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| See who's cited our work at [[http://scholar.google.com/citations?hl=en&user=22M9eisAAAAJ&view_op=list_works&pagesize=100|Google Scholar]] and our [[https://orcid.org/0000-0003-0185-8861|ORCID]] profile. = Peer-reviewed Articles and Preprints = |
See who's cited our work at [[http://scholar.google.com/citations?hl=en&user=22M9eisAAAAJ&view_op=list_works&pagesize=100|Google Scholar]] and our [[https://orcid.org/0000-0003-0185-8861|ORCID]] profile. (Also, check out our latest publications in progress - [[#preprints|preprints]]) = Peer-reviewed Articles = == 2025 == 1. '''Cytoscape Web: bringing network biology to the browser'''<<BR>>Ono K, Fong D, Gao C, Churas C, Pillich R, Lenkiewicz J, Pratt D, Pico AR, Hanspers K, Xin Y, Morris J, '''Kucera M''', '''Franz M''', '''Lopes C''', '''Bader G''', Ideker T, Chen J<<BR>>[[https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkaf365/8123447|Nucleic Acids Res. 2025 May 1:gkaf365]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/40308211/|PubMed Abstract]] - [[attachment:NAR_cyto_April2025.pdf|PDF]]<<BR>>'''SOFTWARE''','''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>> 1. '''PRMT5 promotes full-length HTT expression by repressing multiple proximal intronic polyadenylation sites'''<<BR>>Yadav M, !AlQazzaz MA, Ciamponi FE, Ho JC, Maron MI, '''Sababi AM''', !MacLeod G, Ahmadi M, Bullivant G, Tano V, Langley SR, Sánchez-Osuna M, Sachamitr P, Kushida M, Bardile CF, Pouladi MA, Kurtz R, Richards L, Pugh T, Tyers M, Angers S, Dirks PB, '''Bader GD''', Truant R, Massirer KB, Barsyte-Lovejoy D, Shechter D, Harding RJ, Arrowsmith CH, Prinos P<<BR>>[[https://academic.oup.com/nar/article/53/8/gkaf347/8122723|Nucleic Acids Res. 2025 Apr 22;53(8)]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/40304179/|PubMed Abstract]] - [[attachment:NAR_April2025.pdf|PDF]]<<BR>>'''SINGLE CELL GENOMICS'''<<BR>><<BR>> 1. '''Metformin reduces the competitive advantage of Dnmt3aR878H HSPCs'''<<BR>>Hosseini M, '''Voisin V''', Chegini A, Varesi A, Cathelin S, Ayyathan DM, Liu ACH, Yang Y, Wang V, Maher A, Grignano E, Reisz JA, D'Alessandro A, Young K, Wu Y, Fiumara M, Ferrari S, Naldini L, Gaiti F, Pai S, Egan G, Schimmer AD, '''Bader GD''', Dick JE, Xie SZ, Trowbridge JJ, Chan SM<<BR>>[[https://www.nature.com/articles/s41586-025-08871-w|Nature. 2025 Apr 16.]]<<BR>> [[https://pubmed.ncbi.nlm.nih.gov/40240595/|PubMed Abstract]] - [[attachment:Nature_April2025.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>> 1. '''Elevated mitochondrial membrane potential is a therapeutic vulnerability in Dnmt3a-mutant clonal hematopoiesis'''<<BR>>Young KA, Hosseini M, Mistry JJ, Morganti C, Mills TS, Cai X, James BT, Nye GJ, Fournier NR, '''Voisin V''', Chegini A, Schimmer AD, '''Bader GD''', Egan G, Mansour MR, Challen GA, Pietras EM, Fisher-Wellman KH, Ito K, Chan SM, Trowbridge JJ<<BR>> [[https://www.nature.com/articles/s41467-025-57238-2|Nat Commun. 2025 Apr 16;16(1):3306]]<<BR>> [[https://pubmed.ncbi.nlm.nih.gov/40240771/|PubMed Abstract]] - [[attachment:NatComm_April2025.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>> 1. '''Transfer learning improves performance in volumetric electron microscopy organelle segmentation across tissues'''<<BR>> '''Xie R''', Mulcahy B, Darbandi A, Marwah S, Ali F, '''Lee Y''', Parlakgul G, Hotamisligil GS, Wang B, MacParland S, Zhen M, '''Bader GD'''<<BR>>[[https://academic.oup.com/bioinformaticsadvances/article/5/1/vbaf021/8104107|Bioinform Adv. 2025 Apr 2;5(1)]]<<BR>> [[https://pubmed.ncbi.nlm.nih.gov/40196751/|PubMed Abstract]] - [[attachment:bioinfoadv_April2025.pdf|PDF]]<<BR>>'''VOLUMETRIC ELECTRON MICROSCOPY'''<<BR>><<BR>> 1. '''Approaches to identify scenarios for data science implementations within healthcare settings: recommendations based on experiences at multiple academic institutions'''<<BR>>Sung L, Brudno M, Caesar MCW, Verma AA, Buchsbaum B, Retnakaran R, Giannakeas V, Kushki A, '''Bader GD''', Lasthiotakis H, Mamdani M, Strug L<<BR>> [[https://www.frontiersin.org/journals/digital-health/articles/10.3389/fdgth.2025.1511943/full|Front Digit Health. 2025 Mar 14;7:1511943]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/40161559/|PubMed Abstract]] - [[attachment:frontdig_April2025.pdf|PDF]]<<BR>>'''DATA SCIENCE'''<<BR>><<BR>> 1. '''A single-nucleus and spatial transcriptomic atlas of the COVID-19 liver reveals topological, functional, and regenerative organ disruption in patients'''<<BR>>Pita-Juarez Y, Karagkouni D, Kalavros N, Melms JC, Niezen S, Delorey TM, Essene AL, Brook OR, Pant D, Skelton-Badlani D, Naderi P, Huang P, Pan L, Hether T, Andrews TS, Ziegler CGK, Reeves J, Myloserdnyy A, Chen R, Nam A, Phelan S, Liang Y, Gregory M, He S, Patrick M, Rane T, Wardhani A, Amin AD, Biermann J, Hibshoosh H, Veregge M, Kramer Z, Jacobs C, Yalcin Y, Phillips D, Slyper M, Subramanian A, Ashenberg O, Bloom-Ackermann Z, Tran VM, Gomez J, Sturm A, Zhang S, Fleming SJ, Warren S, Beechem J, Hung D, Babadi M, Padera RF Jr, !MacParland SA, '''Bader GD''', Imad N, Solomon IH, Miller E, Riedel S, Porter CBM, Villani AC, Tsai LT, Hide W, Szabo G, Hecht J, Rozenblatt-Rosen O, Shalek AK, Izar B, Regev A, Popov YV, Jiang ZG, Vlachos IS<<BR>>[[https://genomebiology.biomedcentral.com/articles/10.1186/s13059-025-03499-5|Genome Biol. 2025 Mar 14;26(1):56]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/40087773/|PubMed Abstract]] - [[attachment:Genomebio_March2025.pdf|PDF]]<<BR>> '''SINGLE CELL GENOMICS'''<<BR>><<BR>> 1. '''Interpretable single-cell factor decomposition using sciRED'''<<BR>> '''Pouyabahar D''', Andrews T, '''Bader GD'''<<BR>>[[https://www.nature.com/articles/s41467-025-57157-2|Nat Commun. 2025 Feb 22;16(1):1878]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/39987196/|PubMed Abstract]] - [[attachment:NatureCom_february2025.pdf|PDF]]<<BR>> '''SINGLE CELL GENOMICS'''<<BR>><<BR>> == 2024 == 1. '''Single-cell transcriptome analysis reveals CD34 as a marker of human sinoatrial node pacemaker cardiomyocytes'''<<BR>>Lim AA, '''Pouyabahar D''', Ashraf M, Huang K, Lohbihler M, Murareanu BM, Chang ML, Kwan M, Alibhai FJ, '''Tran T''', Mazine A, Laflamme MA, '''Bader GD''', Laksman Z, Protze S<<BR>>[[https://www.nature.com/articles/s41467-024-54337-4|Nat Commun. 2024 Nov 27;15(1):10206]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/39604360/|PubMed Abstract]] - [[attachment:NatureCom_november2024_number2.pdf|PDF]]<<BR>> '''SINGLE CELL GENOMICS'''<<BR>><<BR>> 1. '''The commitment of the human cell atlas to humanity'''<<BR>>Amit I, Ardlie K, Arzuaga F, Awandare G, '''Bader G''', Bernier A, Carninci P, Donnelly S, Eils R, Forrest ARR, Greely HT, Guigo R, Hacohen N, Haniffa M, Kirby ES, Knoppers BM, Kriegstein A, Lein ES, Linnarsson S, Majumder PP, Merad M, Meyer K, Mhlanga MM, Nolan G, Ntusi NAB, Pe'er D, Prabhakar S, Raven-Adams M, Regev A, Rozenblatt-Rosen O, Saha S, Saltzman A, Shalek AK, Shin JW, Stunnenberg H, Teichmann SA, Tickle T, Villani AC, Wells C, Wold B, Yang H, Zhuang X<<BR>> [[https://www.nature.com/articles/s41467-024-54306-x|Nat Commun. 2024 Nov 20;15(1)]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/39567491/|PubMed Abstract]] - [[attachment:NatureCom_november2024.pdf|PDF]]<<BR>> '''SINGLE CELL GENOMICS'''<<BR>><<BR>> 1. '''Specifications of standards in systems and synthetic biology: status, developments, and tools in 2024'''<<BR>>Golebiewski M, '''Bader G''', Gleeson P, Gorochowski TE, Keating SM, König M, Myers CJ, Nickerson DP, Sommer B, Waltemath D, Schreiber F<<BR>>[[https://www.degruyter.com/document/doi/10.1515/jib-2024-0015/html|J Integr Bioinform. 2024 Jul 22;21(1)]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/39026464/|PubMed Abstract]] - [[attachment:IntergBioinform_july2024.pdf|PDF]]<<BR>>'''DATA STANDARDS''' <<BR>><<BR>> 1. '''Single-cell atlas of the human brain vasculature across development, adulthood and disease'''<<BR>>Wälchli T, Ghobrial M, Schwab M, Takada S, Zhong H, Suntharalingham S, Vetiska S, Gonzalez DR, Wu R, Rehrauer H, Dinesh A, Yu K, Chen ELY, Bisschop J, Farnhammer F, Mansur A, Kalucka J, Tirosh I, Regli L, Schaller K, Frei K, Ketela T, Bernstein M, Kongkham P, Carmeliet P, Valiante T, Dirks PB, Suva ML, Zadeh G, Tabar V, Schlapbach R, Jackson HW, De Bock K, Fish JE, Monnier PP, '''Bader GD''', Radovanovic I<<BR>>[[https://www.nature.com/articles/s41586-024-07493-y|Nature. 2024 Aug;632(8025):603-613]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/38987604/|PubMed Abstract]] - [[attachment:Nature_july2024.pdf|PDF]]<<BR>>'''SINGLE CELL GENOMICS'''<<BR>><<BR>> 1. '''Fatecode enables cell fate regulator prediction using classification-supervised autoencoder perturbation.'''<<BR>>'''Sadria M''', Layton A, Goyal S, '''Bader GD'''<<BR>>[[https://www.cell.com/cell-reports-methods/fulltext/S2667-2375(24)00184-X|Cell Rep Methods. 2024 Jul 15;4(7):100819]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/38986613/|PubMed Abstract]] - [[attachment:cellrepmethods_July2024.pdf|PDF]]<<BR>> [[https://www.biorxiv.org/content/10.1101/2022.12.16.520772v1|arXiv]] -[[https://www.biorxiv.org/content/10.1101/2022.12.16.520772v1.full.pdf|PDF]]<<BR>>'''SINGLE CELL GENOMICS, SOFTWARE'''<<BR>><<BR>> 1. '''Drugst.One - a plug-and-play solution for online systems medicine and network-based drug repurposing'''<<BR>>Maier A, Hartung M, Abovsky M, Adamowicz K, '''Bader GD''', Baier S, Blumenthal DB, Chen J, Elkjaer ML, Garcia-Hernandez C, Helmy M, Hoffmann M, Jurisica I, Kotlyar M, Lazareva O, Levi H, List M, Lobentanzer S, Loscalzo J, Malod-Dognin N, Manz Q, Matschinske J, Mee M, Oubounyt M, Pastrello C, Pico AR, Pillich RT, Poschenrieder JM, Pratt D, Pržulj N, Sadegh S, Saez-Rodriguez J, Sarkar S, Shaked G, Shamir R, Trummer N, Turhan U, Wang RS, Zolotareva O, Baumbach J<<BR>>[[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10274948/|Nucleic Acids Res. 2024 Jul 5;52(W1):W481-W488]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/38783119/|PubMed Abstract]] - [[attachment:NuclAcid_May2024.pdf|PDF]]<<BR>>[[https://arxiv.org/abs/2305.15453|arXiv]] -[[https://arxiv.org/pdf/2305.15453|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>> 1. '''Single-cell, single-nucleus, and spatial transcriptomics characterization of the immunological landscape in the healthy and PSC human liver'''<<BR>>'''Andrews TS''', Nakib D, Perciani CT, Ma XZ, Liu L, Winter E, Camat D, Chung SW, Lumanto P, Manuel J, Mangroo S, Hansen B, Arpinder B, Thoeni C, Sayed B, Feld J, Gehring A, Gulamhusein A, Hirschfield GM, Ricciuto A, '''Bader GD''', !McGilvray ID, !MacParland S<<BR>>[[https://www.journal-of-hepatology.eu/article/S0168-8278(24)00003-5/fulltext|J Hepatol. 2024 May;80(5):730-743]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/38199298/|PubMed Abstract]] - [[attachment:Jhepatol_May2024.pdf|PDF]]<<BR>>'''SINGLE CELL GENOMICS'''<<BR>><<BR>> 1. '''Multimodal Medical Answer Generation using Large Language Models'''<<BR>>Toma A, '''Xie R''', '''Palayew S''', '''Bader GD''', Wang B<<BR>> [[https://aclanthology.org/2024.clinicalnlp-1.60/|2024. WangLab at MEDIQA-M3G 2024: In Proceedings of the 6th Clinical Natural Language Processing Workshop, pages 624–634]]<<BR>>[[https://aclanthology.org/2024.clinicalnlp-1.60/|Abstract]] - [[attachment:Mediam3g_april2024_2.pdf|PDF]]<<BR>>'''NATURAL LANGUAGE PROCESSING'''<<BR>><<BR>> 1. '''The multimodality cell segmentation challenge: toward universal solutions'''<<BR>>Ma J, '''Xie R''', '''Ayyadhury S''', Ge C, Gupta A, Gupta R, Gu S, Zhang Y, Lee G, Kim J, Lou W, Li H, Upschulte E, Dickscheid T, de Almeida JG, Wang Y, Han L, Yang X, Labagnara M, Gligorovski V, Scheder M, Rahi SJ, Kempster C, Pollitt A, Espinosa L, Mignot T, Middeke JM, Eckardt JN, Li W, Li Z, Cai X, Bai B, Greenwald NF, Van Valen D, Weisbart E, Cimini BA, Cheung T, Brück O, '''Bader GD''', Wang B<<BR>>[[https://www.nature.com/articles/s41592-024-02233-6|Nat Methods. 2024 Jun;21(6):1103-1113]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/38532015/|PubMed Abstract]] - [[attachment:NatMethods_March2024.pdf|PDF]]<<BR>>'''COMPUTER VISION''','''SINGLE CELL GENOMICS'''<<BR>><<BR>> 1. '''Integrated transcriptomics uncovers an enhanced association between the prion protein gene expression and vesicle dynamics signatures in glioblastomas'''<<BR>>Boccacino JM, Dos Santos Peixoto R, Fernandes CFL, Cangiano G, Sola PR, Coelho BP, Prado MB, Melo-Escobar MI, de Sousa BP, '''Ayyadhury S''', '''Bader GD''', Shinjo SMO, Marie SKN, da Rocha EL, Lopes MH<<BR>> [[https://bmccancer.biomedcentral.com/articles/10.1186/s12885-024-11914-6|BMC Cancer. 2024 Feb 13;24(1):199]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/38347462/|PubMed Abstract]] - [[attachment:BMCCancer_Feb2024.pdf|PDF]]<<BR>>'''SINGLE CELL GENOMICS'''<<BR>><<BR>> == 2023 == 1. '''Single-nucleus multiomic atlas of frontal cortex in amyotrophic lateral sclerosis with a deep learning-based decoding of alternative polyadenylation mechanisms'''<<BR>>!McKeever PM, '''Sababi AM''', Sharma R, Khuu N, Xu Z, Shen SY, Xiao S, !McGoldrick P, Orouji E, Ketela T, Sato C, Moreno D, Visanji N, Kovacs GG, Keith J, Zinman L, Rogaeva E, Goodarzi H, '''Bader GD''', Robertson J<<BR>> [[https://www.biorxiv.org/content/10.1101/2023.12.22.573083v1|bioRxiv [Preprint]. 2023 Dec 23,2023]]<<BR>> [[https://pubmed.ncbi.nlm.nih.gov/38187588/|PubMed Abstract]] - [[attachment:Biorxiv_Dec2023.pdf|PDF]]<<BR>> '''SINGLE CELL GENOMICS'''<<BR>><<BR>> 1. '''Spatially Resolved Gene Expression Prediction from Histology Images via Bi-modal Contrastive Learning'''<<BR>> '''Xie R''', Pang K, Chung SW, Perciani C, !MacParland S, Wang B, '''Bader GD'''<<BR>>[[https://proceedings.neurips.cc/paper_files/paper/2023/hash/df656d6ed77b565e8dcdfbf568aead0a-Abstract-Conference.html|Proceedings of the Thirty-seventh Conference on Neural Information Processing Systems]] - [[https://proceedings.neurips.cc/paper_files/paper/2023/file/df656d6ed77b565e8dcdfbf568aead0a-Paper-Conference.pdf|PDF]]<<BR>>[[https://arxiv.org/abs/2306.01859|arXiv]] -[[https://arxiv.org/pdf/2306.01859.pdf|PDF]]<<BR>>[[https://neurips.cc/virtual/2023/poster/70961|Poster]] <<BR>>'''SPATIAL TRANSCRIPTOMICS'''<<BR>><<BR>> 1. '''Adversarial training improves model interpretability in single-cell RNA-seq analysis'''<<BR>>'''Sadria M''', Layton A, '''Bader GD''' <<BR>>[[https://academic.oup.com/bioinformaticsadvances/article/3/1/vbad166/7444320|Bioinform Adv. 2023 Nov 23;3(1)]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/38099262/|PubMed Abstract]] - [[attachment:Bioinformadv_Nov2023.pdf|PDF]]<<BR>>'''SINGLE CELL GENOMICS'''<<BR>><<BR>> 1. '''Open Domain Multi-document Summarization: A Comprehensive Study of Model Brittleness under Retrieval'''<<BR>>'''Giorgi J''', Soldaini L, Wang B, '''Bader G''', Lo K, Wang L, and Cohan A<<BR>> [[https://aclanthology.org/2023.findings-emnlp.549/|Findings of the Association for Computational Linguistics: EMNLP Dec 2023, pages 8177–8199]]<<BR>>[[https://arxiv.org/abs/2212.10526|arXiv. 2022 Dec 20]]<<BR>>[[attachment:Compling_Dec2023.pdf|PDF]] <<BR>>'''NATURAL LANGUAGE PROCESSING'''<<BR>><<BR>> 1. '''A rat liver cell atlas reveals intrahepatic myeloid heterogeneity''' <<BR>>'''Pouyabahar D''', Chung SW, Pezzutti OI, Perciani CT, Wang X, Ma XZ, Jiang C, Camat D, Chung T, Sekhon M, Manuel J, Chen XC, !McGilvray ID, !MacParland SA, '''Bader GD'''<<BR>>[[https://www.sciencedirect.com/science/article/pii/S2589004223022903|iScience. 2023 Oct 14;26(11):108213]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/38026201/|PubMed Abstract]] - [[attachment:iscience_Oct2023.pdf|PDF]] <<BR>>'''SINGLE CELL GENOMICS'''<<BR>><<BR>> 1. '''Fate specification of GFAP-negative primitive neural stem cells and their progeny at clonal resolution'''<<BR>>Yammine S, Burns I, Gosio J, Peluso A, Merritt D, '''Innes B''', Coles B, Yan WR, '''Bader GD''', Morshead C, van der Kooy D<<BR>>[[https://www.liebertpub.com/doi/10.1089/scd.2023.0038|Stem Cells Dev. 2023 Oct;32(19-20):606-621]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/37551982/|PubMed Abstract]] - [[attachment:StemCell_Aug2023.pdf|PDF]] <<BR>>'''SINGLE CELL GENOMICS'''<<BR>><<BR>> 1. '''Distinct shared and compartment-enriched oncogenic networks drive primary versus metastatic breast cancer'''<<BR>>Jiang Z, Ju Y, Ali A, Chung PED, Skowron P, Wang DY, Shrestha M, Li H, '''Liu JC''', Vorobieva I, Ghanbari-Azarnier R, Mwewa E, Koritzinsky M, Ben-David Y, Woodgett JR, Perou CM, Dupuy A, '''Bader GD''', Egan SE, Taylor MD, Zacksenhaus E<<BR>>[[https://www.nature.com/articles/s41467-023-39935-y|Nat Commun. 2023 Jul 18;14(1):4313]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/37463901/|PubMed Abstract]] - [[attachment:Natcomm_July2023.pdf|PDF]] <<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>> 1. '''Robust segregation of donor and recipient cells from single-cell RNA-sequencing of transplant samples'''<<BR>>Wilson GW, Duong A, Moshkelgosha S, '''Bader G''', Keshavjee S, Martinu T, Juvet SC, Yeung JC<<BR>>[[https://www.frontiersin.org/articles/10.3389/frtra.2023.1161146/full|Front. Transplant., 12 June 2023 Volume 2 - 2023]]<<BR>>[[attachment:Fronttrans_June2023.pdf|PDF]] <<BR>>'''SINGLE CELL GENOMICS'''<<BR>><<BR>> 1. '''MAESTER: Masked Autoencoder Guided Segmentation at Pixel Resolution for Accurate, Self-Supervised Subcellular Structure Recognition'''<<BR>>'''Xie R''', Pang K, '''Bader GD''', Wang B<<BR>> [[https://openaccess.thecvf.com/content/CVPR2023/html/Xie_MAESTER_Masked_Autoencoder_Guided_Segmentation_at_Pixel_Resolution_for_Accurate_CVPR_2023_paper.html|Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR), 2023, pp. 3292-3301]]<<BR>>[[attachment:CCVF_June2023.pdf|PDF]] <<BR>>'''COMPUTER VISION'''<<BR>><<BR>> 1. '''Multiplatform molecular profiling uncovers two subgroups of malignant peripheral nerve sheath tumors with distinct therapeutic vulnerabilities'''<<BR>>Suppiah S, Mansouri S, Mamatjan Y, '''Liu JC''', Bhunia MM, Patil V, Rath P, Mehani B, Heir P, Bunda S, Velez-Reyes GL, Singh O, Ijad N, Pirouzmand N, Dalcourt T, Meng Y, Karimi S, Wei Q, Nassiri F, Pugh TJ, '''Bader GD''', Aldape KD, Largaespada DA, Zadeh G<<BR>>[[https://www.nature.com/articles/s41467-023-38432-6|Nat Commun. 2023 May 10;14(1):2696]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/37164978/|PubMed Abstract]] - [[attachment:Natcomm_May2023.pdf|PDF]] <<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>> 1. '''Multi-scale systems genomics analysis predicts pathways, cell types, and drug targets involved in normative variation in peri-adolescent human cognition'''<<BR>> '''Pai S''', Hui S, Weber P, Narayan S, '''Whitley O''', Li P, Labrie V, Baumbach J, Wheeler AL, '''Bader GD'''<<BR>>[[https://academic.oup.com/cercor/advance-article/doi/10.1093/cercor/bhad142/7145898?login=false| Cereb Cortex. 2023 Apr 27]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/37106565/|PubMed Abstract]] - [[attachment:cereb_cortex_April2023.pdf|PDF]] <<BR>>'''PRECISION MEDICINE'''<<BR>><<BR>> 1. '''Genotyping SARS-CoV-2 Variants Using Ratiometric Nucleic Acid Barcode Panels'''<<BR>>Kozlowski HN, Malekjahani A, Li VYC, Lekuti AA, Perusini S, Bell NG, '''Voisin V''', '''Pouyabahar D''', '''Pai S''', '''Bader GD''', Mubareka S, Gubbay JB, Chan WCW<<BR>>[[https://pubs.acs.org/doi/10.1021/acs.analchem.2c04630|Anal Chem. 2023 Apr 11;95(14):5877-5885]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/37000033/|PubMed Abstract]] - [[attachment:anal_chem_April2023.pdf|PDF]] <<BR>>'''COVID-19'''<<BR>><<BR>> 1. '''Cytoscape.js 2023 update: a graph theory library for visualisation and analysis. Bioinformatics'''<<BR>>'''Franz M''', '''Lopes CT''', '''Fong D''', '''Kucera M''', '''Cheung M''', Siper MC, Huck G, '''Dong Y''', Sumer O, '''Bader GD'''<<BR>> [[https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btad031/6988031|Bioinformatics 2023 Jan 1;39(1)]] <<BR>>[[https://pubmed.ncbi.nlm.nih.gov/36645249/|PubMed Abstract]] - [[attachment:bioinformatics_Jan2023.pdf|PDF]] <<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>> |
