Bioinformatics, Volume 28

Volume 28, Number 1, January 2012

• Yang Chen, Jin Gu, Dan Li, Shao Li:
  Time-course network analysis reveals TNF-α can promote G₁/S transition of cell cycle in vascular endothelial cells. 1-4
  

• Minzhu Xie, Jing Li, Tao Jiang:
  Detecting genome-wide epistases based on the clustering of relatively frequent items. 5-12
  

• Guohui Yao, Liang Ye, Hongyu Gao, Patrick Minx, Wesley C. Warren, George M. Weinstock:
  Graph accordance of next-generation sequence assemblies. 13-16
  
• David Langenberger, Sachin Pundhir, Claus Thorn Ekstrøm, Peter F. Stadler, Steve Hoffmann, Jan Gorodkin:
  deepBlockAlign: a tool for aligning RNA-seq profiles of read block patterns. 17-24
  
• Natsuhiro Ichinose, Tetsushi Yada, Osamu Gotoh:
  Large-scale motif discovery using DNA Gray code and equiprobable oligomers. 25-31
  
• Dapeng Li, Tonghua Li, Peisheng Cong, Wenwei Xiong, Jiangming Sun:
  A novel structural position-specific scoring matrix for the prediction of protein secondary structures. 32-39
  
• Arief Gusnanto, Henry M. Wood, Yudi Pawitan, Pamela Rabbitts, Stefano Berri:
  Correcting for cancer genome size and tumour cell content enables better estimation of copy number alterations from next-generation sequence data. 40-47
  

• Ryan M. Ames, Daniel Money, Vikramsinh P. Ghatge, Simon Whelan, Simon C. Lovell:
  Determining the evolutionary history of gene families. 48-55
  

• Gabriel Cuellar-Partida, Fabian A. Buske, Robert C. McLeay, Tom Whitington, William Stafford Noble, Timothy L. Bailey:
  Epigenetic priors for identifying active transcription factor binding sites. 56-62
  
• Ming Hu, Yu Zhu, Jeremy M. G. Taylor, Jun S. Liu, Zhaohui S. Qin:
  Using Poisson mixed-effects model to quantify transcript-level gene expression in RNA-Seq. 63-68
  

• Stefan Maetschke, Martin Simonsen, Melissa J. Davis, Mark A. Ragan:
  Gene Ontology-driven inference of protein-protein interactions using inducers. 69-75
  
• Nicola Soranzo, Fahimeh Ramezani, Giovanni Iacono, Claudio Altafini:
  Decompositions of large-scale biological systems based on dynamical properties. 76-83
  
• Emmanuelle Becker, Benoît Robisson, Charles E. Chapple, Alain Guénoche, Marie-Christine Brun:
  Multifunctional proteins revealed by overlapping clustering in protein interaction network. 84-90
  
• Muhammad Tahir, Asifullah Khan, Abdul Majid:
  Protein subcellular localization of fluorescence imagery using spatial and transform domain features. 91-97
  
• Xiujun Zhang, Xing-Ming Zhao, Kun He, Le Lu, Yongwei Cao, Jingdong Liu, Jin-Kao Hao, Zhi-Ping Liu, Luonan Chen:
  Inferring gene regulatory networks from gene expression data by path consistency algorithm based on conditional mutual information. 98-104
  
• Edward Y. Chen, Huilei Xu, Simon Gordonov, Maribel P. Lim, Matthew H. Perkins, Avi Ma'ayan:
  Expression2Kinases: mRNA profiling linked to multiple upstream regulatory layers. 105-111
  

• Daniel J. Stekhoven, Peter Bühlmann:
  MissForest - non-parametric missing value imputation for mixed-type data. 112-118
  

• Xavier Rafael-Palou, Michael P. Schroeder, Núria López-Bigas:
  SVGMap: configurable image browser for experimental data. 119-120
  
• Kun Liang, Sündüz Keles:
  Detecting differential binding of transcription factors with ChIP-seq. 121-122
  
• Francesco Vezzi, Cristian Del Fabbro, Alexandru I. Tomescu, Alberto Policriti:
  rNA: a fast and accurate short reads numerical aligner. 123-124
  

• Yongan Zhao, Haixu Tang, Yuzhen Ye:
  RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data. 125-126
  
• Manal Kalkatawi, Farania Rangkuti, Michael Schramm, Boris R. Jankovic, Allan Kamau, Rajesh Chowdhary, John A. C. Archer, Vladimir B. Bajic:
  Dragon PolyA Spotter: predictor of poly(A) motifs within human genomic DNA sequences. 127-129
  
• Marc Torrent, Paolo Di Tommaso, David Pulido, Victòria M. Nogués, Cédric Notredame, Ester Boix, David Andreu:
  AMPA: an automated web server for prediction of protein antimicrobial regions. 130-131
  
• Mattia C. F. Prosperi, Marco Salemi:
  QuRe: software for viral quasispecies reconstruction from next-generation sequencing data. 132-133
  

• Céline Bellenguez, Amy Strange, Colin Freeman, Peter Donnelly, Chris C. A. Spencer:
  A robust clustering algorithm for identifying problematic samples in genome-wide association studies. 134-135
  

• Brian Pratt, J. Jeffry Howbert, Natalie I. Tasman, Erik J. Nilsson:
  MR-Tandem: parallel X!Tandem using Hadoop MapReduce on Amazon Web Services. 136-137
  
• Walter Georgescu, John P. Wikswo, Vito Quaranta:
  CellAnimation: an open source MATLAB framework for microscopy assays. 138-139
  

• Stephanie A. Canny, Yasel Cruz, Mark R. Southern, Patrick R. Griffin:
  PubChem promiscuity: a web resource for gathering compound promiscuity data from PubChem. 140-141
  

• E. Dassi, A. Malossini, A. Re, Tommaso Mazza, T. Tebaldi, L. Caputi, A. Quattrone:
  AURA: Atlas of UTR Regulatory Activity. 142-144
  

• Xiang Wan, Can Yang, Weichuan Yu:
  Comments on 'An empirical comparison of several recent epistatic interaction detection methods'. 145-146
  

• Yue Wang, Guimei Liu, Mengling Feng, Limsoon Wong:
  Response: an empirical comparison of several recent epistatic interaction detection methods. 147-148
  

• Marie Brown, David C. Wedge, Royston Goodacre, Douglas B. Kell, Philip N. Baker, Louise C. Kenny, Mamas A. Mamas, Ludwig Neyses, Warwick B. Dunn:
  Automated workflows for accurate mass-based putative metabolite identification in LC/MS-derived metabolomic datasets. 149
  
• Farhad Hormozdiari, Faraz Hach, Süleyman Cenk Sahinalp, Evan E. Eichler, Can Alkan:
  Sensitive and fast mapping of di-base encoded reads. 150
  

Volume 28, Number 2, January 2012

• Gerard Wong, Christopher Leckie, Adam Kowalczyk:
  FSR: feature set reduction for scalable and accurate multi-class cancer subtype classification based on copy number. 151-159
  
• David R. Riley, Samuel V. Angiuoli, Jonathan Crabtree, Julie C. Dunning Hotopp, Herve Tettelin:
  Using Sybil for interactive comparative genomics of microbes on the web. 160-166
  

• Jiarui Ding, Ali Bashashati, Andrew Roth, Arusha Oloumi, Kane Tse, Thomas Zeng, Gholamreza Haffari, Martin Hirst, Marco A. Marra, Anne Condon, Sam Aparicio, Sohrab P. Shah:
  Feature-based classifiers for somatic mutation detection in tumour-normal paired sequencing data. 167-175
  
• Yi-Fei Huang, Geoffrey Brian Golding:
  Inferring sequence regions under functional divergence in duplicate genes. 176-183
  
• David T. Jones, Daniel W. A. Buchan, Domenico Cozzetto, Massimiliano Pontil:
  PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments. 184-190
  

• Benjamin Albrecht, Celine Scornavacca, Alberto Cenci, Daniel H. Huson:
  Fast computation of minimum hybridization networks. 191-197
  

• Anna Philips, Kaja Milanowska, Grzegorz Lach, Michal Boniecki, Kristian Rother, Janusz M. Bujnicki:
  MetalionRNA: computational predictor of metal-binding sites in RNA structures. 198-205
  

• Mark Maienschein-Cline, Jie Zhou, Kevin P. White, Roger Sciammas, Aaron R. Dinner:
  Discovering transcription factor regulatory targets using gene expression and binding data. 206-213
  
• Geert Geeven, Ronald E. van Kesteren, August B. Smit, Mathisca C. M. de Gunst:
  Identification of context-specific gene regulatory networks with GEMULA - gene expression modeling using LAsso. 214-221
  
• Bettina Grün, Theresa Scharl, Friedrich Leisch:
  Modelling time course gene expression data with finite mixtures of linear additive models. 222-228
  

• Hua Wang, Feiping Nie, Heng Huang, Sungeun Kim, Kwangsik Nho, Shannon L. Risacher, Andrew J. Saykin, Li Shen:
  Identifying quantitative trait loci via group-sparse multitask regression and feature selection: an imaging genetics study of the ADNI cohort. 229-237
  

• Jose L. Rubio-Guivernau, Vasily Gurchenkov, Miguel A. Luengo-Oroz, Louise Duloquin, Paul Bourgine, Andrés Santos, Nadine Peyriéras, María J. Ledesma-Carbayo:
  Wavelet-based image fusion in multi-view three-dimensional microscopy. 238-245
  

• José Caldas, Nils Gehlenborg, Eeva Kettunen, Ali Faisal, Mikko Rönty, Andrew G. Nicholson, Sakari Knuutila, Alvis Brazma, Samuel Kaski:
  Data-driven information retrieval in heterogeneous collections of transcriptomics data links SIM2s to malignant pleural mesothelioma. 246-253
  
