Bioinformatics, Volume 24

Volume 24, Number 1, 1 January 2008

Genome Analysis

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

Genome Analysis

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

Sequence Analysis

• 
  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, Richard G. H. Immink, Gerco 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

Phylogenetics

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

Structural Bioinformatics

• 
  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

Gene Expression

• 
  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

Genetics and Population Analysis

• 
  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

Systems Biology

• 
  Meng Wang, Xiaobo Zhou, Fuhai Li, Jeremy F. 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

Data and Text Mining

• 
  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

Genome Analysis

• 
  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

Phylogenetics

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

Gene Expression

• 
  James Long, Mitchell Roth:
  Synthetic microarray data generation with RANGE and NEMO. 132-134
• 
  Nicola Lama, Mark A. 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

Genetics and Population Analysis

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

Data and Text Mining

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

Database and Ontologies

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

Erratum

• 
  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

Genome Analysis

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

Sequence Analysis

• 
  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

Gene Expression

• 
  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

Systems Biology

• 
  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

Data and Text Mining

• 
  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

Databases and Ontologies

• 
  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

Structural Bioinformatics

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

Gene Expression

• 
  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

Genetics and Population Analysis

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

Systems Biology

• 
  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

Data and Text Mining

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

Databases and Ontologies

• 
  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

Sequence Analysis

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

Genome Analysis

• 
  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

Sequence Analysis

• 
  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, Lindi 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

Structural Bioinformatics

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

Gene Expression

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

Genetics and Population Analysis

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

Systems Biology

• 
  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

Data and Text Mining

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

Genome Analysis

• 
  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

Structural Bioinformatics

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

Gene Expression

• 
  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

Genetics and Population Analysis

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

Systems Biology

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

Databases and Ontologies

• 
  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

Sequence Analysis

• 
  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

Genome Analysis

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

Sequence Analysis

• 
  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

Structural Bioinformatics

• 
  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

Gene Expression

• 
  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

Systems Biology

• 
  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

Data and Text Mining

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

Genome Analysis

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

Sequence Analysis

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

Phylogenetics

• 
  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

Structural Bioinformatics

• 
  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

Gene Expression

• 
  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

Systems Biology

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

Volume 24, Number 5, 1 March 2008

Genome Analysis

• 
  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

Sequence Analysis

• 
  J. D. Fischer, Christian 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

Structural Bioinformatics

• 
  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

Gene Expression

• 
  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

Systems Biology

• 
  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

Genome Analysis

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

Sequence Analysis

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

Phylogenetics

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

Gene Expression

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

Genetics and Population Analysis

• 
  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

Data and Text Mining

• 
  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

Databases and Ontologies

• 
  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

Discovery Note: Systems Biology

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

Original Papers: Genome Analysis

• 
  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 S. 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

Sequence Analysis

• 
  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

Phylogenetics

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

Systems Biology

• 
  Vladislav Vyshemirsky, Mark A. 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

Data and Text Mining

• 
  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

Applications Notes: Genome Analysis

• 
  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

Sequence Analysis

• 
  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

Phylogenetics

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

Structural Bioinformatics

• 
  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

Gene Expression

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

Systems Biology

• 
  Andrei Yu. Zinovyev, Eric Viara, Laurence Calzone, Emmanuel Barillot:
  BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks. 876-877
• 
  Deepayan Sarkar, Nolwenn 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

Data and Text Mining

• 
  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

Database and Ontologies

• 
  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

Original Papers: Genome Analysis

• 
  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

Sequence Analysis

• 
  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

Structural Bioinformatics

• 
  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

Gene Expression

• 
  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

Genetics and Population Analysis

• 
  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

Systems Biology

• 
  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

Data and Text Mining

• 
  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

Databases and Ontologies

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

Applications Notes: Genome Analysis

• 
  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

Sequence Analysis

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

Phylogenetics

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

Data and Text Mining

• 
  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

Databases and Ontologies

• 
  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

Letters to the Editor: Gene Expression

• 
  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

Original Papers: Genome Analysis:

• 
  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

Sequence Analysis

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

Gene Expression

• 
  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

Systems Biology

• 
  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

Applications Notes: Genome Analysis

• 
  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

Structural Bioinformatics

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

Genetics and Population Analysis

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

Systems Biology

• 
  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

Data and Text Mining

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

Databases and Ontologies

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

Volume 24, Number 9, 1 May 2008

Sequence Analysis

• 
  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

Structural Bioinformatics

• 
  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

Gene Expression

• 
  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

Systems Biology

• 
  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

Data and Text Mining

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

Applications Notes: Structural Bioinformatics

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

Gene Expression

• 
  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

Genetics and Population Analysis

• 
  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

Data and Text Mining

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

Databases and Ontologies

• 
  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

Corrigendum

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

Volume 24, Number 10, 15 May 2008

Discovery Note: Data and Text Mining

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

Original Papers: Genome Analysis

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

Sequence Analysis

• 
  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

Phylogenetics

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

Structural Bioinformatics

• 
  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

Gene Expression

• 
  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

Systems Biology

• 
  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

Data and Text Mining

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

Databases and Ontologies

• 
  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, Alberto Riva, Raffaella Rizzi, Paola Bonizzoni, Graziano Pesole:
  ASPicDB: A database resource for alternative splicing analysis. 1300-1304

