Events Archive

Integrative Modeling of Multi-platform Genomics Data for Cancer Survival

Thursday, January 30, 2014 4:00pm - 4:00pm
Swig Boardroom - CIT 241
Yen-Tsung Huang
Assistant Professor of Epidemiology 
Brown University 
“Integrative ...

Systematic approaches to uncover mechanisms underlying complex immune-mediated diseases

Wednesday, January 29, 2014 4:00pm - 4:00pm
Swig Boardroom - CIT 241
...

Data-driven approaches for uncovering protein interactions and protein interaction specificities

Wednesday, January 22, 2014 4:00pm - 4:00pm
Swig Boardroom - CIT 241
Mona Singh
Professor of Computer Science
Lewis-Sigler Institute for Integrative Genomics
Dept of Computer Science, Princeton University
"Data-driven ...

CCMB Research Day 2014

Tuesday, January 21, 2014 8:30am - 8:30am
Watson-CIT Building, Swig Boardroom - CIT 241
8:30 - 9:00 - Breakfast - CIT 245
9:00 - 9:15 - Introductions: David Savitz (Vice President of Research), and Ben Raphael (Director, CCMB)
9:15 - 9:45 - Algorithms, Statistics, and Computation

Evolution of Ribosomal RNA: rRNA conserved nucleotide elements highlight functional sites in the ribosome

Wednesday, December 11, 2013 4:00pm - 4:00pm
Swig Boardroom - CIT 241
Susan Gerbi
Professor of Biology
George Eggleston Professor of Biochemistry, Molecular Biology, Cell Biology, & Biochemistry
Brown University 
"Evolution ...

A predictive fitness model for influenza

Thursday, December 05, 2013 4:00pm - 4:00pm
SWIG Boardroom (CIT 241)
Marta Luksza
Dana Pe'er Lab of Computational Systems Biology
Columbia University
"A ...

The Fossilized Birth-Death Process: A Coherent Model of Fossil Calibration for Divergence Time Estimation

Wednesday, November 20, 2013 4:00pm - 4:00pm
Swig Boardroom - CIT 241
Tracy Heath
Postdoctoral Researcher
Department of Integrative Biology
University of California Berkeley
"The ...

Postdoctoral Interview Seminar

Friday, November 15, 2013 12:00pm - 12:00pm
Swig Boardroom - CIT 241
Matthew Reyna
Department of Mathematical Sciences
Rensselaer  Polytechnic Institute
"High-order ...

The role of genomic repeats in host gene regulation

Thursday, November 14, 2013 4:00pm - 4:00pm
SWIG Boardroom (CIT 241)
Guillaume Bourque
Associate Professor, Department of Human Genetics
McGill University & Genome Quebec Innovation Center
 "The ...

Analyzing Long Term Fitness Trajectories in Experimental Populations

Wednesday, November 13, 2013 4:00pm - 4:00pm
Swig Boardroom - CIT 241
Mike Wiser - Ph.D. Candidate
Dr. Richard Lenski's Lab
Experimental Evolution
Michigan State University
"Analyzing ...

Phylogenetics and functional genomics in non-model organisms

Thursday, November 07, 2013 4:00pm - 4:00pm
SWIG Boardroom (CIT 241)
Casey Dunn, Assistant Professor of Biology
Dunn Lab, Brown University
Dept of Ecology & Evolutionary Biology

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

Modeling a path from genotype to phenotype using sparsity-enforced linear regression

Wednesday, November 06, 2013 4:00pm - 4:00pm
Swig Boardroom - CIT 241
Suzannah Rutherford 
Affiliate, Division of Basic Sciences
Fred Hutchinson Cancer Research Center

Modeling ...

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

Thursday, October 24, 2013 4:00pm - 4:00pm
SWIG Boardroom (CIT 241)
Matthew Stephens
 Professor, Dept of Human Genetics, Dept of Statistics
University of Chicago
"A ...

Identifying the role of functional microbial clades in Ulcerative Colitis

Wednesday, October 23, 2013 4:00pm - 4:00pm
Swig Boardroom - CIT 241
Susan Huse
Assistant Professor of Pathology & Laboratory Medicine
(Research)
Brown University, Bio Med Pathology & Laboratory Medicine
“Identifying ...

Mito-Nuclear Co-evolution, Epistasis and Systems Biology

Thursday, October 17, 2013 4:00pm - 4:00pm
SWIG Boardroom (CIT 241)
David Rand
Professor of Biology
Brown University

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

Protein-DNA Interactions: Experimental and Computational Approaches

Thursday, October 10, 2013 4:00pm - 4:00pm
SWIG Boardroom (CIT 241)
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

Genomic approaches to investigating disease resistance in oysters

Thursday, October 03, 2013 4:00pm - 4:00pm
SWIG Boardroom (CIT 241)
Marta Gomez-Chiarri
Professor,  Department of Fisheries, Animal & Veterinary Science
University of Rhode Island
"Genomic ...