• Nathan Harmston, Wendy Filsell, Michael P. H. Stumpf:
  Which species is it? Species-driven gene name disambiguation using random walks over a mixture of adjacency matrices. 254-260
  
• Jean-Philippe Carralot, Arnaud Ogier, Annette Boese, Auguste Genovesio, Priscille Brodin, Peter Sommer, Thierry Dorval:
  A novel specific edge effect correction method for RNA interference screenings. 261-268
  

• Fidel Ramírez, Glenn Lawyer, Mario Albrecht:
  Novel search method for the discovery of functional relationships. 269-276
  

• Yan W. Asmann, Sumit Middha, Asif Hossain, Saurabh Baheti, Ying Li, High-Seng Chai, Zhifu Sun, Patrick H. Duffy, Ahmed A. Hadad, Asha Nair, Xiaoyu Liu, Yuji Zhang, Eric W. Klee, Krishna R. Kalari, Jean-Pierre Kocher:
  TREAT: a bioinformatics tool for variant annotations and visualizations in targeted and exome sequencing data. 277-278
  
• Pablo Librado, F. G. Vieira, Julio Rozas:
  BadiRate: estimating family turnover rates by likelihood-based methods. 279-281
  
• Aristotelis Tsirigos, Niina Haiminen, Erhan Bilal, Filippo Utro:
  GenomicTools: a computational platform for developing high-throughput analytics in genomics. 282-283
  

• R. W. W. Brouwer, M. C. G. N. van den Hout, F. G. Grosveld, W. F. J. van IJcken:
  NARWHAL, a primary analysis pipeline for NGS data. 284-285
  

• Chi-Ho Ngan, David R. Hall, Brandon Zerbe, Laurie E. Grove, Dima Kozakov, Sandor Vajda:
  FTSite: high accuracy detection of ligand binding sites on unbound protein structures. 286-287
  

• Laurent Gatto, Kathryn S. Lilley:
  MSnbase-an R/Bioconductor package for isobaric tagged mass spectrometry data visualization, processing and quantitation. 288-289
  

• Christopher Whelan, Kemal Sönmez:
  Computing graphlet signatures of network nodes and motifs in Cytoscape with GraphletCounter. 290-291
  
• Dominique F. Chu, Nicolae Radu Zabet, Tobias von der Haar:
  A novel and versatile computational tool to model translation. 292-293
  
• Lu Zhang, Shengchang Gu, Yuan Liu, Bingqiang Wang, Francisco Azuaje:
  Gene set analysis in the cloud. 294-295
  

• Nigel F. Reuel, Peter Bojo, Jingqing Zhang, Ardemis A. Boghossian, Jin-Ho Ahn, Jong-Ho Kim, Michael S. Strano:
  NoRSE: noise reduction and state evaluator for high-frequency single event traces. 296-297
  
• H. E. L. Lischer, Laurent Excoffier:
  PGDSpider: an automated data conversion tool for connecting population genetics and genomics programs. 298-299
  

• Christian M. Reidys, Fenix W. D. Huang, Jørgen E. Andersen, Robert C. Penner, Peter F. Stadler, Markus E. Nebel:
  Addendum: topology and prediction of RNA pseudoknots. 300
  

Volume 28, Number 3, February 2012

• Xin Wei, Ann F. Hoffman, Shannon M. Hamilton, Qing Xiang, Yang He, W. Venus So, Sung-Sau So, David Mark:
  A simple statistical test to infer the causality of target/phenotype correlation from small molecule phenotypic screens. 301-305
  

• Olga Shevchuk, Louisa Roselius, Gabriele Günther, Johannes Klein, Dieter Jahn, Michael Steinert, Richard Münch:
  InFiRe - a novel computational method for the identification of insertion sites in transposon mutagenized bacterial genomes. 306-310
  

• David E. Larson, Christopher C. Harris, Ken Chen, Daniel C. Koboldt, Travis E. Abbott, David J. Dooling, Timothy J. Ley, Elaine R. Mardis, Richard K. Wilson, Li Ding:
  SomaticSniper: identification of somatic point mutations in whole genome sequencing data. 311-317
  
• Antonio Marco, Sam Griffiths-Jones:
  Detection of microRNAs in color space. 318-323
  

• Ryotaro Koike, Motonori Ota:
  SCPC: a method to structurally compare protein complexes. 324-330
  
• Ke Chen, Marcin J. Mizianty, Lukasz A. Kurgan:
  Prediction and analysis of nucleotide-binding residues using sequence and sequence-derived structural descriptors. 331-341
  
• V. M. Gonçalves-Almeida, Douglas E. V. Pires, Raquel Cardoso de Melo Minardi, Carlos Henrique da Silveira, Wagner Meira Jr., Marcelo M. Santoro:
  HydroPaCe: understanding and predicting cross-inhibition in serine proteases through hydrophobic patch centroids. 342-349
  
• J. W. Heal, J. E. Jimenez-Roldan, Stephen A. Wells, R. B. Freedman, Rudolf A. Römer:
  Inhibition of HIV-1 protease: the rigidity perspective. 350-357
  

• Gengxin Li, Joel Gelernter, Henry R. Kranzler, Hongyu Zhao:
  M³: an improved SNP calling algorithm for Illumina BeadArray data. 358-365
  

• Wei Liu, Mahesan Niranjan:
  Gaussian process modelling for bicoid mRNA regulation in spatio-temporal Bicoid profile. 366-372
  
• Alla Karnovsky, Terry E. Weymouth, Tim Hull, V. Glenn Tarcea, Giovanni Scardoni, Carlo Laudanna, Maureen A. Sartor, Kathleen A. Stringer, H. V. Jagadish, Charles F. Burant, Brian D. Athey, Gilbert S. Omenn:
  Metscape 2 bioinformatics tool for the analysis and visualization of metabolomics and gene expression data. 373-380
  
• Kathrin Ballerstein, Axel von Kamp, Steffen Klamt, Utz-Uwe Haus:
  Minimal cut sets in a metabolic network are elementary modes in a dual network. 381-387
  
• Mario Latendresse, Markus Krummenacker, Miles Trupp, Peter D. Karp:
  Construction and completion of flux balance models from pathway databases. 388-396
  

• Natalia Jiménez-Lozano, Joan Segura, José Ramón Macías, Juanjo Vega, José María Carazo:
  Integrating human and murine anatomical gene expression data for improved comparisons. 397-402
  
• Yupeng Wang, Sandeep J. Joseph, Xinyu Liu, Michael Kelley, Romdhane Rekaya:
  SNPxGE²: a database for human SNP-coexpression associations. 403-410
  
• Nestor Milyaev, David Osumi-Sutherland, Simon Reeve, Nicholas Burton, Richard A. Baldock, J. Douglas Armstrong:
  The Virtual Fly Brain browser and query interface. 411-415
  

• Yongbing Zhao, Jiayan Wu, Junhui Yang, Shixiang Sun, Jing-Fa Xiao, Jun Yu:
  PGAP: pan-genomes analysis pipeline. 416-418
  
• Mikhail G. Dozmorov, Lukas R. Cara, Cory B. Giles, Jonathan D. Wren:
  GenomeRunner: automating genome exploration. 419-420
  
• F. Anthony San Lucas, Gao Wang, Paul Scheet, Bo Peng:
  Integrated annotation and analysis of genetic variants from next-generation sequencing studies with variant tools. 421-422
  
• Valentina Boeva, Tatiana Popova, Kevin Bleakley, Pierre Chiche, Julie Cappo, Gudrun Schleiermacher, Isabelle Janoueix-Lerosey, Olivier Delattre, Emmanuel Barillot:
  Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data. 423-425
  

• Carlos Prieto, Carlos García-Estrada, Diego Lorenzana, Juan Francisco Martín:
  NRPSsp: non-ribosomal peptide synthase substrate predictor. 426-427
  
• Benjamin Kreck, George Marnellos, Julia Richter, Felix Krueger, Reiner Siebert, Andre Franke:
  B-SOLANA: an approach for the analysis of two-base encoding bisulfite sequencing data. 428-429
  
• Yuanxin Xi, Christoph Bock, Fabian Müller, Deqiang Sun, Alexander Meissner, Wei Li:
  RRBSMAP: a fast, accurate and user-friendly alignment tool for reduced representation bisulfite sequencing. 430-432
  
• Robert Schmieder, Yan Wei Lim, Robert A. Edwards:
  Identification and removal of ribosomal RNA sequences from metatranscriptomes. 433-435
  
• Antonio Gonzalez, Jesse Stombaugh, Christian L. Lauber, Noah Fierer, Rob Knight:
  SitePainter: a tool for exploring biogeographical patterns. 436-438
  

• Conan K. Wang, Saroja K. Weeratunga, Chris M. Pacheco, Andreas Hofmann:
  DMAN: a Java tool for analysis of multi-well differential scanning fluorimetry experiments. 439-440
  
• Julia T. Philip, Charles H. Pence, Holly V. Goodson:
  MTBindingSim: simulate protein binding to microtubules. 441-443
  

• Christian Fuchsberger, Daniel Taliun, Peter P. Pramstaller, Cristian Pattaro:
  GWAtoolbox: an R package for fast quality control and handling of genome-wide association studies meta-analysis data. 444-445
  

• Enrico Glaab, Reinhard Schneider:
  PathVar: analysis of gene and protein expression variance in cellular pathways using microarray data. 446-447
  

• Sarala M. Wimalaratne, Pierre Grenon, Robert Hoehndorf, Georgios V. Gkoutos, Bernard de Bono:
  An infrastructure for ontology-based information systems in biomedicine: RICORDO case study. 448-450
  
• Kai Xia, Andrey A. Shabalin, Shunping Huang, Vered Madar, Yi-Hui Zhou, Wei Wang, Fei Zou, Wei Sun, Patrick F. Sullivan, Fred A. Wright:
  seeQTL: a searchable database for human eQTLs. 451-452
  

