Louise Pape
425 Henry Mall Rm 3445
Madison, WI 53706
Phone: 608-265-7935


Karen Nafzger
425 Henry Mall Rm 3420
Madison, WI 53706
Phone: 608-262-4366



Our seminar is held during the Fall and Spring semester, and all are welcome to attend.

Tuesdays, 4:00 p.m.

Genetics/Biotechnology Center Auditorium or Room 1360 Biotechnology Center, 425 Henry Mall

SPRING 2019   

Jan. 22 Presentations by Chris Magnano and Kendall Park, CIBM predoctoral fellows (Computer Sciences Department, UW-Madison), Choosing Parameters for Useful Pathways in Biological Pathway Prediction (CM); Human-Computer Interaction Challenges in Machine Learning Clinical Decision Support (KP), Room 1360 Biotechnology Center

Jan. 29 Presentation by Simon Foucart, PhD, Associate Professor (Department of Mathematics, Texas A&M University), Sparse Recovery Techniques In Metagenomics, Auditorium

Feb. 5 Presentation by Ashley Kates, PhD CIBM postdoctoral fellows (Department of Medicine, UWSMPH), From Probiotics to FMT: Harnessing Microbes to Prevent Bacterial Infections, Room 1360 Biotechnology Center

Feb. 12 Presentation by Jane Tang, PhD, Assistant Professor (Dept. of Biostatistics and Medical Informatics, UW-Madison), Zero-Inflated Generalized Dirichlet Multinomial (ZIGDM) Regression Model for Microbiome Compositional Data, Auditorium

Feb. 19 Presentation by Miaoyan Wang, PhD, Assistant Professor (Department of Statistics, UW-Madison), Three-way Clustering of Muti-Tissue Multi-Individual Gene Expression Data Using Tensor Decomposition, Auditorium

Feb. 26 Presentation by Sebastian Raschka, PhD, Assistant Professor (Department of Statistics, UW-Madison), Discovering Patterns of Molecular Recognition: Protein-ligand Interfaces Are Polarized and Favor Hydrogen Bond Donors on the Protein Side, Auditorium

Mar. 5 Presentation by Catherine Arnott Smith, PhD, Professor (The Information School, UW-Madison; Discovery Fellow, Wisconsin Institutes for Discovery), Title TBA

Mar. 12 Presentation by David Schneider, MD, MS, FACS, Assistant Professor (Depaertment of Surgery, UW School of Medicine and Public Health), Adventures in Natural Language Processing, Auditorium

Mar. 19 No seminar, spring break

Mar. 26 Presentation by Andrew Hasley, PhD, CIBM postdoctoral fellow (Dept. of Genetics, UW-Madison), Actually, Data Science CAN Be Accessible: Barriers to Inclusion of People with Disabilities in the Data Science Workforce Pipeline and Ideas for Lowering Them, Rm. 1360 Biotech

Apr. 2 Presentation by Mostafa Zamanian, PhD, Assistant Professor (Department of Pathobiological Sciences, UW School of Veterinary Medicine), Genomic Perspectives on Drug Target Discovery in Neglected Tropical Parasites, Auditorium

Apr. 9 Presentation by Lauren Baker, PhD, CIBM postdoctoral fellow (Department of Surgical Sciences, UW School of Veterinary Medicine)Leveraging the Canine Model for Genetic Dissection of ACL Rupture, Rm. 1360 Biotech

Apr. 16 Presentation by Erin Zwick, CIBM predoctoral fellow (Epidemiology PhD Program), Computational Modelling of Complex Transmission Dynamics in a Tuberculosis Epidemic, Rm. 1360 Biotech

Apr. 23 Presentation by David R. Bell, PhD, Associate Professor (Department of Kinesiology, UW-Madison), Applications of GPS Technology in Sport Performance and Rehabilitation, Auditorium

Apr. 30 Presentation by Deborah Chasman, PhD, CIBM postdoctoral fellow (Department of Ob-Gyn, UWSMPH), Inferring Molecular and Immunologic Signatures for Early Life Farm Exposure, Rm. 1360 Biotech

FALL 2018   

Sept. 11 Introductory Session I, Room 1360 Biotechnology Center

Sept. 18 Introductory Session II, 1360 Biotech Center

Sept. 25 Presentations by Samamntha Anderson and Niklas Gahm, CIBM predoctoral fellows (Biochemistry (SA); Biomedical Eng. (NG), Understanding Sequence, Structure, and Energetics of Membrane Protein Interactions (SA); Sequential Tissue Erosion Imaging for Thick Fluorescent Biological Samples (NG), Room 1360 Biotechnology Center

Oct. 2 Presentation by Brody Holohan, PhD, CIBM postdoctoral fellow (Center for Human Genetics, Marshfield Clinic Research Inst.), Fear and Loathing in Personalized Medicine: A Savage Journey to the Heart of the New American Dream, Auditorium

Oct. 9 Presentation by Joe Austerweil, Assistant Professor (Dept. of Psychology, University of Wisconsin-Madison), Analyzing Healthy and Pathological Memory Retrieval as (Censored) Random Walks over Different Knowledge Structures, Auditorium

Oct. 16 Presentation by Jesse Meyer, PhD, CIBM postdoctoral fellow (Genome Center of Wisconsin, University of Wisconsin-Madison), Vignettes of Computation in Systems Biology, 1360 Biotech Center

Oct. 23 No seminar, CIBM Retreat is Oct. 26

Oct. 30 Amy Cochran, PhD, Assistant Scientist (Dept. of Biostatistics & Medical Informatics, University of Wisconsin-Madison), Computational Phenotyping in Mental Health, Auditorium

Nov. 8 3:30 pm, Presentation by Marie Davidian, PhD, J. Stuart Hunter Distinguished Professor (Dept. of Statistics, North Carolina State University), David Demets Lectures, The Right Treatment for the Right Patient at the Right Time: Precision Medicine Through Treatment Regimes and SMARTs, 1325 Health Sciences Learning Center

Nov. 9 9:00 am, Presentation by Marie Davidian, PhD, J. Stuart Hunter Distinguished Professor (Dept. of Statistics, North Carolina State University), David Demets Lectures, Machine Learning-based Estimation of Optimal Treatment Regimes With Censored Survival Outcome, Biotechnology Center Auditorium

