Bioinformatics, Volume 25

Volume 25, Number 1, January 2009

Discovery Note - Sequence Analysis

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

Original Papers

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

Gene Expression

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

Genetics and Population Analysis

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

Systems Biology

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

Data and Text Mining

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

Applications Note - Genome Analysis

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

Sequence Analysis

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

Phylogenetics

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

Gene Expression

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

Genetics and Population Analysis

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

Systems Biology

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

Data and Text Mining

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

ISCB News

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

Letters to the Editor - Phylogenetics

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

Erratum

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

Volume 25, Number 2, January 2009

Discovery Notes - Sequence Analysis

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

Databases and Ontologies

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

Original Papers - Genome Analysis

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

Sequence Analysis

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

Phylogenetics

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

Structural Bioinformatics

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

Gene Expression

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

Genetics and Population Analysis

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

Systems Biology

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

Data and Text Mining

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

Applications Note - Genome Analysis

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

Sequence Analysis

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

Gene Expression

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

Genetics and Population Analysis

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

Systems Biology

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

Databases and Ontologies

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

Volume 25, Number 3, February 2009

Discovery Note - Sequence Analysis

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

Original Papers

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

Phylogenetics

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

Gene Expression

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

Genetics and Population Analysis

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

Systems Biology

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

Data and Text Mining

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

Databases and Ontologies

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

Applications Note - Structural Bioinformatics

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

Gene Expression

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

Systems Biology

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

Volume 25, Number 4, February 2009

Review - Data and Text Mining

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

Editorial

• 
  Alex Bateman,John Quackenbush:
  Editorial.429

Discovery Note - Gene Expression

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

Original Papers - Genome Analysis

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

Sequence Analysis

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

Structural Bioinformatics

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

Gene Expression

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

Genetics and Population Analysis

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

Systems Biology

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

Data and Text Mining

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

Applications Note - Genome Analysis

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

Phylogenetics

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

Structural Bioinformatics

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

Gene Expression

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

Genetics and Population Analysis

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

Databases and Ontologies

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

Volume 25, Number 5, March 2009

Discovery Note - Sequence Analysis

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

Original Papers - Genome Analysis

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

Sequence Analysis

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

Phylogenetics

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

Structural Bioinformatics

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

Structural Bioinformatics and Data Mining

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

Gene Expression

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

Data and Text Mining

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

Databases and Ontologies

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

Applications Note - Genome Analysis

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

Sequence Analysis

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

Phylogenetics

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

Structural Bioinformatics

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

Gene Expression

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

Genetics and Population Analysis

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

Systems Biology

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

Databases and Ontologies

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

Letter to the Editor - Gene Expression

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

Volume 25, Number 6, March 2009

Editorial

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

Original Papers - Genome Analysis

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

Sequence Analysis

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

Phylogenetics

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

Structural Bioinformatics

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

Gene Expression

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

Systems Biology

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

Data and Text Mining

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

Applications Note - Sequence Analysis

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

Gene Expression

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

Systems Biology

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

Data and Text Mining

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

Volume 25, Number 7, April 2009

Discovery Note - Genome Analysis

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

Original Papers

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

Gene Expression

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

Systems Biology

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

Data and Text Mining

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

Structural Bioinformatics

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

Applications Note - Genome Analysis

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

Sequence Analysis

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

Phylogenetics

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

Data and Text Mining

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

Databases and Ontologies

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

Volume 25, Number 8, April 2009

Original Papers - Genome Analysis

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

Structural Bioinformatics

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

Gene Expression

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

Genetics and Population Analysis

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

Systems Biology

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

Data and Text Mining

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

Applications Note - Gene Expression

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

Genome Analysis

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

Sequence Analysis

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

Structural Bioinformatics

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

Gene Expression

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

Systems Biology

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

Data and Text Mining

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

Databases and Ontologies

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

Volume 25, Number 9, May 2009

Original Papers - Genome Analysis

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

Sequence Analysis

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

Structural Bioinformatics

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

Gene Expression

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

Systems Biology

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

Data and Text Mining

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

Applications Note - Genome Analysis

• 
  Igor B. Kuznetsov,Michael McDuffie,Roxana Moslehi:
  A web server for inferring the humanN-acetyltransferase-2 (NAT2) enzymatic phenotype fromNAT2 genotype.1185-1186
• 
  Ilya Plyusnin,Liisa Holm,Matti Kankainen:
  LOCP - locating pilus operons in Gram-positive bacteria.1187-1188

Sequence Analysis

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

Phylogenetics

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

Structural Bioinformatics

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

Gene Expression

• 
  Jeffrey T. Leek:
  Thetspair package for finding top scoring pair classifiers inR.1203-1204

Systems Biology

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

Databases and Ontologies

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

Corrigendum

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

Volume 25, Number 10, May 2009

Discovery Note - Genome Analysis

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

Sequence Analysis

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

Original Papers - Genome Analysis

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

Sequence Analysis

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

Structural Bioinformatics

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

Gene Expression

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

Genetics and Population Analysis

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

Systems Biology

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

Data and Text Mining

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

Databases and Ontologies

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

Applications Note - Sequence Analysis

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

Data and Text Mining

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

Volume 25, Number 11, June 2009

Discovery Note - Sequence Analysis

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

Original Papers - Genome Analysis

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

Sequence Analysis

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

Phylogenetics

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

Genetics and Population Analysis

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

Systems Biology

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

Data and Text Mining

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

Applications Note - Genome Analysis

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

Sequence Analysis

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

Structural Bioinformatics

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

Gene Expression

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

Genetics and Population Analysis

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

Systems Biology

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

Data and Text Mining

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

Erratum

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

Volume 25, Number 12, June 2009

ISMB/ECCB 2009 Conference Proceedings, June 27 TO July 2, 2009, Stockholm, Sweden - Editorial

• 
  Dan Gusfield,Anna Tramontano:
  Editorial.

Original Papers

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

Comparative genomics

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

Databases and Ontologies

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

Evolution and Phylogeny

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

Gene Regulation and transcriptomics

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

Other Bioinformatics Applications and Methods

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

Population genomics

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

Protein Interactions and Molecular Networks

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

Protein Structure and Function

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

Sequence Analysis and Alignment

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

Editorial

• 
  Alex Bateman,Matt Wood:
  Cloud computing.1475

Review Gene Expression

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

Original Papers - Genome Analysis

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

Sequence Analysis

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

Structural Bioinformatics

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

Systems Biology

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

Data and Text Mining

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

Applications Note - Genome Analysis

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

Sequence Analysis

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

Phylogenetics

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

Structural Bioinformatics

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

Genetics and Population Analysis

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

Databases and Ontologies

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

ISCB News

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

Erratum

• 
  Zheng Guo,Lei Wang,Yongjin Li,Xue Gong,Chen Yao,Wencai Ma,Dong Wang,Yanhui Li,Jing Zhu,Min Zhang,Da Yang,Shaoqi Rao,Jing Wang:
  Edge-based scoring and searching method for identifying condition-responsive protein-protein interaction sub-network.1574

Volume 25, Number 13, July 2009

Review - Data and Text Mining

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

Original Papers - Genome Analysis

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

Sequence Analysis

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

Structural Bioinformatics

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

Gene Expression

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

Genetics and Population Analysis

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

Systems Biology

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

Applications Note - Structural Bioinformatics

• 
  Jordi Camps,Oliver Carrillo,Agustí Emperador,Laura Orellana,Adam Hospital,Manuel Rueda,Damjan Cicin-Sain,Marco D'Abramo,Josep Lluis Gelpí,Modesto Orozco:
  FlexServ: an integrated tool for the analysis of protein flexibility.1709-1710

Data and Text Mining

• 
  Natalia Becker,Wiebke Werft,Grischa Toedt,Peter Lichter,Axel Benner:
  penalizedSVM: a R-package for feature selection SVM classification.1711-1712

Corrigendum

• 
  Eric P. Nawrocki,Diana L. Kolbe,Sean R. Eddy:
  Infernal 1.0: inference of RNA alignments.1713

Volume 25, Number 14, July 2009

Original Papers - Genome Analysis

• 
  Hyungwon Choi,Alexey I. Nesvizhskii,Debashis Ghosh,Zhaohui S. Qin:
  Hierarchical hidden Markov model with application to joint analysis of ChIP-chip and ChIP-seq data.1715-1721
• 
  Mohammed Monzoorul Haque,Tarini Shankar Ghosh,Dinakar Komanduri,Sharmila S. Mande:
  SOrt-ITEMS: Sequence orthology based approach for improved taxonomic estimation of metagenomic sequences.1722-1730
• 
  Marty C. Brandon,Douglas C. Wallace,Pierre Baldi:
  Data structures and compression algorithms for genomic sequence data.1731-1738

Sequence Analysis

• 
  Meghana Chitale,Troy Hawkins,Changsoon Park,Daisuke Kihara:
  ESG: extended similarity group method for automated protein function prediction.1739-1745
• 
  Verónica Becher,Alejandro Deymonnaz,Pablo Ariel Heiber:
  Efficient computation of all perfect repeats in genomic sequences of up to half a gigabyte, with a case study on the human genome.1746-1753
• 
  Heng Li,Richard Durbin:
  Fast and accurate short read alignment with Burrows-Wheeler transform.1754-1760

Structural Bioinformatics

• 
  Anna E. Lobley,Michael I. Sadowski,David T. Jones:
  pGenTHREADER and pDomTHREADER: new methods for improved protein fold recognition and superfamily discrimination.1761-1767

