BMC Bioinformatics, Volume 7

Volume 7, 2006

• Micah Hamady, Erin Peden, Rob Knight, Ravinder Singh:
  Fast-Find: A novel computational approach to analyzing combinatorial motifs. 1
  
• Pall F. Jonsson, Tamara Cavanna, Daniel Zicha, Paul A. Bates:
  Cluster analysis of networks generated through homology: automatic identification of important protein communities involved in cancer metastasis. 2
  
• Ramón Díaz-Uriarte, Sara Alvarez de Andrés:
  Gene selection and classification of microarray data using random forest. 3
  
• Lakshmi K. Matukumalli, John J. Grefenstette, David L. Hyten, Ik-Young Choi, Perry B. Cregan, Curtis P. Van Tassell:
  Application of machine learning in SNP discovery. 4
  
• Heladia Salgado, Alberto Santos-Zavaleta, Socorro Gama-Castro, Martín Peralta-Gil, Mónica I. Peñaloza-Spínola, Agustino Martínez-Antonio, Peter D. Karp, Julio Collado-Vides:
  The comprehensive updated regulatory network of Escherichia coli K-12. 5
  
• Giacomo Gamberoni, Sergio Storari, Stefano Volinia:
  Finding biological process modifications in cancer tissues by mining gene expression correlations. 6
  
• Jie Zheng, Jan T. Svensson, Kavitha Madishetty, Timothy J. Close, Tao Jiang, Stefano Lonardi:
  OligoSpawn: a software tool for the design of overgo probes from large unigene datasets. 7
  
• Staal A. Vinterbo, Stephan Dreiseitl, Lucila Ohno-Machado:
  Approximation properties of haplotype tagging. 8
  
• Feng-Biao Guo, Chun-Ting Zhang:
  ZCURVE_V: a new self-training system for recognizing protein-coding genes in viral and phage genomes. 9
  
• James A. Casbon, Gavin E. Crooks, Mansoor A. S. Saqi:
  A high level interface to SCOP and ASTRAL implemented in Python. 10
  
• Andrean Goede, Elke Michalsky, Ulrike Schmidt, Robert Preissner:
  SuperMimic - Fitting peptide mimetics into protein structures. 11
  
• Zihua Hu, Gail R. Willsky:
  Utilization of two sample t-test statistics from redundant probe sets to evaluate different probe set algorithms in GeneChip studies. 12
  
• Feng Li, Maoyu Li, Zhiqiang Xiao, Pengfei Zhang, Jianling Li, Zhuchu Chen:
  Construction of a nasopharyngeal carcinoma 2D/MS repository with Open Source XML Database - Xindice. 13
  
• Oliver Sander, Ingolf Sommer, Thomas Lengauer:
  Local protein structure prediction using discriminative models. 14
  
• James J. Yang, Mark C. K. Yang:
  An improved procedure for gene selection from microarray experiments using false discovery rate criterion. 15
  
• Markus Brameier, Josien Haan, Andrea Krings, Robert M. MacCallum:
  Automatic discovery of cross-family sequence features associated with protein function. 16
  
• Brian Tjaden:
  An approach for clustering gene expression data with error information. 17
  
• Yuan-Yuan Li, Lei Qin, Zong-Ming Guo, Lei Liu, Hao Xu, Pei Hao, Jiong Su, Yixiang Shi, Wei-Zhong He, Yi-Xue Li:
  In silico discovery of human natural antisense transcripts. 18
  
• Morgan N. Price, Adam P. Arkin, Eric J. Alm:
  OpWise: Operons aid the identification of differentially expressed genes in bacterial microarray experiments. 19
  
• Youfang Cao, Shi Liu, Lida Zhang, Jie Qin, Jiang Wang, Kexuan Tang:
  Prediction of protein structural class with Rough Sets. 20
  
• Patrick Durand, Laurent Labarre, Alain Meil, Jean-Louis Divol, Yves Vandenbrouck, Alain Viari, Jérôme Wojcik:
  GenoLink: a graph-based querying and browsing system for investigating the function of genes and proteins. 21
  
• Alexei A. Adzhubei, Jon K. Laerdahl, Anna V. Vlasova:
  preAssemble: a tool for automatic sequencer trace data processing. 22
  
• Li-Xuan Qin, Richard P. Beyer, Francesca N. Hudson, Nancy J. Linford, Daryl E. Morris, Kathleen F. Kerr:
  Evaluation of methods for oligonucleotide array data via quantitative real-time PCR. 23
  
• Kyaw Tun, Pawan K. Dhar, Maria Concetta Palumbo, Alessandro Giuliani:
  Metabolic pathways variability and sequence/networks comparisons. 24
  
• Jason C. Ting, Ying Ye, George H. Thomas, Ingo Ruczinski, Jonathan Pevsner:
  Analysis and visualization of chromosomal abnormalities in SNP data with SNPscan. 25
  
• Xia Li, Shaoqi Rao, Wei Jiang, Chuanxing Li, Yun Xiao, Zheng Guo, Qingpu Zhang, Lihong Wang, Lei Du, Jing Li, Li Li, Tianwen Zhang, Qing K. Wang:
  Discovery of time-delayed gene regulatory networks based on temporal gene expression profiling. 26
  
• Hongbo Zhu, Francisco S. Domingues, Ingolf Sommer, Thomas Lengauer:
  NOXclass: prediction of protein-protein interaction types. 27
  
• Nicolas Thierry-Mieg:
  A new pooling strategy for high-throughput screening: the Shifted Transversal Design. 28
  
• Thomas Mailund, Gerth Stølting Brodal, Rolf Fagerberg, Christian N. S. Pedersen, Derek Phillips:
  Recrafting the neighbor-joining method. 29
  
• Ming Yi, Jay D. Horton, Jonathan C. Cohen, Helen H. Hobbs, Robert M. Stephens:
  WholePathwayScope: a comprehensive pathway-based analysis tool for high-throughput data. 30
  
• Bradford C. Powell, Clyde A. Hutchison III:
  Similarity-based gene detection: using COGs to find evolutionarily-conserved ORFs. 31
  
• Xian Wang, Ao Li, Zhaohui Jiang, Huanqing Feng:
  Missing value estimation for DNA microarray gene expression data by Support Vector Regression imputation and orthogonal coding scheme. 32
  
