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Program

18 January (Monday)

8:00 - 9:00 Registration

9:00 - 12:00 Morning session
Industry Track
Chair: Vijay Chandru
Tutorials
Chairs: Nagasuma Chandra & N. Srinivasan
9:00 - 10:30
Session I
Healthcare & Curatorial Bioinformatics

Personalized Medicine in Breast Cancer - 'omics' signatures as prognosticators,Vaijayanti Gupta, Strand Life Sciences

Curated Pathway Database and its use in Drug Discovery, Prashant Naik, Jubilant Biosys

Current and future trends in Bio curation, Jignesh Bhate, Molecular Connections

Detection of heteroplasmy in mitochondrial genome sequences, Vamsi Veeramachaneni, Strand Life Sciences

Tutorial 1: Inferring gene networks with probabilistic graphical models, Chen-Hsiang Yeang, Institute of Statistical Science, Academia Sinica, Taiwan Tutorial 2: Symbolic methods in systems biology, Sriram Iyengar, University of Texas, Houston, USA
10:30 - 12:00
Tutorial 3: Gene expression data analysis, Jyothi Bajpai Dikshit, Strand Life Sciences, India Tutorial 4: Recombinomics: recombinations-based population genomics, Asif Javed, IBM TJ Watson Research Center, USA

12:00 - 1:00
Registration + Lunch

1:00 - 4:00 Afternoon session
Industry Track
Chair: Ramesh Hariharan
Tutorials
Chairs: Saikat Chakrabarti & Indira Ghosh
1:00 - 2:30
Session II
Algorithmics/Analytics & Data Integrators

LIMS – Improving Lab Efficiency, Maya Krishnan, Persistent Systems

An information-theoretic framework for genomic island detection, Alpan Raval, Keck Graduate Institute, D E Shaw Research

Are you ready for “in litero” drug discovery?, Srinivasan Parthiban, Reverse Informatics

Tutorial 5: Protein structural analysis, K. Sekar, Indian Institute of Science Bangalore, India Tutorial 6: Text mining tools in biology, Martin Krallinger and Ashish Tendulkar, Spanish National Cancer Research Centre, Spain
2:30 - 4:00
Tutorial 7: DNA structural attributes, Craig Benham and Ak Prashanth, University of California, Davis, USA Tutorial 8: Metabolic modelling - flux analysis, Pramod Wangikar, IIT Bombay, India

4:00 - 4:30
Registration

4:30 - 7:00 Evening session
Chair: D.N. Rao
4:30 - 4:40
Welcome Remarks
4:40 - 5:40
Keynote: Pinakpani Chakrabarti
Protein-protein interactions - structural features, residue conservation and energy contribution, and location of the binding site
5:40 - 7:00
Welcome High-Tea

19 January (Tuesday)

8:00 - 8:40
Registration + Poster Setup

8:40 - 12:00 Morning session
8:40 - 9:40
Keynote: Sorin Istrail, Brown University, USA
The Regulatory Genome and the Computer: Theory and Practice
Chair: Manju Bansal
9:40 - 9:55
Break
9:55 - 12:00
S1: Patterns and Motifs
Chair: Chiranjiv Bhattacharya
S2: Gene Regulation
Chair: Krishnaswamy
9:55 - 10:20
S1.1 Christina Boucher and James King. Fast motif recognition via application of statistical thresholds S2.1 Vinod Chandra S. S., Reshmi G, Sreenathan S, M. Radhakrishana Pillai and Achuthsankar S. Nair. MTar: a computational microRNA target prediction architecture for human transcriptome
10:20 - 10:45
S1.2 Daniel Brown and Daniil Golod. Decoding HMMs using the k best paths: algorithms and applications S2.2 Junhee Seok, Amit Kaushal, Ronald Davis and Wenzhong Xiao. Knowledge-based analysis of microarray for the discovery of transcriptional regulations
10:45 - 11:10
S1.3 Won-Hyong Chung and Seong-Bae Park. Hit integration for identifying optimal spaced seeds S2.3 Trupti Joshi, Zhe Yan, Marc Libault, Janine Sherrier, Andrew Farmer, Greg May, Blake Meyers, Dong Xu and Gary Stacey. Prediction of novel miRNAs and associated target genes in Glycine max
11:10 - 11:35
S1.4 Daniel Brown and Jakub Truszkowski. New decoding algorithms for hidden Markov models using distance measures on labellings S2.4 Sumeet Agarwal, Candida Vaz, Alok Bhattacharya and Ashwin Srinivasan. Prediction of novel precursor miRNAs using a context-sensitive hidden Markov model (CSHMM)
11:35 - 12:00
S1.5* Jianjun Hu and Fan Zhang. BeyesMotif: De novo protein sorting motif discovery from impure datasets S2.5 Chih-Hung Hsieh, Tien-Hao Chang, Chi-Yeh Wu and Yen-Jen Oyang. Predicting microRNA precursors with a generalized Gaussian components based density estimation algorithm

