BMC Bioinformatics, Volume 10 - Supplements

Volume 10, Number S-1, 2009

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

• 
  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

• 
  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

• 
  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

• 
  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.
• 
  Francesco Rubino, Marcella Attimonelli:
  RegExpBlasting (REB), a Regular Expression Blasting algorithm based on multiply aligned sequences.
• 
  Endre Sebestyén, Tibor Nagy, Sándor Suhai, Endre Barta:
  DoOPSearch: a web-based tool for finding and analysing common conserved motifs in the promoter regions of different chordate and plant genes.
• 
  Sandra P. Calderon-Copete, George Wigger, Christof Wunderlin, Tobias Schmidheini, Joachim Frey, Michael A. Quail, Laurent Falquet:
  The Mycoplasma conjunctivae genome sequencing, annotation and analysis.
• 
  Zhe Li, He Zhang, Song Ge, Xiaocheng Gu, Ge Gao, Jingchu Luo:
  Expression pattern divergence of duplicated genes in rice.
• 
  María José Nueda, Patricia Sebastián, Sonia Tarazona, Francisco García-García, Joaquín Dopazo, Alberto Ferrer, Ana Conesa:
  Functional assessment of time course microarray data.
• 
  Ernesto Picardi, Flavio Mignone, Graziano Pesole:
  EasyCluster: a fast and efficient gene-oriented clustering tool for large-scale transcriptome data.
• 
  Charalampos N. Moschopoulos, Georgios A. Pavlopoulos, Reinhard Schneider, Spiridon D. Likothanassis, Sophia Kossida:
  GIBA: a clustering tool for detecting protein complexes.
• 
  Dimosthenis Tsagkrasoulis, Panagiotis Zerefos, George Loudos, Antonia Vlahou, Marc Baumann, Sophia Kossida:
  'Brukin2D': a 2D visualization and comparison tool for LC-MS data.
• 
  Helena Strömbergsson, Gerard J. Kleywegt:
  A chemogenomics view on protein-ligand spaces.
• 
  Gregory A. C. Singer, Mehrdad Hajibabaei:
  iBarcode.org: web-based molecular biodiversity analysis.
• 
  Monica Santamaria, Saverio Vicario, Graziano Pappadà, Gaetano Scioscia, Claudio Scazzocchio, Cecilia Saccone:
  Towards barcode markers in Fungi: an intron map of Ascomycota mitochondria.
• 
  Ziomara P. Gerdtzen, J. Cristian Salgado, Axel Osses, Juan A. Asenjo, Ivan Rapaport, Barbara A. Andrews:
  Modeling heterocyst pattern formation in cyanobacteria.
• 
  Franck Picard, Vincent Miele, Jean-Jacques Daudin, Ludovic Cottret, Stéphane Robin:
  Deciphering the connectivity structure of biological networks using MixNet.
• 
  Alvaro Martinez Barrio, Erik Lagercrantz, Göran O. Sperber, Jonas Blomberg, Erik Bongcam-Rudloff:
  Annotation and visualization of endogenous retroviral sequences using the Distributed Annotation System (DAS) and eBioX.
• 
  Steve Pettifer, David Thorne, Philip McDermott, James Marsh, Alice Villéger, Douglas B. Kell, Teresa K. Attwood:
  Visualising biological data: a semantic approach to tool and database integration.
• 
  Maria G. Roubelakis, Pantelis Zotos, Georgios Papachristoudis, Ioannis Michalopoulos, Kalliopi I. Pappa, Nicholas P. Anagnou, Sophia Kossida:
  Human microRNA target analysis and gene ontology clustering by GOmir, a novel stand-alone application.
• 
  Roberto Barbera, Giacinto Donvito, Alberto Falzone, Giuseppe La Rocca, Luciano Milanesi, Giorgio Pietro Maggi, Saverio Vicario:
  The GENIUS Grid Portal and robot certificates: a new tool for e-Science.
• 
  Giovanni Minervini, Giuseppe Evangelista, Laura Villanova, Debora Slanzi, Davide De Lucrezia, Irene Poli, Pier Luigi Luisi, Fabio Polticelli:
  Massive non-natural proteins structure prediction using grid technologies.
• 
  Marcello Castellano, Giuseppe Mastronardi, Roberto Bellotti, Gianfranco Tarricone:
  A bioinformatics knowledge discovery in text application for grid computing.
• 
  Vincenzo Lagani, Alberto Montesanto, Fausta Di Cianni, Víctor Moreno, Stefano Landi, Domenico Conforti, Giuseppina Rose, Giuseppe Passarino:
  A novel similarity-measure for the analysis of genetic data in complex phenotypes.
• 
  Antonio Turi, Corrado Loglisci, Eliana Salvemini, Giorgio Grillo, Donato Malerba, Domenica D'Elia:
  Computational annotation of UTR cis-regulatory modules through Frequent Pattern Mining.

