BMC Bioinformatics, Volume 9 - Supplements

Volume 9, Number S-1, 2008

Asia Pacific Bioinformatics Network (APBioNet) Sixth International Conference on Bioinformatics (InCoB2007)

• 
  Shoba Ranganathan, Michael Gribskov, Tin Wee Tan:
  Bioinformatics research in the Asia Pacific: a 2007 update.
• 
  Byoung-Chul Kim, Woo-Yeon Kim, Daeui Park, Won-Hyong Chung, Kwang-Sik Shin, Jong Bhak:
  SNP@Promoter: a database of human SNPs (Single Nucleotide Polymorphisms) within the putative promoter regions.
• 
  Richard Tzong-Han Tsai, Hsi-Chuan Hung, Hong-Jie Dai, Yi-Wen Lin, Wen-Lian Hsu:
  Exploiting likely-positive and unlabeled data to improve the identification of protein-protein interaction articles.
• 
  Madhavi Ganapathiraju, Narayanaswamy Balakrishnan, Raj Reddy, Judith Klein-Seetharaman:
  Transmembrane helix prediction using amino acid property features and latent semantic analysis.
• 
  Christopher J. O. Baker, Kanagasabai Rajaraman, Wee Tiong Ang, Anitha Veeramani, Hong Sang Low, Markus R. Wenk:
  Towards ontology-driven navigation of the lipid bibliosphere.
• 
  Qingwei Xu, Yixiang Shi, Qiang Lu, Guoqing Zhang, Qing-ming Luo, Yixue Li:
  GORouter: an RDF model for providing semantic query and inference services for Gene Ontology and its associations.
• 
  Olivo Miotto, Tin Wee Tan, Vladimir Brusic:
  Rule-based knowledge aggregation for large-scale protein sequence analysis of influenza A viruses.
• 
  Shu-Hwa Chen, Chen-Zen Lo, Ming-Chi Tsai, Chao A. Hsiung, Chung-Yen Lin:
  The unique probe selector: a comprehensive web service for probe design and oligonucleotide arrays.
• 
  Hongya Zhao, Kwok-Leung Chan, Lee-Ming Cheng, Hong Yan:
  Multivariate hierarchical Bayesian model for differential gene expression analysis in microarray experiments.
• 
  Shivashankar H. Nagaraj, Robin B. Gasser, Alasdair J. Nisbet, Shoba Ranganathan:
  In silico analysis of expressed sequence tags from Trichostrongylus vitrinus (Nematoda): comparison of the automated ESTExplorer workflow platform with conventional database searches.
• 
  Rafael Ördög, Zoltan Szabadka, Vince Grolmusz:
  Analyzing the simplicial decomposition of spatial protein structures.
• 
  Paul D. Yoo, Abdur R. Sikder, Bing Bing Zhou, Albert Y. Zomaya:
  Improved general regression network for protein domain boundary prediction.
• 
  Vijayalakshmi Chelliah, William R. Taylor:
  Functional site prediction selects correct protein models.
• 
  Siavoush Dastmalchi, W. Bret Church, Michael B. Morris:
  Modelling the structures of G protein-coupled receptors aided by three-dimensional validation.
• 
  Khar Heng Choo, Joo Chuan Tong, Shoba Ranganathan:
  Modeling Escherichia coli signal peptidase complex with bound substrate: determinants in the mature peptide influencing signal peptide cleavage.
• 
  Naveena Yanamala, Kalyan C. Tirupula, Judith Klein-Seetharaman:
  Preferential binding of allosteric modulators to active and inactive conformational states of metabotropic glutamate receptors.
• 
  Arumugam Madhumalar, Derek John Smith, Chandra Verma:
  Stability of the core domain of p53: insights from computer simulations.
• 
  Olivo Miotto, A. T. Heiny, Tin Wee Tan, J. Thomas August, Vladimir Brusic:
  Identification of human-to-human transmissibility factors in PB2 proteins of influenza A by large-scale mutual information analysis.
• 
  Guanglan Zhang, Asif M. Khan, Kellathur N. Srinivasan, A. T. Heiny, Kenneth X. Lee, Chee Keong Kwoh, J. Thomas August, Vladimir Brusic:
  Hotspot Hunter: a computational system for large-scale screening and selection of candidate immunological hotspots in pathogen proteomes.
• 
  Woo-Yeon Kim, Sungsoo Kang, Byoung-Chul Kim, Jeehyun Oh, Seong-Woong Cho, Jong Bhak, Jong-Soon Choi:
  SynechoNET: integrated protein-protein interaction database of a model cyanobacterium Synechocystis sp. PCC 6803.
• 
  Chen Wang, Jianhua Xuan, Li Chen, Po Zhao, Yue Joseph Wang, Robert Clarke, Eric P. Hoffman:
  Motif-directed network component analysis for regulatory network inference.
• 
  Lesheng Kong, Shoba Ranganathan:
  Tandem duplication, circular permutation, molecular adaptation: how Solanaceae resist pests via inhibitors.
• 
  Dadabhai T. Singh, Rahul Trehan, Bertil Schmidt, Timo Bretschneider:
  Comparative phyloinformatics of virus genes at micro and macro levels in a distributed computing environment.

