Past Seminars


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

DateSpeakerInstitutionHost Presentation Title
9/10Sheng ZhongUCSD, Jacobs School of EngineeringScarlett ZouRainbow-seq: combining cell lineage tracking with single-cell RNA sequencing in preimplantation embryos.
9/17Anne West

Duke University, Dept of Neurobiology-Cancelled

Paul Magwene“Measuring, manipulating, and modeling chromatin regulation of neuronal gene expression”
9/24Ting LuUniversity of Illinois at Urbana-Champaign, Dept of BioengineeringLingchong You Bottom-up Assembly of Microbial Communities: Modeling, Analysis and Engineering
10/1Saurabh SinhaUniversity of Illinois at Urbana-Champaign, Dept of Computer ScienceYuning ZhangStatistical and biophysics-inspired methods for exploring gene regulatory mechanisms
10/8No SeminarFall Break 2018
10/15Michael GreenbergWashington University, Depts of Biochemistry and Molecular BiophysicsDebraj GhoseUnderstanding Familial Cardiomyopathies from the Ground Up
10/22Mike LoveUNC-Chapel Hill, Dept of GeneticsGreg WrayAdaptive priors for estimating effect sizes with sequence count data
10/29Amy GoldbergDuke University, Dept of Evolutionary AnthropologyJenny TungMechanistic models of recent admixture histories
11/5Pablo IglesiasJohn Hopkins University, Dept of Electrical & Computer EngineeringKyle MoranControlling the set point of coupled excitable systems: relations to wave propagation and morphology of protrusions in migrating cells
11/12Cavin Ward-CavinessEPA/CBB AlumniDebraj GhoseEnvironmental ‘Omics: exploring the molecular mediators and modifiers of environmental exposures.
11/19Alberto BartesaghiDuke University, Depts of Computer Science & BiochemistryPaul MagweneExpanding the structural biology toolbox with high-resolution cryo-electron microscopy.
11/26Craig LoweDuke University, Dept of Molecular Genetics & MicrobiologyPaul MagweneFinding copy number variants relevant to vertebrate evolution and human disease
12/3Dennis WrightUniversity of Connecticut, Dept of Pharmaceutical SciencesBruce Donald“Targeting Drug Resistant Pathogens”
12/10Anne WestDuke University, Dept of Neurobiology-Cancelled Due to WeatherPaul Magwene“Measuring, manipulating, and modeling chromatin regulation of neuronal gene expression”


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

1/8Winter Break - No Seminar
1/15MLK Day No Seminar
1/22Michael BrentWashington UniversityAmy SchmidTranscription Factor Networks: We know much less than we think we do. But help is on the way!
2/12Scott McIsaacCalico LabsPaul Magwene"Mitotic Aging"
2/19Rahul KulkarniU Mass-BostonJosh SocolarFluctuations and rare events in stochastic models of gene expression
2/26Anthony FodorUNC-CharlotteLawrence David"Reproducibility and Effect Size in Studies of the Host Associated Microbiome".
3/5Neville SanjanaNew York Genome CenterSayan MukherjeeNew frontiers in functional genomics using high-throughput genome engineering
3/12Spring Break - No Seminar
3/19Ziv Bar-JosephCarnegie Mellon UniversityLawrence David"Reconstructing developmental regulatory networks from scRNA-Seq data"
3/26Scott SchmidlerDuke University

Bayesian Analysis of Shapes and Cur  ves: Applications to Protein Evolution and Microbial Phenonomics

4/2Peter DevreotesJohns Hopkins UniversityDebraj GhoseExcitable networks in directed cell migration
4/9Ken DillStony Brook UniversityTerry OasCell growth and evolution depends on proteome physical chemistry.

Fall 2017 SCHEDULE

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

9/11Town Hall MeetingPaul MagweneFor CBB Students Only
9/18Paul MedvedevPenn State UniversityAlex HarteminkAssembly of Big Genomic Data
10/2Benoit RouxUniversity of ChicagoPatrick Charbonneau Molecular Dynamics Studies of P-type ATPase Ion Pumps
10/9Fall Break
10/16Angela DePaceHarvard Medical SchoolStefano Di Talia Precision and Plasticity in Animal Transcription
10/23Hilmar LappDuke University/GCBPaul Magwene Towards computational science with phenotype descriptions: From large-scale candidate gene discovery to reproducible data synthesis for morphological trait evolution
10/30Alan BoyleUniversity of MichiganKyle Moran "Identifying Negative Regulatory Elements"
11/6Tim ElstonUNCDebraj GhoseCompetition, coexistence, and bistability in polarity establishment
11/13Srini TuragaHoward Hughes Medical InstituteGraham HoltFrom biological neural networks to artificial neural networks
12/4David OrlandoSyros PharmaceuticalsKyle Moran Translating transcriptional inhibition into new therapies
12/18Winter Break