Volume 10, Number S-7, 2009

UT-ORNL-KBRIN Bioinformatics Summit 2009

• 
  Bing Wang, Steve Valentine, Sriram Raghuraman, Manolo Plasencia, Xiang Zhang:
  Prediction of peptide drift time in ion mobility-mass spectrometry.
• 
  Nishchal K. Verma, Pooja Agrawal, Yan Cui:
  Fuzzy rule based unsupervised approach for gene saliency.
• 
  Sungbo Jung:
  Parallelized pairwise sequence alignment using CUDA on multiple GPUs.
• 
  Elissaveta G. Arnaoudova, Philip J. Bowens, Roger G. Chui, Randy D. Dinkins, Uljana Hesse, Jerzy W. Jaromczyk, Mitchell Martin, Paul Maynard, Neil Moore, Christopher L. Schardl:
  Visualizing and sharing results in bioinformatics projects: GBrowse and GenBank exports.
• 
  Sujoy Roy, Lijing Xu, Ramin Homayouni:
  LSI based framework to predict gene regulatory information.
• 
  Mohammed Yeasin, Haritha Malempati, Ramin Homayouni, Mohammad S. Sorower:
  A systematic study on latent semantic analysis model parameters for mining biomedical literature.
• 
  Ramy K. Aziz, Leslie Klis McNeil:
  Reconstructing the virulome of the human pathogen Streptococcus pyogenes using NMPDR subsystems-based annotation.
• 
  Heba M. Amin, Abdel-Gawad M. Hashem, Ramy K. Aziz:
  Bioinformatics determination of ETEC signature genes as potential targets for molecular diagnosis and reverse vaccinology.
• 
  Julia Krushkal, Yanhua Qu, Peter Brown, Sreedhar Sontineni, Toshiyuki Ueki, Katy Juarez, Ching Leang, Enrique Merino, Jeanette Peeples, Jose F. Barbe, Ronald M. Adkins, Derek R. Lovley:
  Bioinformatic analysis of gene regulation in Geobacter sulfurreducens.
• 
  ReddySailaja Marpuri, Claire A. Rinehart:
  Comparison of annotation terms between automated and curated E. coli K12 databases.
• 
  Teeradache Viangteeravat, Ian M. Brooks, Somchan Vuthipadadon, Eunice Y. Huang, Ebony Smith, Ramin Homayouni, Chanchai McDonald:
  Slim-Prim: an integrated data system for clinical and translational research.
• 
  Julie B. Schuck, Chia-Hui Lin, William T. Penberthy, Xiaohong Li, Nigel G. F. Cooper, Michael E. Smith:
  Microarray analysis and quantitative real-time PCR validation of gene expression during auditory hair cell regeneration in zebrafish (Danio rerio).
• 
  Ronald M. Adkins, Julia Krushkal, Grant Somes, John Fain, John Morrison, Chad Klauser, Everett F. Magann:
  Extensive parent-of-origin genetic effects on fetal growth.
• 
  Sirshendu Majumdar, I. Maria Johnson, Gipsy Majumdar, William J. Valentine, Rajendra Raghow:
  Molecular dissection of cardiac hypertrophy induced by interleukin-18.
• 
  Dorothy N. Kakoola, Nataliya Lenchik, Anita Curcio-Brint, Ivan Gerling:
  Transcriptional profiling of CD4 T-lymphocytes reveals abnormal gene expression in young prediabetic NOD mice.
• 
  Antony T. Athippozhy, Liping Huang, Tianyong Zhao, Clavia Ruth Wooton-Kee, Paiboon Jungsuwadee, Arnold J. Stromberg, Mary Vore:
  Utilizing a mixed model approach to compare the lactating rat transcriptome against age-matched control virgins.
• 
  Vinhthuy Phan:
  Motif Tool Manager: a web-based platform for motif discovery.
• 
  Jarret Glasscock, Ryan Richt, Matthew T. Hickenbotham:
  Flipping NextGen: using biological systems to characterize NextGen sequencing technologies.
• 
  Eric C. Rouchka, Julia Krushkal:
  Proceedings of the Eighth Annual UT-ORNL-KBRIN Bioinformatics Summit 2009.

