Bioinformatics, Volume 21

Volume 21, Number 1, January 2005

Editorials

• 
  Alfonso Valencia,Alex Bateman:
  Increasing the Impact ofBioinformatics.1-1

Original Papers - Genome Analysis

• 
  Albert D. G. de Roos:
  Origins of introns based on the definition of exon modules and their conserved interfaces.2-9

Sequence Analysis

• 
  Kuo-Chen Chou:
  Using amphiphilic pseudo amino acid composition to predict enzyme subfamily classes.10-19
• 
  Chin Lung Lu,Yen Pin Huang:
  A memory-efficient algorithm for multiple sequence alignment with constraints.20-30
• 
  Pavel Sumazin,Gengxin Chen,Naoya Hata,Andrew D. Smith,Theresa Zhang,Michael Q. Zhang:
  DWE: Discriminating Word Enumerator.31-38
• 
  Åsa K. Björklund,Daniel Soeria-Atmadja,Anna Zorzet,Ulf Hammerling,Mats G. Gustafsson:
  Supervised identification of allergen-representative peptides for in silico detection of potentially allergenic proteins.39-50

Structural Bioinformatics

• 
  Luonan Chen,Tianshou Zhou,Yun Tang:
  Protein structure alignment by deterministic annealing.51-62

Gene Expression

• 
  Wenjiang J. Fu,Edward R. Dougherty,Bani K. Mallick,Raymond J. Carroll:
  How many samples are needed to build a classifier: a general sequential approach.63-70
• 
  Min Zou,Suzanne D. Conzen:
  A new dynamic Bayesian network (DBN) approach for identifying gene regulatory networks from time course microarray data.71-79
• 
  Toni Reverter-Gomez,S. M. McWilliam,Wes Barris,Brian P. Dalrymple:
  A rapid method for computationally inferring transcriptome coverage and microarray sensitivity.80-89

Genetics And Population Analysis

• 
  Kui Zhang,Fengzhu Sun,Hongyu Zhao:
  HAPLORE: a program for haplotype reconstruction in general pedigrees without recombination.90-103

Data And Text Mining

• 
  Ramin Homayouni,Kevin Heinrich,Lai Wei,Michael W. Berry:
  Gene clustering by Latent Semantic Indexing of MEDLINE abstracts.104-115

Databases And Ontologies

• 
  Yongqun He,Richard R. Vines,Alice R. Wattam,Georgiy V. Abramochkin,Allan Dickerman,J. Dana Eckart,Bruno W. S. Sobral:
  PIML: the Pathogen Information Markup Language.116-121

Applications Notes - Sequence Analysis

• 
  Robert Belshaw,Aris Katzourakis:
  BlastAlign: a program that usesblast to align problematic nucleotide sequences.122-123

Gene Expression

• 
  Scott J. Tebbutt,Igor V. Opushnyev,Ben W. Tripp,Ayaz M. Kassamali,Wendy L. Alexander,Marilyn I. Andersen:
  SNP Chart: an integrated platform for visualization and interpretation of microarray genotyping data.124-127

Genetics And Population Analysis

• 
  Marie-Françoise Jourjon,Sylvain Jasson,Jacques Marcel,Baba Ngom,Brigitte Mangin:
  MCQTL: multi-allelic QTL mapping in multi-cross design.128-130
• 
  Kui Zhang,Zhaohui S. Qin,Ting Chen,Jun S. Liu,Michael S. Waterman,Fengzhu Sun:
  HapBlock: haplotype block partitioning and tag SNP selection software using a set of dynamic programming algorithms.131-134

Systems Biology

• 
  Vincent J. Carey,Jeff Gentry,Elizabeth Whalen,Robert Gentleman:
  Network structures and algorithms in Bioconductor.135-136

Databases And Ontologies

• 
  Slobodan Vucetic,Zoran Obradovic,Vladimir Vacic,Predrag Radivojac,Kang Peng,Lilia M. Iakoucheva,Marc S. Cortese,J. David Lawson,Celeste J. Brown,Jason G. Sikes,Crystal D. Newton,A. Keith Dunker:
  DisProt: a database of protein disorder.137-140

