Bioinformatics, Volume 25

Volume 25, Number 1, January 2009

• Francesca Diella, Sophie Chabanis-Davidson, Katja Luck, Claudia Chica, Chenna Ramu, Claus Nerlov, Toby J. Gibson:
  KEPE - a motif frequently superimposed on sumoylation sites in metazoan chromatin proteins and transcription factors. 1-5
  

• Nawar Malhis, Yaron S. N. Butterfield, Martin Ester, Steven J. M. Jones:
  Slider - maximum use of probability information for alignment of short sequence reads and SNP detection. 6-13
  
• Anna M. Ritz, Gregory Shakhnarovich, Arthur R. Salomon, Benjamin J. Raphael:
  Discovery of phosphorylation motif mixtures in phosphoproteomics data. 14-21
  
• Anton V. Persikov, Robert Osada, Mona Singh:
  Predicting DNA recognition by Cys₂His₂ zinc finger proteins. 22-29
  
• Jiansheng Wu, Hongde Liu, Xueye Duan, Yan Ding, Hongtao Wu, Yunfei Bai, Xiao Sun:
  Prediction of DNA-binding residues in proteins from amino acid sequences using a random forest model with a hybrid feature. 30-35
  

• Chikara Furusawa, Naoaki Ono, Shingo Suzuki, Tomoharu Agata, Hiroshi Shimizu, Tetsuya Yomo:
  Model-based analysis of non-specific binding for background correction of high-density oligonucleotide microarrays. 36-41
  
• A. Marie Fitch, M. Beatrix Jones:
  Shortest path analysis using partial correlations for classifying gene functions from gene expression data. 42-47
  
• Adam L. Asare, Zhong Gao, Vincent J. Carey, Richard Wang, Vicki Seyfert-Margolis:
  Power enhancement via multivariate outlier testing with gene expression arrays. 48-53
  

• James A. Koziol, Anne C. Feng, Zhenyu Jia, Yipeng Wang, Seven Goodison, Michael McClelland, Dan Mercola:
  The wisdom of the commons: ensemble tree classifiers for prostate cancer prognosis. 54-60
  
• Ling-Yun Wu, Xiaobo Zhou, Fuhai Li, Xiaorong Yang, Chung-Che Chang, Stephen T. C. Wong:
  Conditional random pattern algorithm for LOH inference and segmentation. 61-67
  
• Sharlee Climer, Gerold Jäger, Alan R. Templeton, Weixiong Zhang:
  How frugal is mother nature with haplotypes? 68-74
  

• Adi L. Tarca, Sorin Draghici, Purvesh Khatri, Sonia S. Hassan, Pooja Mittal, Jung-sun Kim, Chong Jai Kim, Juan Pedro Kusanovic, Roberto Romero:
  A novel signaling pathway impact analysis. 75-82
  
• Hao Zhang, Claus Lundegaard, Morten Nielsen:
  Pan-specific MHC class I predictors: a benchmark of HLA class I pan-specific prediction methods. 83-89
  
• Ross P. Carlson:
  Decomposition of complex microbial behaviors into resource-based stress responses. 90-97
  
• Xuebing Wu, Qifang Liu, Rui Jiang:
  Align human interactome with phenome to identify causative genes and networks underlying disease families. 98-104
  
• Jingkai Yu, Russell L. Finley Jr.:
  Combining multiple positive training sets to generate confidence scores for protein-protein interactions. 105-111
  

• Rachel Cavill, Hector C. Keun, Elaine Holmes, John C. Lindon, Jeremy K. Nicholson, Timothy M. D. Ebbels:
  Genetic algorithms for simultaneous variable and sample selection in metabonomics. 112-118
  

• Tim J. Carver, Nick Thomson, Alan J. Bleasby, Matthew Berriman, Julian Parkhill:
  DNAPlotter: circular and linear interactive genome visualization. 119-120
  

• Iain Melvin, Jason Weston, Christina S. Leslie, William Stafford Noble:
  RANKPROP: a web server for protein remote homology detection. 121-122
  
• Gang-Qing Hu, Xiaobin Zheng, Huaiqiu Zhu, Zhen-Su She:
  Prediction of translation initiation site for microbial genomes with TriTISA. 123-125
  

• Iain Milne, Dominik Lindner, Micha Bayer, Dirk Husmeier, Gráinne McGuire, David F. Marshall, Frank Wright:
  TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops. 126-127
  

• G. Golfier, Sophie Lemoine, A. van Miltenberg, A. Bendjoudi, J. Rossier, Stéphane Le Crom, M.-C. Potier:
  Selection of oligonucleotides for whole-genome microarrays with semi-automatic update. 128-129
  
• Charles Addo-Quaye, Webb Miller, Michael J. Axtell:
  CleaveLand: a pipeline for using degradome data to find cleaved small RNA targets. 130-131
  

• Manuel A. R. Ferreira, Shaun Purcell:
  A multivariate test of association. 132-133
  
• Christine Herold, Tim Becker:
  Genetic association analysis with FAMHAP: a major program update. 134-136
  

• Jing Gao, Alexander S. Ade, V. Glenn Tarcea, Terry E. Weymouth, Barbara R. Mirel, H. V. Jagadish, David J. States:
  Integrating and annotating the interactome using the MiMI plugin for cytoscape. 137-138
  
• Rutger W. W. Brouwer, Sacha A. F. T. van Hijum, Oscar P. Kuipers:
  MINOMICS: visualizing prokaryote transcriptomics and proteomics data in a genomic context. 139-140
  

• Brigitte Waegele, Irmtraud Dunger-Kaltenbach, Gisela Fobo, Corinna Montrone, Hans-Werner Mewes, Andreas Ruepp:
  CRONOS: the cross-reference navigation server. 141-143
  

• Clare Sansom:
  ISMB 2008 conference report. 144-146
  

• Anne Kupczok, Arndt von Haeseler:
  Comment on 'A congruence index for testing topological similarity between trees'. 147-149
  
• Damien M. de Vienne, Tatiana Giraud, Olivier C. Martin:
  In response to comment on 'A congruence index for testing topological similarity between trees'. 150-151
  

• Luis F. de Figueiredo, Stefan Schuster, Christoph Kaleta, David A. Fell:
  Can sugars be produced from fatty acids? A test case for pathway analysis tools. 152-158
  

Volume 25, Number 2, January 2009

• Alex Bateman, Robert D. Finn, Peter J. Sims, Therese Wiedmer, Andreas Biegert, Johannes Söding:
  Phospholipid scramblases and Tubby-like proteins belong to a new superfamily of membrane tethered transcription factors. 159-162
  

• Richard S. P. Horler, Andrew Butcher, Nikitas Papangelopoulos, Peter D. Ashton, Gavin H. Thomas:
  EchoLOCATION: an in silico analysis of the subcellular locations of Escherichia coli proteins and comparison with experimentally derived locations. 163-166
  

• Xiaohui Xie, Paul Rigor, Pierre Baldi:
  MotifMap: a human genome-wide map of candidate regulatory motif sites. 167-174
  

• William H. Majoros, Uwe Ohler:
  Complexity reduction in context-dependent DNA substitution models. 175-182
  
• Shijie Zhang, Wei Su, Jiong Yang:
  ARCS-Motif: discovering correlated motifs from unaligned biological sequences. 183-189
  

• Yufeng Wu:
  A practical method for exact computation of subtree prune and regraft distance. 190-196
  
• Alex Webb, John M. Hancock, Christopher C. Holmes:
  Phylogenetic inference under recombination using Bayesian stochastic topology selection. 197-203
  

• Ganesan Pugalenthi, E. Ke Tang, Ponnuthurai N. Suganthan, Saikat Chakrabarti:
  Identification of structurally conserved residues of proteins in absence of structural homologs using neural network ensemble. 204-210
  

• Maureen A. Sartor, George D. Leikauf, Mario Medvedovic:
  LRpath: a logistic regression approach for identifying enriched biological groups in gene expression data. 211-217
  
• Sebastian Böcker, Matthias C. Letzel, Zsuzsanna Lipták, Anton Pervukhin:
  SIRIUS: decomposing isotope patterns for metabolite identification. 218-224
  

• Filip Van Nieuwerburgh, E. Goetghebeur, Mado Vandewoestyne, Dieter Deforce:
  Impact of allelic dropout on evidential value of forensic DNA profiles using RMNE. 225-229
  
• S. Yilmaz, P. Jonveaux, C. Bicep, L. Pierron, Malika Smaïl-Tabbone, Marie-Dominique Devignes:
  Gene-disease relationship discovery based on model-driven data integration and database view definition. 230-236
  
• Lina Chen, Liangcai Zhang, Yan Zhao, Liangde Xu, Yukui Shang, Qian Wang, Wan Li, Hong Wang, Xia Li:
  Prioritizing risk pathways: a novel association approach to searching for disease pathways fusing SNPs and pathways. 237-242
  

• Kevin Y. Yip, Mark Gerstein:
  Training set expansion: an approach to improving the reconstruction of biological networks from limited and uneven reliable interactions. 243-250
  
• Donald A. Barkauskas, Hyun Joo An, Scott R. Kronewitter, Maria Lorna de Leoz, Helen K. Chew, Ralph W. de Vere White, Gary S. Leiserowitz, Suzanne Miyamoto, Carlito B. Lebrilla, David M. Rocke:
  Detecting glycan cancer biomarkers in serum samples using MALDI FT-ICR mass spectrometry data. 251-257
  