Nov. 13 Daniel Conn, PhD, CIBM postdoctoral fellow (Dept. of Biostatistics & Medical Informatics, University of Wisconsin-Madison), Zero-Inflated Random Forests for Single Cell RNA-Seq Modeling, Auditorium

Nov. 20 Presentation by Yin Li, PhD, Assistant Professor (Dept. of Biostatistics and Medical Informatics, University of Wisconsin-Madison Activity Recognition from a First Person Perspective

Nov. 27 Presentation by Karl Broman, Steps toward Reproducible Research, Auditorium

Dec. 4 Presentation by Reed Stubbendieck, PhD, CIBM postdoctoral fellow (Dept. of Bacteriology, UW-Madison), Microbial Competition from Below Your Toes to Inside Your Nose, Auditorium

SPRING 2018   

Jan. 23 Ross Kleiman, CIBM predoctoral fellow (Computer Sciences), Practical Information for the Application of Machine Learning, 1360 Biotech Center

Jan. 30, Matthew Bernstein, CIBM fellow (Computer Sciences), Room 1360 Gen/Biotech Bldg., Towards Cell-type Prediction with Public RNA-seq Data, 1360 Biotech Center

Feb. 6 Presentation by Maria Chikina (University of Pittsburgh), 10:45 am, Learning Interpretable Representations Of Biological Data, Auditorium

Feb. 13 Presentation by Molly Carroll, PhD, CIBM fellow (Biomedical Engineering, UW-Madison), Investigations of Paracrine Signaling Between Alternatively Activated Macrophages and Ovarian Cancer in the Metastatic Microenvironment, Auditorium

Feb. 20 9:30 am, Orchard View Room, Discovery Building, 330 N. Orchard St., Presentation by Ellen Wright Clayton, J.D., M.D. (Craig-Weaver Professor of Pediatrics; Professor of Law; Professor of Health Policy, Vanderbilt Univ.), Lessons (Not) to be Learned from the Debate about Genetic Privacy

Feb. 27 Presentation by Seong Jae Hwang, CIBM Fellow (Computer Sciences Department), Some Latent Representations in Medical Image Analysis and Computer Vision , Rm. 1360 Biotechnology Center

Mar 6  Presentation by Burcu Darst, CIBM Fellow (Population Health Sciences), Metabolomics, Genomics, and Risk for Alzheimer’s Disease, Room 1360 Biotech Center

Mar 13  Presentation by Guanhua Chen, PhD (Assistant Professor, Biostatistics and Medical Informatics), Statistical Learning for Heterogeneous Biomedical Data

Mar 20   Presentation by Jamie Fox, PhD, CIBM fellow (Marshfield Clinic Reseach Institute), Precision Medicine Studies: Examination of Variants within the Gene: SLC5A2 , Auditorium

Mar 27   No seminar, Spring Break

Apr 3   Presentation by Lindsay Traeger, PhD, CIBM fellow (Dept. of Bacteriology), Identifying Host Genetic Elements that Control the Gut Microbiome , Room 1360 Biotech Center

Apr 10 Presentation by Qiongshi Lu, PhD (Assistant Professor, Dept. of Biostatistics and Medical Informatics), Improving Genetic Association Analysis Through Integration of Functional Annotations and Biobank Data

Apr 17   Presentation by Ryan Bannen, PhD (Roche, Madison WI), Sequencing Target Enrichment in the Wild

Apr 24 Presentation by Steven Darnell, PhD (Senior Scientist, DNAStar), Being Flexible in a Rigid World: Using Ensembles to Improve Protein Structure Modeling

May 1    Presentation by Philip Romero, PhD (Assistant Professor, Biochemistry), Data-driven Protein Engineering s

FALL 2017   

Sept. 12  Introductory Session I, Note room change: Room 117, 445 Henry Mall

Sept. 19, Introductory Session II, Room 1360 Gen/Biotech Bldg.

Sept. 26 Presentation by Andrew Hasley, PhD (Genetics, UW-Madison), How Is A Fish Made?: Exploring Mechanisms of Early Development using the Zebrafish (Danio rerio)

Oct. 3   No seminar. CIBM Retreat is Oct. 6

Oct. 10 Presentation by Qaiongshi Lu, PhD (Assistant Professor, Dept. of Biostatistics & Medical Informatics, UW-Madison), Title TBA

Oct. 17 Presentation by Michael Veling (Biochemistry), Machine Learning Implicates Oct1p in Coenzyme Q Biosynthesis, 1360 Biotechnology center

Oct. 24 Presentation by Rich Caruana, PhD (Senior Researcher, Microsoft Research), Friends Don’t Let Friends Deploy Black-Box Models: The Importance of Intelligibility in Machine Learning for Healthcare, 9:30 am, Orchard View Room, Discovery Building, 330 N. Charter St.

Oct. 31  Presentations by Christopher Endemann (Computer Sciences), Kurt Weiss, PhD (Morgridge Institute for Research), High Speed Image Acquisition and Processing with Light Sheet Microscopy (KR), 1360 Biotechnology Center

Nov. 7   Presentation by Jeffrey Albert, PhD (Professor, Department of Population and Quantitative Health Sciences, Case Western Reserve University), Generalized Causal Mediation and Path Analysis, Biotechnology Center Auditorium

Nov. 14   Presentation by Steven Schrodi, PhD (Center for Human Genetics, Marshfield Clinic Research Foundation), Biotechnology Center Auditorium, A Survey of Four Disease Genetics Investigations using the Personalized Medicine Research Project

Nov. 21   Presentation by Joshua Medow, MD, MSc (Associate Professor, Dept. of Neurological Surgery, UWSMPH), Biotechnology Center Auditorium, The Digital Intern: Development of a Complex Real-Time Medical Management Decision Support Tool

Nov. 28 Open Discussion on CIBM seminars & program–suggestions & feedback, 1360 Biotechnology Center

Dec. 5    Presentation by Finn Kuusisto, PhD (Postdoctoral Research Associate, Regenerative Biology Lab, Morgridge Inst. for Research), Machine Learning and Data Mining in Cell Reprogramming and Bio-Engineered Tissue Models

PAST Seminars - Spring 2017   

Jan. 17    Presentation by John Rees (past Senior Director/Health Sciences Architecture, Oracle Sciences Global Business Unit)

