Past CIBM Seminar presenters are listed below with the seminar title, their name and affiliation in parenthesis, if it is not UW-Madison, and their area of specialization.

A Bayesian Network to Improve Early Detection of Breast Cancer | Elizabeth Burnside | Radiology; Biostatistics and Medical Informatics
A New DNA Word Design Strategy Using Random de Bruijn Sequences | Christine Heitsch | Math and Chemistry
A Reductionist Approach to E. coli Functional Genomics | Fred Blattner | Genetics
A Single Fluorochrome System for Genomic Analysis | Dalia Dhingra | Chemistry
A Species-Generalized Probabilistic Model-Based Definition of CpG Islands | Rafael Irizarry (Johns Hopkins University) | Biostatistics
A Statistical Framework for the Analysis of ChIP Seq Data | Pei Fen Kuan | Biostatistics and Medical Informatics
A Unified Approach to Discovery and Classification of Tumor Types using Gene Expression Data | Roxana Alexandridis | Bacteriology
Adaptive High-Throughput Peptide Screening and Analysis via Active Learning | Burr Settles | Biostatistics and Medical Informatics
Advanced Nonlinear Programming Methods for Chemical Process Optimization | Lorenz Biegler (Carnegie Mellon University) | Chemical Engineering
An Abductive Approach to Explaining Genome-Wide Experimental Observations | Deborah Chasman | Computer Sciences
An Automated Decision -Tree Approach to Predicting Protein Interaction Hot Spots | Steve Darnell | Biochemistry
An Integrated Computational and Biophysical Approach to the Structural Study of Integral Membrane Proteins | Alessandro Senes | Biochemistry
Analysis of Gene Copy Number Abnormalities in Cancer: Computational Challenges | Dimitri Semizarov (Abbott Laboratories) | Global Pharmaceutical Research and Development
Analysis of Intracellular Signal Transduction at Various Scales of Biological Complexity | Jason Haugh (North Carolina State University) | Chemical Engineering
Application of the Gaussian Network Model and a Variation of Normal Mode Analysis for Refinement of Protein Structures | Ryan Bannen | Biochemistry
Aquaporin Water Channels from Atomic Structure to Malaria | Peter Agre (Director, Johns Hopkins Malaria Research Institute) | Medicine
ASAP, Community Annotation and Analysis of Genomes | Nicole Perna | Animal Health; Biomedical Sciences; Genome Center
Better Living Through Design: Visualizing Biomedical Data for Patient Care, Public Health, and Research | David Pieczkiewicz (Marshfield Clinic Research Foundation) | Biomedical Engineering
Bio-electronic Interfaces for Direct Electronic Sensing | Robert Hamers | Chemistry
Biophysical and Computational Studies of Virus Particles and their Maturation: Insights into Elegantly Programmed Nano-machines | John E. Johnson (The Scripps Research Institutte) | Molecular Biology
Cancer Genomics: Discovery and Characterization of Structural Alterations in the Solid Tumor Oligodendroglioma via Single Molecule Analysis | Nicholas Shera | Laboratory for Molecular and Computational Genomics
Case Studies in Bayesian Phylogenetics | Bret Larget | Statistics; Botany
Clinical Decision Support, Medical Knowledge Representation and Workflow Technology (A Seminar in Clinical Informatics: A Subfield of Biomedical Informatics) | Vojtech Huser (Marshfield Clinic Research Foundation) | Biostatistics and Medical Informatics
Cognate Site Identifier (CSI) Array: A High-Throughput Technique to Determine the Comprehensive Sequence Specificity of DNA- Binding Molecules | Chris Warren | Biochemistry
Comparative Genomics of the Environmental Stress Response in Ascomycete fungi | Dana Wohlbach | Genetics