Volume 28, Number 4, February 2012

• Wilson Wen Bin Goh, Hirotaka Oikawa, Judy Chia Ghee Sng, Marek J. Sergot, Limsoon Wong:
  The role of miRNAs in complex formation and control. 453-456
  

• Thomas J. Hardcastle, Krystyna A. Kelly, David C. Baulcombe:
  Identifying small interfering RNA loci from high-throughput sequencing data. 457-463
  
• Tim Carver, Simon R. Harris, Matthew Berriman, Julian Parkhill, Jacqueline A. McQuillan:
  Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data. 464-469
  
• Alberto Magi, Lorenzo Tattini, Tommaso Pippucci, Francesca Torricelli, Matteo Benelli:
  Read count approach for DNA copy number variants detection. 470-478
  

• Yanju Zhang, Eric-Wubbo Lameijer, Peter A. C. 't Hoen, Zemin Ning, P. Eline Slagboom, Kai Ye:
  PASSion: a pattern growth algorithm-based pipeline for splice junction detection in paired-end RNA-Seq data. 479-486
  
• Phil Arnold, Ionas Erb, Mikhail Pachkov, Nacho Molina, Erik van Nimwegen:
  MotEvo: integrated Bayesian probabilistic methods for inferring regulatory sites and motifs on multiple alignments of DNA sequences. 487-494
  
• Benjamin P. Blackburne, Simon Whelan:
  Measuring the distance between multiple sequence alignments. 495-502
  

• Ian Walsh, Alberto J. M. Martin, Tomás Di Domenico, Silvio C. E. Tosatto:
  ESpritz: accurate and fast prediction of protein disorder. 503-509
  
• Tim Harder, Mikael Borg, Wouter Boomsma, Peter Røgen, Thomas Hamelryck:
  Fast large-scale clustering of protein structures using Gauss integrals. 510-515
  
• Sikander Hayat, Arne Elofsson:
  BOCTOPUS: improved topology prediction of transmembrane β barrel proteins. 516-522
  
• Sudhakar Sahoo, Andreas Alexander Albrecht:
  Approximating the set of local minima in partial RNA folding landscapes. 523-530
  

• Tiejun Tong, Liang Chen, Hongyu Zhao:
  Improved mean estimation and its application to diagonal discriminant analysis. 531-537
  
• Isaac S. Kohane, Vladimir I. Valtchinov:
  Quantifying the white blood cell transcriptome as an accessible window to the multiorgan transcriptome. 538-545
  

• Lipi R. Acharya, Thair Judeh, Guangdi Wang, Dongxiao Zhu:
  Optimal structural inference of signaling pathways from unordered and overlapping gene sets. 546-556
  
• Thomas Handorf, Edda Klipp:
  Modeling mechanistic biological networks: An advanced Boolean approach. 557-563
  

• Youting Sun, Jianqiu Zhang, Ulisses Braga-Neto, Edward R. Dougherty:
  BPDA2d - a 2D global optimization-based Bayesian peptide detection algorithm for liquid chromatograph-mass spectrometry. 564-572
  
• Raivo Kolde, Sven Laur, Priit Adler, Jaak Vilo:
  Robust rank aggregation for gene list integration and meta-analysis. 573-580
  

• Leila Taher, Leelavati Narlikar, Ivan Ovcharenko:
  CLARE: Cracking the LAnguage of Regulatory Elements. 581-583
  

• Thilo Muth, Juan A. García-Martín, Antonio Rausell, David de Juan, Alfonso Valencia, Florencio Pazos:
  JDet: interactive calculation and visualization of function-related conservation patterns in multiple sequence alignments and structures. 584-586
  
• J. Huang, V. Renault, J. Sengenès, Nizar Touleimat, S. Michel, Mark G. Lathrop, J. Tost:
  MeQA: a pipeline for MeDIP-seq data quality assessment and analysis. 587-588
  
• Evarist Planet, Camille Stephan-Otto Attolini, Oscar Reina, Oscar Flores, David Rossell:
  htSeqTools: high-throughput sequencing quality control, processing and visualization in R. 589-590
  
• Athina Theodosiou, Vasilis J. Promponas:
  LaTcOm: a web server for visualizing rare codon clusters in coding sequences. 591-592
  
• Weichun Huang, Leping Li, Jason R. Myers, Gabor T. Marth:
  ART: a next-generation sequencing read simulator. 593-594
  

• Miquel Ràmia, Pablo Librado, Sònia Casillas, Julio Rozas, Antonio Barbadilla:
  PopDrowser: the Population Drosophila Browser. 595-596
  

• Sun Kim, Dongseop Kwon, Soo-Yong Shin, W. John Wilbur:
  PIE the search: searching PubMed literature for protein interaction information. 597-598
  
• Jamie K. Teer, Eric D. Green, James C. Mullikin, Leslie G. Biesecker:
  VarSifter: Visualizing and analyzing exome-scale sequence variation data on a desktop computer. 599-600
  

• Christian Schaefer, Alice Meier, Burkhard Rost, Yana Bromberg:
  SNPdbe: constructing an nsSNP functional impacts database. 601-602
  

Volume 28, Number 5, March 2012

• Natasha Latysheva, Vivien L. Junker, William J. Palmer, Geoffrey A. Codd, Daniel Barker:
  The evolution of nitrogen fixation in cyanobacteria. 603-606
  

• Maria D. Chikina, Olga G. Troyanskaya:
  An effective statistical evaluation of ChIPseq dataset similarity. 607-613
  
• Katelyn McNair, Barbara A. Bailey, Robert A. Edwards:
  PHACTS, a computational approach to classifying the lifestyle of phages. 614-618
  
• Anne-Katrin Emde, Marcel H. Schulz, David Weese, Ruping Sun, Martin Vingron, Vera M. Kalscheuer, Stefan A. Haas, Knut Reinert:
  Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS. 619-627
  

• Raymond Wan, Vo Ngoc Anh, Kiyoshi Asai:
  Transformations for the compression of FASTQ quality scores of next-generation sequencing data. 628-635
  
• Søren Mørk, Ian Holmes:
  Evaluating bacterial gene-finding HMM structures as probabilistic logic programs. 636-642
  
• Na You, Gabriel Murillo, Xiaoquan Su, Xiaowei Zeng, Jian Xu, Kang Ning, Shoudong Zhang, Jiankang Zhu, Xinping Cui:
  SNP calling using genotype model selection on high-throughput sequencing data. 643-650
  
• Ergun Gumus, Olcay Kursun, Ahmet Sertbas, Duran Ustek:
  Application of canonical correlation analysis for identifying viral integration preferences. 651-655
  
• Jonathan Göke, Marcel H. Schulz, Julia Lasserre, Martin Vingron:
  Estimation of pairwise sequence similarity of mammalian enhancers with word neighbourhood counts. 656-663
  

• Zhe Zhang, Lin Wang, Yang Gao, Jie Zhang, Maxim Zhenirovskyy, Emil Alexov:
  Predicting folding free energy changes upon single point mutations. 664-671
  

• Maxime Garcia, Raphaelle Millat-Carus, François Bertucci, Pascal Finetti, Daniel Birnbaum, Ghislain Bidaut:
  Interactome-transcriptome integration for predicting distant metastasis in breast cancer. 672-678
  

• Alex L. B. Leach, James P. J. Chong, Kelly R. Redeker:
  SSuMMo: rapid analysis, comparison and visualization of microbial communities. 679-686
  

• Serguei Sokol, Pierre Millard, Jean-Charles Portais:
  influx_s: increasing numerical stability and precision for metabolic flux analysis in isotope labelling experiments. 687-693
  
• Kakajan Komurov:
  Modeling community-wide molecular networks of multicellular systems. 694-700
  
• Mei-Ju May Chen, Lih-Ching Chou, Tsung-Ting Hsieh, Ding-Dar Lee, Kai-Wei Liu, Chi-Yuan Yu, Yen-Jen Oyang, Huai-Kuang Tsai, Chien-Yu Chen:
  De novo motif discovery facilitates identification of interactions between transcription factors in Saccharomyces cerevisiae. 701-708
  

• Christian Senger, Björn A. Grüning, Anika Erxleben, Kersten Döring, Hitesh Patel, Stephan Flemming, Irmgard Merfort, Stefan Günther:
  Mining and evaluation of molecular relationships in literature. 709-714
  

• Todd F. DeLuca, Jike Cui, Jae-Yoon Jung, Kristian Che St. Gabriel, Dennis P. Wall:
  Roundup 2.0: enabling comparative genomics for over 1800 genomes. 715-716
  
• Thomas Hentrich, Julia M. Schulze, Eldon Emberly, Michael S. Kobor:
  CHROMATRA: a Galaxy tool for visualizing genome-wide chromatin signatures. 717-718
  
• Gary K. Chen:
  A scalable and portable framework for massively parallel variable selection in genetic association studies. 719-720
  
• Dongwan Hong, Arang Rhie, Sung-Soo Park, Jongkeun Lee, Young Seok Ju, Sujung Kim, Saet-Byeol Yu, Thomas Bleazard, Hyun Seok Park, Hwanseok Rhee, Hyonyong Chong, Kap-Seok Yang, Yeon-Su Lee, In-Hoo Kim, Jin Soo Lee, Jong-Il Kim, Jeong-Sun Seo:
  FX: an RNA-Seq analysis tool on the cloud. 721-723
  
• Vladimir Makarov, Tina O'Grady, Guiqing Cai, Jayon Lihm, Joseph D. Buxbaum, Seungtai Yoon:
  AnnTools: a comprehensive and versatile annotation toolkit for genomic variants. 724-725
  

