Location: Common Lab Area, 6th Floor (CCBR)
Email: <daniele DOT merico AT gmail DOT com>
Linked-In: Daniele Merico
Mouse Heart Disease Model Project (Transcriptomics, Proteomics, miRNA, Pathways)
- Gianluca Colombo (UNIMIB - DISCo, Milano, Italy)
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)
p63 Transcription Factor Transcriptional Program
- Roberto Mantovani (UNIMI - DSBB, Milano, Italy)
- Alessandro Terrinoni (Universita La Sapienza, Roma, Italy)
R Code Directory
Microarray Data Analysis
Gene-set Enrichment Analysis
- Empty Slot
--- Old Version ---
Present Reasearch Projects
- 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
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:
- 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:
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:
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.
CCBR - Banting & Best Dept. of Medical Research
- Visiting PhD student
PhD student (Program of Cellular and Molecular Biology)
Roberto Mantovani's Lab
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...)