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 Löwenberg, 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 E. 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
  
• Jonathan M. Carlson, Arijit Chakravarty, Radhika S. Khetani, Robert H. Gross:
  Bounded search for de novo identification of degenerate cis-regulatory elements. 254
  
• Nicolas Sapay, Yann Guermeur, Gilbert Deléage:
  Prediction of amphipathic in-plane membrane anchors in monotopic proteins using a SVM classifier. 255
  
• Catherine M. Conway, Deirdre O'Shea, Sallyann O'Brien, Darragh K. Lawler, Graham D. Dodrill, Anthony O'Grady, Helen Barrett, Christian Gulmann, Lorraine O'Driscoll, William M. Gallagher, Elaine W. Kay, Daniel G. O'Shea:
  The development and validation of the Virtual Tissue Matrix, a software application that facilitates the review of tissue microarrays on line. 256
  
• Alberto Pasamontes, Santiago Garcia-Vallvé:
  Use of a multi-way method to analyze the amino acid composition of a conserved group of orthologous proteins in prokaryotes. 257
  
• Jing Li, Yingyao Zhou, Robert C. Elston:
  Haplotype-based quantitative trait mapping using a clustering algorithm. 258
  
• Feng-Chi Chen, Trees-Juen Chuang:
  The effects of multiple features of alternatively spliced exons on the K_A/K_S ratio test. 259
  
• Nicholas R. Anderson, Peter Tarczy-Hornoch, Roger Eugene Bumgarner:
  On the persistence of supplementary resources in biomedical publications. 260
  
• Matthew E. Ritchie, Dileepa S. Diyagama, Jody Neilson, Ryan van Laar, Alexander Dobrovic, Andrew J. Holloway, Gordon K. Smyth:
  Empirical array quality weights in the analysis of microarray data. 261
  
• Changhui Yan, Michael Terribilini, Feihong Wu, Robert L. Jernigan, Drena Dobbs, Vasant Honavar:
  Predicting DNA-binding sites of proteins from amino acid sequence. 262
  
• Kasper Munch, Anders Krogh:
  Automatic generation of gene finders for eukaryotic species. 263
  
• Pierre Neuvial, Philippe Hupé, Isabel Brito, Stéphane Liva, Elodie Manié, Caroline Brennetot, François Radvanyi, Alain Aurias, Emmanuel Barillot:
  Spatial normalization of array-CGH data. 264
  
• Anne-Kathrin Schultz, Ming Zhang, Thomas Leitner, Carla Kuiken, Bette T. Korber, Burkhard Morgenstern, Mario Stanke:
  A jumping profile Hidden Markov Model and applications to recombination sites in HIV and HCV genomes. 265
  
• Jason Gertz, Justin C. Fay, Barak A. Cohen:
  Phylogeny based discovery of regulatory elements. 266
  
• Alexander García Castro, Philippe Rocca-Serra, Robert Stevens, Chris F. Taylor, Karim Nashar, Mark A. Ragan, Susanna-Assunta Sansone:
  The use of concept maps during knowledge elicitation in ontology development processes - the nutrigenomics use case. 267
  
• Jianghui Xiong, Simon Rayner, Kunyi Luo, Yinghui Li, Shanguang Chen:
  Genome wide prediction of protein function via a generic knowledge discovery approach based on evidence integration. 268
  
• Hyunju Lee, Minghua Deng, Fengzhu Sun, Ting Chen:
  An integrated approach to the prediction of domain-domain interactions. 269
  
• Debra L. Fulton, Yvonne Y. Li, Matthew R. Laird, Benjamin G. S. Horsman, Fiona M. Roche, Fiona S. L. Brinkman:
  Improving the specificity of high-throughput ortholog prediction. 270
  
• Peilin Jia, Tieliu Shi, Yu-Dong Cai, Yixue Li:
  Demonstration of two novel methods for predicting functional siRNA efficiency. 271
  
• Didier Filopon, Annabelle Mérieau, Gilles Bernot, Jean-Paul Comet, Rozenne LeBerre, Benoit Guery, Benoit Polack, Janine Guespin-Michel:
  Epigenetic acquisition of inducibility of type III cytotoxicity in P. aeruginosa. 272
  
• David W. Kane, Moses M. Hohman, Ethan G. Cerami, Michael W. McCormick, Karl F. Kuhlmman, Jeff A. Byrd:
  Agile methods in biomedical software development: a multi-site experience report. 273
  
• Jianping Hua, James Lowey, Zixiang Xiong, Edward R. Dougherty:
  Noise-injected neural networks show promise for use on small-sample expression data. 274
  
• Thomas J. Boyle, Zhirong Bao, John I. Murray, Carlos L. Araya, Robert H. Waterston:
  AceTree: a tool for visual analysis of Caenorhabditis elegans embryogenesis. 275
  
• Michal J. Okoniewski, Crispin J. Miller:
  Hybridization interactions between probesets in short oligo microarrays lead to spurious correlations. 276
  
• Elon Portugaly, Amir Harel, Nathan Linial, Michal Linial:
  EVEREST: automatic identification and classification of protein domains in all protein sequences. 277
  
• Kai Wang, Ram Samudrala:
  Automated functional classification of experimental and predicted protein structures. 278
  
• Weichun Huang, David M. Umbach, Uwe Ohler, Leping Li:
  Optimized mixed Markov models for motif identification. 279
  
• David J. Reiss, Nitin S. Baliga, Richard Bonneau:
  Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks. 280
  
• Irena Spasic, Warwick B. Dunn, Giles Velarde, Andy Tseng, Helen Jenkins, Nigel Hardy, Stephen G. Oliver, Douglas B. Kell:
  MeMo: a hybrid SQL/XML approach to metabolomic data management for functional genomics. 281
  
• Joern Toedling, Peter Rhein, Richard Ratei, Leonid Karawajew, Rainer Spang:
  Automated in-silico detection of cell populations in flow cytometry readouts and its application to leukemia disease monitoring. 282
  
• Pavana Polineni, Prathyusha Aragonda, Suresh R. Xavier, Richard Furuta, David L. Adelson:
  The bovine QTL viewer: a web accessible database of bovine Quantitative Trait Loci. 283
  
• Sok June Oh, Je-Gun Joung, Jeong Ho Chang, Byoung-Tak Zhang:
  Construction of phylogenetic trees by kernel-based comparative analysis of metabolic networks. 284
  
• Alan Villalobos, Jon E. Ness, Claes Gustafsson, Jeremy Minshull, Sridhar Govindarajan:
  Gene Designer: a synthetic biology tool for constructing artificial DNA segments. 285
  
• Bruz Marzolf, Eric W. Deutsch, Patrick Moss, David Campbell, Michael H. Johnson, Timothy Galitski:
  SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology. 286
  
• Hailong Meng, Arunava Banerjee, Lei Zhou:
  BLISS: biding site level identification of shared signal-modules in DNA regulatory sequences. 287
  
• Liam J. McGuffin, Richard T. Smith, Kevin Bryson, Søren-Aksel Sørensen, David T. Jones:
  High throughput profile-profile based fold recognition for the entire human proteome. 288
  
• Lennart Martens, Geert Monsieur, Christophe Ampe, Kris Gevaert, Joël Vandekerckhove:
  Cell_motility: a cross-platform, open source application for the study of cell motion paths. 289
  
