| Date |
Title
|
Speaker
|
Affiliation
|
Notes
|
2009 |
|
|
|
|
| April 7 |
Computer Models of Evolution |
Irwin Kuntz |
UCSF Molecular Design Institute |
|
| March 20 |
Analyzing Stochastic Switches and Trajectories in Gene
Regulatory Networks |
Brian Munsky, PhD |
Los Alamos National Laboratory |
1 pm
3073 BST3 |
| March 18 |
From Natural to Synthetic Gene Networks: New Approaches to Gene Expression Control |
Gabor Balazsi |
The University of Texas, MD Anderson Cancer Center |
4 pm
6014 BST3 |
| March 17 |
Understanding Adaptive Immunity: A Crossword of the Physical and Life Sciences (Jointly sponsored by the Departments of Computational Biology and Immunology) |
Arup Chakraborty, PhD |
Massachusetts Institute of Technology |
4 pm
6014 BST3 |
| Febuary 26 |
Cooperative Folding Kinetics of BBL Protein and Peripheral Subunit-binding Domain Homologues |
Iksoo Chang, PhD |
Pusan National University, Korea |
4 pm
6014 BST3 |
| Febuary 24 |
Computational Modeling of Signaling Processes in Cells |
Jason Haugh, PhD |
North Carolina State University |
4 pm
6014 BST3 |
| Febuary 17 |
Multivalent Histone Methylation Models of Gene Expression |
Stefan Bekiranov |
University of Virginia Health System |
4 pm
6014 BST3 |
| January 13 |
Protein Flexibility and Drug Design: How to Hit a Moving Target |
Heather Carlson |
University of Michigan College of Pharmacy |
4 pm
6014 BST3 |
2008 |
|
|
|
|
| December 2 |
The Evolutionary Design of Proteins |
Rama Ranganathan |
University of Texas Southwestern Medical Center |
4 pm
6014 BST3 |
| November 11 |
Graphical Models for Biomolecular Systems |
Chris Langmead |
Carnegie Mellon University |
4 pm
6014 BST3 |
| November 4 |
Computational Enzymology: Thinking Outside the ActiveSite |
Troy Wymore |
Pittsburgh Supercomputing Center |
4 pm
S100A BST |
| September 30 |
Exploring the control circuit of cell migration with top-down mathematical modeling |
Yu-Li Wang |
Carnegie Mellon University |
4 pm
6014 BST3 |
| September 8 |
Mega-Scale Agent-Based Model Simulations of Complex Bio Systems on Graphics Processing Units |
Roshan D'Souza |
Michigan Technological University |
4 pm
6014 BST3 |
| April 15 |
Optimization in the New Biology |
Nick Sahinidis |
Carnegie Mellon University |
4 pm
6014 BST3 |
| April 11 |
From Acetylcholinesterase to Intrinsically Unfolded Proteins (and Back Again) |
Israel Silman |
Weizmann Institute of Science |
2 pm
6014 BST3 |
| April 1 |
Dynamical Contributions to Enzyme Catalysis: Critical Tests of A Problematic Hypothesis |
Arieh Warshel |
University of Southern California |
4 pm
6014 BST3 |
| March 31 |
Viral Infections And MicroRNAs |
Sebastien Pfeffer |
IBMP-CNRS |
11 am
6014 BST3 |
| March 18 |
Population Effects On Bacterial Thermotaxis |
Hanna Salman |
University of Pittsburgh |
4 pm
6014 BST3 |
| March 4 |
Driving Forces for Polyglutamine Oligomerization and Implications for Aggregation |
Rohit Pappu |
Washington University |
4 pm
6014 BST3 |
| February 26 |
Drug discovery: changing approaches and the roles of biology and chemistry |
Christopher Lipinski |
Melior Discovery |
4 pm
6014 BST3 |
| February 12 |
Information theoretic methods in molecular, structural, and neuro-biology |
Ilya Nemenman |
Los Alamos National Laboratory |
4 pm
6014 BST3 |
| January 16 |
How do you Strip a Protein out of a Biological Membrane? |
Jeffrey Brodsky |
The Pittsburgh Biophysical Theory Club |
4 pm
6014 BST3 |
| January 15 |
Modeling Actin Cytoskeleton Dynamics in Fission Yeast |
Dimitrios Vavylonis |
Lehigh University |
4 pm
6014 BST3 |
2007 |
|
|
|
|
| December 5 |
"How membranes can mediate interactions between proteins" and "Discrete State Model of Coupled Ion Permeation and Fast Gating in ClC Chloride Channels" |
Merkus Deserno & Rob Coalson |
The Pittsburgh Biophysical Theory Club |
4 pm
Eberly 307 |
| November 13 |
Data-Driven Predictive Modeling of Anatomical Joints (or What Can Computer Graphics Research Do for Biomedical Research?) |
