Bioinformatics, Volume 23

Volume 23, Number 1, January 2007

Discovery Note - Genome Analysis

• 
  Passoupathy Rajendrakumar, Akshaya Kumar Biswal, Sena M. Balachandran, Kommoju Srinivasarao, Raman M. Sundaram:
  Simple sequence repeats in organellar genomes of rice: frequency and distribution in genic and intergenic regions. 1-4

Original Papers - Sequence Analysis

• 
  Waibhav Tembe, Nela Zavaljevski, Elizabeth A. Bode, Catherine Chase, Jeanne Geyer, Leonard P. Wasieloski, Gary Benson, Jaques Reifman:
  Oligonucleotide fingerprint identification for microarray-based pathogen diagnostic assays. 5-13

Phylogenetics

• 
  Daniel Barker, Andrew Meade, Mark Pagel:
  Constrained models of evolution lead to improved prediction of functional linkage from correlated gain and loss of genes. 14-20

Gene Expression

• 
  M. Juanita Martinez, Andrew D. Smith, Bilan Li, Michael Q. Zhang, Kevin S. Harrod:
  Computational prediction of novel components of lung transcriptional networks. 21-29
• 
  Yijun Sun, Steve Goodison, Jian Li, Li Liu, William G. Farmerie:
  Improved breast cancer prognosis through the combination of clinical and genetic markers. 30-37
• 
  Hyuna Yang, Gary A. Churchill:
  Estimating p-values in small microarray experiments. 38-43
• 
  Paul Fogel, S. Stanley Young, Douglas M. Hawkins, Nathalie Ledirac:
  Inferential, robust non-negative matrix factorization analysis of microarray data. 44-49
• 
  Xiaowen Liu, Lusheng Wang:
  Computing the maximum similarity bi-clusters of gene expression data. 50-56

Genetics and Population Analysis

• 
  Jianping Hua, David W. Craig, Marcel Brun, Jennifer Webster, Victoria Zismann, Waibhav Tembe, Keta Joshipura, Matthew J. Huentelman, Edward R. Dougherty, Dietrich A. Stephan:
  SNiPer-HD: improved genotype calling accuracy by an expectation-maximization algorithm for high-density SNP arrays. 57-63
• 
  Johannes Dietter, Manuel Mattheisen, Robert Fürst, Franz Rüschendorf, Thomas F. Wienker, Konstantin Strauch:
  Linkage analysis using sex-specific recombination fractions with GENEHUNTER-MODSCORE. 64-70
• 
  Yujin Chung, Seung Yeoun Lee, Robert C. Elston, Taesung Park:
  Odds ratio based multifactor-dimensionality reduction method for detecting gene-gene interactions. 71-76

Systems Biology

• 
  Jens Hollunder, Maik Friedel, Andreas Beyer, Christopher T. Workman, Thomas Wilhelm:
  DASS: efficient discovery and p-value calculation of substructures in unordered data. 77-83
• 
  Tianhai Tian, Songlin Xu, Junbin Gao, Kevin Burrage:
  Simulated maximum likelihood method for estimating kinetic rates in gene expression. 84-91
• 
  John E. Beasley, Francisco J. Planes:
  Recovering metabolic pathways via optimization. 92-98

Data and Text Mining

• 
  Ruhong Zhou, Laxmi Parida, Kush Kapila, Sudhir P. Mudur:
  PROTERAN: animated terrain evolution for visual analysis of patterns in protein folding trajectory. 99-106
• 
  Dae-Won Kim, Ki Young Lee, Kwang H. Lee, Doheon Lee:
  Towards clustering of incomplete microarray data without the use of imputation. 107-113
• 
  Cheolhwan Oh, Stanislaw H. Zak, Hamid Mirzaei, Charles R. Buck, Fred E. Regnier, Xiang Zhang:
  Neural network prediction of peptide separation in strong anion exchange chromatography. 114-118

Applications Note - Genome Analysis

• 
  Guillaume Achaz, Frédéric Boyer, Eduardo P. C. Rocha, Alain Viari, Eric Coissac:
  Repseek, a tool to retrieve approximate repeats from large DNA sequences. 119-121
• 
  Gabriela G. Loots, Ivan Ovcharenko:
  ECRbase: database of evolutionary conserved regions, promoters, and transcription factor binding sites in vertebrate genomes. 122-124
• 
  C. T. Kuenne, Rohit Ghai, Trinad Chakraborty, Torsten Hain:
  GECO-linear visualization for comparative genomics. 125-126

Phylogenetics

• 
  Ivica Letunic, Peer Bork:
  Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. 127-128

Genetics and Population Analysis

• 
  Pak Chung Sham, Sio Iong Ao, Johnny S. H. Kwan, P. Kao, F. Cheung, Pui-Yee Fong, Michael K. Ng:
  Combining functional and linkage disequilibrium information in the selection of tag SNPs. 129-131

Volume 23, Number 2, January 2007

ECCB 2006 Conference Proceedings, January 21-24, Eilat, Israel

• 
  ECCB 2006. 1-2
• 
  ECCB 2006 Organization. 3-4

Original Papers

• 
  Sebastian Böcker:
  Simulating multiplexed SNP discovery rates using base-specific cleavage and mass spectrometry. 5-12
• 
  Yanay Ofran, Burkhard Rost:
  ISIS: interaction sites identified from sequence. 13-16
• 
  Huzefa Rangwala, George Karypis:
  Incremental window-based protein sequence alignment algorithms. 17-23
• 
  Ariel S. Schwartz, Lior Pachter:
  Multiple alignment by sequence annealing. 24-29
• 
  Dina Sokol, Gary Benson, Justin Tojeira:
  Tandem repeats over the edit distance. 30-35
• 
  Yanni Sun, Jeremy Buhler:
  Designing patterns for profile HMM search. 42-43
• 
  Abha Singh Bais, Steffen Grossmann, Martin Vingron:
  Simultaneous alignment and annotation of cis-regulatory regions. 44-49
• 
  Thomas Faraut, Simon de Givry, Patrick Chabrier, Thomas Derrien, Francis Galibert, Christophe Hitte, Thomas Schiex:
  A comparative genome approach to marker ordering. 50-56
• 
  Matan Gavish, Amnon Peled, Benny Chor:
  Genetic code symmetry and efficient design of GC-constrained coding sequences. 57-63
• 
  Filip Hermans, Elena Tsiporkova:
  Merging microarray cell synchronization experiments through curve alignment. 64-70
• 
  Macha Nikolski, David James Sherman:
  Family relationships: should consensus reign? - consensus clustering for protein families. 71-76
• 
  Doron Lipson, Zohar Yakhini, Yonatan Aumann:
  Optimization of probe coverage for high-resolution oligonucleotide aCGH. 77-83
• 
  Chun Ye, Eleazar Eskin:
  Discovering tightly regulated and differentially expressed gene sets in whole genome expression data. 84-90
• 
  Nir Yosef, Zohar Yakhini, Anya Tsalenko, Vessela N. Kristensen, Anne-Lise Børresen-Dale, Eytan Ruppin, Roded Sharan:
  A supervised approach for identifying discriminating genotype patterns and its application to breast cancer data. 91-98
• 
  Andreas Hildebrandt, Ralf Blossey, Sergej Rjasanow, Oliver Kohlbacher, Hans-Peter Lenhof:
  Electrostatic potentials of proteins in water: a structured continuum approach. 99-103
• 
  Rafael Najmanovich, Abdellah Allali-Hassani, Richard J. Morris, Ludmila Dombrovsky, Patricia W. Pan, Masoud Vedadi, Alexander N. Plotnikov, Aled M. Edwards, Cheryl H. Arrowsmith, Janet M. Thornton:
  Analysis of binding site similarity, small-molecule similarity and experimental binding profiles in the human cytosolic sulfotransferase family. 104-109
• 
  José Carlos Clemente, Kenji Satou, Gabriel Valiente:
  Phylogenetic reconstruction from non-genomic data. 110-115
• 
  Pawel Górecki, Jerzy Tiuryn:
  Inferring phylogeny from whole genomes. 116-122
• 
  Guohua Jin, Luay Nakhleh, Sagi Snir, Tamir Tuller:
  Efficient parsimony-based methods for phylogenetic network reconstruction. 123-128
• 
  Matthias Bernt, Daniel Merkle, Martin Middendorf:
  Using median sets for inferring phylogenetic trees. 129-135
• 
  Matan Ninio, Eyal Privman, Tal Pupko, Nir Friedman:
  Phylogeny reconstruction: increasing the accuracy of pairwise distance estimation using Bayesian inference of evolutionary rates. 136-141
• 
  Saharon Rosset:
  Efficient inference on known phylogenetic trees using Poisson regression. 142-147
• 
  Tomer Hertz, Chen Yanover:
  Identifying HLA supertypes by learning distance functions. 148-155
• 
  Keith Noto, Mark Craven:
  Learning probabilistic models of cis-regulatory modules that represent logical and spatial aspects. 156-162
• 
  Barak Raveh, Ofer Rahat, Ronen Basri, Gideon Schreiber:
  Rediscovering secondary structures as network motifs - an unsupervised learning approach. 163-169
• 
  Eitan Hirsh, Roded Sharan:
  Identification of conserved protein complexes based on a model of protein network evolution. 170-176
• 
  Natasa Przulj:
  Biological network comparison using graphlet degree distribution. 177-183
• 
  Oleg Rokhlenko, Ydo Wexler, Zohar Yakhini:
  Similarities and differences of gene expression in yeast stress conditions. 184-190
• 
  Oliver Kohlbacher, Knut Reinert, Clemens Gröpl, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Marc Sturm:
  TOPP - the OpenMS proteomics pipeline. 191-197
• 
  Jennifer Listgarten, Radford M. Neal, Sam T. Roweis, Peter Wong, Andrew Emili:
  Difference detection in LC-MS data for protein biomarker discovery. 198-204
• 
  Fabian Birzele, Jan E. Gewehr, Gergely Csaba, Ralf Zimmer:
  Vorolign - fast structural alignment using Voronoi contacts. 205-211
• 
  Angela Enosh, Sarel Jacob Fleishman, Nir Ben-Tal, Dan Halperin:
  Prediction and simulation of motion in pairs of transmembrane alpha-helices. 212-218
• 
  Iddo Friedberg, Tim Harder, Rachel Kolodny, Einat Sitbon, Zhanwen Li, Adam Godzik:
  Using an alignment of fragment strings for comparing protein structures. 219-224
• 
  Etai Jacob, Ron Unger:
  A tale of two tails: why are terminal residues of proteins exposed? 225-230
• 
  Annalisa Marsico, Dirk Labudde, K. Tanuj Sapra, Daniel J. Muller, Michael Schroeder:
  A novel pattern recognition algorithm to classify membrane protein unfolding pathways with high-throughput single-molecule force spectroscopy. 231-236
• 
  Dietrich Rebholz-Schuhmann, Harald Kirsch, Miguel Arregui, Sylvain Gaudan, Mark Riethoven, Peter Stoehr:
  EBIMed - text crunching to gather facts for proteins from Medline. 237-244

Editorials

• 
  Alfonso Valencia, Alex Bateman:
  Editorial. 133

Original Papers - Genome Analysis

• 
  Helge G. Roider, Aditi Kanhere, Thomas Manke, Martin Vingron:
  Predicting transcription factor affinities to DNA from a biophysical model. 134-141
• 
  Snorre A. Helvik, Ola R. Snøve Jr., Pål Sætrom:
  Reliable prediction of Drosha processing sites improves microRNA gene prediction. 142-149

Sequence Analysis

• 
  Richard J. Dixon, Ian C. Eperon, Nilesh J. Samani:
  Complementary intron sequence motifs associated with human exon repetition: a role for intragenic, inter-transcript interactions in gene expression. 150-155
• 
  Michael Farrar:
  Striped Smith-Waterman speeds database searches six times over other SIMD implementations. 156-161
• 
  Xu Zhang, Tamer Kahveci:
  QOMA: quasi-optimal multiple alignment of protein sequences. 162-168

Phylogenetics

• 
  Zhu Yang, John D. O'Brien, Xiaobin Zheng, Huaiqiu Zhu, Zhen-Su She:
  Tree and rate estimation by local evaluation of heterochronous nucleotide data. 169-176

Structural Bioinformatics

• 
  Joo Chuan Tong, Tin Wee Tan, Shoba Ranganathan:
  In silico grouping of peptide/HLA class I complexes using structural interaction characteristics. 177-183

Gene Expression

• 
  Jorn R. de Haan, Ron Wehrens, Susanne Bauerschmidt, Ester Piek, René C. van Schaik, Lutgarde M. C. Buydens:
  Interpretation of ANOVA models for microarray data using PCA. 184-190
• 
  Andreas W. Schreiber, Ute Baumann:
  A framework for gene expression analysis. 191-197

Systems Biology

• 
  Peng Qiu, Z. Jane Wang, K. J. Ray Liu, Zhang-Zhi Hu, Cathy H. Wu:
  Dependence network modeling for biomarker identification. 198-206
• 
  Feng Luo, Yunfeng Yang, Chin-Fu Chen, Roger L. Chang, Jizhong Zhou, Richard H. Scheuermann:
  Modular organization of protein interaction networks. 207-214
• 
  Xiaotu Ma, Hyunju Lee, Li Wang, Fengzhu Sun:
  CGI: a new approach for prioritizing genes by combining gene expression and protein-protein interaction data. 215-221
• 
  Ai Li, Steve Horvath:
  Network neighborhood analysis with the multi-node topological overlap measure. 222-231

Data and Text Mining

• 
  Yuanyuan Tian, Richard C. McEachin, Carlos Santos, David J. States, Jignesh M. Patel:
  SAGA: a subgraph matching tool for biological graphs. 232-239

Applications Note - Genome Analysis

• 
  Frank M. You, Ming-Cheng Luo, Yong Qiang Gu, Gerard R. Lazo, Karin Deal, Jan Dvorak, Olin D. Anderson:
  GenoProfiler: batch processing of high-throughput capillary fingerprinting data. 240-242
• 
  Nicolás Bellora, Domènec Farré, M. Mar Albà:
  PEAKS: identification of regulatory motifs by their position in DNA sequences. 243-244

Structural Bioinformatics

• 
  Sinae Kim, Jerry W. Tsai, Ioannis Kagiampakis, Patricia LiWang, Marina Vannucci:
  Detecting protein dissimilarities in multiple alignments using Bayesian variable selection. 245-246

Gene Expression

• 
  R. Cathelin, Fabrice Lopez, Christophe Klopp:
  AGScan: a pluggable microarray image quantification software based on the ImageJ library. 247-248

Genetics and Population Analysis

• 
  Reagan J. Kelly, Douglas M. Jacobsen, Yan V. Sun, Jennifer A. Smith, Sharon L. R. Kardia:
  KGraph: a system for visualizing and evaluating complex genetic associations. 249-251
• 
  K. Hao, Xiaojun Di, Simon Cawley:
  LdCompare: rapid computation of single- and multiple-marker r² and genetic coverage. 252-254
• 
  Shaun Purcell, Mark J. Daly, Pak Chung Sham:
  WHAP: haplotype-based association analysis. 255-256

