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 Research Projects

• 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

• Pathway analysis for cancer data (Guidos-Danska)

  • Data directory

Open Research Projects

• Google Summer of Code 2010

  • Semantic Network Summary Directory

Ideas Notes Links

• Ideas for Enrichment Analysis

• Wall of Ideas (multi-project)

• Papers to read

• Connectorium

• To-do notes

• Misc Notes

Internal Exchanges

• Yeast expression data (Chris)

Past Collaborations

• NF-Y (TF) targets: integrative analysis of ChIP-chip and transcript array data

  • Roberto Mantovani (UNIMI - DSBB, Milano, Italy)

• Functional Landscape of p63 Transcription Factor Targets

  • Roberto Mantovani (UNIMI - DSBB, Milano, Italy)
  • Alessandro Terrinoni (Universita La Sapienza, Roma, 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)

• Clinical Phenotype Ontology

  • Gianluca Colombo (UNIMIB - DISCo, Milano, Italy)

Public Data Resources

Functional Gene-sets

• Gene set collections

Neurological Gene-sets

• Neurobiologically-relevant gene-sets (2011)

Educational

Microarray Analysis

• OBI (Ontario Biomedical Institute): R Programming, Microarray Analysis, Pathway and Network Analysis

  • Introduction to R Programming - I

  • Introduction to R Programming - II

  • Introduction to R Programming - III

  • Microarray Analysis using R Part I: Exploratory Analysis (OBI course Summer 2010)

  • Microarray Analysis using R Part II: Differential Expression (OBI course Summer 2010)

  • Pathway Analysis (OBI course Spring 2010)

  • Note: if you are interested in attending the full online version of these courses, please visit the OBI web site

• Overview of Microarray Data Analysis (CCBR graduate lecture)

Pathway Analysis Readings

• Pathway Analysis: Introduction and References

Statistics

• CBW Statistics 2011 Ottawa

  • Introduction to R

  • Exploratory Data Analysis

  • Inferential Statistics

  • pdf print outs: M1 M2 M3

R Code Directory (Public)

Microarray Data Analysis

• Affymetrix Microarray Data Processing

• Hierarchical Clustering using Pearson Correlaton

Gene-set Enrichment Analysis

Data Formatting

• gene sets

  • Generate gene set collections from Bioconductor libraries

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

• expression matrix

  • Convert Affy IDs to Entrez-Gene and add symbols and full names

Tests

• Fisher's Exact Test (with empirical FDR q-value included)

ID Conversion

• Entrez-Gene ID and Symbols

Network Visualization

• Format gene expression data and ppi interaction data for visualization in Cytoscape (OBI Course)

R Computational Efficiency

• Simulation to time vectorization advantages

CV and Publications

• Complete CV (includes Publications)

Trivia & Amenities

• Is there a link holding together biology, computer science, mathematics, statistics and... cooking? The answer is yes

• Another cup of caffeine..?

• How not to build an ontology: The Celestial Emporium of Benevolent Knowledge's Taxonomy

• Something I always remind myself in pathway analysis (on bad days): Videmus nunc per speculum et in aenigmate
• Entia non sunt multiplicanda praeter necessitatem (Occam's Razor). It can be roughly translated into: curb your enthusiasm.
• Natural marvels
  • Marvels of cruelty:

    • Ichneumonidae

    • Emerald wasp

  • (Almost) indestructible life forms:

    • Tardigrades

  • Pseudo-Zombies!
    these parasites modify the host behavior to infect other hosts

    • Zombie Ants

    • Snail Parasite

    • Infective tumors in Tazmanian Devils

• Si Hoc Legere Scis Nimium Eruditionis Habes :p

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