Liz Marai |
University of Pittsburgh |
4 pm
6014 BST3 |
| November 7 |
"Rule-based modeling of biochemical networks" and "Simulations of a molecular switch with mutually exclusive folding" |
James Faeder & Lillian Chong |
University of Pittsburgh Departments of Computational Biology and Chemistry |
4 pm
Eberly 307 |
| November 6 |
Computational studies of protein function and Dynamics Perturbation Analysis |
Michael Wall |
Los Alamos National Laboratory |
4 pm
6014 BST3 |
| October 31 |
Stochastic Robustness of NF-kB Signaling |
Tomasz Lipniacki |
Institute of Fundamental Technological Research |
12 pm
6014 BST3 |
| October 3 |
The reason to use model-free analysis & Soft modes near the buckling transition of icosahedral shells |
Reiko Ishima & Michael Widom |
The Pittsburgh Biophysical Theory Club |
4 pm
Eberly 307 |
| September 9 |
Adapter Proteins of IRS family: a key junction of mitogenic and survival RTK pathways |
Nikolay Borisov |
Thomas Jefferson University |
4 pm
6014 BST3 |
| August 16 |
Protein folding physics, structure prediction, and ligand binding |
Ken Dill |
University of California |
3 pm
6014 BST3 |
| August 8 |
Stretching to understand proteins |
Marek Cieplak |
Polish Academy of Sciences |
11 am
6014 BST3 |
| May 15 |
Molecular Recognition: Informatics, Entropy,and Design |
Michael K. Gilson |
University of Maryland |
4 pm
6014 BST3 |
| May 1 |
Multi - resolution Protein Modeling by Combining Theory and Experiment |
Cecilia Clementi |
Rice University |
4 pm
6014 BST3 |
| Apr. 12 |
Ruled - based Modeling of Signal Transduction |
James Faeder |
Los Alamos National Laboratory |
12:30 pm
3073 BST3 |
| Apr. 10 |
Coupling Between Protein and Solvent Dynamics: Microscopic Insights from Molecular Dynamics Simulations |
Gustavo Carri |
University of Akron |
2 pm
6014 BST3 |
| Mar. 28 |
Collapse or Collaborate: Using Synthetic Biology and Mathematical Analysis to Study Cooperation |
Wenying Shou |
Memorial Sloan - Kettering Cancer left |
12 pm
6014 BST3 |
| Mar. 27 |
One - hit Cell Death in Neurogdegeneration: Evaluation, Implications, and Possible Mechanisms |
Geoffrey Clarke |
University of Toronto |
2 pm
6014 BST3 |
| Mar. 16 |
Whole - Genome Analyses and Evolutionary Dynamics of Influenza A |
Elodie Ghedin |
University of Pittsburgh |
11 am
6014 BST3 |
| Mar. 13 |
Molecular Interactions: From Transcriptional Regulation to Protein-protein docking |
Zhipeng Weng |
Boston University |
4 pm
6014 BST3 |
| Mar. 2 |
The Multiscale Challenge for Biomolecular Systems: A Systematic Approach |
Gregory Voth |
University of Utah |
11 am
6014 BST3 |
| Feb. 8 |
Computational Methods for Reconstructing Biomolecular Systems and Studying their Evolution |
Chen - Hsiang Yeang |
University of California, Santa Cruz |
11 am
6014 BST3 |
| Feb. 23 |
How Much Got There and What Did It Do: Computational and Mathematical Techniques in Oncology Drug Discovery |
Arijit Chakravarty |
Millenium Pharmaceuticals |
11 am
6014 BST3 |
| Feb. 21 |
CaMKII mediates electrical remodeling post-infarction: From in vivo to in silico and back |
Thomas J. Hund |
Washington University |
10 am
6014 BST3 |
| Feb. 19 |
Function and Evolution of Cis-Regulatory Sequences in the Human Genome: from Extreme Conservation to Human-Specific Divergence |
Shyam Prabhakar |
Lawrence Berkeley National Laboratory |
11 am
6014 BST3 |
| Feb. 16 |
Understanding Biological Networks from a Spectral Graph-Theoretic Perspective |
Chakra Chennubhotla |
University of Pittsburgh |
10 am
6014 BST3 |
| Feb. 5 |
Deciphering Information Encoded in Dark Matter of the Human Genome |
Xiaohui Xie |
Broad Institute of MIT and Harvard |
12 pm
6014 BST3 |
| Feb. 1 |
Genome and Development at Single-Cell Resolution: Automated lineaging and it’s Applications in C. elegans |
Zhirong Bao |
University of Washington |
3 pm
6014 BST3 |
| Jan. 5 |
