BMC Bioinformatics, Volume 5

Volume 5, 2004

• Andrew Butterfield, Vivek Vedagiri, Edward Lang, Cath Lawrence, Matthew J. Wakefield, Alexander Isaev, Gavin A. Huttley:
  PyEvolve: a toolkit for statistical modelling of molecular evolution. 1
  
• Vadim Alexandrov, Mark Gerstein:
  Using 3D Hidden Markov Models that explicitly represent spatial coordinates to model and compare protein structures. 2
  
• Bin Li, Warren J. Gallin:
  VKCDB: Voltage-gated potassium channel database. 3
  
• France Denoeud, Gilles Vergnaud:
  Identification of polymorphic tandem repeats by direct comparison of genome sequence from different bacterial strains : a web-based resource. 4
  
• Tomokazu Konishi:
  Three-parameter lognormal distribution ubiquitously found in cDNA microarray data and its application to parametric data treatment. 5
  
• Daniel A. Pollard, Casey M. Bergman, Jens Stoye, Susan E. Celniker, Michael B. Eisen:
  Benchmarking tools for the alignment of functional noncoding DNA. 6
  
• Benjamin Schuster-Böckler, Jörg Schultz, Sven Rahmann:
  HMM Logos for visualization of protein families. 7
  
• Estienne C. Swart, Winston A. Hide, Cathal Seoighe:
  FRAGS: estimation of coding sequence substitution rates from fragmentary data. 8
  
• Romesh Stanislaus, Liu Hong Jiang, Martha Swartz, John M. Arthur, Jonas S. Almeida:
  An XML standard for the dissemination of annotated 2D gel electrophoresis data complemented with mass spectrometry results. 9
  
• Radu Dobrin, Qasim K. Beg, Albert-László Barabási, Zoltán N. Oltvai:
  Aggregation of topological motifs in the Escherichia coli transcriptional regulatory network. 10
  
• Erich J. Baker, Leslie Galloway, Barbara Jackson, Denise Schmoyer, Jay Snoddy:
  MuTrack: a genome analysis system for large-scale mutagenesis in the mouse. 11
  
• Andreas Petri, Jan Fleckner, Mads Wichmann Matthiessen:
  Array-A-Lizer: A serial DNA microarray quality analyzer. 12
  
• Bryan Chi, Ronald J. deLeeuw, Bradley P. Coe, Calum MacAulay, Wan L. Lam:
  SeeGH - A software tool for visualization of whole genome array comparative genomic hybridization data. 13
  
• Afshin Nadershahi, Scott C. Fahrenkrug, Lynda B. M. Ellis:
  Comparison of computational methods for identifying translation initiation sites in EST data. 14
  
• Sara Light, Per Kraulis:
  Network analysis of metabolic enzyme evolution in Escherichia coli. 15
  
• Bing Zhang, Denise Schmoyer, Stefan Kirov, Jay Snoddy:
  GOTree Machine (GOTM): a web-based platform for interpreting sets of interesting genes using Gene Ontology hierarchies. 16
  
• Zhenjun Hu, Joseph C. Mellor, Jie Wu, Charles DeLisi:
  VisANT: an online visualization and analysis tool for biological interaction data. 17
  
• Dominic J. Allocco, Isaac S. Kohane, Atul J. Butte:
  Quantifying the relationship between co-expression, co-regulation and gene function. 18
  
• Jules J. Berman, Milton Datta, Andre Kajdacsy-Balla, Jonathan Melamed, Jan Orenstein, Kevin Dobbin, Ashok Patel, Rajiv Dhir, Michael J. Becich:
  The tissue microarray data exchange specification: implementation by the Cooperative Prostate Cancer Tissue Resource. 19
  
• Gaëlle Lelandais, Philippe Marc, Pierre Vincens, Claude Jacq, Stéphane Vialette:
  MiCoViTo: a tool for gene-centric comparison and visualization of yeast transcriptome states. 20
  
• Kamesh Munagala, Robert Tibshirani, Patrick O. Brown:
  Cancer characterization and feature set extraction by discriminative margin clustering. 21
  
• Rainer Merkl:
  SIGI: score-based identification of genomic islands. 22
  
• Shaun Mahony, James O. McInerney, Terry J. Smith, Aaron Golden:
  Gene prediction using the Self-Organizing Map: automatic generation of multiple gene models. 23
  
• David Adalsteinsson, David McMillen, Timothy C. Elston:
  Biochemical Network Stochastic Simulator (BioNetS): software for stochastic modeling of biochemical networks. 24
  
• Remko de Knikker, Youjun Guo, Jin-long Li, Albert K. H. Kwan, Kevin Y. Yip, David W. Cheung, Kei-Hoi Cheung:
  A web services choreography scenario for interoperating bioinformatics applications. 25
  
• Michael Wagner, Dayanand N. Naik, Alex Pothen, Srinivas Kasukurti, Raghu Ram Devineni, Bao-Ling Adam, O. John Semmes, George L. Wright Jr.:
  Computational protein biomarker prediction: a case study for prostate cancer. 26
  
