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CIBM Seminar Series - Fall 2009

The Computation and Informatics in Biology and Medicine seminar course (BMI 915, cross-listed in CS, Bioch, CBE, BME, and Gen) is designed to bring together trainees and trainers in the CIBM Program and other interested faculty and students for cross-disciplinary exposure to current research in computer science, biostatistics, engineering, biological sciences and biomedical research problems related to bioinformatics and computational biology.

When (except when noted): Tuesdays, 4:00 p.m.
Where (except where noted): Genetics/Biotechnology Center Auditorium, 425 Henry Mall

This is the schedule for the Spring Semester, 2009. Titles and abstracts will be added as the semester goes on, so please check back for more information.

Date	Presenter	Title	Announcement (download)
Sept. 8th	General Discussion - Introductory Session, Room 1360, 425 Henry Mall	*Note Room change
Sept. 15th	Greg Cipriano (Computer Sciences, UW-Madison)	Multiscale Surface Techniques: Labeling and Matching the Protein Surface	Talk announcement (.pdf)
Sept. 22nd Rm. 1610 Eng. Hall	Lorenz Biegler (Prof., Chemical Engineering, Carnegie Mellon Univ.)	Advanced Nonlinear Programming Methods for Chemical Process Optimization
Sept. 29th	Pei Fen Kuan, PhD (Biostatistics & Medical Informatics, UW-Madison)	A Statistical Framework for the Analysis of ChIP Seq Data	Talk announcement (.pdf)
Oct. 6th	Michael White (Genetics, UW-Madison)
Oct. 13th	no seminar; CIBM Retreat, Oct. 16th
Oct. 20th
Oct. 20th	Demian Riccardi, PhD (Biochemistry, UW-Madison)	X-ray Crystallography: It's Not Just about Structure Anymore	Talk announcement (.pdf)
Mon., Oct. 26th 1240 CS	Michael Gribskov (Prof. of Biological Sciences, Purdue Univ.)	XIOS: A Graph-Theoretical Approach to Identifying Conserved RNA Structures
Nov. 3rd	Walter Block (Associate Professor, Biomedical Engineering, UW-Madison)	Rapid Magnetic Resonance Imaging (MRI): Using Numerical Methods to Move from Anatomy to Physiological Function	Talk announcement (.pdf)
Nov. 10th	Pamela Kreeger (Assistant Professor, Biomedical Engineering, UW-Madison)	Systems Biology Analysis of Signaling in Cancer: Extension to ER Cross-talk	Talk announcement (.pdf)
Th., Nov. 19th	NOTE - different day and time! 1:30 p.m., Biotechnology Center Auditoriim
Th., Nov. 19th	Aviv Regev, PhD (Assistant Professor, MIT; Broad Institute)	Modular Biology: The Function and Evolution of Regulatory Networks
Nov. 24th	Maribella Domenech (Biomedical Engineering, UW-Madison)
Dec. 1st
Dec. 1st	Deborah Chasman (Computer Sciences, UW-Madison)
Dec. 8th	David Pieczkiewicz, PhD (Marshfield Clinic Research Foundation)
Past Seminars - Spring 2009
Jan. 20th	General Discussion - Introductory Session, Room 117, 445 Henry Mall	*Note Room change
Jan. 27th	Nagesh Adluru, PhD (Biostatistics & Medical Informatics, UW-Madison)	Techniques for Extracting Contours and Merging Maps
Feb. 3	Alessandro Senes (Asst. Prof., Biochemistry, UW-Madison)	An Integrated Computational and Biophysical Approach to the Structural Study of Integral Membrane Proteins
Feb. 10th	Shane Hubler (Mathematics, UW-Madison)	Counting Peptides
Feb. 17th	Vanissa Ortiz (Chemical & Biol. Eng., UW-Madison)	Molecular Origins of DNA Flexibility: Sequence Effects on Conformational and Mechanical Properties
Feb. 24th	Douglas B. Weibel (Ass't. Prof., Biochemistry, UW-Madison)	Dissecting the Origins of Emergent Behavior in Populations of Bacteria
March 3rd
March 3rd	Burr Settles, PhD (Biostatistics & Medical Informatics, UW-Madison)	Adaptive High-Throughput Peptide Screening and Analysis via Active Learning
