Differences between revisions 89 and 111 (spanning 22 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

Project Directory

Private Research Projects

Mouse Heart Disease Model Project (Transcriptomics, Proteomics, miRNA, Pathways)
Enrichment Map: Network Visualization of Enrichment Results
Visualization of BioPAX encoded Pathways
Functional Enrichment and Pathway Analysis in human genetics
- De-novo CNV in Autism: Pathway Analysis
- Neuropsychological Disorders Meta-Analysis

Open Research Projects

Google Summer of Code 2010
- Semantic Network Summary Directory

Open Ideas And Links

Internal Exchanges

Yeast expression data (Chris)

Past Collaborations

NF-Y (TF) targets: integrative analysis of ChIP-chip and transcript array data
- Roberto Mantovani (UNIMI - DSBB, Milano, Italy)
Functional Landscape of p63 Transcription Factor Targets
- Roberto Mantovani (UNIMI - DSBB, Milano, Italy)
- Alessandro Terrinoni (Universita La Sapienza, Roma, Italy)
Functional Landscape of RET Receptor Transcriptional Program
- Marco Antoniotti (UNIMIB - DISCo, Milano, Italy)
- Maria Grazia Borrello (Istituto Tumori - Milano, Italy)
- Gariboldi Manuela (Istituto Tumori / IFOM/IEO - Milano, Italy)
Clinical Phenotype Ontology
- Gianluca Colombo (UNIMIB - DISCo, Milano, Italy)

Educational

Note: if you are interested in attending the full online version of these courses, please visit the OBI web site

R Code Directory (Public)

Microarray Data Analysis

Gene-set Enrichment Analysis

Data Formatting

Public Data Resources

Gene set collections

Online Supplementary Information

Pinto et al, Nature 2010: Enrichment Test Code

CV and Publications

Complete CV (includes Publications)

Trivia & Amenities

Is there a link holding together biology, computer science, mathematics, statistics and... coking? The answer is yes
How not to build an ontology: The Celestial Emporium of Benevolent Knowledge's Taxonomy
Si Hoc Legere Scis Nimium Eruditionis Habes
Datta. Dayadhvam. Damyata. Shantih shantih shantih.
Lorem ipsum. Opera sine nomine scripta
This is the Bader-lab, not the Baader-meinhof, if you had any doubt
It's a cruel yet marvelous world:
- Ichneumonidae
- Emerald wasp
Indestructible life forms:
- Tardigrades
Zombie Ants!

Old Version

Old version of this page

CategoryHomepage

-  ⇤ ← Revision 89 as of 2010-03-30 21:46:50 → 
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+   ← Revision 111 as of 2010-10-12 22:12:30 → ⇥
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-Deletions are marked like this.
+Additions are marked like this.
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+ * [[ProjectLinks|Connectorium]]
 * [[ToDoNotes|To-do notes]]
=== Internal Exchanges ===
 * [[Yeast_Chris|Yeast expression data (Chris)]]
-Line 27:
+Line 31:
- * '''Clinical Phenotype Ontology'''
   * Gianluca Colombo (UNIMIB - DISCo, Milano, Italy)
+ * '''NF-Y (TF) targets: integrative analysis of ChIP-chip and transcript array data'''
   * Roberto Mantovani (UNIMI - DSBB, Milano, Italy)
 * '''Functional Landscape of p63 Transcription Factor Targets'''
   * Roberto Mantovani (UNIMI - DSBB, Milano, Italy)
   * Alessandro Terrinoni (Universita La Sapienza, Roma, Italy)
-Line 33:
+Line 40:
- * '''Functional Landscape of p63 Transcription Factor Targets'''
   * Roberto Mantovani (UNIMI - DSBB, Milano, Italy)
   * Alessandro Terrinoni (Universita La Sapienza, Roma, Italy)
+ * '''Clinical Phenotype Ontology'''
   * Gianluca Colombo (UNIMIB - DISCo, Milano, Italy)

== Educational ==
 * [[attachment:MicroarrayAnalysis_Rprog_L2.ppt|Introduction to R Programming - II]]
 * [[attachment:CCBR_GeneExpressionLecture_2009_06.ppt|Overview of Microarray Data Analysis (CCBR graduate lecture)]]
 * [[attachment:MicroarrayAnalysis_Rprog_L4_v03.ppt|Microarray Analysis using R Part I: Exploratory Analysis (OBI course Summer 2010)]]
 * [[attachment:MicroarrayAnalysis_Rprog_L5_v03.ppt|Microarray Analysis using R Part II: Differential Expression (OBI course Summer 2010)]]
 * [[attachment:OBI_EnrPathwAnalysis_I_v13.ppt|Pathway Analysis (OBI course Spring 2010)]]

Note: if you are interested in attending the full online version of these courses, please visit the [[http://ontariobiomedical.com/030~Courses/010~Bioinformatics_and_Genome_Analysis/|OBI web site]]
-Line 42:
+Line 57:
-==== Data Formats ====
 * [[DanieleMerico/Code/Bioc2GMT|Generate gene set collections from Bioconductor libraries]]
 * [[DanieleMerico/Code/Read_GMT|Reads a GMT file into a R list object, or binary matrix]]
+==== Data Formatting ====
 * gene sets
   * [[DanieleMerico/Code/Bioc2GMT|Generate gene set collections from Bioconductor libraries]]
   * [[DanieleMerico/Code/Read_GMT|Reads a GMT file into a R list object, or binary matrix]]
 * expression matrix
   * [[DanieleMerico/Code/Affy2GSEA|Convert Affy IDs to Entrez-Gene and add symbols and full names]]
-Line 46:
+Line 64:
- * [[DanieleMerico/Code/Enr_FET|Test a set of experimental genes for enrichment using Fisher's Exact Test (with empirical FDR q-value included)]]
+ * [[DanieleMerico/Code/Enr_FET|Fisher's Exact Test (with empirical FDR q-value included)]]
-Line 49:
+Line 67:
+=== Network Visualization ===
 * [[DanieleMerico/Code/NetworkGexpr_01|Format gene expression data and ppi interaction data for visualization in Cytoscape (OBI Course)]]
-Line 50:
+Line 70:
-== Educational Material ==
 * [[attachment:CCBR_GeneExpressionLecture_2009_06.ppt|CCBR course on Microarray Data Analysis]]
 * [[attachment:OBI_EnrPathwAnalysis_I_v13.ppt|OBI course on Pathway Analysis]]
+== Public Data Resources ==
 * [[GeneSetDB_02|Gene set collections]]

== Online Supplementary Information ==
 * Pinto et al, Nature 2010: [[Suppl/CNV_Pinto2010|Enrichment Test Code]]
-Line 58:
+Line 81:
- * is there a link holding together biology, computer science, mathematics, statistics and... coking? The answer is [[EdibleEnrichmentMaps|yes]]
+ * Is there a link holding together biology, computer science, mathematics, statistics and... coking? The answer is [[EdibleEnrichmentMaps|yes]]
-Line 62:
+Line 85:
+ * Lorem ipsum. Opera sine nomine scripta
 * This is the Bader-lab, not the Baader-meinhof, if you had any doubt
 * It's a cruel yet marvelous world: 
   * [[http://en.wikipedia.org/wiki/Ichneumonidae|Ichneumonidae]]
   * [[http://en.wikipedia.org/wiki/Emerald_cockroach_wasp|Emerald wasp]]
 * Indestructible life forms:
   * [[http://en.wikipedia.org/wiki/Tardigrades|Tardigrades]]
 * [[http://en.wikipedia.org/wiki/Cordyceps_unilateralis|Zombie Ants!]]