Daniele Merico

Contact

Location: Common Lab Area, 6th Floor (CCBR)BR Email: MailTo(daniele DOT merico AT gmail DOT com)BR Skype: the-amerigoBR 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

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:

  • Improved set-enrichment methods
  • Pathway profiling
  • Network profiling

  • Identification of miRNA candidates, BR integrating predictions and miRNA expression patterns with taregt expression patterns

• Active Cell Map (pathway & network: topology, expression profiling, activity patterns, etc...) BR Supervised by: [:GaryBader:Gary Bader].

Ongoing Collaborative Projects: BR

• [:DanieleMerico/OntoBioMed: Biomedical Ontologies], bridging clinics and molecular biosciences

Past Research Projects

Projects @UNIMIB:

• Analysis of Time-course Microarray DataBR 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.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.BR Ref & Links: [http://www.nature.com/emboj/journal/v25/n21/pdf/7601375a.pdf p63 EMBO Paper]

  • [:DanieleMerico/Mantor/p63_Saos: Saos p63 microarray analysis]

• The Landscape of NF-Y BindingBR 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.]

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.

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)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

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.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 studentBR [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

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