BMC Bioinformatics, Volume 10 - Supplements

Volume 10, Number S-1, 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 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, Simin 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, Mao-zu 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, Genographic Consortium:
  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

• 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, Clement 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 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 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

• 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

• 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 Matthews, Tiffani L. Williams:
  Using tree diversity to compare phylogenetic heuristics.
  
• Cornelia Caragea, Jivko Sinapov, Drena Dobbs, Vasant 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 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

• Christopher Brewster, Simon Jupp, Joanne S. Luciano, David 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

• 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 S. 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, Victor 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

• 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, Chris 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 Brooks, Somchan Vuthipadadon, Eunice 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.