Computational and Experimental Models for Macromolecular Recognition | Lynn Ten Eyck (University of California-San Diego, San Diego Supercomputer Center) | Pharmacology; Computational Science Research
Computational Challenges in Discovering the Genetic Basis of Complex Traits in Inbred Mouse Strains | Eleazar Eskin (UCLA) | Computer Science; Human Genetics
Computer Simulation of | Daniel McFarlin | Biostatistics and Medical Informatics, and Oncology
Computer Vision Algorithms for Phenotyping  the Model Plant Arabidopsis | Nathan Miller | Biomedical Engineering Graduate Program
Computers as Puzzle Solvers: The Challenge of Efficient Search | Richard Karp (University of California- Berkeley) | Computer Sciences
Computing the Conformational Entropy of the Folded and Unfolded Ensembles of a Protein Using Lie Groups | Gregory Chirikjian (Johns Hopkins University) | Computer Sciences
Conformational Flexibility of Proteins in Crystallography and Computational Models | Dmitry Kondrashov | Biochemistry
Conservation and Evolution of Cis-regulatory Elements in Diverse Fungi | Audrey Gasch | Genetics; Genome Center
Control of Global Transcription in Escherichia coli | Timothy Durfee | Genetics
Counting Peptides | Shane Hubler | Mathematics
Cryptographic Accuracy Annotations for Electronically Exchanged Personal Health Information | David Haight | Industrial and Systems Engineering
Data Analysis with Latent Topic Models: Genes, Bugs, and Art | David Andrzejewski | Computer Sciences
De Novo Peptide Sequencing using Tandem Mass Spectrometry Data | Gheorghe Craciun | Mathematics; Biomolecular Chemistry
Design and Evaluation of Double-Stranded DNA Microarrays | Chris Warren | Biochemistry
Designing and Evaluating a Method for Multiple Genome Comparison | Aaron Darling | Computer Sciences
Detecting Messenger and MicroRNA Targeting Relationships from Observational Microarray Data Studies | Stephen Stanhope | Statistics
Development and Applications of Escherichia coli Metabolic Models | Jennifer Reed (University of California-San Diego) | Biomedical Engineering
Development of a SNPChip | Henry Zeringue | Biomedical Engineering
Discovery and Characterization of a Causative Mutation for Bovine Dwarfism in Cyclic GMP-dependant, Type II, Protein Kinase (PRKG2) | James Koltes | Biochemistry
Dissecting the Origins of Emergent Behavior in Populations of Bacteria | Douglas B. Weibel | Biochemistry
Driven Assembly of Nanoscale Objects, and its Application in Nanotechnology | Juan de Pablo | Chemical and Biological Engineering
Efficient Modeling of Solvent Environments | Michael Feig (Michigan State University) | Biochemistry and Molecular Biology; Chemistry
Engineering Added Dimensions into Magnetic Resonance Imaging | Walter Block | Biomedical Engineering and Medical Physics
Engineering the p53 Cancer Prevention Protein using Structure Based Features and Active Learning | Sam Danziger (University of California, Irvine) | Biomedical Engineering
Ensemble Refinement of Protein Crystal Structures: Validation and Application | Elena Levin | Biochemistry
Exploring the Flexibility of DNA with Molecular Dynamics Simulations | Vanessa Ortiz | Chemical and Biological Engineering
Extending Pictorial Structures for the Interpretation of Crystallographic Density Maps | Frank DiMaio | Computer Sciences
Finding Relations in Biomedical Literature Using Inductive Logic Programming | Louis Oliphant | Computer Science
Fractionation in Radiation Treatment Planning | Michael Ferris | Computer Sciences and Industrial Engineering
From Genome to Organism: A Virus-World View | John Yin | Chemical and Biological Engineering
From Sequence Information to Gene Expression | Jun Liu (Harvard University) | Statistics
Gene Mapping in the Post-Genomic Era | Brian Yandell | Statistics; Horticulture