Systems Biology

• 
  Seth Falcon, Robert Gentleman:
  Using GOstats to test gene lists for GO term association. 257-258

Data and Text Mining

• 
  Christopher S. Poultney, Rodrigo A. Gutiérrez, Manpreet S. Katari, Miriam L. Gifford, W. Bradford Paley, Gloria M. Coruzzi, Dennis E. Shasha:
  Sungear: interactive visualization and functional analysis of genomic datasets. 259-261
• 
  J. A. Falkner, J. W. Falkner, P. C. Andrews:
  ProteomeCommons.org IO Framework: reading and writing multiple proteomics data formats. 262-263
• 
  Yuliya V. Karpievitch, Elizabeth G. Hill, Adam J. Smolka, Jeffrey S. Morris, Kevin R. Coombes, Keith A. Baggerly, Jonas S. Almeida:
  PrepMS: TOF MS data graphical preprocessing tool. 264-265

Corrigendum

• 
  CASPAR: a hierarchical Bayesian approach to predict survival times in cancer from gene expression data. 266

Volume 23, Number 3, 1 February 2007

Discovery Notes - Sequence Analysis

• 
  Richard Thilakaraj, Krishnan Raghunathan, Sharmila Anishetty, Pennathur Gautam:
  In silico identification of putative metal binding motifs. 267-271

Structural Bioinformatics

• 
  Alexander P. Gultyaev, Hans A. Heus, René C. L. Olsthoorn:
  An RNA conformational shift in recent H5N1 influenza A viruses. 272-276

Data and Text Mining

• 
  Roger Higdon, Eugene Kolker:
  A predictive model for identifying proteins by a single peptide match. 277-280

Original Papers - Genome Analysis

• 
  Liang Goh, Susan K. Murphy, Sayan Mukherjee, Terrence S. Furey:
  Genomic sweeping for hypermethylated genes. 281-288

Sequence Analysis

• 
  Jaebum Kim, Saurabh Sinha:
  Indelign: a probabilistic framework for annotation of insertions and deletions in a multiple alignment. 289-297

Gene Expression

• 
  Ian B. Jeffery, Stephen F. Madden, Paul A. McGettigan, Guy Perrière, Aedín C. Culhane, Desmond G. Higgins:
  Integrating transcription factor binding site information with gene expression datasets. 298-305
• 
  Zhen Jiang, Robert Gentleman:
  Extensions to gene set enrichment. 306-313
• 
  Gilad Lerman, Joseph McQuown, Alexandre Blais, Brian D. Dynlacht, Guangliang Chen, Bud Mishra:
  Functional genomics via multiscale analysis: application to gene expression and ChIP-on-chip data. 314-320
• 
  Zhongxue Chen, Monnie McGee, Qingzhong Liu, Richard H. Scheuermann:
  A distribution free summarization method for Affymetrix GeneChip^® arrays. 321-327
• 
  Kenneth Lo, Raphael Gottardo:
  Flexible empirical Bayes models for differential gene expression. 328-335

Systems Biology

• 
  L. Jason Steggles, Richard Banks, Oliver Shaw, Anil Wipat:
  Qualitatively modelling and analysing genetic regulatory networks: a Petri net approach. 336-343
• 
  Christian Klukas, Falk Schreiber:
  Dynamic exploration and editing of KEGG pathway diagrams. 344-350
• 
  Andrea L. Knorr, Rishi Jain, Ranjan Srivastava:
  Bayesian-based selection of metabolic objective functions. 351-357
• 
  Neda Bagheri, Jörg Stelling, Francis J. Doyle III:
  Quantitative performance metrics for robustness in circadian rhythms. 358-364

Data and Text Mining

• 
  Katrin Fundel, Robert Küffner, Ralf Zimmer:
  RelEx - Relation extraction using dependency parse trees. 365-371

Applications Notes - Sequence Analysis

• 
  Kazutaka Katoh, Hiroyuki Toh:
  PartTree: an algorithm to build an approximate tree from a large number of unaligned sequences. 372-374

Structural Bioinformatics

• 
  Kreshna Gopal, Erik McKee, Tod D. Romo, Reetal Pai, Jacob N. Smith, James C. Sacchettini, Thomas R. Ioerger:
  Crystallographic protein model-building on the web. 375-377
• 
  Lisa Fukui, Yuan Chen:
  NvMap: automated analysis of NMR chemical shift perturbation data. 378-380
• 
  Wolfgang Rieping, Michael Habeck, Benjamin Bardiaux, Aymeric Bernard, Therese E. Malliavin, Michael Nilges:
  ARIA2: Automated NOE assignment and data integration in NMR structure calculation. 381-382
• 
  Stephen A. Cammer:
  SChiSM2: creating interactive web page annotations of molecular structure models using Jmol. 383-384
• 
  Emidio Capriotti, Rita Casadio:
  K-Fold: a tool for the prediction of the protein folding kinetic order and rate. 385-386

Gene Expression

• 
  Giorgio Valentini:
  Mosclust: a software library for discovering significant structures in bio-molecular data. 387-389
• 
  Ignacio Medina, David Montaner, Joaquín Tárraga, Joaquín Dopazo:
  Prophet, a web-based tool for class prediction using microarray data. 390-391

Systems Biology

• 
  Iliana Avila-Campillo, Kevin Drew, John Lin, David J. Reiss, Richard Bonneau:
  BioNetBuilder: automatic integration of biological networks. 392-393
• 
  Olivier Garcia, Cosmin Saveanu, Melissa S. Cline, Micheline Fromont-Racine, Alain Jacquier, Benno Schwikowski, Tero Aittokallio:
  GOlorize: a Cytoscape plug-in for network visualization with Gene Ontology-based layout and coloring. 394-396

Databases and Ontologies

• 
  Areum Han, Woo-Yeon Kim, Seong-Min Park:
  SNP2NMD: A database of human single nucleotide polymorphisms causing nonsense-mediated mRNA decay. 397-399

Volume 23, Number 4, 15 February 2007

Review - Databases and Ontologies

• 
  Isabelle Rivals, Léon Personnaz, Lieng Taing, Marie-Claude Potier:
  Enrichment or depletion of a GO category within a class of genes: which test? 401-407

Original Papers - Genome Analysis

• 
  Shuichi Takitoh, Shogo Fujii, Yoichi Mase, Junichi Takasaki, Toshimasa Yamazaki, Yozo Ohnishi, Masao Yanagisawa, Yusuke Nakamura, Naoyuki Kamatani:
  Accurate automated clustering of two-dimensional data for single-nucleotide polymorphism genotyping by a combination of clustering methods: evaluation by large-scale real data. 408-413

Sequence Analysis

• 
  Yvan Saeys, Pierre Rouzé, Yves Van de Peer:
  In search of the small ones: improved prediction of short exons in vertebrates, plants, fungi and protists. 414-420

Structural Bioinformatics

• 
  Noga Kowalsman, Miriam Eisenstein:
  Inherent limitations in protein-protein docking procedures. 421-426
• 
  José Ignacio Garzón, Julio A. Kovacs, Ruben Abagyan, Pablo Chacón:
  ADP_EM: fast exhaustive multi-resolution docking for high-throughput coverage. 427-433
• 
  Hisanori Kiryu, Taishin Kin, Kiyoshi Asai:
  Robust prediction of consensus secondary structures using averaged base pairing probability matrices. 434-441

Gene Expression

• 
  Nitai D. Mukhopadhyay, Snigdhansu Chatterjee:
  Causality and pathway search in microarray time series experiment. 442-449
• 
  Jun Liu, Sanjay Ranka, Tamer Kahveci:
  Markers improve clustering of CGH data. 450-457
• 
  Jangsun Baek, Young Sook Son, Geoffrey J. McLachlan:
  Segmentation and intensity estimation of microarray images using a gamma-t mixture model. 458-465
• 
  Shuangge Ma, Jian Huang:
  Clustering threshold gradient descent regularization: with applications to microarray studies. 466-472
• 
  Huai Li, Yu Sun, Ming Zhan:
  The discovery of transcriptional modules by a two-stage matrix decomposition approach. 473-479

Systems Biology

• 
  Orland R. Gonzalez, Christoph Küper, Kirsten Jung, Prospero C. Naval Jr., Eduardo Mendoza:
  Parameter estimation using Simulated Annealing for S-system models of biochemical networks. 480-486

Data and Text Mining

• 
  Michael V. Doran, Daniela Stan Raicu, Jacob D. Furst, Raffaella Settimi, Matthew Schipma, Darrell P. Chandler:
  Oligonucleotide microarray identification of Bacillus anthracis strains using support vector machines. 487-492

Applications Notes - Genome Analysis

• 
  Matteo Brilli, Renato Fani, Pietro Liò:
  MotifScorer: using a compendium of microarrays to identify regulatory motifs. 493-495
• 
  André Müller, Karlheinz Holzmann, Hans A. Kestler:
  Visualization of genomic aberrations using Affymetrix SNP arrays. 496-497
• 
  Thomas Derrien, Catherine André, Francis Galibert, Christophe Hitte:
  AutoGRAPH: an interactive web server for automating and visualizing comparative genome maps. 498-499
• 
  René L. Warren, Granger G. Sutton, Steven J. M. Jones, Robert A. Holt:
  Assembling millions of short DNA sequences using SSAKE. 500-501

Sequence Analysis

• 
  Tancred Frickey, Georg Weiller:
  Mclip: motif detection based on cliques of gapped local profile-to-profile alignments. 502-503
• 
  Zong Hong Zhang, Judice L. Y. Koh, Guanglan Zhang, Khar Heng Choo, Martti T. Tammi, Joo Chuan Tong:
  AllerTool: a web server for predicting allergenicity and allergic cross-reactivity in proteins. 504-506

Phylogenetics

• 
  Fang Fang, Jing Ding, Vladimir N. Minin, Marc A. Suchard, Karin S. Dorman:
  cBrother: relaxing parental tree assumptions for Bayesian recombination detection. 507-508
• 
  Mahesh Panchal:
  The automation of Nested Clade Phylogeographic Analysis. 509-510
• 
  Pawel Górecki, Jerzy Tiuryn:
  URec: a system for unrooted reconciliation. 511-512

Structural Bioinformatics

• 
  Stefan J. Suhrer, Markus Wiederstein, Manfred J. Sippl:
  QSCOP - SCOP quantified by structural relationships. 513-514
• 
  Alessandro Pandini, Laura Bonati, Franca Fraternali, Jens Kleinjung:
  MinSet: a general approach to derive maximally representative database subsets by using fragment dictionaries and its application to the SCOP database. 515-516

Genetics and Population Analysis

• 
  Winston Lau, Tai-Yue Kuo, William Tapper, Simon J. Cox, Andrew Collins:
  Exploiting large scale computing to construct high resolution linkage disequilibrium maps of the human genome. 517-519
• 
  Garrett Hellenthal, Matthew Stephens:
  msHOT: modifying Hudson's ms simulator to incorporate crossover and gene conversion hotspots. 520-521
• 
  Vincent J. Carey, Martin Morgan, Seth Falcon, Ross Lazarus, Robert Gentleman:
  GGtools: analysis of genetics of gene expression in bioconductor. 522-523

Systems Biology

• 
  Tetsuro Toyoda, Yoshiki Mochizuki, Keith Player, Naohiko Heida, Norio Kobayashi, Yoshiyuki Sakaki:
  OmicBrowse: a browser of multidimensional omics annotations. 524-526

Volume 23, Number 5, March 2007

Discovery Note - Structural Bioinformatics

• 
  Jerzy Orlowski, Michal J. Boniecki, Janusz M. Bujnicki:
  I-Ssp6803I: the first homing endonuclease from the PD-(D/E)XK superfamily exhibits an unusual mode of DNA recognition. 527-530

Original Papers - Sequence Analysis

• 
  Jing Zhang, Bo Jiang, Ming Li, John Tromp, Xuegong Zhang, Michael Q. Zhang:
  Computing exact P-values for DNA motifs. 531-537
• 
  David T. Jones:
  Improving the accuracy of transmembrane protein topology prediction using evolutionary information. 538-544
• 
  Evan Keibler, Manimozhiyan Arumugam, Michael R. Brent:
  The Treeterbi and Parallel Treeterbi algorithms: efficient, optimal decoding for ordinary, generalized and pair HMMs. 545-554

Structural Bioinformatics

• 
  Julie Bernauer, Jérôme Azé, Joël Janin, Anne Poupon:
  A new protein-protein docking scoring function based on interface residue properties. 555-562
• 
  Jianping Chen, Xi Zhang, Ariel Fernández:
  Molecular basis for specificity in the druggable kinome: sequence-based analysis. 563-572
• 
  Simon J. Cockell, Baldo Oliva, Richard M. Jackson:
  Structure-based evaluation of in silico predictions of protein-protein interactions using Comparative Docking. 573-581
• 
  T. Sobha Rani, S. Durga Bhavani, Raju S. Bapi:
  Analysis of E.coli promoter recognition problem in dinucleotide feature space. 582-588

Gene Expression

• 
  Jie Zhou, Hanchuan Peng:
  Automatic recognition and annotation of gene expression patterns of fly embryos. 589-596

Systems Biology

• 
  Minghui Li, Lei Lin, Xiaolong Wang, Tao Liu:
  Protein-protein interaction site prediction based on conditional random fields. 597-604
• 
  Matthias E. Futschik, Gautam Chaurasia, Hanspeter Herzel:
  Comparison of human protein-protein interaction maps. 605-611

Data and Text Mining

• 
  Debojyoti Dutta, Ting Chen:
  Speeding up tandem mass spectrometry database search: metric embeddings and fast near neighbor search. 612-618
• 
  Habtom W. Ressom, Rency S. Varghese, Steven K. Drake, Glen L. Hortin, Mohamed Abdel-Hamid, Christopher A. Loffredo, Radoslav Goldman:
  Peak selection from MALDI-TOF mass spectra using ant colony optimization. 619-626

Applications Note - Genome Analysis

• 
  Robert B. Scharpf, Jason C. Ting, Jonathan Pevsner, Ingo Ruczinski:
  SNPchip: R classes and methods for SNP array data. 627-628

Sequence Analysis

• 
  Niko Välimäki, Wolfgang Gerlach, Kashyap Dixit, Veli Mäkinen:
  Compressed suffix tree - a basis for genome-scale sequence analysis. 629-630
• 
  Liping Du, Hongxia Zhou, Hong Yan:
  OMWSA: detection of DNA repeats using moving window spectral analysis. 631-633
• 
  Seungwoo Hwang, Zhenkun Gou, Igor B. Kuznetsov:
  DP-Bind: a web server for sequence-based prediction of DNA-binding residues in DNA-binding proteins. 634-636