Jan. 24  Presentations by Matthew Bernstein and Erin Zwick, CIBM predoctoral fellows (Computer Sciences; Epidemiology), Quantifying the effect of chemotherapy on tuberculosis sanatoria admissions (EZ); Normalizing sample-specific metadata for the Sequence Read Archive (MB)

Jan. 31  Presentation by Burcu Darst and Ross Kleiman, CIBM predoctoral fellows (Population Health; Computer Sciences), A Longitudinal Multi-omics Examination of β-Amyloid Deposition and Cognitive Decline in the Years Prior to Alzheimer’s Disease (BD); High-Throughput Machine Learning from Electronic Health Records (RK)

Feb. 7 Presentation by Anthony Cesnik, CIBM predoctoral ellow (to be confirmed; Chemistry), Assembling and Quantifying Proteoform Families Reveals Changes in Cell Machinery from Intact Protein Mass Spectrometry Data

Feb. 14 Presentation by John Pool, PhD, Assistant Professor (Genetics), Expanding the Toolkit of Evolutionary Genomics

Feb. 21   Presentation by Samson Condon, CIBM predoctoral fellow (Biochemistry), Coevolutionary Analysis and Structural Prediction of the Bacterial Divisome Proteins FtsB and FtsL

Feb. 28    Katherine Overmyer, PhD, CIBM postdoctoral fellow (Genome Center of Wisconsin), Multi-omic Analysis of the Human Oral Microbiome

Mar. 7    Presentation by Seong Jae Hwang and Yuriy Sverchkov, PhD, CIBM fellows (Computer Sciences [SJH]; Biostatistics & Medical Informatics [YS]), Medical Image Analysis of Brain Images and Structural Networks for Alzheimer's disease (SJH); Context-Specific Nested Effects Models (YS)

March 14    Presentation by Melissa Skala, PhD, Associate Professor (Biomedical Engineering, UW-Madison; Morgridge Institute for Research), Optical Coherence Tomography of in vivo and in vitro Models

March 21 No seminar, Spring Break

March 28    Presentation by Deborah Chasman, PhD, CIBM Postdoctoral Fellow (Wisconsin Institute for Discovery), Multi-task Learning for in silico Prediction of Chromatin Contact Counts

April 4    Presentation by Ophelia Venturelli, PhD, Assistant Professor (Biochemistry), Deciphering Microbial Interactions that Shape Human Gut Microbiome Stability and Dynamics

April 11    Presentation by Jamie Fox, PhD, CIBM Postdoctoral Fellow (Marshfield Clinic Research Foundation), Title TBA

April 18    Presentation by Adham Abdelrahim, BDS, MSc, CIBM Postdoctoral Fellow (Institute for Oral and Systemic Health, Marshfield Clinic Research Foundation), Feasibility Assessment of a TeleDental Approach to Address Non-traumatic Dental Condition Visits

April 25    Presentation by Robert Striker, MD, PhD (Associate Professor, Department of Medicine, Unit of Infectious Disease, UWSMPH) Will We Know When We've Cured HIV If We Get There??

FALL 2016   

Sept. 6  Introductory Session I, Note room change: Room 1360 Biotechnology Center, 425 Henry Mall

Sept. 13Introductory Session II, Note room change: Room 1408 Genetics/Biotechnology Center Building, 425 Henry Mall

Sept. 20 Presentation by Lauren Baker, DVM (UW School of Veterinary Medicine), Genome-Wide Association Study of ACL Rupture in the Canine Model<

Sept. 27 Presentation by Paul Raccuglia (Research Scientist, Cobalt Speech and Language), Machine-learning-assisted Materials Discovery using Failed Experiments

Oct. 4   No seminar CIBM Retreat is Oct. 7

Oct. 11 Presentation by Lindsay Traeger, PhD, A Tail of Two Voltages: Understanding the Molecular Nature of Electric Organs Using Genomic, Transcriptomic, and Proteomic Approach<

Oct. 18 Big Privacy: Policy Meets Data Science Symposium (Center for Predictive Computational Phenotyping), 1-4:30 Wisconsin Institute for Discovery,

<Oct. 25   Presentation by Aaron Darling, PhD (Associate Professor in Computational Genomics and Bioinformatics, University of Technology Sydney), Metagenomics, Variational Inference, Hi-C, and Babies: Towards Population Genomics of our Uncultured Friends

Nov. 1   Presentation by Corinne Engelman, PhD (Associate Professor, Population Health Science, UW-Madison), Big Data and Alzheimer’s Disease

Nov. 8    Presentation by Benjamin Hackel, PhD (Assistant Professor, Chem. Eng. & Materials Science, University of Minnesota), Engineering Synthetic Ligands for Molecular Imaging, 1610 Engineering Hall

Nov. 15    Presentation by Niklas Gahm; Maryse Lapierre-Landry, Biomedical Engineering, UW-Madison, Leveraging Computation to Improve Light Microscopy (NG); Depth-resolved Analytical Model and Correction Algorithm for Photothermal Optical Coherence Tomography (ML-L), Room 1360

Nov. 22    9:30 am, Presentation by James Rehg, PhD (Professor, School of Interactive Computing, Director of the Center for Behavioral Imaging, co-Director of the Center for Computational Health, and co-Director of the Computational Perception Lab, Georgia Institute of Technology), Big Data in Behavioral Medicine, Rm. 3280 Wisconsin Institutes for Discovery,

Nov. 29    Presentation by Pamela Kreeger, PhD (Associate Professor, Biomedical Engineering) Multi-cellular Interactions in High Grade Serous Ovarian Cancer

SPRING 2016   

Jan. 27    Presentation by Julie Mitchell, PhD, Associate Professor (Depts. of Biochemistry and Math, UW-Madison), Data Driven Approaches to Molecular Biophysics

Feb. 1  David Lewis, PhD (David Lewis Consulting), Note Room and Time Change: CS Room 3310, 2:30 pm E-Discovery in the Law: Challenge Problems

Feb. 9 Presentation by Yuriy Sverchkov, PhD (Dept. of Biostatistics and Medical Informatics), Room 1360 Biotechnology Center, Machine learning of biological networks from gene knockout data and selection of gene knockout experiments by active machine learning

Feb. 16 Presentation by Christian Metallo, PhD (Assistant Professor, Bioengineering, UC San Diego), Note Room Change: Room 3310, 1610 Engineering Hall, Understanding Disease Mechanisms using Isotope Tracing and Flux Analysis

