BMC Bioinformatics, Volume 10 - Supplements

Volume 10, Number S-1, 2009

Selected papers from the Seventh Asia-Pacific Bioinformatics Conference (APBC 2009)

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  Michael Q. Zhang, Michael S. Waterman, Xuegong Zhang:
  The Seventh Asia Pacific Bioinformatics Conference (APBC2009).
• 
  Robert Warren, David Sankoff:
  Genome aliquoting with double cut and join.
• 
  G. X. Yu:
  Pathogenic Bacillus anthracis in the progressive gene losses and gains in adaptive evolution.
• 
  Chin-Hsien Tai, James J. Vincent, Changhoon Kim, Byungkook Lee:
  SE: an algorithm for deriving sequence alignment from a pair of superimposed structures.
• 
  Guan Ning Lin, Zhipeng Cai, Guohui Lin, Sounak Chakraborty, Dong Xu:
  ComPhy: prokaryotic composite distance phylogenies inferred from whole-genome gene sets.
• 
  Krister M. Swenson, Yokuki To, Jijun Tang, Bernard M. E. Moret:
  Maximum independent sets of commuting and noninterfering inversions.
• 
  Krister M. Swenson, Bernard M. E. Moret:
  Inversion-based genomic signatures.
• 
  Harris T. Lin, J. Gordon Burleigh, Oliver Eulenstein:
  Triplet supertree heuristics for the tree of life.
• 
  Martin Bader:
  Sorting by reversals, block interchanges, tandem duplications, and deletions.
• 
  Dimitrios P. Papamichail, Georgios P. Papamichail:
  Improved algorithms for approximate string matching (extended abstract).
• 
  Feng Yue, Jian Shi, Jijun Tang:
  Simultaneous phylogeny reconstruction and multiple sequence alignment.
• 
  Daniel H. Huson, Daniel C. Richter, Suparna Mitra, Alexander F. Auch, Stephan C. Schuster:
  Methods for comparative metagenomics.
• 
  Chengpeng Bi:
  DNA motif alignment by evolving a population of Markov chains.
• 
  Benjamin G. Jackson, Patrick S. Schnable, Srinivas Aluru:
  Parallel short sequence assembly of transcriptomes.
• 
  Francis Y. L. Chin, Henry C. M. Leung, Wei-Lin Li, Siu-Ming Yiu:
  Finding optimal threshold for correction error reads in DNA assembling.
• 
  Mohammad Sajjad Hossain, Navid Azimi, Steven Skiena:
  Crystallizing short-read assemblies around seeds.
• 
  Wendi Wang, Peiheng Zhang, Xinchun Liu:
  Short read DNA fragment anchoring algorithm.
• 
  Hao Zheng, Xingyi Hang, Ji Zhu, Minping Qian, Wubin Qu, Chenggang Zhang, Minghua Deng:
  REMAS: a new regression model to identify alternative splicing events from exon array data.
• 
  Md. Rafiul Hassan, M. Maruf Hossain, James Bailey, Geoff MacIntyre, Joshua Wing Kei Ho, Kotagiri Ramamohanarao:
  A voting approach to identify a small number of highly predictive genes using multiple classifiers.
• 
  Martin H. van Vliet, Lodewyk F. A. Wessels, Marcel J. T. Reinders:
  Knowledge driven decomposition of tumor expression profiles.
• 
  Yanni Zhu, Xiaotong Shen, Wei Pan:
  Network-based support vector machine for classification of microarray samples.
• 
  Fan Yang, Hua-zhen Wang, Hong Mi, Cheng-de Lin, Wei-wen Cai:
  Using random forest for reliable classification and cost-sensitive learning for medical diagnosis.
• 
  Yinglei Lai, Sarah E. Eckenrode, Jin-Xiong She:
  A statistical framework for integrating two microarray data sets in differential expression analysis.
• 
  Reija Autio, Sami Kilpinen, Matti Saarela, Olli-P. Kallioniemi, Sampsa Hautaniemi, Jaakko Astola:
  Comparison of Affymetrix data normalization methods using 6, 926 experiments across five array generations.
• 
  Chun-Chi Liu, Jianjun Hu, Mrinal Kalakrishnan, Haiyan Huang, Xianghong Jasmine Zhou:
  Integrative disease classification based on cross-platform microarray data.
• 
  Wensheng Zhang, Hong-Bin Fang, Jiuzhou Song:
  Principal component tests: applied to temporal gene expression data.
• 
  Smitha Dharan, Achuthsankar S. Nair:
  Biclustering of gene expression data using reactive greedy randomized adaptive search procedure.