Structural Bioinformatics

• 
  Ganesan Pugalenthi, Ponnuthurai N. Suganthan, Ramanathan Sowdhamini, Saikat Chakrabarti:
  SMotif: a server for structural motifs in proteins. 637-638

Gene Expression

• 
  Eugene Novikov, Emmanuel Barillot:
  Software package for automatic microarray image analysis (MAIA). 639-640

Genetics and Population Analysis

• 
  Brian S. Yandell, Tapan Mehta, Samprit Banerjee, Daniel Shriner, Ramprasad Venkataraman, Jee Young Moon, W. Whipple Neely, Hao Wu, Randy von Smith, Nengjun Yi:
  R/qtlbim: QTL with Bayesian Interval Mapping in experimental crosses. 641-643
• 
  Juan R. González, Lluís Armengol, Xavier Solé, Elisabet Guinó, Josep M. Mercader, Xavier Estivill, Víctor Moreno:
  SNPassoc: an R package to perform whole genome association studies. 654-655

Systems Biology

• 
  Henning Schmidt:
  SBaddon: high performance simulation for the Systems Biology Toolbox for MATLAB. 646-647
• 
  Heinrich J. Huber, Markus Rehm, Martin Plchút, Heiko Düssmann, Jochen H. M. Prehn:
  APOPTO-CELL - a simulation tool and interactive database for analyzing cellular susceptibility to apoptosis. 648-650

Data and Text Mining

• 
  Jan E. Gewehr, Martin Szugat, Ralf Zimmer:
  BioWeka - extending the Weka framework for bioinformatics. 651-653

Databases and Ontologies

• 
  David Guzman, Dominic Veit, Viviane Knerr, Gerhard Kindle, Benjamin Gathmann, Anne-Marie Eades-Perner, Bodo Grimbacher:
  The ESID Online Database network. 654-655

Volume 23, Number 6, 15 March 2007

Original Papers - Genome Analysis

• 
  E. S. Venkatraman, Adam B. Olshen:
  A faster circular binary segmentation algorithm for the analysis of array CGH data. 657-663
• 
  Matthew A. Care, Chris J. Needham, Andrew J. Bulpitt, David R. Westhead:
  Deleterious SNP prediction: be mindful of your training data! 664-672
• 
  Arthur L. Delcher, Kirsten A. Bratke, Edwin C. Powers, Steven Salzberg:
  Identifying bacterial genes and endosymbiont DNA with Glimmer. 673-679

Sequence Analysis

• 
  Joan Hérisson, Guillaume Payen, Rachid Gherbi:
  A 3D pattern matching algorithm for DNA sequences. 680-686
• 
  Kai Ye, Walter A. Kosters, Adriaan P. IJzerman:
  An efficient, versatile and scalable pattern growth approach to mine frequent patterns in unaligned protein sequences. 687-693
• 
  Andrzej K. Brodzik:
  Quaternionic periodicity transform: an algebraic solution to the tandem repeat detection problem. 694-700

Structural Bioinformatics

• 
  Yungki Park, Volkhard Helms:
  On the derivation of propensity scales for predicting exposed transmembrane residues of helical membrane proteins. 701-708
• 
  Ahmet Sacan, Ozgur Ozturk, Hakan Ferhatosmanoglu, Yusu Wang:
  LFM-Pro: a tool for detecting significant local structural sites in proteins. 709-716
• 
  Evgeny B. Krissinel:
  On the relationship between sequence and structure similarities in proteomics. 717-723

Gene Expression

• 
  István A. Bogdán, Daniel Coca, Jenny Rivers, Robert J. Beynon:
  Hardware acceleration of processing of mass spectrometric data for proteomics. 724-731
• 
  Shigeyuki Matsui, Masaaki Ito, Hiroyuki Nishiyama, Hajime Uno, Hirokazu Kotani, Jun Watanabe, Parry Guilford, Anthony Reeve, Masanori Fukushima, Osamu Ogawa:
  Genomic characterization of multiple clinical phenotypes of cancer using multivariate linear regression models. 732-738
• 
  Peng Liu, J. T. Gene Hwang:
  Quick calculation for sample size while controlling false discovery rate with application to microarray analysis. 739-746
• 
  Dong Hua, Yinglei Lai:
  An ensemble approach to microarray data-based gene prioritization after missing value imputation. 747-754

Systems Biology

• 
  Yanxin Shi, Tom M. Mitchell, Ziv Bar-Joseph:
  Inferring pairwise regulatory relationships from multiple time series datasets. 755-763

Applications Notes: Genome Analysis

• 
  Shengyin Gu, Iain Anderson, Victor Kunin, Michael J. Cipriano, Simon Minovitsky, Gunther H. Weber, Nina Amenta, Bernd Hamann, Inna Dubchak:
  TreeQ-VISTA: an interactive tree visualization tool with functional annotation query capabilities. 764-766

Sequence Analysis

• 
  Rafael Navajas-Pérez, Cristina Rubio-Escudero, José Luis Aznarte, Manuel Ruiz Rejón, Manuel A. Garrido-Ramos:
  SatDNA Analyzer: a computing tool for satellite-DNA evolutionary analysis. 767-768

Structural Bioinformatics

• 
  Raik Grünberg, Michael Nilges, Johan Leckner:
  Biskit - A software platform for structural bioinformatics. 769-770

Gene Expression

• 
  Charles Girardot, Oleg Sklyar, Sophie Grosz, Wolfgang Huber, Eileen E. M. Furlong:
  CoCo: a web application to display, store and curate ChIP-on-chip data integrated with diverse types of gene expression data. 771-773

Genetics and Population Analysis

• 
  Augustin Luna, Kristin K. Nicodemus:
  snp.plotter: an R-based SNP/haplotype association and linkage disequilibrium plotting package. 774-776

Systems Biology

• 
  Andre S. Ribeiro, Jason Lloyd-Price:
  SGN Sim, a Stochastic Genetic Networks Simulator. 777-779

Data and Text Mining

• 
  Young C. Song, Edward A. Kawas, Benjamin M. Good, Mark D. Wilkinson, Scott J. Tebbutt:
  DataBiNS: a BioMoby-based data-mining workflow for biological pathways and non-synonymous SNPs. 780-782

Databases and Ontologies

• 
  Jean-Pierre Gauthier, Fabrice Legeai, Alain Zasadzinski, Claude Rispe, Denis Tagu:
  AphidBase: a database for aphid genomic resources. 783-784

Volume 23, Number 7, 1 April 2007

Discovery Notes: Phylogenetics

• 
  Farhat Habib, Andrew D. Johnson, Ralf Bundschuh, Daniel Janies:
  Large scale genotype-phenotype correlation analysis based on phylogenetic trees. 785-788

Structural Bioinformatics

• 
  George Nicola, Ilya A. Vakser:
  A simple shape characteristic of protein-protein recognition. 789-792

Original Papers: Genome Analysis

• 
  Kristian Hanekamp, Uta Bohnebeck, Bánk Beszteri, Klaus Valentin:
  PhyloGena - a user-friendly system for automated phylogenetic annotation of unknown sequences. 793-801

Sequence Analysis

• 
  Jimin Pei, Nick V. Grishin:
  PROMALS: towards accurate multiple sequence alignments of distantly related proteins. 802-808
• 
  Alex Bateman, Robert D. Finn:
  SCOOP: a simple method for identification of novel protein superfamily relationships. 809-814

Phylogenetics:

• 
  Bas E. Dutilh, Vera van Noort, René T. J. M. van der Heijden, T. Boekhout, Berend Snel, Martijn A. Huynen:
  Assessment of phylogenomic and orthology approaches for phylogenetic inference. 815-824
• 
  Robert G. Beiko, Robert L. Charlebois:
  A simulation test bed for hypotheses of genome evolution. 825-831

Structural Bioinformatics

• 
  Juris Viksna, David R. Gilbert:
  Assessment of the probabilities for evolutionary structural changes in protein folds. 832-841

Gene Expression

• 
  Takashi Yoneya, Hiroshi Mamitsuka:
  A hidden Markov model-based approach for identifying timing differences in gene expression under different experimental factors. 842-849
• 
  Serban Nacu, Rebecca Critchley-Thorne, Peter P. Lee, Susan P. Holmes:
  Gene expression network analysis and applications to immunology. 850-858

Systems Biology

• 
  Andreas Schlicker, Carola Huthmacher, Fidel Ramírez, Thomas Lengauer, Mario Albrecht:
  Functional evaluation of domain-domain interactions and human protein interaction networks. 859-865
• 
  Shawn Martin, Zhaoduo Zhang, Anthony Martino, Jean-Loup Faulon:
  Boolean dynamics of genetic regulatory networks inferred from microarray time series data. 866-874
• 
  Pratap R. Patnaik:
  Robustness analysis of the E.coli chemosensory system to perturbations in chemoattractant concentrations. 875-881

Databases and Ontologies

• 
  A. Antofie, M. Lateur, R. Oger, Andrea Patocchi, C. E. Durel, W. E. Van de Weg:
  A new versatile database created for geneticists and breeders to link molecular and phenotypic data in perennial crops: the AppleBreed DataBase. 882-891

Applications Notes - Genome Analysis

• 
  Mark A. van de Wiel, Kyung In Kim, Sjoerd J. Vosse, Wessel N. van Wieringen, Saskia M. Wilting, Bauke Ylstra:
  CGHcall: calling aberrations for array CGH tumor profiles. 892-894

Sequence Analysis

• 
  Christian R. Ingrell, Martin L. Miller, Ole Nørregaard Jensen, Nikolaj Blom:
  NetPhosYeast: prediction of protein phosphorylation sites in yeast. 895-897

Phylogenetics

• 
  Jan P. Meier-Kolthoff, Alexander F. Auch, Daniel H. Huson, Markus Göker:
  COPYCAT : cophylogenetic analysis tool. 898-900

Structural Bioinformatics

• 
  José Ignacio Garzón, Julio A. Kovacs, Ruben Abagyan, Pablo Chacón:
  DFprot: a webtool for predicting local chain deformability. 901-902

Gene Expression

• 
  Pedro A. F. Galante, Jeff Trimarchi, Constance L. Cepko, Sandro J. de Souza, Lucila Ohno-Machado, Winston Patrick Kuo:
  Automatic correspondence of tags and genes (ACTG): a tool for the analysis of SAGE, MPSS and SBS data. 903-905

Systems Biology

• 
  Anuj R. Shah, Mudita Singhal, Kyle R. Klicker, Eric G. Stephan, H. Steven Wiley, Katrina M. Waters:
  Enabling high-throughput data management for systems biology: The Bioinformatics Resource Manager. 906-909
• 
  Alfredo Ferro, Rosalba Giugno, Giuseppe Pigola, Alfredo Pulvirenti, Dmitry Skripin, Gary D. Bader, Dennis E. Shasha:
  NetMatch: a Cytoscape plugin for searching biological networks. 910-912

Databases and Ontologies

• 
  Alexander D. Diehl, Jamie A. Lee, Richard H. Scheuermann, Judith A. Blake:
  Ontology development for biological systems: immunology. 913-915

Corrigendum

• 
  Feng Luo, Yunfeng Yang, Chin-Fu Chen, Roger L. Chang, Jizhong Zhou, Richard H. Scheuermann:
  Modular organization of protein interaction networks. 916

Volume 23, Number 8, 15 April 2007

Sequence Analysis

• 
  Minmei Hou, Piotr Berman, Chih-Hao Hsu, Robert S. Harris:
  HomologMiner: looking for homologous genomic groups in whole genomes. 917-925
• 
  Elfar Torarinsson, Jakob Hull Havgaard, Jan Gorodkin:
  Multiple structural alignment and clustering of RNA sequences. 926-932
• 
  Andrija Tomovic, Edward J. Oakeley:
  Position dependencies in transcription factor binding sites. 933-941
• 
  Chun-Wei Tung, Shinn-Ying Ho:
  POPI: predicting immunogenicity of MHC class I binding peptides by mining informative physicochemical properties. 942-949

Structural Bioinformatics

• 
  Mónika Fuxreiter, Peter Tompa, István Simon:
  Local structural disorder imparts plasticity on linear motifs. 950-956

Gene Expression

• 
  Monica Nicolau, Robert Tibshirani, Anne-Lise Børresen-Dale, Stefanie S. Jeffrey:
  Disease-specific genomic analysis: identifying the signature of pathologic biology. 957-965
• 
  Jun S. Song, Kaveh Maghsoudi, Wei Li, Edward Fox, John Quackenbush, Xiaole Shirley Liu:
  Microarray blob-defect removal improves array analysis. 966-971
• 
  Sijian Wang, Ji Zhu:
  Improved centroids estimation for the nearest shrunken centroid classifier. 972-979
• 
  Jelle J. Goeman, Peter Bühlmann:
  Analyzing gene expression data in terms of gene sets: methodological issues. 980-987
• 
  Thomas E. Royce, Joel S. Rozowsky, Mark Gerstein:
  Assessing the need for sequence-based normalization in tiling microarray experiments. 988-997
• 
  Dorothy S. V. Wong, Frederick K. Wong, Graham R. Wood:
  A multi-stage approach to clustering and imputation of gene expression profiles. 998-1005

Genetics and Population Analysis

• 
  Susann Stjernqvist, Tobias Rydén, Martin Sköld, Johan Staaf:
  Continuous-index hidden Markov modelling of array CGH copy number data. 1006-1014

Data and Text Mining

• 
  Hua Xu, Jungwei Fan, George Hripcsak, Eneida A. Mendonça, Marianthi Markatou, Carol Friedman:
  Gene symbol disambiguation using knowledge-based profiles. 1015-1022

Genome Analysis

• 
  Robert P. Davey, George Savva, Jo L. Dicks, Ian N. Roberts:
  MPP: a microarray-to-phylogeny pipeline for analysis of gene and marker content datasets. 1023-1025

Sequence Analysis

• 
  Jan Krumsiek, Roland Arnold, Thomas Rattei:
  Gepard: a rapid and sensitive tool for creating dotplots on genome scale. 1026-1028
• 
  Arijit Chakravarty, Jonathan M. Carlson, Radhika S. Khetani, Charles E. DeZiel, Robert H. Gross:
  SPACER: identification of cis-regulatory elements with non-contiguous critical residues. 1029-1031
• 
  Dmitri A. Papatsenko:
  ClusterDraw web server: a tool to identify and visualize clusters of binding motifs for transcription factors. 1032-1034

Structural Bioinformatics

• 
  Pascal Auffinger, Yaser Hashem:
  SwS: a solvation web service for nucleic acids. 1035-1037

Genetics and Population Analysis

• 
  D. A. Tregouet, V. Garelle:
  A new JAVA interface implementation of THESIAS: testing haplotype effects in association studies. 1038-1039

Systems Biology

• 
  Aaron Barsky, Jennifer L. Gardy, Robert E. W. Hancock, Tamara Munzner:
  Cerebral: a Cytoscape plugin for layout of and interaction with biological networks using subcellular localization annotation. 1040-1042

