December 18 - 20, 2006 New Delhi

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Programme

Preliminary Programme for the Conference. Details such as Session Chairs and Talk titles will be added as we go along.
In all sessions, there will be additional contributed talks.

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International Conference on Bioinformatics-2006

December 18th 20th, 2006 

Hotel Ashok, New Delhi, India

December 18th 2006

8.00 - 9.00 amRegistration
9.00 - 9.30 amTea/Coffee
9.30 - 10.30 am Inauguration
10.30 11.30 am
Plenary Lecture 
Chairperson M.Vijayan, IISc, Bangalore
Speaker  Gene Myers, HHMI, Janelia Farms
Imaging-Based Systems Biology
11.30 am 1.30 pm
SESSION IA    Computational Biology 1
Chairperson Sachin Maheswari, IIT, New Delhi.
11.30 - 12.15 pm Special Lecture  David Sankoff, Ottawa, Canada
Removing Noise and Ambiguities from Comparative Maps in Rearrangement Analysis.
12.15 - 12.45 pmLaxmi Parida, IBM TJ Watson Research Center, USA
Permutations in Bioinformatics
12.45 - 1.00 pmVineeth Surendranath, Max Planck Institute, Germany
Noise and silence : towards a unified framework for functional studies using Mass Spectrometry and RNAi
1.00 - 1.15 pmManoj Hariharan, IGIB, New Delhi.
Miracle a algorithm for miRNA target prediction based on transcript accessibility.
11.30 - 1.30 pm SESSION IB    Structural Bioinformatics 1
Chairperson Awadhesh Surolia, NII, Delhi
11.30 - 12.00 NoonSpeakers  Dinakar Salunke, NII, New Delhi
"Molecular Mimicry and Vaccine Design"
12.00 - 12.15 pm Kalidas. Y, Indian Institute of Science, Bangalore.
CavityGrid: A new grid based algorithm for detecting binding cavities
12.15 - 12.30 pmAbdur Sikder, University of Sydney, Australia.
"Improving the Performance of Domain Discovery of Protein Domain Boundary Assignment Using Inter Domain Linker Index"
12.30 - 1.00 pmPinak Chakrabarti, Bose Institute, Kolkata.
1.00 - 1.30 pmRama Ranganathan, University of Texas Southwestern Medical Center, Dallas.
11.30 - 1.30 pmSESSION - IC Datamining & Databases
ChairpersonTan Tin Wee, NUS, Singapore
11.30 - 12.00 noonSpeakers 

K. Sekar, Indian Institute of Science, Bangalore.
SAP: Structure Analysis Package

12.00 - 12.30 pmRavi Sachidanandam, Cold Spring Harbor Laboratory, NY.
Splice Rack: Insights into splicing and evolution from
a splice site database
12:30 - 1.00 pmShoba Ranganathan, McQuarrie University, Sydney.
1.00 - 1.30 pmDebasisa Mohanty, NII, New Delhi
1.30 2.30 pm LunchAPBioNet Annual General Meeting
http://www.apbionet.org/agm/2006agm.html
2.30 4.00 pm POSTER SESSION & TEA
4.00 6.00 pm SESSION IIA  Genomics & Proteomics 1
Chairperson Akhilesh Tyagi,  UDSC, New Delhi     
4.00 - 4.45 pmSpecial Lecture :Akhilesh Pandey, Johns Hopkins University, Maryland.
*Approaching Systems Biology: Vignettes from an Indo-US Collaboration
4.45 - 5.15 pmSpeakers  Srinivasan Ramachandran, IGIB, New Delhi.
Application of machine learning and statistical methods for analyzing complete sequences of genomes and proteomes
5.15 - 5.30 pmS. Krishnaswamy , Madurai Kamraj University, Tamil Nadu.
Sequence and Structure based sub-classification of HNH domains
5.30 - 5.45 pm

Elayanambi Sundaramoorthy, IGIB, New Delhi.
The Molecular Target Hypothesis revisited: A Proteome wide search for homocysteine mediated Protein structural alterations

4.00 - 6.00 pm SESSION IIB  Protein Folding and Structure Prediction
Chairperson

V.S.Chauhan, ICGEB, New Delhi.