• Henry R. Bigelow, Adam S. Wenick, Allan Wong, Oliver Hobert:
  CisOrtho: A program pipeline for genome-wide identification of transcription factor target genes using phylogenetic footprinting. 27
  
• Shashi B. Pandit, Rana Bhadra, V. S. Gowri, S. Balaji, B. Anand, Narayanaswamy Srinivasan:
  SUPFAM: A database of sequence superfamilies of protein domains. 28
  
• Pantelis G. Bagos, Theodore Liakopoulos, Ioannis C. Spyropoulos, Stavros J. Hamodrakas:
  A Hidden Markov Model method, capable of predicting and discriminating beta-barrel outer membrane proteins. 29
  
• Jan C. Biro, Josephine M. K. Biro:
  Frequent occurrence of recognition Site-like sequences in the restriction endonucleases. 30
  
• Feng Gao, Barrett C. Foat, Harmen J. Bussemaker:
  Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data. 31
  
• Petri Törönen:
  Selection of informative clusters from hierarchical cluster tree with gene classes. 32
  
• Alberto Riva, Isaac S. Kohane:
  A SNP-centric database for the investigation of the human genome. 33
  
• Rainer Breitling, Anna Amtmann, Pawel Herzyk:
  Iterative Group Analysis (iGA): A simple tool to enhance sensitivity and facilitate interpretation of microarray experiments. 34
  
• Anirban Bhaduri, Ganesan Pugalenthi, Ramanathan Sowdhamini:
  PASS2: an automated database of protein alignments organised as structural superfamilies. 35
  
• Ching Yu Austin Huang, Joel F. Studebaker, Anton Yuryev, Jianping Huang, Kathryn E. Scott, Jennifer Kuebler, Shobha Varde, Steven Alfisi, Craig A. Gelfand, Mark Pohl, Michael T. Boyce-Jacino:
  Auto-validation of fluorescent primer extension genotyping assay using signal clustering and neural networks. 36
  
• Artem Cherkasov, Steven J. M. Jones:
  Structural characterization of genomes by large scale sequence-structure threading. 37
  
• Lan V. Zhang, Sharyl L. Wong, Oliver D. King, Frederick P. Roth:
  Predicting co-complexed protein pairs using genomic and proteomic data integration. 38
  
• Alexander V. Diemand, Holger Scheib:
  MolTalk - a programming library for protein structures and structure analysis. 39
  
• Sohrab P. Shah, David Y. M. He, Jessica N. Sawkins, Jeffrey C. Druce, Gerald Quon, Drew Lett, Grace X. Y. Zheng, Tao Xu, B. F. Francis Ouellette:
  Pegasys: software for executing and integrating analyses of biological sequences. 40
  
• Marc N. Offman, Ramil N. Nurtdinov, Mikhail S. Gelfand, Dmitrij Frishman:
  No statistical support for correlation between the positions of protein interaction sites and alternatively spliced regions. 41
  
• Leah Barrera, Chris Benner, Yong-Chuan Tao, Elizabeth A. Winzeler, Yingyao Zhou:
  Leveraging two-way probe-level block design for identifying differential gene expression with high-density oligonucleotide arrays. 42
  
• J. Daniel Navarro, Naveen Talreja, Suraj Peri, B. M. Vrushabendra, B. P. Rashmi, N. Padma, Vineeth Surendranath, Chandra Kiran Jonnalagadda, P. S. Kousthub, Nandan Deshpande, K. Shanker, Akhilesh Pandey:
  BioBuilder as a database development and functional annotation platform for proteins. 43
  
• Olga V. Matveeva, Brian T. Foley, Vladimir A. Nemtsov, Raymond F. Gesteland, Senya Matsufuji, John F. Atkins, Aleksey Y. Ogurtsov, Svetlana A. Shabalina:
  Identification of regions in multiple sequence alignments thermodynamically suitable for targeting by consensus oligonucleotides: application to HIV genome. 44
  
• Timothy J. Harlow, J. Peter Gogarten, Mark A. Ragan:
  A hybrid clustering approach to recognition of protein families in 114 microbial genomes. 45
  
• Guohui Zhou, Xinyu Wen, Hang Liu, Michael J. Schlicht, Martin J. Hessner, Peter J. Tonellato, Milton W. Datta:
  B.E.A.R. GeneInfo: A tool for identifying gene-related biomedical publications through user modifiable queries. 46
  
• Jörg Rahnenführer, Daniel Bozinov:
  Hybrid clustering for microarray image analysis combining intensity and shape features. 47
  
• Timothy Hughes, Young Hyun, David A. Liberles:
  Visualising very large phylogenetic trees in three dimensional hyperbolic space. 48
  
• Christopher S. Coffey, Patricia R. Hebert, Marylyn D. Ritchie, Harlan M. Krumholz, J. Michael Gaziano, Paul M. Ridker, Nancy J. Brown, Douglas E. Vaughan, Jason H. Moore:
  An application of conditional logistic regression and multifactor dimensionality reduction for detecting gene-gene Interactions on risk of myocardial infarction: The importance of model validation. 49
  