Feb. 23   Presentation by Tim Rhoads, PhD (Genome Center of Wisconsin) bsp; Metaproteomics: The Oral Microbiotic Proteome as a Tool to Investigate Systemic Disease

Mar. 1    Presentation by Sara Knaack, PhD (Wisconsin Institute for Discovery); TAn Evolutionary Analysis of Animal Epigenomes

March 8    Presentation by Anthony Cesnik (Chemistry) and Samson Condon (Biochemistry), CIBM predoctoral fellows, Combining RNA-Seq Proteogenomics and Global Post-Translational Modification (AC); Coevolutionary Analysis and Structural Prediction of the Bacterial Divisome (SC)

March 15    Presentation by Laurence Loewe, PhD, Assistant Professor (Wisconsin Institute for Discovery; Genetics, UW-Madison) How to Simulate Time Series in Gene Regulatory Networks using Evolvix

March 22 No seminar, Spring Break

March 29    Presentation by Federico Rey, PhD (Assistant Professor, Bacteriology)Causes and Consequences of our Microbial Differences

April 5    Presentation by Peter Muir, PhD (Professor, Surgical Sciences, UW School of Veterinary Medicine) Man’s Best Friend: Dogs and Complex Trait GWAS

April 12    Presentation by Gary Pack, PhD, CIBM postdoctoral fellow (Dept. of Biostatistics & Medical Informatics, UW-Madison; Marshfield Clinic Research Foundation), Scalable Automatic Image Analysis for Discovery of Imaging Phenotypes Associated with Inflammatory Disease

April 19    Presentation by Presentation by Layla Barkal, CIBM predoctoral fellow (Biomedical Engineering) Microfluidic tools for parsing host-fungal interactions

April 26    Presentation by Guilherme del Fiol, PhD (Assistant Professor, Dept. of Biomedical Informatics, Univ. of Utah), Providing on-demand access to online evidence resources within EHR systems via “Infobuttons”

FALL 2015   

Sept. 8  Introductory Session I, Note room change: Room 1360 Biotechnology Center, 425 Henry Mall

Sept. 15  Introductory Session II, Note room change: Room 1360 Biotechnology Center, 425 Henry Mall

Sept. 22 Presentation by Max He, PhD (Associate Research Scientist-Bioinformatics, Marshfield Clinic Research Foundation), Biotechnology Center Auditorium Big Data Analytics for Genomic Medicines,

Sept. 29   No Matter Where, The Health Care Documentary. Discussion led by Patti Brennan, PhD, RN, FAAN, Moehlman Bascom Professor, UW-Madison (video made by Kevin B. Johnson, MD, MS, filmmaker; Chair of Biomedical Informatics, Chief Information Officer, Vanderbilt University Medical Center), Biotechnology Center Auditorium

Oct. 6   No seminar CIBM Retreat is Oct. 9

Oct. 13   Presentation by Ross Kleiman and Paul Bennett (Computer Sciences, UW-Madison), Pan-Diagnostic Machine Learning

Oct. 20    Presentation by Seong Jae Hwang and Katherine Overmyer, PhD, A Projection free Method for Generalized Eigenvalue Problem with a Nonsmooth Regularizer (SJH); Integrating 'omics to Better Understand the Physiology of Health and Disease (KO)

Oct. 27    Presentation by David Beebe, PhD (Professor) and Jay Warrick, PhD (Assistant Scientist), Department of Biomedical Engineering, UW-Madison Microsale Technologies for Patient Pample Analysis: Doing More with Less

Nov. 3   Presentation by Vincent Chen, PhD (Department of Biochemistry, UW-Madison), NMR Metabolomics of Caloric Restriction in Rhesus Macaques

Nov. 10    Presentation by Jamie Fox, PhD (Marshfield Clinic Research Foundation), Room 1360 Biotechnology Center, Understanding the Genetic Etiology of T1 and T2D through PheWAS and its Application in Drug Repurposing

Nov. 17    Presentation by Alex Cobian (Computer Sciences, UW-Madison),  Machine Learning Approaches for Patient Risk Assessment Using EHR Data

Nov. 24    Presentation by Richard Wang (Laboratory of Genetics, UW-Madison), Title TBA

Dec. 1    Presentation by Megan McClean, PhD (Assistant Professor, Biomedical Engineering, UW-Madison, Elucidating Principles of Biological Signal Processing using Microfluidic and Optogenetic Tools


SPRING 2015   

Jan. 20  Presentation by Nils Gehlenborg, PhD (Research Associate, the Center for Biomedical Informatics, Harvard Medical School Wisconsin Inst. for Discovery, H.F. DeLuca Forum

Jan. 27    Presentation by Gary Pack, PhD, CIBM postdoctoral fellow (Dept. of Biostatistics & Medical Informatics, UW-Madison; Marshfield Clinic Research Foundation) Genomics, Dental and Medical Imaging: Pleiotrophic Models for the Prediction of Alzheimer’s Disease

Feb. 3  Smita Krishnaswamy, PhD (Postdoctoral Research Scientist, Columbia University), Note Room Change: Wisconsin Inst. for Discovery Building, H.F. DeLuca forum Unlocking Cellular Computation and Information Processing through Multidimensional Single-Cell Data

Feb. 10 Presentation by Ferhat Ay, PhD (Postdoctorate Computing Innovation Fellow, Noble Lab, Genome Sciences, University of Washington), Note Room Change: Wisconsin Inst. for Discovery Building, H.F. DeLuca forum, Genome Architecture in Action: Gene Regulation via 3D Chromatin Organization in Human, Mouse and Malaria ParasitesA

Feb. 17   Presentation by John Beasley, MD (Clinical Professor, Department of Family Medicine, and UW I-Practise (Improving PrimAry Care Through Industrial and Systems Engineering)), EHRs – From Meaningful Use to Rational Use

Feb. 24   Presentation by Slavash Mirarab, PhD Student (Department of Computer Science, University of Texas at Austin), Species Tree Estimation from Genome Scale Data

March 3   Wenxiu Ma, PhD, Postdoctoral Fellow, Department of Genome Sciences, University of Washington), Note Room Change: Wisconsin Inst. for Discovery Building, H.F. DeLuca forum, Zooming into the 3D Genome Architecture and Gene Regulation