• Attila Frigyesi, Srinivas Veerla, David Lindgren, Mattias Höglund:
  Independent component analysis reveals new and biologically significant structures in micro array data. 290
  
• Marco Masseroli, Halil Kilicoglu, François-Michel Lang, Thomas C. Rindflesch:
  Argument-predicate distance as a filter for enhancing precision in extracting predications on the genetic etiology of disease. 291
  
• Jun Wang, Peter D. Keightley, Toby Johnson:
  MCALIGN2: Faster, accurate global pairwise alignment of non-coding DNA sequences based on explicit models of indel evolution. 292
  
• Stefan Günther, Christian Senger, Elke Michalsky, Andrean Goede, Robert Preissner:
  Representation of target-bound drugs by computed conformers: implications for conformational libraries. 293
  
• Koji Kadota, Jiazhen Ye, Yuji Nakai, Tohru Terada, Kentaro Shimizu:
  ROKU: a novel method for identification of tissue-specific genes. 294
  
• Chin Lung Lu, Yen-Lin Huang, Tsui Ching Wang, Hsien-Tai Chiu:
  Analysis of circular genome rearrangement by fusions, fissions and block-interchanges. 295
  
• Richard A. Notebaart, Frank H. J. van Enckevort, Christof Francke, Roland J. Siezen, Bas Teusink:
  Accelerating the reconstruction of genome-scale metabolic networks. 296
  
• Sayed-Amir Marashi, Changiz Eslahchi, Hamid Pezeshk, Mehdi Sadeghi:
  Impact of RNA structure on the prediction of donor and acceptor splice sites. 297
  
• Alla Bulashevska, Roland Eils:
  Predicting protein subcellular locations using hierarchical ensemble of Bayesian classifiers based on Markov chains. 298
  
• Huilin Xiong, Xue-wen Chen:
  Kernel-based distance metric learning for microarray data classification. 299
  
• Patrik Rydén, Henrik Andersson, Mattias Landfors, Linda Näslund, Blanka Hartmanová, Laila Noppa, Anders Sjöstedt:
  Evaluation of microarray data normalization procedures using spike-in experiments. 300
  
• Scott Montgomerie, Shan Sundararaj, Warren J. Gallin, David S. Wishart:
  Improving the accuracy of protein secondary structure prediction using structural alignment. 301
  
• Andreas Schlicker, Francisco S. Domingues, Jörg Rahnenführer, Thomas Lengauer:
  A new measure for functional similarity of gene products based on Gene Ontology. 302
  
• Pierre Nicolas, Fengzhu Sun, Lei M. Li:
  A model-based approach to selection of tag SNPs. 303
  
• Shih-Hau Chiu, Chien-Chi Chen, Gwo-Fang Yuan, Thy-Hou Lin:
  Association algorithm to mine the rules that govern enzyme definition and to classify protein sequences. 304
  
• I. Saira Mian, Elizabeth A. Worthey, Reza Salavati:
  Taking U out, with two nucleases? 305
  
• Peter Johansson, Jari Häkkinen:
  Improving missing value imputation of microarray data by using spot quality weights. 306
  
• Gabriela G. Loots, Patrick S. G. Chain, Shalini Mabery, Amy Rasley, Emilio Garcia, Ivan Ovcharenko:
  Array2BIO: from microarray expression data to functional annotation of co-regulated genes. 307
  
• Daniel J. Kliebenstein, Marilyn A. L. West, Hans van Leeuwen, Olivier Loudet, R. W. Doerge, Dina A. St Clair:
  Identification of QTLs controlling gene expression networks defined a priori. 308
  
• Hendrik Marks, Xin-Ying Ren, Hans Sandbrink, Mariëlle C. W. van Hulten, Just M. Vlak:
  In silico identification of putative promoter motifs of White Spot Syndrome Virus. 309
  
• Stefano Lise, Alice Walker-Taylor, David T. Jones:
  Docking protein domains in contact space. 310
  
• Oliver Laule, Matthias Hirsch-Hoffmann, Tomas Hruz, Wilhelm Gruissem, Philip Zimmermann:
  Web-based analysis of the mouse transcriptome using Genevestigator. 311
  
• Natalia V. Petrova, Cathy H. Wu:
  Prediction of catalytic residues using Support Vector Machine with selected protein sequence and structural properties. 312
  
• Eric Beitz:
  Subfamily logos: visualization of sequence deviations at alignment positions with high information content. 313
  
• Keith A. Jolley, Martin C. J. Maiden:
  AgdbNet - antigen sequence database software for bacterial typing. 314
  
• Jakob Fredslund:
  PHY*FI: fast and easy online creation and manipulation of phylogeny color figures. 315
  
• Martin Petrek, Michal Otyepka, Pavel Banás, Pavlína Kosinová, Jaroslav Koca, Jirí Damborský:
  CAVER: a new tool to explore routes from protein clefts, pockets and cavities. 316
  
• Baolin Wu, Nianjun Liu, Hongyu Zhao:
  PSMIX: an R package for population structure inference via maximum likelihood method. 317
  
• Julie D. Thompson, Arnaud Muller, Andrew M. Waterhouse, James B. Procter, Geoffrey J. Barton, Frédéric Plewniak, Olivier Poch:
  MACSIMS : multiple alignment of complete sequences information management system. 318
  
• Chung-Tsai Su, Chien-Yu Chen, Yu-Yen Ou:
  Protein disorder prediction by condensed PSSM considering propensity for order or disorder. 319
  
• Chia Huey Ooi, Madhu Chetty, Shyh Wei Teng:
  Differential prioritization between relevance and redundancy in correlation-based feature selection techniques for multiclass gene expression data. 320
  
• George W. Jackson, Roger J. McNichols, George E. Fox, Richard C. Willson:
  Bacterial genotyping by 16S rRNA mass cataloging. 321
  
• Vincent Nègre, Thierry Hotelier, Anne-Nathalie Volkoff, Sylvie Gimenez, François Cousserans, Kazuei Mita, Xavier Sabau, Janick Rocher, Miguel López-Ferber, Emmanuelle d'Alençon, Pascaline Audant, Cécile Sabourault, Vincent Bidegainberry, Frédérique Hilliou, Philippe Fournier:
  SPODOBASE : an EST database for the lepidopteran crop pest Spodoptera. 322
  
• Satoshi Miyazaki, Yutaka Kuroda, Shigeyuki Yokoyama:
  Identification of putative domain linkers by a neural network - application to a large sequence database. 323
  
• Qiwen Dong, Xiaolong Wang, Lei Lin:
  Novel knowledge-based mean force potential at the profile level. 324
  
• Thomas Karopka, Juliane Fluck, Heinz-Theodor Mevissen, Änne Glass:
  The Autoimmune Disease Database: a dynamically compiled literature-derived database. 325
  
• Claudia L. Kleinman, Nicolas Rodrigue, Cécile Bonnard, Hervé Philippe, Nicolas Lartillot:
  A maximum likelihood framework for protein design. 326
  
• Chaochun Wei, Michael R. Brent:
  Using ESTs to improve the accuracy of de novo gene prediction. 327
  
• Min Wang, Stephen R. Master, Lewis A. Chodosh:
  Computational expression deconvolution in a complex mammalian organ. 328
  
