Academic Year 2013 Seminars

Academic Year 2013 Seminars:

Wednesday, September 19
5:00 p.m. - SWIG Boardroom (CIT 241)

D.E. Shaw Research Event

D.E. ShawD.E. ShawD. E. Shaw Research is an independent research laboratory that conducts basic scientific research in the field of computational biochemistry under the direct scientific leadership of Dr. David E. Shaw.  Our group is currently focusing on molecular simulations involving proteins and other biological macromolecules of potential interest from both a scientific and a pharmaceutical perspective.  Members of the lab include computational chemists and biologists, computer scientists and applied mathematicians, and computer architects and engineers, all working collaboratively within a tightly coupled interdisciplinary research environment.


Wednesday, September 26
4:00 p.m. - SWIG Boardroom (CIT 241)

Daniel UdwaryDaniel Udwary Daniel Udwary
Assistant Professor of Pharmacognosy
Department of Biomedical  & Pharmaceutical Sciences
University of Rhode Island

"SMOR: A database and web analysis tool to identify bacterial secondary metabolism and enable drug discovery" 

Hosted by Sorin Istrail

Wednesday, October 3
4:00 p.m. - SWIG Boardroom (CIT 241) 

Marta Gomez-ChiarriMarta Gomez-Chiarri

Marta Gomez-Chiarri
Professor,  Department of Fisheries, Animal & Veterinary Science
University of Rhode Island

"Genomic approaches to investigating disease resistance in oysters"

Hosted by Sorin Istrail

Wednesday, October 10
4:00 p.m. - SWIG Boardroom (CIT 241)

Gary StormoGary Stormo

Gary Stormo
Center for Genome Sciences, Dept of Genetics
School of Medicine, Washington University

"Protein-DNA Interactions: Experimental and Computational Approaches" 

Hosted by Sorin Istrail

Wednesday, October 17
4:00 p.m. - SWIG Boardroom (CIT 241)

David RandDavid RandDavid Rand
Professor of Biology
Brown University

“Mito-Nuclear Co-evolution, Epistasis and Systems Biology”


Wednesday, October 24
4:00 p.m. - SWIG Boardroom (CIT 241)

Matthew StephensMatthew Stephens
 Matthew Stephens
 Professor, Dept of Human Genetics, Dept of Statistics
University of Chicago

"A unified framework for testing multiple phenotypes for association
with genetic variants."

Hosted by Sorin Istrail

Wednesday, November 7
4:00 p.m. - SWIG Boardroom (CIT 241)

Casey DunnCasey Dunn
Casey Dunn, Assistant Professor of Biology
Dunn Lab, Brown University
Dept of Ecology & Evolutionary Biology

 "Phylogenetics and functional genomics in non-model organisms".

Wednesday, November 14
4:00 p.m. - SWIG Boardroom (CIT 241)

Guillaume BorqueGuillaume Borque

Guillaume Bourque
Associate Professor, Department of Human Genetics
McGill University & Genome Quebec Innovation Center

 "The role of genomic repeats in host gene regulation"

Hosted by Ben Raphael

Wednesday, December 5
4:00 p.m. - SWIG Boardroom (CIT 241)

Marta LukszaMarta Luksza

Marta Luksza
Dana Pe'er Lab of Computational Systems Biology
Columbia University

"A predictive fitness model for influenza"

Hosted by Daniel Weinreich

Prospective Postdoctoral Seminars:

Fernando Mendez (University of Arizona) - Tuesday, January 8th - 10:00 - 11:00 am - SWIG Boardroom CIT 241

Julia Roman (University of Washington) - Wednesday, January 9th - 12:00 - 1:00 pm - SWIG Boardroom CIT 241

Wednesday, January 23
4:00 p.m. - SWIG Boardroom (CIT 241) 

Brian TjadenBrian Tjaden
Brian Tjaden
Theresa Mall Mullarkey Associate Professor of Computer Science
Wellsley College

"The Elusive Gene"

Hosted by Erica Larschan & Ben Raphael 

Wednesday, March 13
4:00 p.m. - SWIG Boardroom (CIT 241)

Julius LucksJulius LucksJulius Lucks, Assistant Professor
Dept of Chemical & Biomolecular Engineering, James C. & Rebecca Q. Morgan Sesquicentennial Faculty Fellow
Cornell University 

"A Platform for Engineering RNA Regulatory Networks using High Throughput RNA Structure Characterization"

Hosted by Chip Lawrence

Wednesday, March 20
4:00 p.m. - SWIG Boardroom (CIT 241)

Eric StoneEric Stone

Eric Stone
Associate Professor of Genetics
Bioinformatics Research Center
North Carolina State University

"Down the rabbit hole in support of Drosophila systems genetics"

Hosted by David Rand

Wednesday, April 3
4:00 p.m. - SWIG Boardroom (CIT 241)

Ben EvansBen EvansBen Evans
Associate Professor, Biology Department
McMaster University 
Ontario, Canada

"Monkey sex chromosomes: the impact of social system and demography on genome evolution."