Databases and Ontologies

• 
  Andrea Caprera, Barbara Lazzari, Alessandra Stella, Ivan Merelli, Alexandre R. Caetano, Paola Mariani:
  GoSh: a web-based database for goat and sheep EST sequences. 1043-1045

Corrigenda

• 
  Guohua Jin, Luay Nakhleh, Sagi Snir, Tamir Tuller:
  Maximum likelihood of phylogenetic networks. 1046-1047
• 
  Kevin Y. Yip, Haiyuan Yu, Philip M. Kim, Martin H. Schultz, Mark Gerstein:
  The tYNA platform for comparative interactomics: a web tool for managing, comparing and mining multiple networks. 1048

Volume 23, Number 9, 1 May 2007

Discovery Note: Systems Biology

• 
  Qingzhao Wang, Yudi Yang, Hongwu Ma, Xue-Ming Zhao:
  Metabolic network properties help assign weights to elementary modes to understand physiological flux distributions. 1049-1052

Genome Analysis

• 
  Gangman Yi, Sing-Hoi Sze, Michael R. Thon:
  Identifying clusters of functionally related genes in genomes. 1053-1060
• 
  Genis Parra, Keith Bradnam, Ian Korf:
  CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. 1061-1067

Sequence Analysis

• 
  Mitsuhiro Kanazawa, Hisae Anyoji, Atsushi Ogiwara, Umpei Nagashima:
  De novo peptide sequencing using ion peak intensity and amino acid cleavage intensity ratio. 1068-1072
• 
  Jason S. Papadopoulos, Richa Agarwala:
  COBALT: constraint-based alignment tool for multiple protein sequences. 1073-1079
• 
  Saskia de Groot, Thomas Mailund, Jotun Hein:
  Comparative annotation of viral genomes with non-conserved gene structure. 1080-1089

Structural Bioinformatics

• 
  Jian Qiu, Martial Hue, Asa Ben-Hur, Jean-Philippe Vert, William Stafford Noble:
  A structural alignment kernel for protein structures. 1090-1098
• 
  Richard E. Smith, Simon C. Lovell, David F. Burke, Rinaldo W. Montalvão, Tom L. Blundell:
  Andante: reducing side-chain rotamer search space during comparative modeling using environment-specific substitution probabilities. 1099-1105

Gene Expression

• 
  Xin Zhou, David P. Tuck:
  MSVM-RFE: extensions of SVM-RFE for multiclass gene selection on DNA microarray data. 1106-1114

Systems Biology

• 
  Jiusheng Chen, Haoran Zheng, Haiyan Liu, Junqing Niu, Jianping Liu, Tie Shen, Bin Rui, Yunyu Shi:
  Improving metabolic flux estimation via evolutionary optimization for convex solution space. 1115-1123
• 
  Bill Andreopoulos, Aijun An, Xiaogang Wang, Michalis Faloutsos, Michael Schroeder:
  Clustering by common friends finds locally significant proteins mediating modules. 1124-1131

Data and Text Mining

• 
  Kyle J. Gaulton, Karen L. Mohlke, Todd J. Vision:
  A computational system to select candidate genes for complex human traits. 1132-1140
• 
  Je-Gun Joung, Kyu Baek Hwang, Jin-Wu Nam, Soo-Jin Kim, Byoung-Tak Zhang:
  Discovery of microRNA-mRNA modules via population-based probabilistic learning. 1141-1147

Databases and Ontologies

• 
  Christopher D. Fjell, Robert E. W. Hancock, Artem Cherkasov:
  AMPer: a database and an automated discovery tool for antimicrobial peptides. 1148-1155

Applications Note: Genome Analysis

• 
  Alejandro A. Schäffer, Edward Stallknecht Rice, William J. Cook, Richa Agarwala:
  rh_tsp_map 3.0: end-to-end radiation hybrid mapping with improved speed and quality control. 1156-1158
• 
  Romain Fremez, Thomas Faraut, Gwennaele Fichant, Jérôme Gouzy, Yves Quentin:
  Phylogenetic exploration of bacterial genomic rearrangements. 1172-1174

Sequence Analysis

• 
  Markus Brameier, Andrea Krings, Robert M. MacCallum:
  NucPred - Predicting nuclear localization of proteins. 1159-1160

Gene Expression

• 
  Evert-Jan Blom, Dinne W. J. Bosman, Sacha A. F. T. van Hijum, Rainer Breitling, Lars Tijsma, Remko Silvis, Jos B. T. M. Roerdink, Oscar P. Kuipers:
  FIVA: Functional Information Viewer and Analyzer extracting biological knowledge from transcriptome data of prokaryotes. 1161-1163
• 
  Wolfram Stacklies, Henning Redestig, Matthias Scholz, Dirk Walther, Joachim Selbig:
  pcaMethods - a bioconductor package providing PCA methods for incomplete data. 1164-1167
• 
  Diego Diez, Rebeca Alvarez, Ana Dopazo:
  Codelink: an R package for analysis of GE healthcare gene expression bioarrays. 1168-1169
• 
  Tancred Frickey, Georg Weiller:
  Analyzing microarray data using CLANS. 1170-1171

Systems Biology

• 
  Ying Sun, Shuqi Zhao, Huashan Yu, Ge Gao, Jingchu Luo:
  ABCGrid: Application for Bioinformatics Computing Grid. 1175-1177

Databases and Ontologies

• 
  Paul M. K. Gordon, Quang Trinh, Christoph W. Sensen:
  Semantic Web Service provision: a realistic framework for Bioinformatics programmers. 1178-1180

Volume 23, Number 10, 15 May 2007

Genome Analysis

• 
  Suresh B. Mudunuri, Hampapathalu A. Nagarajaram:
  IMEx: Imperfect Microsatellite Extractor. 1181-1187

Sequence Analysis

• 
  Leping Li, Yu Liang, Robert L. Bass:
  GAPWM: a genetic algorithm method for optimizing a position weight matrix. 1188-1194
• 
  Shengzhong Feng, Elisabeth R. M. Tillier:
  A fast and flexible approach to oligonucleotide probe design for genomes and gene families. 1195-1202

Structural Bioinformatics

• 
  Jan E. Gewehr, Volker Hintermair, Ralf Zimmer:
  AutoSCOP: automated prediction of SCOP classifications using unique pattern-class mappings. 1203-1210
• 
  Yoshihiro Yamanishi, Francis R. Bach, Jean-Philippe Vert:
  Glycan classification with tree kernels. 1211-1216

Gene Expression

• 
  Wuyan Zhang, Alicia L. Carriquiry, Dan Nettleton, Jack C. M. Dekkers:
  Pooling mRNA in microarray experiments and its effect on power. 1217-1224
• 
  Jiajun Liu, Jacqueline M. Hughes-Oliver, J. Alan Menius Jr.:
  Domain-enhanced analysis of microarray data using GO annotations. 1225-1234
• 
  Alicia Oshlack, Adrien E. Chabot, Gordon K. Smyth, Yoav Gilad:
  Using DNA microarrays to study gene expression in closely related species. 1235-1242
• 
  Yinglei Lai, Bao-Ling Adam, Robert H. Podolsky, Jin-Xiong She:
  A mixture model approach to the tests of concordance and discordance between two large-scale experiments with two-sample groups. 1243-1250

Genetics and Population Analysis

• 
  Min Lin, Hongying Li, Wei Hou, Julie A. Johnson, Rongling Wu:
  Modeling sequence-sequence interactions for drug response. 1251-1257

Systems Biology

• 
  Ross P. Carlson:
  Metabolic systems cost-benefit analysis for interpreting network structure and regulation. 1258-1264
• 
  Yufei Xiao, Edward R. Dougherty:
  The impact of function perturbations in Boolean networks. 1265-1273

Data and Text Mining

• 
  James Zijun Wang, Zhidian Du, Rapeeporn Payattakool, Philip S. Yu, Chin-Fu Chen:
  A new method to measure the semantic similarity of GO terms. 1274-1281

Databases and Ontologies

• 
  Baris E. Suzek, Hongzhan Huang, Peter B. McGarvey, Raja Mazumder, Cathy H. Wu:
  UniRef: comprehensive and non-redundant UniProt reference clusters. 1282-1288

Applications Notes: Sequence Analysis

• 
  Triinu Koressaar, Maido Remm:
  Enhancements and modifications of primer design program Primer3. 1289-1291

Structural Bioinformatics

• 
  Liang-Tsung Huang, M. Michael Gromiha, Shinn-Ying Ho:
  iPTREE-STAB: interpretable decision tree based method for predicting protein stability changes upon mutations. 1292-1293

Genetics and Population Analysis

• 
  Yurii S. Aulchenko, Stephan Ripke, Aaron Isaacs, Cornelia M. van Duijn:
  GenABEL: an R library for genome-wide association analysis. 1294-1296

Systems Biology

• 
  Henning Schmidt, Gunnar Drews, Julio Vera, Olaf Wolkenhauer:
  SBML export interface for the systems biology toolbox for MATLAB. 1297-1298
• 
  François Le Fèvre, Serge Smidtas, Vincent Schächter:
  Cyclone: java-based querying and computing with Pathway/Genome databases. 1299-1300

Databases and Ontologies

• 
  Sarah Cohen Boulakia, Olivier Biton, Susan B. Davidson, Christine Froidevaux:
  BioGuideSRS: querying multiple sources with a user-centric perspective. 1301-1303
• 
  Kevin Le Brigand, Pascal Barbry:
  Mediante: a web-based microarray data manager. 1304-1306
• 
  Qihui Zhu, Anyuan Guo, Ge Gao, Yingfu Zhong, Meng Xu, Minren Huang, Jingchu Luo:
  DPTF: a database of poplar transcription factors. 1307-1308

Volume 23, Number 11, June 2007

Systems Biology

• 
  Niels Grabe, Karsten Neuber:
  Simulating psoriasis by altering transit amplifying cells. 1309-1312

Sequence Analysis

• 
  Edmund S. Jackson, William J. Fitzgerald:
  A sequential Monte Carlo EM approach to the transcription factor binding site identification problem. 1313-1320

Structural Bioinformatics

• 
  Stanley Ng Kwang Loong, Santosh K. Mishra:
  De novo SVM classification of precursor microRNAs from genomic pseudo hairpins using global and intrinsic folding measures. 1321-1330
• 
  Shuoyong Shi, Yi Zhong, Indraneel Majumdar, S. Sri Krishna, Nick V. Grishin:
  Searching for three-dimensional secondary structural patterns in proteins with ProSMoS. 1331-1338

Gene Expression

• 
  Xiuwen Zheng, Hung-Chung Huang, Wenyuan Li, Peng Liu, Quan-Zhen Li, Ying Liu:
  Modeling nonlinearity in dilution design microarray data. 1339-1347
• 
  George Vasmatzis, Eric W. Klee, Dagmar M. Kube, Terry M. Therneau, Farhad Kosari:
  Quantitating tissue specificity of human genes to facilitate biomarker discovery. 1348-1355
• 
  Daniel M. Kemp, N. R. Nirmala, Joseph D. Szustakowski:
  Extending the pathway analysis framework with a test for transcriptional variance implicates novel pathway modulation during myogenic differentiation. 1356-1362
• 
  Ian A. Wood, Peter M. Visscher, Kerrie L. Mengersen:
  Classification based upon gene expression data: bias and precision of error rates. 1363-1370

Systems Biology

• 
  Filippo Castiglione, Karen Duca, Abdul Salam Jarrah, Reinhard C. Laubenbacher, Donna Hochberg, David Thorley-Lawson:
  Simulating Epstein-Barr virus infection with C-ImmSim. 1371-1377
• 
  Ralf Steuer, Adriano Nunes Nesi, Alisdair R. Fernie, Thilo Gross, Bernd Blasius, Joachim Selbig:
  From structure to dynamics of metabolic pathways: application to the plant mitochondrial TCA cycle. 1378-1385

Data and Text Mining

• 
  Alexander V. Alekseyenko, Christopher J. Lee:
  Nested Containment List (NCList): a new algorithm for accelerating interval query of genome alignment and interval databases. 1386-1393
• 
  Peicheng Du, Rajagopalan Sudha, Michael B. Prystowsky, Ruth Hogue Angeletti:
  Data reduction of isotope-resolved LC-MS spectra. 1394-1400
• 
  Martin Sköld, Tobias Rydén, Viktoria Samuelsson, Charlotte Bratt, Lars Ekblad, Håkan Olsson, Bo Baldetorp:
  Regression analysis and modelling of data acquisition for SELDI-TOF mass spectrometry. 1401-1409
• 
  Hagit Shatkay, Annette Höglund, Scott Brady, Torsten Blum, Pierre Dönnes, Oliver Kohlbacher:
  SherLoc: high-accuracy prediction of protein subcellular localization by integrating text and protein sequence data. 1410-1417

Databases and Ontologies

• 
  Ewa Urbanczyk-Wochniak, Lloyd W. Sumner:
  MedicCyc: a biochemical pathway database for Medicago truncatula. 1418-1423

Applications Notes: Genome Analysis

• 
  Nathan Day, Andrew Hemmaplardh, Robert E. Thurman, John A. Stamatoyannopoulos, William Stafford Noble:
  Unsupervised segmentation of continuous genomic data. 1424-1426

Sequence Analysis

• 
  Reed A. Cartwright:
  Ngila: global pairwise alignments with logarithmic and affine gap costs. 1427-1428

Structural Bioinformatics

• 
  Michal J. Pietal, Irina Tuszynska, Janusz M. Bujnicki:
  PROTMAP2D: visualization, comparison and analysis of 2D maps of protein structure. 1429-1430

Gene Expression

• 
  Joachim L. Schultze, Daniela Eggle:
  IlluminaGUI: Graphical User Interface for analyzing gene expression data generated on the Illumina platform. 1431-1433

Data and Text Mining

• 
  Patrick R. Leary, David P. Remsen, Catherine N. Norton, David J. Patterson, Indra Neil Sarkar:
  uBioRSS: Tracking taxonomic literature using RSS. 1434-1436

Databases and Ontologies

• 
  Maxim V. Shapovalov, Adrian A. Canutescu, Roland L. Dunbrack Jr.:
  BioDownloader: bioinformatics downloads and updates in a few clicks. 1437-1439

Volume 23, Number 12, 15 June 2007

Genetics and Population Analysis

• 
  Jan Freudenberg, Ying-Hui Fu, Louis J. Ptácek:
  Human recombination rates are increased around accelerated conserved regions - evidence for continued selection? 1441-1443

Genome Analysis

• 
  Zhi-Qiang Ye, Shuqi Zhao, Ge Gao, Xiao-Qiao Liu, Robert E. Langlois, Hui Lu, Liping Wei:
  Finding new structural and sequence attributes to predict possible disease association of single amino acid polymorphism (SAP). 1444-1450
• 
  Yuhyun Park, Sean R. Downing, Dohyun Kim, William C. Hahn, Cheng Li, Philip W. Kantoff, L. J. Wei:
  Simultaneous and exact interval estimates for the contrast of two groups based on an extremely high dimensional variable: application to mass spec data. 1451-1458
• 
  Yuanyuan Xiao, Mark R. Segal, Yee Hwa Yang, Ru-Fang Yeh:
  A multi-array multi-SNP genotyping algorithm for Affymetrix SNP microarrays. 1459-1467
• 
  Avril Coghlan, Richard Durbin:
  Genomix: a method for combining gene-finders' predictions, which uses evolutionary conservation of sequence and intron-exon structure. 1468-1475