Gene Expression

• 
  Emma Steele,Allan Tucker,Peter A. C. 't Hoen,Martijn J. Schuemie:
  Literature-based priors for gene regulatory networks.1768-1774
• 
  Insuk Sohn,Jinseog Kim,Sin-Ho Jung,Changyi Park:
  Gradient lasso for Cox proportional hazards model.1775-1781
• 
  Jun Wan,C. Jimmy Lin,Donald J. Zack,Jiang Qian:
  Relating periodicity of nucleosome organization and gene regulation.1782-1788
• 
  Dikla Dotan-Cohen,Simon Kasif,Avraham A. Melkman:
  Seeing the forest for the trees: using the Gene Ontology to restructure hierarchical clustering.1789-1795

Genetics and Population Analysis

• 
  Gilles Guillot:
  On the inference of spatial structure from population genetics data.1796-1801

Letters to the Editor - Genetics and Population Analysis

• 
  Eric Durand,Chibiao Chen,Olivier François:
  Comment on 'On the inference of spatial structure from population genetics data'.1802-1804
• 
  Gilles Guillot:
  Response to comment on 'On the inference of spatial structure from population genetics data'.1805-1806

Original Papers - Genetics and Population Analysis

• 
  József Bukszár,Joseph L. McClay,Edwin J. C. G. van den Oord:
  Estimating the posterior probability that genome-wide association findings are true or false.1807-1813

Systems Biology

• 
  Philip Bachman,Ying Liu:
  Structure discovery in PPI networks using pattern-based network decomposition.1814-1821
• 
  Bor-Sen Chen,Chia-Hung Chang,Hsiao-Ching Lee:
  Robust synthetic biology design: stochastic game theory approach.1822-1830

Applications Note - Genome Analysis

• 
  Aziz Mithani,Gail M. Preston,Jotun Hein:
  Rahnuma: hypergraph-based tool for metabolic pathway prediction and network comparison.1831-1832
• 
  Marília D. V. Braga:
  baobabLUNA: the solution space of sorting by reversals.1833-1835
• 
  Ed Lee,Nomi L. Harris,Mark Gibson,Raymond Chetty,Suzanna Lewis:
  Apollo: a community resource for genome annotation editing.1836-1837
• 
  Kun He,Xueyong Li,Junli Zhou,Xingwang Deng,Hongyu Zhao,Jingchu Luo:
  NTAP: for NimbleGen tiling array ChIP-chip data analysis.1838-1840
• 
  Michael F. Lawrence,Robert Gentleman,Vincent J. Carey:
  rtracklayer: an R package for interfacing with genome browsers.1841-1842

Sequence Analysis

• 
  Gang-Qing Hu,Jiangtao Guo,Yongchu Liu,Huaiqiu Zhu:
  MetaTISA: Metagenomic Translation Initiation Site Annotator for improving gene start prediction.1843-1845
• 
  Seong-Hyeuk Nam,Dae-Won Kim,Tae-Sung Jung,Young-Sang Choi,Dong-Wook Kim,Han-Suk Choi,Sang-Haeng Choi,Hong-Seog Park:
  PESTAS: a web server for EST analysis and sequence mining.1846-1848

Volume 25, Number 15, August 2009

Original Papers - Genome Analysis

• 
  Suparna Mitra,Bernhard Klar,Daniel H. Huson:
  Visual and statistical comparison of metagenomes.1849-1855
• 
  Taro L. Saito,Jun Yoshimura,Shin Sasaki,Budrul Ahsan,Atsushi Sasaki,Reginaldo Kuroshu,Shinichi Morishita:
  UTGB toolkit for personalized genome browsers.1856-1861

Sequence Analysis

• 
  Jessica H. Fong,Aron Marchler-Bauer:
  CORAL: aligning conserved core regions across domain families.1862-1868
• 
  Andrew F. Neuwald:
  Rapid detection, classification and accurate alignment of up to a million or more related protein sequences.1869-1875

Structural Bioinformatics

• 
  Andrea Zen,Cesira de Chiara,Annalisa Pastore,Cristian Micheletti:
  Using dynamics-based comparisons to predict nucleic acid binding sites in proteins: an application to OB-fold domains.1876-1883

Genetics and Population Analysis

• 
  Kristin K. Nicodemus,James D. Malley:
  Predictor correlation impacts machine learning algorithms: implications for genomic studies.1884-1890

Systems Biology

• 
  Guimei Liu,Limsoon Wong,Hon Nian Chua:
  Complex discovery from weighted PPI networks.1891-1897
• 
  Chang H. Seo,Jeong-Rae Kim,Man-Sun Kim,Kwang-Hyun Cho:
  Hub genes with positive feedbacks function as master switches in developmental gene regulatory networks.1898-1904
• 
  Wandaliz Torres-García,Weiwen Zhang,George C. Runger,Roger H. Johnson,Deirdre R. Meldrum:
  Integrative analysis of transcriptomic and proteomic data ofDesulfovibrio vulgaris: a non-linear model to predict abundance of undetected proteins.1905-1914
• 
  Christoph Kaleta,Stephan Richter,Peter Dittrich:
  Using chemical organization theory for model checking.1915-1922
• 
  Andreas Raue,Clemens Kreutz,Thomas Maiwald,Julie Bachmann,Marcel Schilling,Ursula Klingmüller,Jens Timmer:
  Structural and practical identifiability analysis of partially observed dynamical models by exploiting the profile likelihood.1923-1929

Data and Text Mining

• 
  Tianwei Yu,Youngja Park,Jennifer M. Johnson,Dean P. Jones:
  apLCMS - adaptive processing of high-resolution LC/MS data.1930-1936
• 
  Rene Hussong,Barbara Gregorius,Andreas Tholey,Andreas Hildebrandt:
  Highly accelerated feature detection in proteomics data sets using modern graphics processing units.1937-1943
• 
  Shanfeng Zhu,Jia Zeng,Hiroshi Mamitsuka:
  Enhancing MEDLINE document clustering by incorporating MeSH semantic similarity.1944-1951
• 
  Chongzhi Zang,Dustin E. Schones,Chen Zeng,Kairong Cui,Keji Zhao,Weiqun Peng:
  A clustering approach for identification of enriched domains from histone modification ChIP-Seq data.1952-1958

Applications Note - Genome Analysis

• 
  Oscar M. Rueda,Ramón Díaz-Uriarte:
  RJaCGH: Bayesian analysis of aCGH arrays for detecting copy number changes and recurrent regions.1959-1960
• 
  Melanie Bahlo,C. J. Bromhead:
  Generating linkage mapping files from Affymetrix SNP chip data.1961-1962

Sequence Analysis

• 
  Rodrigo Gouveia-Oliveira,Francisco S. Roque,Rasmus Wernersson,Thomas Sicheritz-Pontén,Peter Wad Sackett,Anne Mølgaard,Anders Gorm Pedersen:
  InterMap3D: predicting and visualizing co-evolving protein residues.1963-1965
• 
  Ruiqiang Li,Chang Yu,Yingrui Li,Tak Wah Lam,Siu-Ming Yiu,Karsten Kristiansen,Jun Wang:
  SOAP2: an improved ultrafast tool for short read alignment.1966-1967
• 
  Samuel A. Assefa,Thomas M. Keane,Thomas D. Otto,Chris Newbold,Matthew Berriman:
  ABACAS: algorithm-based automatic contiguation of assembled sequences.1968-1969

Phylogenetics

• 
  Rodrigo Santamaría,Roberto Therón:
  Treevolution: visual analysis of phylogenetic trees.1970-1971
• 
  Salvador Capella-Gutiérrez,José M. Silla-Martínez,Toni Gabaldón:
  trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses.1972-1973

Structural Bioinfomatics

• 
  Kévin Darty,Alain Denise,Yann Ponty:
  VARNA: Interactive drawing and editing of the RNA secondary structure.1974-1975
• 
  Semin Lee,Tom L. Blundell:
  Ulla: a program for calculating environment-specific amino acid substitution tables.1976-1977

Gene Expression

• 
  Lasse Folkersen,Diego Diez,Craig E. Wheelock,Jesper Z. Haeggström,Susumu Goto,Per Eriksson,Anders Gabrielsen:
  GeneRegionScan: a Bioconductor package for probe-level analysis of specific, small regions of the genome.1978-1979
• 
  Véronique Dupierris,Christophe Masselon,Magali Court,Sylvie Kieffer-Jaquinod,Christophe Bruley:
  A toolbox for validation of mass spectrometry peptides identification and generation of database: IRMa.1980-1981

Genetics and Population Analysis

• 
  Michael Matschiner,Walter Salzburger:
  TANDEM: integrating automated allele binning into genetics and genomics workflows.1982-1983

Systems Biology

• 
  Stephan Saalfeld,Albert Cardona,Volker Hartenstein,Pavel Tomancak:
  CATMAID: collaborative annotation toolkit for massive amounts of image data.1984-1986
• 
  François Le Fèvre,Serge Smidtas,Cyril Combe,Maxime Durot,Florence d'Alché-Buc,Vincent Schächter:
  CycSim - an online tool for exploring and experimenting with genome-scale metabolic models.1987-1988
• 
  Qiong Cheng,Robert W. Harrison,Alexander Zelikovsky:
  MetNetAligner: a web service tool for metabolic network alignments.1989-1990
• 
  Giorgos L. Papadopoulos,Panagiotis Alexiou,Manolis Maragkakis,Martin Reczko,Artemis G. Hatzigeorgiou:
  DIANA-mirPath: Integrating human and mouse microRNAs in pathways.1991-1993
• 
  Georgios A. Pavlopoulos,Charalampos N. Moschopoulos,Sean D. Hooper,Reinhard Schneider,Sophia Kossida:
  jClust: a clustering and visualization toolbox.1994-1996