Volume 10, Number S-8, 2009

Proceedings of the European Conference on Computational Biology (ECCB) 2008 Workshop: Annotations, interpretation and management of mutations (AIMM)

• 
  Christopher J. O. Baker, Dietrich Rebholz-Schuhmann:
  Between proteins and phenotypes: annotation and interpretation of mutations. 0
• 
  Martin Krallinger, José M. G. Izarzugaza, Carlos Rodríguez Penagos, Alfonso Valencia:
  Extraction of human kinase mutations from literature, databases and genotyping studies. 1
• 
  Süveyda Yeniterzi, Osman Ugur Sezerman:
  EnzyMiner: automatic identification of protein level mutations and their impact on target enzymes from PubMed abstracts. 2
• 
  Rainer Winnenburg, Conrad Plake, Michael Schroeder:
  Improved mutation tagging with gene identifiers applied to membrane protein stability prediction. 3
• 
  Kevin Nagel, Antonio Jimeno-Yepes, Dietrich Rebholz-Schuhmann:
  Annotation of protein residues based on a literature analysis: cross-validation against UniProtKb. 4
• 
  José M. G. Izarzugaza, Anja Baresic, Lisa E. M. McMillan, Corin Yeats, Andrew B. Clegg, Christine A. Orengo, Andrew C. R. Martin, Alfonso Valencia:
  An integrated approach to the interpretation of Single Amino Acid Polymorphisms within the framework of CATH and Gene3D. 5
• 
  Anna Bauer-Mehren, Laura Inés Furlong, Michael Rautschka, Ferran Sanz:
  From SNPs to pathways: integration of functional effect of sequence variations on models of cell signalling pathways. 6
• 
  Anshu Bhardwaj, Mitali Mukerji, Shipra Sharma, Jinny Paul, Chaitanya S. Gokhale, Achal K. Srivastava, Shrish Tiwari:
  MtSNPscore: a combined evidence approach for assessing cumulative impact of mitochondrial variations in disease. 7
• 
  Yana Bromberg, Burkhard Rost:
  Correlating protein function and stability through the analysis of single amino acid substitutions. 8
• 
  Joke Reumers, Joost Schymkowitz, Frederic Rousseau:
  Using structural bioinformatics to investigate the impact of non synonymous SNPs and disease mutations: scope and limitations. 9
• 
  Omar Haq, Ronald M. Levy, Alexandre V. Morozov, Michael Andrec:
  Pairwise and higher-order correlations among drug-resistance mutations in HIV-1 subtype B protease. 10