March 10th	Eagu Kim (Biostatistics & Medical Informatics, UW-Madison)	Inverse Parametric Alignment for Accurate Biological Sequence Comparison
March 24th	Jerry Zhu (Ass't. Prof., Computer Sciences, UW-Madison)	HAMLET (Human, Animal, and Machine Learning: Experiment and Theory)
March 31st	Vojtech Huser (Marshfield Clinic Research Foundation)	Clinical Decision Support, Medical Knowledge Representation and Workflow Technology (A Seminar in Clinical Informatics – A Subfield of Biomedical Informatics)
April 7th
April 7th	Ragesh Chowhardy (Marshfield Clinic Research Foundation)	Genome-wide Analysis of Histone Gene Promoters
April 14th	Brian Teague (CMB Program); Jay Warrick (Biomed Eng)	Human Genome Structural Polymorphism Discovery Using Optical Mapping (B. Teague); Enhancing Arrayed Micro-culture Experiments using Microfluidics and Java (J. Warrick)
April 21st
April 21st	Amitabh Varshney, PhD (Professor of Computer Science, University of Maryland, College Park)	Visual Insights for Computational Biology
April 28th	Gary Pack (Computer Sciences, UW-Madison)	Semiparametric Kernel Methods for Constructing Structural Connectivity Networks in Diffusion Tensor MRI
May 5th 2:30 PM	Wilma Olson, PhD (Professor, Dept. of Chemistry, Rutgers University)	Multi-scale Perspectives of DNA Sequence
Past Seminars - Fall 2008
Sept. 9	General Discussion - Introductory Session, Room 1360 Biotechnology Center	*Note Room change
Sept. 16	Ben-Tzion Karsh (Assoc. Prof., Industrial & Systems Eng., UW-Madison)	Violating Bar Coded Medication Administration Safety Protocols
Sept. 23	Michael Coen, Asst. Prof., Biostatistics & Medical Infomratics; Computer Sciences, UW-Madison	Modern Machine Learning for the Biostatistical Masses
Sept. 30	John E. Johnson (Professor, Department of Molecular Biology, The Scripps Research Institutte)	Biophysical and Computational Studies of Virus Particles and their Maturation: Insights into Elegantly Programmed Nano-machines
Oct. 7	Julie Mitchell (Ass't. Prof., Biochemistry; Mathematics, UW-Madison)	Using Mathematical Tools to Gain Insight into Binding Specificity in Protein-Protein and Protein-DNA Interactions
Oct. 14	No seminar this week
Oct. 21
Oct. 21	Jignesh Patel (Assoc. Professor, Computer Sciences, UW-Madison)	Towards Scalable Biological Data Management
Oct. 28	Dana Wohlbach (Genetics, UW-Madison)	Comparative genomics of the environmental stress response in Ascomycete fungi
Fri., Nov. 7	NOTE - different day and time! 12:00 p.m., 5275 Medical Sciences Center, 1300 Univ. Ave.
Fri., Nov. 7	Eleazar Eskin (Assistant Professor, Departments of Computer Science; Human Genetics, UCLA)	Computational Challenges in Discovering the Genetic Basis of Complex Traits in Inbred Mouse Strains
Nov. 11	NOTE - different time! 3:30 pm (Optional seminar)
Nov. 11	Peter Agre (Director, Johns Hopkins Malaria Research Institute)	Aquaporin Water Channels-from Atomic Structure to Malaria Room 1111 Biotech, 3:30 pm
Nov. 18	Michael Daily (Chemistry, UW-Madison)	Systematic Analysis of Motions and Communication Networks in a Benchmark Set of Allosteric Proteins
Nov. 21
Nov. 21	Rafael Irizarry (Professor of Biostatistics, Johns Hopkins University)	A Species-Generalized Probabilistic Model-Based Definition of CpG Islands (12 pm, Rm. 5275 MSC)
Dec. 2
Dec. 2	Eric Lantz (Computer Sciences, UW-Madison)	Modeling HIV Adaptation for Improved Vaccine Design
Past Seminars - Spring 2008
Jan. 22	General Discussion - Introductory Session, Room 1360 Biotechnology Center	*Note Room change
Jan. 29	Stephen Stanhope (Statistics, UW-Madison)	Detecting Messenger and MicroRNA Targeting Relationships from Observational Microarray Data Studies
Feb. 5	Ryan J. Kershner, Ph.D. , Asst. Prof., Mechanical Engineering, UW-Madison	Site Selective Adsorption of DNA Nanostructures on Lithographically Patterned Substrates