Spring 2017 Schedule

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

DateSpeakerInstitutionTitle of Presentation
1/16No SeminarMLK
1/23Tomas GedeonMontana State UniversityDynamics of gene regulatory networks with unknown parameters
1/30Amy SchmidDuke University“Calm under stress: how regulatory networks control cellular decision-making in archaeal extremophiles.”
2/13Geoffrey GinsburgDuke UniversityNovel genomic paradigms for early detection and diagnosis of acute infectious disease
2/20Vanni BucciUniversity of Massachusetts DartmouthMathematical microbiomics: facilitating the discovery and the optimization of microbiome-based therapies
2/27Kris WoodDuke University

Controlling the evolution of tumors treated with targeted therapies

3/6Charles GersbachDuke University

Genome and Epigenome Editing for Gene Therapy and Cell Programming

3/13No SeminarSpring Break
3/20Diana FuscoUC Berkeley "Evolution at the expanding frontier".
3/27Katie PollardUniversity of California San FranciscoMost transcription factors recognize DNA shape
4/3Martha BulykHarvard Medical School“Variation and evolution in transcription factor-DNA interactions”
4/10Angela DePace-CancelledHarvard Medical SchoolPrecision and plasticity in animal transcription


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

DateSpeakerInstitutionTitle of Presentation
9/19Gevorg GrigoryanDartmouthReverse Engineering Nature towards Programing Protein Molecules
9/26Hana El-SamadUniversity of California, San Francisco”Anticipators and Procrastinators, Synthetic Biology and Big Data”
10/3Richard BertramFlorida StateInteraction of Metabolic, Electrical, and Calcium Signaling Pathways in the Production of Rhythmic Insulin Secretion
10/24Alexander HarteminkDuke University

Efficiently surveying the chromatin landscape

10/31Anshul KundajeStanford UniversityInterpretable, integrative deep learning models for regulatory genomics and epigenomics
11/7Chris RaoUniversity of IllinoisDNA sensing in bacteria
11/14James FerrellStanford UniversityTrigger Waves in Apoptosis
11/21Raluca GordanDuke UniversitySibling rivalry in transcription factor families
11/28Adam PhilippyNIH/NHGRISingle-Molecule Sequencing: Finished Genomes and Mobile DNA Sensors
12/5Shirley LiuHarvard UniversityComputational biology in CRISPR screens and cancer immunology
12/12Arjun RajUniversity of PennsylvaniaSingle cell analysis of therapy resistance in cancer


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

DateSpeakerInstitutionTitle of Presentation
1/25Stephen LisbergerDuke University, Dept of NeurobiologyComputational and experimental analysis of neural codes in the functioning brain
2/1Andreas PfenningCarnegie Mellon University & CBB AlumniGenomic insights into the immune basis of Alzheimer’s disease and aging
2/8Jichun XieDuke University, Dept of Biostatistics and BioinformaticsMultiple Testing of General Dependence by Quantile-Based Contingency Tables with an Application in Elucidating Gene Regulatory Network
2/15Geoff GinsburgDuke University, Center for Applied Genomics & Precision Medicine.  Cancelled due to weatherNovel Genomic Paradigms for Early Detection of Acute and Chronic Disease
2/22Corina TarnitaPrinceton University, Dept of Ecology & Evolutionary BiologyLack of ecological and life history information can lead to the illusion of social success in Dictyostelium discoideum
2/29Massimo VergassolaUCSD, Dept of PhysicsSymmetry and adaptation in the touch response of C. elegans
3/7Sean EddyHHMI Janelia Farms“Sequence homology searches: the future of deciphering the past”
3/21Sri KosuriUCLA, Dept of Chemistry & BiochemistrySynthetic Approaches to Understanding Sequence-Function Relationships
3/28Jason LocasaleDuke University, Dept of Pharmacology & Cancer BiologyAn integrative analysis of metabolism in health and cancer
4/4Xiling ShenDuke University, Dept of Biomedical EngineeringSpatiotemporal Control of Cancer and Stem Cells
4/11Todd WassonLawrence Livermore & CBB Alumni"Modeling heterogeneous data at scale: applications in sepsis prediction"
4/18Martha BulykHarvard Medical School, Depts of Medicine & Pathology  (Cancelled)Reschedule date coming for Fall 2016