Sequence Anlysis

• 
  Edward Wijaya, Kanagasabai Rajaraman, Siu-Ming Yiu, Wing-Kin Sung:
  Detection of generic spaced motifs using submotif pattern mining. 1476-1485

Gene Expression

• 
  Lifeng Wang, Guang Chen, Hongzhe Li:
  Group SCAD regression analysis for microarray time course gene expression data. 1486-1494
• 
  Hyunsoo Kim, Haesun Park:
  Sparse non-negative matrix factorizations via alternating non-negativity-constrained least squares for microarray data analysis. 1495-1502
• 
  Di Huang, Tommy W. S. Chow:
  Identifying the biologically relevant gene categories based on gene expression and biological data: an example on prostate cancer. 1503-1510
• 
  Wai-Ki Ching, Shuqin Zhang, Michael K. Ng, Tatsuya Akutsu:
  An approximation method for solving the steady-state probability distribution of probabilistic Boolean networks. 1511-1518

Genetics and Population Analysis

• 
  Alexandra Goll, Peter Bauer:
  Two-stage designs applying methods differing in costs. 1519-1526
• 
  Jian Yang, Jun Zhu, Robert W. Williams:
  Mapping the genetic architecture of complex traits in experimental populations. 1527-1536

Systems Biology

• 
  Zhi Wei, Hongzhe Li:
  A Markov random field model for network-based analysis of genomic data. 1537-1544

Databases and Ontologies

• 
  Martin S. Taylor, William Valdar, Ashish Kumar, Jonathan Flint, Richard Mott:
  Management, presentation and interpretation of genome scans using GSCANDB. 1545-1549

Genome Analysis

• 
  Frank J. Sørensen, Claus L. Andersen, Carsten Wiuf:
  SNPTools: a software tool for visualization and analysis of microarray data. 1550-1552

Sequence Analysis

• 
  Matthew Goode, Allen G. Rodrigo:
  SQUINT: a multiple alignment program and editor. 1553-1555

Phylogenetics

• 
  Pere Puigbò, Santiago Garcia-Vallvé, James O. McInerney:
  TOPD/FMTS: a new software to compare phylogenetic trees. 1556-1558

Gene Expression

• 
  Andrzej Kudlicki, Maga Rowicka, Zbyszek Otwinowski:
  SCEPTRANS: an online tool for analyzing periodic transcription in yeast. 1559-1561
• 
  Steven Eschrich, Andrew M. Hoerter:
  Libaffy: software for processing Affymetrix(R) GeneChip(R) data. 1562-1564

Genetics and Population Analysis

• 
  Liming Liang, Sebastian Zöllner, Gonçalo R. Abecasis:
  GENOME: a rapid coalescent-based whole genome simulator. 1565-1567

Databases and Ontologies

• 
  Robert D. Finn, James W. Stalker, David K. Jackson, Eugene Kulesha, Jody Clements, Roger Pettett:
  ProServer: a simple, extensible Perl DAS server. 1568-1570

Erratum

• 
  Jie Zhou, Hanchuan Peng:
  Automatic recognition and annotation of gene expression patterns of fly embryos. 1571-1572

Volume 23, Number 13, July 2007

Genome Analysis

• 
  Daniel C. Richter, Stephan C. Schuster, Daniel H. Huson:
  OSLay: optimal syntenic layout of unfinished assemblies. 1573-1579

Sequence Analysis

• 
  Bruno A. Gaëta, Harald R. Malming, Katherine J. L. Jackson, Michael E. Bain, Patrick Wilson, Andrew M. Collins:
  iHMMune-align: hidden Markov model-based alignment and identification of germline genes in rearranged immunoglobulin gene sequences. 1580-1587

Structural Bioinformatics

• 
  Hisanori Kiryu, Yasuo Tabei, Taishin Kin, Kiyoshi Asai:
  Murlet: a practical multiple alignment tool for structural RNA sequences. 1588-1598

Gene Expression

• 
  Irit Fishel, Alon Kaufman, Eytan Ruppin:
  Meta-analysis of gene expression data: a predictor-based approach. 1599-1606
• 
  Vasyl Pihur, Susmita Datta, Somnath Datta:
  Weighted rank aggregation of cluster validation measures: a Monte Carlo cross-entropy approach. 1607-1615

Systems Biology

• 
  Roger Guimerà, Marta Sales-Pardo, Luís A. Nunes Amaral:
  A network-based method for target selection in metabolic networks. 1616-1622
• 
  André Fujita, João Ricardo Sato, Humberto Miguel Garay-Malpartida, Pedro Alberto Morettin, Mari Cleide Sogayar, Carlos Eduardo Ferreira:
  Time-varying modeling of gene expression regulatory networks using the wavelet dynamic vector autoregressive method. 1623-1630
• 
  Zhen-Ping Li, Shi-Hua Zhang, Yong Wang, Xiang-Sun Zhang, Luonan Chen:
  Alignment of molecular networks by integer quadratic programming. 1631-1639
• 
  Nicola Soranzo, Ginestra Bianconi, Claudio Altafini:
  Comparing association network algorithms for reverse engineering of large-scale gene regulatory networks: synthetic versus real data. 1640-1647

Data and Text Mining

• 
  Vladimir Makarenkov, Pablo Zentilli, Dmytro Kevorkov, Andrei V. Gagarin, Nathalie Malo, Robert Nadon:
  An efficient method for the detection and elimination of systematic error in high-throughput screening. 1648-1657
• 
  Vetle I. Torvik, Neil R. Smalheiser:
  A quantitative model for linking two disparate sets of articles in MEDLINE. 1658-1665
• 
  Khuloud Jaqaman, Jonas F. Dorn, Eugenio Marco, Peter K. Sorger, Gaudenz Danuser:
  Phenotypic clustering of yeast mutants based on kinetochore microtubule dynamics. 1666-1673

Databases and Ontologies

• 
  Thomas Bittner, Louis J. Goldberg:
  The qualitative and time-dependent character of spatial relations in biomedical ontologies. 1674-1682

Genome Analysis

• 
  Robert Kofler, Christian Schlötterer, Tamas Lelley:
  SciRoKo: a new tool for whole genome microsatellite search and investigation. 1683-1685

Sequence Analysis

• 
  Anna Gambin, Piotr Wojtalewicz:
  CTX-BLAST: context sensitive version of protein BLAST. 1686-1688
• 
  Ed Dicks, Jon W. Teague, Philip Stephens, Keiran Raine, Andrew D. Yates, C. Mattocks, P. Tarpey, Adam P. Butler, Andrew Menzies, David Richardson, Andrew M. Jenkinson, Helen Davies, Sarah Edkins, Simon A. Forbes, Kristian A. Gray, Christopher Greenman, Rebecca Shepherd, Michael R. Stratton, P. Andrew Futreal, Richard Wooster:
  AutoCSA, an algorithm for high throughput DNA sequence variant detection in cancer genomes. 1689-1691
• 
  Ben J. Hayes, Kjetil Nilsen, Paul R. Berg, Eli Grindflek, Sigbjørn Lien:
  SNP detection exploiting multiple sources of redundancy in large EST collections improves validation rates. 1692-1693

Structural Bioinformatics

• 
  Bruno Contreras-Moreira, Pierre-Alain Branger, Julio Collado-Vides:
  TFmodeller: comparative modelling of protein-DNA complexes. 1694-1696

Gene Expression

• 
  Sang-Bae Kim, Sungjin Yang, Seon-Kyu Kim, Sang Cheol Kim, Hyun Goo Woo, David J. Volsky, Seon-Young Kim, In-Sun Chu:
  GAzer: gene set analyzer. 1697-1699
• 
  Hui Zhao, Kristof Engelen, Bart De Moor, Kathleen Marchal:
  CALIB: a Bioconductor package for estimating absolute expression levels from two-color microarray data. 1700-1701
• 
  Anne-Laure Boulesteix:
  WilcoxCV: an R package for fast variable selection in cross-validation. 1702-1704

Systems Biology

• 
  Bobbie-Jo M. Webb-Robertson, Elena S. Peterson, Mudita Singhal, Kyle R. Klicker, Christopher S. Oehmen, Joshua N. Adkins, Susan L. Havre:
  PQuad - a visual analysis platform for proteomic data exploration of microbial organisms. 1705-1707
• 
  Falk Hüffner, Sebastian Wernicke, Thomas Zichner:
  FASPAD: fast signaling pathway detection. 1708-1709

Databases and Ontologies

• 
  Jing-Xian Zhang, Wei-Juan Huang, Jing-Hua Zeng, Wen-Hui Huang, Yi Wang, Rui Zhao, Bu-Cong Han, Qing-Feng Liu, Yuzong Chen, Zhi Liang Ji:
  DITOP: drug-induced toxicity related protein database. 1710-1712

Volume 23, Number 14, 15 July 2007

REVIEW: Sequence Analysis

• 
  Sudhir Kumar, Joel Dudley:
  Bioinformatics software for biologists in the genomics era. 1713-1717

Sequence Analysis

• 
  Lee Aaron Newberg, William A. Thompson, Sean Conlan, Thomas M. Smith, Lee Ann McCue, Charles E. Lawrence:
  A phylogenetic Gibbs sampler that yields centroid solutions for cis-regulatory site prediction. 1718-1727
• 
  Sepp Hochreiter, Martin Heusel, Klaus Obermayer:
  Fast model-based protein homology detection without alignment. 1728-1736
• 
  Libi Hertzberg, Shai Izraeli, Eytan Domany:
  STOP: searching for transcription factor motifs using gene expression. 1737-1743

Phylogenetics

• 
  Xiaomeng Wu, Zhipeng Cai, Xiu-Feng Wan, Tin Hoang, Randy Goebel, Guohui Lin:
  Nucleotide composition string selection in HIV-1 subtyping using whole genomes. 1744-1752

Structural Bioinformatics

• 
  Peter M. Kasson, Afra Zomorodian, Sanghyun Park, Nina Singhal, Leonidas J. Guibas, Vijay S. Pande:
  Persistent voids: a new structural metric for membrane fusion. 1753-1759
• 
  Ganesh Bagler, Somdatta Sinha:
  Assortative mixing in Protein Contact Networks and protein folding kinetics. 1760-1767

Gene Expression

• 
  Martin Schumacher, Harald Binder, Thomas Gerds:
  Assessment of survival prediction models based on microarray data. 1768-1774
• 
  Feng Tai, Wei Pan:
  Incorporating prior knowledge of predictors into penalized classifiers with multiple penalty terms. 1775-1782
• 
  Mark P. Brynildsen, Tung-Yun Wu, Shi-Shang Jang, James C. Liao:
  Biological network mapping and source signal deduction. 1783-1791
• 
  María José Nueda, Ana Conesa, Johan A. Westerhuis, Huub C. J. Hoefsloot, Age K. Smilde, Manuel Talón, Alberto Ferrer:
  Discovering gene expression patterns in time course microarray experiments by ANOVA-SCA. 1792-1800

Genetics and Population Analysis

• 
  Mattias Jakobsson, Noah A. Rosenberg:
  CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. 1801-1806
• 
  Donna M. Toleno, Peter L. Morrell, Michael T. Clegg:
  Error detection in SNP data by considering the likelihood of recombinational history implied by three-site combinations. 1807-1814

Databases and Ontologies

• 
  Ashwini Bhasi, Ram Vinay Pandey, Suriya Prabha Utharasamy, Periannan Senapathy:
  EuSplice: a unified resource for the analysis of splice signals and alternative splicing in eukaryotic genes. 1815-1823
• 
  Roman A. Laskowski:
  Enhancing the functional annotation of PDB structures in PDBsum using key figures extracted from the literature. 1824-1827

Genome Analysis

• 
  Timothy R. O'Connor, John J. Wyrick:
  ChromatinDB: a database of genome-wide histone modification patterns for Saccharomyces cerevisiae. 1828-1830
• 
  Arnaud Kerhornou, Roderic Guigó:
  BioMoby web services to support clustering of co-regulated genes based on similarity of promoter configurations. 1831-1833

Sequence Analysis

• 
  Francois Beaussart, January 3rd Weiner, Erich Bornberg-Bauer:
  Automated Improvement of Domain ANnotations using context analysis of domain arrangements (AIDAN). 1834-1836

Structural Bioinformatics

• 
  Eran Eyal, Shmuel Pietrokovski, Ivet Bahar:
  Rapid assessment of correlated amino acids from pair-to-pair (P2P) substitution matrices. 1837-1839
• 
  Dominik Gront, Andrzej Kolinski:
  T-Pile - a package for thermodynamic calculations for biomolecules. 1840-1842

Gene Expression

• 
  Zuoshuang Xiang, Zhaohui S. Qin, Yongqun He:
  CRCView: a web server for analyzing and visualizing microarray gene expression data using model-based clustering. 1843-1845
• 
  Sean R. Davis, Paul S. Meltzer:
  GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor. 1846-1847

Genetics and Population Analysis

• 
  Tiago Rodrigues Antao, Albano Beja-Pereira, Gordon Luikart:
  MODELER4SIMCOAL2: A user-friendly, extensible modeler of demography and linked loci for coalescent simulations. 1848-1850
• 
  August E. Woerner, Murray P. Cox, Michael F. Hammer:
  Recombination-filtered genomic datasets by information maximization. 1851-1853
• 
  Edward H. Trager, Ritu Khanna, Adrian Marrs, Lawrence Siden, Kari E. H. Branham, Anand Swaroop, Julia E. Richards:
  Madeline 2.0 PDE: a new program for local and web-based pedigree drawing. 1854-1856

Systems Biology

• 
  Guillermo Rodrigo, Javier Carrera, Alfonso Jaramillo:
  Genetdes: automatic design of transcriptional networks. 1857-1858
• 
  Ravishankar Rao Vallabhajosyula, Herbert M. Sauro:
  Stochastic simulation GUI for biochemical networks. 1859-1861

Data and Text Mining

• 
  J. Gregory Caporaso, William A. Baumgartner Jr., David A. Randolph, K. Bretonnel Cohen, Lawrence Hunter:
  MutationFinder: a high-performance system for extracting point mutation mentions from text. 1862-1865

Databases and Ontologies

• 
  Feng Gao, Chun-Ting Zhang:
  DoriC: a database of oriC regions in bacterial genomes. 1866-1867
• 
  Dilvan A. Moreira, Mark A. Musen:
  OBO to OWL: a protégé OWL tab to read/save OBO ontologies. 1868-1870

Volume 23, Number 15, August 2007

Sequence Analysis

• 
  Isabelle Callebaut, Jean Paul Mornon, Philippe Monget:
  Isolated ZP-N domains constitute the N-terminal extensions of Zona Pellucida proteins. 1871-1874

