Bioinformatics, Volume 24

Volume 24, Number 1, 1 January 2008

• Christoph Bock, Thomas Lengauer:
  Computational epigenetics. 1-10
  

• Michael L. Tress, Jan-Jaap Wesselink, Adam Frankish, Gonzalo López, Nick Goldman, Ari Löytynoja, Tim Massingham, Fabio Pardi, Simon Whelan, Jennifer Harrow, Alfonso Valencia:
  Determination and validation of principal gene products. 11-17
  

• Kai Ye, K. Anton Feenstra, Jaap Heringa, Adriaan P. IJzerman, Elena Marchiori:
  Multi-RELIEF: a method to recognize specificity determining residues from multiple sequence alignments using a Machine-Learning approach for feature weighting. 18-25
  
• Aalt D. J. van Dijk, Cajo J. F. ter Braak, R. G. Immink, G. C. Angenent, Roeland C. H. J. van Ham:
  Predicting and understanding transcription factor interactions based on sequence level determinants of combinatorial control. 26-33
  
• Koen Deforche, Ricardo Camacho, Kristel Van Laethem, Philippe Lemey, Andrew Rambaut, Yves Moreau, Anne-Mieke Vandamme:
  Estimation of an in vivo fitness landscape experienced by HIV-1 under drug selective pressure useful for prediction of drug resistance evolution during treatment. 34-41
  
• Aleksey V. Zimin, Douglas R. Smith, Granger G. Sutton, James A. Yorke:
  Assembly reconciliation. 42-45
  
• Kuo-ching Liang, Xiaodong Wang, Dimitris Anastassiou:
  A profile-based deterministic sequential Monte Carlo algorithm for motif discovery. 46-55
  

• Nicolas Rodrigue, Hervé Philippe, Nicolas Lartillot:
  Uniformization for sampling realizations of Markov processes: applications to Bayesian implementations of codon substitution models. 56-62
  

• Dante Mantini, Francesca Petrucci, Piero Del Boccio, Damiana Pieragostino, Marta Di Nicola, Alessandra Lugaresi, Giorgio Federici, Paolo Sacchetta, Carmine Di Ilio, Andrea Urbani:
  Independent component analysis for the extraction of reliable protein signal profiles from MALDI-TOF mass spectra. 63-70
  

• Ryan M. Kelley, Hoda Feizi, Trey Ideker:
  Correcting for gene-specific dye bias in DNA microarrays using the method of maximum likelihood. 71-77
  
• Manuela Hummel, Reinhard Meister, Ulrich Mansmann:
  GlobalANCOVA: exploration and assessment of gene group effects. 78-85
  

• Guohui Lin, Zhanyong Wang, Lusheng Wang, Yu-Lung Lau, Wanling Yang:
  Identification of linked regions using high-density SNP genotype data in linkage analysis. 86-93
  

• Meng Wang, Xiaobo Zhou, Fuhai Li, Jeremy Huckins, Randall W. King, Stephen T. C. Wong:
  Novel cell segmentation and online SVM for cell cycle phase identification in automated microscopy. 94-101
  
• Pedro Alves, Randy J. Arnold, David E. Clemmer, Yixue Li, James P. Reilly, Quanhu Sheng, Haixu Tang, Zhiyin Xun, Rong Zeng, Predrag Radivojac:
  Fast and accurate identification of semi-tryptic peptides in shotgun proteomics. 102-109
  

• Michal Draminski, Alvaro Rada-Iglesias, Stefan Enroth, Claes Wadelius, Jacek Koronacki, Henryk Jan Komorowski:
  Monte Carlo feature selection for supervised classification. 110-117
  
• Seonho Kim, Juntae Yoon, Jihoon Yang:
  Kernel approaches for genic interaction extraction. 118-126
  

• Cedric Simillion, Koen Janssens, Lieven Sterck, Yves Van de Peer:
  i-ADHoRe 2.0: an improved tool to detect degenerated genomic homology using genomic profiles. 127-128
  

• Luke J. Harmon, Jason T. Weir, Chad D. Brock, Richard E. Glor, Wendell Challenger:
  GEIGER: investigating evolutionary radiations. 129-131
  

• James Long, Mitchell Roth:
  Synthetic microarray data generation with RANGE and NEMO. 132-134
  
• Nicola Lama, Mark Girolami:
  vbmp: Variational Bayesian Multinomial Probit Regression for multi-class classification in R. 135-136
  
• Xiaojiang Xu, Yingdong Zhao, Richard M. Simon:
  Gene Set Expression Comparison kit for BRB-ArrayTools. 137-139
  

• Chun Li, Mingyao Li:
  GWAsimulator: a rapid whole-genome simulation program. 140-142
  

• Fabien Jourdan, Rainer Breitling, Michael P. Barrett, David Gilbert:
  MetaNetter: inference and visualization of high-resolution metabolomic networks. 143-145
  

• Daniel F. Schwarz, Oliver Hädicke, Jeanette Erdmann, Andreas Ziegler, Daniel Bayer, Steffen Möller:
  SNPtoGO: characterizing SNPs by enriched GO terms. 146-148
  

• Peng Liu, J. T. Gene Hwang:
  Gene expression: Quick calculation for sample size while controlling false discovery rate with application to microarray analysis. 149
  

Volume 24, Number 2, 15 January 2008

• Athanasia C. Tzika, Raphaël Helaers, Yves Van de Peer, Michel C. Milinkovitch:
  MANTIS: a phylogenetic framework for multi-species genome comparisons. 151-157
  

• Jana Hertel, Ivo L. Hofacker, Peter F. Stadler:
  SnoReport: computational identification of snoRNAs with unknown targets. 158-164
  
• Xiaowo Wang, Jin Gu, Michael Q. Zhang, Yanda Li:
  Identification of phylogenetically conserved microRNA cis-regulatory elements across 12 Drosophila species. 165-171
  
• Dean Laslett, Björn Canbäck:
  ARWEN: a program to detect tRNA genes in metazoan mitochondrial nucleotide sequences. 172-175
  

• Anagha Joshi, Yves Van de Peer, Tom Michoel:
  Analysis of a Gibbs sampler method for model-based clustering of gene expression data. 176-183
  
• Jaehee Kim, Haseong Kim:
  Clustering of change patterns using Fourier coefficients. 184-191
  
• Dan Nettleton, Justin Recknor, James M. Reecy:
  Identification of differentially expressed gene categories in microarray studies using nonparametric multivariate analysis. 192-201
  

• Changyu Shen, Zhiping Wang, Ganesh Shankar, Xiang Zhang, Lang Li:
  A hierarchical statistical model to assess the confidence of peptides and proteins inferred from tandem mass spectrometry. 202-208
  
• Simon Hardy, Pierre N. Robillard:
  Petri net-based method for the analysis of the dynamics of signal propagation in signaling pathways. 209-217
  
• Denise Scholtens, Tony Chiang, Wolfgang Huber, Robert Gentleman:
  Estimating node degree in bait-prey graphs. 218-224
  
• Jean-Loup Faulon, Milind Misra, Shawn Martin, Ken Sale, Rajat Sapra:
  Genome scale enzyme-metabolite and drug-target interaction predictions using the signature molecular descriptor. 225-233
  

• Hanchuan Peng, Fuhui Long, Xiao Liu, Stuart K. Kim, Eugene W. Myers:
  Straightening Caenorhabditis elegans images. 234-242
  
• Mounir Errami, Justin M. Hicks, Wayne G. Fisher, David Trusty, Jonathan D. Wren, Tara C. Long, Harold R. Garner:
  Déjà vu - A study of duplicate citations in Medline. 243-249
  
• Ichigaku Takigawa, Hiroshi Mamitsuka:
  Probabilistic path ranking based on adjacent pairwise coexpression for metabolic transcripts analysis. 250-257
  
• Giuseppe Jurman, Stefano Merler, Annalisa Barla, Silvano Paoli, Antonio Galea, Cesare Furlanello:
  Algebraic stability indicators for ranked lists in molecular profiling. 258-264
  

• Da Yang, Yanhui Li, Hui Xiao, Qing Liu, Min Zhang, Jing Zhu, Wencai Ma, Chen Yao, Jing Wang, Dong Wang, Zheng Guo, Baofeng Yang:
  Gaining confidence in biological interpretation of the microarray data: the functional consistence of the significant GO categories. 265-271
  

• Annamária F. Ángyán, András Perczel, Sándor Pongor, Zoltán Gáspári:
  Fast protein fold estimation from NMR-derived distance restraints. 272-275
  

• Wolfgang Raffelsberger, Yannick Krause, Luc Moulinier, David Kieffer, Anne-Laure Morand, Laurent Brino, Olivier Poch:
  RReportGenerator: automatic reports from routine statistical analysis using R. 276-278
  

• Christian Fuchsberger, Mario Falchi, Lukas Forer, Peter P. Pramstaller:
  PedVizApi: a Java API for the interactive, visual analysis of extended pedigrees. 279-281
  

• Yassen Assenov, Fidel Ramírez, Sven-Eric Schelhorn, Thomas Lengauer, Mario Albrecht:
  Computing topological parameters of biological networks. 282-284
  
• Thomas W. Evans, Colin S. Gillespie, Darren J. Wilkinson:
  The SBML discrete stochastic models test suite. 285-286
  