• Thomas W. Chittenden, Eleanor Howe, Jennifer M. Taylor, Jessica C. Mar, Martin J. Aryee, Harold Gómez, Razvan Sultana, John C. Braisted, Sarita J. Nair, John Quackenbush, Chris Holmes:
  nEASE: a method for gene ontology subclassification of high-throughput gene expression data. 726-728
  
• Dan Wang, Li Yan, Qiang Hu, Lara E. Sucheston, Michael J. Higgins, Christine B. Ambrosone, Candace S. Johnson, Dominic J. Smiraglia, Song Liu:
  IMA: an R package for high-throughput analysis of Illumina's 450K Infinium methylation data. 729-730
  

• Michal Komorowski, Justina Zurauskiene, Michael P. H. Stumpf:
  StochSens - matlab package for sensitivity analysis of stochastic chemical systems. 731-733
  
• Rogan Carr, Elhanan Borenstein:
  NetSeed: a network-based reverse-ecology tool for calculating the metabolic interface of an organism with its environment. 734-735
  
• Christoph Bueschl, Bernhard Kluger, Franz Berthiller, Gerald Lirk, Stephan Winkler, Rudolf Krska, Rainer Schuhmacher:
  MetExtract: a new software tool for the automated comprehensive extraction of metabolite-derived LC/MS signals in metabolomics research. 736-738
  

• Sergey Kozhenkov, Michael Baitaluk:
  Mining and integration of pathway diagrams from imaging data. 739-742
  
• Adrian Benton, John H. Holmes, S. Hill, Annie Chung, Lyle Ungar:
  medpie: an information extraction package for medical message board posts. 743-744
  
• Yasubumi Sakakibara, Tsuyoshi Hachiya, Miho Uchida, Nobuyoshi Nagamine, Yohei Sugawara, Masahiro Yokota, Masaomi Nakamura, Kris Popendorf, Takashi Komori, Kengo Sato:
  COPICAT: a software system for predicting interactions between proteins and chemical compounds. 745-746
  

• Sentil Balaji, Charles Mcclendon, Rajesh Chowdhary, Jun S. Liu, Jinfeng Zhang:
  IMID: integrated molecular interaction database. 747-749
  
• Mustafa H. Syed, Tatiana V. Karpinets, Morey Parang, Michael R. Leuze, Byung-Hoon Park, Doug Hyatt, Steven D. Brown, Steve Moulton, Michael D. Galloway, Edward C. Uberbacher:
  BESC knowledgebase public portal. 750-751
  
• David van der Spoel, Paul J. van Maaren, Carl Caleman:
  GROMACS molecule & liquid database. 752-753
  

Volume 28, Number 6, March 2012

• Charles C. Berry, Nicolas A. Gillet, Anat Melamed, Niall Gormley, Charles R. M. Bangham, Frederic D. Bushman:
  Estimating abundances of retroviral insertion sites from DNA fragment length data. 755-762
  
• Santi González, Bàrbara Montserrat-Sentís, Friman Sánchez, Montserrat Puiggròs, Enrique Blanco, Alex Ramírez, David Torrents:
  ReLA, a local alignment search tool for the identification of distal and proximal gene regulatory regions and their conserved transcription factor binding sites. 763-770
  

• Martin Reczko, Manolis Maragkakis, Panagiotis Alexiou, Ivo Grosse, Artemis G. Hatzigeorgiou:
  Functional microRNA targets in protein coding sequences. 771-776
  
• E. E. R. Philipp, L. Kraemer, D. Mountfort, M. Schilhabel, S. Schreiber, Philip Rosenstiel:
  The Transcriptome Analysis and Comparison Explorer - T-ACE: a platform-independent, graphical tool to process large RNAseq datasets of non-model organisms. 777-783
  

• David Ryan Koes, Carlos J. Camacho:
  Small-molecule inhibitor starting points learned from protein-protein interaction inhibitor structure. 784-791
  
• Matthew G. Seetin, David H. Mathews:
  TurboKnot: rapid prediction of conserved RNA secondary structures including pseudoknots. 792-798
  

• Sutirtha Chakraborty, Somnath Datta, Susmita Datta:
  Surrogate variable analysis using partial least squares (SVA-PLS) in gene expression studies. 799-806
  
• Yihan Li, Debashis Ghosh:
  Assumption weighting for incorporating heterogeneity into meta-analysis of genomic data. 807-814
  
• Kyungpil Kim, Keni Jiang, Siew Leng Teng, Lewis J. Feldman, Haiyan Huang:
  Using biologically interrelated experiments to identify pathway genes in Arabidopsis. 815-822
  
• Ka Yee Yeung, T. A. Gooley, A. Zhang, Adrian E. Raftery, J. P. Radich, V. G. Oehler:
  Predicting relapse prior to transplantation in chronic myeloid leukemia by integrating expert knowledge and expression data. 823-830
  

• Christopher J. R. Illingworth, Ville Mustonen:
  A method to infer positive selection from marker dynamics in an asexual population. 831-837
  
• Chul Joo Kang, Paul Marjoram:
  Exact coalescent simulation of new haplotype data from existing reference haplotypes. 838-844
  
• Clara S. Tang, Manuel A. R. Ferreira:
  A gene-based test of association using canonical correlation analysis. 845-850
  

• Martin Simonsen, Stefan Maetschke, Mark A. Ragan:
  Automatic selection of reference taxa for protein-protein interaction prediction with phylogenetic profiling. 851-857
  
• Alfredo Rodríguez, David Sosa, Leda Torres, Bertha Molina, Sara Frías, Luis Mendoza:
  A Boolean network model of the FA/BRCA pathway. 858-866
  

• Thanh Thieu, Sneha Joshi, Samantha Warren, Dmitry Korkin:
  Literature mining of host-pathogen interactions: comparing feature-based supervised learning and language-based approaches. 867-875
  

• Matti Niemenmaa, Aleksi Kallio, André Schumacher, Petri Klemelä, Eija Korpelainen, Keijo Heljanko:
  Hadoop-BAM: directly manipulating next generation sequencing data in the cloud. 876-877
  
• Chi-Man Liu, Thomas K. F. Wong, Edward Wu, Ruibang Luo, Siu-Ming Yiu, Yingrui Li, Bingqiang Wang, Chang Yu, Xiaowen Chu, Kaiyong Zhao, Ruiqiang Li, Tak Wah Lam:
  SOAP3: ultra-fast GPU-based parallel alignment tool for short reads. 878-879
  

• Grzegorz Chojnowski, Janusz M. Bujnicki, Matthias Bochtler:
  RIBER/DIBER: a software suite for crystal content analysis in the studies of protein-nucleic acid complexes. 880-881
  

• Jeffrey T. Leek, W. Evan Johnson, Hilary S. Parker, Andrew E. Jaffe, John D. Storey:
  The sva package for removing batch effects and other unwanted variation in high-throughput experiments. 882-883
  
• Björn Schwalb, Daniel Schulz, Mai Sun, Benedikt Zacher, Sebastian Dümcke, Dietmar E. Martin, Patrick Cramer, Achim Tresch:
  Measurement of genome-wide RNA synthesis and decay rates with Dynamic Transcriptome Analysis (DTA). 884-885
  

• Michael C. Turchin, Joel Hirschhorn:
  Gencrypt: one-way cryptographic hashes to detect overlapping individuals across samples. 886-888
  

• Kumar Chandan, Martijn P. van Iersel, Mirit I. Aladjem, Kurt W. Kohn, Augustin Luna:
  PathVisio-Validator: a rule-based validation plugin for graphical pathway notations. 889-890
  
• Matthew DeJongh, Benjamin Bockstege, Paul Frybarger, Nicholas Hazekamp, Joshua Kammeraad, Travis McGeehan:
  CytoSEED: a Cytoscape plugin for viewing, manipulating and analyzing metabolic models created by the Model SEED. 891-892
  
• Aleksandar Stojmirovic, Alexander Bliskovsky, Yi-Kuo Yu:
  CytoSaddleSum: a functional enrichment analysis plugin for Cytoscape based on sum-of-weights scores. 893-894
  

• Michael Hartung, Anika Gross, Erhard Rahm:
  CODEX: exploration of semantic changes between ontology versions. 895-896
  
• Mehdi Pirooznia, Tao Wang, Dimitrios Avramopoulos, David Valle, Gareth Thomas, Richard L. Huganir, Fernando S. Goes, James B. Potash, Peter P. Zandi:
  SynaptomeDB: an ontology-based knowledgebase for synaptic genes. 897-899
  

• Christophe Dessimoz, Toni Gabaldón, David S. Roos, Erik L. L. Sonnhammer, Javier Herrero:
  Toward community standards in the quest for orthologs. 900-904
  

• Isaac S. Kohane, Vladimir I. Valtchinov:
  Quantifying the white blood cell transcriptome as an accessible window to the multiorgan transcriptome. 905
  

Volume 28, Number 7, April 2012

• Andrew Roth, Jiarui Ding, Ryan D. Morin, Anamaria Crisan, Gavin Ha, Ryan Giuliany, Ali Bashashati, Martin Hirst, Gulisa Turashvili, Arusha Oloumi, Marco A. Marra, Sam Aparicio, Sohrab P. Shah:
  JointSNVMix: a probabilistic model for accurate detection of somatic mutations in normal/tumour paired next-generation sequencing data. 907-913
  

• Zhi Liu, Ahmed Abbas, Bing-Yi Jing, Xin Gao:
  WaVPeak: picking NMR peaks through wavelet-based smoothing and volume-based filtering. 914-920
  

• Daniel C. Jones, Walter L. Ruzzo, Xinxia Peng, Michael G. Katze:
  A new approach to bias correction in RNA-Seq. 921-928
  
