Carnegie Mellon University

Past Seminars

October 13, 2006 Chris Bailey-Kellogg Dartmouth University Embedding Computation in Studies of Protein Structure and Function
October 20, 2006 Russell Schwartz Carnegie Mellon Near-perfect Phylogeny Construction from Genetic Variation Data
November 3, 2006 Lillian Chong University of Pittsburgh Exploring protein recognition events using theory and simulation
Nov 10, 2006 @ MI Nathan Urban Carnegie Mellon Noise-induced neuronal synchronization
Nov 17, 2006 @ BST3 Carlos J. Camacho University of Pittsburgh 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 Models and algorithms for genomic sequences, proteins and networks of protein interactions
Jan 19, 2007 @ MI Andy Walsh Carnegie Mellon Visualization and Exploration of Large Multiple Sequence Alignments
February 2, 2006 @ BST3 Ziv Bar-Joseph Carnegie Mellon Data integration for understanding dynamic biological systems
February 9, 2007 @ MI Tao Jiang University of California, Riverside 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 The Multiscale Challenge for Biomolecular Systems: A Systematic Approach
March 16, 2007 @ BST3 Elodie Ghedin University of Pittsburgh Whole-Genome Analyses and Evolutionary Dynamics of Influenza A
March 30, 2007 @ BST3 Ivan Maly University of Pittsburgh How T-Killer Cells Deliver the Kiss of Death: A Quantitative Systems Perspective
April 13, 2007 @ MI Jing Li Case Western Reserve University Multi-Stage Design and Multi-Stage Analysis of Genome-Wide Association Studies
April 20, 2007 @ MI Ron Dror D.E. Shaw Research Scalable Algorithms for Fast Molecular Dynamics Simulations
April 27, 2007 @ MI David J. States University of Michigan Integrating Genomics and Proteomics: Novel Translation Products Identified by Mass Spectrometry
May 4, 2007 @ BST3 Joel Bader Johns Hopkins University Exploratory Data Analysis for Biological Networks
Date/Location Speaker Affiliation Title of Talk Host
Aug. 31, 2007 @ BST3 Nir Friedman Hebrew University Natural history and evolutionary principles of gene duplication in fungi Naftali Kaminski
Sep. 7, 2007 @ MI Shlomo Ta’asan Carnegie Mellon University Mathematical modeling approaches for systems biology
Sep. 17, 2007 @ MI Pratul K. Agarwal Oak Ridge National Laboratory 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 Molecular simulations of bacterial cytoplasm Lillian Chong
Oct. 5, 2007 @ MI Dmitri Chklovskii HHMI – Janelia Farms High-throughput reconstruction of brain circuits: How machine vision will revolutionize neuroscience Justin Crowley
Oct. 12, 2007 @ MI Ming Li University of Waterloo Modern homology search Chris Langmead
Oct. 19, 2007 @ MI Bud Mishra New York University SMASH: Single Molecule Approach to Sequencing by Hybridization Chris Langmead
Oct. 26, 2007 @ MI Uwe Ohler Duke University Motifs and patterns: Using sequence and image data to understand gene regulation in eukaryotes Eric Xing
Nov. 2, 2007 @ MI Olga Troyanskaya Princeton University Combining genomic data, computation, and experiments to discover novel biology Eric Xing
Nov. 9, 2007 @ MI Jeffrey Skolnick Georgia Institute of Technology Prediction of protein structure and function on a proteomic scale Chris Langmead
Nov. 16, 2007 @ BST3 Gary An Northwestern University 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 Brains, Meaning and Corpus Statistics
Dec. 7, 2007 Gregory Voth University of Utah The Multiscale Challenge for Biomolecular Systems: A Systematic Approach Hagai Meirovitch
Jan. 18, 2008 @ MI Nancy Zhang Stanford University A multisample change-point model for DNA copy number analysis Eric Xing
Jan. 25, 2008 @ MI Olga Troyanskaya Princeton University Combining genomic data, computation, and experiments to discover novel biology Eric Xing
Feb. 1, 2008 @ Mauldin Auditorium (NSH 1305) Ivet Bahar University of Pittsburgh Supramolecular Machinery: Insights from Elastic Network Models
Feb. 8, 2008 @ BST3 Harmen Bussemaker Columbia University Data-driven biophysical modeling of (post-)transcriptional networks James Faeder
Feb. 15, 2008 @ BST3 Bruce Tidor Massachusets Inst. of Technology Electrostatics in ligand binding and design Carlos Camacho
Feb. 22, 2008 @ BST3 Takis Benos University of Pittsburgh What can evolution say about gene regulation? From DNA signals to gene networks
Feb. 29, 2008 @ BST3 Thomas E. Cheatham, III University of Utah 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 Computational analysis of eukaryotic transcriptional regulation and its evolution Russell Schwartz
Mar. 21, 2008 @ MI Mark Gerstein Yale University Human Genome Annotation Eric Xing
Mar. 28, 2008 @ BST3 Marcelo Magnasco Rockefeller University 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 Mapping gene regulatory pathways by assembly of physical and genetic interactions Ziv Bar-Joseph
Date/Location Speaker Affiliation Title of Talk Host
Sep. 5, 2008 Saul Kravitz J. Craig Venter Institute  Environmental Metagenomics Background, Results, and Tools Russell Schwartz
Oct. 10, 2008 Xiaole Shirley Liu Harvard University ChIPing the Human Cistrome Bino John
Oct. 24, 2008 Guy Salama University of Pittsburgh Sex, Calcium and Cardiac Arrhythmias Carlos Camacho
Nov. 7, 2008 Jie Liang Univ. of Illinois at Chicago Computational Characterization of Structure, Function, and Dynamics of Proteins Carlos Camacho
Nov. 14, 2008 Julio Fernandez Columbia University Force-clamp spectroscopy of single proteins Carlos Camacho
Nov. 21, 2008 Jeffry Madura Duquesne University Biomolecular Simulations Ivet Bahar
Dec. 5, 2008 Fritz Roth Harvard University Systematic analysis of genetic interactions in yeast Ziv Bar-Joseph
Jan. 23, 2009 Steven Altschuler U.T. Southwestern Interpreting cellular heterogeneity CPCB Students
Feb. 6, 2009 Su-In Lee Carnegie Mellon University Individual Genetic Variation and Gene Regulation: From Networks to Mechanisms
Feb. 13, 2009 Carl Kingsford University of Maryland, College Park Protein Annotation Prediction By Clustering Within Interaction Networks Chris Langmead
Feb. 20, 2009 Anthony Nicholls OpenEye Scientfic Software Polarization. Obvious to Faraday, yet intractable in force fields? Lillian Chong
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 Alejandro Schaeffer NCBI Database Indexing and Masking to Improve the Speed and Result Quality of Production MegaBLAST Searches of the Human and Mouse Genomes Russell Schwartz
Apr. 3, 2009 David Odde University of Minnesota Self-organization of the mitotic spindle: Integrated modeling and microscopy studies CPCB Students
May 28, 2009 Francois Fages INRIA-Paris-Rocquencourt A computational method based on temporal logic for parameter search and robustness analysis of biological models Chris Langmead
Date/Location Speaker Affiliation Title of Talk Host
Sep. 25, 2009 Emma Lundberg Royal Institute of Technology, Stockholm A Human Protein Atlas Robert F. Murphy
Oct. 9, 2009 Bhaskar DasGupta University of Illinois at Chicago Synthesizing and simplifying biological networks from pathway level information Russell Schwartz
Oct. 23, 2009 David Baker University of Washington From Prediction of Structure to Design of Function Chris Langmead
Oct. 30, 2009 Naren Ramakrishnan Virginia Tech How do I remember thee? Let me count the ways. Chris Langmead
Nov. 6, 2009 Peter Park Children's Hospital Boston ChIP-sequencing: data analysis and applications Bino John
Nov. 13, 2009 Shirley Luckhart University of California, Davis The potential for application of systems biology to modeling malaria parasite-host interactions James Faeder
Nov. 20, 2009 Gregoire Altan-Bonnet Memorial Sloan-Kettering Cancer Center System Imunobiology: how integrated cytokine regulation enforces self/non-self discrimination in the immune system James Faeder
Dec. 4, 2009 Eddie Homes Penn State University Life on the Edge: The Evolutionary Biology of RNA Viruses Takis Benos
Dec. 11, 2009 Tomasz Lipniacki Inst. of Fundamental Tech. Research, Warsaw, Poland  Spatial Gradients in Kinase Cascade Regulation James Faeder
Jan. 29, 2010 Quaid Morris University of Toronto Predicting the targets of mRNA-binding proteins Eric Xing
Feb. 12, 2010 Tandy Warnow University of Texas, Austin Simultaneous Alignment and Phylogeneic Tree Estimation Chris Langmead
Feb. 19, 2010 Daniel Erlanson Carmot Therapeutics, Inc.  Starting small, dreaming big: fragment-based drug discovery CPCB Students
Feb. 26, 2010 Andrey Rzhetsky University of Chicago Mining texts and experiments to understand human disease Bino John
Mar. 5, 2010 David Case Rutgers University Simulating biomolecules with implicit solvent models Lillian Chong
Mar. 19, 2010 Rohit Pappu Washington University in St. Louis Conformational equilibria of archetypal intrinsically disordered proteins Dan Zuckerman
Mar. 26, 2010 Nancy Amato Texas A&M University Using Motion Planning to Study Molecular Motions Chris Langmead
Apr. 2, 2010 Mona Singh Princeton University Predicting and analyzing cellular networks Eric Xing
Apr. 23, 2010 Michael Q. Zhang Cold Harbor Spring Laboratory Defining the regulatory network of the tissue-specific splicing factors Fox-1 and Fox-2 Bino John
Apr. 30, 2010 Martha Bulyk Harvard Medical School Transcription factor-DNA interactions: cis regulatory codes in genomes Bino John
Date/Location Speaker Affiliation Title of Talk Host
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 Ruth Nussinov National Institutes of Health Allostery and conformational control of ubiquitination in the cullin-RING E3 ligase machinery Carlos Camacho
Oct. 1, 2010 Yiannis Kaznessis University of Minnesota Mathematical Models in Synthetic Biology Takis Benos
Oct. 8, 2010 Jeff Gray Johns Hopkins University Fundamentals and applications of protein structure prediction Carlos Camacho
Oct. 22, 2010 Michael Gilson University of California, San Diego Modeling molecular recognition: Free energy, entropy and mechanical stress Chris Langmead
Oct. 29, 2010 Billy Day University of Pittsburgh Discovery, design, synthesis and biological evaluation of new microtubule stabilizers Takis Benos
Nov. 5, 2010