• Erdahl T. Teber, Edward Crawford, Kent B. Bolton, Derek Van Dyk, Peter R. Schofield, Vimal Kapoor, W. Bret Church:
  Djinn Lite: a tool for customised gene transcript modelling, annotation-data enrichment and exploration. 33
  
• Holger Conzelmann, Julio Saez-Rodriguez, Thomas Sauter, Boris N. Kholodenko, Ernst Dieter Gilles:
  A domain-oriented approach to the reduction of combinatorial complexity in signal transduction networks. 34
  
• Kyoungmi Kim, Grier P. Page, T. Mark Beasley, Stephen Barnes, Katherine E. Scheirer, David B. Allison:
  A proposed metric for assessing the measurement quality of individual microarrays. 35
  
• Domenico Catalano, Flavio Licciulli, Antonio Turi, Giorgio Grillo, Cecilia Saccone, Domenica D'Elia:
  MitoRes: a resource of nuclear-encoded mitochondrial genes and their products in Metazoa. 36
  
• Xiao I. Liu, Neeraj Korde, Ursula Jakob, Lars I. Leichert:
  CoSMoS: Conserved Sequence Motif Search in the proteome. 37
  
• Hao-Teng Chang, Tun-Wen Pai, Tan-Chi Fan, Bo-Han Su, Pei-Chih Wu, Chuan Yi Tang, Chun-Tien Chang, Shi-Hwei Liu, Margaret Dah-Tsyr Chang:
  A reinforced merging methodology for mapping unique peptide motifs in members of protein families. 38
  
• Alison A. Motsinger, Stephen L. Lee, George Mellick, Marylyn D. Ritchie:
  GPNN: Power studies and applications of a neural network method for detecting gene-gene interactions in studies of human disease. 39
  
• Xiaobo Zhou, James Chou, Stephen T. C. Wong:
  Protein structure similarity from principle component correlation analysis. 40
  
• Monica Chagoyen, Pedro Carmona-Saez, Hagit Shatkay, José María Carazo, Alberto D. Pascual-Montano:
  Discovering semantic features in the literature: a foundation for building functional associations. 41
  
• Harald Barsnes, Svein-Ole Mikalsen, Ingvar Eidhammer:
  MassSorter: a tool for administrating and analyzing data from mass spectrometry experiments on proteins with known amino acid sequences. 42
  
• Tim Van den Bulcke, Koen Van Leemput, Bart Naudts, Piet van Remortel, Hongwu Ma, Alain Verschoren, Bart De Moor, Kathleen Marchal:
  SynTReN: a generator of synthetic gene expression data for design and analysis of structure learning algorithms. 43
  
• Ryung S. Kim, Hongkai Ji, Wing Hung Wong:
  An improved distance measure between the expression profiles linking co-expression and co-regulation in mouse. 44
  
• Olivier Croce, Michaël Lamarre, Richard Christen:
  Querying the public databases for sequences using complex keywords contained in the feature lines. 45
  
• Wen-Yu Chung, Réka Albert, István Albert, Anton Nekrutenko, Kateryna D. Makova:
  Rapid and asymmetric divergence of duplicate genes in the human gene coexpression network. 46
  
• Ross I. Brinkworth, Alan L. Munn, Bostjan Kobe:
  Protein kinases associated with the yeast phosphoproteome. 47
  
• James A. Casbon, Mansoor A. S. Saqi:
  On single and multiple models of protein families for the detection of remote sequence relationships. 48
  
• Jeanette N. McClintick, Howard J. Edenberg:
  Effects of filtering by Present call on analysis of microarray experiments. 49
  
• Xing Qiu, Yuanhui Xiao, Alexander Gordon, Andrei Yakovlev:
  Assessing stability of gene selection in microarray data analysis. 50
  
• Kristofer Hallén, Johan Björkegren, Jesper Tegnér:
  Detection of compound mode of action by computational integration of whole-genome measurements and genetic perturbations. 51
  
• Bor-Sen Chen, Yu-Chao Wang:
  On the attenuation and amplification of molecular noise in genetic regulatory networks. 52
  
• Marcin von Grotthuss, Dariusz Plewczynski, Krzysztof Ginalski, Leszek Rychlewski, Eugene I. Shakhnovich:
  PDB-UF: database of predicted enzymatic functions for unannotated protein structures from structural genomics. 53
  
• Pedro Carmona-Saez, Monica Chagoyen, Andrés Rodríguez, Oswaldo Trelles, José María Carazo, Alberto D. Pascual-Montano:
  Integrated analysis of gene expression by association rules discovery. 54
  
• Michael Baitaluk, Xufei Qian, Shubhada Godbole, Alpan Raval, Animesh Ray, Amarnath Gupta:
  PathSys: integrating molecular interaction graphs for systems biology. 55
  
• Steffen Klamt, Julio Saez-Rodriguez, Jonathan A. Lindquist, Luca Simeoni, Ernst Dieter Gilles:
  A methodology for the structural and functional analysis of signaling and regulatory networks. 56
  
• Yanan Yu, Mya Breitbart, Pat McNairnie, Forest Rohwer:
  FastGroupII: A web-based bioinformatics platform for analyses of large 16S rDNA libraries. 57
  
• Bin Zheng, David C. McLean Jr, Xinghua Lu:
  Identifying biological concepts from a protein-related corpus with a probabilistic topic model. 58
  
• Hemant Ishwaran, J. Sunil Rao, Udaya B. Kogalur:
  BAMarray^TM: Java software for Bayesian analysis of variance for microarray data. 59
  
• Kim W. Carter, Pamela A. McCaskie, Lyle J. Palmer:
  JLIN: A java based linkage disequilibrium plotter. 60
  
• Phillip McClurg, Mathew T. Pletcher, Tim Wiltshire, Andrew I. Su:
  Comparative analysis of haplotype association mapping algorithms. 61
  
• Mario Stanke, Oliver Schöffmann, Burkhard Morgenstern, Stephan Waack:
  Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources. 62
  
• Claes R. Andersson, Anders Isaksson, Mats G. Gustafsson:
  Bayesian detection of periodic mRNA time profiles without use of training examples. 63
  
• Christoph Gille, Peter N. Robinson:
  HotSwap for bioinformatics: A STRAP tutorial. 64
  