Applications Notes: Genome Analysis

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

Sequence Analysis

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

Structural Bioinformatics

• 
  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

Gene Expression

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

Systems Biology

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

Databases and Ontologies

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

Corrigendum

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

Volume 24, Number 11, 1 June 2008

Review: Gene Expression

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

Original Papers: Sequence Analysis

• 
  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

Structural Bioinformatics

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

Gene Expression

• 
  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

Systems Biology

• 
  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

Data and Text Mining

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

Databases and Ontologies

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

Applications Notes: Genome Analysis

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

Sequence Analysis

• 
  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

Structural Bioinformatics

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

Genetics and Population Analysis

• 
  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

Data and Text Mining

• 
  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

Databases and Ontologies

• 
  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

Discovery Note: Sequence Analysis

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

Original Papers: Sequence Analysis

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

Systems Biology

• 
  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

Databases and Ontologies

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

Applications Notes: Sequence Analysis

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

Structural Bioinformatics

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

Gene Expression

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

Systems Biology

• 
  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

Databases and Ontologies

• 
  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

Sequence Analysis

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

Phylogenetics

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

Structural Bioinformatics

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

Gene Expression

• 
  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

Systems Biology

• 
  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

Data and Text Mining

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

Applications Note - Sequence Analysis

• 
  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

Phylogenetics

• 
  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

Gene Expression

• 
  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

Genetics and Population Analysis

• 
  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

Systems Biology

• 
  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

Data and Text Mining

• 
  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

Erratum

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

Volume 24, Number 14, 15 July 2008

Genome Analysis

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

Sequence Analysis

• 
  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

Structural Bioinformatics

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

Gene Expression

• 
  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

Genetics and Population Analysis

• 
  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

Systems Biology

• 
  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

Data and Text Mining

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

Sequence Analysis

• 
  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

Phylogenetics

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

Genetics and Population Analysis

• 
  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

Systems Biology

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

Databases and Ontologies

• 
  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

Systems Biology

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

Gene Expression

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

Volume 24, Number 15, 1 August 2008

Genome Analysis

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

Sequence Analysis

• 
  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

Gene Expression

• 
  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

Systems Biology

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

Data and Text Mining

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

Genome Analysis

• 
  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

Structural Bioinformatics

• 
  Josep Ramón 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

Gene Expression

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

Genetics and Population Analysis

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

Systems Biology

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

Databases and Ontologies

• 
  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

Discovery Note: Genome Analysis

• 
  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

Original Papers: Genome Analysis

• 
  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

Sequence Analysis

• 
  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

Structural Bioinformatics

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

Genetics and Population Analysis

• 
  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

Data and Text Mining

• 
  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

Applications Note: Structural Bioinformatics

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

Genetics and Population Analysis

• 
  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

Databases and Ontologies

• 
  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

Review Paper: Data and Text Mining

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

Original Papers: Genome Analysis

• 
  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

Sequence Analysis

• 
  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

Structural Bioinformatics

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

Gene Expression

• 
  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

Genetics and Population Analysis

• 
  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

Systems Biology

• 
  Mario A. Marchisio, Jörg Stelling:
  Computational design of synthetic gene circuits with composable parts. 1903-1910
• 
  Heng Lian, William A. Thompson, Robert E. 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 A. Girolami:
  BioBayes: A software package for Bayesian inference in systems biology. 1933-1934

Data and Text Mining

• 
  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

Applications Note: Sequence Analysis

• 
  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

Structural Bioinformatics

• 
  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

Gene Expression

• 
  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

Genetics and Population Analysis

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

Systems Biology

• 
  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

Data and Text Mining

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

Databases and Ontologies

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

Volume 24, Number 18, 15 September 2008

Original Papers - Sequence Analysis

• 
  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

Structural Bioinformatics

• 
  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

Gene Expression

• 
  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 A. Kocher, Dennis A. Wigle, Vipin Kumar, Rui Kuang:
  Robust and efficient identification of biomarkers by classifying features on graphs. 2023-2029

Genetics and Population Analysis

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

Systems Biology

• 
  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

Data and Text Mining

• 
  Kathrin Fenner, Junfeng Gao, Stefan Kramer, Lynda B. M. Ellis, Lawrence P. Wackett:
  Data-driven extraction of relative reasoning rules to limit combinatorial explosion in biodegradation pathway prediction. 2079-2085
• 
  Hagit Shatkay, Fengxia Pan, Andrey Rzhetsky, W. John Wilbur:
  Multi-dimensional classification of biomedical text: Toward automated, practical provision of high-utility text to diverse users. 2086-2093

Applications Note- Sequence Analysis

• 
  Marco Lippi, Andrea Passerini, Marco Punta, Burkhard Rost, Paolo Frasconi:
  MetalDetector: a web server for predicting metal-binding sites and disulfide bridges in proteins from sequence. 2094-2095
• 
  Richard C. G. Holland, Thomas A. Down, Matthew R. Pocock, Andreas Prlic, David S. Huen, Keith James, Sylvain Foisy, Andreas Dräger, Andy Yates, Michael L. Heuer, Mark J. Schreiber:
  BioJava: an open-source framework for bioinformatics. 2096-2097

Phylogenetics

• 
  Campbell O. Webb, David D. Ackerly, Steven W. Kembel:
  Phylocom: software for the analysis of phylogenetic community structure and trait evolution. 2098-2100

Structural Bioinformatics

• 
  Romain Gautier, Dominique Douguet, Bruno Antonny, Guillaume Drin:
  HELIQUEST: a web server to screen sequences with specific alpha-helical properties. 2101-2102

Gene Expression

• 
  William D. Nelson, Kert Viele, Bert C. Lynn:
  An integrated approach for automating validation of extracted ion chromatographic peaks. 2103-2104

Genetics and Population Analysis

• 
  Ryan Abo, Stacey Knight, Jathine Wong, Angela Cox, Nicola J. Camp:
  hapConstructor: automatic construction and testing of haplotypes in a Monte Carlo framework. 2105-2107

Systems Biology

• 
  Torsten Blum, Oliver Kohlbacher:
  MetaRoute: fast search for relevant metabolic routes for interactive network navigation and visualization. 2108-2109
• 
  Hector Ramos, P. Shannon, Ruedi Aebersold:
  The protein information and property explorer: an easy-to-use, rich-client web application for the management and functional analysis of proteomic data. 2110-2111
• 
  Robert Kincaid, Allan Kuchinsky, Michael L. Creech:
  VistaClara: an expression browser plug-in for Cytoscape. 2112-2114
• 
  Jan Krumsiek, Caroline C. Friedel, Ralf Zimmer:
  ProCope - protein complex prediction and evaluation. 2115-2116
• 
  Bing Xiong, Ke Liu, Jie Wu, David L. Burk, Hualiang Jiang, Jingkang Shen:
  DrugViz: a Cytoscape plugin for visualizing and analyzing small molecule drugs in biological networks. 2117-2118

Databases and Ontologies

• 
  Rafael C. Jiménez, Antony F. Quinn, Alexander García Castro, Alberto Labarga, Kieran O'Neill, Fernando Martinez, Gustavo A. Salazar, Henning Hermjakob:
  Dasty2, an Ajax protein DAS client. 2119-2121
• 
  Catherine M. Lloyd, James R. Lawson, Peter J. Hunter, Poul M. F. Nielsen:
  The CellML Model Repository. 2122-2123