• Blazej Bulka, Marie desJardins, Stephen J. Freeland:
  An interactive visualization tool to explore the biophysical properties of amino acids and their contribution to substitution matrices. 329
  
• Seon-Young Kim, YongSung Kim:
  Genome-wide prediction of transcriptional regulatory elements of human promoters using gene expression and promoter analysis data. 330
  
• Thorsten Schmidt, Dmitrij Frishman:
  PROMPT: a protein mapping and comparison tool. 331
  
• Chen-Hsiang Yeang, Martin Vingron:
  A joint model of regulatory and metabolic networks. 332
  
• Mathieu Miron, Owen Z. Woody, Alexandre Marcil, Carl Murie, Robert Sladek, Robert Nadon:
  A methodology for global validation of microarray experiments. 333
  
• Hua Xu, Marianthi Markatou, Rositsa Dimova, Hongfang Liu, Carol Friedman:
  Machine learning and word sense disambiguation in the biomedical domain: design and evaluation issues. 334
  
• Mattia Pelizzola, Norman Pavelka, Maria Foti, Paola Ricciardi-Castagnoli:
  AMDA: an R package for the automated microarray data analysis. 335
  
• Mridul K. Kalita, Gowthaman Ramasamy, Sekhar Duraisamy, Virander S. Chauhan, Dinesh Gupta:
  ProtRepeatsDB: a database of amino acid repeats in genomes. 336
  
• Roel G. W. Verhaak, Mathijs A. Sanders, Maarten A. Bijl, Ruud Delwel, Sebastiaan Horsman, Michael J. Moorhouse, Peter van der Spek, Bob Löwenberg, Peter J. M. Valk:
  HeatMapper: powerful combined visualization of gene expression profile correlations, genotypes, phenotypes and sample characteristics. 337
  
• Cheryl Wolting, C. Jane McGlade, David Tritchler:
  Cluster analysis of protein array results via similarity of Gene Ontology annotation. 338
  
• Elaine C. Meng, Eric F. Pettersen, Gregory S. Couch, Conrad C. Huang, Thomas E. Ferrin:
  Tools for integrated sequence-structure analysis with UCSF Chimera. 339
  
• D. Casciari, Michele Seeber, Francesca Fanelli:
  Quaternary structure predictions of transmembrane proteins starting from the monomer: a docking-based approach. 340
  
• Randi Vita, Kerrie Vaughan, Laura Zarebski, Nima Salimi, Ward Fleri, Howard Grey, Muthu Sathiamurthy, John Mokili, Huynh-Hoa Bui, Philip E. Bourne, Julia V. Ponomarenko, Romulo de Castro Jr., Russell K. Chan, John Sidney, Stephen S. Wilson, Scott Stewart, Scott Way, Björn Peters, Alessandro Sette:
  Curation of complex, context-dependent immunological data. 341
  
• Jianjun Hu, Yifeng D. Yang, Daisuke Kihara:
  EMD: an ensemble algorithm for discovering regulatory motifs in DNA sequences. 342
  
• Peter D. Wentzell, Tobias K. Karakach, Sushmita Roy, M. Juanita Martinez, Christopher P. Allen, Margaret Werner-Washburne:
  Multivariate curve resolution of time course microarray data. 343
  
• Philipp Heuser, Dietmar Schomburg:
  Optimised amino acid specific weighting factors for unbound protein docking. 344
  
• Pavlos Pavlidis, Panayiota Poirazi:
  Individualized markers optimize class prediction of microarray data. 345
  
• Peter L. Chang, Andrew W. Rinne, T. Gregory Dewey:
  Structure alignment based on coding of local geometric measures. 346
  
• Zuoshuang Xiang, Wenjie Zheng, Yongqun He:
  BBP: Brucella genome annotation with literature mining and curation. 347
  
• Rohit Ghai, Hannes Lindemann, Trinad Chakraborty:
  Integrated functional visualization of eukaryotic genomes. 348
  
• Matti Nykter, Tommi Aho, Miika Ahdesmäki, Pekka Ruusuvuori, Antti Lehmussola, Olli Yli-Harja:
  Simulation of microarray data with realistic characteristics. 349
  
• Alexander F. Auch, Stefan R. Henz, Barbara R. Holland, Markus Göker:
  Genome BLAST distance phylogenies inferred from whole plastid and whole mitochondrion genome sequences. 350
  
• Hee Shin Kim, Jay E. Mittenthal, Gustavo Caetano-Anollés:
  MANET: tracing evolution of protein architecture in metabolic networks. 351
  
• Pierluigi Lollini, Santo Motta, Francesco Pappalardo:
  Discovery of cancer vaccination protocols with a genetic algorithm driving an agent based simulator. 352
  
• Anne-Mette K. Hein, Sylvia Richardson:
  A powerful method for detecting differentially expressed genes from GeneChip arrays that does not require replicates. 353
  
• Pavel Pospisil, Lakshmanan K. Iyer, S. James Adelstein, Amin I. Kassis:
  A combined approach to data mining of textual and structured data to identify cancer-related targets. 354
  
• Taner Z. Sen, Andrzej Kloczkowski, Robert L. Jernigan:
  Functional clustering of yeast proteins from the protein-protein interaction network. 355
  
• W. John Wilbur, Andrey Rzhetsky, Hagit Shatkay:
  New directions in biomedical text annotation: definitions, guidelines and corpus construction. 356
  
• Tomas Ohlson, Varun Aggarwal, Arne Elofsson, Robert M. MacCallum:
  Improved alignment quality by combining evolutionary information, predicted secondary structure and self-organizing maps. 357
  
• Tadayoshi Fushiki, Hironori Fujisawa, Shinto Eguchi:
  Identification of biomarkers from mass spectrometry data using a "common" peak approach. 358
  
• Ian B. Jeffery, Desmond G. Higgins, Aedín C. Culhane:
  Comparison and evaluation of methods for generating differentially expressed gene lists from microarray data. 359
  
• Silpa Suthram, Tomer Shlomi, Eytan Ruppin, Roded Sharan, Trey Ideker:
  A direct comparison of protein interaction confidence assignment schemes. 360
  
• Paul Marjoram, Jing Chang, Peter W. Laird, Kimberly D. Siegmund:
  Cluster analysis for DNA methylation profiles having a detection threshold. 361
  
• Pin-Hao Chi, Chi-Ren Shyu, Dong Xu:
  A fast SCOP fold classification system using content-based E-Predict algorithm. 362
  
• Monica Chagoyen, Pedro Carmona-Saez, Concha Gil, José María Carazo, Alberto D. Pascual-Montano:
  A literature-based similarity metric for biological processes. 363
  
• Ingolf Sommer, Stefano Toppo, Oliver Sander, Thomas Lengauer, Silvio C. E. Tosatto:
  Improving the quality of protein structure models by selecting from alignment alternatives. 364
  
• Sylvain Pitre, Frank K. H. A. Dehne, Albert Chan, James Cheetham, Alex Duong, Andrew Emili, Marinella Gebbia, Jack Greenblatt, Matthew Jessulat, Nevan J. Krogan, Xuemei Luo, Ashkan Golshani:
  PIPE: a protein-protein interaction prediction engine based on the re-occurring short polypeptide sequences between known interacting protein pairs. 365
  