• Allegra Via, Manuela Helmer-Citterich:
  A structural study for the optimisation of functional motifs encoded in protein sequences. 50
  
• Shandar Ahmad, M. Michael Gromiha, Hamed Fawareh, Akinori Sarai:
  ASAView: Database and tool for solvent accessibility representation in proteins. 51
  
• Srikanth Celamkoti, Sashidhara Kundeti, Anjan Purkayastha, Raja Mazumder, Charles Buck, Donald Seto:
  GeneOrder3.0: Software for comparing the order of genes in pairs of small bacterial genomes. 52
  
• Igor Dozmorov, Nicholas Knowlton, Yuhong Tang, Michael Centola:
  Statistical monitoring of weak spots for improvement of normalization and ratio estimates in microarrays. 53
  
• Jeffrey P. Townsend:
  Resolution of large and small differences in gene expression using models for the Bayesian analysis of gene expression levels and spotted DNA microarrays. 54
  
• Vincent Nègre, Christoph Grunau:
  eL-DASionator: an LDAS upload file generator. 55
  
• Lachlan James M. Coin, Alex Bateman, Richard Durbin:
  Enhanced protein domain discovery using taxonomy. 56
  
• Davide Corà, Ferdinando Di Cunto, Paolo Provero, Lorenzo Silengo, Michele Caselle:
  Computational identification of transcription factor binding sites by functional analysis of sets of genes sharing overrep-resented upstream motifs. 57
  
• Laurent Fourrier, Cristina Benros, Alexandre G. de Brevern:
  Use of a structural alphabet for analysis of short loops connecting repetitive structures. 58
  
• Ian Korf:
  Gene finding in novel genomes. 59
  
• Kellie J. Archer, Catherine I. Dumur, Viswanathan Ramakrishnan:
  Graphical technique for identifying a monotonic variance stabilizing transformation for absolute gene intensity signals. 60
  
• Artem Cherkasov, Steven J. M. Jones:
  An approach to large scale identification of non-obvious structural similarities between proteins. 61
  
• Gavin C. Conant, Andreas Wagner:
  A fast algorithm for determining the best combination of local alignments to a query sequence. 62
  
• Tristan Mary-Huard, Jean-Jacques Daudin, Stéphane Robin, Frédérique Bitton, Eric Cabannes, Pierre Hilson:
  Spotting effect in microarray experiments. 63
  
• Yvan Saeys, Sven Degroeve, Dirk Aeyels, Pierre Rouzé, Yves Van de Peer:
  Feature selection for splice site prediction: A new method using EDA-based feature ranking. 64
  
• Gordana Pavlovic-Lazetic, Nenad S. Mitic, Milos V. Beljanski:
  Bioinformatics analysis of SARS coronavirus genome polymorphism. 65
  
• Qinghua Cui, Tianzi Jiang, Bing Liu, Songde Ma:
  Esub8: A novel tool to predict protein subcellular localizations in eukaryotic organisms. 66
  
• Meena K. Sakharkar, Pandjassarame Kangueane:
  Genome SEGE: A database for 'intronless' genes in eukaryotic genomes. 67
  
• Andrea Bisognin, Stefania Bortoluzzi, Gian Antonio Danieli:
  Detection of chromosomal regions showing differential gene expression in human skeletal muscle and in alveolar rhabdomyosarcoma. 68
  
• Thomas Lütteke, Claus-Wilhelm von der Lieth:
  pdb-care (PDB CArbohydrate REsidue check): a program to support annotation of complex carbohydrate structures in PDB files. 69
  
• Yingchun Liu, Markus Ringnér:
  Multiclass discovery in array data. 70
  
• Robin D. Dowell, Sean R. Eddy:
  Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction. 71
  
• Lars Kiemer, Ole Lund, Søren Brunak, Nikolaj Blom:
  Coronavirus 3CL^pro proteinase cleavage sites: Possible relevance to SARS virus pathology. 72
  
• Daniel A. Pollard, Casey M. Bergman, Jens Stoye, Susan E. Celniker, Michael B. Eisen:
  Correction: Benchmarking tools for the alignment of functional noncodingDNA. 73
  
• Junbai Wang, Leonardo A. Meza-Zepeda, Stine H. Kresse, Ola Myklebost:
  M-CGH: Analysing microarray-based CGH experiments. 74
  
• Drew Lett, Michael Hsing, Frederic Pio:
  Interaction profile-based protein classification of death domain. 75
  
• Michelle L. Green, Peter D. Karp:
  A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases. 76
  
• Helene H. Thygesen, Aeilko H. Zwinderman:
  Comparing transformation methods for DNA microarray data. 77
  
• Kai Huang, Robert F. Murphy:
  Boosting accuracy of automated classification of fluorescence microscope images for location proteomics. 78
  
