Differences between revisions 18 and 53 (spanning 35 versions)

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

--- New Version: Under Construction ---

Project Directory

Mouse Heart Pathway Project
Bio PAX Visualization

Code Directory

Microarray Data Analysis

Hierarchical Clustering using Pearson Correlaton

--- 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.
- Enrichment Method for Time-Series

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:
- NETTAB 2007 presentation;
- published papers & proceedings.

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:
- The histone like NF-Y is a bifunctional transcription factor.
- A balance between NF-Y and p53 governs the pro- and anti-apoptotic transcriptional response.
Link to the Mantor Works Directory

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)
- Pearson Correlation and the Dot Product
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.

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.
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

CategoryHomepage

-  ⇤ ← Revision 18 as of 2007-11-12 14:51:19 → 
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+   ← Revision 53 as of 2009-10-14 22:29:51 → ⇥
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  Comment:
-Deletions are marked like this.
+Additions are marked like this.
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-#acl All:read
== Daniele Merico ==
+#acl All:read DanieleMerico:write,delete,revert
= Daniele Merico =
 Line 7:
-__Location__: Emili 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]]
+__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 12:
-=== 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].
+== --- New Version: Under Construction --- ==
-Line 19:
+Line 14:
-__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.
+== 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__:
-Line 25:
+Line 58:
-   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 (code-name ''Mantor'').<<BR>>
 Ref & Links: [[http://www.nature.com/emboj/journal/v25/n21/pdf/7601375a.pdf|p63 EMBO Paper]]
-Line 28:
+Line 61:
-__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.]]
-Line 37:
+Line 67:
-=== Work Logs ===
(To be filled yet...)
+ * [[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.
-Line 46:
+Line 79:
+   * [[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)
-Line 48:
+Line 84:
- * 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)
-Line 53:
+Line 89:
- * [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]])
-Line 55:
+Line 91:
-Go to the [:DmHowtoDirectory: How To Directory] for tips with R programming.
+Go to my [[DanieleMerico/HowtoDirectory| How To Directory]] for tips with R programming.

[[DanieleMerico/CytoMemo| Cytoscape Memos]]
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+Line 104:
-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]]
+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>>
-Line 74:
+Line 112:
-For more details, please have a look at my CV: [attachment:DanieleMericoCV.PDF CV.PDF].
+For more details, please have a look at my CV: [[attachment:DanieleMericoCV.PDF|CV.PDF]].
-Line 79:
+Line 117:
- * Università di Milano ([http://www.unimi.it UNIMI]) - Dipartimento di Scienze Biomolecolari e Biotecnologie ([http://bimib.disco.unimib.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://www.sbb.unimi.it/ BiMIB Group] (Bioinformatics at Milano-Bicocca)
+ * 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)
-Line 87:
+Line 125:
+The [[http://en.wikipedia.org/wiki/Celestial_Emporium_of_Benevolent_Recognition|Celestial Emporium of Benevolent Knowledge's Taxonomy]]: 
how not to build an ontology
-Line 93:
+Line 134:
- * write runes (still have to learn ideograms...)
+ * write [[http://en.wikipedia.org/wiki/Tengwar/|runes]] (still have to learn ideograms...)