Olag G.Weist


University of Notre Dame  Computational chemistry as a data integrator in epigenetics Carlos Camacho and Zoltan Oltvai
Dec. 3, 2010

 Klaus Palme

University of Freiburg, Germany The magic role of auxin and beyond  Robert F. Murphy
Jan. 14, 2011

 Kris Dahl

Carnegie Mellon University Computational approaches to determine multiscale structural changes in the nucleus associated with aging
Jan. 21, 2011 Russell Malmberg University of Georgia  Computational Searches for Non-Coding RNA; Ecological Genetics of Pitcher Plants Robert F. Murphy
Feb. 4, 2011

 Jinbo Xu 

Toyota Technological Institute at Chicago  Probabilistic Graphical Model for Protein Structure Prediction Chris Langmead
Feb. 11, 2011

 Gary Bader

University of Toronto Predicting protein-protein interactions from the genome for evolutionary analysis Bino John
Feb. 18, 2011

 David J.Klinke

West Virginia University  A Bayesian Perspective on Understanding How Cells Make Decisions James Faeder
Feb. 25, 2011 Richard H. Lathrop University of California, Irvine  Predicting Positive p53 Cancer Rescue Regions Using Most Informative Positive (MIP) Active Learning Robert F. Murphy
Mar. 4, 2011

 Jorg Langowski

German Cancer Research Center  Coarse-grained modeling of the nucleosome and chromatin fiber James Faeder
Mar. 18, 2011

Timothy Hughes 

University of Toronto Exploring the protein-nucleic acid interactome Takis Benos
Mar. 25, 2011

Teresa Head-Gordon

University of California, Berkeley From Monomer Structure to Polymorphism: Computational and Experimental Studies of the Alzheimer’s Aβ Peptide Dan Zuckerman
Apr. 1, 2011

Christina Leslie 

Memorial Sloan-Kettering Cancer Center  Modeling microRNA-mediated regulation and dysregulation of gene expression in cancer Takis Benos
Apr. 8, 2011

Tamer Kahveci

University of Florida Computational strategies for understanding how biological networks function. Ziv Bar-Joseph
Apr. 22, 2011

Li-San Wang

University of Pennsylvania Gene expression in aging and aging-associated disorders Kathryn Roeder
May 5, 2011

Ioannis Tsamardinos

Vanderbilt University Towards Integrative Causal Analysis of Heterogeneous Datasets and Prior Knowledge

Date/Location Speaker Affiliation Title of Talk Host
Sep. 9, 2011 Wei Yang Florida State University Orthogonal Space Sampling of Long TimeScale Biomolecular Processes Dan Zuckerman
Sep. 16, 2011 Frank Alber University of Southern California Exploring the higher order genome organization Bino John
Oct. 7, 2011 Wendy Cornell Merck Comparison of 2D, 3D, and QSAR Methods for Virtual Screening Maria Kurnikova
Oct. 14, 2011 Daphne Koller Stanford University Learning richly structured representations from weakly annotated data
Nov. 11, 2011 Jayajit Das Battelle Center for Mathematical Medicine  From Models to Mechanisms: Understanding cell signaling responses Jim Faeder
Dec. 2, 2011 Steve Andrews Fred Hutchinson Cancer Research Center  Modeling cell biology with spatial and stochastic detail James Faeder
Jan. 27, 2012