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| 1. '''PLAG1 dampens protein synthesis to promote human hematopoietic stem cell self-renewal'''<<BR>>Keyvani Chahi A, Belew MS, Xu J, Chen HTT, Rentas S, '''Voisin V''', Krivdova G, Lechman ER, Marhon SA, De Carvalho D, Dick JE, '''Bader GD''', Hope K<<BR>> [[https://ashpublications.org/blood/article/doi/10.1182/blood.2021014698/485426/PLAG1-dampens-protein-synthesis-to-promote-human|Blood. 2022 May 31]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/35639948/|PubMed Abstract]] - [[attachment:Blood_May2022.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>> | 1. '''Single-cell profiling of healthy human kidney reveals features of sex-based transcriptional programs and tissue-specific immunity'''<<BR>> !McEvoy CM, Murphy JM, Zhang L, Clotet-Freixas S, Mathews JA, An J, Karimzadeh M, '''Pouyabahar D''', Su S, Zaslaver O, Röst H, Arambewela R, Liu LY, Zhang S, Lawson KA, Finelli A, Wang B, !MacParland SA, '''Bader GD''', Konvalinka A, Crome SQ<<BR>>[[https://www.nature.com/articles/s41467-022-35297-z|Nat Commun. 2022 Dec 10;13(1):7634]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/36496458/|PubMed Abstract]] - [[attachment:NatureCom_Dec2022.pdf|PDF]]<<BR>>'''SINGLE CELL GENOMICS'''<<BR>><<BR>> 1. '''Loss of Epigenetic Regulation Disrupts Lineage Integrity, Induces Aberrant Alveogenesis, and Promotes Breast Cancer'''<<BR>>Langille E, Al-Zahrani KN, Ma Z, Liang M, Uuskula-Reimand L, Espin R, Teng K, Malik A, Bergholtz H, Ghamrasni SE, Afiuni-Zadeh S, Tsai R, Alvi S, Elia A, Lü Y, Oh RH, Kozma KJ, Trcka D, Narimatsu M, '''Liu JC''', Nguyen T, Barutcu S, Loganathan SK, Bremner R, '''Bader GD''', Egan SE, Cescon DW, Sørlie T, Wrana JL, Jackson HW, Wilson MD, Witkiewicz AK, Knudsen ES, Pujana MA, Wahl GM, Schramek D<<BR>>[[https://aacrjournals.org/cancerdiscovery/article/12/12/2930/711188/Loss-of-Epigenetic-Regulation-Disrupts-Lineage|Cancer Discov. 2022 Dec 2;12(12):2930-2953]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/36108220/|PubMed Abstract]] - [[attachment:CancerDis_Dec2022.pdf|PDF]]<<BR>>'''CANCER MUTATIONS'''<<BR>><<BR>> 1. '''Neuron-specific protein network mapping of autism risk genes identifies shared biological mechanisms and disease-relevant pathologies'''<<BR>>Murtaza N, Cheng AA, Brown CO, Meka DP, Hong S, Uy JA, El-Hajjar J, Pipko N, Unda BK, Schwanke B, Xing S, Thiruvahindrapuram B, Engchuan W, Trost B, Deneault E, Calderon de Anda F, Doble BW, Ellis J, Anagnostou E, '''Bader GD''', Scherer SW, Lu Y, Singh KK<<BR>>[[https://www.cell.com/cell-reports/fulltext/S2211-1247(22)01552-2|Cell Rep. 2022 Nov 22;41(8):111678]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/36417873/|PubMed Abstract]] - [[attachment:CellRep_Nov2022.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>> 1. '''Neurons and glial cells acquire a senescent signature after repeated mild traumatic brain injury in a sex-dependent manner'''<<BR>>Schwab N, Taskina D, Leung E, '''Innes BT''', '''Bader GD''', Hazrati LN<<BR>>[[https://www.frontiersin.org/articles/10.3389/fnins.2022.1027116/full#:~:text=all%206%20Articles-,Neurons%20and%20glial%20cells%20acquire%20a%20senescent%20signature%20after%20repeated,in%20a%20sex%2Ddependent%20manner&text=Mild%20traumatic%20brain%20injury%20(mTBI,and%20risk%20of%20neurodegenerative%20disease.|Front Neurosci. 2022 Nov 3;16:1027116]]<<BR>> [[https://pubmed.ncbi.nlm.nih.gov/36408415/|PubMed Abstract]] - [[attachment:FrontNeuro_Nov2022.pdf|PDF]]<<BR>>'''SINGLE CELL GENOMICS'''<<BR>><<BR>> 1. '''BIONIC: biological network integration using convolutions'''<<BR>>'''Forster DT''', Li SC, Yashiroda Y, Yoshimura M, Li Z, Isuhuaylas LAV, Itto-Nakama K, Yamanaka D, Ohya Y, Osada H, Wang B, '''Bader GD''', Boone C<<BR>>[[https://www.nature.com/articles/s41592-022-01616-x|Nat Methods. 2022 Oct;19(10):1250-1261]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/36192463/|PubMed Abstract]] - [[attachment:NatMethodsOct2022.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>> 1. '''Single-cell atlas of human liver development reveals pathways directing hepatic cell fates'''<<BR>>Wesley BT, Ross ADB, Muraro D, Miao Z, Saxton S, Tomaz RA, Morell CM, Ridley K, Zacharis ED, Petrus-Reurer S, Kraiczy J, Mahbubani KT, Brown S, Garcia-Bernardo J, Alsinet C, Gaffney D, Horsfall D, Tysoe OC, Botting RA, Stephenson E, Popescu DM, !MacParland S, '''Bader G''', !McGilvray ID, Ortmann D, Sampaziotis F, Saeb-Parsy K, Haniffa M, Stevens KR, Zilbauer M, Teichmann SA, Vallier L<<BR>>[[https://www.nature.com/articles/s41556-022-00989-7|Nat Cell Biol. 2022 Oct;24(10):1487-1498]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/36109670/|PubMed Abstract]] - [[attachment:NatCellBio_Sept2022.pdf|PDF]]<<BR>>'''SINGLE CELL GENOMICS'''<<BR>><<BR>> 1. '''PLAG1 dampens protein synthesis to promote human hematopoietic stem cell self-renewal'''<<BR>>Keyvani Chahi A, Belew MS, Xu J, Chen HTT, Rentas S, '''Voisin V''', Krivdova G, Lechman E, Marhon SA, De Carvalho DD, Dick JE, '''Bader GD''', Hope KJ<<BR>>[[https://ashpublications.org/blood/article/140/9/992/485426/PLAG1-dampens-protein-synthesis-to-promote-human|Blood. 2022 Sep 1;140(9):992-1008]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/36055193/|PubMed Abstract]] - [[attachment:Blood_Sept2022.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>> 1. '''Modeling human multi-lineage heart field development with pluripotent stem cells'''<<BR>>Yang D, Gomez-Garcia J, Funakoshi S, '''Tran T''', Fernandes I, '''Bader GD''', Laflamme MA, Keller GM<<BR>> [[https://www.sciencedirect.com/science/article/pii/S1934590922003435?via%3Dihub|Cell Stem Cell. 2022 Sep 1;29(9):1382-1401]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/36055193/|PubMed Abstract]] - [[attachment:StemCell_Sept2022.pdf|PDF]]<<BR>>'''SINGLE CELL GENOMICS'''<<BR>><<BR>> 1. '''Unraveling the Complexity of Liver Disease One Cell at a Time'''<<BR>>Atif J, Thoeni C, '''Bader GD''', !McGilvray ID, !MacParland SA<<BR>>[[https://www.thieme-connect.com/products/ejournals/abstract/10.1055/s-0042-1755272|Semin Liver Dis. 2022 Aug;42(3):250-270]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/36008091/|PubMed Abstract]] - [[attachment:SeminLiver_Aug2022.pdf|PDF]]<<BR>>'''SINGLE CELL GENOMICS'''<<BR>><<BR>> 1. '''Uncovering the Contribution of Moderate-Penetrance Susceptibility Genes to Breast Cancer by Whole-Exome Sequencing and Targeted Enrichment Sequencing of Candidate Genes in Women of European Ancestry'''<<BR>>Dumont M, Weber-Lassalle N, Joly-Beauparlant C, Ernst C, Droit A, Feng BJ, Dubois S, Collin-Deschesnes AC, Soucy P, Vallée M, Fournier F, Lemaçon A, Adank MA, Allen J, Altmüller J, Arnold N, Ausems MGEM, Berutti R, Bolla MK, Bull S, Carvalho S, Cornelissen S, Dufault MR, Dunning AM, Engel C, Gehrig A, Geurts-Giele WRR, Gieger C, Green J, Hackmann K, Helmy M, Hentschel J, Hogervorst FBL, Hollestelle A, Hooning MJ, Horváth J, Ikram MA, Kaulfuß S, Keeman R, Kuang D, Luccarini C, Maier W, Martens JWM, Niederacher D, Nürnberg P, Ott CE, Peters A, Pharoah PDP, Ramirez A, Ramser J, Riedel-Heller S, Schmidt G, Shah M, Scherer M, Stäbler A, Strom TM, Sutter C, Thiele H, van Asperen CJ, van der Kolk L, van der Luijt RB, Volk AE, Wagner M, Waisfisz Q, Wang Q, Wang-Gohrke S, Weber BHF, Genome Of The Netherlands Project, Ghs Study Group, Devilee P, Tavtigian S, '''Bader GD''', Meindl A, Goldgar DE, Andrulis IL, Schmutzler RK, Easton DF, Schmidt MK, Hahnen E, Simard J<<BR>>[[https://www.mdpi.com/2072-6694/14/14/3363|Cancers (Basel). 2022 Jul 11;14(14)]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/35884425/|PubMed Abstract]] - [[attachment:Cancers_July2022.pdf|PDF]]<<BR>>'''CANCER MUTATIONS'''<<BR>><<BR>> 1. '''Comprehensive multi-cohort transcriptional meta-analysis of muscle diseases identifies a signature of disease severity'''<<BR>>Walsh CJ, Batt J, Herridge MS, Mathur S, '''Bader GD''', Hu P, Khatri P, Dos Santos CC<<BR>>[[https://www.nature.com/articles/s41598-022-15003-1|Sci Rep. 2022 Jul 4;12(1):11260]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/35789175/|PubMed Abstract]] - [[attachment:Scireports_July2022.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>> 1. '''OpenPIP: An Open-source Platform for Hosting, Visualizing and Analyzing Protein Interaction Data'''<<BR>>'''Helmy M''', Mee M, Ranjan A, Hao T, Vidal M, Calderwood MA, Luck K, '''Bader GD'''<<BR>>[[https://www.sciencedirect.com/science/article/pii/S0022283622001838|J Mol Biol. 2022 Jun 15;434(11):167603]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/35662469/|PubMed Abstract]] - [[attachment:JMB_June2022.pdf|PDF]]<<BR>>'''PROTEIN INTERACTION'''<<BR>><<BR>> 1. '''The metabolic enzyme hexokinase 2 localizes to the nucleus in AML and normal haematopoietic stem and progenitor cells to maintain stemness'''<<BR>>Thomas GE, Egan G, García-Prat L, Botham A, '''Voisin V''', Patel PS, Hoff FW, Chin J, Nachmias B, Kaufmann KB, Khan DH, Hurren R, Wang X, Gronda M, !MacLean N, O'Brien C, Singh RP, Jones CL, Harding SM, Raught B, Arruda A, Minden MD, '''Bader GD''', Hakem R, Kornblau S, Dick JE, Schimmer AD<<BR>> [[https://www.nature.com/articles/s41556-022-00925-9|Nat Cell Biol. 2022 Jun 6]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/35668135/|PubMed Abstract]] - [[attachment:NatureCellBio_June2022.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>> 1. '''A sequence-to-sequence approach for document-level relation extraction'''<<BR>>'''Giorgi, John''' and '''Bader, Gary''' and Wang, Bo<<BR>>[[https://aclweb.org/aclwiki/BioNLP_Workshop|BioNLP @ ACL May 2022]]<<BR>>[[https://aclanthology.org/2022.bionlp-1.2/|ACL Anthology]] - [[https://aclanthology.org/2022.bionlp-1.2.pdf|PDF]]<<BR>>'''NATURAL LANGUAGE PROCESSING'''<<BR>><<BR>> |
| Line 12: | Line 114: |
| 1. '''IPO11 regulates the nuclear import of BZW1/2 and is necessary for AML cells and stem cells'''<<BR>>Nachmias B, Khan DH, '''Voisin V''', Mer AS, Thomas GE, Segev N, St-Germain J, Hurren R, Gronda M, Botham A, Wang X, Maclean N, Seneviratne AK, Duong N, Xu C, Arruda A, Orouji E, Algouneh A, Hakem R, Shlush L, Minden MD, Raught B, '''Bader GD''', Schimmer AD<<BR>> [[https://www.nature.com/articles/s41375-022-01513-4|Leukemia. 2022 Feb 12]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/35152270/|PubMed Abstract]] - [[attachment:leukemia_Feb2022.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>> | 1. '''IPO11 regulates the nuclear import of BZW1/2 and is necessary for AML cells and stem cells'''<<BR>>Nachmias B, Khan DH, '''Voisin V''', Mer AS, Thomas GE, Segev N, St-Germain J, Hurren R, Gronda M, Botham A, Wang X, Maclean N, Seneviratne AK, Duong N, Xu C, Arruda A, Orouji E, Algouneh A, Hakem R, Shlush L, Minden MD, Raught B, '''Bader GD''', Schimmer AD<<BR>> [[https://www.nature.com/articles/s41375-022-01513-4|Leukemia. 2022 Feb 12]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/35152270/|PubMed Abstract]] - [[attachment:leukemia_Feb2022.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>> |
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| 1. '''A flexible search system for high-accuracy identification of biological entities and molecules'''<<BR>>'''Franz M''', '''Wong JV''', Siper MC, Dallago C,Giorgi J, Demir E, Chris Sander C, '''Bader GD'''<<BR>> [[https://joss.theoj.org/papers/10.21105/joss.03756#| Journal of Open Source Software, 6(67), 3756]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/34860157/|PubMed Abstract]] - [[attachment:JOSS_Nov2021.pdf|PDF]]<<BR>>'''SOFTWARE'''<<BR>><<BR>> | 1. '''A flexible search system for high-accuracy identification of biological entities and molecules'''<<BR>>'''Franz M''', '''Wong JV''', Siper MC, Dallago C,Giorgi J, Demir E, Chris Sander C, '''Bader GD'''<<BR>> [[https://joss.theoj.org/papers/10.21105/joss.03756#|Journal of Open Source Software, 6(67), 3756]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/34860157/|PubMed Abstract]] - [[attachment:JOSS_Nov2021.pdf|PDF]]<<BR>>'''SOFTWARE'''<<BR>><<BR>> |
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| 1. '''scNetViz: from single cells to networks using Cytoscape'''<<BR>>Choudhary K, Meng EC, Diaz-Mejia JJ, '''Bader GD''', Pico AR, Morris JH<<BR>>[[https://f1000research.com/articles/10-448|F1000Res. 2021 Jun 7;10:ISCB Comm J-448]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/34912541/|PubMed Abstract]] - [[attachment:F1000_June2021.pdf|PDF]]<<BR>>'''SINGLE CELL GENOMICS'''<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>> | 1. '''scNetViz: from single cells to networks using Cytoscape'''<<BR>>Choudhary K, Meng EC, Diaz-Mejia JJ, '''Bader GD''', Pico AR, Morris JH<<BR>>[[https://f1000research.com/articles/10-448|F1000Res. 2021 Jun 7;10:ISCB Comm J-448]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/34912541/|PubMed Abstract]] - [[attachment:F1000_June2021.pdf|PDF]]<<BR>>'''SINGLE CELL GENOMICS'''<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>> |
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| <<Anchor(preprints)>> = Preprints = == 2025 == 1. '''From FAIR to CURE: Guidelines for Computational Models of Biological Systems'''<<BR>>Sauro HM, Agmon E, Blinov ML, Gennari JH, Hellerstein J, Heydarabadipour A, Hunter P, Jardine BE, May E, Nickerson DP, Smith LP, '''Bader GD''', Bergmann F, Boyle PM, Dräger A, Faeder JR, Feng S, Freire J, Fröhlich F, Glazier JA, Gorochowski TE, Helikar T, Hoops S, Imoukhuede P, Keating SM, Konig M, Laubenbacher R, Loew LM, Lopez CF, Lytton WW, !McCulloch A, Mendes P, Myers CJ, Myers JG, Mulugeta L, Niarakis A, van Niekerk DD, Olivier BG, Patrie AA, Quardokus EM, Radde N, Rohwer JM, Sahle S, Schaff JC, Sego TJ, Shin J, Snoep JL, Vadigepalli R, Wiley HS, Waltemath D, Moraru I<<BR>>[[https://arxiv.org/abs/2502.15597|ArXiv [Preprint]. 2025 Feb 21:arXiv:2502.15597v1]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/40034129/|PubMed Abstract]]- [[attachment:preprintbioarxiv_march2026.pdf|PDF]]<<BR>>'''DATA STANDARD'''<<BR>><<BR>> == 2024 == 1. '''Interpretable single-cell factor decomposition using sciRED'''<<BR>>'''Pouyabahar D''', Andrews T, '''Bader GD'''<<BR>> [[https://www.biorxiv.org/content/10.1101/2024.08.01.605536v1|bioRxiv [Preprint]. 2024 Aug 6:2024.08.01.605536]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/39149356/|PubMed Abstract]]-[[attachment:preprintbioarxiv_August2024.pdf|PDF]]<<BR>>'''SINGLE CELL GENOMICS'''<<BR>><<BR>> 1. '''Direct lineage conversion of postnatal mouse cortical astrocytes to oligodendrocyte lineage cells'''<<BR>>Bajohr J, Scott EY, Olfat A, '''Sadria M''', Lee K, Fahim M, Taha HT, Casasbuenas DL, Derham A, Yuzwa SA, '''Bader GD''', Maryam Faiz<<BR>>[[https://www.biorxiv.org/content/10.1101/2024.05.28.596294v1.abstract|bioRxiv [Preprint]. May 2024 - 2024.05.28.596294]]<<BR>>[[attachment:preprint_May2024.pdf|PDF]]<<BR>>'''SINGLE CELL GENOMICS'''<<BR>><<BR>> 1. '''Deep Lineage: Single-Cell Lineage Tracing and Fate Inference Using Deep Learning'''<<BR>> '''Sadria M''', Zhang A, '''Bader GD''' <<BR>>[[https://www.biorxiv.org/content/10.1101/2024.04.25.591126v1.abstract|bioRxiv [Preprint]. April 2024 - 2024.04.25.591126]]<<BR>>[[attachment:preprint_April2024.pdf|PDF]]<<BR>>'''SINGLE CELL GENOMICS'''<<BR>><<BR>> 1. '''Single-cell analysis of an engineered organoid-based model of pancreatic cancer identifies hypoxia as a contributing factor in the determination of transcriptional subtypes'''<<BR>>Natalie Landon-Brace N, '''Innes BT''', Latour S, Cadavid JL, Co IL, Tan CM, Nowlan F, Drissler S, Notta F, Jackson HW, '''Bader GD''', !McGuigan AP<<BR>>[[https://www.biorxiv.org/content/10.1101/2024.03.05.583412v1.abstract|bioRxiv [Preprint]. March 2024 - 2024.03.14.584861]]<<BR>>[[attachment:preprint_March2024.pdf|PDF]]<<BR>>'''SINGLE CELL GENOMICS'''<<BR>><<BR>> 1. '''PRMT5 is required for full-length HTT expression by repressing multiple proximal intronic polyadenylation sites'''<<BR>>!AlQazzaz MA, Ciamponi FE, Ho JC, Maron MI, Yadav M, '''Sababi AM''', !MacLeod G, Ahmadi M, Bullivant G, Tano V, Langley SR, Sánchez-Osuna M, Sachamitr P, Kushida M, Richards L, Bardile CF, Pouladi MA, Pugh T, Tyers M, Angers S, Dirks PB, '''Bader GD''', Massirer KB, Barsyte-Lovejoy D, Shechter D, Harding RJ, Arrowsmith CH, Prinos P<<BR>>[[https://www.biorxiv.org/content/10.1101/2024.03.14.584861v1.article-info|bioRxiv [Preprint]. March 2024 - 2024.03.05.583412]]<<BR>>[[attachment:preprint_March2024_2.pdf|PDF]]<<BR>>'''SINGLE CELL GENOMICS'''<<BR>><<BR>> 1. '''Metformin reduces the clonal fitness of Dnmt3aR878H hematopoietic stem and progenitor cells by reversing their aberrant metabolic and epigenetic state'''<<BR>>Hosseini M, '''Voisin V''', Chegini A, Varesi A, Cathelin S, Ayyathan DM, Liu ACH, Yang Y, Wang V, Maher A, Grignano E, Reisz JA, D'Alessandro A, Young K, Wu Y, Fiumara M, Ferrari S, Naldini L, Gaiti F, Pai S, Schimmer AD, '''Bader GD''', Dick JE, Xie SZ, Trowbridge JJ, Chan SM <<BR>>[[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10889081/|Preprint 2024 Feb 6]]<<BR>> [[https://pubmed.ncbi.nlm.nih.gov/38405837/|PubMed Abstract]] - [[attachment:preprint_Feb2024.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS, SINGLE CELL GENOMICS'''<<BR>><<BR>> == 2023 == 1. '''Cell networks in the mouse liver during partial hepatectomy'''<<BR>>Li B, Rodrigo-Torres D, Pelz C, '''Innes B''', Canaday P, Chai S, Zandstra P, '''Bader GD''', Grompe M<<BR>> [[https://www.biorxiv.org/content/10.1101/2023.07.16.549116v1|bioRxiv [Preprint]. 2023 Jul]] <<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/37503083|PubMed Abstract]] - [[attachment:Mouseliver_BioarxivJuly2023.pdf|PDF]]<<BR>><<BR>> 1. '''Drugst.One -- A plug-and-play solution for online systems medicine and network-based drug repurposing'''<<BR>>Maier A, Hartung M, Abovsky M, Adamowicz K, '''Bader GD''', Baier S, Blumenthal DB, Chen J, Elkjaer ML, Garcia-Hernandez C, Hoffmann M, Jurisica I, Kotlyar M, Lazareva O, Levi H, List M, Lobentanzer S, Loscalzo J, Malod-Dognin N, Manz Q, Matschinske J, Oubounyt M, Pico AR, Pillich RT, Poschenrieder JM, Pratt D, Pržulj N, Sadegh S, Saez-Rodriguez J, Sakar S, Shaked G, Shamir R, Trummer N, Turhan U, Wang R, Zolotareva O, Baumbach J<<BR>>[[https://arxiv.org/abs/2305.15453|ArXiv [Preprint]. 2023 May 24]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/37332567|PubMed Abstract]] - [[attachment:drugstone_BioarxivJune202023.pdf|PDF]]<<BR>> == 2022 == 1. '''A single-nucleus and spatial transcriptomic atlas of the COVID-19 liver reveals topological, functional, and regenerative organ disruption in patients'''<<BR>>Pita-Juarez Y, Karagkouni D, Kalavros N, Melms JC, Niezen S, Delorey TM, Essene AL, Brook OR, Pant D, Skelton-Badlani D, Naderi P, Huang P, Pan L, Hether T, Andrews TS, Ziegler CGK, Reeves J, Myloserdnyy A, Chen R, Nam A, Phelan S, Liang Y, Amin AD, Biermann J, Hibshoosh H, Veregge M, Kramer Z, Jacobs C, Yalcin Y, Phillips D, Slyper M, Subramanian A, Ashenberg O, Bloom-Ackermann Z, Tran VM, Gomez J, Sturm A, Zhang S, Fleming SJ, Warren S, Beechem J, Hung D, Babadi M, Padera RF, !MacParland SA, '''Bader GD''', Imad N, Solomon IH, Miller E, Riedel S, Porter CBM, Villani AC, Tsai LT, Hide W, Szabo G, Hecht J, Rozenblatt-Rosen O, Shalek AK, Izar B, Regev A, Popov Y, Jiang ZG, Vlachos IS<<BR>>[[https://www.biorxiv.org/content/10.1101/2022.10.27.514070v1|bioRxiv Preprint. 2022 Oct 28]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/36324805|PubMed Abstract]] - [[attachment:BioarxivOct282022.pdf|PDF]]<<BR>>'''COVID-19'''<<BR>><<BR>> |
|
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| 1. 2023 '''Duncan Forster''' - BIONIC: Biological Network Integration using Convolutions - [[attachment:Forster_Duncan_Terell_202311_PhD_thesis.pdf|PDF]], University of Toronto, Department of Molecular Genetics<<BR>><<BR>> 1. 2023 '''Brendan Innes''' - Intercellular Signaling Networks of a Tissue from Single-Cell Transcriptomics - [[attachment:Innes_Brendan_T_202406_PhD_thesis.pdf|PDF]], University of Toronto, Department of Molecular Genetics<<BR>><<BR>> 1. 2022 '''Owen Whitley''' - Transcriptional and Multi -Omic Heterogeneity in Glioblastoma Stem Cells - [[attachment:Whitley_Owen_Kenneth Nora_202211_PhD_thesis.pdf|PDF]], University of Toronto, Department of Molecular Genetics<<BR>><<BR>> 1. 2021 '''Gurnit Atwal''' - Automatic tumour typing based on patterns of somatic passenger mutations - [[attachment:Atwal_Gurnit_202106_PhD_Thesis.pdf|PDF]], University of Toronto, Department of Molecular Genetics<<BR>><<BR>> 1. 2021 '''Stuart Matan-Lithwick''' - Identifying Novel Genes and Pathways Correlated with Group 3 and Group 4 Medulloblastoma Metastasis to the Spine - [[attachment:Lithwick__Stuart_Aaron (Matan-Lithwick)_202106_PhD_thesis.pdf|PDF]], University of Toronto, Department of Molecular Genetics<<BR>><<BR>> 1. 2020 '''Patryk Skowron''' - Deciphering Genetic Drivers in Primary and Metastatic Medulloblastoma - [[attachment:Skowron_Patryk_ _202006_PhD_thesis.pdf|PDF]], University of Toronto, Laboratory Medicine and Pathobiology<<BR>><<BR>> 1. 2020 '''Lucas Hu''' - Biochemical Profile-Based Computational Inference of Protein Complexes - [[attachment:Hu_Zhongming_ _202006_PhD_thesis.pdf|PDF]], University of Toronto, Department of Molecular Genetics<<BR>><<BR>> |
|
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| 1. 2019 '''Thinh Ngoc Tran''' - Pathway-based Lineage Analysis of Time-course Single-Cell RNA Sequencing Data - [[attachment:Tran_Thinh_N_201911_MSc_thesis.pdf|PDF]], University of Toronto, Molecular Genetics<<BR>><<BR>> 1. 2018 '''Catherine Ross''' - Detecting Signals of Coevolution within Immune Response Pathways in the African-American Ancestral Population - [[attachment:Ross_Catherine_201806_MSc_thesis.pdf|PDF]], University of Toronto, Molecular Genetics<<BR>><<BR>> |
|
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| 1. 2015 '''David Shih''' - Molecular Classification and Clinical Genomics of Medulloblastoma - [[attachment:Shih_J._H._David_201511_PhD_thesis.pdf|PDF]], University of Toronto, Laboratory Medicine and Pathobiology<<BR>><<BR>> 1. 2015 '''Marina Olhovsky''' - Using Text Mining of PubMed Abstracts as an Evidence Source in Computational Predictions of WW Domain-Mediated Protein-Protein Interactions - [[attachment:Olhovsky_Marina_2015_Masters.pdf|PDF]], York University, Graduate Program in Biology<<BR>><<BR>> |
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2025
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Ono K, Fong D, Gao C, Churas C, Pillich R, Lenkiewicz J, Pratt D, Pico AR, Hanspers K, Xin Y, Morris J, Kucera M, Franz M, Lopes C, Bader G, Ideker T, Chen J
Nucleic Acids Res. 2025 May 1:gkaf365
PubMed Abstract - PDF
SOFTWARE,PATHWAY AND NETWORK ANALYSIS
PRMT5 promotes full-length HTT expression by repressing multiple proximal intronic polyadenylation sites
Yadav M, AlQazzaz MA, Ciamponi FE, Ho JC, Maron MI, Sababi AM, MacLeod G, Ahmadi M, Bullivant G, Tano V, Langley SR, Sánchez-Osuna M, Sachamitr P, Kushida M, Bardile CF, Pouladi MA, Kurtz R, Richards L, Pugh T, Tyers M, Angers S, Dirks PB, Bader GD, Truant R, Massirer KB, Barsyte-Lovejoy D, Shechter D, Harding RJ, Arrowsmith CH, Prinos P
Nucleic Acids Res. 2025 Apr 22;53(8)
PubMed Abstract - PDF
SINGLE CELL GENOMICS
Metformin reduces the competitive advantage of Dnmt3aR878H HSPCs
Hosseini M, Voisin V, Chegini A, Varesi A, Cathelin S, Ayyathan DM, Liu ACH, Yang Y, Wang V, Maher A, Grignano E, Reisz JA, D'Alessandro A, Young K, Wu Y, Fiumara M, Ferrari S, Naldini L, Gaiti F, Pai S, Egan G, Schimmer AD, Bader GD, Dick JE, Xie SZ, Trowbridge JJ, Chan SM
Nature. 2025 Apr 16.
