Genes and Proteins

• Genomics and Proteomics
• Bioinformatics Analysis of Proteomics Data
• Pharmaceutical Applications

Proteomics Techniques

• Proteomics Analysis
• 2-D Gel Electrophoresis
• Spectrometry
• Phage Display
• Yeast 2-Hybrid System
• Lab on a Chip (LOC) Technologies
• Microfluidic LOCs
• Biochips and Microarrays
• Additional Proteomics Technologies: Bioinformatics; Functional Genomics; and Structural Genomics

Introduction

Bioinformatics Analysis of Proteomics Data

• Introduction
• Proteomic Methods

Pharmaceutical Applications

• Bioinformatics Analysis of Proteomics Data
• Studying Proteins Versus Studying Genes

Proteomics Techniques

• Identifying Novel Therapeutics
• Drug Discovery

Phage Display; Yeast 2-Hybrid System

• Proteomics Techniques
• 2-D Gel Electrophoresis
• Spectrometry

Lab-on-a-Chip (LOC) Technologies

• Phage Display
• Yeast 2-Hybrid System

Cal Tech's Beckman Institute: MRI Shows Gene Expression Anywhere in Organism

GeneProt: New Method Automates Mass Spec

University of Michigan: New Protein Separation Faster Than 2-D Gels

Cytogen: Ligand Target Cloning

Hybrigenics

Lexicon: Gene-Trapping Technique Detects Rare Proteins

RheoGene: Multiplexed Gene -Regulation Technology for Studying Complex Gene Interactions

• Cal Tech's Beckman Institute: MRI Shows Gene Expression Anywhere in Organism

HTS Biosystems: Surface Plasmon Resonance

• GeneProt: New Method Automates Mass Spec

Rosemount: Mass Spectrometer on a Chip

• University of Michigan: New Protein Separation Faster Than 2-D Gels

Caliper Technologies: Microfluidics and Lab on a Chip

• Cytogen: Ligand Target Cloning

Johns Hopkins; NYU; Mount Sinai: Bisubstrates Squelch Errant Enzymes

• With Institut Pasteur: Hybrigenics Named Exclusive Licensee To Protein-Interactions Patent
• Bacterial Two-Hybrid System Better Than Yeast
• Protein Interactions Mapped out in H. pylori
• Map of Protein Interactions Between HIV and Host Cells
• With Lynx Therapeutics: Obesity
• With XTL: Hepatitis C Virus (HCV) Therapeutics

SUNY and University of Tokyo: Making Novel Proteins Using a 21st-Century Amino Acid

• Lexicon: Gene-Trapping Technique Detects Rare Proteins

Vanderbilt University: New Technology Expands Molecular Photography Options

• RheoGene: Multiplexed Gene -Regulation Technology for Studying Complex Gene Interactions

Virginia Tech: Dried Cells; Tissues Could Solve Biological Materials Storage; Transport Problems

• HTS Biosystems: Surface Plasmon Resonance
• With Dyax Corp: Phage Display for Antibody Chips
• With Boston Probes and Applied Biosystems: Peptide Nucleic Acid (PNA) Technology
• Mitsubishi Chemical: Purchase and Distribution Agreement

Whitehead Institute and Mass General: Interaction Sequence Tags

• Rosemount: Mass Spectrometer on a Chip

Phylos

• With Structural Genomix: High-Throughput Protein Analysis
• Conflict with Aclara Resolved

Harvard University: Protein Chips Probe Protein Function

• Johns Hopkins; NYU; Mount Sinai: Bisubstrates Squelch Errant Enzymes

University of Pennsylvania: IDAT Detects Proteins at Unprecedented Resolution

• SUNY and University of Tokyo: Making Novel Proteins Using a 21st-Century Amino Acid

Caliper and Structural Genomix High Throughput Proteomics Labchip

• Vanderbilt University: New Technology Expands Molecular Photography Options

Detection on a Chip: Microphotonics

• Virginia Tech: Dried Cells; Tissues Could Solve Biological Materials Storage; Transport Problems

Hoffman-La Roche: Bacteria Chips to Study Antibiotics

• Whitehead Institute and Mass General: Interaction Sequence Tags

EMBL Begets Cellzome: TAP Method Yields Low-Abundance Proteins and Multicomponent Complexes

• Alternative to Phage Display
• Protein-Expression Chip
• Antibody-Like Protein Scaffolds for Cancer Treatment