Ernest Fraenkel


Massachusetts Institute of Technology  Integrating ‘Omic’ Data to Reveal Disease Mechanisms Eric Xing
Feb. 3, 2012

Adrian Lee 

University of Pittsburgh Genomic and Proteomic Systems Biology in Breast Cancer Bino John
Feb. 17, 2012

Donald Hamelberg

Georgia State University  Enzyme conformational dynamics in catalysis Lillian Chong
Feb. 24, 2012 Kevin White University of Chicago Integrating Genomic Networks to Identify Biomarkers and Drug Targets Ziv Bar-Joseph
Mar. 2, 2012

Meera Sitharam 

University of Florida EASAL: Entropy computation for Assembly Configuration spaces via Stratified Convex Parametrizations Maria Kurnikova
Mar. 23, 2012

Teresa Head-Gordon

University of California, Berkeley  From Monomer Structure to Polymorphism: Computational and Experimental Studies of the Alzheimer's Aβ Peptide Dan Zuckerman
Mar. 30, 2012

 Jing Li 

Case Western Reserve University Rare variant discovery and calling by sequencing pooled samples with overlaps Robert F. Murphy
Apr. 13, 2012

Laurence Loewe

University of Wisconsin Evolutionary Systems Biology James Faeder
Apr. 27, 2012 Michael McManus University of California, San Francisco  Mammalian small RNA Pathways Bino John
Date/Location Speaker Affiliation Title of Talk Host
Sep. 21, 2012 Carl Kingsford Carnegie Mellon University Computational Challenges Comprehending Chromosome Conformation Capture Constraints Ziv Bar-Joseph
Sep. 28, 2012 Curtis Huttenhower Harvard University Bug bytes: bioinformatics for meta’omics and microbial community analysis Russell Schwartz
Oct. 12, 2012 Huan-Xing Zhou Florida State University Simulation and Modeling of Ion Channel Functional Mechanisms and Transport Pei Tang
Oct.26, 2012 Eric Schadt Mount Sinai Hospital  Moving towards a better understanding of human disease in the era of big data Robert F. Murphy
Nov. 2, 2012 Matthew J. Lazzara University of Pennsylvania  Analysis of Time Scales in EGF Receptor Signaling Dynamics James Faeder
Nov. 9, 2012  David Pollock  University of Colorado Adaptation, coevolution, and convergence in the context of protein thermodynamics Nathan Clark
Nov. 16, 2012 Tomas Babak  Stanford University Global mapping of allele-specific expression as a tool for understanding epigenetics Bino John
Nov. 30, 2012 Joel McManus Carnegie Mellon University Evolution of post-transcriptional gene regulatory networks Ziv Bar-Joseph
Dec. 7, 2012 Jianpeng Ma Baylor College of Medicine Sean Xie
Feb 1, 2013 Luisa Hiller Carnegie Mellon University  Genomic Plasticity: To Be or Not to Be Joel McManus
Feb 8, 2013 Dennis Kostka University of Pittsburgh Finding and characterizing genomic regions with signatures of accelerated evolution Takis Benos
Mar. 1, 2013 Zia Khan University of Chicago Quantitative Proteomics Provides a New Window into How Genetic Differences Impact Protein-Levels Between Species Joel McManus
Mar. 8, 2013 Ranajeet Ghose City College of New York  Regulation of Protein Tyrosine Kinase Signaling in Bacteria Carlos Camacho
Mar. 22, 2013 Vineet Bafna University of California, San Diego The breakage fusion bridge and other exotic structural variations: combinatorics and cancer genomics R. Ravi
Mar. 29, 2013 Christine Vogel New York University  The Ups and Downs of Human Protein Expression Regulation Joel McManus
Apr. 5, 2013 Alan M. Grossfield University of Rochester Medical Center  Multiscale modeling of GPCRs Daniel Zuckerman
Apr. 12, 2013 Josh Akey University of Washington  Interpreting comprehensive catalogs of genetic variation in humans and yeast Nathan Clark
Apr. 26, 2013 Takis Benos University of Pittsburgh The Importance of Being microRNA: From disease markers and gene network regulators to therapeutic agents
Date/Location Speaker Affiliation Title of Talk Host
Aug. 30, 2013 Pierre Baldi  University of California, Irvine Deep Learning: Theory, Algorithms, and Biological Applications Ziv Bar-Joseph
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 Eric Deeds University of Kansas  The evolution of crosstalk in signaling networks James Faeder
Sep. 27, 2013 Judith LaLonde Bryn Mawr College Antagonism of HIV-1 Entry: Targeting Hotspots at the CD4-gp120 Protein-Protein Interface Indira Shrivastava
Oct. 4, 2013 Wing Wong  Stanford University Characterization of hESC transcriptome by hybrid sequencing Robert F. Murphy
Oct. 11, 2013 Matthew Stephens  University of Chicago  Assessing association between genetic variants and multiple phenotypes Seyoung Kim
Oct. 25, 2013 Anthony M. Dean  University of Minnesota Evolution of Catalytic Mechanisms Nathan Clark
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 Raul Rabadan Columbia University The Topology of Evolution Elodie Ghedin
Dec. 6, 2013 Ido Golding Baylor College of Medicine Quantitative Adventures in Gene Regulation Hanna Salman
Jan. 24, 2014 Kaspar Hansen   Johns Hopkins University Statistical analysis of epigenomewide data Dennis Kostka
Jan. 31, 2014 Arijit Chakravarty Takeda Pharmaceuticals  An evolving view of cancer: how mathematical modeling helps effective drug development in the face of tumor evolution Karen Thickman
Feb. 7, 2014 Julia Zeitlinger Stowers Institute for Medical Research Genome-wide approaches to understand gene regulation during development Veronica Hinman
Feb. 21, 2014 Ge Yang Carnegie Mellon University  Image-based computational analysis of regulatory mechanisms of axonal transport
Feb. 28, 2014 Ilya Shmulevich Institute for Systems Biology  Integrative Analysis and Interactive Exploration of Data from The Cancer Genome Atlas Dan Zuckerman
Mar. 21, 2014 Seyoung Kim University of Washington Learning network features reveals novel biomarkers for survival, chemosensitivity and surgical resectability phenotypes in cancer Su-In Lee 
Mar. 28, 2014 Nathan A.Baker Pacific Northwest National Laboratory  Geometric flow for biomolecular solvation Carlos Camacho
Apr. 18, 2014 Hector Corrado Bravo University of Maryland Exploring tumor epigenetic heterogeneity by cell-specific methylation pattern reconstruction Russell Schwartz
Apr. 25, 2014 David H. Matthews University of Rochester Medical Center RNA Molecular Mechanics: Estimating Free Energy Changes Facilitates Comparison with Experiments Dan Zuckerman
Date Speaker Affiliation Title of Talk Host
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 Andrew VanDemark University of Pittsburgh, Biological Sciences The molecular basis of Paf1C chromatin recruitment Nathan Clark
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 Lucy Forrest NIH-NINDS  How repetition helps: computational studies of pseudo-symmetrical membrane proteins Dan Zuckerman
Oct. 10, 2014 Jennifer Gallaghe West Virginia University Harnessing the genetic diversity of yeast to uncover mechanisms of adaptation Joel McManus
Oct. 24, 2014 Alain Laederach University of North Carolina at Chapel Hill What your riboSNitches may say about you
Oct. 31, 2014 Hongzhe Li Microbiome, Metagenomics and High-Dimensional Compositional Data Analysis Kathryn Roeder
Nov. 7, 2014 Byron Yu Carnegie Mellon University, Electrical & Computer Engineering / Biomedical Engineering  Dimensionality reduction for large-scale neural recordings Joel McManus
Nov. 11, 2014 Michael Rust University of Chicago Input Processing by a Three-Protein Circadian Clock James Faeder
Nov. 21, 2014 Junhyong Kim University of Pennsylvania Single Cell Variation and Cellular Phenotype  Joel McManus
Jan. 16, 2015 Da Yang University of Pittsburgh  Characterizing the genetic and epigenetic landscapes of miRNAs in cancer
Jan. 23, 2015 Steven Salzberg Johns Hopkins University Transcriptome Assembly: Computational Challenges of Next-Generation Sequence Data Carl Kingsford
Jan. 1, 2015 Herve Tettelin University of Maryland Comparative and functional genomics of Mycobacterium massiliense serial clinical isolates Luisa Hiller
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 Haiyuan Yu Cornell University Understanding molecular mechanisms of human disease mutations through 3D protein networks​ Maria Chikina
Feb. 27, 2015 Remo Rohs University of Southern California, Molecular and Computational Biology Quantitative modeling of transcription factor binding specificities using DNA shape Ivet Bahar
Mar. 27, 2015 Ryan Gutenkunst University of Arizona  Inferring natural selection on and within protein networks by coupling network- and population-scale models with genomic data Nathan Clark
Apr. 3, 2015 Michael Miller Bayesian Deformable Templates in Computational Anatomy: Application for Neurodegenerative Diseases and BrainClouds Robert F. Murphy
Apr. 10, 2015 Binhua Zhou University of Kentucky Epithelial-mesenchymal Transition in Breast Cancer Progression and Metastasis Jianhua Xing
Apr. 24, 2015 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 Takis Benos
Date/Location Speaker Affiliation Host
September 11, 2015

