Conference location: Niagara Falls Conference Center

Program (tentative)

Aug. 1 Sunday, 2010

  • 13:30 - 17:00 Registration

Aug. 2 Monday, 2010

  • 9:00 - 18:00 Four Workshops
    Workshop1: Gene Network and Pathway Generation and Analysis
    Workshop2: International Workshop on Graph Theoretic Approaches for Biological Network Analysis (IWBNA 2010)
    Workshop3: Immunoinformatics and Computational Immunology Workshop (ICIW 2010)
    Workshop4: Protein-protein interaction data: management, querying and analysis
  • 12:00 - 13:00 Lunch
  • 13:00 - 14:30 Tutorial: Next Generation Sequencing Data Analysis
    Dr. Jing Li, Case Western Reserve University
    Dr. Kung Huang, The Ohio State University
  • 14:30 - 16:00 Tutorial: Intelligent Pattern Recognition and Applications
    Dr. Patrick S.P. Wang, Northeast University

Aug. 3 Tuesday, 2010

  • 9:00 - 09:15 Opening Remarks
    Aidong Zhang, State University of New York at Buffalo
    Mark Borodovsky, Georgia Tech
  • 9:15 - 10:15 Keynote speech - Analysis of Molecular Networks
    Mark Gerstein, Yale University
    Session Chair: Mark Borodovsky, Georgia Tech
  • 10:15 - 10:30 Coffee Break
  • 10:30 - 12:00 Three parallel paper sessions
    Session 1: Paper Presentations (Session chair: Umit Catalyurek, The Ohio State University)
    1. Relational Operators for Prioritizing Candidate Biomarkers in High-Throughput Differential Expression Data,Getiria Onsongo, University of Minnesota; Hongwei Xie, University of Minnesota; Timothy J. Griffin, University of Minnesota ; John V. Carlis, University of Minnesota
    2. An Annotated k-deep Prefix Tree for (1-k)-mer Based Sequence Comparisons, Adrienne Breland, University of Nevada; Karen Schlauch, University of Nevada; Monica Nicolescu, University of Nevada; Frederick C. Harris Jr. , University of Nevada
    3. A Graph and Hierarchical Clustering based Approach for Population Structure Inference, Jun Wang, Harbin Institute of Technology; Mao-zu Guo, Harbin Institute of Technology (short paper)
    4. Comparison of Discrete- and Continuous-State Stochastic Methods to Model Neuronal Signal Transduction, Tiina Manninen, Tampere University of Technology; Daniel X. Keller, Ecole Polytechnique Federale de Lausanne (short paper)

    Session 2: Paper Presentations (Session chair: Jonathan Dennis, Florida State University)
    1. Functional Similarities of Reaction Sets in Metabolic Pathways, Ferhat Ay, University of Florida at Gainesville; Tamer Kahveci, University of Florida at Gainesville
    2. Analyzing Metabolite Measurements for Automated Prediction of Underlying Biological Mechanisms, Ali Cakmak, Case Western Reserve University; Arun Dsouza, Case Western Reserve University; Richard W. Hanson, Case Western Reserve University; Z. Meral Ozsoyoglu, Case Western Reserve University
    3. Enhanced Flux Balance Analysis to Model Metabolic Networks, Nishanth Ulhas Nair, EPFL; Navin Goyal, Microsoft Research India; Nagasuma R. Chandra, Indian Institute of Science (short paper)
    4. Compositional Modelling of Signalling Pathways in Timed Concurrent Constraint Programming, Davide Chiarugi, Universita di Siena; Moreno Falaschi, Universita di Siena; Carlos Olarte, Universidad Javeria; Catuscia Palamidessi, LIX, Ecole Polytechnique (short paper)