• Svetlana A. Shabalina, Alexey N. Spiridonov, Aleksey Y. Ogurtsov:
  Computational models with thermodynamic and composition features improve siRNA design. 65
  
• Hanno Teeling, Frank Oliver Glöckner:
  RibAlign: a software tool and database for eubacterial phylogeny based on concatenated ribosomal protein subunits. 66
  
• Christian V. Forst, Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler:
  Algebraic comparison of metabolic networks, phylogenetic inference, and metabolic innovation. 67
  
• Mikael Bodén, Zheng Yuan, Timothy L. Bailey:
  Prediction of protein continuum secondary structure with probabilistic models based on NMR solved structures. 68
  
• Feng He, An-Ping Zeng:
  In search of functional association from time-series microarray data based on the change trend and level of gene expression. 69
  
• Aaron Birkland, Golan Yona:
  BIOZON: a system for unification, management and analysis of heterogeneous biological data. 70
  
• Paul Shafer, Timothy Isganitis, Golan Yona:
  Hubs of knowledge: using the functional link structure in Biozon to mine for biologically significant entities. 71
  
• Zuozhou Chen, Weilin Wang, Xuefeng Bruce Ling, Jane Jijun Liu, Liangbiao Chen:
  GO-Diff: Mining functional differentiation between EST-based transcriptomes. 72
  
• Daniel P. Berrar, Ian Bradbury, Werner Dubitzky:
  Instance-based concept learning from multiclass DNA microarray data. 73
  
• Brandon W. Higgs, Jennifer W. Weller, Jeffrey L. Solka:
  Spectral embedding finds meaningful (relevant) structure in image and microarray data. 74
  
• Andrew E. Firth, Chris M. Brown:
  Detecting overlapping coding sequences in virus genomes. 75
  
• Chengpeng Bi, Peter K. Rogan:
  BIPAD: A web server for modeling bipartite sequence elements. 76
  
• Donglin Liu, Joel H. Graber:
  Quantitative comparison of EST libraries requires compensation for systematic biases in cDNA generation. 77
  
• Pedro Carmona-Saez, Roberto D. Pascual-Marqui, Francisco Tirado, José María Carazo, Alberto D. Pascual-Montano:
  Biclustering of gene expression data by non-smooth non-negative matrix factorization. 78
  
• Gareth Palidwor, Emmanuel G. Reynaud, Miguel A. Andrade-Navarro:
  Taxonomic colouring of phylogenetic trees of protein sequences. 79
  
• Jie Wu, Zhenjun Hu, Charles DeLisi:
  Gene annotation and network inference by phylogenetic profiling. 80
  
• G. W. Patton, Robert M. Stephens, I. A. Sidorov, X. Xiao, Richard A. Lempicki, D. S. Dimitrov, Robert H. Shoemaker, G. Tudor:
  Transcriptomic response to differentiation induction. 81
  
• Alistair R. R. Forrest, Darrin F. Taylor, J. Lynn Fink, M. Milena Gongora, Cameron Flegg, Rohan D. Teasdale, Harukazu Suzuki, Mutsumi Kanamori, Chikatoshi Kai, Yoshihide Hayashizaki, Sean M. Grimmond:
  PhosphoregDB: The tissue and sub-cellular distribution of mammalian protein kinases and phosphatases. 82
  
• Jing Huang, Wen Wei, Joyce Chen, Jane Zhang, Guoying Liu, Xiaojun Di, Rui Mei, Shumpei Ishikawa, Hiroyuki Aburatani, Keith W. Jones, Michael H. Shapero:
  CARAT: A novel method for allelic detection of DNA copy number changes using high density oligonucleotide arrays. 83
  
• Grier P. Page, Jode W. Edwards, Gary L. Gadbury, Prashanth Yelisetti, Jelai Wang, Prinal Trivedi, David B. Allison:
  The PowerAtlas: a power and sample size atlas for microarray experimental design and research. 84
  
• Joshua S. Yuan, Ann Reed, Feng Chen, C. Neal Stewart Jr.:
  Statistical analysis of real-time PCR data. 85
  
• Ricardo Z. N. Vêncio, Tie Koide, Suely L. Gomes, Carlos A. de B. Pereira:
  BayGO: Bayesian analysis of ontology term enrichment in microarray data. 86
  
• Delong Liu, Shyamal D. Peddada, Leping Li, Clarice R. Weinberg:
  Phase analysis of circadian-related genes in two tissues. 87
  
• Jonathan P. Bollback:
  SIMMAP: Stochastic character mapping of discrete traits on phylogenies. 88
  
• Michael E. Bradley, Steven A. Benner:
  Integrating protein structures and precomputed genealogies in the Magnum database: Examples with cellular retinoid binding proteins. 89
  
• Shann-Ching Chen, Robert F. Murphy:
  A graphical model approach to automated classification of protein subcellular location patterns in multi-cell images. 90
  
• Sudhir Varma, Richard Simon:
  Bias in error estimation when using cross-validation for model selection. 91
  
• Richard Tzong-Han Tsai, Shih-Hung Wu, Wen-Chi Chou, Yu-Chun Lin, Ding He, Jieh Hsiang, Ting-Yi Sung, Wen-Lian Hsu:
  Various criteria in the evaluation of biomedical named entity recognition. 92
  
• Howard Salis, Vassilios Sotiropoulos, Yiannis N. Kaznessis:
  Multiscale Hy3S: Hybrid stochastic simulation for supercomputers. 93
  
• Stefan M. Stanley, Timothy L. Bailey, John S. Mattick:
  GONOME: measuring correlations between GO terms and genomic positions. 94
  
• E. Ke Tang, Ponnuthurai N. Suganthan, Xin Yao:
  Gene selection algorithms for microarray data based on least squares support vector machine. 95
  
• Anders Bengtsson, Henrik Bengtsson:
  Microarray image analysis: background estimation using quantile and morphological filters. 96
  
• Richard G. Côté, Philip Jones, Rolf Apweiler, Henning Hermjakob:
  The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries. 97
  
• Patrick Martin, Kim E. Boulukos, Philippe Pognonec:
  REtools: A laboratory program for restriction enzyme work: enzyme selection and reaction condition assistance. 98
  
• Ghislain Bidaut, Karsten Suhre, Jean-Michel Claverie, Michael F. Ochs:
  Determination of strongly overlapping signaling activity from microarray data. 99
  