Genetic Maps: Past, Present, and Future | Karl Broman | Biostatistics and Medical Informatics; Genetics
Genome Analysis by Proteomic Methods and Genome Fingerprint Scanning | Michael Giddings (University of North Carolina-Chapel Hill) | Microbiology and Immunology; Biomedical Engineering
Genome-Wide Analysis of Histone Gene Promoters | Ragesh Chowhardy (Marshfield Clinic Research Foundation) | Biomedical Engineering
Genomic Network Tomography | Robert Nowak | Electrical and Computer Engineering
Geovisualization and Public Health Informatics: Tools to Inform Decisions | Lori Severtson | School of Nursing
Gleaning Relational Information from Biomedical Text | Mark Goadrich | Computer Sciences
HAMLET (Human, Animal, and Machine Learning: Experiment and Theory) | Jerry Zhu | Computer Sciences
High Throughput Microfluidics for Biological Assays | Jay Warrick | Biomedical Engineering
Human Genome Structural Polymorphism Discovery Using Optical Mapping (B. Teague);Enhancing Arrayed Micro-Culture Experiments using Microfluidics and Java (J. Warrick) | Brian Teague; Jay Warrick | Biomedical Engineering
Identification of Genes Common to Multiple Diseases | Craig A. Struble (Marquette University) | Mathematics, Statistics and Computer Science
Identifying Human Genomic Variation By Optical Mapping | Steve Goldstein | Biotechnology Center
Image Informatics for Multidimensional Light Microscopy | Kevin Elicieri | Laboratory for Optical and Computational Instrumentation
Image-Based Analysis of the Topology and Morphology of Diseased Lungs | William Mullally (Boston University) | Computer Science
Imaging and Visualizing Micro- Vascular Architectures | Michael Gleicher and Garet Lahvis | Computer Sciences; Surgery
Information Topology in Computational Biology | Amir Assadi | Mathematics
Integrating Molecular Markers for Association Studies of Complex Disease | Bret Payseur | Genetics
Interpretation of Molecular Dynamics through Diffuse X-ray Scattering | Jason McCoy | Biochemistry
Inverse Parametric Alignment for Accurate Biological Sequence Comparison | Eagu Kim | Biostatistics and Medical Informatics
Investigations of Brain Connectivity Using Diffusion-Tensor MRI | Andrew Alexander | Medical Physics
Learning Classifiers for Non- IID Data: Applications to Computer Aided Diagnosis (CAD) Problems | Glenn Fung (Siemens Medical Solutions USA) | Biomedical Engineering
Learning Ensembles of First- Order Clauses for Recall- Precision Curves: A Case Study in Biomedical Information Extraction | Mark Goadrich | Computer Sciences
Learning Models of cis-Regulatory Modules from Sequence Data | Keith Noto | Computer Sciences
Learning Regulatory Network Models that Represent Regulator States and Roles | Keith Noto | Computer Sciences
Learning Semantic Indicators for Information Extraction | Burr Settles | Computer Sciences
Linking Lay People to the Professional Literature: An Application of Natural Language Processing to Free-Text E-Mail | Patricia Brennan | Biostatistics; Medical Informatics; Nursing; Industrial Engineering
Many Low-Barrier Local Motions Cooperate to Produce the Adenylate Kinase Conformational Transition | Michael Daily | Chemistry
Medical Informatics within a Population Health Context: Building Wisconsin’s Strategic Framework | Larry Hanrahan, (Chief, Bureau of Health Information and Policy, Division of Public Health, Health, and Family Services) | Epidemiologist
Mining the Protein Data Bank and TargetDB with a Structural Genomics Focus | Ryan Bannen | Biochemistry
Modeling Gene Regulatory Pathways | Irene Ong | Computer Sciences
Modeling HIV Adaptation for Improved Vaccine Design | Eric Lantz | Computer Sciences
