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Sequence and gene expression analysis

   
 

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Protein interaction and clinical data analysis

   
   
   
 

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Post-Genome Knowledge Discovery
(January – June 2002)

Sub-theme 1. Sequence and gene expression analysis (Jan - Feb 2002)

 

  Special Workshop on Language of DNA (18 - 20 February 2002)

 

 Jointly organized by Institute for Mathematical Sciences (IMS) and Genome Institute of Singapore (GIS)

 

The DNA of a cell contains all the instructions necessary to recreate life. As such, the sequence of a genome's DNA provides a form of information transfer with its own alphabet (i.e., nucleotides), words (i.e., codons), and sentences (i.e., genes). Thus, the efforts to decode the meaning of DNA sequence is an exercise analogous to that of cryptography seeking to derive meaning from a collection of seemingly randomly recurring symbols.


Previous deciphering efforts have been basic and focused on the immediate meaning of a focal sequence. This is akin to the translation of a text on a word-by-word basis. As we advance in this understanding, we start to see higher order meaning through the nuances of gene expression and splice changes. Moreover, the structure and organization of the DNA sequences within and across species provides a clue as to the fundamental rules that governed the creation of life.


Linguistics is a branch of science that has long sought to define the architecture and laws of language structure. There is ample evidence to indicate that both the dimensions and units of linguistic structure appear genetically embedded in the human species. Therefore, the analysis of the structure of language has provided a window into the make-up of the Homo Sapien mind, and perhaps a set of useful strategies to unearth similar structures.


Experimentally, therefore, both the disciplines of genomics and linguistics seek to uncover order and information from a sea of noise. Genomics, by virtue of its origins in physical and biological sciences, has had the benefit of rigorous computational tools and laboratory validation in its investigations. Unlike genomics, however, the intuitive understanding of language in all of us permitted linguists to convincingly reconstruct rules governing the transmission of higher order meaning, while unlike cryptography, genomics can use experimental strategies to uncover the relation between form and meaning.


This workshop on the Language of DNA will explore the investigative strategies used by these diverse fields of genomics and linguistics in identifying meaning from recurrent strings of information. A series of short talks will be presented in a multidisciplinary manner touching on linguistics, genomics, computation and molecular biology. The goal will be to synthesize novel conceptual approaches to uncovering higher order meaning from DNA sequence information. These presentations will be followed by extensive discussions with the audience, aimed at deepening mutual understanding and exploring the possibility of forging novel investigative strategies in genomic research.

 

Senior Discussants:

 

  • Vlad Bajic, Ph.D. (Laboratories for Information Technology)(formerly KRDL)
  • Matthew Huang, Ph.D. (Beijing Genome Institute)
  • Prasanna Kolatkar, Ph.D. (Genome Institute of Singapore)
  • Edison Liu, M.D. (Genome Institute of Singapore)
  • Philip Long, Ph.D. (Genome Institute of Singapore)
  • Lance Miller, Ph.D. (Genome Institute of Singapore)
  • Karuvannur Mohanan, Ph.D. (Department of English Language & Literature, National University of Singapore)
  • Tan Kian Lee, Ph.D. (Department of Computer Science, National University of Singapore)

 

Schedule of Speakers

 

Monday, 18 February 2002

Venue: 

The Big One

 

Laboratories for Information Technology (formerly KRDL)
21 Heng Mui Keng Terrace
Singapore 119613

 

1:30 - 2:00pm

Registration

2:00 - 2:15pm

The goals of the conference
The fundamental laws of genomic information
Edison Liu, Genome Institute of Singapore

2:15 - 2:45pm

Exploring language structure: questions and methodology
Karuvannur Mohanan, Department of English Language & Literature, National University of Singapore

2:45 - 3:10pm

Expression array technology: searching for structure in gene expression data
Lance Miller, Genome Institute of Singapore

3:10 - 3:25pm

 -- Coffee Break --

3:25 - 3:50pm

Estrogen response element: a challenging task of computer modeling and recognition
Vlad Bajic, Laboratories for Information Technology (formerly KRDL) and Lin Chin Yo, Genome Institute of Singapore 

3:50 - 4:15pm

Some applications of machine learning to molecular biology
Philip Long, Genome Institute of Singapore

4:15 - 4:35pm

Hierarchical machine learning for characterising FAD-binding proteins
Aik Choon Tan and David Gilbert, Bioinformatics Group, Department of Computing, City University. London, U.K.

4:35 - 5:15pm

Group discussion

 

Tuesday, 19 February 2002

Venue: 

The Big One

 

Laboratories for Information Technology (formerly KRDL)
21 Heng Mui Keng Terrace
Singapore 119613

 

2:00 - 2:30pm

Strategies of unearthing laws of language structure
Karuvannur Mohanan, Department of English Language & Literature, National University of Singapore

2:30 - 3:00pm

Databases and information discovery
Limsoon Wong, Laboratories for Information Technology (formerly KRDL)

3:00 - 3:30pm

Exploiting synteny in genome-by-genome ortholog pairing
Karuturi Radha Krishna Murthy, Department of Computer Science, National University of Singapore

3:30 - 3:45pm

 -- Coffee Break --

3:45 - 4:10pm

S. pombe (yeast) functional genomics
Lin Kui, Genome Institute of Singapore and Jian Hua Liu, Institute of Molecular Agrobiology

4:10 - 4:30pm

The zebrafish database at GIS
Kuang Yuyu, Genome Institute of Singapore

4:30 - 4:50pm

Genetic diversity of the HLA locus
Ren Ee Chee, Genome Institute of Singapore

4:50 - 5:30pm

Group discussion

 

Wednesday, 20 February 2002

Venue: 

The Big One

 

Laboratories for Information Technology (formerly KRDL)
21 Heng Mui Keng Terrace
Singapore 119613

 

2:00 - 2:30pm

Universal laws and interaction between laws in language structure
Karuvannur Mohanan, Department of English Language & Literature, National University of Singapore

2:30 - 3:00pm

BLASTing your sequence: how fast can you go?
Tan Kian Lee, Department of Computer Science, National University of Singapore

3:00 - 3:20pm

Annotation for the Fugu
Tania Oh, Genome Institute of Singapore

3:20 - 3:35pm

 -- Coffee Break --

3:35 - 3:55pm

How the brain processes language: lessons from functional brain imaging

Michael Chee, Genome Institute of Singapore

3:55 - 4:55pm

Human Genome Project: how it was done and what did we learn
Matthew Huang, Beijing Genome Institute

4:55 - 5:30pm

Wrapping up
Edison Liu, Genome Institute of Singapore
Karuvannur Mohanan, Department of English Language & Literature, National University of Singapore
Matthew Huang, Beijing Genome Institute

 

 

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