• Francesca Diella, Scott Cameron, Christine Gemünd, Rune Linding, Allegra Via, Bernhard Küster, Thomas Sicheritz-Pontén, Nikolaj Blom, Toby J. Gibson:
  Phospho.ELM: A database of experimentally verified phosphorylation sites in eukaryotic proteins. 79
  
• Barry Zeeberg, Joseph Riss, David W. Kane, Kimberly J. Bussey, Edward Uchio, W. Marston Linehan, J. Carl Barrett, John N. Weinstein:
  Mistaken Identifiers: Gene name errors can be introduced inadvertently when using Excel in bioinformatics. 80
  
• Hongying Jiang, Youping Deng, Huann-Sheng Chen, Lin Tao, Qiuying Sha, Jun Chen, Chung-Jui Tsai, Shuanglin Zhang:
  Joint analysis of two microarray gene-expression data sets to select lung adenocarcinoma marker genes. 81
  
• Tomokazu Konishi:
  Correction: Three-parameter lognormal distribution ubiquitously found in cDNA microarray data and its application to parametric data treatment. 82
  
• Lisa C. Romero, Thanh Vinh Nguyen, Benoit Deville, Oluwasanmi Ogunjumo, Anthony A. James:
  The MB2 gene family of Plasmodium species has a unique combination of S1 and GTP-binding domains. 83
  
• Eric H. Baehrecke, Niem Dang, Ketan Babaria, Ben Shneiderman:
  Visualization and analysis of microarray and gene ontology data with treemaps. 84
  
• Hao Zhu, Peter Y. H. Pang, Yan Sun, Pawan Dhar:
  Asynchronous adaptive time step in quantitative cellular automata modeling. 85
  
• Keith A. Jolley, Man-Suen Chan, Martin C. J. Maiden:
  mlstdbNet - distributed multi-locus sequence typing (MLST) databases. 86
  
• R. Henrik Nilsson, Balaji Rajashekar, Karl-Henrik Larsson, Björn M. Ursing:
  galaxieEST: addressing EST identity through automated phylogenetic analysis. 87
  
• Daniela Fera, Namhee Kim, Nahum Shiffeldrim, Julie Zorn, Uri Laserson, Hin Hark Gan, Tamar Schlick:
  RAG: RNA-As-Graphs web resource. 88
  
• Peisen Zhang, Huitao Sheng, Ryuhei Uehara:
  A double classification tree search algorithm for index SNP selection. 89
  
• Oleg N. Reva, Burkhard Tümmler:
  Global features of sequences of bacterial chromosomes, plasmids and phages revealed by analysis of oligonucleotide usage patterns. 90
  
• Luis Sánchez-Pulido, Ana María Rojas, Karel H. M. van Wely, Carlos Martínez-A, Alfonso Valencia:
  SPOC: A widely distributed domain associated with cancer, apoptosis and transcription. 91
  
• Matthias Wjst:
  Target SNP selection in complex disease association studies. 92
  
• Matthew J. Cockerill:
  Delayed impact: ISI's citation tracking choices are keeping scientists in the dark. 93
  
• Olivier Andrieu, Anna-Sophie Fiston, Dominique Anxolabéhère, Hadi Quesneville:
  Detection of transposable elements by their compositional bias. 94
  
• Marie-Christine Brun, Carl Herrmann, Alain Guénoche:
  Clustering proteins from interaction networks for the prediction of cellular functions. 95
  
• Ryan Brodie, Alex J. Smith, Rachel L. Roper, Vasily Tcherepanov, Chris Upton:
  Base-By-Base: Single nucleotide-level analysis of whole viral genome alignments. 96
  
• Dankyu Yoon, Sung-Gon Yi, Ju-Han Kim, Taesung Park:
  Two-stage normalization using background intensities in cDNA microarray data. 97
  
• Dariusz Plewczynski, Leszek Rychlewski, Yuzhen Ye, Lukasz Jaroszewski, Adam Godzik:
  Integrated web service for improving alignment quality based on segments comparison. 98
  
• Bin Yao, Sanjay N. Rakhade, Qunfang Li, Sharlin Ahmed, Raul Krauss, Sorin Draghici, Jeffrey A. Loeb:
  Accuracy of cDNA microarray methods to detect small gene expression changes induced by neuregulin on breast epithelial cells. 99
  
• Rainer Breitling, Anna Amtmann, Pawel Herzyk:
  Graph-based iterative Group Analysis enhances microarray interpretation. 100
  
• Artem Cherkasov, Shannan J. Ho Sui, Robert C. Brunham, Steven J. M. Jones:
  Structural characterization of genomes by large scale sequence-structure threading: application of reliability analysis in structural genomics. 101
  
• Baozhen Qiao, Ronald M. Weigel:
  A computer simulation analysis of the accuracy of partial genome sequencing and restriction fragment analysis in estimating genetic relationships: an application to papillomavirus DNA sequences. 102
  
• Chao Lu:
  Improving the scaling normalization for high-density oligonucleotide GeneChip expression microarrays. 103
  
• Jens Reeder, Robert Giegerich:
  Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics. 104
  
