1. BCB 2010: Niagara Falls, NY, USA

Keynote speeches, panel and tutorials

• Mark Gerstein:
  Analysis of molecular networks. 1
  
• Bob Cottingham:
  Bioinformatics - transition from algorithmic to data intensive science. 2
  
• Vipin Kumar:
  Personalized medicine - challenges and opportunities for informatics research. 3-4
  
• Jing Li, Kun Huang:
  Next generation sequencing data analysis. 5
  
• Patrick Wang:
  Intelligent pattern recognition and applications. 6
  

Regular papers

• Fatih Altiparmak, Michael Gibas, Hakan Ferhatosmanoglu:
  Relationship preserving feature selection for unlabelled clinical trials time-series. 7-16
  
• Irtisha Singh, Oznur Tastan, Judith Klein-Seetharaman:
  Comparison of virus interactions with human signal transduction pathways. 17-24
  
• Getiria Onsongo, Hongwei Xie, Timothy J. Griffin, John V. Carlis:
  Relational operators for prioritizing candidate biomarkers in high-throughput differential expression data. 25-34
  
• Yue Li, Gary S. Tyson, Jinfeng Zhang:
  Effect of sequences on the shape of protein energy landscapes. 35-42
  
• Jeremy W. Wang, Kyle J. Moore, Qi Zhang, Fernando Pardo-Manuel de Villena, Wei Wang, Leonard McMillan:
  Genome-wide compatible SNP intervals and their properties. 43-52
  
• Yifeng Li, Numanul Subhani, Alioune Ngom, Luis Rueda:
  Alignment-based versus variation-based transformation methods for clustering microarray time-series data. 53-61
  
• Wei Liu, Anuj Srivastava, Jinfeng Zhang:
  Protein structure alignment using elastic shape analysis. 62-70
  
• Pamela F. Marcott, Jacquelyn S. Fetrow, Richard F. Loeser, Edward E. Allen:
  Computational modeling of the effects of oxidative stress on the IGF-1 signaling pathway in human articular chondrocytes. 71-78
  
• Adrienne Breland, Karen Schlauch, Monica N. Nicolescu, Frederick C. Harris Jr.:
  An annotated k-deep prefix tree for (1-k)-mer based sequence comparisons. 79-85
  
• Choujun Zhan, Lam Fat Yeung:
  A parameter estimation approach for non-linear systems biology models using spline approximation. 86-91
  
• Nirmalya Bandyopadhyay, A. Mark Settles, Tamer Kahveci:
  RepFrag: a graph based method for finding repeats and transposons from fragmented genomes. 92-101
  
• Ferhat Ay, Tamer Kahveci:
  Functional similarities of reaction sets in metabolic pathways. 102-111
  
• Vamsi Kundeti, Sanguthevar Rajasekaran, Hieu Dinh:
  On the border length minimization problem (BLMP) on a square array. 112-119
  
• Shaolei Teng, Hong Luo, Liangjiang Wang:
  Random forest-based prediction of protein sumoylation sites from sequence features. 120-126
  
• Sharlee Climer, Alan R. Templeton, Weixiong Zhang:
  SplittingHeirs: inferring haplotypes by optimizing resultant dense graphs. 127-136
  
• Ali Cakmak, Arun Dsouza, Richard W. Hanson, Z. Meral Özsoyoglu:
  Analyzing metabolite measurements for automated prediction of underlying biological mechanisms. 137-146
  
• Markus Chimani, Sven Rahmann, Sebastian Böcker:
  Exact ILP solutions for phylogenetic minimum flip problems. 147-153
  
• Kimon Frousios, Costas S. Iliopoulos, Laurent Mouchard, Solon P. Pissis, German Tischler:
  REAL: an efficient REad ALigner for next generation sequencing reads. 154-159
  
