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IMA Tutorial
Tools for Model and Data Integration in the Genome Sciences/Information Integration Technologies for Complex Systems
September 15-19, 2003


Probability and Statistics in Complex Systems: Genomics, Networks, and Financial Engineering, September 1, 2003 - June 30, 2004

Tools for Model and Data Integration in the Genome Sciences

Monday-Thursday, September 15-18, 2003

Michael A. Newton
Department of Biostatistics and Medical Informatics
University of Wisconsin-Madison
newton@stat.wisc.edu

Simon Tavaré
Program in Molecular and Computational Biology
University of Southern California
stavare@usc.edu
http://www-hto.usc.edu/people/Tavare.html

Robert Gentleman
Department of Biostatistics
Harvard University
rgentlem@jimmy.harvard.edu
http://biosun1.harvard.edu/~rgentlem/HTML/home.html

Information Integration Technologies for Complex Systems

Friday, September 19, 2003

Sallie Keller-McNulty
Group Leader for the Statistical Sciences Group
Los Alamos National Laboratory
sallie@lanl.gov
http://www.lanl.gov/orgs/d/d1/people/skeller.shtml

Alyson Gabbard Wilson
Statistical Sciences Group
Los Alamos National Laboratory
agw@lanl.gov

http://www.stat.lanl.gov/people/awilson.shtml

The first four days of the tutorial, Tools for Model and Data Integration in the Genome Sciences, will provide an introduction to molecular biology and molecular technology for mathematicians and statisticians. The aim is to give a broad overview of the problems being addressed in the post-genomic era, such as array technology in human disease, mass spectrometry for protein sequencing and high throughput variation detection, regulatory networks, signal detection and comparative genomics and proteomics. The final day, on Information Integration Technologies for Complex Systems, will develop, present, and discuss a framework for the integration of experience, models and information in the highly dynamic context of contemporary scientific discovery driven by vast amounts and rapidly changing acquired information.

On the evening of September 15 there will be a lecture by Leroy Hood aimed at the general public and entitled After the Human Genome Project: Systems Biology and Predictive, Preventive and Personalized Medicine.

KICKOFF TUTORIAL SCHEDULE
Monday Tuesday
MONDAY, SEPTEMBER 15
All talks are in Lecture Hall EE/CS 3-180 unless otherwise noted.
8:30 Coffee and Registration

Reception Room EE/CS 3-176

9:15 Douglas N. Arnold, Scot Adams, and Organizers Welcome and Introduction
9:30 Simon Tavaré
University of Southern California

Intro to Molecular Biology 1

Slides:   ima1.pdf

10:20
Discussion
10:30 Coffee Break Reception Room EE/CS 3-176
11:00 Robert Gentleman
Harvard University

Basic Introduction to R and Its Philosophy

Lecture 1 Slides:   pdf

11:50
Discussion
12:00
Lunch Break
1:30 Arkady Khodursky
University of Minnesota

Microarrays: Biological, Technologicial and Analytical Issues

Slides:   pdf

2:20
Discussion
2:30 Coffee Break Reception Room EE/CS 3-176
3:00 Robert Gentleman
Harvard University

Basic Introduction to R and Its Philosophy

Lecture 2 Slides:   pdf

3:50
Discussion
4:00 Group Photo click here   Slides Format  
4:10-5-30 IMA Tea and more  
7:00-8:00 pm IMA Public Lecture:
Leroy Hood
President, Institute for Systems Biology, Seattle, Washington

After the Human Genome Project: Systems Biology and Predictive, Preventive and Personalized Medicine

Smith Hall 100, 7-8 pm

TUESDAY, SEPTEMBER 16
All talks are in Lecture Hall EE/CS 3-180 unless otherwise noted.
8:30 Coffee

Reception Room EE/CS 3-176

9:30 Charles Geyer
University of Minnesota
Introduction to Markov Chain Monte Carlo
10:20
Discussion
10:30 Coffee Break Reception Room EE/CS 3-176
11:00 Simon Tavaré
University of Southern California

Intro to Molecular Biology 2

Slides:   ima2.pdf

11:50
Discussion
12:00
Lunch Break
1:30 Robert Gentleman
Harvard University

Bioconductor, with Array Analysis

Lecture 3 Slides:   pdf

2:20
Discussion
2:30 Coffee Break Reception Room EE/CS 3-176
3:00 Simon Tavaré
University of Southern California

Genetic Variation and the HapMap Project 1

Slides:   ima3.pdf

3:50
Discussion
4:00 Walk along the Mississippi
WEDNESDAY, SEPTEMBER 17
All talks are in Lecture Hall EE/CS 3-180 unless otherwise noted.
8:30 Coffee

Reception Room EE/CS 3-176

9:30 Michael A. Newton
University of Wisconsin-Madison

Stochastic Computation Case Study 1: Dectecting Motifs, Lawrence-Liu Model

Slides:   start. pdf    loh.pdf

10:20
Discussion
10:30 Coffee Break Reception Room EE/CS 3-176
11:00 Robert Gentleman
Harvard University