• Kishore J. Doshi, Jamie J. Cannone, Christian W. Cobaugh, Robin Ray Gutell:
  Evaluation of the suitability of free-energy minimization using nearest-neighbor energy parameters for RNA secondary structure prediction. 105
  
• Ruslan Sadreyev, Nick V. Grishin:
  Estimates of statistical significance for comparison of individual positions in multiple sequence alignments. 106
  
• Roberto H. Higa, Roberto C. Togawa, Arnaldo J. Montagner, Juliana F. Palandrani, Igor K. S. Okimoto, Paula R. Kuser, Michel E. B. Yamagishi, Adauto L. Mancini, Goran Neshich:
  STING Millennium Suite: integrated software for extensive analyses of 3d structures of proteins and their complexes. 107
  
• Bahrad A. Sokhansanj, J. Patrick Fitch, Judy N. Quong, Andrew A. Quong:
  Linear fuzzy gene network models obtained from microarray data by exhaustive search. 108
  
• Shane C. Dillon, Alex Bateman:
  The Hotdog fold: wrapping up a superfamily of thioesterases and dehydratases. 109
  
• James Lyons-Weiler, Satish Patel, Michael J. Becich, Tony E. Godfrey:
  Tests for finding complex patterns of differential expression in cancers: towards individualized medicine. 110
  
• Laurent Gautier, Morten Møller, Lennart Friis-Hansen, Steen Knudsen:
  Alternative mapping of probes to genes for Affymetrix chips. 111
  
• Jibin Sun, An-Ping Zeng:
  IdentiCS - Identification of coding sequence and in silico reconstruction of the metabolic network directly from unannotated low-coverage bacterial genome sequence. 112
  
• Robert C. Edgar:
  MUSCLE: a multiple sequence alignment method with reduced time and space complexity. 113
  
• Alexandre G. de Brevern, Serge A. Hazout, Alain Malpertuy:
  Influence of microarrays experiments missing values on the stability of gene groups by hierarchical clustering. 114
  
• Zhaoyang Feng, Christopher J. Cronin, John H. Wittig Jr., Paul W. Sternberg, William R. Schafer:
  An imaging system for standardized quantitative analysis of C. elegans behavior. 115
  
• Arunachalam Vinayagam, Rainer König, Jutta Moormann, Falk Schubert, Roland Eils, Karl-Heinz Glatting, Sándor Suhai:
  Applying Support Vector Machines for Gene ontology based gene function prediction. 116
  
• Kristian Flikka, Fekadu Yadetie, Astrid Lægreid, Inge Jonassen:
  XHM: A system for detection of potential cross hybridizations in DNA microarrays. 117
  
• Carsten O. Daub, Ralf Steuer, Joachim Selbig, Sebastian Kloska:
  Estimating mutual information using B-spline functions - an improved similarity measure for analysing gene expression data. 118
  
• Ricardo Z. N. Vêncio, Helena Brentani, Diogo F. C. Patrão, Carlos A. de B. Pereira:
  Bayesian model accounting for within-class biological variability in Serial Analysis of Gene Expression (SAGE). 119
  
• Yasuyuki Tomita, Shuta Tomida, Yuko Hasegawa, Yoichi Suzuki, Taro Shirakawa, Takeshi Kobayashi, Hiroyuki Honda:
  Artificial neural network approach for selection of susceptible single nucleotide polymorphisms and construction of prediction model on childhood allergic asthma. 120
  
• Huajun Wang, Hui Huang:
  SED, a normalization free method for DNA microarray data analysis. 121
  
• Xinghua Lu, Chengxiang Zhai, Vanathi Gopalakrishnan, Bruce G. Buchanan:
  Automatic annotation of protein motif function with Gene Ontology terms. 122
  
• Richard J. Edwards, Denis C. Shields:
  GASP: Gapped Ancestral Sequence Prediction for proteins. 123
  
• Michael V. Osier, Hongyu Zhao, Kei-Hoi Cheung:
  Handling multiple testing while interpreting microarrays with the Gene Ontology Database. 124
  
• Julie Aubert, Avner Bar-Hen, Jean-Jacques Daudin, Stéphane Robin:
  Determination of the differentially expressed genes in microarray experiments using local FDR. 125
  
• Sudhir Varma, Richard Simon:
  Iterative class discovery and feature selection using Minimal Spanning Trees. 126
  
• Anuradha Vivekanandan Giri, Sharmila Anishetty, Pennathur Gautam:
  Functionally specified protein signatures distinctive for each of the different blue copper proteins. 127
  
• Martin Schmollinger, Kay Nieselt, Michael Kaufmann, Burkhard Morgenstern:
  DIALIGN P: Fast pair-wise and multiple sequence alignment using parallel processors. 128
  
• Saurabh Sinha, Mark D. Schroeder, Ulrich Unnerstall, Ulrike Gaul, Eric D. Siggia:
  Cross-species comparison significantly improves genome-wide prediction of cis-regulatory modules in Drosophila. 129
  