Letter to the Editor- Genome Analysis

• 
  Miguel Pignatelli, Gabriel Aparício, Ignacio Blanquer, Vicente Hernández, Andrés Moya, Javier Tamames:
  Metagenomics reveals our incomplete knowledge of global diversity. 2124-2125

Volume 24, Number 19, 1 October 2008

Editorial

• 
  Jonathan D. Wren, Alex Bateman:
  Databases, data tombs and dust in the wind. 2127-2128

Original Papers - Genome Analysis

• 
  Alejandro Cruz-Marcelo, Rudy Guerra, Marina Vannucci, Yiting Li, Ching C. Lau, Tsz-Kwong Man:
  Comparison of algorithms for pre-processing of SELDI-TOF mass spectrometry data. 2129-2136
• 
  Holger Fröhlich, Mark Fellmann, Holger Sültmann, Annemarie Poustka, Tim Beißbarth:
  Predicting pathway membership via domain signatures. 2137-2142
• 
  Chandra Erdman, John W. Emerson:
  A fast Bayesian change point analysis for the segmentation of microarray data. 2143-2148
• 
  Laurent Jacob, Jean-Philippe Vert:
  Protein-ligand interaction prediction: an improved chemogenomics approach. 2149-2156

Sequence Analysis

• 
  Martin Peifer, John E. Karro, H. H. von Grünberg:
  Is there an acceleration of the CpG transition rate during the mammalian radiation? 2157-2164
• 
  Virpi Ahola, Tero Aittokallio, Mauno Vihinen, Esa Uusipaikka:
  Model-based prediction of sequence alignment quality. 2165-2171
• 
  Karl Frank, Manfred J. Sippl:
  High-performance signal peptide prediction based on sequence alignment techniques. 2172-2176

Phylogenetics

• 
  Andrew D. Fernandes, William R. Atchley:
  Site-specific evolutionary rates in proteins are better modeled as non-independent and strictly relative. 2177-2183

Structural Bioinformatics

• 
  Michael Hirsch, Michael Habeck:
  Mixture models for protein structure ensembles. 2184-2192

Gene Expression

• 
  Jianhua Hu:
  Cancer outlier detection based on likelihood ratio test. 2193-2199
• 
  Benjamin Haibe-Kains, Christine Desmedt, Christos P. Sotiriou, Gianluca Bontempi:
  A comparative study of survival models for breast cancer prognostication based on microarray data: does a single gene beat them all? 2200-2208

Genetics and Population Analysis

• 
  Eleni Giannoulatou, Christopher Yau, Stefano Colella, Jiannis Ragoussis, Christopher C. Holmes:
  GenoSNP: a variational Bayes within-sample SNP genotyping algorithm that does not require a reference population. 2209-2214
• 
  Zhihong Ding, Thomas Mailund, Yun S. Song:
  Efficient whole-genome association mapping using local phylogenies for unphased genotype data. 2215-2221
• 
  Gilles Guillot:
  Inference of structure in subdivided populations at low levels of genetic differentiation - the correlated allele frequencies model revisited. 2222-2228

Systems Biology

• 
  Marco Terzer, Jörg Stelling:
  Large-scale computation of elementary flux modes with bit pattern trees. 2229-2235
• 
  Diogo A. R. S. Latino, Qing-You Zhang, João Aires-de-Sousa:
  Genome-scale classification of metabolic reactions and assignment of EC numbers with self-organizing maps. 2236-2244
• 
  Albert Gevorgyan, Mark G. Poolman, David A. Fell:
  Detection of stoichiometric inconsistencies in biomolecular models. 2245-2251

Applications Note - Genome Analysis

• 
  Simon Moxon, Frank Schwach, Tamas Dalmay, Daniel MacLean, David J. Studholme, Vincent Moulton:
  A toolkit for analysing large-scale plant small RNA datasets. 2252-2253

Sequence Analysis

• 
  Wencheng Li, Bo Yang, Shaoguang Liang, Yonghua Wang, Chris Whiteley, Yicheng Cao, Xiaoning Wang:
  BLogo: a tool for visualization of bias in biological sequences. 2254-2255
• 
  Patrick Ng, Uri Keich:
  GIMSAN: a Gibbs motif finder with significance analysis. 2256-2257

Structural Bioinformatics

• 
  Doroteya K. Staykova, Jonas Fredriksson, Martin Billeter:
  PRODECOMPv3: decompositions of NMR projections for protein backbone and side-chain assignments and structural studies. 2258-2259

Gene Expression

• 
  Lin S. Chen, John D. Storey:
  Eigen-R² for dissecting variation in high-dimensional studies. 2260-2262
• 
  Ananyo Choudhury, Ansuman Lahiri:
  Arabidopsis thaliana regulatory element analyzer. 2263-2264

Systems Biology

• 
  Faruck Morcos, Charles Lamanna, Marcin Sikora, Jesús A. Izaguirre:
  Cytoprophet: a Cytoscape plug-in for protein and domain interaction networks inference. 2265-2266

Data and Text Mining

• 
  Anastasia Alexandridou, George T. Tsangaris, Konstantinos N. Vougas, Konstantina S. Nikita, George M. Spyrou:
  Peptide Finder: mapping measured molecular masses to peptides and proteins. 2267-2269

Databases and Ontologies

• 
  Tiago L. Moda, Leonardo G. Torres, Alexandre E. Carrara, Adriano D. Andricopulo:
  PK/DB: database for pharmacokinetic properties and predictive in silico ADME models. 2270-2271
• 
  Gabriel F. Berriz, Frederick P. Roth:
  The Synergizer service for translating gene, protein and other biological identifiers. 2272-2273

Corrigenda

• 
  Sofia Wichert, Konstantinos Fokianos, Korbinian Strimmer:
  Identifying periodically expressed transcripts in microarray time series data. 2274
• 
  Kristoffer Forslund, Erik L. L. Sonnhammer:
  Predicting protein function from domain content. 2275

