Events Archive

Publishing for Impact

Wednesday, January 27, 2016 12:00pm - 1:00pm
Watson CIT - SWIG Boardroom (CIT241)

 

"Publishing for Impact"
(There will be a Q&A for postdocs and grad students following the seminar with refreshments provided) 

Inference of Population Size Trajectories from Genomic Data

Wednesday, December 09, 2015 4:00pm - 5:00pm
Watson CIT - SWIG Boardroom (CIT241)

 

Inference of Population Size Trajectories from Genomic Data

"Aneuploidy and Adaptation in Yeast"

Wednesday, November 18, 2015 4:00pm - 5:00pm
Watson CIT - SWIG Boardroom (CIT241)

 

"Aneuploidy and Adaptation in Yeast"

Using Graphical Models to Combine Exome and Gene Expression Increases the Power of Disease Mechanism Discovery

Wednesday, November 11, 2015 4:00pm - 5:00pm
Watson CIT - SWIG Boardroom (CIT241)

Identifying genes associated with complex human diseases is one of the main challenges of human genetics and computational medicine. To answer this question, millions of genetic variants get screened to identify a few of importance. To increase the power of identifying genes associated with diseases and to account for other potential sources of protein function aberrations, we propose a novel factor-graph based model, where much of the biological knowledge is incorporated through factors and priors.

Mitonuclear Variation and Hypoxia in Flies

Wednesday, November 04, 2015 4:00pm - 5:00pm
Watson CIT - SWIG Boardroom (CIT241)
Mitochondria are involved in almost all cellular processes due to their role in ATP production- providing the majority of the energy currency of cells. However, it is now apparent that mitochondria are important in sensing and mediating signaling pathways ...

Recent Advances in Data Management for Data Exploration

Wednesday, October 28, 2015 4:00pm - 5:00pm
Watson CIT - SWIG Boardroom (CIT241)

Tim Kraska
Assistant Professor, Computer Science

Andrew Crotty
Ph.D. student, Computer Science

"Recent Advances in Data Management for Data Exploration"

D.E. Shaw Research Information Session

Thursday, October 01, 2015 5:30pm - 7:30pm
Watson CIT - SWIG Boardroom (CIT241)
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 on molecular ...

Michael DeGiorgio - "Statistical Techniques for Identifying Adaptive Alleles with an Application to Human Evolution"

Wednesday, September 30, 2015 4:00pm - 5:00pm
Watson CIT - SWIG Boardroom (CIT241)

"Statistical Techniques for Identifying Adaptive Alleles with an Application to Human Evolution"

"Incorporating experimental data into the online protein-folding game Foldit"

Friday, May 15, 2015 12:00pm - 1:00pm
Sidney Frank Hall, Room 220 (Nathan Marcuvitz Auditorium)

CCMB & MPPB Department

Seminar Series 2014- 2015

PRESENT:

Dr. Firas Khatib

"Incorporating experimental data into the online protein-folding game Foldit"

Friday, May 15, 2015 Marcuvitz Auditorium, Sidney Frank Hall 220

Hosted by Nicolas Fawzi

 

Brown University 250th Anniversary Symposium: The Next 250 Years

Tuesday, May 12, 2015 12:00am - Thursday, May 14, 2015 12:00am
CIT, Room 368
Brown University 250th Anniversary Symposium: The Next 250 Years
May 12−15, 2015
14 John von Neumann Lectures on Economics, Physics, Computer Science, and Brain and
Neuroscience unified by John von Neumann’s vision of “Computation ...

Computational Biology Degree Day

Wednesday, April 29, 2015 5:00pm - 7:00pm
MacMillan Hall, Room 115

What do you do with a degree in Computational Biology? Join the Computational Biology Department Undergraduate Group to hear from alums about what they've done since Brown! Food will be served.

Andrew Beck - "Extensive rewiring of epithelial-stromal coexpression networks in breast cancer"

Wednesday, April 29, 2015 4:00pm - 5:00pm
Alpert Medical Building, Case Study Room 270

"Extensive rewiring of epithelial-stromal coexpression networks in breast cancer"

Sevinc Ercan - "Regulation of X Chromosome Chromatin Structure and Transcription in C. elegans."

Wednesday, April 22, 2015 4:00pm - 5:00pm
Watson CIT - SWIG Boardroom (CIT241)

"Regulation of X chromosome chromatin structure and transcription in C. elegans."

Su-In Lee - "Identifying network features reveals novel markers for clinical phenotypes in cancer."