Da-Wei Li, Ph.D.


Ohio State University David Koes, Ph.D.
September 25, 2015 David Klinke, Ph.D. West Virginia University Tim Lezon, Ph.D.
October 2, 2015 Dr. Jason Shoemaker, Ph.D. University of Pittsburgh Pitt
October 9, 2015 Caros Lopez, Ph.D. Vanderbilt University James Faeder, Ph.D.
October 16, 2015 Vaughn Cooper, Ph.D. University of Pittsburgh Pitt
October 30, 2015 Ben Raphael, Ph.D. Brown University Russell Schwartz, Ph.D.
November 6, 2015 KC Huang, Ph.D.  Stanford University Hanna Salman, Ph.D.
November 13, 2015 Gaundenz Danuser, Ph.D.  UT Southwestern Ge Yang, Ph.D.
November 20, 2015 Roy Wollman, Ph.D.  University of California – San Diego Robin E. C. Lee, Ph.D.
December 11, 2015 Sui Huang, MD, Ph.D.  Institute for Systems Biology Philip LeDuc, Ph.D.
January 15, 2016 Natasa Miskov-Zivanov, Ph.D. University of Pittsburgh,
Electrical and Computer Engineering
Jim Faeder, Ph.D.
January 22, 2016 William Hlavacek, Ph.D. Los Alamos National Labratory Jim Faeder, Ph.D.
January 29, 2016 Arvind Ramanathan Oak Ridge National Laboratory CMU
February 5, 2016 Jan Liphardt, Ph.D. Stanford University Jianhua Xing, Ph.D.
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.
February 26, 2016 Jennifer Listgarten, Ph.D.  Microsoft Research Seyoung Kim, Ph.D.
March 18, 2016 Jian Ma, Ph.D.  Carnegie Mellon University CMU
March 25, 2016 Andreas Pfenning, Ph.D.  Carnegie Mellon University CMU
April 1, 2016 Tim Hughes, Ph.D. University of Toronto  C. Joel McManus, Ph.D.
April 8, 2016 Oleg Igoshin, Ph.D.  Rice University Jianhua Xing, Ph.D.
April 22, 2016 Jonathon Pritchard, Ph.D  Stanford University Student Nominated
Host: AJ Sedgewick
Date/Location Speaker Title of Talk Host
September 9, 2016

Dr. Min Xu, Carnegie Mellon University

 “Molecular resolution structural pattern mining inside single cells” CMU
September 16, 2016

Dr. Tandy Warnow, University of Illinois, Urbana-Champaign

“Grand Challenges in Phylogenomics” Dr. Russell Schwartz
September 23, 2016

Dr. Miler Lee, Biological Sciences, Pitt 

“Eggs, embryos, and pluripotency: gene regulation during early development” Dr. Nathan Clark
September 30, 2016

Dr. Sara Mostafavi, University of British Columbia

“Inferring molecular and cellular networks to understand complex traits” Dr. Maria Chikina
October 7, 2016

Dr. Jian Liu, NIH, National Heart, Lung, and Blood Inst.

“Spatial-temporal regulation of mitotic spindle assembly checkpoint” Dr. Jianhua Xing
October 14, 2016

Dr. Olexandr,  Isayev, University of North Carolina at Chapel Hill

“Accurate prediction of protein kinase inhibitors with deep convolutional neural networks” Dr. David Koes
October 28, 2016

Dr. Jasmine Zhou, University of Southern California

 “Make Big Data Useful: Horizontal and Vertical Integration of Genomics Data” Dr. Jian Ma
November 4, 2016

Dr. Wei Chen, University of Pittsburgh 

“Statistical Issues in Genome-Wide Association Studies of AMD Progression” Dr. Jian Ma
November 11, 2016

Dr. Stacey Finley, University of Southern California 

 “Predicting cancer signaling dynamics using computational systems biology” Dr. Jim Faeder
November 18, 2016

Dr. Su-In Lee, University of Washington

“From Big Data to Precision Oncology using Machine Learning” Dr. Jian Ma
December 2, 2016

Dr. Joanna Kelley, Washington State University

“Genomics in extreme environments: gene regulation and the evolution of hydrogen sulfide loving fish” Dr. Nathan Clark
December 9, 2016

Dr. Bin Zhang, MIT  

“Towards Predictive Modeling of Three Dimensional Genome Organization” Dr. Ivet Bahar / Dr. Jianhua Xing
February 3, 2017