• Sook Jung, Christopher Jesudurai, Margaret Staton, Zhidian Du, Stephen Ficklin, Ilhyung Cho, Albert Abbott, Jeffrey Tomkins, Dorrie Main:
  GDR (Genome Database for Rosaceae): integrated web resources for Rosaceae genomics and genetics research. 130
  
• Thomas A. Down, Tim J. P. Hubbard:
  What can we learn from noncoding regions of similarity between genomes? 131
  
• Michael P. Cummings, Daniel S. Myers:
  Simple statistical models predict C-to-U edited sites in plant mitochondrial RNA. 132
  
• Mark W. E. J. Fiers, Gijs A. Kleter, Herman Nijland, Jan Peter Nap, Roeland C. H. J. van Ham:
  Allermatch(tm), a webtool for the prediction of potential allergenicity according to current FAO/WHO Codex alimentarius guidelines. 133
  
• Yanlin Huang, David Kowalski:
  PATTERNFINDER: combined analysis of DNA regulatory sequences and double-helix stability. 134
  
• Gustavo Camps-Valls, Alistair M. Chalk, Antonio J. Serrano-López, José David Martín-Guerrero, Erik L. L. Sonnhammer:
  Profiled support vector machines for antisense oligonucleotide efficacy prediction. 135
  
• Bing Liu, Qinghua Cui, Tianzi Jiang, Songde Ma:
  A combinational feature selection and ensemble neural network method for classification of gene expression data. 136
  
• Michael P. Cummings, Mark R. Segal:
  Few amino acid positions in rpoB are associated with most of the rifampin resistance in Mycobacterium tuberculosis. 137
  
• Christiana K. Magkrioti, Ioannis C. Spyropoulos, Vassiliki A. Iconomidou, Judith H. Willis, Stavros J. Hamodrakas:
  cuticleDB: a relational database of Arthropod cuticular proteins. 138
  
• Neil R. Smalheiser, Vetle I. Torvik:
  A population-based statistical approach identifies parameters characteristic of human microRNA-mRNA interactions. 139
  
• Paul P. Gardner, Robert Giegerich:
  A comprehensive comparison of comparative RNA structure prediction approaches. 140
  
• Christian A. Rees, Janos Demeter, John C. Matese, David Botstein, Gavin Sherlock:
  GeneXplorer: an interactive web application for microarray data visualization and analysis. 141
  
• Anu Sharma, Gyan Prakash Srivastava, Vineet K. Sharma, Srinivasan Ramachandran:
  ArrayD: A general purpose software for Microarray design. 142
  
• Céline Keime, Francesca Damiola, Dominique Mouchiroud, Laurent Duret, Olivier Gandrillon:
  Identitag, a relational database for SAGE tag identification and interspecies comparison of SAGE libraries. 143
  
• Keith A. Baggerly, Li Deng, Jeffrey S. Morris, C. Marcelo Aldaz:
  Overdispersed logistic regression for SAGE: Modelling multiple groups and covariates. 144
  
• Jonathan D. Wren:
  Extending the mutual information measure to rank inferred literature relationships. 145
  
• Diane E. Oliver, Gaurav Bhalotia, Ariel S. Schwartz, Russ B. Altman, Marti A. Hearst:
  Tools for loading MEDLINE into a local relational database. 146
  
• Hao Chen, Burt M. Sharp:
  Content-rich biological network constructed by mining PubMed abstracts. 147
  
• Dietmar E. Martin, Philippe Demougin, Michael N. Hall, Michel Bellis:
  Rank Difference Analysis of Microarrays (RDAM), a novel approach to statistical analysis of microarray expression profiling data. 148
  
• Laurent Noé, Gregory Kucherov:
  Improved hit criteria for DNA local alignment. 149
  
• Florian Meereis, Michael Kaufmann:
  PCOGR: Phylogenetic COG ranking as an online tool to judge the specificity of COGs with respect to freely definable groups of organisms. 150
  
• Ihab A. B. Awad, Christian A. Rees, Tina Hernandez-Boussard, Catherine A. Ball, Gavin Sherlock:
  Caryoscope: An Open Source Java application for viewing microarray data in a genomic context. 151
  
• Sergey V. Anisimov, Alexei A. Sharov:
  Incidence of "quasi-ditags" in catalogs generated by Serial Analysis of Gene Expression (SAGE). 152
  
• Gareth Williams, Patrick Doherty:
  Inter-residue distances derived from fold contact propensities correlate with evolutionary substitution costs. 153
  
• Nan Lin, Baolin Wu, Ronald Jansen, Mark Gerstein, Hongyu Zhao:
  Information assessment on predicting protein-protein interactions. 154
  
• Tuangthong Wattarujeekrit, Parantu K. Shah, Nigel Collier:
  PASBio: predicate-argument structures for event extraction in molecular biology. 155
  
• Michael Hsing, Joel L. Bellenson, Conor Shankey, Artem Cherkasov:
  Modeling of cell signaling pathways in macrophages by semantic networks. 156
  