Volume 9, Number S-2, 2008

Italian Society of Bioinformatics (BITS): Annual Meeting 2007

• 
  Graziano Pesole, Manuela Helmer-Citterich:
  Bioinformatics in Italy: BITS2007, the fourth annual meeting of the Italian Society of Bioinformatics.
• 
  Gabriele Ausiello, Pier Federico Gherardini, Paolo Marcatili, Anna Tramontano, Allegra Via, Manuela Helmer-Citterich:
  FunClust: a web server for the identification of structural motifs in a set of non-homologous protein structures.
• 
  Ezio Bartocci, Flavio Corradini, Emilia Entcheva, Radu Grosu, Scott A. Smolka:
  CellExcite: an efficient simulation environment for excitable cells.
• 
  Alberto Bertoni, Giorgio Valentini:
  Discovering multi-level structures in bio-molecular data through the Bernstein inequality.
• 
  Luigi Buonaguro, Alessandro Monaco, Eleonora Aricò, Ena Wang, Maria Lina Tornesello, George K. Lewis, Francesco M. Marincola, Franco M. Buonaguro:
  Gene expression profile of peripheral blood mononuclear cells in response to HIV-VLPs stimulation.
• 
  Emidio Capriotti, Piero Fariselli, Ivan Rossi, Rita Casadio:
  A three-state prediction of single point mutations on protein stability changes.
• 
  Maria Luisa Chiusano, Nunzio D'Agostino, Alessandra Traini, Concetta Licciardello, Enrico Raimondo, Mario Aversano, Luigi Frusciante, Luigi Monti:
  ISOL@: an Italian SOLAnaceae genomics resource.
• 
  Bernard Degryse, Juan Fernández-Recio, Valentina Citro, Francescol Blasi, Maria Vittoria Cubellis:
  In silico docking of urokinase plasminogen activator and integrins.
• 
  Barbara Lazzari, Andrea Caprera, Alberto Vecchietti, Ivan Merelli, Francesca Barale, Luciano Milanesi, Alessandra Stella, Carlo Pozzi:
  Version VI of the ESTree db: an improved tool for peach transcriptome analysis.
• 
  Svetlin Manavski, Giorgio Valle:
  CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment.
• 
  Paolo Marcatili, Giovanni Bussotti, Anna Tramontano:
  The MoVIN server for the analysis of protein interaction networks.
• 
  Margherita Mutarelli, Luigi Cicatiello, Lorenzo Ferraro, Olì M. V. Grober, Maria Ravo, Angelo M. Facchiano, Claudia Angelini, Alessandro Weisz:
  Time-course analysis of genome-wide gene expression data from hormone-responsive human breast cancer cells.
• 
  Alessandro Orro, Guia Guffanti, Erika Salvi, Fabio Macciardi, Luciano Milanesi:
  SNPLims: a data management system for genome wide association studies.
• 
  Ernesto Picardi, Carla Quagliariello:
  Is plant mitochondrial RNA editing a source of phylogenetic incongruence? An answer from in silico and in vivo data sets.
• 
  Paolo Romano, Domenico Marra:
  SWS: accessing SRS sites contents through Web Services.

Volume 9, Number S-3, 2008

Proceedings of the Second International Symposium on Languages in Biology and Medicine (LBM) 2007

• 
  Jian Su, Christopher J. O. Baker:
  The Second International Symposium on Languages in Biology and Medicine (LBM) 2007.
• 
  Yoshimasa Tsuruoka, John McNaught, Sophia Ananiadou:
  Normalizing biomedical terms by minimizing ambiguity and variability.
• 
  Antonio Jimeno-Yepes, Ernesto Jiménez-Ruiz, Vivian Lee, Sylvain Gaudan, Rafael Berlanga Llavori, Dietrich Rebholz-Schuhmann:
  Assessment of disease named entity recognition on a corpus of annotated sentences.
• 
  Hongning Wang, Minlie Huang, Shilin Ding, Xiaoyan Zhu:
  Exploiting and integrating rich features for biological literature classification.
• 
  Kanae Oda, Jin-Dong Kim, Tomoko Ohta, Daisuke Okanohara, Takuya Matsuzaki, Yuka Tateisi, Jun'ichi Tsujii:
  New challenges for text mining: mapping between text and manually curated pathways.
• 
  Sampo Pyysalo, Antti Airola, Juho Heimonen, Jari Björne, Filip Ginter, Tapio Salakoski:
  Comparative analysis of five protein-protein interaction corpora.
• 
  Jong-Chan Park, Tak-Eun Kim, Jinah Park:
  Monitoring the evolutionary aspect of the Gene Ontology to enhance predictability and usability.
• 
  Ai Kawazoe, Hutchatai Chanlekha, Mika Shigematsu, Nigel Collier:
  Structuring an event ontology for disease outbreak detection.
• 
  Julien Gobeill, Imad Tbahriti, Frédéric Ehrler, Anaïs Mottaz, Anne-Lise Veuthey, Patrick Ruch:
  Gene Ontology density estimation and discourse analysis for automatic GeneRiF extraction.
• 
  Richárd Farkas, György Szarvas:
  Automatic construction of rule-based ICD-9-CM coding systems.
• 
  Hui Yang, Goran Nenadic, John A. Keane:
  Identification of transcription factor contexts in literature using machine learning approaches.

