Past Seminar Series

October 13, 2006 Chris Bailey-Kellogg Dartmouth University homepage Embedding Computation in Studies of Protein Structure and Function
October 20, 2006 Russell Schwartz Carnegie Mellon homepage Near-perfect Phylogeny Construction from Genetic Variation Data
November 3, 2006 Lillian Chong University of Pittsburgh homepage Exploring protein recognition events using theory and simulation
Nov 10, 2006 @ MI Nathan Urban Carnegie Mellon homepage Noise-induced neuronal synchronization
Nov 17, 2006 @ BST3 Carlos J. Camacho University of Pittsburgh homepage The molecular regulation of the action potential and refractoriness by the Shaker K+ channel: Rated R for XXXtructures (no cartoons)
Dec 1, 2006 @ BST3 Ronald Wetzel University of Pittsburgh Protein aggregation – challenges to our understanding of protein structure and behavior
Jan 5, 2007 @ BST3 Serafim Batzoglou Stanford University homepage Models and algorithms for genomic sequences, proteins and networks of protein interactions
Jan 19, 2007 @ MI Andy Walsh Carnegie Mellon homepage Visualization and Exploration of Large Multiple Sequence Alignments
February 2, 2006 @ BST3 Ziv Bar-Joseph Carnegie Mellon homepage Data integration for understanding dynamic biological systems
February 9, 2007 @ MI Tao Jiang University of California, Riverside homepage A High-Throughput Combinatorial Approach to Genome-Wide Ortholog Assignment
February 23, 2007 @ BST3 Arijit Chakravarty Millenium Pharmaceuticals How much got there and what did it do: computational and mathematical techniques in Oncology drug discovery
March 2, 2007 @ BST3 Gregory Voth University of Utah homepage The Multiscale Challenge for Biomolecular Systems: A Systematic Approach
March 16, 2007 @ BST3 Elodie Ghedin University of Pittsburgh homepage Whole-Genome Analyses and Evolutionary Dynamics of Influenza A
March 30, 2007 @ BST3 Ivan Maly University of Pittsburgh homepage How T-Killer Cells Deliver the Kiss of Death: A Quantitative Systems Perspective
April 13, 2007 @ MI Jing Li Case Western Reserve University homepage Multi-Stage Design and Multi-Stage Analysis of Genome-Wide Association Studies
April 20, 2007 @ MI Ron Dror D.E. Shaw Research homepage Scalable Algorithms for Fast Molecular Dynamics Simulations
April 27, 2007 @ MI David J. States University of Michigan homepage Integrating Genomics and Proteomics: Novel Translation Products Identified by Mass Spectrometry
May 4, 2007 @ BST3 Joel Bader Johns Hopkins University homepage Exploratory Data Analysis for Biological Networks
Date/Location Speaker Affiliation homepage Title of Talk Host
Aug. 31, 2007 @ BST3 Nir Friedman Hebrew University homepage Natural history and evolutionary principles of gene duplication in fungi Naftali Kaminski
Sep. 7, 2007 @ MI Shlomo Ta’asan Carnegie Mellon University homepage Mathematical modeling approaches for systems biology
Sep. 17, 2007 @ MI Pratul K. Agarwal Oak Ridge National Laboratory homepage Enzymes: an integrated view of structure, dynamics and function Maria Kurnikova
Sep. 21, 2007 @ BST3 James Faeder University of Pittsburgh Rule-based modeling of signal-transduction systems
Sep. 28, 2007 @ BST3 Adrian Elcock University of Iowa homepage Molecular simulations of bacterial cytoplasm Lillian Chong
Oct. 5, 2007 @ MI Dmitri Chklovskii HHMI – Janelia Farms homepage High-throughput reconstruction of brain circuits: How machine vision will revolutionize neuroscience Justin Crowley
Oct. 12, 2007 @ MI Ming Li University of Waterloo homepage Modern homology search Chris Langmead
Oct. 19, 2007 @ MI Bud Mishra New York University homepage SMASH: Single Molecule Approach to Sequencing by Hybridization Chris Langmead
Oct. 26, 2007 @ MI Uwe Ohler Duke University homepage Motifs and patterns: Using sequence and image data to understand gene regulation in eukaryotes Eric Xing