Feb. 12	Nathan Miller (Biomedical Engineering Graduate Program)	Computer Vision Algorithms for Phenotyping the Model Plant Arabidopsis
Feb. 19	Gregory S. Chirikjian, Ph.D. (Johns Hopkins University)	Computing the Conformational Entropy of the Folded and Unfolded Ensembles of a Protein Using Lie Groups
Feb. 26	No seminar this week
Mar. 4
Mar. 4	David Andrzejewski (Computer Sciences, UW-Madison)	Data Analysis with Latent Topic Models: Genes, Bugs, and Art
Mar. 11	David Pieczkiewicz, PhD (Marshfield Clinic Research Foundation)	Better Living Through Design: Visualizing Biomedical Data for Patient Care, Public Health, and Research
Mar. 18	No seminar, Spring Break
Mar. 25
Mar. 25	Vanessa Ortiz, PhD (Chemical & Biological Engineering, UW-Madison)	Exploring the Flexibility of DNA with Molecular Dynamics Simulations
Apr. 1	Ameet Soni (Computer Sciences, UW-Madison)	Protein Recognition in Electron-Density Maps using Spherical-Harmonic Decompositions
Apr. 8
Apr. 8	Gary A. Churchill, Ph.D. (The Jackson Laboratory)	On the Subspecific Origin of the Laboratory Mouse
Apr. 15
Apr. 15	Vikas Singh, PhD (Ass't Prof., Dept. of Biostatistics & Med. Informatics, UW-Madison)	Some Aggregation Problems in Clustering and Structural Graphs
Apr. 22
Apr. 22	Karl Broman, PhD (Assoc. Prof., Depts. of Biostatistics and Medical Informatics; Genetics, UW-Madison)	Genetic Maps: Past, Present and Future
Apr. 29
Apr. 29	Demian Riccardi, PhD (Biochemistry, UW-Madison)
Past Seminars - Fall 2007
Sept. 4	General Discussion - Introductory Session, Room 1360 Biotechnology Center	*Note Room change
Fri., Sept. 14	NOTE - different day and time! 2:25 p.m., B235 Van Vleck Hall, 480 Lincoln Drive
Fri., Sept. 14	Michael Feig (Assistant Professor, Departments of Biochemistry & Molecular Biology; Chemistry, Michigan State Univ.)	Efficient Modeling of Solvent Environments
Sept. 18	Colin Dewey (Ass't. Prof., Biostatistics & Medical Informatics, UW-Madison)	On the Complexity of the Human Genome: New Insights from the ENCODE Project
Sept. 25	David Haight (Dept. of Industrial and Systems Engineering)	Cryptographic Accuracy Annotations for Electronically Exchanged Personal Health Information
Fri., Oct. 5	NOTE - different day and time! 12:00 p.m., 5275 MSC, 1300 Univ. Avenue
Fri., Oct. 5	James Gee (Associate Professor of Radiologic Science and Computer and Information Science, U. Penn.)	Symmetric Image Normalization in the Space of Diffeomorphisms
Oct. 9	Greg Cipriano (Computer Sciences, UW-Madison)	Molecular Surface Abstraction
Oct. 16
Oct. 16	No seminar, CIBM Retreat is Fri., Oct. 19th
Oct. 23	David DeMets (Biostatistics and Medical Informatics, UW-Madison)	Selecting the Statistical Analysis Based on the Research Question
Oct. 30	Ed Huttlin (Biochemistry, UW-Madison)	Monitoring Bacterial Protein Turnover at a Proteomic Scale Using Metabolic Labeling and the AMT Approach
Nov. 6
Nov. 6	Adam Smith (Computer Sciences, UW-Madison)	Similarity Queries for Temporal Toxicogenomic Expression Profiles
Nov. 13	Brian Teague (Laboratory for Molecular and Computational Genomics, UW-Madison)	Optical Mapping: The Human Genome Under the Microscope
Nov. 20
Nov. 20	Dimitri Semizarov, PhD (Global Pharmaceutical Research and Development), Abbott Laboratories)	Analysis of Gene Copy Number Abnormalities in Cancer: Computational Challenges
Nov. 27
Nov. 27	Chris Warren (Department of Biochemistry, UW-Madison)	Cognate Site Identifier (CSI) Array: A High-Throughput Technique to Determine the Comprehensive Sequence Specificity of DNA-Binding Molecules
Dec. 4
Dec. 4	Sean McIlwain (Computer Sciences Department, UW-Madison)	Using Dynamic Programming to Annotate Mass Spectra
Past Seminars - Spring 2007