Volume 9, Number S-4, 2008

A Semantic Web for Bioinformatics: Goals, Tools, Systems, Applications

• 
  Nicola Cannata, Michael Schroeder, Roberto Marangoni, Paolo Romano:
  A Semantic Web for bioinformatics: goals, tools, systems, applications.
• 
  Dimitra Alexopoulou, Thomas Wächter, Laura Pickersgill, Cecilia Eyre, Michael Schroeder:
  Terminologies for text-mining; an experiment in the lipoprotein metabolism domain.
• 
  Adrien Coulet, Malika Smaïl-Tabbone, Pascale Benlian, Amedeo Napoli, Marie-Dominique Devignes:
  Ontology-guided data preparation for discovering genotype-phenotype relationships.
• 
  Federica Viti, Ivan Merelli, Andrea Caprera, Barbara Lazzari, Alessandra Stella, Luciano Milanesi:
  Ontology-based, Tissue MicroArray oriented, image centered tissue bank.
• 
  Ismael Navas-Delgado, Raúl Montañez, Almudena Pino-Ángeles, Aurelio A. Moya-García, José Luis Urdiales, Francisca Sánchez-Jiménez, José Francisco Aldana Montes:
  AMMO-Prot: amine system project 3D-model finder.
• 
  Andrea Splendiani:
  RDFScape: Semantic Web meets Systems Biology.
• 
  Andrea Bracciali, Marcello Brunelli, Enrico Cataldo, Pierpaolo Degano:
  Stochastic models for the in silico simulation of synaptic processes.
• 
  Chiara Bodei, Andrea Bracciali, Davide Chiarugi:
  On deducing causality in metabolic networks.
• 
  Mirko Francesconi, Daniel Remondini, Nicola Neretti, John M. Sedivy, Leon N. Cooper, Ettore Verondini, Luciano Milanesi, Gastone C. Castellani:
  Reconstructing networks of pathways via significance analysis of their intersections.
• 
  Alfredo Ferro, Rosalba Giugno, Misael Mongiovì, Alfredo Pulvirenti, Dmitry Skripin, Dennis E. Shasha:
  GraphFind: enhancing graph searching by low support data mining techniques.
• 
  Sara Brunetti, Elena Lodi, Elisa Mori, Maria Stella:
  PARPST: a PARallel algorithm to find peptide sequence tags.
• 
  Tiziana Margaria, Christian Kubczak, Bernhard Steffen:
  Bio-jETI: a service integration, design, and provisioning platform for orchestrated bioinformatics processes.
• 
  Anna-Lena Lamprecht, Tiziana Margaria, Bernhard Steffen, Alexander Sczyrba, Sven Hartmeier, Robert Giegerich:
  GeneFisher-P: variations of GeneFisher as processes in Bio-jETI.

Volume 9, Number S-5, 2008

Proceedings of the 10th Bio-Ontologies Special Interest Group Workshop 2007. Ten years past and looking to the future

• 
  Mikel Egaña Aranguren, Erick Antezana, Martin Kuiper, Robert Stevens:
  Ontology Design Patterns for bio-ontologies: a case study on the Cell Cycle Ontology.
• 
  David P. Hill, Barry Smith, Monica S. McAndrews-Hill, Judith A. Blake:
  Gene Ontology annotations: what they mean and where they come from.
• 
  Anaïs Mottaz, Yum Lina Yip, Patrick Ruch, Anne-Lise Veuthey:
  Mapping proteins to disease terminologies: from UniProt to MeSH.
• 
  Catia Pesquita, Daniel Faria, Hugo P. Bastos, António E. N. Ferreira, André O. Falcão, Francisco M. Couto:
  Metrics for GO based protein semantic similarity: a systematic evaluation.
• 
  Irena Spasic, Daniel Schober, Susanna-Assunta Sansone, Dietrich Rebholz-Schuhmann, Douglas B. Kell, Norman W. Paton:
  Facilitating the development of controlled vocabularies for metabolomics technologies with text mining.