Volume 10, Number S-9, 2009

Proceedings of the 2009 AMIA Summit on Translational Bioinformatics

• 
  Yves A. Lussier, Indra Neil Sarkar:
  Selected proceedings of the 2009 Summit on Translational Bioinformatics. 0
• 
  Hsun-Hsien Chang, Marco Ramoni:
  Transcriptional network classifiers. 1
• 
  Eunjung Lee, Hyunchul Jung, Predrag Radivojac, Jong-Won Kim, Doheon Lee:
  Analysis of AML genes in dysregulated molecular networks. 2
• 
  Suresh K. Bhavnani, Felix Eichinger, Sebastian Martini, Paul Saxman, H. V. Jagadish, Matthias Kretzler:
  Network analysis of genes regulated in renal diseases: implications for a molecular-based classification. 3
• 
  Adam D. Grossman, Mitchell J. Cohen, Geoffrey T. Manley, Atul J. Butte:
  Infection in the intensive care unit alters physiological networks. 4
• 
  Angela K. Dean, Stephen E. Harris, Ivo Kalajzic, Jianhua Ruan:
  A systems biology approach to the identification and analysis of transcriptional regulatory networks in osteocytes. 5
• 
  Xinan Yang, Yong Huang, James L. Chen, Jianming Xie, Xiao Sun, Yves A. Lussier:
  Mechanism-anchored profiling derived from epigenetic networks predicts outcome in acute lymphoblastic leukemia. 6
• 
  Angel Janevski, Sitharthan Kamalakaran, Nilanjana Banerjee, Vinay Varadan, Nevenka Dimitrova:
  PAPAyA: a platform for breast cancer biomarker signature discovery, evaluation and assessment. 7
• 
  Casey Lynnette Overby, Peter Tarczy-Hornoch, Dina Demner-Fushman:
  The potential for automated question answering in the context of genomic medicine: an assessment of existing resources and properties of answers. 8
• 
  Erik Pitzer, Ronilda Lacson, Christian Hinske, Jihoon Kim, Pedro A. F. Galante, Lucila Ohno-Machado:
  Towards large-scale sample annotation in gene expression repositories. 9
• 
  Ronilda Lacson, Erik Pitzer, Christian Hinske, Pedro A. F. Galante, Lucila Ohno-Machado:
  Evaluation of a large-scale biomedical data annotation initiative. 10
• 
  Terry H. Shen, Christopher S. Carlson, Peter Tarczy-Hornoch:
  Evaluating the accuracy of a functional SNP annotation system. 11
• 
  Brett R. South, Shuying Shen, Makoto Jones, Jennifer H. Garvin, Matthew H. Samore, Wendy Webber Chapman, Adi V. Gundlapalli:
  Developing a manually annotated clinical document corpus to identify phenotypic information for inflammatory bowel disease. 12
• 
  Xiaoyan Wang, George Hripcsak, Carol Friedman:
  Characterizing environmental and phenotypic associations using information theory and electronic health records. 13
• 
  Nigam H. Shah, Nipun Bhatia, Clément Jonquet, Daniel L. Rubin, Annie P. Chiang, Mark A. Musen:
  Comparison of concept recognizers for building the Open Biomedical Annotator. 14
• 
  Bo Jin, Alvin Strasburger, Steven J. Laken, F. Andrew Kozel, Kevin A. Johnson, Mark S. George, Xinghua Lu:
  Feature selection for fMRI-based deception detection. 15
• 
  Jonathan L. Lustgarten, Shyam Visweswaran, Robert P. Bowser, William R. Hogan, Vanathi Gopalakrishnan:
  Knowledge-based variable selection for learning rules from proteomic data. 16
• 
  Pavithra Shivakumar, Michael Krauthammer:
  Structural similarity assessment for drug sensitivity prediction in cancer. 17

Volume 10, Number S-10, 2009

Semantic Web Applications and Tools for Life Sciences, 2008

• 
  Albert Burger, Paolo Romano, Adrian Paschke, Andrea Splendiani:
  Semantic Web Applications and Tools for Life Sciences, 2008 - Introduction. 1
• 
  Jamie P. McCusker, Joshua A. Phillips, Alejandra N. González-Beltrán, Anthony Finkelstein, Michael Krauthammer:
  Semantic web data warehousing for caGrid. 2
• 
  Nadia Anwar, Ela Hunt:
  Francisella tularensis novicida proteomic and transcriptomic data integration and annotation based on semantic web technologies. 3
• 
  Antonio Jimeno-Yepes, Ernesto Jiménez-Ruiz, Rafael Berlanga Llavori, Dietrich Rebholz-Schuhmann:
  Reuse of terminological resources for efficient ontological engineering in Life Sciences. 4
• 
  María del Mar Roldán García, Ismael Navas-Delgado, Amine Kerzazi, Othmane Chniber, Joaquin J. Molina-Castro, José Francisco Aldana Montes:
  KA-SB: from data integration to large scale reasoning. 5
• 
  George Zheng, Athman Bouguettaya:
  Service-based analysis of biological pathways. 6
• 
  Heiko Dietze, Michael Schroeder:
  GoWeb: a semantic search engine for the life science web. 7
• 
  Anna-Lena Lamprecht, Tiziana Margaria, Bernhard Steffen:
  Bio-jETI: a framework for semantics-based service composition. 8
• 
  Marco Roos, M. Scott Marshall, Andrew P. Gibson, Martijn J. Schuemie, Edgar Meij, Sophia Katrenko, Willem Robert van Hage, Konstantinos Krommydas, Pieter W. Adriaans:
  Structuring and extracting knowledge for the support of hypothesis generation in molecular biology. 9
• 
  Kei-Hoi Cheung, H. Robert Frost, M. Scott Marshall, Eric Prud'hommeaux, Matthias Samwald, Jun Zhao, Adrian Paschke:
  A journey to Semantic Web query federation in the life sciences. 10
• 
  Erick Antezana, Ward Blondé, Mikel Egaña, Alistair Rutherford, Robert Stevens, Bernard De Baets, Vladimir Mironov, Martin Kuiper:
  BioGateway: a semantic systems biology tool for the life sciences. 11
• 
  Karen Sutherland, Kenneth McLeod, Gus Ferguson, Albert Burger:
  Knowledge-driven enhancements for task composition in bioinformatics. 12
• 
  José Antonio Miñarro-Giménez, Marisa Madrid, Jesualdo Tomás Fernández-Breis:
  OGO: an ontological approach for integrating knowledge about orthology. 13
• 
  Helen Oliver, Gayo Diallo, Ed de Quincey, Dimitra Alexopoulou, Bianca Habermann, Patty Kostkova, Michael Schroeder, Simon Jupp, Khaled Khelif, Robert Stevens, Gawesh Jawaheer, Gemma Madle:
  A user-centred evaluation framework for the Sealife semantic web browsers. 14