Dr. Zachary Freyberg, University of Pittsburgh

“Opening a new window into the secretory cell with in situ cryo imaging” Dr. Ivet Bahar
February 17, 2017

Dr. Ross Curtis,

February 24, 2017

Dr. Nikolay Dokholyan, UNC – Chapel Hill

“Control of cellular networks by structural disorder” Dr. Carlos Camacho
March 3, 2017

Dr. Gene Yeo, University of California, San Diego

“Insights into RNA processing from large-scale protein-RNA interactions” Dr. Joel McManus
March 24, 2017

Dr. George Tseng, University of Pittsburgh

 “Omics data integration for disease subtype discovery and marker detection” Dr. Jian Ma
March 31, 2017

Dr.Cenk Sahinalp, Indiana University

 “Algorithms for Precision Genomics with Scalability, Security and Privacy Constraints” Dr. Russell Schwartz
April 7, 2017

Dr.Hannah Carter, UC San Diego

“Interaction Landscape of Inherited Polymorphisms with Somatic Events in Cancer” Dr. Anne-Ruxandra Carvunis
April 14, 2017

Dr. Anne-Ruxandra Carvunis, University of Pittsburgh

April 21, 2017

Dr. Ingo Greger, MRC Lab. of Molecular Biology

Dr. Ivet Bahar
Date Speaker Host Title
Sept. 15, 2017
6014 BST3
Dr. Jintao Liu Postdoctoral Scholar, University of California, San Diego Dr. Jim Faeder Pitt “Emergent dynamics in bacterial communities”
 Sept. 22, 2017  NO SEMINAR
 Sept. 29 2017 Dr. Adam Siepel Professor & Chair, Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory Dr. Nathan Clark Pitt “New methods for measuring natural selection and predicting deleterious variants in noncoding regions of the human genome.”
 Oct. 6 2017
GHC 6115
Dr. Kayhan Batmanghelich Professor, University of Pittsburgh Dr. Andreas Pfenning CMU  “Generative Method to Discover Genetically Driven Image Biomarkers”
 Oct. 13, 2017 Dr. Daniel Jarosz Stanford University Dr. Anne-Ruxandra Carvunis Pitt “Remembering the past: A new form of protein-based inheritance”
 Nov. 3, 2017
GHC 6115
Dr. Luay Nakhleh Rice University Dr. Jian Ma CMU
 Nov. 10, 2017 Dr. Jason Ernst UCLA Dr. Russell Schwartz CMU “Computational Approaches for Deciphering the Non-coding Genome”
 Nov. 17, 2017
BST3 6014
Dr. Xuedong Liu UC Boulder Dr. Jianhua Xing Pitt “Autocrine and Paracrine Signaling During Cell Migration”
 Dec. 1, 2017 Dr. Jean Yang CMU
 Dec. 4, 2017
11:00 AM – GHC 4303 Note: Joining this seminar will count as attendance credit, however attendance it is NOT mandatory.
Dr. Giri Narasimhan Bioinformatics Research Group (BioRG) School of Computing and Information Sciences Florida International University CMU Microbial “Social Networks”
 Dec. 8, 2017 Dr. Sarah Slavoff Yale University Dr. Anne-Ruxandra Carvunis Pitt “Discovery and Characterization of Microproteins”
 Dec. 15, 2017
 Jan. 26, 2018 Dr. Andrew J. Spakowitz Stanford University Dr. Jianhua Xing Pitt “Multi-scale Modeling of Chromosomal DNA in Prokaryotic and Eukaryotic Cells”
 Feb. 2, 2018
GHC 8102