Hosted by Will Fairbrother

Wednesday, April 10
4:00 p.m. - SWIG Boardroom (CIT 241)

David MathewsDavid MathewsDavid Mathews
 Associate Professor, Dept of Biochemistry and Biophysics
University of Rochester, Medical Center

“RNA Partition Functions: Structure Prediction Beyond a Single Lowest Free Energy Structure”

Hosted by Chip Lawrence

Wednesday, April 24
4:00 p.m. - SWIG Boardroom (CIT 241)
James PadburyJames Padbury

James Padbury
Oh-Zopfi Professor of Pediatrics & Perinatal Research
Brown University
Chair for Research Women and Infants' Hospital


“Bioinformatic Approach to Complex Diseases”

Friday, May 3 - All Day
Evolution of Cancer Symposium
Alpert Medical School - Lecture Hall 170

Presented with the Department of Pathology & Laboratory Medicine

See Schedule Here

Wednesday, May 8
4:00 p.m. - SWIG Boardroom (CIT 241)

Shamil SunyaevShamil SunyaevShamil Sunyaev
Associate Professor, Division of Genetics, Dept. of Medicine
Brigham & Women's Hospital & Harvard Medical School


"Human germ line and somatic mutation rates: evolution, biology and statistical genetics"

Hosted by Will Fairbrother 

Wednesday, May 15
4:00 p.m. - SWIG Boardroom (CIT 241)

Frederick RothFrederick RothFrederick P (Fritz) Roth
Professor, Donnelly Centre for Cellular & Biomedical Research
University of Toronto

 "The Dark Side of the Interactome, Barcode Fusion Genetics, and Prix Fixe Menus"

Hosted by Ben Raphael


Thursday, August 16th, 2012
11:00 a.m. - SWIG Boardroom (CIT241)

Jian MaJian MaAssistant Professor, Dept of Bioengineering
University of Illinois at Urbana-Champaign
College of Engineering

"Self-training Algorithm for Splice Junction Detection Using RNA-seq"

RNA-seq has proven to be a powerful technique for transcriptome profiling based on next-generation sequencing (NGS) technologies. However, due to the short length of NGS reads, it is challenging to accurately map RNA-seq reads to splice junctions (SJs), which is a critically important step in the analysis of alternative splicing (AS) and isoform construction. In this presentation, I will introduce a new method that we recently developed, called TrueSight. Both simulations and real data evaluations showed that TrueSight achieved higher sensitivity and specificity than other methods. We applied TrueSight to discover novel splice forms in honey bee transcriptomes and found that 65% of honey bee multi-exon genes are alternatively spliced. Utilizing new high coverage transcriptome profiling data and gene models improved by TrueSight, our quantitative analysis revealed that the expression ratio of the splice variants of a single gene is significantly correlated with various genomic features. We believe this new tool will be highly useful to comprehensively study the biology of alternative splicing.


Tuesday, August 7, 2012
1:00 p.m. - SWIG Boardroom (CIT 241)

Sagi SnirSagi Snir Professor, Department of Evolutionary & Environmental Biology
University of Haifa

"Using Computational Tools for Piecing Together Small Trees into the Large Tree of Life"

The reconstruction of evolutionary trees is a fundamental task in Biology. The increasing amount of available genomic sequences over thousands of taxa, gave rise to the task of large scale phylogenetic reconstruction. Since accurate reconstruction is limited to few dozens of taxa, the supertree approach, aims at accurately reconstructing small trees over overlapping taxa sets and subsequently amalgamate these trees into a tree over the full taxa set. Perhaps the simplest version of this task that is still widely applicable, yet quite challenging, is quartet based reconstruction. This problem lies at the root of many tree reconstruction methods and theoretical as well as experimental results have been reported. Nevertheless, fundamental problems such as dealing with conflicting quartet trees or even with arbitrary congruent quartet trees remain problematic. In a series of works we have developed a graph theoretically based approach for the supertree task.  Our approach is based on a divide and conquer algorithm where our divide step uses a semi-definite programming (SDP) formulation of MaxCut in a graph representing relationships between the organisms. We devised an extremely fast SDP-like heuristic that allows us to extend the input data from several thousands of quartet trees over few dozens of species to tens of millions of quartet trees over thousands of species. These results are promising in the realm of large scale phylogenetic reconstruction. Based on works with Satish Rao and Raphy Yuster. The talk is self-contained and requires no prior knowledge in Biology.

Summer Seminar: Friday, June 7th

2:00 p.m. - SWIG Boardroom, CIT 241

Alexander SchoenhuthAlexander SchoenhuthDr. Alexander Schönhuth
Scienctific Staff Member 
Life Sciences Group, Centrum Wiskunde & Informatica

Ancestry-aware variant calling and genotyping in the 'Genome of the Netherlands'

The 'Genome of the Netherlands' (GoNL) is a Dutch collaboration that
aims at characterizing and cataloging genetic variation in the Dutch
population. The resulting variant catalogue will add substantially to our
understanding of genetic variability in the context of population
history, acquisition of de novo variation and GWAS interpretation.
250 Dutch families, consisting of trios and mono-/dizygotic twin
quartets, have been sequenced to 12x coverage per individual.
Here, we will report on results of the analysis of structural variants and
indels. We focus on ancestry- and population-aware variant calling in
particular and present novel, statistical approaches by which to
combine high-precision variant calling and genotyping with Mendelian
statistics. Indels of size 20 to 100 bp pose particular
statistical challenges, both in ancestry-related and generic settings.
We present MATE-CLEVER (Multiple-Allele-Attentive Clique-Enumerating
Variant Finder) as a tool that tackles this challenge by combining
enhanced algorithmic engineering with Bayesian statistics.


Hosted by Ben Raphael & Iman Hajirasouliha

Special Seminar:  Friday, July 19th
12:00 p.m. - SWIG Boardroom, CIT 241

Michael StifflerMichael Stiffler Michael Stiffler, Ph.D.
Postdoctoral Researcher, Ranganathan Laboratory
Green Center for Systems Biology, UT Southwestern Medical Center

"Selection Strength Defines the Robustness and Evolvability of Beta-lactamase"


Hosted by Dan Weinreich