Volume 10, Number S-11, 2009

Proceedings of the Sixth Annual MCBIOS Conference. Transformational Bioinformatics: Delivering Value from Genomes

• 
  Jonathan D. Wren, Yuriy Gusev, Raphael D. Isokpehi, Daniel Berleant, Ulisses M. Braga-Neto, Dawn Wilkins, Susan Bridges:
  Proceedings of the 2009 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference. 1
• 
  Teresia J. Buza, Ranjit Kumar, Cathy R. Gresham, Shane C. Burgess, Fiona M. McCarthy:
  Facilitating functional annotation of chicken microarray data. 2
• 
  Zhanyou Xu, Dandan Zhang, Jun Hu, Xin Zhou, Xia Ye, Kristen L. Reichel, Nathan R. Stewart, Ryan D. Syrenne, Xiaohan Yang, Peng Gao, Weibing Shi, Crissa Doeppke, Robert W. Sykes, Jason N. Burris, Joseph J. Bozell, (Max) Zong-Ming Cheng, Douglas G. Hayes, Nicole Labbe, Mark Davis, C. Neal Stewart Jr., Joshua S. Yuan:
  Comparative genome analysis of lignin biosynthesis gene families across the plant kingdom. 3
• 
  Andy D. Perkins, Michael A. Langston:
  Threshold selection in gene co-expression networks using spectral graph theory techniques. 4
• 
  Sudhir R. Chowbina, Xiaogang Wu, Fan Zhang, Peter M. Li, Ragini Pandey, Harini N. Kasamsetty, Jake Y. Chen:
  HPD: an online integrated human pathway database enabling systems biology studies. 5
• 
  Andrey A. Ptitsyn:
  Computational analysis of gene expression space associated with metastatic cancer. 6
• 
  T. J. Jankun-Kelly, Andrew D. Lindeman, Susan M. Bridges:
  Exploratory visual analysis of conserved domains on multiple sequence alignments. 7
• 
  Lauren A. Bright, Shane C. Burgess, Bhanu Chowdhary, Cyprianna E. Swiderski, Fiona M. McCarthy:
  Structural and functional-annotation of an equine whole genome oligoarray. 8
• 
  Bart H. J. van den Berg, Chamali Thanthiriwatte, Prashanti Manda, Susan M. Bridges:
  Comparing gene annotation enrichment tools for functional modeling of agricultural microarray data. 9
• 
  Amin Zollanvari, Mary Jane Cunningham, Ulisses M. Braga-Neto, Edward R. Dougherty:
  Analysis and modeling of time-course gene-expression profiles from nanomaterial-exposed primary human epidermal keratinocytes. 10
• 
  Natàlia Garcia-Reyero, Ira R. Adelman, Dalma Martinovic, Li Liu, Nancy D. Denslow:
  Site-specific impacts on gene expression and behavior in fathead minnows (Pimephales promelas) exposed in situ to streams adjacent to sewage treatment plants. 11
• 
  Zhiguang Li, Zhenqiang Su, Zhining Wen, Leming M. Shi, Tao Chen:
  Microarray platform consistency is revealed by biologically functional analysis of gene expression profiles. 12
• 
  Mutlu Mete, Leah Hennings, Horace J. Spencer III, Umit Topaloglu:
  Automatic identification of angiogenesis in double stained images of liver tissue. 13
• 
  Shweta S. Chavan, Michael A. Bauer, Marco Scutari, Radhakrishnan Nagarajan:
  NATbox: a network analysis toolbox in R. 14
• 
  Bernard Chen, Matthew Johnson:
  Protein local 3D structure prediction by Super Granule Support Vector Machines (Super GSVM). 15
• 
  Xin Zhou, Zhen Su, R. Douglas Sammons, Yanhui Peng, Patrick J. Tranel, C. Neal Stewart Jr., Joshua S. Yuan:
  Novel software package for cross-platform transcriptome analysis (CPTRA). 16
• 
  Ken Pendarvis, Ranjit Kumar, Shane C. Burgess, Bindu Nanduri:
  An automated proteomic data analysis workflow for mass spectrometry. 17
• 
  Lifeng Zhang, Daniel Berleant, Jing Ding, Tuan Cao, Eve Syrkin Wurtele:
  PathBinder - text empirics and automatic extraction of biomolecular interactions. 18
• 
  Cuilan Gao, Xin Dang, Yixin Chen, Dawn Wilkins:
  Graph ranking for exploratory gene data analysis. 19
• 
  Brandon M. Malone, Andy D. Perkins, Susan M. Bridges:
  Integrating phenotype and gene expression data for predicting gene function. 20

