Past Seminars | Duke GCB

FALL 2018 SCHEDULE

Time: 11:30am - 12:30pm
Place: 4233 French

Date	Speaker	Institution	Host	Presentation Title
9/10	Sheng Zhong	UCSD, Jacobs School of Engineering	Scarlett Zou	Rainbow-seq: combining cell lineage tracking with single-cell RNA sequencing in preimplantation embryos.
9/17	Anne West	Duke University, Dept of Neurobiology-Cancelled	Paul Magwene	“Measuring, manipulating, and modeling chromatin regulation of neuronal gene expression”
9/24	Ting Lu	University of Illinois at Urbana-Champaign, Dept of Bioengineering	Lingchong You	Bottom-up Assembly of Microbial Communities: Modeling, Analysis and Engineering
10/1	Saurabh Sinha	University of Illinois at Urbana-Champaign, Dept of Computer Science	Yuning Zhang	Statistical and biophysics-inspired methods for exploring gene regulatory mechanisms
10/8	No Seminar	Fall Break 2018
10/15	Michael Greenberg	Washington University, Depts of Biochemistry and Molecular Biophysics	Debraj Ghose	Understanding Familial Cardiomyopathies from the Ground Up
10/22	Mike Love	UNC-Chapel Hill, Dept of Genetics	Greg Wray	Adaptive priors for estimating effect sizes with sequence count data
10/29	Amy Goldberg	Duke University, Dept of Evolutionary Anthropology	Jenny Tung	Mechanistic models of recent admixture histories
11/5	Pablo Iglesias	John Hopkins University, Dept of Electrical & Computer Engineering	Kyle Moran	Controlling the set point of coupled excitable systems: relations to wave propagation and morphology of protrusions in migrating cells
11/12	Cavin Ward-Caviness	EPA/CBB Alumni	Debraj Ghose	Environmental ‘Omics: exploring the molecular mediators and modifiers of environmental exposures.
11/19	Alberto Bartesaghi	Duke University, Depts of Computer Science & Biochemistry	Paul Magwene	Expanding the structural biology toolbox with high-resolution cryo-electron microscopy.
11/26	Craig Lowe	Duke University, Dept of Molecular Genetics & Microbiology	Paul Magwene	Finding copy number variants relevant to vertebrate evolution and human disease
12/3	Dennis Wright	University of Connecticut, Dept of Pharmaceutical Sciences	Bruce Donald	“Targeting Drug Resistant Pathogens”
12/10	Anne West	Duke University, Dept of Neurobiology-Cancelled Due to Weather	Paul Magwene	“Measuring, manipulating, and modeling chromatin regulation of neuronal gene expression”

SPRING 2018 SCHEDULE

Time: 11:30am - 12:30pm
Place: 4233 French

Date	Speaker	Institution	Host	Title
1/8	Winter Break - No Seminar
1/15	MLK Day No Seminar
1/22	Michael Brent	Washington University	Amy Schmid	Transcription Factor Networks: We know much less than we think we do. But help is on the way!
1/29
2/5
2/12	Scott McIsaac	Calico Labs	Paul Magwene	"Mitotic Aging"
2/19	Rahul Kulkarni	U Mass-Boston	Josh Socolar	Fluctuations and rare events in stochastic models of gene expression
2/26	Anthony Fodor	UNC-Charlotte	Lawrence David	"Reproducibility and Effect Size in Studies of the Host Associated Microbiome".
3/5	Neville Sanjana	New York Genome Center	Sayan Mukherjee	New frontiers in functional genomics using high-throughput genome engineering
3/12	Spring Break - No Seminar
3/19	Ziv Bar-Joseph	Carnegie Mellon University	Lawrence David	"Reconstructing developmental regulatory networks from scRNA-Seq data"
3/26	Scott Schmidler	Duke University		Bayesian Analysis of Shapes and Cur ves: Applications to Protein Evolution and Microbial Phenonomics
4/2	Peter Devreotes	Johns Hopkins University	Debraj Ghose	Excitable networks in directed cell migration
4/9	Ken Dill	Stony Brook University	Terry Oas	Cell growth and evolution depends on proteome physical chemistry.
4/16