• Peter Li, Tom Oinn, Stian Soiland, Douglas B. Kell:
  Automated manipulation of systems biology models using libSBML within Taverna workflows. 287-289
  
• Kevin Y. Yip, Prianka Patel, Philip M. Kim, Donald M. Engelman, Drew McDermott, Mark Gerstein:
  An integrated system for studying residue coevolution in proteins. 290-292
  
• Sema Kachalo, Ranran Zhang, Eduardo D. Sontag, Réka Albert, Bhaskar DasGupta:
  NET-SYNTHESIS: a software for synthesis, inference and simplification of signal transduction networks. 293-295
  

• Dietrich Rebholz-Schuhmann, Miguel Arregui, Sylvain Gaudan, Harald Kirsch, Antonio Jimeno-Yepes:
  Text processing through Web services: calling Whatizit. 296-298
  

• Unitsa Sangket, Amornrat Phongdara, Wilaiwan Chotigeat, Darran Nathan, Woo-Yeon Kim, Jong Bhak, Chumpol Ngamphiw, Sissades Tongsima, Asif M. Khan, Honghuang Lin, Tin Wee Tan:
  Automatic synchronization and distribution of biological databases and software over low-bandwidth networks among developing countries. 299-301
  

Volume 24, Number 3, 1 February 2008

• Shuji Fujita, Hideo Iba:
  Putative promoter regions of miRNA genes involved in evolutionarily conserved regulatory systems among vertebrates. 303-308
  

• Roger Pique-Regi, Jordi Monso-Varona, Antonio Ortega, Robert C. Seeger, Timothy Triche, Shahab Asgharzadeh:
  Sparse representation and Bayesian detection of genome copy number alterations from microarray data. 309-318
  

• Gabriel Moreno-Hagelsieb, Kristen Latimer:
  Choosing BLAST options for better detection of orthologs as reciprocal best hits. 319-324
  
• Xiaowei Wang, Issam M. El Naqa:
  Prediction of both conserved and nonconserved microRNA targets in animals. 325-332
  
• S. D. Dunn, L. M. Wahl, Gregory B. Gloor:
  Mutual information without the influence of phylogeny or entropy dramatically improves residue contact prediction. 333-340
  
• Tak-Ming Chan, Kwong-Sak Leung, Kin-Hong Lee:
  TFBS identification based on genetic algorithm with combined representations and adaptive post-processing. 341-349
  
• Utz J. Pape, Sven Rahmann, Martin Vingron:
  Natural similarity measures between position frequency matrices with an application to clustering. 350-357
  
• Laurent Jacob, Jean-Philippe Vert:
  Efficient peptide-MHC-I binding prediction for alleles with few known binders. 358-366
  

• Hisanori Kiryu, Taishin Kin, Kiyoshi Asai:
  Rfold: an exact algorithm for computing local base pairing probabilities. 367-373
  

• Fangxin Hong, Rainer Breitling:
  A comparison of meta-analysis methods for detecting differentially expressed genes in microarray experiments. 374-382
  

• F. F. Vale, P. Encarnação, J. M. B. Vítor:
  A new algorithm for cluster analysis of genomic methylation: the Helicobacter pylori case. 383-388
  

• Anatoly L. Mayburd, Inna Golovchikova, James L. Mulshine:
  Successful anti-cancer drug targets able to pass FDA review demonstrate the identifiable signature distinct from the signatures of random genes and initially proposed targets. 389-395
  
• David J. Reiss, Marc T. Facciotti, Nitin S. Baliga:
  Model-based deconvolution of genome-wide DNA binding. 396-403
  
• Peng Wei, Wei Pan:
  Incorporating gene networks into statistical tests for genomic data via a spatially correlated mixture model. 404-411
  

• Li Wang, Ji Zhu, Hui Zou:
  Hybrid huberized support vector machines for microarray classification and gene selection. 412-419
  

• Tae-Min Kim, Yu-Chae Jung, Mun-Gan Rhyu, Myeong Ho Jung, Yeun-Jun Chung:
  GEAR: genomic enrichment analysis of regional DNA copy number changes. 420-421
  
• Lukas A. Mueller, Adri A. Mills, Beth Skwarecki, Robert M. Buels, Naama Menda, Steven D. Tanksley:
  The SGN comparative map viewer. 422-423
  
• Jacques Oberto:
  BAGET: a web server for the effortless retrieval of prokaryotic gene context and sequence. 424-425
  

• Manfred J. Sippl, Markus Wiederstein:
  A note on difficult structure alignment problems. 426-427
  

• Daniele Masotti, Christine Nardini, Simona Rossi, Elena Bonora, Giovanni Romeo, Stefano Volinia, Luca Benini:
  TOM: enhancement and extension of a tool suite for in silico approaches to multigenic hereditary disorders. 428-429
  
• Paolo Magni, Fulvia Ferrazzi, Lucia Sacchi, Riccardo Bellazzi:
  TimeClust: a clustering tool for gene expression time series. 430-432
  
• Rudi Alberts, Gonzalo Vera, Ritsert C. Jansen:
  affyGG: computational protocols for genetical genomics with Affymetrix arrays. 433-434
  

• Xiaoquan Wen, Dan L. Nicolae:
  Association studies for untyped markers with TUNA. 435-437
  

• Tianming Liu, Jingxin Nie, Gang Li, Lei Guo, Stephen T. C. Wong:
  ZFIQ: a software package for zebrafish biology. 438-439
  

• Julia Stoyanovich, Itsik Pe'er:
  MutaGeneSys: estimating individual disease susceptibility based on genome-wide SNP array data. 440-442
  
• J. Stuart Aitken, Yin Chen, Jonathan Bard:
  OBO Explorer: an editor for open biomedical ontologies in OWL. 443-444
  
• Quentin Kaas, Jan-C. Westermann, Reena Halai, Conan K. L. Wang, David J. Craik:
  ConoServer, a database for conopeptide sequences and structures. 445-446
  
• David Salgado, Gregory Gimenez, François Coulier, Christophe Marcelle:
  COMPARE, a multi-organism system for cross-species data comparison and transfer of information. 447-449
  
• Gil Alterovitz, Adnaan Jiwaji, Marco Ramoni:
  Automated programming for bioinformatics algorithm deployment. 450-451
  

Volume 24, Number 4, 15 February 2008

• Sushama Michael, Gilles Travé, Chenna Ramu, Claudia Chica, Toby J. Gibson:
  Discovery of candidate KEN-box motifs using Cell Cycle keyword enrichment combined with native disorder prediction and motif conservation. 453-457
  
• Saraswathi Abhiman, Lakshminarayan M. Iyer, L. Aravind:
  BEN: a novel domain in chromatin factors and DNA viral proteins. 458-461
  

• James Robert White, Michael Roberts, James A. Yorke, Mihai Pop:
  Figaro: a novel statistical method for vector sequence removal. 462-467
  

• Xuehui Li, Tamer Kahveci, A. Mark Settles:
  A novel genome-scale repeat finder geared towards transposons. 468-476
  
• Ido Ginodi, Tal Vider-Shalit, Lea Tsaban, Yoram Louzoun:
  Precise score for the prediction of peptides cleaved by the proteasome. 477-483
  
• Sumedha Gunewardena, Zhaolei Zhang:
  A hybrid model for robust detection of transcription factor binding sites. 484-491
  
• Walter Pirovano, K. Anton Feenstra, Jaap Heringa:
  PRALINE^TM: a strategy for improved multiple alignment of transmembrane proteins. 492-497
  
• Rotem Rubinstein, András Fiser:
  Predicting disulfide bond connectivity in proteins by correlated mutations analysis. 498-504
  
• Yu-Chieh Liao, Min-Shi Lee, Chin-Yu Ko, Chao A. Hsiung:
  Bioinformatics models for predicting antigenic variants of influenza A/H3N2 virus. 505-512
  

• Arlo Z. Randall, Jianlin Cheng, Michael J. Sweredoski, Pierre Baldi:
  TMBpro: secondary structure, beta-contact and tertiary structure prediction of transmembrane beta-barrel proteins. 513-520
  
• Konrad Hinsen:
  Structural flexibility in proteins: impact of the crystal environment. 521-528
  

• Jeffrey S. Morris, Brittan N. Clark, Howard B. Gutstein:
  Pinnacle: a fast, automatic and accurate method for detecting and quantifying protein spots in 2-dimensional gel electrophoresis data. 529-536
  
• Jelle J. Goeman, Ulrich Mansmann:
  Multiple testing on the directed acyclic graph of gene ontology. 537-544
  

• Debayan Datta, Hongyu Zhao:
  Statistical methods to infer cooperative binding among transcription factors in Saccharomyces cerevisiae. 545-552
  
• Hao Xiong, Yoonsuck Choe:
  Structural systems identification of genetic regulatory networks. 553-560
  
• Vasyl Pihur, Somnath Datta, Susmita Datta:
  Reconstruction of genetic association networks from microarray data: a partial least squares approach. 561-568
  

• Yuntao Qian, Robert F. Murphy:
  Improved recognition of figures containing fluorescence microscope images in online journal articles using graphical models. 569-576
  

