Workshops

Six Workshops are planned to be held in conjunction with ACM-BCB 2013.
  • Workshop on Accelerating Bioinformatics Applications Enabled by NextGen-Sequencing (NGS 2013)

  • Fourth Immunoinformatics and Computational Immunology Workshop (ICIW 2013)

    • Regular Papers

    1. iAtheroSim: atherosclerosis process simulator on smart devices, Francesco Pappalardo; Marzio Pennisi; Ferdinando Chiacchio; Salvatore Musumeci; Santo Motta;
    2. Characterizing Amino Acid Variations in Aligned Pattern Clusters of Scavenger Receptors, En-Shiun Annie Lee; Fiona Whelan; Dawn Bowdish; Andrew K. C. Wong;
    3. Biomarkers in immunology: from concepts to applications, Ping Zhang; Lou Chitkushev; Vladimir Brusic; Guang Lan Zhang”, “Ping.Zhang@csiro.au;
    4. Landscape of neutralizing assessment of monoclonal antibodies against dengue virus, Jing Sun; Guang Lan Zhang; Lars Ronn Olsen; Ellis L. Reinherz; Vladimir Brusic;
    5. HPVdb: Data Source and Analysis Platform for T-cell based Vaccine Target Discovery in Human Papillomavirus, Guang Lan Zhang; Angelika Riemer; Derin B. Keskin; Ellis L. Reinherz; Vladimir Brusic.

    Poster Abstracts

    1. DNA Vaccine Design For Chikungunya Virus Based On The Conserved Epitopes Derived from Structural Protein, Parvez Singh Slathia;
    2. Enhanced affinity of docking HLA B*57:01 pit with putative self peptide structures by hypersensitivity causative drug of Abacavir and its in silico alikes, Chen-Chieh Fan, Chun-Fan Chang, Hsueh-Ting Chu, Thai-Yen Ling, Cheng-Yan Kao;
    3. Defining Functional Redundancy of Epitope Data as Potential Antigenic Cross-Reactivity, Salvador Eugenio C. Caoili;
    4. Highly Immunogenic Vaccine for Prevention and Therapy of Malignant Mesothelioma, A.S. De Groot, P. Bertino, P. Hoffman, M. Carbone, A.G. Siccardi, F. Terry, L.P. Cousens, L. Moise, and W. Martin;
    5. iVAX: A Sophisticated Suite of Online Vaccine Design Tools, A.S. De Groot, F. Terry, D. Spero, L. Moise, and W. Martin;
    6. In Silico High Throughput Pre-clinical Determination of Monoclonal Antibody Immunogenicity, L.P. Cousens, F. Terry, M. Ardito, W. Martin, and A.S. De Groot;
    7. Cross-reactive influenza H1N1 T cell epitopes identified by immunoinformatic methods stimulate CD4+ T cell responses, Anne S. De Groot, Christine Boyle, Matthew Ardito, Frances Terry, Howard Latimer, Ryan Tassone, Mindy Cote, Leonard Moise, an dWilliam D. Martin;
    8. The Two-Faced T Cell Epitope: Examining the Host-Microbe Interface with JanusMatrix, Andres H. Gutierrez, Chris Bailey-Kellogg, Lenny Moise, Frances Terry, Karim Abdel Hady, Qiben Leng, Marcelo B. Sztein, Phyllis Losikoff, Nathan Verberkmoes, William D. Martin, Alan Rothman, and Anne S. De Groot;
    9. In Silicoprediction of HLA-DP and -DQ epitope content is poorly correlated with clinical immunogenicity of therapeutic proteins, A.S. De Groot, R. Tassone, L. P. Cousens, F. Terry, R. Martin, M.T. Ardito, and W.D. Martin.


  • Computational Structural Bioinformatics Workshop (CSBW 2013)

    • Regular Papers

    1. Fast and Accurate Structure-Based Prediction of Resistance to the HIV-1 Integrase Inhibitor Raltegravir, Majid Masso
    2. Improving the Prediction of Kinase Binding Affinity Using Homology Models, Jeffrey Chyan;Mark Moll;Lydia Kavraki
    3. A Constrained K-shortest Path Algorithm to Rank the Topologies of the Protein Secondary Structure Elements Detected in CryoEM Volume Maps, Kamal Al Nasr;Lin Chen;Jing He
    4. Exploring the Structure Space of Wildtype Ras Guided by Experimental Data, Rudy Clausen;Amarda Shehu
    5. Beta-sheet Detection and Representation from Medium Resolution Cryo-EM Density Maps, Dong Si;Jing He
    6. An Evolutionary Conservation and Rigidity Analysis Machine Learning Approach for Detecting Critical Protein Residues, Nurit Haspel; Bahar Akbal-Delibas; and Filip Jagodzinski
    7. Informatics-driven Protein-protein Docking, Irina Hashmi;Amarda Shehu
    8. Multi-Resolution Rigidity-Based Sampling of Protein Conformational Paths, Dong Luo;Nurit Haspel
    9. A Combined Molecular Dynamics, Rigidity Analysis Approach for Studying Protein Complexes, Brian Orndorff;Filip Jagodzinski


  • 6th International Workshop on Biomolecular Network Analysis (IWBNA 2013)

    • Regular Papers

    1. Identifying Pathway Proteins in Networks using Convergence, Kathryn Dempsey;Hesham Ali
    2. A Neural-network Algorithm for All k Shortest Paths Problem, Kun Zhao;Abdoul Sylla
    3. Revealing Protein Structures by Co-Occurrence Clustering of Aligned Pattern Clusters, Sanderz Fung;En-Shiun Annie Lee;Andrew K.C. Wong
    4. Comparative analysis of network algorithms to address modularity with gene expression temporal data, Suhaib Mohammed


  • Parallel and Cloud-based Bioinformatics and Biomedicine (ParBio 2013)

    • Regular Papers

    1. Vascular Modeling, Simulation, and Visualization for Enhanced Brain Imaging, Thomas Marrinan; Ian Gould; Chih-Yang Hsu; Andreas Linninger; and Andrew Johnson
    2. MEGADOCK-GPU: Acceleration of Protein-Protein Docking Calculation on GPUs, Takehiro Shimoda; Takashi Ishida; Shuji Suzuki; Masahito Ohue; and Yutaka Akiyama
    3. pXAlign: A parallel implementation of XAlign, Aditi Magikar; and John Springer


  • Workshop on Epigenomics and Cell Function (ECF 2013)

    • Regular Paper

    1. Relating mammalian replication program to large-scale chromatin folding, Benjamin Audit; Antoine Baker; Rasha Boulos; Hanna Julienne; Alain Arneodo; Chun-Long Chen; Yves D'Aubenton-Carafa; Arach Goldar; Guillaume Guilbaud; Olivier Hyrien

    Short abstract

    1. Chromatin structure fully determines replication timing program in human cells, Sven Bilke; Yevgeniy Gindin; Paul Meltzer

    Highlight abstracts

    1. Unsupervised pattern discovery in human chromatin structure through genomic segmentation, Michael M. Hoffman; Orion J. Buske; Jie Wang; Zhiping Weng; Jeff Bilmes; William Stafford Noble
    2. Bayesian Inference of Spatial Organizations of Chromosomes, Zhaohui Qin; Ming Hu; Jun Liu; Bing Ren; Ke Deng; Siddarth Selvaraj; Jesse Dixon; Jennifer Fang