Sequence Analysis

• 
  John A. Capra, Mona Singh:
  Predicting functionally important residues from sequence conservation. 1875-1882
• 
  Xing Xu, Yongmei Ji, Gary D. Stormo:
  RNA Sampler: a new sampling based algorithm for common RNA secondary structure prediction and structural alignment. 1883-1891
• 
  Uta Schulze, Bettina Hepp, Cheng Soon Ong, Gunnar Rätsch:
  PALMA: mRNA to genome alignments using large margin algorithms. 1892-1900

Structural Bioinformatics

• 
  James A. R. Dalton, Richard M. Jackson:
  An evaluation of automated homology modelling methods at low target-template sequence similarity. 1901-1908
• 
  Mainak Guharoy, Pinak Chakrabarti:
  Secondary structure based analysis and classification of biological interfaces: identification of binding motifs in protein-protein interactions. 1909-1918
• 
  Gennady Verkhivker:
  Exploring sequence-structure relationships in the tyrosine kinome space: functional classification of the binding specificity mechanisms for cancer therapeutics. 1919-1926

Gene Expression

• 
  Attila Gyenesei, Ulrich Wagner, Simon Barkow-Oesterreicher, Etzard Stolte, Ralph Schlapbach:
  Mining co-regulated gene profiles for the detection of functional associations in gene expression data. 1927-1935
• 
  Peter Sykacek, R. Clarkson, Cristin G. Print, R. A. Furlong, Gos Micklem:
  Bayesian modelling of shared gene function. 1936-1944
• 
  J. G. Liao, Khew-Voon Chin:
  Logistic regression for disease classification using microarray data: model selection in a large p and small n case. 1945-1951

Genetics and Population Analysis

• 
  Marko Laakso, Sari Tuupanen, Auli Karhu, Rainer Lehtonen, Lauri A. Aaltonen, Sampsa Hautaniemi:
  Computational identification of candidate loci for recessively inherited mutation using high-throughput SNP arrays. 1952-1961
• 
  Scotland C. Leman, Marcy K. Uyenoyama, Michael Lavine, Yuguo Chen:
  The evolutionary forest algorithm. 1962-1968

Systems Biology

• 
  Maciej Dobrzynski, Jordi Vidal Rodríguez, Jaap A. Kaandorp, Joke G. Blom:
  Computational methods for diffusion-influenced biochemical reactions. 1969-1977
• 
  Sebastian Wernicke, Florian Rasche:
  Simple and fast alignment of metabolic pathways by exploiting local diversity. 1978-1985
• 
  Jianhua Hu, Xuming He, Keith A. Baggerly, Kevin R. Coombes, Bryan T. J. Hennessy, Gordon B. Mills:
  Non-parametric quantification of protein lysate arrays. 1986-1994

Data and Text Mining

• 
  Mark F. Burkart, Jonathan D. Wren, Jason I. Herschkowitz, Charles M. Perou, Harold R. Garner:
  Clustering microarray-derived gene lists through implicit literature relationships. 1995-2003
• 
  Nobuyoshi Nagamine, Yasubumi Sakakibara:
  Statistical prediction of protein-chemical interactions based on chemical structure and mass spectrometry data. 2004-2012

Genome Analysis

• 
  Xiaohui Cai, Haiyan Hu, Xiaoman Shawn Li:
  Tree Gibbs Sampler: identifying conserved motifs without aligning orthologous sequences. 2013-2014

Sequence Analysis

• 
  Markus Fischer, Michael Knoll, Demet Sirim, Florian Wagner, Sonja Funke, Jürgen Pleiss:
  The Cytochrome P450 Engineering Database: a navigation and prediction tool for the cytochrome P450 protein family. 2015-2017

Structural Bioinformatics

• 
  John-Marc Chandonia:
  StrBioLib: a Java library for development of custom computational structural biology applications. 2018-2020

Data and Text Mining

• 
  Matthew E. Monroe, Nikola Tolic, Navdeep Jaitly, Jason L. Shaw, Joshua N. Adkins, Richard D. Smith:
  VIPER: an advanced software package to support high-throughput LC-MS peptide identification. 2021-2023
• 
  Jiajing Wang, Huai Li, Yitan Zhu, Malik Yousef, Michael Nebozhyn, Michael M. Showe, Louise C. Showe, Jianhua Xuan, Robert Clarke, Yue Joseph Wang:
  VISDA: an open-source caBIG^TM analytical tool for data clustering and beyond. 2024-2027

Corrigendum

• 
  Qifang Xu, Adrian A. Canutescu, Zoran Obradovic, Roland L. Dunbrack Jr.:
  ProtBuD: a database of biological unit structures of protein families and superfamilies. 2028
• 
  Xin Zhou, David P. Tuck:
  MSVM-RFE: extensions of SVM-RFE for multiclass gene selection on DNA microarray data. 2029

Volume 23, Number 16, 15 August 2007

Sequence Analysis

• 
  Wendy S. W. Wong, Rasmus Nielsen:
  Finding cis-regulatory modules in Drosophila using phylogenetic hidden Markov models. 2031-2037

Structural Bioinformatics

• 
  Alessio Ceroni, Fabrizio Costa, Paolo Frasconi:
  Classification of small molecules by two- and three-dimensional decomposition kernels. 2038-2045
• 
  Shuichi Hirose, Kana Shimizu, Satoru Kanai, Yutaka Kuroda, Tamotsu Noguchi:
  POODLE-L: a two-level SVM prediction system for reliably predicting long disordered regions. 2046-2053
• 
  Eva Freyhult, Vincent Moulton, Peter Clote:
  Boltzmann probability of RNA structural neighbors and riboswitch detection. 2054-2062

Gene Expression

• 
  Rosalia Maglietta, Ada Piepoli, Domenico Catalano, Piepoli Licciulli, Massimo Carella, Sabino Liuni, Graziano Pesole, Francesco Perri, Nicola Ancona:
  Statistical assessment of functional categories of genes deregulated in pathological conditions by using microarray data. 2063-2072
• 
  Yiyong Zhou, Corentin Cras-Méneur, Mitsuru Ohsugi, Gary D. Stormo, M. Alan Permutt:
  A global approach to identify differentially expressed genes in cDNA (two-color) microarray experiments. 2073-2079
• 
  Hege M. Bøvelstad, Ståle Nygård, H. L. Størvold, Magne Aldrin, Ørnulf Borgan, Arnoldo Frigessi, Ole Christian Lingjærde:
  Predicting survival from microarray data - a comparative study. 2080-2087
• 
  Yonghong Wang, Ze-Hong Miao, Yves Pommier, Ernest S. Kawasaki, Audrey Player:
  Characterization of mismatch and high-signal intensity probes associated with Affymetrix genechips. 2088-2095
• 
  Laura Elo, Henna Järvenpää, Matej Oresic, Riitta Lahesmaa, Tero Aittokallio:
  Systematic construction of gene coexpression networks with applications to human T helper cell differentiation process. 2096-2103
• 
  James J. Chen, Taewon Lee, Robert R. Delongchamp, Tao Chen, Chen-An Tsai:
  Significance analysis of groups of genes in expression profiling studies. 2104-2112

Genetics and Population Analysis

• 
  Brett A. McKinney, David M. Reif, Bill C. White, James E. Crowe Jr., Jason H. Moore:
  Evaporative cooling feature selection for genotypic data involving interactions. 2113-2120

Systems Biology

• 
  Zheng Guo, Yongjin Li, Xue Gong, Chen Yao, Wencai Ma, Dong Wang, Yanhui Li, Jing Zhu, Min Zhang, Da Yang, Jing Wang:
  Edge-based scoring and searching method for identifying condition-responsive protein-protein interaction sub-network. 2121-2128
• 
  Vachiranee Limviphuvadh, Seigo Tanaka, Susumu Goto, Kunihiro Ueda, Minoru Kanehisa:
  The commonality of protein interaction networks determined in neurodegenerative disorders (NDDs). 2129-2138
• 
  Oleg Rokhlenko, Tomer Shlomi, Roded Sharan, Eytan Ruppin, Ron Y. Pinter:
  Constraint-based functional similarity of metabolic genes: going beyond network topology. 2139-2146

Data and Text Mining

• 
  Minca Mramor, Gregor Leban, Janez Demsar, Blaz Zupan:
  Visualization-based cancer microarray data classification analysis. 2147-2154
• 
  Kyu-Won Kim, Hun-Ki Chung, Gyu-Taek Cho, Kyung-Ho Ma, Dorothy Chandrabalan, Jae-Gyun Gwag, Tae-San Kim, Eun-Gi Cho, Yong-Jin Park:
  PowerCore: a program applying the advanced M strategy with a heuristic search for establishing core sets. 2155-2162

Databases and Ontologies

• 
  Haiyuan Yu, Ronald Jansen, Gustavo Stolovitzky, Mark Gerstein:
  Total ancestry measure: quantifying the similarity in tree-like classification, with genomic applications. 2163-2173
• 
  Long Yang, Gulei Jin, Xiangqian Zhao, Yan Zheng, Zhaohua Xu, Weiren Wu:
  PIP: a database of potential intron polymorphism markers. 2174-2177

Genome Analysis

• 
  François Enault, Romain Fremez, Eric Baranowski, Thomas Faraut:
  Alvira: comparative genomics of viral strains. 2178-2179
• 
  Adrian Schneider, Christophe Dessimoz, Gaston H. Gonnet:
  OMA Browser - Exploring orthologous relations across 352 complete genomes. 2180-2182
• 
  Mark J. Dunning, Mike L. Smith, Matthew E. Ritchie, Simon Tavaré:
  beadarray: R classes and methods for Illumina bead-based data. 2183-2184

Gene Expression

• 
  Manhong Dai, Pinglang Wang, Elvis Jakupovic, Stanley J. Watson, Fan Meng:
  Web-based GeneChip analysis system for large-scale collaborative projects. 2185-2187

Genetics and Population Analysis

• 
  Clément Rezvoy, Delphine Charif, Laurent Guéguen, Gabriel A. B. Marais:
  MareyMap: an R-based tool with graphical interface for estimating recombination rates. 2188-2189
• 
  Jason M. Laramie, Jemma B. Wilk, Anita L. DeStefano, Richard H. Myers:
  HaploBuild: an algorithm to construct non-contiguous associated haplotypes in family based genetic studies. 2190-2192

Systems Biology

• 
  Lukasz Salwínski, David Eisenberg:
  The MiSink Plugin: Cytoscape as a graphical interface to the Database of Interacting Proteins. 2193-2195

Data and Text Mining

• 
  Marti A. Hearst, Anna Divoli, Harendra Guturu, Alex Ksikes, Preslav Nakov, Michael A. Wooldridge, Jerry Ye:
  BioText Search Engine: beyond abstract search. 2196-2197

Databases and Ontologies

• 
  John Day-Richter, Midori A. Harris, Melissa A. Haendel, Suzanna Lewis:
  OBO-Edit - an ontology editor for biologists. 2198-2200

Corrigendum

• 
  George Nicola, Ilya A. Vakser:
  A simple shape characteristic of protein-protein recognition. 2201

Erratum

• 
  Ross P. Carlson:
  Metabolic systems cost-benefit analysis for interpreting network structure and regulation - Erratum. 2202

Volume 23, Number 17, 1 September 2007

Structural Bioinformatics

• 
  Huan-Xiang Zhou, Sanbo Qin:
  Interaction-site prediction for protein complexes: a critical assessment. 2203-2209

Sequence Analysis

• 
  Jian Feng, Daniel Q. Naiman, Bret Cooper:
  Probability-based pattern recognition and statistical framework for randomization: modeling tandem mass spectrum/peptide sequence false match frequencies. 2210-2217

Structural Bioinformatics

• 
  Zhuqing Zhang, Hao Chen, Luhua Lai:
  Identification of amyloid fibril-forming segments based on structure and residue-based statistical potential. 2218-2225
• 
  Christina Kiel, Luis Serrano:
  Prediction of Ras-effector interactions using position energy matrices. 2226-2230
• 
  Anna V. Glyakina, Sergiy O. Garbuzynskiy, Michail Yu. Lobanov, Oxana V. Galzitskaya:
  Different packing of external residues can explain differences in the thermostability of proteins from thermophilic and mesophilic organisms. 2231-2238

Gene Expression

• 
  Anat Reiner-Benaim, Daniel Yekutieli, Noah E. Letwin, Gregory I. Elmer, Norman H. Lee, Neri Kafkafi, Yoav Benjamini:
  Associating quantitative behavioral traits with gene expression in the brain: searching for diamonds in the hay. 2239-2246
• 
  George C. Tseng:
  Penalized and weighted K-means for clustering with scattered objects and prior information in high-throughput biological data. 2247-2255
• 
  Claudio Lottaz, Joern Toedling, Rainer Spang:
  Annotation-based distance measures for patient subgroup discovery in clinical microarray studies. 2256-2264
• 
  Antonis Daskalakis, Dionisis A. Cavouras, Panagiotis Bougioukos, Spiros Kostopoulos, Dimitris Glotsos, Ioannis Kalatzis, George C. Kagadis, Christos Argyropoulos, George Nikiforidis:
  Improving gene quantification by adjustable spot-image restoration. 2265-2272
• 
  Andreas Buness, Ruprecht Kuner, Markus Ruschhaupt, Annemarie Poustka, Holger Sültmann, Achim Tresch:
  Identification of aberrant chromosomal regions from gene expression microarray studies applied to human breast cancer. 2273-2280

Systems Biology

• 
  Julio Vera, Raul Curto, Marta Cascante, Néstor V. Torres:
  Detection of potential enzyme targets by metabolic modelling and optimization: Application to a simple enzymopathy. 2281-2289
• 
  Wei Sun, Tianwei Yu, Ker-Chau Li:
  Detection of eQTL modules mediated by activity levels of transcription factors. 2290-2297
• 
  Dongxiao Zhu, Youjuan Li, Hua Li:
  Multivariate correlation estimator for inferring functional relationships from replicated genome-wide data. 2298-2305
• 
  Eric Yang, Panagiota T. Foteinou, K. R. King, Martin L. Yarmush, Ioannis P. Androulakis:
  A novel non-overlapping bi-clustering algorithm for network generation using living cell array data. 2306-2313
• 
  Pao-Yang Chen, Charlotte M. Deane, Gesine Reinert:
  A statistical approach using network structure in the prediction of protein characteristics. 2314-2321

Data and Text Mining

• 
  Chad L. Myers, Olga G. Troyanskaya:
  Context-sensitive data integration and prediction of biological networks. 2322-2330

Genome Analysis

• 
  Namshin Kim, Christopher J. Lee:
  QPRIMER: a quick web-based application for designing conserved PCR primers from multigenome alignments. 2331-2333

Sequence Analysis

• 
  Wenjie Deng, David C. Nickle, Gerald H. Learn, Brandon Maust, James I. Mullins:
  ViroBLAST: a stand-alone BLAST web server for flexible queries of multiple databases and user's datasets. 2334-2336

