Differences between revisions 337 and 599 (spanning 262 versions)

Contents

Peer-reviewed Articles
Preprints
Textbook Chapters
Theses

See who's cited our work at Google Scholar and our ORCID profile. (Also, check out our latest publications in progress - preprints)

Peer-reviewed Articles

2023

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 Mar 31.
PubMed Abstract - PDF
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
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, El Ghamrasni S, Afiuni-Zadeh S, Tsai R, Alvi S, Elia A, Lu 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, Sorlie T, Wrana JL, Jackson HW, Wilson MD, Witkiewicz AK, Knudsen ES, Pujana MA, Wahl GM, Schramek D
Cancer Discov. 2022 Sep 15
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

-  ⇤ ← Revision 337 as of 2017-09-12 14:22:36 → 
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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]]
+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]])
 Line 8:
+== 2023 ==
 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 Mar 31.]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/37000033/|PubMed Abstract]] -  [[attachment:anal_chem_April2023.pdf|PDF]] <<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>>

== 2022 ==
 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. '''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, El Ghamrasni S, Afiuni-Zadeh S, Tsai R, Alvi S, Elia A, Lu 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, Sorlie T, Wrana JL, Jackson HW, Wilson MD, Witkiewicz AK, Knudsen ES, Pujana MA, Wahl GM, Schramek D<<BR>>[[https://aacrjournals.org/cancerdiscovery/article/doi/10.1158/2159-8290.CD-21-0865/709222/Loss-of-epigenetic-regulation-disrupts-lineage|Cancer Discov. 2022 Sep 15]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/36108220/|PubMed Abstract]] -  [[attachment:CancerDis_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>>

 1. '''Identification of the global miR-130a targetome reveals a role for TBL1XR1 in hematopoietic stem cell self-renewal and t(8;21) AML'''<<BR>>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<<BR>>[[https://www.cell.com/cell-reports/fulltext/S2211-1247(22)00214-5|Cell Rep. 2022 Mar 8;38(10)]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/35263585/|PubMed Abstract]] - [[attachment:CellRep_March2022.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>>

 1. '''A Shared Transcriptional Identity for Forebrain and Dentate Gyrus Neural Stem Cells from Embryogenesis to Adulthood'''<<BR>>Borrett MJ, Tahmasian N, '''Innes BT''', '''Bader GD''', Kaplan DR, Miller FD<<BR>>[[https://www.eneuro.org/content/early/2022/01/12/ENEURO.0271-21.2021.long|eNeuro. 2022 Jan 13:ENEURO.0271-21.2021]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/35027446/|PubMed Abstract]] - [[attachment:eneuro_Jan2022.pdf|PDF]]<<BR>>'''SINGLE CELL GENOMICS'''<<BR>><<BR>>

 1. '''Hypophosphorylated pRb knock-in mice exhibit hallmarks of aging and vitamin C-preventable diabetes'''<<BR>>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<<BR>>[[https://www.embopress.org/doi/full/10.15252/embj.2020106825|EMBO J. 2022 Jan 13]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/35023164/|PubMed Abstract]] - [[attachment:EMBO_Jan2022.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>>

== 2021 ==
 1. '''Temporal profiling of therapy resistance in human medulloblastoma identifies novel targetable drivers of recurrence'''<<BR>>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<<BR>>[[https://www.science.org/doi/full/10.1126/sciadv.abi5568?af=R|Sci Adv. 2021 Dec 10;7(50)]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/34878832/|PubMed Abstract]] - [[attachment:SciAdv_Dec2021.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>>

 1. '''Author-sourced capture of pathway knowledge in computable form using Biofactoid'''<<BR>>'''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<<BR>>[[https://elifesciences.org/articles/68292|Elife. 2021 Dec 3;10]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/34860157/|PubMed Abstract]] - [[attachment:Elife_Dec2021.pdf|PDF]]<<BR>>'''SOFTWARE'''<<BR>><<BR>>

 1. '''Single-Cell, Single-Nucleus, and Spatial RNA Sequencing of the Human Liver Identifies Cholangiocyte and Mesenchymal Heterogeneity'''<<BR>>'''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<<BR>>[[https://aasldpubs.onlinelibrary.wiley.com/doi/full/10.1002/hep4.1854|Hepatol Commun. 2021 Nov 18]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/34792289/|PubMed Abstract]] - [[attachment:HepatoCom_Nov2021.pdf|PDF]]<<BR>>'''SINGLE CELL GENOMICS'''<<BR>><<BR>>

 1. '''The Reactome pathway knowledgebase 2022'''<<BR>>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<<BR>>[[https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkab1028/6426058|Nucleic Acids Res. 2021 Nov 12]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/34788843/|PubMed Abstract]] - [[attachment:NucleicAcid_Nov2021.pdf|PDF]]<<BR>>'''PATHWAY DATABASE'''<<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>>

 1. '''A microfluidic platform enables comprehensive gene expression profiling of mouse retinal stem cells'''<<BR>>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<<BR>>[[https://pubs.rsc.org/en/content/articlelanding/2021/lc/d1lc00790d|Lab Chip. 2021 Oct 15]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/34651637/|PubMed Abstract]] - [[attachment:LabChip_Oct2021.pdf|PDF]]<<BR>>'''SINGLE CELL GENOMICS'''<<BR>><<BR>>

 1. '''A roadmap for the Human Developmental Cell Atlas'''<<BR>>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<<BR>> [[https://www.nature.com/articles/s41586-021-03620-1|Nature. 2021 Sep;597(7875):196-205]]<<BR>> [[https://pubmed.ncbi.nlm.nih.gov/34497388/|PubMed Abstract]] - [[attachment:Nature_Sept2021.pdf|PDF]]<<BR>>'''SINGLE CELL GENOMICS'''<<BR>><<BR>>

 1. '''A clinically applicable integrative molecular classification of meningiomas'''<<BR>>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<<BR>>[[https://www.nature.com/articles/s41586-021-03850-3|Nature. 2021 Aug 25]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/34433969/|PubMed Abstract]] - [[attachment:Nature_Aug2021.pdf|PDF]]<<BR>>'''SINGLE CELL GENOMICS'''<<BR>><<BR>>

 1. '''DeCLUTR: Deep Contrastive Learning for Unsupervised Textual Representations'''<<BR>>'''John Giorgi''', Osvald Nitski, Bo Wang, '''Gary Bader'''<<BR>>[[https://aclanthology.org/2021.acl-long.72/|ACL/IJCNLP. 2021 Aug 1]]<<BR>>[[https://aclanthology.org/2021.acl-long.72/|ACL Anthology]] - [[https://aclanthology.org/2021.acl-long.72.pdf|PDF]]<<BR>>'''NATURAL LANGUAGE PROCESSING'''<<BR>><<BR>>

 1. '''TFEB-mediated endolysosomal activity controls human hematopoietic stem cell fate'''<<BR>>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<<BR>>[[https://www.sciencedirect.com/science/article/pii/S1934590921002885?via=ihub|Cell Stem Cell. 2021 Jul 28:S1934-5909(21)00288-5.]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/34343492/|PubMed Abstract]] - [[attachment:CellStemcell_Aug2021.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>>

 1. '''Nicotinamide phosphoribosyltransferase inhibitors selectively induce apoptosis of AML stem cells by disrupting lipid homeostasis'''<<BR>>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<<BR>>[[https://www.sciencedirect.com/science/article/pii/S1934590921002745|Cell Stem Cell. 2021 Jul 12:S1934-5909(21)]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/34293334/|PubMed Abstract]] - [[attachment:CellStemcell_July2021.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>>

 1. '''Control of tissue development and cell diversity by cell cycle dependent transcriptional filtering'''<<BR>>'''Abou Chakra M''', '''Isserlin R''', '''Tran TN''', '''Bader GD'''<<BR>> [[https://elifesciences.org/articles/64951|Elife. 2021 Jul 2;10:e64951]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/34212855/|PubMed Abstract]] - [[attachment:Elife_July2021.pdf|PDF]]<<BR>>'''MATHEMATICAL MODELLING'''<<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>>

 1. '''Surveilling and Tracking COVID-19 Patients Using a Portable Quantum Dot Smartphone Device'''<<BR>>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<<BR>> [[https://pubs.acs.org/doi/10.1021/acs.nanolett.1c01280|Nano Lett. 2021 Jun 10]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/34110166/|PubMed Abstract]] - [[attachment:NanoLett_June2021.pdf|PDF]]<<BR>>'''COVID-19'''<<BR>><<BR>>