• Niranjan Nagarajan, Uri Keich:
  FAST: Fourier transform based algorithms for significance testing of ungapped multiple alignments. 577-578
  

• Yuri R. Bendaña, Ian Holmes:
  Colorstock, SScolor, Ratón: RNA alignment visualization tools. 579-580
  

• Johan A. A. Nylander, James C. Wilgenbusch, Dan L. Warren, David L. Swofford:
  AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics. 581-583
  

• Dominik Gront, Andrzej Kolinski:
  Utility library for structural bioinformatics. 584-585
  
• Liam J. McGuffin:
  The ModFOLD server for the quality assessment of protein structural models. 586-587
  

• Priit Adler, Jüri Reimand, Jürgen Jänes, Raivo Kolde, Hedi Peterson, Jaak Vilo:
  KEGGanim: pathway animations for high-throughput data. 588-590
  
• Sebastian Böcker, Zsuzsanna Lipták, Marcel Martin, Anton Pervukhin, Henner Sudek:
  DECOMP - from interpreting Mass Spectrometry peaks to solving the Money Changing Problem. 591-593
  

• Maxim Kalaev, Michael E. Smoot, Trey Ideker, Roded Sharan:
  NetworkBLAST: comparative analysis of protein networks. 594-596
  

Volume 24, Number 5, 1 March 2008

• Qian Liu, Aaron J. Mackey, David S. Roos, Fernando C. N. Pereira:
  Evigan: a hidden variable model for integrating gene evidence for eukaryotic gene prediction. 597-605
  
• Onur Sakarya, Kenneth S. Kosik, Todd H. Oakley:
  Reconstructing ancestral genome content based on symmetrical best alignments and Dollo parsimony. 606-612
  

• J. D. Fischer, C. E. Mayer, Johannes Söding:
  Prediction of protein functional residues from sequence by probability density estimation. 613-620
  
• Igor V. Tetko, Igor V. Rodchenkov, Mathias C. Walter, Thomas Rattei, Hans-Werner Mewes:
  Beyond the "best" match: machine learning annotation of protein sequences by integration of different sources of information. 621-628
  
• Leping Li, Robert L. Bass, Yu Liang:
  fdrMotif: identifying cis-elements by an EM algorithm coupled with false discovery rate control. 629-636
  
• Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler:
  Using native and syntenically mapped cDNA alignments to improve de novo gene finding. 637-644
  

• Arun Siddharth Konagurthu, Peter J. Stuckey, Arthur M. Lesk:
  Structural search and retrieval using a tableau representation of protein folding patterns. 645-651
  
• Julie Bernauer, Ranjit Prasad Bahadur, Francis Rodier, Joël Janin, Anne Poupon:
  DiMoVo: a Voronoi tessellation-based method for discriminating crystallographic and biological protein-protein interactions. 652-658
  
• Changjun Chen, Yi Xiao:
  Observation of multiple folding pathways of beta-hairpin trpzip2 from independent continuous folding trajectories. 659-665
  

• Yinglei Lai:
  Genome-wide co-expression based prediction of differential expressions. 666-673
  
• Jainab Khatun, Eric Hamlett, Morgan C. Giddings:
  Incorporating sequence information into the scoring function: a hidden Markov model for improved peptide identification. 674-681
  
• Laurent Bréhélin, Olivier Gascuel, Olivier Martin:
  Using repeated measurements to validate hierarchical gene clusters. 682-688
  

• Ramazan Saeed, Charlotte M. Deane:
  An assessment of the uses of homologous interactions. 689-695
  
• Nicolas Thierry-Mieg, Gilles Bailly:
  Interpool: interpreting smart-pooling results. 696-703
  
• Andreas Kremling, Katja Bettenbrock, Ernst Dieter Gilles:
  A feed-forward loop guarantees robust behavior in Escherichia coli carbohydrate uptake. 704-710
  

• Simon Gog, Martin Bader, Enno Ohlebusch:
  GENESIS: genome evolution scenarios. 711-712
  

• Ruiqiang Li, Yingrui Li, Karsten Kristiansen, Jun Wang:
  SOAP: short oligonucleotide alignment program. 713-714
  

• Stephen A. Smith, Casey W. Dunn:
  Phyutility: a phyloinformatics tool for trees, alignments and molecular data. 715-716
  
• J. D. Moore, R. G. Allaby:
  TreeMos: a high-throughput phylogenomic approach to find and visualize phylogenetic mosaicism. 717-718
  

• Peter Langfelder, Bin Zhang, Steve Horvath:
  Defining clusters from a hierarchical cluster tree: the Dynamic Tree Cut package for R. 719-720
  

• Jian Yang, Chengcheng Hu, Han Hu, Rongdong Yu, Zhen Xia, Xiuzi Ye, Jun Zhu:
  QTLNetwork: mapping and visualizing genetic architecture of complex traits in experimental populations. 721-723
  
• Mario Falchi, Christian Fuchsberger:
  Jenti: an efficient tool for mining complex inbred genealogies. 724-726
  

• Martijn J. Schuemie, Jan A. Kors:
  Jane: suggesting journals, finding experts. 727-728
  
• Giorgio Valentini, Nicolò Cesa-Bianchi:
  HCGene: a software tool to support the hierarchical classification of genes. 729-731
  
• Alexander Lüdemann, Katrin Strassburg, Alexander Erban, Joachim Kopka:
  TagFinder for the quantitative analysis of gas chromatography - mass spectrometry (GC-MS)-based metabolite profiling experiments. 732-737
  

• Sorin Draghici, Adi L. Tarca, Longfei Yu, Stephen Ethier, Roberto Romero:
  KUTE-BASE: storing, downloading and exporting MIAME-compliant microarray experiments in minutes rather than hours. 738-740
  

Volume 24, Number 6, 15 March 2008

• Scott Grandison, Richard J. Morris:
  Biological pathway kinetic rate constants are scale-invariant. 741-743
  

• Jeong-Hyeon Choi, Sun Kim, Haixu Tang, Justen Andrews, Don G. Gilbert, John Colbourne:
  A machine-learning approach to combined evidence validation of genome assemblies. 744-750
  
• Robin Andersson, Carl E. G. Bruder, Arkadiusz Piotrowski, Uwe Menzel, Helena Nord, Johanna Sandgren, Torgeir R. Hvidsten, Teresita Diaz de Ståhl, Jan P. Dumanski, Henryk Jan Komorowski:
  A segmental maximum a posteriori approach to genome-wide copy number profiling. 751-758
  
• Henrik Bengtsson, Rafael A. Irizarry, Benilton Carvalho, Terence P. Speed:
  Estimation and assessment of raw copy numbers at the single locus level. 759-767
  
• Guillem Rigaill, Philippe Hupé, Anna Almeida, Philippe La Rosa, Jean-Philippe Meyniel, Charles Decraene, Emmanuel Barillot:
  ITALICS: an algorithm for normalization and DNA copy number calling for Affymetrix SNP arrays. 768-774
  

• Nanjiang Shu, Tuping Zhou, Sven Hovmöller:
  Prediction of zinc-binding sites in proteins from sequence. 775-782
  
• Anuj R. Shah, Christopher S. Oehmen, Bobbie-Jo M. Webb-Robertson:
  SVM-HUSTLE - an iterative semi-supervised machine learning approach for pairwise protein remote homology detection. 783-790
  
• Tak Wah Lam, Wing-Kin Sung, Siu-Lung Tam, Chi-Kwong Wong, Siu-Ming Yiu:
  Compressed indexing and local alignment of DNA. 791-797
  
• Mark N. Wass, Michael J. E. Sternberg:
  ConFunc - functional annotation in the twilight zone. 798-806
  
• Andreas Biegert, Johannes Söding:
  De novo identification of highly diverged protein repeats by probabilistic consistency. 807-814
  
• Bruce R. Southey, Jonathan V. Sweedler, Sandra L. Rodriguez-Zas:
  Prediction of neuropeptide cleavage sites in insects. 815-825
  

• Hadas Birin, Zohar Gal-Or, Isaac Elias, Tamir Tuller:
  Inferring horizontal transfers in the presence of rearrangements by the minimum evolution criterion. 826-832
  

• Vladislav Vyshemirsky, Mark Girolami:
  Bayesian ranking of biochemical system models. 833-839
  
• Julio Saez-Rodriguez, Arthur Goldsipe, Jeremy Muhlich, Leonidas G. Alexopoulos, Bjorn Millard, Douglas A. Lauffenburger, Peter K. Sorger:
  Flexible informatics for linking experimental data to mathematical models via DataRail. 840-847
  
• Henning Schmidt, Mads F. Madsen, Sune Danø, Gunnar Cedersund:
  Complexity reduction of biochemical rate expressions. 848-854
  

• Frank M. Graziano, Samira Y. Kettoola, Judy M. Munshower, Jack T. Stapleton, George Towfic:
  Effect of spatial distribution of T-Cells and HIV load on HIV progression. 855-860
  

• Gavin C. Conant, Kenneth H. Wolfe:
  GenomeVx: simple web-based creation of editable circular chromosome maps. 861-862
  
• Gipsi Lima-Mendez, Jacques van Helden, Ariane Toussaint, Raphaël Leplae:
  Prophinder: a computational tool for prophage prediction in prokaryotic genomes. 863-865
  