March 10    Presentation by Layla Barkal (Biomedical Engineering; MSTP) and Samson Condon (Biochemistry), ; Microscale Metabolomics (LB); Combining Multiple Sequence Alignments with Computational Modeling to Predict the Structures of Transmembrane Helix Homodimers (SC)

March 17    Presentation by Yuao Luo (Computer Science and Artificial Intelligence Lab, MIT) Improving Accuracy and Interpretability with Subgraph Mining and Factorization Models

March 27   Presentation by Quaid Morris, PhD (University of Torongo), Reconstructing the Evolutionary History of Tumors

March 31    No seminar, Spring Break

April 7    Presentation by Yuriy Sverchov, PhD (Biostatistics & Medical Informatics) and Matthew Bernstein (Computer Sciences), Probabilistic Methods for Transcriptome Analysis with RNA-seq (MB); Active Learning for Uncovering Biological Networks (YS)

April 14    Presentation by Kimberly Shoenbill, MD (Clinical Investigations Graduate Program), Machine Learning Analysis of Lifestyle Modification in Hypertension Treatment

April 21    Presentation by Anna Merrill, PhD, Quantitative Omics Strategies for Investigating the Oral Microbiome in Dental and Systemic Diseases

April 28    Presentation by Catie Minogue, A Protein Expression Atlas of Medicago truncatula

FALL 2014   

Sept. 2  Introductory Session I, Note room change: Room 1360 Biotechnology Center, 425 Henry Mall

Sept. 9  CANCELLED: Room 1240 Computer Sciences Building, 1210 Dayton St., Court Cutting, MD (Professor of Plastic Surgery, NYU School of Medicine, The Role of Computational Science in Cognitive Training for Surgical Practices

Sept. 16  Introductory Session II, Note Room Change: Room 1360 Biotechnology Center, 425 Henry Mall

Sept. 23 Presentation by Nagesh Adluru, PhD (Assistant Scientist, Waisman Laboratory for Brain Imaging and Behavior, UW-Madison), Effective Priors in Diffusion Image Science of the Brain

Sept. 30   Presentation by Anthony Gitter, PhD (Assistant Professor, Department of Biostatistics and Medical Informatics; Morgridge Institute for Research), Synthesizing Signaling Pathways from Temporal Phosphoproteomic Data

Oct. 7   Presentation by Anna Merrill, PhD ((Biotechnology Center, UW-Madison), ) NeuCode Labeling for Multiplexed, Global Protein Quantification

Oct. 14   No seminar. CIBM Annual Retreat is Fri., Oct. 17

Oct. 21    Presentation by Timothy Rhoads, PhD (Genome Center), Quantitative Proteomics with NeuCode: Investigation of Ascaroside Signaling in C. elegans

Oct. 28    Presentation by Kurt Weiss, PhD (Department of Psychiatry, UW-Madison) Ultrastructural Analysis of Sleep Deprived Brain Tissue Using Automated Image Segmentation Techniques

Nov. 4   Presentation by Caitlin Pepperell, MD (Assistant Professor of Medical Microbiology & Immunology and Medicine, UW-Madison), Title TBA

Nov. 11    Presentation by James Cimino (Laboratory for Informatics Development, NLM), Leveraging Ontologies to Deliver Knowledge to the Bedside and Data to the Researcher

Nov. 18    Presentation by Anthony Cesnik (Chemistry) and Barbara Wendelberger (Statistical and Computational Biology and Medicine Special Committee Program), In-Depth Identification of Protein Sequence Variants and Posttranslational Modifications; Exploring Neural Effective Connectivity in Patients with Balance Dysfunction Using Dynamic Causal Modeling in fMRI

Nov. 25    Presentation by Ricardo Pizarro, Neural Mass Modeling of Sensory Networks using μECoG Data

Dec. 2    Presentation by Laura McLay, PhD, Associate Professor, Industrial & Systems Engineering, UW-Madison, Delivering Emergency Medical Services: Research, Application, and Outreach

SPRING 2014   

Jan. 21  Anthony Gitter, PhD (Postdoctoral Associate, Department of Biomedical Engineering, MIT; Microsoft Research New England), Linking the Signaling Cascades and Dynamic Regulatory Networks Controlling Infection Response, Wisconsin Inst. for Discovery, H.F. DeLuca Forum, 330 North Orchard St.

Jan. 28  Note Room Change: Wisconsin Inst. for Discovery, H.F. DeLuca Forum, 330 North Orchard St., Jian Peng, PhD, Unraveling the Mechanism of Chaperone-Mediated Protein Homeostasis, Wisconsin Inst. for Discovery, H.F. DeLuca Forum

Feb. 4  Note Room Change: Wisconsin Inst. for Discovery, H.F. DeLuca Forum, 330 North Orchard St., Mengjie Chen, PhD Candidate (Computational Biology & Bioinformatics, Yale University), Profiling and Accounting for Heterogeneity in the Analysis of Cancer Sequencing Data,

Feb. 11 Presentation by Vincent Chen, PhD (Department of Biochemistry, UW-Madison), Computational Tools for Validation and Correction of Macromolecular 3D Structures

Feb. 18   Presentation by Ricardo Pizarro (Department of Biomedical Engineering) and Richard Wang (Department of Genetics, UW-Madison), Neural Mass Modeling of Sensory Networks using micro-ECoG Data (R.Pizarro); Modeling the Genetic Architecture of Hybridization Barriers (R. Wang)

Feb. 25   Christina Kendziorski, PhD (Professor, Dept. of Biostatistics & Medical Informatics) Pathway-Index Models for Construction of Patient-Specific Risk Profiles

March 4    Presentation by A. Pasha Hosseinbor, PhD (Waisman Center) and Sara Knaack, PhD (Wisconsin Institute for Discovery), The 4D Hyperspherical Diffusion Wavelet: A New Method for Detection of Localized Anatomical Variation (Hosseinbor); Multiclustering Analysis of Epigenome Dynamic (Knaack)

March 11    Presentation by Nathanael Fillmore (Computer Sciences Department, UW-Madison), Evaluation of de Novo Transcriptome Assemblies from RNA-Seq Data

March 18    Spring Break, no seminar

March 25    Colin Dewey, PhD (Associate Professor, Depts. of Biostatistics & Medical Informatics; Computer Sciences), Bypassing Genomics: The New Era of Transcriptomics with RNA-Seq and Genome-Free Computational Methods