Models and algorithms for genomic sequences, proteins and networks of protein interactions |
Serafim Batzoglou |
Stanford University |
11 am
6014 BST3 |
2006 |
|
|
|
|
| Dec. 15 |
Microtubule Array in the Interphase Cell: Spatial and Temporal Organization |
Prof. Ivan A. Vorobjev |
Laboratory of Cell Motility, A.N. Belozersky Institute, Moscow State University |
11 am - 12 pm
6014 BST3 |
| Dec. 12 |
How Does Voltage Open and Close Potassium Channels? |
Michael Grabe |
Dept. of Biological Sciences, Univ. of Pittsburgh |
4 - 5 pm
Room 6014 BST3 |
| Dec. 5 |
Adventures in Reverse Engineering of Biochemical Networks |
Pedro Mendes |
Virginia Bioinformatics Institute, Virginia Tech |
3 - 4 pm
Room 6014 BST3 |
| Nov. 29 |
Computing rates from reaction coordinates with milestoning |
Ron Elber |
Cornell University |
|
| Nov. 14 |
Understanding HIV protease inhibition: computational studies of structural dynamics and drug binding |
Carlos L. Simmerling |
left for Structural Biology, Stony Brook University |
4 - 5 pm
Room 6014 BST3 |
| Oct. 31 |
Models of G - Protein Coupled Receptor Structure and Function: Past, Present, and Future |
Marta Filizola |
Cornell University |
4 - 5 pm
Room 6014 BST3 |
| Oct. 24 |
Dynamics Of Cellular Traction Forces |
Micah Dembo |
Boston University |
4 - 5 pm
Room 6014 BST3 |
| Sep. 12 |
Nucleosome Energy Level Diagrams and Chromatin Structure |
Thomas Bishop |
Dept. Environmental Health Sciences, Tulane University, New Orleans, LA |
4 - 5 pm
Room 6014 BST3 |
| Aug. 28 |
Computational analysis on residue contacts in protein structures: Applications to structure prediction, folding and stability |
M. Michael Gromiha |
Computational Biology Research left (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo |
12 - 1 pm
Room 6014 BST3 |
| Apr. 17 |
Single pair FRET (spFRET) for the elucidation of protein/DNA dynamics: recent results andunpublished directions |
Sanford Leuba |
University of PittsburghDept. of Cell Biology and Physiology |
12 - 1 pm |
| Mar. 30 |
Estimation of the stiffness of bacterial flagella using flow - induced deformation |
MunJu Kim |
University of Utah, Salt Lake CityDept. of Mathematics |
11 am - 12 pm |
| Feb. 24 |
Modeling Biological Develo pment Using the Cellular Potts Model |
James Glazier |
Indiana Biocomplexity Institute |
12 - 1 pm |
2005 |
|
|
|
|
| Dec. 8 |
Statistically Significant Short BlocksDiscovered in the Non - Coding Parts of the Human Genome have one or moreInstances within nearly all known genes and relate to Specific Biological Processes |
Isidore Rigoutsos |
IBM's Computational Biology left |
12 - 1 pm |
| Dec. 1 |
Routes are Trees:The Parsing Perspectives on Protein Folding |
Julia Hockenmaier |
University of PennsylvaniaInstitute for Research in Cognitive Science |
3:30 - 4:30 pm |
| Nov. 16 |
Multi - scale Modeling of DNA |
Wilma Olson |
Rutgers UniversityDepartment of Chemistry |
3 - 4 pm |
| Nov. 10 |
Common Functional Dynamics in Proteases |
Cristian Micheletti |
Statistical and Biological Physics International School for Advanced Studies |
12 - 1 pm |
| Nov. 9 |
Understanding Molecular Evolutionfrom First Principles |
Eugene Shakhnovich |
Harvard UniversityDepartment of Chemistry |
12 - 1 pm |
| Nov. 7 |
Prediction of Secondary Structures of Proteins Using a Two - Stage Method |
Metin Turkay |
Koc Universityleft for Computational Biology and Bioinfromatics |
4 - 5 pm |
| Sep. 29 |
How Cells Eat Stuff: Experimental and Theoretical Studies of Phagocytosis |
Marc Herant |
Boston UniversityBiomedical Engineering |
|
| Sep. 20 |
Algorithmic Challenges in Structural Molecular Biology and Proteomics |
Bruce R. Donald |
Dartmouth Universityleft for Structural Biology and Comp. Biology |
12 - 1 pm |
| June 1 |
The Stochastic Dynamics of Molecular Motors |
Michael Fisher |
University of MarylandInstitute of Physical Science & Technology |
12 - 1 pm
S120 BST |
| May 9 |