Volume 9, Number S-6, 2008

Symposium of Computations in Bioinformatics and Bioscience (SCBB07)

• 
  Guoqing Lu, Jun Ni:
  Highlighting computations in bioscience and bioinformatics: review of the Symposium of Computations in Bioinformatics and Bioscience (SCBB07).
• 
  Manika Govil, Alberto M. Segre, Veronica J. Vieland:
  MLIP: using multiple processors to compute the posterior probability of linkage.
• 
  Yao-Lin Chang, Huai-Kuang Tsai, Cheng-Yan Kao, Yung-Chiang Chen, Yuh-Jyh Hu, Jinn-Moon Yang:
  Evolutionary conservation of DNA-contact residues in DNA-binding domains.
• 
  Maozu Guo, Jian-Fu Li, Yang Liu:
  A topological transformation in evolutionary tree search methods based on maximum likelihood combining p-ECR and neighbor joining.
• 
  Fei Gu, Hang Chen, Jun Ni:
  Protein structural class prediction based on an improved statistical strategy.
• 
  George Chin Jr., Daniel G. Chavarría-Miranda, Grant C. Nakamura, Heidi J. Sofia:
  BioGraphE: high-performance bionetwork analysis using the Biological Graph Environment.
• 
  Guo-Zheng Li, Hao-Hua Meng, Wen-Cong Lu, Jack Y. Yang, Mary Qu Yang:
  Asymmetric bagging and feature selection for activities prediction of drug molecules.
• 
  Xue-Qiang Zeng, Guo-Zheng Li, Jack Y. Yang, Mary Qu Yang, Gengfeng Wu:
  Dimension reduction with redundant gene elimination for tumor classification.
• 
  Mary Qu Yang, James Taylor, Laura Elnitski:
  Comparative analyses of bidirectional promoters in vertebrates.
• 
  Hiroyuki Mishima, Andrew C. Lidral, Jun Ni:
  Application of the Linux cluster for exhaustive window haplotype analysis using the FBAT and Unphased programs.
• 
  Takeshi Arikuma, Sumi Yoshikawa, Ryuzo Azuma, Kentaro Watanabe, Kazumi Matsumura, Akihiko Konagaya:
  Drug interaction prediction using ontology-driven hypothetical assertion framework for pathway generation followed by numerical simulation.
• 
  Fang-Xiang Wu:
  Genetic weighted k-means algorithm for clustering large-scale gene expression data.
• 
  Fang-Xiang Wu, Pierre Gagné, Arnaud Droit, Guy G. Poirier:
  Quality assessment of peptide tandem mass spectra.
• 
  Xutao Deng, Jun Xu, Charles Wang:
  Improving the power for detecting overlapping genes from multiple DNA microarray-derived gene lists.
• 
  Guoqing Lu, Shunpu Zhang, Xiang Fang:
  An improved string composition method for sequence comparison.
• 
  Lily R. Liang, Vinay Mandal, Yi Lu, Deepak Kumar:
  MCM-test: a fuzzy-set-theory-based approach to differential analysis of gene pathways.
• 
  Chang F. Quo, May D. Wang:
  Quantitative analysis of numerical solvers for oscillatory biomolecular system models.
• 
  Todd H. Stokes, J. T. Torrance, Henry Li, May D. Wang:
  ArrayWiki: an enabling technology for sharing public microarray data repositories and meta-analyses.
• 
  Gregory A. Wilkin, Xiuzhen Huang:
  A practical comparison of two K-Means clustering algorithms.