Erratum

• 
  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. 2276

Volume 24, Number 20, 15 October 2008

Discovery Note - Sequence Analysis

• 
  Antonina Andreeva, Henning Tidow:
  A novel CHHC Zn-finger domain found in spliceosomal proteins and tRNA modifying enzymes. 2277-2280

Original Papers - Genome Analysis

• 
  Zhibin Huang, Yong Wu, Joseph Robertson, Liang Feng, Russell L. Malmberg, Liming Cai:
  Fast and accurate search for non-coding RNA pseudoknot structures in genomes. 2281-2287

Sequence Analysis

• 
  Edward Wijaya, Siu-Ming Yiu, Ngo Thanh Son, Kanagasabai Rajaraman, Wing-Kin Sung:
  MotifVoter: a novel ensemble method for fine-grained integration of generic motif finders. 2288-2295
• 
  Qi Dai, Yanchun Yang, Tian-Ming Wang:
  Markov model plus k-word distributions: a synergy that produces novel statistical measures for sequence comparison. 2296-2302
• 
  François Fauteux, Mathieu Blanchette, Martina V. Stromvik:
  Seeder: discriminative seeding DNA motif discovery. 2303-2307
• 
  K. C. Dukka Bahadur, Dennis R. Livesay:
  Improving position-specific predictions of protein functional sites using phylogenetic motifs. 2308-2316

Phylogenetics

• 
  Si Quang Le, Olivier Gascuel, Nicolas Lartillot:
  Empirical profile mixture models for phylogenetic reconstruction. 2317-2323

Structural Bioinformatics

• 
  Vinay Pulim, Bonnie Berger, Jadwiga R. Bienkowska:
  Optimal contact map alignment of protein-protein interfaces. 2324-2328
• 
  Tuo Zhang, Hua Zhang, Ke Chen, Shiyi Shen, Jishou Ruan, Lukasz A. Kurgan:
  Accurate sequence-based prediction of catalytic residues. 2329-2338
• 
  Ryan M. Bannen, Vanitha Suresh, George N. Phillips Jr., Stephen J. Wright, Julie C. Mitchell:
  Optimal design of thermally stable proteins. 2339-2343

Gene Expression

• 
  Han Xu, Chia-Lin Wei, Feng Lin, Wing-Kin Sung:
  An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data. 2344-2349

Genetics and Population Analysis

• 
  Iuliana Ionita-Laza, Nan M. Laird, Benjamin A. Raby, Scott T. Weiss, Christoph Lange:
  On the frequency of copy number variants. 2350-2355
• 
  Meijuan Li, Cavan Reilly, Timothy Hanson:
  A semiparametric test to detect associations between quantitative traits and candidate genes in structured populations. 2356-2362

Systems Biology

• 
  Jaroslaw Smieja, Mohammad Jamaluddin, Allan R. Brasier, Marek Kimmel:
  Model-based analysis of interferon-beta induced signaling pathway. 2363-2369
• 
  Juan Cui, Qi Liu, David Puett, Ying Xu:
  Computational prediction of human proteins that can be secreted into the bloodstream. 2370-2375
• 
  Shuye Pu, Karen Ronen, James Vlasblom, Jack Greenblatt, Shoshana J. Wodak:
  Local coherence in genetic interaction patterns reveals prevalent functional versatility. 2376-2383
• 
  Kristen A. Wieghaus, Erwin P. Gianchandani, Mikell A. Paige, Milton L. Brown, Edward A. Botchwey, Jason A. Papin:
  Novel pathway compendium analysis elucidates mechanism of pro-angiogenic synthetic small molecule. 2384-2390

Applications Note - Genome Analysis

• 
  Jasmina Bogojeska, Adrian Alexa, André Altmann, Thomas Lengauer, Jörg Rahnenführer:
  Rtreemix: an R package for estimating evolutionary pathways and genetic progression scores. 2391-2392

Sequence Analysis

• 
  Anika Jöcker, Fabian Hoffmann, Andreas Groscurth, Heiko Schoof:
  Protein function prediction and annotation in an integrated environment powered by web services (AFAWE). 2393-2394
• 
  Hui Jiang, Wing Hung Wong:
  SeqMap: mapping massive amount of oligonucleotides to the genome. 2395-2396
• 
  Yana Bromberg, Guy Yachdav, Burkhard Rost:
  SNAP predicts effect of mutations on protein function. 2397-2398

Phylogenetics

• 
  Thasso Griebel, Malte Brinkmeyer, Sebastian Böcker:
  EPoS: a modular software framework for phylogenetic analysis. 2399-2400
• 
  Matthias Wolf, Benjamin Ruderisch, Thomas Dandekar, Jörg Schultz, Tobias Müller:
  ProfDistS: (profile-) distance based phylogeny on sequence - structure alignments. 2401-2402
• 
  Ádám Novák, István Miklós, Rune B. Lyngsø, Jotun Hein:
  StatAlign: an extendable software package for joint Bayesian estimation of alignments and evolutionary trees. 2403-2404

Gene Expression

• 
  Wuming Gong, Yongliang Ren, Haiyan Zhou, Yejun Wang, Shuli Kang, Tongbin Li:
  siDRM: an effective and generally applicable online siRNA design tool. 2405-2406

Genetics and Population Analysis

• 
  Jérôme Wojcik, Karl Forner:
  ExactFDR: exact computation of false discovery rate estimate in case-control association studies. 2407-2408

Databases and Ontologies

• 
  Jing Zhang, Tao Ma, Yanda Li, Shao Li:
  dbNEI2.0: building multilayer network for drug-NEI-disease. 2409-2411
• 
  Siyuan Zheng, Jia Sheng, Chuan Wang, Xiaojing Wang, Yao Yu, Yun Li, Alex Michie, Jianliang Dai, Yang Zhong, Pei Hao, Lei Liu, Yixue Li:
  MPSQ: a web tool for protein-state searching. 2412-2413
• 
  Chaka Tang, Josephine F. Reyes, Fabio Luciani, Andrew R. Francis, Mark M. Tanaka:
  spolTools: online utilities for analyzing spoligotypes of the Mycobacterium tuberculosis complex. 2414-2415
• 
  Guangyong Zheng, Kang Tu, Qing Yang, Yun Xiong, Chaochun Wei, Lu Xie, Yangyong Zhu, Yixue Li:
  ITFP: an integrated platform of mammalian transcription factors. 2416-2417
• 
  Jason Persampieri, Deborah I. Ritter, Daniel Lees, Jessica Lehoczky, Qiang Li, Su Guo, Jeffrey H. Chuang:
  cneViewer: a database of conserved non-coding elements for studies of tissue-specific gene regulation. 2418-2419