Genome - Wide Post Transcriptional Gene Regulation by microRNAS |
Bino John |
Memorial Sloan Kettering Cancer leftComputational Biology left |
12 - 1 pm
Herberman Conference left |
| May 5 |
Computationally Optimized DNA Assembly |
Richard Lathrop |
University of California, IrvineDept. of Information and Computer Science |
12 - 1 pm
S123 BST |
| April 14 |
The Plasticity and Structure of Metabolic Networks |
Eivind Almaas |
University of Notre DameDepartment of Physics |
10 - 11 am
S100A BST |
| Mar. 28 |
A Ran GTP gradient facilitates the Search - and - Capture of Chromosomes |
Alex Mogilner |
Univerisity of CaliforniaDept. of Math & left for Genetics & Develo pment |
12 - 1 pm
S123 BST |
| Mar. 16 |
Genome - Wide Post Transcriptional Gene Regulation by microRNAS |
Bino John |
Memorial Sloan Kettering Cancer leftComputational Biology left |
3 - 4 pm
S100 BST |
| Mar. 15 |
Modeling side chain conformations and structural analysis of mutants using contact surface areas |
Eran Eyal |
Weizmann Institute of ScienceDept. of Plant Science |
12 - 1 pm
S123 BST |
| Mar. 14 |
Functional Organization of Transcriptional - regulatory Networks |
Zoltan N. Oltvai |
University of Pittsburgh School of MedicineDepartment of Pathology |
3 - 4 pm
S123 BST |
| Feb. 24 |
Model Systems for Virtual Screening |
Brian Shoichet |
UCSFDept. of Pharmaceutical Chemistry |
12 - 1 pm
S123 BST |
| Jan. 21 |
Computational Investigations of Protein Regulation by Post Transitional Phosphorylation |
Matt Jacobson |
UCSFDept. of Pharmaceutical Chemistry |
12 - 1:30 pm
S123 BST |
2004 |
|
|
|
|
| Nov. 4 |
Simulating, Refining and Modeling Protein Structures at Multi - resolution and Multi - length Scales |
Jianpeng Ma |
Rice UniversityBaylor College of Medicine |
|
| Oct. 5 |
Cue - Signal - Response Analysis of Cell Decision Processes |
Dr. Douglas Lauffenburger |
MITDept. |
12 - 1:30 pm
S100A BST |
| Sep. 15 |
Molecular Modeling and Simulations of Membrane Proteins |
Dr. Indira Shrivastava |
NCI/NIH |
10 - 11am
995 BST |
| Aug. 13 |
Klaus Schulten |
|
Beckman Institute for Advanced Science and Tech. |
|
| June 15 |
Informatics in Biomed Science and Healthcare: Spanning from the Molecular to the Clinical |
Ivet Bahar/ Gregory F. Cooper |
CCBB, Pitt |
Frick Fine Arts Building Auditorium |
| April 15 |
Folded to bind: In silico predictionsof protein - protein interactions |
Carlos J. Camacho |
Boston UniversityDept. of Biomedical Engineering |
1:30 - 2:30 pm
E119 5BST |
| Mar. 4 |
Interrogative Cell Signaling:How cells perceive their context |
Steven Wiley |
Biomolecular Systems InitiativePacific Northwest National Laboratory |
12 - 1 pm
S 100A BST |
| Mar. 2 |
Gene Fossils: A Comprehensive Survey of Pseudogenes in the Human Genome |
Zhaolei Zhang |
Yale UniversityDepartment of Mol Biophysics & Biochem |
BST 1195 |
| Mar. 1 |
Comp Approaches To Cytoskeleton - Signaling Interactions Underlying Cell Polarity |
Ivan V. Maly |
MITBiological Eng'g Division |
BST E1295 |
| Feb. 26 |
Continuum Electrostatics and Membrane Peptides/Proteins |
Wonpil Im |
The Scripps Res Ins.Department of Molecular Biology |
BST 995 |
| Feb. 13 |
Surprising instabilities in prion proteins:Evidence from comp methods applied to se - quences and NMR structures |
Dr. Ruxandra Dima |
University of MarylandInstitute of Physical Sci and TechnolDept. of Chem. and Biochem |
12 - 1 pm
E 1295 BST |
| Feb. 12 |
Regulation of the Eukaryotic Cell Cycle: Theory, Computation and Experiment |
John Tyson |
Virginia Polytechnic Institute & State UniversityDept. of Biology |
12 - 1 pm
S 123 BST |
| Jan. 22 |
Water in confinement:from nanotubes to proteins |
Gerhard Hummer |
Laboratory of Chemical Physics, NIH |
12 - 1 pm
BST South 100A |
| Jan. 14 |
Integrative Modeling of Spatial Self - organization in the Cytoskeleton and Cell Signaling |
Ivan V. Maly |
MIT Biological Eng'g DivisionDepts of Biology and Chem Eng'g |
12 - 1 pm
BST South 100A |