• Jorge Duitama, Thomas Huebsch, Gayle McEwen, Eun-Kyung Suk, Margret R. Hoehe:
  ReFHap: a reliable and fast algorithm for single individual haplotyping. 160-169
  
• Bin Yang, Yu Peng, Henry C. M. Leung, Siu-Ming Yiu, Junjie Qin, Ruiqiang Li, Francis Y. L. Chin:
  MetaCluster: unsupervised binning of environmental genomic fragments and taxonomic annotation. 170-179
  
• Bin Song, Sanjay Ranka, Tamer Kahveci:
  Enzymatic target identification with dynamic states. 180-187
  
• Li An, Desmond J. Smith, Hongbo Xie, Vasileios Megalooikonomou, Zoran Obradovic:
  Identifying gene functions using functional expression profiles obtained by voxelation. 188-197
  
• J. Gordon Burleigh, Mukul S. Bansal, Oliver Eulenstein, Todd J. Vision:
  Inferring species trees from gene duplication episodes. 198-203
  
• Trilce Estrada, Roger Armen, Michela Taufer:
  Automatic selection of near-native protein-ligand conformations using a hierarchical clustering and volunteer computing. 204-213
  
• Dong Yue, Hui Liu, Mingzhu Lu, Philip Chen, Yidong Chen, Yufei Huang:
  A Bayesian decision fusion approach for microRNA target prediction. 214-221
  
• Daniel A. Ashlock, Sheridan K. Houghten:
  Ring optimization of edit metric codes in DNA. 222-229
  
• Kuan Yang, João C. Setubal:
  Homology prediction refinement and reconstruction of gene content and order of ancestral bacterial genomes. 230-236
  
• Tae-Hyuk Ahn, Adrian Sandu:
  Parallel stochastic simulations of budding yeast cell cycle: load balancing strategies and theoretical analysis. 237-246
  
• Venu Satuluri, Srinivasan Parthasarathy, Duygu Ucar:
  Markov clustering of protein interaction networks with improved balance and scalability. 247-256
  
• Cornelia Caragea, Adrian Silvescu, Doina Caragea, Vasant Honavar:
  Semi-supervised sequence classification using abstraction augmented Markov models. 257-264
  
• Doruk Bozdag, Ashwin S. Kumar, Ümit V. Çatalyürek:
  Comparative analysis of biclustering algorithms. 265-274
  
• Omar Odibat, Chandan K. Reddy, Craig N. Giroux:
  Differential biclustering for gene expression analysis. 275-284
  
• Ameet Soni, Craig A. Bingman, Jude W. Shavlik:
  Guiding belief propagation using domain knowledge for protein-structure determination. 285-294
  
• Xuefeng Zhou, Jianhua Ruan, Weixiong Zhang:
  Promoter prediction based on a multiple instance learning scheme. 295-301
  
• Fangrui Ma, Jitender S. Deogun:
  The solution space of genome sequence alignment and LIS graph decomposition. 302-311
  
• Ankit Agrawal, Alok N. Choudhary, Xiaoqiu Huang:
  Derived distribution points heuristic for fast pairwise statistical significance estimation. 312-321
  
• Mi-Young Kim, Qing Dou, Osmar R. Zaïane, Randy Goebel:
  Unsupervised mapping of sentences to biomedical concepts based on integrated information retrieval model and clustering. 322-329
  

Short papers

• Isa Kemal Pakatci, Wei Wang, Leonard McMillan:
  Gene set analysis using principal components. 330-333
  
• Ulisses Dias, Zanoni Dias:
  An improved 1.375-approximation algorithm for the transposition distance problem. 334-337
  
• Jinchao Feng, Kebin Jia:
  Spectrally resolved bioluminescence tomography with Huber-Markov random-field regularization. 338-341
  
• Ying-Wooi Wan, Swetha Bose, James Denvir, Nancy Lan Guo:
  A novel network model for molecular prognosis. 342-345
  
• Jun Wang, Maozu Guo:
  A graph and hierarchical clustering based approach for population structure inference. 346-349
  