• 
  Corinna Kolárik, Roman Klinger, Martin Hofmann-Apitius:
  Identification of histone modifications in biomedical text for supporting epigenomic research.
• 
  Quan Wang, Lin Wan, Dayong Li, Lihuang Zhu, Minping Qian, Minghua Deng:
  Searching for bidirectional promoters in Arabidopsis thaliana.
• 
  Hong Sun, Tijl De Bie, Valerie Storms, Qiang Fu, Thomas Dhollander, Karen Lemmens, Annemieke Verstuyf, Bart De Moor, Kathleen Marchal:
  ModuleDigger: an itemset mining framework for the detection of cis-regulatory modules.
• 
  Zhiming Dai, Xianhua Dai, Qian Xiang, Jihua Feng, Yangyang Deng, Jiang Wang, Caisheng He:
  Transcriptional interaction-assisted identification of dynamic nucleosome positioning.
• 
  Brian J. Parker, Jiayu Wen:
  Predicting microRNA targets in time-series microarray experiments via functional data analysis.
• 
  Chi Yu Chan, C. Steven Carmack, Dang D. Long, Anil Maliyekkel, Yu Shao, Igor B. Roninson, Ye Ding:
  A structural interpretation of the effect of GC-content on efficiency of RNA interference.
• 
  Je-Gun Joung, Zhangjun Fei:
  Computational identification of condition-specific miRNA targets based on gene expression profiles and sequence information.
• 
  Sabah Kadri, Veronica F. Hinman, Panayiotis V. Benos:
  HHMMiR: efficient de novo prediction of microRNAs using hierarchical hidden Markov models.
• 
  Dandan Song, Yang Yang, Bin Yu, Binglian Zheng, Zhidong Deng, Bao-Liang Lu, Xuemei Chen, Tao Jiang:
  Computational prediction of novel non-coding RNAs in Arabidopsis thaliana.
• 
  Fei Xia, Yong Dou, Xingming Zhou, Xuejun Yang, Jiaqing Xu, Yang Zhang:
  Fine-grained parallel RNAalifold algorithm for RNA secondary structure prediction on FPGA.
• 
  Unyanee Poolsap, Yuki Kato, Tatsuya Akutsu:
  Prediction of RNA secondary structure with pseudoknots using integer programming.
• 
  Fenix W. D. Huang, Linda Y. M. Li, Christian M. Reidys:
  Sequence-structure relations of pseudoknot RNA.
• 
  Weitao Sun, Jing He:
  Reduction of the secondary structure topological space through direct estimation of the contact energy formed by the secondary structures.
• 
  Jhang-Wei Huang, Chwan-Chuen King, Jinn-Moon Yang:
  Co-evolution positions and rules for antigenic variants of human influenza A/H3N2 viruses.
• 
  Pengfei Han, Xiuzhen Zhang, Zhi-Ping Feng:
  Predicting disordered regions in proteins using the profiles of amino acid indices.
• 
  Thai Quang Tung, Doheon Lee:
  A method to improve protein subcellular localization prediction by integrating various biological data sources.
• 
  Liling Zhao, Jihua Wang, Xianghua Dou, Zanxia Cao:
  Studying the unfolding process of protein G and protein L under physical property space.
• 
  Jian Tian, Ningfeng Wu, Jun Guo, Yunliu Fan:
  Prediction of amyloid fibril-forming segments based on a support vector machine.
• 
  Yi Jia, Jun Huan, Vincent Buhr, Jintao Zhang, Leonidas N. Carayannopoulos:
  Towards comprehensive structural motif mining for better fold annotation in the "twilight zone" of sequence dissimilarity.
• 
  Qian Xu, Derek Hao Hu, Hong Xue, Weichuan Yu, Qiang Yang:
  Semi-supervised protein subcellular localization.
• 
  Krongsakda Phakthanakanok, Khanok Ratanakhanokchai, Khin Lay Kyu, Pornthep Sompornpisut, Aaron Watts, Surapong Pinitglang:
  A computational analysis of SARS cysteine proteinase-octapeptide substrate interaction: implication for structure and active site binding mechanism.
• 
  An-Min Zou, Fang-Xiang Wu, Jiarui Ding, Guy G. Poirier:
  Quality assessment of tandem mass spectra using support vector machine (SVM).
• 
  Yan Fu, Wei Jia, Zhuang Lu, Haipeng Wang, Zuofei Yuan, Hao Chi, You Li, Liyun Xiu, Wenping Wang, Chao Liu, Leheng Wang, Ruixiang Sun, Wen Gao, Xiaohong Qian, Si-Min He:
  Efficient discovery of abundant post-translational modifications and spectral pairs using peptide mass and retention time differences.