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Elevated mitochondrial membrane potential is a therapeutic vulnerability in Dnmt3a-mutant clonal hematopoiesis
Young KA, Hosseini M, Mistry JJ, Morganti C, Mills TS, Cai X, James BT, Nye GJ, Fournier NR, Voisin V, Chegini A, Schimmer AD, Bader GD, Egan G, Mansour MR, Challen GA, Pietras EM, Fisher-Wellman KH, Ito K, Chan SM, Trowbridge JJ
Nat Commun. 2025 Apr 16;16(1):3306
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Transfer learning improves performance in volumetric electron microscopy organelle segmentation across tissues
Xie R, Mulcahy B, Darbandi A, Marwah S, Ali F, Lee Y, Parlakgul G, Hotamisligil GS, Wang B, MacParland S, Zhen M, Bader GD
Bioinform Adv. 2025 Apr 2;5(1)
PubMed Abstract - PDF
VOLUMETRIC ELECTRON MICROSCOPY
Approaches to identify scenarios for data science implementations within healthcare settings: recommendations based on experiences at multiple academic institutions
Sung L, Brudno M, Caesar MCW, Verma AA, Buchsbaum B, Retnakaran R, Giannakeas V, Kushki A, Bader GD, Lasthiotakis H, Mamdani M, Strug L
Front Digit Health. 2025 Mar 14;7:1511943
PubMed Abstract - PDF
DATA SCIENCE
A single-nucleus and spatial transcriptomic atlas of the COVID-19 liver reveals topological, functional, and regenerative organ disruption in patients
Pita-Juarez Y, Karagkouni D, Kalavros N, Melms JC, Niezen S, Delorey TM, Essene AL, Brook OR, Pant D, Skelton-Badlani D, Naderi P, Huang P, Pan L, Hether T, Andrews TS, Ziegler CGK, Reeves J, Myloserdnyy A, Chen R, Nam A, Phelan S, Liang Y, Gregory M, He S, Patrick M, Rane T, Wardhani A, Amin AD, Biermann J, Hibshoosh H, Veregge M, Kramer Z, Jacobs C, Yalcin Y, Phillips D, Slyper M, Subramanian A, Ashenberg O, Bloom-Ackermann Z, Tran VM, Gomez J, Sturm A, Zhang S, Fleming SJ, Warren S, Beechem J, Hung D, Babadi M, Padera RF Jr, MacParland SA, Bader GD, Imad N, Solomon IH, Miller E, Riedel S, Porter CBM, Villani AC, Tsai LT, Hide W, Szabo G, Hecht J, Rozenblatt-Rosen O, Shalek AK, Izar B, Regev A, Popov YV, Jiang ZG, Vlachos IS
Genome Biol. 2025 Mar 14;26(1):56
PubMed Abstract - PDF
SINGLE CELL GENOMICS
Interpretable single-cell factor decomposition using sciRED
Pouyabahar D, Andrews T, Bader GD
Nat Commun. 2025 Feb 22;16(1):1878
PubMed Abstract - PDF
SINGLE CELL GENOMICS
2024
Single-cell transcriptome analysis reveals CD34 as a marker of human sinoatrial node pacemaker cardiomyocytes
Lim AA, Pouyabahar D, Ashraf M, Huang K, Lohbihler M, Murareanu BM, Chang ML, Kwan M, Alibhai FJ, Tran T, Mazine A, Laflamme MA, Bader GD, Laksman Z, Protze S
Nat Commun. 2024 Nov 27;15(1):10206
PubMed Abstract - PDF
SINGLE CELL GENOMICS
The commitment of the human cell atlas to humanity
Amit I, Ardlie K, Arzuaga F, Awandare G, Bader G, Bernier A, Carninci P, Donnelly S, Eils R, Forrest ARR, Greely HT, Guigo R, Hacohen N, Haniffa M, Kirby ES, Knoppers BM, Kriegstein A, Lein ES, Linnarsson S, Majumder PP, Merad M, Meyer K, Mhlanga MM, Nolan G, Ntusi NAB, Pe'er D, Prabhakar S, Raven-Adams M, Regev A, Rozenblatt-Rosen O, Saha S, Saltzman A, Shalek AK, Shin JW, Stunnenberg H, Teichmann SA, Tickle T, Villani AC, Wells C, Wold B, Yang H, Zhuang X
Nat Commun. 2024 Nov 20;15(1)
PubMed Abstract - PDF
SINGLE CELL GENOMICS
Specifications of standards in systems and synthetic biology: status, developments, and tools in 2024
Golebiewski M, Bader G, Gleeson P, Gorochowski TE, Keating SM, König M, Myers CJ, Nickerson DP, Sommer B, Waltemath D, Schreiber F
J Integr Bioinform. 2024 Jul 22;21(1)
PubMed Abstract - PDF
DATA STANDARDS
Single-cell atlas of the human brain vasculature across development, adulthood and disease
Wälchli T, Ghobrial M, Schwab M, Takada S, Zhong H, Suntharalingham S, Vetiska S, Gonzalez DR, Wu R, Rehrauer H, Dinesh A, Yu K, Chen ELY, Bisschop J, Farnhammer F, Mansur A, Kalucka J, Tirosh I, Regli L, Schaller K, Frei K, Ketela T, Bernstein M, Kongkham P, Carmeliet P, Valiante T, Dirks PB, Suva ML, Zadeh G, Tabar V, Schlapbach R, Jackson HW, De Bock K, Fish JE, Monnier PP, Bader GD, Radovanovic I
Nature. 2024 Aug;632(8025):603-613
PubMed Abstract - PDF
SINGLE CELL GENOMICS
Fatecode enables cell fate regulator prediction using classification-supervised autoencoder perturbation.
Sadria M, Layton A, Goyal S, Bader GD
Cell Rep Methods. 2024 Jul 15;4(7):100819
PubMed Abstract - PDF
arXiv -PDF
SINGLE CELL GENOMICS, SOFTWARE
Drugst.One - a plug-and-play solution for online systems medicine and network-based drug repurposing
Maier A, Hartung M, Abovsky M, Adamowicz K, Bader GD, Baier S, Blumenthal DB, Chen J, Elkjaer ML, Garcia-Hernandez C, Helmy M, Hoffmann M, Jurisica I, Kotlyar M, Lazareva O, Levi H, List M, Lobentanzer S, Loscalzo J, Malod-Dognin N, Manz Q, Matschinske J, Mee M, Oubounyt M, Pastrello C, Pico AR, Pillich RT, Poschenrieder JM, Pratt D, Pržulj N, Sadegh S, Saez-Rodriguez J, Sarkar S, Shaked G, Shamir R, Trummer N, Turhan U, Wang RS, Zolotareva O, Baumbach J
Nucleic Acids Res. 2024 Jul 5;52(W1):W481-W488
PubMed Abstract - PDF
arXiv -PDF
PATHWAY AND NETWORK ANALYSIS
Single-cell, single-nucleus, and spatial transcriptomics characterization of the immunological landscape in the healthy and PSC human liver
Andrews TS, Nakib D, Perciani CT, Ma XZ, Liu L, Winter E, Camat D, Chung SW, Lumanto P, Manuel J, Mangroo S, Hansen B, Arpinder B, Thoeni C, Sayed B, Feld J, Gehring A, Gulamhusein A, Hirschfield GM, Ricciuto A, Bader GD, McGilvray ID, MacParland S
J Hepatol. 2024 May;80(5):730-743
PubMed Abstract - PDF
SINGLE CELL GENOMICS
Multimodal Medical Answer Generation using Large Language Models
Toma A, Xie R, Palayew S, Bader GD, Wang B
2024. WangLab at MEDIQA-M3G 2024: In Proceedings of the 6th Clinical Natural Language Processing Workshop, pages 624–634
Abstract - PDF
NATURAL LANGUAGE PROCESSING
The multimodality cell segmentation challenge: toward universal solutions
Ma J, Xie R, Ayyadhury S, Ge C, Gupta A, Gupta R, Gu S, Zhang Y, Lee G, Kim J, Lou W, Li H, Upschulte E, Dickscheid T, de Almeida JG, Wang Y, Han L, Yang X, Labagnara M, Gligorovski V, Scheder M, Rahi SJ, Kempster C, Pollitt A, Espinosa L, Mignot T, Middeke JM, Eckardt JN, Li W, Li Z, Cai X, Bai B, Greenwald NF, Van Valen D, Weisbart E, Cimini BA, Cheung T, Brück O, Bader GD, Wang B
Nat Methods. 2024 Jun;21(6):1103-1113
PubMed Abstract - PDF
COMPUTER VISION,SINGLE CELL GENOMICS
Integrated transcriptomics uncovers an enhanced association between the prion protein gene expression and vesicle dynamics signatures in glioblastomas
Boccacino JM, Dos Santos Peixoto R, Fernandes CFL, Cangiano G, Sola PR, Coelho BP, Prado MB, Melo-Escobar MI, de Sousa BP, Ayyadhury S, Bader GD, Shinjo SMO, Marie SKN, da Rocha EL, Lopes MH
BMC Cancer. 2024 Feb 13;24(1):199
PubMed Abstract - PDF
SINGLE CELL GENOMICS
2023
Single-nucleus multiomic atlas of frontal cortex in amyotrophic lateral sclerosis with a deep learning-based decoding of alternative polyadenylation mechanisms
McKeever PM, Sababi AM, Sharma R, Khuu N, Xu Z, Shen SY, Xiao S, McGoldrick P, Orouji E, Ketela T, Sato C, Moreno D, Visanji N, Kovacs GG, Keith J, Zinman L, Rogaeva E, Goodarzi H, Bader GD, Robertson J
bioRxiv [Preprint]. 2023 Dec 23,2023
PubMed Abstract - PDF
SINGLE CELL GENOMICS
Spatially Resolved Gene Expression Prediction from Histology Images via Bi-modal Contrastive Learning
Xie R, Pang K, Chung SW, Perciani C, MacParland S, Wang B, Bader GD
Proceedings of the Thirty-seventh Conference on Neural Information Processing Systems - PDF
arXiv -PDF
Poster
SPATIAL TRANSCRIPTOMICS
Adversarial training improves model interpretability in single-cell RNA-seq analysis
Sadria M, Layton A, Bader GD
Bioinform Adv. 2023 Nov 23;3(1)
PubMed Abstract - PDF
SINGLE CELL GENOMICS
Open Domain Multi-document Summarization: A Comprehensive Study of Model Brittleness under Retrieval
Giorgi J, Soldaini L, Wang B, Bader G, Lo K, Wang L, and Cohan A
Findings of the Association for Computational Linguistics: EMNLP Dec 2023, pages 8177–8199
arXiv. 2022 Dec 20
PDF
NATURAL LANGUAGE PROCESSING
A rat liver cell atlas reveals intrahepatic myeloid heterogeneity
Pouyabahar D, Chung SW, Pezzutti OI, Perciani CT, Wang X, Ma XZ, Jiang C, Camat D, Chung T, Sekhon M, Manuel J, Chen XC, McGilvray ID, MacParland SA, Bader GD
iScience. 2023 Oct 14;26(11):108213
PubMed Abstract - PDF
SINGLE CELL GENOMICS
Fate specification of GFAP-negative primitive neural stem cells and their progeny at clonal resolution
Yammine S, Burns I, Gosio J, Peluso A, Merritt D, Innes B, Coles B, Yan WR, Bader GD, Morshead C, van der Kooy D
Stem Cells Dev. 2023 Oct;32(19-20):606-621
PubMed Abstract - PDF
SINGLE CELL GENOMICS
Distinct shared and compartment-enriched oncogenic networks drive primary versus metastatic breast cancer
Jiang Z, Ju Y, Ali A, Chung PED, Skowron P, Wang DY, Shrestha M, Li H, Liu JC, Vorobieva I, Ghanbari-Azarnier R, Mwewa E, Koritzinsky M, Ben-David Y, Woodgett JR, Perou CM, Dupuy A, Bader GD, Egan SE, Taylor MD, Zacksenhaus E
Nat Commun. 2023 Jul 18;14(1):4313
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Robust segregation of donor and recipient cells from single-cell RNA-sequencing of transplant samples
Wilson GW, Duong A, Moshkelgosha S, Bader G, Keshavjee S, Martinu T, Juvet SC, Yeung JC
Front. Transplant., 12 June 2023 Volume 2 - 2023
PDF
SINGLE CELL GENOMICS
MAESTER: Masked Autoencoder Guided Segmentation at Pixel Resolution for Accurate, Self-Supervised Subcellular Structure Recognition
Xie R, Pang K, Bader GD, Wang B
Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR), 2023, pp. 3292-3301
PDF
COMPUTER VISION
Multiplatform molecular profiling uncovers two subgroups of malignant peripheral nerve sheath tumors with distinct therapeutic vulnerabilities
Suppiah S, Mansouri S, Mamatjan Y, Liu JC, Bhunia MM, Patil V, Rath P, Mehani B, Heir P, Bunda S, Velez-Reyes GL, Singh O, Ijad N, Pirouzmand N, Dalcourt T, Meng Y, Karimi S, Wei Q, Nassiri F, Pugh TJ, Bader GD, Aldape KD, Largaespada DA, Zadeh G
Nat Commun. 2023 May 10;14(1):2696
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Multi-scale systems genomics analysis predicts pathways, cell types, and drug targets involved in normative variation in peri-adolescent human cognition
Pai S, Hui S, Weber P, Narayan S, Whitley O, Li P, Labrie V, Baumbach J, Wheeler AL, Bader GD
Cereb Cortex. 2023 Apr 27
PubMed Abstract - PDF
PRECISION MEDICINE
Genotyping SARS-CoV-2 Variants Using Ratiometric Nucleic Acid Barcode Panels
Kozlowski HN, Malekjahani A, Li VYC, Lekuti AA, Perusini S, Bell NG, Voisin V, Pouyabahar D, Pai S, Bader GD, Mubareka S, Gubbay JB, Chan WCW
Anal Chem. 2023 Apr 11;95(14):5877-5885
PubMed Abstract - PDF
COVID-19
Cytoscape.js 2023 update: a graph theory library for visualisation and analysis. Bioinformatics
Franz M, Lopes CT, Fong D, Kucera M, Cheung M, Siper MC, Huck G, Dong Y, Sumer O, Bader GD
Bioinformatics 2023 Jan 1;39(1)
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
2022
Single-cell profiling of healthy human kidney reveals features of sex-based transcriptional programs and tissue-specific immunity
McEvoy CM, Murphy JM, Zhang L, Clotet-Freixas S, Mathews JA, An J, Karimzadeh M, Pouyabahar D, Su S, Zaslaver O, Röst H, Arambewela R, Liu LY, Zhang S, Lawson KA, Finelli A, Wang B, MacParland SA, Bader GD, Konvalinka A, Crome SQ
Nat Commun. 2022 Dec 10;13(1):7634
PubMed Abstract - PDF
SINGLE CELL GENOMICS
Loss of Epigenetic Regulation Disrupts Lineage Integrity, Induces Aberrant Alveogenesis, and Promotes Breast Cancer
Langille E, Al-Zahrani KN, Ma Z, Liang M, Uuskula-Reimand L, Espin R, Teng K, Malik A, Bergholtz H, Ghamrasni SE, Afiuni-Zadeh S, Tsai R, Alvi S, Elia A, Lü Y, Oh RH, Kozma KJ, Trcka D, Narimatsu M, Liu JC, Nguyen T, Barutcu S, Loganathan SK, Bremner R, Bader GD, Egan SE, Cescon DW, Sørlie T, Wrana JL, Jackson HW, Wilson MD, Witkiewicz AK, Knudsen ES, Pujana MA, Wahl GM, Schramek D
Cancer Discov. 2022 Dec 2;12(12):2930-2953
PubMed Abstract - PDF
CANCER MUTATIONS
Neuron-specific protein network mapping of autism risk genes identifies shared biological mechanisms and disease-relevant pathologies
Murtaza N, Cheng AA, Brown CO, Meka DP, Hong S, Uy JA, El-Hajjar J, Pipko N, Unda BK, Schwanke B, Xing S, Thiruvahindrapuram B, Engchuan W, Trost B, Deneault E, Calderon de Anda F, Doble BW, Ellis J, Anagnostou E, Bader GD, Scherer SW, Lu Y, Singh KK
Cell Rep. 2022 Nov 22;41(8):111678
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Neurons and glial cells acquire a senescent signature after repeated mild traumatic brain injury in a sex-dependent manner
Schwab N, Taskina D, Leung E, Innes BT, Bader GD, Hazrati LN
Front Neurosci. 2022 Nov 3;16:1027116
PubMed Abstract - PDF
SINGLE CELL GENOMICS
BIONIC: biological network integration using convolutions
Forster DT, Li SC, Yashiroda Y, Yoshimura M, Li Z, Isuhuaylas LAV, Itto-Nakama K, Yamanaka D, Ohya Y, Osada H, Wang B, Bader GD, Boone C
Nat Methods. 2022 Oct;19(10):1250-1261
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Single-cell atlas of human liver development reveals pathways directing hepatic cell fates
Wesley BT, Ross ADB, Muraro D, Miao Z, Saxton S, Tomaz RA, Morell CM, Ridley K, Zacharis ED, Petrus-Reurer S, Kraiczy J, Mahbubani KT, Brown S, Garcia-Bernardo J, Alsinet C, Gaffney D, Horsfall D, Tysoe OC, Botting RA, Stephenson E, Popescu DM, MacParland S, Bader G, McGilvray ID, Ortmann D, Sampaziotis F, Saeb-Parsy K, Haniffa M, Stevens KR, Zilbauer M, Teichmann SA, Vallier L
Nat Cell Biol. 2022 Oct;24(10):1487-1498
PubMed Abstract - PDF
SINGLE CELL GENOMICS
PLAG1 dampens protein synthesis to promote human hematopoietic stem cell self-renewal
Keyvani Chahi A, Belew MS, Xu J, Chen HTT, Rentas S, Voisin V, Krivdova G, Lechman E, Marhon SA, De Carvalho DD, Dick JE, Bader GD, Hope KJ
Blood. 2022 Sep 1;140(9):992-1008
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Modeling human multi-lineage heart field development with pluripotent stem cells
Yang D, Gomez-Garcia J, Funakoshi S, Tran T, Fernandes I, Bader GD, Laflamme MA, Keller GM
Cell Stem Cell. 2022 Sep 1;29(9):1382-1401
PubMed Abstract - PDF
SINGLE CELL GENOMICS
Unraveling the Complexity of Liver Disease One Cell at a Time
Atif J, Thoeni C, Bader GD, McGilvray ID, MacParland SA
Semin Liver Dis. 2022 Aug;42(3):250-270
PubMed Abstract - PDF
SINGLE CELL GENOMICS
Uncovering the Contribution of Moderate-Penetrance Susceptibility Genes to Breast Cancer by Whole-Exome Sequencing and Targeted Enrichment Sequencing of Candidate Genes in Women of European Ancestry
Dumont M, Weber-Lassalle N, Joly-Beauparlant C, Ernst C, Droit A, Feng BJ, Dubois S, Collin-Deschesnes AC, Soucy P, Vallée M, Fournier F, Lemaçon A, Adank MA, Allen J, Altmüller J, Arnold N, Ausems MGEM, Berutti R, Bolla MK, Bull S, Carvalho S, Cornelissen S, Dufault MR, Dunning AM, Engel C, Gehrig A, Geurts-Giele WRR, Gieger C, Green J, Hackmann K, Helmy M, Hentschel J, Hogervorst FBL, Hollestelle A, Hooning MJ, Horváth J, Ikram MA, Kaulfuß S, Keeman R, Kuang D, Luccarini C, Maier W, Martens JWM, Niederacher D, Nürnberg P, Ott CE, Peters A, Pharoah PDP, Ramirez A, Ramser J, Riedel-Heller S, Schmidt G, Shah M, Scherer M, Stäbler A, Strom TM, Sutter C, Thiele H, van Asperen CJ, van der Kolk L, van der Luijt RB, Volk AE, Wagner M, Waisfisz Q, Wang Q, Wang-Gohrke S, Weber BHF, Genome Of The Netherlands Project, Ghs Study Group, Devilee P, Tavtigian S, Bader GD, Meindl A, Goldgar DE, Andrulis IL, Schmutzler RK, Easton DF, Schmidt MK, Hahnen E, Simard J
Cancers (Basel). 2022 Jul 11;14(14)
PubMed Abstract - PDF
CANCER MUTATIONS
Comprehensive multi-cohort transcriptional meta-analysis of muscle diseases identifies a signature of disease severity
Walsh CJ, Batt J, Herridge MS, Mathur S, Bader GD, Hu P, Khatri P, Dos Santos CC
Sci Rep. 2022 Jul 4;12(1):11260
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
OpenPIP: An Open-source Platform for Hosting, Visualizing and Analyzing Protein Interaction Data
Helmy M, Mee M, Ranjan A, Hao T, Vidal M, Calderwood MA, Luck K, Bader GD
J Mol Biol. 2022 Jun 15;434(11):167603
PubMed Abstract - PDF
PROTEIN INTERACTION
The metabolic enzyme hexokinase 2 localizes to the nucleus in AML and normal haematopoietic stem and progenitor cells to maintain stemness
Thomas GE, Egan G, García-Prat L, Botham A, Voisin V, Patel PS, Hoff FW, Chin J, Nachmias B, Kaufmann KB, Khan DH, Hurren R, Wang X, Gronda M, MacLean N, O'Brien C, Singh RP, Jones CL, Harding SM, Raught B, Arruda A, Minden MD, Bader GD, Hakem R, Kornblau S, Dick JE, Schimmer AD
Nat Cell Biol. 2022 Jun 6
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
A sequence-to-sequence approach for document-level relation extraction
Giorgi, John and Bader, Gary and Wang, Bo
BioNLP @ ACL May 2022
ACL Anthology - PDF
NATURAL LANGUAGE PROCESSING
Identification of the global miR-130a targetome reveals a role for TBL1XR1 in hematopoietic stem cell self-renewal and t(8;21) AML
Krivdova G, Voisin V, Schoof EM, Marhon SA, Murison A, McLeod JL, Gabra MM, Zeng AGX, Aigner S, Yee BA, Shishkin AA, Van Nostrand EL, Hermans KG, Trotman-Grant AC, Mbong N, Kennedy JA, Gan OI, Wagenblast E, De Carvalho DD, Salmena L, Minden MD, Bader GD, Yeo GW, Dick JE, Lechman ER
Cell Rep. 2022 Mar 8;38(10)
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
IPO11 regulates the nuclear import of BZW1/2 and is necessary for AML cells and stem cells
Nachmias B, Khan DH, Voisin V, Mer AS, Thomas GE, Segev N, St-Germain J, Hurren R, Gronda M, Botham A, Wang X, Maclean N, Seneviratne AK, Duong N, Xu C, Arruda A, Orouji E, Algouneh A, Hakem R, Shlush L, Minden MD, Raught B, Bader GD, Schimmer AD
Leukemia. 2022 Feb 12
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
A Shared Transcriptional Identity for Forebrain and Dentate Gyrus Neural Stem Cells from Embryogenesis to Adulthood
Borrett MJ, Tahmasian N, Innes BT, Bader GD, Kaplan DR, Miller FD
eNeuro. 2022 Jan 13:ENEURO.0271-21.2021
PubMed Abstract - PDF
SINGLE CELL GENOMICS
Hypophosphorylated pRb knock-in mice exhibit hallmarks of aging and vitamin C-preventable diabetes
Jiang Z, Li H, Schroer SA, Voisin V, Ju Y, Pacal M, Erdmann N, Shi W, Chung PED, Deng T, Chen NJ, Ciavarra G, Datti A, Mak TW, Harrington L, Dick FA, Bader GD, Bremner R, Woo M, Zacksenhaus E
EMBO J. 2022 Jan 13
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
2021
Temporal profiling of therapy resistance in human medulloblastoma identifies novel targetable drivers of recurrence
Bakhshinyan D, Adile AA, Liu J, Gwynne WD, Suk Y, Custers S, Burns I, Singh M, McFarlane N, Subapanditha MK, Qazi MA, Vora P, Kameda-Smith MM, Savage N, Desmond KL, Tatari N, Tran D, Seyfrid M, Hope K, Bock NA, Venugopal C, Bader GD, Singh SK
Sci Adv. 2021 Dec 10;7(50)
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Author-sourced capture of pathway knowledge in computable form using Biofactoid
Wong JV, Franz M, Siper MC, Fong D, Durupinar F, Dallago C, Luna A, Giorgi J, Rodchenkov I, Babur Ö, Bachman JA, Gyori BM, Demir E, Bader GD, Sander C
Elife. 2021 Dec 3;10
PubMed Abstract - PDF
SOFTWARE
Single-Cell, Single-Nucleus, and Spatial RNA Sequencing of the Human Liver Identifies Cholangiocyte and Mesenchymal Heterogeneity
Andrews TS, Atif J, Liu JC, Perciani CT, Ma XZ, Thoeni C, Slyper M, Eraslan G, Segerstolpe A, Manuel J, Chung S, Winter E, Cirlan I, Khuu N, Fischer S, Rozenblatt-Rosen O, Regev A, McGilvray ID, Bader GD, MacParland SA
Hepatol Commun. 2021 Nov 18
PubMed Abstract - PDF
SINGLE CELL GENOMICS
The Reactome pathway knowledgebase 2022
Gillespie M, Jassal B, Stephan R, Milacic M, Rothfels K, Senff-Ribeiro A, Griss J, Sevilla C, Matthews L, Gong C, Deng C, Varusai T, Ragueneau E, Haider Y, May B, Shamovsky V, Weiser J, Brunson T, Sanati N, Beckman L, Shao X, Fabregat A, Sidiropoulos K, Murillo J, Viteri G, Cook J, Shorser S, Bader G, Demir E, Sander C, Haw R, Wu G, Stein L, Hermjakob H, D'Eustachio P
Nucleic Acids Res. 2021 Nov 12
PubMed Abstract - PDF
PATHWAY DATABASE
A flexible search system for high-accuracy identification of biological entities and molecules
Franz M, Wong JV, Siper MC, Dallago C,Giorgi J, Demir E, Chris Sander C, Bader GD
Journal of Open Source Software, 6(67), 3756
PubMed Abstract - PDF
SOFTWARE
A microfluidic platform enables comprehensive gene expression profiling of mouse retinal stem cells
Coles BLK, Labib M, Poudineh M, Innes BT, Belair-Hickey J, Gomis S, Wang Z, Bader GD, Sargent EH, Kelley SO, van der Kooy D
Lab Chip. 2021 Oct 15
PubMed Abstract - PDF
SINGLE CELL GENOMICS
A roadmap for the Human Developmental Cell Atlas
Haniffa M, Taylor D, Linnarsson S, Aronow BJ, Bader GD, Barker RA, Camara PG, Camp JG, Chédotal A, Copp A, Etchevers HC, Giacobini P, Göttgens B, Guo G, Hupalowska A, James KR, Kirby E, Kriegstein A, Lundeberg J, Marioni JC, Meyer KB, Niakan KK, Nilsson M, Olabi B, Pe'er D, Regev A, Rood J, Rozenblatt-Rosen O, Satija R, Teichmann SA, Treutlein B, Vento-Tormo R, Webb S
Nature. 2021 Sep;597(7875):196-205
PubMed Abstract - PDF
SINGLE CELL GENOMICS
A clinically applicable integrative molecular classification of meningiomas
Nassiri F, Liu J, Patil V, Mamatjan Y, Wang JZ, Hugh-White R, Macklin AM, Khan S, Singh O, Karimi S, Corona RI, Liu LY, Chen CY, Chakravarthy A, Wei Q, Mehani B, Suppiah S, Gao A, Workewych AM, Tabatabai G, Boutros PC, Bader GD, de Carvalho DD, Kislinger T, Aldape K, Zadeh G
Nature. 2021 Aug 25
PubMed Abstract - PDF
SINGLE CELL GENOMICS
DeCLUTR: Deep Contrastive Learning for Unsupervised Textual Representations
John Giorgi, Osvald Nitski, Bo Wang, Gary Bader
ACL/IJCNLP. 2021 Aug 1
ACL Anthology - PDF
NATURAL LANGUAGE PROCESSING
TFEB-mediated endolysosomal activity controls human hematopoietic stem cell fate
García-Prat L, Kaufmann KB, Schneiter F, Voisin V, Murison A, Chen J, Chan-Seng-Yue M, Gan OI, McLeod JL, Smith SA, Shoong MC, Parris D, Pan K, Zeng AGX, Krivdova G, Gupta K, Takayanagi SI, Wagenblast E, Wang W, Lupien M, Schroeder T, Xie SZ, Dick JE
Cell Stem Cell. 2021 Jul 28:S1934-5909(21)00288-5.
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Nicotinamide phosphoribosyltransferase inhibitors selectively induce apoptosis of AML stem cells by disrupting lipid homeostasis
Subedi A, Liu Q, Ayyathan DM, Sharon D, Cathelin S, Hosseini M, Xu C, Voisin V, Bader GD, D'Alessandro A, Lechman ER, Dick JE, Minden MD, Wang JCY, Chan SM
Cell Stem Cell. 2021 Jul 12:S1934-5909(21)
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Control of tissue development and cell diversity by cell cycle dependent transcriptional filtering
Abou Chakra M, Isserlin R, Tran TN, Bader GD
Elife. 2021 Jul 2;10:e64951
PubMed Abstract - PDF
MATHEMATICAL MODELLING
scNetViz: from single cells to networks using Cytoscape
Choudhary K, Meng EC, Diaz-Mejia JJ, Bader GD, Pico AR, Morris JH
F1000Res. 2021 Jun 7;10:ISCB Comm J-448
PubMed Abstract - PDF
SINGLE CELL GENOMICS
PATHWAY AND NETWORK ANALYSIS
Surveilling and Tracking COVID-19 Patients Using a Portable Quantum Dot Smartphone Device
Zhang Y, Malekjahani A, Udugama BN, Kadhiresan P, Chen H, Osborne M, Franz M, Kucera M, Plenderleith S, Yip L, Bader GD, Tran V, Gubbay JB, McGeer A, Mubareka S, Chan WCW
Nano Lett. 2021 Jun 10
PubMed Abstract - PDF
COVID-19
Generation of mature compact ventricular cardiomyocytes from human pluripotent stem cells
Funakoshi S, Fernandes I, Mastikhina O, Wilkinson D, Tran T, Dhahri W, Mazine A, Yang D, Burnett B, Lee J, Protze S, Bader GD, Nunes SS, Laflamme M, Keller G
Nat Commun. 2021 May 26;12(1):3155
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Tutorial: guidelines for annotating single-cell transcriptomic maps using automated and manual methods
Clarke ZA, Andrews TS, Atif J, Pouyabahar D, Innes BT, MacParland SA, Bader GD
Nat Protoc. 2021 May 24.
