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| == Project Directory (Private) == | == Project Directory == === Private Research Projects === |
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| * 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]] |
* [[DanieleMerico/PathGenetics|Functional Enrichment and Pathway Analysis in human genetics]] * Pathway analysis for cancer data (Guidos-Danska) * [[CancerStemCellProject|Data directory]] === Open Research Projects === * Google Summer of Code 2010 * [[GSoC2010_Directory|Semantic Network Summary Directory]] === Ideas Notes Links === * [[IdeaEnr|Ideas for Enrichment Analysis]] * [[IdeaWall|Wall of Ideas (multi-project)]] * [[PapersToRead|Papers to read]] * [[ProjectLinks|Connectorium]] * [[ToDoNotes|To-do notes]] * [[MiscNotes|Misc Notes]] === Internal Exchanges === * [[Yeast_Chris|Yeast expression data (Chris)]] |
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| * '''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) |
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| * '''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) |
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| == Educational == === Microarray Analysis === * OBI (Ontario Biomedical Institute): R Programming, Microarray Analysis, Pathway and Network Analysis * [[attachment:MicroarrayAnalysis_Rprog_L1_U.ppt|Introduction to R Programming - I]] * [[attachment:MicroarrayAnalysis_Rprog_L2.ppt|Introduction to R Programming - II]] * [[attachment:MicroarrayAnalysis_Rprog_L3_U.ppt|Introduction to R Programming - III]] * [[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]] * [[attachment:CCBR_GeneExpressionLecture_2009_06.ppt|Overview of Microarray Data Analysis (CCBR graduate lecture)]] === Pathway Analysis Readings === * [[PathwayAnalysisReadings|Pathway Analysis: Introduction and References]] === Statistics === * CBW Statistics 2011 Ottawa * [[attachment:CBW_2011_Mod1_IntroductionR_DM_v06.ppt|Introduction to R]] * [[attachment:CBW_2011_Mod2_ExplAnalysis_DM_v07.ppt|Exploratory Data Analysis]] * [[attachment:CBW_2011_Mod3_HypTest_DM_v12.ppt|Inferential Statistics]] * pdf print outs: [[attachment:CBW_2011_Mod1_IntroductionR_DM_v06_print.pdf|M1]] [[attachment:CBW_2011_Mod2_ExplAnalysis_DM_v07_print.pdf|M2]] [[attachment:CBW_2011_Mod3_HypTest_DM_v12_print.pdf|M3]] |
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| * [[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]] ==== Tests ==== * [[DanieleMerico/Code/Enr_FET|Fisher's Exact Test (with empirical FDR q-value included)]] |
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| === Network Visualization === * [[DanieleMerico/Code/NetworkGexpr_01|Format gene expression data and ppi interaction data for visualization in Cytoscape (OBI Course)]] === R Computational Efficiency === * [[/Code/Efficiency_Vectorization|Simulation to time vectorization advantages]] |
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| == 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]] |
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| * Is there a link holding together biology, computer science, mathematics, statistics and... cooking? The answer is [[EdibleEnrichmentMaps|yes]] * [[http://en.wikipedia.org/wiki/File:Caffeinated_spiderwebs.jpg|Another cup of caffeine..?]] |
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| * Something I always remind myself in pathway analysis (on bad days): Videmus nunc per speculum et in aenigmate * Entia non sunt multiplicanda praeter necessitatem (Occam's Razor). It can be roughly translated into: curb your enthusiasm. * Natural marvels * Marvels of cruelty: * [[http://en.wikipedia.org/wiki/Ichneumonidae|Ichneumonidae]] * [[http://en.wikipedia.org/wiki/Emerald_cockroach_wasp|Emerald wasp]] * (Almost) indestructible life forms: * [[http://en.wikipedia.org/wiki/Tardigrades|Tardigrades]] * Pseudo-Zombies! <<BR>> these parasites modify the host behavior to infect other hosts * [[http://en.wikipedia.org/wiki/Cordyceps_unilateralis|Zombie Ants]] * [[http://en.wikipedia.org/wiki/Leucochloridium_paradoxum| Snail Parasite]] * [[http://en.wikipedia.org/wiki/Devil_facial_tumor_disease| Infective tumors in Tazmanian Devils]] * Si Hoc Legere Scis Nimium Eruditionis Habes :p |
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)
Functional Enrichment and Pathway Analysis in human genetics
- Pathway analysis for cancer data (Guidos-Danska)
Open Research Projects
- Google Summer of Code 2010
Ideas Notes Links
Internal Exchanges
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
Microarray Analysis
- OBI (Ontario Biomedical Institute): R Programming, Microarray Analysis, Pathway and Network Analysis
Microarray Analysis using R Part I: Exploratory Analysis (OBI course Summer 2010)
Microarray Analysis using R Part II: Differential Expression (OBI course Summer 2010)
Note: if you are interested in attending the full online version of these courses, please visit the OBI web site
Overview of Microarray Data Analysis (CCBR graduate lecture)
Pathway Analysis Readings
Statistics
- CBW Statistics 2011 Ottawa
R Code Directory (Public)
Microarray Data Analysis
Gene-set Enrichment Analysis
Data Formatting
- gene sets
- expression matrix
Tests
ID Conversion
Network Visualization
R Computational Efficiency
Public Data Resources
CV and Publications
Trivia & Amenities
Is there a link holding together biology, computer science, mathematics, statistics and... cooking? The answer is yes
How not to build an ontology: The Celestial Emporium of Benevolent Knowledge's Taxonomy
- Something I always remind myself in pathway analysis (on bad days): Videmus nunc per speculum et in aenigmate
- Entia non sunt multiplicanda praeter necessitatem (Occam's Razor). It can be roughly translated into: curb your enthusiasm.
- Natural marvels
- Marvels of cruelty:
- (Almost) indestructible life forms:
Pseudo-Zombies!
these parasites modify the host behavior to infect other hosts
- Si Hoc Legere Scis Nimium Eruditionis Habes :p
