SPRING 2020
Time: 11:30am - 12:30pm
Place: 4233 French
Fall 2019
Date | Speaker | Institution | Host | Presentation Title |
9/9 | No seminar | |||
9/16 | Valerie Dagget | University of Washington | Melyssa Minto | Dynameomics: From Simulation of All Protein Folds to the Design of Amyloid Inhibitors and Diagnostics |
9/23 | Jeffrey Gray | Johns Hopkins University | Patrick Charbonneau | Prediction of Protein-Protein Complex Structures and Protein Crystal Design |
9/30 | Rafael Irizarry | Harvard University | Harshit Sahay | Statistical Approaches for Single Cell Technologies |
10/7 | No Seminar | |||
10/14 | David Gifford | MIT | Alex Hartemink | Machine Learning Based Therapeutic Design |
10/21 | Lorin Crawford | Brown University | Melyssa Minto | Deep Learning Methods for Fine Mapping and Discovery in Genomic Association Studies |
10/28 | Mona Singh | Princeton University | Alejandro Ochoa | Integrative Methods for deciphering disease networks |
11/4 | Jane Kondev | Brandeis University | Danny Lew | How Cells Measure Length |
11/11 | Haiyan Huang | University of California Berkeley | Jichun Xie | GeneFishing: a method to reconstruct context-specific portraits of biological processes and its application to cholesterol metabolism |
11/18 | Tony Capra | Vanderbilt University | Greg Wray | Diagnosing the Legacy of Neanderthal Interbreeding on Modern Humans |
11/25 | Christina Williams | Durham VA | Beth Hauser | TBA |
12/2 | TBA | |||
12/9 | Oleg Igoshin | Rice University | Lingchong You | Design principles of cellular differentiation control: Lessons from Bacillus subtilis |
SPRING 2019 SCHEDULE
Date | Speaker | Institution | Host | Presentation Title |
1/14 | Anne West | Duke University, Dept of Neurobiology | Paul Magwene | “Measuring, manipulating, and modeling chromatin regulation of neuronal gene expression” |
1/21 | No Seminar | MLK Holiday | ||
1/28 | Molly Prezworski | Columbia | Sayan Mukherjee | "An evolutionary perspective on meiotic recombination in vertebrates" |
2/4 | Alex Ochoa | Duke University, Dept of B&B | Tim Reddy | "Relatedness and differentiation in arbitrary population structures" |
2/11 | John Marioni | CRUK/EMBL | Jenny Tung | Using Single Cell Genomics to understand cell fate decisions in early mammalian development. |
2/18 | Zhiping Weng | U Mass Medical School | Harshit Sahay | An Atlas of polymerase III-transcribed Alu elements across human cell types and tissues |
2/25 | ||||
3/4 | Neeraj (Neil) Surana | Duke University, Dept of Pediatrics | Paul Magwene | “Determining causality within the microbiome: Finding the needle in the haystack” |
3/11 | No Seminar | Spring Break | ||
3/18 | Michael Beer | John Hopkins , Dept of Biomedical Engineering | Harshit Sahay | Using Machine Learning to Predict the Impact of Non-coding Genetic Variation and Enhancer-Promoter Interactions |
3/25 | Deborah Winter | Northwestern | Kyle Moran | “Modeling the Gene Regulatory Networks of Macrophages in Health and Disease” |
4/1 | Enrique De La Cruz | Yale | Danny Lew | How cells break the filament bones that power their movement |
4/8 | Xihong Lin | Harvard | Mengqi Zhang | Analysis of Massive Data from Genome, Exposome and Phenome: Challenges and Opportunities |
4/15 | Hongyu Zhao | Yale | Beth Hauser | “Dissecting Genetic Architecture of Complex Diseases From Genome Wide Association Studies” |
FALL 2018 SCHEDULE
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
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
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
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
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
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
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
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
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 |