• Qian Xiang, Xianhua Dai:
  Modeling the competitive effects of nucleosomes on transcription factors binding. 350-353
  
• Guo-Zheng Li, Mingyu You, Lei Ge, Jack Y. Yang, Mary Qu Yang:
  Feature selection for semi-supervised multi-label learning with application to gene function analysis. 354-357
  
• Nishanth Ulhas Nair, Navin Goyal, Nagasuma R. Chandra:
  Enhanced flux balance analysis to model metabolic networks. 358-361
  
• Jinane Mounsef, Lina J. Karam, Patricia Estes, Daniela Zamescu:
  Shape analysis and classification of lgl-type and wild-type neurons. 362-365
  
• Emad Ramadan, Christopher Osgood, Alex Pothen:
  Discovering overlapping modules and bridge proteins in proteomic networks. 366-369
  
• Syed Toufeeq Ahmed, Radhika Nair, Chintan Patel, Sheela P. Kanwar, Jörg Hakenberg, Hasan Davulcu:
  Semantic classification and dependency parsing enabled automated bio-molecular event extraction from text. 370-373
  
• Rachel A. Black, David J. John, Jacquelyn S. Fetrow, James L. Norris:
  Examining effects of variability on systems biology modeling algorithms. 374-377
  
• Yang Liu, Michael K. Ng, Jin Zhou:
  SNP specific extraction and analysis using shrunken dissimilarity measure. 378-381
  
• Zejin Jason Ding, Yan-Qing Zhang:
  An effective filtering gene selection method for microarray data via shuffling and statistical analysis. 382-385
  
• Yu Zhang, Xiuwen Liu, Justin A. Fincher, Jonathan H. Dennis:
  DNA sequence feature selection for intrinsic nucleosome positioning signals using AdaBoost. 386-389
  
• Jason E. McDermott, Bob Baddeley, Susan L. Stevens, Antonio Sanfilippo, Rick Riensche, Mary P. Stenzel-Poore, Ronald C. Taylor, Russ Jensen:
  An integrated approach to predictive genomic analytics. 390-393
  
• Tiina Manninen, Daniel X. Keller:
  Comparison of discrete- and continuous-state stochastic methods to model neuronal signal transduction. 394-397
  
• Kathryn Dempsey, Benjamin Currall, Richard Hallworth, Hesham H. Ali:
  An intelligent data-centric approach toward identification of conserved motifs in protein sequences. 398-401
  
• Michael Krone, Carsten Dachsbacher, Thomas Ertl:
  Parallel computation and interactive visualization of time-varying solvent excluded surfaces. 402-405
  
• Wendy Ashlock, Suprakash Datta:
  Using Fourier phase analysis on genomic sequences to identify retroviruses. 406-409
  
• Vijender Chaitankar, Preetam Ghosh, Chaoyang Zhang, Ping Gong, Edward J. Perkins:
  Effects of cDNA microarray time-series data size on gene regulatory network inference accuracy. 410-413
  
• Davide Chiarugi, Moreno Falaschi, Carlos Olarte, Catuscia Palamidessi:
  Compositional modelling of signalling pathways in timed concurrent constraint programming. 414-417
  
• Narayan Ganesan, Roger D. Chamberlain, Jeremy Buhler, Michela Taufer:
  Accelerating HMMER on GPUs by implementing hybrid data and task parallelism. 418-421
  
• Mehdi Kargar, Aijun An:
  Evaluation of different complexity measures for signal detection in genome sequences. 422-425
  
• Qinmin Vivian Hu, Jimmy Xiangji Huang:
  Genomics information retrieval using a Bayesian model for learning and re-ranking. 426-429
  
• Ping Gong, Fuliang Xie, Baohong Zhang, Edward J. Perkins:
  In silico identification of microRNAs from expressed sequence tags of three earthworm species. 430-434
  