PubMed Abstract - PDF
SINGLE CELL GENOMICS
SBGN Bricks Ontology as a tool to describe recurring concepts in molecular networks
Rougny A, Touré V, Albanese J, Waltemath D, Shirshov D, Sorokin A, Bader GD, Blinov ML, Mazein A
Brief Bioinform. 2021 Mar 24
PubMed Abstract - PDF
DATA STANDARDS
Distinct DNA methylation patterns associated with treatment resistance in metastatic castration resistant prostate cancer
Peter MR, Bilenky M, Davies A, Isserlin R, Bader GD, Fleshner NE, Hirst M, Zoubeidi A, Bapat B
Sci Rep. 2021 Mar 23;11(1):6630
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
The transcriptional landscape of Shh medulloblastoma
Skowron P, Farooq H, Cavalli FMG, Morrissy AS, Ly M, Hendrikse LD, Wang EY, Djambazian H, Zhu H, Mungall KL, Trinh QM, Zheng T, Dai S, Stucklin ASG, Vladoiu MC, Fong V, Holgado BL, Nor C, Wu X, Abd-Rabbo D, Bérubé P, Wang YC, Luu B, Suarez RA, Rastan A, Gillmor AH, Lee JJY, Zhang XY, Daniels C, Dirks P, Malkin D, Bouffet E, Tabori U, Loukides J, Doz FP, Bourdeaut F, Delattre OO, Masliah-Planchon J, Ayrault O, Kim SK, Meyronet D, Grajkowska WA, Carlotti CG, de Torres C, Mora J, Eberhart CG, Van Meir EG, Kumabe T, French PJ, Kros JM, Jabado N, Lach B, Pollack IF, Hamilton RL, Rao AAN, Giannini C, Olson JM, Bognár L, Klekner A, Zitterbart K, Phillips JJ, Thompson RC, Cooper MK, Rubin JB, Liau LM, Garami M, Hauser P, Li KKW, Ng HK, Poon WS, Yancey Gillespie G, Chan JA, Jung S, McLendon RE, Thompson EM, Zagzag D, Vibhakar R, Ra YS, Garre ML, Schüller U, Shofuda T, Faria CC, López-Aguilar E, Zadeh G, Hui CC, Ramaswamy V, Bailey SD, Jones SJ, Mungall AJ, Moore RA, Calarco JA, Stein LD, Bader GD, Reimand J, Ragoussis J, Weiss WA, Marra MA, Suzuki H, Taylor MD
Nat Commun. 2021 Mar 19;12(1):1749
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Biological and therapeutic implications of a unique subtype of NPM1 mutated AML
Mer AS, Heath EM, Madani Tonekaboni SA, Dogan-Artun N, Nair SK, Murison A, Garcia-Prat L, Shlush L, Hurren R, Voisin V, Bader GD, Nislow C, Rantalainen M, Lehmann S, Gower M, Guidos CJ, Lupien M, Dick JE, Minden MD, Schimmer AD, Haibe-Kains B
Nat Commun. 2021 Feb 16;12(1):1054
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
PRMT5 inhibition disrupts splicing and stemness in glioblastoma
Sachamitr P, Ho JC, Ciamponi FE, Ba-Alawi W, Coutinho FJ, Guilhamon P, Kushida MM, Cavalli FMG, Lee L, Rastegar N, Vu V, Sánchez-Osuna M, Coulombe-Huntington J, Kanshin E, Whetstone H, Durand M, Thibault P, Hart K, Mangos M, Veyhl J, Chen W, Tran N, Duong BC, Aman AM, Che X, Lan X, Whitley O, Zaslaver O, Barsyte-Lovejoy D, Richards LM, Restall I, Caudy A, Röst HL, Bonday ZQ, Bernstein M, Das S, Cusimano MD, Spears J, Bader GD, Pugh TJ, Tyers M, Lupien M, Haibe-Kains B, Artee Luchman H, Weiss S, Massirer KB, Prinos P, Arrowsmith CH, Dirks PB
Nat Commun. 2021 Feb 12;12(1):979
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Sphingosine-1-phosphate receptor 3 potentiates inflammatory programs in normal and leukemia stem cells to promote differentiation
Xie SZ, Kaufmann KB, Wang W, Chan-Seng-Yue M, Gan OI, Laurenti E, Garcia-Prat L, Takayanagi SI, Ng SWK, Xu C, Zeng AGX, Jin L, McLeod J, Wagenblast E, Mitchell A, Kennedy JA, Liu Q, Boutzen H, Kleinau M, Jargstorf J, Holmes G, Zhang Y, Voisin V, Bader GD, Wang JCY, Hannun YA, Luberto C, Schroeder T, Minden MD, Dick JE
Blood Cancer Discov. 2021 Jan 1;2(1):32-53
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Gradient of Developmental and Injury Response transcriptional states defines functional vulnerabilities underpinning glioblastoma heterogeneity
Richards LM,Whitley OKN, MacLeod G, Cavalli FMG, Coutinho F, Jaramillo J, Svergun N, Riverin M, Croucher D, Kushida M, Yu K, Guilhamon P, Rastegar N, Ahmadi M, Bhatti J, Bozek D, Li N, Lee L, Che C, Luis E, Park N, Xu Z, Ketela T, Moore R, Marra M, Spears, Cusimano M, Das S, Bernstein M, Haibe-Kains B, Lupien M, Luchman H, Weiss S, Angers S, Dirks PB, Bader GD, Pugh TJ.
Nature Cancer 2021 Feb;2(2):157-173
PubMed Abstract - PDF
SINGLE CELL GENOMICS
2020
Large-scale survey and database of high affinity ligands for peptide recognition modules
Teyra J, Kelil A, Jain S, Helmy M, Jajodia R, Hooda Y, Gu J, D'Cruz AA, Nicholson SE, Min J, Sudol M, Kim PM, Bader GD, Sidhu SS
Mol Syst Biol. 2020 Dec;16(12)
PubMed Abstract - PDF
PROTEIN INTERACTION PREDICTION
CD200 expression marks leukemia stem cells in human AML
Ho JM, Dobson SM, Voisin V, McLeod J, Kennedy JA, Mitchell A, Jin L, Eppert K, Bader G, Minden MD, Dick JE, Wang JCY
Blood Adv. 2020 Nov 10;4(21):5402-5413
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
netDx: Software for building interpretable patient classifiers by multi-'omic data integration using patient similarity networks
Pai S, Weber P, Isserlin R, Kaka H, Hui S, Shah MA, Giudice L, Giugno R, Nøhr AK, Baumbach J, Bader GD
F1000Res. 2020 Oct 15;9:1239
PubMed Abstract - PDF
PRECISION MEDICINE
Functional genomic landscape of cancer-intrinsic evasion of killing by T cells
Lawson KA, Sousa CM, Zhang X, Kim E, Akthar R, Caumanns JJ, Yao Y, Mikolajewicz N, Ross C, Brown KR, Zid AA, Fan ZP, Hui S, Krall JA, Simons DM, Slater CJ, De Jesus V, Tang L, Singh R, Goldford JE, Martin S, Huang Q, Francis EA, Habsid A, Climie R, Tieu D, Wei J, Li R, Tong AHY, Aregger M, Chan KS, Han H, Wang X, Mero P, Brumell JH, Finelli A, Ailles L, Bader G, Smolen GA, Kingsbury GA, Hart T, Kung C, Moffat J
Nature. 2020 Sep 23
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Tempora: Cell trajectory inference using time-series single-cell RNA sequencing data
Tran TN, Bader GD
PLoS Comput Biol. 2020 Sep 9;16(9)
PubMed Abstract - PDF
SINGLE CELL GENOMICS
Dynamics of the cell-free DNA methylome of metastatic prostate cancer during androgen-targeting treatment
Peter MR, Bilenky M, Isserlin R, Bader GD, Shen SY, De Carvalho DD, Hansen AR, Hu P, Fleshner NE, Joshua AM, Hirst M, Bapat B
Epigenomics. 2020 Sep 1.
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Wnt activation as a therapeutic strategy in medulloblastoma
Manoranjan B, Venugopal C, Bakhshinyan D, Adile AA, Richards L, Kameda-Smith MM, Whitley O, Dvorkin-Gheva A, Subapanditha M, Savage N, Tatari N, McKenna D, Bassey-Archibong B, Winegarden N, Hallett R, Provias JP, Yarascavitch B, Ajani O, Fleming A, Bader GD, Pugh TJ, Doble BW, Singh SK
Nat Commun. 2020 Aug 28;11(1):4323
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Single-Cell Profiling Shows Murine Forebrain Neural Stem Cells Reacquire a Developmental State when Activated for Adult Neurogenesis
Borrett MJ, Innes BT, Jeong D, Tahmasian N, Storer MA, Bader GD, Kaplan DR, Miller FD
Cell Rep. 2020 Aug 11;32(6):108022
PubMed Abstract - PDF
SINGLE CELL GENOMICS
Meta-analysis of gene expression profiles of lean and obese PCOS to identify differentially regulated pathways and risk of comorbidities
Idicula-Thomas S, Gawde U, Bhaye S, Pokar K, Bader GD
Comput Struct Biotechnol J. 2020;18:1735-1745
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Generation of Functional Liver Sinusoidal Endothelial Cells from Human Pluripotent Stem-Cell-Derived Venous Angioblasts
Gage BK, Liu JC, Innes BT, MacParland SA, McGilvray ID, Bader GD, Keller GM
Cell Stem Cell. 2020;S1934-5909(20)30274-5
PubMed Abstract - PDF
SINGLE CELL GENOMICS
Distinct fibroblast functional states drive clinical outcomes in ovarian cancer and are regulated by TCF21
Hussain A, Voisin V, Poon S, Karamboulas C, Bui NHB, Meens J, Dmytryshyn J, Ho VW, Tang KH, Paterson J, Clarke BA, Bernardini MQ, Bader GD, Neel BG, Ailles LE
J Exp Med. 2020 Aug 3;217(8)
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Disrupting Mitochondrial Copper Distribution Inhibits Leukemic Stem Cell Self-Renewal
Singh RP, Jeyaraju DV, Voisin V, Hurren R, Xu C, Hawley JR, Barghout SH, Khan DH, Gronda M, Wang X, Jitkova Y, Sharon D, Liyanagae S, MacLean N, Seneviratene AK, Mirali S, Borenstein A, Thomas GE, Soriano J, Orouji E, Minden MD, Arruda A, Chan SM, Bader GD, Lupien M, Schimmer AD
Cell Stem Cell. 2020 May 12
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
BraInMap Elucidates the Macromolecular Connectivity Landscape of Mammalian Brain
Pourhaghighi R, Ash PEA, Phanse S, Goebels F, Hu LZM, Chen S, Zhang Y, Wierbowski SD, Boudeau S, Moutaoufik MT, Malty RH, Malolepsza E, Tsafou K, Nathan A, Cromar G, Guo H, Abdullatif AA, Apicco DJ, Becker LA, Gitler AD, Pulst SM, Youssef A, Hekman R, Havugimana PC, White CA, Blum BC, Ratti A, Bryant CD, Parkinson J, Lage K, Babu M, Yu H, Bader GD, Wolozin B, Emili A.
Cell Syst. 2020 Apr 22;10(4):333-350
PubMed Abstract - PDF
PROTEIN INTERACTION
Mitochondrial carrier homolog 2 (MTCH2) is necessary for AML survival
Khan DH, Mullokandov M, Wu Y, Voisin V, Gronda MV, Hurren R, Wang X, MacLean N, Jeyaraju DV, Jitkova Y, Xu GW, Laister RC, Seneviratne A, Blatman Z, Ketala T,Bader GD, Marhon SA, Carvalho DD, Minden MD, Gross A, Schimmer AD
Blood. 2020 Apr 16
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Medulloblastoma Arises from the Persistence of a Rare and Transient Sox2(+) Granule Neuron Precursor
Selvadurai HJ, Luis E, Desai K, Lan X, Vladoiu MC, Whitley O, Galvin C, Vanner RJ, Lee L, Whetstone H, Kushida M, Nowakowski T, Diamandis P, Hawkins C, Bader G, Kriegstein A, Taylor MD, Dirks PB
Cell Rep. 2020 Apr 14;31(2):107511
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
A reference map of the human binary protein interactome
Luck K, Kim DK, Lambourne L, Spirohn K, Begg BE, Bian W, Brignall R, Cafarelli T, Campos-Laborie FJ, Charloteaux B, Choi D, Coté AG, Daley M, Deimling S, Desbuleux A, Dricot A, Gebbia M, Hardy MF, Kishore N, Knapp JJ, Kovács IA, Lemmens I, Mee MW, Mellor JC, Pollis C, Pons C, Richardson AD, Schlabach S, Teeking B, Yadav A, Babor M, Balcha D, Basha O, Bowman-Colin C, Chin SF, Choi SG, Colabella C, Coppin G, D'Amata C, De Ridder D, De Rouck S, Duran-Frigola M, Ennajdaoui H, Goebels F, Goehring L, Gopal A, Haddad G, Hatchi E, Helmy M, Jacob Y, Kassa Y, Landini S, Li R, van Lieshout N, MacWilliams A, Markey D, Paulson JN, Rangarajan S, Rasla J, Rayhan A, Rolland T, San-Miguel A, Shen Y, Sheykhkarimli D, Sheynkman GM, Simonovsky E, Taşan M, Tejeda A, Tropepe V, Twizere JC, Wang Y, Weatheritt RJ, Weile J, Xia Y, Yang X, Yeger-Lotem E, Zhong Q, Aloy P, Bader GD, De Las Rivas J, Gaudet S, Hao T, Rak J, Tavernier J, Hill DE, Vidal M, Roth FP, Calderwood MA
Nature.2020 Apr;580(7803):402-408
PubMed Abstract - PDF
PROTEIN INTERACTION
The mitochondrial peptidase, neurolysin, regulates respiratory chain supercomplexformation and is necessary for AML viability
Mirali S, Botham A, Voisin V, Xu C, St-Germain J, Sharon D, Hoff FW, Qiu Y, Hurren R, Gronda M, Jitkova Y, Nachmias B, MacLean N, Wang X, Arruda A, Minden MD, Horton TM, Kornblau SM, Chan SM, Bader GD, Raught B, Schimmer AD
Sci Transl Med. 2020 Apr 8;12(538)
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Nanoparticle Uptake in a Spontaneous and Immunocompetent Woodchuck Liver Cancer Model
Liu LY, Ma XZ, Ouyang B, Ings DP, Marwah S, Liu J, Chen AY, Gupta R, Manuel J, Chen XC, Gage BK, Cirlan I, Khuu N, Chung S, Camat D, Cheng M, Sekhon M, Zagorovsky K, Abdou Mohamed MA, Thoeni C, Atif J, Echeverri J, Kollmann D, Fischer S, Bader GD, Chan WCW, Michalak TI, McGilvray ID, MacParland SA
ACS Nano. 2020 Apr 7
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Relapse fated latent diagnosis subclones in acute B lineage leukaemia are drug tolerant and possess distinct metabolic programs
Dobson SM, Garcia-Prat L, Vanner RJ, Wintersinger J, Waanders E, Gu Z, McLeod J, Gan OI, Grandal I, Payne-Turner D, Edmonson MN, Ma X, Fan Y, Voisin V, Chan-Seng-Yue M, Xie SZ, Hosseini M, Abelson S, Gupta P, Rusch M, Shao Y, Olsen SR, Neale G, Chan SM, Bader G, Easton J, Guidos CJ, Danska JS, Zhang J, Minden MD, Morris Q, Mullighan CG, Dick JE
Cancer Discov. 2020 Feb 21
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Potential Therapeutic Targets for Lung Repair During Human Ex Vivo Lung Perfusion
Wong A, Zamel R, Yeung J, Bader GD, Dos Santos CC, Bai X, Wang Y, Keshavjee S, Liu M
Eur Respir J. 2020 Feb 14
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
A network analysis to identify mediators of germline-driven differences in breast cancer prognosis.
Escala-Garcia M, Abraham J, Andrulis IL, Anton-Culver H, Arndt V, Ashworth A, Auer PL, Auvinen P, Beckmann MW, Beesley J, Behrens S, Benitez J, Bermisheva M,Blomqvist C, Blot W, Bogdanova NV, Bojesen SE, Bolla MK, Børresen-Dale AL, Brauch H, Brenner H, Brucker SY, Burwinkel B, Caldas C, Canzian F, Chang-Claude J, Chanock SJ, Chin SF, Clarke CL, Couch FJ, Cox A, Cross SS, Czene K, Daly MB, Dennis J, Devilee P, Dunn JA, Dunning AM, Dwek M, Earl HM, Eccles DM, Eliassen AH, Ellberg C, Evans DG, Fasching PA, Figueroa J, Flyger H, Gago-Dominguez M, Gapstur SM, García-Closas M, García-Sáenz JA, Gaudet MM, George A, Giles GG, Goldgar DE, González-Neira A, Grip M, Guénel P, Guo Q, Haiman CA, Håkansson N, Hamann U, Harrington PA, Hiller L, Hooning MJ, Hopper JL, Howell A, Huang CS, Huang G, Hunter DJ, Jakubowska A, John EM, Kaaks R, Kapoor PM, Keeman R, Kitahara CM, Koppert LB, Kraft P, Kristensen VN, Lambrechts D, Le Marchand L, Lejbkowicz F, Lindblom A, Lubiński J, Mannermaa A, Manoochehri M, Manoukian S, Margolin S, Martinez ME, Maurer T, Mavroudis D, Meindl A, Milne RL, Mulligan AM, Neuhausen SL, Nevanlinna H, Newman WG, Olshan AF, Olson JE, Olsson H, Orr N, Peterlongo P, Petridis C, Prentice RL, Presneau N, Punie K, Ramachandran D, Rennert G, Romero A, Sachchithananthan M, Saloustros E, Sawyer EJ, Schmutzler RK, Schwentner L, Scott C, Simard J, Sohn C, Southey MC, Swerdlow AJ, Tamimi RM, Tapper WJ, Teixeira MR, Terry MB, Thorne H, Tollenaar RAEM, Tomlinson I, Troester MA, Truong T, Turnbull C, Vachon CM, van der Kolk LE, Wang Q, Winqvist R, Wolk A, Yang XR, Ziogas A, Pharoah PDP, Hall P, Wessels LFA, Chenevix-Trench G, Bader GD, Dörk T, Easton DF, Canisius S, Schmidt MK
Nat Commun. 2020 Jan 16;11(1):312
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Pathway Commons 2019 Update: integration, analysis and exploration of pathway data
Rodchenkov I, Babur O, Luna A, Aksoy BA, Wong JV, Fong D, Franz M, Siper MC, Cheung M, Wrana M, Mistry H, Mosier L, Dlin J, Wen Q, O'Callaghan C, Li W, Elder G, Smith PT, Dallago C, Cerami E, Gross B, Dogrusoz U, Demir E, Bader GD, Sander C
Nucleic Acids Res. 2020 Jan 8
PubMed Abstract - PDF
PATHWAY DATABASE
2019
End-to-end Named Entity Recognition and Relation Extraction using Pre-trained Language Models
John Giorgi, Xindi Wang, Nicola Sahar, Won Young Shin, Gary D. Bader, Bo Wang
arXiv. 2019 Dec 20
arXiv - PDF
NATURAL LANGUAGE PROCESSING
Sphingolipid Modulation Activates Proteostasis Programs to Govern Human Hematopoietic Stem Cell Self-Renewal
Xie SZ, Garcia-Prat L, Voisin V, Ferrari R, Gan OI, Wagenblast E, Kaufmann KB, Zeng AGX, Takayanagi SI, Patel I, Lee EK, Jargstorf J, Holmes G, Romm G, Pan K, Shoong M, Vedi A, Luberto C, Minden MD, Bader GD, Laurenti E, Dick JE
Cell Stem Cell. 2019 Oct 11
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Single-cell transcriptomic profiling of the aging mouse brain
Ximerakis M, Lipnick SL, Innes BT, Simmons SK, Adiconis X, Dionne D, Mayweather BA, Nguyen L, Niziolek Z, Ozek C, Butty VL, Isserlin R, Buchanan SM, Levine SS, Regev A, Bader GD, Levin JZ, Rubin LL
Nat Neurosci. 2019 Oct;22(10):1696-1708
PubMed Abstract - PDF
SINGLE CELL GENOMICS
Rewiring of the Human Mitochondrial Interactome during Neuronal Reprogramming Reveals Regulators of the Respirasome and Neurogenesis
Moutaoufik MT, Malty R, Amin S, Zhang Q, Phanse S, Gagarinova A, Zilocchi M, Hoell L, Minic Z, Gagarinova M, Aoki H, Stockwell J, Jessulat M, Goebels F, Broderick K, Scott NE, Vlasblom J, Musso G, Prasad B, Lamantea E, Garavaglia B, Rajput A, Murayama K, Okazaki Y, Foster LJ, Bader GD, Cayabyab FS, Babu M
iScience. 2019 Sep 4;19:1114-1132
PubMed Abstract - PDF
NETWORK ANALYSIS SOFTWARE
Benchmarking to the Gold Standard: Hyaluronan-Oxime Hydrogels Recapitulate Xenograft Models with In Vitro Breast Cancer Spheroid Culture
Baker AEG, Bahlmann LC, Tam RY, Liu JC, Ganesh AN, Mitrousis N, Marcellus R, Spears M, Bartlett JMS, Cescon DW, Bader GD, Shoichet MS
Adv Mater. 2019 Jul 19;31(36)
PubMed Abstract - PDF
NETWORK ANALYSIS SOFTWARE
EPIC: software toolkit for elution profile-based inference of protein complexes
Hu LZ, Goebels F, Tan JH, Wolf E, Kuzmanov U, Wan C, Phanse S, Xu C, Schertzberg M, Fraser AG, Bader GD, Emili A
Nat Methods. 2019 July 15
PubMed Abstract - PDF
NETWORK ANALYSIS SOFTWARE
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019
Schreiber F, Sommer B, Bader GD, Gleeson P, Golebiewski M, Hucka M, Keating SM, König M, Myers C, Nickerson D, Waltemath D. J
Integr Bioinform. 2019 Jul 13
PubMed Abstract - PDF
DATA STANDARDS
Towards reliable named entity recognition in the biomedical domain
Giorgi JM, Bader GD
Bioinformatics. 2019 Jun 20
PubMed Abstract - PDF
TEXT MINING
Bmi1 regulates human glioblastoma stem cells through activation of differential gene networks in CD133+ brain tumor initiating cells
Vora P, Seyfrid M, Venugopal C, Qazi MA, Salim S, Isserlin R, Subapanditha M, O'Farrell E, Mahendram S, Singh M, Bakhshinyan D, Chokshi C, McFarlane N, Dvorkin-Gheva A, Brown KR, Murty N, Moffat J, Bader GD, Singh SK
J Neurooncol. 2019 May 21
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
The Mitochondrial Transacylase, Tafazzin, Regulates for AML Stemness by Modulating Intracellular Levels of Phospholipids
Seneviratne AK, Xu M, Henao JJA, Fajardo VA, Hao Z, Voisin V, Xu GW, Hurren R, Kim S, MacLean N, Wang X, Gronda M, Jeyaraju D, Jitkova Y, Ketela T, Mullokandov M, Sharon D, Thomas G, Chouinard-Watkins R, Hawley JR, Schafer C, Yau HL, Khuchua Z, Aman A, Al-Awar R, Gross A, Claypool SM, Bazinet R, Lupien M, Chan S, De Carvalho DD, Minden MD, Bader GD, Stark KD, LeBlanc P, Schimmer AD
Cell Stem Cell. 2019 Mar 19
PubMed Abstract -PDF
PATHWAY AND NETWORK ANALYSIS
Exploring targets of TET2-mediated methylation reprogramming as potential discriminators of prostate cancer progression
Kamdar S, Isserlin R, Van der Kwast T, Zlotta AR, Bader GD, Fleshner NE, Bapat B
Clin Epigenetics. 2019 Mar 27;11(1):54
PubMed Abstract -PDF
PATHWAY AND NETWORK ANALYSIS
netDx: interpretable patient classification using integrated patient similarity networks
Pai S, Hui S, Isserlin R, Shah MA, Kaka H, Bader GD
Mol Syst Biol. 2019 Mar 14;15(3):e8497
PubMed Abstract -PDF
PRECISION MEDICINE
Evaluation of methods to assign cell type labels to cell clusters from single-cell RNA-sequencing data.
Diaz-Mejia JJ, Meng EC, Pico AR, MacParland SA, Ketela T, Pugh TJ, Bader GD, Morris JH
F1000Res. 2019 Mar 15;8. pii: ISCB Comm J-296
PubMed Abstract -PDF
SINGLE CELL GENOMICS
Powerful gene set analysis in GWAS with the Generalized Berk-Jones statistic
Sun R, Hui S, Bader GD, Lin X, Kraft P
PLoS Genet. 2019 Mar 15;15(3)
PubMed Abstract -PDF
PATHWAY AND NETWORK ANALYSIS
Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and EnrichmentMap
Reimand J, Isserlin R, Voisin V, Kucera M, Tannus-Lopes C, Rostamianfar A, Wadi L, Meyer M, Wong J, Xu C, Merico D, Bader GD
Nat Protoc. 2019 Feb;14(2):482-517
PubMed Abstract -PDF
PATHWAY AND NETWORK ANALYSIS
ARGLU1 is a transcriptional coactivator and splicing regulator important for stress hormone signaling and development
Magomedova L, Tiefenbach J, Zilberman E, Le Billan F, Voisin V, Saikali M, Boivin V, Robitaille M, Gueroussov S, Irimia M, Ray D, Patel R, Xu C, Jeyasuria P, Bader GD, Hughes TR, Morris QD, Scott MS, Krause H, Angers S, Blencowe BJ, Cummins CL
Nucleic Acids Res. 2019 Jan 30
PubMed Abstract -PDF
PATHWAY AND NETWORK ANALYSIS
2018
Induction of rod versus cone photoreceptor-specific progenitors from retinal precursor cells
Khalili S, Ballios BG, Belair-Hickey J, Donaldson L, Liu J, Coles BLK, Grisé KN, Baakdhah T, Bader GD, Wallace VA, Bernier G, Shoichet MS, van der Kooy D
Stem Cell Res. 2018 Nov 13;33:215-227
PubMed Abstract -PDF
PATHWAY AND NETWORK ANALYSIS
The Relative Contributions of Cell-Dependent Cortical Microcircuit Aging to Cognition and Anxiety
Shukla R, Prevot TD, French L, Isserlin R, Rocco BR, Banasr M, Bader GD, Sibille E
Biol Psychiatry. 2018 Oct 5
PubMed Abstract -PDF
PATHWAY AND NETWORK ANALYSIS
Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations
MacParland SA, Liu, JC, Ma X, Innes BT, Bartczak AM, Gage BK, Manuel J, Khuu N, Echeverri J, Linares I, Gupta R, Cheng ML, Liu LY, Camat D, Chung SW, Seliga RK, Shao Z, Lee E, Ogawa S, Ogawa M, Wilson MD, Fish JE, Selzner M, Ghanekar A, Grant D, Greig P, Sapisochin G, Selzner N, Winegarden N, Adeyi O, Keller G, Bader GD, McGilvray ID
Nat Commun. 2018 Oct 22;9(1):4383
PubMed Abstract -PDF
SINGLE CELL GENOMICS
scClustViz - Single-cell RNAseq cluster assessment and visualization
Innes BT, Bader GD
F1000Res. 2018 Sep 21;7
PubMed Abstract -PDF
SINGLE CELL GENOMICS
The Human Cell Atlas White Paper
Aviv Regev, Sarah Teichmann, Orit Rozenblatt-Rosen, Michael Stubbington, Kristin Ardlie, Ido Amit, Paola Arlotta, Gary Bader, Christophe Benoist, Moshe Biton, Bernd Bodenmiller, Benoit Bruneau, Peter Campbell, Mary Carmichael, Piero Carninci, Leslie Castelo-Soccio, Menna Clatworthy, Hans Clevers, Christian Conrad, Roland Eils, Jeremy Freeman, Lars Fugger, Berthold Goettgens, Daniel Graham, Anna Greka, Nir Hacohen, Muzlifah Haniffa, Ingo Helbig, Robert Heuckeroth, Sekar Kathiresan, Seung Kim, Allon Klein, Bartha Knoppers, Arnold Kriegstein, Eric Lander, Jane Lee, Ed Lein, Sten Linnarsson, Evan Macosko, Sonya MacParland, Robert Majovski, Partha Majumder, John Marioni, Ian McGilvray, Miriam Merad, Musa Mhlanga, Shalin Naik, Martijn Nawijn, Garry Nolan, Benedict Paten, Dana Pe'er, Anthony Philippakis, Chris Ponting, Steve Quake, Jayaraj Rajagopal, Nikolaus Rajewsky, Wolf Reik, Jennifer Rood, Kourosh Saeb-Parsy, Herbert Schiller, Steve Scott, Alex Shalek, Ehud Shapiro, Jay Shin, Kenneth Skeldon, Michael Stratton, Jenna Streicher, Henk Stunnenberg, Kai Tan, Deanne Taylor, Adrian Thorogood, Ludovic Vallier, Alexander van Oudenaarden, Fiona Watt, Wilko Weicher, Jonathan Weissman, Andrew Wells, Barbara Wold, Ramnik Xavier, Xiaowei Zhuang, Human Cell Atlas Organizing Committee
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SINGLE CELL GENOMICS, PREPRINT
Single-Cell RNA Sequencing: A New Window into Cell Scale Dynamics
Dasgupta S, Bader GD, Goyal S
Biophys J. 2018 Aug 7;115(3):429-435
PubMed Abstract -PDF
SINGLE CELL GENOMICS
The Cytoscape Automation app article collection.