Jan. 23	Glenn Fung, PhD, Siemens Medical Solutions USA	Learning Classifiers for Non-IID Data: Applications to Computer Aided Diagnosis (CAD) Problems
Jan. 30	General Discussion, Room 1360 Biotechnology Center	*Note room change: Room 1360
Feb. 6	Elena Levin (Biochemistry, UW-Madison)	Ensemble Refinement of Protein Crystal Structures: Validation and Application
Feb. 13	Jennifer Reed (Dept. of Biomedical Engineering, UC-San Diego)	Development and Applications of Escherichia coli Metabolic Models
Feb. 20	Nicholas Shera (Laboratory for Molecular and Computational Genomics, UW-Madison)	Cancer Genomics: Discovery and Characterization of Structural Alterations in the Solid Tumor Oligodendroglioma via Single Molecule Analysis
Feb. 27	Juan de Pablo (Chemical & Biological Engineering, UW-Madison)	Driven Assembly of Nanoscale Objects, and its Application in Nanotechnology
March 6
March 6	Lori Severtson (School of Nursing, UW-Madison)	Geovisualization & Public Health Informatics: Tools to Inform Decisions
March 13	Jay Warrick (Biomedical Engineering, UW-Madison)	High Throughput Microfluidics for Biological Assays
March 20	Hong Yu (Ass't. Prof., Health Sciences, UW-Milwaukee)	Question Answering Systems for Physicians and Biomedical Researchers
March 27
March 27	Antonio Piccolboni, Affymetrix	Multivariate Segmentation in the Analysis of Transcription Tiling Array Data
April 3
April 3	No Class, Spring Break
April 10	William Mullally (Computer Science, Boston University)	Image-Based Analysis of the Topology and Morphology of Diseased Lungs
April 17
April 17	Sunduz Keles (Statistics; Biostatistics & Medical Informatics, UW-Madison)	Statistical Model Enhancements for Motif Finding
April 24
April 24	Kevin Elicieri (Laboratory for Optical and Computational Instrumentation, UW-Madison)	Image Informatics for Multidimensional Light Microscopy
May 1
May 1	Bret Payseur (Ass't. Prof., Dept. of Genetics, UW-Madison)	Integrating Molecular Markers for Association Studies of Complex Disease
Past Seminars - Fall 2006
Sept. 5	General Discussion, Room 1360 Biotechnology Center	*Note room change
Sept. 12	General Discussion, Room 1360 Biotechnology Center	*Note room change: Room 1360
Sept. 21	NOTE - different day and time! 3:30 p.m., Thursday, B1118 Biochemistry
Sept. 21	Terence Hwa , Ph.D. (Professor, Center for Theoretical Biological Physics, UC San Diego)	Quantitative Studies of Bacterial Gene Regulation
Sept. 26	Gheorghe Craciun , Ph.D. (Assistant Professor, Mathematics; Biomolecular Chemistry, UW-Madison)	De Novo Peptide Sequencing using Tandem Mass Spectrometry Data
Oct. 3	NOTE - different room! 4:00 pm 1800 Engineering Hall, 1415 Engineering Drive
Oct. 3	Jason Haugh, Ph.D. (Associate Professor, Chemical Engineering, North Carolina State University),	Analysis of Intracellular Signal Transduction at Various Scales of Biological Complexity
Oct. 10	No seminar - CIBM Retreat Fri., Oct. 13th
Oct. 17 Cancelled	Hong Yu Ph.D. (Ass't. Professor, Computer Science, UW-Milwaukee)	Beyond Information Retrieval - Medical Question Answering	Cancelled
Oct. 24	Aaron Bryden (Computer Sciences, UW-Madison)	Tools for Understanding Protein Structure and Functional Studies
Oct. 31
Oct. 31	Sarah Cunningham (Biophysics, UW-Madison)	Recursive Motifs in Metabolic Networks
Nov. 7	Steve Darnell (Biochemistry, UW-Madison)	An Automated Decision-Tree Approach to Predicting Protein Interaction Hot Spots
Nov. 14	Colin Dewey, PhD (Biostatistics & Medical Informatics, UW-Madison)	The Genome Alignment Problem
Nov. 21
Nov. 21	Robert Nowak , PhD (Electrical & Comp. Engineering, UW-Madison)	Genomic Network Tomography
Nov. 28
Nov. 28	Dmitry Kondrashov, Ph.D. (Biochemistry, UW-Madison)	Conformational Flexibility of Proteins in Crystallography and Computational Models