Nov. 2, 2007 @ MI Olga Troyanskaya Princeton University homepage Combining genomic data, computation, and experiments to discover novel biology Eric Xing
Nov. 9, 2007 @ MI Jeffrey Skolnick Georgia Institute of Technology homepage Prediction of protein structure and function on a proteomic scale Chris Langmead
Nov. 16, 2007 @ BST3 Gary An Northwestern University homepage Dynamic Knowledge Representation using Agent Based Modeling: A Multi-scale Modeling Architecture for Acute Inflammation Yoram Vodovotz
Nov. 30, 2007 @ MI Tom Mitchell Carnegie Mellon University homepage Brains, Meaning and Corpus Statistics
Dec. 7, 2007 Gregory Voth University of Utah homepage The Multiscale Challenge for Biomolecular Systems: A Systematic Approach Hagai Meirovitch
Jan. 18, 2008 @ MI Nancy Zhang Stanford University homepage A multisample change-point model for DNA copy number analysis Eric Xing
Jan. 25, 2008 @ MI Olga Troyanskaya Princeton University homepage Combining genomic data, computation, and experiments to discover novel biology Eric Xing
Feb. 1, 2008 @ Mauldin Auditorium (NSH 1305) Ivet Bahar University of Pittsburgh homepage Supramolecular Machinery: Insights from Elastic Network Models
Feb. 8, 2008 @ BST3 Harmen Bussemaker Columbia University homepage Data-driven biophysical modeling of (post-)transcriptional networks James Faeder
Feb. 15, 2008 @ BST3 Bruce Tidor Massachusets Inst. of Technology homepage Electrostatics in ligand binding and design Carlos Camacho
Feb. 22, 2008 @ BST3 Takis Benos University of Pittsburgh homepage What can evolution say about gene regulation? From DNA signals to gene networks
Feb. 29, 2008 @ BST3 Thomas E. Cheatham, III University of Utah homepage Promise and peril in the simulation of nucleic acids and protein structure, dynamics and interactions Carlos Camacho
Mar. 7, 2008 @ MI Sridhar Hannenhalli University of Pennsylvania homepage Computational analysis of eukaryotic transcriptional regulation and its evolution Russell Schwartz
Mar. 21, 2008 @ MI Mark Gerstein Yale University homepage Human Genome Annotation Eric Xing
Mar. 28, 2008 @ BST3 Marcelo Magnasco Rockefeller University homepage Sparse time-frequency representations and the neural coding of sound. Bino John
Apr. 4, 2008 @ BST3 Marti Head GlaxoSmithKline Structure-Based Design at GSK Lillian Chong
May 13, 2008 @ MI Trey Ideker University of California, San Diego homepage Mapping gene regulatory pathways by assembly of physical and genetic interactions Ziv Bar-Joseph
Date Speaker
Sep. 5, 2008 Host: Russell Schwartz Saul Kravitz | J. Craig Venter Institute | Environmental Metagenomics Background, Results, and Tools
Oct. 10, 2008 Host: Bino John Xiaole Shirley Liu | Harvard University | ChIPing the Human Cistrome
Oct. 24, 2008 Host: Carlos Camacho Guy Salama | University of Pittsburgh | Sex, Calcium and Cardiac Arrhythmias
Nov. 7, 2008 Host: Carlos Camacho Jie Liang | Univ. of Illinois at Chicago | Computational Characterization of Structure, Function, and Dynamics of Proteins
Nov. 14, 2008 Host: Carlos Camacho Julio Fernandez | Columbia University | Force-clamp spectroscopy of single proteins
Nov. 21, 2008 Host: Ivet Bahar Jeffry Madura | Duquesne University | Biomolecular Simulations
Dec. 5, 2008 Host: Ziv Bar-Joseph Fritz Roth | Harvard University | Systematic analysis of genetic interactions in yeast
Jan. 23, 2009 Host: CPCB Students Steven Altschuler | U. T. Southwestern |  Interpreting cellular heterogeneity
Feb. 6, 2009 Su-In Lee | Carnegie Mellon UniversityIndividual Genetic Variation and Gene Regulation: From Networks to Mechanisms
Feb. 13, 2009 Host: Chris Langmead Carl Kingsford| University of Maryland, College Park | Protein Annotation Prediction By Clustering Within Interaction Networks
Feb. 20, 2009 Host: Lillian Chong Anthony Nicholls, | OpenEye Scientific Software | Polarization. Obvious to Faraday, yet intractable in force fields?
