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InCoB 2006 -International Conference on Bioinformatics


The Fifth International Conference on Bioinformatics (InCoB 2006) was held from 18th – 20th Dec. 2006 at Hotel Ashok, New Delhi. The conference was jointly organized by Department of Biotechnology, Govt. of India New Delhi, Jawaharlal Nehru University, New Delhi and Indian Institute of Technology Delhi, under the aegis of Asia Pacific Bioinformatics Network (APBionet). The conference was inaugurated by Honourable Minister for Science and Technology and Earth Sciences, Mr. Kapil Sibal.

About 1000 participants including 700 students attended the conference. During the three days of conference about 400 scientific presentations were made on seven different Bioinformatics topics, which included Computational Biology, Structural Bioinformatics, Datamining and Databases, Genomics and Proteomics, Protein Folding and Structure Prediction, Systems Biology and Molecular simulations.  In addition, majority of the presentations were in the form of posters. A number of awards were also distributed for outstanding posters. The highlight of the conference was the lectures given by 12 leading experts in their respective fields as Plenary speakers. These experts were drawn from US, UK, France, Canada, Israel and Japan. Apart from plenary lectures 16 symposia were also held involving about 50 presentations.  

The opening speaker for session on Computational Biology I-A was Prof. Gene Myers (Imaging-Based Systems Biology) from Howard Hughes Medical Institute, chaired by Prof. Sachin Maheshwari from IIT Delhi. He described the use of advanced light and electron microscopy to visualize the meso-scale of the cell and development of small organs at the resolution of individual cells. He presented his group’s findings on imaging projects and potential implications for such work for the future of molecular biology. The next speaker was Prof. David Sankoff from Department of Mathematics, University of Ottawa. His talk highlighted the removal of noise and ambiguities from comparative maps in rearrangement analysis of genomes. Dr. Laxmi Parida from IBM TJ Watson Research Center delivered a talk on Permutations in Bioinformatics. She discussed the problem of common gene clusters across species, phylogeny within populations, modeling of complex control of transcription via motifs, identified the underlying mathematical problems and showed results of applying the proposed mathematical solutions to biological data. The opening speaker for the session on  Structural Bioinformatics I chaired by Prof. Awadhesh Surolia from NII, New Delhi was Dr. Dinakar Salunke from National Institute of Immunology. He addressed the gathering on molecular mimicry and vaccine design and mentioned the integration of the current understanding of the molecular processes associated with the body’s self-defense and the physicochemical basis of molecular mimicry would provide sound theoretical basis for design strategies towards next-generation vaccine. Dr. Abdur Sikder from School of Information Technologies, University of Sydney spoke on improving the performance of domain discovery of protein domain boundary assignment using inter-domain linker index. The first speaker for the session on Datamining and Databases chaired by Prof. Tan Tin Wee, University of Singapore, was Dr. Sekar from IISc Bangalore. He spoke on Structure Analysis Package (SAP), a computing engine developed in his lab to calculate and display various structural and functional regions in the three-dimensional protein structures available in the PDB. Dr. D. Mohanty delivered a talk on Knowledge-Based Computational Resources for Understanding Biosynthesis of Complex Metabolites and spoke on the research work carried out in his lab in experimental characterization of metabolic products of several uncharacterized proteins from Mycobacterium tuberculosis which has provided guidelines for site directed mutagenesis experiments to engineer biosynthesis of rationally altered metabolites.

