Academic Year 2014 Seminars

Wednesday, August 21, 2013
4:00 p.m. Swig Boardroom - CIT 241  

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


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

Hosted by Sorin Istrail

Wednesday, September 4, 2013
4:00 p.m. - Swig Boardroom - CIT 241


Casey DunnCasey Dunn

Casey Dunn
Manning Assistant Professor of Biology
Department of Ecology & Evolutionary Biology



Mark HowisonMark Howison

Mark Howison
Application Scientist
Brown University Center for Computation & Visualization


"Bayesian sequence assembly and assessment by Markov Chain Monte Carlo sampling"

Hosted by the CCMB

Wednesday, September 18, 2013
4:00 p.m. - Swig Boardroom  - CIT 241


Angela BrooksAngela BrooksAngela Brooks
Post Doctoral Associate - Broad Institute
Cambridge, MA 


"Somatic mutations that affect RNA splicing in human cancers"

Hosted by Ben Raphael

Wednesday, September 25, 2013
4:00 p.m. - Swig Boardroom - CIT 241


Brian AtheyBrian AtheyBrian 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”

Hosted by Ben Raphael & Ed Hawrot

Postodoctoral Interview Seminar:
Thursday, October 3, 2013
1:00 p.m. - Swig Boardroom - CIT 241 

Son PhamSon Pham

Son K. Pham
Department of Computer Science & Engineering
University of California San Diego

"De Bruijn Graphs in Genome Assembly and Comparison"

Hosted by Ben Raphael

Wednesday, October 23, 2013

4:00 p.m. - Swig Boardroom - CIT 241


Susan HuseSusan HuseSusan Huse
Assistant Professor of Pathology & Laboratory Medicine
Brown University, Bio Med Pathology & Laboratory Medicine

“Identifying the role of functional microbial clades in Ulcerative Colitis”

Hosted by David Rand

Wednesday, November 6, 2013
4:00 p.m. - Swig Boardroom - CIT 241


Suzannah Rutherford 
Affiliate, Division of Basic Sciences
Fred Hutchinson Cancer Research Center

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

Hosted by David Rand

Wednesday, November 13, 2013
4:00 p.m. - Swig Boardroom - CIT 241

Michael WiserMichael Wiser Mike Wiser - Ph.D. Candidate
Dr. Richard Lenski's Lab
Experimental Evolution
Michigan State University

"Analyzing Long Term Fitness Trajectories in Experimental Populations"

Hosted by Daniel Weinreich 


Postdoctoral Interview Seminar
Friday, November 15, 2013
12:00 p.m. - Swig Boardroom - CIT 241

Matthew ReynaMatthew Reyna Matthew Reyna
Department of Mathematical Sciences
Rensselaer  Polytechnic Institute

"High-order discontinuous Galerkin methods for solving partial differential equations"

Hosted by Ben Raphael

Wednesday, November 20, 2013
4:00 p.m. - Swig Boardroom - CIT 241

Tracy HeathTracy Heath Tracy Heath
Postdoctoral Researcher
Department of Integrative Biology
University of California Berkeley

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

Hosted by Casey Dunn 

Wednesday, December 11, 2013
4:00 p.m. - Swig Boardroom - CIT 241


Susan GerbiSusan GerbiSusan Gerbi
Professor of Biology
George Eggleston Professor of Biochemistry, Molecular Biology, Cell Biology, & Biochemistry
Brown University 

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


Hosted by David Rand 

Tuesday, January 21 

CCMB Seminars AY 14:

POSTPONED Due to Weather

Wednesday, January 22, 2014
4:00 - Swig Boardroom - CIT 241

Mona SinghMona SinghMona Singh
Professor of Computer Science
Lewis-Sigler Institute for Integrative Genomics
Dept of Computer Science, Princeton University

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

Hosted by Ben Raphael

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

Chris CotsapasChris CotsapasChris Cotsapas
Assistant Professor of Neurology and of  Genetics
Yale School of Medicine 


"Systematic approaches to uncover mechanisms underlying complex immune-mediated diseases"

Hosted by Ben Raphael

4:00 p.m. - Swig Boardroom - CIT 241

Yen-Tsung HuangYen-Tsung HuangYen-Tsung Huang
Assistant Professor of Epidemiology 
Brown University



“Integrative Modeling of Multi-platform Genomics Data for Cancer Survival”

 Hosted by Jean Wu

Wednesday, February 12, 2014
4:00 p.m. - Swig Boardroom - CIT 241 

Lauren AlpertLauren Alpert

Lauren Alpert
Graduate Student in Applied Mathematics
Brown University

Using A Bayesian Hierarchical Model to Assess Scientific Reproducibility

Hosted by Chip Lawrence


Wendesday, February 19, 2014
4:00 p.m. - Swig Boardroom - CIT 241

Mike SchatzMike SchatzMichael Schatz
Assistant Professor 
Simons Center for Quantitative Biology
Cold Spring Harbor Laboratory

