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| == Daniele Merico == | = Daniele Merico = |
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| __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]] |
__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 === __Main Projects @CCBR__: * '''Active Cell Map''' (pathway & network: topology, expression profiling, activity patterns, etc...) Supervised by: [:GaryBader:Gary Bader]. * '''MouseHeartPathwayProject'''[[BR]] and specifically [:MouseHeartPathwayProject/NetworkProfilingTrack: Network Profiling Track][[BR]] 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]] * 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) |
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| __Almost-completed or on-going Projects @UNIMI/UNIMIB__: * Analysis of Time-course Microarray Data With Italo Zoppis. Supervised by: Marco Antoniotti. * enahncements of the GOALIE approach to time-course data analysis * critically revisiting the GOALIE approach: [[BR]] [:DanieleMerico/GOALIErevisited: a survey of transcriptional regulation of GO terms during yest cell cycle] * the PIFS data-set analysis (with the CDC of Atlanta & University of South Wales) * The p63 Network With Alessandra Viganò. Supervised by: Roberto Mantovani. 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)]] == 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)]] |
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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. 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]. * The Landscape of NF-Y Binding With: Michele Ceribelli, Diletta Dolfini. Supervised by: Roberto Mantovani. Ref & Links: (2 accepted papers) |
== 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. * It's a cruel yet marvelous world: * [[http://en.wikipedia.org/wiki/Ichneumonidae|Ichneumonidae]] * [[http://en.wikipedia.org/wiki/Emerald_cockroach_wasp|Emerald wasp]] * This is the Bader-lab, not the Baader-meinhof, if you had any doubt |
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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. |
== Old Version == [[/Old|Old version of this page]] |
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| === Knowledge Sharing === Here's the knowledge & expertise I wish to share with anybody who wants to. __Computational techniques & resources__: * PCA (Principal Correspondence Analysis) & CA (Correspondence Analysis) * Correlation Measures (Pearson, Spearman) * Distance Measures (quantitative: Euclidean, correlation-based; binary: Hamming, 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 (hirerarchical, K-means, CLICK, etc...) * Statistical tests (t-test, Fisher's) * Gene Ontology I usually program with: * [http://cran.r-project.org/ R] (see also [http://www.bioconductor.org/ Bioconductor]) Go to my [:DanieleMerico/HowtoDirectory: How To Directory] for tips with R programming. __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 === 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
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
Gene-set Enrichment Analysis
Data Formatting
- gene sets
- expression matrix
Tests
ID Conversion
Network Visualization
Educational Material
Public Data-sets
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.
- It's a cruel yet marvelous world:
- This is the Bader-lab, not the Baader-meinhof, if you had any doubt