12:00 - 1:30
Poster Session 1 + Lunch

1:30 - 3:35 Afternoon session
1:30 - 3:35
S3: Interactomics I
Chair: Debnath Pal
S4: Functional Genomics I
Chair: S. Ramakumar
1:30 - 1:55
S3.1 Tien-Hao Chang, Yu-Tang Syu and Bo-Chang Lin. Predicting the protein-protein interactions using primary structures with predicted protein surface S4.1* Nitin Bhardwaj, Mark Gerstein and Hui Lu. Genome-wide sequence-based prediction of peripheral proteins using a novel semi-supervised learning technique
1:55 - 2:20
S3.2 Byungkyu Park and Kyungsook Han. An ontology-based search engine for protein-protein interactions S4.2 Matteo Comin and Davide Verzotto. Classification of protein sequences by means of irredundant patterns
2:20 - 2:45
S3.3 Yezhou Huang and Shao Li. Detection of pathway network biomarker for angiogenesis based on the comprehensive pathway network S4.3 Sneh Lata, Nitish Mishra and Gajendra Raghava. AntiBP2: Improved version of antibacterial peptide prediction
2:45 - 3:10
S3.4 Adi Mano, Tamir Tuller, Oded Beja and Ron Pinter. Comparative classification of species and the study of pathway evolution based on the alignment of metabolic pathways S4.4 Chia-Hao Chin, Chin-Wen Ho, Ming-Tat Ko and Chung-Yen Lin. A hub-attachment based method to detect functional modules from confidence-scored protein interactions and expression profiles
3:10 - 3:35
S3.5 Giovanni Ciriello, Claudio Gallina and Concettina Guerra. Analysis of interactions between ribosomal proteins and RNA structural motifs S4.5 Jayesh Pandey, Mehmet Koyuturk and Ananth Grama. Functional characterization and topological modularity of molecular interaction networks

3:35 - 4:05
Break + Poster Dismantle

4:05 - 6:45 Evening session
4:05 - 5:05
Keynote: Miklós Csűrös, Université de Montréal, Canada
Counting along phylogenies: ancestral reconstruction of numerical characters
Chair: Yathindra
5:05 - 6:45
S5: Genomics & Metagenomics
Chair: Pramod Wangikar
S6: Proteomics
Chair: Dipankar Chatterjee
5:05 - 5:30
S5.1 Inkyung Jung, Dongsup Kim, Akihisa Matsuyama and Minoru Yoshida. PostMod: sequence based prediction of kinase-specific phosphorylation sites with indirect relationship S6.1 Xiaowen Liu, Baozhen Shan, Lei Xin and Bin Ma. Better score function for peptide identification with ETD MS/MS spectra
5:30 - 5:55
S5.2 Suparna Mitra, Max Schubach and Daniel Huson. Short clones or long clones? A simulation study on the use of paired reads in metagenomics S6.2 Suyu Mei. Amino acid classification based spectrum kernel fusion for large-scale protein subcelluar localization
5:55 - 6:20
S5.3 Aridaman Pandit and Somdatta Sinha. Using genomic signatures for HIV-1 sub-typing S6.3 Wen-Ching Chan, Chun-Nan Hsu, Ueng-Cheng Yang, Wen-Chang Lin, Po-Huang Liang and Yan-Ping Shih. Learning to predict expression efficacy of vectors in recombinant
6:20 - 6:45
S5.4 Tina P G and Tessamma Thomas. Discrete wavelet transform de-noising in eukaryotic gene splicing. S6.4 Hiroto Saigo, Masahiro Hattori, Hisashi Kashima and Koji Tsuda. Reaction graph kernels predict EC numbers of unknown enzymatic reactions in plant secondary metabolism