Modeling Patterns in Single- Nucleotide Polymorphism Data for Predicting Cancer Susceptibility: A Case Study in Multiple Myelomas | Michael Waddell | Computer Sciences
Modeling the Regulation of Ribosomal Synthesis: In vivo Insights from in vitro Data | Patrick Suthers | Chemical and Biol Eng
Modern Machine Learning for the Biostatistical Masses | Michael Coen | Biostatistics and Medical Informatics; Computer Sciences
Modular Biology: The Function and Evolution of Regulatory Networks | Aviv Regev (MIT; Broad Institute) | Biology
Molecular Simulations of Mechanochemical Coupling in Myosin | Qiang Cui | Chemistry
Monitoring Bacterial Protein Turnover at a Proteomic Scale Using Metabolic Labeling and the AMT Approach | Ed Huttlin | Biochemistry
Multi-Chamber Platform for the Study of Interactions between Cancer Cells and the Surrounding Microenvironment | Maribella Domenech | Biomedical Engineering
Multi-Level Dynamics of Viral Infections | Eric Haseltine | Chemical and Biological Engineering
Multi-Scale Perspectives of DNA Sequence | Wilma Olson (Rutgers University) | Chemistry
Multiscale Surface Techniques: Labeling and Matching the Protein Surface | Greg Cipriano | Computer Sciences
Multivariate Segmentation in the Analysis of Transcription Tiling Array Data | Antonio Piccolboni, Affymetrix | Genetics
New Computational Methods in NMR | Hamid Eghbalnia | Biochemistry
On the Complexity of the Human Genome: New Insights from the ENCODE Project | Colin Dewey | Biostatistics and Medical Informatics
On the Subspecific Origin of the Laboratory Mouse | Gary Churchill (The Jackson Laboratory) | Biology
Optical Mapping: The Human Genome Under the Microscope | Brian Teague | Laboratory for Molecular and Computational Genomics
Optimization and Evaluation of Simple Models of Protein Motion Using X-ray Crystal Data | Dmitry Kondrashov | Biochemistry
Our Genomic Future | Craig Venter (President of the Center for the Advancement of Genomics) | Genomics
Personal Genome and Synthetic Biology Projects | George Church (Harvard Medical School) | Medicine
PQR Trees and DNA Physical Mapping | Joao Meidanis (Institute of Computing, UNICAMP, Campinas, Brazil) | Bioinformatics
Predicting Bacterial Transcription Units Using Sequence and Expression Data | Joseph Bockhorst | Computer Sciences
Predicting Protein Interactions using the Docking Mesh Evaluator (DoME) | Roummel Marcia | Biochemistry
Privacy Issues in the Implementation of Electronic Health Records | David Haight | Industrial Engineering
Protein Recognition in Electron-Density Maps using Spherical- Harmonic Decompositions | Ameet Soni | Computer Sciences
Proteins, The Unfolding Story | George Rose (Johns Hopkins University) | Biochemistry
Proteomics, Ovarian Cancer, and Experimental Design | Keith A. Baggerly (Anderson Cancer) | Biostatistics and Applied Mathematics
Public Health Communication and the Potential Power of Informatics Tools | Lori Severtson | School of Nursing
Quantitative proteomics | Ruedi Aebersold (Institute for Systems Biology, Affiliate University of Washington) | Systems Biology
Quantitative Studies of Bacterial Gene Regulation | Terence Hwa (University of California-San Diego) | Center for Theoretical Biological Physics
Question Answering Systems for Physicians and Biomedical Researchers | Hong Yu (UW-Milwaukee) | Health Sciences
Rapid Magnetic Resonance Imaging (MRI): Using Numerical Methods to Move from Anatomy to Physiological Function | Walter Block | Biomedical Engineering
Realistic Simulation of Biological Macromolecules in Solution | David A. C. Beck (University of Washington) | Biochemistry
Recent Usability Studies at Marshfield Clinic | David Pieczkiewicz (Marshfield Clinic Research Foundation) | Medicine