• Alberto D. Pascual-Montano, Pedro Carmona-Saez, Monica Chagoyen, Francisco Tirado, José María Carazo, Roberto D. Pascual-Marqui:
  bioNMF: a versatile tool for non-negative matrix factorization in biology. 366
  
• Michal Dabrowski, Stein Aerts, Bozena Kaminska:
  Prediction of a key role of motifs binding E2F and NR2F in down-regulation of numerous genes during the development of the mouse hippocampus. 367
  
• Naoto Tanaka, Takashi Abe, Satoru Miyazaki, Hideaki Sugawara:
  G-InforBIO: integrated system for microbial genomics. 368
  
• Martin Hoffmann, Dirk Pohlers, Dirk Koczan, Hans-Jürgen Thiesen, Stefan Wölfl, Raimund W. Kinne:
  Robust computational reconstitution - a new method for the comparative analysis of gene expression in tissues and isolated cell fractions. 369
  
• David Chen, Hans-Michael Müller, Paul W. Sternberg:
  Automatic document classification of biological literature. 370
  
• Catherine Lozupone, Micah Hamady, Rob Knight:
  UniFrac - An online tool for comparing microbial community diversity in a phylogenetic context. 371
  
• Katrin Fundel, Ralf Zimmer:
  Gene and protein nomenclature in public databases. 372
  
• Jeyakumar Natarajan, Daniel P. Berrar, Werner Dubitzky, Catherine J. Hack, Yonghong Zhang, Catherine DeSesa, James R. Van Brocklyn, Eric G. Bremer:
  Text mining of full-text journal articles combined with gene expression analysis reveals a relationship between sphingosine-1-phosphate and invasiveness of a glioblastoma cell line. 373
  
• Zhaotao Cai, Xizeng Mao, Songgang Li, Liping Wei:
  Genome comparison using Gene Ontology (GO) with statistical testing. 374
  
• Arun M. Jesubatham, Mark D. Burow:
  PeanutMap: an online genome database for comparative molecular maps of peanut. 375
  
• Daniel A. Pollard, Alan M. Moses, Venky N. Iyer, Michael B. Eisen:
  Detecting the limits of regulatory element conservation and divergence estimation using pairwise and multiple alignments. 376
  
• Derrick K. Rollins, Dongmei Zhai, Alrica L. Joe, Jack W. Guidarelli, Abhishek Murarka, Ramon Gonzalez:
  A novel data mining method to identify assay-specific signatures in functional genomic studies. 377
  
• Xujing Wang, Shuang Jia, Lisa Meyer, Bixia Xiang, Li-Yen Chen, Nan Jiang, Carol Moreno, Howard J. Jacob, Soumitra Ghosh, Martin J. Hessner:
  Comprehensive quality control utilizing the prehybridization third-dye image leads to accurate gene expression measurements by cDNA microarrays. 378
  
• Li-Yeh Chuang, Cheng-Hong Yang, Yu-Huei Cheng, De-Leung Gu, Phei-Lang Chang, Ke-Hung Tsui, Hsueh-Wei Chang:
  V-MitoSNP: visualization of human mitochondrial SNPs. 379
  
• Ralf Steuer, Peter Humburg, Joachim Selbig:
  Validation and functional annotation of expression-based clusters based on gene ontology. 380
  
• Shawn Cokus, Sherri Rose, David Haynor, Niels Grønbech-Jensen, Matteo Pellegrini:
  Modelling the network of cell cycle transcription factors in the yeast Saccharomyces cerevisiae. 381
  
• Elijah Roberts, John Eargle, Dan Wright, Zaida Luthey-Schulten:
  MultiSeq: unifying sequence and structure data for evolutionary analysis. 382
  
• B. Jayashree, Praveen T. Reddy, Y. Leeladevi, Jonathan H. Crouch, V. Mahalakshmi, Hutokshi K. Buhariwalla, K. E. Eshwar, Emma Mace, Rolf Folksterma, S. Senthilvel, Rajeev K. Varshney, K. Seetha, R. Rajalakshmi, V. P. Prasanth, Subhash Chandra, L. Swarupa, P. SriKalyani, David A. Hoisington:
  Laboratory Information Management Software for genotyping workflows: applications in high throughput crop genotyping. 383
  
• Srinivas Veerla, Mattias Höglund:
  Analysis of promoter regions of co-expressed genes identified by microarray analysis. 384
  
• Kai Wang, Ram Samudrala:
  Incorporating background frequency improves entropy-based residue conservation measures. 385
  
• Jing Zhao, Hong Yu, Jianhua Luo, Zhi-Wei Cao, Yi-Xue Li:
  Hierarchical modularity of nested bow-ties in metabolic networks. 386
  
• Nicola Ancona, Rosalia Maglietta, Ada Piepoli, Annarita D'Addabbo, R. Cotugno, M. Savino, Sabino Liuni, Massimo Carella, Graziano Pesole, Francesco Perri:
  On the statistical assessment of classifiers using DNA microarray data. 387
  
• Jochen Jaeger, Rainer Spang:
  Selecting normalization genes for small diagnostic microarrays. 388
  
• Michael Beckstette, Robert Homann, Robert Giegerich, Stefan Kurtz:
  Fast index based algorithms and software for matching position specific scoring matrices. 389
  
• Kuo Ping Chiu, Chee-Hong Wong, Qiongyu Chen, Pramila Ariyaratne, Hong Sain Ooi, Chia-Lin Wei, Wing-Kin Sung, Yijun Ruan:
  PET-Tool: a software suite for comprehensive processing and managing of Paired-End diTag (PET) sequence data. 390
  
• Sébastien Lemieux:
  Probe-level linear model fitting and mixture modeling results in high accuracy detection of differential gene expression. 391
  
• Jung-Hsien Chiang, Jyh-Wei Shin, Heng-Hui Liu, Chong-Liang Chin:
  GeneLibrarian: an effective gene-information summarization and visualization system. 392
  
• Idan Menashe, Ronny Aloni, Doron Lancet:
  A probabilistic classifier for olfactory receptor pseudogenes. 393
  
• Qingfeng Chen, Yi-Ping Phoebe Chen:
  Mining frequent patterns for AMP-activated protein kinase regulation on skeletal muscle. 394
  
• Jinwook Seo, Eric P. Hoffman:
  Probe set algorithms: is there a rational best bet? 395
  
• Matthieu Defrance, Hélène Touzet:
  Predicting transcription factor binding sites using local over-representation and comparative genomics. 396
  
• Susmita Datta, Somnath Datta:
  Methods for evaluating clustering algorithms for gene expression data using a reference set of functional classes. 397
  
• Tim Hulsen, Jacob de Vlieg, Peter M. A. Groenen:
  PhyloPat: phylogenetic pattern analysis of eukaryotic genes. 398
  
• Hiro Takahashi, Takeshi Nemoto, Teruhiko Yoshida, Hiroyuki Honda, Tadashi Hasegawa:
  Cancer diagnosis marker extraction for soft tissue sarcomas based on gene expression profiling data by using projective adaptive resonance theory (PART) filtering method. 399
  
• Robin D. Dowell, Sean R. Eddy:
  Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints. 400
  
• Akira R. Kinjo, Ken Nishikawa:
  CRNPRED: highly accurate prediction of one-dimensional protein structures by large-scale critical random networks. 401
  