4.00 - 4.30 pm Speakers     Saraswathi Vishveshwara, IISc, Bangalore
Dynamics of Protein Structure Network: From Equilibrium and Unfolding Simulations on Lysozyme
4.30 - 5.00 pmN Gautham, University of Madras, Chennai
Exploring Conformational Space Using a Mean Field Technique with MOLS Sampling
5.00 - 5.30 pmG.P.S.Raghawa, IMTECH, Chandigarh
"Prediction of proteins secreted by classical and non-classical pathways"
5.30 - 5.45 pm

Elizabeth Jacob, RRL, Kerala
"An alignment free technique for protein classification using chaos game representation"

4.00 - 6.00 pmSESSION - IIC Systems Biology 1
Chairperson

R Ramaswamy, JNU, New Delhi

4.00 - 4.30 pmSpeakersA. Kinoshita, Keio University, Fujisawa, Japan.
Hypoxic response of human red blood cell metabolism assessed by
metabolomics  and simulation
4.30 - 5.00 pm Pawan Dhar, RIKEN, Yokohama
Design principles of molecular networks
5.00 - 5.30 pmSomdatta Sinha, CCMB, Hyderabad
Modelling collective behaviour in interacting cell systems
5.30 - 6.00 pmJohn Reinitz, Stony Brook University, NY.
Variation and Transcriptional Control in Drosophila Segment Determination
6.00 - 6.45 pm Plenary lecture  Chairperson:
Samir Bramhachari, IGIB, Delhi
Speaker   Michael Waterman, University of Southern California, Los Angeles, USA
Constructing a Restriction Map of the Maize Genome
 

December 19th 2006             

9.15 10.00 am Plenary lectures  Chairperson:
S.C.Purohit, C-DAC, New Delhi
Speakers  D L Beveridge, Wesleyan University, Middletown
Molecular Dynamics Simulations of the 136 Unique Tetranucleotide Sequences of DNA Oligonucleotides: Dynamical Structures, Hydration, Ion Atmosphere, and Sequence Context Effects of the 10 Unique Dinucleotide Steps
10.00 - 10.45 am Ravi Iyengar, Mount Saimi School of Medicine, New York
Dynamic Topology of Biological Networks: Functional Consequences
10.45 11.15 am Tea/Coffee
11.15 1.30 pm SESSION IIIA Molecular Simulations
Chairperson Ashok Thakur, Kolkata
11.15 - 12.00 noon Special Lecture : Richard Lavery, CNRS, Paris (Special Lecture)
Probing Biomolecular Mechanics
12.00 - 12.30 pmSpeakers  B Jayaram, IIT, New Delhi
Gene to Drug In Silico: A Molecular Bioinformatics Approach
12.30 - 1.00 pmDevapriya Chaudhury, JNU, New Delhi
Use of Optimised Elastic Network Models for the interpretation of protein structure and dynamics
1.00 -1.30 pm Rajinder Joshi, C-DAC, Pune
MD Simulations - Studies of Peptide Nucleic acids.
11.15 - 1.30 pm SESSION IIIB  Computational Biology 2
Chairperson

