Joint RFBR-DST Workshop on the Systems Biology and Genome Informatics
"Predictive Biology using Systems and Integrative Analysis and Methods"

November 15-19, 2010,
Chandigarh. India



Organizers:
Institute for Microbial Technology (CSIR), Chandigarh, India
Institute of Genomics and Integrative Biology (CSIR), New Delhi, India

Russian coordinators:
Prof. Nikolay Kolchanov, Academician, IC&G SB RAS, Novosibirsk, Russia
Dr. Dmitry Afonnikov, Head, Evolutionary Bioinformatics, IC&G SB RAS, Novosibirsk, Russia

Indian coordinators:
Dr. G.P.S. Raghava, Head Bioinformatics Centre, Institute of Microbial Technology(CSIR), Chandigarh, India
Dr. S. Ramachandran, Institute of Genomics and Integrative Biology, New Delhi, India

Background:

Infectious diseases pose one of the world's leading healthcare problems. In the last years, new knowledge about the genomic structure of pathogenic microorganisms, their metabolic and functional features, and details of interactions of their DNA, RNA, proteins, metabolites and drug-like molecules has accumulated in basic and applied medicine in Russia and India. The integration of this knowledge at the systems level, thorough analysis and annotation using modern mathematical and computational methods will help in developing new approaches and predict new drug-like molecules to combat pathogens. At this junction, to better integrate the efforts of the Russian and Indian partners in resolution of the issues of tuberculosis and other infectious diseases, the Indo-Russian Joint Workshop Predictive Biology using Systems and Integrative analysis and Methods will be held.

The aim of this workshop will be experience exchange and integration of the efforts of leading scientists in the area of bioinformatics, protein research and computational genomics in Russia and India. The seminar will be implemented within the framework of the approaches of systems biology and genome informatics for studying microbial pathogen - human immune system interactions, developing new methods for combating tuberculosis and other infectious diseases. This workshop will continue the success of the previous meeting "Systems Biology and Genome Informatics of M. tuberculosis and other infectious diseases" held in 2008 in Novosibirsk.

Objective:

The infectious diseases are among the top causes of people death for countries such as Russia and India. In the last years, most dangerous threats like tuberculosis have increased worldwide due microbial adaptation and change. Moreover, new pathogenic organisms emerge from the dynamic interaction between the classical epidemiological triad of agent, host, and the environment. Traditional approaches to treatment of new forms of infections and emerged threats proved to be not consistently efficient. A well coordinated and an integrate approach is essential to tackle the threat of hazardous infections. The doors of modern biology have opened almost endless potential. The new experimental techniques of high-throughput biological data analysis (microarrays, protein mass-spectrometry, ChIP and next generation sequencing methods) provide a lot of knowledge on pathogen-host interactions, disease pathogenesis, immune responses etc. However, the obtained knowledge is fragmented. To create an overall picture of the complex network of interactions involved in infectious disease, we need to combine the current knowledge and fill in the gaps. The underlying basis of integration is Systems Biology. The new paradigm of integration of novel experimental, theoretical and computational methods of analysis from molecular entities to the levels of cell and organism provide predictive power and offer promise. Emphasis on these developments is worldwide, involving Russia and India. However close international collaboration, exchange of information and experience between multidisciplinary scientists would provide breakthroughs in this research area.

The following topics will be addressed in the workshop

Novel Integrative Methods in drug discovery
Systems analysis of host-pathogen interactions
Annotation to prediction of metabolites
Intrinsically disordered regions in proteins and their roles in protein-protein interactions
Microanalysis of protein-protein interacting surfaces
Computational platforms for integrative analysis
Machine intelligence for biological predictions
Genome sequence analysis as foundation for systems biology

List of Russian Participants

Prof. Nikolai Kochanov, Director, Institute of Cytology and Genetics, Novosibirsk
Dr. Dmitry Afonnikov, Institute of Cytology and Genetics, Novosibirsk
Prof. Sergey Deyev, Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Moscow
Prof. Alexander Efimov, Institute of Protein Research, Pushchino
Prof. Roman Efremov, Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Moscow
Dr. Vladimir Ivanisenko, Institute of Cytology and Genetics, Novosibirsk
Prof. Alex Ivanov, Institute of Biomedical Chemistry RAMS, Moscow
Dr. Alex Kochetov, Institute of Cytology and Genetics, Novosibirsk
Prof. Vsevolod Makeev, Institute of genetics and selection of industrial microorganisms, GosNIIgenetika, Moscow
Dr. Yurii Matushkin, Institute of Cytology and Genetics, Novosibirsk

List of Indian Participants

Samir K. Brahmachari, Council of Scientific and Industrial Research, New Delhi India.
Prof. Alok Bhattacharya, Jawaharlal Nehru University, New Delhi, India
Dr. Nagasuma Chandra, Indian Institute of Science, Bengluru, India
Dr. Andrew M. Lynn, Jawaharalal Nehru University, New Delhi, India
Dr. Shekhar C. Mande, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
Dr. Debasisa Mohanty, National Institute of Immunology, New Delhi, India.
Dr. G.P.S. Raghava, Institute of Microbial technology, CSIR, Chandigarh, India
Dr. S. Ramachandran, Institute of Genomics and Integrative Biology, Delhi, India
Dr. R. Ravishankar, Central Drug Research Institute, Lucknow, India
Dr. RamaSubbu Sankar, Indian Institute of Technology, Kanpur, India
Dr. Vinod Scaria, Institute of Genomics and Integrative Biology, Delhi, India