• Davide Baù, Alberto J. M. Martin, Catherine Mooney, Alessandro Vullo, Ian Walsh, Gianluca Pollastri:
  Distill: a suite of web servers for the prediction of one-, two- and three-dimensional structural features of proteins. 402
  
• Mark K. Titulaer, Ivar Siccama, Lennard J. Dekker, Angelique L. C. T. van Rijswijk, Ron M. A. Heeren, Peter A. E. Sillevis Smitt, Theo M. Luider:
  A database application for pre-processing, storage and comparison of mass spectra derived from patients and controls. 403
  
• Wenjie Shu, Xiaochen Bo, Rujia Liu, Dongsheng Zhao, Zhiqiang Zheng, Shengqi Wang:
  RDMAS: a web server for RNA deleterious mutation analysis. 404
  
• Chris J. Needham, James R. Bradford, Andrew J. Bulpitt, Matthew A. Care, David R. Westhead:
  Predicting the effect of missense mutations on protein function: analysis with Bayesian networks. 405
  
• James Thompson, Shuba Gopal:
  Correction: genetic algorithm learning as a robust approach to RNA editing site site prediction. 406
  
• Stuart G. Baker, Barnett S. Kramer:
  Identifying genes that contribute most to good classification in microarrays. 407
  
• Kannan Tharakaraman, Leonardo Mariño-Ramírez, Sergey Sheetlin, David Landsman, John L. Spouge:
  Scanning sequences after Gibbs sampling to find multiple occurrences of functional elements. 408
  
• Stephan Hutter, Albert J. Vilella, Julio Rozas:
  Genome-wide DNA polymorphism analyses using VariScan. 409
  
• Eric D. Scheeff, Philip E. Bourne:
  Application of protein structure alignments to iterated hidden Markov model protocols for structure prediction. 410
  
• Sung-Kyu Kim, Jin-Wu Nam, Je-Keun Rhee, Wha-Jin Lee, Byoung-Tak Zhang:
  miTarget: microRNA target gene prediction using a support vector machine. 411
  
• Cheong Xin Chan, Robert G. Beiko, Mark A. Ragan:
  Detecting recombination in evolving nucleotide sequences. 412
  
• Angela Re, Davide Corà, Alda Maria Puliti, Michele Caselle, Isabella Sbrana:
  Correlated fragile site expression allows the identification of candidate fragile genes involved in immunity and associated with carcinogenesis. 413
  
• Shigeyuki Oba, Shin Ishii:
  Semi-supervised discovery of differential genes. 414
  
• G. P. S. Raghava, Geoffrey J. Barton:
  Quantification of the variation in percentage identity for protein sequence alignments. 415
  
• Mary E. Dolan, Constance C. Holden, M. Kate Beard, Carol J. Bult:
  Genomes as geography: using GIS technology to build interactive genome feature maps. 416
  
• Rui Jiang, Hua Yang, Fengzhu Sun, Ting Chen:
  Searching for interpretable rules for disease mutations: a simulated annealing bump hunting strategy. 417
  
• Jussi Paananen, Markus Storvik, Garry Wong:
  CROPPER: a metagene creator resource for cross-platform and cross-species compendium studies. 418
  
• Thomas Down, Bernard Leong, Tim J. P. Hubbard:
  A machine learning strategy to identify candidate binding sites in human protein-coding sequence. 419
  
• Evan S. Snitkin, Adam M. Gustafson, Joseph C. Mellor, Jie Wu, Charles DeLisi:
  Comparative assessment of performance and genome dependence among phylogenetic profiling methods. 420
  
• Wei-Sheng Wu, Wen-Hsiung Li, Bor-Sen Chen:
  Computational reconstruction of transcriptional regulatory modules of the yeast cell cycle. 421
  
• Florent Baty, Michaël Facompré, Jan Wiegand, Joseph Schwager, Martin H. Brutsche:
  Analysis with respect to instrumental variables for the exploration of microarray data structures. 422
  
• Pierre-Étienne Jacques, Sébastien Rodrigue, Luc Gaudreau, Jean Goulet, Ryszard Brzezinski:
  Detection of prokaryotic promoters from the genomic distribution of hexanucleotide pairs. 423
  
• Maksim V. Plikus, Zina Zhang, Cheng-Ming Chuong:
  PubFocus: semantic MEDLINE/PubMed citations analytics through integration of controlled biomedical dictionaries and ranking algorithm. 424
  
• Jiangning Song, Kevin Burrage:
  Predicting residue-wise contact orders in proteins by support vector regression. 425
  
• Alex Lewin, Ian C. Grieve:
  Grouping Gene Ontology terms to improve the assessment of gene set enrichment in microarray data. 426
  
• William A. Stokes, Benjamin S. Glick:
  MICA: desktop software for comprehensive searching of DNA databases. 427
  
• Peter S. Klosterman, Andrew V. Uzilov, Yuri R. Bendaña, Robert K. Bradley, Sharon Chao, Carolin Kosiol, Nick Goldman, Ian Holmes:
  XRate: a fast prototyping, training and annotation tool for phylo-grammars. 428
  
• Julian Mintseris, Michael B. Eisen:
  Design of a combinatorial DNA microarray for protein-DNA interaction studies. 429
  
• Hiraku Morisawa, Mikako Hirota, Tosifusa Toda:
  Development of an open source laboratory information management system for 2-D gel electrophoresis-based proteomics workflow. 430
  
• Tamás Arányi, András Váradi, István Simon, Gábor E. Tusnády:
  The BiSearch web server. 431
  
• Prabakaran Subramani, Rajendra Sahu, Shekhar Verma:
  Feature selection using Haar wavelet power spectrum. 432
  
• Todd J. Treangen, Xavier Messeguer:
  M-GCAT: interactively and efficiently constructing large-scale multiple genome comparison frameworks in closely related species. 433
  
• Srinka Ghosh, Heather A. Hirsch, Edward A. Sekinger, Kevin Struhl, Thomas R. Gingeras:
  Rank-statistics based enrichment-site prediction algorithm developed for chromatin immunoprecipitation on chip experiments. 434
  
• Isabel K. Darcy, Jeff Chang, Nathan Druivenga, Colin McKinney, Ram K. Medikonduri, Stacy Mills, Junalyn Navarra-Madsen, Arun Ponnusamy, Jesse Sweet, Travis Thompson:
  Coloring the Mu transpososome. 435
  
• Olivier Lespinet, Bernard Labedan:
  ORENZA: a web resource for studying ORphan ENZyme activities. 436
  
• Denis C. Bauer, Mikael Bodén, Ricarda Thier, Elizabeth M. Gillam:
  STAR: predicting recombination sites from amino acid sequence. 437
  
• Jifeng Tang, Ben Vosman, Roeland E. Voorrips, C. Gerard van der Linden, Jack A. M. Leunissen:
  QualitySNP: a pipeline for detecting single nucleotide polymorphisms and insertions/deletions in EST data from diploid and polyploid species. 438
  
• François Chevenet, Marie-Christine Brun, Anne-Laure Bañuls, Bernard Jacq, Richard Christen:
  TreeDyn: towards dynamic graphics and annotations for analyses of trees. 439
  