• Henrik Bengtsson, Ola Hössjer:
  Methodological study of affine transformations of gene expression data with proposed robust non-parametric multi-dimensional normalization method. 100
  
• Yian A. Chen, Cheng-Chung Chou, Xinghua Lu, Elizabeth H. Slate, Konan Peck, Wenying Xu, Eberhard O. Voit, Jonas S. Almeida:
  A multivariate prediction model for microarray cross-hybridization. 101
  
• Richard P. Auburn, Roslin R. Russell, Bettina Fischer, Lisa A. Meadows, Santiago Sevillano Matilla, Steven Russell:
  SimArray: a user-friendly and user-configurable microarray design tool. 102
  
• Arthur Chun-Chieh Shih, D. T. Lee, Laurent Lin, Chin-Lin Peng, Shiang-Heng Chen, Yu-Wei Wu, Chun-Yi Wong, Meng-Yuan Chou, Tze-Chang Shiao, Mu-Fen Hsieh:
  SinicView: A visualization environment for comparisons of multiple nucleotide sequence alignment tools. 103
  
• Joan Teyra, Andreas Doms, Michael Schroeder, M. Teresa Pisabarro:
  SCOWLP: a web-based database for detailed characterization and visualization of protein interfaces. 104
  
• Roel G. W. Verhaak, Frank J. T. Staal, Peter J. M. Valk, Bob Lowenberg, Marcel J. T. Reinders, Dick de Ridder:
  The effect of oligonucleotide microarray data pre-processing on the analysis of patient-cohort studies. 105
  
• Robert Tibshirani:
  A simple method for assessing sample sizes in microarray experiments. 106
  
• Rasmus Goll, Trine Olsen, Guanglin Cui, Jon Florholmen:
  Evaluation of absolute quantitation by nonlinear regression in probe-based real-time PCR. 107
  
• Teresa W. Haynes, Debra J. Knisley, Edith Seier, Yue Zou:
  A quantitative analysis of secondary RNA structure using domination based parameters on trees. 108
  
• Björn H. Junker, Christian Klukas, Falk Schreiber:
  VANTED: A system for advanced data analysis and visualization in the context of biological networks. 109
  
• Michael Spitzer, Stefan Lorkowski, Paul Cullen, Alexander Sczyrba, Georg Fuellen:
  IsoSVM - Distinguishing isoforms and paralogs on the protein level. 110
  
• Scott A. Becker, Nathan D. Price, Bernhard O. Palsson:
  Metabolite coupling in genome-scale metabolic networks. 111
  
• Hidenori Inaoka, Yutaka Fukuoka, Isaac S. Kohane:
  Lower expression of genes near microRNA in C. elegans germline. 112
  
• Kenzie D. MacIsaac, Ting Wang, D. Benjamin Gordon, David K. Gifford, Gary D. Stormo, Ernest Fraenkel:
  An improved map of conserved regulatory sites for Saccharomyces cerevisiae. 113
  
• Victor X. Jin, Gregory A. Singer, Francisco J. Agosto-Perez, Sandya Liyanarachchi, Ramana V. Davuluri:
  Genome-wide analysis of core promoter elements from conserved human and mouse orthologous pairs. 114
  
• Chun Liang, Feng Sun, Haiming Wang, Junfeng Qu, Robert M. Freeman Jr, Lee H. Pratt, Marie-Michèle Cordonnier-Pratt:
  MAGIC-SPP: a database-driven DNA sequence processing package with associated management tools. 115
  
• Haiying Wang, Huiru Zheng, David Simpson, Francisco Azuaje:
  Machine learning approaches to supporting the identification of photoreceptor-enriched genes based on expression data. 116
  
• Zhengdong Zhang, George W. Jackson, George E. Fox, Richard C. Willson:
  Microbial identification by mass cataloging. 117
  
• Areejit Samal, Shalini Singh, Varun Giri, Sandeep Krishna, Nandula Raghuram, Sanjay Jain:
  Low degree metabolites explain essential reactions and enhance modularity in biological networks. 118
  
• Rainer König, Gunnar Schramm, Marcus Oswald, Hanna Seitz, Sebastian Sager, Marc Zapatka, Gerhard Reinelt, Roland Eils:
  Discovering functional gene expression patterns in the metabolic network of Escherichia coli with wavelets transforms. 119
  
• Sebastiaan Horsman, Michael J. Moorhouse, Victor C. L. de Jager, Peter van der Spek, Frank Grosveld, John Strouboulis, Eleni Z. Katsantoni:
  TF Target Mapper: A BLAST search tool for the identification of Transcription Factor target genes. 120
  
• Maike Tech, Peter Meinicke:
  An unsupervised classification scheme for improving predictions of prokaryotic TIS. 121
  
• Xiaochen Bo, Shaoke Lou, Daochun Sun, Wenjie Shu, Jing Yang, Shengqi Wang:
  Selection of antisense oligonucleotides based on multiple predicted target mRNA structures. 122
  
• Harvey J. Motulsky, Ronald E. Brown:
  Detecting outliers when fitting data with nonlinear regression - a new method based on robust nonlinear regression and the false discovery rate. 123
  
• Jiangning Song, Kevin Burrage, Zheng Yuan, Thomas Huber:
  Prediction of cis/trans isomerization in proteins using PSI-BLAST profiles and secondary structure information. 124
  
• Michael Meissner, Michael Schmuker, Gisbert Schneider:
  Optimized Particle Swarm Optimization (OPSO) and its application to artificial neural network training. 125
  
• Richard J. Fox, Matthew W. Dimmic:
  A two-sample Bayesian t-test for microarray data. 126
  
• Ulrika Wickenberg-Bolin, Hanna Göransson, Mårten Fryknäs, Mats G. Gustafsson, Anders Isaksson:
  Improved variance estimation of classification performance via reduction of bias caused by small sample size. 127
  
• Ramazan Saeed, Charlotte M. Deane:
  Protein protein interactions, evolutionary rate, abundance and age. 128
  
• Robert Urbanczik:
  SNA - a toolbox for the stoichiometric analysis of metabolic networks. 129
  
• Takuji Yamada, Minoru Kanehisa, Susumu Goto:
  Extraction of phylogenetic network modules from the metabolic network. 130
  