Letter to the Editor - Genome Analysis

• 
  Yang Xie:
  Comments on "On correcting the overestimation of the permutation-based false discovery rate estimator". 2420

Erratum

• 
  Vladislav Vyshemirsky, Mark A. Girolami:
  Bayesian ranking of biochemical system models. 2421

Volume 24, Number 21, 1 November 2008

Discovery Notes - Sequence Analysis

• 
  Robson Francisco de Souza, Vivek Anantharaman, Sandro José de Souza, L. Aravind, Frederico J. Gueiros-Filho:
  AMIN domains have a predicted role in localization of diverse periplasmic protein complexes. 2423-2426
• 
  Fanny Jadeau, Emmanuelle Bechet, Alain J. Cozzone, Gilbert Deléage, Christophe Grangeasse, Christophe Combet:
  Identification of the idiosyncratic bacterial protein tyrosine kinase (BY-kinase) family signature. 2427-2430

Original Papers - Sequence Analysis

• 
  Hao Lin, Zefeng Zhang, Michael Q. Zhang, Bin Ma, Ming Li:
  ZOOM! Zillions of oligos mapped. 2431-2437
• 
  Osamu Gotoh:
  Direct mapping and alignment of protein sequences onto genomic sequence. 2438-2444
• 
  Sriram Sankararaman, Kimmen Sjölander:
  INTREPID - INformation-theoretic TREe traversal for Protein functional site IDentification. 2445-2452

Structural Bioinformatics

• 
  Sol Katzman, Christian Barrett, Grant Thiltgen, Rachel Karchin, Kevin Karplus:
  PREDICT-2ND: a tool for generalized protein local structure prediction. 2453-2459
• 
  Mirabela Rusu, Stefan Birmanns, Willy Wriggers:
  Biomolecular pleiomorphism probed by spatial interpolation of coarse models. 2460-2466

Gene Expression

• 
  Chang-Tsun Li, Yinyin Yuan, Roland Wilson:
  An unsupervised conditional random fields approach for clustering gene expression time series. 2467-2473
• 
  Xi Chen, Lily Wang, Jonathan D. Smith, Bing Zhang:
  Supervised principal component analysis for gene set enrichment of microarray data with continuous or survival outcomes. 2474-2481
• 
  Elissa J. Cosgrove, Yingchun Zhou, Timothy S. Gardner, Eric D. Kolaczyk:
  Predicting gene targets of perturbations via network-based filtering of mRNA expression compendia. 2482-2490
• 
  Antonio Reverter, Eva K. F. Chan:
  Combining partial correlation and an information theory approach to the reversed engineering of gene co-expression networks. 2491-2497

Genetics and Population Analysis

• 
  Zachary A. Szpiech, Mattias Jakobsson, Noah A. Rosenberg:
  ADZE: a rarefaction approach for counting alleles private to combinations of populations. 2498-2504

Systems Biology

• 
  Gautam Goel, I-Chun Chou, Eberhard O. Voit:
  System estimation from metabolic time-series data. 2505-2511

Data and Text Mining

• 
  Alona Fyshe, Yifeng Liu, Duane Szafron, Russell Greiner, Paul Lu:
  Improving subcellular localization prediction using text classification and the gene ontology. 2512-2517
• 
  Justin Klekota, Frederick P. Roth:
  Chemical substructures that enrich for biological activity. 2518-2525

Databases and Ontologies

• 
  Brendan Elliott, Mustafa Kirac, Ali Cakmak, Gökhan Yavas, Stephen Mayes, En Cheng, Yuan Wang, Chirag Gupta, Gultekin Özsoyoglu, Z. Meral Özsoyoglu:
  PathCase: pathways database system. 2526-2533

Applications Note - Genome Analysis

• 
  Darren Kessner, Matt Chambers, Robert Burke, David B. Agus, Parag Mallick:
  ProteoWizard: open source software for rapid proteomics tools development. 2534-2536
• 
  Alan P. Boyle, Justin Guinney, Gregory E. Crawford, Terrence S. Furey:
  F-Seq: a feature density estimator for high-throughput sequence tags. 2537-2538

Phylogenetics

• 
  Salvador Ramírez-Flandes, Osvaldo Ulloa:
  Bosque: integrated phylogenetic analysis software. 2539-2541
• 
  Liang Liu:
  BEST: Bayesian estimation of species trees under the coalescent model. 2542-2543

Gene Expression

• 
  Denis C. Bauer, Timothy L. Bailey:
  STREAM: Static Thermodynamic REgulAtory Model of transcription. 2544-2545

Systems Biology

• 
  Dorothea Emig, Melissa S. Cline, Thomas Lengauer, Mario Albrecht:
  Integrating expression data with domain interaction networks. 2546-2548
• 
  Holger Fröhlich, Tim Beißbarth, Achim Tresch, Dennis Kostka, Juby Jacob, Rainer Spang, Florian Markowetz:
  Analyzing gene perturbation screens with nested effects models in R and bioconductor. 2549-2550
• 
  Anthony D. Hill, Jonathan R. Tomshine, Emma M. B. Weeding, Vassilios Sotiropoulos, Yiannis N. Kaznessis:
  SynBioSS: the synthetic biology modeling suite. 2551-2553
• 
  Guillermo Rodrigo, Javier Carrera, Kristala Jones Prather, Alfonso Jaramillo:
  DESHARKY: automatic design of metabolic pathways for optimal cell growth. 2554-2556
• 
  Tian Xia, Julie A. Dickerson:
  OmicsViz: Cytoscape plug-in for visualizing omics data across species. 2557-2558

Data and Text Mining

• 
  Yoshimasa Tsuruoka, Jun'ichi Tsujii, Sophia Ananiadou:
  FACTA: a text search engine for finding associated biomedical concepts. 2559-2560