• Gavin Brelstaff, Manuele Bicego, Nicola Culeddu, Matilde Chessa:
  Bag of Peaks: interpretation of NMR spectrometry. 258-264
  
• Sach Mukherjee, Steven Pelech, Richard M. Neve, Wen-Lin Kuo, Safiyyah Ziyad, Paul T. Spellman, Joe W. Gray, Terence P. Speed:
  Sparse combinatorial inference with an application in cancer biology. 265-271
  

• Nobutaka Kitamura, Kouhei Akazawa, Akinori Miyashita, Ryozo Kuwano, Shin-ichi Toyabe, Junichiro Nakamura, Norihito Nakamura, Tatsuhiko Sato, M. Aminul Hoque:
  Programs for calculating the statistical powers of detecting susceptibility genes in case-control studies based on multistage designs. 272-273
  

• Scott Christley, Yiming Lu, Chen Li, Xiaohui Xie:
  Human genomes as email attachments. 274-275
  

• Wubin Qu, Zhiyong Shen, Dongsheng Zhao, Yi Yang, Chenggang Zhang:
  MFEprimer: multiple factor evaluation of the specificity of PCR primers. 276-278
  
• Tim F. Rayner, Faisal Ibne Rezwan, Margus Lukk, Xiangqun Zheng Bradley, Anna Farne, Ele Holloway, James Malone, Eleanor Williams, Helen E. Parkinson:
  MAGETabulator, a suite of tools to support the microarray data format MAGE-TAB. 279-280
  

• Oliver S. P. Davis, Robert Plomin, Leonard C. Schalkwyk:
  The SNPMaP package for R: a framework for genome-wide association using DNA pooling on microarrays. 281-283
  
• Wei Chen, Liming Liang, Gonçalo R. Abecasis:
  GWAS GUI: graphical browser for the results of whole-genome association studies with high-dimensional phenotypes. 284-285
  

• Bartek Wilczynski, Norbert Dojer:
  BNFinder: exact and efficient method for learning Bayesian networks. 286-287
  

• Seth Carbon, Amelia Ireland, Christopher J. Mungall, ShengQiang Shu, Brad Marshall, Suzanna Lewis:
  AmiGO: online access to ontology and annotation data. 288-289
  

Volume 25, Number 3, February 2009

• Bogumil Kaczkowski, Elfar Torarinsson, Kristin Reiche, Jakob Hull Havgaard, Peter F. Stadler, Jan Gorodkin:
  Structural profiles of human miRNA families from pairwise clustering. 291-294
  

• Benedict Paten, Javier Herrero, Kathryn Beal, Ewan Birney:
  Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment. 295-301
  
• Denise Y. F. Mak, Gary Benson:
  All hits all the time: parameter-free calculation of spaced seed sensitivity. 302-308
  

• Jumamurat R. Bayjanov, Michiel Wels, Marjo Starrenburg, Johan E. T. van Hylckama Vlieg, Roland J. Siezen, Douwe Molenaar:
  PanCGH: a genotype-calling algorithm for pangenome CGH data. 309-314
  

• Stan Pounds, Cheng Cheng, Charles Mullighan, Susana C. Raimondi, Sheila Shurtleff, James R. Downing:
  Reference alignment of SNP microarray signals for copy number analysis of tumors. 315-321
  
• Krzysztof Wabnik, Torgeir R. Hvidsten, Anna M. Kedzierska, Jelle Van Leene, Geert De Jaeger, Gerrit T. S. Beemster, Henryk Jan Komorowski, Martin T. R. Kuiper:
  Gene expression trends and protein features effectively complement each other in gene function prediction. 322-330
  
• Kun-hong Liu, Chun-Gui Xu:
  A genetic programming-based approach to the classification of multiclass microarray datasets. 331-337
  

• Junghyun Namkung, Kyunga Kim, Sung-Gon Yi, Wonil Chung, Min-Seok Kwon, Taesung Park:
  New evaluation measures for multifactor dimensionality reduction classifiers in gene-gene interaction analysis. 338-345
  

• Ekaterina Myasnikova, Svetlana Surkova, Lena Panok, Maria Samsonova, John Reinitz:
  Estimation of errors introduced by confocal imaging into the data on segmentation gene expression in Drosophila. 346-352
  
• Mahesh Yaragatti, Ted Sandler, Lyle H. Ungar:
  A predictive model for identifying mini-regulatory modules in the mouse genome. 353-357
  
• Hu Li, Choong Yong Ung, Xiao Hua Ma, Bao Wen Li, Boon Chuan Low, Zhi Wei Cao, Yu Zong Chen:
  Simulation of crosstalk between small GTPase RhoA and EGFR-ERK signaling pathway via MEKK1. 358-364
  
• David Goldberg, Marshall W. Bern, Simon J. North, Stuart M. Haslam, Anne Dell:
  Glycan family analysis for deducing N-glycan topology from single MS. 365-371
  
• Hailiang Huang, Joel S. Bader:
  Precision and recall estimates for two-hybrid screens. 372-378
  

• Anthony Y. C. Kuk, Han Zhang, Yaning Yang:
  Computationally feasible estimation of haplotype frequencies from pooled DNA with and without Hardy-Weinberg equilibrium. 379-386
  
• Je-Gun Joung, Zhangjun Fei:
  Identification of microRNA regulatory modules in Arabidopsis via a probabilistic graphical model. 387-393
  
• Yusuke Miyao, Kenji Sagae, Rune Sætre, Takuya Matsuzaki, Jun'ichi Tsujii:
  Evaluating contributions of natural language parsers to protein-protein interaction extraction. 394-400
  
• Age K. Smilde, Henk A. L. Kiers, S. Bijlsma, C. M. Rubingh, M. J. van Erk:
  Matrix correlations for high-dimensional data: the modified RV-coefficient. 401-405
  

• Davide Bolchini, Anthony Finkelstein, Vito Perrone, Sylvia Nagl:
  Better bioinformatics through usability analysis. 406-412
  

• Christopher Reynolds, David Damerell, Susan Jones:
  ProtorP: a protein-protein interaction analysis server. 413-414
  

• Audrey Kauffmann, Robert Gentleman, Wolfgang Huber:
  arrayQualityMetrics - a bioconductor package for quality assessment of microarray data. 415-416
  

• Julien Chiquet, Alexander Smith, Gilles Grasseau, Catherine Matias, Christophe Ambroise:
  SIMoNe: Statistical Inference for MOdular NEtworks. 417-418
  
• Martino Barenco, E. Papouli, S. Shah, Daniel Brewer, C. J. Miller, Michael Hubank:
  rHVDM: an R package to predict the activity and targets of a transcription factor. 419-420
  

Volume 25, Number 4, February 2009

• Robert P. Guralnick, Andrew W. Hill:
  Biodiversity informatics: automated approaches for documenting global biodiversity patterns and processes. 421-428
  

• Alex Bateman, John Quackenbush:
  Editorial. 429
  

• Fuxiao Xin, Meng Li, Curtis Balch, Michael Thomson, Meiyun Fan, Yunlong Liu, Scott M. Hammond, Sun Kim, Kenneth P. Nephew:
  Computational analysis of microRNA profiles and their target genes suggests significant involvement in breast cancer antiestrogen resistance. 430-434
  

• Helge G. Roider, Thomas Manke, Sean O'Keeffe, Martin Vingron, Stefan A. Haas:
  PASTAA: identifying transcription factors associated with sets of co-regulated genes. 435-442
  

• Norman E. Davey, Denis C. Shields, Richard J. Edwards:
  Masking residues using context-specific evolutionary conservation significantly improves short linear motif discovery. 443-450
  
• Tala Bakheet, Andrew J. Doig:
  Properties and identification of human protein drug targets. 451-457
  
• René L. Warren, Brad H. Nelson, Robert A. Holt:
  Profiling model T-cell metagenomes with short reads. 458-464
  
• Michiaki Hamada, Hisanori Kiryu, Kengo Sato, Toutai Mituyama, Kiyoshi Asai:
  Prediction of RNA secondary structure using generalized centroid estimators. 465-473
  

• Dirk Stratmann, Carine van Heijenoort, Eric Guittet:
  NOEnet-Use of NOE networks for NMR resonance assignment of proteins with known 3D structure. 474-481
  

• Daniel M. Gatti, Andrey A. Shabalin, Tieu-Chong Lam, Fred A. Wright, Ivan Rusyn, Andrew B. Nobel:
  FastMap: Fast eQTL mapping in homozygous populations. 482-489
  
• Anagha Joshi, Riet De Smet, Kathleen Marchal, Yves Van de Peer, Tom Michoel:
  Module networks revisited: computational assessment and prioritization of model predictions. 490-496
  

• Mingyao Li, Kai Wang, Struan F. A. Grant, Hakon Hakonarson, Chun Li:
  ATOM: a powerful gene-based association test by combining optimally weighted markers. 497-503
  
• Can Yang, Zengyou He, Xiang Wan, Qiang Yang, Hong Xue, Weichuan Yu:
  SNPHarvester: a filtering-based approach for detecting epistatic interactions in genome-wide association studies. 504-511
  

• Simon Rogers, Richard A. Scheltema, Mark A. Girolami, Rainer Breitling:
  Probabilistic assignment of formulas to mass peaks in metabolomics experiments. 512-518
  
• Oliver Kotte, Matthias Heinemann:
  A divide-and-conquer approach to analyze underdetermined biochemical models. 519-525
  