Demchak B, Otasek D, Pico AR, Bader GD, Ono K, Settle B, Sage E, Morris JH, Longabaugh W, Lopes C, Kucera M, Treister A, Schwikowski B, Molenaar P, Ideker T.
F1000Res. 2018 Jun 20;7:800
PubMed Abstract -PDF
PATHWAY AND NETWORK ANALYSIS
Mammary molecular portraits reveal lineage-specific features and progenitor cell vulnerabilities
Casey AE, Sinha A, Singhania R, Livingstone J, Waterhouse P, Tharmapalan P,Cruickshank J, Shehata M, Drysdale E, Fang H, Kim H, Isserlin R, Bailey S, Medina T, Deblois G, Shiah YJ, Barsyte-Lovejoy D, Hofer S, Bader G, Lupien M, Arrowsmith C, Knapp S, De Carvalho D, Berman H, Boutros PC, Kislinger T, Khokha R
J Cell Biol. 2018 Jun 19
PubMed Abstract -PDF
PATHWAY AND NETWORK ANALYSIS
GeneMANIA update 2018
Franz M, Rodriguez H, Lopes C, Zuberi K, Montojo J, Bader GD, Morris Q
Nucleic Acids Res. 2018 Jun 15
PubMed Abstract -PDF
PATHWAY AND NETWORK ANALYSIS
Transfer learning for biomedical named entity recognition with neural networks
Giorgi JM, Bader GD
Bioinformatics. 2018 Jun 1
PubMed Abstract -PDF
Patient Similarity Networks for Precision Medicine
Pai S, Bader GD
J Mol Biol. 2018 May 31
PubMed Abstract -PDF
PRECISION MEDICINE
Identification of CDC25 as a Common Therapeutic Target for Triple-Negative Breast Cancer
Liu JC, Granieri L, Shrestha M, Wang DY, Vorobieva I, Rubie EA, Jones R, Ju Y, Pellecchia G, Jiang Z, Palmerini CA, Ben-David Y, Egan SE, Woodgett JR, Bader GD, Datti A, Zacksenhaus E
Cell Rep. 2018 Apr 3;23(1):112-126
PubMed Abstract -PDF
PATHWAY AND NETWORK ANALYSIS
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017
Schreiber F, Bader GD, Gleeson P, Golebiewski M, Hucka M, Keating SM, Novère NL, Myers C, Nickerson D, Sommer B, Waltemath D
J Integr Bioinform. 2018 Mar 29
PubMed Abstract -PDF
DATA STANDARDS
Whole transcriptome analysis reveals differential gene expression profile reflecting macrophage polarization in response to influenza A H5N1 virus infection
Zhang N, Bao YJ, Tong AH, Zuyderduyn S, Bader GD, Malik Peiris JS, Lok S, Lee SM
BMC Med Genomics. 2018 Feb 23;11(1):20
PubMed Abstract -PDF
PATHWAY AND NETWORK ANALYSIS
2017
Developmental Emergence of Adult Neural Stem Cells as Revealed by Single-Cell Transcriptional Profiling
Yuzwa SA, Borrett MJ, Innes BT, Voronova A, Ketela T, Kaplan DR, Bader GD, Miller FD
Cell Rep. 2017 Dec 26;21(13):3970-3986
PubMed Abstract -PDF
SINGLE CELL GENOMICS
A Map of Human Mitochondrial Protein Interactions Linked to Neurodegeneration Reveals New Mechanisms of Redox Homeostasis and NF-κB Signaling
Malty RH, Aoki H, Kumar A, Phanse S, Amin S, Zhang Q, Minic Z, Goebels F, Musso G, Wu Z, Abou-Tok H, Meyer M, Deineko V, Kassir S, Sidhu V, Jessulat M, Scott NE, Xiong X, Vlasblom J, Prasad B, Foster LJ, Alberio T, Garavaglia B, Yu H, Bader GD, Nakamura K, Parkinson J, Babu M
Cell Syst. 2017 Nov 7. pii:S2405-4712(17)30447-7
PubMed Abstract -PDF
Association analysis identifies 65 new breast cancer risk loci
Michailidou K, Lindström S, Dennis J, Beesley J, Hui S, Kar S, Lemaçon A,Soucy P, Glubb D, Rostamianfar A, Bolla MK, Wang Q, Tyrer J, Dicks E, Lee A, Wang Z, Allen J, Keeman R, Eilber U, French JD, Qing Chen X, Fachal L, McCue K, McCart Reed AE, Ghoussaini M, Carroll JS, Jiang X, Finucane H, Adams M, Adank MA, Ahsan H, Aittomäki K, Anton-Culver H, Antonenkova NN, Arndt V, Aronson KJ, Arun B, Auer PL, Bacot F, Barrdahl M, Baynes C, Beckmann MW, Behrens S, Benitez J, Bermisheva M, Bernstein L, Blomqvist C, Bogdanova NV, Bojesen SE, Bonanni B, Børresen-Dale AL, Brand JS, Brauch H, Brennan P, Brenner H, Brinton L, Broberg P, Brock IW, Broeks A, Brooks-Wilson A, Brucker SY, Brüning T, Burwinkel B, Butterbach K, Cai Q, Cai H, Caldés T, Canzian F, Carracedo A, Carter BD, Castelao JE, Chan TL, David Cheng TY, Seng Chia K, Choi JY, Christiansen H, Clarke CL; NBCS Collaborators, Collée M, Conroy DM, Cordina-Duverger E, Cornelissen S, Cox DG, Cox A, Cross SS, Cunningham JM, Czene K, Daly MB, Devilee P, Doheny KF, Dörk T, Dos-Santos-Silva I, Dumont M, Durcan L, Dwek M, Eccles DM, Ekici AB, Eliassen AH, Ellberg C, Elvira M, Engel C, Eriksson M, Fasching PA, Figueroa J, Flesch-Janys D, Fletcher O, Flyger H, Fritschi L, Gaborieau V, Gabrielson M, Gago-Dominguez M, Gao YT, Gapstur SM, García-Sáenz JA, Gaudet MM, Georgoulias V, Giles GG, Glendon G, Goldberg MS, Goldgar DE, González-Neira A, Grenaker Alnæs GI, Grip M, Gronwald J, Grundy A, Guénel P, Haeberle L, Hahnen E, Haiman CA, Håkansson N, Hamann U, Hamel N, Hankinson S, Harrington P, Hart SN, Hartikainen JM, Hartman M, Hein A, Heyworth J, Hicks B, Hillemanns P, Ho DN, Hollestelle A, Hooning MJ, Hoover RN, Hopper JL, Hou MF, Hsiung CN, Huang G, Humphreys K, Ishiguro J, Ito H, Iwasaki M, Iwata H, Jakubowska A, Janni W, John EM, Johnson N, Jones K, Jones M, Jukkola-Vuorinen A, Kaaks R, Kabisch M, Kaczmarek K, Kang D, Kasuga Y, Kerin MJ, Khan S, Khusnutdinova E, Kiiski JI, Kim SW, Knight JA, Kosma VM, Kristensen VN, Krüger U, Kwong A, Lambrechts D, Le Marchand L, Lee E, Lee MH, Lee JW, Neng Lee C, Lejbkowicz F, Li J, Lilyquist J, Lindblom A, Lissowska J, Lo WY, Loibl S, Long J, Lophatananon A, Lubinski J, Luccarini C, Lux MP, Ma ESK, MacInnis RJ, Maishman T, Makalic E, Malone KE, Kostovska IM, Mannermaa A, Manoukian S, Manson JE, Margolin S, Mariapun S, Martinez ME, Matsuo K, Mavroudis D, McKay J, McLean C, Meijers-Heijboer H, Meindl A, Menéndez P, Menon U, Meyer J, Miao H, Miller N,Taib NAM, Muir K, Mulligan AM, Mulot C, Neuhausen SL, Nevanlinna H, Neven P, Nielsen SF, Noh DY, Nordestgaard BG, Norman A, Olopade OI, Olson JE, Olsson H, Olswold C, Orr N, Pankratz VS, Park SK, Park-Simon TW, Lloyd R, Perez JIA, Peterlongo P, Peto J, Phillips KA, Pinchev M, Plaseska-Karanfilska D, Prentice R, Presneau N, Prokofyeva D, Pugh E, Pylkäs K, Rack B, Radice P, Rahman N, Rennert G, Rennert HS, Rhenius V, Romero A, Romm J, Ruddy KJ, Rüdiger T, Rudolph A, Ruebner M, Rutgers EJT, Saloustros E, Sandler DP, Sangrajrang S, Sawyer EJ, Schmidt DF, Schmutzler RK, Schneeweiss A, Schoemaker MJ, Schumacher F, Schürmann P, Scott RJ, Scott C, Seal S, Seynaeve C, Shah M, Sharma P, Shen CY, Sheng G, Sherman ME, Shrubsole MJ, Shu XO, Smeets A, Sohn C, Southey MC, Spinelli JJ, Stegmaier C, Stewart-Brown S, Stone J, Stram DO, Surowy H, Swerdlow A, Tamimi R, Taylor JA, Tengström M, Teo SH, Beth Terry M, Tessier DC, Thanasitthichai S, Thöne K, Tollenaar RAEM, Tomlinson I, Tong L, Torres D, Truong T, Tseng CC, Tsugane S, Ulmer HU, Ursin G, Untch M, Vachon C, van Asperen CJ, Van Den Berg D, van den Ouweland AMW, van der Kolk L, van der Luijt RB, Vincent D, Vollenweider J, Waisfisz Q, Wang-Gohrke S, Weinberg CR, Wendt C, Whittemore AS, Wildiers H, Willett W, Winqvist R, Wolk A, Wu AH, Xia L, Yamaji T, Yang XR, Har Yip C, Yoo KY, Yu JC, Zheng W, Zheng Y, Zhu B, Ziogas A, Ziv E; ABCTB Investigators; ConFab/AOCS Investigators, Lakhani SR, Antoniou AC, Droit A, Andrulis IL, Amos CI, Couch FJ, Pharoah PDP, Chang-Claude J, Hall P, Hunter DJ, Milne RL, García-Closas M, Schmidt MK, Chanock SJ, Dunning AM, Edwards SL, Bader GD, Chenevix-Trench G, Simard J, Kraft P, Easton DF
Nature. 2017 Oct 23
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Identification of ten variants associated with risk of estrogen-receptor-negative breast cancer
Milne RL, Kuchenbaecker KB, Michailidou K, Beesley J, Kar S, Lindström S, Hui S, Lemaçon A, Soucy P, Dennis J, Jiang X, Rostamianfar A, Finucane H, Bolla MK, McGuffog L, Wang Q, Aalfs CM; ABCTB Investigators, Adams M, Adlard J, Agata S, Ahmed S, Ahsan H, Aittomäki K, Al-Ejeh F, Allen J, Ambrosone CB, Amos CI, Andrulis IL, Anton-Culver H, Antonenkova NN, Arndt V, Arnold N, Aronson KJ, Auber B, Auer PL, Ausems MGEM, Azzollini J, Bacot F, Balmaña J, Barile M, Barjhoux L, Barkardottir RB, Barrdahl M, Barnes D, Barrowdale D, Baynes C, Beckmann MW, Benitez J, Bermisheva M, Bernstein L, Bignon YJ, Blazer KR, Blok MJ, Blomqvist C, Blot W, Bobolis K, Boeckx B, Bogdanova NV, Bojesen A, Bojesen SE, Bonanni B, Børresen-Dale AL, Bozsik A, Bradbury AR, Brand JS, Brauch H, Brenner H, Bressac-de Paillerets B, Brewer C, Brinton L, Broberg P, Brooks-Wilson A, Brunet J, Brüning T, Burwinkel B, Buys SS, Byun J, Cai Q, Caldés T, Caligo MA, Campbell I, Canzian F, Caron O, Carracedo A, Carter BD, Castelao JE, Castera L, Caux-Moncoutier V, Chan SB, Chang-Claude J, Chanock SJ, Chen X, Cheng TD, Chiquette J, Christiansen H, Claes KBM, Clarke CL, Conner T, Conroy DM, Cook J, Cordina-Duverger E, Cornelissen S, Coupier I, Cox A, Cox DG, Cross SS, Cuk K, Cunningham JM, Czene K, Daly MB, Damiola F, Darabi H, Davidson R, De Leeneer K, Devilee P, Dicks E, Diez O, Ding YC, Ditsch N, Doheny KF, Domchek SM, Dorfling CM, Dörk T, Dos-Santos-Silva I, Dubois S, Dugué PA, Dumont M, Dunning AM, Durcan L, Dwek M, Dworniczak B, Eccles D, Eeles R, Ehrencrona H, Eilber U, Ejlertsen B, Ekici AB, Eliassen AH; EMBRACE, Engel C, Eriksson M, Fachal L, Faivre L, Fasching PA, Faust U, Figueroa J, Flesch-Janys D, Fletcher O, Flyger H, Foulkes WD, Friedman E, Fritschi L, Frost D, Gabrielson M, Gaddam P, Gammon MD, Ganz PA, Gapstur SM, Garber J, Garcia-Barberan V, García-Sáenz JA, Gaudet MM, Gauthier-Villars M, Gehrig A; GEMO Study Collaborators, Georgoulias V, Gerdes AM, Giles GG, Glendon G, Godwin AK, Goldberg MS, Goldgar DE, González-Neira A, Goodfellow P, Greene MH, Alnæs GIG, Grip M, Gronwald J, Grundy A, Gschwantler-Kaulich D, Guénel P, Guo Q, Haeberle L, Hahnen E, Haiman CA, Håkansson N, Hallberg E, Hamann U, Hamel N, Hankinson S, Hansen TVO, Harrington P, Hart SN, Hartikainen JM, Healey CS; HEBON, Hein A, Helbig S, Henderson A, Heyworth J, Hicks B, Hillemanns P, Hodgson S, Hogervorst FB, Hollestelle A, Hooning MJ, Hoover B, Hopper JL, Hu C, Huang G, Hulick PJ, Humphreys K, Hunter DJ, Imyanitov EN, Isaacs C, Iwasaki M, Izatt L, Jakubowska A, James P, Janavicius R, Janni W, Jensen UB, John EM, Johnson N, Jones K, Jones M, Jukkola-Vuorinen A, Kaaks R, Kabisch M, Kaczmarek K, Kang D, Kast K; kConFab/AOCS Investigators, Keeman R, Kerin MJ, Kets CM, Keupers M, Khan S, Khusnutdinova E, Kiiski JI, Kim SW, Knight JA, Konstantopoulou I, Kosma VM, Kristensen VN, Kruse TA, Kwong A, Lænkholm AV, Laitman Y, Lalloo F, Lambrechts D, Landsman K, Lasset C, Lazaro C, Le Marchand L, Lecarpentier J, Lee A, Lee E, Lee JW, Lee MH, Lejbkowicz F, Lesueur F, Li J, Lilyquist J, Lincoln A, Lindblom A, Lissowska J, Lo WY, Loibl S, Long J, Loud JT, Lubinski J, Luccarini C, Lush M, MacInnis RJ, Maishman T, Makalic E, Kostovska IM, Malone KE, Manoukian S, Manson JE, Margolin S, Martens JWM, Martinez ME, Matsuo K, Mavroudis D, Mazoyer S, McLean C, Meijers-Heijboer H, Menéndez P, Meyer J, Miao H, Miller A, Miller N, Mitchell G, Montagna M, Muir K, Mulligan AM, Mulot C, Nadesan S, Nathanson KL; NBSC Collaborators, Neuhausen SL, Nevanlinna H, Nevelsteen I, Niederacher D, Nielsen SF, Nordestgaard BG, Norman A, Nussbaum RL, Olah E, Olopade OI, Olson JE, Olswold C, Ong KR, Oosterwijk JC, Orr N, Osorio A, Pankratz VS, Papi L, Park-Simon TW, Paulsson-Karlsson Y, Lloyd R,Pedersen IS, Peissel B, Peixoto A, Perez JIA, Peterlongo P, Peto J, Pfeiler G,Phelan CM, Pinchev M, Plaseska-Karanfilska D, Poppe B, Porteous ME, Prentice R, Presneau N, Prokofieva D, Pugh E, Pujana MA, Pylkäs K, Rack B, Radice P, Rahman N, Rantala J, Rappaport-Fuerhauser C, Rennert G, Rennert HS, Rhenius V, Rhiem K, Richardson A, Rodriguez GC, Romero A, Romm J, Rookus MA, Rudolph A, Ruediger T,Saloustros E, Sanders J, Sandler DP, Sangrajrang S, Sawyer EJ, Schmidt DF, Schoemaker MJ, Schumacher F, Schürmann P, Schwentner L, Scott C, Scott RJ, Seal S, Senter L, Seynaeve C, Shah M, Sharma P, Shen CY, Sheng X, Shimelis H,Shrubsole MJ, Shu XO, Side LE, Singer CF, Sohn C, Southey MC, Spinelli JJ, Spurdle AB, Stegmaier C, Stoppa-Lyonnet D, Sukiennicki G, Surowy H, Sutter C, Swerdlow A, Szabo CI, Tamimi RM, Tan YY, Taylor JA, Tejada MI, Tengström M, Teo SH, Terry MB, Tessier DC, Teulé A, Thöne K, Thull DL, Tibiletti MG, Tihomirova L, Tischkowitz M, Toland AE, Tollenaar RAEM, Tomlinson I, Tong L, Torres D, Tranchant M, Truong T, Tucker K, Tung N, Tyrer J, Ulmer HU, Vachon C, van Asperen CJ, Van Den Berg D, van den Ouweland AMW, van Rensburg EJ, Varesco L, Varon-Mateeva R, Vega A, Viel A, Vijai J, Vincent D, Vollenweider J, Walker L, Wang Z, Wang-Gohrke S, Wappenschmidt B, Weinberg CR, Weitzel JN, Wendt C, Wesseling J, Whittemore AS, Wijnen JT, Willett W, Winqvist R, Wolk A, Wu AH, Xia L, Yang XR, Yannoukakos D, Zaffaroni D, Zheng W, Zhu B, Ziogas A, Ziv E, Zorn KK, Gago-Dominguez M, Mannermaa A, Olsson H, Teixeira MR, Stone J, Offit K, Ottini L, Park SK, Thomassen M, Hall P, Meindl A, Schmutzler RK, Droit A, Bader GD, Pharoah PDP, Couch FJ, Easton DF, Kraft P, Chenevix-Trench G, García-Closas M, Schmidt MK, Antoniou AC, Simard J
Nat Genet. 2017 Oct 23
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Comprehensive Analysis of the Human SH3 Domain Family Reveals a Wide Variety of Non-canonical Specificities
Teyra J, Huang H, Jain S, Guan X, Dong A, Liu Y, Tempel W, Min J, Tong Y, Kim PM, Bader GD, Sidhu SS
Structure. 2017 Aug 28. S0969-2126(17)30251-4
PubMed Abstract - PDF
PROTEIN INTERACTION
microRNA-143/145 loss induces Ras signaling to promote aggressive Pten-deficient basal-like breast cancer
Wang S, Liu JC, Ju Y, Pellecchia G, Voisin V, Wang DY, Leha L R, Ben-David Y, Bader GD, Zacksenhaus E
JCI Insight. 2017 Aug 3;2(15)
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
ASCL1 Reorganizes Chromatin to Direct Neuronal Fate and Suppress Tumorigenicity of Glioblastoma Stem Cells
Park NI, Guilhamon P, Desai K, McAdam RF, Langille E, O'Connor M, Lan X,Whetstone H, Coutinho FJ, Vanner RJ, Ling E, Prinos P, Lee L, Selvadurai H, Atwal G, Kushida M, Clarke ID, Voisin V, Cusimano MD, Bernstein M, Das S, Bader G, Arrowsmith CH, Angers S, Huang X, Lupien M, Dirks PB
Cell Stem Cell. 2017 Aug 3;21(2):209-224
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Tracing the origins of relapse in acute myeloid leukaemia to stem cells
Shlush LI, Mitchell A, Heisler L, Abelson S, Ng SWK, Trotman-Grant A, Medeiros JJF, Rao-Bhatia A, Jaciw-Zurakowsky I, Marke R, McLeod JL, Doedens M, Bader G, Voisin V, Xu C, McPherson JD, Hudson TJ, Wang JCY, Minden MD, Dick JE
Nature. 2017 Jul 6;547(7661):104-108
PubMed Abstract - PDF
Intertumoral Heterogeneity within Medulloblastoma Subgroups
Cavalli FMG, Remke M, Rampasek L, Peacock J, Shih DJH, Luu B, Garzia L,Torchia J, Nor C, Morrissy AS, Agnihotri S, Thompson YY, Kuzan-Fischer CM, Farooq H, Isaev K, Daniels C, Cho BK, Kim SK, Wang KC, Lee JY, Grajkowska WA, Perek-Polnik M, Vasiljevic A, Faure-Conter C, Jouvet A, Giannini C, Nageswara Rao AA, Li KKW, Ng HK, Eberhart CG, Pollack IF, Hamilton RL, Gillespie GY, Olson JM, Leary S, Weiss WA, Lach B, Chambless LB, Thompson RC, Cooper MK, Vibhakar R, Hauser P, van Veelen MC, Kros JM, French PJ, Ra YS, Kumabe T, López-Aguilar E, Zitterbart K, Sterba J, Finocchiaro G, Massimino M, Van Meir EG, Osuka S, Shofuda T, Klekner A, Zollo M, Leonard JR, Rubin JB, Jabado N, Albrecht S, Mora J, Van Meter TE, Jung S, Moore AS, Hallahan AR, Chan JA, Tirapelli DPC, Carlotti CG, Fouladi M, Pimentel J, Faria CC, Saad AG, Massimi L, Liau LM, Wheeler H, Nakamura H, Elbabaa SK, Perezpeña-Diazconti M, Chico Ponce de León F, Robinson S, Zapotocky M, Lassaletta A, Huang A, Hawkins CE, Tabori U, Bouffet E, Bartels U, Dirks PB, Rutka JT, Bader GD, Reimand J, Goldenberg A, Ramaswamy V, Taylor MD
Cancer Cell. 2017 Jun 12;31(6):737-754
PubMed Abstract - PDF
CANCER MUTATIONS
Spatial heterogeneity in medulloblastoma
Morrissy AS, Cavalli FM, Remke M, Ramaswamy V, Shih DJ, Holgado BL, Farooq H, Donovan LK, Garzia L, Agnihotri S, Kiehna EN, Mercier E, Mayoh C, Papillon-Cavanagh S, Nikbakht H, Gayden T, Torchia J, Picard D, Merino DM, Vladoiu M, Luu B, Wu X, Daniels C, Horswell S, Thompson YY, Hovestadt V, Northcott PA, Jones DT, Peacock J, Wang X, Mack SC, Reimand J, Albrecht S, Fontebasso AM, Thiessen N, Li Y, Schein JE, Lee D, Carlsen R, Mayo M, Tse K, Tam A, Dhalla N, Ally A, Chuah E, Cheng Y, Plettner P, Li HI, Corbett RD, Wong T, Long W, Loukides J, Buczkowicz P, Hawkins CE, Tabori U, Rood BR, Myseros JS, Packer RJ, Korshunov A, Lichter P, Kool M, Pfister SM, Schüller U, Dirks P, Huang A, Bouffet E, Rutka JT, Bader GD, Swanton C, Ma Y, Moore RA, Mungall AJ, Majewski J, Jones SJ, Das S, Malkin D, Jabado N, Marra MA, Taylor MD
Nat Genet. 2017 Apr 10
PubMed Abstract - PDF
CANCER MUTATIONS
Integrative cancer pharmacogenomics to infer large-scale drug taxonomy
El-Hachem N, Gendoo DM, Soltan Ghoraie L, Safikhani Z, Smirnov P, Chung C, Deng K, Fang A, Birkwood E, Ho C, Isserlin R, Bader G, Goldenberg A, Haibe-Kains B
Cancer Res. 2017 Mar 17
PubMed Abstract - PDF
NETWORK ANALYSIS
Leveraging increased cytoplasmic nucleoside kinase activity to target mtDNA and oxidative phosphorylation in AML
Liyanage SU, Hurren R, Voisin V, Bridon G, Wang X, Xu C, MacLean N, Siriwardena TP, Gronda M, Yehudai D, Sriskanthadevan S, Avizonis D, Shamas-Din A, Minden MD, Bader GD, Laposa R, Schimmer AD
Blood. 2017 Mar 10
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Integrated analysis of proteome, phosphotyrosine-proteome, tyrosine-kinome and tyrosine-phosphatome in acute myeloid leukemia
Tong J, Helmy M, Cavalli FM, Jin L, St-Germain J, Karisch R, Taylor P, Minden MD, Taylor MD, Neel BG, Bader GD, Moran MF
Proteomics. 2017 Feb 7.