Feb. 27, 2009 Ge Yang, | Carnegie Mellon University | Computational analysis of axonal transport based on large-scale genetic screen and model-driven computer vision
Mar. 20, 2009 Host: Russell Schwartz Alejandro Schaeffer, | NCBI | Database Indexing and Masking to Improve the Speed and Result Quality of Production MegaBLAST Searches of the Human and Mouse Genomes
Apr. 3, 2009 Host: CPCB Students David Odde, | University of Minnesota | Self-organization of the mitotic spindle: Integrated modeling and microscopy studies
May 28, 2009 Host: Christopher Langmead Francois Fages, | INRIA-Paris-Rocquencourt | A computational method based on temporal logic for parameter search and robustness analysis of biological models
Date Speaker
Sep. 25, 2009 Host: Robert F. Murphy Emma Lundberg |Royal Inst. of Technology, Stockholm| A Human Protein Atlas
Oct. 9, 2009 Host: Russell Schwartz Bhaskar DasGupta | University of Illinois at Chicago | Synthesizing and simplifying biological networks from pathway level information
Oct. 23, 2009 Host: Chris Langmead David Baker | University of Washington |From Prediction of Structure to Design of Function
Oct. 30, 2009 Host: Chris Langmead Naren Ramakrishnan | Virginia Tech | How do I remember thee? Let me count the ways.
Nov. 6, 2009 Host: Bino John Peter Park | Children’s Hospital Boston | ChIP-sequencing: data analysis and applications
Nov. 13, 2009 Host: James Faeder Shirley Luckhart | University of California, Davis | The potential for application of systems biology to modeling malaria parasite-host interactions
Nov. 20, 2009 Host: James Faeder Gregoire Altan-Bonnett | Memorial Sloan-Kettering Cancer Center | System Imunobiology: how integrated cytokine regulation enforces self/non-self discrimination in the immune system
Dec. 4, 2009 Host: Takis Benos Eddie Holmes | Penn State University | Life on the Edge: The Evolutionary Biology of RNA Viruses
Dec. 11, 2009 Host: James Faeder Tomasz Lipniacki | Inst. of Fundamental Tech. Research, Warsaw, Poland | Spatial Gradients in Kinase Cascade Regulation
Jan. 29, 2010 Host:Eric Xing Quaid Morris | University of Toronto | Predicting the targets of mRNA-binding proteins
Feb. 12, 2010 Host: Chris Langmead Tandy Warnow | University of Texas, Austin | Simultaneous Alignment and Phylogeneic Tree Estimation
Feb. 19, 2010 Host: CPCB Students Daniel Erlanson | Carmot Therapeutics, Inc. |  Starting small, dreaming big: fragment-based drug discovery
Feb. 26, 2010 Host: Bino John Andrey Rzhetsky | University of Chicago | Mining texts and experiments to understand human disease
Mar. 5, 2010 Host: Lillian Chong David Case | Rutgers University | Simulating biomolecules with implicit solvent models
Mar. 19, 2010 Host: Dan Zuckerman Rohit Pappu | Washington University in St. Louis | Conformational equilibria of archetypal intrinsically disordered proteins
Mar. 26, 2010 Host: Chris Langmead Nancy Amato | Texas A&M University |  Using Motion Planning to Study Molecular Motions
Apr. 2, 2010 Host: Eric Xing Mona Singh | Princeton University | Predicting and analyzing cellular networks
Apr. 23, 2010 Host: Bino John Michael Q. Zhang | Cold Spring Harbor Laboratory | Defining the regulatory network of the tissue-specific splicing factors Fox-1 and Fox-2
Apr. 30, 2010 Host: Bino John Martha Bulyk | Harvard Medical School |  Transcription factor-DNA interactions: cis regulatory codes in genomes
Date/Location Speaker
Sep. 10, 2010 Carlos Camacho | University of Pittsburgh | Drug Discovery in the 21st Century: Novel compounds and high hit rates in real time
Sep. 17, 2010 Host: Carlos Camacho Ruth Nussinov | National Institutes of HealthAllostery and conformational control of ubiquitination in the cullin-RING E3 ligase machinery
Oct. 1, 2010 Host: Takis Benos Yiannis Kaznessis | University of Minnesota | Mathematical Models in Synthetic Biology