Recursive Motifs in Metabolic Networks | Sarah Cunningham | Biophysics
Selecting the Statistical Analysis Based on the Research Question | David DeMets | Biostatistics and Medical Informatics
Self-Tuning Method for One- Chip SNP Identification | Michael Molla | Computer Sciences
Semiparametric Kernel Methods for Constructing Structural Connectivity Networks in Diffusion Tensor MRI | Gary Pack | Computer Sciences
Similarity Queries for Temporal Toxicogenomic Expression Profiles | Adam Smith | Computer Sciences
Site Selective Adsorption of DNA Nanostructures on Lithographically Patterned Substrates | Ryan J. Kershner | Mechanical Engineering
Some Aggregation Problems in Clustering and Structural Graphs | Vikas Singh | Biostatistics and Medical Informatics
Statistical Methods for the Design and Analysis of Microarray Experiments | Christiana Kendziorski | Biostatistics and Medical Informatics
Statistical Model Enhancements for Motif Finding | Sunduz Keles | Statistics; Biostatistics and Medical Informatics
Structural Genomics Wisconsin-Style | George Phillips | Biochemistry
Symmetric Image Normalization in the Space of Diffeomorphisms | James Gee (University Pennsylvania) | Radiologic Science and Computer and Information Science
Systematic Analysis of Motions and Communication Networks in a Benchmark Set of Allosteric Proteins | Michael Daily | Chemistry
Systems Biology Analysis of Signaling in Cancer: Extension to ER Cross-talk | Pamela Kreeger | Biomedical Engineering
Systems Biology of Receptor Tyrosine Kinase Signaling: Can We Navigate | Boris Kholodenko (Thomas Jefferson University) | Biology
Techniques for Extracting Contours and Merging Maps | Nagesh Adluru | Biostatistics and Medical Informatics
Temporal Discrimination of Microarray Data for Toxicogenomics | Adam Smith | Computer Sciences
The Condor View of Grid Computing | Miron Livny | Computer Sciences
The Genetics of Speciation among Three Subspecies of House Mice | Michael White | Genetics
The Genome Alignment Problem | Colin Dewey | Biostatistics and Medical Informatics
The Robot Scientist Project | Ross King (The University of Wales) | Computer Sciences
The Spectrum and Integration of Biomedical Ontologies | Christopher Chute (Mayo Clinic) | Medical Informatics
There’s No Place like ‘Ome | Mark Boguski (University of Washington- Seattle) | Biochemistry
Tools for Understanding Protein Structure and Functional Studies | Aaron Bryden | Computer Sciences
Towards Scalable Biological Data Management | Jignesh Patel | Computer Sciences
Transport and Collective Dynamics in Suspensions of Swimming Microorganisms | Michael Graham | Chemical and Biological Engineering
Using Dynamic Programming to Annotate Mass Spectra | Sean McIlwain | Computer Sciences Department
Using Mathematical Tools to Gain Insight into Binding Specificity in Protein-Protein and Protein-DNA Interactions | Julie Mitchell | Biochemistry; Mathematics
Using NMR Data for Biological Investigations: Toward a Probabilistic Approach | Hamid Eghbalnia | Biochemistry
Using Proteomics for Diagnosis | Sean McIlwain | Computer Sciences
Violating Bar Coded Medication Administration Safety Protocols | Ben- Tzion Karsh | Industrial and Systems Engineering
Visual Insights for Computational Biology | Amitabh Varshney (University of Maryland, College Park) | CMB Program
WUN Bioinformatics Video Seminar: The Proteome and the Metabolome | Janet Thorton (Director of European Bioinformatics Institute) | Bioinformatics
XIOS: A Graph-Theoretical Approach to Identifying Conserved RNA Structures | Michael Gribskov (Purdue University) | Biological Sciences
X-ray Crystallography: It’s Not Just about Structure Anymore | Demian Riccardi | Biochemistry