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Advanced topics in Bioinformatics and Computational Biology

Laxmi Parida, IBM Watson Research Center, Yorktown Heights, NY, USA

Daniele Merico, The Centre for Applied Genomics (TCAG), Toronto (ON), Canada

Jim Schaff, Center for Cell Analysis & Modeling, University of Connecticut Health Center, Farmington, CT, USA

Laxmi Parida:

Laxmi is leading the Computational Genomics Group in the Computational Biology Center at the IBM T, J. Watson and a visiting professor at the Courant Institute of Mathematical Sciences, New York. She received her Ph.D. in the area of Computational Genomics from New York University in 1998 and received the Janet Fabri Award for an outstanding thesis in computer science. She is also a recipient of the Sandra Belestein award for notable achievement in mathematical and computer science by a woman. She has authored over hundred research papers, and holds several patents related to her algorithmic work.  Her professional activities include organizing/chairing leading conferences in the area of computational biology and computer science;  advisory board  membership of computer science departments; evaluation panels of NIH/NSF bodies, amongst others.  Her research has focused on algorithmics and statistics in the area of computational genomics. Her research monograph “Pattern discovery in Bioinformatics: Theory and Algorithms” on her contributions to the field juxtaposed with  the  latest developments in this  area,  was published by Chapman Hall in August, 2007 (the book has been on the computer science best selling list  since its publication).




Daniele Merico:

Daniele Merico received his Bachelor's degree in Molecular Biotechnology and his Master's degree in Bioinformatics from Universita di Milano-Bicocca (2003 and 2005, respectively). He then received his Molecular and Cellular Biology PhD from Universita di Milano (2009).

Daniele Merico was a post-doctoral fellow under the supervision of Drs. Gary D. Bader and Andrew Emili (Donnelly Centre, University of Toronto, Toronto, Canada) from 2009 to 2011. His post-doctoral activity focused on pathway and network analysis of gene expression microarray and proteomics data applied to cardiomiopathy and tumor mouse models.

Since 2011, Daniele Merico manages the bioinformatics core facility at TCAG (The Centre for Applied Genomics, Hospital for Sick Children, Toronto, Canada), under the direction of Dr. Stephen W. Scherer. As a core facility manager, he is responsible for the next generation sequencing (NGS) analysis pipelines, including human whole exome and whole genome resequencing and variant annotation, RNA-seq, ChIP-seq, methyl-seq, de-novo transcriptome and genome assembly. His current research interests are focused on genome annotation for clinical applications, disease gene discovery for rare disorders, as well as pathway/network analysis of rare genetic variants in autism and schizophrenia.

Daniele Merico has authored or co-authored 18 peer-reviewed Pubmed-indexed journal articles, 3 peer-reviewed journal articles indexed by other services, as well as 4 peer-reviewed articles published as conference proceedings.






Jim Schaff:

My research interests center on the development of abstractions, formalisms and numerical methods in biological modeling and simulatoin. I am the founding developer of the Virtual Cell project and currently lead our software development group.

We are also developing a suite of tools for the quantitative analysis of microscopy experiments which transparently leverage VCell technologies. The Virtual FRAP (VFRAP) tools is the first of these application, and facilitates the analysis of FRAP (Fluorescence Redistribution After Photobleaching) experiments.

I have been involved in the development of SBML from its inception and now serve as one of the SBML editors. Currently I am working toward the development of an SBML Level 3 extension for spatial modeling.






For information: Prof.ssa Paola Bonizzoni





Period and location


June 26 2013, 14.00-17.00 : Seminar Room, 1st Floor

June 27 2013, 10.30-12.30 and 14.30-16.30: Seminar Room, 1st Floor

June 28, 2013 10.00-13.00: Seminar Room, 1st Floor

September 9-10, 2013: Seminar Room, 1st Floor

September 23,2013: Seminar Room, 1st Floor

September 24, 2013: T024 Room, Ground Floor



Department of Computer Science, Systems and Communication – University of Milano-Bicocca

Viale Sarca,336 U14, 20126 Milano

Topic - Aim organization


Genomic data of populations is becoming more accessible, whether it is of human, animal or plant origin. The potential impact of the availability of this extensive genomic data ranges from understanding  virus populations in hosts to plant breeding and animal husbandry at one end to personalized medicine at the  other.  Indeed, a correct understanding of the data is essential to make these wide spectrum of applications a viable reality.


Part 1 

Discrete Methods for Population Genomics (Laxmi Parida)

In this course, we explore the use of discrete methods in the area of population genomics. In particular, we will study the use of random graphs and the new insights it brings to the table about understanding genetic history abstracted in a topological structure (combinatorial network). This can be utilized for non-redundant simulations of population evolution, i.e., avoiding computations in the simulator that are “redundant”. This process is not only computationally efficient but also mathematically clean and elegant.


I will discuss yet another class of algorithms in the area of simulations of extant populations satisfying certain statistical characteristics such as, linkage disequilibrium distributions, Fixation Index ( Fisher’s Fst) etc. We will apply discrete methods for non-generative modeling of this class of problems.


This is an emerging cross-disciplinary area, thus rich with (particularly computational) research questions that are of vital interest to biologists, population geneticists and others.


Population Models                                                   


            I.             a. The Wright-Fisher, Moran populations

                         b. Haploid models; uniparental vs. biparental

                         c. Descriptor topologies: trees, networks (ARGs)

                         d. The generic random graph model

                         e.  Minimal descriptors




           II.    Constructing descriptors (simulations)                  

                         a.Uni-parental tree model for non-recombining loci

                         b. Coalescent models

                                 i.    With mutations

                                 ii.    And recombinations

                         c. Simulating via minimal descriptors




          III.    Reconstructing descriptors                                              

                       a. On limits to inference (human data)

                       b.A discrete algorithm for ARG reconstruction

                         (DSR Algorithm)



         IV.    Discrete methods in plant genomics                              

                      a.Simulating crossovers (Kosambi interference model)

                      b.Haplotypes from genotypes in a mapping population for QTL estimation (with iXora)




Part 2

Gene lists, Pathways and their Annotations (Daniele Merico)

September 9-10, 2013

Many research programs often slow or stall after generating a gene list. The course covers the bioinformatics concepts and tools available for annotating and determining functional enrichment of a gene list and analyzing networks. The workshop is focused on the principles and concepts required for analyzing and conducting pathway analysis on a gene list from any organism, although focus will be on human and model Eukaryotic organisms. Specifically, we will focus on 1) getting more information about a gene list, 2) finding out how a set of genes is connected, 3) discovering what's enriched in a gene list (and using it for hypothesis generation) and 4) extending or refining a gene list. An analysis flow chart will be developed throughout the course.

Students will be required to complete the Cytoscape tutorials:


Part 3

Modeling and Simulation of Cellular Systems (Jim Schaff)

September 23-24, 2013

The simulation of biological systems is one of the most foundational parts of any Systems Biology integrative approaches to biomedical research.  There are many systems available for the development of biological simulations based on different underlying paradigms.  The goal of this short course is to acquaint users with the VCell system, one of the prominent systems for biological simulations.  A few different biological models will be presented alongside the various possibilities offered by VCell pertaining their simulations.



Final Examination



Short project that will be discussed with Laxmi Parida




Pratical activities





Pratical activities

Educational Material


Slides from the professor +  other references

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20126 Milano - Edificio U14 - ultimo aggiornamento di questa pagina 23/07/2013