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 anin 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 microRNAcis-regulatory elements across 12Drosophila 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 V. 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:
  StraighteningCaenorhabditis 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 ofmiRNA 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: theHelicobacter 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 forin 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 inSaccharomyces 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: identifyingcis-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 improvede 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 ofbeta-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 inEscherichia 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 viaDataRail.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 ofPlasmodium 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: asearchable 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 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:
  OnE-values for tandem MS scoring schemes.1652-1653

Gene Expression

• 
  Jainab Khatun,Morgan C. Giddings:
  In response to "OnE-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 thePlasmodium 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 ofDrosophila 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 inEscherichia 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 theCpG 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: aCytoscape 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 predictivein 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 plusk-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 theMycobacterium 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 withDIY 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 generatingF_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: anin 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: aCytoscape 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 forOryza 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