• Andrew F. Neuwald, Jun S. Liu:
  Gapped alignment of protein sequence motifs through Monte Carlo optimization of a hidden Markov model. 157
  
• Yin Liu, Hongyu Zhao:
  A computational approach for ordering signal transduction pathway components from genomics and proteomics Data. 158
  
• Kyu Baek Hwang, Sek Won Kong, Steven A. Greenberg, Peter J. Park:
  Combining gene expression data from different generations of oligonucleotide arrays. 159
  
• Ki-Yeol Kim, Byoung-Jin Kim, Gwan-Su Yi:
  Reuse of imputed data in microarray analysis increases imputation efficiency. 160
  
• Jer-Ming Chia, Prasanna R. Kolatkar:
  Implications for domain fusion protein-protein interactions based on structural information. 161
  
• Andreas M. Boehm, Robert P. Galvin, Albert Sickmann:
  Extractor for ESI quadrupole TOF tandem MS data enabled for high throughput batch processing. 162
  
• Hanno Teeling, Jost Waldmann, Thierry Lombardot, Margarete Bauer, Frank Oliver Glöckner:
  TETRA: a web-service and a stand-alone program for the analysis and comparison of tetranucleotide usage patterns in DNA sequences. 163
  
• Yuanhui Xiao, Robert D. Frisina, Alexander Gordon, Lev Klebanov, Andrei Yakovlev:
  Multivariate search for differentially expressed gene combinations. 164
  
• Zhining Wang, Mark G. Lewis, Martin E. Nau, Alma Arnold, Maryanne T. Vahey:
  Identification and utilization of inter-species conserved (ISC) probesets on Affymetrix human GeneChip^(r) platforms for the optimization of the assessment of expression patterns in non human primate (NHP) samples. 165
  
• Ian Holmes:
  A probabilistic model for the evolution of RNA structure. 166
  
• Saikat Chakrabarti, Nitin Bhardwaj, Prem A. Anand, Ramanathan Sowdhamini:
  Improvement of alignment accuracy utilizing sequentially conserved motifs. 167
  
• Dominik Seelow, Raffaello Galli, Siegrun Mebus, Hans-Peter Sperling, Hans Lehrach, Silke Sperling:
  d-matrix - database exploration, visualization and analysis. 168
  
• Peter Meinicke, Maike Tech, Burkhard Morgenstern, Rainer Merkl:
  Oligo kernels for datamining on biological sequences: a case study on prokaryotic translation initiation sites. 169
  
• Saurabh Sinha, Mathieu Blanchette, Martin Tompa:
  PhyME: A probabilistic algorithm for finding motifs in sets of orthologous sequences. 170
  
• Chunlin Wang, Elliot J. Lefkowitz:
  SS-Wrapper: a package of wrapper applications for similarity searches on Linux clusters. 171
  
• Yi Lu, Shiyong Lu, Farshad Fotouhi, Youping Deng, Susan J. Brown:
  Incremental genetic K-means algorithm and its application in gene expression data analysis. 172
  
• Sierra D. Stoneberg Holt, Jason A. Holt:
  The InDeVal insertion/deletion evaluation tool: a program for finding target regions in DNA sequences and for aiding in sequence comparison. 173
  
• Nicolas Le Novère, Marco Donizelli:
  The Molecular Pages of the mesotelencephalic dopamine consortium (DopaNet). 174
  
• Julien Gagneur, Steffen Klamt:
  Computation of elementary modes: a unifying framework and the new binary approach. 175
  
• Charu G. Kumar, Richard LeDuc, George Gong, Levan Roinishivili, Harris A. Lewin, Lei Liu:
  ESTIMA, a tool for EST management in a multi-project environment. 176
  
• Henrik Bengtsson, Göran Jönsson, Johan Vallon-Christersson:
  Calibration and assessment of channel-specific biases in microarray data with extended dynamical range. 177
  
• David M. A. Martin, Matthew Berriman, Geoffrey J. Barton:
  GOtcha: a new method for prediction of protein function assessed by the annotation of seven genomes. 178
  
• Maurizio Pellegrino, Paolo Provero, Lorenzo Silengo, Ferdinando Di Cunto:
  CLOE: Identification of putative functional relationships among genes by comparison of expression profiles between two species. 179
  
• Neal O. Jeffries:
  Performance of a genetic algorithm for mass spectrometry proteomics. 180
  
• Manuel Middendorf, Etay Ziv, Carter Adams, Jen Hom, Robin Koytcheff, Chaya Levovitz, Gregory Woods, Linda Chen, Chris Wiggins:
  Discriminative topological features reveal biological network mechanisms. 181
  
• Manisha Desai, Mary J. Emond:
  A new mixture model approach to analyzing allelic-loss data using Bayes factors. 182
  
• Richard Chung, Golan Yona:
  Protein family comparison using statistical models and predicted structural information. 183
  
• Albert Burger, Duncan Davidson, Yiya Yang, Richard A. Baldock:
  Integrating partonomic hierarchies in anatomy ontologies. 184
  