    Session 3: Paper Presentations (Session chair: Doina Caragea, Kansas State University)
    1. MetaCluster: Unsupervised Binning of Environmental Genomic Fragments and Taxonomic Annotation, Bin Yang*, Southeast University &The University of Hong Kong; Yu Peng, The University of Hong Kong ; Henry C.M. Leung, The University of Hong Kong ; S.M. Yiu, The University of Hong Kong ; Junjie Qin, BGI-Shenzhen; Ruiqiang Li, BGI-Shenzhen; Francis Y.L. Chin, The University of Hong Kong
    2. Relationship Preserving Feature Selection for Unlabelled Clinical Trials Time-Series, Fatih Altiparmak, ASELSAN A.S.; Michael Gibas, The Ohio State University; Hakan Ferhatosmanoglu, The Ohio State University
    3. An Improved 1.375-Approximation Algorithm for the Transposition Distance Problem, Ulisses Dias, Virginia Tech; Zanoni Dias, University of Campinas (short paper)
    4. Evaluation of Different Complexity Measures for Signal Detection in Genome Sequences, Mehdi Kargar, York University; Aijun An, York University (short paper)

  • 12:00 - 13:00 Lunch Break
  • 13:00 - 14:30 Three parallel paper sessions
    Session 4: Paper Presentations (Session chair: Young-Rae Cho, Baylor University)
    1. Protein Structure Alignment Using Elastic Shape Analysis, Wei Liu, Florida State University; Anuj Srivastava, Florida State University ; Jinfeng Zhang, Florida State University
    2. Random Forest-Based Prediction of Protein Sumoylation Sites from Sequence Features; Shaolei Teng, Clemson University; Hong Luo, Clemson University; Liangjiang Wang, Clemson University
    3. Discovering Overlapping Modules and Bridge Proteins in Proteomic Networks, Emad Ramadan, Yale University; Christopher Osgood, Old Dominion University; Alex Pothen, Purdue University (short paper)
    4. A Novel Network Model for Molecular Prognosis, Ying-Wooi Wan, West Virginia University; Swetha Bose, West Virginia University; James Denvir, West Virginia University; Nancy Lan Guo, West Virginia University (short paper)

    Session 5: Paper Presentations (Session chair: Olatunde Okediji, Albany State University)
    1. Comparison of Virus Interactions with Human Signal Transduction Pathways, Irtisha Singh, Carnegie Mellon University; Oznur Tastan, Carnegie Mellon University; Judith Klein-Seetharaman, University of Pittsburgh
    2. Computational Modeling of the Effects of Oxidative Stress on the IGF-1 Signaling Pathway in Human Articular Chondrocytes, Pamela F. Marcott, Wake Forest University; Jacquelyn, S. Fetrow, Wake Forest University; Richard F. Loeser, Wake Forest University; Edward E. Allen, Wake Forest University
    3. An Intelligent Data-Centric Approach toward Identification of Conserved Motifs in Protein Sequences, Kathryn Dempsey, University of Nebraska at Omaha; Benjamin Currall, Creighton University; Richard Hallworth, Creighton University; Hesham Ali, University of Nebraska at Omaha (short paper)
    4. Systematic Data Integration Platform for Functional Glycomics, Mahesh Visvanathan, University of Kansas; Gerhald H. Lushington, University of Kansas; George R. Bousfield, Wichita State University (short paper)