• Bai Zhang, Huai Li, Rebecca B. Riggins, Ming Zhan, Jianhua Xuan, Zhen Zhang, Eric P. Hoffman, Robert Clarke, Yue Joseph Wang:
  Differential dependency network analysis to identify condition-specific topological changes in biological networks. 526-532
  

• Sascha Steinbiss, Gordon Gremme, Christin Schärfer, Malte Mader, Stefan Kurtz:
  AnnotationSketch: a genome annotation drawing library. 533-534
  
• Michael S. Barker, Katrina M. Dlugosch, A. Chaitanya C. Reddy, Sarah N. Amyotte, Loren H. Rieseberg:
  SCARF: maximizing next-generation EST assemblies for evolutionary and population genomic analyses. 535-536
  

• Jeremy M. Brown, Robert ElDabaje:
  PuMA: Bayesian analysis of partitioned (and unpartitioned) model adequacy. 537-538
  

• Benjamin M. Bulheller, Jonathan D. Hirst:
  DichroCalc - circular and linear dichroism online. 539-540
  

• Daniel M. Gatti, Myroslav Sypa, Ivan Rusyn, Fred A. Wright, William T. Barry:
  SAFEGUI: resampling-based tests of categorical significance in gene expression data made easy. 541-542
  
• Ryosuke R. Ishiwata, Masaki S. Morioka, Soichi Ogishima, Hiroshi Tanaka:
  BioCichlid: central dogma-based 3D visualization system of time-course microarray data on a hierarchical biological network. 543-544
  
• Qihao Qi, Yingdong Zhao, Ming-Chung Li, Richard M. Simon:
  Non-negative matrix factorization of gene expression profiles: a plug-in for BRB-ArrayTools. 545-547
  
• E. Ryder, H. Spriggs, E. Drummond, D. St Johnston, Steven Russell:
  The Flannotator - a gene and protein expression annotation tool for Drosophila melanogaster. 548-549
  
• Evert-Jan Blom, Jos B. T. M. Roerdink, Oscar P. Kuipers, Sacha A. F. T. van Hijum:
  MOTIFATOR: detection and characterization of regulatory motifs using prokaryote transcriptome data. 550-551
  

• Gilles Guillot, Matthieu Foll:
  Correcting for ascertainment bias in the inference of population structure. 552-554
  

• Uma Mudunuri, Anney Che, Ming Yi, Robert M. Stephens:
  bioDBnet: the biological database network. 555-556
  
• Jeff Heard, William Kaufmann, Xiaojun Guan:
  A novel method for large tree visualization. 557-558
  

Volume 25, Number 5, March 2009

• Shahar Alon, Eli Eisenberg, Jasmine Jacob-Hirsch, Gideon Rechavi, Gad Vatine, Reiko Toyama, Steven L. Coon, David C. Klein, Yoav Gothilf:
  A new cis-acting regulatory element driving gene expression in the zebrafish pineal gland. 559-562
  

• Shamim Ahmed, Ayumu Saito, Miho Suzuki, Naoto Nemoto, Koichi Nishigaki:
  Host-parasite relations of bacteria and phages can be unveiled by Oligostickiness, a measure of relaxed sequence similarity. 563-570
  
• Xu Ling, Xin He, Dong Xin:
  Detecting gene clusters under evolutionary constraint in a large number of genomes. 571-577
  
• Leila Taher, Ivan Ovcharenko:
  Variable locus length in the human genome leads to ascertainment bias in functional inference for non-coding elements. 578-584
  

• Xue-wen Chen, Jong Cheol Jeong:
  Sequence-based prediction of protein interaction sites with an integrative method. 585-591
  

• Fuxia Cheng, Stefanie Hartmann, Mayetri Gupta, Joseph G. Ibrahim, Todd J. Vision:
  A hierarchical model for incomplete alignments in phylogenetic inference. 592-598
  
• Naoki Sato:
  Gclust: trans-kingdom classification of proteins using automatic individual threshold setting. 599-605
  

• Lee-Wei Yang, Eran Eyal, Ivet Bahar, Akio Kitao:
  Principal component analysis of native ensembles of biomolecular structures (PCA_NEST): insights into functional dynamics. 606-614
  
• Izhar Wallach, Ryan H. Lilien:
  The protein-small-molecule database, a non-redundant structural resource for the analysis of protein-ligand binding. 615-620
  
• Ryan Brenke, Dima Kozakov, Gwo-Yu Chuang, Dmitri Beglov, David R. Hall, Melissa R. Landon, Carla Mattos, Sandor Vajda:
  Fragment-based identification of druggable 'hot spots' of proteins using Fourier domain correlation techniques. 621-627
  

• Wataru Nishima, Guoying Qi, Steven Hayward, Akio Kitao:
  DTA: dihedral transition analysis for characterization of the effects of large main-chain dihedral changes in proteins. 628-635
  

• Satwik Rajaram:
  A novel meta-analysis method exploiting consistency of high-throughput experiments. 636-642
  

• Theodore Alexandrov, Jens Decker, Bart J. A. Mertens, André M. Deelder, Rob A. E. M. Tollenaar, Peter Maass, Herbert Thiele:
  Biomarker discovery in MALDI-TOF serum protein profiles using discrete wavelet transformation. 643-649
  
• Li Zhang, Qingyi Wei, Li Mao, Wenbin Liu, Gordon B. Mills, Kevin R. Coombes:
  Serial dilution curve: a new method for analysis of reverse phase protein array data. 650-654
  

• Claude Chelala, Arshad Khan, Nicholas R. Lemoine:
  SNPnexus: a web database for functional annotation of newly discovered and public domain single nucleotide polymorphisms. 655-661
  

• Olivier Martin, Armand Valsesia, Amalio Telenti, Ioannis Xenarios, Brian J. Stevenson:
  AssociationViewer: a scalable and integrated software tool for visualization of large-scale variation data in genomic context. 662-663
  
• Morgan G. I. Langille, Fiona S. L. Brinkman:
  IslandViewer: an integrated interface for computational identification and visualization of genomic islands. 664-665
  

• J. Stenberg, M. Zhang, H. Ji:
  Disperse - a software system for design of selector probes for exon resequencing applications. 666-667
  
• Parvez Anandam, Elfar Torarinsson, Walter L. Ruzzo:
  Multiperm: shuffling multiple sequence alignments while approximately preserving dinucleotide frequencies. 668-669
  
• Jérôme Gouzy, Sébastien Carrère, Thomas Schiex:
  FrameDP: sensitive peptide detection on noisy matured sequences. 670-671
  

• Jacqueline L. Whalley, Stephen Brooks, Robert G. Beiko:
  Radié: visualizing taxon properties and parsimonious mappings using a radial phylogenetic tree. 672-673
  

• Charles E. Chapple, Roderic Guigó, Alain Krol:
  SECISaln, a web-based tool for the creation of structure-based alignments of eukaryotic SECIS elements. 674-675
  
• Martin Mann, Cameron Smith, Mohamad Rabbath, Marlien Edwards, Sebastian Will, Rolf Backofen:
  CPSP-web-tools: a server for 3D lattice protein studies. 676-677
  

• Nora Rieber, Bettina Knapp, Roland Eils, Lars Kaderali:
  RNAither, an automated pipeline for the statistical analysis of high-throughput RNAi screens. 678-679
  

• Mehdi Sargolzaei, Flavio S. Schenkel:
  QMSim: a large-scale genome simulator for livestock. 680-681
  

• Nils Gehlenborg, Wei Yan, Inyoul Y. Lee, Hyuntae Yoo, Kay Nieselt, Daehee Hwang, Ruedi Aebersold, Leroy Hood:
  Prequips - an extensible software platform for integration, visualization and analysis of LC-MS/MS proteomics data. 682-683
  
• Alexander Lachmann, Avi Ma'ayan:
  KEA: kinase enrichment analysis. 684-686
  
• Sebastian Mirschel, Katrin Steinmetz, Michael Rempel, Martin Ginkel, Ernst Dieter Gilles:
  PROMOT: modular modeling for systems biology. 687-689
  

• Emilie Chautard, Lionel Ballut, Nicolas Thierry-Mieg, Sylvie Ricard-Blum:
  MatrixDB, a database focused on extracellular protein-protein and protein-carbohydrate interactions. 690-691
  
• ClarLynda R. Williams-DeVane, Maritja A. Wolf, Ann M. Richard:
  DSSTox chemical-index files for exposure-related experiments in ArrayExpress and Gene Expression Omnibus: enabling toxico-chemogenomics data linkages. 692-694
  
• Hanchuan Peng, Fuhui Long, Eugene W. Myers:
  VANO: a volume-object image annotation system. 695-697
  

• Stan Pounds, Cheng Cheng:
  Erratum: sample size determination for the false discovery rate. 698-699
  

Volume 25, Number 6, March 2009

• David M. Rocke, Trey Ideker, Olga G. Troyanskaya, John Quackenbush, Joaquín Dopazo:
  Papers on normalization, variable selection, classification or clustering of microarray data. 701-702
  

• Eva Budinska, Eva Gelnarova, Michael G. Schimek:
  MSMAD: a computationally efficient method for the analysis of noisy array CGH data. 703-713
  
• Tong Tong Wu, Yi Fang Chen, Trevor Hastie, Eric M. Sobel, Kenneth Lange:
  Genome-wide association analysis by lasso penalized logistic regression. 714-721
  