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

DateSpeakerInstitutionTitle of Presentation
9/14Tandy WarnowUniversity of Illinois, Depts of Computer Science & BioengineeringNew methods for estimating species trees from genome-scale data
9/21Lawrence CarinDuke University, Dept of Electrical and Computer EngineeringDeep Poisson Learning with Application to Analyzing the Medical Record
9/28Deepak VooraDuke University, Dept of Medicine-CardiologyUsing aspirin as a probe: A new take on an old drug
10/5Edo KussellNYU, Dept of BiologyEvolution of Genomic Binding Landscapes by Global Selection
10/19Barak CohenWashington University St. Louis, Dept of GeneticsWhy don’t transcription factors get lost? Specificity of cis-regulation in large genomes
10/26Marc RyserDuke University, Dept of MathematicsTreat or wait? Model-based Risk Projections for Active Surveillance in Patients with Ductal Carcinoma in Situ
11/2Hana El-SamadUCSF, Depts of Biochemistry & Biophysics (Cancelled)Anticipators and Procrastinators:  Cellular Decision Making in Multivariate Environments
11/9Lucy BaPenn State, Depts of Biochemistry, Molecular BiologyRegulatory Mechanism and Functional Significance of Divergent Gene Pairs
11/16Kirill KorolevBoston University, Dept of PhysicsThe tug-of-war between deleterious and beneficial mutations in cancer
11/23Murat AcarYale University, Dept Of Molecular, Cellular & Developmental BiologyNetwork-dosage compensation and gene network evolution in the context of a canonical gene network
11/30Sayan MukherjeeDuke University, Dept of Statistical ScienceNonlinear mixed models for statistical genetics and pedigree analysis from low coverage sequencing data
12/7Greg FieldDuke University, Dept of NeurobiologyCircuitry and Computation in the Mammalian Retina
12/14Christina LeslieSloan Kettering, Computational BiologyDecoding epigenetic and transcriptional programs in cellular differentiation


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

DateSpeakerInstitutionTitle of Presentation
1/12Jason BelskyCBB PhD Student, David MacAlpine GroupGenome-wide chromatin footprinting reveals dynamics of replication origin chromatin architecture induced by pre-RC assembly
1/26Dan KnightsUniversity of Minnesota, Depts of Computer Science and Engineering and the Biotechnology InstituteHacking the Microbiome: Discovering Microbial Diagnostics and Therapeutics
2/2Rob DunnNorth Carolina State University, Dept of BiologyUsing 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
2/9Allison Ashley-KochDuke University, Center for Human Disease ModelingGenetic and Genomic Dissection of Chiari Malformation Type 1
2/16Samuel RamirezCBB PhD Student, Daniel Lew GroupModeling the spatiotemporal dynamics of Rho-GTPases activity at dendritic spines
2/23Hashim al-HashimiDuke University, Director of the Center for RNA Biology, Depts of Biochemistry and ChemistryThe Dynamic Nature of DNA and RNA Structure and its Fundamental Importance to Biology
3/2Martin PolzMIT, Dept of Civil and Environmental EngineeringDefining Bacterial Populations as Genetic, Ecological and Social Units
3/23Kevin LuoCBB PhD Student, Alex Hartemink GroupPredicting transcription factor occupancy using DNase digestion data - from binary to continuous perspective
3/23Jianling ZhongCBB PhD Student, Alex Hartemink GroupA genome-wide nucleosome map for Saccharomyces cerevisiae on DNase-seq data
3/30Li MaDuke University, Dept of Statistical ScienceEffective detection of cross-sample differences
4/6Dennis Frank-ItoDuke University, Dept of SurgeryInvestigating Physiological Responses in Ear, Nose and Throat Using Computational Fluid Dynamics Modeling
4/13Matt EatonCBB Alumni, Computational Biologist at Syros Pharmaceuticals and MITEpigenome-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

DateSpeakerInstitutionTitle of Presentation
9/8Jeff GoreMIT, Dept of PhysicsCooperation, cheating, and collapse in microbial populations
9/15Stefano Di TaliaDuke University, Dept of Cell BiologyControl of cell division and cell differentiation during embryonic development
9/22Mike HauserDuke University, Molecular Physiology Institute, Depts of Medicine, MGM, and B&BQuantitative methods for analysis of genetic susceptibility to glaucoma
10/6John ChoderaMemorial Sloan Kettering Cancer CenterRedesigning Drug Design
10/20Steven SalzbergJohns Hopkins University School of Medicine, Director, Center for Computational BiologyTranscriptome Assembly: Computational Challenges of Next-Generation Sequence Data
10/27Katherine HellerDuke University, Dept of Statistical ScienceBayesian Machine Learning Methods for Epidemiology, Cognition and Neuroscience
11/3Chaitanya AcharyaCBB PhD Student, Andrew Allen GroupJoint analysis of genotype and tissue-specific variability using a novel score test to map eQTL
11/10Rustom AntiaEmory University, Dept of BiologyA population biological view of immunological memory and vaccination
11/17Remo RohsUSC, Dept of Molecular and Computational BiologyQuantitative modeling of transcription factor binding specificities using DNA shape
11/24Andrea MoffittCBB PhD Student, Sandeep Dave GroupIntegrating Transcriptomic, Genomic and Epigenomic Information to Characterize Signatures of Lymphomas
12/1Zach SchollCBB PhD Student, Piotr Marszalek and Weito Yang GroupsExploring multi-domain protein unfolding and refolding using single-molecule experiments and simulations