Databases and Ontologies

• 
  Mehdi Pirooznia, Tanwir Habib, Edward J. Perkins, Youping Deng:
  GOfetcher: a database with complex searching facility for gene ontology. 2561-2563
• 
  C. Nelson Hayes, Diego Diez, Nicolas Joannin, Wataru Honda, Minoru Kanehisa, Mats Wahlgren, Craig E. Wheelock, Susumu Goto:
  varDB: a pathogen-specific sequence database of protein families involved in antigenic variation. 2564-2565

Letters to the Editor - Gene Expression

• 
  Harald Binder, Martin Schumacher:
  Comment on "network-constrained regularization and variable selection for analysis of genomic data". 2566-2568

Systems Biology

• 
  Caiyan Li, Hongzhe Li:
  In Response to Comment on "Network-constrained regularization and variable selection for analysis of genomic data". 2569

Volume 24, Number 22, 15 November 2008

Original Papers - Genome Analysis

• 
  Christina Beargie, Tsunglin Liu, Mark Corriveau, Ha Youn Lee, Jonatha Gott, Ralf Bundschuh:
  Genome annotation in the presence of insertional RNA editing. 2571-2578

Phylogenetics

• 
  Aurélien Mazurie, Danail Bonchev, Benno Schwikowski, Gregory A. Buck:
  Phylogenetic distances are encoded in networks of interacting pathways. 2579-2585

Gene Expression

• 
  Assaf P. Oron, Zhen Jiang, Robert Gentleman:
  Gene set enrichment analysis using linear models and diagnostics. 2586-2591

Systems Biology

• 
  Ryo Yoshida, Masao Nagasaki, Rui Yamaguchi, Seiya Imoto, Satoru Miyano, Tomoyuki Higuchi:
  Bayesian learning of biological pathways on genomic data assimilation. 2592-2601
• 
  Katrin Sameith, Philipp Antczak, Elliot Marston, Nil Turan, Dieter Maier, Tanja Stankovic, Francesco Falciani:
  Functional modules integrating essential cellular functions are predictive of the response of leukaemia cells to DNA damage. 2602-2607
• 
  Ta-tsen Soong, Kazimierz O. Wrzeszczynski, Burkhard Rost:
  Physical protein-protein interactions predicted from microarrays. 2608-2614
• 
  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. 2615-2621

Data and Text Mining

• 
  Seesandra V. Rajagopala, Johannes Goll, N. D. Deve Gowda, Kumar C. Sunil, Björn Titz, Arnab Mukherjee, Sharmila S. Mary, Naresh Raviswaran, Chetan S. Poojari, Srinivas Ramachandra, Svetlana Shtivelband, Stephen M. Blazie, Julia Hofmann, Peter Uetz:
  MPI-LIT: a literature-curated dataset of microbial binary protein--protein interactions. 2622-2627

Applications Note - Genome Analysis

• 
  Craig E. Jones, Julian Schwerdt, Tessa Arwen Bretag, Ute Baumann, Alfred L. Brown:
  GOSLING: a rule-based protein annotator using BLAST and GO. 2628-2629

Sequence Analysis

• 
  Martin Madera:
  Profile Comparer: a program for scoring and aligning profile hidden Markov models. 2630-2631

Structural Bioinformatics

• 
  Francesco Sirocco, Silvio C. E. Tosatto:
  TESE: generating specific protein structure test set ensembles. 2632-2633
• 
  Shiyong Liu, Ying Gao, Ilya A. Vakser:
  DOCKGROUND protein-protein docking decoy set. 2634-2635

Gene Expression

• 
  Edi Prifti, Jean-Daniel Zucker, Karine Clément, Corneliu Henegar:
  FunNet: an integrative tool for exploring transcriptional interactions. 2636-2638
• 
  Xin Zhou, Zhen Su:
  tCal: transcriptional probability calculator using thermodynamic model. 2639-2640

Systems Biology

• 
  Daehee Hwang, Ning Zhang, Hookeun Lee, Eugene Yi, Hui Zhang, Inyoul Y. Lee, Leroy Hood, Ruedi Aebersold:
  MS-BID: a Java package for label-free LC-MS-based comparative proteomic analysis. 2641-2642

Data and Text Mining

• 
  Ricardo Martínez, Nicolas Pasquier, Claude Pasquier:
  GenMiner: mining non-redundant association rules from integrated gene expression data and annotations. 2643-2644

Databases and Ontologies

• 
  Samone Khouangsathiene, Carlo Pearson, Summer Street, Betsy Ferguson, Christopher Dubay:
  MonkeySNP: a web portal for non-human primate single nucleotide polymorphisms. 2645-2646
• 
  Khalid Belhajjame, Andrew R. Jones, Norman W. Paton:
  A toolkit for capturing and sharing FuGE experiments. 2647-2649

German Conference on Bioinformatics: Systems Biology

• 
  Holger Fröhlich, Mark Fellmann, Holger Sültmann, Annemarie Poustka, Tim Beißbarth:
  Estimating large-scale signaling networks through nested effect models with intervention effects from microarray data. 2650-2656

Sequence Analysis

• 
  Hakim Tafer, Ivo L. Hofacker:
  RNAplex: a fast tool for RNA-RNA interaction search. 2657-2663

Volume 24, Number 23, December 2008

Original Papers - Genome Analysis

• 
  Yan Lin, George C. Tseng, Soo Yeon Cheong, Lora J. H. Bean, Stephanie L. Sherman, Eleanor Feingold:
  Smarter clustering methods for SNP genotype calling. 2665-2671
• 
  Tim J. Carver, Matthew Berriman, Adrian Tivey, Chinmay Patel, Ulrike Böhme, Bart Barrell, Julian Parkhill, Marie-Adèle Rajandream:
  Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database. 2672-2676

Sequence Analysis

• 
  Robert K. Bradley, Lior Pachter, Ian H. Holmes:
  Specific alignment of structured RNA: stochastic grammars and sequence annealing. 2677-2683
• 
  Lucie N. Hutchins, Sean M. Murphy, Priyam Singh, Joel H. Graber:
  Position-dependent motif characterization using non-negative matrix factorization. 2684-2690
• 
  Ching-Tai Chen, Ei-Wen Yang, Hung-Ju Hsu, Yi-Kun Sun, Wen-Lian Hsu, An-Suei Yang:
  Protease substrate site predictors derived from machine learning on multilevel substrate phage display data. 2691-2697