 1. '''Generation of mature compact ventricular cardiomyocytes from human pluripotent stem cells'''<<BR>>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<<BR>> [[https://www.nature.com/articles/s41467-021-23329-z|Nat Commun. 2021 May 26;12(1):3155]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/34039977/|PubMed Abstract]] - [[attachment:NatureComm_May2021.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>>

 1. '''Tutorial: guidelines for annotating single-cell transcriptomic maps using automated and manual methods'''<<BR>> '''Clarke ZA''', '''Andrews TS''', Atif J, '''Pouyabahar D''', '''Innes BT''', !MacParland SA, '''Bader GD'''<<BR>> [[https://www.nature.com/articles/s41596-021-00534-0|Nat Protoc. 2021 May 24.]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/34031612/|PubMed Abstract]] - [[attachment:NatureProt_May2021.pdf|PDF]]<<BR>>'''SINGLE CELL GENOMICS'''<<BR>><<BR>>

 1. '''SBGN Bricks Ontology as a tool to describe recurring concepts in molecular networks'''<<BR>>Rougny A, Touré V, Albanese J, Waltemath D, Shirshov D, Sorokin A, '''Bader GD''', Blinov ML, Mazein A<<BR>>[[https://academic.oup.com/bib/advance-article/doi/10.1093/bib/bbab049/6184415|Brief Bioinform. 2021 Mar 24]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/33758926/|PubMed Abstract]] - [[attachment:briefbioinfo_Mar2021.pdf|PDF]]<<BR>>'''DATA STANDARDS''' <<BR>><<BR>>

 1. '''Distinct DNA methylation patterns associated with treatment resistance in metastatic castration resistant prostate cancer'''<<BR>>Peter MR, Bilenky M, Davies A, '''Isserlin R''', '''Bader GD''', Fleshner NE, Hirst M, Zoubeidi A, Bapat B<<BR>> [[https://www.nature.com/articles/s41598-021-85812-3|Sci Rep. 2021 Mar 23;11(1):6630]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/33758253/|PubMed Abstract]] - [[attachment:Scireport_Mar2021.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>>

 1. '''The transcriptional landscape of Shh medulloblastoma'''<<BR>>'''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<<BR>>[[https://www.nature.com/articles/s41467-021-21883-0|Nat Commun. 2021 Mar 19;12(1):1749]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/33741928/|PubMed Abstract]] - [[attachment:NatureCom_Mar2021.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>>

 1. '''Biological and therapeutic implications of a unique subtype of NPM1 mutated AML'''<<BR>>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<<BR>> [[https://www.nature.com/articles/s41467-021-21233-0|Nat Commun. 2021 Feb 16;12(1):1054]]<<BR>> [[https://pubmed.ncbi.nlm.nih.gov/33594052/|PubMed Abstract]] - [[attachment:NatureCom_Feb2021_2.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>>

 1. '''PRMT5 inhibition disrupts splicing and stemness in glioblastoma'''<<BR>>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 <<BR>> [[https://www.nature.com/articles/s41467-021-21204-5|Nat Commun. 2021 Feb 12;12(1):979]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/33579912/|PubMed Abstract]] - [[attachment:NatureCom_Feb2021.pdf|PDF]]<<BR>> '''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>>

 1. '''Sphingosine-1-phosphate receptor 3 potentiates inflammatory programs in normal and leukemia stem cells to promote differentiation'''<<BR>>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<<BR>>[[https://bloodcancerdiscov.aacrjournals.org/content/2/1/32|Blood Cancer Discov. 2021 Jan 1;2(1):32-53]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/33458693/|PubMed Abstract]] - [[attachment:BloodCancer_Jan2021.pdf|PDF]]<<BR>> '''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>>

 1. '''Gradient of Developmental and Injury Response transcriptional states defines functional vulnerabilities underpinning glioblastoma heterogeneity'''<<BR>> 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.<<BR>>[[https://www.nature.com/articles/s43018-020-00154-9|Nature Cancer 2021 Feb;2(2):157-173]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/35122077/|PubMed Abstract]] - [[attachment:Naturecancer_Jan2021.pdf|PDF]]<<BR>>'''SINGLE CELL GENOMICS'''<<BR>><<BR>>

== 2020 ==
 1. '''Large-scale survey and database of high affinity ligands for peptide recognition modules'''<<BR>>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<<BR>>[[https://www.embopress.org/doi/full/10.15252/msb.20199310|Mol Syst Biol. 2020 Dec;16(12)]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/33438817/|PubMed Abstract]] - [[attachment:MolSysBio_Dec2020.pdf|PDF]]<<BR>> '''PROTEIN INTERACTION PREDICTION'''<<BR>><<BR>>

 1. '''CD200 expression marks leukemia stem cells in human AML'''<<BR>>Ho JM, Dobson SM, '''Voisin V''', !McLeod J, Kennedy JA, Mitchell A, Jin L, Eppert K, '''Bader G''', Minden MD, Dick JE, Wang JCY<<BR>>[[https://ashpublications.org/bloodadvances/article/4/21/5402/469828/CD200-expression-marks-leukemia-stem-cells-in|Blood Adv. 2020 Nov 10;4(21):5402-5413]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/33147339/|PubMed Abstract]] - [[attachment:Bloodadv_Nov2020.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>>

 1. '''netDx: Software for building interpretable patient classifiers by multi-'omic data integration using patient similarity networks'''<<BR>>'''Pai S''', Weber P, '''Isserlin R''', '''Kaka H''', '''Hui S''', '''Shah MA''', Giudice L, Giugno R, Nøhr AK, Baumbach J, '''Bader GD'''<<BR>>[[https://f1000research.com/articles/9-1239/v2|F1000Res. 2020 Oct 15;9:1239]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/33628435/|PubMed Abstract]] - [[attachment:f1000_Oct2020.pdf|PDF]]<<BR>> '''PRECISION MEDICINE'''<<BR>><<BR>>

 1. '''Functional genomic landscape of cancer-intrinsic evasion of killing by T cells'''<<BR>>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<<BR>> [[https://www.nature.com/articles/s41586-020-2746-2|Nature. 2020 Sep 23]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/32968282/|PubMed Abstract]] - [[attachment:Nature_Sep2020.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>>

 1. '''Tempora: Cell trajectory inference using time-series single-cell RNA sequencing data'''<<BR>>'''Tran TN''', '''Bader GD'''<<BR>>[[https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008205|PLoS Comput Biol. 2020 Sep 9;16(9)]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/32903255/|PubMed Abstract]] - [[attachment:Plos_comp_bio_Sep2020.pdf|PDF]]<<BR>>'''SINGLE CELL GENOMICS'''<<BR>><<BR>>

 1. '''Dynamics of the cell-free DNA methylome of metastatic prostate cancer during androgen-targeting treatment'''<<BR>>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 <<BR>>[[https://www.futuremedicine.com/doi/abs/10.2217/epi-2020-0173|Epigenomics. 2020 Sep 1.]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/32867540/|PubMed Abstract]] - [[attachment:epigenomics_Sep2020.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>>

 1. '''Wnt activation as a therapeutic strategy in medulloblastoma'''<<BR>> 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<<BR>>[[https://www.nature.com/articles/s41467-020-17953-4|Nat Commun. 2020 Aug 28;11(1):4323]]<<BR>> [[https://pubmed.ncbi.nlm.nih.gov/32859895/|PubMed Abstract]] - [[attachment:nature_com_Aug2020.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>>

 1. '''Single-Cell Profiling Shows Murine Forebrain Neural Stem Cells Reacquire a Developmental State when Activated for Adult Neurogenesis'''<<BR>> Borrett MJ, '''Innes BT''', Jeong D, Tahmasian N, Storer MA, '''Bader GD''', Kaplan DR, Miller FD<<BR>> [[https://www.sciencedirect.com/science/article/pii/S221112472031007X|Cell Rep. 2020 Aug 11;32(6):108022]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/32783944/|PubMed Abstract]] - [[attachment:Cell_rep_Aug2020.pdf|PDF]]<<BR>>'''SINGLE CELL GENOMICS'''<<BR>><<BR>>

 1. '''Meta-analysis of gene expression profiles of lean and obese PCOS to identify differentially regulated pathways and risk of comorbidities'''<<BR>> '''Idicula-Thomas S''', Gawde U, Bhaye S, Pokar K, '''Bader GD'''<<BR>>[[https://www.sciencedirect.com/science/article/pii/S2001037020303123|Comput Struct Biotechnol J. 2020;18:1735-1745]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/32695266/|PubMed Abstract]] - [[attachment:Comp_struct_bio_July2020.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>>