• Irini A. Doytchinova, Pingping Guan, Darren R. Flower:
  EpiJen: a server for multistep T cell epitope prediction. 131
  
• Christian L. Barrett, Nathan D. Price, Bernhard O. Palsson:
  Network-level analysis of metabolic regulation in the human red blood cell using random sampling and singular value decomposition. 132
  
• Yanni Sun, Jeremy Buhler:
  Choosing the best heuristic for seeded alignment of DNA sequences. 133
  
• Seo Young Kim, Jae Won Lee, Jong Sung Bae:
  Effect of data normalization on fuzzy clustering of DNA microarray data. 134
  
• Peisen Zhang, Jinghui Zhang, Huitao Sheng, James J. Russo, Brian Osborne, Kenneth H. Buetow:
  Gene functional similarity search tool (GFSST). 135
  
• Feng-Chi Chen, Chuang-Jong Chen, Jar-Yi Ho, Trees-Juen Chuang:
  Identification and evolutionary analysis of novel exons and alternative splicing events using cross-species EST-to-genome comparisons in human, mouse and rat. 136
  
• Frank F. Millenaar, John Okyere, Sean T. May, Martijn van Zanten, Laurentius A. C. J. Voesenek, Anton J. M. Peeters:
  How to decide? Different methods of calculating gene expression from short oligonucleotide array data will give different results. 137
  
• Min Lin, Rongling Wu:
  A joint model for nonparametric functional mapping of longitudinal trajectory and time-to-event. 138
  
• Yuliya V. Karpievitch, Jonas S. Almeida:
  mGrid: A load-balanced distributed computing environment for the remote execution of the user-defined Matlab code. 139
  
• Minsuk Lee, Weiqing Wang, Hong Yu:
  Exploring supervised and unsupervised methods to detect topics in biomedical text. 140
  
• Tilman Lamparter:
  A computational approach to discovering the functions of bacterial phytochromes by analysis of homolog distributions. 141
  
• Stephan Waack, Oliver Keller, Roman Asper, Thomas Brodag, Carsten Damm, Wolfgang Florian Fricke, Katharina Surovcik, Peter Meinicke, Rainer Merkl:
  Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models. 142
  
• Rahul Siddharthan:
  Sigma: multiple alignment of weakly-conserved non-coding DNA sequence. 143
  
• Markus Seiler, Alexander Mehrle, Annemarie Poustka, Stefan Wiemann:
  The 3of5 web application for complex and comprehensive pattern matching in protein sequences. 144
  
• James Thompson, Shuba Gopal:
  Genetic algorithm learning as a robust approach to RNA editing site prediction. 145
  
• Aaron N. Chang, Jason McDermott, Zachary Frazier, Michal Guerquin, Ram Samudrala:
  INTEGRATOR: interactive graphical search of large protein interactomes over the Web. 146
  
• J. R. Semeiks, A. Rizki, Mina J. Bissell, I. Saira Mian:
  Ensemble attribute profile clustering: discovering and characterizing groups of genes with similar patterns of biological features. 147
  
• Wendy S. W. Wong, Raazesh Sainudiin, Rasmus Nielsen:
  Identification of physicochemical selective pressure on protein encoding nucleotide sequences. 148
  
• Kevin A. Greer, Matthew R. McReynolds, Heddwen L. Brooks, James B. Hoying:
  CARMA: A platform for analyzing microarray datasets that incorporate replicate measures. 149
  
• Colleen D. Behrsin, Chris J. Brandl, David W. Litchfield, Brian H. Shilton, Lindi M. Wahl:
  Development of an unbiased statistical method for the analysis of unigenic evolution. 150
  
• Jason M. Doherty, Lynn K. Carmichael, Jason C. Mills:
  GOurmet: A tool for quantitative comparison and visualization of gene expression profiles based on gene ontology (GO) distributions. 151
  
• Kevin A. Snyder, Howard J. Feldman, Michel Dumontier, John J. Salama, Christopher W. V. Hogue:
  Domain-based small molecule binding site annotation. 152
  
• Huynh-Hoa Bui, John Sidney, Kenny Dinh, Scott Southwood, Mark J. Newman, Alessandro Sette:
  Predicting population coverage of T-cell epitope-based diagnostics and vaccines. 153
  
• Richard E. Kennedy, Kellie J. Archer, Michael F. Miles:
  Empirical validation of the S-Score algorithm in the analysis of gene expression data. 154
  
• Erik Arner, Martti T. Tammi, Anh-Nhi Tran, Ellen Kindlund, Björn Andersson:
  DNPTrapper: an assembly editing tool for finishing and analysis of complex repeat regions. 155
  
• Shigeyuki Matsui:
  Predicting survival outcomes using subsets of significant genes in prognostic marker studies with microarrays. 156
  
• Helene H. Thygesen, Aeilko H. Zwinderman:
  Modeling Sage data with a truncated gamma-Poisson model. 157
  
• Lars Malmström, György Marko-Varga, Gunilla Westergren-Thorsson, Thomas Laurell, Johan Malmström:
  2DDB - a bioinformatics solution for analysis of quantitative proteomics data. 158
  
• Enrique M. Muro, Carolina Perez-Iratxeta, Miguel A. Andrade-Navarro:
  Amplification of the Gene Ontology annotation of Affymetrix probe sets. 159
  
• Pieter Monsieurs, Gert Thijs, Abeer A. Fadda, Sigrid C. J. De Keersmaecker, Jozef Vanderleyden, Bart De Moor, Kathleen Marchal:
  More robust detection of motifs in coexpressed genes by using phylogenetic information. 160
  
• Arunachalam Vinayagam, Coral del Val, Falk Schubert, Roland Eils, Karl-Heinz Glatting, Sándor Suhai, Rainer König:
  GOPET: A tool for automated predictions of Gene Ontology terms. 161
  
• Beltran Rodriguez-Brito, Forest Rohwer, Robert Edwards:
  An application of statistics to comparative metagenomics. 162
  
• Yu Xue, Ao Li, Lirong Wang, Huanqing Feng, Xuebiao Yao:
  PPSP: prediction of PK-specific phosphorylation site with Bayesian decision theory. 163
  