20 January (Wednesday)

8:00 - 8:40
Registration + Poster Setup

8:40 - 12:00 Morning session
8:40 - 9:40
Keynote: Frank Eisenhaber
Discovering biomolecular mechanisms with computational biology
Chair: Alok Bhattacharya
9:40 - 9:55
Break
9:55 - 12:00
S7: Disease Studies
Chair: P. Gautam
S8: Association Studies
Chair: V. Nagaraja
9:55 - 10:20
S7.1 Henry Han. Nonnegative principal component analysis for mass spectral serum profiles and biomarker discovery S8.1* Pengyi Yang, Bingbing Zhou, Zili Zhang and Albert Zomaya. A multi-filter enhanced genetic ensemble system for gene selection and sample classification of microarray data
10:20 - 10:45
S7.2 Sayak Ganguli, Manjita Mazumder, Protip Basu, Paushali Roy, Sayani Mitra and Abhijit Datta. In silico screening of herbal and nanoparticle lead compounds for effectivity against H5N1, H1N1 neuraminidase and telomerase S8.2 Can Yang, Xiang Wan, Qiang Yang, Hong Xue and Weichuan Yu. Identifying main effects and epistatic interactions from large-scale SNP data via adaptive group Lasso
10:45 - 11:10
S7.3 Ramkrishna Mitra, Sanghamitra Bandyopadhyay, Ujjwal Maulik and Michael Q. Zhang. SFSSClass: An integrated approach for miRNA based tumor classification S8.3 Li Yongjin and Patra Jagdish. Integration of multiple data sources to prioritize candidate genes using discounted rating system
11:10 - 11:35
S7.4 Aarti Garg, Rupinder Tewari and Gajendra P.S. Raghava. Virtual screening of potential drug-like inhibitors against Lysine/DAP pathway of Mycobacterium tuberculosis S8.4 Yixuan Chen, Xin Li and Jing Li. A novel approach for haplotype-based association analysis using family data
11:35 - 12:00
S7.5 Anil Sorathiya, Pietro Lio` and Andrea Bracciali. In silico approaches to anti-HIV and Tuberculosis therapies S8.5 Michael Riel-Mehan, Juan Nunez-Iglesias, Chao Dai, Michael Waterman and Jasmine Zhou. An integrative modular approach to systematically predict gene-phenotype associations

12:00 - 1:30
Poster Session 2 + Lunch

1:30 - 3:35 Afternoon session
1:30 - 3:35
S9: Interactomics II
Chair: Jayant Haritsa
S10: Functional Genomics II
Chair: R. Sankararamakrishnan
1:30 - 1:55
S9.1 Vishwesh Kulkarni, Venkatesh Kareenhalli, Pushkar Malakar, Lucy Pao, Michael Safonov and Ganesh Vishwanathan. Stability analysis of GAL regulatory pathway in Saccharomyces Cerevisiae and K. Lactis S10.1 Yang Yang, Jiayuan Zhao, Robyn Morgan, Wenbo Ma and Tao Jiang. Computational prediction of type III secreted proteins from gram-negative bacteria
1:55 - 2:20
S9.2 Mitra Kabir, Nasimul Noman and Hitoshi Iba. Reverse engineering gene regulatory network from microarray data using linear time-variant model S10.2 Nitish Mishra and Gajendra Raghava. Prediction of FAD interacting residues in a protein from its primary sequence using evolutionary information
2:20 - 2:45
S9.3 Thahir P. Mohamed, Jaime G. Carbonell and Madhavi Ganapathiraju. Active learning for human protein-protein interaction prediction S10.3 Padma Priya Paragi Vedanthi and Dr. Mukesh Doble. Comparison of PGH2 binding site in prostaglandin synthases
2:45 - 3:10
S9.4 Corban G. Rivera, Rachit Vakil and Joel S. Bader. NeMo: network module identification in Cytoscape S10.4 Hatice U Osmanbeyoglu, Jessica A Wehner, Jaime G. Carbonell and Madhavi Ganapathiraju. Active machine learning for transmembrane helix prediction
3:10 - 3:35
S9.5 Ravi Gupta, Priyankara Wikramasinghe, Anirban Bhattacharya, Francisco Agosto-Perez, Sharmistha Pal and Ramana Davuluri. Annotation of gene promoters by integrative data-mining of ChIP-seq Pol II enrichment data S10.5 Pingzhao Hu, Hui Jiang and Andrew Emili. Predicting protein functions by relaxation labelling protein interaction network

3:35 - 4:05
Break + Poster Dismantle

4:05 - 5:05 Evening session
4:05 - 5:05
Keynote: Thangaraj Kumarasamy, CCMB, Hyderabad, India
The Peopling of India: Genetics and health perspectives
Chair: Sharat Chandra