• 
  Wouter Meuleman, Judith Y. M. N. Engwegen, Marie-Christine W. Gast, Lodewyk F. A. Wessels, Marcel J. T. Reinders:
  Analysis of mass spectrometry data using sub-spectra.
• 
  Taiji Suzuki, Masashi Sugiyama, Takafumi Kanamori, Jun Sese:
  Mutual information estimation reveals global associations between stimuli and biological processes.
• 
  Hong-Hee Won, Inho Park, Eunjung Lee, Jong-Won Kim, Doheon Lee:
  Comparative analysis of the JAK/STAT signaling through erythropoietin receptor and thrombopoietin receptor using a systems approach.
• 
  Dongxiao Zhu:
  Semi-supervised gene shaving method for predicting low variation biological pathways from genome-wide data.
• 
  Hongning Wang, Minlie Huang, Xiaoyan Zhu:
  Extract interaction detection methods from the biological literature.
• 
  Pei Hao, Siyuan Zheng, Jie Ping, Kang Tu, Christian Gieger, Rui Wang-Sattler, Yang Zhong, Yixue Li:
  Human gene expression sensitivity according to large scale meta-analysis.
• 
  Jisu Kim, De-Shuang Huang, Kyungsook Han:
  Finding motif pairs in the interactions between heterogeneous proteins via bootstrapping and boosting.
• 
  Yanping Xi, Yi-Ping Phoebe Chen, Ming Cao, Weirong Wang, Fei Wang:
  Analysis on relationship between extreme pathways and correlated reaction sets.
• 
  Gunnar W. Klau:
  A new graph-based method for pairwise global network alignment.
• 
  Kelvin Xi Zhang, B. F. Francis Ouellette:
  GAIA: a gram-based interaction analysis tool - an approach for identifying interacting domains in yeast.
• 
  Sebastian Böcker, Sebastian Briesemeister, Gunnar W. Klau:
  On optimal comparability editing with applications to molecular diagnostics.
• 
  Zixiang Xu, Xiao Sun, Shihai Yu:
  Genome-scale analysis to the impact of gene deletion on the metabolism of E. coli: constraint-based simulation approach.
• 
  Jing Chen, Guangcheng Xi:
  An unsupervised partition method based on association delineated revised mutual information.
• 
  Tomasz Gambin, Krzysztof Walczak:
  A new classification method using array Comparative Genome Hybridization data, based on the concept of Limited Jumping Emerging Patterns.
• 
  Rui Jiang, Wanwan Tang, Xuebing Wu, Wenhui Fu:
  A random forest approach to the detection of epistatic interactions in case-control studies.
• 
  Jan Freudenberg, Mingyi Wang, Yaning Yang, Wentian Li:
  Partial correlation analysis indicates causal relationships between GC-content, exon density and recombination rate in the human genome.
• 
  Wentian Li, Annette Lee, Peter K. Gregersen:
  Copy-number-variation and copy-number-alteration region detection by cumulative plots.
• 
  Wenhui Huang, Pengyuan Wang, Zhen Liu, Liqing Zhang:
  Identifying disease associations via genome-wide association studies.
• 
  Erdahl T. Teber, Jason Y. Liu, Sara Ballouz, Diane Fatkin, Merridee A. Wouters:
  Comparison of automated candidate gene prediction systems using genes implicated in type 2 diabetes by genome-wide association studies.
• 
  Reija Autio, Matti Saarela, Anna-Kaarina Järvinen, Sampsa Hautaniemi, Jaakko Astola:
  Advanced analysis and visualization of gene copy number and expression data.
• 
  Jun Wang, Maozu Guo, Chun-yu Wang:
  CGTS: a site-clustering graph based tagSNP selection algorithm in genotype data.
• 
  Laxmi Parida, Asif Javed, Marta Melé, Francesc Calafell, Jaume Bertranpetit:
  Minimizing recombinations in consensus networks for phylogeographic studies.
• 
  Chih Lee, Ali Abdool, Chun-Hsi Huang:
  PCA-based population structure inference with generic clustering algorithms.
• 
  Søren Besenbacher, Christian N. S. Pedersen, Thomas Mailund:
  A fast algorithm for genome-wide haplotype pattern mining.
• 
  Quan Long, Qingrun Zhang, Jurg Ott:
  Detecting disease-associated genotype patterns.