• Shuji Kawaguchi, Kei Iida, Erimi Harada, Kousuke Hanada, Akihiro Matsui, Masanori Okamoto, Kazuo Shinozaki, Motoaki Seki, Tetsuro Toyoda:
  Positional correlation analysis improves reconstruction of full-length transcripts and alternative isoforms from noisy array signals or short reads. 929-937
  

• Degui Zhi, Jihua Wu, Nianjun Liu, Kui Zhang:
  Genotype calling from next-generation sequencing data using haplotype information of reads. 938-946
  

• John L. Van Hemert, Julie A. Dickerson:
  Discriminating response groups in metabolic and regulatory pathway networks. 947-954
  
• Shiwen Zhao, Shao Li:
  A co-module approach for elucidating drug-disease associations and revealing their molecular basis. 955-961
  
• Andy C. W. Lai, Alex N. Nguyen Ba, Alan M. Moses:
  Predicting kinase substrates using conservation of local motif density. 962-969
  
• Feng He, Jie Ren, Wei Wang, Jun Ma:
  Evaluating the Drosophila Bicoid morphogen gradient system through dissecting the noise in transcriptional bursts. 970-975
  
• Robert J. Weatheritt, Katja Luck, E. Petsalaki, Norman E. Davey, Toby J. Gibson:
  The identification of short linear motif-mediated interfaces within the human interactome. 976-982
  
• Guy Naamati, Yitzhak Friedman, Ohad Balaga, Michal Linial:
  Susceptibility of the human pathways graphs to fragmentation by small sets of microRNAs. 983-990
  

• Maria Liakata, Shyamasree Saha, Simon Dobnik, Colin R. Batchelor, Dietrich Rebholz-Schuhmann:
  Automatic recognition of conceptualization zones in scientific articles and two life science applications. 991-1000
  
• Theofanis Karaletsos, Oliver Stegle, Christine Dreyer, John M. Winn, Karsten M. Borgwardt:
  ShapePheno: unsupervised extraction of shape phenotypes from biological image collections. 1001-1008
  
• Nima Aghaeepour, Pratip K. Chattopadhyay, Anuradha Ganesan, Kieran O'Neill, Habil Zare, Adrin Jalali, Holger H. Hoos, Mario Roederer, Ryan R. Brinkman:
  Early immunologic correlates of HIV protection can be identified from computational analysis of complex multivariate T-cell flow cytometry assays. 1009-1016
  

• Anne Niknejad, Aurélie Comte, Gilles Parmentier, Julien Roux, Frederic B. Bastian, Marc Robinson-Rechavi:
  vHOG, a multispecies vertebrate ontology of homologous organs groups. 1017-1020
  

• William K. M. Lai, Jonathan E. Bard, Michael J. Buck:
  ArchTEx: accurate extraction and visualization of next-generation sequence data. 1021-1023
  
• Ruping Sun, Michael I. Love, Tomasz Zemojtel, Anne-Katrin Emde, Ho-Ryun Chung, Martin Vingron, Stefan A. Haas:
  Breakpointer: using local mapping artifacts to support sequence breakpoint discovery from single-end reads. 1024-1025
  

• Conan K. Wang, Ursula Broder, Saroja K. Weeratunga, Robin B. Gasser, Alex Loukas, Andreas Hofmann:
  SBAL: a practical tool to generate and edit structure-based amino acid sequence alignments. 1026-1027
  
• Sang-Mun Chi, Dougu Nam:
  WegoLoc: accurate prediction of protein subcellular localization using weighted Gene Ontology terms. 1028-1030
  
• Kian Huat Lim, William G. Fairbrother:
  Spliceman - a computational web server that predicts sequence variations in pre-mRNA splicing. 1031-1032
  
• Martin Wu, Alexandra J. Scott:
  Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2. 1033-1034
  
• Raoul J. P. Bonnal, Jan Aerts, George Githinji, Naohisa Goto, Daniel MacLean, Chase A. Miller, Hiroyuki Mishima, Massimiliano Pagani, Ricardo Ramirez-Gonzalez, Geert Smant, Francesco Strozzi, Rob Syme, Rutger A. Vos, Trevor J. Wennblom, Ben J. Woodcroft, Toshiaki Katayama, Pjotr Prins:
  Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics. 1035-1037
  

• Alessandro Barbato, Pascal Benkert, Torsten Schwede, Anna Tramontano, Jan Kosinski:
  Improving your target-template alignment with MODalign. 1038-1039
  
• Franck Samson, Richard Shrager, Chin-Hsien Tai, Vichetra Sam, Byungkook Lee, Peter J. Munson, Jean-François Gibrat, Jean Garnier:
  DOMIRE: a web server for identifying structural domains and their neighbors in proteins. 1040-1041
  

• Danny Arends, K. Joeri van der Velde, Pjotr Prins, Karl W. Broman, Steffen Möller, Ritsert C. Jansen, Morris A. Swertz:
  xQTL workbench: a scalable web environment for multi-level QTL analysis. 1042-1044
  
• John Bunge, Linda Woodard, Dankmar Böhning, James A. Foster, Sean Connolly, Heather K. Allen:
  Estimating population diversity with CatchAll. 1045-1047
  

• Darren J. Creek, Andris Jankevics, Karl E. V. Burgess, Rainer Breitling, Michael P. Barrett:
  IDEOM: an Excel interface for analysis of LC-MS-based metabolomics data. 1048-1049
  
• Eero Lihavainen, Jarno Mäkelä, Johannes N. Spelbrink, Andre S. Ribeiro:
  Mytoe: automatic analysis of mitochondrial dynamics. 1050-1051
  

• Till Bald, Johannes Barth, Anna Niehues, Michael Specht, Michael Hippler, Christian Fufezan:
  pymzML - Python module for high-throughput bioinformatics on mass spectrometry data. 1052-1053
  

• Valentin Guignon, Gaëtan Droc, Michael Alaux, Franc-Christophe Baurens, Olivier Garsmeur, Claire Poiron, Tim Carver, Mathieu Rouard, Stéphanie Bocs:
  Chado Controller: advanced annotation management with a community annotation system. 1054-1056
  

Volume 28, Number 8, April 2012

• Hanchuan Peng, Alex Bateman, Alfonso Valencia, Jonathan D. Wren:
  Bioimage informatics: a new category in Bioinformatics. 1057
  

• William Ritchie, Dadi Gao, John E. J. Rasko:
  Defining and providing robust controls for microRNA prediction. 1058-1061
  

• Dominik Beck, Miriam Brandl, Lies Boelen, Ashwin Unnikrishnan, John E. Pimanda, Jason W. H. Wong:
  Signal analysis for genome-wide maps of histone modifications measured by ChIP-seq. 1062-1069
  

• Vitaly L. Galinsky:
  YOABS: yet other aligner of biological sequences - an efficient linearly scaling nucleotide aligner. 1070-1077
  
• Vincent Miele, Simon Penel, Vincent Daubin, Franck Picard, Daniel Kahn, Laurent Duret:
  High-quality sequence clustering guided by network topology and multiple alignment likelihood. 1078-1085
  
• Marcel H. Schulz, Daniel Zerbino, Martin Vingron, Ewan Birney:
  Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. 1086-1092
  

• Hisanori Kiryu, Kiyoshi Asai:
  Rchange: algorithms for computing energy changes of RNA secondary structures in response to base mutations. 1093-1101
  

• Ruijie Liu, Ana-Teresa Maia, Roslin Russell, Carlos Caldas, Bruce A. Ponder, Matthew E. Ritchie:
  Allele-specific expression analysis methods for high-density SNP microarray data. 1102-1108
  
• Zhongxue Chen, Qingzhong Liu, Saralees Nadarajah:
  A new statistical approach to detecting differentially methylated loci for case control Illumina array methylation data. 1109-1113
  
• Leonid Chindelevitch, Daniel Ziemek, Ahmed Enayetallah, Ranjit Randhawa, Ben Sidders, Christoph Brockel, Enoch S. Huang:
  Causal reasoning on biological networks: interpreting transcriptional changes. 1114-1121
  
• Jeffrey T. Chang:
  Deriving transcriptional programs and functional processes from gene expression databases. 1122-1129
  

• J. Vanlier, C. A. Tiemann, Peter A. J. Hilbers, Natal A. W. van Riel:
  An integrated strategy for prediction uncertainty analysis. 1130-1135
  
• J. Vanlier, C. A. Tiemann, Peter A. J. Hilbers, Natal A. W. van Riel:
  A Bayesian approach to targeted experiment design. 1136-1142
  

• Jan Kölling, Daniel Langenkämper, Sylvie Abouna, Michael Khan, Tim W. Nattkemper:
  WHIDE - a web tool for visual data mining colocation patterns in multivariate bioimages. 1143-1150
  
• Loris Nanni, Sheryl Brahnam, Alessandra Lumini:
  Combining multiple approaches for gene microarray classification. 1151-1157
  
• Seongho Kim, Imhoi Koo, Xiaoli Wei, Xiang Zhang:
  A method of finding optimal weight factors for compound identification in gas chromatography-mass spectrometry. 1158-1163
  

• Xiaobei Zhao, Albin Sandelin:
  GMD: measuring the distance between histograms with applications on high-throughput sequencing reads. 1164-1165
  
• Konstantin Okonechnikov, Olga Golosova, Mikhail Fursov:
  Unipro UGENE: a unified bioinformatics toolkit. 1166-1167
  
• Volker Steiß, Thomas Letschert, Helmut Schäfer, Roman Pahl:
  PERMORY-MPI: a program for high-speed parallel permutation testing in genome-wide association studies. 1168-1169
  

• Oscar Westesson, Lars Barquist, Ian Holmes:
  HandAlign: Bayesian multiple sequence alignment, phylogeny and ancestral reconstruction. 1170-1171
  

• Yingjie Lin, Seungyeul Yoo, Roberto Sanchez:
  SiteComp: a server for ligand binding site analysis in protein structures. 1172-1173
  

