Chapter Web Links for
Genomics, Proteomics & Bioinformatics

Minidystrophin gene PNAS Dec. 2000 publication

• BLAST
  
  
• Fred Sanger
  
  
• Norm Dovichi at the University of Washington, Seattle
  
  
• Movie of picking clones from libraries for sequencing
  
  
• Movie of mass production of template DNA
  
  
• The Human Genome Project
  • Nature Publication of Public Domain Human Genome
  • Human Map Viewer
    
  • Human Genome Projectšs Genome Browser based at the University of California Santa Cruz
  • List of species with sequenced genomes
  • Ensemble Genome Browser
  • ElectronicPCR
  • Department of Energy (DOE)
  • National Institutes of Health (NIH)
  • Welcome Trust of Britain
    
    
• The Institute for Genomics Research (TIGR)
  
  
• Celera
  • Science Publication of Celera's Human Genome
    
    
• UniGene
  
  
• EST database
  
  
• FlyBase
  
  
• Berkeley Drosophila Genome Project
  
  
• Joint Genome Institute (JGI)
  
  
• Company that hopes to make DNA sequencing will be routine in clinical settings
  
  
• NCBI (the National Center for Biotechnology Information)
  
  
• PubMed
  
  
• OMIM: Online Mendelian Inheritance in Man(kind)
  
  
• GeneCard at the Weizmann Institute in Israel list of mirror sites
  
  
• LocusLink
  
  
• ORF Finder
  
  
• Entrez
  
  
• BLAST2
  
  
• PREDATOR secondary structure prediction method
  
  
• Kyte Doolittle Plot, by William R. Pearson at Medical School at the University of Virginia
  
  
• Conserved Domain (CD) search
  
  
• PDB (Protein DataBase)
  
  
• Human-Mouse Homology page
  
  
• Entrez Structure
  
  
• Gene Ontology
  
  
• Proteome Database Home Page
  
  
• Yeast PD
  
  
• Clusters of Orthologous Groups (COG)
  
  
• Swiss-Prot
  
  
• Enzyme Commission
  
  
• Phylogenetic Tree program by the Swiss Computational Biochemistry Research Group
  
  
• GeneMark by Mark Borodovsky at Georgia Tech
  
  
• Gustavo Glusman at the Institute for Systems Biology
  
  
• Doron Lancet at the Weizmann Institute
  
  
• Genotator
  
  
• HGP glossary

3.2 What have we learned from the human genome draft sequences?

• PHRED and PHRAP software programs
  
  
• Phil Green at the University of Washington
  
  
• TIGR challenges bacterial origin of human genes: TIGR web site OR Science Abstract
  
  
• Rosetta Inpharmatics
  
  
• The Sanger Center
  
  
• Stanley Prusiner at University of California, San Francisco
  • Nobel Prize Link
    
    
• George Church at Harvard University
  
  
• Gary Ruvkun at the Massachusetts General Hospital
  
  
• US Patent and Trademark Office
  
  
• Prader-Willi Syndrome (PWS)
  
  
• Angelman Syndrome (AS)
  
  
• List of imprinted genes
  
  
• Shirley Tilghman at Princeton University
  
  
• Human Epigenome Consortium
  
  
• Albert de la Chapelleweb at Ohio State Universtiy
  
  
• Yusuke Nakamura at the University of Tokyo
  
  
• Beckwith-Wiedemann Syndrome
  
  
• Eric Lander at MIT
  
  
• Rudolf Jaenish at MIT
  
  
• Christopher Wilson at the University of Washington
  

Takao Shinozawa at Gumma University in Kiryu, Japan


RIKEN Genome Sciences Centre


Buchnera Genmome


Comprehensive Microbial Resource (CMR)


Stewart Cole at the Pasteur Institute, Paris


M. leprae web site at Sanger Centre


M. leprae web sites at the Pasteur Institute


John Glass and the Ureaplasma urealyticum genome


NCBI Entrez Taxonomy


Svante Pääbo at Max Planck Institute for Evolutionary Anthropology


Phylogenetic Tree Terminology


Human mtDNA genomes: MITOMAP and mtDB

CDC page on Anthrax


Andreas Manz at Imperial College, London


David Burke at the University of Michigan


Phillip Belgrader at the Lawrence Livermore National Laboratory


Rapid detection device use by US FDA


William Rosenzweig and Russell Vreeland at West Chester University


Wilmar Salo in Duluth Minnesota


Kathleen Eisenbach at the University of Arkansas Medical School


Filarial Genome Project


New diseases identified in humans


Laura Richman and Gary Hayward at Johns Hopkins Medical School


Robert Lanciotti at the National Center for Infectious Diseases in Fort Collins, Colorado