Volume 10, Number S-2, 2009

Selected Proceedings of the First Summit on Translational Bioinformatics 2008

• 
  Atul J. Butte, Indra Neil Sarkar, Marco Ramoni, Yves A. Lussier, Olga G. Troyanskaya:
  Selected proceedings of the First Summit on Translational Bioinformatics 2008.
• 
  Nigam H. Shah, Clément Jonquet, Annie P. Chiang, Atul J. Butte, Rong Chen, Mark A. Musen:
  Ontology-driven indexing of public datasets for translational bioinformatics.
• 
  Parsa Mirhaji, Min Zhu, Mattew Vagnoni, Elmer V. Bernstam, Jiajie Zhang, Jack W. Smith:
  Ontology driven integration platform for clinical and translational research.
• 
  Daniel L. Rubin, Ion-Florin Talos, Michael Halle, Mark A. Musen, Ron Kikinis:
  Computational neuroanatomy: ontology-based representation of neural components and connectivity.
• 
  Isaac Kunz, Ming-Chin Lin, Lewis J. Frey:
  Metadata mapping and reuse in caBIG^TM.
• 
  Jianji Yang, Aaron M. Cohen, William R. Hersh:
  Evaluation of a gene information summarization system by users during the analysis process of microarray datasets.
• 
  Yael Garten, Russ B. Altman:
  Pharmspresso: a text mining tool for extraction of pharmacogenomic concepts and relationships from full text.
• 
  Alberto Malovini, Angelo Nuzzo, Fulvia Ferrazzi, Annibale A. Puca, Riccardo Bellazzi:
  Phenotype forecasting with SNPs data through gene-based Bayesian networks.
• 
  Lee T. Sam, Eneida A. Mendonça, Jianrong Li, Judith A. Blake, Carol Friedman, Yves A. Lussier:
  PhenoGO: an integrated resource for the multiscale mining of clinical and biological data.
• 
  Peter L. Elkin, Mark S. Tuttle, Brett E. Trusko, Steven H. Brown:
  BioProspecting: novel marker discovery obtained by mining the bibleome.
• 
  Vitali Sintchenko, Blanca Gallego, Grace Chung, Enrico W. Coiera:
  Towards bioinformatics assisted infectious disease control.
• 
  Yang Liu, Lee T. Sam, Jianrong Li, Yves A. Lussier:
  Robust methods for accurate diagnosis using pan-microbiological oligonucleotide microarrays.
• 
  Hannah J. Tipney, Sonia M. Leach, Weiguo Feng, Richard A. Spritz, Trevor Williams, Lawrence Hunter:
  Leveraging existing biological knowledge in the identification of candidate genes for facial dysmorphology.
• 
  Benjamin J. Keller, Richard C. McEachin:
  Identifying hypothetical genetic influences on complex disease phenotypes.
• 
  Yueyi I. Liu, Paul H. Wise, Atul J. Butte:
  The "etiome": identification and clustering of human disease etiological factors.

Volume 10, Number S-3, 2009

Second International Workshop on Data and Text Mining in Bioinformatics (DTMBio) 2008

• 
  Ankit Agrawal, Xiaoqiu Huang:
  Pairwise statistical significance of local sequence alignment using multiple parameter sets and empirical justification of parameter set change penalty.
• 
  Sangwoo Kim, Doheon Lee:
  Mining metastasis related genes by primary-secondary tumor comparisons from large-scale databases.
• 
  Jay Urbain, Ophir Frieder, Nazli Goharian:
  Passage relevance models for genomics search.
• 
  Weisi Duan, Min Song, Alexander Yates:
  Fast max-margin clustering for unsupervised word sense disambiguation in biomedical texts.
• 
  Jorge Amigo, Christopher Phillips, Antonio Salas, Ángel Carracedo:
  Viability of in-house datamarting approaches for population genetics analysis of SNP genotypes.
• 
  Hojung Nam, Ki Young Lee, Doheon Lee:
  Identification of temporal association rules from time-series microarray data sets.