Volume 9, Number S-7, 2008

UT-ORNL-KBRIN Bioinformatics Summit 2008

• 
  Eric C. Rouchka, Julia Krushkal, Daniel Goldowitz:
  Proceedings of the Seventh Annual UT-ORNL-KBRIN Bioinformatics Summit 2008.
• 
  Elina Tjioe, Michael W. Berry, Ramin Homayouni, Kevin Heinrich:
  Using a literature-based NMF model for discovering gene functional relationships.
• 
  Weikuan Gu, Ivan Gerling, Yan Jiao, Peng Gao, Qing Xiong:
  Candidate genes within known QTL of type 1 diabetes from mouse models.
• 
  Zachary S. Ware, Lisbeth A. Selby, Jerzy W. Jaromczyk:
  MedSurv: a software application for creating, conducting and managing medical surveys and questionnaires.
• 
  Brandon Barker, Jim Lund:
  Genomic analysis of gene regulation complexity.
• 
  Chanchai McDonald, Anand Kulkarni, Teeradache Viangteeravat:
  Scientific Laboratory Information Management System: Tissue Bank.
• 
  Nourtan Abdeltawab, Rita Kansal, Sarah Rowe, Lidia Gardner, Charity Brannen, Mohammed Nooh, Santhosh Mukundan, Hossam Abdelsamed, Ramy Attia, William Taylor, Lu Lu, Robert W. Williams, Malak Kotb:
  Bioinformatics analysis of immune response to group A streptococcal sepsis integrating quantitative trait loci mapping with genome-wide expression studies.
• 
  Sham S. Kakar, Siva K. Panguluri, Sabine J. Waigel:
  Global profile of genes regulated by securin.
• 
  Rami N. Mahdi, Eric C. Rouchka:
  Buffered codons in human transcriptional units.
• 
  Ronald M. Adkins, Julia Krushkal, Chad Klauser, Everett F. Magann, Grant Somes, John Fain, John Morrison:
  Haplotypes of the imprinted insulin gene are associated with size for gestational age and umbilical cord IGF-II levels.
• 
  Dana Marshall, Jeremy Peirce, Fang Zhou, Lu Lu, Robert W. Williams, Kenneth F. Manly, John Stuart:
  QTL mapping arthritis traits in CXB mice.
• 
  Siddharth Pratap, Scott M. Williams, Shawn E. Levy:
  Evaluation of pooled allelotyping versus individual genotyping for genome-wide association analysis of complex disease.
• 
  Stan Pounds, Cheng Cheng, Wenjian Yang, Arzu Onar, Christine Hartford, Susana C. Raimondi, Mary Relling:
  A permutation-based method to identify loss-of-heterozygosity using paired genotype microarray data.
• 
  Christy M. Bogard, Eric C. Rouchka, Benjamin Arazi:
  Random number generation for DNA-based security circuitry.
• 
  Mariofanna G. Milanova:
  Model of visual attention for video sequences.
• 
  Julie B. Schuck, Michael E. Smith, Xiaohong Li, Nigel G. F. Cooper:
  Microarray analysis of gene expression during auditory hair cell regeneration in zebrafish (Danio rerio).
• 
  Dorothy N. Kakoola, Nataliya Lenchik, Anita Curcio-Brint, Ivan Gerling:
  Analysis of the transcriptome of CD4 T-Lymphocytes from young Non-Obese Diabetic (NOD) mice suggests a key role for cytokines and apoptosis.
• 
  Jim Lund:
  Identifying regulatory elements and gene boundaries with comparative genomic sequence analysis.
• 
  Jonathan Quiton, Claire Rinehart, Joseph Chavarria-Smith, Nancy Rice:
  Gene classification for microarray data with multiple time measurements.
• 
  Shesh N. Rai, Stanley Pounds:
  Robust detection method for differential expression studies.
• 
  Mohammed Yeasin, Bhanu Vanteru, Jahangheer S. Shaik, Faruk Ahmed:
  i-SEGOPubmed: a web interface for semantic enabled browsing of PubMed using Gene Ontology.
• 
  Erik S. Gough, Cheolhwan Oh, Jing He, Catherine P. Riley, Charles R. Buck, Xiang Zhang:
  Proteome discovery pipeline for mass spectrometry-based proteomics.
• 
  Xinnan Niu, K. Jill McAfee, Dexter T. Duncan, Michael Assink, Andrew J. Link:
  A computational and analysis tool for proteomics research.
• 
  Pongsathorn Chotikasemsri, Claire Rinehart:
  Modeling mis-folded lysozyme aggregates.
• 
  Victor X. Jin, Alina Rabinovich, Henny O'Geen, Sushma Iyengar, Peggy J. Farnham:
  De novo identification of in vivo binding sites from ChIP-chip data.
• 
  Joseph Morris, Eric C. Rouchka, David Schultz:
  Techniques for the analysis of trichome Pelagonium xhortorum expressed sequence tags.

Volume 9, Number S-8, 2008

Selected proceedings of the Fifth International Workshop on Data Integration in the Life Sciences 2008

• 
  Amos Bairoch, Sarah Cohen Boulakia, Christine Froidevaux:
  Review of the selected proceedings of the Fifth International Workshop on Data Integration in the Life Sciences 2008.
• 
  Samira Jaeger, Sylvain Gaudan, Ulf Leser, Dietrich Rebholz-Schuhmann:
  Integrating protein-protein interactions and text mining for protein function prediction.
• 
  Andrew M. Jenkinson, Mario Albrecht, Ewan Birney, Hagen Blankenburg, Thomas A. Down, Robert D. Finn, Henning Hermjakob, Tim J. P. Hubbard, Rafael C. Jiménez, Philip Jones, Andreas Kähäri, Eugene Kulesha, José R. Macías, Gabrielle A. Reeves, Andreas Prlic:
  Integrating biological data - the Distributed Annotation System.