De Bruijn Graphs in Genome Assembly and Comparison

Thursday, October 03, 2013 1:00pm - 1:00pm
Swig Boardroom - CIT 241
Son K. Pham
Department of Computer Science & Engineering
University of California San Diego
"De ...

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

Thursday, September 26, 2013 4:00pm - 4:00pm
SWIG Boardroom (CIT 241)
 Daniel Udwary
Assistant Professor of Pharmacognosy
Department of Biomedical  & Pharmaceutical Sciences
University of Rhode Island
"SMOR: ...

The tranSMART Platform and the tranSMART Foundation: Global Cyberinfrastructure for Integrative Informatics Analysis

Wednesday, September 25, 2013 4:00pm - 4:00pm
Swig Boardroom - CIT 241

 

Brian Athey
Professor & Chair, Computational Medicine and Bioinformatics (DCM&B)
Professor, Psychiatry and Internal Medicine
Associate Director, Michigan Institute for Clinical Health Research (MICHR)
University of Michigan Medical School

 

"The tranSMART Platform and the tranSMART Foundation: Global Cyberinfrastructure for Integrative Informatics Analysis" 

Somatic mutations that affect RNA splicing in human cancers

Wednesday, September 18, 2013 4:00pm - 4:00pm
Swig Boardroom - CIT 241

 

Angela Brooks
Post Doctoral Associate - Broad Institute
Cambridge, MA 

"Somatic mutations that affect RNA splicing in human cancers" 

 

D.E. Shaw Research Event

Friday, September 13, 2013 5:00pm - 5:00pm
SWIG Boardroom (CIT 241)
D. 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 ...

Bayesian sequence assembly and assessment by Markov Chain Monte Carlo sampling

Wednesday, September 04, 2013 4:00pm - 4:00pm
Swig Boardroom - CIT 241
"Bayesian sequence assembly and assessment by Markov Chain Monte Carlo sampling"
Hosted ...

Complexity & Information: Genetics, circulating RNA & the analysis of data

Wednesday, August 21, 2013 4:00pm - 4:00pm
Swig Boardroom - CIT 241

 

David J. Galas
Principal Scientist, Pacific Northwest Diabetes Research Institute
Seattle, WA 

"Complexity & Information: Genetics, circulating RNA & the analysis of data"

Hosted by Sorin Istrail 

 

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

Friday, August 16, 2013 11:00am - 11:00am
SWIG Boardroom (CIT241)
Assistant 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 ...

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

Wednesday, May 15, 2013 4:00pm - 4:00pm
SWIG Boardroom (CIT 241)
Frederick P (Fritz) Roth
Professor, Donnelly Centre for Cellular & Biomedical Research
University of Toronto
 "The ...

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

Wednesday, May 08, 2013 4:00pm - 4:00pm
SWIG Boardroom (CIT 241)

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

Evolution of Cancer Symposium

Friday, May 03, 2013 12:00am - 12:00am
Alpert Medical School - Lecture Hall 170

Presented with the Department of Pathology & Laboratory Medicine

Bioinformatic Approach to Complex Diseases

Wednesday, April 24, 2013 4:00pm - 4:00pm
SWIG Boardroom (CIT 241)
James Padbury
Oh-Zopfi Professor of Pediatrics & Perinatal Research
Brown University
Chair for Research Women and Infants' Hospital
 
“Bioinformatic ...

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

Wednesday, April 10, 2013 4:00pm - 4:00pm
SWIG Boardroom (CIT 241)
David 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 ...

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

Wednesday, April 03, 2013 4:00pm - 4:00pm
SWIG Boardroom (CIT 241)
Ben Evans
Associate Professor, Biology Department
McMaster University 
Ontario, Canada
"Monkey ...

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

Wednesday, March 13, 2013 4:00pm - 4:00pm
SWIG Boardroom (CIT 241)
Julius Lucks, Assistant Professor
Dept of Chemical & Biomolecular Engineering, James C. & Rebecca Q. Morgan Sesquicentennial Faculty Fellow
Cornell University 
"A ...

The Elusive Gene

Wednesday, January 23, 2013 4:00pm - 4:00pm
SWIG Boardroom (CIT 241)
Brian Tjaden
Theresa Mall Mullarkey Associate Professor of Computer Science
Wellsley College

"The ...

Archaic introgression and natural selection: Patterns of variation at the immune genes OAS1 and STAT2

Tuesday, January 08, 2013 10:00am - 11:00am
SWIG Boardroom CIT 241
Fernando Mendez (University of Arizona) - Tuesday, January 8th - 10:00 - 11:00 am - SWIG Boardroom CIT 241
Archaic ...

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

Tuesday, August 07, 2012 1:00pm - 1:00pm
SWIG Boardroom (CIT 241)
Dr. Alexander Schönhuth
Scienctific Staff Member 
Life Sciences Group, Centrum Wiskunde & Informatica
Amsterdam
Ancestry-aware variant calling and genotyping in the 'Genome of the Netherlands'
The ...

Selection Strength Defines the Robustness and Evolvability of Beta-lactamase

Tuesday, August 07, 2012 1:00pm - 1:00pm
SWIG Boardroom (CIT 241)
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 ...

