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= Daniele Merico =
=== Contact ===
__Location__: Common Lab Area, 6th Floor (CCBR)<
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__Email__: <><
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__Skype__: the-amerigo<
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__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]]<
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== Project Directory ==
=== Private Research Projects ===
* [[DanieleMerico/MouseHeart|Mouse Heart Disease Model Project]] (Transcriptomics, Proteomics, miRNA, Pathways)
* [[EnrichmentMap|Enrichment Map: Network Visualization of Enrichment Results]]
* [[DanieleMerico/PathwayViz|Visualization of BioPAX encoded Pathways]]
* Functional Enrichment and Pathway Analysis in human genetics
* [[DanieleMerico/Autism_CNV|De-novo CNV in Autism: Pathway Analysis]]
* [[DanieleMerico/Asylum_CNV|Neuropsychological Disorders Meta-Analysis]]
=== Open Research Projects ===
* Google Summer of Code 2010
* [[GSoC2010_Directory|Semantic Network Summary Directory]]
=== Open Ideas And Links ===
* [[IdeaWall|Wall of Ideas (multi-project)]]
* [[PapersToRead|Papers to read]]
* [[ProjectLinks|Connectorium]]
=== Internal Exchanges ===
* [[Yeast_Chris|Yeast expression data (Chris)]]
== Past Collaborations ==
* '''Clinical Phenotype Ontology'''
* Gianluca Colombo (UNIMIB - DISCo, Milano, 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)
* '''Functional Landscape of p63 Transcription Factor Targets'''
* Roberto Mantovani (UNIMI - DSBB, Milano, Italy)
* Alessandro Terrinoni (Universita La Sapienza, Roma, Italy)
== R Code Directory (Public) ==
=== Microarray Data Analysis ===
* [[DanieleMerico/HowtoDirectory/ExprSet|Affymetrix Microarray Data Processing]]
* [[DanieleMerico/Code/Hierarchical_Pearson|Hierarchical Clustering using Pearson Correlaton]]
=== Gene-set Enrichment Analysis ===
==== 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]]
==== Tests ====
* [[DanieleMerico/Code/Enr_FET|Fisher's Exact Test (with empirical FDR q-value included)]]
=== ID Conversion ===
* [[DanieleMerico/Code/Conv_Eg_Symbols|Entrez-Gene ID and Symbols]]
=== Network Visualization ===
* [[DanieleMerico/Code/NetworkGexpr_01|Format gene expression data and ppi interaction data for visualization in Cytoscape (OBI Course)]]
== 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-sets ==
* [[GeneSetDB_01|Gene set collections]]
== CV and Publications ==
* [[attachment:cvDanieleMericoEng29General.pdf|Complete CV (includes Publications)]]
== Trivia & Amenities ==
* is there a link holding together biology, computer science, mathematics, statistics and... coking? The answer is [[EdibleEnrichmentMaps|yes]]
* How not to build an ontology: The [[http://en.wikipedia.org/wiki/Celestial_Emporium_of_Benevolent_Recognition|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:
* [[http://en.wikipedia.org/wiki/Ichneumonidae|Ichneumonidae]]
* [[http://en.wikipedia.org/wiki/Emerald_cockroach_wasp|Emerald wasp]]
== Old Version ==
[[/Old|Old version of this page]]
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