Bioinformatics, Volume 23

Volume 23, Number 1, January 2007

• 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
  

• 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
  

• 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
  

• 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
  

• 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
  

• 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
  

• 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
  

• 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
  

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

• Pak Chung Sham, Sio Iong Ao, J. 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. 1-2
  
• ECCB 2006 Organization. 3-4
  

• 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 J. 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
  

• Alfonso Valencia, Alex Bateman:
  Editorial. 133
  

• 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
  

• 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
  

• 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
  

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

• 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
  

• 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
  

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

• 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
  

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

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

• 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, X. Di, S. 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
  

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

• Christopher S. Poultney, Rodrigo A. Gutiérrez, Manpreet S. Katari, Miriam L. Gifford, W. Bradford Paley, Gloria M. Coruzzi, Dennis 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
  

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

Volume 23, Number 3, 1 February 2007

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

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

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

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

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

• 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
  

• 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
  

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

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

• 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
  

• 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
  

• 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
  

• 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

• 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
  

• 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
  

• 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
  

• 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
  

• 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
  

• 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
  

• 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
  

• 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
  

• 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
  

• 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
  

• 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
  

• Winston Lau, Tai-Yue Kuo, William Tapper, Simon 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
  

• 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

• Jerzy Orlowski, Michal 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
  

• 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
  

• 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
  

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

• 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
  

• 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
  

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

• 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
  

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

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

• 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
  

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

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

• D. Guzman, D. Veit, V. Knerr, G. Kindle, B. Gathmann, A. M. Eades-Perner, B. Grimbacher:
  The ESID Online Database network. 654-655
  

Volume 23, Number 6, 15 March 2007

• 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
  

• 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
  

• 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
  

• 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
  

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

• 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
  

• 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
  

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

• 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
  

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

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

• 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
  

• 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

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

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

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

• 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
  

• 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
  

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

• 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 Lee, Susan Holmes:
  Gene expression network analysis and applications to immunology. 850-858
  

• 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
  

• A. Antofie, M. Lateur, R. Oger, A. 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
  

• 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
  

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

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

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

• 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
  

• 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, G. D. Bader, Dennis Shasha:
  NetMatch: a Cytoscape plugin for searching biological networks. 910-912
  

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

• 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

• 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
  

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

• 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, X. 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
  

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

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

• Robert 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
  

• 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
  

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

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

• 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
  

• 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
  

• 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

• 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
  

• 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
  

• 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
  

• 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
  

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

• 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
  

• 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
  

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

• Alejandro A. Schäffer, Edward Stallknecht Rice, William 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
  

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

• 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
  

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

• 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

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

• 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
  

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

• Wuyan Zhang, Alicia 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 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
  

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

• 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
  

• 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
  

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

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

• 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
  

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

• 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
  

• 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

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

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

• 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
  

• 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
  

• 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
  

• 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
  

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

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

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

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

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

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

• 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

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

• 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
  

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

• 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
  
• D. 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
  

• 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
  

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

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

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

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

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

• 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
  

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

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

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

Volume 23, Number 13, July 2007

Proceedings 15th International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB), Vienna, Austria, July 21-25, 2007. 2007
Contents

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

• 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
  

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

• 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
  

• Roger Guimerà, Marta Sales-Pardo, Luis 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
  

• 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, E. Marco, Peter K. Sorger, Gaudenz Danuser:
  Phenotypic clustering of yeast mutants based on kinetochore microtubule dynamics. 1666-1673
  

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

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

• Anna Gambin, Piotr Wojtalewicz:
  CTX-BLAST: context sensitive version of protein BLAST. 1686-1688
  
• E. Dicks, Jon W. Teague, P. Stephens, K. Raine, A. Yates, C. Mattocks, P. Tarpey, A. Butler, Andrew Menzies, D. Richardson, A. Jenkinson, H. Davies, S. Edkins, Simon A. Forbes, K. Gray, C. Greenman, Rebecca Shepherd, Michael R. Stratton, P. Andrew Futreal, R. 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
  

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

• 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
  

• 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
  

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

Volume 23, Number 14, 15 July 2007

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

• 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
  

• 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
  

• 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
  

• 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
  

• 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
  

• 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
  

• 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
  

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

• 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
  

• 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 Davis, Paul S. Meltzer:
  GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor. 1846-1847
  

• Tiago 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
  

• 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
  

• 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
  

• 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

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

• 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
  

• 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
  

• 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, C. 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
  

• 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
  

• 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
  

• 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