    Session 6: Paper Presentations (Session chair: Qunfeng Dong, University of North Texas)
    1. Effect of Sequences on the Shape of Protein Energy Landscapes, Yue Li, Florida State University; Gary Tyson, Florida State University; Jinfeng Zhang, Florida State University
    2. Automatic Selection of Near-Native Protein-Ligand Conformations using a Hierarchical Clustering and Volunteer Computing, Trilce Estrada, University of Delaware; Roger Armen, University of Michigan at Ann Arbor; Michela Taufer, University of Delaware
    3. Genomics Information Retrieval Using a Bayesian Model for Learning and Re-ranking Qinmin Vivian Hu, York University; Xiangji Jimmy Huang, York University (short paper)
    4. Accelerating HMMER on GPUs by Implementing Hybrid Data and Task Parallelism, Narayan Ganesan, University of Delaware; Roger Chamberlain, Washington University in St. Louis; Jeremy Buhler, Washington University in St. Louis; Michela Taufer, University of Delaware (short paper)
  • 14:30 - 14:50 Break
  • 14:50 - 16:20 Three parallel paper sessions
    Session 7: Paper Presentations (Session chair: Zhongming Zhao, Vanderbilt University)
    1. Genome-Wide Compatible SNP Intervals and Their Properties, Jeremy Wang, University of North Carolina at Chapel Hill; Fernando Pardo-Manual de Villena, University of North Carolina at Chapel Hill; Kyle J. Moore, University of North Carolina at Chapel Hill; Wei Wang, University of North Carolina at Chapel Hill; Qi Zhang, University of North Carolina at Chapel Hill; Leonard McMillan, University of North Carolina at Chapel Hill
    2. The Solution Space of Genome Sequence Alignment and LIS Graph Decomposition, Fangrui Ma, University of Nebraska-Lincoln; Jitender Deogun, University of Nebraska-Lincoln
    3. Gene Set Analysis Using Principal Components, Isa Kemal Pakatci, University of North Carolina at Chapel Hill; Wei Wang, University of North Carolina at Chapel Hill; Leonard McMillan, University of North Carolina at Chapel Hill (short paper)
    4. An Integrated Approach to Predictive Genomic Analytics, Jason E. McDermott, Pacific Northwest National Lab; Antonio Sanfilippo, Pacific Northwest National Lab; Ronald Taylor, Pacific Northwest National Laboratory; Bob Baddeley, Pacific Northwest National Laboratory; Rick Riensche, Pacific Northwest National Laboratory; Russ Jensen, Pacific Northwest National Laboratory; Susan Stevens. Oregon Health & Science University; Mary Stenzel-Poore, Oregon Health & Science University (short paper)

    Session 8: Paper Presentations (Session chair: Preetam Ghosh, University of Southern Mississippi)
    1. A Parameter Estimation Approach for Non-linear Systems Biology Models Using Spline Approximation, Choujun Zhan, City University of Hong Kong; Lam Fat Yeung, City University of Hong Kong
    2. Inferring Species Trees From Gene Duplication Episodes, John Burleigh, University of Florida; Mukul Bansal, Tel Aviv University; Oliver Eulenstein, Iowa State University; Todd J. Vision, University of North Carolina at Chapel Hill
    3. Examining Effects of Variability on Systems Biology Modeling Algorithms, David J. John, Wake Forest University; Rachel A. Black, Wake Forest University; Jacquelyn S. Fetrow, Wake Forest University; James L. Norris, Wake Forest University (short paper)
    4. Spectrally Resolved Bioluminescence Tomography with Huber-Markov Random-Field Regularization, Jinchao Feng, Beijing University of Technology; Kebin Jia, Beijing University of Technology (short paper)

    Session 9: Paper Presentations (Session chair: Li Liao, University of Delaware)
    1. Alignment-Based versus Variation-based Transformation Methods for Clustering Microarray Time-Series Data, Yifeng Li, University of Windsor; Numanul Subhani, University of Windsor; Alioune Ngom, University of Windsor; Luis Rueda, University of Windsor
    2. Derived Distribution Points Heuristic for Fast Pairwise Statistical Significance Estimation Ankit Agrawal, Northwestern University; Alok Choudhary, Northwestern University; Xiaoqiu Huang, Iowa State University
    3. Effects of cDNA Microarray Time-Series Data Size on Gene Regulatory Network Inference Accuracy, Vijender Chaitankar, The University of Southern Mississippi, Preetam Ghosh, University of Southern Mississippi, Chaoyang Zhang, The University of Southern Mississippi; Ping Gong, SpecPro Inc.; Edward J. Perkins, E.R.D.C Vicksburg, MS (short paper)
    4. Semantic Classification and Dependency Parsing enabled Automated Bio-Molecular Event Extraction from Text, Syed Toufeeq Ahmed, Arizona State University; Radhika Nair, Arizona State University; Chintan Patel, Arizona State University; Sheela P. Kanwar, Arizona State University; Jorg Hakenberg, Arizona State University; Hasan Davulcu, Arizona State University (short paper)
  • 16:20 - 16:40 Coffee Break
  • 16:40 - 17:40 Panel - Personalized Medicine - Challenges and Opportunities for Informatics Research
    Panel chair: Dr. Vipin Kumar, University of Minnesota
    Panelists: Mark Borodovsky, Georgia Tech
    Vladimir Brusic, Harvard University
    Robert Cottingham, Oak Bridge National Laboratory
    Mark Gerstein, Yale University
    Peter Li, Mayo Clinic
  • 18:00 - 20:00 Poster session and reception, Session Chair: Sun Kim, Indiana University
  • (35 posters, see the list of posters at the end of the schedule)