• Thomas LaFramboise, Wendy Winckler, Roman K. Thomas:
  A flexible rank-based framework for detecting copy number aberrations from array data. 722-728
  

• Inkyung Jung, Dongsup Kim:
  SIMPRO: simple protein homology detection method by using indirect signals. 729-735
  

• Thomas Pommier, Björn Canbäck, Per Lundberg, Åke Hagström, Anders Tunlid:
  RAMI: a tool for identification and characterization of phylogenetic clusters in microbial communities. 736-742
  

• Jinyan Li, Qian Liu:
  'Double water exclusion': a hypothesis refining the O-ring theory for the hot spots at protein interfaces. 743-750
  

• Yang Xie, Xinlei Wang, Michael Story:
  Statistical methods of background correction for Illumina BeadArray data. 751-757
  
• Katharina Podwojski, Arno Fritsch, Daniel C. Chamrad, Wolfgang Paul, Barbara Sitek, Kai Stühler, Petra Mutzel, Christian Stephan, Helmut E. Meyer, Wolfgang Urfer, Katja Ickstadt, Jörg Rahnenführer:
  Retention time alignment algorithms for LC/MS data must consider non-linear shifts. 758-764
  
• Davis J. McCarthy, Gordon K. Smyth:
  Testing significance relative to a fold-change threshold is a TREAT. 765-771
  

• David R. Bickel, Zahra Montazeri, Pei-Chun Hsieh, Mary Beatty, Shai J. Lawit, Nicholas J. Bate:
  Gene network reconstruction from transcriptional dynamics under kinetic model uncertainty: a case for the second derivative. 772-779
  
• Peter Gennemark, Dag Wedelin:
  Benchmarks for identification of ordinary differential equations from time series data. 780-786
  
• V. V. Mihaleva, H. A. Verhoeven, R. C. H. de Vos, R. D. Hall, Roeland C. H. J. van Ham:
  Automated procedure for candidate compound selection in GC-MS metabolomics based on prediction of Kovats retention index. 787-794
  
• Zhirong Sun, Jie Luo, Yun Zhou, Junjie Luo, Ke Liu, Wenting Li:
  Exploring phenotype-associated modules in an oral cavity tumor using an integrated framework. 795-800
  
• Brian C. Haynes, Michael R. Brent:
  Benchmarking regulatory network reconstruction with GRENDEL. 801-807
  

• Shuo Chen, Ming Li, Don Hong, Dean Billheimer, Huiming Li, Baogang J. Xu, Yu Shyr:
  A novel comprehensive wave-form MS data processing method. 808-814
  
• Joachim Wermter, Katrin Tomanek, Udo Hahn:
  High-performance gene name normalization with GENO. 815-821
  

• Lucian Ilie, Silvana Ilie:
  Fast computation of neighbor seeds. 822-823
  
• Jacques Lagnel, Costas S. Tsigenopoulos, Ioannis Iliopoulos:
  NOBLAST and JAMBLAST: New Options for BLAST and a Java Application Manager for BLAST results. 824-826
  

• Christine Porzelius, Harald Binder, Martin Schumacher:
  Parallelized prediction error estimation for evaluation of high-dimensional models. 827-829
  

• Sabine Dietmann, Elisabeth Georgii, Alexey V. Antonov, Koji Tsuda, Hans-Werner Mewes:
  The DICS repository: module-assisted analysis of disease-related gene lists. 830-831
  
• X. Wu, M. Watson:
  CORNA: testing gene lists for regulation by microRNAs. 832-833
  
• Armando Reyes-Palomares, Raúl Montañez, Alejandro Real-Chicharro, Othmane Chniber, Amine Kerzazi, Ismael Navas Delgado, Miguel Angel Medina, José Francisco Aldana Montes, Francisca Sánchez-Jiménez:
  Systems biology metabolic modeling assistant: an ontology-based tool for the integration of metabolic data in kinetic modeling. 834-835
  
• J. Vanlier, F. Wu, Feng Qi, K. C. Vinnakota, Yu Han, Ranjan K. Dash, F. Yang, Daniel A. Beard:
  BISEN: Biochemical Simulation Environment. 836-837
  

• Junguk Hur, Adam D. Schuyler, David J. States, Eva L. Feldman:
  SciMiner: web-based literature mining tool for target identification and functional enrichment analysis. 838-840
  

Volume 25, Number 7, April 2009

• Xiaohua Douglas Zhang, Joseph F. Heyse:
  Determination of sample size in genome-scale RNAi screens. 841-844
  

• Kuo-Ho Yen, Chung-Liang Ho, Chiang Lee:
  The analysis of inconsistencies between cytogenetic annotations and sequence mapping by defining the imprecision zones of cytogenetic banding. 845-852
  
• Tsuyoshi Hachiya, Yasunori Osana, Kris Popendorf, Yasubumi Sakakibara:
  Accurate identification of orthologous segments among multiple genomes. 853-860
  
• Henrik Bengtsson, Amrita Ray, Paul T. Spellman, Terence P. Speed:
  A single-sample method for normalizing and combining full-resolution copy numbers from multiple platforms, labs and analysis methods. 861-867
  
• Chen Yanover, Mona Singh, Elena Zaslavsky:
  M are better than one: an ensemble-based motif finder and its application to regulatory element prediction. 868-874
  

• João Pedro de Magalhães, João Curado, George M. Church:
  Meta-analysis of age-related gene expression profiles identifies common signatures of aging. 875-881
  
• Shuangge Ma, Michael R. Kosorok:
  Identification of differential gene pathways with principal component analysis. 882-889
  
• Harald Binder, Arthur Allignol, Martin Schumacher, Jan Beyersmann:
  Boosting for high-dimensional time-to-event data with competing risks. 890-896
  
• Chen-An Tsai, James J. Chen:
  Multivariate analysis of variance test for gene set analysis. 897-903
  
• Ruth Heller, Elisabetta Manduchi, Dylan S. Small:
  Matching methods for observational microarray studies. 904-909
  

• Joshua Colvin, Michael I. Monine, James R. Faeder, William S. Hlavacek, Daniel D. Von Hoff, Richard G. Posner:
  Simulation of large-scale rule-based models. 910-917
  
• Shuhei Kimura, Satoshi Nakayama, Mariko Hatakeyama:
  Genetic network inference as a series of discrimination tasks. 918-925
  
• Géraldine Del Mondo, Damien Eveillard, Irena Rusu:
  Homogeneous decomposition of protein interaction networks: refining the description of intra-modular interactions. 926-932
  

• Elisabeth Georgii, Sabine Dietmann, Takeaki Uno, Philipp Pagel, Koji Tsuda:
  Enumeration of condition-dependent dense modules in protein interaction networks. 933-940
  
• Michael Netzer, Gunda Millonig, Melanie Osl, Bernhard Pfeifer, Siegfried Praun, Johannes Villinger, Wolfgang Vogel, Christian Baumgartner:
  A new ensemble-based algorithm for identifying breath gas marker candidates in liver disease using ion molecule reaction mass spectrometry. 941-947
  

• Hiromi Arai, Satoru Watanabe, Takanori Kigawa, Masayuki Yamamura:
  A new modeling method in feature construction for the HSQC spectra screening problem. 948-953
  

• Touati Benoukraf, Pierre Cauchy, Romain Fenouil, Adrien Jeanniard, Frederic Koch, Sébastien Jaeger, Denis Thieffry, Jean Imbert, Jean-Christophe Andrau, Salvatore Spicuglia, Pierre Ferrier:
  CoCAS: a ChIP-on-chip analysis suite. 954-955
  
• Kashi Vishwanath Revanna, Vivek Krishnakumar, Qunfeng Dong:
  A web-based software system for dynamic gene cluster comparison across multiple genomes. 956-957
  
• Masumi Itoh, Hidemi Watanabe:
  CGAS: comparative genomic analysis server. 958-959
  
• Andrés Esteban-Marcos, Aaron E. Darling, Mark A. Ragan:
  Seevolution: visualizing chromosome evolution. 960-961
  
• Andrew C. Stewart, Brian Osborne, Timothy D. Read:
  DIYA: a bacterial annotation pipeline for any genomics lab. 962-963
  
• Lukas Käll, John D. Storey, William Stafford Noble:
  QVALITY: non-parametric estimation of q-values and posterior error probabilities. 964-966
  

• Davide Campagna, Alessandro Albiero, Alessandra Bilardi, Elisa Caniato, Claudio Forcato, Svetlin Manavski, Nicola Vitulo, Giorgio Valle:
  PASS: a program to align short sequences. 967-968
  
• Hugh L. Eaves, Yuan Gao:
  MOM: maximum oligonucleotide mapping. 969-970
  

• Laura Salter Kubatko, Bryan C. Carstens, L. Lacey Knowles:
  STEM: species tree estimation using maximum likelihood for gene trees under coalescence. 971-973
  

• David J. States, Alexander S. Ade, Zachary C. Wright, Aaron V. Bookvich, Brian D. Athey:
  MiSearch adaptive pubMed search tool. 974-976
  
• Georgios A. Pavlopoulos, Evangelos Pafilis, Michael Kuhn, Sean D. Hooper, Reinhard Schneider:
  OnTheFly: a tool for automated document-based text annotation, data linking and network generation. 977-978
  

• Joo Chuan Tong, Shen Jean Lim, Hon Cheng Muh, Fook Tim Chew, Martti T. Tammi:
  Allergen Atlas: a comprehensive knowledge center and analysis resource for allergen information. 979-980
  