• William W. Cohen, Einat Minkov:
  A graph-search framework for associating gene identifiers with documents. 440
  
• Paul M. Harrison:
  Exhaustive assignment of compositional bias reveals universally prevalent biased regions: analysis of functional associations in human and Drosophila. 441
  
• Manju R. Mamtani, Tushar P. Thakre, Mrunal Y. Kalkonde, Manik A. Amin, Yogeshwar V. Kalkonde, Amit P. Amin, Hemant Kulkarni:
  A simple method to combine multiple molecular biomarkers for dichotomous diagnostic classification. 442
  
• Rachel S. G. Sealfon, Matthew A. Hibbs, Curtis Huttenhower, Chad L. Myers, Olga G. Troyanskaya:
  GOLEM: an interactive graph-based gene-ontology navigation and analysis tool. 443
  
• Tim Hulsen, Jacob de Vlieg, Jack A. M. Leunissen, Peter M. A. Groenen:
  Testing statistical significance scores of sequence comparison methods with structure similarity. 444
  
• Kalyan Gayen, K. V. Venkatesh:
  Analysis of optimal phenotypic space using elementary modes as applied to Corynebacterium glutamicum. 445
  
• Michael Hackenberg, Christopher Previti, Pedro Luis Luque-Escamilla, Pedro Carpena, José Martínez-Aroza, José L. Oliver:
  CpGcluster: a distance-based algorithm for CpG-island detection. 446
  
• Xiyin Wang, Xiaoli Shi, Zhe Li, Qihui Zhu, Lei Kong, Wen Tang, Song Ge, Jingchu Luo:
  Statistical inference of chromosomal homology based on gene colinearity and applications to Arabidopsis and rice. 447
  
• Babak Shahbaba, Radford M. Neal:
  Gene function classification using Bayesian models with hierarchy-based priors. 448
  
• Jianjun Hu, Haifeng Li, Michael S. Waterman, Xianghong Jasmine Zhou:
  Integrative missing value estimation for microarray data. 449
  
• Stéphane Descorps-Declère, Danielle Ziébelin, François Rechenmann, Alain Viari:
  Genepi: a blackboard framework for genome annotation. 450
  
• Jian Huang, Alex Gutteridge, Wataru Honda, Minoru Kanehisa:
  MIMOX: a web tool for phage display based epitope mapping. 451
  
• Min Wu, Cheng Thao, Xiangming Mu, Ethan V. Munson:
  A fisheye viewer for microarray-based gene expression data. 452
  
• Alessandro Coppe, Gian Antonio Danieli, Stefania Bortoluzzi:
  REEF: searching REgionally Enriched Features in genomes. 453
  
• Thomas Mailund, Søren Besenbacher, Mikkel H. Schierup:
  Whole genome association mapping by incompatibilities and local perfect phylogenies. 454
  
• Huzefa Rangwala, George Karypis:
  Building multiclass classifiers for remote homology detection and fold recognition. 455
  
• You Jung Kim, Jignesh M. Patel:
  A framework for protein structure classification and identification of novel protein structures. 456
  
• Zhi Liang, Meng Xu, Maikun Teng, Liwen Niu:
  Comparison of protein interaction networks reveals species conservation and divergence. 457
  
• Yu Xue, Hu Chen, Changjiang Jin, Zhirong Sun, Xuebiao Yao:
  NBA-Palm: prediction of palmitoylation site implemented in Naïve Bayes algorithm. 458
  
• Carol L. Ecale Zhou, Marisa Lam, Jason Smith, Adam Zemla, Matthew D. Dyer, Thomas A. Kuczmarski, Elizabeth A. Vitalis, Thomas R. Slezak:
  MannDB - A microbial database of automated protein sequence analyses and evidence integration for protein characterization. 459
  
• Degui Zhi, S. Sri Krishna, Haibo Cao, Pavel A. Pevzner, Adam Godzik:
  Representing and comparing protein structures as paths in three-dimensional space. 460
  
• Chunguang Liang, Thomas Dandekar:
  inGeno - an integrated genome and ortholog viewer for improved genome to genome comparisons. 461
  
• Aijazuddin Syed, Chris Upton:
  Java GUI for InterProScan (JIPS): A tool to help process multiple InterProScans and perform ortholog analysis. 462
  
• Ji Wan, Wen Liu, Qiqi Xu, Yongliang Ren, Darren R. Flower, Tongbin Li:
  SVRMHC prediction server for MHC-binding peptides. 463
  
• Simon Katz, Rafael A. Irizarry, Xue Lin, Mark Tripputi, Mark W. Porter:
  A summarization approach for Affymetrix GeneChip data using a reference training set from a large, biologically diverse database. 464
  
• Stephan Weise, Ivo Grosse, Christian Klukas, Dirk Koschützki, Uwe Scholz, Falk Schreiber, Björn H. Junker:
  Meta-All: a system for managing metabolic pathway information. 465
  
• Charles Richard Bradshaw, Vineeth Surendranath, Bianca Habermann:
  ProFAT: a web-based tool for the functional annotation of protein sequences. 466
  
• Sophie Lemoine, Florence Combes, Nicolas Servant, Stéphane Le Crom:
  Goulphar: rapid access and expertise for standard two-color microarray normalization methods. 467
  
• Lakshmi K. Matukumalli, John J. Grefenstette, David L. Hyten, Ik-Young Choi, Perry B. Cregan, Curtis P. Van Tassell:
  SNP-PHAGE - High throughput SNP discovery pipeline. 468
  
• André Fujita, João Ricardo Sato, Leonardo de Oliveira Rodrigues, Carlos Eduardo Ferreira, Mari Cleide Sogayar:
  Evaluating different methods of microarray data normalization. 469
  
• Vidar Beisvag, Frode K. R. Jünge, Hallgeir Bergum, Lars Jølsum, Stian Lydersen, Clara-Cecilie Günther, Heri Ramampiaro, Mette Langaas, Arne K. Sandvik, Astrid Lægreid:
  GeneTools - application for functional annotation and statistical hypothesis testing. 470
  
• Paulo A. S. Nuin, Zhouzhi Wang, Elisabeth R. M. Tillier:
  The accuracy of several multiple sequence alignment programs for proteins. 471
  
• Ikuo Uchiyama, Toshio Higuchi, Ichizo Kobayashi:
  CGAT: a comparative genome analysis tool for visualizing alignments in the analysis of complex evolutionary changes between closely related genomes. 472
  
• Coral del Val, Vladimir Yurjevich Kuryshev, Karl-Heinz Glatting, Peter Ernst, Agnes Hotz-Wagenblatt, Annemarie Poustka, Sándor Suhai, Stefan Wiemann:
  CAFTAN: a tool for fast mapping, and quality assessment of cDNAs. 473
  
• Oleksiy Kohany, Andrew J. Gentles, Lukasz Hankus, Jerzy Jurka:
  Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor. 474
  
• Kim Kultima, Birger Scholz, Henrik Alm, Karl Sköld, Marcus Svensson, Alan R. Crossman, Erwan Bezard, Per E. Andrén, Ingrid Lönnstedt:
  Normalization and expression changes in predefined sets of proteins using 2D gel electrophoresis: A proteomic study of L-DOPA induced dyskinesia in an animal model of Parkinson's disease using DIGE. 475
  