Oct. 8, 2010 Host: Carlos Camacho Jeff Gray | Johns Hopkins University | Fundamentals and applications of protein structure prediction
Oct. 22, 2010 Host: Chris Langmead Michael Gilson | University of California, San Diego | Modeling molecular recognition: Free energy, entropy and mechanical stress
Oct. 29, 2010 Host: Takis Benos Billy Day | University of Pittsburgh | Discovery, design, synthesis and biological evaluation of new microtubule stabilizers
Nov. 5, 2010 Hosts: Carlos Camacho and Zoltan Oltvai Olaf G. Weist | University of Notre Dame |  Computational chemistry as a data integrator in epigenetics
Dec. 3, 2010 Host: Robert F. Murphy Klaus Palme | University of Freiburg, Germany | The magic role of auxin and beyond
Jan. 14, 2011 Kris Dahl | Carnegie Mellon University | Computational approaches to determine multiscale structural changes in the nucleus associated with aging
Jan. 21, 2011 Host: Robert F. Murphy Russell Malmberg | University of Georgia | Computational Searches for Non-Coding RNA; Ecological Genetics of Pitcher Plants
Feb. 4, 2011 Host: Chris Langmead Jinbo Xu | Toyota Technological Institute at Chicago | Probabilistic Graphical Model for Protein Structure Prediction
Feb. 11, 2011 Host: Bino John Gary Bader | University of Toronto | Predicting protein-protein interactions from the genome for evolutionary analysis
Feb. 18, 2011 Host: James Faeder David J. Klinke | West Virginia University |  A Bayesian Perspective on Understanding How Cells Make Decisions
Feb. 25, 2011 Host: Robert F. Murphy Richard H. Lathrop | University of California, Irvine | Predicting Positive p53 Cancer Rescue Regions Using Most Informative Positive (MIP) Active Learning
Mar. 4, 2011 Host: James Faeder Jorg Langowski | German Cancer Research Center | Coarse-grained modeling of the nucleosome and chromatin fiber
Mar. 18, 2011 Host: Takis Benos Timothy Hughes | University of Toronto | Exploring the protein-nucleic acid interactome
Mar. 25, 2011 Host: Dan Zuckerman Teresa Head-Gordon | University of California, Berkeley | From Monomer Structure to Polymorphism: Computational and Experimental Studies of the Alzheimer’s Aβ Peptide
Apr. 1, 2011 Host: Takis Benos Christina Leslie | Memorial Sloan-Kettering Cancer Center | Modeling microRNA-mediated regulation and dysregulation of gene expression in cancer
Apr. 8, 2011 Host: Ziv Bar-Joseph Tamer Kahveci | University of Florida | Computational strategies for understanding how biological networks function.
Apr. 22, 2011 Host: Kathryn Roeder Li-San Wang | University of Pennsylvania | Gene expression in aging and aging-associated disorders
May 5, 2011 Ioannis Tsamardinos | Vanderbilt University | Towards Integrative Causal Analysis of Heterogeneous Datasets and Prior Knowledge
Date/Location Speaker
Sep. 9, 2011 Host: Dan Zuckerman Wei Yang | Florida State University | Orthogonal Space Sampling of Long TimeScale Biomolecular Processes
Sep. 16, 2011 Host: Bino John Frank Alber | University of Southern California | Exploring the higher order genome organization
Oct. 7, 2011 Host: Maria Kurnikova Wendy Cornell | Merck | Comparison of 2D, 3D, and QSAR Methods for Virtual Screening
Oct. 14, 2011 Daphne Koller | Stanford University | Learning richly structured representations from weakly annotated data
Nov. 11, 2011 Host: Jim Faeder Jayajit Das | Battelle Center for Mathematical Medicine | From Models to Mechanisms: Understanding cell signaling responses
Dec. 2, 2011 Host: James Faeder Steve Andrews | Fred Hutchinson Cancer Research CenterModeling cell biology with spatial and stochastic detail
Jan. 27, 2012 Host: Eric Xing Ernest Fraenkel | Massachusetts Institute of Technology | Integrating ‘Omic’ Data to Reveal Disease Mechanisms
Feb. 3, 2012 Host: Bino John Adrian Lee | University of Pittsburgh | Genomic and Proteomic Systems Biology in Breast Cancer
Feb. 17, 2012 Host: Lillian Chong Donald Hamelberg | Georgia State University | Enzyme conformational dynamics in catalysis