Volume 10, Number S-12, 2009

Bioinformatics Methods for Biomedical Complex System Applications

• 
  Luciano Milanesi, Paolo Romano, Gastone C. Castellani, Daniel Remondini, Pietro Liò:
  Trends in modeling Biomedical Complex Systems. 0
• 
  Chiara Balestrieri, Lilia Alberghina, Marco Vanoni, Ferdinando Chiaradonna:
  Data recovery and integration from public databases uncovers transformation-specific transcriptional downregulation of cAMP-PKA pathway-encoding genes. 1
• 
  Ivan Merelli, Andrea Caprera, Alessandra Stella, Marcello Del Corvo, Luciano Milanesi, Barbara Lazzari:
  The Human EST Ontology Explorer: a tissue-oriented visualization system for ontologies distribution in human EST collections. 2
• 
  Federica Chiappori, Pasqualina D'Ursi, Ivan Merelli, Luciano Milanesi, Ermanna Rovida:
  In silico saturation mutagenesis and docking screening for the analysis of protein-ligand interaction: the Endothelial Protein C Receptor case study. 3
• 
  Filippo Menolascina, Domenico Bellomo, Thomas Maiwald, Vitoantonio Bevilacqua, Caterina Ciminelli, Angelo Paradiso, Stefania Tommasi:
  Developing optimal input design strategies in cancer systems biology with applications to microfluidic device engineering. 4
• 
  Angelo Nuzzo, Alberto Riva, Riccardo Bellazzi:
  Phenotypic and genotypic data integration and exploration through a web-service architecture. 5
• 
  Emanuel Schwarz, F. Markus Leweke, Sabine Bahn, Pietro Liò:
  Clinical bioinformatics for complex disorders: a schizophrenia case study. 6
• 
  Marco Mesiti, Ernesto Jiménez-Ruiz, Ismael Sanz, Rafael Berlanga Llavori, Paolo Perlasca, Giorgio Valentini, David Manset:
  XML-based approaches for the integration of heterogeneous bio-molecular data. 7
• 
  Ettore Mosca, Gloria Bertoli, Eleonora Piscitelli, Laura Vilardo, Rolland A. Reinbold, Ileana Zucchi, Luciano Milanesi:
  Identification of functionally related genes using data mining and data integration: a breast cancer case study. 8
• 
  Michele Ceccarelli, Antonio d'Acierno, Angelo M. Facchiano:
  A scale space approach for unsupervised feature selection in mass spectra classification for ovarian cancer detection. 9
• 
  Luca Corradi, Valentina Mirisola, Ivan Porro, Livia Torterolo, Marco Fato, Paolo Romano, Ulrich Pfeffer:
  Survival Online: a web-based service for the analysis of correlations between gene expression and clinical and follow-up data. 10
• 
  Alessandra Tiengo, Nicola Barbarini, Sonia Troiani, Luisa Rusconi, Paolo Magni:
  A Perl procedure for protein identification by Peptide Mass Fingerprinting. 11
• 
  Concita Cantarella, Leandra Sepe, Francesca Fioretti, Maria Carla Ferrari, Giovanni Paolella:
  Analysis and modelling of motility of cell populations with MotoCell. 12
• 
  Federico M. Stefanini, Danila Coradini, Elia Biganzoli:
  Conditional independence relations among biological markers may improve clinical decision as in the case of triple negative breast cancers. 13
• 
  Liliana Ironi, Luigi Panzeri:
  A computational framework for qualitative simulation of nonlinear dynamical models of gene-regulatory networks. 14
• 
  Matteo D'Antonio, Marco Masseroli:
  Extraction, integration and analysis of alternative splicing and protein structure distributed information. 15
• 
  Roberta Alfieri, Matteo Barberis, Ferdinando Chiaradonna, Daniela Gaglio, Luciano Milanesi, Marco Vanoni, Edda Klipp, Lilia Alberghina:
  Towards a systems biology approach to mammalian cell cycle: modeling the entrance into S phase of quiescent fibroblasts after serum stimulation. 16
• 
  Alejandro Real-Chicharro, Iván Ruiz Mostazo, Ismael Navas-Delgado, Amine Kerzazi, Othmane Chniber, Francisca Sánchez-Jiménez, Miguel Angel Medina, José Francisco Aldana Montes:
  Protopia: a protein-protein interaction tool. 17