• Micah Hamady, M. D. Betterton, Rob Knight:
  Using the nucleotide substitution rate matrix to detect horizontal gene transfer. 476
  
• Patrick Durand, Frédéric Mahé, Anne-Sophie Valin, Jacques Nicolas:
  Browsing repeats in genomes: Pygram and an application to non-coding region analysis. 477
  
• Illés J. Farkas, Chuang Wu, Chakra Chennubhotla, Ivet Bahar, Zoltán N. Oltvai:
  Topological basis of signal integration in the transcriptional-regulatory network of the yeast, Saccharomyces cerevisiae. 478
  
• Kosaku Shinoda, Nozomu Yachie, Takeshi Masuda, Naoyuki Sugiyama, Masahiro Sugimoto, Tomoyoshi Soga, Masaru Tomita:
  HybGFS: a hybrid method for genome-fingerprint scanning. 479
  
• Jean-François Lucier, Lucien Junior Bergeron, Francis P. Brière, Rodney Ouellette, Sherif Abou Elela, Jean-Pierre Perreault:
  RiboSubstrates: a web application addressing the cleavage specificities of ribozymes in designated genomes. 480
  
• Fabien Campagne, Lucy Skrabanek:
  Mining expressed sequence tags identifies cancer markers of clinical interest. 481
  
• Andrea Sackmann, Monika Heiner, Ina Koch:
  Application of Petri net based analysis techniques to signal transduction pathways. 482
  
• Maria Rodriguez-Fernandez, Jose A. Egea, Julio R. Banga:
  Novel metaheuristic for parameter estimation in nonlinear dynamic biological systems. 483
  
• Virpi Ahola, Tero Aittokallio, Mauno Vihinen, Esa Uusipaikka:
  A statistical score for assessing the quality of multiple sequence alignments. 484
  
• Rakesh Kaundal, Amar S. Kapoor, Gajendra P. S. Raghava:
  Machine learning techniques in disease forecasting: a case study on rice blast prediction. 485
  
• Kazuhito Shida:
  GibbsST: a Gibbs sampling method for motif discovery with enhanced resistance to local optima. 486
  
• Rodrigo Malig, Cristian Varela, Eduardo Agosin, Francisco Melo:
  Accurate and unambiguous tag-to-gene mapping in serial analysis of gene expression. 487
  
• Sylvain Brohée, Jacques van Helden:
  Evaluation of clustering algorithms for protein-protein interaction networks. 488
  
• Tim F. Rayner, Philippe Rocca-Serra, Paul T. Spellman, Helen C. Causton, Anna Farne, Ele Holloway, Rafael A. Irizarry, Junmin Liu, Donald Maier, Michael Miller, Kjell Petersen, John Quackenbush, Gavin Sherlock, Christian J. Stoeckert Jr., Joseph White, Patricia L. Whetzel, Farrell Wymore, Helen E. Parkinson, Ugis Sarkans, Catherine A. Ball, Alvis Brazma:
  A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB. 489
  
• Philipp N. Seibel, Jan Krüger, Sven Hartmeier, Knut Schwarzer, Kai Löwenthal, Henning Mersch, Thomas Dandekar, Robert Giegerich:
  XML schemas for common bioinformatic data types and their application in workflow systems. 490
  
• Zhengdeng Lei, Yang Dai:
  Assessing protein similarity with Gene Ontology and its use in subnuclear localization prediction. 491
  
• Yang Jin, Ryan T. McDonald, Kevin Lerman, Mark A. Mandel, Steven Carroll, Mark Y. Liberman, Fernando C. Pereira, Raymond S. Winters, Peter S. White:
  Automated recognition of malignancy mentions in biomedical literature. 492
  
• Na Liu, Tianming Wang:
  A method for rapid similarity analysis of RNA secondary structures. 493
  
• Anna Lovrics, Attila Csikasz-Nagy, István Gy Zsély, Judit Zádor, Tamás Turányi, Béla Novák:
  Time scale and dimension analysis of a budding yeast cell cycle model. 494
  
• Markus Fischer, Quan K. Thai, Melanie Grieb, Jürgen Pleiss:
  DWARF - a data warehouse system for analyzing protein families. 495
  
• Filip Pattyn, Jasmien Hoebeeck, Piet Robbrecht, Evi Michels, Anne De Paepe, Guy Bottu, David Coornaert, Robert Herzog, Frank Speleman, Jo Vandesompele:
  methBLAST and methPrimerDB: web-tools for PCR based methylation analysis. 496
  
• Ethan G. Cerami, Gary D. Bader, Benjamin E. Gross, Chris Sander:
  cPath: open source software for collecting, storing, and querying biological pathways. 497
  
• Philipp N. Seibel, Tobias Müller, Thomas Dandekar, Jörg Schultz, Matthias Wolf:
  4SALE - A tool for synchronous RNA sequence and secondary structure alignment and editing. 498
  
• Saikat Chakrabarti, Christopher J. Lanczycki, Anna R. Panchenko, Teresa M. Przytycka, Paul A. Thiessen, Stephen H. Bryant:
  State of the art: refinement of multiple sequence alignments. 499
  
• Sreedevi Thiyagarajan, Miloslav Karhanek, Michael Akhras, Ronald W. Davis, Nader Pourmand:
  PathogenMIPer: a tool for the design of molecular inversion probes to detect multiple pathogens. 500
  
• Jesper Salomon, Darren R. Flower:
  Predicting Class II MHC-Peptide binding: a kernel based approach using similarity scores. 501
  
• Soon-Heng Tan, Hugo Willy, Wing-Kin Sung, See-Kiong Ng:
  A correlated motif approach for finding short linear motifs from protein interaction networks. 502
  
• Petras J. Kundrotas, Emil Alexov:
  Predicting residue contacts using pragmatic correlated mutations method: reducing the false positives. 503
  
• Yi-Ju Li, Puting Xu, Xuejun Qin, Donald E. Schmechel, Christine M. Hulette, Jonathan L. Haines, Margaret A. Pericak-Vance, John R. Gilbert:
  A comparative analysis of the information content in long and short SAGE libraries. 504
  
• Bartek Wilczynski, Torgeir R. Hvidsten, Andriy Kryshtafovych, Jerzy Tiuryn, Henryk Jan Komorowski, Krzysztof Fidelis:
  Using local gene expression similarities to discover regulatory binding site modules. 505
  
• Julio Saez-Rodriguez, Sebastian Mirschel, Rebecca Hemenway, Steffen Klamt, Ernst Dieter Gilles, Martin Ginkel:
  Visual setup of logical models of signaling and regulatory networks with ProMoT. 506
  
• Jonathan G. Lees, Andrew J. Miles, Robert W. Janes, B. A. Wallace:
  Novel methods for secondary structure determination using low wavelength (VUV) circular dichroism spectroscopic data. 507
  
• Kai Xia, Dong Dong, Jing-Dong J. Han:
  IntNetDB v1.0: an integrated protein-protein interaction network database generated by a probabilistic model. 508
  
• Michael Watson:
  CoXpress: differential co-expression in gene expression data. 509
  
• Björn Kolbeck, Patrick May, Tobias Schmidt-Goenner, Thomas Steinke, Ernst-Walter Knapp:
  Connectivity independent protein-structure alignment: a hierarchical approach. 510
  