Dec. 5	Mark Goadrich (Computer Sciences, UW-Madison)	Gleaning Relational Information from Biomedical Text
Past Seminars - Fall 2005
Sept. 6	General Discussion, Room 1360 Biotechnology Center	*Note room change
Sept. 13	General Discussion, Room 1360 Biotechnology Center	*Note room change: Room 1360
Sept. 20	Bret Larget, Ph.D. (Assoc. Professor, Depts. of Statistics; Botany, UW-Madison)	Case Studies in Bayesian Phylogenetics	Talk announcement (.pdf)
Sept. 27	Hamid Eghbalnia , Ph.D. (Assistant Scientist, Biochemistry, UW-Madison)	Using NMR data for biological investigations: toward a probabilistic approach	Talk announcement (.pdf)
Oct. 4	Robert Hamers, Ph.D. (Professor, Department of Chemistry, UW-Madison)	Bio-electronic Interfaces for Direct Electronic Sensing	Talk announcement (.pdf)
Oct. 11	Roxana Alexandridis, Ph.D. (Department of Bacteriology, UW-Madison)	A Unified Approach to Discovery and Classification of Tumor Types using Gene Expression Data	Talk announcement (.pdf)
Oct. 18	Jun Liu, Ph.D. (Professor, Department of Statistics, Harvard University)	From Sequence Information to Gene Expression	Talk announcement (.pdf)
Oct. 25	No seminar (CIBM Retreat Oct. 28th)
Nov. 1
Nov. 1	Larry Hanrahan, Ph.D. (Chief Epidemiologist, Bureau of Health Information and Policy, Division of Public Health, Department of Health and Family Services)	Medical Informatics within a Population Health Context: Building Wisconsin’s Strategic Framework
Nov. 8	Keith Noto (CIBM Predoctoral Fellow, Computer Sciences, UW-Madison)	Learning Models of cis-Regulatory Modules from Sequence Data	Talk announcement (.pdf)
Nov. 15	David Haight (CIBM Predoctoral Fellow, Industrial Engineering, UW-Madison)	Privacy Issues in the Implementation of Electronic Health Records	Talk announcement (.pdf)
Nov. 21	NOTE - different day and time! 3:30 p.m., Mon., B1118 Biochemistry
Nov. 21	Boris Kholodenko, Ph.D. (Thomas Jefferson University)	Systems Biology of Receptor Tyrosine Kinase Signaling: Can We Navigate Through Molecular Jungles?
Nov. 29
Nov. 29	Dmitry Kondrashov, Ph.D. (CIBM Postdoctoral Fellow, Biochemistry, UW-Madison)	Optimization and Evaluation of Simple Models of Protein Motion Using X-Ray Crystal Data	Talk announcement (.pdf)
Dec. 6	George Phillips, Ph.D. (Professor, Dept. of Biochemistry, UW-Madison0	Structural Genomics Wisconsin-Style
Dec. 12	NOTE - different day and time! 3:30 p.m., Mon., B1118 Biochemistry
Dec. 12	George Rose , Ph.D. (Johns Hopkins University)	Proteins, The Unfolding Story
Past Seminars - Spring 2005
Jan. 18	Roummel Marcia, Ph.D. (CIBM Postdoctoral Fellow, Dept. of Biochemistry)	Predicting Protein Interactions using the Docking Mesh Evaluator (DoME)	Talk announcement (.pdf)
Jan. 25	General Discussion, Room 1360 Biotechnology Center	*Note room change: Room 1360
Feb. 1	Adam Smith (Dept. of Computer Sciences, UW-Madison)	Temporal Discrimination of Microarray Data for Toxicogenomics	Talk announcement (.pdf)
Feb. 8	Lori Severtson, Ph.D. (CIBM Postdoctoral Fellow, School of Nursing)	Public Health Communication and the Potential Power of Informatics Tools	Talk announcement (.pdf)
Feb. 15	Christiana Kendziorski, Ph.D. (Ass't Professor, Depts. of Biostatistics and Medical Informatics)	Statistical Methods for the Design and Analysis of Microarray Experiments	Talk announcement (.pdf)
Feb. 22	Patrick Suthers ( Dept. of Chemical & Biol. Eng.)	Modeling the Regulation of Ribosomal Synthesis: In vivo Insights from in vitro Data	Talk announcement (.pdf)
March 1	Craig A. Struble, Ph.D. (Assistant Professor, Department of Mathematics, Statistics and Computer Science, Marquette University)	Identification of Genes Common to Multiple Diseases	Talk announcement (.pdf)