Data and Text Mining

• 
  Yoshinobu Kano,William A. Baumgartner Jr.,Luke McCrohon,Sophia Ananiadou,K. Bretonnel Cohen,Lawrence Hunter,Jun'ichi Tsujii:
  U-Compare: share and compare text mining tools with UIMA.1997-1998

Volume 25, Number 16, August 2009

Original Papers - Genome Analysis

• 
  Eugene Andres Houseman,Brock C. Christensen,Margaret R. Karagas,Margaret R. Wrensch,Heather H. Nelson,Joseph Wiemels,Shichun Zheng,John K. Wiencke,Karl T. Kelsey,Carmen J. Marsit:
  Copy number variation has little impact on bead-array-based measures of DNA methylation.1999-2005

Sequence Analysis

• 
  Yanglan Gan,Jihong Guan,Shuigeng Zhou:
  A pattern-based nearest neighbor search approach for promoter prediction using DNA structural profiles.2006-2012

Gene Expression

• 
  Stan Pounds,Cheng Cheng,Xueyuan Cao,Kristine R. Crews,William Plunkett,Varsha Gandhi,Jeffrey Rubnitz,Raul C. Ribeiro,James R. Downing,Jatinder Lamba:
  PROMISE: a tool to identify genomic features with a specific biologically interesting pattern of associations with multiple endpoint variables.2013-2019
• 
  Chuan Lu,Ross D. King:
  An investigation into the population abundance distribution of mRNAs, proteins, and metabolites in biological systems.2020-2027
• 
  Yuliya V. Karpievitch,Jeff Stanley,Thomas Taverner,Jianhua Huang,Joshua N. Adkins,Charles Ansong,Fred Heffron,Thomas O. Metz,Wei-Jun Qian,Hyunjin Yoon,Richard D. Smith,Alan R. Dabney:
  A statistical framework for protein quantitation in bottom-up MS-based proteomics.2028-2034
• 
  Kathleen F. Kerr:
  Comments on the analysis of unbalanced microarray data.2035-2041

Systems Biology

• 
  Ritwik Layek,Aniruddha Datta,Ranadip Pal,Edward R. Dougherty:
  Adaptive intervention in probabilistic boolean networks.2042-2048
• 
  Nicola Bonzanni,Elzbieta Krepska,K. Anton Feenstra,Wan J. Fokkink,Thilo Kielmann,Henri E. Bal,Jaap Heringa:
  Executing multicellular differentiation: quantitative predictive modelling ofC.elegans vulval development.2049-2056
• 
  Thomas Sütterlin,Simone Huber,Hartmut Dickhaus,Niels Grabe:
  Modeling multi-cellular behavior in epidermal tissue homeostasis via finite state machines in multi-agent systems.2057-2063

Databases and Ontologies

• 
  David S. DeLuca,Elena Beisswanger,Joachim Wermter,Peter A. Horn,Udo Hahn,Rainer Blasczyk:
  MaHCO: an ontology of the major histocompatibility complex for immunoinformatic applications and text mining.2064-2070

Applications Note - Genome Analysis

• 
  Anna I. Rissman,Bob Mau,Bryan S. Biehl,Aaron E. Darling,Jeremy D. Glasner,Nicole T. Perna:
  Reordering contigs of draft genomes using the Mauve Aligner.2071-2073

Sequence Analysis

• 
  Kathryn E. Holt,Yik Y. Teo,Heng Li,Satheesh Nair,Gordon Dougan,John Wain,Julian Parkhill:
  Detecting SNPs and estimating allele frequencies in clonal bacterial populations by sequencing pooled DNA.2074-2075
• 
  Yong Wang,Ruslan Sadreyev,Nick V. Grishin:
  PROCAIN server for remote protein sequence similarity search.2076-2077
• 
  Heng Li,Bob Handsaker,Alec Wysoker,Tim Fennell,Jue Ruan,Nils Homer,Gabor T. Marth,Gonçalo R. Abecasis,Richard Durbin:
  The Sequence Alignment/Map format and SAMtools.2078-2079

Systems Biology

• 
  Nils Hoffmann,Jens Stoye:
  ChromA: signal-based retention time alignment for chromatography-mass spectrometry data.2080-2081

Data and Text Mining

• 
  Raul Rodriguez-Esteban,Ivan Iossifov:
  Figure mining for biomedical research.2082-2084
• 
  Woonghee Lee,William M. Westler,Arash Bahrami,Hamid Eghbalnia,John L. Markley:
  PINE-SPARKY: graphical interface for evaluating automated probabilistic peak assignments in protein NMR spectroscopy.2085-2087

Databases and Ontologies

• 
  Claudia Andreini,Ivano Bertini,Gabriele Cavallaro,Gemma L. Holliday,Janet M. Thornton:
  Metal-MACiE: a database of metals involved in biological catalysis.2088-2089
• 
  Steve Pettifer,David Thorne,Philip McDermott,Terri K. Attwood,J. Baran,Jan Christian Bryne,Taavi Hupponen,D. Mowbray,Gert Vriend:
  An active registry for bioinformatics web services.2090-2091
• 
  Audrey Kauffmann,Tim F. Rayner,Helen E. Parkinson,Misha Kapushesky,Margus Lukk,Alvis Brazma,Wolfgang Huber:
  Importing ArrayExpress datasets into R/Bioconductor.2092-2094

German Conference on Bioinformatics - Sequence Analysis

• 
  Steffen Heyne,Sebastian Will,Michael Beckstette,Rolf Backofen:
  Lightweight comparison of RNAs based on exact sequence-structure matches.2095-2102
• 
  Utz J. Pape,Holger Klein,Martin Vingron:
  Statistical detection of cooperative transcription factors with similarity adjustment.2103-2109

Structural Bioinformatics

• 
  Thomas Fober,Marco Mernberger,Gerhard Klebe,Eyke Hüllermeier:
  Evolutionary construction of multiple graph alignments for the structural analysis of biomolecules.2110-2117

Gene Expression

• 
  Michael Seifert,Jens Keilwagen,Marc Strickert,Ivo Grosse:
  Utilizing gene pair orientations for HMM-based analysis of promoter array ChIP-chip data.2118-2125
• 
  Sebastian J. Schultheiß,Wolfgang Busch,Jan U. Lohmann,Oliver Kohlbacher,Gunnar Rätsch:
  KIRMES: kernel-based identification of regulatory modules in euchromatic sequences.2126-2133

Genetics and Population Analysis

• 
  Markus Riester,Peter F. Stadler,Konstantin Klemm:
  FRANz: reconstruction of wild multi-generation pedigrees.2134-2139

Systems Biology

• 
  Caroline C. Friedel,Ralf Zimmer:
  Identifying the topology of protein complexes from affinity purification assays.2140-2146

Corrigendum Systems Biology

• 
  Lee-Wei Yang,Eran Eyal,Ivet Bahar,Akio Kitao:
  Principal component analysis of native ensembles of biomolecular structures (PCA_NEST): insights into functional dynamics.2147

Volume 25, Number 17, September 2009

Original Papers - Genome Analysis

• 
  Henrik Bengtsson,Pratyaksha Wirapati,Terence P. Speed:
  A single-array preprocessing method for estimating full-resolution raw copy numbers from all Affymetrix genotyping arrays including GenomeWideSNP 5 & 6.2149-2156
• 
  Jan Schröder,Heiko Schröder,Simon J. Puglisi,Ranjan Sinha,Bertil Schmidt:
  SHREC: a short-read error correction method.2157-2163
• 
  Reid F. Thompson,Masako Suzuki,Kevin W. Lau,John M. Greally:
  A pipeline for the quantitative analysis of CG dinucleotide methylation using mass spectrometry.2164-2170
• 
  Don Gilbert,Andreas Rechtsteiner:
  Comments on sequence normalization of tiling array expression.2171-2173

Sequence Analysis

• 
  Xiaowen Liu,Yonghua Han,Denis Yuen,Bin Ma:
  Automated protein (re)sequencing with MS/MS and a homologous database yields almost full coverage and accuracy.2174-2180
• 
  Liang-Tsung Huang,M. Michael Gromiha:
  Reliable prediction of protein thermostability change upon double mutation from amino acid sequence.2181-2187
• 
  Te-Chin Chu,Tsunglin Liu,D. T. Lee,Greg C. Lee,Arthur Chun-Chieh Shih:
  GR-Aligner: an algorithm for aligning pairwise genomic sequences containing rearrangement events.2188-2193
• 
  Nava Whiteford,Tom Skelly,Christina Curtis,Matthew E. Ritchie,Andrea Löhr,Alexander Wait Zaranek,Irina I. Abnizova,Clive Brown:
  Swift: primary data analysis for the Illumina Solexa sequencing platform.2194-2199
• 
  Christophe N. Magnan,Arlo Z. Randall,Pierre Baldi:
  SOLpro: accurate sequence-based prediction of protein solubility.2200-2207

Gene Expression

• 
  Jun Liu,Nirmalya Bandyopadhyay,Sanjay Ranka,Michael Baudis,Tamer Kahveci:
  Inferring progression models for CGH data.2208-2215
• 
  David L. Gold,Jeffrey C. Miecznikowski,Song Liu:
  Error control variability in pathway-based microarray analysis.2216-2221
• 
  Ali Torkamani,Nicholas J. Schork:
  Prestige centrality-based functional outlier detection in gene expression analysis.2222-2228

