Differences between revisions 42 and 54 (spanning 12 versions)

Daniele Merico

Contact

Location: Common Lab Area, 6th Floor (CCBR)
Email: <daniele DOT merico AT gmail DOT com>
Skype: the-amerigo
Linked-In: Daniele Merico

--- New Version: Under Construction ---

Project Directory

Code Directory

Microarray Data Analysis

Hierarchical Clustering using Pearson Correlaton

--- Old Version ---

Research Projects

Present Reasearch Projects

Projects @CCBR:

Mouse Heart Pathway Project (Main Directory of my work)
With: Ruth Isserlin. Supervised by: Andrew Emili and Gary Bader.
I am specifically working on the gene expression analysis using:
- Set-enrichment
- Identification of active miRNAs
- Pathway profiling
- Network profiling
Active Cell Map (pathway & network: topology, expression profiling, activity patterns, etc...)
Supervised by: Gary Bader.
- Enrichment Method for Time-Series

Ongoing Collaborative Projects:

Biomedical Ontologies, bridging clinics and molecular biosciences

Past Research Projects

Projects @UNIMIB:

Analysis of Time-course Microarray Data
With Italo Zoppis. Supervised by: Marco Antoniotti.
- enahncements of the GOALIE approach to time-course data analysis
- the PIFS data-set analysis (with the CDC of Atlanta & University of South Wales)
Clinical Phenotype Ontology for Cerebrovascular Disorders (NEUROWEB Project)
With Gianluca Colombo, Giuseppe "Beppe" Frisoni, Flavio De Paoli, Marco Antoniotti. Supervised by: Giancarlo Mauri.
Ref & Links:
- NETTAB 2007 presentation;
- published papers & proceedings.

Projects @UNIMI:

The p63 Network
With Alessandra Viganò. Supervised by: Roberto Mantovani (code-name Mantor).
Ref & Links: p63 EMBO Paper
The Landscape of NF-Y Binding
With: Michele Ceribelli, Diletta Dolfini. Supervised by: Roberto Mantovani.
Ref & Links:
- The histone like NF-Y is a bifunctional transcription factor.
- A balance between NF-Y and p53 governs the pro- and anti-apoptotic transcriptional response.
Link to the Mantor Works Directory

Activity Reports

Work logs, concerning on-going reserach activity, will be visible only to lab members.
Memoranda, concerning paper and seminar summaries, or more general considerations, will be kept more open.

Knowledge Sharing

Here's the knowledge & expertise I wish to share with anybody who wants to.

Computational techniques & resources:

PCA (Principal Correspondence Analysis) & CA (Correspondence Analysis)
Correlation Measures (Pearson, Spearman)
- Pearson Correlation and the Dot Product
Distance Measures (continuous data: Euclidean, correlation-based; binary data: Hamming, Jaccard-based; sets: Jaccard-based)
- a few tips on distances (especially for binary strings)
Standard Affymetrix Microarray Analysis
- (CEL files handling, Normalization, Signal computation (e.g. rma), Exploratory Analysis, Differentially Expressed Genes)
Clustering (hierarchical, K-means, CLICK, etc...)
Statistical tests (t-test, Fisher's, Kolmogorov-Smirnov)
Gene Ontology

I usually program with:

R (see also Bioconductor)

Go to my How To Directory for tips with R programming.

Cytoscape Memos

Biological Systems and Pathologies I've been working on (in order of confidence):

Mammalian Immune System (focus on Dendritic Cells)
Ischemic Stroke & Atherosclerosis
Mammalian Chromatin Modification
Yeast Cell Cycle

Resume & CV

I was born in Saronno (VA, Italy) in 29/07/1981. I lived, studied and worked in the Milan metropolitan area till November 2007. I got my BSc in Molecular Biotechnologies (July 2003) and my MSc Bioinformatics (July 2005) at Università di Milano-Bicocca. I started my PhD in Molecular and Cellular Biology at Università di Milano in 2005.
My scientific interests are:

Pathways and Networks
Human Phenotypes
Expression Data and Transcriptional Regulation
Biomedical Knowledge Engineering & Representation
Philosophy and Sociology of Science

For more details, please have a look at my CV: CV.PDF.