            Prof. Akhilesh Tyagi, University of Delhi, chaired Session II- A on  Genomics and Proteomics. The session started with a talk by Dr. Aklilesh Pandey from Johns Hopkins University, Baltimore. He presented briefly several ‘firsts’ as case studies from his highly successful Indo-US model of collaborative research,  ranging from analysis of protein interaction networks and signal transduction to Cancer Biology and Therapeutics. Dr. Srinivasan Ramachandran from IGIB, spoke on application of machine learning and statistical methods for analyzing complete sequences of genomes and proteomes. Prof. Krishnaswamy from Madurai Kamaraj University spoke on Sequence and Structure based sub-classification of HNH domains. Prof. Saraswathi Vishveshwara from IISc Bangalore talked on Dynamics of Protein Structure Network: From Equilibrium and Unfolding Simulations on Lysozyme. Her talk highlighted on the network changes that take place during unfolding and such an analysis provided insights into details of the changes occurring in the protein tertiary structure at the level of amino acid side chain interactions, which could prove to be  valuable method to identify residues important for stability and folding of proteins. Prof. N. Gautham from University of Madras, spoke on Exploring Conformational Space using a Mean Field Technique with Mols sampling and its applications. The first speaker for Session II-C on Systems Biology -1 chaired by Prof. Ram Ramaswamy, JNU, New Delhi, was Prof. Kinoshita from Japan. He spoke on the Hypoxic Response of Human Red Blood Cell Metabolism Assessed by Metabolomics and Simulation.   The next speaker of the session was Dr. Pawan Dhar from Riken, Japan. He talked on Design principles of Molecular Networks and discussed the application of his work in the direction of Computer Aided Design of Biological Systems. Dr. Somdatta Sinha from CCMB, Hyderabad addressed the gathering on modeling collective behavior in interacting cell systems. Prof. Michael Waterman of University of Southern California presented his plenary talk on Constructing a Restriction Map of the Maize Genome. The chairman was Prof. Samir Bramhachari, IGIB, New Delhi.  

Prof. David Beveridge from Wesleyan University delivered his plenary talk on 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. His talk highlighted the outcome of ABC (Ascona B-DNA Consortium) resulting in a database, which contains almost a microsecond of dynamics and more than half a terabyte of information, representing a unique resource for understanding the dynamical structure of DNA, including the hydration and ion atmosphere.  Dr. Ravi Iyengar from Mount Sinai School of Medicine spoke on Dynamic Topology of Biological Networks and Functional Consequences. The session was chaired by Dr. S.C. Purohit, CDAC, Pune.   

Session IIIA on Molecular Simulations started with a lecture by Prof. Richard Lavery from CNRS, Paris. This session was chaired by Prof. Ashok Thakur, Kolkata. Prof. Lavery emphasized on the different methods to calculate mechanical properties of biomacromolecules and presented results of his research on both nucleic acids and proteins to suggest that nature indeed uses mechanics to control function. The next talk was by Prof B. Jayaram from IIT Delhi. He presented the science behind the softwares developed at IIT Delhi for three different biological applications, genome analysis, protein tertiary structure prediction of small proteins and drug design. The next speaker, Dr. Devapriya Choudhury, spoke on Use of Optimised Elastic Network Models for the Interpretation of Protein Structure and Dynamics. Dr. Rajinder Joshi from CDAC, New Delhi gave his presentation on MD simulations: Studies of Peptide Nucleic Acids. The opening speaker of session IIIB on Computational Biology 2 chaired by Dr. Judith Klein-Seetharam, Carnegie Melon, was Dr. Rahul Siddharthan from Chennai. He spoke on Phylogibbs-Mp, a motif finder capable of predicting Cis-regulatory modules (CRMs) as well as predicting the binding cites within those CRMs and the performance of Phylogibbs-Mp in predicting well known enhancers.  Dr. Gad Landau from Israel spoke on Indexing Genotypes for Haplotype Research. Session III C on Structural Bioinformatics I chaired by Prof. P. Gautam, Anna University, Chennai, witnessed the opening speaker as Dr. N. Srinivasan from IISc Bangalore. His talk covered recognition, classification and domain structures of protein kinases encoded in the genomes of several eukaryotic and prokaryotic organisms. Dr. Bostjan Kobe from Queensland, Australia spoke on prediction of substrate specificities of protein kinases. A talk on Prediction of Protein Structure Using backbone Fragment Library and a Multilayered Learning Algorithm was delivered by Prof. Pramod Wangikar from IIT Bombay. The plenary talk delivered by Prof. Yoshiyuki Sakaki from Genomics Sciences Center, RIKEN, Japan featured progress made by the centre in the area of Systems Biology of Signal Transduction pathways and Molecular Dynamics Protein Simulation. Prof. Manju Bansal from IISc Bangalore initiated session IV A chaired by Prof. Ram Kumar.  She addressed the gathering on Promoter Identification in Bacterial genomes: Role of DNA Structure vs Sequence. Dr. Chaitanya Hiremath from Pune spoke on Abbreviated Profile of Drugs (APOD): A Numerical and Graphical Representation for Comparing Compounds. Dr. Sarah Teichmann from MRC Laboratory of Molecular Biology, UK presented her talk on Evolution and Dynamics of Transcription Factor Repertoires. Dr. Gabriela Alexe from IBM TJ Watson Research center initiated Session IV B on Microarray analysis with his talk on Molecular Profiles of Breast Cancer Progression. Prof. Karmeshu, JNU, New Delhi, chaired the session.  This was followed by a talk by Dr. Narinder Singh Sahni from JNU who spoke on Gene Ontology Based Prediction and Analysis of Microarray data.   Prof. Rajani Joshi from IIT Povai delivered her talk on Mining the Gene-Protein data and showcased two softwares developed in her lab for protein domain predictions.   