Volume 9, Number S-9, 2008

Proceedings of the Fifth Annual MCBIOS Conference. Systems Biology: Bridging the Omics

• 
  Jonathan D. Wren, Dawn Wilkins, James C. Fuscoe, Susan Bridges, Stephen Winters-Hilt, Yuriy Gusev:
  Proceedings of the 2008 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference.
• 
  Ronald L. Frank, Cyriac Kandoth, Fikret Erçal:
  Validation of an NSP-based (negative selection pattern) gene family identification strategy.
• 
  Vinayak Kulkarni, Mounir Errami, Robert Barber, Harold R. Garner:
  Exhaustive prediction of disease susceptibility to coding base changes in the human genome.
• 
  Mikhail G. Dozmorov, Kimberly D. Kyker, Paul J. Hauser, Ricardo Saban, David D. Buethe, Igor Dozmorov, Michael Centola, Daniel J. Culkin, Robert E. Hurst:
  From microarray to biology: an integrated experimental, statistical and in silico analysis of how the extracellular matrix modulates the phenotype of cancer cells.
• 
  Tianxiao Huan, Andrey Y. Sivachenko, Scott H. Harrison, Jake Yue Chen:
  ProteoLens: a visual analytic tool for multi-scale database-driven biological network data mining.
• 
  Daniel Quest, Kathryn Dempsey, Mohammad Shafiullah, Dhundy Bastola, Hesham H. Ali:
  MTAP: The Motif Tool Assessment Platform.
• 
  Arun Rawat, Georg J. Seifert, Youping Deng:
  Novel implementation of conditional co-regulation by graph theory to derive co-expressed genes from microarray data.
• 
  Andrey A. Ptitsyn, Michael M. Weil, Douglas H. Thamm:
  Systems biology approach to identification of biomarkers for metastatic progression in cancer.
• 
  Zhenqiang Su, Huixiao Hong, Hong Fang, Leming M. Shi, Roger Perkins, Weida Tong:
  Very Important Pool (VIP) genes - an application for microarray-based molecular signatures.
• 
  Leming M. Shi, Wendell D. Jones, Roderick V. Jensen, Stephen C. Harris, Roger Perkins, Federico M. Goodsaid, Lei Guo, Lisa J. Croner, Cecilie Boysen, Hong Fang, Feng Qian, Shashi Amur, Wenjun Bao, Catalin C. Barbacioru, Vincent Bertholet, Xiaoxi Megan Cao, Tzu-Ming Chu, Patrick J. Collins, Xiao-hui Fan, Felix W. Frueh:
  The balance of reproducibility, sensitivity, and specificity of lists of differentially expressed genes in microarray studies.
• 
  Cory B. Giles, Jonathan D. Wren:
  Large-scale directional relationship extraction and resolution.
• 
  Brian Roux, Stephen Winters-Hilt:
  Hybrid MM/SVM structural sensors for stochastic sequential data.
• 
  Alexander G. Churbanov, Stephen Winters-Hilt:
  Clustering ionic flow blockade toggles with a Mixture of HMMs.
• 
  Jerzy S. Zielinski, Nidhal Bouaynaya, Dan Schonfeld, William D. O'Neill:
  Time-dependent ARMA modeling of genomic sequences.
• 
  Minho Chae, Robert J. Shmookler Reis, John J. Thaden:
  An iterative block-shifting approach to retention time alignment that preserves the shape and area of gas chromatography-mass spectrometry peaks.
• 
  Christopher A. Bottoms, Dong Xu:
  Wanted: unique names for unique atom positions. PDB-wide analysis of diastereotopic atom names of small molecules containing diphosphate.
• 
  Huixiao Hong, Zhenqiang Su, Weigong Ge, Leming M. Shi, Roger Perkins, Hong Fang, Joshua Xu, James J. Chen, Tao Han, Jim Kaput, James C. Fuscoe, Weida Tong:
  Assessing batch effects of genotype calling algorithm BRLMM for the Affymetrix GeneChip Human Mapping 500 K array set using 270 HapMap samples.
• 
  Andrey A. Ptitsyn:
  Comprehensive analysis of circadian periodic pattern in plant transcriptome.
• 
  Mutlu Mete, Fusheng Tang, Xiaowei Xu, Nurcan Yuruk:
  A structural approach for finding functional modules from large biological networks.
• 
  Taewon Lee, Varsha G. Desai, Cruz Velasco, Robert J. S. Reis, Robert R. Delongchamp:
  Testing for treatment effects on gene ontology.

Volume 9, Number S-10, 2008

Highlights from the Fourth International Society for Computational Biology (ISCB) Student Council Symposium