Fall 2017 SCHEDULE

Time: 11:30am - 12:30pm
Place: 4233 French

Date	Speaker	Institution	Host	Title
9/4
9/11	Town Hall Meeting		Paul Magwene	For CBB Students Only
9/18	Paul Medvedev	Penn State University	Alex Hartemink	Assembly of Big Genomic Data
9/25
10/2	Benoit Roux	University of Chicago	Patrick Charbonneau	Molecular Dynamics Studies of P-type ATPase Ion Pumps
10/9	Fall Break
10/16	Angela DePace	Harvard Medical School	Stefano Di Talia	Precision and Plasticity in Animal Transcription
10/23	Hilmar Lapp	Duke University/GCB	Paul Magwene	Towards computational science with phenotype descriptions: From large-scale candidate gene discovery to reproducible data synthesis for morphological trait evolution
10/30	Alan Boyle	University of Michigan	Kyle Moran	"Identifying Negative Regulatory Elements"
11/6	Tim Elston	UNC	Debraj Ghose	Competition, coexistence, and bistability in polarity establishment
11/13	Srini Turaga	Howard Hughes Medical Institute	Graham Holt	From biological neural networks to artificial neural networks
11/20
11/27
12/4	David Orlando	Syros Pharmaceuticals	Kyle Moran	Translating transcriptional inhibition into new therapies
12/11
12/18	Winter Break

Spring 2017 Schedule

Time: 11:30am - 12:30pm
Place: 4233 French

Date	Speaker	Institution	Title of Presentation
1/16	No Seminar	MLK
1/23	Tomas Gedeon	Montana State University	Dynamics of gene regulatory networks with unknown parameters
1/30	Amy Schmid	Duke University	“Calm under stress: how regulatory networks control cellular decision-making in archaeal extremophiles.”
2/6
2/13	Geoffrey Ginsburg	Duke University	Novel genomic paradigms for early detection and diagnosis of acute infectious disease
2/20	Vanni Bucci	University of Massachusetts Dartmouth	Mathematical microbiomics: facilitating the discovery and the optimization of microbiome-based therapies
2/27	Kris Wood	Duke University	Controlling the evolution of tumors treated with targeted therapies
3/6	Charles Gersbach	Duke University	Genome and Epigenome Editing for Gene Therapy and Cell Programming
3/13	No Seminar	Spring Break
3/20	Diana Fusco	UC Berkeley	"Evolution at the expanding frontier".
3/27	Katie Pollard	University of California San Francisco	Most transcription factors recognize DNA shape
4/3	Martha Bulyk	Harvard Medical School	“Variation and evolution in transcription factor-DNA interactions”
4/10	Angela DePace-Cancelled	Harvard Medical School	Precision and plasticity in animal transcription

FALL 2016 SCHEDULE

Time: 11:30am - 12:30pm
Place: CBB Seminar will meet in Gross Hall Room 103 for the fall semester

Date	Speaker	Institution	Title of Presentation
9/19	Gevorg Grigoryan	Dartmouth	Reverse Engineering Nature towards Programing Protein Molecules
9/26	Hana El-Samad	University of California, San Francisco	”Anticipators and Procrastinators, Synthetic Biology and Big Data”
10/3	Richard Bertram	Florida State	Interaction of Metabolic, Electrical, and Calcium Signaling Pathways in the Production of Rhythmic Insulin Secretion
10/24	Alexander Hartemink	Duke University	Efficiently surveying the chromatin landscape
10/31	Anshul Kundaje	Stanford University	Interpretable, integrative deep learning models for regulatory genomics and epigenomics
11/7	Chris Rao	University of Illinois	DNA sensing in bacteria
11/14	James Ferrell	Stanford University	Trigger Waves in Apoptosis
11/21	Raluca Gordan	Duke University	Sibling rivalry in transcription factor families
11/28	Adam Philippy	NIH/NHGRI	Single-Molecule Sequencing: Finished Genomes and Mobile DNA Sensors
12/5	Shirley Liu	Harvard University	Computational biology in CRISPR screens and cancer immunology
12/12	Arjun Raj	University of Pennsylvania	Single cell analysis of therapy resistance in cancer