Aug. 4 Wednesday, 2010

  • 9:00 - 10:00 Keynote speech - Transition from Algorithmic to Data Intensive Science
    Robert Cottingham, Oak Bridge National Laboratory
    Session Chair: Gultekin Ozsoyoglu, Case Western Reserve University
  • 10:00 - 10:20 Coffee Break
  • 10:20 - 11:50 Three parallel paper sessions
    Session 10: Paper Presentations (Session chair: Vasant Honavar, Iowa State University)
    1. On the Border Length Minimization Problem (BLMP) on a Square Array, Vamsi Kundeti, University of Connecticut; Sanguthevar Rajasekaran, University of Connecticut; Hieu Dinh, University of Connecticut
    2. Markov Clustering of Protein Interaction Networks with Improved Balance and Scalability, Venu Satuluri, The Ohio State University; Srinivasan Parthasarathy, The Ohio State University, OH; Duygu Ucar, University of Iowa
    3. Feature Selection for Semi-Supervised Multi-Label Learning with Application to Gene Function Analysis, Guo-Zheng Li, Tongji University; Mingyu You, Tongji University; Lei Ge, Shanghai University; Jack Y Yang, Harvard University ; Mary Qu Yang, Purdue University (short paper)
    4. Using Fourier Phase Analysis on Genomic Sequences to Identify Retroviruses, Wendy Ashlock, York University; Suprakash Datta, York University (short paper)

    Session 11: Paper Presentations (Session chair: David Tuck, Yale University)
    1. REAL: An Efficient REad ALigner for Next Generation Sequencing Reads, Kimon Frousios, King's College London; Costas Iliopoulos, King's College London; Laurent Mouchard, Universite de Rauen; Solon P. Pissis, King's College London; German Tischler, King's College London
    2. Parallel Stochastic Simulations of Budding Yeast Cell Cycle: Load Balancing Strategies and Theoretical Analysis, Tae-Hyuk Ahn, Virginia Polytechnic Institute and State University; Adrian Sandu, Virginia Polytechnic Institute and State University
    3. Shape Analysis and Classification of lgl-Type and Wild-Type Neurons, Jinane Mounsef, Arizona State University; Lina Karam, Arizona State University; Patricia Estes, University of Arizona; Daniela Zarnescu, University of Arizona (short paper)
    4. DNA Sequence Feature Selection for Intrinsic Nucleosome Positioning Signals Using AdaBoost, Yu Zhang, Florida State University; Xiuwen Liu, Florida State University; Justin Fincher, Florida State University; Jonathan Dennis, Florida State University (short paper)

    Session 12: Paper Presentations (Session chair: Jake Chen, Indiana-Purdue University)
    1. Enzymatic Target Identification with Dynamic States, Bin Song, University of Florida at Gainesville; Sanjay Ranka, University of Florida at Gainesville; Tamer Kahveci, University of Florida at Gainesville
    2. Comparative Analysis of Biclustering Algorithms, Doruk Bozdag, The Ohio State University; Ashwin Kumar, The Ohio State University; Umit Catalyurek, The Ohio State University
    3. Compositional Modelling of Signalling Pathways in Timed Concurrent Constraint Programming, Davide Chiarugi, Universita di Siena; Moreno Falaschi, Universita di Siena; Carlos Olarte, Universidad Javeriana; Catuscia Palamidessi, Ecole Polytechnique (short paper)
    4. Parallel Computation and Interactive Visualization of Time-varying Solvent Excluded Surfaces, Michael Krone*, University of Stuttgart; Carsten Dachsbacher, Karlsruhe Institute of Technology; Thomas Ertl, University of Stuttgart (short paper)
  • 11:50 - 13:00 Lunch Break
  • 13:00 - 14:15 Three parallel paper sessions
    Session 13: Paper Presentations (Session chair: Wei Wang, University of North Carolina, Chapel Hill)
    1. Guiding Belief Propagation using Domain Knowledge for Protein-Structure Determination, Ameet Soni, University of Wisconsin-Madison; Craig Bingman, University of Wisconsin-Madison; Jude Shavlik, University of Wisconsin-Madison
    2. A Bayesian Decision Fusion Approach for microRNA Target Prediction, Dong Yue, University of Texas at San Antonio; Hui Lui, China University of Mining and Technology; MingZhu Lu, University of Texas at San Antonio; Philip Chen, University of Macau; Yidong Chen, University of Texas Health Science Center at San Antonio; Yufei Huang, University of Texas at San Antonio
    3. Semi-supervised Sequence Classification using Abstraction Augmented Markov Models, Cornelia Caragea*, Iowa State University; Adrian Silvescu, Iowa State University; Doina Caragea, Kansas State University; Vasant Honavar, Iowa State University