Systems Biology

• 
  Lars Kaderali,Eva Dazert,Ulf Zeuge,Michael Frese,Ralf Bartenschlager:
  Reconstructing signaling pathways from RNAi data using probabilistic Boolean threshold networks.2229-2235
• 
  Xuerui Yang,Yang Zhou,Rong Jin,Christina Chan:
  Reconstruct modular phenotype-specific gene networks by knowledge-driven matrix factorization.2236-2243

Data and Text Mining

• 
  Lun Yang,Langlai Xu,Lin He:
  A CitationRank algorithm inheriting Google technology designed to highlight genes responsible for serious adverse drug reaction.2244-2250
• 
  Lianyi Han,Yanli Wang,Stephen H. Bryant:
  A survey of across-target bioactivity results of small molecules in PubChem.2251-2255
• 
  Zheng Rong Yang,Ganjana Lertmemongkolchai,Gladys Tan,Philip L. Felgner,Richard W. Titball:
  A genetic programming approach forBurkholderia Pseudomallei diagnostic pattern discovery.2256-2262

Databases and Ontologies

• 
  Sarala M. Wimalaratne,Matt D. B. Halstead,Catherine M. Lloyd,Edmund J. Crampin,Poul M. F. Nielsen:
  Biophysical annotation and representation of CellML models.2263-2270
• 
  Victor M. Markowitz,Konstantinos Mavrommatis,Natalia Ivanova,I-Min A. Chen,Ken Chu,Nikos Kyrpides:
  IMG ER: a system for microbial genome annotation expert review and curation.2271-2278

Applications Note - Genome Analysis

• 
  Bertil Schmidt,Ranjan Sinha,Bryan Beresford-Smith,Simon J. Puglisi:
  A fast hybrid short read fragment assembly algorithm.2279-2280
• 
  Davide Rambaldi,Francesca D. Ciccarelli:
  FancyGene: dynamic visualization of gene structures and protein domain architectures on genomic loci.2281-2282

Sequence Analysis

• 
  Daniel C. Koboldt,Ken Chen,Todd Wylie,David E. Larson,Michael D. McLellan,Elaine R. Mardis,George M. Weinstock,Richard K. Wilson,Li Ding:
  VarScan: variant detection in massively parallel sequencing of individual and pooled samples.2283-2285

Phylogenetics

• 
  Nicolas Lartillot,Thomas Lepage,Samuel Blanquart:
  PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating.2286-2288

Systems Biology

• 
  Mieszko Lis,Maxim N. Artyomov,Srinivas Devadas,Arup K. Chakraborty:
  Efficient stochastic simulation of reaction-diffusion processes via direct compilation.2289-2291
• 
  Neil Swainston,Pedro Mendes:
  libAnnotationSBML: a library for exploiting SBML annotations.2292-2293

Corrigendum - Systems Biology

• 
  Macha Nikolski,David James Sherman:
  Family relationships: should consensus reign? - consensus clustering for protein families.2294

Volume 25, Number 18, September 2009

Discovery Note - Genome Analysis

• 
  Hiromi Nishida,Takayuki Motoyama,Shogo Yamamoto,Hiroyuki Aburatani,Hiroyuki Osada:
  Genome-wide maps of mono- and di-nucleosomes ofAspergillus fumigatus.2295-2297

Sequence Analysis

• 
  David Langenberger,Clara Bermudez-Santana,Jana Hertel,Steve Hoffmann,Philipp Khaitovich,Peter F. Stadler:
  Evidence for human microRNA-offset RNAs in small RNA sequencing data.2298-2301

Original Papers - Sequence Analysis

• 
  Lauren M. Bragg,Glenn Stone:
  k-link EST clustering: evaluating error introduced by chimeric sequences under different degrees of linkage.2302-2308
• 
  Zhen Xia,Gulei Jin,Jun Zhu,Ruhong Zhou:
  Using a mutual information-based site transition network to map the genetic evolution of influenza A/H3N2 virus.2309-2317
• 
  Ivan V. Kulakovskiy,Alexander V. Favorov,Vsevolod J. Makeev:
  Motif discovery and motif finding from genome-mapped DNase footprint data.2318-2325

Structural Bioinformatics

• 
  Marco Lippi,Paolo Frasconi:
  Prediction of protein beta-residue contacts by Markov logic networks with grounding-specific weights.2326-2333

Gene Expression

• 
  Cenny Taslim,Jiejun Wu,Pearlly Yan,Greg Singer,Jeffrey D. Parvin,Tim Hui-Ming Huang,Shili Lin,Kun Huang:
  Comparative study on ChIP-seq data: normalization and binding pattern characterization.2334-2340
• 
  Pierre Nicolas,Aurélie Leduc,Stéphane Robin,Simon Rasmussen,Hanne Jarmer,Philippe Bessières:
  Transcriptional landscape estimation from tiling array data using a model of signal shift and drift.2341-2347
• 
  Galina V. Glazko,Frank Emmert-Streib:
  Unite and conquer: univariate and multivariate approaches for finding differentially expressed gene sets.2348-2354
• 
  A. H. M. Mahbub Latif,Frank Bretz,Edgar Brunner:
  Robustness considerations in selecting efficient two-color microarray designs.2355-2361
• 
  Xiaofeng Dai,Olli Yli-Harja,Andre S. Ribeiro:
  Determining noisy attractors of delayed stochastic gene regulatory networks from multiple data sources.2362-2368
• 
  Jennifer Toolan Judy,Hongkai Ji:
  TileProbe: modeling tiling array probe effects using publicly available data.2369-2375

Genetics and Population Analysis

• 
  Øivind Skare,Nuala Sheehan,Thore Egeland:
  Identification of distant family relationships.2376-2382

Systems Biology

• 
  Stefan Jäger,Qingfeng Song,Su-Shing Chen:
  DYNAMIK: a software environment for cell DYNAmics, Motility, and Information tracKing, with an application to Ras pathways.2383-2388
• 
  Zhihui Wang,Christina M. Birch,Jonathan Sagotsky,Thomas S. Deisboeck:
  Cross-scale, cross-pathway evaluation using an agent-based non-small cell lung cancer model.2389-2396
• 
  Kevin Bleakley,Yoshihiro Yamanishi:
  Supervised prediction of drug-target interactions using bipartite local models.2397-2403

Data and Text Mining

• 
  Curtis Huttenhower,Matthew A. Hibbs,Chad L. Myers,Amy A. Caudy,David C. Hess,Olga G. Troyanskaya:
  The impact of incomplete knowledge on evaluation: an experimental benchmark for protein function prediction.2404-2410

Databases and Ontologies

• 
  David S. DeLuca,Britta Eiz-Vesper,Nektarios Ladas,Barbara Anna-Maria Khattab,Rainer Blasczyk:
  High-throughput minor histocompatibility antigen prediction.2411-2417
• 
  José A. Encinar,G. Fernandez-Ballester,Ignacio E. Sánchez,E. Hurtado-Gomez,Francois Stricher,Pedro Beltrão,Luis Serrano:
  ADAN: a database for prediction of protein-protein interaction of modular domains mediated by linear motifs.2418-2424
• 
  Xiaoqin Xia,Michael McClelland,Steffen Porwollik,Wenzhi Song,Xianling Cong,Yipeng Wang:
  WebArrayDB: cross-platform microarray data analysis and public data repository.2425-2429

Applications Note - Genome Analysis

• 
  Jong Hyun Kim,Woo-Cheol Kim,Michael S. Waterman,Sanghyun Park,Lei M. Li:
  HAPLOWSER: a whole-genome haplotype browser for personal genome and metagenome.2430-2431

Sequence Analysis

• 
  Nestor Zaburannyy,Bohdan Ostash,Victor Fedorenko:
  TTA Lynx: a web-based service for analysis of actinomycete genes containing rare TTA codon.2432-2433
• 
  Heinrich Magnus Manske,Dominic Kwiatkowski:
  SNP-o-matic.2434-2435
• 
  Quan Long,Daniel G. MacArthur,Zemin Ning,Chris Tyler-Smith:
  HI: haplotype improver using paired-end short reads.2436-2437
• 
  Antonio Martínez-Alcántara,Efren Ballesteros,Chen Feng,Mark Rojas,H. Koshinsky,Viacheslav Fofanov,Paul Havlak,Yuriy Fofanov:
  PIQA: pipeline for Illumina G1 genome analyzer data quality assessment.2438-2439

Phylogenetics

• 
  Lin Himmelmann,Dirk Metzler:
  TreeTime: an extensible C++ software package for Bayesian phylogeny reconstruction with time-calibration.2440-2441

Gene Expression

• 
  Andrew A. Pohl,Charles W. Sugnet,Tyson Clark,Kayla E. Smith,Pauline A. Fujita,Melissa S. Cline:
  Affy exon tissues: exon levels in normal tissues in human, mouse and rat.2442-2443

Genetics and Population Analysis

• 
  David Zamar,Ben W. Tripp,George Ellis,Denise Daley:
  Path: a tool to facilitate pathway-based genetic association analysis.2444-2446

Systems Biology

• 
  Aleksandar Stojmirovic,Yi-Kuo Yu:
  ITM Probe: analyzing information flow in protein networks.2447-2449
• 
  Hong Sun,Karen Lemmens,Tim Van den Bulcke,Kristof Engelen,Bart De Moor,Kathleen Marchal:
  ViTraM: visualization of transcriptional modules.2450-2451
• 
  Lucian P. Smith,Frank T. Bergmann,Deepak Chandran,Herbert M. Sauro:
  Antimony: a modular model definition language.2452-2454