April 1    Presentation by Yuriy Sverchkov, Intelligent Systems Program, University of Pittsburgh, Explanation of Differences Across a Pair of Groups

April 8   Presentation by Aubrey Barnard (Computer Sciences Department, UW-Madison), Identifying Adverse Drug Events in Observational Medical Data

April 15    Presentation by Shravan Sukumar (Department of Biochemistry, UW-Madison, Markers of Specificity in Protein-DNA Interactions

April 22    Presentation by Kimberly Shoenbill, MD (Clinical Investigations Program, UWSMPH), Machine Learning Analysis of Lifestyle Modification in Hypertension Treatment

April 29    Presentation by Deborah Chasman (Department of Computer Science, Inferring Stress-Activated Signaling Subnetworks in Yeast

FALL 2013   

Sept. 3  Introduction of Participants, Room 1210 MSC, 1300 University Avenue

Sept. 10  Sean McIlwain, PhD (Researcher, Great Lakes Bioenergy Research Center), Accurately Identifying Cross-linked Peptides from the Analysis of Mass Spectrometry Data

Sept. 17  Presentation by Scott Hebbring, PhD (Faculty, Marshfield Clinic Research Foundation), The Development of Phenome-Wide Approaches for the Study of Human Genetics

Sept. 24 Presentation by David DeMets, PhD (Professor, Department of Biostatistics & Medical Informatics, UWSMPH), This Could Happen Anywhere: Evolution of Translational 'OMICS' & Lessons Learned from the Duke Saga

Oct. 1    Introductory Session 2, Room 1210 Medical Sciences Center, 1300 University Ave.

Oct. 15    Maxwell Collins (Computer Sciences Department, UW-Madison) Distributed Methods for Vision Problems with Orthogonality Constraints

Oct. 22    Peggy Peissig, PhD (Marshfield Clinic Research Foundation), Relational Machine Learning for Electronic Health Record Phenotyping

Oct. 29    David O’Connor, PhD (Professor, Department of Pathology & Laboratory Medicine, UWSMPH), Mauritian Macaque Genomics: Implications for Understanding Protective Cellular Immune Responses to HIV/AIDS

Nov. 8    Presentation by Yalin Wong, PhD ( - Assistant Professor, Computer Science & Engineering, Arizona State University), 12:00 Noon, Room 140 Bardeen, Computational Conformal Geometry with its Applications in Shape Analysis

Nov. 12    Presentation by Cheng Guan Koay, PhD (Assistant Scientist, Medical Physics), Pseudometrically Constrained Centroidal Voronoi Tessellations and Its Application to Sampling Designs in MR Imaging

Nov. 19    Presentation by Paul Wilson, PhD (Professor, Engineering Physics, UW-Madison), The Advanced Computing Infrastructure: Shared Solutions for Shared Success

Nov. 26    Presentation by Michael Newton, PhD (Professor, Statistics; Biostatistics and Medical Informatics), Two Problems in High-Dimensional Statistics: A Specific One on the Analysis of Gene Function, and a General One on Ranking and Selection

Dec. 3    Presentation by Jie Liu (Computer Sciences Department, Department of Radiology, UW-Madison), Statistical Methods for Genome-wide Association Studies and Personalized Medicine

SPRING 2013   

Jan. 22  Presentation by Wolfgang Gaggl, PhD (Medical College of Wisconsin), Functional MRI, Connectivity, and DTI in Clinical Practice

Jan. 29  Presentation by Pascale Carayon, PhD, Assistant Professor (Biomedical Engineering), Designing Health Information Technology for Clinicians and Patients: A Human Factors Engineering Viewpoint

Feb. 5  Introduction of Participants, Room 1210 Medical Sciences Center, 1300 University Avenue

Feb. 12  Presentation by Catie Vincent, CIBM Predoctoral Trainee (Chemistry), and Nathanael Fillmore, CIBM Predoctoral Trainee (Computer Sciences), The Utilization of Machine Learning for the Prediction of Sequence-Informative Fragment Ions Greatly Improves Peptide Identification by Mass Spectrometry; Evaluation of de novo Transcriptome Assemblies from RNA-Seq Data

Feb. 19 Presentation by Jeremy Weiss, CIBM Predoctoral Trainee (Computer Sciences; Medicine), Statistical Timeline Analysis: Clinical Event Prediction from Electronic Health Records

Feb. 26    Presentation by Nicholas A. Davis (Division of Information Technology, UW-Madison), The Unique Challenges of Information Security in Healthcare Environments

March 5    Presentation by Sriraam Natarajan (Assistant Professor, Translational Sciences Institute, Wake Forest University School of Medicine), Statistical Relational Learning for Predictive Personalized Medicine

March 8    **Note Different Day and Room** 140 Bardeen, 12:00 noon. Presentation by James M. Regh, PhD, Professor (School of Interactive Computing, College of Computing Georgia Institute of Technology), Behavior Imaging and the Study of Autism

March 12    Presentation by Ishmael Amarreh (Dept. of Biomedical Engineering, UW-Madison) Title TBA

March 19    Presentation by Gary Pack, PhD, Semiparametric Geometric Methods for Extracting and Modeling White Matter Volumetric Structures of the Brain

March 26    No seminar - Spring Break

April 2    Presentation by Alan Wolf, PhD (Director, New Media Center Program; collaborator and consultant on technology projects at the Institute for Biology Education), Electronic Laboratory Notebooks: Moving from paper to bytes

April 9    Presentation by Dana Wohlbach, PhD (Assistant Scientist, Genetics, UW-Madison), Comparative Analysis of Multiomics Analysis of Natural Variation in Yeast to Understand Bottlenecks to Bioenergy Production

April 16    Presentation by Dolores Severtson, PhD (Assistant Professor, School of Nursing, UW-Madison), and Jeff Myers (Wisc. Department of Natural Resources), Modeling Estimated Cancer Risk from Air Pollution & Designing Maps to Communicate the Uncertainty of the Modeled Estimates

April 23    Presentation by Jeremy Goecks, PhD (Postdoctoral Researcher, Departments of Biology, and Mathematics & Computer Science), Interactive Computing for High-Performance Medical Genomics

Th., May 2    **Note different day and room ** Presentation by Deborah Estrin (Professor of Computer Science, CornellNYC Tech), CS Building, Room 1240, 4:00 pmSensemaking for Mobile Health