Wednesday, April 01, 2015 4:00pm - 5:00pm
Watson CIT - SWIG Boardroom (CIT241)

"Identifying network features reveals novel markers for clinical phenotypes in cancer."

Toby Bloom - "Infrastructure for the Next Generation of Genomic Analysis"

Wednesday, March 18, 2015 4:00pm - 5:00pm
Watson CIT - SWIG Boardroom (CIT241)

"Infrastructure for the Next Generation of Genomic Analysis"

Massively parallel sequencing technologies now enable the generation of tens of terabytes of raw data per day, with, on average, 3 times that amount of processed data.  Earlier genomics infrastructure projects focused on handling such large volumes of data efficiently, and on performing vast amounts of processing with algorithms that are not embarrassingly parallel, and with combinations of data and genomes that required constant shuffling of data.

Neil Sarkar - "Imputing Knowledge from Biological and Health Data"

Tuesday, March 17, 2015 4:00pm - 5:00pm
Watson CIT - SWIG Boardroom (CIT241)

"Imputing Knowledge from Biological and Health Data"

Rameen Beroukhim - "The Genomic Landscape of Endometrial Cancer Progression"

Wednesday, March 11, 2015 4:00pm - 5:00pm
Watson CIT - SWIG Boardroom (CIT241)

"The Genomic Landscape of Endometrial Cancer Progression"

 

Most cancer deaths are due to metastatic disease, but most of our understanding of the cancer genome derives from primary tumors.  We have performed systematic analyses of genomic alterations to characterize patterns of tumor evolution in endometrial cancer from hyperplastic lesions to primary tumors and their paired metastases.  These indicate potential novel driver genes and indicate principles governing the spread of endometrial cancers past their primary site.
Hosted by Ben Raphael

Stefan Canzar

Wednesday, March 04, 2015 4:00pm - 5:00pm
Watson CIT - SWIG Boardroom (CIT241)

"Transcript Assembly with CIDANE: Scoring the Impossible"

CCMB Seminar - Sara Sheehan

Wednesday, February 18, 2015 4:00pm - 5:00pm
Watson CIT - SWIG Boardroom (CIT241)

February 18, 2015, 4:00 pm - Swig Boardroom - CIT 241

Sara Sheehan
Simons Institute for the Theory of Computing
University of California, Berkeley

Title & Abstract TBA

Hosted by Sohini Ramachandran

"Pathway Regulatory Evolution between Long-Diverged Species."

Wednesday, February 11, 2015 4:00pm - 5:00pm
Watson CIT - SWIG Boardroom (CIT241)

February 11, 2015, 4:00 pm - Swig Boardroom - CIT 241

Rachel Brem
Associate Professor
Buck Institute for Research on Aging

"Pathway Regulatory Evolution between Long-Diverged Species."

Hosted by Ben Raphael

Sequence Comparison in the Time of Deluge

Monday, November 17, 2014 4:00pm - 4:00pm
Swig Boardroom - CIT 241
Alberto Apostolico
Georgia Tech College of Computing
School of Computational Science & Engineering

The Genetic Architecture of Schizophrenia: Insights from a Population Isolate

Wednesday, November 12, 2014 4:00pm - 4:00pm
Swig Boardroom - CIT 241
Todd Lencz
Feinstein Institute for Medical Research and Albert Einstein College of Medicine

 

Hosted by Eric Morrow.

Nakka & McKerrow Research Presentations

Wednesday, November 05, 2014 4:00pm - 4:00pm
Swig Boardroom - CIT 241
Wilson McKerrow:

"Genomic dumpster diving: A probabilistic treatment of repetitive sequence"
Many next generation sequencing pipelines begin by aligning reads to a reference genome using bowtie, bwa or another ...

Ancestry in the Americas and its Impact on Medical Traits

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

 

Computational Modeling of the Metabolism and Evolution of Microorganisms

Wednesday, October 15, 2014 4:00pm - 4:00pm
Swig Boardroom - CIT 241
Ying Zhang
Assistant Professor, Cell and Molecular Biology
University of Rhode Island 
Microorganisms ...

Random Walk Distances in Data Clustering and Applications

Wednesday, October 01, 2014 4:00pm - 4:00pm
Swig Boardroom - CIT 241
Anastasios Matzavinos
Assistant Professor, Applied Mathematics
Brown University 
 Clustering data into groups of similarity is well recognized as an important step in many diverse applications, including biomedical ...

