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: an in silico analysis of the subcellular locations of Escherichia 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 in Drosophila. 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, Baowen 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 deducing N-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 in Arabidopsis 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 for Drosophila 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 new cis-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 by Oligostickiness, 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

•