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
2016
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016
Schreiber F, Bader GD, Gleeson P, Golebiewski M, Hucka M, Le Novère N, Myers C, Nickerson D, Sommer B, Walthemath D
J Integr Bioinform. 2016 Dec 18;13(3):289
PubMed Abstract - PDF
DATA STANDARDS
Integrated (epi)-Genomic Analyses Identify Subgroup-Specific Therapeutic Targets in CNS Rhabdoid Tumors
Torchia J, Golbourn B, Feng S, Ho KC, Sin-Chan P, Vasiljevic A, Norman JD, Guilhamon P, Garzia L, Agamez NR, Lu M, Chan TS, Picard D, de Antonellis P, Khuong-Quang DA, Planello AC, Zeller C, Barsyte-Lovejoy D, Lafay-Cousin L, Letourneau L, Bourgey M, Yu M, Gendoo DM, Dzamba M, Barszczyk M, Medina T, Riemenschneider AN, Morrissy AS, Ra YS, Ramaswamy V, Remke M, Dunham CP, Yip S, Ng HK, Lu JQ, Mehta V, Albrecht S, Pimentel J, Chan JA, Somers GR, Faria CC, Roque L, Fouladi M, Hoffman LM, Moore AS, Wang Y, Choi SA, Hansford JR, Catchpoole D, Birks DK, Foreman NK, Strother D, Klekner A, Bognár L, Garami M, Hauser P, Hortobágyi T, Wilson B, Hukin J, Carret AS, Van Meter TE, Hwang EI, Gajjar A, Chiou SH, Nakamura H, Toledano H, Fried I, Fults D, Wataya T, Fryer C, Eisenstat DD, Scheinemann K, Fleming AJ, Johnston DL, Michaud J, Zelcer S, Hammond R, Afzal S, Ramsay DA, Sirachainan N, Hongeng S, Larbcharoensub N, Grundy RG, Lulla RR, Fangusaro JR, Druker H, Bartels U, Grant R, Malkin D, McGlade CJ, Nicolaides T, Tihan T, Phillips J, Majewski J, Montpetit A, Bourque G, Bader GD, Reddy AT, Gillespie GY, Warmuth-Metz M, Rutkowski S, Tabori U, Lupien M, Brudno M, Schüller U, Pietsch T, Judkins AR, Hawkins CE, Bouffet E, Kim SK, Dirks PB, Taylor MD, Erdreich-Epstein A, Arrowsmith CH, De Carvalho DD, Rutka JT, Jabado N,Huang A
Cancer Cell. 2016 Dec 12;30(6):891-908
PubMed Abstract - PDF
Global neuroscience and mental health research: a bibliometrics case study
Buchan AMJ, Jurczyk E, Isserlin R, Bader GD
Scientometrics 109 (1), 515-531
PDF
NETWORK ANALYSIS SOFTWARE
AutoAnnotate: A Cytoscape app for summarizing networks with semantic annotations
Kucera M, Isserlin R, Arkhangorodsky A, Bader GD
F1000Res. 2016 Jul 15;5:1717
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Ten Simple Rules for Developing Public Biological Databases
Helmy M, Crits-Christoph A, Bader GD
PLoS Comput Biol. 2016 Nov 10;12(11)
PubMed Abstract -PDF
RB1 deficiency in triple-negative breast cancer induces mitochondrial protein translation
Jones RA, Robinson TJ, Liu JC, Shrestha M, Voisin V, Ju Y, Chung PE, Pellecchia G, Fell VL, Bae S, Muthuswamy L, Datti A, Egan SE, Jiang Z, Leone G, Bader GD, Schimmer A, Zacksenhaus E
J Clin Invest. 2016 Aug 29
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Ectopic miR-125a Expression Induces Long-Term Repopulating Stem Cell Capacity in Mouse and Human Hematopoietic Progenitors
Wojtowicz EE, Lechman ER, Hermans KG, Schoof EM, Wienholds E, Isserlin R, van Veelen PA, Broekhuis MJ, Janssen GM, Trotman-Grant A, Dobson SM, Krivdova G, Elzinga J, Kennedy J, Gan OI, Sinha A, Ignatchenko V, Kislinger T, Dethmers-Ausema B, Weersing E, Alemdehy MF, de Looper HW, Bader GD, Ritsema M, Erkeland SJ, Bystrykh LV, Dick JE, de Haan G
Cell Stem Cell. 2016 Jul 12. pii: S1934-5909(16)30158-8
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Transcriptomic analysis reveals abnormal muscle repair and remodeling in survivors of critical illness with sustained weakness
Walsh CJ, Batt J, Herridge MS, Mathur S, Bader GD, Hu P, Dos Santos CC
Sci Rep. 2016 Jul 14;6:29334
PubMed Abstract - PDF
Inhibition of Dopamine Receptor D4 Impedes Autophagic Flux, Proliferation, and Survival of Glioblastoma Stem Cells
Dolma S, Selvadurai HJ, Lan X, Lee L, Kushida M, Voisin V, Whetstone H, So M, Aviv T, Park N, Zhu X, Xu C, Head R, Rowland KJ, Bernstein M, Clarke ID, Bader G, Harrington L, Brumell JH, Tyers M, Dirks PB
Cancer Cell. 2016 Jun 13;29(6):859-73
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Frequent mutations in acetylation and ubiquitination sites suggest novel driver mechanisms of cancer
Narayan S, Bader GD, Reimand J
Genome Med. 2016 May 12;8(1):55
PubMed Abstract - PDF
CANCER MUTATIONS
Musashi-2 attenuates AHR signalling to expand human haematopoietic stem cells
Rentas S, Holzapfel NT, Belew MS, Pratt GA, Voisin V, Wilhelm BT, Bader GD, Yeo GW, Hope KJ
Nature. 2016 Apr 28;532(7600):508-11
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
HOX gene complement and expression in the planarian Schmidtea mediterranea
Currie KW, Brown DD, Zhu S, Xu C, Voisin V, Bader GD, Pearson BJ
Evodevo. 2016 Mar 30;7:7
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Social Network: a Cytoscape app for visualizing co-authorship networks
Kofia V, Isserlin R, Buchan AM, Bader GD
F1000Res. 2015 Aug 5;4:481
PubMed Abstract - PDF
NETWORK ANALYSIS SOFTWARE
Predicting physiologically relevant SH3 domain mediated protein-protein interactions in yeast
Jain S, Bader GD
Bioinformatics. 2016 Feb 9
PubMed Abstract - PDF
PROTEIN INTERACTION PREDICTION
miR-126 Regulates Distinct Self-Renewal Outcomes in Normal and Malignant Hematopoietic Stem Cells
Lechman ER, Gentner B, Ng SW, Schoof EM, van Galen P, Kennedy JA, Nucera S, Ciceri F, Kaufmann KB, Takayama N, Dobson SM, Trotman-Grant A, Krivdova G, Elzinga J, Mitchell A, Nilsson B, Hermans KG, Eppert K, Marke R, Isserlin R, Voisin V, Bader GD, Zandstra PW, Golub TR, Ebert BL, Lu J, Minden M, Wang JC, Naldini L, Dick JE
Cancer Cell. 2016 Apr 11;29(4):602-606
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Landscape of Human Breast Cancer Drivers, Vulnerabilities, and Resistance
Marcotte R, Sayad A, Brown KR, Sanchez-Garcia F, Reimand J, Haider M, Virtanen C, Bradner JE, Bader GD, Mills GB, Pe'er D, Moffat J, Neel BG
Cell. 2016 Jan 14;164(1-2):293-309
PubMed Abstract - PDF
CANCER MUTATIONS
Divergent clonal selection dominates medulloblastoma at recurrence
Morrissy AS, Garzia L, Shih DJ, Zuyderduyn S, Huang X, Skowron P, Remke M, Cavalli FM, Ramaswamy V, Lindsay PE, Jelveh S, Donovan LK, Wang X, Luu B, Zayne K, Li Y, Mayoh C, Thiessen N, Mercier E, Mungall KL, Ma Y, Tse K, Zeng T, Shumansky K, Roth AJ, Shah S, Farooq H, Kijima N, Holgado BL, Lee JJ, Matan-Lithwick S, Liu J, Mack SC, Manno A, Michealraj KA, Nor C, Peacock J, Qin L, Reimand J, Rolider A, Thompson YY, Wu X, Pugh T, Ally A, Bilenky M, Butterfield YS, Carlsen R, Cheng Y, Chuah E, Corbett RD, Dhalla N, He A, Lee D, Li HI, Long W, Mayo M, Plettner P, Qian JQ, Schein JE, Tam A, Wong T, Birol I, Zhao Y, Faria CC, Pimentel J, Nunes S, Shalaby T, Grotzer M, Pollack IF, Hamilton RL, Li XN, Bendel AE, Fults DW, Walter AW, Kumabe T, Tominaga T, Collins VP, Cho YJ, Hoffman C, Lyden D, Wisoff JH, Garvin JH, Stearns DS, Massimi L, Schüller U, Sterba J, Zitterbart K, Puget S, Ayrault O, Dunn SE, Tirapelli DP, Carlotti CG, Wheeler H, Hallahan AR, Ingram W, MacDonald TJ, Olson JJ, Van Meir EG, Lee JY, Wang KC, Kim SK, Cho BK, Pietsch T, Fleischhack G, Tippelt S, Ra YS, Bailey S, Lindsey JC, Clifford SC, Eberhart CG, Cooper MK, Packer RJ, Massimino M, Garre ML, Bartels U, Tabori U, Hawkins CE, Dirks P, Bouffet E, Rutka JT, Wechsler-Reya RJ, Weiss WA, Collier LS, Dupuy AJ, Korshunov A, Jones DT, Kool M, Northcott PA, Pfister SM, Largaespada DA, Mungall AJ, Moore RA, Jabado N, Bader GD, Jones SJ, Malkin D, Marra MA, Taylor MD
Nature. 2016 Jan 13. doi: 10.1038/nature16478
PubMed Abstract - PDF
CANCER MUTATIONS
2015
NetMatchStar: an enhanced Cytoscape network querying app
Rinnone F, Micale G, Bonnici V, Bader GD, Shasha D, Ferro A, Pulvirenti A,Giugno R F1000Res.2015 Aug 5;4:479
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Specifications of Standards in Systems and Synthetic Biology
Schreiber F, Bader GD, Golebiewski M, Hucka M, Kormeier B, Le Novère N, Myers C, Nickerson D, Sommer B, Waltemath D, Weise S
J Integr Bioinform. 2015 Sep 4;12(2):258
PubMed Abstract - PDF
DATA STANDARDS
Identification of CD146 as a marker enriched for tumor-propagating capacity reveals targetable pathways in primary human sarcoma
Wei Q, Tang YJ, Voisin V, Sato S, Hirata M, Whetstone H, Han I, Ailles L, Bader GD, Wunder J, Alman BA
Oncotarget. 2015 Oct 26.
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Antitumor activity of the novel multi-kinase inhibitor EC-70124 in triple negative breast cancer
Cuenca-López MD, Serrano-Heras G, Montero JC, Corrales-Sánchez V, Gomez-Juarez M, Gascón-Escribano MJ, Morales JC, Voisin V, Núñez LE, Morís F, Bader GD, Pandiella A, Ocaña A
Oncotarget. 2015 Sep 29;6(29):27923-37
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Systematic analysis of somatic mutations impacting gene expression in 12 tumour types
Ding J, McConechy MK, Horlings HM, Ha G, Chun Chan F, Funnell T, Mullaly SC, Reimand J, Bashashati A, Bader GD, Huntsman D, Aparicio S, Condon A, Shah SP
Nat Commun. 2015 Oct 5;6:8554
PubMed Abstract - PDF
CANCER MUTATIONS
Cytoscape.js: a graph theory library for visualisation and analysis
Franz M, Lopes CT, Huck G, Dong Y, Sumer O, Bader GD
Bioinformatics 2015 Sep 28
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
EAG2 potassium channel with evolutionarily conserved function as a brain tumor target
Huang X, He Y, Dubuc AM, Hashizume R, Zhang W, Reimand J, Yang H, Wang TA,Stehbens SJ, Younger S, Barshow S, Zhu S, Cooper MK, Peacock J, Ramaswamy V, Garzia L, Wu X, Remke M, Forester CM, Kim CC, Weiss WA, James CD, Shuman MA, Bader GD, Mueller S, Taylor MD, Jan YN, Jan LY
Nat Neurosci 2015 Aug 10
PubMed Abstract - PDF
CANCER MUTATIONS
GreedyPlus: An Algorithm for the Alignment of Interface Interaction Networks
Law B, Bader GD
Sci Rep 2015 Jul 13;5:12074
PubMed Abstract - PDF
PROTEIN INTERACTIONS
Inferring interaction type in gene regulatory networks using co-expression data
Khosravi P, Gazestani VH, Pirhaji L, Law B, Sadeghi M, Bader GD,Goliaei B
Algorithms Mol Biol 2015 Jul 8;10:23
PubMed Abstract - PDF
GENE REGULATORY INTERACTIONS
Canadian Open Genetics Repository (COGR): a unified clinical genomics database as a community resource for standardising and sharing genetic interpretations
Lerner-Ellis J, Wang M, White S, Lebo MS; Canadian Open Genetics Repository Group
J Med Genet 2015 Jul;52(7):438-45
PubMed Abstract - PDF
CANCER MUTATIONS
Pathway and network analysis of cancer genomes
Mutation Consequences and Pathway Analysis working group of the International Cancer Genome Consortium
Nat Methods 2015 Jun 30;12(7):615-21
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Cardioprotective Signature of Short-Term Caloric Restriction
Noyan H, El-Mounayri O, Isserlin R, Arab S, Momen A, Cheng HS, Wu J, Afroze T,Li RK, Fish JE, Bader GD, Husain M
PLoS One 2015 Jun 22;10(6)
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Inhibition of the Mitochondrial Protease ClpP as a Therapeutic Strategy for Human Acute Myeloid Leukemia
Cole A, Wang Z, Coyaud E, Voisin V, Gronda M, Jitkova Y, Mattson R, Hurren R, Babovic S, Maclean N, Restall I, Wang X, Jeyaraju DV, Sukhai MA, Prabha S, Bashir S, Ramakrishnan A, Leung E, Qia YH, Zhang N, Combes KR, Ketela T, Lin F, Houry WA, Aman A, Al-Awar R, Zheng W, Wienholds E, Xu CJ, Dick J, Wang JC, Moffat J, Minden MD, Eaves CJ, Bader GD, Hao Z, Kornblau SM, Raught B, Schimmer AD
Cancer Cell 2015 Jun 8;27(6):864-76
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
MIMP: predicting the impact of mutations on kinase-substrate phosphorylation
Wagih O, Reimand J, Bader GD
Nat Methods 2015 Jun;12(6):531-3
PubMed Abstract - PDF
CANCER MUTATIONS
Molecular Classification of Ependymal Tumors across All CNS Compartments, Histopathological Grades, and Age Groups
Pajtler KW, Witt H, Sill M, Jones DT, Hovestadt V, Kratochwil F, Wani K, Tatevossian R, Punchihewa C, Johann P, Reimand J, Warnatz HJ, Ryzhova M, Mack S, Ramaswamy V, Capper D, Schweizer L, Sieber L, Wittmann A, Huang Z, van Sluis P, Volckmann R, Koster J, Versteeg R, Fults D, Toledano H, Avigad S, Hoffman LM, Donson AM, Foreman N, Hewer E, Zitterbart K, Gilbert M, Armstrong TS, Gupta N, Allen JC, Karajannis MA, Zagzag D, Hasselblatt M, Kulozik AE, Witt O, Collins VP, von Hoff K, Rutkowski S, Pietsch T, Bader G, Yaspo ML, von Deimling A, Lichter P, Taylor MD, Gilbertson R, Ellison DW, Aldape K, Korshunov A, Kool M, Pfister SM
Cancer Cell 2015 May 11;27(5):728-43
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Metabolomic profiling in liver of adiponectin knockout mice uncovers lysophospholipid metabolism as an important target of adiponectin action
Liu Y, Sen S, Wannaiampikul S, Palanivel R, Hoo RL, Isserlin R, Bader GD, Tungtrongchitr R, Deshaies Y, Xu A, Sweeney G
Biochem J 2015 Jul 1;469(1):71-82
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Long read nanopore sequencing for detection of HLA and CYP2D6 variants and haplotypes
Ammar R, Paton TA, Torti D, Shlien A, Bader GD
F1000Res 2015 Jan 21;4:17
PubMed Abstract - PDF
DNA SEQUENCING
Molecular subgroups of atypical teratoid rhabdoid tumours in children: an integrated genomic and clinicopathological analysis
Torchia J, Picard D, Lafay-Cousin L, Hawkins CE, Kim SK, Letourneau L, Ra YS, Ho KC, Chan TS, Sin-Chan P, Dunham CP, Yip S, Ng HK, Lu JQ, Albrecht S, Pimentel J, Chan JA, Somers GR, Zielenska M, Faria CC, Roque L, Baskin B, Birks D, Foreman N, Strother D, Klekner A, Garami M, Hauser P, Hortobágyi T, Bognár L, Wilson B, Hukin J, Carret AS, Van Meter TE, Nakamura H, Toledano H, Fried I, Fults D, Wataya T, Fryer C, Eisenstat DD, Scheineman K, Johnston D, Michaud J, Zelcer S,Hammond R, Ramsay DA, Fleming AJ, Lulla RR, Fangusaro JR, Sirachainan N, Larbcharoensub N, Hongeng S, Barakzai MA, Montpetit A, Stephens D, Grundy RG, Schüller U, Nicolaides T, Tihan T, Phillips J, Taylor MD, Rutka JT, Dirks P, Bader GD, Warmuth-Metz M, Rutkowski S, Pietsch T, Judkins AR, Jabado N, Bouffet E, Huang A
Lancet Oncol 2015 May;16(5):569-82
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Promoting Coordinated Development of Community-Based Information Standards for Modeling in Biology: The COMBINE Initiative
Hucka M, Nickerson DP, Bader GD, Bergmann FT, Cooper J, Demir E, Garny A, Golebiewski M, Myers CJ, Schreiber F, Waltemath D, Le Novère N
Front Bioeng Biotechnol 2015 Feb 24;3:19
PubMed Abstract - PDF
DATA STANDARDS
IL-7 coordinates proliferation, differentiation and Tcra recombination during thymocyte β-selection
Boudil A, Matei IR, Shih HY, Bogdanoski G, Yuan JS, Chang SG, Montpellier B,Kowalski PE, Voisin V, Bashir S, Bader GD, Krangel MS, Guidos CJ
Nat Immunol 2015 Apr;16(4):397-405
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
A Progesterone-CXCR4 Axis Controls Mammary Progenitor Cell Fate in the Adult Gland.
Shiah YJ, Tharmapalan P, Casey AE, Joshi PA, McKee TD, Jackson HW, Beristain AG, Chan-Seng-Yue MA, Bader GD, Lydon JP, Waterhouse PD, Boutros PC, Khokha R
Stem Cell Reports. 2015 Mar 10;4(3):313-322
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Evolutionary Constraint and Disease Associations of Post-Translational Modification Sites in Human Genomes
Reimand J, Wagih O, Bader GD
PLoS Genet 2015 Jan 22;11(1)
PubMed Abstract - PDF
CANCER MUTATIONS
Single cell-derived clonal analysis of human glioblastoma links functional and genomic heterogeneity
Meyer M, Reimand J, Lan X, Head R, Zhu X, Kushida M, Bayani J, Pressey JC, Lionel AC, Clarke ID, Cusimano M, Squire JA, Scherer SW, Bernstein M, Woodin MA, Bader GD, Dirks PB
Proc Natl Acad Sci U S A 2015 Jan 20;112(3):851-6
Pubmed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
2014
Systems analysis reveals down-regulation of a network of pro-survival miRNAs drives the apoptotic response in dilated cardiomyopathy
Isserlin R, Merico D, Wang D, Vuckovic D, Bousette N, Gramolini AO, Bader GD, Emili A
Mol Biosyst 2015 Jan;11(1):239-51
Pubmed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Combined deletion of Pten and p53 in mammary epithelium accelerates triple-negative breast cancer with dependency on eEF2K
Liu JC, Voisin V, Wang S, Wang DY, Jones RA, Datti A, Uehling D, Al-Awar R, Egan SE, Bader GD, Tsao M, Mak TW, Zacksenhaus E
EMBO Mol Med 2014 Oct 20;6(12):1542-60
Pubmed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Novel function discovery with GeneMANIA: a new integrated resource for gene function prediction in Escherichia coli
James Vlasblom, Khalid Zuberi, Harold Rodriguez, Roland Arnold, Alla Gagarinova, Viktor Deineko, Ashwani Kumar, Elisa Leung, Kamran Rizzolo, Bahram Samanfar, Luke Chang, Sadhna Phanse, Ashkan Golshani, Jack F. Greenblatt, Walid A. Houry, Andrew Emili, Quaid Morris, Gary Bader, Mohan Babu
Bioinformatics 2015 Feb 1;31(3):306-10
Pubmed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
The Cytoscape app article collection
Pico AR, Bader GD, Demchak B, Guitart Pla O, Hull T, Longabaugh W, Lopes C,Lotia S, Molenaar P, Montojo J, Morris JH, Ono K, Schwikowski B, Welker D, Ideker T.
F1000Res 2014 Jul 1;3:138.
Pubmed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
GeneMANIA: Fast gene network construction and function prediction for Cytoscape
Jason Montojo,Khalid Zuberi, Harold Rodriguez, Gary D. Bader, Quaid Morris
F1000Res 2014 Jul 1;3:153
Pubmed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Enrichment Map - a Cytoscape app to visualize and explore OMICs pathway enrichment results
Isserlin R, Merico D, Voisin V, Bader GD
F1000Res 2014 Jul 1;3:141
Pubmed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Intercellular network structure and regulatory motifs in the human hematopoietic system
Qiao W, Wang W, Laurenti E, Turinsky AL, Wodak SJ, Bader GD, Dick JE, Zandstra PW
Mol Syst Biol 2014 Jul 15;10(7):741
Pubmed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma
Northcott PA, Lee C, Zichner T, Stütz AM, Erkek S, Kawauchi D, Shih DJ, Hovestadt V, Zapatka M, Sturm D, Jones DT, Kool M, Remke M, Cavalli FM, Zuyderduyn S, Bader GD, VandenBerg S, Esparza LA, Ryzhova M, Wang W, Wittmann A, Stark S, Sieber L, Seker-Cin H, Linke L, Kratochwil F, Jäger N, Buchhalter I, Imbusch CD, Zipprich G, Raeder B, Schmidt S, Diessl N, Wolf S, Wiemann S, Brors B, Lawerenz C, Eils J, Warnatz HJ, Risch T, Yaspo ML, Weber UD, Bartholomae CC, von Kalle C, Turányi E, Hauser P, Sanden E, Darabi A, Siesjö P, Sterba J, Zitterbart K, Sumerauer D, van Sluis P, Versteeg R, Volckmann R, Koster J, Schuhmann MU, Ebinger M, Grimes HL, Robinson GW, Gajjar A, Mynarek M, von Hoff K, Rutkowski S, Pietsch T, Scheurlen W, Felsberg J, Reifenberger G, Kulozik AE, von Deimling A, Witt O, Eils R, Gilbertson RJ, Korshunov A, Taylor MD, Lichter P, Korbel JO, Wechsler-Reya RJ, Pfister SM
Nature 2014 Jul 24;511(7510):428-34
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Quiescent Sox2+ Cells Drive Hierarchical Growth and Relapse in Sonic Hedgehog Subgroup Medulloblastoma
Vanner RJ, Remke M, Gallo M, Selvadurai HJ, Coutinho F, Lee L, Kushida M, Head R, Morrissy S, Zhu X, Aviv T, Voisin V, Clarke ID, Li Y, Mungall AJ, Moore RA, Ma Y, Jones SJ, Marra MA, Malkin D, Northcott PA, Kool M, Pfister SM, Bader G, Hochedlinger K, Korshunov A, Taylor MD, Dirks PB
Cancer Cell 2014 Jul 14;26(1):33-47
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Network Assessor: an automated method for quantitative assessment of a network's potential for gene function prediction
Montojo J, Zuberi K, Shao Q, Bader GD, Morris Q
Front Genet 2014 May 16;5:123
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
A draft map of the human proteome
Kim MS, Pinto SM, Getnet D, Nirujogi RS, Manda SS, Chaerkady R, Madugundu AK, Kelkar DS, Isserlin R, Jain S, Thomas JK, Muthusamy B, Leal-Rojas P, Kumar P, Sahasrabuddhe NA, Balakrishnan L, Advani J, George B, Renuse S, Selvan LD, Patil AH, Nanjappa V, Radhakrishnan A, Prasad S, Subbannayya T, Raju R, Kumar M, Sreenivasamurthy SK, Marimuthu A, Sathe GJ, Chavan S, Datta KK, Subbannayya Y, Sahu A, Yelamanchi SD, Jayaram S, Rajagopalan P, Sharma J, Murthy KR, Syed N, Goel R, Khan AA, Ahmad S, Dey G, Mudgal K, Chatterjee A, Huang TC, Zhong J, Wu X, Shaw PG, Freed D, Zahari MS, Mukherjee KK, Shankar S, Mahadevan A, Lam H, Mitchell CJ, Shankar SK, Satishchandra P, Schroeder JT, Sirdeshmukh R, Maitra A, Leach SD, Drake CG, Halushka MK, Prasad TS, Hruban RH, Kerr CL, Bader GD, Iacobuzio-Donahue CA, Gowda H, Pandey A
Nature 2014 May 29;509(7502):575-81
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Mapping the cellular response to small molecules using chemogenomic fitness signatures
Lee AY, St Onge RP, Proctor MJ, Wallace IM, Nile AH, Spagnuolo PA, Jitkova Y, Gronda M, Wu Y, Kim MK, Cheung-Ong K, Torres NP, Spear ED, Han MK, Schlecht U, Suresh S, Duby G, Heisler LE, Surendra A, Fung E, Urbanus ML, Gebbia M, Lissina E, Miranda M, Chiang JH, Aparicio AM, Zeghouf M, Davis RW, Cherfils J, Boutry M, Kaiser CA, Cummins CL, Trimble WS, Brown GW, Schimmer AD, Bankaitis VA, Nislow C, Bader GD, Giaever G
Science 2014 Apr 11;344(6180):208-11
PubMed Abstract - PDF
CHEMICAL GENOMICS
Prediction and Experimental Characterization of nsSNPs Altering Human PDZ-Binding Motifs
Gfeller D, Ernst A, Jarvik N, Sidhu SS, Bader GD
PLoS One 2014 Apr 10;9(4):e94507
PubMed Abstract - PDF
FUNCTIONAL MUTATION ANALYSIS
HyperModules: identifying clinically and phenotypically significant network modules with disease mutations for biomarker discovery
Leung A, Bader GD, Reimand J
Bioinformatics 2014 Apr 8
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Genome sequencing of SHH medulloblastoma predicts genotype-related response to smoothened inhibition
Kool M, Jones DT, Jäger N, Northcott PA, Pugh TJ, Hovestadt V, Piro RM, Esparza LA, Markant SL, Remke M, Milde T, Bourdeaut F, Ryzhova M, Sturm D, Pfaff E, Stark S, Hutter S, Seker-Cin H, Johann P, Bender S, Schmidt C, Rausch T, Shih D, Reimand J, Sieber L, Wittmann A, Linke L, Witt H, Weber UD, Zapatka M, König R, Beroukhim R, Bergthold G, van Sluis P, Volckmann R, Koster J, Versteeg R, Schmidt S, Wolf S, Lawerenz C, Bartholomae CC, von Kalle C, Unterberg A, Herold-Mende C, Hofer S, Kulozik AE, von Deimling A, Scheurlen W, Felsberg J, Reifenberger G, Hasselblatt M, Crawford JR, Grant GA, Jabado N, Perry A, Cowdrey C, Croul S, Zadeh G, Korbel JO, Doz F, Delattre O, Bader GD, McCabe MG, Collins VP, Kieran MW, Cho YJ, Pomeroy SL, Witt O, Brors B, Taylor MD, Schüller U, Korshunov A, Eils R, Wechsler-Reya RJ, Lichter P, Pfister SM, ICGC PedBrain Tumor Project
Cancer Cell 2014 Mar 17;25(3):393-405
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Highlights of B/D-HPP and HPP Resource Pillar Workshops at Yokohama 12th Annual HUPO World Congress of Proteomics
Aebersold R, Bader GD, Edwards AM, van Eyk J, Kussman M, Qin J, Omenn GS
Proteomics 2014 May;14(9):975-88
PubMed Abstract - PDF
PROTEOMICS
Epigenomic alterations define lethal CIMP-positive ependymomas of infancy
Mack SC, Witt H, Piro RM, Gu L, Zuyderduyn S, Stütz AM, Wang X, Gallo M, Garzia L, Zayne K, Zhang X, Ramaswamy V, Jäger N, Jones DT, Sill M, Pugh TJ, Ryzhova M, Wani KM, Shih DJ, Head R, Remke M, Bailey SD, Zichner T, Faria CC, Barszczyk M, Stark S, Seker-Cin H, Hutter S, Johann P, Bender S, Hovestadt V, Tzaridis T, Dubuc AM, Northcott PA, Peacock J, Bertrand KC, Agnihotri S, Cavalli FM, Clarke I, Nethery-Brokx K, Creasy CL, Verma SK, Koster J, Wu X, Yao Y, Milde T, Sin-Chan P, Zuccaro J, Lau L, Pereira S, Castelo-Branco P, Hirst M, Marra MA, Roberts SS, Fults D, Massimi L, Cho YJ, Van Meter T, Grajkowska W, Lach B, Kulozik AE, von Deimling A, Witt O, Scherer SW, Fan X, Muraszko KM, Kool M, Pomeroy SL, Gupta N, Phillips J, Huang A, Tabori U, Hawkins C, Malkin D, Kongkham PN, Weiss WA, Jabado N, Rutka JT, Bouffet E, Korbel JO, Lupien M, Aldape KD, Bader GD, Eils R, Lichter P, Dirks PB, Pfister SM, Korshunov A, Taylor MD
Nature 2014 Feb 27;506(7489):445-50
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
2013
TCGA pan-cancer project, thread 2: Network models
Reimand J, Bader GD, Adam Margolin, Abel Gonzalez-Perez, David Tamborero, Nuria Lopez-Bigas, John Weinstein, Joshua Stuart, Myles Axton
Nature Genetics (2013) doi:10.1038/ng.2787
CANCER MUTATIONS, NETWORKS
Coordinate microRNA-mediated regulation of protein complexes in prostate cancer
Alshalalfa M, Bader GD, Bismar TA, Alhajj R
PLoS One 2013 Dec 31;8(12):e84261
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Comprehensive identification of mutational cancer driver genes across 12 tumor types
Tamborero D, Gonzalez-Perez A, Perez-Llamas C, Deu-Pons J, Kandoth C, Reimand J, Lawrence MS, Getz G, Bader GD, Ding L, Lopez-Bigas N
Sci Rep 2013 Oct 2;3:2650
PubMed Abstract - PDF
CANCER MUTATIONS
The mutational landscape of phosphorylation signaling in cancer
Reimand J, Wagih O, Bader GD
Sci Rep 2013 Oct 2;3:2651
PubMed Abstract - PDF
CANCER MUTATIONS, NETWORKS
Using biological pathway data with paxtools
Demir E, Babur O, Rodchenkov I, Aksoy BA, Fukuda KI, Gross B, Sümer OS, Bader GD, Sander C.