Volume 10, Number S-4, 2009

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (BIBM) 2008

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  Oscar Harari, Coral del Val, Rocío Romero-Záliz, Dongwoo Shin, Henry Huang, Eduardo A. Groisman, Igor Zwir:
  Identifying promoter features of co-regulated genes with similar network motifs.
• 
  Pavel P. Kuksa, Pai-Hsi Huang, Vladimir Pavlovic:
  Efficient use of unlabeled data for protein sequence classification: a comparative study.
• 
  Seung-Jin Sul, Suzanne J. Matthews, Tiffani L. Williams:
  Using tree diversity to compare phylogenetic heuristics.
• 
  Cornelia Caragea, Jivko Sinapov, Drena Dobbs, Vasant G. Honavar:
  Mixture of experts models to exploit global sequence similarity on biomolecular sequence labeling.
• 
  Xiaotong Lin, Mei Liu, Xue-wen Chen:
  Assessing reliability of protein-protein interactions by integrative analysis of data in model organisms.
• 
  Rui-Sheng Wang, Guangxu Jin, Xiang-Sun Zhang, Luonan Chen:
  Modeling post-transcriptional regulation activity of small non-coding RNAs in Escherichia coli.
• 
  Jung Hun Oh, Jean Gao:
  A kernel-based approach for detecting outliers of high-dimensional biological data.
• 
  Feng Luo, Bo Li, Xiu-Feng Wan, Richard H. Scheuermann:
  Core and periphery structures in protein interaction networks.
• 
  Junwan Liu, Zhoujun Li, Xiaohua Hu, Yiming Chen:
  Biclustering of microarray data with MOSPO based on crowding distance.
• 
  Li An, Hongbo M. Xie, Mark H. Chin, Zoran Obradovic, Desmond J. Smith, Vasileios Megalooikonomou:
  Analysis of multiplex gene expression maps obtained by voxelation.

Volume 10, Number S-5, 2009

Proceedings of the Bio-Ontologies Special Interest Group Workshop 2008: Knowledge in Biology

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  Christopher Brewster, Simon Jupp, Joanne S. Luciano, David M. Shotton, Robert D. Stevens, Ziqi Zhang:
  Issues in learning an ontology from text.
• 
  Tim Beck, Hugh Morgan, Andrew Blake, Sara Wells, John M. Hancock, Ann-Marie Mallon:
  Practical application of ontologies to annotate and analyse large scale raw mouse phenotype data.
• 
  Cecilia N. Arighi, Hongfang Liu, Darren A. Natale, Winona C. Barker, Harold J. Drabkin, Judith A. Blake, Barry Smith, Cathy H. Wu:
  TGF-beta signaling proteins and the Protein Ontology.
• 
  Xiaoyan A. Qu, Ranga Chandra Gudivada, Anil G. Jegga, Eric K. Neumann, Bruce J. Aronow:
  Inferring novel disease indications for known drugs by semantically linking drug action and disease mechanism relationships.
• 
  Robert Hoehndorf, Joshua Bacher, Michael Backhaus, Sergio E. Gregorio Jr., Frank Loebe, Kay Prüfer, Alexandr Uciteli, Johann Visagie, Heinrich Herre, Janet Kelso:
  BOWiki: an ontology-based wiki for annotation of data and integration of knowledge in biology.
• 
  Weijian Xuan, Manhong Dai, Barbara Mirel, Jean Song, Brian D. Athey, Stanley J. Watson, Fan Meng:
  Open Biomedical Ontology-based Medline exploration.

Volume 10, Number S-6, 2009

European Molecular Biology Network (EMBnet) Conference 2008: 20th Anniversary Celebration. Leading applications and technologies in bioinformatics

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  Domenica D'Elia, Andreas Gisel, Nils-Einar Eriksson, Sophia Kossida, Kimmo Mattila, Lubos Klucar, Erik Bongcam-Rudloff:
  The 20^th anniversary of EMBnet: 20 years of bioinformatics for the Life Sciences community.
• 
  Teresa Maria Creanza, David Stephen Horner, Annarita D'Addabbo, Rosalia Maglietta, Flavio Mignone, Nicola Ancona, Graziano Pesole:
  Statistical assessment of discriminative features for protein-coding and non coding cross-species conserved sequence elements.
• 
  Simon Penel, Anne-Muriel Arigon, Jean-François Dufayard, Anne-Sophie Sertier, Vincent Daubin, Laurent Duret, Manolo Gouy, Guy Perrière:
  Databases of homologous gene families for comparative genomics.
• 
  Göran O. Sperber, Anders Lövgren, Nils-Einar Eriksson, Farid Benachenhou, Jonas Blomberg:
  RetroTector online, a rational tool for analysis of retroviral elements in small and medium size vertebrate genomic sequences.
•