• 
  Lucia Peixoto, Nils Gehlenborg, Sarath Chandra Janga:
  Highlights from the Fourth International Society for Computational Biology Student Council Symposium at the Sixteenth Annual International Conference on Intelligent Systems for Molecular Biology.
• 
  Young-Rae Cho, Lei Shi, Aidong Zhang:
  Functional module detection by functional flow pattern mining in protein interaction networks.
• 
  Sebastian Pechmann, Emmanuel D. Levy, Gian Gaetano Tartaglia, Michele Vendruscolo:
  Competition between protein aggregation and protein complex formation.
• 
  Preti Jain, Gopi K. Podila, Maria R. Davis:
  Comparative analysis of non-classically secreted proteins in Botrytis cinerea and symbiotic fungus Laccaria bicolor.
• 
  Surya Saha, Susan Bridges, Zenaida Magbanua, Daniel G. Peterson:
  Discovering relationships among dispersed repeats using spatial association rule mining.
• 
  David Ruau, Corinna Kolárik, Heinz-Theodor Mevissen, Emmanuel Müller, Ira Assent, Ralph Krieger, Thomas Seidl, Martin Hofmann-Apitius, Martin Zenke:
  Public microarray repository semantic annotation with ontologies employing text mining and expression profile correlation.
• 
  Phil Hyoun Lee, Hagit Shatkay:
  Ranking single nucleotide polymorphisms by potential deleterious effects.
• 
  Fabio De Bona, Stephan Ossowski, Korbinian Schneeberger, Gunnar Rätsch:
  Optimal spliced alignments of short sequence reads.
• 
  Regina Bohnert, Georg Zeller, Richard M. Clark, Kevin L. Childs, Victor Jun M. Ulat, Renee Stokowski, Dennis Ballinger, Kelly Frazer, David Cox, Richard M. Bruskiewich, C. Robin Buell, Jan Leach, Hei Leung, Kenneth L. McNally, Detlef Weigel, Gunnar Rätsch:
  Revealing sequence variation patterns in rice with machine learning methods.
• 
  Magali Michaut, Samuel Kerrien, Luisa Montecchi-Palazzi, Corinne Cassier-Chauvat, Franck Chauvat, Jean-Christophe Aude, Pierre Legrain, Henning Hermjakob:
  InteroPORC: an automated tool to predict highly conserved protein interaction networks.
• 
  Danny A. Bitton, Michal J. Okoniewski, Yvonne Connolly, Crispin J. Miller:
  Exon level integration of proteomics and microarray data.
• 
  Anne-Laure Abraham, Joël Pothier, Eduardo P. C. Rocha:
  Protein evolution driven by symmetric structural repeats.
• 
  Tobias Rausch, Anne-Katrin Emde, Knut Reinert:
  Robust consensus computation.
• 
  Bridget Chukualim, Nick Peters, Christiane Hertz-Fowler, Matthew Berriman:
  TrypanoCyc - a metabolic pathway database for Trypanosoma brucei.
• 
  Lixia Yao, Andrey Rzhetsky:
  Quantitative systems-level determinants of drug targets.

Volume 9, Number S-11, 2008

Proceedings of the BioNLP 08 ACL Workshop: Themes in biomedical language processing

• 
  Dina Demner-Fushman, Sophia Ananiadou, K. Bretonnel Cohen, John Pestian, Jun'ichi Tsujii, Bonnie L. Webber:
  Themes in biomedical natural language processing: BioNLP08.
• 
  Antti Airola, Sampo Pyysalo, Jari Björne, Tapio Pahikkala, Filip Ginter, Tapio Salakoski:
  All-paths graph kernel for protein-protein interaction extraction with evaluation of cross-corpus learning.
• 
  Angus Roberts, Robert J. Gaizauskas, Mark Hepple, Yikun Guo:
  Mining clinical relationships from patient narratives.
• 
  Peter T. Corbett, Ann A. Copestake:
  Cascaded classifiers for confidence-based chemical named entity recognition.
• 
  Yutaka Sasaki, Yoshimasa Tsuruoka, John McNaught, Sophia Ananiadou:
  How to make the most of NE dictionaries in statistical NER.
• 
  Xinglong Wang, Michael Matthews:
  Distinguishing the species of biomedical named entities for term identification.
• 
  Mark Stevenson, Yikun Guo, Robert J. Gaizauskas, David Martínez:
  Disambiguation of biomedical text using diverse sources of information.
• 
  Yoshimasa Tsuruoka, Jun'ichi Tsujii, Sophia Ananiadou:
  Accelerating the annotation of sparse named entities by dynamic sentence selection.
• 
  Veronika Vincze, György Szarvas, Richárd Farkas, György Móra, János Csirik:
  The BioScope corpus: biomedical texts annotated for uncertainty, negation and their scopes.
• 
  Halil Kilicoglu, Sabine Bergler:
  Recognizing speculative language in biomedical research articles: a linguistically motivated perspective.
• 
  Aurélie Névéol, Sonya E. Shooshan, Vincent Claveau:
  Automatic inference of indexing rules for MEDLINE.