• Virginie M. Aris, Michael J. Cody, Jeff Cheng, James J. Dermody, Patricia Soteropoulos, Michael Recce, Peter P. Tolias:
  Noise filtering and nonparametric analysis of microarray data underscores discriminating markers of oral, prostate, lung, ovarian and breast cancer. 185
  
• Alessandro Dal Palù, Agostino Dovier, Federico Fogolari:
  Constraint Logic Programming approach to protein structure prediction. 186
  
• James Wasmuth, Mark L. Blaxter:
  prot4EST: Translating Expressed Sequence Tags from neglected genomes. 187
  
• Enda D. Kelly, Fabian Sievers, Ross McManus:
  Haplotype frequency estimation error analysis in the presence of missing genotype data. 188
  
• Bernett T. K. Lee, Tin Wee Tan, Shoba Ranganathan:
  DEDB: a database of Drosophila melanogaster exons in splicing graph form. 189
  
• Tomas Radivoyevitch:
  A two-way interface between limited Systems Biology Markup Language and R. 190
  
• Yian A. Chen, David J. Mckillen, Shuyuan Wu, Matthew J. Jenny, Robert Chapman, Paul S. Gross, Gregory W. Warr, Jonas S. Almeida:
  Optimal cDNA microarray design using expressed sequence tags for organisms with limited genomic information. 191
  
• Gregory M. Cooper, Senthil A. G. Singaravelu, Arend Sidow:
  ABC: software for interactive browsing of genomic multiple sequence alignment data. 192
  
• Thomas Breslin, Patrik Edén, Morten Krogh:
  Comparing functional annotation analyses with Catmap. 193
  
• John A. Berger, Sampsa Hautaniemi, Anna-Kaarina Järvinen, Henrik Edgren, Sanjit K. Mitra, Jaakko Astola:
  Optimized LOWESS normalization parameter selection for DNA microarray data. 194
  
• Joachim Theilhaber, Anatoly Ulyanov, Anish Malanthara, Jack Cole, Dapeng Xu, Robert Nahf, Michael Heuer, Christoph Brockel, Steven Bushnell:
  GECKO: a complete large-scale gene expression analysis platform. 195
  
• Noam Kaplan, Moriah Friedlich, Menachem Fromer, Michal Linial:
  A functional hierarchical organization of the protein sequence space. 196
  
• Sara Cheek, Yuan Qi, S. Sri Krishna, Lisa N. Kinch, Nick V. Grishin:
  SCOPmap: Automated assignment of protein structures to evolutionary superfamilies. 197
  
• Rohit Ghai, Torsten Hain, Trinad Chakraborty:
  GenomeViz: visualizing microbial genomes. 198
  
• Hongwu Ma, Jan Buer, An-Ping Zeng:
  Hierarchical structure and modules in the Escherichia coli transcriptional regulatory network revealed by a new top-down approach. 199
  
• James A. Casbon, Mansoor A. S. Saqi:
  Analysis of superfamily specific profile-profile recognition accuracy. 200
  
• Kayvan Najarian, Maryam Zaheri, Ali Ajdari Rad, Siamak Najarian, Javad Dargahi:
  A novel Mixture Model Method for identification of differentially expressed genes from DNA microarray data. 201
  
• Rajalakshmi Gurunathan, Bernard Van Emden, Sethuraman Panchanathan, Sudhir Kumar:
  Identifying spatially similar gene expression patterns in early stage fruit fly embryo images: binary feature versus invariant moment digital representations. 202
  
• Norman Pavelka, Mattia Pelizzola, Caterina Vizzardelli, Monica Capozzoli, Andrea Splendiani, Francesca Granucci, Paola Ricciardi-Castagnoli:
  A power law global error model for the identification of differentially expressed genes in microarray data. 203
  
• Gary W. Stuart, Michael W. Berry:
  An SVD-based comparison of nine whole eukaryotic genomes supports a coelomate rather than ecdysozoan lineage. 204
  
• Taner Z. Sen, Andrzej Kloczkowski, Robert L. Jernigan, Changhui Yan, Vasant Honavar, Kai-Ming Ho, Cai-Zhuang Wang, Yungok Ihm, Haibo Cao, Xun Gu, Drena Dobbs:
  Predicting binding sites of hydrolase-inhibitor complexes by combining several methods. 205
  
• William H. Majoros, Steven Salzberg:
  An empirical analysis of training protocols for probabilistic gene finders. 206
  
• Jose C. Nacher, Nobuhisa Ueda, Takuji Yamada, Minoru Kanehisa, Tatsuya Akutsu:
  Clustering under the line graph transformation: application to reaction network. 207
  
• Antigoni L. Elefsinioti, Pantelis G. Bagos, Ioannis C. Spyropoulos, Stavros J. Hamodrakas:
  A database for G proteins and their interaction with GPCRs. 208
  
• Hao Li, Constance L. Wood, Thomas V. Getchell, Marilyn L. Getchell, Arnold J. Stromberg:
  Analysis of oligonucleotide array experiments with repeated measures using mixed models. 209
  

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