"Algorithms for Genome Assembly and Disease Analytics"

Hosted by Ben Raphael

Wednesday, March 12, 2014
4:00 p.m. - Swig Boardroom - CIT 241

Kathleen AsklandKathleen Askland

Kathleen Askland
Assistant Professor of Psychiatry & Human Behavior
Brown University

"The Computational Challenges of Complex Genetic Architectures"

Hosted by Ben Raphael


Wednesday, April 2, 2014

4:00 p.m. - Swig Boardroom - CIT 241


Zheyang WuZheyang Wu

Zheyang Wu
Assistant Professor of Mathematical Sciences
Worcester Polytechnic Institute

"The Pattern of Genetic Effects and the Power of Genetic Association Studies"

Hosted by Jean Wu

Wednesday, April 9, 2014
4:00 p.m. - Swig Boardroom - CIT 241


Uwe OhlerUwe Ohler

 Uwe Ohler
Associate Professor in Biostatistics & Bioinformatics
Duke University

"Decoding Transcription Regulation:  From Global Maps to Single-Nucleotide Resolution"

Hosted by Will Fairbrother

Wednesday, April 16, 2014
4:00 p.m. - Swig Boardroom - CIT 241


Chao Cheng
Assistant Professor of Genetics
Geisel School of Medicine at Dartmouth University 

“From ChIP-seq data to transcriptional regulation”

Hosted by Jean Wu

Wednesday, April 30, 2014
4:00 p.m. - Swig Boardroom - CIT 241

Peter ParkPeter ParkPeter Park
Associate Professor of Pediatrics
Center for Biomedical Informatics
Harvard Medical School

"Discovering somatic variation in cancer genomes using whole-genome sequencing”

Hosted by Erica Larschan 


Wednesday, May 7, 2014
4:00 p.m. - Swig Boardroom - CIT 241

Franziska MichorFranziska Michor

Franziska Michor
 Associate Professor
Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute
Department of Biostatistics, Harvard School of Public Health

"Towards a mechanistic understanding of cancer genome evolution"

Hosted by MCB/CCMB

Tuesday, May 20, 2014
4:00 pm - Swig Boardroom - CIT 241

Remo RohsRemo RohsRemo Rohs
Assistant Professor of Biological Sciences, Chemistry, Physics & Astronomy, and Computer Science
University of Southern California

"Quantitative Modeling of Transcription Factor Binding Specificites Using DNA Shape"


Hosted by Erica Larschan 

Wednesday, May 28, 2014
4:00 pm - Swig Boardroom - CIT 241

Teresa PrzytyckaTeresa PrzytyckaTeresa Przytycka
Senior Investigator, NCBI, NLM, NIH
Computational Biology Branch

"Towards Network Level Modeling of Tumor Heterogeneity"

Hosted by Ben Raphael

Monday, June 23rd
11:00 am in the SWIG Boardroom (CIT 241)
CCMB Postdoctoral candidate Seminar


Yun-Ching Chen
Department of Biomedical Engineering, Institute for Computational Medicine
Johns Hopkins University

"Methods for Genome Interpretation: causal gene discovery and personal phenotype prediction".

His research areas are as follows:
Lab website is
My research includes two main projects. One is a likelihood ratio model for identifying disease-associated genes in sequence-based case-control studies ( The other is a probabilistic model for personal phenotype prediction. The paper is currently under review but we used this model to participated CAGI 2012-13 competition PGP challenge ( yielding the best prediction.

Here is the abstract of the second project:
Genetic screening is becoming possible on an unprecedented scale. However, its utility remains controversial. Although most variant genotypes cannot be easily interpreted, many individuals pursue interpreting their genetic information.  Initiatives such as the Personal Genome Project (PGP) and Illumina's Understand Your Genome are sequencing thousands of adults, collecting phenotypic information and developing computational pipelines to identify the most important variant genotypes harbored by each individual. These pipelines consider database and allele frequency annotations and bioinformatics classifications. We propose that the next step will be to integrate these different sources of information to estimate the probability that an individual has specific phenotypes of clinical interest.  To this end, we have designed a Bayesian probabilistic model to predict the probability of dichotomous phenotypes. When applied to a cohort from PGP, predictions of Gilbert syndrome, Graves' disease, non-Hodgkin lymphoma, and various blood groups were accurate, as individuals manifesting the phenotype in question exhibited the highest, or among the highest, predicted probabilities.  Thirty-eight PGP phenotypes (26%) were predicted with area-under-the-ROC curve (AUC) > 0.7, and 23 (15.8%) of these were statistically significant, based on permutation tests.  Moreover, in a Criticial Assessment of Genome Interpretation (CAGI) blinded prediction experiment, the models were used to match 77 PGP genomes to phenotypic profiles, generating the most accurate prediction of 16 submissions, according to an independent assessor.  While the models are currently not sufficiently accurate for diagnostic utility, we expect their performance to improve with growth of publicly available genomics data and model refinement by domain experts.