 1. '''Generation of Functional Liver Sinusoidal Endothelial Cells from Human Pluripotent Stem-Cell-Derived Venous Angioblasts'''<<BR>> Gage BK, '''Liu JC, Innes BT''', !MacParland SA, !McGilvray ID, '''Bader GD''', Keller GM <<BR>> [[https://www.cell.com/cell-stem-cell/fulltext/S1934-5909(20)30274-5|Cell Stem Cell. 2020;S1934-5909(20)30274-5]]<<BR>>[[https://pubmed.ncbi.nlm.nih.gov/32640183/|PubMed Abstract]] - [[attachment:cellstem_July2020.pdf|PDF]]<<BR>>'''SINGLE CELL GENOMICS'''<<BR>><<BR>>

 1. '''Distinct fibroblast functional states drive clinical outcomes in ovarian cancer and are regulated by TCF21'''<<BR>>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<<BR>>[[https://rupress.org/jem/article/doi/10.1084/jem.20191094/151793/Distinct-fibroblast-functional-states-drive|J Exp Med. 2020 Aug 3;217(8)]]<<BR>> [[https://pubmed.ncbi.nlm.nih.gov/32434219/|PubMed Abstract]] - [[attachment:jexm_May2020.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>>

 1. '''Disrupting Mitochondrial Copper Distribution Inhibits Leukemic Stem Cell Self-Renewal'''<<BR>>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<<BR>>[[https://www.sciencedirect.com/science/article/abs/pii/S1934590920301491?via=ihub|Cell Stem Cell. 2020 May 12]]<<BR>>[[https://www.ncbi.nlm.nih.gov/pubmed/32416059|PubMed Abstract]] - [[attachment:cellstem_May2020.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>>

 1. '''!BraInMap Elucidates the Macromolecular Connectivity Landscape of Mammalian Brain'''<<BR>>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.<<BR>>  [[https://www.cell.com/cell-systems/fulltext/S2405-4712(20)30109-5|Cell Syst. 2020 Apr 22;10(4):333-350]]<<BR>>[[https://www.ncbi.nlm.nih.gov/pubmed/32325033|PubMed Abstract]] - [[attachment:CellSys_April2020.pdf|PDF]]<<BR>>'''PROTEIN INTERACTION'''<<BR>><<BR>>

 1. '''Mitochondrial carrier homolog 2 (MTCH2) is necessary for AML survival'''<<BR>>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 <<BR>>[[https://ashpublications.org/blood/article/doi/10.1182/blood.2019000106/454408/Mitochondrial-carrier-homolog-2-MTCH2-is-necessary|Blood. 2020 Apr 16]]<<BR>>[[https://www.ncbi.nlm.nih.gov/pubmed/32299104|PubMed Abstract]] - [[attachment:Blood_April2020.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>>

 1. '''Medulloblastoma Arises from the Persistence of a Rare and Transient Sox2(+) Granule Neuron Precursor''' <<BR>>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<<BR>> [[https://www.cell.com/cell-reports/fulltext/S2211-1247(20)30401-0|Cell Rep. 2020 Apr 14;31(2):107511]]<<BR>>[[https://www.ncbi.nlm.nih.gov/pubmed/32294450|PubMed Abstract]] - [[attachment:CellReports_April2020.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>>

 1. '''A reference map of the human binary protein interactome'''<<BR>> 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<<BR>> [[https://www.nature.com/articles/s41586-020-2188-x|Nature.2020 Apr;580(7803):402-408]]<<BR>>[[https://www.ncbi.nlm.nih.gov/pubmed/32296183|PubMed Abstract]] - [[attachment:Natuer_April2020.pdf|PDF]]<<BR>>'''PROTEIN INTERACTION'''<<BR>><<BR>>

 1. '''The mitochondrial peptidase, neurolysin, regulates respiratory chain supercomplexformation and is necessary for AML viability'''<<BR>>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<<BR>>[[https://stm.sciencemag.org/content/12/538/eaaz8264.short|Sci Transl Med. 2020 Apr 8;12(538)]]<<BR>> [[https://www.ncbi.nlm.nih.gov/pubmed/32269163|PubMed Abstract]] - [[attachment:SciTranslmed_April2020.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>>

 1. '''Nanoparticle Uptake in a Spontaneous and Immunocompetent Woodchuck Liver Cancer Model'''<<BR>>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<<BR>> [[https://pubs.acs.org/doi/10.1021/acsnano.0c00468|ACS Nano. 2020 Apr 7]]<<BR>>[[https://www.ncbi.nlm.nih.gov/pubmed/32255624|PubMed Abstract]] - [[attachment:Nano_April2020.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>>

 1. '''Relapse fated latent diagnosis subclones in acute B lineage leukaemia are drug tolerant and possess distinct metabolic programs'''<<BR>>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 <<BR>>[[https://cancerdiscovery.aacrjournals.org/content/early/2020/02/21/2159-8290.CD-19-1059.long|Cancer Discov. 2020 Feb 21]]<<BR>>[[https://www.ncbi.nlm.nih.gov/pubmed/32086311|PubMed Abstract]] - [[attachment:CancerDisc_Feb2020.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>>

 1. '''Potential Therapeutic Targets for Lung Repair During Human Ex Vivo Lung Perfusion'''<<BR>>Wong A, Zamel R, Yeung J, '''Bader GD''', Dos Santos CC, Bai X, Wang Y, Keshavjee S, Liu M<<BR>>[[https://erj.ersjournals.com/content/early/2020/01/16/13993003.02222-2019.long|Eur Respir J. 2020 Feb 14]] <<BR>> [[https://www.ncbi.nlm.nih.gov/pubmed/32060066|PubMed Abstract]] - [[attachment:EurRespir_Feb2020.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>>

 1. '''A network analysis to identify mediators of germline-driven differences in breast cancer prognosis.'''<<BR>> 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<<BR>> [[https://www.nature.com/articles/s41467-019-14100-6|Nat Commun. 2020 Jan 16;11(1):312]]<<BR>> [[https://www.ncbi.nlm.nih.gov/pubmed/31949161|PubMed Abstract]] - [[attachment:NatComm_Jan2020.pdf|PDF]]<<BR>> '''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>>

 1. '''Pathway Commons 2019 Update: integration, analysis and exploration of pathway data'''<<BR>>'''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<<BR>>[[https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkz946/5606621|Nucleic Acids Res. 2020 Jan 8]]<<BR>> [[https://www.ncbi.nlm.nih.gov/pubmed/31647099|PubMed Abstract]] - [[attachment:NucAcid_Oct2019.pdf|PDF]]<<BR>> '''PATHWAY DATABASE'''<<BR>><<BR>>

== 2019 ==
 1. '''End-to-end Named Entity Recognition and Relation Extraction using Pre-trained Language Models'''<<BR>>'''John Giorgi''', Xindi Wang, Nicola Sahar, Won Young Shin, '''Gary D. Bader''', Bo Wang<<BR>>[[https://arxiv.org/abs/1912.13415|arXiv. 2019 Dec 20]]<<BR>>[[https://arxiv.org/abs/1912.13415|arXiv]] - [[https://arxiv.org/pdf/1912.13415|PDF]]<<BR>>'''NATURAL LANGUAGE PROCESSING'''<<BR>><<BR>>
 1. '''Sphingolipid Modulation Activates Proteostasis Programs to Govern Human Hematopoietic Stem Cell Self-Renewal'''<<BR>>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<<BR>>[[https://www.sciencedirect.com/science/article/pii/S1934590919303935|Cell Stem Cell. 2019 Oct 11]]<<BR>> [[https://www.ncbi.nlm.nih.gov/pubmed/31631013|PubMed Abstract]] - [[attachment:stemcell_Oct2019.pdf|PDF]]<<BR>> '''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>>

 1. '''Single-cell transcriptomic profiling of the aging mouse brain'''<<BR>>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<<BR>>  [[https://www.nature.com/articles/s41593-019-0491-3|Nat Neurosci. 2019 Oct;22(10):1696-1708]]<<BR>>[[https://www.ncbi.nlm.nih.gov/pubmed/31551601|PubMed Abstract]] - [[attachment:iNatneuro_Oct2019.pdf|PDF]]<<BR>>[[https://www.biorxiv.org/content/10.1101/440032v1|{{attachment:bioarxiv.png|https://www.biorxiv.org/content/10.1101/440032v1|width="50"}}]]<<BR>>'''SINGLE CELL GENOMICS'''<<BR>><<BR>>