Dr. Heng Huang

University of Pittsburgh

Dr. Jian Ma CMU Large-Scale Machine Learning Algorithms for Biomedical Data Science
 Feb. 9, 2018 Dr. Jan Skotheim Stanford University Dr. Robin Lee Pitt On the Biosynthetic Mechanism Coupling Cell Growth to Division
 Feb 16, 2018
 Feb. 23, 2018 No Seminar – CPCB Open House
 Mar. 2, 2018 No Seminar – CPCB Open House
 Mar. 23, 2018
Tepper, Room 152
Dr. Sushmita Roy Assistant Professor, Biostatistics and Medical Informatics, Systems Biology University of Wisconsin Dr. Jian Ma CMU Inference of regulatory network dynamics in developmental and evolutionary lineages
 Mar. 30, 2018
GHC 6115
Dr. Lydia Tapia Assistant Professor, University of New Mexico Dr. Russell Schwartz CMU Robotics Inspired Methods for Modeling Molecular Motion: From Molecular Docking to Antibody Assembly
 April 6, 2018 Dr. Xiaosong Wang Associate Professor, Pathology University of Pittsburgh Pitt Integrative concept signature analysis for the discovery of driving genetic aberrations and causal pathways in cancer
 April 13, 2018 Dr. Kathryn Miller-Jensen Yale University Dr. Robin Lee Pitt Exploring regulation of HIV latency with single-cell systems biology
 April 27, 2018
NSH 3305
Dr. David Gifford MIT Dr. Ziv Bar-Joseph CMU Therapeutic Antibody Design Using High-Capacity Machine Learning
Date Speaker Host Title
 September 14, 2018 Warren Ruder
University of Pittsburgh
Russell Schwartz (CMU) Modeling Emergent Behavior in Synthetic Biological Systems
 September 21, 2018 Bokai Zhu
University of Pittsburgh
Robin Lee (Pitt) Unveiling “Musica universalis” of the Cell: A Brief History of Biological 12h Rhythms
 October 5, 2018 Chad Myers
University of Minnesota
 Anne-Ruxandra Carvunis (Pitt)  Translating insights from yeast to discover genetic interactions in humans
 October 12, 2018 Ryan Suderman
 James Faeder (Pitt) Understanding the limits of information transmission in cellular signaling networks
 November 2, 2018 Robert Jernigan
Iowa State University
Ivet Bahar (Pitt) Improving Protein Sequence Matching to Aid Genome-Based Medicine
 November 9, 2018 Guo-Cheng Yuan
Harvard University
 Jian Ma (CMU) Systematic Mapping of Cellular States and Regulatory Circuits
 November 16, 2018 Brian Munsky
Colorado State University
James Faeder (Pitt) Using Stochastic Models to Interpret, Predict and Design Single-cell Experiments.
November 30, 2018 Aaron Wise  MetaSchool Event (Pitt) Oh the places you can go:  A bioinformatics odyssey  
December 7, 2018 Peter Kekenes-Huskey
University of Kentucky
 Jacob Durrant (Pitt) Understanding cardiac calcium signaling through computation: The Calcium, Calmodulin, Calcineurin signaling ‘triad’”
 January 18, 2019 Rachel Gottschalk
University of Pittsburgh
Robin Lee (Pitt) Quantitative control of macrophage signaling and inflammatory thresholds
 January 25, 2019 Iman Hajirasouliha, Ph.D.
Weill Cornell Medicine
 Hosein Mohimani (CMU) Novel algorithms and applications of Linked-Read genomics and metagenomics
 February 1, 2019 Will Fairbrother
Brown University
 Joel McManus (CMU) Pathogenic variations often disrupt splicing – implications for clinical genetics and evolutionary models of regulatory signals
 February 8, 2019 James Taylor
Johns Hopkins University
 Jian Ma (CMU) Making large-scale genomic analysis accessible, transparent, and reproducible
 February 15, 2019 Jacob Stewart-Ornstein
University of Pittsburgh
Hillman Cancer Center
 Hosein Mohimani (CMU) Conservation and divergence in p53 and DNA damage signaling dynamics
 March 22, 2019 Alberto Bartesaghi
Duke University
 Robert F. Murphy (CMU) Workflows for high-resolution structure determination by single particle Cryo-EM
 March 29, 2019 Dennis Vitkup
Columbia University
 Robin Lee (Pitt) Phenotypic evolution of bacteria and ecological dynamics of microbiomes
 April 5, 2019 Paul Medvedev
Penn State University
 Hosein Mohimani (CMU)  
 April 19, 2019 Wei Chen
University of Pittsburgh
 Jianhua Xing (Pitt) Clustering Single-Cell Sequencing Data from Population Studies
 April 26, 2019
Bo Huang
University of California, San Francisco
 Jianhua Xing (Pitt) Mapping the inner world of cells
Date Speaker Host Title
 August 30, 2019 Hu Cang
The Salk Institute
Jianhua Xing (Pitt) Visualizing the Organization of Mitotic Chromosomes by Super-resolution Microscopy
 September 6, 2019 John Chodera
Memorial Sloan Kettering Cancer Center
Lillian Chong (Pitt) Harnessing 100,000 computers around the world to probe kinase activation, inhibition, and resistance
 September 13, 2019 Dennis Kostka (SVC Seminar) S100A, Thomas E. Starzl Biomedical Science Tower Computational Genomics Yields Insights into Developmental Gene Regulation
 September 20, 2019 Itsik Pe’er
Columbia University
Ziv Bar-Joseph (CMU) Approximating Microbial Dynamics in the Simplex
 September 27, 2019 Virginia Burger
XtalPi Inc.
Joseph Ayoob (Pitt) The first six years since PhD
 October 4, 2019 Kin Fai
Ohio State University
Jian Ma (CMU) Applications and analyses of Third Generation Sequencing data to transcriptome and epigenetics research
 October 25, 2019 Ken Chen
University of Texas
 Russell Schwartz (CMU) Modeling single-cell copy number evolution reveals novel insight of oncogenesis
 November 1, 2019 Elizabeth A. Heller
Penn Epigenetics Institute
Andreas Pfenning (CMU) Locus-specific neuroepigenetic editing for the study of reward pathophysiology
 November 8, 2019 Hatice Ulku Osmanbeyoglu
University of Pittsburgh
James Faeder (Pitt) Systems biology approaches to dissect regulatory pathways in cancer
 November 15, 2019 Jacob Stewart-Ornstein (SVC Seminar)
University of Pittsburgh
*Mandatory for 1st year students only
 S100A, Thomas E. Starzl Biomedical Science Tower  Dynamics in DNA Damage Signaling Regulate the Response to Radiation
December 6, 2019 Lei Shi
NIH - National Institute on Drug Abuse
 Pei Tang (Pitt) Protein dynamics in determining key pharmacological properties of their ligands
 January 17, 2020 Devin Sullivan
Encodia, Inc.
Josh Kangas (CMU) A global journey with interstellar adventures
 January 24, 2020 Olexandr Isayev
Carnegie Mellon University
David Koes (hosted at CMU) Accelerating Drug Discovery with Machine Learning and AI
 January 31, 2020 Anastasia Baryshnikova
Calico Labs
Omer Acar (Pitt) Genome-wide phenotypic screens: the total greater than the sum of the parts
 February 7, 2020 Vineet Bafna
University of California San Diego
Hosein Mohimani (CMU) Mechanisms of oncogene amplification in cancer
 February 28, 2020 Rajiv McCoy
Johns Hopkins University
 Oana Carja (CMU) Functional and fitness effects of human genetic variation
 March 20, 2020
Elana Fertig
Johns Hopkins University
Maria Chikina (Pitt)
 March 27, 2020
Shuchang Liu
University of Pittsburgh
Takis Benos (Pitt) Fusion transcripts detection from short-read and long-read sequencing data
 April 3, 2020
Anshul Kundaje
Stanford University
Omer Acar (CMU)
 April 10, 2020
Zongqi Xia
University of Pittsburgh
James Faeder (Pitt)
Date Speaker Host Title
 September 4, 2020 Debbie Winter
Northwestern University
Andreas Pfenning (CMU)  “Modelling the Gene Regulatory Networks of Microglia and Other Macrophages in Health and Disease.”
 September 11, 2020
Pitt SVC Seminar (optional)
Registration Required:
Maria Chikina
University of Pittsburgh
University of Pittsburgh  “Finding Concise Descriptors in Genomic Data”
 September 18, 2020 Judy Day
University of Tennessee, Knoxville
Yoram Vodovotz (Pitt)  “Insights from mathematical modeling of inflammation: from sepsis to COVID-19″
 September 25, 2020 Denise Okafor
Pennsylvania State University
Omer Acar (Pitt)  “Ligand interactions that determine transcriptional outcomes”
 October 2, 2020 Julia Mahamid Min Xu (CMU)  “Molecular views into cellular functions by in-cell cryo-electron tomography.”
 October 9, 2020 Tongli Zhang
University of Cincinnati
Jianhua Xing (Pitt)  “Integrating mechanistic modeling and machine learning to understand complex biological systems with ‘small data’”
 October 16, 2020 No Seminar (no classes, CMU)
 October 23, 2020 No Seminar 
 October 30, 2020 Daisuke Kihara Min Xu (CMU)  “Protein 3D structure modeling for medium-resolution cryo-EM density maps”
 November 6, 2020 Aaron Streets
UC Berkeley
James Faeder (Pitt)  “Imaging and sequencing single cells – microfluidics for multi-modal single-cell analysis”
 November 13, 2020 Jessica Gibson
Ariel Precision Medicine
Joseph Ayoob / James Faeder (Pitt)  “Challenges and Opportunities for Modeling Complex Systems in a Clinical Product”
 November 20, 2020 Donald Hamelberg
Georgia State University
Ivet Bahar (Pitt)  “Perturbing the Conformational Ensemble to Understand and Tune Protein Function”
 November 27, 2020 No Seminar (Thanksgiving Break)
 December 4, 2020 Kevin Janes
University of Virginia
 Rachel Gottschalk (Pitt)  “Complete kinetic modeling of an RNA pathogen”
 December 11, 2020 No Seminar (no classes, PITT)
 December 18, 2020 No Seminar (Winter Break)
 December 25, 2020 No Seminar (Winter Break)
 January 1, 2021 No Seminar (Winter Break)
 January 8, 2021 No Seminar (Winter break)
 January 15, 2021 No Seminar (Winter break)
 January 22, 2021 No Seminar (No classes, CMU)
 January 29, 2021 No Seminar (No classes, CMU)
 February 5, 2021 Chaitanya Gokhale
Max Planck Institute for Evolutionary Biology 
Oana Carja (CMU) Eco-evolutionary dynamics | from cells to societies”
 February 12, 2021 David Van Valen
California Institute of Technology
Jianhua Xing (Pitt)  “Single-cell biology in a software 2.0 world”
 February 19, 2021 No Seminar (Open House)
 February 26, 2021 No Seminar
 March 5, 2021 Tae Hyun Hwang
Cleveland Clinic
Russell Schwartz (CMU) “Spatial transcriptome, single cell and digital pathology approaches to understand mechanisms of response and resistance to Immunotherapy and cell therapy: Opportunities and challenges for machine learning and AI scientists”
 March 12, 2021 Tzviya Zeev Ben Mordehai
University of Oxford
Min Xu (CMU) “The remarkable multi-scale architecture of mammalian sperm and implications for motility”
 March 19, 2021 No Seminar (No classes, CMU)
 March 26, 2021 Claudia Bank
Gulbenkian Institute & Universität Bern
Oana Carja (CMU) “Fitness landscapes and the predictability of evolution”
 April 2, 2021 Shilpa Garg
University of Copenhagen
Min Xiu (CMU) Efficient, high-resolution bioinformatic approaches for integrative sequencing analysis of complex diseases
 April 9, 2021 Sandra Safo
University of Minnesota
Omer Acar (Pitt) SIDA and SIDANet: New Discriminant Analysis Methods for Multi-class, Multi-view Structured Data
 April 16, 2021 No Seminar (no classes, CMU) 
 April 23, 2021 John Hogenesch
Cincinnati Children’s Hospital Medical Center
Bokai Zhu (Pitt) Computational problems in circadian biology
 April 30, 2021 Aly Azeem Khan
Toyota Technological Institute at Chicago
Hatice Osmanbeyoglu (Pitt) New computational approaches to understand immune function