• Bram Slabbinck, Peter Dawyndt, M. Martens, Paul De Vos, Bernard De Baets:
  TaxonGap: a visualization tool for intra- and inter-species variation among individual biomarkers. 866-867
  

• Mark Derthick:
  Interactive visualization software for exploring phylogenetic trees and clades. 868-869
  

• Manfred J. Sippl, Stefan J. Suhrer, Markus Gruber, Markus Wiederstein:
  A discrete view on fold space. 870-871
  
• Manfred J. Sippl:
  On distance and similarity in fold space. 872-873
  

• Yongsung Joo, James G. Booth, Younghwan Namkoong, George Casella:
  Model-based Bayesian clustering (MBBC). 874-875
  

• Andrei Zinovyev, Eric Viara, Laurence Calzone, Emmanuel Barillot:
  BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks. 876-877
  
• Deepayan Sarkar, N. Le Meur, Robert Gentleman:
  Using flowViz to visualize flow cytometry data. 878-879
  
• Benjamin J. Bornstein, Sarah M. Keating, Akiya Jouraku, Michael Hucka:
  LibSBML: an API Library for SBML. 880-881
  

• HyungJun Cho, Yang-jin Kim, Hee Jung Jung, Sang-Won Lee, Jae Won Lee:
  OutlierD: an R package for outlier detection using quantile regression on mass spectrometry data. 882-884
  

• Erick Antezana, Mikel Egaña, Bernard De Baets, Martin Kuiper, Vladimir Mironov:
  ONTO-PERL: An API for supporting the development and analysis of bio-ontologies. 885-887
  

Volume 24, Number 7, 1 April 2008

• Hyunju Lee, Sek Won Kong, Peter J. Park:
  Integrative analysis reveals the direct and indirect interactions between DNA copy number aberrations and gene expression changes. 889-896
  

• Ketil Malde:
  The effect of sequence quality on sequence alignment. 897-900
  
• Ian M. Overton, Gianandrea Padovani, Mark A. Girolami, Geoffrey J. Barton:
  ParCrys: a Parzen window density estimation approach to protein crystallization propensity prediction. 901-907
  
• Kai Ye, Gert Vriend, Adriaan P. IJzerman:
  Tracing evolutionary pressure. 908-915
  

• Michael Stout, Jaume Bacardit, Jonathan D. Hirst, Natalio Krasnogor:
  Prediction of recursive convex hull class assignments for protein residues. 916-923
  
• Sitao Wu, Yang Zhang:
  A comprehensive assessment of sequence-based and template-based methods for protein contact prediction. 924-931
  

• Osamu Hirose, Ryo Yoshida, Seiya Imoto, Rui Yamaguchi, Tomoyuki Higuchi, Stephen D. Charnock-Jones, Cristin G. Print, Satoru Miyano:
  Statistical inference of transcriptional module-based gene networks from time course gene expression profiles by using state space models. 932-942
  
• Yuan Ji, Yiling Lu, Gordon B. Mills:
  Bayesian models based on test statistics for multiple hypothesis testing problems. 943-949
  
• Andrew W. Dowsey, Michael J. Dunn, Guang-Zhong Yang:
  Automated image alignment for 2D gel electrophoresis in a high-throughput proteomics pipeline. 950-957
  
• Joshua N. Sampson, Steven G. Self:
  Identifying trait clusters by linkage profiles: application in genetical genomics. 958-964
  

• Yu Zhang:
  Tree-guided Bayesian inference of population structures. 965-971
  
• Shu-Yi Su, David J. Balding, Lachlan J. M. Coin:
  Disease association tests by inferring ancestral haplotypes using a hidden markov model. 972-978
  

• Bing Zhang, Byung-Hoon Park, Tatiana V. Karpinets, Nagiza F. Samatova:
  From pull-down data to protein interaction networks and complexes with biological relevance. 979-986
  
• Yung-Keun Kwon, Kwang-Hyun Cho:
  Quantitative analysis of robustness and fragility in biological networks based on feedback dynamics. 987-994
  

• Juby Jacob, Marcel Jentsch, Dennis Kostka, Stefan Bentink, Rainer Spang:
  Detecting hierarchical structure in molecular characteristics of disease using transitive approximations of directed graphs. 995-1001
  

• Norio Kobayashi, Tetsuro Toyoda:
  Statistical search on the Semantic Web. 1002-1010
  

• Qing Xiong, Yuhui Qiu, Weikuan Gu:
  PGMapper: a web-based tool linking phenotype to genes. 1011-1013
  
• Weil R. Lai, Vidhu Choudhary, Peter J. Park:
  CGHweb: a tool for comparing DNA copy number segmentations from multiple algorithms. 1014-1015
  

• David He, John Parkinson:
  SubSeqer: a graph-based approach for the detection and identification of repetitive elements in low-complexity sequences. 1016-1017
  

• Liam J. Revell, Alexis S. Harrison:
  PCCA: a program for phylogenetic canonical correlation analysis. 1018-1020
  

• Anoop M. Mayampurath, Navdeep Jaitly, Samuel O. Purvine, Matthew E. Monroe, Kenneth J. Auberry, Joshua N. Adkins, Richard D. Smith:
  DeconMSn: a software tool for accurate parent ion monoisotopic mass determination for tandem mass spectra. 1021-1023
  

• Jongsun Park, Jaejin Park, Suwang Jang, Seryun Kim, Sunghyung Kong, Jaeyoung Choi, Kyohun Ahn, Juhyeon Kim, Seungmin Lee, Sunggon Kim, Bongsoo Park, Kyongyong Jung, Soonok Kim, Seogchan Kang, Yong-Hwan Lee:
  FTFD: an informatics pipeline supporting phylogenomic analysis of fungal transcription factors. 1024-1025
  
• Bongshin Lee, Kristy Brown, Yetrib Hathout, Jinwook Seo:
  GOTreePlus: an interactive gene ontology browser. 1026-1028
  

• Radhakrishnan Nagarajan, Meenakshi Upreti:
  Comment on causality and pathway search in microarray time series experiment. 1029-1032
  
• Nitai D. Mukhopadhyay, Snigdhansu Chatterjee:
  Reply to "Comment on causality and pathway search in microarray time series experiment". 1033
  

Volume 24, Number 8, 15 April 2008

• Gennady Denisov, Brian Walenz, Aaron L. Halpern, Jason R. Miller, Nelson Axelrod, Samuel Levy, Granger G. Sutton:
  Consensus generation and variant detection by Celera Assembler. 1035-1040
  
• Jan Mrázek, Shaohua Xie, Xiangxue Guo, Anuj Srivastava:
  AIMIE: a web-based environment for detection and interpretation of significant sequence motifs in prokaryotic genomes. 1041-1048
  

• Yossef Kliger, Eyal Gofer, Assaf Wool, Amir Toporik, Avihay Apatoff, Moshe Olshansky:
  Predicting proteolytic sites in extracellular proteins: only halfway there. 1049-1055
  

• Jin Xu, Xinping Cui:
  Robustified MANOVA with applications in detecting differentially expressed genes from oligonucleotide arrays. 1056-1062
  
• Matthias E. Futschik, Hanspeter Herzel:
  Are we overestimating the number of cell-cycling genes? The impact of background models on time-series analysis. 1063-1069
  
• Peicheng Du, Gustavo Stolovitzky, Peter Horvatovich, Rainer Bischoff, Jihyeon Lim, Frank Suits:
  A noise model for mass spectrometry based proteomics. 1070-1077
  

• Guido Sanguinetti, Josselin Noirel, Phillip C. Wright:
  MMG: a probabilistic tool to identify submodules of metabolic pathways. 1078-1084
  
• Pang-Kai Liu, Feng-Sheng Wang:
  Inference of biochemical network models in S-system using multiobjective optimization approach. 1085-1092
  
• Desmond J. Higham, Marija Rasajski, Natasa Przulj:
  Fitting a geometric graph to a protein-protein interaction network. 1093-1099
  

• Tony Chiang, Nianhua Li, Sandra E. Orchard, Samuel Kerrien, Henning Hermjakob, Robert Gentleman, Wolfgang Huber:
  Rintact: enabling computational analysis of molecular interaction data from the IntAct repository. 1100-1101
  
• James A. Morris, Simon A. Gayther, Ian J. Jacobs, Christopher Jones:
  A suite of Perl modules for handling microarray data. 1102-1103
  

• Wolfgang Rieping, Michael Nilges, Michael Habeck:
  ISD: a software package for Bayesian NMR structure calculation. 1104-1105
  

• Julie A. Douglas, Conner I. Sandefur:
  PedMine - a simulated annealing algorithm to identify maximally unrelated individuals in population isolates. 1106-1108
  

• Gang Liu, Sriram Neelamegham:
  In silico Biochemical Reaction Network Analysis (IBRENA): a package for simulation and analysis of reaction networks. 1109-1111
  
• David P. Nickerson, Alberto Corrias, Martin L. Buist:
  Reference descriptions of cellular electrophysiology models. 1112-1114
  

• Arek Gladki, Pawel Siedlecki, Szymon Kaczanowski, Piotr Zielenkiewicz:
  e-LiSe - an online tool for finding needles in the "(Medline) haystack". 1115-1117
  