 1. '''Rewiring of the Human Mitochondrial Interactome during Neuronal Reprogramming Reveals Regulators of the Respirasome and Neurogenesis'''<<BR>>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<<BR>>[[https://www.sciencedirect.com/science/article/pii/S2589004219303360|iScience. 2019 Sep 4;19:1114-1132]]<<BR>>[[https://www.ncbi.nlm.nih.gov/pubmed/31536960|PubMed Abstract]] - [[attachment:iScience_Sept2019.pdf|PDF]]<<BR>>'''NETWORK ANALYSIS SOFTWARE'''<<BR>><<BR>>

 1. '''Benchmarking to the Gold Standard: Hyaluronan-Oxime Hydrogels Recapitulate Xenograft Models with In Vitro Breast Cancer Spheroid Culture'''<<BR>>Baker AEG, Bahlmann LC, Tam RY, '''Liu JC''', Ganesh AN, Mitrousis N, Marcellus R, Spears M, Bartlett JMS, Cescon DW, '''Bader GD''', Shoichet MS<<BR>>[[https://onlinelibrary.wiley.com/doi/full/10.1002/adma.201901166|Adv Mater. 2019 Jul 19;31(36)]]<<BR>>[[https://www.ncbi.nlm.nih.gov/pubmed/31322299|PubMed Abstract]] - [[attachment:AdvMater_July2019.pdf|PDF]]<<BR>>'''NETWORK ANALYSIS SOFTWARE'''<<BR>><<BR>>

 1. '''EPIC: software toolkit for elution profile-based inference of protein complexes'''<<BR>>'''Hu LZ''', '''Goebels F''', Tan JH, Wolf E, Kuzmanov U, Wan C, Phanse S, '''Xu C''', Schertzberg M, Fraser AG, '''Bader GD''', Emili A <<BR>>[[https://www.nature.com/articles/s41592-019-0461-4|Nat Methods. 2019 July 15]] <<BR>> [[https://www.ncbi.nlm.nih.gov/pubmed/31308550|PubMed Abstract]] - [[attachment:NatureMethod_July2019.pdf|PDF]]<<BR>>'''NETWORK ANALYSIS SOFTWARE'''<<BR>><<BR>>

 1. '''Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019'''<<BR>>Schreiber F, Sommer B, '''Bader GD''', Gleeson P, Golebiewski M, Hucka M, Keating SM, König M, Myers C, Nickerson D, Waltemath D. J<<BR>> [[https://www.degruyter.com/view/j/jib.ahead-of-print/jib-2019-0035/jib-2019-0035.xml?format=INT|Integr Bioinform. 2019 Jul 13]]<<BR>>[[https://www.ncbi.nlm.nih.gov/pubmed/31301675|PubMed Abstract]] - [[attachment:InteBioinfo_July2019.pdf|PDF]]<<BR>>'''DATA STANDARDS''' <<BR>><<BR>>

 1. '''Towards reliable named entity recognition in the biomedical domain'''<<BR>>'''Giorgi JM''', '''Bader GD'''<<BR>>[[https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btz504/5520946|Bioinformatics. 2019 Jun 20]] <<BR>>[[https://www.ncbi.nlm.nih.gov/pubmed/31218364|PubMed Abstract]] - [[attachment:Bioinfo_June2019.pdf|PDF]]<<BR>>'''TEXT MINING'''<<BR>><<BR>>

 1. '''Bmi1 regulates human glioblastoma stem cells through activation of differential gene networks in CD133+ brain tumor initiating cells'''<<BR>> 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<<BR>> [[https://link.springer.com/article/10.1007/s11060-019-03192-1|J Neurooncol. 2019 May 21]]<<BR>>[[https://www.ncbi.nlm.nih.gov/pubmed/31115870|PubMed Abstract]] - [[attachment:JNeruor_May2019.pdf|PDF]]<<BR>> '''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>>

 1. '''The Mitochondrial Transacylase, Tafazzin, Regulates for AML Stemness by Modulating Intracellular Levels of Phospholipids'''<<BR>>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<<BR>> [[https://www.cell.com/cell-stem-cell/pdfExtended/S1934-5909(19)30072-4|Cell Stem Cell. 2019 Mar 19]]<<BR>>[[https://www.ncbi.nlm.nih.gov/pubmed/30930145|PubMed Abstract]] -[[attachment:Cellstem_April2019.pdf|PDF]]<<BR>> '''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>>

 1. '''Exploring targets of TET2-mediated methylation reprogramming as potential discriminators of prostate cancer progression'''<<BR>> Kamdar S, '''Isserlin R''', Van der Kwast T, Zlotta AR, '''Bader GD''', Fleshner NE, Bapat B<<BR>>[[https://clinicalepigeneticsjournal.biomedcentral.com/articles/10.1186/s13148-019-0651-z|Clin Epigenetics. 2019 Mar 27;11(1):54]]<<BR>>[[https://www.ncbi.nlm.nih.gov/pubmed/30917865|PubMed Abstract]] -[[attachment:ClinEpi_Mar2019.pdf|PDF]]<<BR>> '''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>>

 1. '''netDx: interpretable patient classification using integrated patient similarity networks'''<<BR>> '''Pai S''', '''Hui S''', '''Isserlin R''', '''Shah MA''', '''Kaka H''', '''Bader GD'''<<BR>>[[http://msb.embopress.org/content/15/3/e8497.long|Mol Syst Biol. 2019 Mar 14;15(3):e8497]]<<BR>>[[https://www.ncbi.nlm.nih.gov/pubmed/30872331|PubMed Abstract]] -[[attachment:MSB_Mar2019.pdf|PDF]]<<BR>> [[https://www.biorxiv.org/content/10.1101/084418v4|{{attachment:bioarxiv.png|https://www.biorxiv.org/content/10.1101/084418v4|width="50"}}]]<<BR>>'''PRECISION MEDICINE'''<<BR>><<BR>>

 1. '''Evaluation of methods to assign cell type labels to cell clusters from single-cell RNA-sequencing data.''' <<BR>> Diaz-Mejia JJ, Meng EC, Pico AR, !MacParland SA, Ketela T, Pugh TJ, '''Bader GD''', Morris JH<<BR>>[[https://f1000research.com/articles/8-296|F1000Res. 2019 Mar 15;8. pii: ISCB Comm J-296]] <<BR>>[[https://www.ncbi.nlm.nih.gov/pubmed/31508207|PubMed Abstract]] -[[attachment:f1000_Mar2019.pdf|PDF]]<<BR>>'''SINGLE CELL GENOMICS'''<<BR>><<BR>>

 1. '''Powerful gene set analysis in GWAS with the Generalized Berk-Jones statistic'''<<BR>>Sun R, '''Hui S''', '''Bader GD''', Lin X, Kraft P<<BR>>[[https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1007530|PLoS Genet. 2019 Mar 15;15(3)]]<<BR>>[[https://www.ncbi.nlm.nih.gov/pubmed/30875371|PubMed Abstract]] -[[attachment:PlosGenet_Mar2019.pdf|PDF]]<<BR>> '''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>>

 1. <<Anchor(EM_2019)>> '''Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and !EnrichmentMap'''<<BR>>'''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'''<<BR>>[[https://www.nature.com/articles/s41596-018-0103-9|Nat Protoc. 2019 Feb;14(2):482-517]]<<BR>>[[https://www.ncbi.nlm.nih.gov/pubmed/30664679|PubMed Abstract]] -[[attachment:NatProt_Jan2019.pdf|PDF]]<<BR>>[[https://www.biorxiv.org/content/early/2017/12/12/232835|{{attachment:bioarxiv.png|https://www.biorxiv.org/content/early/2017/12/12/232835|width="50"}}]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>>

 1. '''ARGLU1 is a transcriptional coactivator and splicing regulator important for stress hormone signaling and development'''<<BR>>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<<BR>>[[https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkz010/5304305|Nucleic Acids Res. 2019 Jan 30]]<<BR>>[[https://www.ncbi.nlm.nih.gov/pubmed/30698747|PubMed Abstract]] -[[attachment:NucleicAcids_Jan2019.pdf|PDF]]<<BR>> '''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>>

== 2018 ==
 1. '''Induction of rod versus cone photoreceptor-specific progenitors from retinal precursor cells'''<<BR>>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<<BR>> [[https://www.sciencedirect.com/science/article/pii/S1873506118302733|Stem Cell Res. 2018 Nov 13;33:215-227]] <<BR>>[[https://www.ncbi.nlm.nih.gov/pubmed/30453152|PubMed Abstract]] -[[attachment:Stemcell_Nov2018.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>>