Feb. 24, 2012 Host: Ziv Bar-Joseph Kevin White | University of Chicago | Integrating Genomic Networks to Identify Biomarkers and Drug Targets
Mar. 2, 2012 Host: Maria Kurnikova Meera Sitharam | University of FloridaEASAL: Entropy computation for Assembly Configuration spaces via Stratified Convex Parametrizations
Mar. 23, 2012 Host: Dan Zuckerman Teresa Head-Gordon | University of California, Berkeley | From Monomer Structure to Polymorphism: Computational and Experimental Studies of the Alzheimer’s Aβ Peptide
Mar. 30, 2012 Host: Robert F. Murphy Jing Li | Case Western Reserve University |  Rare variant discovery and calling by sequencing pooled samples with overlaps
Apr. 13, 2012 Host: James Faeder Laurence Loewe | University of Wisconsin | Evolutionary Systems Biology
Apr. 27, 2012 Host: Bino John Michael McManus | University of California, San FranciscoMammalian small RNA Pathways
Date Speaker
Sep. 21, 2012 Host: Ziv Bar-Joseph Carl Kingsford | Carnegie Mellon UniversityComputational Challenges Comprehending Chromosome Conformation Capture Constraints
Sep. 28, 2012 Host: Russell Schwartz Curtis Huttenhower | Harvard University | Bug bytes: bioinformatics for meta’omics and microbial community analysis
Oct. 12, 2012 Host: Pei Tang Huan-Xiang Zhou | Florida State University | Simulation and Modeling of Ion Channel Functional Mechanisms and Transport
Oct.26, 2012 Host: Robert F. Murphy Eric Schadt | Mount Sinai Hospital | Moving towards a better understanding of human disease in the era of big data
Nov. 2, 2012 Host: James Faeder Matthew J. Lazzara | University of Pennsylvania | Analysis of Time Scales in EGF Receptor Signaling Dynamics
Nov. 9, 2012 Host: Nathan Clark David Pollock | University of Colorado | Adaptation, coevolution, and convergence in the context of protein thermodynamics
Nov. 16, 2012 Host: Bino John Tomas Babak | Stanford University | Global mapping of allele-specific expression as a tool for understanding epigenetics
Nov. 30, 2012 Host: Ziv Bar-Joseph Joel McManus | Carnegie Mellon University | Evolution of post-transcriptional gene regulatory networks
Dec. 7, 2012 Host: Sean Xie Jianpeng Ma | Baylor College of Medicine
Feb 1, 2013 Host: Joel McManus Luisa Hiller | Carnegie Mellon University | Genomic Plasticity: To Be or Not to Be
Feb 8, 2013 Host: Takis Benos Dennis Kostka | University of Pittsburgh |  Finding and characterizing genomic regions with signatures of accelerated evolution
Mar. 1, 2013 Host: Joel McManus Zia Kahn | University of ChicagoQuantitative Proteomics Provides a New Window into How Genetic Differences Impact Protein-Levels Between Species
Mar. 8, 2013 Host: Carlos Camacho Ranajeet Ghose | City College of New York | Regulation of Protein Tyrosine Kinase Signaling in Bacteria
Mar. 22, 2013 Host: R. Ravi Vineet Bafna | University of California, San DiegoThe breakage fusion bridge and other exotic structural variations: combinatorics and cancer genomics
Mar. 29, 2013 Host: Joel McManus Christine Vogel | New York University | The Ups and Downs of Human Protein Expression Regulation
Apr. 5, 2013 Host: Daniel Zuckerman Alan M. Grossfield | University of Rochester Medical Center | Multiscale modeling of GPCRs
Apr. 12, 2013 Host: Nathan Clark Josh Akey | University of Washington | Interpreting comprehensive catalogs of genetic variation in humans and yeast
Apr. 26, 2013 Takis Benos | University of PittsburghThe Importance of Being microRNA: From disease markers and gene network regulators to therapeutic agents
Date Speaker
Aug. 30, 2013 Host: Ziv Bar-Joseph Pierre Baldi | University of California, Irvine | Deep Learning: Theory, Algorithms, and Biological Applications
Sep. 6, 2013 Hanna Salman | University of Pittsburgh | Mechanisms of bacterial migration in temperature gradients