FALL 2012   

Sept. 4  Introduction of Participants, Room 117, 445 Henry Mall

Sept. 11  Presentation by Anna Rissman, CIBM Predoctoral Fellow (Department of Genetics) Interpreting Differential Expression Associated with Variants of a Non-Coding Mammary Cancer Susceptibility Locus

Sept. 18  Presentation by John Doyle, Professor of Control and Dynamical Systems, Electrical Engineering, Bioengineering (Caltech), WID Building Forum, Universal Laws and Architectures

Sept. 25 Presentation by Christopher Rao (Associate Professor, Department of Chemical and Biological Engineering, University of Illinois, Champagne-Urbana), 1227 Engineering Hall, Design and Diversity in Bacterial Signaling Networks

Oct. 2    Presentation by Benjamin Mueller, CIBM Predoctoral Fellow (Department of Biochemistry) Modeling C-alpha-H.....O Mediated Transmembrane Dimers

Oct. 16    Presentation by Kevin Ponto, PhD, Assistant Professor (School of Human Ecology, UW-Madison) Rethinking 3D

Oct. 23    Presentation by Maureen Smith, MD, MPH, PhD, Associate Professor (Population Health Sciences, UW School of Medicine and Public Health), Health Services Research: Integrating Clinical, Administrative, and Survey Data for Research on Improving Health Care

Oct. 30    Presentation by Amit Acharya, BDS, MS, PhD, Director, Dental Informatics Postdoctoral Fellowship Program; Dental Informatics Research and Training Program, Biomedical Informatics Research Center (Marshfield Clinic Research Foundation), Computation and Informatics in Dentistry: A Specialized Area of Research Focus!

Nov. 6   Presentation by Takeo Kanade, Professor (Robotics Institute, Carnegie Mellon University), Rm. 1240 Computer Science Building, First-Person Vision

Nov. 13    Presentation by Chris Hinrichs (Department of Computer Sciences, How Machine Learning Methods Can Reshape Neuroimaging-Based Clinical Trials

Nov. 20    Presentation by David Devilbiss, PhD, Assistant Scientist (Department of Psychology, UW-Madison), Lost Moments in Time: The Effects of Stress on PFC Neural Coding

Nov. 30    Presentation by Christina Leslie, PhD (Computational Biology Program, Memorial Sloan Kettering Cancer Center), 12:00 Noon, Room 140 Bardeen, Deciphering co- and post-transcriptional regulatory programs in normal and cancer cells

Dec. 4    Presentation by Murray Brilliant, PhD, Director at the Center for Human Genetics (Marshfield Clinic Research Foundation), Personalized Medicine at the Marshfield Clinic: Research and Implementation

PAST SEMINARS    Spring 2012

Jan. 24  Introduction of Participants, Room 1360 Biotechnology Center

Jan. 31  Presentation by Kyle Hoffman (Chemical and Biological Engineering), The Interaction of Islet Amyloid Polypeptide with Phospholipid Bilayers and Micelles

Feb. 7  Presentation by Moo K. Chung, PhD (Associate Professor, Department of Biostatistics & Medical Informatics) Persistent Homology and Its Application to Characterizing Abnormal Brain Cortical Thickness and Network in Autism

Feb. 14 Presentation by Elizabeth S. Burnside, MD MPh (Associate Professor, Radiology; Biostatistics and Medical Informatics), Using Multi-relational Data and Machine Learning to Improve Breast Cancer Diagnosis

Feb. 21    Presentation by Collin Timm, CIBM Predoctoral Trainee (Chemical and Biological Engineering), Quantitative Transcription and Replication Dynamics of Vesicular Stomatitis Virus – Towards a Predictive Model of Viral Growth

Feb. 28    Presentation by M. Elizabeth Meyerand, PhD  (Professor and Chair, Department of Biomedical Engineering), A MRI study of Sustained Neuromodulation Induced by Electrical Tongue Stimulation in Balance Disorders

March 6    Presentation by Gang Luo, PhD (IBM T.J. Watson Research Center), Intelligent Personal Health Records

March 13    Presentation by Sushmita Roy (Assistant Professor, Department of Biostatistics and Medical Informatics, UW-Madison), Computational Approaches to Modeling Gene Regulation in One and Many Species

Fr., March 23   **Note different time and room** 12 pm, 140 Bardeen, 1215 Linden Drive Russell Greiner, Professor (Professor, Department of Computing Science; Center for Machine Learning, University of Alberta), Budgeted Learning Of Effective Classifiers

March 27    Presentation by Kendrick Boyd, CIBM predoctoral fellow (Department of Computer Sciences), Precision-Recall Space and Empirical Algorithm Evaluation

April 3    No seminar, Spring Break

April 10    Presentation by Deborah Muganda, CIBM predoctoral fellow (Department of Computer Sciences), Computing Clustered Alignments of Gene-Expression Time Series

April 17    Presentation by Garret Suen (Assistant Professor, Department of Bacteriology, UW-Madison) How Much Cow is in it? The Systems Biology of the Rumen Ecosystem

April 24    Presentation by Deborah Chasman (Department of Computer Sciences) Inferring Host Subnetworks involved in Viral Replication

May 1    Presentation by Brian Teague (Laboratory for Molecular and Computational Genomics), Title TBA

FALL 2011   

Sept. 6  Introduction of Participants, Room 1360 Biotechnology Center

Sept. 13  Presentation by Carolyn Pehlke, CIBM Predoctoral Trainee (Biomedical Engineering), Quantitation of Collagen Alignment: Tools for Characterizing Cancer Progression and Invasion

Sept. 20  Presentation by Sabareesh Subramaniam (Biochemistry), Efficient Conformer Libraries to Improve Protein Sidechain Optimization

Sept. 27  Presentation by Shane Hubler, PhD, CIBM Postdoctoral Trainee (Chemistry) The Effects of Stress on Translation – A Systems Approach

Oct. 4    No seminar – CIBM Retreat is Fri., Oct. 7th

Oct. 11    Presentation by Kevin Ponto, PhD, CIBM Postdoctoral Trainee (Computer Sciences), Effective Replays and Summarization of Virtual Experiences

Oct. 18    Presentation by Laurence Loewe, PhD, Assistant Professor (Genetics; Systems Biology, Wisconsin Inst. for Discovery), Computational Approaches to understanding Distributions of Mutational Effects