NEN Life Science: Analyzing Gene Expression or Copy Number on a Chip

• Harvard University: Protein Chips Probe Protein Function

Functional Genomics

Human Genome Sciences Wins AIDS-Receptor Drug Target Patent

Agritope: Functional Genomics for Plants

Devgen NV: Belgian Firm Focuses on Functional Genomics

Paradigm Genetics: 150 Plant Gene Functions per Week

CuraGen: Functional Genomics for Therapeutics

Rigel and Pfizer: Allergies

DOE Grants Focus on Microbial Waste Remediation; Carbon Management; Energy Production; Biotech

Genset: Protein Takes Fat off Obese Mice

MDS Proteomics Links with Zyomyx; IBM

Arqule and Acadia: G-Protein-Receptors as Drug Targets

Neotherapeutics: Therapies for Neurodegenerative Disease

Neogene Technologies: G-Protein-Coupled Receptors

Cereon Genomics: Arabidopsis Data Released through Public-Private Partnership

Exelixis: Functional Genomics in Drosophila

Aurora Patents Gene Tagging System

UPenn: Pure-Blood Microchips

Cadus Pharmaceutical: Orphan Receptors and G-Protein

Mycota Biosciences: Functional Genomics in Fungus to Find Drug Targets

Mendel Biotech: Technology Makes Plants More Weatherproof

Hyseq Protein May Reduce Blood Clotting

Structural Genomics

Protein Folding

NIGMS: $150 Million for Multicenter Protein Structure Initiative

University of Washington: Computational Method may Hold Key to Predicting Protein Folding

Berkeley Lab's Advanced Light Source Accelerates X-Ray Crystallography

University of California-Santa Cruz: New Images Reveal the Workings of Cellular Protein Factories

Keio University; Teikyo University Biotechnology Center: Snapshots of a Molecular Motor

Integrative Proteomics: X-Ray; NMR; Mass Spec for Target ID

Wistar Institute: X-Ray Structure Reveals Similarities in Molecules Linked to Cancers

NIAID; St. Jude's; St. Andrews: Advance in Tackling Common Viral Respiratory Disease

Structural Bioinformatics Patents NMR 3-D Structure Technology

Bioinformatics and Computational Proteomics

Incyte Genomics

Turbogenomics: Turbo-Charged Blast Sequence Comparison

Celera Genomics: Now Proteomics

Entigen Provides Services to Smaller Research Groups

GeneData AG: Collaboration Targets Antibacterials

Alphagene Identifies 264 New Genes

Lion Bioscience Provides System to Nestle and Bayer

Geneformatics: Protein Structure Prediction

Proteome and Spotfire: Databases and Analytic Software

Netgenics

Shanghai Genecore: Complicated Genealogy

Norwegian Radium Hospital: Mining the Biobibliome

National Center for Genome Resources: ISYS Integrates Bioinformatics Tools; Databases

McGill University Launches Centre for Bioinformatics

Compugen and UCSF: New Chemokine Binds HIV Co-Receptors

Millennium Pharmaceuticals

ZymoGenetics Runs the Gamut of Protein R&D

Proteome Systems: Australians Build Proteomics Capabilities

Gemini Genomics and Large Scale Biology Corp. Isolate 70 Disease Proteins

Myriad Genetics

Eos Uses Morphosys Combinatorial Antibody Library

MitoKor: Alzheimer's Disease

Oxford Glycosciences

Sunesis Pharmaceuticals

Morphochem AG

Scriptgen Becomes Anadys and Expands

Fraunhofer Institute Pinpoints Candida Pathogenicity Proteins

Genetrace Systems Acquires Strata Biosciences

Axcell Maps Interactions Of WW Domain Proteins

Large Scale Biology Corp.; Navy; NIH Look for Stem-Cell Factors

Syngenta and Myriad: Rice Proteomics May Mean Better Cereal Crops

Ciphergen Biosystems: Biomarkers

Beyond Proteomics: Glycomics

UPenn Scientists Show How Chaperonins Catch Protein-Folding Errors

Newcastle University: Fragments of Dinosaur Protein can Survive in Bone Fossils

Scripps: Expanding E. Coli's Amino Acid Repertoire Paves Way for Engineered Proteins

Gladstone Institute; UCSF: HIV Viral Protein Plays Offense and Defense Against Immune System

UCSD: Protein Responsible for Failing Heart

Ceres Pharmaceuticals: Powerful New Vaccines from Yeast

Cellular Signaling Alliance Unites Researchers Via Internet

University of Illinois: New Mechanism for Cell Signaling

NCI Intensifies Informatics

Xenometrix Wins US Gene-Profiling Patent

PNNL: Top Role in Biological Sciences Initiative

Dana-Farber Cancer Institute: Molecular Gateways to Death

Markets

Barriers to Commercialization

Appendix A: Contacts

Appendix B: Recent Patents in Proteomics and Bioinformatics

Appendix C and D: Website URLs and Publications