• Mahesh Visvanathan, Sasidhar R. Siddam, In-Hee Lee, Gerald H. Lushington, George R. Bousfield:
  Systematic data integration platform for functional glycomics. 435-438
  

Posters

• Changjiang Zhang, Kimberly Forsten-Williams, Bing Zhao, Michael Fannon, Jun Zhang:
  Coupling between heparan sulfate proteoglycans and FGF-2 receptors is key to FGF-2 capture under flow: a computational study. 439-441
  
• Alex Rudniy, Min Song, James Geller:
  Shortest path edit distance for detecting duplicate biological entities. 442-444
  
• Tianchuan Du, Shuju Bai, Ebrahim Khosravi:
  Docking arachidonic acid to 8R-lipoxygenase using internal coordinate mechanics. 445-447
  
• Heejoon Chae, Kwangmin Choi, Sun Kim, Haleh Ashki:
  EGGSlicer: predicting biologically meaningful gene sets from gene clusters using gene ontology information. 448-450
  
• Preetam Ghosh, Amit Kumar, Bhaswati Datta, Vijayaraghavan Rangachari:
  Estimating the dynamics of protofibril elongation involved in Aβ42 peptide aggregation in Alzheimer's disease. 451-453
  
• En Cheng, Ali Cakmak, Z. Meral Özsoyoglu:
  Efficient query evaluation for DAG-shaped hierarchies. 454-456
  
• Guillaume Santini, Henry Soldano, Joël Pothier:
  Use of ternary similarities in graph based clustering for protein structural family classification. 457-459
  
• Mei Xiao, Jung Soh, Morgan L. Taschuk, Andrei L. Turinsky, Trish E. Parsons, Benedikt Hallgrímsson, Christoph W. Sensen:
  Visualization of biological shape transformation by 3D model morphing. 460-462
  
• Fan Zhang, Mu Wang, Jake Y. Chen:
  Breast cancer plasma protein biomarker discovery by coupling LC-MS/MS proteomics and systems biology. 463-465
  
• Haoni Li, Peng Li, Chaoyang Zhang, Nan Wang, Ping Gong, Edward J. Perkins:
  Performance evaluation of the time-delayed dynamic Bayesian network approach to inferring gene regulatory networks from time series microarray data. 466-468
  
• Justin A. Fincher, Gary Tyson, Jonathan H. Dennis:
  A computational exploration of gene regulation by nucleosome position. 469-471
  
• Jingshan Huang, Ming Tan, Dejing Dou, Lei He, Christopher Townsend, Patrick J. Hayes:
  Ontology for MicroRNA Target prediction in human cancer. 472-474
  
• Marko Gosak, Marko Marhl, Christelle Guibert, Marie Billaud, Etienne Roux:
  Pulmonary artery smooth muscle responses to KCl under normoxic and hypoxic conditions studied by means of a spatial network model. 475-477
  
• Wolfgang Hankeln, Pier Luigi Buttigieg, Ivaylo Kostadinov, Renzo Kottmann, Pelin Yilmaz, Melissa Beth Duhaime, Frank Oliver Glöckner:
  Applying graph theoretic approaches to microbial metagenomes: ecological perspectives on function. 478-480
  
• Cen Li, Suk Jai Seo, Ralph Butler:
  Hunting for truly relevant articles in bioinformatics literature: a preliminary study. 481-483
  
• Alex Rodionov, Alexandr Bezginov, Jonathan Rose, Elisabeth R. M. Tillier:
  Faster coevolution detection of proteins using maximum similar cliques. 484-486
  
• David Hala, Duane B. Huggett, Dalma Martinovic:
  In silico predicted essential genes required for zebrafish (Danio rerio) steroid hormone production. 487-489
  
• Mohamad Qayoom, Qi Zhang, Christopher Taylor:
  F-statistics algorithm for gene clustering evaluation. 490-492
  