 1. '''The Relative Contributions of Cell-Dependent Cortical Microcircuit Aging to Cognition and Anxiety'''<<BR>>Shukla R, Prevot TD, French L, '''Isserlin R''', Rocco BR, Banasr M, '''Bader GD''', Sibille E <<BR>>[[https://www.biologicalpsychiatryjournal.com/article/S0006-3223(18)31890-0/fulltext|Biol Psychiatry. 2018 Oct 5]]<<BR>>[[https://www.ncbi.nlm.nih.gov/pubmed/30446205|PubMed Abstract]] -[[attachment:Psychiatry_Nov2018.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>>

 1. '''Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations'''<<BR>>!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<<BR>>[[https://www.nature.com/articles/s41467-018-06318-7|Nat Commun. 2018 Oct 22;9(1):4383]]<<BR>>[[https://www.ncbi.nlm.nih.gov/pubmed/30348985|PubMed Abstract]] -[[attachment:NatureCom_Oct2018.pdf|PDF]]<<BR>>'''SINGLE CELL GENOMICS'''<<BR>><<BR>>

 1. '''scClustViz - Single-cell RNAseq cluster assessment and visualization'''<<BR>>'''Innes BT''', '''Bader GD'''<<BR>> [[https://f1000research.com/articles/7-1522/v2|F1000Res. 2018 Sep 21;7]]<<BR>>[[https://www.ncbi.nlm.nih.gov/pubmed/31016009|PubMed Abstract]] -[[attachment:f1000_April2019.pdf|PDF]]<<BR>> '''SINGLE CELL GENOMICS'''<<BR>><<BR>>

 1. '''The Human Cell Atlas White Paper'''<<BR>>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<<BR>>[[https://arxiv.org/abs/1810.05192|{{attachment:bioarxiv.png|https://arxiv.org/abs/1810.05192|width="50"}}]]-[[attachment:website_pdf.pdf|PDF]]<<BR>>'''SINGLE CELL GENOMICS, PREPRINT'''<<BR>><<BR>>

 1. '''Single-Cell RNA Sequencing: A New Window into Cell Scale Dynamics'''<<BR>>Dasgupta S, '''Bader GD''', Goyal S<<BR>>[[https://www.sciencedirect.com/science/article/pii/S0006349518307653|Biophys J. 2018 Aug 7;115(3):429-435]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/30033145|PubMed Abstract]] -[[attachment:Biophyd_July2018.pdf|PDF]]<<BR>>'''SINGLE CELL GENOMICS'''<<BR>><<BR>>

 1. '''The Cytoscape Automation app article collection.'''<<BR>>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.<<BR>> [[https://f1000research.com/articles/7-800/v1|F1000Res. 2018 Jun 20;7:800]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/29983926|PubMed Abstract]] -[[attachment:f1000_July2018.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>>

 1. '''Mammary molecular portraits reveal lineage-specific features and progenitor cell vulnerabilities'''<<BR>>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<<BR>>[[http://jcb.rupress.org/content/early/2018/06/18/jcb.201804042|J Cell Biol. 2018 Jun 19]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/29921600|PubMed Abstract]] -[[attachment:JCB_June2018.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>>

 1. <<Anchor(GeneMANIA_2018)>> '''GeneMANIA update 2018'''<<BR>>'''Franz M''', '''Rodriguez H''', '''Lopes C''', Zuberi K, Montojo J, '''Bader GD''', Morris Q<<BR>>[[https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gky311/5038280|Nucleic Acids Res. 2018 Jun 15]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/29912392|PubMed Abstract]] -[[attachment:NAR_June2018.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>>

 1. '''Transfer learning for biomedical named entity recognition with neural networks'''<<BR>>'''Giorgi JM, Bader GD'''<<BR>>[[https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty449/5026661|Bioinformatics. 2018 Jun 1]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/29868832|PubMed Abstract]] -[[attachment:Bioinformatics_June2018.pdf|PDF]]<<BR>> [[https://www.biorxiv.org/content/early/2018/02/12/262790|{{attachment:bioarxiv.png|https://www.biorxiv.org/content/early/2018/02/12/262790|width="50"}}]]<<BR>><<BR>>

 1. '''Patient Similarity Networks for Precision Medicine'''<<BR>>'''Pai S, Bader GD'''<<BR>> [[https://www.sciencedirect.com/science/article/pii/S0022283618305321|J Mol Biol. 2018 May 31]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/29860027|PubMed Abstract]] -[[attachment:JMB_June2018.pdf|PDF]]<<BR>> [[https://www.biorxiv.org/content/early/2018/05/25/084418|{{attachment:bioarxiv.png|https://www.biorxiv.org/content/early/2018/05/25/084418|width="50"}}]] <<BR>>'''PRECISION MEDICINE'''<<BR>><<BR>>

 1. '''Identification of CDC25 as a Common Therapeutic Target for Triple-Negative Breast Cancer'''<<BR>> '''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<<BR>>[[http://www.cell.com/cell-reports/fulltext/S2211-1247(18)30381-4?_returnURL=https://linkinghub.elsevier.com/retrieve/pii/S2211124718303814?showall=true|Cell Rep. 2018 Apr 3;23(1):112-126]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/29617654|PubMed Abstract]] -[[attachment:Cellrep_April2018.pdf|PDF]] <<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>>

 1. '''Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017'''<<BR>>Schreiber F, '''Bader GD''', Gleeson P, Golebiewski M, Hucka M, Keating SM, Novère NL, Myers C, Nickerson D, Sommer B, Waltemath D<<BR>>[[https://www.degruyter.com/view/j/jib.ahead-of-print/jib-2018-0013/jib-2018-0013.xml|J Integr Bioinform. 2018 Mar 29]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/29596055|PubMed Abstract]] -[[attachment:IntegrativeBio_April2018.pdf|PDF]] <<BR>>'''DATA STANDARDS''' <<BR>><<BR>>

 1. '''Whole transcriptome analysis reveals differential gene expression profile reflecting macrophage polarization in response to influenza A !H5N1 virus infection'''<<BR>>Zhang N, Bao YJ, Tong AH, '''Zuyderduyn S''', '''Bader GD''', Malik Peiris JS, Lok S, Lee SM<<BR>>[[https://bmcmedgenomics.biomedcentral.com/articles/10.1186/s12920-018-0335-0|BMC Med Genomics. 2018 Feb 23;11(1):20]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/29475453|PubMed Abstract]] -[[attachment:BMC_medicalgenom_Feb2018.pdf|PDF]] <<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>>
-Line 9:
+Line 208:
-. '''Comprehensive Analysis of the Human SH3 Domain Family Reveals a Wide Variety of Non-canonical Specificities'''<<BR>>Teyra J, Huang H, '''Jain S''', Guan X, Dong A, Liu Y, Tempel W, Min J, Tong Y, Kim PM, '''Bader GD''', Sidhu SS[[http://www.cell.com/structure/abstract/S0969-2126(17)30251-4|Structure. 2017 Aug 28.
pii: S0969-2126(17)30251-4]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/28890361|PubMed Abstract]] - [[attachment:Structure_September2017.pdf|PDF]]<<BR>>'''PROTEIN INTERACTION'''<<BR>><<BR>>
+. '''Developmental Emergence of Adult Neural Stem Cells as Revealed by Single-Cell Transcriptional Profiling'''<<BR>>Yuzwa SA, Borrett MJ, '''Innes BT''', Voronova A, Ketela T, Kaplan DR, '''Bader GD''', Miller FD<<BR>>[[http://www.cell.com/cell-reports/fulltext/S2211-1247(17)31813-2|Cell Rep. 2017 Dec 26;21(13):3970-3986]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/29281841|PubMed Abstract]] -[[attachment:CellRe_December2017.pdf|PDF]]<<BR>>'''SINGLE CELL GENOMICS'''<<BR>><<BR>>

 1. '''A Map of Human Mitochondrial Protein Interactions Linked to Neurodegeneration Reveals New Mechanisms of Redox Homeostasis and NF-κB Signaling'''<<BR>>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<<BR>>[[http://www.cell.com/cell-systems/fulltext/S2405-4712(17)30447-7|Cell Syst. 2017 Nov 7. pii:S2405-4712(17)30447-7]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/29128334|PubMed Abstract]] -[[attachment:Cell_November2017.pdf|PDF]]<<BR>><<BR>>