PLoS Comput Biol 2013;9(9):e1003194
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
The BioPAX Validator
Rodchenkov I, Demir E, Sander C, Bader GD
Bioinformatics 2013 Oct 15;29(20):2659-60
PubMed Abstract - PDF
DATA STANDARD
Computational approaches to identify functional genetic variants in cancer genomes
Gonzalez-Perez A, Mustonen V, Reva B, Ritchie GR, Creixell P, Karchin R, Vazquez M, Fink JL, Kassahn KS, Pearson JV, Bader GD, Boutros PC, Muthuswamy L, Ouellette BF, Reimand J, Linding R, Shibata T, Valencia A, Butler A, Dronov S, Flicek P, Shannon NB, Carter H, Ding L, Sander C, Stuart JM, Stein LD, Lopez-Bigas N; International Cancer Genome Consortium Mutation Pathways and Consequences Subgroup of the Bioinformatics Analyses Working Group
Nature Methods 2013 Aug;10(8):723-9
PubMed Abstract - PDF
CANCER MUTATIONS
GeneMANIA prediction server 2013 update
Zuberi K, Franz M, Rodriguez H, Montojo J, Lopes CT, Bader GD, Morris Q
Nucleic Acids Res 2013 Jul;41(Web Server issue):W115-22
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Cytoscape App Store
Lotia S, Montojo J, Dong Y, Bader GD, Pico AR
Bioinformatics 2013 May 15;29(10):1350-1
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
SH3 interactome conserves general function over specific form
Xin X, Gfeller D, Cheng J, Tonikian R, Sun L, Guo A, Lopez L, Pavlenco A, Akintobi A, Zhang Y, Rual JF, Currell B, Seshagiri S, Hao T, Yang X, Shen YA, Salehi-Ashtiani K, Li J, Cheng AT, Bouamalay D, Lugari A, Hill DE, Grimes ML, Drubin DG, Grant BD, Vidal M, Boone C, Sidhu SS, Bader GD
Mol Syst Biol 2013 Apr 2;9:652
Pubmed Abstract - PDF
Interactions in Intact Database
PROTEIN INTERACTION PREDICTION
Metabolic adaptation to chronic inhibition of mitochondrial protein synthesis in acute myeloid leukemia cells
Jhas B, Sriskanthadevan S, Skrtic M, Sukhai MA, Voisin V, Jitkova Y, Gronda M, Hurren R, Laister RC, Bader GD, Minden MD, Schimmer AD.
PLoS One 2013;8(3):e58367
Pubmed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Systematic analysis of somatic mutations in phosphorylation signaling predicts novel cancer drivers
Reimand J, Bader GD
Mol Syst Biol 2013;9:637
PubMed Abstract - PDF
Research Highlight in Genome Medicine (2013)
CANCER MUTATIONS, SIGNALING NETWORKS
Predicting PDZ domain mediated protein interactions from structure
Hui S, Xing X, Bader GD
BMC Bioinformatics 2013 Jan 21;14:27
PubMed Abstract - PDF
PROTEIN INTERACTION PREDICTION
Integrative pathway dissection of molecular mechanisms of moxLDL-induced vascular smooth muscle phenotype transformation
Karagiannis GS, Weile J, Bader GD, Minta J.
BMC Cardiovasc Disord 2013 Jan 16;13:4
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
GESTODIFFERENT: A Cytoscape plugin for the generation and the identification of Gene Regulatory Networks describing a stochastic cell differentiation process
Marco Antoniotti, Gary D. Bader, Giulio Caravagna, Silvia Crippa, Alex Graudenzi and Giancarlo Mauri
Bioinformatics 2013 Feb 15;29(4):513-4
PubMed Abstract - PDF
NETWORK SIMULATION
2012
The Biology/Disease-driven Human Proteome Project (B/D-HPP): Enabling Protein Research for the Life Sciences Community
Aebersold R, Bader GD, Edwards AM, van Eyk JE, Kussmann M, Qin J, Omenn GS
J Proteome Res 2013 Jan 4;12(1):23-7
PubMed Abstract - PDF
PROTEOMICS
Chromatin is an ancient innovation conserved between Archaea and Eukarya
Ammar R, Torti D, Tsui K, Gebbia M, Durbic T, Bader GD, Giaever G, Nislow C
Elife 2012 Dec 13;1:e00078
PubMed Abstract - PDF
ANALYSIS OF ARCHAEAL CHROMATIN
Attenuation of miR-126 Activity Expands HSC In Vivo without Exhaustion
Lechman ER, Gentner B, van Galen P, Giustacchini A, Saini M, Boccalatte FE, Hiramatsu H, Restuccia U, Bachi A, Voisin V, Bader GD, Dick JE, Naldini L
Cell Stem Cell 2012 Nov 7
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
A travel guide to Cytoscape plugins
Saito R, Smoot ME, Ono K, Ruscheinski J, Wang PL, Lotia S, Pico AR, Bader GD, Ideker T
Nat Methods 2012 Nov;9(11):1069-76
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Detecting microRNAs of high influence on protein functional interaction networks: a prostate cancer case study
Alshalalfa M, Bader GD, Goldenberg A, Morris Q, Alhajj R
BMC Syst Biol 2012 Aug 28;6:112
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Disruption of Abi1/Hssh3bp1 expression induces prostatic intraepithelial neoplasia in the conditional Abi1/Hssh3bp1 KO mice
Xiong X, Chorzalska A, Dubielecka PM, White JR, Vedvyas Y, Hedvat CV, Haimovitz-Friedman A, Koutcher JA, Reimand J, Bader GD, Sawicki JA, Kotula L
Oncogenesis 2012 Sep 3;1:e26
PubMed Abstract - PDF
CANCER GENOMICS
Subgroup-specific structural variation across 1,000 medulloblastoma genomes
Northcott PA, Shih DJ, Peacock J, Garzia L, Morrissy AS, Zichner T, Stütz AM, Korshunov A, Reimand J, Schumacher SE, Beroukhim R, Ellison DW, Marshall CR, Lionel AC, Mack S, Dubuc A, Yao Y, Ramaswamy V, Luu B, Rolider A, Cavalli FM, Wang X, Remke M, Wu X, Chiu RY, Chu A, Chuah E, Corbett RD, Hoad GR, Jackman SD, Li Y, Lo A, Mungall KL, Nip KM, Qian JQ, Raymond AG, Thiessen NT, Varhol RJ, Birol I, Moore RA, Mungall AJ, Holt R, Kawauchi D, Roussel MF, Kool M, Jones DT, Witt H, Fernandez-L A, Kenney AM, Wechsler-Reya RJ, Dirks P, Aviv T, Grajkowska WA, Perek-Polnik M, Haberler CC, Delattre O, Reynaud SS, Doz FF, Pernet-Fattet SS, Cho BK, Kim SK, Wang KC, Scheurlen W, Eberhart CG, Fèvre-Montange M, Jouvet A, Pollack IF, Fan X, Muraszko KM, Gillespie GY, Di Rocco C, Massimi L, Michiels EM, Kloosterhof NK, French PJ, Kros JM, Olson JM, Ellenbogen RG, Zitterbart K, Kren L, Thompson RC, Cooper MK, Lach B, McLendon RE, Bigner DD, Fontebasso A, Albrecht S, Jabado N, Lindsey JC, Bailey S, Gupta N, Weiss WA, Bognár L, Klekner A, Van Meter TE, Kumabe T, Tominaga T, Elbabaa SK, Leonard JR, Rubin JB, Liau LM, Van Meir EG, Fouladi M, Nakamura H, Cinalli G, Garami M, Hauser P, Saad AG, Iolascon A, Jung S, Carlotti CG, Vibhakar R, Ra YS, Robinson S, Zollo M, Faria CC, Chan JA, Levy ML, Sorensen PH, Meyerson M, Pomeroy SL, Cho YJ, Bader GD, Tabori U, Hawkins CE, Bouffet E, Scherer SW, Rutka JT, Malkin D, Clifford SC, Jones SJ, Korbel JO, Pfister SM, Marra MA, Taylor MD
Nature 2012 Aug 2;488(7409):49-56
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
A Comparative Transcriptomic Analysis Reveals Conserved Features of Stem Cell Pluripotency in Planarians and Mammals
Labbé RM, Irimia M, Currie KW, Lin A, Zhu SJ, Brown DD, Ross EJ, Voisin V, Bader GD, Blencowe BJ, Pearson BJ
Stem Cells 2012 Jun 13
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Multiple Genetic Interaction Experiments Provide Complementary Information Useful for Gene Function Prediction
Michaut M, Bader GD
PLoS Comput Biol 8(6): e1002559
PubMed Abstract - PDF
GENETIC INTERACTIONS
Domain-mediated protein interaction prediction: From genome to network
Reimand J, Hui S, Jain S, Law B, Bader GD
FEBS Lett 2012 May 3
PubMed Abstract - PDF
PROTEIN INTERACTIONS
Seventeen-gene signature from enriched Her2/Neu mammary tumor-initiating cells predicts clinical outcome for human HER2+:ERα- breast cancer
Liu JC, Voisin V, Bader GD, Deng T, Pusztai L, Symmans WF, Esteva FJ, Egan SE, Zacksenhaus E
Proc Natl Acad Sci U S A 2012 Mar 28
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Phosphorylation sites of higher stoichiometry are more conserved
Tan CS, Bader GD
Nat Methods 2012 Mar 27;9(4):317
PubMed Abstract -PDF
PHOSPHOPROTEOMICS
Mapping the Hsp90 Genetic Interaction Network in Candida albicans Reveals Environmental Contingency and Rewired Circuitry
Diezmann S, Michaut M, Shapiro RS, Bader GD, Cowen LE
PLoS Genet 2012 Mar;8(3):e1002562
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
2011
MUSI: an integrated system for identifying multiple specificity from very large peptide or nucleic acid data sets
Kim T, Tyndel MS, Huang H, Sidhu SS, Bader GD, Gfeller D, Kim PM
Nucleic Acids Res 2011 Dec 30
PubMed Abstract - PDF
DOMAIN SPECIFICITY SOFTWARE
Meeting report from the first meetings of the Computational Modeling in Biology Network (COMBINE)
Le Novère N, Hucka M, Anwar N, Bader GD, Demir E, Moodie S, Sorokin A
Stand Genomic Sci 2011 Nov 30;5(2):230-42
PubMed Abstract - PDF
DATA STANDARD
clusterMaker: a multi-algorithm clustering plugin for Cytoscape
Morris JH, Apeltsin L, Newman AM, Baumbach J, Wittkop T, Su G, Bader GD, Ferrin TE
BMC Bioinformatics 2011 Nov 9;12(1):436
PubMed Abstract -PDF
NETWORK ANALYSIS SOFTWARE
Compound Prioritization Methods Increase Rates of Chemical Probe Discovery in Model Organisms
Iain M. Wallace, Malene L. Urbanus, Genna M. Luciani,Andrew R. Burns,Mitchell K.L. Han, Hao Wang, Kriti Arora, Lawrence E. Heisler, Michael Proctor, Robert P. St. Onge, Terry Roemer, Peter J. Roy,Carolyn L. Cummins, Gary D. Bader, Corey Nislow, Guri Giaever
Cell Chemistry & Biology 2011 18, 1273–1283
PubMed Abstract - PDF
Chemistry & Biology 2011 18:10, 1204-1205 Commentary on paper
CHEMICAL GENOMICS
NetSlim: high-confidence curated signaling maps
Raju R, Nanjappa V, Balakrishnan L, Radhakrishnan A, Thomas JK, Sharma J, Tian M, Palapetta SM, Subbannayya T, Sekhar NR, Muthusamy B, Goel R, Subbannayya Y, Telikicherla D, Bhattacharjee M, Pinto SM, Syed N, Srikanth MS, Sathe GJ, Ahmad S, Chavan SN, Sameer Kumar GS, Marimuthu A, Prasad TS, Harsha HC, Rahiman BA, Ohara O, Bader GD, Sujatha Mohan S, Schiemann WP, Pandey A
Database (Oxford) 2011 Sep 29;2011(0):bar032
PubMed Abstract - PDF
PATHWAY DATABASE
Delineation of Two Clinically and Molecularly Distinct Subgroups of Posterior Fossa Ependymoma
Witt H, Mack SC, Ryzhova M, Bender S, Sill M, Isserlin R, Benner A, Hielscher T, Milde T, Remke M, Jones DTW, Northcott PA, Garzia L, Bertrand KC, Wittmann A, Yao Y, Roberts SS, Massimi L, Van Meter T, Weiss WA, Gupta N, Grajkowska W, Lach B, Cho YJ, von Deimling A, Kulozik AE, Witt O, Bader GD, Hawkins CE, Tabori U, Guha A, Rutka JT, Lichter P, Korshunov A, Taylor MD, Pfister SM
Cancer Cell, Volume 20, Issue 2, 143-157, 16 August 2011
PubMed Abstract - PDF
PATHWAY ANALYSIS
A comprehensive manually curated reaction map of RANKL/RANK-signaling pathway
Raju R, Balakrishnan L, Nanjappa V, Bhattacharjee M, Getnet D, Muthusamy B, Kurian Thomas J, Sharma J, Rahiman BA, Harsha HC, Shankar S, Prasad TS, Mohan SS, Bader GD, Wani MR, Pandey A
Database (Oxford) 2011 Jul 8;2011
PubMed Abstract -PDF
PATHWAY DATABASE
PSICQUIC and PSISCORE: accessing and scoring molecular interactions
Aranda B, Blankenburg H, Kerrien S, Brinkman FS, Ceol A, Chautard E, Dana JM, De Las Rivas J, Dumousseau M, Galeota E, Gaulton A, Goll J, Hancock RE, Isserlin R, Jimenez RC, Kerssemakers J, Khadake J, Lynn DJ, Michaut M, O'Kelly G, Ono K, Orchard S, Prieto C, Razick S, Rigina O, Salwinski L, Simonovic M, Velankar S, Winter A, Wu G, Bader GD, Cesareni G, Donaldson IM, Eisenberg D, Kleywegt GJ, Overington J, Ricard-Blum S, Tyers M, Albrecht M, Hermjakob H
Nature Methods 2011 Jun 29;8(7):528-9
Pubmed Abstract - PDF
PROTEIN INTERACTIONS
Response to Comment on Positive Selection of Tyrosine Loss in Metazoan Evolution,
Tan CS, Schoof EM, Creixell P, Pasculescu A, Lim WA, Pawson T, Bader GD and Linding R
Science 332(6032):917, 20 May 2011
PDF
NETWORK EVOLUTION
The multiple-specificity landscape of modular peptide recognition domains
Gfeller D, Butty F, Wierzbicka M, Verschueren E, Vanhee P, Huang H, Ernst A, Dar N, Stagljar I, Serrano L, Sidhu SS, Bader GD, Kim PM
Molecular Systems Biology 7:484, 26 April 2011
PubMed Abstract - PDF
PROTEIN INTERACTION PREDICTION
WordCloud: a Cytoscape plugin to create a visual semantic summary of networks
Oesper L, Merico D, Isserlin R, Bader GD
Source Code for Biology and Medicine 2011, 6:7, 7 April 2011
PubMed Abstract -PDF
NETWORK ANALYSIS SOFTWARE
Protein Complexes are Central in the Yeast Genetic Landscape
Michaut M, Baryshnikova A, Costanzo M, Myers CL, Andrews BJ, Boone C, Bader GD
PLoS Computational Biology 7(2): e1001092 Feb 24 2011
February 2011 Issue Cover
PubMed Abstract - PDF
GENETIC INTERACTION NETWORK ANALYSIS
Bringing order to protein disorder through comparative genomics and genetic interactions
Bellay J*, Han S*, Michaut M*, Kim T, Costanzo M, Andrews BJ, Boone C, Bader GD, Myers CL, Kim PM
Genome Biology 12(2):R14 Feb 15 2011
PubMed Abstract - PDF
PROTEIN DISORDER AND COMPARATIVE GENOMICS
Too Many Roads Not Taken
Edwards AM, Isserlin R, Bader GD, Frye SV, Willson TM, Yu FH
Nature. (470) 163-165 Feb 9 2011
PubMed Abstract - PDF
Full Paper on arxiv.org
BIBLIOMETRIC ANALYSIS
The Biomolecular Interaction Network Database in PSI-MI 2.5
Isserlin R, El-Badrawi RA, Bader GD
Database 2011 Jan 12;2011:baq037
PubMed Abstract - PDF
PROTEIN INTERACTION DATABASE
2010
A regression framework incorporating quantitative and negative interaction data improves prediction of quantitative PDZ domain-peptide interaction from primary sequence
Shao X, Tan CS, Voss C, Li SS, Deng N, Bader GD
Bioinformatics 2010 Dec 2
PubMed Abstract - PDF
PROTEIN INTERACTION PREDICTION
Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation
Merico D, Isserlin R, Stueker O, Emili A, Bader GD
PLoS One 2010 Nov 15;5(11):e13984
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
An improved method for scoring protein-protein interactions using semantic similarity within the Gene Ontology
Jain S, Bader GD
BMC Bioinformatics 2010 Nov 15;11(1):562
PubMed Abstract -PDF
PROTEIN INTERACTION PREDICTION
Quantitative analysis of fitness and genetic interactions in yeast on a genome scale
Baryshnikova A, Costanzo M, Kim Y, Ding H, Koh J, Toufighi K, Youn JY, Ou J, San Luis BJ, Bandyopadhyay S, Hibbs M, Hess D, Gingras AC, Bader GD, Troyanskaya OG, Brown GW, Andrews B, Boone C, Myers CL
Nat Methods 2010 Nov 14
PubMed Abstract -PDF
GENETIC INTERACTION NETWORK ANALYSIS
Pathway Commons, a web resource for biological pathway data
Cerami EG, Gross BE, Demir E, Rodchenkov I, Babur O, Anwar N, Schultz N, Bader GD, Sander C
Nucleic Acids Res 2010 Nov 10
PubMed Abstract - PDF
PATHWAY DATABASE
Proteome scanning to predict PDZ domain interactions using support vector machines
Hui S, Bader GD
BMC Bioinformatics 2010 Oct 12;11(1):50
PubMed Abstract - PDF
PROTEIN INTERACTION PREDICTION
GeneMANIA Cytoscape Plugin: Fast gene function predictions on the desktop
Montojo J, Zuberi K, Rodriguez H, Kazi F, Wright G, Donaldson SL, Morris Q, Bader GD
Bioinformatics 2010 Nov 15;26(22):2927-8
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Dynamic interaction networks in a hierarchically organized tissue
Kirouac DC, Ito C, Csaszar E, Roch A, Yu M, Sykes EA, Bader GD, Zandstra PW
Mol Syst Biol 2010 Oct 5;6:417
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Functional complex between YAP2 and ZO-2 is PDZ domain dependent, regulates YAP2 nuclear localization and signaling
Oka T, Remue E, Meerschaert K, Vanloo B, Boucherie C, Gfeller D, Bader GD, Sidhu S, Vandekerckhove J, Gettemans J, Sudol M
Biochem J 2010 Sep 24
PubMed Abstract - PDF
PROTEIN INTERACTION PREDICTION
The BioPAX community standard for pathway data sharing
Demir E, Cary MP, Paley S, Fukuda K, Lemer C, Vastrik I, Wu G, D'Eustachio P, Schaefer C, Luciano J, Schacherer F, Martinez-Flores I, Hu Z, Jimenez-Jacinto V, Joshi-Tope G, Kandasamy K, Lopez-Fuentes AC, Mi H, Pichler E, Rodchenkov I, Splendiani A, Tkachev S, Zucker J, Gopinath G, Rajasimha H, Ramakrishnan R, Shah I, Syed M, Anwar N, Babur O, Blinov M, Brauner E, Corwin D, Donaldson S, Gibbons F, Goldberg R, Hornbeck P, Luna A, Murray-Rust P, Neumann E, Reubenacker O, Samwald M, van Iersel M, Wimalaratne S, Allen K, Braun B, Whirl-Carrillo M, Cheung KH, Dahlquist K, Finney A, Gillespie M, Glass E, Gong L, Haw R, Honig M, Hubaut O, Kane D, Krupa S, Kutmon M, Leonard J, Marks D, Merberg D, Petri V, Pico A, Ravenscroft D, Ren L, Shah N, Sunshine M, Tang R, Whaley R, Letovksy S, Buetow KH, Rzhetsky A, Schachter V, Sobral BS, Dogrusoz U, McWeeney S, Aladjem M, Birney E, Collado-Vides J, Goto S, Hucka M, Novère NL, Maltsev N, Pandey A, Thomas P, Wingender E, Karp PD, Sander C, Bader GD
Nat Biotechnol 2010 Sep;28(9):935-42
PubMed Abstract - PDF
DATA STANDARD
Coevolution of PDZ domain–ligand interactions analyzed by high-throughput phage display and deep sequencing
Ernst A, Gfeller D, Kan Z, Seshagiri S, Kim PM, Bader GD, Sidhu SS
Mol. BioSyst., 2010, Advance Article
PubMed Abstract - PDF
PROTEIN INTERACTION NETWORK EVOLUTION
Cytoscape Web: an interactive web-based network browser
Lopes CT, Franz M, Kazi F, Donaldson SL, Morris Q, Bader GD
Bioinformatics 2010 Jul 23
PubMed Abstract - PDF
NETWORK VISUALIZATION
The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function
Warde-Farley D, Donaldson SL, Comes O, Zuberi K, Badrawi R, Chao P, Franz M, Grouios C, Kazi F, Lopes CT, Maitland A, Mostafavi S, Montojo J, Shao Q, Wright G, Bader GD, Morris Q
Nucleic Acids Res 2010 Jul 1;38 Suppl:W214-20
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Functional impact of global rare copy number variation in autism spectrum disorders
Pinto D, Pagnamenta AT, Klei L, Anney R, Merico D, Regan R, Conroy J, Magalhaes TR, Correia C, Abrahams BS, Almeida J, Bacchelli E, Bader GD, Bailey AJ, Baird G, Battaglia A, Berney T, Bolshakova N, Bölte S, Bolton PF, Bourgeron T, Brennan S, Brian J, Bryson SE, Carson AR, Casallo G, Casey J, Chung BH, Cochrane L, Corsello C, Crawford EL, Crossett A, Cytrynbaum C, Dawson G, de Jonge M, Delorme R, Drmic I, Duketis E, Duque F, Estes A, Farrar P, Fernandez BA, Folstein SE, Fombonne E, Freitag CM, Gilbert J, Gillberg C, Glessner JT, Goldberg J, Green A, Green J, Guter SJ, Hakonarson H, Heron EA, Hill M, Holt R, Howe JL, Hughes G, Hus V, Igliozzi R, Kim C, Klauck SM, Kolevzon A, Korvatska O, Kustanovich V, Lajonchere CM, Lamb JA, Laskawiec M, Leboyer M, Le Couteur A, Leventhal BL, Lionel AC, Liu XQ, Lord C, Lotspeich L, Lund SC, Maestrini E, Mahoney W, Mantoulan C, Marshall CR, McConachie H, McDougle CJ, McGrath J, McMahon WM, Merikangas A, Migita O, Minshew NJ, Mirza GK, Munson J, Nelson SF, Noakes C, Noor A, Nygren G, Oliveira G, Papanikolaou K, Parr JR, Parrini B, Paton T, Pickles A, Pilorge M, Piven J, Ponting CP, Posey DJ, Poustka A, Poustka F, Prasad A, Ragoussis J, Renshaw K, Rickaby J, Roberts W, Roeder K, Roge B, Rutter ML, Bierut LJ, Rice JP, Salt J, Sansom K, Sato D, Segurado R, Sequeira AF, Senman L, Shah N, Sheffield VC, Soorya L, Sousa I, Stein O, Sykes N, Stoppioni V, Strawbridge C, Tancredi R, Tansey K, Thiruvahindrapduram B, Thompson AP, Thomson S, Tryfon A, Tsiantis J, Van Engeland H, Vincent JB, Volkmar F, Wallace S, Wang K, Wang Z, Wassink TH, Webber C, Weksberg R, Wing K, Wittemeyer K, Wood S, Wu J, Yaspan BL, Zurawiecki D, Zwaigenbaum L, Buxbaum JD, Cantor RM, Cook EH, Coon H, Cuccaro ML, Devlin B, Ennis S, Gallagher L, Geschwind DH, Gill M, Haines JL, Hallmayer J, Miller J, Monaco AP, Nurnberger Jr JI, Paterson AD, Pericak-Vance MA, Schellenberg GD, Szatmari P, Vicente AM, Vieland VJ, Wijsman EM, Scherer SW, Sutcliffe JS, Betancur C
Nature 2010 Jul 15;466(7304):368-72
PubMed Abstract - PDF
Nature Blogs - In the news (The Globe and Mail)
PATHWAY AND NETWORK ANALYSIS
A predictive model for drug bioaccumulation and bioactivity in Caenorhabditis elegans
Burns AR, Wallace IM, Wildenhain J, Tyers M, Giaever G, Bader GD, Nislow C, Cutler SR, Roy PJ
Nat Chem Biol 2010 May 30
PubMed Abstract - PDF
NCB_News&Views.pdf
CHEMICAL GENOMICS
International network of cancer genome projects
International Cancer Genome Consortium
Nature 2010 Apr 15;464(7291):993-8
PubMed Abstract - PDF
CANCER GENOMICS
Pathway analysis of dilated cardiomyopathy using global proteomic profiling and enrichment maps
Isserlin R, Merico D, Alikhani-Koupaei R, Gramolini A, Bader GD, Emili A
Proteomics 2010, March 10(6):1316-27
Pubmed Abstract - PDF
PATHWAY ANALYSIS
The Genetic Landscape of a Cell
Costanzo M, Baryshnikova A, Bellay J, Kim Y, Spear ED, Sevier CS, Ding H, Koh JL, Toufighi K, Mostafavi S, Prinz J, St Onge RP, VanderSluis B, Makhnevych T, Vizeacoumar FJ, Alizadeh S, Bahr S, Brost RL, Chen Y, Cokol M, Deshpande R, Li Z, Lin ZY, Liang W, Marback M, Paw J, San Luis BJ, Shuteriqi E, Tong AH, van Dyk N, Wallace IM, Whitney JA, Weirauch MT, Zhong G, Zhu H, Houry WA, Brudno M, Ragibizadeh S, Papp B, Pál C, Roth FP, Giaever G, Nislow C, Troyanskaya OG, Bussey H, Bader GD, Gingras AC, Morris QD, Kim PM, Kaiser CA, Myers CL, Andrews BJ, Boone C
Science 2010 Jan 22;327(5964):425-31
PubMed Abstract - PDF
GENETIC INTERACTION NETWORK ANALYSIS
NetPath: a public resource of curated signal transduction pathways
Kandasamy K, Mohan S, Raju R, Keerthikumar S, Kumar GS, Venugopal AK, Telikicherla D, Navarro DJ, Mathivanan S, Pecquet C, Gollapudi SK, Tattikota SG, Mohan S, Padhukasahasram H, Subbannayya Y, Goel R, Jacob HK, Zhong J, Sekhar R, Nanjappa V, Balakrishnan L, Subbaiah R, Ramachandra YL, Rahiman A, Keshava Prasad TS, Lin JX, Houtman JC, Desiderio S, Renauld JC, Constantinescu S, Ohara O, Hirano T, Kubo M, Singh S, Khatri P, Draghici S, Bader GD, Sander C, Leonard WJ, Pandey A
Genome Biology 2010 Jan 12;11(1):R3
PubMed Abstract - PDF
PATHWAY DATABASE
DRYGIN: a database of quantitative genetic interaction networks in yeast
Koh JL, Ding H, Costanzo M, Baryshnikova A, Toufighi K, Bader GD, Myers CL, Andrews BJ, Boone C