    Session 14: Paper Presentations (Session chair: Meral Ozsoyoglu, Case Western Reserve University)
    1. Identify Gene Functions using Functional Expression Profiles obtained by Voxelation, Li An, Temple University; Hongbo Xie, Temple University; Zoran Obradovic , Temple University; Desmond Smith, UCLA; Vasileios Megalooikonomou, Temple University
    2. Differential Biclustering for Gene Expression Analysis, Omar Odibat, Wayne State University; Chandan K. Reddy, Wayne State University; Craig N. Giroux, Karmanos Cancer Institute.
    3. RepFrag: A Graph based Method for Finding Repeats and Transposons from Fragmented Genomes, Nirmalya Bandyopadhyay, University of Florida; A. Mark Settles, University of Florida; Tamer Kahveci, University of Florida

    Session 15: Paper Presentations (Session chair: Jing Li, Case Western Reserve University)
    1. Exact ILP Solutions for Phylogenetic Minimum Flip Problems, Markus Chimani, Friedrich-Schiller-University; Sven Rahmann, TU Dortmund; Sebastian Bocker, Friedrich-Schiller-University
    2. SplittingHeirs: Inferring Haplotypes by Optimizing Resultant Dense Graphs, Sharlee Climer, Washington University ; Alan R. FfTempleton, Washington University; Weixiong Zhang, Washington University
    3. ReFHap: A Reliable and Fast Algorithm for Single Individual Haplotyping, Jorge Duitama, University of Connecticut; Thomas Huebsch, Max Planck Institute for Molecular Genetics; Gayle McEwen, Max Planck Institute for Molecular Genetics; Eun-Kyung Suk, Max Planck Institute for Molecular Genetics; Margret Hoehe, Max Planck Institute for Molecular Genetics
  • 14:15 - 14:30 Break
  • 14:30 - 16:00 Two parallel paper sessions
    Session 16: Paper Presentations (Session chair: Michael Buck, SUNY at Buffalo)
    1. Ring Optimization of Edit Metric Codes in DNA, Daniel Ashlock, University of Guelph; Sheridan K. Houghten, Brock University
    2. Unsupervised Mapping of Sentences to Biomedical Concepts based on Integrated Information Retrieval Model and Clustering, Mi-Young Kim, University of Alberta; Qing Dou, University of Alberta; Osmar R. Zaiane, U. of Alberta; Randy Goebel, University of Alberta
    3. Modeling the Competitive Effects of Nucleosomes on Transcription Factors Binding, Qian Xiang, Sun Yat-Sen University; XianHua Dai, Sun Yat-Sen University (short paper)
    4. SNP Specific Extraction and Analysis using Shrunken Dissimilarity Measure, Yang Liu, Hong Kong Baptist University; Michael K. Ng, Hong Kong Baptist University; Jin Zhou, University of Jinan(short paper)