 1. '''Association analysis identifies 65 new breast cancer risk loci'''<<BR>>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<<BR>>[[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature24284.html|Nature. 2017 Oct 23]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/29059683|PubMed Abstract]] - [[attachment:Nature_October2017.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>>

 1. '''Identification of ten variants associated with risk of estrogen-receptor-negative breast cancer'''<<BR>>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<<BR>>[[https://www.nature.com/articles/ng.3785|Nat Genet. 2017 Oct 23]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/29058716|PubMed Abstract]] - [[attachment:NatureGenetics_Octoboer2017.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>>

 1. '''Comprehensive Analysis of the Human SH3 Domain Family Reveals a Wide Variety of Non-canonical Specificities'''<<BR>>Teyra J, Huang H, '''Jain S''', Guan X, Dong A, Liu Y, Tempel W, Min J, Tong Y, Kim PM, '''Bader GD''', Sidhu SS<<BR>>[[http://www.cell.com/structure/abstract/S0969-2126(17)30251-4|Structure. 2017 Aug 28. S0969-2126(17)30251-4]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/28890361|PubMed Abstract]] - [[attachment:Structure_September2017.pdf|PDF]]<<BR>>'''PROTEIN INTERACTION'''<<BR>><<BR>>
-Line 14:
+Line 220:
-. '''ASCL1 Reorganizes Chromatin to Direct Neuronal Fate and Suppress Tumorigenicity of Glioblastoma Stem Cells'''<<BR>> 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<<BR>>[[http://www.cell.com/cell-stem-cell/fulltext/S1934-5909(17)30230-8|Cell Stem Cell. 2017 Jul 11. pii: S1934-5909(17)30230-8.]]<<BR>> [[http://www.ncbi.nlm.nih.gov/pubmed/28712938|PubMed Abstract]] - [[attachment:Cell_July2017.pdf|PDF]]<<BR>> '''PATHWAY AND NETWORK ANALYSIS '''  <<BR>><<BR>>
+. '''ASCL1 Reorganizes Chromatin to Direct Neuronal Fate and Suppress Tumorigenicity of Glioblastoma Stem Cells'''<<BR>> 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<<BR>>[[http://www.cell.com/cell-stem-cell/fulltext/S1934-5909(17)30230-8|Cell Stem Cell. 2017 Aug 3;21(2):209-224]]<<BR>> [[http://www.ncbi.nlm.nih.gov/pubmed/28712938|PubMed Abstract]] - [[attachment:Cell_July2017.pdf|PDF]]<<BR>> '''PATHWAY AND NETWORK ANALYSIS '''  <<BR>><<BR>>
-Line 20:
+Line 226:
-. '''Spatial heterogeneity in medulloblastoma'''<<BR>>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<<BR>> [[http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.3838.html|Nat Genet. 2017 Apr 10]]<<BR>> [[http://www.ncbi.nlm.nih.gov/pubmed/28394352|PubMed Abstract]] - [[attachment:NatureGenetics_April2017.pdf|PDF]]<<BR>>'''CANCER MUTATIONS'''  <<BR>><<BR>>

 1. '''Integrative cancer pharmacogenomics to infer large-scale drug taxonomy'''<<BR>>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<<BR>>[[http://cancerres.aacrjournals.org/content/early/2017/03/17/0008-5472.CAN-17-0096.long| Cancer Res. 2017 Mar 17 ]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/28314784|PubMed Abstract]] - [[attachment:CancerResearch_March2017.pdf|PDF]]<<BR>>'''NETWORK ANALYSIS'''<<BR>><<BR>>
+. '''Spatial heterogeneity in medulloblastoma'''<<BR>>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<<BR>> [[http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.3838.html|Nat Genet. 2017 Apr 10]]<<BR>> [[http://www.ncbi.nlm.nih.gov/pubmed/28394352|PubMed Abstract]] - [[attachment:NatureGenetics_April2017.pdf|PDF]]<<BR>>'''CANCER MUTATIONS'''  <<BR>><<BR>>

 1. '''Integrative cancer pharmacogenomics to infer large-scale drug taxonomy'''<<BR>>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<<BR>>[[http://cancerres.aacrjournals.org/content/early/2017/03/17/0008-5472.CAN-17-0096.long|Cancer Res. 2017 Mar 17]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/28314784|PubMed Abstract]] - [[attachment:CancerResearch_March2017.pdf|PDF]]<<BR>> [[https://www.biorxiv.org/content/early/2017/01/05/046219|{{attachment:bioarxiv.png|https://www.biorxiv.org/content/early/2017/01/05/046219|width="50"}}]]<<BR>>'''NETWORK ANALYSIS'''<<BR>><<BR>>
-Line 32:
+Line 237:
-Line 35:
+Line 239:
+. '''Global neuroscience and mental health research: a bibliometrics case study'''<<BR>> Buchan AMJ, Jurczyk E, '''Isserlin R''', '''Bader GD'''<<BR>>[[https://link.springer.com/article/10.1007/s11192-016-2094-z|Scientometrics 109 (1), 515-531]]<<BR>>[[attachment:Scientometrics_Oct2016.pdf|PDF]]<<BR>>'''NETWORK ANALYSIS SOFTWARE'''<<BR>><<BR>>
-Line 43:
+Line 249:
-.  '''Transcriptomic analysis reveals abnormal muscle repair and remodeling in survivors of critical illness with sustained weakness'''<<BR>> Walsh CJ, Batt J, Herridge MS, Mathur S, '''Bader GD''', Hu P, Dos Santos CC<<BR>>[[http://www.nature.com/articles/srep29334|Sci Rep. 2016 Jul 14;6:29334]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/27411715|PubMed Abstract]] - [[attachment:ScirepJuly2016.pdf|PDF]]<<BR>><<BR>>

 1.  '''Inhibition of Dopamine Receptor D4 Impedes Autophagic Flux, Proliferation, and Survival of Glioblastoma Stem Cells'''<<BR>> 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<<BR>>[[http://www.sciencedirect.com/science/article/pii/S1535610816302070|Cancer Cell. 2016 Jun 13;29(6):859-73]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/27300435|PubMed Abstract]] - [[attachment:CancerCellJune2016.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>>
+. '''Transcriptomic analysis reveals abnormal muscle repair and remodeling in survivors of critical illness with sustained weakness'''<<BR>> Walsh CJ, Batt J, Herridge MS, Mathur S, '''Bader GD''', Hu P, Dos Santos CC<<BR>>[[http://www.nature.com/articles/srep29334|Sci Rep. 2016 Jul 14;6:29334]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/27411715|PubMed Abstract]] - [[attachment:ScirepJuly2016.pdf|PDF]]<<BR>><<BR>>