Nucleic Acids Res 2010 Jan;38(Database issue):D502-7
PubMed Abstract - PDF
GENETIC INTERACTION NETWORK DATABASE
2009
Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of uncharacterized endocytosis proteins
Tonikian R, Xin X, Toret CP, Gfeller D, Landgraf C, Panni S, Paoluzi S, Castagnoli L, Yu H, Winsor B, Vidal M, Davidson AR, Gerstein MB, Bader GD, Volkmer R, Cesareni G, Drubin DG, Kim PM, Sidhu SS, Boone C
PLoS Biology 2009 Oct Vol. 7, No. 10, e1000218
PubMed Abstract - PDF
PROTEIN-PROTEIN INTERACTION ANALYSIS
How to visually interpret biological data using networks
Merico D, Gfeller D, Bader GD
Nature Biotechnology 2009 Oct 27, 921-924
PubMed Abstract - PDF
Data: http://www.baderlab.org/NetworkPrimerNBT
NETWORK PRIMER
Rapid evolution of functional complexity in a domain family
Ernst A, Sazinsky SL, Hui S, Currell B, Dharsee M, Seshagiri S, Bader GD, Sidhu SS
Science Signaling 2009 Sep 8;2(87):ra50
PubMed Abstract - PDF
PROTEIN INTERACTION NETWORK EVOLUTION
Positive Selection of Tyrosine Loss in Metazoan Evolution
Tan CS, Pasculescu A, Lim WA, Pawson T, Bader GD, Linding R
Science. Sep 25;325(5948):1686-8
PubMed Abstract - PDF
PROTEIN INTERACTION NETWORK EVOLUTION
Comparative Analysis Reveals Conserved Protein Phosphorylation Networks Implicated in Multiple Diseases
Tan CS, Bodenmiller B, Pasculescu A, Jovanovic M, Hengartner MO, Jørgensen C, Bader GD, Aebersold R, Pawson T, Linding R
Science Signaling 2(81):r39 (2009)
PubMed Abstract - PDF
PROTEIN INTERACTION NETWORK EVOLUTION
2008
A Specificity Map for the PDZ Domain Family
Tonikian R, Zhang Y, Sazinsky SL, Currell B, Yeh JH, Reva B, Held HA, Appleton BA, Evangelista M, Wu Y, Xin X, Chan AC, Seshagiri S, Lasky LA, Sander C, Boone C, Bader GD, Sidhu SS
PLoS Biology Vol. 6, No. 9, e239
PubMed Abstract - PDF
PROTEIN-PROTEIN INTERACTION ANALYSIS
Cytoscape ESP: simple search of complex biological networks
Ashkenazi M, Bader GD, Kuchinsky A, Moshelion M, States DJ
Bioinformatics 2008 Jun 15;24(12):1465-6
PubMed Abstract - PDF
NETWORK ANALYSIS SOFTWARE
Computational prediction of protein-protein interactions
Skrabanek L, Saini HK, Bader GD, Enright AJ
Molecular Biotechnology 2008 Jan;38(1):1-17
PubMed Abstract - PDF
REVIEW
2007
Integration of biological networks and gene expression data using Cytoscape
Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C, Christmas R, Avila-Campilo I, Creech M, Gross B, Hanspers K, Isserlin R, Kelley R, Killcoyne S, Lotia S, Maere S, Morris J, Ono K, Pavlovic V, Pico AR, Vailaya A, Wang PL, Adler A, Conklin BR, Hood L, Kuiper M, Sander C, Schmulevich I, Schwikowski B, Warner GJ, Ideker T, Bader GD
Nature Protocols 2007;2(10):2366-82
PubMed Abstract - PDF
NETWORK ANALYSIS SOFTWARE
Broadening the Horizon - Level 2.5 of the HUPO-PSI Format for Molecular Interactions
Kerrien S, Orchard S, Montecchi-Palazzi L, Aranda B, Quinn AF, Vinod N, Bader GD, Xenarios I, Wojcik J, Sherman D, Tyers M, Salama JJ, Moore S, Ceol A, Chatr-Aryamontri A, Oesterheld M, Stumpflen V, Salwinski L, Nerothin J, Cerami E, Cusick ME, Vidal M, Gilson M, Armstrong J, Woollard P, Hogue C, Eisenberg D, Cesareni G, Apweiler R, Hermjakob H
BMC Biology 2007 Oct 9;5(1):44
PubMed Abstract - PDF
DATA STANDARD
The minimum information required for reporting a molecular interaction experiment (MIMIx)
Orchard S, Salwinski L, Kerrien S, Montecchi-Palazzi L, Oesterheld M, Stumpflen V, Ceol A, Chatr-Aryamontri A, Armstrong J, Woollard P, Salama JJ, Moore S, Wojcik J, Bader GD, Vidal M, Cusick ME, Gerstein M, Gavin AC, Superti-Furga G, Greenblatt J, Bader J, Uetz P, Tyers M, Legrain P, Fields S, Mulder N, Gilson M, Niepmann M, Burgoon L, Rivas Jde L, Prieto C, Perreau VM, Hogue C, Mewes HW, Apweiler R, Xenarios I, Eisenberg D, Cesareni G, Hermjakob H
Nat Biotechnol 2007 Aug;25(8):894-8
PubMed Abstract - PDF
DATA STANDARD
Germ-line DNA copy number variation frequencies in a large North American population
Zogopoulos G, Ha KC, Naqib F, Moore S, Kim H, Montpetit A, Robidoux F, Laflamme P, Cotterchio M, Greenwood C, Scherer SW, Zanke B, Hudson TJ, Bader GD, Gallinger S
Hum Genet 2007 Nov;122(3-4):345-53
PubMed Abstract - PDF
GENOMICS
From bytes to bedside: data integration and computational biology for translational cancer research
Mathew JP, Taylor BS, Bader GD, Pyarajan S, Antoniotti M, Chinnaiyan AM, Sander C, Burakoff SJ, Mishra B
PLoS Comput Biol 2007 Feb 23;3(2):e12
PubMed Abstract - PDF
CANCER REVIEW
NetMatch: a Cytoscape Plugin for Searching Biological Networks
Ferro A, Giugno R, Pigola G, Pulvirenti A, Skripin D, Bader GD, Shasha D
Bioinformatics 2007 Apr 1;23(7):910-2
PubMed Abstract - PDF
Download software
NETWORK ANALYSIS SOFTWARE
Computational prediction of cancer-gene function
Hu P, Bader G, Wigle DA, Emili A
Nature Reviews Cancer 2007 Jan;7(1):23-34
PubMed Abstract - PDF
CANCER REVIEW
2006
cPath: open source software for collecting, storing, and querying biological pathways
Cerami EG, Bader GD, Gross BE, Sander C
BMC Bioinformatics 2006, 7:497
PubMed Abstract - PDF
PATHWAY SOFTWARE
Pathguide: a Pathway Resource List
Bader GD, Cary MP, Sander C
Nucleic Acids Research 2006 Jan 1;34(Database issue):D504-6
PubMed Abstract - PDF
PATHWAY WEBSITE
2005
Pathway information for systems biology
Cary MP, Bader GD, Sander C
FEBS Lett 2005 Mar 21;579(8):1815-20
PubMed Abstract - PDF
PATHWAY REVIEW
2004
Global Mapping of the Yeast Genetic Interaction Network
Tong AH, Lesage G, Bader GD, Ding H, Xu H, Xin X, Young J, Berriz GF, Brost RL, Chang M, Chen Y, Cheng X, Chua G, Friesen H, Goldberg DS, Haynes J, Humphries C, He G, Hussein S, Ke L, Krogan N, Li Z, Levinson JN, Lu H, Menard P, Munyana C, Parsons AB, Ryan O, Tonikian R, Roberts T, Sdicu AM, Shapiro J, Sheikh B, Suter B, Wong SL, Zhang LV, Zhu H, Burd CG, Munro S, Sander C, Rine J, Greenblatt J, Peter M, Bretscher A, Bell G, Roth FP, Brown GW, Andrews B, Bussey H, Boone C
Science 2004 Feb 6;303(5659):808-813
PubMed Abstract - PDF
Science Perspective PDF
GENETIC INTERACTION NETWORK ANALYSIS
The HUPO PSI Molecular Interaction Format - a community standard for the representation of protein interaction data
Hermjakob H, Montecchi-Palazzi L, Bader G, Wojcik J, Salwinski L, Ceol A, Moore S, Orchard S, Sarkans U, Von Mering C, Roechert B, Poux S, Jung E, Mersch H, Kersey P, Lappe M, Li Y, Zeng R, Rana D, Nikolski M, Husi H, Brun C, Shanker K, Grant SG, Sander C, Bork P, Zhu W, Pandey A, Brazma A, Jacq B, Vidal M, Sherman D, Legrain P, Cesareni G, Xenarios I, Eisenberg D, Steipe B, Hogue C, Apweiler R
Nature Biotechnology 2004 Feb;22(2):177-83
PubMed Abstract - PDF
DATA STANDARD
2003
Playing tag with the yeast proteome
Andrews BJ, Bader GD, Boone C
Nature Biotechnology Nov;21(11):1297-1299
PubMed Abstract - PDF
REVIEW
Functional Genomics and Proteomics: Charting a Multidimensional Map of the Cell
Bader GD, Heilbut A, Andrews B, Tyers M, Hughes T, Boone C
Trends in Cell Biology Jul, 2003 13(7):344-56
PubMed Abstract - PDF
REVIEW
PreBIND and Textomy - mining the biomedical literature for protein-protein interactions using a support vector machine
Donaldson I, Martin J, De Bruijn B, Wolting C, Lay V, Tuekam B, Zhang S, Baskin B, Bader GD, Michalickova K, Pawson T, Hogue CW
BMC Bioinformatics Mar 27, 2003 4(1):11
PubMed Abstract - PDF
TEXT MINING SOFTWARE
Functional genomics of intracellular peptide recognition domains with combinatorial biology methods
Sidhu SS, Bader GD, Boone C
Current Opinion in Chemical Biology 2003 Feb;7(1):97-102
PubMed Abstract - PDF
REVIEW
An automated method for finding molecular complexes in large protein interaction networks
Bader GD, Hogue CWV
BMC Bioinformatics 2003 Jan 13;4(1):2
PubMed Abstract - PDF
ALGORITHM
BIND-The Biomolecular Interaction Network Database
Bader GD, Betel D, Hogue CWV
Nucleic Acids Research Jan 1, 2003 31(1):248-250
PubMed Abstract - PDF
INTERACTION DATABASE
2002
SeqHound: biological sequence and structure database as a platform for bioinformatics research
Michalickova K, Bader GD, Dumontier M, Lieu H, Betel D, Isserlin R, Hogue CW
BMC Bioinformatics 2002, 3:32 (25 October 2002)
PubMed Abstract - PDF
PROTEIN DATABASE
Analyzing yeast protein–protein interaction data obtained from different sources
Bader GD, Hogue CW
Nature Biotechnology 2002 Oct;20(10):991-997
PubMed Abstract - PDF
META-ANALYSIS
A Combined Experimental and Computational Strategy to Define Protein Interaction Networks for Peptide Recognition Modules
Tong AH, Drees B, Nardelli G, Bader GD, Brannetti B, Castagnoli L, Evangelista M, Ferracuti S, Nelson B, Paoluzi S, Quondam M, Zucconi A, Hogue CW, Fields S, Boone C, Cesareni G
Science 2002 Jan 11;295(5553):321-324
PubMed Abstract - PDF
Science Perspective PDF
PROTEIN INTERACTION PREDICTION
Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry
Ho Y, Gruhler A, Heilbut A, Bader GD, Moore L, Adams SL, Millar A, Taylor P, Bennett K, Boutilier K, Yang L, Wolting C, Donaldson I, Schandorff S, Shewnarane J, Vo M, Taggart J, Goudreault M, Muskat B, Alfarano C, Dewar D, Lin Z, Michalickova K, Willems AR, Sassi H, Nielsen PA, Rasmussen KJ, Andersen JR, Johansen LE, Hansen LH, Jespersen H, Podtelejnikov A, Nielsen E, Crawford J, Poulsen V, Sorensen BD, Matthiesen J, Hendrickson RC, Gleeson F, Pawson T, Moran MF, Durocher D, Mann M, Hogue CW, Figeys D, Tyers M
Nature 2002 Jan 10;415(6868): 180-183
PubMed Abstract - PDF
Nature News and Views PDF
PROTEIN INTERACTION NETWORK ANALYSIS
2001
Systematic Genetic Analysis with Ordered Arrays of Yeast Deletion Mutants
Tong AH, Evangelista M, Parsons AB, Xu H, Bader GD, Page N, Robinson M, Raghibizadeh S, Hogue CW, Bussey H, Andrews B, Tyers M, Boone C
Science 2001 Dec 14;294(5550):2364-8
PubMed Abstract - PDF
GENETIC INTERACTION NETWORK ANALYSIS
BIND - The Biomolecular Interaction Network Database
Bader GD, Donaldson I, Wolting C, Ouellette BF, Pawson T, Hogue CW
Nucleic Acids Research Jan 1, 2001 29(1):242-245
PubMed Abstract - PDF
INTERACTION DATABASE
2000
BIND - A data specification for storing and describing biomolecular interactions, molecular complexes and pathways
Bader GD, Hogue CW
Bioinformatics 2000 May;16(5):465-77
PubMed Abstract - PDF
INTERACTION DATABASE
Preprints
2025
From FAIR to CURE: Guidelines for Computational Models of Biological Systems
Sauro HM, Agmon E, Blinov ML, Gennari JH, Hellerstein J, Heydarabadipour A, Hunter P, Jardine BE, May E, Nickerson DP, Smith LP, Bader GD, Bergmann F, Boyle PM, Dräger A, Faeder JR, Feng S, Freire J, Fröhlich F, Glazier JA, Gorochowski TE, Helikar T, Hoops S, Imoukhuede P, Keating SM, Konig M, Laubenbacher R, Loew LM, Lopez CF, Lytton WW, McCulloch A, Mendes P, Myers CJ, Myers JG, Mulugeta L, Niarakis A, van Niekerk DD, Olivier BG, Patrie AA, Quardokus EM, Radde N, Rohwer JM, Sahle S, Schaff JC, Sego TJ, Shin J, Snoep JL, Vadigepalli R, Wiley HS, Waltemath D, Moraru I
ArXiv [Preprint]. 2025 Feb 21:arXiv:2502.15597v1
PubMed Abstract- PDF
DATA STANDARD
2024
Interpretable single-cell factor decomposition using sciRED
Pouyabahar D, Andrews T, Bader GD
bioRxiv [Preprint]. 2024 Aug 6:2024.08.01.605536
PubMed Abstract-PDF
SINGLE CELL GENOMICS
Direct lineage conversion of postnatal mouse cortical astrocytes to oligodendrocyte lineage cells
Bajohr J, Scott EY, Olfat A, Sadria M, Lee K, Fahim M, Taha HT, Casasbuenas DL, Derham A, Yuzwa SA, Bader GD, Maryam Faiz
bioRxiv [Preprint]. May 2024 - 2024.05.28.596294
PDF
SINGLE CELL GENOMICS
Deep Lineage: Single-Cell Lineage Tracing and Fate Inference Using Deep Learning
Sadria M, Zhang A, Bader GD
bioRxiv [Preprint]. April 2024 - 2024.04.25.591126
PDF
SINGLE CELL GENOMICS
Single-cell analysis of an engineered organoid-based model of pancreatic cancer identifies hypoxia as a contributing factor in the determination of transcriptional subtypes
Natalie Landon-Brace N, Innes BT, Latour S, Cadavid JL, Co IL, Tan CM, Nowlan F, Drissler S, Notta F, Jackson HW, Bader GD, McGuigan AP
bioRxiv [Preprint]. March 2024 - 2024.03.14.584861
PDF
SINGLE CELL GENOMICS
PRMT5 is required for full-length HTT expression by repressing multiple proximal intronic polyadenylation sites
AlQazzaz MA, Ciamponi FE, Ho JC, Maron MI, Yadav M, Sababi AM, MacLeod G, Ahmadi M, Bullivant G, Tano V, Langley SR, Sánchez-Osuna M, Sachamitr P, Kushida M, Richards L, Bardile CF, Pouladi MA, Pugh T, Tyers M, Angers S, Dirks PB, Bader GD, Massirer KB, Barsyte-Lovejoy D, Shechter D, Harding RJ, Arrowsmith CH, Prinos P
bioRxiv [Preprint]. March 2024 - 2024.03.05.583412
PDF
SINGLE CELL GENOMICS
Metformin reduces the clonal fitness of Dnmt3aR878H hematopoietic stem and progenitor cells by reversing their aberrant metabolic and epigenetic state
Hosseini M, Voisin V, Chegini A, Varesi A, Cathelin S, Ayyathan DM, Liu ACH, Yang Y, Wang V, Maher A, Grignano E, Reisz JA, D'Alessandro A, Young K, Wu Y, Fiumara M, Ferrari S, Naldini L, Gaiti F, Pai S, Schimmer AD, Bader GD, Dick JE, Xie SZ, Trowbridge JJ, Chan SM
Preprint 2024 Feb 6
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS, SINGLE CELL GENOMICS
2023
Cell networks in the mouse liver during partial hepatectomy
Li B, Rodrigo-Torres D, Pelz C, Innes B, Canaday P, Chai S, Zandstra P, Bader GD, Grompe M
bioRxiv [Preprint]. 2023 Jul
PubMed Abstract - PDF
Drugst.One -- A plug-and-play solution for online systems medicine and network-based drug repurposing
Maier A, Hartung M, Abovsky M, Adamowicz K, Bader GD, Baier S, Blumenthal DB, Chen J, Elkjaer ML, Garcia-Hernandez C, Hoffmann M, Jurisica I, Kotlyar M, Lazareva O, Levi H, List M, Lobentanzer S, Loscalzo J, Malod-Dognin N, Manz Q, Matschinske J, Oubounyt M, Pico AR, Pillich RT, Poschenrieder JM, Pratt D, Pržulj N, Sadegh S, Saez-Rodriguez J, Sakar S, Shaked G, Shamir R, Trummer N, Turhan U, Wang R, Zolotareva O, Baumbach J
ArXiv [Preprint]. 2023 May 24
PubMed Abstract - PDF
2022
A single-nucleus and spatial transcriptomic atlas of the COVID-19 liver reveals topological, functional, and regenerative organ disruption in patients
Pita-Juarez Y, Karagkouni D, Kalavros N, Melms JC, Niezen S, Delorey TM, Essene AL, Brook OR, Pant D, Skelton-Badlani D, Naderi P, Huang P, Pan L, Hether T, Andrews TS, Ziegler CGK, Reeves J, Myloserdnyy A, Chen R, Nam A, Phelan S, Liang Y, Amin AD, Biermann J, Hibshoosh H, Veregge M, Kramer Z, Jacobs C, Yalcin Y, Phillips D, Slyper M, Subramanian A, Ashenberg O, Bloom-Ackermann Z, Tran VM, Gomez J, Sturm A, Zhang S, Fleming SJ, Warren S, Beechem J, Hung D, Babadi M, Padera RF, MacParland SA, Bader GD, Imad N, Solomon IH, Miller E, Riedel S, Porter CBM, Villani AC, Tsai LT, Hide W, Szabo G, Hecht J, Rozenblatt-Rosen O, Shalek AK, Izar B, Regev A, Popov Y, Jiang ZG, Vlachos IS
bioRxiv Preprint. 2022 Oct 28
PubMed Abstract - PDF
COVID-19
Textbook Chapters
2020
Biological Networks and Pathways
Bader GD.
in Bioinformatics 4th Eds. Andreas D. Baxevanis, Gary D. Bader, and David Wishart. John Wiley and Sons, New Jersey
NETWORK ANALYSIS
2018
Automated Computational Inference of Multi-protein Assemblies from Biochemical Co-purification Data
Goebels F., Hu L., Bader G., Emili A.
Methods Mol Bio 2018;1764:391-399 - PubMed Abstract - PDF
NETWORK ANALYSIS SOFTWARE
2014
Biological network exploration with Cytoscape 3
Su G, Morris JH, Demchak B, Bader GD
Curr Protoc Bioinformatics 2014 Sep 8;47:8.13.1-8.13.24 - PubMed Abstract - PDF
NETWORK ANALYSIS SOFTWARE
2011
Displaying chemical information on a biological network using cytoscape
Wallace IM, Bader GD, Giaever G, Nislow C
Methods Mol Biol 2011;781:363-76 - PubMed Abstract - PDF Supplemental Website
NETWORK ANALYSIS SOFTWARE
Visualizing Gene-Set Enrichment Results Using the Cytoscape Plug-in Enrichment Map
Merico D, Isserlin R, Bader GD
Methods Mol Biol 2011;781:257-77 - PubMed Abstract - PDF
NETWORK ANALYSIS SOFTWARE
2008
Exploring Biological Networks with Cytoscape Software
Natalie Yeung, Melissa S. Cline, Allan Kuchinsky, Michael E. Smoot, and Gary D. Bader
Current Protocols in Bioinformatics - PubMed Abstract - PDF
John Wiley & Sons, Inc.
NETWORK ANALYSIS SOFTWARE
2006
BioPAX - Biological Pathway Data Exchange Format
Gary D. Bader, Michael Cary, Chris Sander
Encyclopedia of Genomics, Proteomics and Bioinformatics
Humana Press, New Jersey
DATA STANDARD
2005
Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
Rowan Christmas, Iliana Avila-Campillo, Hamid Bolouri, Benno Schwikowski, Mark Anderson, Ryan Kelley, Nerius Landys, Chris Workman, Trey Ideker, Ethan Cerami, Rob Sheridan, Gary D. Bader, and Chris Sander
Am Assoc Cancer Res Educ Book 2005: 12-16
NETWORK ANALYSIS SOFTWARE
Exploiting Synthetic Genetic Interactions to Predict Pathways and Complexes
Gary D. Bader, Amy Tong, Lan V. Zhang, Frederick P. Roth, Brenda Andrews and Charles Boone
in Protein-Protein Interactions: A Molecular Cloning Manual, 2nd Edition
Ed. Erica Golemis, Cold Spring Harbor Laboratory Press, New York, USA
GENETIC INTERACTION NETWORK ANALYSIS
2004
Interaction Databases, in Genomics and Bioinformatics, 2nd Edition
Gary D. Bader, Christopher W.V. Hogue
in Volume 5B of the Series: Biotechnology, 2nd Edition
Eds Rehm, H.-J., Reed, G., Pühler, A., Stadler, P. Wiley-VCH, Germany
INTERACTION DATABASE
Intermolecular Interactions and Biological Pathways
Gary D. Bader, Anton J. Enright
in Bioinformatics 3E Eds. Andreas D. Baxevanis and B.F.Francis Ouellette. John Wiley and Sons, New Jersey
INTERACTION DATABASE
Computational Prediction of Protein-Protein Interactions
Anton J. Enright, Lucy Skrabanek, Gary D. Bader
in The Proteomics Handbook Ed. John Walker. (Humana Press, New Jersey)
PROTEIN INTERACTION PREDICTION
2003
Peptide Recognition Module Networks: Combining Phage Display with Two-hybrid Analysis to Define Protein-Protein Interactions
Gary D. Bader, Amy Hin Yan Tong, Gianni Cesareni, Christopher W.V. Hogue, Stanley Fields, Charles Boone
in Handbook of Cell Signaling
Eds. Ralph Bradshaw and Edward Dennis. (San Diego: Academic/Elsevier Press)
PDF
PROTEIN INTERACTION PREDICTION
2002
Interaction Databases
Gary D. Bader, Christopher W.V. Hogue
Chapter 18, in Genomics and Bioinformatics (Volume 5B of the Series: Biotechnology, 2nd Edition.)
Eds. Rehm, H.-J., Reed, G., Pühler, A., Stadler, P.
Wiley-VCH, Germany
INTERACTION DATABASE
Theses
2023 Duncan Forster - BIONIC: Biological Network Integration using Convolutions - PDF, University of Toronto, Department of Molecular Genetics
2023 Brendan Innes - Intercellular Signaling Networks of a Tissue from Single-Cell Transcriptomics - PDF, University of Toronto, Department of Molecular Genetics
2022 Owen Whitley - Transcriptional and Multi -Omic Heterogeneity in Glioblastoma Stem Cells - PDF, University of Toronto, Department of Molecular Genetics
2021 Gurnit Atwal - Automatic tumour typing based on patterns of somatic passenger mutations - PDF, University of Toronto, Department of Molecular Genetics
2021 Stuart Matan-Lithwick - Identifying Novel Genes and Pathways Correlated with Group 3 and Group 4 Medulloblastoma Metastasis to the Spine - PDF, University of Toronto, Department of Molecular Genetics
2020 Patryk Skowron - Deciphering Genetic Drivers in Primary and Metastatic Medulloblastoma - PDF, University of Toronto, Laboratory Medicine and Pathobiology
2020 Lucas Hu - Biochemical Profile-Based Computational Inference of Protein Complexes - PDF, University of Toronto, Department of Molecular Genetics
2019 Brian Law - Protein-Protein Interaction Network Alignment and Evolution - PDF, University of Toronto, Department of Computer Science
2019 Thinh Ngoc Tran - Pathway-based Lineage Analysis of Time-course Single-Cell RNA Sequencing Data - PDF, University of Toronto, Molecular Genetics
2018 Catherine Ross - Detecting Signals of Coevolution within Immune Response Pathways in the African-American Ancestral Population - PDF, University of Toronto, Molecular Genetics
2018 Shobhit Jain - Computational Models For Domain-Peptide Mediated Protein-Protein Interactions - PDF, University of Toronto, Department of Computer Science
2015 David Shih - Molecular Classification and Clinical Genomics of Medulloblastoma - PDF, University of Toronto, Laboratory Medicine and Pathobiology
2015 Marina Olhovsky - Using Text Mining of PubMed Abstracts as an Evidence Source in Computational Predictions of WW Domain-Mediated Protein-Protein Interactions - PDF, York University, Graduate Program in Biology
2013 Omar Wagih - Assessing the impact of single nucleotide variants on kinase–substrate phosphorylation - PDF, University of Toronto, Department of Computer Science
2013 Shirley Hui - Computational Prediction of PDZ Mediated Protein-Protein Interactions - PDF, University of Toronto, Department of Molecular Genetics
2013 Ron Ammar - Understanding Genome Structure and Response to Perturbation - PDF, University of Toronto, Department of Molecular Genetics
2013 Anastasia Baryshnikova - Mapping Genetic Interaction Networks in Yeast - PDF, University of Toronto, Department of Molecular Genetics
2012 Chris Tan - Characterizing the Evolutionary Dynamics of Protein Phosphorylation Sites for Functional Phospho-proteomics - PDF, University of Toronto, Department of Molecular Genetics
2011 Xiaojian Shao - Prediction of Protein-Nucleic Acids and Protein-Protein Interactions Using Kernel Methods - PDF (in Mandarin), China Agricultural University and the University of Toronto