Judith Klein-Seetharam, Carnegie Melon  University,  Pittsburgh, USA

11.15 - 11.45 amSpeakers Rahul Siddharthan, IMSc, Chennai.
PhyloGibbs-MP: Detecting cis-regulatory modules by Gibbs sampling
11.45 - 12.00 amT. Shashi Rekha, University of Hyderabad, AP.
Comparative Analysis of Splice Site Regions by Information Theory
12.00 - 12.15 pmAbha Singh Bais, Max Planck Institute for Molecular Genetics< Berlin.
Incorporating evolution of transcription factor binding sites into annotated alignments
12.15 - 12.30 pmAarti Singh, School of Computer Engineering, Nanyang  Technological University, Singapore
GPU- accelerated volunteer computing model for implementing parallelizable Bioinformatics applications
12.30 - 1.00 pmGad Landau, The University of Haifa
Indexing Genotypes for Haplotype search
11.15 - 1.30 SESSION - IIIC  

Structural Bioinformatics 1

ChairpersonP.Gautam, Anna University, Chennai
11.15 - 11.45 amSpeakers N. Srinivasan, IISc, Bangalore
Kinomics
11.45 - 12.15 pmBostjan Kobe, Queensland, Brisbane
Prediction of substrate specificities of protein kinases
12.15 - 12.45 pmPramod Wangikar, IIT, Mumbai
Prediction of Protein Structure Using Backbone Fragment Library and a Multilayered Learning Algorithm
12.45 - 1.00 pmBiswa Ranjan Meher, Indian Institute of Technology, Guwahati.
Effect of simulation protocol and force field on the flap dynamics of HIV-1 protease
1.00 -1.15 pmTarini Shankar Ghosh, IIT Kanpur
Interactions of End-to-End and End-to-Middle Helix Pairs: Crystal Structure Analysis
1:15 - 1:30Lennart Nilsson, Karolinska Institute, Stockholm, Sweden
1.30 2.30 pm Lunch
2.30 3.30 pm Poster Session
3.30 4.15 pm Plenary Lecture
Chairperson
N. Vijayaditya, New Delhi
Speaker  Y. Sakaki, RIKEN, Yokohama
From molecular simulation to network simulation
4.15 6.00 pm SESSION IV A Structural Bioinformatics 2
Chairperson  T.P.Singh, AIIMS, New Delhi
4.15 - 4.45 pm Speakers  Manju Bansal, IISc, Bangalore
Promoter identification in bacterial genomes: Role of DNA structure vs sequence
4.45 - 5.00 pmChaitanya Hiremath, University of Pune.
Abbreviated Profile Of Drugs (APOD): A numerical and graphical representation for comparing compounds
5.00 - 5.15 pmGaurav Chopra, Stanford University, CA.
Stability of Aromatic Rich Short Peptide Segments in Hydrophobic Collapse (POSTER)
5:15 - 5:30 pmAnita Suresh, Bioinformatics Institute, Singapore
Modelling study of dimerization in mammalian defensins
5.30 - 6.00 pm Sarah A. Teichmann, MRC Laboratory of Molecular Biology, Cambridge, UK.
Evolution and dynamics of transcription factor repertoires
4.15 - 6.00 pm SESSION IV B Microarray Analysis
Chairperson Karmeshu, JNU, New Delhi.
4.15 - 4.45 pm Speakers  Gabriela Alexe, IBM T.J. Watson Research Center,  NY
Molecular profiles of breast cancer progression
4.45 - 5.15 pmNarinder Sahni, JNU, New Delhi
Gene Ontology Based Prediction and Analysis of Microarray Data, GO-PAM
5.15 - 5.30 pmSaraswathi Sundararajan, Nanyang Technological University, Singapore.
Particle Swarm Optimization (PSO) and ELM based two-step approach for cancer classification
5.30 - 5.45 pmShubhra Sankar Ray, ISI, Kolkata.
Gene Ordering in Partitive Clustering using MicroarrayExpressions
5.45 - 6.00 pmRamesh Hariharan, Strand Lifesciences, Bangalore
Building Tools for Expression and Pathway Analysis
4.15 - 6.00 pmSession IV C Bioinformatics Products and Tools 1
Chairperson Ashok Kolaskar, University of Pune.
 