Affiliations

CCBR - Banting & Best Dept. of Medical Research
- Visiting PhD student
Università di Milano (UNIMI) - Dipartimento di Scienze Biomolecolari e Biotecnologie (DSBB)
- PhD student (Program of Cellular and Molecular Biology)
  Roberto Mantovani's Lab
Università di Milano-Bicocca (UNIMIB) - Dipartimento di Informatica (DISCo)
- External PhD student
  BiMIB Group (Bioinformatics at Milano-Bicocca)

Trivia & Amenities

The Celestial Emporium of Benevolent Knowledge's Taxonomy: how not to build an ontology

I like to...

travel, and discover new cultures
meet people
discuss ideas
take more than 45' to have lunch or dinner
swim, walk, trek
write runes (still have to learn ideograms...)
drink beer
throw snowballs (look out...)
laugh

CategoryHomepage

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-Deletions are marked like this.
+Additions are marked like this.
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-__Location__: Common Lab Area, 6th Floor (CCBR)[[BR]]
__Email__: [[MailTo(daniele DOT merico AT gmail DOT com)]][[BR]]
__Skype__: the-amerigo[[BR]]
__Linked-In__: [http://www.linkedin.com/profile?viewProfile=&key=4048991&goback=%2Econ-*3conbro*40*4*051*4false*4*02*40%2Ebcc_2220874_1/ Daniele Merico][[BR]]
+__Location__: Common Lab Area, 6th Floor (CCBR)<<BR>>
__Email__: <<MailTo(daniele DOT merico AT gmail DOT com)>><<BR>>
__Skype__: the-amerigo<<BR>>
__Linked-In__: [[http://www.linkedin.com/profile?viewProfile=&key=4048991&goback=%2Econ-*3conbro*40*4*051*4false*4*02*40%2Ebcc_2220874_1/|Daniele Merico]]<<BR>>

== --- New Version: Under Construction --- ==

== Project Directory ==
 * [[Mouse Heart Project|DanieleMerico/MouseHeart]]
 * [[Bio PAX Visualization|DanieleMerico/PathwayViz]]

== Code Directory ==
=== Microarray Data Analysis ===
 * [[DanieleMerico/Code/Hierarchical_Pearson|Hierarchical Clustering using Pearson Correlaton]]