Bioconductor, with Array Analysis

Slides:   pdf

11:50
Discussion
12:00
Lunch Break
1:30 Michael A. Newton
University of Wisconsin-Madison

Stochastic Computation Case Study 2: Phylogenetics, Bayesian Analysis of Trees

Slides:  ima.pdf

2:20
Discussion
2:30 Coffee Break Reception Room EE/CS 3-176
3:00 Simon Tavaré
University of Southern California

Genetic Variation and the HapMap Project 2

Slides:    ima4.pdf

3:50
Discussion
4:00
Robert Gentleman
Harvard University

Hands-on session on "R"
Lind Hall 400

THURSDAY, SEPTEMBER 18
All talks are in Lecture Hall EE/CS 3-180 unless otherwise noted.
8:30 Coffee

Reception Room EE/CS 3-176

9:30 Michael A. Newton
University of Wisconsin-Madison

Stochastic Computation Case Study 3: Cancer Genomics

Slides:   cancer.pdf

10:20
Discussion
10:30 Coffee Break Reception Room EE/CS 3-176
11:00 Robert Gentleman
Harvard University

Graphs and Networks in R

Slides:   pdf

11:50
Discussion
12:00
Lunch Break
1:30 Michael A. Newton
University of Wisconsin-Madison

Stochastic Computation Case Study 4: Gene Expression: Hierarchical Mixture Models

Slides:   arrays.pdf

2:20
Discussion
2:30 Coffee Break Reception Room EE/CS 3-176
3:00 Simon Tavaré
University of Southern California

Approximate Bayesian Computation

Slides:    ima5.pdf

3:50
Discussion
6:00 Workshop Dinner Kikugawa at Riverplace
43 Main St. SE.
Minneapolis

FRIDAY, SEPTEMBER 19
Special Mini-Workshop with Sallie Keller-McNulty and Alyson Gabbard Wilson

All talks are in Lecture Hall EE/CS 3-180 unless otherwise noted.

8:30 Coffee Reception Room EE/CS 3-176
9:00 Sallie Keller-McNulty
Los Alamos National Laboratory
Greg Wilson
Los Alamos National Laboratory

Complex Multidisciplinary R&D: Characterization of the Scientific Method and Decision Processes in this Context

Mapping Decision Spaces: Role of Ethnographic Methods

Sallie Keller-McNulty's Slides:
html    pdf    ps    ppt

Greg Wilson's Slides:
html    pdf    ps    ppts

10:00
Discussion
10:10 Coffee Break Reception Room EE/CS 3-176
10:40 Andrew Koehler
Los Alamos National Laboratory

System Representations: Graphical Models and Metaphors

Slides:  html    pdf    ps    ppt

11:40
Discussion
12:00
Lunch Break
1:30 Alyson Gabbard Wilson
Los Alamos National Laboratory

Quantification/Information Integration: Integration of Hetrogeneous Information Sources through Bayesian Methods

Slides:   pdf

2:30 Short Break  
2:40 Alyson Gabbard Wilson
Los Alamos National Laboratory

Quantification/Information Integration: Integration of Hetrogeneous Information Sources through Bayesian Methods

Slides:   pdf

3:40 Coffee Break Reception Room EE/CS 3-176
4:10 Sallie Keller-McNulty
Los Alamos National Laboratory

Assessment: Optimization and Resource (e.g., R&D) Allocation, including Evolutionary Methods