Volume 21, Number 2, January 2005

Original Papers - Genome Analysis

• 
  Siu-Ming Yiu,Prudence W. H. Wong,Tak Wah Lam,Y. C. Mui,Hsiang-fu Kung,Marie C. M. Lin,Y. T. Cheung:
  Filtering of Ineffective siRNAs and Improved siRNA Design Tool.144-151

Sequence Analysis

• 
  Kuang Lin,Victor A. Simossis,William R. Taylor,Jaap Heringa:
  A simple and fast secondary structure prediction method using hidden neural networks.152-159
• 
  Sung W. Shin,Sam Kim:
  A new algorithm for detecting low-complexity regions in protein sequences.160-170

Gene Expression

• 
  Liat Ein-Dor,Itai Kela,Gad Getz,David Givol,Eytan Domany:
  Outcome signature genes in breast cancer: is there a unique set?.171-178
• 
  Hiro Takahashi,Takeshi Kobayashi,Hiroyuki Honda:
  Construction of robust prognostic predictors by using projective adaptive resonance theory as a gene filtering method.179-186
• 
  Hyunsoo Kim,Gene H. Golub,Haesun Park:
  Missing value estimation for DNA microarray gene expression data: local least squares imputation.187-198

Systems Biology

• 
  J. P. Massar,Michael Travers,Jeff Elhai,Jeff Shrager:
  BioLingua: a programmable knowledge environment for biologists.199-207
• 
  David Orrell,Stephen Ramsey,Pedro de Atauri,Hamid Bolouri:
  A method for estimating stochastic noise in large genetic regulatory networks.208-217
• 
  Shawn Martin,Diana C. Roe,Jean-Loup Faulon:
  Predicting protein-protein interactions using signature products.218-226
• 
  Sascha Ott,Annika Hansen,SunYong Kim,Satoru Miyano:
  Superiority of network motifs over optimal networks and an application to the revelation of gene network evolution.227-238
• 
  Michele Leone,Andrea Pagnani:
  Predicting protein functions with message passing algorithms.239-247

Data And Text Mining

• 
  Lifeng Chen,Hongfang Liu,Carol Friedman:
  Gene name ambiguity of eukaryotic nomenclatures.248-256

Applications Notes - Sequence Analysis

• 
  Sam Griffiths-Jones:
  RALEE--RNA ALignment Editor in Emacs.257-259

Phylogenetics

• 
  Darren P. Martin,Carolyn Williamson,David Posada:
  RDP2: recombination detection and analysis from sequence alignments.260-262

Genetics And Population Analysis

• 
  Jeffrey C. Barrett,B. Fry,Julian B. Maller,Mark J. Daly:
  Haploview: analysis and visualization of LD and haplotype maps.263-265
• 
  Lan-Juan Zhao,Miao-Xin Li,Yan-Fang Guo,Fu-Hua Xu,Jin-Long Li,Hong-Wen Deng:
  SNPP: automating large-scale SNP genotype data management.266-268

Systems Biology

• 
  Steven Vercruysse,Martin Kuiper:
  Simulating genetic networks made easy: network construction with simple building blocks.269-271
• 
  Florian Iragne,Macha Nikolski,Bertrand Mathieu,David Auber,David James Sherman:
  ProViz: protein interaction visualization and exploration.272-274

Databases And Ontologies

• 
  Andrew Young,Nathan Whitehouse,J. Cho,Chad A. Shaw:
  OntologyTraverser: an R package for GO analysis.275-276

Volume 21, Number 3, February 2005

Editorials

• 
  Protein Refinement: A New Challenge For Casp In Its 10th Anniversary.277

Genome Analysis

• 
  Graham J. Etherington,Jo L. Dicks,Ian N. Roberts:
  Recombination Analysis Tool (RAT): a program for the high-throughput detection of recombination.278-281
• 
  Andrew E. Firth,Chris M. Brown:
  Detecting overlapping coding sequences with pairwise alignments.282-292
• 
  Daniel H. Haft,Jeremy D. Selengut,Lauren M. Brinkac,Nikhat Zafar,Owen White:
  Genome Properties: a system for the investigation of prokaryotic genetic content for microbiology, genome annotation and comparative genomics.293-306

Sequence Analysis

• 
  Dustin E. Schones,Pavel Sumazin,Michael Q. Zhang:
  Similarity of position frequency matrices for transcription factor binding sites.307-313