Sep. 13, 2013 Carlos Camacho | University of Pittsburgh | Modeling the assembly and disassembly of multi-domain structures of alpha-actinin-4 explains how external cues regulate actin binding
Sep. 20, 2013 Host: James Faeder Eric Deeds | University of Kansas | The evolution of crosstalk in signaling networks
Sep. 27, 2013 Host: Indira Shrivastava Judith LaLonde | Bryn Mawr College | Antagonism of HIV-1 Entry: Targeting Hotspots at the CD4-gp120 Protein-Protein Interface
Oct. 4, 2013 Host: Robert F. Murphy Wing Wong | Stanford University | Characterization of hESC transcriptome by hybrid sequencing
Oct. 11, 2013 Host: Seyoung Kim Matthew Stephens | University of Chicago | Assessing association between genetic variants and multiple phenotypes
Oct. 25, 2013 Host: Nathan Clark Antony M. Dean | University of Minnesota | Evolution of Catalytic Mechanisms
Nov. 8, 2013 Ziv Bar-Joseph | Carnegie Mellon University | Reconstructing dynamic regulatory networks in development and disease
Nov. 15, 2013 Kathryn Roeder | Carnegie Mellon Universtiy | Statistics and Genetics Open a Window into Autism
Nov. 22, 2013 Host: Elodie Ghedin Raul Rabadan | Columbia University | The Topology of Evolution
Dec. 6, 2013 Host: Hanna Salman Ido Golding | Baylor College of Medicine | Quantitative Adventures in Gene Regulation
Jan. 24, 2014 Host: Dennis Kostka Kaspar Hansen | Johns Hopkins University | Statistical analysis of epigenomewide data
Jan. 31, 2014 Host: Karen Thickman Arijit Chakravarty | Takeda Pharmaceuticals | An evolving view of cancer: how mathematical modeling helps effective drug development in the face of tumor evolution
Feb. 7, 2014 Host: Veronica Hinman Julia Zeitlinger | Stowers Institute for Medical Research | Genome-wide approaches to understand gene regulation during development
Feb. 21, 2014 Ge Yang | Carnegie Mellon University | Image-based computational analysis of regulatory mechanisms of axonal transport
Feb. 28, 2014 Host: Dan Zuckerman Ilya Shmulevich | Institute for Systems Biology | Integrative Analysis and Interactive Exploration of Data from The Cancer Genome Atlas
Mar. 21, 2014 Host: Seyoung Kim Su-In Lee | University of Washington | Learning network features reveals novel biomarkers for survival, chemosensitivity and surgical resectability phenotypes in cancer
Mar. 28, 2014 Host: Carlos Camacho Nathan A. Baker | Pacific Northwest National Laboratory | Geometric flow for biomolecular solvation
Apr. 18, 2014 Host: Russell Schwartz Hector Corrada Bravo | University of Maryland | Exploring tumor epigenetic heterogeneity by cell-specific methylation pattern reconstruction
Apr. 25, 2014 Host: Dan Zuckerman David H. Matthews | University of Rochester Medical Center | RNA Molecular Mechanics: Estimating Free Energy Changes Facilitates Comparison with Experiments
Date Speaker
Sep. 9, 2014 Jing Xia | Washington University in St. Louis | An integrated approach to identification of small noncoding RNAs and their regulatory networks in human diseases
Sep. 12, 2014 Host: Nathan Clark Andrew VanDemark | University of Pittsburgh, Biological Sciences | The molecular basis of Paf1C chromatin recruitment
Sep. 9, 2014 Robin E. C. Lee | University of Pittsburgh, Computational and Systems Biology | Leveraging cell-to-cell variability to understand TNF-induced signal transduction circuits
Sep. 26, 2014 Laxmi Parida | IBM T.J. Watson Research Center | Population Genomics under the lens of Random-Graphs
Oct. 3, 2014 Host: Dan Zuckerman Lucy Forrest | NIH-NINDS | How repetition helps: computational studies of pseudo-symmetrical membrane proteins
Oct. 10, 2014 Host: Joel McManus Jennifer Gallagher | West Virginia University | Harnessing the genetic diversity of yeast to uncover mechanisms of adaptation
Oct. 24, 2014 Alain Laederach | University of North Carolina at Chapel Hill | What your riboSNitches may say about you
Oct. 31, 2014 Host: Kathryn Roeder Hongzhe Li |Microbiome, Metagenomics and High-Dimensional Compositional Data Analysis