 1. '''Inhibition of Dopamine Receptor D4 Impedes Autophagic Flux, Proliferation, and Survival of Glioblastoma Stem Cells'''<<BR>> 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<<BR>>[[http://www.sciencedirect.com/science/article/pii/S1535610816302070|Cancer Cell. 2016 Jun 13;29(6):859-73]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/27300435|PubMed Abstract]] - [[attachment:CancerCellJune2016.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>>
-Line 51:
+Line 257:
-. '''HOX gene complement and expression in the planarian Schmidtea mediterranea'''<<BR>> Currie KW, Brown DD, Zhu S, '''Xu C''', '''Voisin V''', '''Bader GD''', Pearson BJ<<BR>>[[http://evodevojournal.biomedcentral.com/articles/10.1186/s13227-016-0044-8| Evodevo. 2016 Mar 30;7:7]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/27034770|PubMed Abstract]] - [[attachment:EvodevoMarch2016.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>>
+. '''HOX gene complement and expression in the planarian Schmidtea mediterranea'''<<BR>> Currie KW, Brown DD, Zhu S, '''Xu C''', '''Voisin V''', '''Bader GD''', Pearson BJ<<BR>>[[http://evodevojournal.biomedcentral.com/articles/10.1186/s13227-016-0044-8|Evodevo. 2016 Mar 30;7:7]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/27034770|PubMed Abstract]] - [[attachment:EvodevoMarch2016.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>>
-Line 106:
+Line 312:
-. '''Evolutionary Constraint and Disease Associations of Post-Translational Modification Sites in Human Genomes''' <<BR>>'''Reimand J''', '''Wagih O''', '''Bader GD'''<<BR>> [[http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1004919| PLoS Genet 2015 Jan 22;11(1)]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/25611800| PubMed Abstract]] - [[attachment:plosgeneticsJan2015_Reimand.pdf|PDF]]<<BR>> '''CANCER MUTATIONS'''<<BR>><<BR>>
+. '''Evolutionary Constraint and Disease Associations of Post-Translational Modification Sites in Human Genomes''' <<BR>>'''Reimand J''', '''Wagih O''', '''Bader GD'''<<BR>> [[http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1004919|PLoS Genet 2015 Jan 22;11(1)]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/25611800|PubMed Abstract]] - [[attachment:plosgeneticsJan2015_Reimand.pdf|PDF]]<<BR>> '''CANCER MUTATIONS'''<<BR>><<BR>>
-Line 111:
+Line 317:
-.  '''Systems analysis reveals down-regulation of a network of pro-survival miRNAs drives the apoptotic response in dilated cardiomyopathy'''<<BR>> '''Isserlin R''', Merico D, Wang D, Vuckovic D, Bousette N, Gramolini AO, '''Bader GD''', Emili A<<BR>>  [[http://pubs.rsc.org/en/Content/ArticleLanding/2015/MB/C4MB00265B|Mol Biosyst 2015 Jan;11(1):239-51]] <<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/25361207|Pubmed Abstract]] - [[attachment:mbs2014.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>>
+. '''Systems analysis reveals down-regulation of a network of pro-survival miRNAs drives the apoptotic response in dilated cardiomyopathy'''<<BR>> '''Isserlin R''', Merico D, Wang D, Vuckovic D, Bousette N, Gramolini AO, '''Bader GD''', Emili A<<BR>>  [[http://pubs.rsc.org/en/Content/ArticleLanding/2015/MB/C4MB00265B|Mol Biosyst 2015 Jan;11(1):239-51]] <<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/25361207|Pubmed Abstract]] - [[attachment:mbs2014.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>>
-Line 115:
+Line 321:
-. '''Novel function discovery with GeneMANIA: a new integrated resource for gene function prediction in Escherichia coli'''<<BR>>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<<BR>>[[http://bioinformatics.oxfordjournals.org/content/early/2014/10/13/bioinformatics.btu671.abstract|Bioinformatics 2015 Feb 1;31(3):306-10]]<<BR>> [[http://www.ncbi.nlm.nih.gov/pubmed/25316676|Pubmed Abstract]] - [[attachment:genemania_ecoli.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>>
+. <<Anchor(GeneMANIA_2015)>> '''Novel function discovery with GeneMANIA: a new integrated resource for gene function prediction in Escherichia coli'''<<BR>>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<<BR>>[[http://bioinformatics.oxfordjournals.org/content/early/2014/10/13/bioinformatics.btu671.abstract|Bioinformatics 2015 Feb 1;31(3):306-10]]<<BR>> [[http://www.ncbi.nlm.nih.gov/pubmed/25316676|Pubmed Abstract]] - [[attachment:genemania_ecoli.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>>
-Line 119:
+Line 325:
-. '''GeneMANIA: Fast gene network construction and function prediction for Cytoscape'''<<BR>>'''Jason Montojo''','''Khalid Zuberi''', '''Harold Rodriguez''', '''Gary D. Bader''', Quaid Morris<<BR>>[[http://f1000research.com/articles/3-153/v1|F1000Res 2014 Jul 1;3:153]]<<BR>> [[http://www.ncbi.nlm.nih.gov/pubmed/25254104|Pubmed Abstract]] - [[attachment:Montojo_f10002014.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>>
+. <<Anchor(GeneMANIA_2014)>> '''GeneMANIA: Fast gene network construction and function prediction for Cytoscape'''<<BR>>'''Jason Montojo''','''Khalid Zuberi''', '''Harold Rodriguez''', '''Gary D. Bader''', Quaid Morris<<BR>>[[http://f1000research.com/articles/3-153/v1|F1000Res 2014 Jul 1;3:153]]<<BR>> [[http://www.ncbi.nlm.nih.gov/pubmed/25254104|Pubmed Abstract]] - [[attachment:Montojo_f10002014.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>>
-Line 135:
+Line 341:
-. '''Prediction and Experimental Characterization of nsSNPs Altering Human PDZ-Binding Motifs'''<<BR>> '''Gfeller D''', Ernst A, Jarvik N, Sidhu SS, '''Bader GD''' <<BR>>[[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0094507|PLoS One 2014 Apr 10;9(4):e94507]] <<BR>> [[http://www.ncbi.nlm.nih.gov/pubmed/24722214|PubMed Abstract]] - [[attachment:gfeller_plosone2014.pdf|PDF]] <<BR>> '''FUNCTIONAL MUTATION ANALYSIS'''<<BR>><<BR>>
+. '''Prediction and Experimental Characterization of nsSNPs Altering Human PDZ-Binding Motifs'''<<BR>> '''Gfeller D''', Ernst A, Jarvik N, Sidhu SS, '''Bader GD''' <<BR>>[[http://www.plosone.org/article/info:doi/10.1371/journal.pone.0094507|PLoS One 2014 Apr 10;9(4):e94507]] <<BR>> [[http://www.ncbi.nlm.nih.gov/pubmed/24722214|PubMed Abstract]] - [[attachment:gfeller_plosone2014.pdf|PDF]] <<BR>> '''FUNCTIONAL MUTATION ANALYSIS'''<<BR>><<BR>>
-Line 148:
+Line 354:
-. '''Coordinate microRNA-mediated regulation of protein complexes in prostate cancer'''<<BR>>'''Alshalalfa M''', '''Bader GD''', Bismar TA, Alhajj R<<BR>>[[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0084261|PLoS One 2013 Dec 31;8(12):e84261]] <<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/24391925|PubMed Abstract]] - [[attachment:Alshalalfa_PLOSONE.pdf|PDF]]<<BR>> '''PATHWAY AND NETWORK ANALYSIS''' <<BR>><<BR>>
+. '''Coordinate microRNA-mediated regulation of protein complexes in prostate cancer'''<<BR>>'''Alshalalfa M''', '''Bader GD''', Bismar TA, Alhajj R<<BR>>[[http://www.plosone.org/article/info:doi/10.1371/journal.pone.0084261|PLoS One 2013 Dec 31;8(12):e84261]] <<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/24391925|PubMed Abstract]] - [[attachment:Alshalalfa_PLOSONE.pdf|PDF]]<<BR>> '''PATHWAY AND NETWORK ANALYSIS''' <<BR>><<BR>>
-Line 151:
+Line 357:
-Line 154:
+Line 360:
-. '''Using biological pathway data with paxtools'''<<BR>>Demir E, Babur O, '''Rodchenkov I''', Aksoy BA, Fukuda KI, Gross B, Sümer OS, '''Bader GD''', Sander C.<<BR>>[[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003194|PLoS Comput Biol 2013;9(9):e1003194]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/24068901|PubMed Abstract]] - [[attachment:Demir_paxtools_ploone.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>>
+. '''Using biological pathway data with paxtools'''<<BR>>Demir E, Babur O, '''Rodchenkov I''', Aksoy BA, Fukuda KI, Gross B, Sümer OS, '''Bader GD''', Sander C.<<BR>>[[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003194|PLoS Comput Biol 2013;9(9):e1003194]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/24068901|PubMed Abstract]] - [[attachment:Demir_paxtools_ploone.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>>
-Line 160:
+Line 366:
-. '''GeneMANIA prediction server 2013 update'''<<BR>> '''Zuberi K''', '''Franz M''', '''Rodriguez H''', '''Montojo J''', '''Lopes CT''', '''Bader GD''', Morris Q <<BR>> [[http://nar.oxfordjournals.org/content/41/W1/W115.long|Nucleic Acids Res 2013 Jul;41(Web Server issue):W115-22]]<<BR>> [[http://www.ncbi.nlm.nih.gov/pubmed/23794635|PubMed Abstract]] - [[attachment:Zuberi_genemanis_NAR.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>>
+. <<Anchor(GeneMANIA_2013)>> '''GeneMANIA prediction server 2013 update'''<<BR>> '''Zuberi K''', '''Franz M''', '''Rodriguez H''', '''Montojo J''', '''Lopes CT''', '''Bader GD''', Morris Q <<BR>> [[http://nar.oxfordjournals.org/content/41/W1/W115.long|Nucleic Acids Res 2013 Jul;41(Web Server issue):W115-22]]<<BR>> [[http://www.ncbi.nlm.nih.gov/pubmed/23794635|PubMed Abstract]] - [[attachment:Zuberi_genemanis_NAR.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>>
-Line 164:
+Line 370:
-. '''SH3 interactome conserves general function over specific form'''<<BR>>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'''<<BR>>[[http://www.nature.com/msb/journal/v9/n1/full/msb20139.html|Mol Syst Biol 2013 Apr 2;9:652]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/23549480|Pubmed Abstract]] - [[attachment:Xin_SH3inter_MSB.pdf|PDF]]<<BR>>[[http://www.ebi.ac.uk/intact/search/do/search?searchString=pubid:23549480| Interactions in Intact Database]]<<BR>>'''PROTEIN INTERACTION PREDICTION'''<<BR>><<BR>>