Pan-Cancer to Personalized Cellular Wiring Diagrams of Tumor Cells

Wednesday, September 24, 2014 4:00pm - 4:00pm
Swig Boardroom CIT 241
Josh Stuart
Professor, Biomolecular Engineering Department
University of California, Santa Cruz 
Although many genomic events that directly contribute to cancer onset and progression have been identified, much of the complex ...

Computational Epigenomics and Regulatory Genomics for Deciphering the Non-coding Human Genome

Thursday, July 17, 2014 11:00am - 11:00am
CIT 241 Swig Boardroom
Jason Ernst
Assistant Professor
Biological Chemistry, Computer Science, and Bioinformatics
UCLA
"Computational ...

Finding Active & Co-Active Subnetwork Modules

Wednesday, July 16, 2014 11:00am - 11:00am
CIT 241 Swig Boardroom
Mohammed El-Kebir
PhD student, Amsterdam Institute for Molecules, Medicines and Systems, Algorithmic Computational Biology Group.

"Finding Active & Co-Active Subnetwork Modules" 

CCMB Postdoctoral candidate Seminar

Monday, June 23, 2014 11:00am - 11:00am
SWIG Boardroom (CIT 241)
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 ...

Towards network level modeling of tumor heterogeneity

Wednesday, May 28, 2014 4:00pm - 4:00pm
Swig Boardroom - CIT 241
Teresa Przytycka
Senior Investigator, NCBI, NLM, NIH
Computational Biology Branch
"Towards ...

Quantitative modeling of transcription factor binding specificities using DNA shape

Tuesday, May 20, 2014 4:00pm - 4:00pm
Swig Boardroom - CIT 241
Remo Rohs
Assistant Professor of Biological Sciences, Chemistry, Physics & Astronomy, and Computer Science
University of Southern California
"Quantitative ...

CCMB Symposium - "Modern Genomic Approaches to Heritable Disease"

Monday, May 12, 2014 9:00am - 6:00pm
The Warren Alpert Medical School Building, Lecture Hall 170 - 1st Floor
At its most fundamental level the goal of genetics is to connect genotype to phenotype. Increasingly, this question is being asked in the clinic. Up until recently, hereditary diseases were analyzed by classical genetic methods. Remarkably, the modes ...

Towards a mechanistic understanding of cancer genome evolution

Wednesday, May 07, 2014 4:00pm - 4:00pm
Swig Boardroom - CIT 241
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 ...

Discovering somatic variation in cancer genomes using whole-genome sequencing

Wednesday, April 30, 2014 4:00pm - 4:00pm
Swig Boardroom - CIT 241
Peter Park
Associate Professor of Pediatrics
Center for Biomedical Informatics
Harvard Medical School
"Discovering ...

From ChIP-seq data to transcriptional regulation

Wednesday, April 16, 2014 4:00pm - 4:00pm
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

Decoding transcription regulation: from global maps to single-nucleotide resolution

Wednesday, April 09, 2014 4:00pm - 4:00pm
Swig Boardroom - CIT 241
Uwe Ohler
Associate Professor in Biostatistics & Bioinformatics
Duke University
"Decoding ...

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

Wednesday, April 02, 2014 4:00pm - 4:00pm
Swig Boardroom - CIT 241
Zheyang Wu
Assistant Professor of Mathematical Sciences
Worcester Polytechnic Institute
"The ...

Down the rabbit hole in support of Drosophila systems genetics

Thursday, March 20, 2014 4:00pm - 4:00pm
SWIG Boardroom (CIT 241)
Eric Stone
Associate Professor of Genetics
Bioinformatics Research Center
North Carolina State University
"Down ...

The Computational Challenges of Complex Genetic Architectures

Wednesday, March 12, 2014 4:00pm - 4:00pm
Swig Boardroom - CIT 241
Kathleen Askland
Assistant Professor of Psychiatry & Human Behavior
Brown University

"The ...

Algorithms for genome assembly and disease analytics

Wednesday, February 19, 2014 4:00pm - 4:00pm
Swig Boardroom - CIT 241
Michael Schatz
Assistant Professor 
Simons Center for Quantitative Biology
Cold Spring Harbor Laboratory
"Algorithms ...

Using a Bayesian Hierarchical Model to Assess Scientific Reproducibility

Wednesday, February 12, 2014 4:00pm - 4:00pm
Swig Boardroom - CIT 241
Lauren Alpert
Graduate Student in Applied Mathematics
Brown University
Using ...

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 ...