Nov. 7, 2014 Host: Joel McManus Byron Yu | Carnegie Mellon University, Electrical & Computer Engineering / Biomedical Engineering | Dimensionality reduction for large-scale neural recordings
Nov. 11, 2014 Host: James Faeder Michael Rust | University of Chicago | Input Processing by a Three-Protein Circadian Clock
Nov. 21, 2014 Host: Joel McManus Junhyong Kim | University of Pennsylvania | Single Cell Variation and Cellular Phenotype
Jan. 16, 2015 Da Yang | University of Pittsburgh | Characterizing the genetic and epigenetic landscapes of miRNAs in cancer
Jan. 23, 2015 Host: Carl Kingsford Steven Salzberg | Johns Hopkins University | Transcriptome Assembly: Computational Challenges of Next-Generation Sequence Data
Jan. 1, 2015 Host: Luisa Hiller Herve Tettelin | University of Maryland | Comparative and functional genomics of Mycobacterium massiliense serial clinical isolates
Feb. 6, 2015 Jon P. Boyle | University of Pittsburgh | Moving up and down the ladder: does locus expansion and diversification define species-specific phenotypes in the Apicomplexa? Toxoplasma gondii as a working example
Feb. 13, 2015  Host: Maria Chikina Haiyuan Yu | Cornell University | Understanding molecular mechanisms of human disease mutations through 3D protein networks​
Feb. 27, 2015 Host: Ivet Bahar Remo Rohs | University of Southern California, Molecular and Computational Biology | Quantitative modeling of transcription factor binding specificities using DNA shape
Mar. 27, 2015 Host: Nathan Clark Ryan Gutenkunst | University of Arizona | Inferring natural selection on and within protein networks by coupling network- and population-scale models with genomic data
Apr. 3, 2015 Host: Robert F. Murphy Michael Miller | Bayesian Deformable Templates in Computational Anatomy: Application for Neurodegenerative Diseases and BrainClouds
Apr. 10, 2015 Host: Jianhua Xing Binhua Zhou | University of Kentucky | Epithelial-mesenchymal Transition in Breast Cancer Progression and Metastasis
Apr. 24, 2015 Host: Takis Benos Mehmet Koyuturk | Case Western Reserve University | Network and pathway-based analyses are commonly used as powerful tools to interpret genotype-phenotype associations in a functional context
Date Speaker Host
September 11, 2015 Da-Wei Li, Ph.D. Ohio State University David Koes, Ph.D. Pitt
September 18, 2015 : CANCELED (to be rescheduled) Yong Wan, Ph.D. University of Pittsburgh School of Medicine Ivet Bahar, Ph.D. Pitt
September 25, 2015 6014 BST3 David Klinke, Ph.D. West Virginia University Tim Lezon, Ph.D. Pitt
October 2, 2015 S120 BST Dr. Jason Shoemaker, Ph.D. University of Pittsburgh Pitt
October 9, 2015 6014 BST3 Carlos Lopez, Ph.D. Vanderbilt University James Faeder, Ph.D. Pitt
October 16, 2015 6014 BST3 Vaughn Cooper, Ph.D. University of Pittsburgh  Pitt
October 30, 2015 GHC 6115 Ben Raphael, Ph.D. Brown University  Russell Schwartz, Ph.D. CMU
November 6, 2015 S120 BST KC Huang, Ph.D. Stanford University Hanna Salman, Ph.D. Pitt
November 13, 2015 GHC 6115 Gaudenz Danuser, Ph.D. UT Southwestern Ge Yang, Ph.D. CMU
November 20, 2015 6014 BST3 Roy Wollman, Ph.D. University of California – San Diego Robin E. C. Lee, Ph.D. Pitt
December 4. 2015
December 11, 2015 NSH 3305 Sui Huang, MD, Ph.D. Institute for Systems Biology Philip LeDuc, Ph.D. CMU
January 15, 2016 6014 BST3 Natasa Miskov-Zivanov, Ph.D. University of Pittsburgh, Electrical and Computer Engineering Jim Faeder, Ph.D. Pitt
January 22, 2016 William Hlavacek, Ph.D. Los Alamos National Labratory Jim Faeder, Ph.D. Pitt
January 29, 2016 GHC 6115 Arvind Ramanathan, Ph.D. Oak Ridge National Laboratory CMU
February 5, 2016 6014 BST3 Jan Liphardt, Ph.D. Stanford University Jianhua Xing, Ph.D. Pitt
February 12, 2016 Nancy J. Nersessian Research Associate Harvard University Department of PsychologyRegents’ Professor of Cognitive Science (Emerita) Georgia Institute of Technology  Jim Faeder, Ph.D. Pitt