• Aparna Bhaduri, Kun Qu, Carolyn S. Lee, Alexander Ungewickell, Paul A. Khavari:
  Rapid identification of non-human sequences in high-throughput sequencing datasets. 1174-1175
  

• Mathieu Gautier, Renaud Vitalis:
  rehh: an R package to detect footprints of selection in genome-wide SNP data from haplotype structure. 1176-1177
  

• Johannes Gräßler, Dirk Koschützki, Falk Schreiber:
  CentiLib: comprehensive analysis and exploration of network centralities. 1178-1179
  
• Richard R. Adams:
  SED-ED, a workflow editor for computational biology experiments written in SED-ML. 1180-1181
  

• Hanwen Huang, Xiaosun Lu, Yufeng Liu, Perry Haaland, J. S. Marron:
  R/DWD: distance-weighted discrimination for classification, visualization and batch adjustment. 1182-1183
  

• Markus Krupp, Jens U. Marquardt, Ugur Sahin, Peter R. Galle, John C. Castle, Andreas Teufel:
  RNA-Seq Atlas - a reference database for gene expression profiling in normal tissue by next-generation sequencing. 1184-1185
  
• Nigel Collier, Son Doan:
  GENI-DB: a database of global events for epidemic intelligence. 1186-1188
  
• Scott F. Saccone, Jiaxi Quan, Peter L. Jones:
  BioQ: tracing experimental origins in public genomic databases using a novel data provenance model. 1189-1191
  

Volume 28, Number 9, May 2012

• Pablo Meyer, Julia Hoeng, John Jeremy Rice, Raquel Norel, Jörg Sprengel, Katrin Stolle, Thomas Bonk, Stephanie Corthesy, Ajay K. Royyuru, Manuel C. Peitsch, Gustavo Stolovitzky:
  Industrial methodology for process verification in research (IMPROVER): toward systems biology verification. 1193-1201
  

• Iman Hajirasouliha, Alexander Schönhuth, David de Juan, Alfonso Valencia, Süleyman Cenk Sahinalp:
  Mirroring co-evolving trees in the light of their topologies. 1202-1208
  

• Michael I. Sadowski, William R. Taylor:
  Evolutionary inaccuracy of pairwise structural alignments. 1209-1215
  
• Noah M. Daniels, Raghavendra Hosur, Bonnie Berger, Lenore J. Cowen:
  SMURFLite: combining simplified Markov random fields with simulated evolution improves remote homology detection for beta-structural proteins into the twilight zone. 1216-1222
  
• Bin Li, Feng Liang, Jianhua Hu, Xuming He:
  Reno: regularized non-parametric analysis of protein lysate array data. 1223-1229
  

• William H. Mather, Jeff Hasty, Lev S. Tsimring:
  Fast stochastic algorithm for simulating evolutionary population dynamics. 1230-1238
  

• Hang T. T. Phan, Michael J. E. Sternberg:
  PINALOG: a novel approach to align protein interaction networks - implications for complex detection and function prediction. 1239-1245
  
• Yuan Yuan, Yanxun Xu, Jianfeng Xu, Robyn L. Ball, Han Liang:
  Predicting the lethal phenotype of the knockout mouse by integrating comprehensive genomic data. 1246-1252
  

• David Campos, Sérgio Matos, Ian Lewin, José Luís Oliveira, Dietrich Rebholz-Schuhmann:
  Harmonization of gene/protein annotations: towards a gold standard MEDLINE. 1253-1261
  

• David Osumi-Sutherland, Simon Reeve, Christopher J. Mungall, Fabian Neuhaus, Alan Ruttenberg, Gregory S. X. E. Jefferis, J. Douglas Armstrong:
  A strategy for building neuroanatomy ontologies. 1262-1269
  

• Sabine Ménigaud, Ludovic Mallet, Géraldine Picord, Cécile Churlaud, Alexandre Borrel, Patrick Deschavanne:
  GOHTAM: a website for 'Genomic Origin of Horizontal Transfers, Alignment and Metagenomics'. 1270-1271
  
• Jing-Woei Li, Robert Schmieder, R. Matthew Ward, Joann Delenick, Eric C. Olivares, David Mittelman:
  SEQanswers: an open access community for collaboratively decoding genomes. 1272-1273
  
• Junhee Seok, Weihong Xu, Hong Gao, Ronald W. Davis, Wenzhong Xiao:
  JETTA: junction and exon toolkits for transcriptome analysis. 1274-1275
  

• Kris Popendorf, Yasubumi Sakakibara:
  SAMSCOPE: an OpenGL-based real-time interactive scale-free SAM viewer. 1276-1277
  

• Adam Hospital, Pau Andrio, Carlos Fenollosa, Damjan Cicin-Sain, Modesto Orozco, Josep Lluis Gelpí:
  MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations. 1278-1279
  

• Richard T. Barfield, Varun Kilaru, Alicia K. Smith, Karen N. Conneely:
  CpGassoc: an R function for analysis of DNA methylation microarray data. 1280-1281
  
• Mark Reppell, Michael Boehnke, Sebastian Zöllner:
  FTEC: a coalescent simulator for modeling faster than exponential growth. 1282-1283
  

• Florian Gnad, Javier Estrada, Jeremy Gunawardena:
  Proteus: a web-based, context-specific modelling tool for molecular networks. 1284-1286
  
• Nicolae Radu Zabet, Boris Adryan:
  GRiP: a computational tool to simulate transcription factor binding in prokaryotes. 1287-1289
  
• Stefan Streif, Anton Savchenko, Philipp Rumschinski, Steffen Borchers, Rolf Findeisen:
  ADMIT: a toolbox for guaranteed model invalidation, estimation and qualitative-quantitative modeling. 1290-1291
  

• J. Lamar Barnett, Jialiang Yang, Zhipeng Cai, Tong Zhang, Xiu-Feng Wan:
  AntigenMap 3D: an online antigenic cartography resource. 1292-1293
  
• Pierre Millard, Fabien Letisse, Serguei Sokol, Jean-Charles Portais:
  IsoCor: correcting MS data in isotope labeling experiments. 1294-1296
  

• Catherine Stamoulis, Rebecca A. Betensky:
  A novel signal processing approach for the detection of copy number variations in the human genome. 1297
  

Volume 28, Number 10, May 2012

• Cyril F. Reboul, Khalid Mahmood, James C. Whisstock, Michelle A. Dunstone:
  Predicting giant transmembrane β-barrel architecture. 1299-1302
  

• Hiren J. Joshi, Katy M. Christiansen, Joffrey Fitz, Jun Cao, Anna Lipzen, Joel Martin, A. Michelle Smith-Moritz, Len A. Pennacchio, Wendy S. Schackwitz, Detlef Weigel, Joshua L. Heazlewood:
  1001 Proteomes: a functional proteomics portal for the analysis of Arabidopsis thaliana accessions. 1303-1306
  

• Jason Li, Richard Lupat, Kaushalya C. Amarasinghe, Ella R. Thompson, Maria A. Doyle, Georgina L. Ryland, Richard W. Tothill, Saman K. Halgamuge, Ian G. Campbell, Kylie L. Gorringe:
  CONTRA: copy number analysis for targeted resequencing. 1307-1313
  

• Jie Lin, Donald A. Adjeroh, Bing-Hua Jiang:
  Probabilistic suffix array: efficient modeling and prediction of protein families. 1314-1323
  
• Matthew S. Burriesci, Erik M. Lehnert, John R. Pringle:
  Fulcrum: condensing redundant reads from high-throughput sequencing studies. 1324-1327
  
• Erola Pairo, Joan Maynou, Santiago Marco, Alexandre Perera:
  A subspace method for the detection of transcription factor binding sites. 1328-1335
  
• Hongtao Sun, Jeremy D. Buhler:
  PhyLAT: a phylogenetic local alignment tool. 1336-1344
  

• Bin Pang, Nan Zhao, Dmitry Korkin, Chi-Ren Shyu:
  Fast protein binding site comparisons using visual words representation. 1345-1352
  

• Andrey A. Shabalin:
  Matrix eQTL: ultra fast eQTL analysis via large matrix operations. 1353-1358
  

• Yael Baran, Bogdan Pasaniuc, Sriram Sankararaman, Dara G. Torgerson, Christopher Gignoux, Celeste Eng, William Rodriguez-Cintron, Rocio Chapela, Jean G. Ford, Pedro C. Avila, Jose Rodriguez-Santana, Esteban Gonzàlez Burchard, Eran Halperin:
  Fast and accurate inference of local ancestry in Latino populations. 1359-1367
  
• Hokeun Sun, Shuang Wang:
  Penalized logistic regression for high-dimensional DNA methylation data with case-control studies. 1368-1375
  

• Robert Küffner, Tobias Petri, Pegah Tavakkolkhah, Lukas Windhager, Ralf Zimmer:
  Inferring gene regulatory networks by ANOVA. 1376-1382
  

• Haixuan Yang, Tamás Nepusz, Alberto Paccanaro:
  Improving GO semantic similarity measures by exploring the ontology beneath the terms and modelling uncertainty. 1383-1389
  
• Andrew Sparkes, Amanda Clare:
  AutoLabDB: a substantial open source database schema to support a high-throughput automated laboratory. 1390-1397
  

• Nizar Fawal, Bruno Savelli, Christophe Dunand, Catherine Mathé:
  GECA: a fast tool for gene evolution and conservation analysis in eukaryotic protein families. 1398-1399
  

• Federico Comoglio, Maurizio Rinaldi:
  Rknots: topological analysis of knotted biopolymers with R. 1400-1401
  

• Vincent Xue, Tony Burdett, Margus Lukk, Julie Taylor, Alvis Brazma, Helen E. Parkinson:
  MageComet - web application for harmonizing existing large-scale experiment descriptions. 1402-1403
  