Volume 25, Number 8, April 2009

• Ke-Shiuan Lynn, Li-Lan Li, Yen-Ju Lin, Chiuen-Huei Wang, Shu-Hui Sheng, Ju-Hwa Lin, Wayne Liao, Wen-Lian Hsu, Wen-Harn Pan:
  A neural network model for constructing endophenotypes of common complex diseases: an application to male young-onset hypertension microarray data. 981-988
  
• Rukshan Batuwita, Vasile Palade:
  microPred: effective classification of pre-miRNAs for human miRNA gene prediction. 989-995
  

• Allan Lo, Yi-Yuan Chiu, Einar Andreas Rødland, Ping-Chiang Lyu, Ting-Yi Sung, Wen-Lian Hsu:
  Predicting helix-helix interactions from residue contacts in membrane proteins. 996-1003
  

• Claudia Hundertmark, R. Fischer, Tobias Reinl, Sigrun May, Frank Klawonn, Lothar Jänsch:
  MS-specific noise model reveals the potential of iTRAQ in quantitative proteomics. 1004-1011
  
• Trevis M. Alleyne, Lourdes Peña Castillo, Gwenael Badis, Shaheynoor Talukder, Michael F. Berger, Andrew R. Gehrke, Anthony A. Philippakis, Martha L. Bulyk, Quaid Morris, Timothy R. Hughes:
  Predicting the binding preference of transcription factors to individual DNA k-mers. 1012-1018
  
• Ruth Heller, Elisabetta Manduchi, Gregory R. Grant, Warren J. Ewens:
  A flexible two-stage procedure for identifying gene sets that are differentially expressed. 1019-1025
  
• Hui Jiang, Wing Hung Wong:
  Statistical inferences for isoform expression in RNA-Seq. 1026-1032
  

• Runqing Yang, Xin Wang, Jian Li, Hong-Wen Deng:
  Bayesian robust analysis for genetic architecture of quantitative traits. 1033-1039
  
• Mattia C. F. Prosperi, Roberto D'Autilia, Francesca Incardona, Andrea De Luca, Maurizio Zazzi, Giovanni Ulivi:
  Stochastic modelling of genotypic drug-resistance for human immunodeficiency virus towards long-term combination therapy optimization. 1040-1047
  
• Phil Hyoun Lee, Hagit Shatkay:
  An integrative scoring system for ranking SNPs by their potential deleterious effects. 1048-1055
  
• Richard Bourgon, Eugenio Mancera, Alessandro Brozzi, Lars M. Steinmetz, Wolfgang Huber:
  Array-based genotyping in S.cerevisiae using semi-supervised clustering. 1056-1062
  

• Gábor Boross, Katalin Orosz, Illés J. Farkas:
  Human microRNAs co-silence in well-separated groups and have different predicted essentialities. 1063-1069
  

• Hang Chang, Rosa Anna DeFilippis, Thea D. Tlsty, Bahram Parvin:
  Graphical methods for quantifying macromolecules through bright field imaging. 1070-1075
  

• Jan Gertheiss, Gerhard Tutz:
  Supervised feature selection in mass spectrometry-based proteomic profiling by blockwise boosting. 1076-1077
  

• Björn Nilsson, Mikael Johansson, Fátima Al-Shahrour, Anne E. Carpenter, Benjamin L. Ebert:
  Ultrasome: efficient aberration caller for copy number studies of ultra-high resolution. 1078-1079
  
• Yingfeng Wang, Zhibin Huang, Yong Wu, Russell L. Malmberg, Liming Cai:
  RNATOPS-W: a web server for RNA structure searches of genomes. 1080-1081
  

• Ankit Agrawal, Xiaoqiu Huang:
  PSIBLAST_PairwiseStatSig: reordering PSI-BLAST hits using pairwise statistical significance. 1082-1083
  
• Robert Homann, David Fleer, Robert Giegerich, Marc Rehmsmeier:
  mkESA: enhanced suffix array construction tool. 1084-1085
  

• Sebastian Kelm, Jiye Shi, Charlotte M. Deane:
  iMembrane: homology-based membrane-insertion of proteins. 1086-1088
  

• Theresa Scharl, Friedrich Leisch:
  gcExplorer: interactive exploration of gene clusters. 1089-1090
  

• Gabriela Bindea, Bernhard Mlecnik, Hubert Hackl, Pornpimol Charoentong, Marie Tosolini, Amos Kirilovsky, Wolf-Herman Fridman, Franck Pagès, Zlatko Trajanoski, Jérôme Galon:
  ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. 1091-1093
  

• Hong Li, Guohui Ding, Lu Xie, Yixue Li:
  PAnnBuilder: an R package for assembling proteomic annotation data. 1094-1095
  

• Alexandra Moura, Mário Soares, Carolina Pereira, Nuno Leitão, Isabel Henriques, António Correia:
  INTEGRALL: a database and search engine for integrons, integrases and gene cassettes. 1096-1098
  

Volume 25, Number 9, May 2009

• Mark A. van de Wiel, Rebecca Brosens, Paul H. C. Eilers, Candy Kumps, Gerrit Meijer, Björn Menten, Erik Sistermans, Frank Speleman, Marieke E. Timmerman, Bauke Ylstra:
  Smoothing waves in array CGH tumor profiles. 1099-1104
  

• Cole Trapnell, Lior Pachter, Steven L. Salzberg:
  TopHat: discovering splice junctions with RNA-Seq. 1105-1111
  
• Zhu-Jin Zhang:
  DV-Curve: a novel intuitive tool for visualizing and analyzing DNA sequences. 1112-1117
  
• Tobias Rausch, Sergey Koren, Gennady Denisov, David Weese, Anne-Katrin Emde, Andreas Döring, Knut Reinert:
  A consistency-based consensus algorithm for de novo and reference-guided sequence assembly of short reads. 1118-1124
  
• Cristina Marino Buslje, Javier Santos, José María Delfino, Morten Nielsen:
  Correction for phylogeny, small number of observations and data redundancy improves the identification of coevolving amino acid pairs using mutual information. 1125-1131
  

• Anatoly M. Ruvinsky, Ilya A. Vakser:
  The ruggedness of protein-protein energy landscape and the cutoff for 1/rⁿ potentials. 1132-1136
  
• Jinkyu Kim, Seunghak Yu, Byonghyo Shim, Hanjoo Kim, Hyeyoung Min, Eui-Young Chung, Rhiju Das, Sungroh Yoon:
  A robust peak detection method for RNA structure inference by high-throughput contact mapping. 1137-1144
  

• Michael C. Wu, Lingsong Zhang, Zhaoxi Wang, David Christiani, Xihong Lin:
  Sparse linear discriminant analysis for simultaneous testing for the significance of a gene set/pathway and gene selection. 1145-1151
  
• Ashok Sharma, Robert Podolsky, Jieping Zhao, Richard A. McIndoe:
  A modified hyperplane clustering algorithm allows for efficient and accurate clustering of extremely large datasets. 1152-1157
  

• Igor Ulitsky, Ron Shamir:
  Identifying functional modules using expression profiles and confidence-scored protein interactions. 1158-1164
  

• Bracken M. King, Bruce Tidor:
  MIST: Maximum Information Spanning Trees for dimension reduction of biological data sets. 1165-1172
  
• Mark F. Rogers, Asa Ben-Hur:
  The use of gene ontology evidence codes in preventing classifier assessment bias. 1173-1177
  
• Troy A. Ruths, Derek A. Ruths, Luay Nakhleh:
  GS²: an efficiently computable measure of GO-based similarity of gene sets. 1178-1184
  

• Igor B. Kuznetsov, Michael McDuffie, Roxana Moslehi:
  A web server for inferring the human N-acetyltransferase-2 (NAT2) enzymatic phenotype from NAT2 genotype. 1185-1186
  
• Ilya Plyusnin, Liisa Holm, Matti Kankainen:
  LOCP - locating pilus operons in Gram-positive bacteria. 1187-1188
  

• Andrew M. Waterhouse, James B. Procter, David M. A. Martin, Michele E. Clamp, Geoffrey J. Barton:
  Jalview Version 2 - a multiple sequence alignment editor and analysis workbench. 1189-1191
  
• David Talavera, Roman A. Laskowski, Janet M. Thornton:
  WSsas: a web service for the annotation of functional residues through structural homologues. 1192-1194
  
• Yongjian Guo, Jose M. C. Ribeiro, Jennifer M. Anderson, Stephan Bour:
  dCAS: a desktop application for cDNA sequence annotation. 1195-1196
  
• Robert J. Gifford, Tommy F. Liu, Soo-Yon Rhee, Mark Kiuchi, Stephane Hue, Deenan Pillay, Robert W. Shafer:
  The calibrated population resistance tool: standardized genotypic estimation of transmitted HIV-1 drug resistance. 1197-1198
  

• Martin Lott, Andreas Spillner, Katharina T. Huber, Vincent Moulton:
  PADRE: a package for analyzing and displaying reticulate evolution. 1199-1200
  

• Timothy V. Pyrkov, Anton O. Chugunov, Nikolay A. Krylov, Dmitry E. Nolde, Roman G. Efremov:
  PLATINUM: a web tool for analysis of hydrophobic/hydrophilic organization of biomolecular complexes. 1201-1202
  

