Past Seminars

Fall 2020

Time: 12 - 1pm
Place: Zoom

Date Speaker Institution Host Presentation Title
9/14 Manuel Rivas Stanford University Alejandro Ochoa "Generating effective therapeutic hypotheses from human genetic data"
9/21 David Page Duke University Scott Schmidler Computational Methods for Genotype-Phenotype Associations from Electronic Health Records
9/28 Possu Huang Stanford Niven Singh Protein Design in the Deep Learning Era
10/5 Nuria Lopez-Bigas IRB Barcelona Raluca Gordan Computational analysis of Cancer Genomes
10/12 Su-In Lee University of Washington Miko Liu Explainable Artificial Intelligence for Biology and Health
10/19 Stacey Finley USC- Viterbi Rachel Kositsky Predicting the effects of engineering immune cells using system biology models
10/26 James Lloyd Smith UCLA Amy Goldberg "From SARS to COVID-19 and beyond: unpacking the drivers of emerging viral zoonoses"
11/2 Gurol M. Suel UC San Diego Lingchong You "The role of inorganic ions in bacterial resilience"
11/9 Bill Majoros Duke University TBD Probabilistic Graphical Models for Genetic and Genomic Data
11/16 Olivier Elemento Weill Cornell Miko Liu Towards AI driven precision medicine

SPRING 2020

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

Date Speaker Institution Host Presentation Title
1/27 Zhirong Bao Sloan Kettering Institute Stefano Di Talia Systematic Single-Cell Analysis of Development:  Worm and Beyong
2/10 Stephanie Palmer University of Chicago Greg Field Canceled-Reschedule fall 2020
2/17 Rahul Satija New York Genome Center Greg Wray  Integrated analysis of single-cell data across modalities and technologies
2/24 Adam Cohen Harvard University Debraj Ghose  Synthetic electrophysiology
3/2 Gill Bejerano Stanford University Craig Lowe "Realizing Precision Medicine:  Automated Monogenic patient diagnosis and beyond"
3/16 No Seminar  
3/23 Ekta Khurana-Canceled Cornell Yuning Zhang Non-coding genetic variation
3/30 Ethan Garner-Canceled Harvard University Debraj Ghose

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