Oct. 25    Presentation by Maxwell Collins (Computer Sciences), Cosegmentation in Neuroimaging, and Nathanael Fillmore (Computer Sciences), A Model for Progression and Gene Expression in Cervical Cancer

Fri., Nov. 4    Presentation by Patricia Brennan, PhD (Professor, Dept. of Industrial & Systems Engineering; School of Nursing; Theme Leader, Living Environments Laboratory, Wisconsin Institute for Discovery), 12:00 pm, 3280 Wisconsin Institutes of Discovery, 330 N. Orchard St., The Living Environments Laboratory at the Wisconsin Institutes of Discovery

Nov. 8    Presentation by Costas D. Maranas (Professor, Department of Chemical Engineering, Penn State), 1800 Engineering Hall, 1415 Engineering Dr. Using Computations to Reconstruct, Analyze and Redesign Metabolism

Nov. 15    Presentation by Laura LeGault (Computer Sciences), Inference of Alternative Splicing from RNA-Seq Data with Probabilistic Splice Graphs

Nov. 22    Cancelled: Presentation by David Baumler, PhD, CIBM Postdoctoral Fellow (Genome Center of Wisconsin), Systems Biology: Investigating Modern-Day Disease by Using Metabolic Models of Bacteria from the Past

Nov. 29    Presentation by Kevin Eng, PhD, CIBM Postdoctoral Fellow (Biostatistics & Medical Informatics) Exploratory Genomic Analysis and Modeling of Ovarian Carcinoma

Dec. 6    Presentation by David J. Baumler, PhD, CIBM Postdoctoral Fellow, Genome Center of Wisconsin, Investigating Modern-Day Disease by Using Metabolic Models of Bacteria from the Past

PAST SEMINARS    Spring 2011

Jan. 25  Presentation by Houssam Nassif (Computer Sciences), Characterizing and Predicting Hexose-Binding Sites

Feb. 1  Presentation by Kaitlin Sundling (Biophysics), Analysis of GTP Biosynthetic Gene IMD2 Expression In Yeast

Mo., Feb. 7  3:30 pm Ebling Symposium Center, Microbial Sciences Building, 1550 Linden Dr., Presentation by Abbas Ourmazd (Distinguished Professor of Physics & Electrical Engineering, UW-Milwaukee), Biostructure and Dynamics from Random Snapshots

Feb. 15    Presentation by Nathan Miller (Assistant Scientist, Botany), Data Modeling Root Gravitropism

Feb. 22    Presentation by Ryan Haasl (Genetics), Computer Experiments with Microsatellites

Th., March 3rd, Fri., March 4th    Presentation by Tom Mitchell (Fredkin Professor of AI and Learning Machine Learning Department, Carnegie Mellon University), Never-Ending Learning, Neural Representations of Word Meanings

March 8    Presentation by Darryl Thelen (Associate Professor, Depts. of Mechanical Engineering; Biomedical Engineering; UW-Madison), Computational Biomechanics

March 22     Presentation by Qiuling He (Statistsics) How Many Human Genes Participate in Influenza Virus Replication

Th., March 31st, 4:00 pm, 1240 CS; Fri., April 1st 11:00 am 1240 CS    Presentation by Eric Horvitz (Distinguished Scientist, Micrond Evidence-Based Healthcare (April 1st)

April 5    Presentation by Jie Liang (Professor of Bioengineering, Univ. of Illinois, Chicago) Multi-Scale Computational Study of Biological Systems: Protein Structure, Function, Assemblies, Networks, and Cells 

April 12    Presentation by Bo Li (Computer Sciences)) RSEM: Accurate Quantification of Gene and Isoform Expression from RNA-Seq Data 

April 19    Presentation by Corinne Engelman (Ass’t. Prof., Population Health Sciences, UW Madison) Unraveling the Environmental and Genetic Predictors of Vitamin D 

April 26     Presentation by Tim Patton, CIBM Predoctoral Fellow (Industrial & Systems Engineering)) Towards Cognitive Support for Health Self-management: Representing Knowledge of Health in Everyday Living 

PAST SEMINARS    Fall 2010

Sept. 14  Presentation by Nagesh Adluru, PhD (Biostatistics & Medical Informatics), Techniques for Mapping Brain Connectivity using Diffusion MRI

Sept. 21  Presentation by Bing Ma (Comparative Biomedical Sciences Program), Genomic Approaches to Understanding the Evolution of Host-Microbe Interactions

Sept. 28  Presentation by Bess Berg, CIBM Predoctoral Trainee (Computer Sciences) Learning Predictive Rules from Electronic Health Records

Oct. 8      12:00 noon, 140 Bardeen Medical Laboratories, 1215 Linden Drive, Presentation by Eric A. Stone, PhD (Assistant Professor, Bioinformatics Research Center, Department of Genetics, North Carolina State University), Next-generation Genotyping for Next-generation Sequencing

Oct. 12    No seminar – CIBM Retreat is Fri., Oct. 15th

Oct. 19    Presentation by Ameet Soni (Computer Sciences), Improved Statistical Inference for Protein-Structure Determination

Oct. 26    Presentation by Chris Hinrichs, CIBM Predoctoral Trainee (Computer Sciences), Learning to Recognize Disease Patterns in Medical Imaging: Applications to Alzheimer's Disease Research

Nov. 5      1:30 pm, Biotechnology Center Auditorium, Presentation by Dmitry Kondrashov, PhD (Senior Lecturer, University of Chicago Biological Sciences Collegiate Division), A Multi-Dimensional  Approach to Teaching Mathematics for Biologists

Nov. 9      Presentation by David Baumler, PhD, CIBM Postdoctoral Trainee (Genome Center of Wisconsin)The Evolution of Metabolic Networks of E. coli

Nov. 16    Presentation by Ron Stewart, PhD (Morgridge Institute for Research)RNA-Seq Analysis of the Axolotl Adult Limb and Blastema - Cues and Clues to Regeneration 

Nov. 23    Presentation by Barry D. Van Veen, PhD (Professor, Electrical and Computer Engineering) EEG/MEG Estimation of Cortical Effective Connectivity 

Nov. 30    Presentation by Casian Pantea, PhD (Departments of Mathematics; Biomolecular Chemistry) Computational Methods for Analyzing Bistability in Biochemical Reaction Networks 

Dec. 7      Presentation by David Anderson, PhD (Assistant Professor, Department of Mathematics) Stochastic Models in Biology 

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