Volume 25, Number 19, October 2009

Reviews - Sequence Analysis

• 
  Carsten Kemena,Cédric Notredame:
  Upcoming challenges for multiple sequence alignment methods in the high-throughput era.2455-2465

Systems Biology

• 
  Seth I. Berger,Ravi Iyengar:
  Network analyses in systems pharmacology.2466-2472

Discovery Note - Gene Expression

• 
  Antonio Marco,Charlotte Konikoff,Timothy L. Karr,Sudhir Kumar:
  Relationship between gene co-expression and sharing of transcription factor binding sites inDrosophila melanogaster.2473-2477

Original Papers - Genome Analysis

• 
  David J. Miller,Yanxin Zhang,Guoqiang Yu,Yongmei Liu,Li Chen,Carl D. Langefeld,David M. Herrington,Yue Joseph Wang:
  An algorithm for learning maximum entropy probability models of disease risk that efficiently searches and sparingly encodes multilocus genomic interactions.2478-2485
• 
  Youngchul Kim,Stefan Bekiranov,Jae K. Lee,Taesung Park:
  Double error shrinkage method for identifying protein binding sites observed by tiling arrays with limited replication.2486-2491
• 
  Mei Liu,Xue-wen Chen,Raja Jothi:
  Knowledge-guided inference of domain-domain interactions from incomplete protein-protein interaction networks.2492-2499

Sequence Analysis

• 
  Kristoffer Forslund,Erik L. L. Sonnhammer:
  Benchmarking homology detection procedures with low complexity filters.2500-2505
• 
  Byung-chul Lee,Dongsup Kim:
  A new method for revealing correlated mutations under the structural and functional constraints in proteins.2506-2513
• 
  Yangho Chen,Tade Souaiaia,Ting Chen:
  PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds.2514-2521

Phylogenetics

• 
  Patricia Buendia,Brice Cadwallader,Victor DeGruttola:
  A phylogenetic and Markov model approach for the reconstruction of mutational pathways of drug resistance.2522-2529
• 
  Li-Jung Liang,Robert E. Weiss,Benjamin D. Redelings,Marc A. Suchard:
  Improving phylogenetic analyses by incorporating additional information from genetic sequence databases.2530-2536

Structural Bioinformatics

• 
  Yves Dehouck,Aline Grosfils,Benjamin Folch,Dimitri Gilis,Philippe Bogaerts,Marianne Rooman:
  Fast and accurate predictions of protein stability changes upon mutations using statistical potentials and neural networks: PoPMuSiC-2.0.2537-2543
• 
  José Ignacio Garzón,José Ramón López-Blanco,Carles Pons,Julio A. Kovacs,Ruben Abagyan,Juan Fernández-Recio,Pablo Chacón:
  FRODOCK: a new approach for fast rotational protein-protein docking.2544-2551
• 
  Pablo Carbonell,Antonio del Sol:
  Methyl side-chain dynamics prediction based on protein structure.2552-2558
• 
  Pin-Hao Chi,Bin Pang,Dmitry Korkin,Chi-Ren Shyu:
  Efficient SCOP-fold classification and retrieval using index-based protein substructure alignments.2559-2565

Gene Expression

• 
  Natalia Jiménez-Lozano,Joan Segura,José Ramón Macías,Juanjo Vega,José María Carazo:
  aGEM: an integrative system for analyzing spatial-temporal gene-expression information.2566-2572
• 
  Yuliya V. Karpievitch,Thomas Taverner,Joshua N. Adkins,Stephen J. Callister,Gordon A. Anderson,Richard D. Smith,Alan R. Dabney:
  Normalization of peak intensities in bottom-up MS-based proteomics using singular value decomposition.2573-2580
• 
  Dustin A. Cartwright,Siobhan M. Brady,David A. Orlando,Bernd Sturmfels,Philip N. Benfey:
  Reconstructing spatiotemporal gene expression data from partial observations.2581-2587
• 
  Katrijn Van Deun,Herbert Hoijtink,Lieven Thorrez,Leentje Van Lommel,Frans Schuit,Iven Van Mechelen:
  Testing the hypothesis of tissue selectivity: the intersection-union test and a Bayesian approach.2588-2594

Genetics and Population Analysis

• 
  Jingchun Sun,Peilin Jia,Ayman H. Fanous,Bradley Todd Webb,Edwin J. C. G. van den Oord,Xiangning Chen,József Bukszár,Kenneth S. Kendler,Zhongming Zhao:
  A multi-dimensional evidence-based candidate gene prioritization approach for complex diseases-schizophrenia as a case.2595-2602

Applications Note - Genome Analysis

• 
  Maik Friedel,Swetlana Nikolajewa,Jürgen Sühnel,Thomas Wilhelm:
  DiProGB: the dinucleotide properties genome browser.2603-2604
• 
  Hyunjin Shin,Tao Liu,Arjun K. Manrai,Xiaole Shirley Liu:
  CEAS:cis-regulatory element annotation system.2605-2606

Sequence Analysis

• 
  Martin Morgan,Simon Anders,Michael F. Lawrence,Patrick Aboyoun,Hervé Pagès,Robert Gentleman:
  ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data.2607-2608
• 
  Jill L. Wegrzyn,Jennifer M. Lee,John Liechty,David B. Neale:
  PineSAP - sequence alignment and SNP identification pipeline.2609-2610

Phylogenetics

• 
  Bongshin Lee,Lev Nachmanson,George G. Robertson,Jonathan M. Carlson,David Heckerman:
  PhyloDet: a scalable visualization tool for mapping multiple traits to large evolutionary trees.2611-2612

Gene Expression

• 
  Takehiro Hashimoto,Michiel J. L. de Hoon,Sean M. Grimmond,Carsten O. Daub,Yoshihide Hayashizaki,Geoffrey J. Faulkner:
  Probabilistic resolution of multi-mapping reads in massively parallel sequencing data using MuMRescueLite.2613-2614
• 
  Nicole Cloonan,Qinying Xu,Geoffrey J. Faulkner,Darrin F. Taylor,Dave T. P. Tang,Gabriel Kolle,Sean M. Grimmond:
  RNA-MATE: a recursive mapping strategy for high-throughput RNA-sequencing data.2615-2616
• 
  Mathieu Clément-Ziza,Christophe Malabat,Christian Weber,Ivan Moszer,Tero Aittokallio,Catherine Letondal,Sandrine Rousseau:
  Genoscape: a Cytoscape plug-in to automate the retrieval and integration of gene expression data and molecular networks.2617-2618
• 
  John R. Stevens,Gabriel Nicholas:
  metahdep: meta-analysis of hierarchically dependent gene expression studies.2619-2620

Genetics and Population Analysis

• 
  Matthew E. Ritchie,Benilton S. Carvalho,Kurt N. Hetrick,Simon Tavaré,Rafael A. Irizarry:
  R/Bioconductor software for Illumina's Infinium whole-genome genotyping BeadChips.2621-2623

Erratum Genetics and Population Analysis

• 
  Nicola Bonzanni,Elzbieta Krepska,K. Anton Feenstra,Wan J. Fokkink,Thilo Kielmann,Henri E. Bal,Jaap Heringa:
  Executing multicellular differentiation: quantitative predictive modelling of C.elegans vulval development.2624

Volume 25, Number 20, October 2009

Original Papers - Genome Analysis

• 
  Sanghamitra Bandyopadhyay,Ramkrishna Mitra:
  TargetMiner: microRNA target prediction with systematic identification of tissue-specific negative examples.2625-2631

Sequence Analysis

• 
  Julien Jorda,Andrey V. Kajava:
  T-REKS: identification of Tandem REpeats in sequences with a K-meanS based algorithm.2632-2638

Structural Bioinformatics

• 
  Ami Levy-Moonshine,El-ad David Amir,Chen Keasar:
  Enhancement of beta-sheet assembly by cooperative hydrogen bonds potential.2639-2645
• 
  Fenix W. D. Huang,Jing Qin,Christian M. Reidys,Peter F. Stadler:
  Partition function and base pairing probabilities for RNA-RNA interaction prediction.2646-2654
• 
  Qiwen Dong,Shuigeng Zhou,Jihong Guan:
  A new taxonomy-based protein fold recognition approach based on autocross-covariance transformation.2655-2662
• 
  Cristian Micheletti,Henri Orland:
  MISTRAL: a tool for energy-based multiple structural alignment of proteins.2663-2669

Gene Expression

• 
  Lee Zamparo,Theodore J. Perkins:
  Statistical lower bounds on protein copy number from fluorescence expression images.2670-2676
• 
  Kengo Kinoshita,Takeshi Obayashi:
  Multi-dimensional correlations for gene coexpression and application to the large-scale data of Arabidopsis.2677-2684
• 
  Davide Risso,Maria Sofia Massa,Monica Chiogna,Chiara Romualdi:
  A modified LOESS normalization applied to microRNA arrays: a comparative evaluation.2685-2691
• 
  Guillemette Marot,Jean-Louis Foulley,Claus-Dieter Mayer,Florence Jaffrézic:
  Moderated effect size andP-value combinations for microarray meta-analyses.2692-2699
• 
  Verena Zuber,Korbinian Strimmer:
  Gene ranking and biomarker discovery under correlation.2700-2707
• 
  Chen Zhang,Chunguo Wu,Enrico Blanzieri,You Zhou,Yan Wang,Wei Du,Yanchun Liang:
  Methods for labeling error detection in microarrays based on the effect of data perturbation on the regression model.2708-2714
• 
  Matthieu Defrance,Jacques van Helden:
  info-gibbs: a motif discovery algorithm that directly optimizes information content during sampling.2715-2722