• Georg Schneider, Georg Neuberger, Michael Wildpaner, Sun Tian, Igor N. Berezovsky, Frank Eisenhaber:
  Application of a sensitive collection heuristic for very large protein families: Evolutionary relationship between adipose triglyceride lipase (ATGL) and classic mammalian lipases. 164
  
• Hyunsoo Kim, William Hu, Yuval Kluger:
  Unraveling condition specific gene transcriptional regulatory networks in Saccharomyces cerevisiae. 165
  
• Peng Yue, Eugene Melamud, John Moult:
  SNPs3D: Candidate gene and SNP selection for association studies. 166
  
• Peteris Prusis, Staffan Uhlén, Ramona Petrovska, Maris Lapinsh, Jarl E. S. Wikberg:
  Prediction of indirect interactions in proteins. 167
  
• Kazuharu Arakawa, Yohei Yamada, Kosaku Shinoda, Yoichi Nakayama, Masaru Tomita:
  GEM System: automatic prototyping of cell-wide metabolic pathway models from genomes. 168
  
• Vincent Le Texier, Jean-Jack M. Riethoven, Vasudev Kumanduri, Chellappa Gopalakrishnan, Fabrice Lopez, Daniel Gautheret, Thangavel Alphonse Thanaraj:
  AltTrans: Transcript pattern variants annotated for both alternative splicing and alternative polyadenylation. 169
  
• Thomas J. Lee, Yannick Pouliot, Valerie Wagner, Priyanka Gupta, David W. J. Stringer-Calvert, Jessica D. Tenenbaum, Peter D. Karp:
  BioWarehouse: a bioinformatics database warehouse toolkit. 170
  
• Anton Yuryev, Zufar Mulyukov, Ekaterina Kotelnikova, Sergei Maslov, Sergei Egorov, Alexander Nikitin, Nikolai Daraselia, Ilya Mazo:
  Automatic pathway building in biological association networks. 171
  
• Reidar Andreson, Eric Reppo, Lauris Kaplinski, Maido Remm:
  GENOMEMASKER package for designing unique genomic PCR primers. 172
  
• Andrew V. Uzilov, Joshua M. Keegan, David H. Mathews:
  Detection of non-coding RNAs on the basis of predicted secondary structure formation free energy change. 173
  
• Vicente Arnau, Miguel Gallach, J. Ignasi Lucas, Ignacio Marín:
  UVPAR: fast detection of functional shifts in duplicate genes. 174
  
• Guoli Wang, Andrew V. Kossenkov, Michael F. Ochs:
  LS-NMF: A modified non-negative matrix factorization algorithm utilizing uncertainty estimates. 175
  
• Paul T. Shannon, David J. Reiss, Richard Bonneau, Nitin S. Baliga:
  The Gaggle: An open-source software system for integrating bioinformatics software and data sources. 176
  
• Peter Kharchenko, Lifeng Chen, Yoav Freund, Dennis Vitkup, George M. Church:
  Identifying metabolic enzymes with multiple types of association evidence. 177
  
• Zafer Aydin, Yucel Altunbasak, Mark Borodovsky:
  Protein secondary structure prediction for a single-sequence using hidden semi-Markov models. 178
  
• Sangjo Han, Dongsup Kim:
  AtRTPrimer: database for Arabidopsis genome-wide homogeneous and specific RT-PCR primer-pairs. 179
  
• Alessandro Vullo, Ian Walsh, Gianluca Pollastri:
  A two-stage approach for improved prediction of residue contact maps. 180
  
• Lars Snipen, Dirk Repsilber, Ludvig Nyquist, Ågot Aakra, Andreas Ziegler, Are Halvor Aastveit:
  Detection of divergent genes in microbial aCGH experiments. 181
  
• Wen Liu, Xiangshan Meng, Qiqi Xu, Darren R. Flower, Tongbin Li:
  Quantitative prediction of mouse class I MHC peptide binding affinity using support vector machine regression (SVR) models. 182
  
• Veronica Vinciotti, Xiaohui Liu, Rolf Turk, Emile J. de Meijer, Peter A. C. 't Hoen:
  Exploiting the full power of temporal gene expression profiling through a new statistical test: Application to the analysis of muscular dystrophy data. 183
  
• Ester Vilaprinyó, Rui Alves, Albert Sorribas:
  Use of physiological constraints to identify quantitative design principles for gene expression in yeast adaptation to heat shock. 184
  
• H. Alexander Ebhardt, Kay C. Wiese, Peter J. Unrau:
  Ebbie: automated analysis and storage of small RNA cloning data using a dynamic web server. 185
  
• Jean-Marc Schwartz, Minoru Kanehisa:
  Quantitative elementary mode analysis of metabolic pathways: the example of yeast glycolysis. 186
  
• Xiaojing Yu, Chuan Wang, Yixue Li:
  Classification of protein quaternary structure by functional domain composition. 187
  
• Julien Dutheil, Sylvain Gaillard, Eric Bazin, Sylvain Glemin, Vincent Ranwez, Nicolas Galtier, Khalid Belkhir:
  Bio++: a set of C++ libraries for sequence analysis, phylogenetics, molecular evolution and population genetics. 188
  
• Pantelis G. Bagos, Theodore D. Liakopoulos, Stavros J. Hamodrakas:
  Algorithms for incorporating prior topological information in HMMs: application to transmembrane proteins. 189
  
• Leandro Hermida, Olivier Schaad, Philippe Demougin, Patrick Descombes, Michael Primig:
  MIMAS: an innovative tool for network-based high density oligonucleotide microarray data management and annotation. 190
  
• Jason Ernst, Ziv Bar-Joseph:
  STEM: a tool for the analysis of short time series gene expression data. 191
  
• Sylvia M. Major, Satoshi Nishizuka, Daisaku Morita, Rick Rowland, Margot Sunshine, Uma T. Shankavaram, Frank Washburn, Daniel Asin, Hosein Kouros-Mehr, David W. Kane, John N. Weinstein:
  AbMiner: A bioinformatic resource on available monoclonal antibodies and corresponding gene identifiers for genomic, proteomic, and immunologic studies. 192
  
• Peter Ruzanov, Steven J. M. Jones:
  An interactive tool for visualization of relationships between gene expression profiles. 193
  
• Joseph C. Roden, Brandon W. King, Diane Trout, Ali Mortazavi, Barbara J. Wold, Christopher E. Hart:
  Mining gene expression data by interpreting principal components. 194
  