September 3, 2021
Khanh Dao Duc
Assistant Professor in the Department of Mathematics at the University of British Columbia
Oana Carja (CMU)
Geometric and transport-based methods for ribosome and cryo-EM studies
September 10, 2021
September 17, 2021
German Enciso
Professor in Mathematics and Systems Biology
UC Irvine
 Nathan Lord (PITT)
Absolute concentration robustness controllers for stochastic chemical reaction network systems
September 24, 2021
Mingyao Li
Professor of Biostatistics
Department of Biostatistics, Epidemiology and Informatics
University of Pennsylvania Perelman School of Medicine
Kathryn Roeder (CMU)
“Applications of statistical and machine learning methods in spatial transcriptomics”
October 1, 2021
Dina Schneidman
Assistant Professor, Institute of Life Sciences and
School of Computer Science and
The Hebrew University
of Jerusalem
Yi Shi (PITT)
“Integrative Structure Modeling in the Age of Deep Learning”
October 8, 2021
Stephanie Hicks
Assistant Professor, Department of Biostatistics
Johns Hopkins University
 Steven Smeal (PITT)
“Scalable statistical methods and software for single-cell and spatial data science”
October 15, 2021
No Seminar (Fall Break)
October 22, 2021
Senior Vice Chancellor Seminar
Nathan Lord
Assistant Professor, Department of Computational & Systems Biology
University of Pittsburgh
(Register here)
“Mechanisms of Robust Developmental Patterning”
October 29, 2021
Rajul Satija
Associate Professor of Biology, Center for Genomics and Systems Biology, New York University
 Ziv Bar-Joseph (CMU)
November 5, 2021
No Seminar (no classes, CMU)
November 12, 2021
Kerry Geiler-Samerotte
Arizona State University
Anne-Ruxandra Carvunis (PITT)
November 19, 2021
Angela Brooks
Assistant Professor, Biomolecular Engineering, University of California Santa Cruz
C. Joel McManus (CMU)
“High-throughput and full-length characterization of transcript isoforms, and their function”
November 26, 2021
No Seminar (Thanksgiving Break)
December 3, 2021
Antonia Mey
University of Edinburgh
David Koes (PITT)
“From catalysis to binding affinity predictions: how a molecular dynamics based toolbox can shed light on protein functions and interactions”
December 10, 2021
No Seminar (no classes, CMU)
December 17, 2021
No Seminar (Winter Break)
December 24, 2021
No Seminar (Winter Break)
December 31, 2021
No Seminar (Winter Break)
January 7, 2022
No Seminar (Winter break)
January 14, 2022
No Seminar (Winter break)
January 21, 2022
Adam Phillippy
Senior Investigator, Computational & Statistical Genomics Branch, NHGRI
Carleton Kingsford (CMU)
January 28, 2022
Sergei Pond
Professor, Department of Biology
Temple University
Maria Chikina (PITT)
Evolution of SARS-CoV-2: past present and future
February 4, 2022
Galit Alter
Professor of Medicine
Harvard Medical School
Jishnu Das (PITT)
Using Systems Serology to Define Correlates of Immunity to Respiratory Pathogens
February 11, 2022
Alison Feder
Assistant Professor
Department of Genome Sciences
University of Washington
Oana Carja (CMU)
Evolutionary dynamics of HIV drug resistance through space and time
February 18, 2022
HOLD (Possible Open House)
 February 25, 2022
CPCB Open House
No Seminar
March 4, 2022
No Seminar (No classes, CMU)
March 11, 2022
No Seminar (Spring Break)
March 18, 2022
[TBD] Dr. Mohammed AlQuraishi
Assistant Professor, The Department of Systems Biology, Columbia University
Olexandr Isayev (CMU)
March 25, 2022
Anton Bennett
Dorys McConnell Duberg Professor of Pharmacology and Professor of Comparative Medicine; Co-Director, Program in Integrative Cell Signaling and Neurobiology of Metabolism, Yale School of Medicine
Robert Murphy (CMU)
“Signaling Mechanisms by Protein Tyrosine Phosphatases in Disease”
April 1, 2022
Alexis Battle
Associate Professor, Biomedical Engineering, Johns Hopkins University
Jian Ma (CMU)
April 8, 2022
No Seminar (No classes, CMU)
April 15, 2022
Carlos Lopez
Associate Professor, Biochemistry & Biomedical Informatics
Vanderbilt University
James Faeder (PITT)
April 22, 2022
Emilia Huerta-Sanchez
Associate Professor, Department of Ecology, Evolution, and Organismal Biology, Brown University
Oana Carja (CMU)
April 29, 2022
Nyasha Chambwe
Steven Smeal (CMU)





