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)

• Enrichment Map: Network Visualization of Enrichment Results

• Visualization of BioPAX encoded Pathways

• Functional Enrichment and Pathway Analysis in human genetics

  • De-novo CNV in Autism: Pathway Analysis

  • 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

• Affymetrix Microarray Data Processing

• Hierarchical Clustering using Pearson Correlaton

Gene-set Enrichment Analysis

• Generate gene set collections from Bioconductor libraries

• Reads a GMT file into a R list object, or binary matrix

ID Conversion

• Entrez-Gene ID and Symbols

Educational Material

• CCBR course on Microarray Data Analysis

• OBI course on Pathway Analysis

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.

  • 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

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