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| == Research Projects == === Present Reasearch Projects === __Projects @CCBR__: <<BR>> * '''Mouse Heart Pathway Project''' ([[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>> 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...) <<BR>> Supervised by: [[GaryBader|Gary Bader]]. * [[DanieleMerico/Enrichment_Time| Enrichment Method for Time-Series]] |
== 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]] * [[ToDoNotes|To-do 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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| __Ongoing Collaborative Projects__: <<BR>> * [[DanieleMerico/OntoBioMed| Biomedical Ontologies]], bridging clinics and molecular biosciences === Past Research Projects === __Projects @UNIMIB__: * Analysis of Time-course Microarray Data<<BR>> 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) |
== Educational == * 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)]] |
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| * Clinical Phenotype Ontology for Cerebrovascular Disorders (NEUROWEB Project) With Gianluca Colombo, Giuseppe "Beppe" Frisoni, Flavio De Paoli, Marco Antoniotti. Supervised by: Giancarlo Mauri.<<BR>> Ref & Links: * [[http://www.nettab.org/2007/slides/SemanticWeb_Frisoni.pdf|NETTAB 2007 presentation]]; * [[http://nuke.neurowebkc.eu/Dissemination/tabid/66/Default.aspx/|published papers & proceedings]]. __Projects @UNIMI__: * The p63 Network 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]] |
== 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)]] |
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| * The Landscape of NF-Y Binding<<BR>> With: Michele Ceribelli, Diletta Dolfini. Supervised by: Roberto Mantovani.<<BR>> Ref & Links: * [[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.]] |
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| * [[DanieleMerico/Mantor| Link to the Mantor Works Directory]] | == Public Data Resources == * [[GeneSetDB_02|Gene set collections]] |
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| === Activity Reports === [[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. |
== Online Supplementary Information == * Pinto et al, Nature 2010: [[Suppl/CNV_Pinto2010|Enrichment Test Code]] |
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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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| __Computational techniques & resources__: * PCA (Principal Correspondence Analysis) & CA (Correspondence Analysis) * Correlation Measures (Pearson, Spearman) * [[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) * 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 |
== 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]] * Indestructible life forms: * [[http://en.wikipedia.org/wiki/Tardigrades|Tardigrades]] * [[http://en.wikipedia.org/wiki/Cordyceps_unilateralis|Zombie Ants!]] |
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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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| Go to my [[DanieleMerico/HowtoDirectory| How To Directory]] for tips with R programming. [[DanieleMerico/CytoMemo| 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.<<BR>> 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: [[attachment:DanieleMericoCV.PDF|CV.PDF]]. === Affiliations === * CCBR - Banting & Best Dept. of Medical Research Visiting PhD student * 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) === Trivia & Amenities === The [[http://en.wikipedia.org/wiki/Celestial_Emporium_of_Benevolent_Recognition|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 [[http://en.wikipedia.org/wiki/Tengwar/|runes]] (still have to learn ideograms...) * drink beer * throw snowballs (look out...) * laugh :D |
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
Open Research Projects
- Google Summer of Code 2010
Open Ideas And 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
- 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)
R Code Directory (Public)
Microarray Data Analysis
Gene-set Enrichment Analysis
Data Formatting
- gene sets
- expression matrix
Tests
ID Conversion
Network Visualization
Public Data Resources
Online Supplementary Information
Pinto et al, Nature 2010: Enrichment Test Code
CV and 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:
- Indestructible life forms: