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== Daniele Merico == | = Daniele Merico = |
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=== Research Projects === __Current Projects @CCBR__: |
== Research Projects == === Present Reasearch Projects === __Projects @CCBR__: [[BR]] * '''Mouse Heart Pathway Project'''[[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 [:MouseHeartPathwayProject/NetworkProfilingTrack: Main Directory][[BR]] |
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Supervised by: [:GaryBader:Gary Bader]. * '''MouseHeartPathwayProject'''[[BR]] and specifically [:MouseHeartPathwayProject/NetworkProfilingTrack: Network Profiling Track][[BR]] With: [:RuthIsserlin:Ruth Isserlin] and [http://www.tcag.ca/staffHuP.html Pingzhao Hu]. Supervised by: [http://lambda.med.utoronto.ca/Emili.htm/ Andrew Emili] and [:GaryBader:Gary Bader]. |
Supervised by: [:GaryBader:Gary Bader]. |
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__Almost-completed or on-going Projects @UNIMI/UNIMIB__: * Knowledge Engineering of Human Phenotypes With Gianluca Colombo. Supervised by: Giancarlo Mauri. * Analysis of Time-course Microarray Data With Italo Zoppis. Supervised by: Marco Antoniotti. |
__Ongoing Collaborations__: [[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, 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__: |
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With Alessandra Viganò. Supervised by: Roberto Mantovani. Ref & Links: [http://www.nature.com/emboj/journal/v25/n21/pdf/7601375a.pdf p63 EMBO Paper] |
With Alessandra Viganò. Supervised by: Roberto Mantovani.[[BR]] Ref & Links: [http://www.nature.com/emboj/journal/v25/n21/pdf/7601375a.pdf p63 EMBO Paper] |
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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) |
* 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.] |
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* Distance Measures (quantitative: Euclidean, correlation-based; binary: Hamming, Jaccard-based)[[BR]] | * [: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]] |
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* Clustering (hirerarchical, K-means, CLICK, etc...) * Statistical tests (t-test, Fisher's) |
* Clustering (hierarchical, K-means, CLICK, etc...) * Statistical tests (t-test, Fisher's, Kolmogorov-Smirnov) |
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[:DanieleMerico/CytoMemo: Cytoscape Memos] |
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The [http://en.wikipedia.org/wiki/Celestial_Emporium_of_Benevolent_Recognition Celestial Emporium of Benevolent Knowledge's Taxonomy]: how not to build an ontology |
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 ProjectBR 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
[:MouseHeartPathwayProject/NetworkProfilingTrack: Main Directory]BR
Active Cell Map (pathway & network: topology, expression profiling, activity patterns, etc...) Supervised by: [:GaryBader:Gary Bader].
Ongoing Collaborations: 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, 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]
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