== --- Old Version --- ==
-Line 14:
+Line 26:
-__Projects @CCBR__: [[BR]]
+__Projects @CCBR__: <<BR>>
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+Line 28:
- ([:MouseHeartPathwayProject/NetworkProfilingTrack: Main Directory of my work])[[BR]]
 With: [:RuthIsserlin:Ruth Isserlin]. 
 Supervised by: [http://lambda.med.utoronto.ca/Emili.htm/ Andrew Emili] and [:GaryBader:Gary Bader]. [[BR]]
+ ([[MouseHeartPathwayProject/NetworkProfilingTrack|Main Directory of my work]])<<BR>>
 With: [[RuthIsserlin|Ruth Isserlin]]. 
 Supervised by: [[http://lambda.med.utoronto.ca/Emili.htm/|Andrew Emili]] and [[GaryBader|Gary Bader]]. <<BR>>
-Line 20:
+Line 32:
-   * Improved set-enrichment methods
+   * Set-enrichment
   * Identification of active miRNAs
-Line 23:
+Line 36:
-   * Identification of miRNA candidates, [[BR]]
   integrating predictions and miRNA expression patterns with taregt expression patterns
 * '''Active Cell Map''' (pathway & network: topology, expression profiling, activity patterns, etc...)
 Supervised by: [:GaryBader:Gary Bader].
+ * '''Active Cell Map''' (pathway & network: topology, expression profiling, activity patterns, etc...) <<BR>>
 Supervised by: [[GaryBader|Gary Bader]].
   * [[DanieleMerico/Enrichment_Time| Enrichment Method for Time-Series]]
-Line 28:
+Line 40:
-__Ongoing Collaborations__: [[BR]]
 * [:DanieleMerico/OntoBioMed: Biomedical Ontologies], bridging clinics and molecular biosciences
+__Ongoing Collaborative Projects__: <<BR>>
 * [[DanieleMerico/OntoBioMed| Biomedical Ontologies]], bridging clinics and molecular biosciences
-Line 33:
+Line 45:
- * Analysis of Time-course Microarray Data[[BR]]
+ * Analysis of Time-course Microarray Data<<BR>>
-Line 39:
+Line 51:
- With Gianluca Colombo, Flavio De Paoli, Marco Antoniotti. Supervised by: Giancarlo Mauri.[[BR]]
+ With Gianluca Colombo, Giuseppe "Beppe" Frisoni, Flavio De Paoli, Marco Antoniotti. Supervised by: Giancarlo Mauri.<<BR>>
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+Line 53:
-   * [http://www.nettab.org/2007/slides/SemanticWeb_Frisoni.pdf NETTAB 2007 presentation]; 
   * [http://nuke.neurowebkc.eu/Dissemination/tabid/66/Default.aspx/ published papers & proceedings].
+   * [[http://www.nettab.org/2007/slides/SemanticWeb_Frisoni.pdf|NETTAB 2007 presentation]]; 
   * [[http://nuke.neurowebkc.eu/Dissemination/tabid/66/Default.aspx/|published papers & proceedings]].
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+Line 58:
- With Alessandra Viganò. Supervised by: Roberto Mantovani.[[BR]]
 Ref & Links: [http://www.nature.com/emboj/journal/v25/n21/pdf/7601375a.pdf p63 EMBO Paper]
+ With Alessandra Viganò. Supervised by: Roberto Mantovani (code-name ''Mantor'').<<BR>>
 Ref & Links: [[http://www.nature.com/emboj/journal/v25/n21/pdf/7601375a.pdf|p63 EMBO Paper]]
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+Line 61:
- * The Landscape of NF-Y Binding[[BR]]
 With: Michele Ceribelli, Diletta Dolfini. Supervised by: Roberto Mantovani.[[BR]]
+ * The Landscape of NF-Y Binding<<BR>>
 With: Michele Ceribelli, Diletta Dolfini. Supervised by: Roberto Mantovani.<<BR>>
-Line 52:
+Line 64:
-   * [http://mcb.asm.org/cgi/reprint/MCB.01861-07v1?view=long&pmid=18212061 The histone like NF-Y is a bifunctional transcription factor.]
   * [http://nar.oxfordjournals.org/cgi/content/full/gkm1046v2 A balance between NF-Y and p53 governs the pro- and anti-apoptotic transcriptional response.]
+   * [[http://mcb.asm.org/cgi/reprint/MCB.01861-07v1?view=long&pmid=18212061|The histone like NF-Y is a bifunctional transcription factor.]]
   * [[http://nar.oxfordjournals.org/cgi/content/full/gkm1046v2|A balance between NF-Y and p53 governs the pro- and anti-apoptotic transcriptional response.]]