Systems Biology

• 
  Francisco J. Planes,John E. Beasley:
  An optimization model for metabolic pathways.2723-2729

Applications Note Genome Analysis

• 
  John W. Nicol,Gregg A. Helt,Steven G. Blanchard Jr.,Archana Raja,Ann E. Loraine:
  The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets.2730-2731
• 
  Jacob Almagro-Garcia,Magnus Manske,Celine Carret,Susana G. Campino,Sarah Auburn,Bronwyn L. MacInnis,Gareth Maslen,Arnab Pain,Christopher I. Newbold,Dominic Kwiatkowski,Taane G. Clark:
  SnoopCGH: software for visualizing comparative genomic hybridization data.2732-2733

Sequence Analysis

• 
  Paulo C. Carvalho,Tao Xu,Xuemei Han,Daniel Cociorva,Valmir Carneiro Barbosa,John R. Yates III:
  YADA: a tool for taking the most out of high-resolution spectra.2734-2736
• 
  Erik Kristiansson,Philip Hugenholtz,Daniel Dalevi:
  ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes.2737-2738
• 
  Olivier Sand,Morgane Thomas-Chollier,Jacques van Helden:
  Retrieve-ensembl-seq: user-friendly and large-scale retrieval of single or multi-genome sequences from Ensembl.2739-2740

Structural Bioinformatics

• 
  Filippo Rusconi:
  massXpert 2: a cross-platform software environment for polymer chemistry modelling and simulation/analysis of mass spectrometric data.2741-2742
• 
  Tyanko Aleksiev,Raffaello Potestio,Francesco Pontiggia,Stefano Cozzini,Cristian Micheletti:
  PiSQRD: a web server for decomposing proteins into quasi-rigid dynamical domains.2743-2744
• 
  Zsuzsanna Dosztányi,Bálint Mészáros,István Simon:
  ANCHOR: web server for predicting protein binding regions in disordered proteins.2745-2746

Genetics and Population Analysis

• 
  Joao S. Lopes,David J. Balding,Mark A. Beaumont:
  PopABC: a program to infer historical demographic parameters.2747-2749
• 
  Karol Estrada,Anis Abuseiris,Frank G. Grosveld,André G. Uitterlinden,Tobias A. Knoch,Fernando Rivadeneira:
  GRIMP: a web- and grid-based tool for high-speed analysis of large-scale genome-wide association using imputed data.2750-2752
• 
  Steven Maenhout,Bernard De Baets,Geert Haesaert:
  CoCoa: a software tool for estimating the coefficient of coancestry from multilocus genotype data.2753-2754

Systems Biology

• 
  Eva Grafahrend-Belau,Christian Klukas,Björn H. Junker,Falk Schreiber:
  FBA-SimVis: interactive visualization of constraint-based metabolic models.2755-2757
• 
  Magdalena Feldhahn,Pierre Dönnes,Philipp Thiel,Oliver Kohlbacher:
  FRED - a framework for T-cell epitope detection.2758-2759
• 
  Marc Streit,Alexander Lex,Michael Kalkusch,Kurt Zatloukal,Dieter Schmalstieg:
  Caleydo: connecting pathways and gene expression.2760-2761
• 
  Colm O'Dushlaine,Elaine Kenny,Elizabeth A. Heron,Ricardo Segurado,Michael Gill,Derek W. Morris,Aiden P. Corvin:
  The SNP ratio test: pathway analysis of genome-wide association datasets.2762-2763

Data and Text Mining

• 
  Jan Urban,Jan Vanek,Jirí Soukup,Dalibor Stys:
  Expertomica metabolite profiling: getting more information from LC-MS using the stochastic systems approach.2764-2767

Databases and Ontologies

• 
  Maria Krestyaninova,Andris Zarins,Juris Viksna,Natalja Kurbatova,Peteris Rucevskis,Sudeshna Guha Neogi,Mike Gostev,Teemu Perheentupa,Juha Knuuttila,Amy Barrett,Ilkka Lappalainen,Johan Rung,Karlis Podnieks,Ugis Sarkans,Mark I. McCarthy,Alvis Brazma:
  A System for Information Management in BioMedical Studies - SIMBioMS.2768-2769

Letters to the Editor - Data and Text Mining

• 
  Aurélie Névéol,James G. Mork,Alan R. Aronson:
  Comment on 'MeSH-up: effective MeSH text classification for improved document retrieval'.2770-2771
• 
  Dolf Trieschnigg,Piotr Pezik,Vivian Lee,Franciska de Jong,Wessel Kraaij,Dietrich Rebholz-Schuhmann:
  Response to comment on 'MeSH-up: effective MeSH text classification for improved document retrieval'.2772

Databases and Ontologies

• 
  Brendan Elliott,Mustafa Kirac,Ali Cakmak,Gökhan Yavas,Stephen Mayes,En Cheng,Yuan Wang,Chirag Gupta,Gultekin Özsoyoglu,Z. Meral Özsoyoglu:
  Corrigendum for Elliott, B.et al., 'PathCase pathways database system', Bioinformatics 2008, 24(21) 2526-2533.2773

Volume 25, Number 21, November 2009

Original Papers - Genome Analysis

• 
  Mitsunori Kayano,Ichigaku Takigawa,Motoki Shiga,Koji Tsuda,Hiroshi Mamitsuka:
  Efficiently finding genome-wide three-way gene interactions from transcript- and genotype-data.2735-2743

Sequence Analysis

• 
  Biao Li,Vidhya G. Krishnan,Matthew E. Mort,Fuxiao Xin,Kishore K. Kamati,David N. Cooper,Sean D. Mooney,Predrag Radivojac:
  Automated inference of molecular mechanisms of disease from amino acid substitutions.2744-2750

Structural Bioinformatics

• 
  Aleksandar Poleksic:
  Algorithms for optimal protein structure alignment.2751-2756
• 
  Lisa Bartoli,Piero Fariselli,Anders Krogh,Rita Casadio:
  CCHMM_PROF: a HMM-based coiled-coil predictor with evolutionary information.2757-2763

Gene Expression

• 
  Sandra Waaijenborg,Aeilko H. Zwinderman:
  Correlating multiple SNPs and multiple disease phenotypes: penalized non-linear canonical correlation analysis.2764-2771
• 
  Michael Dannemann,Anna Lorenc,Ines Hellmann,Philipp Khaitovich,Michael Lachmann:
  The effects of probe binding affinity differences on gene expression measurements and how to deal with them.2772-2779
• 
  YounJeong Choi,Christina Kendziorski:
  Statistical methods for gene set co-expression analysis.2780-2786
• 
  Andreas Keller,Christina Backes,Andreas Gerasch,Michael Kaufmann,Oliver Kohlbacher,Eckart Meese,Hans-Peter Lenhof:
  A novel algorithm for detecting differentially regulated paths based on gene set enrichment analysis.2787-2794
• 
  Anindya Bhattacharya,Rajat K. De:
  Bi-correlation clustering algorithm for determining a set of co-regulated genes.2795-2801

Genetics and Population Analysis

• 
  Zhi Wei,Wenguang Sun,Kai Wang,Hakon Hakonarson:
  Multiple testing in genome-wide association studies via hidden Markov models.2802-2808
• 
  Moritz Gerstung,Michael Baudis,Holger Moch,Niko Beerenwinkel:
  Quantifying cancer progression with conjunctive Bayesian networks.2809-2815

Systems Biology

• 
  Irina Surovtsova,Natalia Simus,Thomas Lorenz,Artjom König,Sven Sahle,Ursula Kummer:
  Accessible methods for the dynamic time-scale decomposition of biochemical systems.2816-2823
• 
  Victor Olariu,Daniel Coca,Stephen A. Billings,Peter Tonge,Paul Gokhale,Peter W. Andrews,Visakan Kadirkamanathan:
  Modified variational Bayes EM estimation of hidden Markov tree model of cell lineages.2824-2830
• 
  Ze Tian,TaeHyun Hwang,Rui Kuang:
  A hypergraph-based learning algorithm for classifying gene expression and arrayCGH data with prior knowledge.2831-2838

Applications Note - Genome Analysis

• 
  Timo Lassmann,Yoshihide Hayashizaki,Carsten O. Daub:
  TagDust - a program to eliminate artifacts from next generation sequencing data.2839-2840

Sequence Analysis

• 
  Andrew D. Smith,Wen-Yu Chung,Emily Hodges,Jude Kendall,Gregory J. Hannon,James Hicks,Zhenyu Xuan,Michael Q. Zhang:
  Updates to the RMAP short-read mapping software.2841-2842

Structural Bioinformatics

• 
  David La,Juan Esquivel-Rodríguez,Vishwesh Venkatraman,Bin Li,Lee Sael,Stephen Ueng,Steven Ahrendt,Daisuke Kihara:
  3D-SURFER: software for high-throughput protein surface comparison and analysis.2843-2844

Genetics and Population Analysis

• 
  Mattias Jakobsson:
  COMPASS: a program for generating serial samples under an infinite sites model.2845-2847