March 8	Timothy Durfee, Ph.D. (CIBM Postdoctoral Fellow, Genome Center; Dept. of Genetics	Control of Global Transcription in Escherichia coli	Talk announcement (.pdf)
March 14	Special Seminar. NOTE - different day and time! 3:30 p.m., Mon., B1118 Biochemistry
March 14	Lynn Ten Eyck, Ph.D. (Adjunct Prof., UC-San Diego, Dept. of Pharmacology; Assoc. Director, Computational Science Research, San Diego Supercomputer Center)	Computational and Experimental Models for Macromolecular Recognition
March 15	Christopher Chute, M.D., D.P.H. (Professor of Medical Informatics, Mayo Clinic)	The Spectrum and Integration of Biomedical Ontologies	Talk announcement (.pdf)
March 29	David A. C. Beck (University of Washington)	Realistic Simulation of Biological Macromolecules in Solution	Talk announcement (.pdf)
April 5	Chris Oldfield (CIBM Predoctoral Fellow, Dept. of Biophysics)
April 13	NOTE - different day and time! 2:00 p.m., Wed., Genetics/Biotechnology Ctr Auditorium
April 13	Keith A. Baggerly, Ph.D. (MD Anderson Cancer, Biostatistics and Applied Mathematics)	Proteomics, Ovarian Cancer, and Experimental Design	Talk announcement (.pdf)
April 19	Irene Ong (CIBM Predoctoral Fellow, Dept. of Computer Sciences)	Modeling Gene Regulatory Pathways	Talk announcement (.pdf)
April 27	NOTE - different day and time! 11:00 a.m., Wed., Room 1360, Genetics/Biotechnology Ctr
April 27	Janet Thorton, Director of European Bioinformatics Institute	WUN Bioinformatics Video Seminar: The Proteome and the Metabolome
Past Seminars - Fall 2004
Sept. 8	NOTE - different day and time! 12:00 p.m., Wed., Genetics/Biotech Ctr Auditorium
Sept. 8	Mark Boguski, M.D., Ph.D. (University of Washington, Seattle WA)	There's No Place like 'Ome
Sept. 14	Steve Goldstein, Ph.D. (Biotechnology Center, UW-Madison)	Identifying Human Genomic Variation By Optical Mapping	Talk announcement (.pdf)
Sept. 21	Mark Goadrich (Dept. of Computer Sciences, UW-Madison)	Learning Ensembles of First-Order Clauses for Recall-Precision Curves: A Case Study in Biomedical Information Extraction	Talk announcement (.pdf)
Sept. 28	Qiang Cui , Ph.D. (Ass't. Prof., Dept. of Chem., UW-Madison)	Molecular Simulations of Mechanochemical Coupling in Myosin	Talk announcement (.pdf)
Oct. 6	NOTE - different day and time! 12:00 p.m., Wed., Genetics/Biotech Ctr Auditorium
Oct. 6	George Church , Ph.D. (Prof., Harvard Medical School)	Personal Genome and Synthetic Biology Projects	Talk announcement (.pdf)
Oct. 13	NOTE - different day and time! 12:00 p.m., Wed., Genetics/Biotech Ctr Auditorium
Oct. 13	Ross King, Ph.D. (Prof., Dept. of Computer Sciences, The University of Wales)	The Robot Scientist Project	Talk announcement (.pdf)
Oct. 19	No seminar (CIBM retreat Friday, Oct. 15th)
Oct. 26	Eric Haseltine (Dept. of Chemical & Biol. Engineering, UW-Madison)	Multi-Level Dynamics of Viral Infections	Talk announcement (.pdf)
Nov. 2	Miron Livny (Professor, Dept. of Computer Sciences, UW-Madison)	The Condor View of Grid Computing	Talk announcement (.pdf)
Nov. 9	Elizabeth Burnside (Ass't. Professor, Depts. of Radiology; Biostat. and Medical Informatics, UW-Madison)	A Bayesian Network to Improve Early Detection of Breast Cancer	Talk announcement (.pdf)
Nov. 16	Michael Molla (Dept. of Computer Sciences, UW-Madison)	Self-Tuning Method for One-Chip SNP Identification	Talk announcement (.pdf)
Nov. 23	Ryan Bannen (Dept. of Biochemistry, UW-Madison)	Mining the Protein Data Bank and TargetDB with a Structural Genomics Focus	Talk announcement (.pdf)
Nov. 30	Walter Block (Assistant Professor, Department of Biomedical Eng. & Medical Physics, UW-Madison)	Engineering Added Dimensions into Magnetic Resonance Imaging	Talk announcement (.pdf)