 1. '''Metabolic adaptation to chronic inhibition of mitochondrial protein synthesis in acute myeloid leukemia cells'''<<BR>>Jhas B, Sriskanthadevan S, Skrtic M, Sukhai MA, '''Voisin V''', Jitkova Y, Gronda M, Hurren R, Laister RC, '''Bader GD''', Minden MD, Schimmer AD.<<BR>>[[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0058367|PLoS One 2013;8(3):e58367]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/23520503|Pubmed Abstract]] - [[attachment:Jhas_leuk_plosone.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>>

 1. '''Systematic analysis of somatic mutations in phosphorylation signaling predicts novel cancer drivers'''<<BR>>'''Reimand J, Bader GD'''<<BR>>[[http://www.nature.com/msb/journal/v9/n1/full/msb201268.html|Mol Syst Biol 2013;9:637]] <<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/23340843|PubMed Abstract]] - [[attachment:Reimand_MSB_phosphomutations.pdf|PDF]]<<BR>> [[http://genomemedicine.com/content/5/2/19/abstract|Research Highlight in Genome Medicine (2013)]] <<BR>>
 '''CANCER MUTATIONS, SIGNALING NETWORKS''' <<BR>><<BR>>
+. '''SH3 interactome conserves general function over specific form'''<<BR>>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'''<<BR>>[[http://www.nature.com/msb/journal/v9/n1/full/msb20139.html|Mol Syst Biol 2013 Apr 2;9:652]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/23549480|Pubmed Abstract]] - [[attachment:Xin_SH3inter_MSB.pdf|PDF]]<<BR>>[[http://www.ebi.ac.uk/intact/search/do/search?searchString=pubid:23549480|Interactions in Intact Database]]<<BR>>'''PROTEIN INTERACTION PREDICTION'''<<BR>><<BR>>

 1. '''Metabolic adaptation to chronic inhibition of mitochondrial protein synthesis in acute myeloid leukemia cells'''<<BR>>Jhas B, Sriskanthadevan S, Skrtic M, Sukhai MA, '''Voisin V''', Jitkova Y, Gronda M, Hurren R, Laister RC, '''Bader GD''', Minden MD, Schimmer AD.<<BR>>[[http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058367|PLoS One 2013;8(3):e58367]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/23520503|Pubmed Abstract]] - [[attachment:Jhas_leuk_plosone.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>>

 1. '''Systematic analysis of somatic mutations in phosphorylation signaling predicts novel cancer drivers'''<<BR>>'''Reimand J, Bader GD'''<<BR>>[[http://www.nature.com/msb/journal/v9/n1/full/msb201268.html|Mol Syst Biol 2013;9:637]] <<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/23340843|PubMed Abstract]] - [[attachment:Reimand_MSB_phosphomutations.pdf|PDF]]<<BR>> [[http://genomemedicine.com/content/5/2/19/abstract|Research Highlight in Genome Medicine (2013)]] <<BR>> '''CANCER MUTATIONS, SIGNALING NETWORKS''' <<BR>><<BR>>
-Line 175:
+Line 380:
-Line 179:
+Line 383:
-Line 250:
+Line 453:
-. '''GeneMANIA Cytoscape Plugin: Fast gene function predictions on the desktop'''<<BR>>'''Montojo J''', '''Zuberi K''', '''Rodriguez H''', '''Kazi F''', '''Wright G''', '''Donaldson SL''', Morris Q, '''Bader GD'''<<BR>>[[http://bioinformatics.oxfordjournals.org/cgi/reprint/btq562|Bioinformatics 2010 Nov 15;26(22):2927-8]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/20926419|PubMed Abstract]] - [[attachment:2010_GeneMANIA_Cytoscape_Plugin_Montojo_Bioinformatics_Oct.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>>
+. <<Anchor(GeneMANIA_2010)>> '''GeneMANIA Cytoscape Plugin: Fast gene function predictions on the desktop'''<<BR>>'''Montojo J''', '''Zuberi K''', '''Rodriguez H''', '''Kazi F''', '''Wright G''', '''Donaldson SL''', Morris Q, '''Bader GD'''<<BR>>[[http://bioinformatics.oxfordjournals.org/cgi/reprint/btq562|Bioinformatics 2010 Nov 15;26(22):2927-8]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/20926419|PubMed Abstract]] - [[attachment:2010_GeneMANIA_Cytoscape_Plugin_Montojo_Bioinformatics_Oct.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>>
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-. '''The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function'''<<BR>>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<<BR>>[[http://nar.oxfordjournals.org/cgi/content/abstract/38/suppl_2/W214|Nucleic Acids Res 2010 Jul 1;38 Suppl:W214-20]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/20576703|PubMed Abstract]] - [[attachment:2010_GeneMANIA_Warde-Farley_NAR_Jun.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>>
+. <<Anchor(GeneMANIA_original)>> '''The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function'''<<BR>>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<<BR>>[[http://nar.oxfordjournals.org/cgi/content/abstract/38/suppl_2/W214|Nucleic Acids Res 2010 Jul 1;38 Suppl:W214-20]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/20576703|PubMed Abstract]] - [[attachment:2010_GeneMANIA_Warde-Farley_NAR_Jun.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>>
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-. '''How to visually interpret biological data using networks'''<<BR>> '''Merico D''', '''Gfeller D''', '''Bader GD'''<<BR>>[[http://www.nature.com/nbt/journal/v27/n10/abs/nbt.1567.html|Nature Biotechnology 2009 Oct 27, 921-924]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/19816451|PubMed Abstract]] - [[attachment:2009_Merico_Primer_NatBiotech_Oct.pdf|PDF]]<<BR>> Data: http://www.baderlab.org/NetworkPrimerNBT <<BR>> '''NETWORK PRIMER'''<<BR>><<BR>>
+. <<Anchor(interpret_networks)>> '''How to visually interpret biological data using networks'''<<BR>> '''Merico D''', '''Gfeller D''', '''Bader GD'''<<BR>>[[http://www.nature.com/nbt/journal/v27/n10/abs/nbt.1567.html|Nature Biotechnology 2009 Oct 27, 921-924]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/19816451|PubMed Abstract]] - [[attachment:2009_Merico_Primer_NatBiotech_Oct.pdf|PDF]]<<BR>> Data: http://www.baderlab.org/NetworkPrimerNBT <<BR>> '''NETWORK PRIMER'''<<BR>><<BR>>
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+<<Anchor(preprints)>>
= Preprints =

== 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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+== 2020 ==
 1. '''Biological Networks and Pathways'''<<BR>> '''Bader GD.''' <<BR>>in [[https://www.wiley.com/en-us/Bioinformatics,+4th+Edition-p-9781119335580|Bioinformatics 4th Eds. Andreas D. Baxevanis, Gary D. Bader, and David Wishart. John Wiley and Sons, New Jersey]] <<BR>>'''NETWORK ANALYSIS'''<<BR>>

== 2018 ==
 1. '''Automated Computational Inference of Multi-protein Assemblies from Biochemical Co-purification Data'''<<BR>>'''Goebels F., Hu L., Bader G.,''' Emili A.<<BR>>[[https://link.springer.com/protocol/10.1007/978-1-4939-7759-8_25|Methods Mol Bio 2018;1764:391-399]] - [[https://www.ncbi.nlm.nih.gov/pubmed/29605929|PubMed Abstract]] - [[attachment:automatedcopm.pdf|PDF]]<<BR>>'''NETWORK ANALYSIS SOFTWARE'''
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+. 2019 '''Brian Law''' - Protein-Protein Interaction Network Alignment and Evolution - [[attachment:Law_Brian_201911_PhD_thesis.pdf|PDF]], University of Toronto, Department of Computer Science<<BR>><<BR>>
 1. 2018 '''Shobhit Jain''' - Computational Models For Domain-Peptide Mediated Protein-Protein Interactions - [[attachment:Jain_Shobhit_201806_PhD_thesis.pdf|PDF]], University of Toronto, Department of Computer Science<<BR>><<BR>>