• Anders Lanzén, Tom Oinn:
  The Taverna Interaction Service: enabling manual interaction in workflows. 1118-1120
  

Volume 24, Number 9, 1 May 2008

• Xin Chen, Lingqiong Guo, Zhaocheng Fan, Tao Jiang:
  W-AlignACE: an improved Gibbs sampling algorithm based on more accurate position weight matrices learned from sequence and gene expression/ChIP-chip data. 1121-1128
  
• Haiquan Li, Xinbin Dai, Xuechun Zhao:
  A nearest neighbor approach for automated transporter prediction and categorization from protein sequences. 1129-1136
  

• Victor I. Lesk, Michael J. E. Sternberg:
  3D-Garden: a system for modelling protein-protein complexes based on conformational refinement of ensembles generated with the marching cubes algorithm. 1137-1144
  
• Aleksandar Poleksic, Mark A. Fienup:
  Optimizing the size of the sequence profiles to increase the accuracy of protein sequence alignments generated by profile-profile algorithms. 1145-1153
  

• Andrey A. Shabalin, Håkon Tjelmeland, Cheng Fan, Charles M. Perou, Andrew B. Nobel:
  Merging two gene-expression studies via cross-platform normalization. 1154-1160
  
• Reid F. Thompson, Mark Reimers, Batbayar Khulan, Mathieu Gissot, Todd A. Richmond, Quan Chen, Xin Zheng, Kami Kim, John M. Greally:
  An analytical pipeline for genomic representations used for cytosine methylation studies. 1161-1167
  
• Meaza Demissie, Barbara Mascialino, Stefano Calza, Yudi Pawitan:
  Unequal group variances in microarray data analyses. 1168-1174
  

• Caiyan Li, Hongzhe Li:
  Network-constrained regularization and variable selection for analysis of genomic data. 1175-1182
  
• Cheng-Long Chuang, Chih-Hung Jen, Chung-Ming Chen, Grace S. Shieh:
  A pattern recognition approach to infer time-lagged genetic interactions. 1183-1190
  
• Bayu Jayawardhana, Douglas B. Kell, Magnus Rattray:
  Bayesian inference of the sites of perturbations in metabolic pathways via Markov chain Monte Carlo. 1191-1197
  

• Yuanyuan Xiao, Mark R. Segal:
  Biological sequence classification utilizing positive and unlabeled data. 1198-1205
  

• Christian X. Weichenberger, Piotr Byzia, Manfred J. Sippl:
  Visualization of unfavorable interactions in protein folds. 1206-1207
  

• Federico Abascal, Pedro Carmona-Saez, José María Carazo, Alberto D. Pascual-Montano:
  ChIPCodis: mining complex regulatory systems in yeast by concurrent enrichment analysis of chip-on-chip data. 1208-1209
  

• Angeline M. Loh, Steven Wiltshire, Jon Emery, Kim W. Carter, Lyle J. Palmer:
  Celestial3D: a novel method for 3D visualization of familial data. 1210-1211
  

• Rodrigo Santamaría, Roberto Therón, Luis Quintales:
  BicOverlapper: A tool for bicluster visualization. 1212-1213
  

• Matthew P. Campbell, Louise Royle, Catherine M. Radcliffe, Raymond A. Dwek, Pauline M. Rudd:
  GlycoBase and autoGU: tools for HPLC-based glycan analysis. 1214-1216
  
• Xiang Xu, Jinyu Wu, Jian Xiao, Yi Tan, Qiyu Bao, Fangqing Zhao, Xiaokun Li:
  PlasmoGF: an integrated system for comparative genomics and phylogenetic analysis of Plasmodium gene families. 1217-1220
  
• Hajo N. Krabbenhöft, Steffen Möller, Daniel Bayer:
  Integrating ARC grid middleware with Taverna workflows. 1221-1222
  

• Wataru Fujibuchi, Larisa Kiseleva, Takeaki Taniguchi, Hajime Harada, Paul Horton:
  CellMontage: Similar Expression Profile Search Server. 1223
  

Volume 24, Number 10, 15 May 2008

• Roger Higdon, Gerald van Belle, Eugene Kolker:
  A note on the false discovery rate and inconsistent comparisons between experiments. 1225-1228
  

• Niranjan Nagarajan, Timothy D. Read, Mihai Pop:
  Scaffolding and validation of bacterial genome assemblies using optical restriction maps. 1229-1235
  

• Rahul Satija, Lior Pachter, Jotun Hein:
  Combining statistical alignment and phylogenetic footprinting to detect regulatory elements. 1236-1242
  
• Ying Liu, Eran Eyal, Ivet Bahar:
  Analysis of correlated mutations in HIV-1 protease using spectral clustering. 1243-1250
  
• Pawel Szczesny, Andrei N. Lupas:
  Domain annotation of trimeric autotransporter adhesins - daTAA. 1251-1256
  

• Orland R. Gonzalez, Ralf Zimmer:
  Assigning functional linkages to proteins using phylogenetic profiles and continuous phenotypes. 1257-1263
  

• Theodoros Damoulas, Mark A. Girolami:
  Probabilistic multi-class multi-kernel learning: on protein fold recognition and remote homology detection. 1264-1270
  
• Yungki Park, Volkhard Helms:
  Prediction of the translocon-mediated membrane insertion free energies of protein sequences. 1271-1277
  

• Naoaki Ono, Shingo Suzuki, Chikara Furusawa, Tomoharu Agata, Akiko Kashiwagi, Hiroshi Shimizu, Tetsuya Yomo:
  An improved physico-chemical model of hybridization on high-density oligonucleotide microarrays. 1278-1285
  

• Jongrae Kim, Declan G. Bates, Ian Postlethwaite, Pat Heslop-Harrison, Kwang-Hyun Cho:
  Linear time-varying models can reveal non-linear interactions of biomolecular regulatory networks using multiple time-series data. 1286-1292
  

• Zengyou He, Can Yang, Weichuan Yu:
  Peak bagging for peptide mass fingerprinting. 1293-1299
  

• Tiziana Castrignanò, Mattia D'Antonio, Anna Anselmo, Danilo Carrabino, A. D'Onorio De Meo, Anna Maria D'Erchia, Flavio Licciulli, Marina Mangiulli, Flavio Mignone, Giulio Pavesi, Ernesto Picardi, A. Riva, Raffaella Rizzi, Paola Bonizzoni, Graziano Pesole:
  ASPicDB: A database resource for alternative splicing analysis. 1300-1304
  

• Istvan Albert, Shinichiro Wachi, Cizhong Jiang, B. Franklin Pugh:
  GeneTrack - a genomic data processing and visualization framework. 1305-1306
  

• Richard J. Edwards, Norman E. Davey, Denis C. Shields:
  CompariMotif: quick and easy comparisons of sequence motifs. 1307-1309
  

• Janosch Hennig, Klaus D. M. Hennig, Maria Sunnerhagen:
  MTMDAT: Automated analysis and visualization of mass spectrometry data for tertiary and quaternary structure probing of proteins. 1310-1312
  
• Marco Vassura, Luciano Margara, Pietro di Lena, Filippo Medri, Piero Fariselli, Rita Casadio:
  FT-COMAR: fault tolerant three-dimensional structure reconstruction from protein contact maps. 1313-1315
  

• Alistair M. Chalk, Erik L. L. Sonnhammer:
  siRNA specificity searching incorporating mismatch tolerance data. 1316-1317
  

• Sushmita Roy, Margaret Werner-Washburne, Terran Lane:
  A system for generating transcription regulatory networks with combinatorial control of transcription. 1318-1320
  

• Samuel Patient, Daniela Wieser, Michael Kleen, Ernst Kretschmann, Maria Jesus Martin, Rolf Apweiler:
  UniProtJAPI: a remote API for accessing UniProt data. 1321-1322
  

• Qing Xiong, Yuhui Qiu, Weikuan Gu:
  PGMapper: a web-based tool linking phenotype to genes. 1323
  

Volume 24, Number 11, 1 June 2008

• Sridhar Hannenhalli:
  Eukaryotic transcription factor binding sites - modeling and integrative search methods. 1325-1331
  

• Daniel Dalevi, Niklas Eriksen:
  Expected gene-order distances and model selection in bacteria. 1332-1338
  
• Marianne M. Lee, Michael K. Chan, Ralf Bundschuh:
  Simple is beautiful: a straightforward approach to improve the delineation of true and false positives in PSI-BLAST searches. 1339-1343
  

• Takashi Ishida, Kengo Kinoshita:
  Prediction of disordered regions in proteins based on the meta approach. 1344-1348
  

• Chunqi Chang, Zhi Ding, Yeung Sam Hung, Peter Chin Wan Fung:
  Fast network component analysis (FastNCA) for gene regulatory network reconstruction from microarray data. 1349-1358
  
• Anindya Bhattacharya, Rajat K. De:
  Divisive Correlation Clustering Algorithm (DCCA) for grouping of genes: detecting varying patterns in expression profiles. 1359-1366
  
• Haiyun Wang, Qi Wang, Xia Li, Bairong Shen, Min Ding, Ziyin Shen:
  Towards patterns tree of gene coexpression in eukaryotic species. 1367-1373
  

