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| == Daniele Merico == | #acl All:read DanieleMerico:write,delete,revert = Daniele Merico = |
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| Physical location: Emili Lab Area (6th Floor CCBR)[[BR]] Email: [[MailTo(daniele DOT merico AT gmail DOT com)]][[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]] |
__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>> |
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| === Research Projects === Current Projects @CCBR: * Active Cell Maps (pathway & network: topology, expression profiling, activity patterns, etc...) Supervised by: [:GaryBader:Gary Bader]. * MouseHeartPathwayProject With: [:RuthIsserlin:Ruth Isserlin]. Supervised by: [http://lambda.med.utoronto.ca/Emili.htm/ Andrew Emili] and [:GaryBader:Gary Bader]. |
== 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]] |
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| Almost-completed or on-going Projects @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. |
== 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) |
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| Completed Projects @UNIMI / UNIMIB: | == 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__: <<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) |
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| With Gianluca Colombo, Flavio De Paoli, Marco Antoniotti. Supervised by: Giancarlo Mauri. Links: [http://www.nettab.org/2007/slides/SemanticWeb_Frisoni.pdf/ NETTAB 2007 presentation]; [http://nuke.neurowebkc.eu/Dissemination/tabid/66/Default.aspx/ published papers]. * The Landscape of NF-Y Binding With: Michele Ceribelli, Diletta Dolfini. Supervised by: Roberto Mantovani. |
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. |
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| Expertise on computational techniques & resources: | __Computational techniques & resources__: |
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| * [[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) |
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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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| * [http://cran.r-project.org/ R] (see also [http://www.bioconductor.org/ Bioconductor]) | * [[http://cran.r-project.org/|R]] (see also [[http://www.bioconductor.org/|Bioconductor]]) |
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| Biological Systems and Pathologies I've been working on (in order of confidence): | 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): |
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=== 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 |
Daniele Merico
Contact
Location: Common Lab Area, 6th Floor (CCBR)
Email: <daniele DOT merico AT gmail DOT com>
Skype: the-amerigo
Linked-In: Daniele Merico
Project Directory (Private)
Mouse Heart Disease Model Project (Transcriptomics, Proteomics, miRNA, Pathways)
- Functional Enrichment and Pathway Analysis in human genetics
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
Gene-set Enrichment Analysis
ID Conversion
Publications
- Empty Slot
--- Old Version ---
Research Projects
Present Reasearch Projects
Projects @CCBR:
Mouse Heart Pathway Project (Main Directory of my work)
With: Ruth Isserlin. Supervised by: Andrew Emili and 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: Gary Bader.
Ongoing Collaborative Projects:
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:
Projects @UNIMI:
- The p63 Network
With Alessandra Viganò. Supervised by: Roberto Mantovani (code-name Mantor).
Ref & Links: p63 EMBO Paper The Landscape of NF-Y Binding
With: Michele Ceribelli, Diletta Dolfini. Supervised by: Roberto Mantovani.
Ref & Links:
Activity Reports
Work logs, concerning on-going reserach activity, will be visible only to lab members.
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)
Distance Measures (continuous data: Euclidean, correlation-based; binary data: Hamming, Jaccard-based; sets: Jaccard-based)
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:
R (see also Bioconductor)
Go to my How To Directory for tips with R programming.
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: CV.PDF.
Affiliations
CCBR - Banting & Best Dept. of Medical Research
- Visiting PhD student
Università di Milano (UNIMI) - Dipartimento di Scienze Biomolecolari e Biotecnologie (DSBB)
PhD student (Program of Cellular and Molecular Biology)
Roberto Mantovani's Lab
Università di Milano-Bicocca (UNIMIB) - Dipartimento di Informatica (DISCo)
External PhD student
BiMIB Group (Bioinformatics at Milano-Bicocca)
Trivia & Amenities
The 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 runes (still have to learn ideograms...)
- drink beer
- throw snowballs (look out...)
laugh
