##master-page:HomepageTemplate #format wiki #acl All:read DanieleMerico:write,delete,revert = Daniele Merico = === Contact === __Location__: Common Lab Area, 6th Floor (CCBR)<
> __Email__: <><
> __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]]<
> == Project Directory (Private) == * [[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]] * [[DanieleMerico/CCBR_Collab|Other CCBR Collaborations]] == Collaborations == * '''Pathway Analysis of CNV (Copy Number Variations) in Autism''' * Scherer Lab (Sick Kids) * '''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 === * [[DanieleMerico/Code/Bioc2GMT|Generate gene set collections from Bioconductor libraries]] * [[DanieleMerico/Code/Read_GMT|Reads a GMT file into a list or binary matrix]] === ID Conversion === * [[DanieleMerico/Code/Conv_Eg_Symbols|Entrez-Gene ID and Symbols]] == Publications == * Empty Slot == --- Old Version --- == == Research Projects == === Present Reasearch Projects === __Projects @CCBR__: <
> * '''Mouse Heart Pathway Project''' ([[MouseHeartPathwayProject/NetworkProfilingTrack|Main Directory of my work]])<
> With: [[RuthIsserlin|Ruth Isserlin]]. Supervised by: [[http://lambda.med.utoronto.ca/Emili.htm/|Andrew Emili]] and [[GaryBader|Gary Bader]]. <
> 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...) <
> Supervised by: [[GaryBader|Gary Bader]]. * [[DanieleMerico/Enrichment_Time| Enrichment Method for Time-Series]] __Ongoing Collaborative Projects__: <
> * [[DanieleMerico/OntoBioMed| Biomedical Ontologies]], bridging clinics and molecular biosciences === Past Research Projects === __Projects @UNIMIB__: * Analysis of Time-course Microarray Data<
> 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) * Clinical Phenotype Ontology for Cerebrovascular Disorders (NEUROWEB Project) With Gianluca Colombo, Giuseppe "Beppe" Frisoni, 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]]. __Projects @UNIMI__: * The p63 Network With Alessandra Viganò. Supervised by: Roberto Mantovani (code-name ''Mantor'').<
> Ref & Links: [[http://www.nature.com/emboj/journal/v25/n21/pdf/7601375a.pdf|p63 EMBO Paper]] * The Landscape of NF-Y Binding<
> With: Michele Ceribelli, Diletta Dolfini. Supervised by: Roberto Mantovani.<
> 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.]] * [[DanieleMerico/Mantor| Link to the Mantor Works Directory]] === Activity Reports === [[DanieleMerico/WorkLogDirectory| Work logs]], concerning on-going reserach activity, will be visible only to lab members.<
> [[DanieleMerico/MemorandaDirectory| Memoranda]], concerning paper and seminar summaries, or more general considerations, will be kept more open. === 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) * [[DanieleMerico/HowtoDirectory/PearsonDotP| Pearson Correlation and the Dot Product]] * Distance Measures (continuous data: Euclidean, correlation-based; binary data: Hamming, Jaccard-based; sets: Jaccard-based)<
> * [[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 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. [[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.<
> 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)<
> [[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<
> [[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 ---- CategoryHomepage