West Nile Virus Home Page


Flash animation interactive map of West Nile Virus


Cases of human encephalitis from WNV


Mosquito vectors of WNV


Job ads posted in Science each week

Sites that try to maintain current genome lists

Enhanced Microbial Genomes Library

Institut Pasteur (E. coli)

Institut Pasteur (M. tuberculosis)

Joint Genome Institute

Los Alamos National Lab

NCBI

National Center for Genome Resources

Pedant

Sanger Centre

TIGR

University of Oklahoma

University of Wisconsin: E. coli and Genetics Facutly

Aileen Allsop and John Rosamond of AstraZeneca


Malaria Genome Project Consortium Partners List


Christian Raetz at Duke University


Sidney Altman at Yale University
Nobel Prize for Ribozymes


Ribozyme Pharmaceuticals, Inc.


Cy Stein at Columbia University


Fred Blattner at the University of Wisconsin

Chapter 4 - Genomic Variation (15 second biographies)

4.1 Environmental Case Studies

• Kenine Comstock, Elaine Ostrander at the Fred Hutchinson Cancer Research Institute
  
  
• Sam Wasser at the University of Washington, Seattle
  
  
• David Mann at the Royal Botanic Garden in Edinburgh
  
  
• Ginger Armbrust at the University of Washingtonšs School of Oceanography
  
  
• Online Trends - a compendium of global change.

4.2 Human Genomic Variation

• The SNP Consortium (TSC)
  
  
• OMIM: Online Mendelian Inheritance in Man(kind)
  
  
• Adrian R. Krainer at the Cold Spring Harbor Laboratory in New York
  

4.3 Why the SNP frenzy? Pharmacogenomics!

• William Evans at St. Judešs Childrenšs Hospital
  
  
• Mary Relling at St. Judešs Childrenšs Hospital
  
  
• Incyte Genomics
  

4.4 Is there a genomic component to the ultimate phenotype - death?

• Delany Sisters, Sadie and Bessie
  
  
• Gordon Lithgow form Manchester, England
  
  
• Richard Lenski at Michigan State University
  

4.6 Ethical Consequences of Genomic Variations

• Syngenta
  
  
• Greenpeace
  
  
• The Center for the Application of Molecular Biology to International Agriculture in Melbourne, Australia
  
  
• Metabolix
  
  
• Scientific American article about bioplastics
  
  
• Charles Arntzen at Arizona State University
  
  
• US Patent Office
  
  
• Nextran
  
  
• ELSI or Ethical Legal and Social Issues
  
  
• Steve Hyman, director of the National Institutes of Mental Health
  
  
• Dorothy Nelkin at New York University
  
  
• Peter Neufeld, director of the Innocence Project in New York
  • Innocence Project
    
    
• US Census Bureau
  
  
• NIH recommendations concerning universal CF genetic testing
  
  
• Kari Stefansson at deCODE
  
  
• Google.com
  
  
• Zavos interview by Dateline of NBC News
  
  
• Panos Zavos and Severino Antinori human cloning web site
  
  
• Raelians
  
  
• Ian Wilmut at the Roslin Institute
  
  
• Rudolf Jaenish at MIT
  

Chapter 5 - Genomic DNA Microarrays (15 second biographies)

5.1 Introduction

• Pat Brown at Stanford University
  
  
• GCAT (Genome Consortium for Active Teaching)
  
  
• Yeast Genes can be amplified by PCR using a set of primers that are commercially available
  
  
• Saccharomyces Genome Database Function Junction
  
  
• Saccharomyces Genome Database Expression Connection
  
  
• Entrez PubMed
  
  
• David Botstein at Stanford University
  
  
• Free access to paper by Brown and Botstein, et al., December 2000.
  

5.2 Microarray Data Analysis

• Patrik Dšhaeseleer at the University of New Mexico
  
  
• Shoudan Liang at NASA
  
  
• Roland Somogyi at Incyte Pharmaceuticals
  
  
• David Gilbert at City University in London
  
  
• Michael Schroeder at City University in London
  
  
• Jacques van Helden in Brusselles
  
  
• GenMAPP developed by the Gladstone Institutes at the University of California, San Francisco
  
  
• Timothy Hughes at Rosetta
  • Rosetta Inpharmatics
    
    
• MIPS web site
  
  
• Rosetta Inpharmatics Inc.
  