• Jeffrey T. Leek:
  The tspair package for finding top scoring pair classifiers in R. 1203-1204
  

• Hendrik Hache, Christoph K. Wierling, Hans Lehrach, Ralf Herwig:
  GeNGe: systematic generation of gene regulatory networks. 1205-1207
  
• Tim McComb, Oliver Cairncross, Andrew B. Noske, David L. A. Wood, Brad J. Marsh, Mark A. Ragan:
  Illoura^TM: a software tool for analysis, visualization and semantic querying of cellular and other spatial biological data. 1208-1210
  

• Francesco Piva, Matteo Giulietti, Linda Nocchi, Giovanni Principato:
  SpliceAid: a database of experimental RNA target motifs bound by splicing proteins in humans. 1211-1213
  

• Kristoffer Forslund, Erik L. L. Sonnhammer:
  Predicting protein function from domain content. 1214
  

Volume 25, Number 10, May 2009

• Xiangfeng Wang, Zhihui Yu, Xiaozeng Yang, Xing Wang Deng, Lei Li:
  Transcriptionally active gene fragments derived from potentially fast-evolving donor genes in the rice genome. 1215-1218
  

• Agathe Burgess, Jean Paul Mornon, Geneviève de Saint-Basile, Isabelle Callebaut:
  A concanavalin A-like lectin domain in the CHS1/LYST protein, shared by members of the BEACH family. 1219-1222
  

• Roger Pique-Regi, Antonio Ortega, Shahab Asgharzadeh:
  Joint estimation of copy number variation and reference intensities on multiple DNA arrays using GADA. 1223-1230
  
• Simon Anders:
  Visualization of genomic data with the Hilbert curve. 1231-1235
  

• Diana L. Kolbe, Sean R. Eddy:
  Local RNA structure alignment with incomplete sequence. 1236-1243
  
• Tianjiao Chu, Kimberly Bunce, W. Allen Hogge, David G. Peters:
  Statistical model for whole genome sequencing and its application to minimally invasive diagnosis of fetal genetic disease. 1244-1250
  

• Mingyue Zheng, Xiaomin Luo, Qiancheng Shen, Yong Wang, Yun Du, Weiliang Zhu, Hualiang Jiang:
  Site of metabolism prediction for six biotransformations mediated by cytochromes P450. 1251-1258
  
• Ruslan Sadreyev, Shuoyong Shi, David Baker, Nick V. Grishin:
  Structure similarity measure with penalty for close non-equivalent residues. 1259-1263
  
• Patrik Björkholm, Pawel Daniluk, Andriy Kryshtafovych, Krzysztof Fidelis, Robin Andersson, Torgeir R. Hvidsten:
  Using multi-data hidden Markov models trained on local neighborhoods of protein structure to predict residue-residue contacts. 1264-1270
  
• Julia Handl, Joshua D. Knowles, Simon C. Lovell:
  Artefacts and biases affecting the evaluation of scoring functions on decoy sets for protein structure prediction. 1271-1279
  

• Guido Sanguinetti, Andreas Ruttor, Manfred Opper, Cédric Archambeau:
  Switching regulatory models of cellular stress response. 1280-1286
  

• Alun Thomas:
  A method and program for estimating graphical models for linkage disequilibrium that scale linearly with the number of loci, and their application to gene drop simulation. 1287-1292
  

• Hao Zhang, Ole Lund, Morten Nielsen:
  The PickPocket method for predicting binding specificities for receptors based on receptor pocket similarities: application to MHC-peptide binding. 1293-1299
  
• Paul D. W. Kirk, Michael P. H. Stumpf:
  Gaussian process regression bootstrapping: exploring the effects of uncertainty in time course data. 1300-1306
  

• Zafer Barutçuoglu, Edoardo M. Airoldi, Vanessa Dumeaux, Robert E. Schapire, Olga G. Troyanskaya:
  Aneuploidy prediction and tumor classification with heterogeneous hidden conditional random fields. 1307-1313
  
• Lam C. Tsoi, Michael Boehnke, Richard L. Klein, W. Jim Zheng:
  Evaluation of genome-wide association study results through development of ontology fingerprints. 1314-1320
  

• Hagen Blankenburg, Robert D. Finn, Andreas Prlic, Andrew M. Jenkinson, Fidel Ramírez, Dorothea Emig, Sven-Eric Schelhorn, Joachim Büch, Thomas Lengauer, Mario Albrecht:
  DASMI: exchanging, annotating and assessing molecular interaction data. 1321-1328
  

• György Abrusán, Norbert Grundmann, Luc DeMester, Wojciech Makalowski:
  TEclass - a tool for automated classification of unknown eukaryotic transposable elements. 1329-1330
  
• Micah Hamady, Stephanie A. Wilson, Jesse Zaneveld, Noboru Sueoka, Rob Knight:
  CodonExplorer: an online tool for analyzing codon usage and sequence composition, scaling from genes to genomes. 1331-1332
  
• David N. Messina, Erik L. L. Sonnhammer:
  DASher: a stand-alone protein sequence client for DAS, the Distributed Annotation System. 1333-1334
  
• Eric P. Nawrocki, Diana L. Kolbe, Sean R. Eddy:
  Infernal 1.0: inference of RNA alignments. 1335-1337
  
• Ying Huang, Paul Gilna, Weizhong Li:
  Identification of ribosomal RNA genes in metagenomic fragments. 1338-1340
  

• Hua Xu, Michael A. Freitas:
  Automated diagnosis of LC-MS/MS performance. 1341-1343
  

Volume 25, Number 11, June 2009

• Angelica Lindlöf, Marcus Bräutigam, Aakash Chawade, Olof Olsson, Björn Olsson:
  In silico analysis of promoter regions from cold-induced genes in rice (Oryza sativa L.) and Arabidopsis thaliana reveals the importance of combinatorial control. 1345-1348
  

• Triinu Koressaar, Kai Jõers, Maido Remm:
  Automatic identification of species-specific repetitive DNA sequences and their utilization for detecting microbial organisms. 1349-1355
  

• Eric L. Peterson, Jané Kondev, Julie A. Theriot, Rob Phillips:
  Reduced amino acid alphabets exhibit an improved sensitivity and selectivity in fold assignment. 1356-1362
  
• Michael C. Schatz:
  CloudBurst: highly sensitive read mapping with MapReduce. 1363-1369
  

• Marc A. Suchard, Andrew Rambaut:
  Many-core algorithms for statistical phylogenetics. 1370-1376
  

• Jules Hernández-Sánchez, Jean-Alain Grunchec, Sara Knott:
  A web application to perform linkage disequilibrium and linkage analyses on a computational grid. 1377-1383
  

• E. Shannon Neeley, Steven M. Kornblau, Kevin R. Coombes, Keith A. Baggerly:
  Variable slope normalization of reverse phase protein arrays. 1384-1389
  
• Wei Pan:
  Network-based multiple locus linkage analysis of expression traits. 1390-1396
  

• Smriti R. Ramakrishnan, Christine Vogel, John T. Prince, Rong Wang, Zhihua Li, Luiz O. Penalva, Margaret Myers, Edward M. Marcotte, Daniel P. Miranker:
  Integrating shotgun proteomics and mRNA expression data to improve protein identification. 1397-1403
  
• Irena Spasic, Evangelos Simeonidis, Hanan L. Messiha, Norman W. Paton, Douglas B. Kell:
  KiPar, a tool for systematic information retrieval regarding parameters for kinetic modelling of yeast metabolic pathways. 1404-1411
  
• Dolf Trieschnigg, Piotr Pezik, Vivian Lee, Franciska de Jong, Wessel Kraaij, Dietrich Rebholz-Schuhmann:
  MeSH Up: effective MeSH text classification for improved document retrieval. 1412-1418
  

• Feng-Chi Chen, Yen-Zho Chen, Trees-Juen Chuang:
  CNVVdb: a database of copy number variations across vertebrate genomes. 1419-1421
  

• Peter J. A. Cock, Tiago Antao, Jeffrey T. Chang, Brad A. Chapman, Cymon J. Cox, Andrew Dalke, Iddo Friedberg, Thomas Hamelryck, Frank Kauff, Bartek Wilczynski, Michiel J. L. de Hoon:
  Biopython: freely available Python tools for computational molecular biology and bioinformatics. 1422-1423
  
• You Jung Kim, Nikhil Teletia, Victor Ruotti, Christopher A. Maher, Arul M. Chinnaiyan, Ron M. Stewart, James A. Thomson, Jignesh M. Patel:
  ProbeMatch: rapid alignment of oligonucleotides to genome allowing both gaps and mismatches. 1424-1425
  

• R. Matthew Ward, Eric Venner, Bryce Daines, Stephen Murray, Serkan Erdin, David M. Kristensen, Olivier Lichtarge:
  Evolutionary Trace Annotation Server: automated enzyme function prediction in protein structures using 3D templates. 1426-1427
  
• Massimo Sandal, Fabrizio Benedetti, Marco Brucale, Alberto Gomez-Casado, Bruno Samorì:
  Hooke: an open software platform for force spectroscopy. 1428-1430
  
• Michael C. Ryan, Mark Diekhans, Stephanie Lien, Yun Liu, Rachel Karchin:
  LS-SNP/PDB: annotated non-synonymous SNPs mapped to Protein Data Bank structures. 1431-1432
  
• Xuefeng Xia, Song Zhang, Yu Su, Zhirong Sun:
  MICAlign: a sequence-to-structure alignment tool integrating multiple sources of information in conditional random fields. 1433-1434
  