Structural Bioinformatics

• 
  Mallika Veeramalai, David R. Gilbert:
  A novel method for comparing topological models of protein structures enhanced with ligand information. 2698-2705

Gene Expression

• 
  Elmer Andrés Fernández, María R. Girotti, Juan A. López del Olmo, Andrea S. Llera, Osvaldo L. Podhajcer, Rodolfo J. C. Cantet, Mónica Balzarini:
  Improving 2D-DIGE protein expression analysis by two-stage linear mixed models: assessing experimental effects in a melanoma cell study. 2706-2712

Genetics and Population Analysis

• 
  Jean-Marie Cornuet, Filipe Santos, Mark A. Beaumont, Christian P. Robert, Jean-Michel Marin, David J. Balding, Thomas Guillemaud, Arnaud Estoup:
  Inferring population history with DIY ABC: a user-friendly approach to approximate Bayesian computation. 2713-2719
• 
  YuZhong Zhao, Yun Xu, ZhiHao Wang, Hong Zhang, Guoliang Chen:
  A better block partition and ligation strategy for individual haplotyping. 2720-2725

Systems Biology

• 
  Heiko Neuweger, Stefan P. Albaum, Michael Dondrup, Marcus Persicke, Tony Watt, Karsten Niehaus, Jens Stoye, Alexander Goesmann:
  MeltDB: a software platform for the analysis and integration of metabolomics experiment data. 2726-2732
• 
  Fergal P. Casey, Gerard Cagney, Nevan J. Krogan, Denis C. Shields:
  Optimal stepwise experimental design for pairwise functional interaction studies. 2733-2739
• 
  Gang Liu, Dhananjay D. Marathe, Khushi L. Matta, Sriram Neelamegham:
  Systems-level modeling of cellular glycosylation reaction networks: O-linked glycan formation on natural selectin ligands. 2740-2747
• 
  Eugenio Cinquemani, Andreas Milias-Argeitis, Sean Summers, John Lygeros:
  Stochastic dynamics of genetic networks: modelling and parameter identification. 2748-2754
• 
  Jiri Jablonsky, Petr Susila, Dusan Lazar:
  Impact of dimeric organization of enzyme on its function: the case of photosynthetic water splitting. 2755-2759

Databases and Ontologies

• 
  Sirarat Sarntivijai, Alexander S. Ade, Brian D. Athey, David J. States:
  A bioinformatics analysis of the cell line nomenclature. 2760-2766
• 
  Gabrielle A. Reeves, Karen Eilbeck, Michele Magrane, Claire O'Donovan, Luisa Montecchi-Palazzi, Midori A. Harris, Sandra E. Orchard, Rafael C. Jiménez, Andreas Prlic, Tim J. P. Hubbard, Henning Hermjakob, Janet M. Thornton:
  The Protein Feature Ontology: a tool for the unification of protein feature annotations. 2767-2772

Applications Note - Genome Analysis

• 
  Peng-An Chen, Hsiao-Fei Liu, Kun-Mao Chao:
  CNVDetector: locating copy number variations using array CGH data. 2773-2775

Sequence Analysis

• 
  Brian D. Ondov, Anjana Varadarajan, Karla D. Passalacqua, Nicholas H. Bergman:
  Efficient mapping of Applied Biosystems SOLiD sequence data to a reference genome for functional genomic applications. 2776-2777

Phylogenetics

• 
  Thorhildur Juliusdottir, Fredrik Pettersson, Richard R. Copley:
  POPE - a tool to aid high-throughput phylogenetic analysis. 2778-2779

Structural Bioinformatics

• 
  Liisa Holm, S. Kääriäinen, Päivi Rosenström, A. Schenkel:
  Searching protein structure databases with DaliLite v.3. 2780-2781
• 
  Michaël Heymann, David Paramelle, Gilles Subra, Eric Forest, Jean Martinez, Christophe Geourjon, Gilbert Deléage:
  MSX-3D: a tool to validate 3D protein models using mass spectrometry. 2782-2783

Genetics and Population Analysis

• 
  Marit Holden, Shiwei Deng, Leszek Wojnowski, Bettina Kulle:
  GSEA-SNP: applying gene set enrichment analysis to SNP data from genome-wide association studies. 2784-2785
• 
  Ryan D. Hernandez:
  A flexible forward simulator for populations subject to selection and demography. 2786-2787
• 
  Roby Joehanes, James C. Nelson:
  QGene 4.0, an extensible Java QTL-analysis platform. 2788-2789
• 
  Anna Ramírez-Soriano, Francesc Calafell:
  FABSIM: a software for generating F_ST distributions with various ascertainment biases. 2790-2791

Systems Biology

• 
  Josselin Noirel, Guido Sanguinetti, Phillip C. Wright:
  Identifying differentially expressed subnetworks with MMG. 2792-2793
• 
  Tom S. Price, Julie E. Baggs, Anne M. Curtis, Garret A. FitzGerald, John B. Hogenesch:
  WAVECLOCK: wavelet analysis of circadian oscillation. 2794-2795

Data and Text Mining

• 
  John T. Prince, Edward M. Marcotte:
  mspire: mass spectrometry proteomics in Ruby. 2796-2797
• 
  Yuelin Zhu, Sean R. Davis, Robert M. Stephens, Paul S. Meltzer, Yidong Chen:
  GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus. 2798-2800

Databases and Ontologies

• 
  Dihui Lu, Richard Z. Liu, Victoria Izumi, David A. Fenstermacher, Eric B. Haura, John M. Koomen, Steven Eschrich:
  IPEP: an in silico tool to examine proteolytic peptides for mass spectrometry. 2801-2802
• 
  Geoffrey L. Winsor, Bhavjinder Khaira, Thea Van Rossum, Raymond Lo, Matthew D. Whiteside, Fiona S. L. Brinkman:
  The Burkholderia Genome Database: facilitating flexible queries and comparative analyses. 2803-2804

Letter to the Editor - Systems Biology

• 
  Faruck Morcos, Charles Lamanna, Marcin Sikora, Jesús A. Izaguirre:
  Addendum. Cytoprophet: a Cytoscape plug-in for protein and domain interaction networks inference. 2805