Systems Biology

• 
  Chris J. Myers,Nathan A. Barker,Kevin R. Jones,Hiroyuki Kuwahara,Curtis Madsen,Nam-Phuong D. Nguyen:
  iBioSim: a tool for the analysis and design of genetic circuits.2848-2849
• 
  Tae-Sung Jung,Hock Chuan Yeo,Satty G. Reddy,Wan-Sup Cho,Dong-Yup Lee:
  WEbcoli: an interactive and asynchronous web application forin silico design and analysis of genome-scaleE.coli model.2850-2852
• 
  Nicola Soranzo,Claudio Altafini:
  ERNEST: a toolbox for chemical reaction network theory.2853-2854
• 
  Kim-Anh Lê Cao,Ignacio González,Sébastien Déjean:
  integrOmics: an R package to unravel relationships between two omics datasets.2855-2856
• 
  Giovanni Scardoni,Michele Petterlini,Carlo Laudanna:
  Analyzing biological network parameters with CentiScaPe.2857-2859

Databases and Ontologies

• 
  Kumaran Kandasamy,Shivakumar Keerthikumar,Rajesh Raju,T. S. Keshava Prasad,Y. L. Ramachandra,S. Sujatha Mohan,Akhilesh Pandey:
  PathBuilder - open source software for annotating and developing pathway resources.2860-2862

ISMB/ECCB 2009 Special Interest Group on Short Read Sequencing Report

• 
  Michael Brudno,Paul Medvedev,Jens Stoye,Francisco M. de la Vega:
  A report on the 2009 SIG on short read sequencing and algorithms (Short-SIG).2863-2864

Original Papers

• 
  Kai Ye,Marcel H. Schulz,Quan Long,Rolf Apweiler,Zemin Ning:
  Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads.2865-2871

Sequence Analysis

• 
  Inanç Birol,Shaun D. Jackman,Cydney B. Nielsen,Jenny Q. Qian,Richard Varhol,Greg Stazyk,Ryan D. Morin,Yongjun Zhao,Martin Hirst,Jacqueline E. Schein,Douglas E. Horsman,Joseph M. Connors,Randy D. Gascoyne,Marco A. Marra,Steven J. M. Jones:
  De novo transcriptome assembly with ABySS.2872-2877
• 
  Bas E. Dutilh,Martijn A. Huynen,Marc Strous:
  Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly.2878-2881

Gene Expression

• 
  Gerald T. Quon,Quaid Morris:
  ISOLATE: a computational strategy for identifying the primary origin of cancers using high-throughput sequencing.2882-2889

Volume 25, Number 22, November 2009

Original Papers Systems Biology

• 
  Ruslan Sadreyev,Jamison D. Feramisco,Hensin Tsao,Nick V. Grishin:
  Phenotypic categorization of genetic skin diseases reveals new relations between phenotypes, genes and pathways.2891-2896

Genome Analysis

• 
  Thao T. Tran,Fengfeng Zhou,Sarah Marshburn,Mark Stead,Sidney R. Kushner,Ying Xu:
  De novo computational prediction of non-coding RNA genes in prokaryotic genomes.2897-2905
• 
  Ronglai Shen,Adam B. Olshen,Marc Ladanyi:
  Integrative clustering of multiple genomic data types using a joint latent variable model with application to breast and lung cancer subtype analysis.2906-2912

Sequence Analysis

• 
  Babak Bostan,Russell Greiner,Duane Szafron,Paul Lu:
  Predicting homologous signaling pathways using machine learning.2913-2920

Structural Bioinformatics

• 
  Ofer Rahat,Uri Alon,Yaakov Levy,Gideon Schreiber:
  Understanding hydrogen-bond patterns in proteins using network motifs.2921-2928

Systems Biology

• 
  Shahzia Anjum,Arnaud Doucet,Christopher C. Holmes:
  A boosting approach to structure learning of graphs with and without prior knowledge.2929-2936
• 
  Tarmo Äijö,Harri Lähdesmäki:
  Learning gene regulatory networks from gene expression measurements using non-parametric molecular kinetics.2937-2944
• 
  Alexander Senf,Xue-wen Chen:
  Identification of genes involved in the same pathways using a Hidden Markov Model-based approach.2945-2954

Data and Text Mining

• 
  Smriti R. Ramakrishnan,Christine Vogel,Taejoon Kwon,Luiz O. F. Penalva,Edward M. Marcotte,Daniel P. Miranker:
  Mining gene functional networks to improve mass-spectrometry-based protein identification.2955-2961
• 
  Hisashi Kashima,Yoshihiro Yamanishi,Tsuyoshi Kato,Masashi Sugiyama,Koji Tsuda:
  Simultaneous inference of biological networks of multiple species from genome-wide data and evolutionary information: a semi-supervised approach.2962-2968
• 
  Zengyou He,Weichuan Yu:
  Improving peptide identification with single-stage mass spectrum peaks.2969-2974
• 
  Marco J. L. de Groot,Rogier J. P. van Berlo,Wouter A. van Winden,Peter J. T. Verheijen,Marcel J. T. Reinders,Dick de Ridder:
  Metabolite and reaction inference based on enzyme specificities.2975-2982
• 
  Kristina M. Hettne,Rob H. Stierum,Martijn J. Schuemie,Peter J. M. Hendriksen,Bob J. A. Schijvenaars,Erik M. van Mulligen,Jos Kleinjans,Jan A. Kors:
  A dictionary to identify small molecules and drugs in free text.2983-2991
• 
  Paul E. Anderson,Michael L. Raymer,Benjamin J. Kelly,Nicholas V. Reo,Nicholas J. DelRaso,Travis E. Doom:
  Characterization of¹H NMR spectroscopic data and the generation of synthetic validation sets.2992-3000

Databases and Ontologies

• 
  Feng Tian,Parantu K. Shah,Xiangjun Liu,Nicolas N. Negre,Jia Chen,Oleksiy Karpenko,Kevin P. White,Robert L. Grossman:
  Flynet: a genomic resource forDrosophila melanogaster transcriptional regulatory networks.3001-3004
• 
  Bertrand Néron,Hervé Ménager,Corinne Maufrais,Nicolas Joly,Julien Maupetit,Sébastien Letort,Sébastien Carrère,Pierre Tufféry,Catherine Letondal:
  Mobyle: a new full web bioinformatics framework.3005-3011
• 
  Sarala M. Wimalaratne,Matt D. B. Halstead,Catherine M. Lloyd,Mike T. Cooling,Edmund J. Crampin,Poul M. F. Nielsen:
  A method for visualizing CellML models.3012-3019
• 
  Patrik Björkholm,Erik L. L. Sonnhammer:
  Comparative analysis and unification of domain-domain interaction networks.3020-3025

Applications Note Systems Biology

• 
  Allyson L. Lister,Matthew R. Pocock,Morgan L. Taschuk,Anil Wipat:
  Saint: a lightweight integration environment for model annotation.3026-3027
• 
  Pauli Rämö,Raphael Sacher,Berend Snijder,Boris Begemann,Lucas Pelkmans:
  CellClassifier: supervised learning of cellular phenotypes.3028-3030

Data and Text Mining

• 
  Richard Tzong-Han Tsai,Hong-Jie Dai,Po-Ting Lai,Chi-Hsin Huang:
  PubMed-EX: a web browser extension to enhance PubMed search with text mining features.3031-3032
• 
  Yue Fan,Thomas Brendan Murphy,R. William G. Watson:
  digeR: a graphical user interface R package for analyzing 2D-DIGE data.3033-3034
• 
  Anastasia Alexandridou,George T. Tsangaris,Konstantinos N. Vougas,Konstantina S. Nikita,George M. Spyrou:
  UniMaP: finding unique mass and peptide signatures in the human proteome.3035-3037
• 
  Zhiyong Lu,Natalie Xie,W. John Wilbur:
  Identifying related journals through log analysis.3038-3039

Databases and Ontologies

• 
  Ken Youens-Clark,Benjamin Faga,Immanuel Yap,Lincoln Stein,Doreen Ware:
  CMap 1.01: a comparative mapping application for the Internet.3040-3042
• 
  Gabriel F. Berriz,John E. Beaver,Can Cenik,Murat Tasan,Frederick P. Roth:
  Next generation software for functional trend analysis.3043-3044
• 
  David Binns,Emily Dimmer,Rachael P. Huntley,Daniel Barrell,Claire O'Donovan,Rolf Apweiler:
  QuickGO: a web-based tool for Gene Ontology searching.3045-3046

Corrigendum - Databases and Ontologies

• 
  Andrew F. Neuwald:
  Rapid detection, classification and accurate alignment of up to a million or more related protein sequences.3047

Volume 25, Number 23, December 2009

Review - Gene Expression

• 
  Panagiotis Alexiou,Manolis Maragkakis,Giorgos L. Papadopoulos,Martin Reczko,Artemis G. Hatzigeorgiou:
  Lost in translation: an assessment and perspective for computational microRNA target identification.3049-3055

Discovery Note - Gene Expression

• 
  David Hiller,Hui Jiang,Weihong Xu,Wing Hung Wong:
  Identifiability of isoform deconvolution from junction arrays and RNA-Seq.3056-3059

Data and Text Mining

• 
  Lior Shamir,Catherine A. Wolkow,Ilya G. Goldberg:
  Quantitative measurement of aging using image texture entropy.3060-3063

Original Papers - Sequence Analysis

• 
  Vera Afreixo,Carlos A. C. Bastos,Armando J. Pinho,Sara P. Garcia,Paulo Jorge S. G. Ferreira:
  Genome analysis with inter-nucleotide distances.3064-3070
• 
  Mensur Dlakic:
  HHsvm: fast and accurate classification of profile-profile matches identified by HHsearch.3071-3076
• 
  Nicolas Terrapon,Olivier Gascuel,Eric Maréchal,Laurent Bréhélin:
  Detection of new protein domains using co-occurrence: application toPlasmodium falciparum.3077-3083
• 
  Jia Zeng,Reda Alhajj,Douglas J. Demetrick:
  Adaptive multi-agent architecture for functional sequence motifs recognition.3084-3092

