Paradigm Shift in Biology

Paradigm Shift in Biology

Paradigm Shift in Biology

What’s Really Next

Fundamental Dogma

There are Problems with the HGP . ..

• The actual sequence data makes up only 16% of the content; the other 84% is annotated.

• The is leads to a number of issues:

• How to structure databases for mining
• How to establish control vocabularies to establish integrity of searches
• What new algorithms are needed to facilitate processing and correlating the petabytes (1015 bytes) of information
• How can protein function be extracted for the purposes of diagnostics, drug discovery and therapeutics

• USERS

• of Information

• of Tools

• of Instrumentation

• In-Silico Modeling

• INTERPRETERS

• of Information

Bioinformatics Functional Organization

Rhetorical Question

Business Factoids

Medical Bioinformatics: What is it?

What’s in a name?

Gene Discovery Informatics

IM Intensive Research Groups

Cancer Gene Discovery Knowledgebase

Bioinformatics Architecture

Challenges in High Throughput Biotechnology R&D

• Volume of Data is Growing Rapidly

• Technology is Evolving Rapidly

• Instrumentation, Informatics

• Biological Definitions are Constantly Updated

• New Interactions and Functions Discovered Daily

• New Genes

• Sometimes Homologous to Known Genes ->re-evaluate old data

• Full Value is Realized by Integrating Multiple High-Throughput Platforms

• Sequencing, Functional Screens, Small Molecule Activity

• Up-Front Design of Data and Quality Control Databases is Crucial to Success

• High Data Quality is Essential
• Financially Impossible to Repeat Experiments
• Requires Informatics Specialist who Understands Laboratory Techniques

Recent Informatics Job Description

1999

• 1999
• JGI releases 150 Mbases draft
• Celera releases the sequence of Drosophila (140 Mb)
• Public “draft” effort reaches halfway point (1,500 Mb)
• 20 more Microbial genomes completed (80 Mb but 60,000 genes)
• First release of Celera “shotgun” (9,000 Mb)
• 2000
• Public “draft” completed (1,500 Mb)
• Mouse “draft” begins (500 Mb - comparisons with human)
• Two more Celera shotgun releases ( 18,000 Mb)
• 40 more Microbial genomes sequenced (160 Mb -120,000 genes)

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