    Session 17: Paper Presentations (Session chair: Ping Liang, Brock University)
    1. Homology Prediction Refinement and Reconstruction of Gene Content and Order of Ancestral Bacterial Genomes, Kuan Yang, Virginia Tech; Joao Setubal, Virginia Tech
    2. Promoter Prediction Based on a Multiple Instance Learning Scheme, Xuefeng Zhou, Washington University in St. Louis; Jianhua Ruan, The University of Texas at San Antonio ; Weixiong Zhang, Washington University in Saint Louis
    3. In Silico Identification of microRNAs from Expressed Sequence Tags of Three Earthworm Species, Ping Gong*, SpecPro Inc ; Fuliang Xie, East Carolina University ; Baohong Zhang, East Carolina University; Edward Perkins, E.R.D.C Vicksburg, MS (short paper)
    4. An Effective Filtering Gene Selection Method for Microarray Data via Shuffling and Statistical Analysis, Zejin Jason Ding, Georgia State University; Yan-Qing Zhang, Georgia State University (short paper)
  • 16:00 - 16:20 Coffee Break
  • 16:20 - 17:20 Community meeting on ACM SIG Bioinformatics, Session Chair: Armin Mikler , University of North Texas
    Discussants: Mark Borodovsky, Georgia Tech
    Sun Kim, Indiana University
    Vipin Kumar, University of Minnesota
    Tekin Ozsoyoglu, Case Western Reserve University
    Yi Pan, Georgia State University
    Joe Zhang, University of Southern Mississippi
  • 18:00 - 20:00 Dinner and best paper and poster awards
    Chairs: Mark Borodovsky, Georgia Tech
    Aidong Zhang, State University of New York at Buffalo
    Wei Wang, University of North Carolina, Chapel Hill (present the best paper award)
    Parthasarathy Srinivasan, The Ohio State University (present the best student paper award)
    Sun Kim, Indiana University (present the best poster award)