• Andrew J. Holloway, Alicia Oshlack, Dileepa S. Diyagama, David D. L. Bowtell, Gordon K. Smyth:
  Statistical analysis of an RNA titration series evaluates microarray precision and sensitivity on a whole-array basis. 511
  
• Anne Kümmel, Sven Panke, Matthias Heinemann:
  Systematic assignment of thermodynamic constraints in metabolic network models. 512
  
• Mariano Latorre, Herman Silva, Juan Saba, Carito Guziolowski, Paula Vizoso, Veronica Martinez, Jonathan Maldonado, Andrea Morales, Rodrigo Caroca, Veronica Cambiazo, Reinaldo Campos-Vargas, Mauricio Gonzalez, Ariel Orellana, Julio Retamales, Lee A. Meisel:
  JUICE: a data management system that facilitates the analysis of large volumes of information in an EST project workflow. 513
  
• Francesca Demichelis, Paolo Magni, Paolo Piergiorgi, Mark A. Rubin, Riccardo Bellazzi:
  A hierarchical Naïve Bayes Model for handling sample heterogeneity in classification problems: an application to tissue microarrays. 514
  
• Wei Liu, Dong Li, Jiyang Zhang, Yunping Zhu, Fuchu He:
  SigFlux: A novel network feature to evaluate the importance of proteins in signal transduction networks. 515
  
• Wuming Gong, Yongliang Ren, Qiqi Xu, Yejun Wang, Dong Lin, Haiyan Zhou, Tongbin Li:
  Integrated siRNA design based on surveying of features associated with high RNAi effectiveness. 516
  
• Martin A. Ott, Gert Vriend:
  Correcting ligands, metabolites, and pathways. 517
  
• Pufeng Du, Yanda Li:
  Prediction of protein submitochondria locations by hybridizing pseudo-amino acid composition with various physicochemical features of segmented sequence. 518
  
• Caroline C. Friedel, Ralf Zimmer:
  Inferring topology from clustering coefficients in protein-protein interaction networks. 519
  
• Jean-Philippe Vert, Nicolas Foveau, Christian Lajaunie, Yves Vandenbrouck:
  An accurate and interpretable model for siRNA efficacy prediction. 520
  
• Mohua Podder, William J. Welch, Ruben H. Zamar, Scott J. Tebbutt:
  Dynamic variable selection in SNP genotype autocalling from APEX microarray data. 521
  
• Kenneth W. Berendzen, Kurt Stüber, Klaus Harter, Dierk Wanke:
  Cis-motifs upstream of the transcription and translation initiation sites are effectively revealed by their positional disequilibrium in eukaryote genomes using frequency distribution curves. 522
  
• Edward A. Kawas, Martin Senger, Mark D. Wilkinson:
  BioMoby extensions to the Taverna workflow management and enactment software. 523
  
• Shinsuke Yamada, Osamu Gotoh, Hayato Yamana:
  Improvement in accuracy of multiple sequence alignment using novel group-to-group sequence alignment algorithm with piecewise linear gap cost. 524
  
• Chun Meng Song, Boon Huat Yeo, Erwin Tantoso, Yuchen Yang, Yun Ping Lim, Kuo-Bin Li, Gunaretnam Rajagopal:
  iHAP - integrated haplotype analysis pipeline for characterizing the haplotype structure of genes. 525
  
• Federico E. Turkheimer, Federico Roncaroli, Benoit Hennuy, Christian Herens, Minh Nguyen, Didier Martin, Annick Evrard, Vincent Bours, Jacques Boniver, Manuel Deprez:
  Chromosomal patterns of gene expression from microarray data: methodology, validation and clinical relevance in gliomas. 526
  
• Reed A. Cartwright:
  Logarithmic gap costs decrease alignment accuracy. 527
  
• Keith Noto, Mark Craven:
  A specialized learner for inferring structured cis-regulatory modules. 528
  
• Christophe Dessimoz, Manuel Gil, Adrian Schneider, Gaston H. Gonnet:
  Fast estimation of the difference between two PAM/JTT evolutionary distances in triplets of homologous sequences. 529
  
• Richard Baran, Hayataro Kochi, Natsumi Saito, Makoto Suematsu, Tomoyoshi Soga, Takaaki Nishioka, Martin Robert, Masaru Tomita:
  MathDAMP: a package for differential analysis of metabolite profiles. 530
  
• Gully A. P. C. Burns, Wei-Cheng Cheng, Richard H. Thompson, Larry W. Swanson:
  The NeuARt II system: a viewing tool for neuroanatomical data based on published neuroanatomical atlases. 531
  
• Kevin L. Garwood, Christopher Garwood, Cornelia Hedeler, Tony Griffiths, Neil Swainston, Stephen G. Oliver, Norman W. Paton:
  Model-driven user interfaces for bioinformatics data resources: regenerating the wheel as an alternative to reinventing it. 532
  
• Catalin C. Barbacioru, Yulei Wang, Roger D. Canales, Yongming A. Sun, David N. Keys, Frances Chan, Karen A. Poulter, Raymond R. Samaha:
  Effect of various normalization methods on Applied Biosystems expression array system data. 533
  
• Benjamin M. Good, Edward A. Kawas, Byron Yu-Lin Kuo, Mark D. Wilkinson:
  iHOPerator: user-scripting a personalized bioinformatics Web, starting with the iHOP website. 534
  
• Björn Usadel, Axel Nagel, Dirk Steinhauser, Yves Gibon, Oliver E. Bläsing, Henning Redestig, Nese Sreenivasulu, Leonard Krall, Matthew A. Hannah, Fabien Poree, Alisdair R. Fernie, Mark Stitt:
  PageMan: An interactive ontology tool to generate, display, and annotate overview graphs for profiling experiments. 535
  
• Martin O. Jones, Mark L. Blaxter:
  TaxMan: a taxonomic database manager. 536
  
• Shuangge Ma:
  Empirical study of supervised gene screening. 537
  
• Maureen A. Sartor, Craig R. Tomlinson, Scott C. Wesselkamper, Siva Sivaganesan, George D. Leikauf, Mario Medvedovic:
  Intensity-based hierarchical Bayes method improves testing for differentially expressed genes in microarray experiments. 538
  
• Andreas Keller, Nicole Ludwig, Nicole Comtesse, Andreas Hildebrandt, Eckart Meese, Hans-Peter Lenhof:
  A minimally invasive multiple marker approach allows highly efficient detection of meningioma tumors. 539
  
• I. Emrah Nikerel, Wouter A. van Winden, Walter M. van Gulik, Joseph J. Heijnen:
  A method for estimation of elasticities in metabolic networks using steady state and dynamic metabolomics data and linlog kinetics. 540
  
• Bernhard Haubold, Thomas Wiehe:
  How repetitive are genomes? 541
  
• Lauri Eronen, Floris Geerts, Hannu Toivonen:
  HaploRec: efficient and accurate large-scale reconstruction of haplotypes. 542
  
• Satoshi Niijima, Satoru Kuhara:
  Recursive gene selection based on maximum margin criterion: a comparison with SVM-RFE. 543
  
• Arnim Jenett, Johannes E. Schindelin, Martin Heisenberg:
  The Virtual Insect Brain protocol: creating and comparing standardized neuroanatomy. 544