Structural Bioinformatics

• 
  Kana Shimizu, Shuichi Hirose, Tamotsu Noguchi:
  POODLE-S: web application for predicting protein disorder by using physicochemical features and reduced amino acid set of a position-specific scoring matrix. 2337-2338

Gene Expression

• 
  Laetitia Marisa, Jean-Laurent Ichanté, Nancie Reymond, Lawrence Aggerbeck, Hervé Delacroix, Marie-Hélène Mucchielli-Giorgi:
  MAnGO: an interactive R-based tool for two-colour microarray analysis. 2339-2341
• 
  Kin-On Cheng, Ngai-Fong Law, Wan-Chi Siu, T. H. Lau:
  BiVisu: software tool for bicluster detection and visualization. 2342-2344

Systems Biology

• 
  John H. Morris, Conrad C. Huang, Patricia C. Babbitt, Thomas E. Ferrin:
  structureViz: linking Cytoscape and UCSF Chimera. 2345-2347

Databases and Ontologies

• 
  Jonathan H. Chen, Erik Linstead, Sanjay Joshua Swamidass, Dennis Wang, Pierre Baldi:
  ChemDB update - full-text search and virtual chemical space. 2348-2351

Volume 23, Number 18, 15 September 2007

Sequence Analysis

• 
  Adam James Reid, Corin Yeats, Christine A. Orengo:
  Methods of remote homology detection can be combined to increase coverage by 10% in the midnight zone. 2353-2360
• 
  Andreas Heger, Swapan Mallick, Christopher Andrew Wilton, Liisa Holm:
  The global trace graph, a novel paradigm for searching protein sequence databases. 2361-2367

Phylogenetics

• 
  Xiu-Feng Wan, Guorong Chen, Feng Luo, Michael Emch, Ruben O. Donis:
  A quantitative genotype algorithm reflecting H5N1 Avian influenza niches. 2368-2375

Structural Bioinformatics

• 
  Avner Schlessinger, Marco Punta, Burkhard Rost:
  Natively unstructured regions in proteins identified from contact predictions. 2376-2384

Gene Expression

• 
  Hongfang Liu, Barry Zeeberg, Gang Qu, Akif Günes Koru, Alessandro Ferrucci, Ari B. Kahn, Michael C. Ryan, Antej Nuhanovic, Peter J. Munson, William C. Reinhold, David W. Kane, John N. Weinstein:
  AffyProbeMiner: a web resource for computing or retrieving accurately redefined Affymetrix probe sets. 2385-2390
• 
  Jianqing Fan, Yue Niu:
  Selection and validation of normalization methods for c-DNA microarrays using within-array replications. 2391-2398

Genetics and Population Analysis

• 
  Yun Joo Yoo, Jianming Tang, Richard A. Kaslow, Kui Zhang:
  Haplotype inference for present-absent genotype data using previously identified haplotypes and haplotype patterns. 2399-2406

Systems Biology

• 
  Mohamed Elati, Pierre Neuvial, Monique Bolotin-Fukuhara, Emmanuel Barillot, François Radvanyi, Céline Rouveirol:
  LICORN: learning cooperative regulation networks from gene expression data. 2407-2414
• 
  Grégory Batt, Boyan Yordanov, Ron Weiss, Calin Belta:
  Robustness analysis and tuning of synthetic gene networks. 2415-2422
• 
  Zuoshuang Xiang, Rebecca M. Minter, Xiaoming Bi, Peter J. Woolf, Yongqun He:
  miniTUBA: medical inference by network integration of temporal data using Bayesian analysis. 2423-2432
• 
  Jeongah Yoon, Yaguang Si, Ryan Nolan, Kyongbum Lee:
  Modular decomposition of metabolic reaction networks based on flux analysis and pathway projection. 2433-2440

Data and Text Mining

• 
  Jaroslaw Harezlak, Mike Wang, David Christiani, Xihong Lin:
  Quantitative quality-assessment techniques to compare fractionation and depletion methods in SELDI-TOF mass spectrometry experiments. 2441-2448
• 
  Ziliang Qian, Lingyi Lu, Xiao-Jun Liu, Yu-Dong Cai, Yixue Li:
  An approach to predict transcription factor DNA binding site specificity based upon gene and transcription factor functional categorization. 2449-2454
• 
  Hiroto Saigo, Takeaki Uno, Koji Tsuda:
  Mining complex genotypic features for predicting HIV-1 drug resistance. 2455-2462
• 
  Jian Huang, Arief Gusnanto, Kathleen O'Sullivan, Johan Staaf, Åke Borg, Yudi Pawitan:
  Robust smooth segmentation approach for array CGH data analysis. 2463-2469
• 
  Youjuan Li, Ji Zhu:
  Analysis of array CGH data for cancer studies using fused quantile regression. 2470-2476
• 
  Weijian Xuan, Pinglang Wang, Stanley J. Watson, Fan Meng:
  Medline search engine for finding genetic markers with biological significance. 2477-2484

Sequence Analysis

• 
  Gerton Lunter:
  HMMoC - a compiler for hidden Markov models. 2485-2487
• 
  Andrija Tomovic, Edward J. Oakeley:
  Quality estimation of multiple sequence alignments by Bayesian hypothesis testing. 2488-2490

Structural Bioinformatics

• 
  Jo-Lan Chung, John E. Beaver, Eric D. Scheeff, Philip E. Bourne:
  Con-Struct Map: a comparative contact map analysis tool. 2491-2492

Gene Expression

• 
  Chris Harbron, Kai-Ming Chang, Marie C. South:
  RefPlus: an R package extending the RMA Algorithm. 2493-2494

Systems Biology

• 
  Juan Hernandez-Toro, Carlos Prieto, Javier De Las Rivas:
  APID2NET: unified interactome graphic analyzer. 2495-2497

Data and Text Mining

• 
  Supawadee Ingsriswang, Eakasit Pacharawongsakda:
  sMOL Explorer: an open source, web-enabled database and exploration tool for Small MOLecules datasets. 2498-2500

Databases and Ontologies

• 
  Hongseok Yun, Jeong Wook Lee, Joonwoo Jeong, Jaesung Chung, Jong Myoung Park, Han Na Myoung, Sang Yup Lee:
  EcoProDB: the Escherichia coli protein database. 2501-2503
• 
  Catherine Voegele, Sean V. Tavtigian, D. de Silva, S. Cuber, Alun Thomas, Florence Le Calvez-Kelm:
  A Laboratory Information Management System (LIMS) for a high throughput genetic platform aimed at candidate gene mutation screening. 2504-2506

Volume 23, Number 19, 1 October 2007

REVIEW: Gene Expression

• 
  Yvan Saeys, Iñaki Inza, Pedro Larrañaga:
  A review of feature selection techniques in bioinformatics. 2507-2517

Sequence Analysis

• 
  Kirill Borziak, Igor B. Zhulin:
  FIST: a sensory domain for diverse signal transduction pathways in prokaryotes and ubiquitin signaling in eukaryotes. 2518-2521

Structural Bioinformatics

• 
  Andrzej Kolinski, Dominik Gront:
  Comparative modeling without implicit sequence alignments. 2522-2527

Genome Analysis

• 
  Karin Noy, Daniel P. Fasulo:
  Improved model-based, platform-independent feature extraction for mass spectrometry. 2528-2535

Sequence Analysis

• 
  Pawel Smialowski, Antonio J. Martin-Galiano, Aleksandra Mikolajka, Tobias Girschick, Tad A. Holak, Dmitrij Frishman:
  Protein solubility: sequence based prediction and experimental verification. 2536-2542
• 
  Jurica Zucko, N. Skunca, Tomaz Curk, Blaz Zupan, Paul F. Long, John Cullum, R. H. Kessin, Daslav Hranueli:
  Polyketide synthase genes and the natural products potential of Dictyostelium discoideum. 2543-2549
• 
  Cécile Militon, Sébastien Rimour, Mohieddine Missaoui, Corinne Biderre, Vincent Barra, David R. C. Hill, Anne Moné, Geneviève Gagne, Harald Meier, Eric Peyretaillade, Pierre Peyret:
  PhylArray: phylogenetic probe design algorithm for microarray. 2550-2557

Structural Bioinformatics

• 
  Narcis Fernandez-Fuentes, Brajesh Kumar Rai, Carlos J. Madrid-Aliste, J. Eduardo Fajardo, András Fiser:
  Comparative protein structure modeling by combining multiple templates and optimizing sequence-to-structure alignments. 2558-2565

Gene Expression

• 
  Chunlei Wu, Haitao Zhao, Keith A. Baggerly, Roberto Carta, Li Zhang:
  Short oligonucleotide probes containing G-stacks display abnormal binding affinity on Affymetrix microarrays. 2566-2572
• 
  Thomas Dhollander, Qizheng Sheng, Karen Lemmens, Bart De Moor, Kathleen Marchal, Yves Moreau:
  Query-driven module discovery in microarray data. 2573-2580

Genetics and Population Analysis

• 
  Fred A. Wright, Hanwen Huang, Xiaojun Guan, Kevin Gamiel, Clark D. Jeffries, William T. Barry, Fernando Pardo-Manuel de Villena, Patrick F. Sullivan, Kirk C. Wilhelmsen, Fei Zou:
  Simulating association studies: a data-based resampling method for candidate regions or whole genome scans. 2581-2588
• 
  Seung Yeoun Lee, Yujin Chung, Robert C. Elston, Youngchul Kim, Taesung Park:
  Log-linear model-based multifactor dimensionality reduction method to detect gene-gene interactions. 2589-2595

Systems Biology

• 
  Elizabeth A. Heron, Bärbel Finkenstädt, David A. Rand:
  Bayesian inference for dynamic transcriptional regulation; the Hes1 system as a case study. 2596-2603
• 
  Zachary M. Saul, Vladimir Filkov:
  Exploring biological network structure using exponential random graph models. 2604-2611
• 
  Stefan Hengl, Clemens Kreutz, Jens Timmer, Thomas Maiwald:
  Data-based identifiability analysis of non-linear dynamical models. 2612-2618

Sequence Analysis

• 
  Seung-Hee Bae, Haixu Tang, Jing Wu, Jun Xie, Sun Kim:
  dPattern: transcription factor binding site (TFBS) discovery in human genome using a discriminative pattern analysis. 2619-2621

Phylogenetics

• 
  Matthew N. Bainbridge, René L. Warren, An He, Mikhail Bilenky, Gordon Robertson, Steven J. M. Jones:
  THOR: targeted high-throughput ortholog reconstructor. 2622-2624

Structural Bioinformatics

• 
  Michele Seeber, Marco Cecchini, Francesco Rao, Giovanni Settanni, Amedeo Caflisch:
  Wordom: a program for efficient analysis of molecular dynamics simulations. 2625-2627
• 
  Haitao Cheng, Taner Z. Sen, Robert L. Jernigan, Andrzej Kloczkowski:
  Consensus Data Mining (CDM) Protein Secondary Structure Prediction Server: Combining GOR V and Fragment Database Mining (FDM). 2628-2630

Gene Expression

• 
  Duccio Cavalieri, Cinzia Castagnini, Simona Toti, Karolina Maciag, Thomas Kelder, Luca Gambineri, Samuele Angioli, Piero Dolara:
  Eu.Gene Analyzer a tool for integrating gene expression data with pathway databases. 2631-2632

Genetics and Population Analysis

• 
  Peter J. Bradbury, Zhiwu Zhang, Dallas E. Kroon, Terry M. Casstevens, Yogesh Ramdoss, Edward S. Buckler:
  TASSEL: software for association mapping of complex traits in diverse samples. 2633-2635
• 
  Heiko A. Schmidt, Arndt von Haeseler, Jutta Buschbom:
  pIPHULA - parallel inference of population parameters using a likelihood approach. 2636-2637

Systems Biology

• 
  Julio Vera, Cheng Sun, Yvonne Oertel, Olaf Wolkenhauer:
  PLMaddon: a power-law module for the Matlab^TM SBToolbox. 2638-2640
• 
  Joanna Jakubowska, Ela Hunt, Matthew Chalmers, Martin W. McBride, Anna F. Dominiczak:
  VisGenome: visualization of single and comparative genome representations. 2641-2642

Databases and Ontologies

• 
  Dominik Seelow, Katrin Hoffmann, Tom H. Lindner:
  AssociationDB: web-based exploration of genomic association. 2643-2644
• 
  Milind Misra, Catherine H. Schein:
  Flavitrack: an annotated database of flavivirus sequences. 2645-2647
• 
  Hyrum Carroll, Wesley A. Beckstead, Timothy O'Connor, Mark T. W. Ebbert, Mark J. Clement, Quinn Snell, David A. McClellan:
  DNA reference alignment benchmarks based on tertiary structure of encoded proteins. 2648-2649

Volume 23, Number 20, 15 October 2007

Systems Biology

• 
  Matthew Suderman, Michael T. Hallett:
  Tools for visually exploring biological networks. 2651-2659

Sequence Analysis

• 
  Lakshminarayan M. Iyer, Vivek Anantharaman, L. Aravind:
  The DOMON domains are involved in heme and sugar recognition. 2660-2664

Genome Analysis

• 
  Chris Reed, Viacheslav Fofanov, Catherine Putonti, Sergei Chumakov, Tom Slezak, Yuriy Fofanov:
  Effect of the mutation rate and background size on the quality of pathogen identification. 2665-2671

Sequence Analysis

• 
  Issaac Rajan, Sarang Aravamuthan, Sharmila S. Mande:
  Identification of compositionally distinct regions in genomes using the centroid method. 2672-2677

Structural Bioinformatics

• 
  Csaba Hetényi, Uko Maran, Alfonso T. García-Sosa, Mati Karelson:
  Structure-based calculation of drug efficiency indices. 2678-2685

Gene Expression

• 
  Thomas Tang, Nicolas François, Annie Glatigny, Nicolas Agier, Marie-Hélène Mucchielli-Giorgi, Lawrence Aggerbeck, Hervé Delacroix:
  Expression ratio evaluation in two-colour microarray experiments is significantly improved by correcting image misalignment. 2686-2691
• 
  Matthew A. Hibbs, David C. Hess, Chad L. Myers, Curtis Huttenhower, Kai Li, Olga G. Troyanskaya:
  Exploring the functional landscape of gene expression: directed search of large microarray compendia. 2692-2699
• 
  Matthew E. Ritchie, Jeremy David Silver, Alicia Oshlack, Melissa Holmes, Dileepa S. Diyagama, Andrew J. Holloway, Gordon K. Smyth:
  A comparison of background correction methods for two-colour microarrays. 2700-2707
• 
  Michele Leone, Sumedha, Martin Weigt:
  Clustering by soft-constraint affinity propagation: applications to gene-expression data. 2708-2715
• 
  Duygu Ucar, Isaac Neuhaus, Petra Ross-MacDonald, Charles Tilford, Srinivasan Parthasarathy, Nathan O. Siemers, Rui-Ru Ji:
  Construction of a reference gene association network from multiple profiling data: application to data analysis. 2716-2724
• 
  Giacomo Gamberoni, Evelina Lamma, Gianluca Lodo, Jlenia Marchesini, Nicoletta Mascellani, Simona Rossi, Sergio Storari, Luca Tagliavini, Stefano Volinia:
  Fun&Co: identification of key functional differences in transcriptomes. 2725-2732
• 
  Carla S. Möller-Levet, Catharine M. West, Crispin J. Miller:
  Exploiting sample variability to enhance multivariate analysis of microarray data. 2733-2740