• Penghao Wang, Pengyi Yang, Jean Yee Hwa Yang:
  OCAP: an open comprehensive analysis pipeline for iTRAQ. 1404-1405
  

• Mario Novkovic, Juraj Simunic, Viktor Bojovic, Alessandro Tossi, Davor Juretic:
  DADP: the database of anuran defense peptides. 1406-1407
  
• Maureen A. Sartor, Alexander S. Ade, Zach Wright, David J. States, Gilbert S. Omenn, Brian D. Athey, Alla Karnovsky:
  Metab2MeSH: annotating compounds with medical subject headings. 1408-1410
  
• Bo Qin, Meng Zhou, Ying Ge, Len Taing, Tao Liu, Qian Wang, Su Wang, Junsheng Chen, Lingling Shen, Xikun Duan, Sheng'en Hu, Wei Li, Henry Long, Yong Zhang, X. Shirley Liu:
  CistromeMap: a knowledgebase and web server for ChIP-Seq and DNase-Seq studies in mouse and human. 1411-1412
  

• Feng Feng, Ana Paula Sales, Thomas B. Kepler:
  A Bayesian approach for estimating calibration curves and unknown concentrations in immunoassays. 1413
  

Volume 28, Number 11, June 2012

• Anthony J. Cox, Markus J. Bauer, Tobias Jakobi, Giovanna Rosone:
  Large-scale compression of genomic sequence databases with the Burrows-Wheeler transform. 1415-1419
  

• Yu Peng, Henry C. M. Leung, Siu-Ming Yiu, Francis Y. L. Chin:
  IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. 1420-1428
  
• Alexey A. Gritsenko, Jurgen F. Nijkamp, Marcel J. T. Reinders, Dick de Ridder:
  GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies. 1429-1437
  

• Matthieu Chartier, Francis Gaudreault, Rafael Najmanovich:
  Large-scale analysis of conserved rare codon clusters suggests an involvement in co-translational molecular recognition events. 1438-1445
  
• Anton Aboukhalil, Martha L. Bulyk:
  LOESS correction for length variation in gene set-based genomic sequence analysis. 1446-1454
  
• Binbin Lai, Ruogu Ding, Yang Li, Liping Duan, Huaiqiu Zhu:
  A de novo metagenomic assembly program for shotgun DNA reads. 1455-1462
  

• Valéry Ozenne, Frédéric Bauer, Loïc Salmon, Jie-rong Huang, Malene Ringkjøbing Jensen, Stéphane Segard, Pau Bernadó, Céline Charavay, Martin Blackledge:
  Flexible-meccano: a tool for the generation of explicit ensemble descriptions of intrinsically disordered proteins and their associated experimental observables. 1463-1470
  

• Christian Otto, Kristin Reiche, Jörg Hackermüller:
  Detection of differentially expressed segments in tiling array data. 1471-1479
  
• Haroon Naeem, Ralf Zimmer, Pegah Tavakkolkhah, Robert Küffner:
  Rigorous assessment of gene set enrichment tests. 1480-1486
  
• Andrew E. Teschendorff, Martin Widschwendter:
  Differential variability improves the identification of cancer risk markers in DNA methylation studies profiling precursor cancer lesions. 1487-1494
  

• Jochen Weile, Katherine James, Jennifer Hallinan, Simon J. Cockell, Phillip W. Lord, Anil Wipat, Darren J. Wilkinson:
  Bayesian integration of networks without gold standards. 1495-1500
  
• Xin Liu, Mahesan Niranjan:
  State and parameter estimation of the heat shock response system using Kalman and particle filters. 1501-1507
  
• Bing Liu, Andrei Hagiescu, Sucheendra K. Palaniappan, Bipasa Chattopadhyay, Zheng Cui, Weng-Fai Wong, P. S. Thiagarajan:
  Approximate probabilistic analysis of biopathway dynamics. 1508-1516
  
• Nicolae Radu Zabet, Boris Adryan:
  A comprehensive computational model of facilitated diffusion in prokaryotes. 1517-1524
  

• Simon P. Sadedin, Bernard Pope, Alicia Oshlack:
  Bpipe: a tool for running and managing bioinformatics pipelines. 1525-1526
  
• Vikas Rao Pejaver, Jaehyun An, SungMin Rhee, Ankita Bhan, Jeong-Hyeon Choi, Boshu Liu, Heewook Lee, Pamela J. Brown, David Kysela, Yves V. Brun, Sun Kim:
  GeneclusterViz: a tool for conserved gene cluster visualization, exploration and analysis. 1527-1529
  
• David S. DeLuca, Joshua Z. Levin, Andrey Sivachenko, Tim Fennell, Marc-Danie Nazaire, Chris Williams, Michael Reich, Wendy Winckler, Gad Getz:
  RNA-SeQC: RNA-seq metrics for quality control and process optimization. 1530-1532
  

• Xuesong Hu, Jianying Yuan, Yujian Shi, Jianliang Lu, Binghang Liu, Zhenyu Li, Yanxiang Chen, Desheng Mu, Hao Zhang, Nan Li, Zhen Yue, Fan Bai, Heng Li, Wei Fan:
  pIRS: Profile-based Illumina pair-end reads simulator. 1533-1535
  

• Andrei-Alin Popescu, Katharina T. Huber, Emmanuel Paradis:
  ape 3.0: New tools for distance-based phylogenetics and evolutionary analysis in R. 1536-1537
  

• Osvaldo A. Martin, Jorge A. Vila, Harold A. Scheraga:
  CheShift-2: graphic validation of protein structures. 1538-1539
  
• Emilie Pihan, Lionel Colliandre, Jean-François Guichou, Dominique Douguet:
  e-Drug3D: 3D structure collections dedicated to drug repurposing and fragment-based drug design. 1540-1541
  

• Laurent Jourdren, Maria Bernard, Marie-Agnès Dillies, Stéphane Le Crom:
  Eoulsan: a cloud computing-based framework facilitating high throughput sequencing analyses. 1542-1543
  
• Jian-Bo Pan, Shi-chang Hu, Hao Wang, Quan Zou, Zhi-Liang Ji:
  PaGeFinder: quantitative identification of spatiotemporal pattern genes. 1544-1545
  
• Daryl Waggott, Kenneth Chu, Shaoming Yin, Bradly G. Wouters, Fei-Fei Liu, Paul C. Boutros:
  NanoStringNorm: an extensible R package for the pre-processing of NanoString mRNA and miRNA data. 1546-1548
  

• Gábor Szederkényi, Julio R. Banga, Antonio A. Alonso:
  CRNreals: a toolbox for distinguishability and identifiability analysis of biochemical reaction networks. 1549-1550
  

• Feng Gao, Hao Luo, Chun-Ting Zhang:
  DeOri: a database of eukaryotic DNA replication origins. 1551-1552
  

• Stephen A. Stanhope, Mark Abney:
  GLOGS: a fast and powerful method for GWAS of binary traits with risk covariates in related populations. 1553-1554
  

Volume 28, Number 12, June 2012

• Bonnie Berger:
  Editorial. 1
  
• ISMB 2012 Committee. 2-6
  
• Alexander Herbig, Günter Jäger, Florian Battke, Kay Nieselt:
  GenomeRing: alignment visualization based on SuperGenome coordinates. 7-15
  
• Xiao Cai, Hua Wang, Heng Huang, Chris H. Q. Ding:
  Joint stage recognition and anatomical annotation of drosophila gene expression patterns. 16-24
  
• Linqing Feng, Ting Zhao, Jinhyun Kim:
  Improved synapse detection for mGRASP-assisted brain connectivity mapping. 25-31
  
• Jieyue Li, Liang Xiong, Jeff G. Schneider, Robert F. Murphy:
  Protein subcellular location pattern classification in cellular images using latent discriminative models. 32-39
  
• Yongjin Park, Joel S. Bader:
  How networks change with time. 40-48
  
• Yu-Keng Shih, Srinivasan Parthasarathy:
  A single source k-shortest paths algorithm to infer regulatory pathways in a gene network. 49-58
  
• Jianzhu Ma, Jian Peng, Sheng Wang, Jinbo Xu:
  A conditional neural fields model for protein threading. 59-66
  
• Milana Frenkel-Morgenstern, Alfonso Valencia:
  Novel domain combinations in proteins encoded by chimeric transcripts. 67-74
  
• Fatemeh Miri Disfani, Wei-Lun Hsu, Marcin J. Mizianty, Christopher J. Oldfield, Bin Xue, A. Keith Dunker, Vladimir N. Uversky, Lukasz A. Kurgan:
  MoRFpred, a computational tool for sequence-based prediction and characterization of short disorder-to-order transitioning binding regions in proteins. 75-83
  
• Ryan G. Christensen, Metewo Selase Enuameh, Marcus B. Noyes, Michael H. Brodsky, Scot A. Wolfe, Gary D. Stormo:
  Recognition models to predict DNA-binding specificities of homeodomain proteins. 84-89
  
• Sikander Hayat, Arne Elofsson:
  Ranking models of transmembrane β-barrel proteins using Z-coordinate predictions. 90-96
  
• Arun Siddharth Konagurthu, Arthur M. Lesk, Lloyd Allison:
  Minimum message length inference of secondary structure from protein coordinate data. 97-105
  
• Dorit S. Hochbaum, Chun-Nan Hsu, Yan T. Yang:
  Ranking of multidimensional drug profiling data by fractional-adjusted bi-partitional scores. 106-114
  
• Atsushi Niida, Seiya Imoto, Teppei Shimamura, Satoru Miyano:
  Statistical model-based testing to evaluate the recurrence of genomic aberrations. 115-120
  
• Chirag J. Patel, Rong Chen, Atul J. Butte:
  Data-driven integration of epidemiological and toxicological data to select candidate interacting genes and environmental factors in association with disease. 121-126
  