Prof. Ross King of University of Aberystwyth, UK delivered a plenary talk on The Robot Scientist Project. His talk featured the application of Robot Scientist Principle in predicting the function of genes in a well-understood part of the metabolism of the yeast, S. cerevisiae. Prof. Stanislas Leibler from Rockefeller University delivered his plenary talk on Fluctuations, Information and Survival: some lessons from Bacteria. The plenary talks were chaired by Mr. Ashwin Srinivasan, IBM, India.

Session VA comprised Drug Design speakers. The session was chaired by Dr. Rama Mukherjee, DRF, India.  A talk on Factors Governing the Maximum Number of Metal-bound Carboxylates in Metalloproteins was presented by Dr. Carmay Lim from Taiwan. Dr. Indira Ghosh from Pune University spoke on Virtual High throughput Screening for Lead Identification. The first speaker for session VC on Genomics and Proteomics 2 was Dr. Gyan Bhanot from New Brunswich who delivered his talk on Consensus Ensemble Clustering Reveals Novel mtDNA Phylogeny for N Clade. Dr. H.A. Nagarajaram from CDFD Hyderabad, delivered his talk on An Interesting Saga of Simple Sequence Repeats in Mycobacterial genomes. The session was chaired by Prof. Saroj Mishra from IIT Delhi.                                                  

There were also talks given by different industry emphasizing their products and services. Session IV C was dedicated for Bioinformatics Products and Tools chaired by Prof. A.S. Kolaskar, Pune University. Dr. Ramesh Hariharan from Strand Lifesciences, Bangalore presented charts on Building Tools for Expression and Pathway analysis. Dr. Thomas Werner from Genomatrix Software, Germany spoke on complete microarray analysis pipeline developed as a product. Ms. Kritika from CDAC talked on Genome Grid Computing Portal.  Dr. Sharmila Mande spoke on the Biosuite software developed at TCS.  

All sessions witnessed student platform presentations.

The student community and the scientists working in this area greatly benefited through this conference by being exposed to the latest developments particularly in the area of computational and systems biology, structure prediction and drug design and different aspects of machine learning methods in solving biological problems.  The enthusiasm generated during the conference particularly among the young scientists and students suggest that there is a great potential for a high end generation of human resource as well as for undertaking of hard core research in this area.  Journal of Bioscienes (India) and BMC Bioinformatics are coming out with special issues based on the conference.

The main sponsor of the Conference was Department of Biotechnology (DBT). The other Govt. sponsors were Department of Science and Technology (DST), Department of Information technology (DIT), Council for Scientific and Industrial Research (CSIR) and Indian Council of Medical Research (ICMR). The major private sponsor of the event was Center for Development of Advanced Computing (CDAC). Others included Software Technology Parks of India (STPI), Dabur Research Foundation (DBR), Sun Microsystems, Mascon Life Sciences, Elsevier, HCL Tech, HCL Infinet, Oscimum, Accelrys, Jubiliant Biosys Ltd. and Wiley.   

The conference witnessed participants drawn from academia, industry, government institutions, multinational companies and students and the attendance was four times of the previous InCoB meetings. The organizers of InCoB 2006 thank all the sponsors and participants for making this conference a grand success.


Compiled by:
Dr. Sandhya R. Shenoy, IIT Delhi
Prof. B. Jayaram, IIT Delhi
Prof. Alok Bhattacharya, JNU, New Delhi
Prof. Ram Ramaswamy, JNU, New Delhi
Dr. T. Madhan Mohan, DBT, New Delhi