Phylogenetics

• 
  Christian Blouin,Scott Perry,Allan Lavell,Edward Susko,Andrew J. Roger:
  Reproducing the manual annotation of multiple sequence alignments using a SVM classifier.3093-3098

Structural Bioinformatics

• 
  Christopher Kauffman,George Karypis:
  LIBRUS: combined machine learning and homology information for sequence-based ligand-binding residue prediction.3099-3107
• 
  Kei Yura,Steven Hayward:
  The interwinding nature of protein-protein interfaces and its implication for protein complex formation.3108-3113

Gene Expression

• 
  Darya Chudova,Alexander Ihler,Kevin K. Lin,Bogi Andersen,Padhraic Smyth:
  Bayesian detection of non-sinusoidal periodic patterns in circadian expression data.3114-3120
• 
  Peter J. Park,Sek Won Kong,Toma Tebaldi,Weil R. Lai,Simon Kasif,Isaac S. Kohane:
  Integration of heterogeneous expression data sets extends the role of the retinol pathway in diabetes and insulin resistance.3121-3127
• 
  Stefan P. Albaum,Heiko Neuweger,Benjamin Fränzel,Sita Lange,Dominik Mertens,Christian Trötschel,Dirk Wolters,Jörn Kalinowski,Tim W. Nattkemper,Alexander Goesmann:
  Qupe - a Rich Internet Application to take a step forward in the analysis of mass spectrometry-based quantitative proteomics experiments.3128-3134

Systems Biology

• 
  Markus Leber,Volker Egelhofer,Ida Schomburg,Dietmar Schomburg:
  Automatic assignment of reaction operators to enzymatic reactions.3135-3142
• 
  Jimin Song,Mona Singh:
  How and when should interactome-derived clusters be used to predict functional modules and protein function?3143-3150
• 
  Hojung Nam,Bong Chul Chung,Younghoon Kim,Ki Young Lee,Doheon Lee:
  Combining tissue transcriptomics and urine metabolomics for breast cancer biomarker identification.3151-3157
• 
  Luis F. de Figueiredo,Adam Podhorski,Angel Rubio,Christoph Kaleta,John E. Beasley,Stefan Schuster,Francisco J. Planes:
  Computing the shortest elementary flux modes in genome-scale metabolic networks.3158-3165
• 
  Waqar Ali,Charlotte M. Deane:
  Functionally guided alignment of protein interaction networks for module detection.3166-3173

Data and Text Mining

• 
  Shashank Agarwal,Hong Yu:
  Automatically classifying sentences in full-text biomedical articles into Introduction, Methods, Results and Discussion.3174-3180

Applications Note - Sequence Analysis

• 
  Janne H. Korhonen,Petri Martinmäki,Cinzia Pizzi,Pasi Rastas,Esko Ukkonen:
  MOODS: fast search for position weight matrix matches in DNA sequences.3181-3182

Structural Bioinformatics

• 
  Romina Oliva,Janet M. Thornton,Marialuisa Pellegrini-Calace:
  PoreLogo: a new tool to analyse, visualize and compare channels in transmembrane proteins.3183-3184
• 
  Dario Ghersi,Roberto Sanchez:
  EASYMIFS and SITEHOUND: a toolkit for the identification of ligand-binding sites in protein structures.3185-3186
• 
  Thomas C. Bishop:
  VDNA: The virtual DNA plug-in for VMD.3187-3188

Genetics and Population Analysis

• 
  Dmitry A. Filatov:
  Processing and population genetic analysis of multigenic datasets with ProSeq3 software.3189-3190

Systems Biology

• 
  Victor X. Jin,Jeff Apostolos,Naga Satya Venkateswara Ra Nagisetty,Peggy J. Farnham:
  W-ChIPMotifs: a web application tool forde novo motif discovery from ChIP-based high-throughput data.3191-3193

Databases and Ontologies

• 
  Richard Easty,Nikolay Nikolov:
  Client-side integration of life science literature resources.3194-3196
• 
  Carl Herrmann,Sèverine Bérard,Laurent Tichit:
  SimCT: a generic tool to visualize ontology-based relationships for biological objects.3197-3198
• 
  Ka-Lok Ng,Hsueh-Chuan Liu,Shan-Chih Lee:
  ncRNAppi - a tool for identifying disease-related miRNA and siRNA targeting pathways.3199-3201

Letter to the Editor Systems Biology

• 
  Karoline Faust,Didier Croes,Jacques van Helden:
  In response to 'Can sugars be produced from fatty acids? A test case for pathway analysis tools'.3202-3205

Volume 25, Number 24, December 2009

Original Papers - Genome Analysis

• 
  Jacob F. Degner,John C. Marioni,Athma A. Pai,Joseph K. Pickrell,Everlyne Nkadori,Yoav Gilad,Jonathan K. Pritchard:
  Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data.3207-3212
• 
  Xiaoxiao Kong,Cavan Reilly:
  A Bayesian approach to the alignment of mass spectra.3213-3220
• 
  Mirjana Domazet-Loso,Bernhard Haubold:
  Efficient estimation of pairwise distances between genomes.3221-3227
• 
  Martin Schäfer,Holger Schwender,Sylvia Merk,Claudia Haferlach,Katja Ickstadt,Martin Dugas:
  Integrated analysis of copy number alterations and gene expression: a bivariate assessment of equally directed abnormalities.3228-3235

Sequence Analysis

• 
  Michiaki Hamada,Kengo Sato,Hisanori Kiryu,Toutai Mituyama,Kiyoshi Asai:
  CentroidAlign: fast and accurate aligner for structured RNAs by maximizing expected sum-of-pairs score.3236-3243
• 
  Ian M. Carr,J. I. Robinson,R. Dimitriou,Alexander F. Markham,A. W. Morgan,David T. Bonthron:
  Inferring relative proportions of DNA variants from sequencing electropherograms.3244-3250
• 
  Michael Beckstette,Robert Homann,Robert Giegerich,Stefan Kurtz:
  Significant speedup of database searches with HMMs by search space reduction with PSSM family models.3251-3258

Structural Bioinformatics

• 
  Magdalena A. Jonikas,Randall J. Radmer,Russ B. Altman:
  Knowledge-based instantiation of full atomic detail into coarse-grain RNA 3D structural models.3259-3266

Gene Expression

• 
  Curtis Huttenhower,K. Tsheko Mutungu,Natasha Indik,Woongcheol Yang,Mark Schroeder,Joshua J. Forman,Olga G. Troyanskaya,Hilary A. Coller:
  Detailing regulatory networks through large scale data integration.3267-3274

Genetics and Population Analysis

• 
  Christine Herold,Michael Steffens,Felix F. Brockschmidt,Max P. Baur,Tim Becker:
  INTERSNP: genome-wide interaction analysis guided by a priori information.3275-3281

Systems Biology

• 
  Philip Gerlee,L. Lizana,Kim Sneppen:
  Pathway identification by network pruning in the metabolic network ofEscherichia coli.3282-3288
• 
  Ranjit Randhawa,Clifford A. Shaffer,John J. Tyson:
  Model aggregation: a building-block approach to creating large macromolecular regulatory networks.3289-3295

Data and Text Mining

• 
  Matti Pirinen:
  Estimating population haplotype frequencies from pooled SNP data using incomplete database information.3296-3302
• 
  Alfonso Ibáñez,Pedro Larrañaga,Concha Bielza:
  Predicting citation count ofBioinformatics papers within four years of publication.3303-3309
• 
  Qingliang Li,Yanli Wang,Stephen H. Bryant:
  A novel method for mining highly imbalanced high-throughput screening data in PubChem.3310-3316

Applications Note - Genome Analysis

• 
  Christine Rousseau,Mathieu Gonnet,Marc Le Romancer,Jacques Nicolas:
  CRISPI: a CRISPR interactive database.3317-3318
• 
  Sarbashis Das,Anchal Vishnoi,Alok Bhattacharya:
  ABWGAT: anchor-based whole genome analysis tool.3319-3320
• 
  Yoshihiro Kawahara,Ryuichi Sakate,Akihiro Matsuya,Katsuhiko Murakami,Yoshiharu Sato,Hao Zhang,Takashi Gojobori,Takeshi Itoh,Tadashi Imanishi:
  G-compass: a web-based comparative genome browser between human and other vertebrate genomes.3321-3322

Gene Expression

• 
  Pascal Gellert,Shizuka Uchida,Thomas Braun:
  Exon Array Analyzer: a web interface for Affymetrix exon array analysis.3323-3324
• 
  Heidi Dvinge,Paul Bertone:
  HTqPCR: high-throughput analysis and visualization of quantitative real-time PCR data in R.3325-3326

Systems Biology

• 
  Kevin R. Brown,David Otasek,Muhammad Ali,Michael J. McGuffin,Wing Xie,Baiju Devani,Ian Lawson van Toch,Igor Jurisica:
  NAViGaTOR: Network Analysis, Visualization and Graphing Toronto.3327-3329

Letter to the Editor - Systems Biology

• 
  Luis F. de Figueiredo,Stefan Schuster,Christoph Kaleta,David A. Fell:
  Response to comment on 'Can sugars be produced from fatty acids? A test case for pathway analysis tools'.3330-3331