Slides:   html    pdf    ps    ppt

4:40
Discussion
4:50
Concluding Remarks by Organizers
5:00
End of Tutorial

LIST OF CONFIRMED PARTICIPANTS
NAMEDEPARTMENTAFFILIATION
Scot AdamsInstitute for Mathematics and its Applications University of Minnesota, Twin Cities
Soohan AhnDepartment of Statistics Seoul National University
Bilgin AltundasInstitute for Mathematics and its Applications Schlumberger-Doll
Greg AndersonSchool of Mathematics University of Minnesota, Twin Cities
Douglas ArnoldInstitute for Mathematics and its Applications University of Minnesota, Twin Cities
Donald AronsonInstitute for Mathematics and its Applications University of Minnesota, Twin Cities
Gerard AwanouInstitute for Mathematics and its Applications University of Minnesota, Twin Cities
Karen BallInstitute for Mathematics and its Applications University of Minnesota, Twin Cities
Antar BandyopadhyayInstitute for Mathematics and its Applications University of Minnesota, Twin Cities
Maury BramsonSchool of Mathematics University of Minnesota, Twin Cities
Olga BrezhnevaInstitute for Mathematics and its Applications University of Minnesota, Twin Cities
Dongwei CaoDepartment of Computer Science and Engineering University of Minnesota, Twin Cities
Vladimir CherkasskyDepartment of Electrical and Computer Engineering University of Minnesota, Twin Cities
Laura ChiharaDepartment of Mathematics Carleton College
Donald Connelly University of Minnesota, Twin Cities
Palahela (Daya) DayanandaDepartment of Mathematics University of St. Thomas
Ann DewittDepartment of Genomics 3M
Christian Domnisoru University of St. Thomas
Flora FanBiochemistry, Molecular Biology and Biophysics University of Minnesota, Twin Cities
Shmuel FriedlandDepartment of Mathematics, Statistics, and Computer Science University of Illinois, Chicago
Chetan GadgilSchool of Mathematics University of Minnesota, Twin Cities
Tim GaroniInstitute for Mathematics and its Applications University of Minnesota, Twin Cities
Robert Gentleman Harvard School of Public Health
Charles GeyerSchool of Statistics University of Minnesota, Twin Cities
Ryan Gill University of Louisville
Balaji GopalakrishnanInstitute for Mathematics and its Applications University of Minnesota, Twin Cities
Robert GulliverSchool of Mathematics University of Minnesota, Twin Cities
Chuan-Hsiang HanInstitute for Mathematics and its Applications University of Minnesota, Twin Cities
Leroy Hood Institute for Systems Biology
Fern HuntMathematical and Computational Sciences Division National Institute of Standards and Technology
Naresh JainSchool of Mathematics University of Minnesota, Twin Cities
Lili JuInstitute for Mathematics and its Applications University of Minnesota, Twin Cities
Baris Kazar University of Minnesota, Twin Cities
Sabera KaziWireless and RF Solutions Honeywell
Sallie Keller-McnultyDepartment of Statistical Science Los Alamos National Laboratory
Christina KendziorskiDepartment of Biostatistics and Medical Informatic University of Wisconsin, Madison
Mohammad KhanDepartment of Mathematics Kent State University
Arkady KhodurskyShannon Laboratory Biotechnology Institute University of Minnesota, Twin Cities
Dohyun KimDepartment of Statistics Seoul National University
Andrew Koehler Los Alamos National Laboratory
Thomas KurtzDepartment of Mathematics University of Wisconsin, Madison
Soumendra LahiriDepartment of Statistics Iowa State University
Gary Lam University of Minnesota, Twin Cities
Jeff Lande University of Minnesota, Twin Cities
Taerim LeeDepartment of Statistics Seoul National University
Raoul LePageDepartment of Statistics and Probability Michigan State University
Qingsheng LiDepartment of Microbiology University of Minnesota, Twin Cities
Daniel MakiDepartment of Mathematics Indiana University
Richard McGeheeSchool of Mathematics University of Minnesota, Twin Cities
Sunil MenonES&S Labs Honeywell
Dinkar MylaraswamyHoneywell Technology Center Honeywell
Haewon NamInstitute of Mathematics and Statistics University of Minnesota, Twin Cities
Michael NewtonDepartment of Statistics University of Wisconsin, Madison
Amir NiknejadDepartment of Mathematics University of Illinois, Chicago
Sharareh NoorbaloochiDepartment of Electrical Engineering University of Minnesota, Twin Cities
Lea PopovicInstitute for Mathematics and its Applications University of Minnesota, Twin Cities
Sanjive QaziDepartment of Bioinformatics Parker Hughes Cancer Institute
Arvind Raghavan University of Minnesota, Twin Cities
Shalini RaghavanDepartment of Genomics and Proteomics 3M
Grzegorz RempalaDepartment of Mathematics University of Louisville
David RoeDepartment of Biology University of Minnesota, Twin Cities
Suhas SahaDepartment of Economics University of Minnesota, Twin Cities
Fadil SantosaInstitute for Mathematics and its Applications University of Minnesota, Twin Cities
Arnd ScheelSchool of Mathematics University of Minnesota, Twin Cities
Sashirekha ShanmugaveluDepartment of Computer Engineering University of Minnesota, Twin Cities
Ruth ShawDepartment of Ecology and Evolutionary Biology University of Minnesota, Twin Cities
Jeffrey SilvisSpace Physics Laboratory University of Minnesota, Twin Cities
Tamon StephenInstitute of Mathematics and its Application University of Minnesota, Twin Cities
Simon TavareDepartment of Mathematics University of Southern California
Kenneth Tetrick NONE
Minassie Tewoldebrhan University of Minnesota, Twin Cities
Zheng TuDepartment of Supercomputing Institute University of Minnesota, Twin Cities
Onder UluyolES&S Labs Honeywell
Jing WangInstitute for Mathematics and its Applications University of Minnesota, Twin Cities
Stephen WillsonDepartment of Mathematics Iowa State University
Alyson WilsonStatistical Sciences Group Los Alamos National Laboratory
Greg Wilson Los Alamos National Laboratory
Jie XuDepartment of Animal Science University of Minnesota, Twin Cities
Yuhong YangDepartment of Statistics Iowa State University
Ofer ZeitouniSchool of Mathematics University of Minnesota, Twin Cities
Yongqian ZhangDepartment of Animal Science University of Minnesota, Twin Cities
Jun ZhaoInstitute of Mathematics and its Application University of Minnesota, Twin Cities
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