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| == Daniele Merico == | #acl All:read DanieleMerico:write,delete,revert = Daniele Merico = |
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| Physical location: Emili Lab Area (6th Floor CCBR)[[BR]] Email: [[MailTo(daniele DOT merico AT gmail DOT com)]][[BR]] Skype: the-amerigo 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>> |
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| === Research Projects === Current Projects @CCBR: * Active Cell Maps (pathway & network: topology, expression profiling, activity patterns, etc...) Supervised by: [:GaryBader:Gary Bader]. * MouseHeartPathwayProject With: [:RuthIsserlin:Ruth Isserlin]. Supervised by: [http://lambda.med.utoronto.ca/Emili.htm/ Andrew Emili] and [:GaryBader:Gary Bader]. |
== 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]] * [[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)]] == 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) |
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| Almost-completed or on-going Projects @UNIMIB: * Knowledge Engineering of Human Phenotypes With Gianluca Colombo. Supervised by: Giancarlo Mauri. * Analysis of Time-course Microarray Data With Italo Zoppis. Supervised by: Marco Antoniotti. |
== Public Data Resources == === Functional Gene-sets === * [[GeneSetDB_02|Gene set collections]] === Neurological Gene-sets === * [[NeuroGenes_01|Neurobiologically-relevant gene-sets (2011)]] |
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| Completed Projects @UNIMI / UNIMIB: * Clinical Phenotype Ontology for Cerebrovascular Disorders (NEUROWEB Project) With Gianluca Colombo, Flavio De Paoli, Marco Antoniotti. Supervised by: Giancarlo Mauri. Links: [http://www.nettab.org/2007/slides/SemanticWeb_Frisoni.pdf/ NETTAB 2007 presentation]; [http://nuke.neurowebkc.eu/Dissemination/tabid/66/Default.aspx/ published papers]. * The Landscape of NF-Y Binding With: Michele Ceribelli, Diletta Dolfini. Supervised by: Roberto Mantovani. |
== 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]] == 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)]] === R Computational Efficiency === * [[/Code/Efficiency_Vectorization|Simulation to time vectorization advantages]] |
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| === Knowledge Sharing === Here's the knowledge & expertise I wish to share with anybody who wants to. |
== CV and Publications == * [[attachment:cvDanieleMericoEng29General.pdf|Complete CV (includes Publications)]] |
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| Expertise on computational techniques & resources: * PCA (Principal Correspondence Analysis) & CA (Correspondence Analysis) * Correlation Measures (Pearson, Spearman) * Standard Affymetrix Microarray Analysis (CEL files handling, Normalization, Signal computation (e.g. rma), Exploratory Analysis, Differentially Expressed Genes) * Clustering (hirerarchical, K-means, CLICK, etc...) * Statistical tests (t-test, Fisher's) * Gene Ontology |
== Trivia & Amenities == * 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..?]] * How not to build an ontology: The [[http://en.wikipedia.org/wiki/Celestial_Emporium_of_Benevolent_Recognition|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: * [[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 |
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| I usually program with: * [http://cran.r-project.org/ R] (see also [http://www.bioconductor.org/ Bioconductor]) |
== Old Version == [[/Old|Old version of this page]] |
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| 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 |
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)
Public Data Resources
Functional Gene-sets
Neurological Gene-sets
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
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