• Yanga Byun, Kyungsook Han:
  PseudoViewer3: generating planar drawings of large-scale RNA structures with pseudoknots. 1435-1437
  

• Paul Geeleher, Dermot Morris, John P. Hinde, Aaron Golden:
  BioconductorBuntu: a Linux distribution that implements a web-based DNA microarray analysis server. 1438-1439
  

• Ambra Giovannini, Gaetano Zanghirati, Mark A. Beaumont, Lounès Chikhi, Guido Barbujani:
  A novel parallel approach to the likelihood-based estimation of admixture in population genetics. 1440-1441
  
• Xavier Didelot, Daniel Lawson, Daniel Falush:
  SimMLST: simulation of multi-locus sequence typing data under a neutral model. 1442-1444
  
• John Watkinson, Dimitris Anastassiou:
  Synergy Disequilibrium Plots: graphical visualization of pairwise synergies and redundancies of SNPs with respect to a phenotype. 1445-1446
  
• Vincent J. Carey, Adam R. Davis, Michael F. Lawrence, Robert Gentleman, Benjamin A. Raby:
  Data structures and algorithms for analysis of genetics of gene expression with Bioconductor: GGtools 3.x. 1447-1448
  
• Miao-Xin Li, Lin Jiang, Patrick Yu-Ping Kao, Pak Chung Sham, You-Qiang Song:
  IGG3: a tool to rapidly integrate large genotype datasets for whole-genome imputation and individual-level meta-analysis. 1449-1450
  
• Pablo Librado, Julio Rozas:
  DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. 1451-1452
  

• Frédéric Y. Bois:
  GNU MCSim: Bayesian statistical inference for SBML-coded systems biology models. 1453-1454
  
• Andreas Dräger, Hannes Planatscher, Dieudonné Motsou Wouamba, Adrian Schröder, Michael Hucka, Lukas Endler, Martin Golebiewski, Wolfgang Müller, Andreas Zell:
  SBML2L^AT_EX: Conversion of SBML files into human-readable reports. 1455-1456
  
• Bin Hu, G. Matthew Fricke, James R. Faeder, Richard G. Posner, William S. Hlavacek:
  GetBonNie for building, analyzing and sharing rule-based models. 1457-1460
  
• Xuefeng Bruce Ling, Harvey Cohen, Joseph Jin, Irwin Lau, James Schilling:
  FDR made easy in differential feature discovery and correlation analyses. 1461-1462
  
• Stephan Preibisch, Stephan Saalfeld, Pavel Tomancak:
  Globally optimal stitching of tiled 3D microscopic image acquisitions. 1463-1465
  
• Giorgio F. Gilestro, Chiara Cirelli:
  pySolo: a complete suite for sleep analysis in Drosophila. 1466-1467
  
• Mauro A. A. Castro, José L. Rybarczyk Filho, Rodrigo J. S. Dalmolin, Marialva Sinigaglia, José C. F. Moreira, José C. M. Mombach, Rita M. C. de Almeida:
  ViaComplex: software for landscape analysis of gene expression networks in genomic context. 1468-1469
  

• Jitao David Zhang, Stefan Wiemann:
  KEGGgraph: a graph approach to KEGG PATHWAY in R and bioconductor. 1470-1471
  
• Bas van Breukelen, Henk W. P. van den Toorn, Madalina M. Drugan, Albert J. R. Heck:
  StatQuant: a post-quantification analysis toolbox for improving quantitative mass spectrometry. 1472-1473
  

• Tsuyoshi Hachiya, Yasunori Osana, Kris Popendorf, Yasubumi Sakakibara:
  Accurate identification of orthologous segments among multiple genomes. 1474
  

Volume 25, Number 12, June 2009

• Dan Gusfield, Anna Tramontano:
  Editorial.
  

• Ivan G. Costa, Alexander Schönhuth, Christoph Hafemeister, Alexander Schliep:
  Constrained mixture estimation for analysis and robust classification of clinical time series.
  
• Yang Huang, Stefan Wuchty, Michael T. Ferdig, Teresa M. Przytycka:
  Graph theoretical approach to study eQTL: a case study of Plasmodium falciparum.
  
• Marc A. Schaub, Irene M. Kaplow, Marina Sirota, Chuong B. Do, Atul J. Butte, Serafim Batzoglou:
  A Classifier-based approach to identify genetic similarities between diseases.
  
• Sohrab P. Shah, K-John Cheung Jr., Nathalie A. Johnson, Guillaume Alain, Randy D. Gascoyne, Douglas E. Horsman, Raymond T. Ng, Kevin P. Murphy:
  Model-based clustering of array CGH data.
  
• Tal Vider-Shalit, Ronit Sarid, Kobi Maman, Lea Tsaban, Ran Levi, Yoram Louzoun:
  Viruses selectively mutate their CD8+ T-cell epitopes - a large-scale immunomic analysis.
  

• Jacob M. Joseph, Dannie Durand:
  Family classification without domain chaining.
  
• Manuel Garber, Mitchell Guttman, Michele E. Clamp, Michael C. Zody, Nir Friedman, Xiaohui Xie:
  Identifying novel constrained elements by exploiting biased substitution patterns.
  

• Pan Du, Gang Feng, Jared Flatow, Jie Song, Michelle Holko, Warren A. Kibbe, Simon M. Lin:
  From disease ontology to disease-ontology lite: statistical methods to adapt a general-purpose ontology for the test of gene-ontology associations.
  
• Stefan Schulz, Elena Beisswanger, László van den Hoek, Olivier Bodenreider, Erik M. van Mulligen:
  Alignment of the UMLS semantic network with BioTop: methodology and assessment.
  
• Karin Verspoor, Daniel Dvorkin, K. Bretonnel Cohen, Lawrence Hunter:
  Ontology quality assurance through analysis of term transformations.
  

• Daniel H. Huson, Regula Rupp, Vincent Berry, Philippe Gambette, Christophe Paul:
  Computing galled networks from real data.
  
• Timothy D. O'Connor, Nicholas I. Mundy:
  Genotype-phenotype associations: substitution models to detect evolutionary associations between phenotypic variables and genotypic evolutionary rate.
  

• Abhishek Garg, Kartik Mohanram, Alessandro Di Cara, Giovanni De Micheli, Ioannis Xenarios:
  Modeling stochasticity and robustness in gene regulatory networks.
  
• Aurelie C. Lozano, Naoki Abe, Yan Liu, Saharon Rosset:
  Grouped graphical Granger modeling for gene expression regulatory networks discovery.
  
• Adam A. Smith, Aaron L. Vollrath, Christopher A. Bradfield, Mark Craven:
  Clustered alignments of gene-expression time series data.
  
• Le Song, Mladen Kolar, Eric P. Xing:
  KELLER: estimating time-varying interactions between genes.
  
• Duygu Ucar, Andreas Beyer, Srinivasan Parthasarathy, Christopher T. Workman:
  Predicting functionality of protein-DNA interactions by integrating diverse evidence.
  

• José Caldas, Nils Gehlenborg, Ali Faisal, Alvis Brazma, Samuel Kaski:
  Probabilistic retrieval and visualization of biologically relevant microarray experiments.
  
• Manfred Claassen, Ruedi Aebersold, Joachim M. Buhmann:
  Proteome coverage prediction with infinite Markov models.
  
• Theo A. Knijnenburg, Lodewyk F. A. Wessels, Marcel J. T. Reinders, Ilya Shmulevich:
  Fewer permutations, more accurate P-values.
  
• Aurélien Rizk, Grégory Batt, François Fages, Sylvain Soliman:
  A general computational method for robustness analysis with applications to synthetic gene networks.
  
• Yoshihiro Yamanishi, Masahiro Hattori, Masaaki Kotera, Susumu Goto, Minoru Kanehisa:
  E-zyme: predicting potential EC numbers from the chemical transformation pattern of substrate-product pairs.
  

• Anand Bhaskar, Yun S. Song:
  Multi-locus match probability in a finite population: a fundamental difference between the Moran and Wright-Fisher models.
  
• Dan Geiger, Christopher Meek, Ydo Wexler:
  Speeding up HMM algorithms for genetic linkage analysis via chain reductions of the state space.
  
• Seyoung Kim, Kyung-Ah Sohn, Eric P. Xing:
  A multivariate regression approach to association analysis of a quantitative trait network.
  
• Bogdan Pasaniuc, Sriram Sankararaman, Gad Kimmel, Eran Halperin:
  Inference of locus-specific ancestry in closely related populations.
  
• Suzanne S. Sindi, Elena Helman, Ali Bashir, Benjamin J. Raphael:
  A geometric approach for classification and comparison of structural variants.
  
• Junming Yin, Michael I. Jordan, Yun S. Song:
  Joint estimation of gene conversion rates and mean conversion tract lengths from population SNP data.
  

• Xin Guo, Alexander J. Hartemink:
  Domain-oriented edge-based alignment of protein interaction networks.
  
• Shira Mintz-Oron, Asaph Aharoni, Eytan Ruppin, Tomer Shlomi:
  Network-based prediction of metabolic enzymes' subcellular localization.
  
• Chung-Shou Liao, Kanghao Lu, Michael Baym, Rohit Singh, Bonnie Berger:
  IsoRankN: spectral methods for global alignment of multiple protein networks.
  