• Svetlana Pacifico, Guozhen Liu, Stephen Guest, Jodi R. Parrish, Farshad Fotouhi, Russell L. Finley Jr.:
  A database and tool, IM Browser, for exploring and integrating emerging gene and protein interaction data for Drosophila. 195
  
• Stephen A. Racunas, Nigam Shah, Nina V. Fedoroff:
  A case study in pathway knowledgebase verification. 196
  
• Xuegong Zhang, Xin Lu, Qian Shi, Xiu-qin Xu, Hon-chiu E. Leung, Lyndsay N. Harris, James D. Iglehart, Alexander Miron, Jun S. Liu, Wing Hung Wong:
  Recursive SVM feature selection and sample classification for mass-spectrometry and microarray data. 197
  
• Werner W. V. B. Van Belle, Nina N. A. Anensen, Ingvild I. H. Haaland, Oystein O. B. Bruserud, Kjell-Arild K. A. H. Hogda, Bjorn B. T. G. Tore Gjertsen:
  Correlation analysis of two-dimensional gel electrophoretic protein patterns and biological variables. 198
  
• Tomer Shlomi, Daniel Segal, Eytan Ruppin, Roded Sharan:
  QPath: a method for querying pathways in a protein-protein interaction network. 199
  
• Rachel I. M. van Haaften, Blanche Schroen, Ben J. A. Janssen, Arie van Erk, Jacques J. M. Debets, Hubert J. M. Smeets, Jos F. M. Smits, Arthur van den Wijngaard, Yigal M. Pinto, Chris T. A. Evelo:
  Biologically relevant effects of mRNA amplification on gene expression profiles. 200
  
• Paramvir S. Dehal, Jeffrey L. Boore:
  A phylogenomic gene cluster resource: the Phylogenetically Inferred Groups (PhIGs) database. 201
  
• Chaolin Zhang, Hai-Ri Li, Jian-Bing Fan, Jessica Wang-Rodriguez, Tracy Downs, Xiang-Dong Fu, Michael Q. Zhang:
  Profiling alternatively spliced mRNA isoforms for prostate cancer classification. 202
  
• Pinar Pir, Betül Kirdar, Andrew Hayes, Z. Ilsen Önsan, Kutlu Ö. Ülgen, Stephen G. Oliver:
  Integrative investigation of metabolic and transcriptomic data. 203
  
• Tricia A. Thornton-Wells, Jason H. Moore, Jonathan L. Haines:
  Dissecting trait heterogeneity: a comparison of three clustering methods applied to genotypic data. 204
  
• Casper J. Albers, Ritsert C. Jansen, Jan Kok, Oscar P. Kuipers, Sacha A. F. T. van Hijum:
  SIMAGE: simulation of DNA-microarray gene expression data. 205
  
• Vichetra Sam, Chin-Hsien Tai, Jean Garnier, Jean-François Gibrat, Byungkook Lee, Peter J. Munson:
  ROC and confusion analysis of structure comparison methods identify the main causes of divergence from manual protein classification. 206
  
• Md. Altaf-Ul-Amin, Yoko Shinbo, Kenji Mihara, Ken Kurokawa, Shigehiko Kanaya:
  Development and implementation of an algorithm for detection of protein complexes in large interaction networks. 207
  
• Kang Peng, Predrag Radivojac, Slobodan Vucetic, A. Keith Dunker, Zoran Obradovic:
  Length-dependent prediction of protein intrinsic disorder. 208
  
• Kristina Allen-Brady, Jathine Wong, Nicola J. Camp:
  PedGenie: an analysis approach for genetic association testing in extended pedigrees and genealogies of arbitrary size. 209
  
• Simon Fiddy, David Cattermole, Dong Xie, Xiao Yuan Duan, Richard Mott:
  An integrated system for genetic analysis. 210
  
• Lesley Jones, Darlene R. Goldstein, Gareth P. Hughes, Andrew Strand, Francois Collin, Stephen B. Dunnett, Charles L. Kooperberg, Aaron Aragaki, James M. Olson, Sarah J. Augood, Richard L. M. Faull, Ruth Luthi-Carter, Valentina Moskvina, Angela K. Hodges:
  Assessment of the relationship between pre-chip and post-chip quality measures for Affymetrix GeneChip expression data. 211
  
• Jacob Köhler, Katherine Munn, Alexander Rüegg, Andre Skusa, Barry Smith:
  Quality control for terms and definitions in ontologies and taxonomies. 212
  
• Michael L. Tress, Domenico Cozzetto, Anna Tramontano, Alfonso Valencia:
  An analysis of the Sargasso Sea resource and the consequences for database composition. 213
  
• Peter Steffen, Robert Giegerich:
  Correction: versatile and declarative dynamic programming using pair algebras. 214
  
• Allan A. Sioson, Shrinivasrao P. Mane, Pinghua Li, Wei Sha, Lenwood S. Heath, Hans J. Bohnert, Ruth Grene:
  The statistics of identifying differentially expressed genes in Expresso and TM4: a comparison. 215
  
• Rafal Kustra, Romy Shioda, Mu Zhu:
  A factor analysis model for functional genomics. 216
  
• Richard J. B. Dobson, Patricia B. Munroe, Mark J. Caulfield, Mansoor A. S. Saqi:
  Predicting deleterious nsSNPs: an analysis of sequence and structural attributes. 217
  
• Amrita Pati, Cecilia Vasquez-Robinet, Lenwood S. Heath, Ruth Grene, T. M. Murali:
  XcisClique: analysis of regulatory bicliques. 218
  
• Björn H. Junker, Dirk Koschützki, Falk Schreiber:
  Exploration of biological network centralities with CentiBiN. 219
  
• Aditya Kumar Sehgal, Padmini Srinivasan:
  Retrieval with gene queries. 220
  
• Alexander Churkin, Danny Barash:
  RNAmute: RNA secondary structure mutation analysis tool. 221
  
• Zhuo Zhang, Shiwei Sun, Xiaopeng Zhu, Suhua Chang, Xiaofei Liu, Chungong Yu, Dongbo Bu, Runsheng Chen:
  A novel scoring schema for peptide identification by searching protein sequence databases using tandem mass spectrometry data. 222
  