September 9, 2022 No Seminar
September 16, 2022
Wayne Stallaert
University of Pittsburgh

Nathan Lord (PITT)

Remote Only *Please reference your email for Zoom link 

Mapping cell cycle plasticity during tumorigenesis and treatment

 September 23, 2022
John Barton
UC Riverside
Nathan Lord (PITT)
 September 30, 2022
Wilson Wong
Boston University
Mo Ebrahimkhani (PITT) Mammalian Cell Design using Synthetic Biology
October 7, 2022
Max Staller
University of California, Berkeley
Nathan Lord (PITT)
October 14, 2022
No Seminar (Fall Break, PITT)
October 21, 2022
No Seminar (Fall Break, CMU)
October 28, 2022
No Seminar (CMU Tartan Day)
November 4, 2022

November 11, 2022
Andres Blanco
University of Pennsylvania
Nate Lord (PITT)
November 18, 2022
Satoshi Okawa
Vascular Medicine Institute,
University of Pittsburgh
Nate Lord (PITT)
November 25, 2022
No Seminar (Thanksgiving Break)
December 2, 2022
Amy Goldberg
Duke University
Oana Carja (CMU) & Anne-Ruxandra Carvunis (PITT)
Evolutionary Perspectives on Malaria
December 9, 2022
Lucia Peixoto
Washington State University
Anne-Ruxandra Carvunis (PITT)
December 16, 2022
No Seminar (no classes)
December 23, 2022
No Seminar (Winter Break)
December 30, 2022
No Seminar (Winter Break)
January 6, 2023 No Seminar (Winter Break)
January 13, 2023
No Seminar (Winter Break)
January 20, 2023
Martin Haesemeyer
Ohio State University
Nathan Lord (PITT) A model-free approach to link neural activity to behavioral tasks
January 27, 2023
No Seminar
February 3, 2023
Andrew Kern
University of Oregon

Vaughn Cooper (PITT)


Putting the HAL in Haldane: leverage machine learning for population genetics
February 10, 2023
Wah Chiu
Stanford University
Min Xu (CMU) CryoEM Informs Protein and RNA Folding
February 17, 2023
Phillip Romero
University of Madison Wisconsin
Jose Lugo-Martinez (CMU)
Join Zoom Meeting
Meeting ID: 997 5970 4280
Passcode: SEMINAR
Machine learning to navigate sequence-function landscapes for protein engineering
February 24, 2023
Fei Chen
Broad Institute
Jian Ma (CMU) A new methodology for generating spatially localized single cell genomics data
March 3, 2023
Gaurav Chopra
Purdue University
David Koes (PITT) Targeting Immune Cell Dysfunction in Chronic Inflammation: AI Models to Drugs
March 10, 2023
No Seminar (Spring Break)
March 17, 2023

Dana Pe’er
Sloan Kettering Institute; Alan and Sandra Gerry Metastasis and Tumor Ecosystems Center

Student-selected Speaker (CMU) Beyond cells, the importance of gene programs and tissue context
March 24, 2023
No Seminar
March 31, 2023 Tami Lieberman
Institute for Medical Engineering and Science

Oana Carja (CMU) & Nathan Lord (PITT)
*This talk will be hosted at CMU

De novo mutations in skin microbiomes
 April 7, 2023

Marcella Gomez
University of California, Santa Cruz

Yoram Vodovotz (PITT)
April 14, 2023
No Seminar (Spring Carnival)
April 21, 2023
Sergey Ovchinnikov
John Harvard Distinguished Science Fellow, Harvard University 
Student-selected speaker
*This talk will be hosted at PITT
April 28, 2023

Rommie E. Amaro
University of California, San Diego


Olexandr Isayev (CMU) In Situ Dynamics Reveal Unseen Vulnerabilities of Viral Glycoproteins





September 8, 2023 Martin Zhang
Carnegie Mellon University
Oana Carja (CMU) "Estimating SNP-pair effect correlations across functional annotations"
September 15, 2023
Allen Institute

Jianhua Xing (PITT)

"Integrated intracellular organization dynamics and its variations in human iPS cells"

September 22, 2023
Yun William Yu
Carnegie Mellon University
Oana Carja (CMU)
"Sketching, alignment, and more in bioinformatics"
September 29, 2023
Ginkgo Bioworks
Nathan Lord (PITT) "Charting the path to biology by design: Lessons from building genetic engineering as a service"
October 6, 2023
Johns Hopkins University
Anne-Ruxandra Carvunis (PITT) "Cell motility and shape as a playground for physics"
October 20, 2023
October 27, 2023
Itai Yanai
New York University
Wayne Stallaert (PITT)
"Cell state dynamics and plasticity in tumorigenesis and drug resistance"
University of California, Los Angeles
Jian Ma (CMU) & Kathryn Roeder (CMU) "Enhancing statistical rigor in single-cell data analysis using synthetic negative controls"
Frederick "Fritz" Roth
University of Pittsburgh
Oana Carja (CMU) "Towards a Context-Aware Atlas of Human Variant Effects"
November 24, 2023
December 1, 2023
University of Maryland, Baltimore County

James Faeder  (PITT)

"Automatic inference of spatial and temporal regulatory mechanisms"


NIH, National Cancer Institute
Rachel Gottschalk (PITT) “Building models of CAR-T signal integration, using automatized/dynamic high-dimensional dynamic profiling”
John Kang
UW Medicine, Dept of Radiation Oncology 
*MSTP/CPCB Alumnus
Russell Schwartz (CMU) "Extracting knowledge from unstructured data in oncology"
February 2, 2024

Saulo de Oliveira   AtomwiseSenior Scientist, Senior Manager - Cheminformatics

David Koes (PITT)

"Unlocking tera-scale vHTS screens by a combination of 100%-synthesizability generative AI and reinforcement learning"
Steven Ludtke
Baylor College of Medicine
Min Xu (CMU) "Structural Variability in CryoEM and CryoET: Deep Learning Strategies for Structure in Context"
Andrew White
University of Rochester
*Student Invited Speaker (hosted by CMU)
"Automating chemistry with large language models"
Virginia Burger
CEO & Founder NEQ Bio
*CPCB Alumnus
Russell Schwartz (CMU) "Building a biotech startup to discover drugs targeting intrinsically disordered proteins"
March 1, 2024
March 8, 2024
March 15, 2024


Nicole Creanza
Vanderbilt University
Oana Carja
"The evolution of learned behaviors: computational insights from birds and humans"
March 29, 2024


April 5, 2024

Predrag Radivojac
Northeastern University 

Jose Lugo-Martinez (CMU) "A New Framework for the Use of Variant Interpretation Tools (and Interdependent Evidence) in Clinical Practice"
April 12, 2024
April 19, 2024

Hernan G. Garcia
University of California, Berkeley 

Nathan Lord (PITT) "Using Physics as a Microscope to Dissect Transcriptional Dynamics in Development"