Past Seminars - Spring 2004
Jan. 20	Christine Heitsch (CIBM Postdoctoral Fellow, Depts. of Math and Chemistry)	A New DNA Word Design Strategy Using Random de Bruijn Sequences	Talk announcement (.pdf)
Jan. 27	Burr Settles (CIBM Predoctoral Fellow, Dept. of Computer Sciences)	Learning Semantic Indicators for Information Extraction	Talk announcement (.pdf)
Feb. 3	Ryan Bannen (CIBM Predoctoral Fellow, Dept. of Biochemistry)	Application of the Gaussian Network Model and a Variation of Normal Mode Analysis for Refinement of Protein Structures	Talk announcement (.pdf)
Feb. 10	Aaron Darling (CIBM Predoctoral Fellow, Dept. of Computer Sciences)	Designing and Evaluating a Method for Multiple Genome Comparison	Talk announcement (.pdf)
Feb. 17	Daniel McFarlin (CIBM Postdoctoral Fellow, Depts. of Biostatistics and Medical Informatics, and Oncology)	Computer Simulation of Ras Signaling Kinetics	Talk announcement (.pdf)
Feb. 24	Chris Warren (CIBM Predoctoral Fellow, Dept. of Biochemistry)	Design and Evaluation of Double-Stranded DNA Microarrays	Talk announcement (.pdf)
March 2	Michael Waddell (CIBM Predoctoral Fellow, Dept. of Computer Sciences)	Modeling Patterns in Single-Nucleotide Polymorphism Data for Predicting Cancer Susceptibility: A Case Study in Multiple Myelomas	Talk announcement (.pdf)
March 9	Frank DiMaio (CIBM Predoctoral Fellow, Dept. of Computer Sciences)	Extending Pictorial Structures for the Interpretation of Crystallographic Density Maps	Talk announcement (.pdf)
March 23	Keith Noto (CIBM Predoctoral Fellow, Dept. of Computer Sciences)	Learning Regulatory Network Models that Represent Regulator States and Roles	Talk announcement (.pdf)
March 30	Dalia Dhingra (CIBM Predoctoral Fellow, Dept. of Chemistry)	A Single Fluorochrome System for Genomic Analysis	Talk announcement (.pdf)
April 6	Sean McIlwain (CIBM Predoctoral Fellow, Dept. of Computer Sciences)	Using Proteomics for Diagnosis	Talk announcement (.pdf)
April 13	Richard Karp (Professor, Computer Sciences Div., Univ. of Calif., Berkeley)	Hilldale Lecture: 4 p.m., 1100 Grainger Hall, Computers as Puzzle Solvers: The Challenge of Efficient Search
April 20	Audrey Gasch (Ass't. Prof., Dept. of Genetics, Genome Center of Wisc.)	Conservation and Evolution of Cis-regulatory Elements in Diverse Fungi	Talk announcement (.pdf)
April 27	Jason McCoy (CIBM Predoctoral Fellow, Dept. of Biochemistry)	Interpretation of Molecular Dynamics through Diffuse X-ray Scattering	Talk announcement (.pdf)
Past Seminars - Fall 2003
Sept. 3	NOTE - different day and time! 3:30 p.m., Wed., Genetics/Biotech Center Auditorium
Sept. 3	Fred Blattner (Professor, Department of Genetics)	A reductionist approach to E. coli functional genomics
Sept. 9	Henry Zeringue (Dept. of Biomedical Engineering, CIBM Predoctoral Fellow, UW-Madison)	Development of a SNPChip	Talk announcement (.pdf)
Sept. 16	Michael Ferris (Professor, Dept. of Computer Sciences and Industrial Engineering)	Fractionation in radiation treatment planning	Talk announcement (.pdf)
Sept. 23	Brian Yandell (Professor, Depts. of Statistics and Horticulture)	Gene Mapping in the Post-Genomic Era	Talk announcement (.pdf)
Sept. 30	No seminar (CIBM retreat Friday, Oct. 3rd)
Oct. 7	Andrew L. Alexander (Assistant Professor, Depts. of Medical Physics)	Investigations of Brain Connectivity Using Diffusion-Tensor MRI	Talk announcement (.pdf)
Oct. 14	Nicole Perna (Assistant Professor, Dept. of Animal Health and Biomedical Sciences and Genome Center of Wisconsin)	ASAP, Community Annotation and Analysis of Genomes
Oct. 21	Hamid Eghbalnia (Dept. of Biochemistry, CIBM Postdoctoral Trainee)	New Computational Methods in NMR
Oct. 28	Joao Meidanis (Laboratory of Bioinformatics, Institute of Computing, UNICAMP, Campinas, Brazil)	PQR Trees and DNA Physical Mapping	Talk announcement (.pdf)
Nov. 3	NOTE - different day, time and place! 3:30 p.m., Mon., B1118 Biochem
Nov. 3	Ruedi Aebersold (Institute for Systems Biology, Affiliate Professor, University of Washington)	Quantitative proteomics
Nov. 11	Michael Gleicher (Ass't. Prof., Dept. of Computer Sciences) and Garet P. Lahvis, Ph.D. (Ass't. Prof., Dept. of Surgery, UW-Madison)	Imaging and Visualizing Micro-Vascular Architectures
Nov. 18	Amir Assadi (Professor, Department of Mathematics)	Information Topology in Computational Biology
Nov. 19	NOTE - different day and time! 3:30 p.m., Wed., Genetics/Biotech Center Auditorium
Nov. 19	Craig Venter (President of the Center for the Advancement of Genomics)	Our Genomic Future
Nov. 25	Joseph Bockhorst (Department of Computer Sciences, CIBM Predoctoral Fellow, UW-Madison)	Predicting Bacterial Transcription Units Using Sequence and Expression Data
Dec. 2	Louis Oliphant (Dept. of Computer Sciences, CIBM Predoctoral Fellow)	Finding Relations in Biomedical Literature Using Inductive Logic Programming
Oct. 3	CIBM Annual Retreat (9 AM - 5 PM), Pyle Center, Room 325/326 Talks include:
	9:45-10:45 - Patricia Brennan (Professor, Depts. of Biostatistics and Medical Informatics, Nursing, and Industrial Engineering, UW-Madison)	Linking Lay People to the Professional Literature - An Application of Natural Language Processing to Free-Text E-Mail	Talk announcement (.pdf)
	1:15-2:15 - John Yin (Associate Professor, Dept. of Chemical and Biological Engineering, UW-Madison)	From Genome to Organism: A Virus-world View	Talk announcement (.pdf)
	3:30-4:30 - Michael Giddings (Assistant Professor, Microbiology & Immunology; Biomedical Engineering, University of North Carolina-Chapel Hill)	Genome Analysis by Proteomic Methods and Genome Fingerprint Scanning	Talk announcement (.pdf)