• Jaegyoon Ahn, Youngmi Yoon, Sanghyun Park:
  A novel cancer classifier based on differentially expressed gene network. 493-495
  
• Caroline Baroukh, Anthony Rowe, Yike Guo:
  Process calculi for systems biology. 496-497
  
• Bradley W. Poland, Panayiotis Zagouras, Snehal Naik, Eric Fauman, Karl Richter, Robert M. Peitzsch:
  Alzheimer's disease target selection: a data integration approach. 498
  
• Hyunsoo Kim, Ramana V. Davuluri:
  Data mining of mRNA-Seq and small RNA-Seq data to find microRNA targets. 499-501
  

Workshop on Gene Network and Pathway Generation and Analysis

• Tao Huang, Guohui Ding, Yixue Li, Lei Liu, Eugene Tan, Hongyue Dai, Qi Liu, Zhidong Tu, Lu Xie:
  Dysfunctional gene/protein networks in hepatitis C virus-induced hepatocellular cirrhosis and carcinoma. 502-507
  
• Mahesh Visvanathan, Shanker Rao, Vijay Anand, Gerald H. Lushington, Michael Netzer, Christian Baumgartner, George R. Bousfield:
  A multi-tier data mining workflow to analyze the age related shift from diglycosylated- to tetra-glycosylated-FSH secretion by the anterior pituitary. 508-514
  
• Ronald C. Taylor, Bob Baddeley, Antonio Sanfilippo, Rick Riensche, Marc Verhagen, Jason E. McDermott, Russ Jensen:
  Learning biological networks via bootstrapping with optimized go-based gene similarity. 515-519
  
• Chifeng Ma, Hung-I Harry Chen, Yufei Huang, Yidong Chen:
  Constructing a compound mode-of-action network for personalized drug effectiveness prediction. 520-528
  
• Laura Elnitski, Jens Lichtenberg, Lonnie R. Welch:
  Regulatory network nodes of check point factors in DNA repair pathways. 529-536
  
• Mudita Singhal, Anuj R. Shah, Joshua N. Adkins, Roslyn Brown:
  Using support vector machine for improving protein-protein interaction prediction utilizing domain interactions. 537-545
  
• Praneeth Uppalapati, Yang Xiang, Kun Huang:
  Predicting prognostic markers for glioma using gene co-expression network analysis. 546-551
  
• An Zhou, Larry David, Roger Simon:
  De novo proteomics of neuronal ischemic tolerance. 552-555
  

Workshop on Graph Theoretic Approaches for Biological Network Analysis

• Emad Ramadan, Sudhir Perincheri, David Tuck:
  A hyper-graph approach for analyzing transcriptional networks in breast cancer. 556-562
  
• Taehyong Kim, Murali Ramanathan, Aidong Zhang:
  A graph-based approach for computational model of bone microstructure. 563-568
  
• José P. Pinto, Isabel Rocha, Miguel Rocha:
  A software tool for network topology analysis under a metabolic engineering perspective. 569-578
  
• Emad Ramadan, Sudhir Perincheri, David Tuck:
  Crosstalk measures for analyzing biological networks in breast cancer. 579-586
  
• Young-Rae Cho:
  Topological analysis of structural roles of proteins in interactome networks. 587-593
  
• Adrienne Breland, Karen Schlauch, Mehmet Hadi Gunes, Frederick C. Harris Jr.:
  Fast graph approaches to measure influenza transmission across geographically distributed host types. 594-601
  

Immunoinformatics and Computational Immunology Workshop

• Salvador Eugenio C. Caoili:
  B-cell epitope prediction for peptide-based vaccine design: towards a paradigm of biological outcomes. 602-610
  
• Matthew Ardito, Songhua Zhang, William Martin, Steven F. Moss, Anne S. De Groot, Leonard Moise:
  Immunoinformatic-driven H. pylori vaccine design. 611-615
  