 * [[DanieleMerico/Mantor| Link to the Mantor Works Directory]]
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+Line 70:
-[:DanieleMerico/WorkLogDirectory: Work logs], concerning on-going reserach activity, will be visible only to lab members.[[BR]]
[:DanieleMerico/MemorandaDirectory: Memoranda], concerning paper and seminar summaries, or more general considerations, will be kept more open.
+[[DanieleMerico/WorkLogDirectory| Work logs]], concerning on-going reserach activity, will be visible only to lab members.<<BR>>
[[DanieleMerico/MemorandaDirectory| Memoranda]], concerning paper and seminar summaries, or more general considerations, will be kept more open.
-Line 65:
+Line 79:
-   * [:DanieleMerico/HowtoDirectory/PearsonDotP: Pearson Correlation and the Dot Product]
 * Distance Measures (continuous data: Euclidean, correlation-based; binary data: Hamming, Jaccard-based; sets: Jaccard-based)[[BR]]
   * [:DanieleMerico/HowtoDirectory/Distances: a few tips on distances] (especially for binary strings)
+   * [[DanieleMerico/HowtoDirectory/PearsonDotP| Pearson Correlation and the Dot Product]]
 * Distance Measures (continuous data: Euclidean, correlation-based; binary data: Hamming, Jaccard-based; sets: Jaccard-based)<<BR>>
   * [[DanieleMerico/HowtoDirectory/Distances| a few tips on distances]] (especially for binary strings)
-Line 75:
+Line 89:
- * [http://cran.r-project.org/ R] (see also [http://www.bioconductor.org/ Bioconductor])
+ * [[http://cran.r-project.org/|R]] (see also [[http://www.bioconductor.org/|Bioconductor]])
-Line 77:
+Line 91:
-Go to my [:DanieleMerico/HowtoDirectory: How To Directory] for tips with R programming.
+Go to my [[DanieleMerico/HowtoDirectory| How To Directory]] for tips with R programming.
-Line 79:
+Line 93:
-[:DanieleMerico/CytoMemo: Cytoscape Memos]
+[[DanieleMerico/CytoMemo| Cytoscape Memos]]
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+Line 104:
-I got my BSc in Molecular Biotechnologies (July 2003) and my MSc Bioinformatics (July 2005) at Università di Milano-Bicocca. I started my PhD in Molecular and Cellular Biology at Università di Milano in 2005.[[BR]]
+I got my BSc in Molecular Biotechnologies (July 2003) and my MSc Bioinformatics (July 2005) at Università di Milano-Bicocca. I started my PhD in Molecular and Cellular Biology at Università di Milano in 2005.<<BR>>
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+Line 112:
-For more details, please have a look at my CV: [attachment:DanieleMericoCV.PDF CV.PDF].
+For more details, please have a look at my CV: [[attachment:DanieleMericoCV.PDF|CV.PDF]].
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+Line 117:
- * Università di Milano ([http://www.unimi.it UNIMI]) - Dipartimento di Scienze Biomolecolari e Biotecnologie ([http://www.sbb.unimi.it/ DSBB])
   PhD student (Program of Cellular and Molecular Biology)[[BR]]
   [http://www.bsb.unimi.it/gene_expression.htm Roberto Mantovani's Lab]
 * Università di Milano-Bicocca ([http://www.unimib.it UNIMIB]) - Dipartimento di Informatica ([http://www.disco.unimib.it/ DISCo])
   External PhD student[[BR]]
   [http://bimib.disco.unimib.it/ BiMIB Group] (Bioinformatics at Milano-Bicocca)
+ * Università di Milano ([[http://www.unimi.it|UNIMI]]) - Dipartimento di Scienze Biomolecolari e Biotecnologie ([[http://www.sbb.unimi.it/|DSBB]])
   PhD student (Program of Cellular and Molecular Biology)<<BR>>
   [[http://www.bsb.unimi.it/gene_expression.htm|Roberto Mantovani's Lab]]
 * Università di Milano-Bicocca ([[http://www.unimib.it|UNIMIB]]) - Dipartimento di Informatica ([[http://www.disco.unimib.it/|DISCo]])
   External PhD student<<BR>>
   [[http://bimib.disco.unimib.it/|BiMIB Group]] (Bioinformatics at Milano-Bicocca)
-Line 111:
+Line 125:
-The [http://en.wikipedia.org/wiki/Celestial_Emporium_of_Benevolent_Recognition Celestial Emporium of Benevolent Knowledge's Taxonomy]:
+The [[http://en.wikipedia.org/wiki/Celestial_Emporium_of_Benevolent_Recognition|Celestial Emporium of Benevolent Knowledge's Taxonomy]]:
-Line 120:
+Line 134:
- * write [http://en.wikipedia.org/wiki/Tengwar/ runes] (still have to learn ideograms...)
+ * write [[http://en.wikipedia.org/wiki/Tengwar/|runes]] (still have to learn ideograms...)