Volume 10, Number S-13, 2009

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

• 
  Thomas Abeel, Jeroen de Ridder, Lucia Peixoto:
  Highlights from the 5^th International Society for Computational Biology Student Council Symposium at the 17^th Annual International Conference on Intelligent Systems for Molecular Biology and the 8^th European Conference on Computational Biology. 0
• 
  Sebastian J. Schultheiß, Wolfgang Busch, Jan U. Lohmann, Oliver Kohlbacher, Gunnar Rätsch:
  KIRMES: kernel-based identification of regulatory modules in euchromatic sequences. 0
• 
  Rayan Chikhi, Dominique Lavenier:
  Paired-end read length lower bounds for genome re-sequencing. 0
• 
  T. Van Du Tran, Philippe Chassignet, Jean-Marc Steyaert:
  Prediction of super-secondary structure in alpha-helical and beta-barrel transmembrane proteins. 0
• 
  Martina Koeva, E. Camilla Forsberg, Joshua M. Stuart:
  Core stemness mechanisms revealed through homology. 0
• 
  Phil Hyoun Lee, Jae-Yoon Jung, Hagit Shatkay:
  Functionally informative tag SNP selection using a pareto-optimal approach: playing the game of life. 0
• 
  Teresa Szczepinska, Krzysztof Pawlowski:
  Looking for chromosome spatial organization rules in microarray gene expression data. 0
• 
  Nils Gehlenborg, Alvis Brazma:
  Visualization of large microarray experiments with space maps. 0
• 
  José Caldas, Nils Gehlenborg, Ali Faisal, Alvis Brazma, Samuel Kaski:
  Probabilistic retrieval and visualization of biologically relevant microarray experiments. 0
• 
  Inken Wohlers, Lars Petzold, Francisco S. Domingues, Gunnar W. Klau:
  PAUL: protein structural alignment using integer linear programming and Lagrangian relaxation. 0
• 
  Nikolay Samusik, Yannis Kalaidzidis, Marino Zerial:
  A method for validation for clustering of phenotypic gene knockdown profiles using protein-protein interactions information. 0
• 
  Tom A. Williams, Brian E. Caffrey, Xiaowei Jiang, Christina Toft, Mario A. Fares:
  Phylogenomic inference of functional divergence. 0
• 
  Regina Bohnert, Jonas Behr, Gunnar Rätsch:
  Transcript quantification with RNA-Seq data. 0
• 
  Walter Pirovano, Anneke van der Reijden, K. Anton Feenstra, Jaap Heringa:
  Structure and function analysis of flexible alignment regions in proteins. 0
• 
  Tanya C. Petrossian, Steven G. Clarke:
  Computational methods to identify novel methyltransferases. 0

