|
December 18th 2006 |
| 8.00
- 9.00 am | Registration |
| 9.00
- 9.30 am | Tea/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 pm | Laxmi
Parida, IBM TJ Watson Research Center, USA
Permutations
in Bioinformatics
|
| 12.45
- 1.00 pm | Vineeth
Surendranath, Max Planck Institute, Germany
Noise
and silence : towards a unified framework for functional studies using Mass Spectrometry
and RNAi
|
| 1.00
- 1.15 pm | Manoj
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 Noon | Speakers
| 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 pm | Abdur
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 pm | Pinak Chakrabarti, Bose Institute,
Kolkata. |
| 1.00
- 1.30 pm | Rama
Ranganathan, University of Texas Southwestern Medical Center, Dallas.
|
| 11.30
- 1.30 pm | SESSION
- IC | Datamining
& Databases |
| Chairperson | Tan
Tin Wee, NUS, Singapore |
| 11.30
- 12.00 noon | Speakers
| K.
Sekar, Indian Institute of Science, Bangalore.
SAP:
Structure Analysis Package |
| 12.00
- 12.30 pm | Ravi
Sachidanandam, Cold Spring Harbor Laboratory, NY.
Splice
Rack: Insights into splicing and evolution from
a splice site database |
| 12:30
- 1.00 pm | Shoba
Ranganathan, McQuarrie University, Sydney. |
| 1.00
- 1.30 pm | Debasisa
Mohanty, NII, New Delhi |
| 1.30
– 2.30 pm |
Lunch | APBioNet
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 pm | Special
Lecture : | Akhilesh
Pandey, Johns Hopkins University, Maryland.
*Approaching Systems Biology:
Vignettes from an Indo-US Collaboration |
| 4.45
- 5.15 pm | Speakers | Srinivasan
Ramachandran, IGIB, New Delhi.
Application
of machine learning and statistical methods for analyzing complete sequences of
genomes and proteomes |
| 5.15
- 5.30 pm | S.
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 pm | N
Gautham, University of Madras, Chennai
Exploring
Conformational Space Using a Mean Field Technique with MOLS Sampling |
| 5.00
- 5.30 pm | G.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 pm | SESSION
- IIC | Systems Biology 1 |
| Chairperson |
R
Ramaswamy, JNU, New Delhi |
| 4.00
- 4.30 pm | Speakers | A.
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 pm | Somdatta
Sinha, CCMB, Hyderabad
Modelling
collective behaviour in interacting cell systems |
| 5.30
- 6.00 pm | John
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 pm | Speakers |
B Jayaram, IIT, New Delhi
Gene
to Drug In Silico: A Molecular Bioinformatics Approach |
| 12.30
- 1.00 pm | Devapriya 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 am | Speakers | Rahul Siddharthan, IMSc, Chennai.
PhyloGibbs-MP:
Detecting cis-regulatory modules by Gibbs sampling
|
| 11.45
- 12.00 am | T.
Shashi Rekha, University of Hyderabad, AP.
Comparative
Analysis of Splice Site Regions by Information Theory
|
| 12.00
- 12.15 pm | Abha Singh Bais, Max Planck Institute for
Molecular Genetics< Berlin.
Incorporating
evolution of transcription factor binding sites into annotated alignments |
| 12.15
- 12.30 pm | Aarti
Singh, School of Computer Engineering, Nanyang Technological
University, Singapore
GPU- accelerated volunteer computing model for implementing
parallelizable Bioinformatics applications |
| 12.30
- 1.00 pm | Gad Landau, The University of Haifa
Indexing
Genotypes for Haplotype search |
| 11.15
- 1.30 |
SESSION - IIIC |
Structural
Bioinformatics 1 |
| Chairperson | P.Gautam,
Anna University, Chennai |
| 11.15
- 11.45 am | Speakers | N. Srinivasan, IISc, Bangalore
Kinomics |
| 11.45
- 12.15 pm | Bostjan
Kobe, Queensland, Brisbane
Prediction
of substrate specificities of protein kinases |
| 12.15
- 12.45 pm | Pramod
Wangikar, IIT, Mumbai
Prediction
of Protein Structure Using Backbone Fragment Library and a Multilayered Learning
Algorithm |
| 12.45
- 1.00 pm | Biswa
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 pm | Tarini
Shankar Ghosh, IIT Kanpur
Interactions of
End-to-End and End-to-Middle Helix Pairs: Crystal Structure Analysis |
| 1:15
- 1:30 | Lennart
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 pm | Chaitanya
Hiremath, University of Pune.
Abbreviated
Profile Of Drugs (APOD): A numerical and graphical representation for comparing
compounds |
| 5.00
- 5.15 pm | Gaurav
Chopra, Stanford University, CA.
Stability
of Aromatic Rich Short Peptide Segments in Hydrophobic Collapse (POSTER)
|
| 5:15
- 5:30 pm | Anita
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 pm | Narinder Sahni, JNU, New Delhi
Gene Ontology
Based Prediction and Analysis of Microarray Data, GO-PAM |
| 5.15
- 5.30 pm | Saraswathi
Sundararajan, Nanyang Technological University, Singapore.
Particle
Swarm Optimization (PSO) and ELM based two-step approach for cancer classification
|
| 5.30
- 5.45 pm | Shubhra
Sankar Ray, ISI, Kolkata.
Gene Ordering in
Partitive Clustering using MicroarrayExpressions
|
| 5.45
- 6.00 pm | Ramesh Hariharan, Strand Lifesciences, Bangalore
Building
Tools for Expression and Pathway Analysis |
| 4.15
- 6.00 pm | Session
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 pm | T.Werner,
Genomatix, Munich, Germany
Routine systems-biology based microarray analysis |
| 5.15
- 5.30 pm | M.S.
Janaki CH, C-DAC, Pune
GenomeGrid: A bioinformatics grid computing portal |
| 5.30
- 6.00 pm | Sharmila
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 am | Stanislas
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 pm | Carmay Lim, National Tsing Hua U,
Taipei
Factors
Governing the Maximum Number of Metal-bound Carboxylates in Metalloproteins |
| 12.30
- 1.00 pm | Indira 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 pm | SESSION
- 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 am | Luciano
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 pm | Samta
Malhotra,IISc, Bangalore.
Cytoview: Development
of a Cell Modeling Framework |
| 12.15
- 12.45 pm | Anirvan
Sengupta, Rutgers University, New Brunswick
Modeling
Epigenetic Silencing |
| 11.15
- 1.30 pm | SESSION
- V C | Genomics
and Proteomics 2 |
| Chairperson |
Saroj
Mishra, IIT Delhi, Delhi. |
| 11.15
- 11.45 pm | Speakers | Gyan
Bhanot, CINJ, New Brunswick
Consensus Ensemble Clustering Reveals Novel mtDNA
Phylogeny for the N Clade |
| 11.45
- 12.15 am | H.
A. Nagarajaram, CDFD, Hyderabad
An
Interesting Saga of Simple Sequence Repeats in Mycobacterial Genomes
|
| 12.15
- 12.30 pm | Chanchal
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 pm | Khairina
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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VALEDICTORY FUNCTION
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