Genetics and Population Analysis

• 
  Yik Y. Teo, Michael Inouye, Kerrin S. Small, Rhian Gwilliam, Panagiotis Deloukas, Dominic Kwiatkowski, Taane G. Clark:
  A genotype calling algorithm for the Illumina BeadArray platform. 2741-2746

Systems Biology

• 
  Clemens Kreutz, M. M. Bartolome Rodriguez, Thomas Maiwald, Maxmilian Seidl, H. E. Blum, L. Mohr, Jens Timmer:
  An error model for protein quantification. 2747-2753
• 
  Raman Lall, Julie C. Mitchell:
  Metal reduction kinetics in Shewanella. 2754-2759
• 
  Yizhi Cai, Brian Hartnett, Claes Gustafsson, Jean Peccoud:
  A syntactic model to design and verify synthetic genetic constructs derived from standard biological parts. 2760-2767

Data and Text Mining

• 
  Yoshimasa Tsuruoka, John McNaught, Jun'ichi Tsujii, Sophia Ananiadou:
  Learning string similarity measures for gene/protein name dictionary look-up using logistic regression. 2768-2774
• 
  Ali Cakmak, Gultekin Özsoyoglu:
  Mining biological networks for unknown pathways. 2775-2783
• 
  Norman Warthmann, Joffrey Fitz, Detlef Weigel:
  MSQT for choosing SNP assays from multiple DNA alignments. 2784-2787
• 
  Zhanfeng Wang, Yuan-chin Ivan Chang, Zhiliang Ying, Liang Zhu, Yaning Yang:
  A parsimonious threshold-independent protein feature selection method through the area under receiver operating characteristic curve. 2788-2794

Sequence Analysis

• 
  Madhavi Ganapathiraju, Christopher Jon Jursa, Hassan A. Karimi, Judith Klein-Seetharaman:
  TMpro web server and web service: transmembrane helix prediction through amino acid property analysis. 2795-2796

Structural Bioinformatics

• 
  Ekachai Jenwitheesuk, Ram Samudrala:
  Identification of potential HIV-1 targets of minocycline. 2797-2799

Systems Biology

• 
  Sean Sedwards, Tommaso Mazza:
  Cyto-Sim: a formal language model and stochastic simulator of membrane-enclosed biochemical processes. 2800-2802
• 
  Seth I. Berger, Ravi Iyengar, Avi Ma'ayan:
  AVIS: AJAX viewer of interactive signaling networks. 2803-2805

Volume 23, Number 21, 1 November 2007

Genome Analysis

• 
  Ali Bashir, Yu-Tsueng Liu, Benjamin J. Raphael, Dennis Carson, Vineet Bafna:
  Optimization of primer design for the detection of variable genomic lesions in cancer. 2807-2815

Sequence Analysis

• 
  Ersin Emre Oren, Candan Tamerler, Deniz Sahin, Marketa Hnilova, Urartu Ozgur Safak Seker, Mehmet Sarikaya, Ram Samudrala:
  A novel knowledge-based approach to design inorganic-binding peptides. 2816-2822
• 
  Bo Jiang, Michael Q. Zhang, Xuegong Zhang:
  OSCAR: One-class SVM for accurate recognition of cis-elements. 2823-2828

Structural Bioinformatics

• 
  Michael J. Sweredoski, Kevin J. Donovan, Bao D. Nguyen, A. J. Shaka, Pierre Baldi:
  Minimizing the overlap problem in protein NMR: a computational framework for precision amino acid labeling. 2829-2835
• 
  Hung-Pin Peng, An-Suei Yang:
  Modeling protein loops with knowledge-based prediction of sequence-structure alignment. 2836-2842
• 
  Ke Chen, Lukasz A. Kurgan:
  PFRES: protein fold classification by using evolutionary information and predicted secondary structure. 2843-2850
• 
  Frank DiMaio, Dmitry A. Kondrashov, Eduard Bitto, Ameet Soni, Craig A. Bingman, George N. Phillips Jr., Jude W. Shavlik:
  Creating protein models from electron-density maps using particle-filtering methods. 2851-2858

Gene Expression

• 
  Sanghamitra Bandyopadhyay, Anirban Mukhopadhyay, Ujjwal Maulik:
  An improved algorithm for clustering gene expression data. 2859-2865
• 
  Blaise Hanczar, Jean-Daniel Zucker, Corneliu Henegar, Lorenza Saitta:
  Feature construction from synergic pairs to improve microarray-based classification. 2866-2872
• 
  Kathe E. Bjork, Karen Kafadar:
  Systematic order-dependent effect in expression values, variance, detection calls and differential expression in Affymetrix GeneChips®. 2873-2880
• 
  Mark D. Robinson, Gordon K. Smyth:
  Moderated statistical tests for assessing differences in tag abundance. 2881-2887
• 
  Zhiwen Yu, Hau-San Wong, Hong-Qiang Wang:
  Graph-based consensus clustering for class discovery from gene expression data. 2888-2896
• 
  Willem Talloen, Djork-Arné Clevert, Sepp Hochreiter, Dhammika Amaratunga, Luc Bijnens, Stefan Kass, Hinrich W. H. Göhlmann:
  I/NI-calls for the exclusion of non-informative genes: a highly effective filtering tool for microarray data. 2897-2902
• 
  Jiexin Zhang, Yuan Ji, Li Zhang:
  Extracting three-way gene interactions from microarray data. 2903-2909
• 
  Sangeeta B. English, Atul J. Butte:
  Evaluation and integration of 49 genome-wide experiments and the prediction of previously unknown obesity-related genes. 2910-2917

Genetics and Population Analysis

• 
  Ali Torkamani, Nicholas J. Schork:
  Accurate prediction of deleterious protein kinase polymorphisms. 2918-2925

Systems Biology

• 
  Ming Zheng, Peng Lu, Yanzhou Liu, Joseph Pease, Jonathan Usuka, Guochun Liao, Gary Peltz:
  2D NMR metabonomic analysis: a novel method for automated peak alignment. 2926-2933

Databases and Ontologies

• 
  Atsushi Hijikata, Hiroshi Kitamura, Yayoi Kimura, Ryo Yokoyama, Yuichi Aiba, Yanyuan Bao, Shigeharu Fujita, Koji Hase, Shohei Hori, Yasuyuki Ishii, Osami Kanagawa, Hiroshi Kawamoto, Kazuya Kawano, Haruhiko Koseki, Masato Kubo, Ai Kurita-Miki, Tomohiro Kurosaki, Kyoko Masuda, Mitsumasa Nakata, Keisuke Oboki, Hiroshi Ohno, Mariko Okamoto, Yoshimichi Okayama, Jiyang O-Wang, Hirohisa Saito, Takashi Saito, Machie Sakuma, Katsuaki Sato, Kaori Sato, Ken-ichiro Seino, Ruka Setoguchi, Yuki Tamura, Masato Tanaka, Masaru Taniguchi, Ichiro Taniuchi, Annabelle Teng, Takeshi Watanabe, Hiroshi Watarai, Sho Yamasaki, Osamu Ohara:
  Construction of an open-access database that integrates cross-reference information from the transcriptome and proteome of immune cells. 2934-2941

Genome Analysis

• 
  William R. Jeck, Josephine A. Reinhardt, David A. Baltrus, Matthew T. Hickenbotham, Vincent J. Magrini, Elaine R. Mardis, Jeffery L. Dangl, Corbin D. Jones:
  Extending assembly of short DNA sequences to handle error. 2942-2944
• 
  Taishin Kin, Yukiteru Ono:
  Idiographica: a general-purpose web application to build idiograms on-demand for human, mouse and rat. 2945-2946

Sequence Analysis

• 
  Mark A. Larkin, Gordon Blackshields, Nigel P. Brown, R. Chenna, Paul A. McGettigan, Hamish McWilliam, Franck Valentin, Iain M. Wallace, Andreas Wilm, Rodrigo Lopez, Julie Dawn Thompson, Toby J. Gibson, Desmond G. Higgins:
  Clustal W and Clustal X version 2.0. 2947-2948
• 
  Sergey A. Shiryev, Jason S. Papadopoulos, Alejandro A. Schäffer, Richa Agarwala:
  Improved BLAST searches using longer words for protein seeding. 2949-2951

Phylogenetics

• 
  John P. Archer, David L. Robertson:
  CTree: comparison of clusters between phylogenetic trees made easy. 2952-2953
• 
  Víctor Soria-Carrasco, Gerard Talavera, Javier Igea, Jose Castresana:
  The K tree score: quantification of differences in the relative branch length and topology of phylogenetic trees. 2954-2956
• 
  Matthias Bernt, Daniel Merkle, Kai Ramsch, Guido Fritzsch, Marleen Perseke, Detlef Bernhard, Martin Schlegel, Peter F. Stadler, Martin Middendorf:
  CREx: inferring genomic rearrangements based on common intervals. 2957-2958

Structural Bioinformatics

• 
  Namhee Kim, Jin Sup Shin, Shereef Elmetwaly, Hin Hark Gan, Tamar Schlick:
  RAGPOOLS: RNA-As-Graph-Pools - a web server for assisting the design of structured RNA pools for in vitro selection. 2959-2960

Volume 23, Number 22, 15 November 2007

Genome Analysis

• 
  Alexis A. Rodriguez, Tanuja Bompada, Mustafa H. Syed, Parantu K. Shah, Natalia Maltsev:
  Evolutionary analysis of enzymes using Chisel. 2961-2968

Sequence Analysis

• 
  Lucian Ilie, Silvana Ilie:
  Multiple spaced seeds for homology search. 2969-2977
• 
  Stephen McCauley, Saskia de Groot, Thomas Mailund, Jotun Hein:
  Annotation of selection strengths in viral genomes. 2978-2986
• 
  Malik Yousef, Segun Jung, Andrew V. Kossenkov, Louise C. Showe, Michael K. Showe:
  Naïve Bayes for microRNA target predictions - machine learning for microRNA targets. 2987-2992

Phylogenetics

• 
  Patricia Buendia, Giri Narasimhan:
  Sliding MinPD: building evolutionary networks of serial samples via an automated recombination detection approach. 2993-3000

Structural Bioinformatics

• 
  J. R. Davies, Richard M. Jackson, Kanti V. Mardia, Charles C. Taylor:
  The Poisson Index: a new probabilistic model for protein-ligand binding site similarity. 3001-3008
• 
  Christopher Deutsch, Bala Krishnamoorthy:
  Four-Body Scoring Function for Mutagenesis. 3009-3015

Gene Expression

• 
  Franz F. Roos, Riko Jacob, Jonas Grossmann, Bernd Fischer, Joachim M. Buhmann, Wilhelm Gruissem, Sacha Baginsky, Peter Widmayer:
  PepSplice: cache-efficient search algorithms for comprehensive identification of tandem mass spectra. 3016-3023
• 
  Steffen Grossmann, Sebastian Bauer, Peter N. Robinson, Martin Vingron:
  Improved detection of overrepresentation of Gene-Ontology annotations with parent-child analysis. 3024-3031
• 
  Nandini Raghavan, An M. I. M. De Bondt, Willem Talloen, Dieder Moechars, Hinrich W. H. Göhlmann, Dhammika Amaratunga:
  The high-level similarity of some disparate gene expression measures. 3032-3038
• 
  Shinsheng Yuan, Ker-Chau Li:
  Context-dependent clustering for dynamic cellular state modeling of microarray gene expression. 3039-3047

Genetics and Population Analysis

• 
  Bonnie Kirkpatrick, Carlos Santos Armendariz, Richard M. Karp, Eran Halperin:
  HAPLOPOOL: improving haplotype frequency estimation through DNA pools and phylogenetic modeling. 3048-3055

Systems Biology

• 
  Rui-Sheng Wang, Yong Wang, Xiang-Sun Zhang, Luonan Chen:
  Inferring transcriptional regulatory networks from high-throughput data. 3056-3064

Data and Text Mining

• 
  Richard Pelikan, William L. Bigbee, David Malehorn, James Lyons-Weiler, Milos Hauskrecht:
  Intersession reproducibility of mass spectrometry profiles and its effect on accuracy of multivariate classification models. 3065-3072
• 
  Andrew K. Smith, Kei-Hoi Cheung, Michael Krauthammer, Martin H. Schultz, Mark Gerstein:
  Leveraging the structure of the Semantic Web to enhance information retrieval for proteomics. 3073-3079

Databases and Ontologies

• 
  Lennart J. G. Post, Marco Roos, M. Scott Marshall, Roel van Driel, Timo M. Breit:
  A semantic web approach applied to integrative bioinformatics experimentation: a biological use case with genomics data. 3080-3087

Genome Analysis

• 
  Sungsoo Kang, Sung-Jin Yang, Sangsoo Kim, Jong Bhak:
  CONSORF: a consensus prediction system for prokaryotic coding sequences. 3088-3090
• 
  John E. Major:
  Genomic mutation consequence calculator. 3091-3092

Sequence Analysis

• 
  Matthew R. Huska, Henrik Buschmann, Miguel A. Andrade-Navarro:
  BiasViz: visualization of amino acid biased regions in protein alignments. 3093-3094

Structural Bioinformatics

• 
  Emmanuelle Becker, Aurélie Cotillard, Vincent Meyer, Hocine Madaoui, Raphaël Guérois:
  HMM-Kalign: a tool for generating sub-optimal HMM alignments. 3095-3097

Gene Expression

• 
  Pablo Minguez, Fátima Al-Shahrour, David Montaner, Joaquín Dopazo:
  Functional profiling of microarray experiments using text-mining derived bioentities. 3098-3099
• 
  Shouguo Gao, Xujing Wang:
  TAPPA: topological analysis of pathway phenotype association. 3100-3102
• 
  Wataru Fujibuchi, Larisa Kiseleva, Takeaki Taniguchi, Hajime Harada, Paul Horton:
  CellMontage: similar expression profile search server. 3103-3104

Genetics and Population Analysis

• 
  Miao-Xin Li, Lin Jiang, S.-L. Ho, You-Qiang Song, Pak Chung Sham:
  IGG: A tool to integrate GeneChips for genetic studies. 3105-3107
• 
  Adnane Nemri, Michael M. Neff, Michael Burrell, Jonathan D. G. Jones, David J. Studholme:
  Marker development for the genetic study of natural variation in Arabidopsis thaliana. 3108-3109

Databases and Ontologies

•