Diff for "DanieleMerico" - Bader Lab @ The University of Toronto

Differences between revisions 1 and 29 (spanning 28 versions)

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

Current Projects @CCBR:

Active Cell Map (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].

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.
The p63 Network
- With Alessandra Viganò. Supervised by: Roberto Mantovani.
  Ref & Links: [http://www.nature.com/emboj/journal/v25/n21/pdf/7601375a.pdf p63 EMBO Paper]

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)

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)
Distance Measures (quantitative: Euclidean, correlation-based; binary: Hamming, 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 (hirerarchical, K-means, CLICK, etc...)
Statistical tests (t-test, Fisher's)
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.

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

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

CategoryHomepage

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-Physical location: Emili Lab Area (6th Floor CCBR)
Email: [[MailTo(daniele DOT merico AT gmail DOT com)]]
+__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]]
-Line 9:
+Line 12:
-=== Current Projects ===
Current Projects @CCBR:
 * Active Cell Maps (pathway & network: expression profiling, activity patterns, etc...)
+=== Research Projects ===
__Current Projects @CCBR__:
 * '''Active Cell Map''' (pathway & network: topology, expression profiling, activity patterns, etc...)
-Line 13:
+Line 16:
- * MouseHeartPathwayProject
+ * '''MouseHeartPathwayProject'''
-Line 16:
+Line 19:
-Almost-completed or on-going Projects @UNIMIB:
+__Almost-completed or on-going Projects @UNIMI/UNIMIB__:
-Line 21:
+Line 24:
+ * The p63 Network
   With Alessandra Viganò. Supervised by: Roberto Mantovani.
   Ref & Links: [http://www.nature.com/emboj/journal/v25/n21/pdf/7601375a.pdf p63 EMBO Paper]
-Line 22:
+Line 28:
-Completed Projects @UNIMI / UNIMIB:
+__Completed Projects @UNIMI/UNIMIB__:
-Line 25:
+Line 31:
-  Links: [http://www.nettab.org/2007/slides/SemanticWeb_Frisoni.pdf/ NETTAB 2007 presentation]; 
  [http://nuke.neurowebkc.eu/Dissemination/tabid/66/Default.aspx/ published papers].
+  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].
-Line 29:
+Line 35:
+  Ref & Links: (2 accepted papers)
-Line 30:
+Line 37:
+=== 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)
 * Distance Measures (quantitative: Euclidean, correlation-based; binary: Hamming, 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 (hirerarchical, K-means, CLICK, etc...)
 * Statistical tests (t-test, Fisher's)
 * 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.

__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 ===
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