• Tong Zhou, Jianhong Weng, Xiao Sun, Zuhong Lu:
  Support vector machine for classification of meiotic recombination hotspots and coldspots in Saccharomyces cerevisiaebased on codon composition. 223
  
• Thierry-Pascal Baum, Vivien Hierle, Nicolas Pasqual, Fatena Bellahcene, Denys Chaume, Marie-Paule Lefranc, Evelyne Jouvin-Marche, Patrice-Noël Marche, Jacques Demongeot:
  IMGT/GeneInfo: T cell receptor gamma TRG and delta TRD genes in database give access to all TR potential V(D)J recombinations. 224
  
• Marcin P. Joachimiak, Jennifer L. Weissman, Barnaby C. H. May:
  JColorGrid: software for the visualization of biological measurements. 225
  
• Filippo Rusconi:
  GNU polyxmass: a software framework for mass spectrometric simulations of linear (bio-)polymeric analytes. 226
  
• Tom R. Gaunt, Santiago Rodríguez, Carlos Zapata, Ian N. M. Day:
  MIDAS: software for analysis and visualisation of interallelic disequilibrium between multiallelic markers. 227
  
• Kun Yang, Zhipeng Cai, Jianzhong Li, Guohui Lin:
  A stable gene selection in microarray data analysis. 228
  
• Bertrand R. Huber, Martha L. Bulyk:
  Meta-analysis discovery of tissue-specific DNA sequence motifs from mammalian gene expression data. 229
  
• Yoshiya Matsubara, Shinichi Kikuchi, Masahiro Sugimoto, Masaru Tomita:
  Parameter estimation for stiff equations of biosystems using radial basis function networks. 230
  
• Paul-Ludwig Lott, Marvin Mundry, Christoph Sassenberg, Stefan Lorkowski, Georg Fuellen:
  Simplifying gene trees for easier comprehension. 231
  
• Cheng-Chung Chou, Te-Tsui Lee, Chun-Houh Chen, Hsiang-Yun Hsiao, Yi-Ling Lin, Mei-Shang Ho, Pan-Chyr Yang, Konan Peck:
  Design of microarray probes for virus identification and detection of emerging viruses at the genus level. 232
  
• Hsin-Chou Yang, Chia-Ching Pan, Chin-Yu Lin, Cathy S. J. Fann:
  PDA: Pooled DNA analyzer. 233
  
• Tobias Kind, Oliver Fiehn:
  Metabolomic database annotations viaquery of elemental compositions: Mass accuracy is insufficient even at less than 1 ppm. 234
  
• Carmen Lai, Marcel J. T. Reinders, Laura J. van't Veer, Lodewyk F. A. Wessels:
  A comparison of univariate and multivariate gene selection techniques for classification of cancer datasets. 235
  
• David Tuck, Harriet Kluger, Yuval Kluger:
  Characterizing disease states from topological properties of transcriptional regulatory networks. 236
  
• Jamie A. Lee, Robert S. Sinkovits, Dennis Mock, Eva L. Rab, Jennifer Cai, Peng Yang, Brian Saunders, Robert C. Hsueh, Sangdun Choi, Shankar Subramaniam, Richard H. Scheuermann:
  Components of the antigen processing and presentation pathway revealed by gene expression microarray analysis following B cell antigen receptor (BCR) stimulation. 237
  
• Yi Lu, Adrian E. Platts, G. Charles Ostermeier, Stephen A. Krawetz:
  K-SPMM: a database of murine spermatogenic promoters modules & motifs. 238
  
• Kasper Munch, Paul P. Gardner, Peter Arctander, Anders Krogh:
  A hidden Markov model approach for determining expression from genomic tiling micro arrays. 239
  
• Yadhu Kumar, Ralf Westram, Peter Kipfer, Harald Meier, Wolfgang Ludwig:
  Evaluation of sequence alignments and oligonucleotide probes with respect to three-dimensional structure of ribosomal RNA using ARB software package. 240
  
• Marc Aubry, Annabelle Monnier, Celine Chicault, Marie de Tayrac, Marie-Dominique Galibert, Anita Burgun, Jean Mosser:
  Combining evidence, biomedical literature and statistical dependence: new insights for functional annotation of gene sets. 241
  
• Apostol Gramada, Philip E. Bourne:
  Multipolar representation of protein structure. 242
  
• Jijoy Joseph, Roschen Sasikumar:
  Chaos game representation for comparison of whole genomes. 243
  
• Mohammad Anwar, Truong Nguyen, Marcel Turcotte:
  Identification of consensus RNA secondary structures using suffix arrays. 244
  
• Hao Li, Constance L. Wood, Yushu Liu, Thomas V. Getchell, Marilyn L. Getchell, Arnold J. Stromberg:
  Identification of gene expression patterns using planned linear contrasts. 245
  
• Hiroto Saigo, Jean-Philippe Vert, Tatsuya Akutsu:
  Optimizing amino acid substitution matrices with a local alignment kernel. 246
  
• Erin M. Conlon, Joon J. Song, Jun S. Liu:
  Bayesian models for pooling microarray studies with multiple sources of replications. 247
  
• Huiquan Wang, Craig J. Benham:
  Promoter prediction and annotation of microbial genomes based on DNA sequence and structural responses to superhelical stress. 248
  
• Norbert Dojer, Anna Gambin, Andrzej Mizera, Bartek Wilczynski, Jerzy Tiuryn:
  Applying dynamic Bayesian networks to perturbed gene expression data. 249
  
• David M. Blei, K. Franks, Michael I. Jordan, I. Saira Mian:
  Statistical modeling of biomedical corpora: mining the Caenorhabditis Genetic Center Bibliography for genes related to life span. 250
  
• Martino Barenco, Jaroslav Stark, Daniel Brewer, Daniela Tomescu, Robin Callard, Michael Hubank:
  Correction of scaling mismatches in oligonucleotide microarray data. 251
  
• Yong Zhang, Shaojuan Li, Geir Skogerbø, Zhihua Zhang, Xiaopeng Zhu, Zefeng Zhang, Shiwei Sun, Hongchao Lu, Baochen Shi, Runsheng Chen:
  Phylophenetic properties of metabolic pathway topologies as revealed by global analysis. 252
  
• Shuangge Ma, Xiao Song, Jian Huang:
  Regularized binormal ROC method in disease classificationusing microarray data. 253