List of Poser papers

  1. Coupling Between Heparan Sulfate Proteoglycans and FGF-2 Receptors is Key to FGF-2 Capture under Flow: A Computational Study, Changjiang Zhang, Kimberly Forsten-Williams, Bing Zhao, Michael Fannon and Jun Zhang
  2. Shortest Path Edit Distance for Detecting Duplicate Biological Entities, Alex Rudniy, Min Song, and James Geller
  3. Docking Arachidonic Acid to 8R-Lipoxygenase Using Internal Coordinate Mechanics Tianchuan Du, Shuju Bai, and Ebrahim Khosravi
  4. EGGSlicer: Predicting biologically meaningful gene sets from conserved gene clusters using gene ontology information, Sun Kim, Kwangmin Choi, Heejoon Chae, and Haleh Ashiki
  5. Estimating the dynamics of protofibril elongation involved in A42 peptide aggregation in Alzheimer's disease, Preetam Ghosh, Amit Kumar, Bhaswati Datta, and Vijayaraghavan Rangachari
  6. Efficient Query Evaluation for DAG-shaped Hierarchies, En Cheng, Ali Cakmak, and Meral Ozsoyoglu
  7. Use of ternary similarities in graph based clustering for protein structural family classification, Guillaume Santini, Henry Soldano, and Joel Pothier
  8. Visualization of Biological Shape Transformation by 3D Model Morphing, Mei Xiao, Jung Soh, Morgan Taschuk, Andrei Turinsky, Trish Parsons, Benedikt Hallgr?msson, and Christoph Sensen
  9. Breast Cancer Plasma Protein Biomarker Discovery by Coupling LC-MS/MS Proteomics and Systems Biology, Fan Zhang, Mu Wang, and Jake Y. Chen
  10. Performance Evaluation of the Time-Delayed Dynamic Bayesian Network Approach to Inferring Gene Regulatory Networks from Time Series Microarray Data, Haoni Li, Peng Li, Chaoyang Zhang, Ping Gong, and Edward Perkins
  11. A Computational Exploration of Gene Regulation by Nucleosome Position, Justin A. Fincher, Gary Tyson, and Jonatha H. Dennis
  12. Ontology for MicroRNA Target Prediction in Human Cancer, Jingshan Huang, Ming Tan, Dejing Dou, Lei He, Chris Townsend, and Patrick J. Hayes
  13. Pulmonary artery smooth muscle responses to KCl under normoxic and hypoxic conditions studied by means of a spatial network model, Marko Gosak, Marko Marhl, Christelle Guibert, Marie Billaud, and Etienne Roux
  14. Applying graph theoretic approaches to microbial metagenomes: Ecological perspectives on function, Wolfgang Hankeln, Pier Luigi Buttigieg, Ivaylo Kostadinov, Renzo Kottmann, Pelin Yilmaz, Melissa Beth Duhaime, and Frank Oliver Gl?ckner
  15. Hunting for Truly Relevant Articles in Bioinformatics Literature ? A Preliminary Study Cen Li, Suk Seo, and Ralph Butler
  16. Faster Coevolution Detection of Proteins using Maximum Similar Cliques, Alexandr Bezginov, Elisabeth R.M. Tillier, and Jonathan Rose
  17. In silico Predicted Essential Genes required for Zebrafish (Danio rerio) Steroid Hormone Production, David Hala, Duane B. Huggett, and Dalma Martinovic
  18. F-Statistics Algorithm for Gene Clustering Evaluation, Mohamad Qayoom, Qi Zhang, and Christopher Taylor
  19. A Novel Cancer Classifier based on Differentially Expressed Gene Network, Jaegyoon Ahn, Youngmi Yoon, and Sanghyun Park
  20. Process Calculi for Systems Biology, Caroline Baroukh and Yike Guo
  21. Alzheimer's Disease Target Selection: a data integration approach, Bradley W. Poland, Snehal Naik, Karl Richter, Panayiotis Zagouras, Eric Fauman, and Robert M. Peitzsch
  22. Data mining of mRNA-Seq and small RNA-Seq data to find microRNA targets, Hyunsoo Kim and Ramana V. Davuluri
  23. A novel representation of HLA allele specificity and prediction algorithm for HLA class I binding, David Crockett and Perry Ridge
  24. Feature selection for characterizing HLA class I peptide motif anchors, Perry Ridge and David Crockett
  25. Whole-genome Immunoinformatic Analysis of Mycobacterium tuberculosis Towards Large Scale Identification of Immunodominant CD8 Epitopes, Anat Zvi, David Lewinsohn, Deborah Lewinsohn, and Avigdor Shafferman
  26. Application of Systems Biology for understanding of Disease and selection of Molecular Targets for Therapy, Andreas Heinzel, Johannes Sollner, and Suszan Szathmary
  27. Highly conserved and associated HIV-1 CTL and T-Helper epitopes in global HIV-1 population: Potential candidates for multi-epitope HIV-1 vaccine, Sinu Paul and Helen Piontkivska
  28. Universal Immune System Simulator framework (UISS), Francesco Pappalardo, Marzio Pennisi, and Santo Motta
  29. Structural landscape of immunoglobulin lambda light chains, Anna Chailyan and Paolo Marcatili
  30. Immunological Implications of a Structural Analysis of Two Different Porcine IL1 Proteins Expressed in Macrophages and Embryos, Ataur Katebi, Pawel Gniewek, Michael Zimmermann, Saras Saraswathi, Zhenming Gong, Christopher Tuggle, Andrzej Kloczkowski, and Robert Jernigan
  31. Effective Neutralization and Neutralization Epitope Masking Signatures for four Anti-V3 mAbs, Alpna Agarwal, James Swetnam, Susan Zolla-Pazner, and Timothy Cardozo
  32. Immunological response in normal healthy twins across age, Sanchita Bhattacharya Shai Shen-Orr, Hodel Maecker, Laura Lazzeroni, Gary Swan, J. David Clark, Martin Angst, Atul Butte, and Mark Davis
  33. PopCover: A method for selecting of peptides with optimal Population and Pathogen Coverage, C. Lundegaard, AC Karlsson, Carina Perez, M. Buggert, O. Lund, M. Nielsen
  34. A framework for developing epitope prediction tools, Yasser El-Manzalawy and Vasant Honavar
  35. Rheumatoid Arthritis Molecular Heterogeneity, Sarah Kummerfeld, Jason Hackney, Michael Townsend and Hilary Clark