• Daniele Santoni, Marco Pedicini, Filippo Castiglione:
  Implementation of a regulatory gene network to simulate the TH1/2 differentiation in an agent-based model of hypersensitivity reactions. 1374-1380
  

• Jonathan D. Wren:
  URL decay in MEDLINE - a 4-year follow-up study. 1381-1385
  

• Michael Hackenberg, Rune Matthiesen:
  Annotation-Modules: a tool for finding significant combinations of multisource annotations for gene lists. 1386-1393
  

• William Ritchie, François-Xavier Théodule, Daniel Gautheret:
  Mireval: a web tool for simple microRNA prediction in genome sequences. 1394-1396
  

• Claus Lundegaard, Ole Lund, Morten Nielsen:
  Accurate approximation method for prediction of class I MHC affinities for peptides of length 8, 10 and 11 using prediction tools trained on 9mers. 1397-1398
  
• Frédéric Schütz, Mauro Delorenzi:
  MAMOT: hidden Markov modeling tool. 1399-1400
  

• Lixiao Wang, Uwe H. Sauer:
  OnD-CRF: predicting order and disorder in proteins conditional random fields. 1401-1402
  

• Thibaut Jombart:
  adegenet: a R package for the multivariate analysis of genetic markers. 1403-1405
  
• Gilles Guillot, Filipe Santos, Arnaud Estoup:
  Analysing georeferenced population genetics data with Geneland: a new algorithm to deal with null alleles and a friendly graphical user interface. 1406-1407
  
• Bo Peng, Christopher I. Amos:
  Forward-time simulations of non-random mating populations using simuPOP. 1408-1409
  

• Jung-jae Kim, Piotr Pezik, Dietrich Rebholz-Schuhmann:
  MedEvi: Retrieving textual evidence of relations between biomedical concepts from Medline. 1410-1412
  
• Soyang Ha, Young-Ju Seo, Min-Seok Kwon, Byung-Ha Chang, Cheol Kyu Han, Jeong Hyeok Yoon:
  IDMap: facilitating the detection of potential leads with therapeutic targets. 1413-1415
  
• Andreas Quandt, Patricia Hernandez, Alexandre Masselot, Céline Hernandez, Sergio Maffioletti, Cesare Pautasso, Ron D. Appel, Frédérique Lisacek:
  swissPIT: a novel approach for pipelined analysis of mass spectrometry data. 1416-1417
  

• Jonathan L. Lustgarten, Chad Kimmel, Henrik Ryberg, William R. Hogan:
  EPO-KB: a searchable knowledge base of biomarker to protein links. 1418-1419
  

Volume 24, Number 12, 15 June 2008

• Jacob A. Tennessen:
  Positive selection drives a correlation between non-synonymous/synonymous divergence and functional divergence. 1421-1425
  

• Rainer Malik, Erich A. Nigg, Roman Körner:
  Comparative conservation analysis of the human mitotic phosphoproteome. 1426-1432
  

• Kaname Kojima, Masao Nagasaki, Satoru Miyano:
  Fast grid layout algorithm for biological networks with sweep calculation. 1433-1441
  
• Yong Li, Pankaj Agarwal, Dilip Rajagopalan:
  A global pathway crosstalk network. 1442-1447
  

• Michael Bada, Lawrence Hunter:
  Identification of OBO nonalignments and its implications for OBO enrichment. 1448-1455
  

• Michael Y. Tolstorukov, Vidhu Choudhary, Wilma K. Olson, Victor Zhurkin, Peter J. Park:
  nuScore: a web-interface for nucleosome positioning predictions. 1456-1458
  

• Michael J. Sweredoski, Pierre Baldi:
  PEPITO: improved discontinuous B-cell epitope prediction using multiple distance thresholds and half sphere exposure. 1459-1460
  

• Korbinian Strimmer:
  fdrtool: a versatile R package for estimating local and tail area-based false discovery rates. 1461-1462
  

• Andreas Weidemann, Stefan Richter, Matthias Stein, Sven Sahle, Ralph Gauges, Razif R. Gabdoulline, Irina Surovtsova, Nils Semmelrock, Bruno Besson, Isabel Rojas, Rebecca C. Wade, Ursula Kummer:
  SYCAMORE - a systems biology computational analysis and modeling research environment. 1463-1464
  
• Maital Ashkenazi, Gary D. Bader, Allan Kuchinsky, Menachem Moshelion, David J. States:
  Cytoscape ESP: simple search of complex biological networks. 1465-1466
  
• Martin Klammer, Sanjit Roopra, Erik L. L. Sonnhammer:
  jSquid: a Java applet for graphical on-line network exploration. 1467-1468
  

• Gábor E. Tusnády, Lajos Kalmár, Hédi Hegyi, Peter Tompa, István Simon:
  TOPDOM: database of domains and motifs with conservative location in transmembrane proteins. 1469-1470
  
• Margarita C. Theodoropoulou, Pantelis G. Bagos, Ioannis C. Spyropoulos, Stavros J. Hamodrakas:
  gpDB: a database of GPCRs, G-proteins, effectors and their interactions. 1471-1472
  

Volume 24, Number 13, 1 July 2008

Proceedings 16th International Conference on Intelligent Systems for Molecular Biology (ISMB), Toronto, Canada, July 19-23, 2008. 2008
Contents

• John A. Capra, Mona Singh:
  Characterization and prediction of residues determining protein functional specificity. 1473-1480
  

• Gabriel Cardona, Mercè Llabrés, Francesc Rosselló, Gabriel Valiente:
  A distance metric for a class of tree-sibling phylogenetic networks. 1481-1488
  

• Jiangning Song, Hao Tan, Kazuhiro Takemoto, Tatsuya Akutsu:
  HSEpred: predict half-sphere exposure from protein sequences. 1489-1497
  

• István A. Bogdán, Jenny Rivers, Robert J. Beynon, Daniel Coca:
  High-performance hardware implementation of a parallel database search engine for real-time peptide mass fingerprinting. 1498-1502
  

• Bobbie-Jo M. Webb-Robertson, William R. Cannon, Christopher S. Oehmen, Anuj R. Shah, Vidhya Gurumoorthi, Mary S. Lipton, Katrina M. Waters:
  A support vector machine model for the prediction of proteotypic peptides for accurate mass and time proteomics. 1503-1509
  
• Mattia Zampieri, Nicola Soranzo, Claudio Altafini:
  Discerning static and causal interactions in genome-wide reverse engineering problems. 1510-1515
  
• Junil Kim, Tae-Geon Kim, Sung Hoon Jung, Jeong-Rae Kim, Taesung Park, Pat Heslop-Harrison, Kwang-Hyun Cho:
  Evolutionary design principles of modules that control cellular differentiation: consequences for hysteresis and multistationarity. 1516-1522
  

• Makio Tamura, Patrik D'haeseleer:
  Microbial genotype-phenotype mapping by class association rule mining. 1523-1529
  

• Kay Prüfer, Udo Stenzel, Michael Dannemann, Richard E. Green, Michael Lachmann, Janet Kelso:
  PatMaN: rapid alignment of short sequences to large databases. 1530-1531
  
• Michiel Van Bel, Yvan Saeys, Yves Van de Peer:
  FunSiP: a modular and extensible classifier for the prediction of functional sites in DNA. 1532-1533
  
• Igor B. Kuznetsov:
  ProBias: a web-server for the identification of user-specified types of compositionally biased segments in protein sequences. 1534-1535
  
• Anne-Laure Abraham, Eduardo P. C. Rocha, Joël Pothier:
  Swelfe: a detector of internal repeats in sequences and structures. 1536-1537
  

• Miklós Csürös:
  Malin: maximum likelihood analysis of intron evolution in eukaryotes. 1538-1539
  
• André Wehe, Mukul S. Bansal, J. Gordon Burleigh, Oliver Eulenstein:
  DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony. 1540-1541
  

• Scott Hazelhurst, Winston Hide, Zsuzsanna Lipták, Ramon Nogueira, Richard Starfield:
  An overview of the wcd EST clustering tool. 1542-1546
  
• Pan Du, Warren A. Kibbe, Simon M. Lin:
  lumi: a pipeline for processing Illumina microarray. 1547-1548
  
• Christian Ritz, Andrej-Nikolai Spiess:
  qpcR: an R package for sigmoidal model selection in quantitative real-time polymerase chain reaction analysis. 1549-1551
  

• Samuel Neuenschwander, Frédéric Hospital, Frédéric Guillaume, Jérôme Goudet:
  quantiNemo: an individual-based program to simulate quantitative traits with explicit genetic architecture in a dynamic metapopulation. 1552-1553
  

• Jason M. Gilmore, Deanna L. Auberry, Julia L. Sharp, Amanda M. White, Kevin K. Anderson, Don Simone Daly:
  A Bayesian estimator of protein-protein association probabilities. 1554-1555
  

• Ashoka D. Polpitiya, Wei-Jun Qian, Navdeep Jaitly, Vladislav A. Petyuk, Joshua N. Adkins, David G. Camp II, Gordon A. Anderson, Richard D. Smith:
  DAnTE: a statistical tool for quantitative analysis of -omics data. 1556-1558
  
• Curtis Huttenhower, Mark Schroeder, Maria D. Chikina, Olga G. Troyanskaya:
  The Sleipnir library for computational functional genomics. 1559-1561
  