4.15 - 4.45 Speakers
 
Rajani Joshi, IIT, Mumbai
Mining the GDB and PDB: A Statistical Perspective
4.45 - 5.15 pmT.Werner, Genomatix, Munich, Germany
Routine systems-biology based microarray analysis
5.15 - 5.30 pmM.S. Janaki CH, C-DAC, Pune
GenomeGrid: A bioinformatics grid computing portal
5.30 - 6.00 pmSharmila Mande, TCS, Hyderabad

December 20th 2006

9.15 10.00 am Plenary lecture Chairperson :
Ashwin Srinivasan, IBM Lab. IIT New Delhi.
Speakers  Ross King, U. of Aberystwyth
The Robot Scientist Project
10.00 - 10.45 amStanislas Leibler, Rockefeller University
Fluctuations, Information and Survival: some lessons from bacteria
10.45 11.15 am Tea/Coffee
11.15 1.30 pm SESSION   VA  Drug Design
Chairperson Rama Mukherji,  Dabur India, New Delhi
Accelrys
11.15 - 12.00 am Speaker  Special Lecture :
W. L. Jorgensen, Yale U, New Haven
FEP-guidance for rapid lead optimization of anti-HIV agents
12.00 - 12.30 pmCarmay Lim, National Tsing Hua U, Taipei
Factors Governing the Maximum Number of Metal-bound Carboxylates in Metalloproteins
12.30 - 1.00 pmIndira Ghosh, University of Pune, Pune
Virtual High Throughput Screening: will it help for lead identification?
1.00 - 1.15 pm

Jyothi Devakumar, Jubilant Biosys, Bangalore

11.15 - 1.30 pmSESSION - VB Systems Biology 2
Chairperson N.Balakrishnan, IISc, Bangalore.
11.15 - 11.45 am Speakers Indrani Bose, Bose Institute, Kolkata
The p53-Mdm2 network: from oscillations to apoptosis
11.45 - 12.00 amLuciano Milanesi, CNR - Institute for Biomedical Technologies, Milan, Italy.
A Data Mining Approach for Yeast and Mammalian Cell Cycle Models in Systems Biology
12.00 - 12.15 pmSamta Malhotra,IISc, Bangalore.
Cytoview: Development of a Cell Modeling Framework
12.15 - 12.45 pmAnirvan Sengupta, Rutgers University, New Brunswick
Modeling Epigenetic Silencing
11.15 - 1.30 pmSESSION - V CGenomics and Proteomics 2
Chairperson  Saroj Mishra, IIT Delhi, Delhi.
11.15 - 11.45 pmSpeakersGyan Bhanot, CINJ, New Brunswick
Consensus Ensemble Clustering Reveals Novel mtDNA Phylogeny for the N Clade
11.45 - 12.15 amH. A. Nagarajaram, CDFD, Hyderabad
An Interesting Saga of Simple Sequence Repeats in Mycobacterial Genomes
12.15 - 12.30 pmChanchal Kumar, Max Planck Institute of Biochemistry, Germany.
Quantitative phosphoproteomics as a framework for systems biology
Om Rajora, University of New Brunswick, Canada.
12.30 - 12.45 pmKhairina Tajul-Arifin, National University of Malaysia, Malaysia.
Identification of unique proteins in Burkholderia species by comparative proteomic analysis
12:45-1:15pm Software Technology Parks of India (STPI)
Chairperson: Dr. T. Madhanmohan
Title: Mr. Zindal, DG, STPI, Delhi
1.30 2.30 pm Lunch & APBionet Executive Committee Meeting
2.30 3.30 pm Poster Session
3.30 4.15 pm Plenary lecture  M.Vidyasagar, TCS, Hyderabad.
Speaker  Dan Gusfield, University of California, Davis
Efficient and Practical Algorithms for Studying the History of Recombination in Populations: An introduction to Population Genomics
4.15 - 5.00 pm Michael Gribskov, Purdue University, West Lafayette IN, USA


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