5.3 Cancer and Genomic Microarrays

• Louis Staudt at the National Cancer Institute
  
  
• Ash Alizadeh at Stanford University
  
  
• Mike Eisen at Lawrence Berkeley National Laboratory
  
  
• Charles Perou at Stanford University
  
  
• Therese Sørlie of Oslo Norway
  
  
• Michael Wigler at Cold Spring Harbor Laboratories
  

5.4 Improving Medications with DNA Microarrays

• Marcel Behr at McGill University
  
  
• Lee Hartwell at Fred Hutchinson Cancer Institute
  
  
• John Weinstein at the National Cancer Institute
  
  
• Jeffrey Friedman at Rockefeller University
  
  
• Affimetrix
  

5.5 Can microarrays illuminate the ultimate black box?

• Rat Brain Sagital Sections
  
  
• Carrolee Barlow at the Salk Institute in San Diego
  
  
• Claire Rampon and Joe Tsien at Princeton University
  
  
• Yinghe Hu at the Genomics Institute of Novartis Research Foundation
  
  
• Chiara Cirelli and Giulio Tononi from the University of Pisa, Italy
  
  
• Tomas Prolla and Richard Weindruch at the University of Wisconsin, Madison
  
  
• Cheol-Koo Lee at the University of Wisconsin, Madison
  
  
• R. Adron Harris at the University of Texas, Austin
  
  
• Pat Levitt at the University of Pittsburg
  

Chapter 6 - Proteomics (15 second biographies)

6.1 Introduction

• Gene Ontology
  
  
• Mike Snyder at Yale University
  
  
• Elizabeth Winzeler and Ron Davis at Stanford University
  
  
• Information about C. elegans the nematode worm
  
  
• RNA interference Database
  
  
• Andy Fire at the Carnegie Institute for Embryology
  

6.2 Protein 3D Structures

• Protein Explorer web page
  
  
• German Protein Structure Factory
  
  
• National Institute of General Medical Sciences
  
  
• Protein DataBaseweb (PDB)
  
  
• Dinesh Christendat, Adelinda Yee, and Aled Edwards at the University of Toronto
  
  
• Cheryl Arrowsmith at the University of Toronto
  
  
• Vicki Nienaber at Abbott Laboratories in Illinois
  
  
• Stanley Prusiner at University of California, San Francisco
  • Nobel Prize Link
    
    
• Susan Lindquist of the University of Chicago
  

6.3 Protein-Protein Interactions

• David Eisenberg at UCLA
  
  
• DIP, Database of Interacting Proteins
  
  
• Stan Fields at the University of Washington, Seattle
  
  
• Yeast Protein Database (YPD)
  
  
• Benno Schwikowski at the Institute for Systems Biology
  
  
• Swiss 2D database called Expasy
  

6.4 Measuring Proteins

• Michel Desjardins at the University of Montreal
  
  
• Brian Chait at the Rockefeller University in NYC
  
  
• Rudei Aebersoldweb at the Institute for Systems Biology (ISB) in Seattle
  
  
• Pat Brown at Stanford University
  
  
• Gavin MacBeath at Harvard University
  
  
• Stuart Schreiber at Harvard University
  
  
• Oliver Fiehn at the Max Planck Institute in Potsdam Germany
  
  
• Norm Dovichi at the University of Washington in Seattle
  

Chapter 7 - Genomic Circuits (15 second biographies)

7.1 Circuits Within Single Genes

Sea Urchin Development


Chuck Ettensohn, Carnegie-Mellon Univ.


John Morrill at Univ. of South Florida


Eric Davidson at CalTech


Susan Ernst at Tufts University

Harley McAdams at Stanford

Adam Arkin at Physical Biosciences Division of the Lawrence Berkeley National Laboratory

Timothy Garnder at Boston University

Jim Collins at Boston University

Charles Cantor at Boston University

Stan Leibler in the Physics Department at Princeton University

Brain Anatomy


Upinder Bhalla at the National Center for Biological Sciences, Bangalore, India

Ravi Iyengar at Mount Sinai School of Medicine


Emergent Properties of Networks of Biological Signaling Pathways (publication by Iyengar and Bhalla)

Block Diagram of signaling network


GENESIS

Imaging calcium fluxes in hippocampus


long term potentiation informational web site


UCLA Laboratory of Neuro Imaging


Synapse Web

David Clayton at the University of Illinois, Champaign-Urbana

Kurt Kohn at the National Cancer Institute (NCI)

cell cycle control and DNA repair


Elizabeth Williams and Laurence Hurst at Bath University

European Molecular Biology Laboratory in Germany

Drew Endy at the Molecular Science Institute


T7 Virus Gene List

Malcolm Gladwell, author of the Tipping Point


Molecular Science Institute


Gunter Blobel at Rockefeller University


Seymour Benzer at CalTech


Francis Crick at the Salk Institute


James Watson at Cold Spring Harbor Laboratoty

The Watson School of Biological Sciences


Lee Hartwell at Fred Hutchinson Cancer Institute

Fred Hutchinson Cancer Research Center


Jeremy Edwards and Bernhard Palsson from the University of California in San Diego

Ecocyc

Pathway Database
National Center for Genome Research


The Institue for Systems Biology

Alliance for Cell Signaling
Al Gilman at the University of Texas Southwestern Medical Center


Integrated Genomics