• Lixiao Wang, Uwe H. Sauer:
  OnD-CRF: prediciting order and disorder in proteins conditional random fields. 1562
  

Volume 24, Number 14, 15 July 2008

• Andrew B. Conley, Jittima Piriyapongsa, I. King Jordan:
  Retroviral promoters in the human genome. 1563-1567
  

• Christian Martin, Naryttza N. Diaz, Jörg Ontrup, Tim W. Nattkemper:
  Hyperbolic SOM-based clustering of DNA fragment features for taxonomic visualization and classification. 1568-1574
  

• Christopher S. Miller, David Eisenberg:
  Using inferred residue contacts to distinguish between correct and incorrect protein models. 1575-1582
  

• Huaizhen Qin, Tao Feng, Scott A. Harding, Chung-Jui Tsai, Shuanglin Zhang:
  An efficient method to identify differentially expressed genes in microarray experiments. 1583-1589
  
• Kosaku Shinoda, Masaru Tomita, Yasushi Ishihama:
  Aligning LC peaks by converting gradient retention times to retention index of peptides in proteomic experiments. 1590-1595
  

• Kristin L. Ayers, Kenneth Lange:
  Penalized estimation of haplotype frequencies. 1596-1602
  
• Sophia S. F. Lee, Lei Sun, Rafal Kustra, Shelley B. Bull:
  EM-random forest and new measures of variable importance for multi-locus quantitative trait linkage analysis. 1603-1610
  

• Florian Centler, Christoph Kaleta, Pietro Speroni di Fenizio, Peter Dittrich:
  Computing chemical organizations in biological networks. 1611-1618
  
• Jiguo Cao, Hongyu Zhao:
  Estimating dynamic models for gene regulation networks. 1619-1624
  
• Magali Michaut, Samuel Kerrien, Luisa Montecchi-Palazzi, Franck Chauvat, Corinne Cassier-Chauvat, Jean-Christophe Aude, Pierre Legrain, Henning Hermjakob:
  InteroPORC: automated inference of highly conserved protein interaction networks. 1625-1631
  

• Ludger Evers, Claudia-Martina Messow:
  Sparse kernel methods for high-dimensional survival data. 1632-1638
  

• James Thurmond, Hyejin Yoon, Carla Kuiken, Karina Yusim, Simon Perkins, James Theiler, Tanmoy Bhattacharya, Bette T. Korber, Will Fischer:
  Web-based design and evaluation of T-cell vaccine candidates. 1639-1640
  

• Gregory E. Jordan, William H. Piel:
  PhyloWidget: web-based visualizations for the tree of life. 1641-1642
  

• Carlos Morcillo-Suarez, Josep Alegre, Ricardo Sangros, Elodie Gazave, Rafael de Cid, Roger Milne, Jorge Amigo, Anna Ferrer-Admetlla, Andrés Moreno-Estrada, Michelle Gardner, Ferran Casals, Anna Pérez-Lezaun, David Comas, Elena Bosch, Francesc Calafell, Jaume Bertranpetit, Arcadi Navarro:
  SNP analysis to results (SNPator): a web-based environment oriented to statistical genomics analyses upon SNP data. 1643-1644
  
• Mamoru Kato, Yusuke Nakamura, Tatsuhiko Tsunoda:
  MOCSphaser: a haplotype inference tool from a mixture of copy number variation and single nucleotide polymorphism data. 1645-1646
  

• Ahmet Sacan, Hakan Ferhatosmanoglu, Huseyin Coskun:
  CellTrack: an open-source software for cell tracking and motility analysis. 1647-1649
  

• Sebastian Bauer, Steffen Grossmann, Martin Vingron, Peter N. Robinson:
  Ontologizer 2.0 - a multifunctional tool for GO term enrichment analysis and data exploration. 1650-1651
  

• Mark R. Segal:
  On E-values for tandem MS scoring schemes. 1652-1653
  

• Jainab Khatun, Morgan C. Giddings:
  In response to "On E-value for tandem MS scoring schemes". 1654
  

Volume 24, Number 15, 1 August 2008

• Shuo Jiao, Shunpu Zhang:
  On correcting the overestimation of the permutation-based false discovery rate estimator. 1655-1661
  

• Håkan Viklund, Arne Elofsson:
  OCTOPUS: improving topology prediction by two-track ANN-based preference scores and an extended topological grammar. 1662-1668
  
• Kyoung-Jae Won, Albin Sandelin, Troels Torben Marstrand, Anders Krogh:
  Modeling promoter grammars with evolving hidden Markov models. 1669-1675
  
• Tiago José P. Sobreira, Arthur Gruber:
  Sequence-specific reconstruction from fragmentary databases using seed sequences: implementation and validation on SAGE, proteome and generic sequencing data. 1676-1680
  
• Kristoffer Forslund, Erik L. L. Sonnhammer:
  Predicting protein function from domain content. 1681-1687
  

• Reinhard Schachtner, Dominik Lutter, P. Knollmüller, Ana Maria Tomé, Fabian J. Theis, Gerd Schmitz, Martin Stetter, Pedro Gómez Vilda, Elmar Wolfgang Lang:
  Knowledge-based gene expression classification via matrix factorization. 1688-1697
  
• Anne-Laure Boulesteix, Christine Porzelius, Martin Daumer:
  Microarray-based classification and clinical predictors: on combined classifiers and additional predictive value. 1698-1706
  
• E. Purdom, Ken M. Simpson, Mark D. Robinson, J. G. Conboy, A. V. Lapuk, Terence P. Speed:
  FIRMA: a method for detection of alternative splicing from exon array data. 1707-1714
  

• Francesco Pappalardo, Salvatore Musumeci, Santo Motta:
  Modeling immune system control of atherogenesis. 1715-1721
  

• Derek Greene, Gerard Cagney, Nevan J. Krogan, Padraig Cunningham:
  Ensemble non-negative matrix factorization methods for clustering protein-protein interactions. 1722-1728
  

• Anthony P. Fejes, Gordon Robertson, Mikhail Bilenky, Richard Varhol, Matthew N. Bainbridge, Steven J. M. Jones:
  FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology. 1729-1730
  

• Josep Ramon Goñi, Carlos Fenollosa, Alberto Pérez, David Torrents, Modesto Orozco:
  DNAlive: a tool for the physical analysis of DNA at the genomic scale. 1731-1732
  
• Yiqun Cao, Anna Charisi, Li-Chang Cheng, Tao Jiang, Thomas Girke:
  ChemmineR: a compound mining framework for R. 1733-1734
  

• Carl Murie, Robert Nadon:
  A correction for estimating error when using the Local Pooled Error Statistical Test. 1735-1736
  

• Meizhuo Zhang, Rui Feng, Xiang Chen, Buqu Hu, Heping Zhang:
  LOT: a tool for linkage analysis of ordinal traits for pedigree data. 1737-1739
  

• Marzio Pennisi, Roberto Catanuto, Francesco Pappalardo, Santo Motta:
  Optimal vaccination schedules using simulated annealing. 1740-1742
  

• Johannes Goll, Seesandra V. Rajagopala, Shen C. Shiau, Hank Wu, Brian T. Lamb, Peter Uetz:
  MPIDB: the microbial protein interaction database. 1743-1744
  

Volume 24, Number 16, 15 August 2008

ECCB'08 Proceedings, Seventh European Conference on Computational Biology, 22-26 September 2008, Cagliari, Italy. 2008
Contents

• Meng Li, Hyun-il Henry Paik, Curtis Balch, Yoosung Kim, Lang Li, Tim Hui-Ming Huang, Kenneth P. Nephew, Sun Kim:
  Enriched transcription factor binding sites in hypermethylated gene promoters in drug resistant cancer cells. 1745-1748
  

• Hung-I Harry Chen, Fang-Han Hsu, Yuan Jiang, Mong-Hsun Tsai, Pan-Chyr Yang, Paul S. Meltzer, Eric Y. Chuang, Yidong Chen:
  A probe-density-based analysis method for array CGH data: simulation, normalization and centralization. 1749-1756
  
• Aleksandr Morgulis, George Coulouris, Yan Raytselis, Thomas L. Madden, Richa Agarwala, Alejandro A. Schäffer:
  Database indexing for production MegaBLAST searches. 1757-1764
  

• Duncan P. Brown:
  Efficient functional clustering of protein sequences using the Dirichlet process. 1765-1771
  
• Lee Aaron Newberg:
  Memory-efficient dynamic programming backtrace and pairwise local sequence alignment. 1772-1778
  
• Aalt D. J. van Dijk, D. Bosch, Cajo J. F. ter Braak, A. R. van der Krol, Roeland C. H. J. van Ham:
  Predicting sub-Golgi localization of type II membrane proteins. 1779-1786
  
• Ali Torkamani, Nicholas J. Schork:
  Predicting functional regulatory polymorphisms. 1787-1792
  
• Daniel J. Rigden, Michael Y. Galperin:
  Sequence analysis of GerM and SpoVS, uncharacterized bacterial "sporulation" proteins with widespread phylogenetic distribution. 1793-1797
  

• Liam J. McGuffin:
  Intrinsic disorder prediction from the analysis of multiple protein fold recognition models. 1798-1804
  