Past Seminars

Fall 2002 Spring 2003

Related Seminars

Dept. of Biochemistry	Dept. of Biostatitics and Medical Informatics
Dept. of Chemistry	Dept. of Computer Sciences
School of Engineering	Dept. of Genetics
Dept. of Mathematics	McArdle Laboratory For Cancer Research
Dept. of Statistics	UW Biotechnology Center Bioscience Event Listings

Course Information

Most seminars listed are a part of the course Computation and Informatics in Biology and Medicine (Biostatistics and Medical Informatics 915, cross-listed inCS, Bioch, Gen, CBE, and BME).

Grading:

Students who don’t present: Those students who don’t give a presentation will be assigned an S/U letter grade based on participation and attendance. Each student will be required to evaluate the seminar speakers for sufficiency of background, presentation of the problem, understandability, explanation of methodology, suitability of the scope of the presentation for the audience, and to comment on the presentation and on insights learned. Grading will be done by the instructors.

Students who present: Students will present a seminar on their own research or on a relevant article from the scientific literature. The articles chosen for presentations must be approved in advance by the instructors. The students that give a presentation will be assigned a letter grade A-F based on their presentation, in addition to attendance and participation. Their presentation will be evaluated jointly by the instructors, and the grade for the presentation will be based on the quality and clarity of their presentation, taking into account their oral delivery as well as use of visual aids, their ability to explain the research problem, results and its impact to a multi-disciplinary audience and on their ability to answer questions.

Instructors:

Louise Pape (Department of Genetics and Biotechnology Center);
lpape@facstaff.wisc.edu

George Phillips (Departments of Biochemistry and Computer Sciences);
phillips@biochem.wisc.edu

Jude Shavlik (Computer Sciences Department and Department of Biostatistics and Medical Informatics);
shavlik@cs.wisc.edu

Fred Blattner (Department of Genetics);
fred@genome.wisc.edu

Reading List:

A list of articles recommended by presenters will be distributed prior to their seminars.

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File last modified: September 27, 2003
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