5:15
Buses from conference venue to NCBS campus
6:00
Cultural Event & Banquet (at NCBS campus)

21 January (Thursday)

8:00 - 8:40
Poster Setup

8:40 - 12:00 Morning session
8:40 - 9:40
Keynote: Alexey G. Murzin
Fifty years of protein structure: the ever-changing paradigm of sequence-structure relationship
Chair: M. Vijayan
9:40 - 9:55
Break
9:55 - 12:00
S11: Comparative Genomics
Chair: Marketa Zvelebil
S12: Structural Genomics I
Chair: Umesh Varshney
9:55 - 10:20
S11.1 MS Vijayabaskar and Saraswathi Vishveshwara. Comparative analysis of thermophilic and mesophilic proteins using protein energy networks S12.1 Soja Saghar Soman, K.C. Sivakumar and E Sreekumar. Molecular dynamics simulation studies and in vitro site directed mutagenesis of avian beta-defensin Apl_AvBD2
10:20 - 10:45
S11.2 Xianjun Dong, Altuna Akalin, Yogita Sharma and Boris Lenhard. Translog, a web browser for studying the expression divergence of homologous genes S12.2 Jian-Yi Yang, Zhen-Ling Peng and Xin Chen. Prediction of protein structural classes for low-homology sequences based on predicted secondary structure
10:45 - 11:10
S11.3 Daniel Merkle, Martin Middendorf and Nicolas Wieseke. A parameter-adaptive dynamic programming approach for inferring cophylogenies S12.3 P Sundaramurthy, Shameer Khader, Raashi Sreenivasan, Sunita Gakkar and Ramanathan Sowdhamini. HORI: A web server to compute higher order residue interactions in protein structures
11:10 - 11:35
S11.4 Melvin Zhang and Hon Wai Leong. Bidirectional best hit r-window gene clusters S12.4 LIMIN LI, Wai-Ki Ching, Takako Yamaguchi and Kiyoko F. Aoki-Kinoshita. A weighted q-gram method for glycan structural classification
11:35 - 12:00
  S12.5 Zaixin Lu, Zhiyu Zhao and Bin Fu. Efficient protein alignment algorithm for protein search

12:00 - 1:30
Poster Session 3 + Lunch

1:30 - 3:35 Afternoon session
1:30 - 3:35
S13: Phylogeny
Chair: M.R.N. Murthy
S14: Structural Genomics II
Chair: Raghavan Varadarajan
1:30 - 1:55
S13.1 Suzanne Matthews and Tiffani Williams. MrsRF: an efficient MapReduce algorithm for analyzing large collections of evolutionary trees S14.1 Krishnan S P T, Sze Liang Sim and Bharadwaj Veeravali. Towards high-performance computing for molecular structure prediction using IBM Cell Broadband Engine – an implementation perspective
1:55 - 2:20
S13.2 Martin Bader. Genome rearrangements with duplications S14.2 Abu Dayem Ullah and Kathleen Steinhofel. A hybrid approach to protein folding problem integrating constraint programming with local search
2:20 - 2:45
S13.3 Vaibhav Rajan, Andrew Wei Xu, Yu Lin, Krister Swenson and Bernard Moret. Heuristics for the inversion median problem S14.3 Jing He, Kamal Al Nasr and Weitao Sun. Structure prediction for the helical skeletons detected from the low resolution protein density map
2:45 - 3:10
S13.4 Mukul S. Bansal, J. Gordon Burleigh and Oliver Eulenstein. Efficient genome-scale phylogenetic analysis under the duplication-loss and deep coalescence cost models S14.4 Lei Zhang, James Bailey, Arun S. Konagurthu and Ramamohanarao Kotagiri. A fast indexing approach for protein structure comparison
3:10 - 3:35
S13.5 Yu Lin, Vaibhav Rajan, Krister Swenson and Bernard Moret. Estimating true evolutionary distances under rearrangements, duplications, and losses S14.5 Kalidas Yeturu, Tapani Utriainen, Graham Kemp and Nagasuma Chandra. An automated framework for understanding structural variations in the binding grooves of MHC class II molecules

3:35 - 4:05
Break + Poster Dismantle

4:05 - 5:20 Evening session
4:05 - 5:05
Keynote: Laxmi Parida, IBM T J Watson Research, USA
Graph Theory in Recombinational Population Genomics
Chair: Saraswathi Vishweshwara
5:05 - 5:20
Best Poster Award + Closing Remarks