• Hua Wang, Feiping Nie, Heng Huang, Shannon L. Risacher, Andrew J. Saykin, Li Shen:
  Identifying disease sensitive and quantitative trait-relevant biomarkers from multidimensional heterogeneous imaging genetics data via sparse multimodal multitask learning. 127-136
  
• Seunghak Lee, Eric P. Xing:
  Leveraging input and output structures for joint mapping of epistatic and marginal eQTLs. 137-146
  
• Gregory Darnell, Dat Duong, Buhm Han, Eleazar Eskin:
  Incorporating prior information into association studies. 147-153
  
• Derek Aguiar, Bjarni V. Halldórsson, Eric M. Morrow, Sorin Istrail:
  DELISHUS: an efficient and exact algorithm for genome-wide detection of deletion polymorphism in autism. 154-162
  
• Qian Peng, Joseph R. Ecker:
  Detection of allele-specific methylation through a generalized heterogeneous epigenome model. 163-171
  
• Thomas C. Conway, Jeremy Wazny, Andrew J. Bromage, Martin Tymms, Dhanya Sooraj, Elizabeth D. Williams, Bryan Beresford-Smith:
  Xenome - a tool for classifying reads from xenograft samples. 172-178
  
• Deniz Yörükoglu, Faraz Hach, Lucas Swanson, Colin Collins, Inanç Birol, Süleyman Cenk Sahinalp:
  Dissect: detection and characterization of novel structural alterations in transcribed sequences. 179-187
  
• Roy Ronen, Christina Boucher, Hamidreza Chitsaz, Pavel A. Pevzner:
  SEQuel: improving the accuracy of genome assemblies. 188-196
  
• David Golan, Yaniv Erlich, Saharon Rosset:
  Weighted pooling - practical and cost-effective techniques for pooled high-throughput sequencing. 197-206
  
• Vladimir Reinharz, François Major, Jérôme Waldispühl:
  Towards 3D structure prediction of large RNA molecules: an integer programming framework to insert local 3D motifs in RNA secondary structure. 207-214
  
• Jan Hoinka, Elena Zotenko, Adam Friedman, Zuben E. Sauna, Teresa M. Przytycka:
  Identification of sequence-structure RNA binding motifs for SELEX-derived aptamers. 215-223
  
• Steffen Heyne, Fabrizio Costa, Dominic Rose, Rolf Backofen:
  GraphClust: alignment-free structural clustering of local RNA secondary structures. 224-232
  
• Christopher A. Penfold, Vicky Buchanan-Wollaston, Katherine J. Denby, David L. Wild:
  Nonparametric Bayesian inference for perturbed and orthologous gene regulatory networks. 233-241
  
• Anton Polishko, Nadia Ponts, Karine G. Le Roch, Stefano Lonardi:
  NOrMAL: accurate nucleosome positioning using a modified Gaussian mixture model. 242-249
  
• Tatsunori Hashimoto, Tommi Jaakkola, Richard Sherwood, Esteban O. Mazzoni, Hynek Wichterle, David K. Gifford:
  Lineage-based identification of cellular states and expression programs. 250-257
  
• Aaron Wise, Zoltán N. Oltvai, Ziv Bar-Joseph:
  Matching experiments across species using expression values and textual information. 258-264
  
• Franziska Hufsky, Kai Dührkop, Florian Rasche, Markus Chimani, Sebastian Böcker:
  Fast alignment of fragmentation trees. 265-273
  
• Serita M. Nelesen, Kevin Liu, Li-San Wang, C. Randal Linder, Tandy Warnow:
  DACTAL: divide-and-conquer trees (almost) without alignments. 274-282
  
• Mukul S. Bansal, Eric J. Alm, Manolis Kellis:
  Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss. 283-291
  
• Götz Fabian, Thomas Wächter, Michael Schroeder:
  Extending ontologies by finding siblings using set expansion techniques. 292-300
  

• Ahrim Youn, Richard Simon:
  Estimating the order of mutations during tumorigenesis from tumor genome sequencing data. 1555-1561
  
• Tuobin Wang, Arminja N. Kettenbach, Scott A. Gerber, Chris Bailey-Kellogg:
  MMFPh: a maximal motif finder for phosphoproteomics datasets. 1562-1570
  
• Axel Bernal, Koby Crammer, Fernando Pereira:
  Automated gene-model curation using global discriminative learning. 1571-1578
  
• Zhong-Ru Xie, Ming-Jing Hwang:
  Ligand-binding site prediction using ligand-interacting and binding site-enriched protein triangles. 1579-1585
  
• Xuan Wang, Gordon A. Anderson, Richard D. Smith, Alan R. Dabney:
  A hybrid approach to protein differential expression in mass spectrometry-based proteomics. 1586-1591
  
• Ovidiu D. Iancu, Sunita Kawane, Daniel Bottomly, Robert Searles, Robert Hitzemann, Shannon K. McWeeney:
  Utilizing RNA-Seq data for de novo coexpression network inference. 1592-1597
  
• T. S. Shah, J. Z. Liu, J. A. B. Floyd, James A. Morris, N. Wirth, Jeffrey C. Barrett, C. A. Anderson:
  optiCall: a robust genotype-calling algorithm for rare, low-frequency and common variants. 1598-1603
  
• Bor-Sen Chen, Chia-Chou Wu:
  On the calculation of signal transduction ability of signaling transduction pathways in intracellular communication: systematic approach. 1604-1611
  
• Juliane Siebourg, Gunter Merdes, Benjamin Misselwitz, Wolf-Dietrich Hardt, Niko Beerenwinkel:
  Stability of gene rankings from RNAi screens. 1612-1618
  
• Dennis Egen, Desmond S. Lun:
  Truncated branch and bound achieves efficient constraint-based genetic design. 1619-1623
  
• Tavis K. Anderson, William W. Laegreid, Francesco Cerutti, Fernando A. Osorio, Eric A. Nelson, Jane Christopher-Hennings, Tony L. Goldberg:
  Ranking viruses: measures of positional importance within networks define core viruses for rational polyvalent vaccine development. 1624-1632
  
• Tim Rocktäschel, Michael Weidlich, Ulf Leser:
  ChemSpot: a hybrid system for chemical named entity recognition. 1633-1640
  

• Clemens Kreutz, J. S. Gehring, D. Lang, Ralf Reski, Jens Timmer, Stefan A. Rensing:
  TSSi - an R package for transcription start site identification from 5′ mRNA tag data. 1641-1642
  
• Vittore F. Scolari, Mina Zarei, Matteo Osella, M. Cosentino Lagomarsino:
  NuST: analysis of the interplay between nucleoid organization and gene expression. 1643-1644
  
• Joshua Tan, Durga Kuchibhatla, Fernanda L. Sirota, Westley A. Sherman, Tobias Gattermayer, Chia Yee Kwoh, Frank Eisenhaber, Georg Schneider, Sebastian Maurer-Stroh:
  Tachyon search speeds up retrieval of similar sequences by several orders of magnitude. 1645-1646
  
• Matthew Kearse, Richard Moir, Amy Wilson, Steven Stones-Havas, Matthew Cheung, Shane S. Sturrock, Simon Buxton, Alex Cooper, Sidney Markowitz, Chris Duran, Tobias Thierer, Bruce Ashton, Peter L. Meintjes, Alexei Drummond:
  Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data. 1647-1649
  
• Weizhong Li, Hamish McWilliam, Mickael Goujon, Andrew Cowley, Rodrigo Lopez, William R. Pearson:
  PSI-Search: iterative HOE-reduced profile SSEARCH searching. 1650-1651
  
• Paulo C. Carvalho, John R. Yates III, Valmir C. Barbosa:
  Improving the TFold test for differential shotgun proteomics. 1652-1654
  
• Nicholas Smith, Shawn Witham, Subhra Sarkar, Jie Zhang, Lin Li, Chuan Li, Emil Alexov:
  DelPhi web server v2: incorporating atomic-style geometrical figures into the computational protocol. 1655-1657
  
• Claudia Andreini, Gabriele Cavallaro, Serena Lorenzini:
  FindGeo: a tool for determining metal coordination geometry. 1658-1660
  
• Adrià Cereto-Massagué, Laura Guasch, Cristina Valls, Miquel Mulero, Gerard Pujadas, Santiago Garcia-Vallvé:
  DecoyFinder: an easy-to-use python GUI application for building target-specific decoy sets. 1661-1662
  
• Hadas Zur, Tamir Tuller:
  RFMapp: ribosome flow model application. 1663-1664
  
• Marco Brandizi, Natalja Kurbatova, Ugis Sarkans, Philippe Rocca-Serra:
  graph2tab, a library to convert experimental workflow graphs into tabular formats. 1665-1667
  

Volume 28, Number 13, July 2012

• Catherine A. Hayes, Szilard Nemes, Niclas G. Karlsson:
  Statistical analysis of glycosylation profiles to compare tissue type and inflammatory disease state. 1669-1676
  
• Shreepriya Das, Haris Vikalo:
  OnlineCall: fast online parameter estimation and base calling for illumina's next-generation sequencing. 1677-1683
  

• Ari Löytynoja, Albert J. Vilella, Nick Goldman:
  Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm. 1684-1691
  
• Xiaowen Liu, Alessandro Mammana, Vineet Bafna:
  Speeding up tandem mass spectral identification using indexes. 1692-1697
  
• Christian Otto, Peter F. Stadler, Steve Hoffmann:
  Fast and sensitive mapping of bisulfite-treated sequencing data. 1698-1704
  

• Lars J. Kangas, Thomas O. Metz, Giorgis Isaac, Brian T. Schrom, Bojana Ginovska-Pangovska, Luning Wang, Li Tan, Robert R. Lewis, John H. Miller:
  In silico identification software (ISIS): a machine learning approach to tandem mass spectral identification of lipids. 1705-1713