SPRING 2016 SCHEDULE

Time: 11:30am - 12:30pm
Place: 4233 French

Date	Speaker	Institution	Title of Presentation
1/25	Stephen Lisberger	Duke University, Dept of Neurobiology	Computational and experimental analysis of neural codes in the functioning brain
2/1	Andreas Pfenning	Carnegie Mellon University & CBB Alumni	Genomic insights into the immune basis of Alzheimer’s disease and aging
2/8	Jichun Xie	Duke University, Dept of Biostatistics and Bioinformatics	Multiple Testing of General Dependence by Quantile-Based Contingency Tables with an Application in Elucidating Gene Regulatory Network
2/15	Geoff Ginsburg	Duke University, Center for Applied Genomics & Precision Medicine. Cancelled due to weather	Novel Genomic Paradigms for Early Detection of Acute and Chronic Disease
2/22	Corina Tarnita	Princeton University, Dept of Ecology & Evolutionary Biology	Lack of ecological and life history information can lead to the illusion of social success in Dictyostelium discoideum
2/29	Massimo Vergassola	UCSD, Dept of Physics	Symmetry and adaptation in the touch response of C. elegans
3/7	Sean Eddy	HHMI Janelia Farms	“Sequence homology searches: the future of deciphering the past”
3/21	Sri Kosuri	UCLA, Dept of Chemistry & Biochemistry	Synthetic Approaches to Understanding Sequence-Function Relationships
3/28	Jason Locasale	Duke University, Dept of Pharmacology & Cancer Biology	An integrative analysis of metabolism in health and cancer
4/4	Xiling Shen	Duke University, Dept of Biomedical Engineering	Spatiotemporal Control of Cancer and Stem Cells
4/11	Todd Wasson	Lawrence Livermore & CBB Alumni	"Modeling heterogeneous data at scale: applications in sepsis prediction"
4/18	Martha Bulyk	Harvard Medical School, Depts of Medicine & Pathology (Cancelled)	Reschedule date coming for Fall 2016

FALL 2015 SCHEDULE

Time: 11:30am - 12:30pm
Place: 4233 French

Date	Speaker	Institution	Title of Presentation
9/14	Tandy Warnow	University of Illinois, Depts of Computer Science & Bioengineering	New methods for estimating species trees from genome-scale data
9/21	Lawrence Carin	Duke University, Dept of Electrical and Computer Engineering	Deep Poisson Learning with Application to Analyzing the Medical Record
9/28	Deepak Voora	Duke University, Dept of Medicine-Cardiology	Using aspirin as a probe: A new take on an old drug
10/5	Edo Kussell	NYU, Dept of Biology	Evolution of Genomic Binding Landscapes by Global Selection
10/19	Barak Cohen	Washington University St. Louis, Dept of Genetics	Why don’t transcription factors get lost? Specificity of cis-regulation in large genomes
10/26	Marc Ryser	Duke University, Dept of Mathematics	Treat or wait? Model-based Risk Projections for Active Surveillance in Patients with Ductal Carcinoma in Situ
11/2	Hana El-Samad	UCSF, Depts of Biochemistry & Biophysics (Cancelled)	Anticipators and Procrastinators: Cellular Decision Making in Multivariate Environments
11/9	Lucy Ba	Penn State, Depts of Biochemistry, Molecular Biology	Regulatory Mechanism and Functional Significance of Divergent Gene Pairs
11/16	Kirill Korolev	Boston University, Dept of Physics	The tug-of-war between deleterious and beneficial mutations in cancer
11/23	Murat Acar	Yale University, Dept Of Molecular, Cellular & Developmental Biology	Network-dosage compensation and gene network evolution in the context of a canonical gene network
11/30	Sayan Mukherjee	Duke University, Dept of Statistical Science	Nonlinear mixed models for statistical genetics and pedigree analysis from low coverage sequencing data
12/7	Greg Field	Duke University, Dept of Neurobiology	Circuitry and Computation in the Mammalian Retina
12/14	Christina Leslie	Sloan Kettering, Computational Biology	Decoding epigenetic and transcriptional programs in cellular differentiation