Volume 9, Number S-12, 2008

Seventh International Conference on Bioinformatics (InCoB2008)

• 
  Shoba Ranganathan, Wen-Lian Hsu, Ueng-Cheng Yang, Tin Wee Tan:
  Emerging strengths in Asia Pacific bioinformatics.
• 
  Darby Tien-Hao Chang, Chih-Ching Wang, Jian-Wei Chen:
  Using a kernel density estimation based classifier to predict species-specific microRNA precursors.
• 
  Wing-Sze Leung, Marie C. M. Lin, David Wai-Lok Cheung, Siu-Ming Yiu:
  Filtering of false positive microRNA candidates by a clustering-based approach.
• 
  Yuchen Yang, Yu-Ping Wang, Kuo-Bin Li:
  MiRTif: a support vector machine-based microRNA target interaction filter.
• 
  Dang Hung Tran, Kenji Satou, Tu Bao Ho:
  Finding microRNA regulatory modules in human genome using rule induction.
• 
  Cheng-Wei Cheng, Emily Chia-Yu Su, Jenn-Kang Hwang, Ting-Yi Sung, Wen-Lian Hsu:
  Predicting RNA-binding sites of proteins using support vector machines and evolutionary information.
• 
  Chung-Chin Lu, Wei-Hao Yuan, Te-Ming Chen:
  Extracting transcription factor binding sites from unaligned gene sequences with statistical models.
• 
  A. K. M. A. Baten, Saman K. Halgamuge, Bill C. H. Chang:
  Fast splice site detection using information content and feature reduction.
• 
  Chumpol Ngamphiw, Supasak Kulawonganunchai, Anunchai Assawamakin, Ekachai Jenwitheesuk, Sissades Tongsima:
  VarDetect: a nucleotide sequence variation exploratory tool.
• 
  Chuan-Kun Liu, Yan-Hau Chen, Cheng-Yang Louis Tang, Shu-Chuan Chang, Yi-Jung Lin, Ming-Fang Tsai, Yuan-Tsong Chen, Adam Yao:
  Functional analysis of novel SNPs and mutations in human and mouse genomes.
• 
  Sheng-An Lee, Chen-hsiung Chan, Chi-Hung Tsai, Jin-Mei Lai, Feng-Sheng Wang, Cheng-Yan Kao, Chi-Ying F. Huang:
  Ortholog-based protein-protein interaction prediction and its application to inter-species interactions.
• 
  Darby Tien-Hao Chang, Hsuan-Yu Huang, Yu-Tang Syu, Chih-Peng Wu:
  Real value prediction of protein solvent accessibility using enhanced PSSM features.
• 
  Yong Seok Lee, Tae-Hyung Kim, Tae-Wook Kang, Won-Hyong Chung, Gwang-Sik Shin:
  WSPMaker: a web tool for calculating selection pressure in proteins and domains using window-sliding.
• 
  Uthaman Gowthaman, Mannu Jayakanthan, Durai Sundar:
  Molecular docking studies of dithionitrobenzoic acid and its related compounds to protein disulfide isomerase: computational screening of inhibitors to HIV-1 entry.
• 
  Khar Heng Choo, Shoba Ranganathan:
  Flanking signal and mature peptide residues influence signal peptide cleavage.
• 
  Yumi Mizuno, Igor Kurochkin, Marlis Herberth, Yasushi Okazaki, Christian Schönbach:
  Predicted mouse peroxisome-targeted proteins and their actual subcellular locations.
• 
  Wu Hsiung Wu, Feng Sheng Wang, Maw-Shang Chang:
  Dynamic sensitivity analysis of biological systems.
• 
  Richard Tzong-Han Tsai, Hong-Jie Dai, Chi-Hsin Huang, Wen-Lian Hsu:
  Semi-automatic conversion of BioProp semantic annotation to PASBio annotation.
• 
  Jin Ok Yang, Sohyun Hwang, Jeongsu Oh, Jong Bhak, Tae-Kwon Sohn:
  An integrated database-pipeline system for studying single nucleotide polymorphisms and diseases.
• 
  Xiaojing Wang, Di Wu, Siyuan Zheng, Jing Sun, Lin Tao, Yixue Li, Zhi-Wei Cao:
  Ab-origin: an enhanced tool to identify the sourcing gene segments in germline for rearranged antibodies.
• 
  Shen Jean Lim, Joo Chuan Tong, Fook Tim Chew, Martti T. Tammi:
  The value of position-specific scoring matrices for assessment of protein allegenicity.
• 
  Honghuang Lin, Guanglan Zhang, Songsak Tongchusak, Ellis L. Reinherz, Vladimir Brusic:
  Evaluation of MHC-II peptide binding prediction servers: applications for vaccine research.
• 
  Pei-Chun Hsu, Ueng-Cheng Yang, Kuan-Hui Shih, Chih-Min Liu, Yu-Li Liu, Hai-Gwo Hwu:
  A protein interaction based model for schizophrenia study.
• 
  Jeongheui Lim, Jong Bhak, Hee-Mock Oh, Chang-Bae Kim, Yong-Ha Park, Woon Kee Paek:
  An Integrated Korean Biodiversity and Genetic Information Retrieval System.
• 
  Jitendra Gaikwad, Varun Khanna, Subramanyam Vemulpad, Joanne Jamie, Jim Kohen, Shoba Ranganathan:
  CMKb: a web-based prototype for integrating Australian Aboriginal customary medicinal plant knowledge.