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= Daniele Merico =

=== Contact ===
__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>>

== New Version: Under Construction --- == 

== Project Directory ==
 * Mouse Heart Pathway Project
 * Bio PAX Visualization

== Code Directory ==
=== Microarray Data Analysis ===
 * [[DanieleMerico/Code/Hierarchical_Pearson|Hierarchical Clustering using Pearson Correlaton]]

== --- Old Version --- ==

== 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]]

__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)

 * 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]]

 * 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.]]

 * [[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.<<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 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
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