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

Tuesday, August 07, 2012 1:00pm - 1:00pm
SWIG Boardroom (CIT 241)
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 ...

Evolutionary accessibility and genetic architecture

Tuesday, May 29, 2012 4:00pm - 4:00pm
SWIG Boardroom (CIT 241)
Joachim Krug
Professor, Institute for Theoretical Physics
University of Cologne
"Evolutionary accessibility and genetic architecture"
The adaptive dynamics of a population in the space of genotypes is constrained by epistatic ...

Identifying driver missense mutations in tumor sequencing data with CHASM

Tuesday, May 15, 2012 11:00am - 11:00am
CIT 345
Hannah Carter
Graduate Student - Karchin Lab
Institute for Computational Medicine
Johns Hopkins University
"Identifying driver missense mutations in tumor sequencing data with CHASM"
Large-scale sequencing of cancer genomes ...

Nonclassical Mathematical Tools for Conceptualizing Epistasis

Thursday, April 26, 2012 4:00pm - 4:00pm
SWIG Boardroom
Robert Heckendorn
Associate Professor, Computer Science Department & College of Engineering
University of Idaho
Nonclassical Mathematical Tools for Conceptualizing Epistasis

BEACON, A Center for the Study of Evolution ...

Maintaining Genome Stability: Role of the Fanconi Anemia Pathway

Wednesday, April 25, 2012 4:00pm - 4:00pm
SWIG Boardroom (CIT 241)
Niall Howlett
Assistant Professor, College of the Environment & Life Sciences
University of Rhode Island
Maintaining Genome Stability: Role of the Fanconi Anemia Pathway

The primary research focus of the Howlett laboratory ...

Hybrid Assembly of Bacterial Genomes

Wednesday, April 18, 2012 4:00pm - 4:00pm
SWIG Boardroom (CIT 241)
Ali Bashir
Assistant Professor, Genetics & Genomic Sciences
Mount Sinai School of Medicine 

"Hybrid Assembly of Bacterial Genomes"
Next-generation sequencing technologies have dramatically improved our ability ...

Algorithmic Methods for Structural Variation Detection

Friday, April 13, 2012 2:00pm - 2:00pm
SWIG Boardroom (CIT 241)
Iman Hajirasouliha
CCMB Postdoctoral Seminar
PhD Candidate at Simon Fraser University
Lab for Computational Biology, School of Computing Science
 
"Algorithmic Methods for Structural Variation Detection"

Novel genomic methods for mutation discovery in disorders of cognitive development

Wednesday, April 11, 2012 4:00pm - 4:00pm
SWIG Boardroom (CIT 241)
Eric Morrow
Assistant Professor in Biology and Psychiatry & Human Behavior
Brown University 

"Novel genomic methods for mutation discovery in disorders of cognitive development"

Next-generation sequencing of structural variation in germline and somatic genomes

Wednesday, April 04, 2012 4:00pm - 4:00pm
SWIG Boardroom (CIT 241)
Ira Hall
Assistant Professor, Biochemistry & Molecular Sciences
University of Virginia School of Medicine

"Next-generation sequencing of structural variation in germline and somatic genomes"

Statistical approaches for studying human genetic variation in diverse populations

Wednesday, March 21, 2012 4:00pm - 4:00pm
SWIG Boardroom (CIT 241)
Chaolong Wang
PhD Candidate in Bioinformatics
University of Michigan, Ann Arbor

"Statistical approaches for studying human genetic variation in diverse populations"

The spatial pattern of human genetic variation ...

De-Novo Discovery of Differentially Abundant DNA Binding Sites Including Their Positional Preference

Monday, March 19, 2012 4:00pm - 4:00pm
SWIG Boardroom (CIT 241)
Ivo Grosse
Professor, Institut für Informatik, Martin-Luther-Universität
De-Novo Discovery of Differentially Abundant DNA Binding Sites Including Their Positional Preference

The identification of DNA binding sites ...

Pandemic Influenza Bioinformatics

Wednesday, March 14, 2012 4:00pm - 4:00pm
SWIG Boardroom (CIT 241)
Joel Weltman
Clinical Professor Emeritus of Medicine
Brown University
Pandemic Influenza Bioinformatics

Epidemic influenza is a significant threat to public  health. Because of this threat, thousands of influenza ...

Optimization Algorithms for the Design of Immunotolerant Biotherapies

Wednesday, February 29, 2012 4:00pm - 4:00pm
SWIG Boardroom (CIT 241)
Chris Bailey-Kellogg
Associate Professor
Department of Computer Science
Dartmouth College
"Optimization Algorithms for the Design of Immunotolerant Biotherapies"
The explosive growth of biotherapeutic agents is revolutionizing ...

Graphical Models for Gene Networks and Their Use in Classification

Wednesday, February 22, 2012 4:00pm - 4:00pm
SWIG Boardroom (CIT 241)
Xi Luo
Assistant Professor of Biostatistics
Brown University
"Graphical Models for Gene Networks and Their Use in Classification"

Graphical models use network graphs to represent the statistical dependence structures of ...