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= Daniele Merico =
=== Contact ===
__Location__: Common Lab Area, 6th Floor (CCBR)<
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__Email__: <><
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__Skype__: the-amerigo<
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__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]]<
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== 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]]
== 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 ===
* [[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 R list object, 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__: <
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* '''Mouse Heart Pathway Project'''
([[MouseHeartPathwayProject/NetworkProfilingTrack|Main Directory of my work]])<
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With: [[RuthIsserlin|Ruth Isserlin]].
Supervised by: [[http://lambda.med.utoronto.ca/Emili.htm/|Andrew Emili]] and [[GaryBader|Gary Bader]]. <
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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...) <
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Supervised by: [[GaryBader|Gary Bader]].
* [[DanieleMerico/Enrichment_Time| Enrichment Method for Time-Series]]
__Ongoing Collaborative Projects__: <
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* [[DanieleMerico/OntoBioMed| Biomedical Ontologies]], bridging clinics and molecular biosciences
=== Past Research Projects ===
__Projects @UNIMIB__:
* Analysis of Time-course Microarray Data<
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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.<
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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'').<
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Ref & Links: [[http://www.nature.com/emboj/journal/v25/n21/pdf/7601375a.pdf|p63 EMBO Paper]]
* The Landscape of NF-Y Binding<
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With: Michele Ceribelli, Diletta Dolfini. Supervised by: Roberto Mantovani.<
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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.<
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[[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)<
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* [[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.<
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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)<
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[[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<
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[[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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