February 19, 2016 6014 BST3
February 26, 2016 3305 NSH Jennifer Listgarten, Ph.D. Microsoft Research Seyoung Kim, Ph.D. CMU
March 18, 2016 GHC 4307  Jian Ma, Ph.D. Carnegie Mellon University CMU
March 25, 2016 GHC 4307 Andreas Pfenning, Ph.D. Carnegie Mellon University CMU
April 1, 2016 GHC 4405 Tim Hughes, Ph.D. University of Toronto  C. Joel McManus, Ph.D. CMU
April 8, 2016 Oleg Igoshin, Ph.D. Rice University Jianhua Xing, Ph.D. Pitt
April 22, 2016 Jonathan Pritchard, Ph.D. Stanford University Student Nominated Host: AJ Sedgewick Pitt
Date Speaker Host Title
September 9, 2016 NSH 3305 Dr. Min Xu Carnegie Mellon University CMU  “Molecular resolution structural pattern mining inside single cells”
September 16, 2016 6115 GHC Dr. Tandy Warnow University of Illinois, Urbana-Champaign Dr. Russell Schwartz CMU “Grand Challenges in Phylogenomics”
September 23, 2016 6014 BST3 Dr. Miler Lee Biological Sciences, Pitt Dr. Nathan Clark Pitt “Eggs, embryos, and pluripotency: gene regulation during early development”
September 30, 2016 6014 BST3 Dr. Sara Mostafavi University of British Columbia Dr. Maria Chikina Pitt “Inferring molecular and cellular networks to understand complex traits”
October 7, 2016 6014 BST3 Dr. Jian Liu NIH, National Heart, Lung, and Blood Inst. Dr. Jianhua Xing Pitt “Spatial-temporal regulation of mitotic spindle assembly checkpoint”
October 14, 2016 6014 BST3 Dr. Olexandr Isayev University of North Carolina at Chapel Hill Dr. David Koes Pitt “Accurate prediction of protein kinase inhibitors with deep convolutional neural networks”
October 28, 2016 6115 GHC Dr. Jasmine Zhou University of Southern California Dr. Jian Ma CMU  “Make Big Data Useful: Horizontal and Vertical Integration of Genomics Data”
November 4, 2016 6115 GHC Dr. Wei Chen University of Pittsburgh Dr. Jian Ma CMU  “Statistical Issues in Genome-Wide Association Studies of AMD Progression”
November 11, 2016 6014 BST3 Dr. Stacey Finley University of Southern California Dr. Jim Faeder Pitt  “Predicting cancer signaling dynamics using computational systems biology”
November 18, 2016 6115 GHC  Dr. Su-In Lee University of Washington Dr. Jian Ma CMU  “From Big Data to Precision Oncology using Machine Learning”
December 2, 2016 6014 BST3 Dr. Joanna Kelley Washington State University Dr. Nathan Clark Pitt “Genomics in extreme environments: gene regulation and the evolution of hydrogen sulfide loving fish”
December 9, 2016 6014 BST3 Dr. Bin Zhang MIT Dr. Ivet Bahar / Dr. Jianhua Xing Pitt  “Towards Predictive Modeling of Three Dimensional Genome Organization”
January 20, 2017
February 3, 2017 6014 BST3 Dr. Zachary Freyberg University of Pittsburgh Dr. Ivet Bahar Pitt “Opening a new window into the secretory cell with in situ cryo imaging”
February 10, 2017
February 17, 2017 6014 BST3 Dr. Ross Curtis Pitt
February 24, 2017 6014 BST3 Dr. Nikolay Dokholyan UNC – Chapel Hill Dr. Carlos Camacho Pitt “Control of cellular networks by structural disorder”
March 3, 2017 GHC 6115 Dr. Gene Yeo University of California, San Diego Dr. Joel McManus CMU “Insights into RNA processing from large-scale protein-RNA interactions”
March 24, 2017 GHC 4405 Dr. George Tseng University of Pittsburgh Dr. Jian Ma CMU  “Omics data integration for disease subtype discovery and marker detection”
March 31, 2017 GHC 6115 Dr. Cenk Sahinalp Indiana University Dr. Russell Schwartz CMU  “Algorithms for Precision Genomics with Scalability, Security and Privacy Constraints”
April 7, 2017 6014 BST3 Dr. Hannah Carter UC San Diego Dr. Anne-Ruxandra Carvunis Pitt “Interaction Landscape of Inherited Polymorphisms with Somatic Events in Cancer”
April 14, 2017 6014 BST3 Dr. Anne-Ruxandra Carvunis University of Pittsburgh Pitt
April 21, 2017 6014 BST3 Dr. Ingo Greger MRC Lab. of Molecular Biology Dr. Ivet Bahar Pitt