Volume 24, Number 24, December 2008

Review - Genome Analysis

• 
  Christophe Pichon, Brice Felden:
  Small RNA gene identification and mRNA target predictions in bacteria. 2807-2813

Discovery Note - Systems Biology

• 
  Alexander E. Vinogradov:
  Modularity of cellular networks shows general center-periphery polarization. 2814-2817

Original Papers - Genome Analysis

• 
  Jason R. Miller, Arthur L. Delcher, Sergey Koren, Eli Venter, Brian Walenz, Anushka Brownley, Justin Johnson, Kelvin Li, Clark M. Mobarry, Granger G. Sutton:
  Aggressive assembly of pyrosequencing reads with mates. 2818-2824
• 
  Yu Zhang:
  Poisson approximation for significance in genome-wide ChIP-chip tiling arrays. 2825-2831
• 
  Jhonny R. Demey, José L. Vicente-Villardón, M. P. Galindo-Villardón, Asia Yusely Zambrano:
  Identifying molecular markers associated with classification of genotypes by External Logistic Biplots. 2832-2838

Sequence Analysis

• 
  Paolo Ribeca, Emanuele Raineri:
  Faster exact Markovian probability functions for motif occurrences: a DFA-only approach. 2839-2848
• 
  Anke Busch, Andreas S. Richter, Rolf Backofen:
  IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions. 2849-2856
• 
  Thanh Hai Dang, Koenraad Van Leemput, Alain Verschoren, Kris Laukens:
  Prediction of kinase-specific phosphorylation sites using conditional random fields. 2857-2864

Structural Bioinformatics

• 
  Andrew J. Bordner:
  Predicting small ligand binding sites in proteins using backbone structure. 2865-2871
• 
  Ahmet Sacan, Ismail Hakki Toroslu, Hakan Ferhatosmanoglu:
  Integrated search and alignment of protein structures. 2872-2879

Gene Expression

• 
  Ronglai Shen, Jeremy M. G. Taylor, Debashis Ghosh:
  Reconstructing tumor-wise protein expression in tissue microarray studies using a Bayesian cell mixture model. 2880-2886
• 
  Karen Kapur, Hui Jiang, Yi Xing, Wing Hung Wong:
  Cross-hybridization modeling on Affymetrix exon arrays. 2887-2893

Systems Biology

• 
  Simon Rogers, Mark A. Girolami, Walter Kolch, Katrina M. Waters, Tao Liu, Brian Thrall, H. Steven Wiley:
  Investigating the correspondence between transcriptomic and proteomic expression profiles using coupled cluster models. 2894-2900
• 
  Bärbel Finkenstädt, Elizabeth A. Heron, Michal Komorowski, Kieron D. Edwards, Sanyi Tang, Claire V. Harper, Julian R. E. Davis, Michael R. H. White, Andrew J. Millar, David A. Rand:
  Reconstruction of transcriptional dynamics from gene reporter data using differential equations. 2901-2907

Data and Text Mining

• 
  Melanie Osl, Stephan Dreiseitl, Bernhard Pfeifer, Klaus Weinberger, Helmut Klocker, Georg Bartsch, Georg Schäfer, Bernhard Tilg, Armin Graber, Christian Baumgartner:
  A new rule-based algorithm for identifying metabolic markers in prostate cancer using tandem mass spectrometry. 2908-2914

Applications Note - Genome Analysis

• 
  Robert T. Morris, Timothy R. O'Connor, John J. Wyrick:
  Osiris: an integrated promoter database for Oryza sativa L.. 2915-2917
• 
  Matteo Cesaroni, Davide Cittaro, Alessandro Brozzi, Pier Giuseppe Pelicci, Lucilla Luzi:
  CARPET: a web-based package for the analysis of ChIP-chip and expression tiling data. 2918-2920
• 
  Jonathan M. Cairns, Mark J. Dunning, Matthew E. Ritchie, Roslin Russell, Andy G. Lynch:
  BASH: a tool for managing BeadArray spatial artefacts. 2921-2922

Sequence Analysis

• 
  Jun Kong, Fei Zhu, Jim Stalker, David J. Adams:
  iMapper: a web application for the automated analysis and mapping of insertional mutagenesis sequence data against Ensembl genomes. 2923-2925
• 
  Leming Zhou, Ingrid Mihai, Liliana Florea:
  Effective cluster-based seed design for cross-species sequence comparisons. 2926-2927
• 
  Håkan Viklund, Andreas Bernsel, Marcin J. Skwark, Arne Elofsson:
  SPOCTOPUS: a combined predictor of signal peptides and membrane protein topology. 2928-2929
• 
  Vinhthuy Phan, Nicholas A. Furlotte:
  Motif Tool Manager: a web-based framework for motif discovery. 2930-2931

Phylogenetics

• 
  Jeffrey C. Oliver:
  AUGIST: inferring species trees while accommodating gene tree uncertainty. 2932-2933

Structural Bioinformatics

• 
  Hui Kian Ho, Michael J. Kuiper, Kotagiri Ramamohanarao:
  PConPy - a Python module for generating 2D protein maps. 2934-2935

Genetics and Population Analysis

• 
  Matthew J. Jobin, Joanna L. Mountain:
  REJECTOR: software for population history inference from genetic data via a rejection algorithm. 2936-2937
• 
  Andrew D. Johnson, Robert E. Handsaker, Sara L. Pulit, Marcia M. Nizzari, Christopher J. O'Donnell, Paul I. W. de Bakker:
  SNAP: a web-based tool for identification and annotation of proxy SNPs using HapMap. 2938-2939

Data and Text Mining

• 
  Nigel Collier, Son Doan, Ai Kawazoe, Reiko Matsuda Goodwin, Mike Conway, Yoshio Tateno, Hung Quoc Ngo, Dinh Dien, Asanee Kawtrakul, Koichi Takeuchi, Mika Shigematsu, Kiyosu Taniguchi:
  BioCaster: detecting public health rumors with a Web-based text mining system. 2940-2941

Corrigendum

• 
  Aleksandr Morgulis, George Coulouris, Yan Raytselis, Thomas L. Madden, Richa Agarwala, Alejandro A. Schäffer:
  Database indexing for production MegaBLAST searches. 2942