Volume 10, Number S-14, 2009

Biodiversity Informatics

• 
  Indra Neil Sarkar:
  Biodiversity Informatics: the emergence of a field. 1
• 
  Vishwas Chavan, Peter Ingwersen:
  Towards a data publishing framework for primary biodiversity data: challenges and potentials for the biodiversity informatics community. 2
• 
  Andrew W. Hill, Robert P. Guralnick, Paul Flemons, Reed Beaman, John Wieczorek, Ajay Ranipeta, Vishwas Chavan, David P. Remsen:
  Location, location, location: utilizing pipelines and services to more effectively georeference the world's biodiversity data. 3
• 
  Mehrdad Hajibabaei, Gregory A. C. Singer:
  Googling DNA sequences on the World Wide Web. 4
• 
  Roderic D. M. Page:
  bioGUID: resolving, discovering, and minting identifiers for biodiversity informatics. 5
• 
  Vincent S. Smith, Simon D. Rycroft, Kehan T. Harman, Ben Scott, David Roberts:
  Scratchpads: a data-publishing framework to build, share and manage information on the diversity of life. 6
• 
  Paola Bertolazzi, Giovanni Felici, Emanuel Weitschek:
  Learning to classify species with barcodes. 7
• 
  Ka Hou Chu, Minli Xu, Chi Pang Li:
  Rapid DNA barcoding analysis of large datasets using the composition vector method. 8
• 
  Pavel P. Kuksa, Vladimir Pavlovic:
  Efficient alignment-free DNA barcode analytics. 9
• 
  Frederic Austerlitz, Olivier David, Brigitte Schaeffer, Kevin Bleakley, Madalina Olteanu, Raphaël Leblois, Michel Veuille, Catherine Larédo:
  DNA barcode analysis: a comparison of phylogenetic and statistical classification methods. 10

Volume 10, Number S-15, 2009

Eighth International Conference on Bioinformatics (InCoB2009): Bioinformatics

• 
  Shoba Ranganathan:
  Towards a career in bioinformatics. 1
• 
  Khar Heng Choo, Tin Wee Tan, Shoba Ranganathan:
  A comprehensive assessment of N-terminal signal peptides prediction methods. 2
• 
  Woo-Yeon Kim, Sang-Yoon Kim, Tae-Hyung Kim, Sung-Min Ahn, Ha Na Byun, Deokhoon Kim, Dae-Soo Kim, Yong Seok Lee, Ho Ghang, Daeui Park, Byoung-Chul Kim, Chulhong Kim, Sunghoon Lee, Seong-Jin Kim, Jong Bhak:
  Gevab: a prototype genome variation analysis browsing server. 3
• 
  Merlin Veronika, James Evans, Paul Matsudaira, Roy E. Welsch, Jagath C. Rajapakse:
  Sub-population analysis based on temporal features of high content images. 4
• 
  Byungwook Lee, Doheon Lee:
  Protein comparison at the domain architecture level. 5
• 
  Shubhra Ghosh Dastidar, David P. Lane, Chandra S. Verma:
  Modulation of p53 binding to MDM2: computational studies reveal important roles of Tyr100. 6
• 
  Cheng-Ju Kuo, Maurice H. T. Ling, Kuan-Ting Lin, Chun-Nan Hsu:
  BIOADI: a machine learning approach to identifying abbreviations and definitions in biological literature. 7
• 
  Hsin-Nan Lin, Ching-Tai Chen, Ting-Yi Sung, Shinn-Ying Ho, Wen-Lian Hsu:
  Protein subcellular localization prediction of eukaryotes using a knowledge-based approach. 8
• 
  Richard Tzong-Han Tsai, Po-Ting Lai, Hong-Jie Dai, Chi-Hsin Huang, Yue-Yang Bow, Yen-Ching Chang, Wen-Harn Pan, Wen-Lian Hsu:
  HypertenGene: extracting key hypertension genes from biomedical literature with position and automatically-generated template features. 9
• 
  Varun Khanna, Shoba Ranganathan:
  Physicochemical property space distribution among human metabolites, drugs and toxins. 10
• 
  In-Hwan Paik, Jeongheui Lim, Byung-Sun Chun, Seon-Duck Jin, Jae-Pyoung Yu, Joon-Woo Lee, Jong Bhak, Woon Kee Paek:
  The Korean Bird Information System (KBIS) through open and public participation. 11
• 
  Shen Jean Lim, Asif Mohammad Khan, Mark De Silva, Kuan Siong Lim, Yongli Hu, Chay Hoon Tan, Tin Wee Tan:
  The implementation of e-learning tools to enhance undergraduate bioinformatics teaching and learning: a case study in the National University of Singapore. 12