• Matthew Ardito, Leonard Moise, William Martin, Anne S. De Groot:
  Immunoinformatic approach to a multi-pathogen genome-derived epitope-driven vaccine. 616-620
  
• Michael T. Zimmermann, Aris Skliros, Saras Saraswathi, Andrzej Kloczkowski, Robert L. Jernigan:
  Immunoglobulin functional motions and their effects on the complementarity determining regions. 621-626
  
• Chen Yanover, Mari Malkki, Ted Gooley, Effie W. Petersdorf, Philip Bradley:
  How do amino acid mismatches affect the outcome of hematopoietic cell transplants?: a structural perspective. 627-633
  
• Peng Wang, Björn Peters, John Sidney, Alessandro Sette:
  An automatic computational pipeline to display MHC binding motifs. 634-641
  
• David K. Crockett, Perry G. Ridge:
  A novel representation of HLA allele specificity and prediction algorithm for HLA class I binding. 642-643
  
• Perry G. Ridge, David K. Crockett:
  Feature selection for characterizing HLA class I peptide motif anchors. 644-645
  
• Anat Zvi, David Lewinsohn, Deborah Lewinsohn, Avigdor Shafferman:
  Whole-genome immunoinformatic analysis of Mycobacterium tuberculosis towards large scale identification of immunodominant CD8 epitopes. 646
  
• Andreas Heinzel, Johannes Söllner, Suszan Szathmary:
  Application of systems biology for understanding of disease and selection of molecular targets for therapy. 647
  
• Sinu Paul, Helen Piontkivska:
  Highly conserved and associated HIV-1 CTL and T-Helper epitopes in global HIV-1 population: potential candidates for multi-epitope HIV-1 vaccine. 648
  
• Francesco Pappalardo, Marzio Pennisi, Santo Motta:
  Universal immune system simulator framework (UISS). 649-650
  
• Anna Chailyan, Davide Cirillo, Paolo Marcatili, Anna Tramontano:
  Structural landscape of immunoglobulin lambda light chains. 651-652
  
• Ataur R. Katebi, Pawel Gniewek, Michael Zimmermann, Saras Saraswathi, Zhenming Gong, Christopher K. Tuggle, Andrzej Kloczkowski, Robert L. Jernigan:
  Immunological implications of a structural analysis of two different porcine IL1β proteins expressed in macrophages and embryos. 653-655
  
• Alpna Agarwal, Susan Zolla-Pazner, James Swetnam, Timothy Cardozo:
  Effective neutralization and neutralization epitope masking signatures for four anti-V3 mAbs. 656
  
• Sanchita Bhattacharya, Shai Shen-Orr, Holden Maecker, Laura Lazzeroni, Gary E. Swan, J. David Clark, Martin S. Angst, Atul J. Butte, Mark M. Davis:
  Immunological response in normal healthy twins across age. 657
  
• Claus Lundegaard, M. Buggert, A. C. Karlsson, Ole Lund, Carina Perez, Morten Nielsen:
  PopCover: a method for selecting of peptides with optimal population and pathogen coverage. 658-659
  
• Yasser El-Manzalawy, Vasant Honavar:
  A framework for developing epitope prediction tools. 660-662
  
• Sarah K. Kummerfeld, Jason A. Hackney, Michael J. Townsend, Hilary F. Clark:
  Rheumatoid Arthritis molecular heterogeneity. 663
  

Workshop on Protein-Protein Interaction Data: Management, Querying and Analysis

• Mario Cannataro, Pietro Hiram Guzzi, Pierangelo Veltri:
  Using RDF for managing protein-protein interaction data. 664-670
  
• Vera Tomaino, Pietro Hiram Guzzi, Mario Cannataro, Pierangelo Veltri:
  Experimental comparison of biclustering algorithms for PPI networks. 671-676
  
• Maria Persico:
  A combinatorics based solution for input generation in the context of classification frameworks aimed to learning interacting protein class. 684-689
  

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