List of Special Invitees

Dr. Anshu Bhardwaj, Institute of Genomics and Integrative Biology, Delhi, India
Dr. Amit Nargotra, Indian Institute of Integrative Medicine, Jammu, India
Dr. Ravishankar, Institute of Himalayan Biotechnology, Palampur, India
Shri Zakir Thomas, Council of Scientific and Industrial Research, Delhi, India

Tentative programme of the Joint Indo-Russian Workshop Predictive Biology using Systems and Integrative analysis and Methods Institute for Microbial Technology (CSIR), Chandigarh, India 15-19 November 2010

November 14, 2010
Arrival day
November 15, 2010
Institute for Microbial Technology (CSIR)

Time Speakers and Chair Title
10:00 AM 1:00 PM Visit to IMTECH Laboratories
1:00 PM 2:00 PM LUNCH

Time Speakers and Chair Title
2:00 P.M. 2:10 P.M. Director, IMTECH, Chandigarh Opening Remarks
2:10 P.M. 2:20 P.M. Dr. S. Ramachandran, Dr. G.P.S. Raghava Indian Co-ordinators Indo-Russian Co-operation in the era of Systems analysis for Predictive Biology
2:20 P.M. - 2:30 P.M. Dr. Dmitry Afonnikov, and Prof. Nikolai Kolchanov Russian Co-ordinatior
2:30 P.M. 3:15 P.M. Dr. GPS Raghava Machine intelligence for biological predictions
3:15 P.M. 4:00 P.M. Dr. A. Kochetov Computational genomics: searching for new proteome components (pdf )
4:00 P.M. 4:30 P.M. TEA
4:30 P.M. 5:15 P.M. Dr. Vinod Scaria "Understanding the Biology of Genomes"
5:15 P.M. 6:00 P.M. Dr. Andrew M. Lynn "Information theoretic applications in identifying specificity determining residues"

November 16, 2010
Institute for Microbial Technology (CSIR)

Time Speakers and Chair Title
10:00 A.M. - 10:45 A.M. Dr. Yuri Matushkin Evolution of trophically linked populations of unicellular organisms; translation efficiency in unicellular organisms. (pdf)
10:45 A.M. - 11:30 A.M. Prof. Alexander V. Efimov Modeling of Protein Structure and Protein Folding (pdf)
11:30 A.M. 12:00 P.M. TEA
12:00 P.M. 12:45 P.M. D. Debasisa Mohanty Structure based approach for predicting substrates for protein kinases (pdf)
12:45 P.M. - 2:00 P.M. LANCH
2:00 P.M. 2: 45 P.M. Dr. Vladimir Ivanisenko Reconstruction of molecular genetic networks: text mining as a tool for knowledge discovery (pdf)
2:45 P.M. - 3:30 P.M. Dr. S. Ramachandran Computational platforms for Integrative Analysis in Open Source (pdf )
3:30 P.M. - 4:00 P.M. TEA
4:00 P.M. - 4:45 P.M. Dr. Nagasuma Chandra Networks in M. tuberculosis: Deriving optimal strategies for drug discovery (pdf)
4:45 P.M. 5: 30 P.M. Dr. Anshu Bhardwaj Open Source Drug Discovery (pdf)
Special Dinner

November 17, 2010
IMTECH, Chandigarh

Time Speakers and Chair Title
10:00 A.M. - 10:45 A.M. Dr. Dmitry Afonnikov on behalf of Prof. Nikolai Kolchanov, Russian Organizer The systems biology: integration of experimental and computational approaches (pdf)
10:45 A.M. - 11:30 A.M. Prof. Alok Bhattacharya Comparative genomics and genome evolution of microbes (pdf)
11:30 A.M. - 12:00 P.M. TEA
12:00 P.M. - 12:45 P.M. Dr. Dmitry Afonnikov Prokaryotic adaptation to different environmental conditions at the genomic level: Molecular evolution analysis (pdf)
12:45 P.M. - 2:00 P.M.
2:00 P.M. 2:45 P.M. Prof. Sergey Deev Barnase-barstar module as a platform for targeted delivery of imaging and therapeutic nanoconstructs (pdf)
2:45 P.M. - 3:30 P.M. Dr. R. Ravishankar Rational approach to drug discovery (pdf)
3:30 P.M. - 4:00 P.M. TEA
4:00 P.M. - 4:45 P.M. Prof. Alexis Ivanov Integration of Structure-Based Drug Design and SPR Biosensor Technology in Discovery of New Lead Compounds (pdf)
4:45 P.M. - 5:30 P.M. Dr. RamaSubbu Sankar Using molecular dynamics simulations to understand the specificity of protein-ligand interactions (pdf)

November 18, 2010

Time Speakers and Chair Title
10:00 A.M. - 10:45 A.M. Ms. Nisha Chandran Open source methods and using SysBorg2.0
10:45 A.M. - 11:30 A.M. Prof. Roman Efremov Intrinsic structural heterogeneity of biomembranes is functionally important: a molecular modeling view.(pdf)
11:30 A.M. 12:00 P.M. TEA
12:00 P.M. - 12:45 P.M. Dr. Vsevolod Makeev Improved modulon identification from bacterial expression array data using operon-based reference correlation set
12:45 P.M. - 2:00 P.M. LUNCH
2:00 P.M. - 3:00 P.M. Round table discussion Bioinformatics research in India and Russia: perspectives of mutual collaboration. Sum up report.

November 19, 2010
Individual discussions (and other visits)
Departure.

Financial Support



Russian Foundation for Basic Research



Department of Science and Technology, Ministry of Science and Technology, India