• Scott F. Saccone, Nancy L. Saccone, Gary E. Swan, Pamela A. F. Madden, Alison M. Goate, John P. Rice, Laura J. Bierut:
  Systematic biological prioritization after a genome-wide association study: an application to nicotine dependence. 1805-1811
  

• Jung Hun Oh, Young Bun Kim, Prem Gurnani, Kevin P. Rosenblatt, Jean X. Gao:
  Biomarker selection and sample prediction for multi-category disease on MALDI-TOF data. 1812-1818
  

• Yungki Park, Volkhard Helms:
  MINS2: Revisiting the molecular code for transmembrane-helix recognition by the Sec61 translocon. 1819-1820
  

• Brian W. Lambert, Joseph D. Terwilliger, Kenneth M. Weiss:
  ForSim: a tool for exploring the genetic architecture of complex traits with controlled truth. 1821-1822
  

• Olivier Filangi, Yoann Beausse, Anthony Assi, Ludovic Legrand, Jean-Marc Larré, Véronique Martin, Olivier Collin, Christophe Caron, Hugues Leroy, David Allouche:
  BioMAJ: a flexible framework for databanks synchronization and processing. 1823-1825
  

Volume 24, Number 17, 1 September 2008

• Hanchuan Peng:
  Bioimage informatics: a new area of engineering biology. 1827-1836
  

• Gyan Prakash Srivastava, Juyuan Guo, Huidong Shi, Dong Xu:
  PRIMEGENS-v2: genome-wide primer design for analyzing DNA methylation patterns of CpG islands. 1837-1842
  
• Jie Wu, Douglas H. Sieglaff, Joshua Gervin, Xiaohui S. Xie:
  Discovering regulatory motifs in the Plasmodium genome using comparative genomics. 1843-1849
  

• Jiajian Liu, Gary D. Stormo:
  Context-dependent DNA recognition code for C₂H₂ zinc-finger transcription factors. 1850-1857
  
• James Lara, Robert M. Wohlhueter, Zoya Dimitrova, Yuri Khudyakov:
  Artificial neural network for prediction of antigenic activity for a major conformational epitope in the hepatitis C virus NS3 protein. 1858-1864
  

• David W. Ritchie, Dima Kozakov, Sandor Vajda:
  Accelerating and focusing protein-protein docking correlations using multi-dimensional rotational FFT generating functions. 1865-1873
  

• Huai Li, Ming Zhan:
  Unraveling transcriptional regulatory programs by integrative analysis of microarray and transcription factor binding data. 1874-1880
  
• Shuiwang Ji, Liang Sun, Rong Jin, Sudhir Kumar, Jieping Ye:
  Automated annotation of Drosophila gene expression patterns using a controlled vocabulary. 1881-1888
  
• Blaise Hanczar, Edward R. Dougherty:
  Classification with reject option in gene expression data. 1889-1895
  

• Nils Homer, Waibhav Tembe, Szabolcs Szelinger, Margot Redman, Dietrich A. Stephan, John V. Pearson, Stanley F. Nelson, David W. Craig:
  Multimarker analysis and imputation of multiple platform pooling-based genome-wide association studies. 1896-1902
  

• M. A. Marchisio, Jörg Stelling:
  Computational design of synthetic gene circuits with composable parts. 1903-1910
  
• Heng Lian, William A. Thompson, Robert Thurman, John A. Stamatoyannopoulos, William Stafford Noble, Charles E. Lawrence:
  Automated mapping of large-scale chromatin structure in ENCODE. 1911-1916
  
• Abhishek Garg, Alessandro Di Cara, Ioannis Xenarios, Luis Mendoza, Giovanni De Micheli:
  Synchronous versus asynchronous modeling of gene regulatory networks. 1917-1925
  
• Yung-Keun Kwon, Kwang-Hyun Cho:
  Coherent coupling of feedback loops: a design principle of cell signaling networks. 1926-1932
  
• Vladislav Vyshemirsky, Mark Girolami:
  BioBayes: A software package for Bayesian inference in systems biology. 1933-1934
  

• Theodosios Theodosiou, Nikos Darzentas, Lefteris Angelis, Christos A. Ouzounis:
  PuReD-MCL: a graph-based PubMed document clustering methodology. 1935-1941
  
• Han Zhang, Hsin-Chou Yang, Yaning Yang:
  PoooL: an efficient method for estimating haplotype frequencies from large DNA pools. 1942-1948
  

• Art F. Y. Poon, Fraser I. Lewis, Simon D. W. Frost, Sergei L. Kosakovsky Pond:
  Spidermonkey: rapid detection of co-evolving sites using Bayesian graphical models. 1949-1950
  

• Shantanu Sharma, Feng Ding, Nikolay V. Dokholyan:
  iFoldRNA: three-dimensional RNA structure prediction and folding. 1951-1952
  
• Paolo Marcatili, Alessandra Rosi, Anna Tramontano:
  PIGS: automatic prediction of antibody structures. 1953-1954
  
• Martin Prokop, Jan Adam, Zdenek Kríz, Michaela Wimmerová, Jaroslav Koca:
  TRITON: a graphical tool for ligand-binding protein engineering. 1955-1956
  

• Tae-Min Kim, Seon-Hee Yim, Yong-Bok Jeong, Yu-Chae Jung, Yeun-Jun Chung:
  PathCluster: a framework for gene set-based hierarchical clustering. 1957-1958
  
• Eoghan D. Harrington, Peer Bork:
  Sircah: a tool for the detection and visualization of alternative transcripts. 1959-1960
  

• Dominik Heider, Daniel Kessler, Angelika Barnekow:
  Watermarking sexually reproducing diploid organisms. 1961-1962
  

• Frank T. Bergmann, Herbert M. Sauro:
  Comparing simulation results of SBML capable simulators. 1963-1965
  
• Garrett M. Dancik, Karin S. Dorman:
  mlegp: statistical analysis for computer models of biological systems using R. 1966-1967
  

• Songhua Xu, James P. McCusker, Michael Krauthammer:
  Yale Image Finder (YIF): a new search engine for retrieving biomedical images. 1968-1970
  

• Jung-Wei Fan, Carol Friedman:
  Semantic reclassification of the UMLS concepts. 1971-1973
  

Volume 24, Number 18, 15 September 2008

• Krishna R. Kalari, Thomas L. Casavant, Todd E. Scheetz:
  A knowledge-based approach to predict intragenic deletions or duplications. 1975-1979
  
• Matthew N. Davies, Andrew Secker, Alex Alves Freitas, Edward Clark, Jonathan Timmis, Darren R. Flower:
  Optimizing amino acid groupings for GPCR classification. 1980-1986
  
• Dariusz Przybylski, Burkhard Rost:
  Powerful fusion: PSI-BLAST and consensus sequences. 1987-1993
  

• Xiang Chen, Simin He, Dongbo Bu, Fa Zhang, Zhiyong Wang, Runsheng Chen, Wen Gao:
  FlexStem: improving predictions of RNA secondary structures with pseudoknots by reducing the search space. 1994-2001
  
• Majid Masso, Iosif I. Vaisman:
  Accurate prediction of stability changes in protein mutants by combining machine learning with structure based computational mutagenesis. 2002-2009
  

• Dhammika Amaratunga, Javier Cabrera, Yung-Seop Lee:
  Enriched random forests. 2010-2014
  
• Liang Chen, Tiejun Tong, Hongyu Zhao:
  Considering dependence among genes and markers for false discovery control in eQTL mapping. 2015-2022
  
• TaeHyun Hwang, Hugues Sicotte, Ze Tian, Baolin Wu, Jean-Pierre Kocher, Dennis A. Wigle, Vipin Kumar, Rui Kuang:
  Robust and efficient identification of biomarkers by classifying features on graphs. 2023-2029
  

• Ioanna Tachmazidou, Toby Andrew, Claudio J. Verzilli, Michael R. Johnson, Maria De Iorio:
  Bayesian survival analysis in genetic association studies. 2030-2036
  

• Thomas Maiwald, Jens Timmer:
  Dynamical modeling and multi-experiment fitting with PottersWheel. 2037-2043
  
• Markus W. Covert, Nan Xiao, Tiffany J. Chen, Jonathan R. Karr:
  Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli. 2044-2050
  
• Viviane Galvão, José Garcia Vivas Miranda, Ricardo Ribeiro-dos-Santos:
  Development of a two-dimensional agent-based model for chronic chagasic cardiomyopathy after stem cell transplantation. 2051-2056
  
• Min Zhang, Chen Yao, Zheng Guo, Jinfeng Zou, Lin Zhang, Hui Xiao, Dong Wang, Da Yang, Xue Gong, Jing Zhu, Yanhui Li, Xia Li:
  Apparently low reproducibility of true differential expression discoveries in microarray studies. 2057-2063
  
• Mudassar Iqbal, Alex Alves Freitas, Colin G. Johnson, Massimo Vergassola:
  Message-passing algorithms for the prediction of protein domain interactions from protein-protein interaction data. 2064-2070
  
• Marco Grzegorczyk, Dirk Husmeier, Kieron D. Edwards, Peter Ghazal, Andrew J. Millar:
  Modelling non-stationary gene regulatory processes with a non-homogeneous Bayesian network and the allocation sampler. 2071-2078