SPRING 2015 SCHEDULE

Time: 11:30am - 12:30pm
Place: 4233 French

Date	Speaker	Institution	Title of Presentation
1/12	Jason Belsky	CBB PhD Student, David MacAlpine Group	Genome-wide chromatin footprinting reveals dynamics of replication origin chromatin architecture induced by pre-RC assembly
1/26	Dan Knights	University of Minnesota, Depts of Computer Science and Engineering and the Biotechnology Institute	Hacking the Microbiome: Discovering Microbial Diagnostics and Therapeutics
2/2	Rob Dunn	North Carolina State University, Dept of Biology	Using samples of dust to characterize the lives of people in houses and the clouds of species - be the fungi, bacteria, polln or animals - around them
2/9	Allison Ashley-Koch	Duke University, Center for Human Disease Modeling	Genetic and Genomic Dissection of Chiari Malformation Type 1
2/16	Samuel Ramirez	CBB PhD Student, Daniel Lew Group	Modeling the spatiotemporal dynamics of Rho-GTPases activity at dendritic spines
2/23	Hashim al-Hashimi	Duke University, Director of the Center for RNA Biology, Depts of Biochemistry and Chemistry	The Dynamic Nature of DNA and RNA Structure and its Fundamental Importance to Biology
3/2	Martin Polz	MIT, Dept of Civil and Environmental Engineering	Defining Bacterial Populations as Genetic, Ecological and Social Units
3/23	Kevin Luo	CBB PhD Student, Alex Hartemink Group	Predicting transcription factor occupancy using DNase digestion data - from binary to continuous perspective
3/23	Jianling Zhong	CBB PhD Student, Alex Hartemink Group	A genome-wide nucleosome map for Saccharomyces cerevisiae on DNase-seq data
3/30	Li Ma	Duke University, Dept of Statistical Science	Effective detection of cross-sample differences
4/6	Dennis Frank-Ito	Duke University, Dept of Surgery	Investigating Physiological Responses in Ear, Nose and Throat Using Computational Fluid Dynamics Modeling
4/13	Matt Eaton	CBB Alumni, Computational Biologist at Syros Pharmaceuticals and MIT	Epigenome-guided investigation of human disease: case studies from Alzheimer's Disease, AML, and Breast Cancer

fall 2014 SCHEDULE

Time: 11:30am - 12:30pm
Place: 4233 French

Date	Speaker	Institution	Title of Presentation
9/8	Jeff Gore	MIT, Dept of Physics	Cooperation, cheating, and collapse in microbial populations
9/15	Stefano Di Talia	Duke University, Dept of Cell Biology	Control of cell division and cell differentiation during embryonic development
9/22	Mike Hauser	Duke University, Molecular Physiology Institute, Depts of Medicine, MGM, and B&B	Quantitative methods for analysis of genetic susceptibility to glaucoma
10/6	John Chodera	Memorial Sloan Kettering Cancer Center	Redesigning Drug Design
10/20	Steven Salzberg	Johns Hopkins University School of Medicine, Director, Center for Computational Biology	Transcriptome Assembly: Computational Challenges of Next-Generation Sequence Data
10/27	Katherine Heller	Duke University, Dept of Statistical Science	Bayesian Machine Learning Methods for Epidemiology, Cognition and Neuroscience
11/3	Chaitanya Acharya	CBB PhD Student, Andrew Allen Group	Joint analysis of genotype and tissue-specific variability using a novel score test to map eQTL
11/10	Rustom Antia	Emory University, Dept of Biology	A population biological view of immunological memory and vaccination
11/17	Remo Rohs	USC, Dept of Molecular and Computational Biology	Quantitative modeling of transcription factor binding specificities using DNA shape
11/24	Andrea Moffitt	CBB PhD Student, Sandeep Dave Group	Integrating Transcriptomic, Genomic and Epigenomic Information to Characterize Signatures of Lymphomas
12/1	Zach Scholl	CBB PhD Student, Piotr Marszalek and Weito Yang Groups	Exploring multi-domain protein unfolding and refolding using single-molecule experiments and simulations