• Mikhail Zaslavskiy, Francis R. Bach, Jean-Philippe Vert:
  Global alignment of protein-protein interaction networks by graph matching methods.
  

• Babak Alipanahi, Xin Gao, Emre Karakoç, Logan Donaldson, Ming Li:
  PICKY: a novel SVD-based NMR spectra peak picking method.
  
• Liya Fan, Fa Zhang, Gongming Wang, Zhiyong Liu:
  A framework to refine particle clusters produced by EMAN.
  
• Firas Khatib, Carol A. Rohl, Kevin Karplus:
  Pokefind: a novel topological filter for use with protein structure prediction.
  
• Luca Marsella, Francesco Sirocco, Antonio Trovato, Flavio Seno, Silvio C. E. Tosatto:
  REPETITA: detection and discrimination of the periodicity of protein solenoid repeats by discrete Fourier transform.
  
• Izhar Wallach, Ryan H. Lilien:
  Prediction of sub-cavity binding preferences using an adaptive physicochemical structure representation.
  
• Lei Xie, Li Xie, Philip E. Bourne:
  A unified statistical model to support local sequence order independent similarity searching for ligand-binding sites and its application to genome-based drug discovery.
  

• Thomas Abeel, Yves Van de Peer, Yvan Saeys:
  Toward a gold standard for promoter prediction evaluation.
  
• Wenjie Fu, Pradipta Ray, Eric P. Xing:
  DISCOVER: a feature-based discriminative method for motif search in complex genomes.
  
• Michiaki Hamada, Kengo Sato, Hisanori Kiryu, Toutai Mituyama, Kiyoshi Asai:
  Predictions of RNA secondary structure by combining homologous sequence information.
  
• John Hawkins, Charles E. Grant, William Stafford Noble, Timothy L. Bailey:
  Assessing phylogenetic motif models for predicting transcription factor binding sites.
  
• Shai Lubliner, Eran Segal:
  Modeling interactions between adjacent nucleosomes improves genome-wide predictions of nucleosome occupancy.
  
• Tobias Marschall, Sven Rahmann:
  Efficient exact motif discovery.
  
• Hamidreza Chitsaz, Raheleh Salari, Süleyman Cenk Sahinalp, Rolf Backofen:
  A partition function algorithm for interacting nucleic acid strands.
  
• Oliver Stegle, Linda Payet, Jean-Louis Mergny, David J. C. MacKay, Julian Leon Huppert:
  Predicting and understanding the stability of G-quadruplexes.
  

• Alex Bateman, Matt Wood:
  Cloud computing. 1475
  

• Yong Lu, Peter Huggins, Ziv Bar-Joseph:
  Cross species analysis of microarray expression data. 1476-1483
  

• Rasa Jurgelenaite, Tjeerd Dijkstra, Clemens H. M. Kocken, Tom Heskes:
  Gene regulation in the intraerythrocytic cycle of Plasmodium falciparum. 1484-1491
  

• Ruth V. Spriggs, Yoichi Murakami, Haruki Nakamura, Susan Jones:
  Protein function annotation from sequence: prediction of residues interacting with RNA. 1492-1497
  
• Yasuo Tabei, Kiyoshi Asai:
  A local multiple alignment method for detection of non-coding RNA sequences. 1498-1505
  

• Oriol Fornes, Ramon Aragues, Jordi Espadaler, Marc A. Martí-Renom, Andrej Sali, Baldo Oliva:
  ModLink+: improving fold recognition by using protein-protein interactions. 1506-1512
  
• Nurcan Tuncbag, Attila Gürsoy, Ozlem Keskin:
  Identification of computational hot spots in protein interfaces: combining solvent accessibility and inter-residue potentials improves the accuracy. 1513-1520
  

• Jia Meng, Shou-Jiang Gao, Yufei Huang:
  Enrichment constrained time-dependent clustering analysis for finding meaningful temporal transcription modules. 1521-1527
  
• Aziz Mithani, Gail M. Preston, Jotun Hein:
  A stochastic model for the evolution of metabolic networks with neighbor dependence. 1528-1535
  

• Rajesh Chowdhary, Jinfeng Zhang, Jun S. Liu:
  Bayesian inference of protein-protein interactions from biological literature. 1536-1542
  
• Leon French, Suzanne Lane, Tamryn Law, Lydia Xu, Paul Pavlidis:
  Application and evaluation of automated semantic annotation of gene expression experiments. 1543-1549
  

• Ram Podicheti, Rajesh Gollapudi, Qunfeng Dong:
  WebGBrowse - a web server for GBrowse. 1550-1551
  
• Miguel Pignatelli, Florenci Serras, Andrés Moya, Roderic Guigó, Montserrat Corominas:
  CROC: finding chromosomal clusters in eukaryotic genomes. 1552-1553
  

• Hua Bao, Hui Guo, Jinwei Wang, Renchao Zhou, Xuemei Lu, Suhua Shi:
  MapView: visualization of short reads alignment on a desktop computer. 1554-1555
  

• Blaz Stres, James M. Tiedje, Bostjan Murovec:
  BEsTRF: a tool for optimal resolution of terminal-restriction fragment length polymorphism analysis based on user-defined primer-enzyme-sequence databases. 1556-1558
  

• Semin Lee, Tom L. Blundell:
  BIPA: a database for protein-nucleic acid interaction in 3D structures. 1559-1560
  

• Mark Abney:
  A graphical algorithm for fast computation of identity coefficients and generalized kinship coefficients. 1561-1563
  
• Brandon M. Hall, Chang-Xing Ma, Ping Liang, Keshav K. Singh:
  Fluctuation AnaLysis CalculatOR: a web tool for the determination of mutation rate using Luria-Delbrück fluctuation analysis. 1564-1565
  

• Amanda M. White, James R. Collett, Shannon L. Seurynck-Servoss, Don Simone Daly, Richard C. Zangar:
  ELISA-BASE: an integrated bioinformatics tool for analyzing and tracking ELISA microarray data. 1566-1567
  
• Jayashree Ramana, Dinesh Gupta:
  ProtVirDB: a database of protozoan virulent proteins. 1568-1569
  

• Marie-France Sagot, B. J. Morrison McKay, Gene Myers:
  ISMB/ECCB 2009 Stockholm. 1570-1573
  

• 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. 1574
  

Volume 25, Number 13, July 2009

• Raffaele Giancarlo, Davide Scaturro, Filippo Utro:
  Textual data compression in computational biology: a synopsis. 1575-1586
  

• David V. Lu, Randall H. Brown, Manimozhiyan Arumugam, Michael R. Brent:
  Pairagon: a highly accurate, HMM-based cDNA-to-genome aligner. 1587-1593
  
• Jochen W. Klingelhoefer, Loukas Moutsianas, Christopher C. Holmes:
  Approximate Bayesian feature selection on a large meta-dataset offers novel insights on factors that effect siRNA potency. 1594-1601
  

• Anoop Kumar, Lenore Cowen:
  Augmented training of hidden Markov models to recognize remote homologs via simulated evolution. 1602-1608
  
• Zia Khan, Joshua S. Bloom, Leonid Kruglyak, Mona Singh:
  A practical algorithm for finding maximal exact matches in large sequence datasets using sparse suffix arrays. 1609-1616
  
• Dennis J. Hazelett, Daniel L. Lakeland, Joseph B. Weiss:
  Affinity Density: a novel genomic approach to the identification of transcription factor regulatory targets. 1617-1624
  

• Jairo Rocha, Joan Segura, Richard C. Wilson, Swagata Dasgupta:
  Flexible structural protein alignment by a sequence of local transformations. 1625-1631
  
• Christian Schillinger, Prisca Boisguerin, Gerd Krause:
  Domain Interaction Footprint: a multi-classification approach to predict domain-peptide interactions. 1632-1639
  

• Denis C. Bauer, Timothy L. Bailey:
  Optimizing static thermodynamic models of transcriptional regulation. 1640-1646
  
• Fred P. Davis, Sean R. Eddy:
  A tool for identification of genes expressed in patterns of interest using the Allen Brain Atlas. 1647-1654
  
• Chunrong Cheng, Kui Shen, Chi Song, Jianhua Luo, George C. Tseng:
  Ratio adjustment and calibration scheme for gene-wise normalization to enhance microarray inter-study prediction. 1655-1661
  
• Min Zhang, Lin Zhang, Jinfeng Zou, Chen Yao, Hui Xiao, Qing Liu, Jing Wang, Dong Wang, Chenguang Wang, Zheng Guo:
  Evaluating reproducibility of differential expression discoveries in microarray studies by considering correlated molecular changes. 1662-1668
  

• Long Yang Wu, Hugh A. Chipman, Shelley B. Bull, Laurent Briollais, Kesheng Wang:
  A Bayesian segmentation approach to ascertain copy number variations at the population level. 1669-1679
  

• Chao-Yi Dong, Jisoon Lim, Yoonkey Nam, Kwang-Hyun Cho:
  Systematic analysis of synchronized oscillatory neuronal networks reveals an enrichment for coupled direct and indirect feedback motifs. 1680-1685
  
• Janis Dingel, Olgica Milenkovic:
  List-decoding methods for inferring polynomials in finite dynamical gene network models. 1686-1693
  
• Jonathan D. Wren:
  A global meta-analysis of microarray expression data to predict unknown gene functions and estimate the literature-data divide. 1694-1701
  
• Quanyu Zhao, Hiroyuki Kurata:
  Genetic modification of flux for flux prediction of mutants. 1702-1708