Structural Bioinformatics

• 
  Haiquan Li,Jinyan Li:
  Discovery of stable and significant binding motif pairs from PDB complexes and protein interaction datasets.314-324

Gene Expression

• 
  Anders F. Andersson,Rolf Bernander,Peter Nilsson:
  Dual-genome primer design for construction of DNA microarrays.325-332

Genetics And Population Analysis

• 
  Juan M. Gonzalez,Johannes Zimmermann,Cesareo Saiz-Jimenez:
  Evaluating putative chimeric sequences from PCR-amplified products.333-337

Systems Biology

• 
  Luca Ferrarini,Luca Bertelli,Jacob D. Feala,Andrew D. McCulloch,Giovanni Paternostro:
  A more efficient search strategy for aging genes based on connectivity.338-348
• 
  Matthew J. Beal,Francesco Falciani,Zoubin Ghahramani,Claudia Rangel,David L. Wild:
  A Bayesian approach to reconstructing genetic regulatory networks with hidden factors.349-356
• 
  Antti Pettinen,Tommi Aho,Olli-Pekka Smolander,Tiina Manninen,Antti Saarinen,Kaisa-Leena Taattola,Olli Yli-Harja,Marja-Leena Linne:
  Simulation tools for biochemical networks: evaluation of performance and usability.357-363
• 
  Vicente Arnau,Sergio Mars,Ignacio Marín:
  Iterative Cluster Analysis of Protein Interaction Data.364-378

Databases And Ontologies

• 
  Carla Kuiken,Karina Yusim,Laura Boykin,Russell Richardson:
  The Los Alamos hepatitis C sequence database.379-384

Genome Analysis

• 
  Stefan Weckx,Peter De Rijk,Christine Van Broeckhoven,Jurgen Del-Favero:
  SNPbox: a modular software package for large-scale primer design.385-387
• 
  Madelaine Marchin,Paul T. Kelly,Jianwen Fang:
  Tracker: continuous HMMER and BLAST searching.388-389

Phylogenetics

• 
  C. J. Creevey,James O. McInerney:
  Clann: investigating phylogenetic information through supertree analyses.390-392

Structural Bioinformatics

• 
  Paolo Fontana,Eckart Bindewald,Stefano Toppo,Riccardo Velasco,Giorgio Valle,Silvio C. E. Tosatto:
  The SSEA server for protein secondary structure alignment.393-395

Gene Expression

• 
  Tomaz Curk,Janez Demsar,Qikai Xu,Gregor Leban,Uros Petrovic,Ivan Bratko,Gad Shaulsky,Blaz Zupan:
  Microarray data mining with visual programming.396-398
• 
  Xiaoyun Tang,Lishuang Shen,Julie A. Dickerson:
  BarleyExpress: a web-based submission tool for enriched microarray database annotations.399-401

Genetics And Population Analysis

• 
  Eric W. Price,Ignazio Carbone:
  SNAP: workbench management tool for evolutionary population genetic analysis.402-404
• 
  Tom H. Lindner,Katrin Hoffmann:
  easyLINKAGE: a PERL script for easy and automated two-/multi-point linkage analyses.405-407
• 
  Ian Bradford,Robin Winter,Carl Evans,Jonathan Bard:
  Human-CMouse Gene Searcher: a tool to assist discovery of malformation-associated genes by using phenotype databases.408-409

Systems Biology

• 
  Robert D. Finn,Mhairi Marshall,Alex Bateman:
  iPfam: visualization of protein?Cprotein interactions in PDB at domain and amino acid resolutions.410-412

Data And Text Mining

• 
  Gregor Leban,Ivan Bratko,Uros Petrovic,Tomaz Curk,Blaz Zupan:
  VizRank: finding informative data projections in functional genomics by machine learning.413-414

Databases And Ontologies

• 
  Daniel Shegogue,W. Jim Zheng:
  Capturing biological information with class?Cresponsibility?Ccollaboration cards.415-417
• 
  Abdullah Kahraman,Andrey Avramov,Lyubomir G. Nashev,Dimitar Popov,Rainer Ternes,Hans-Dieter Pohlenz,Bertram Weiss:
  PhenomicDB: a multi-species genotype/phenotype database for comparative phenomics.418-420

Volume 21, Number 4, February 2005

SAC 2004 Papers

• 
  Jyotsna Kasturi,Raj Acharya:
  Clustering of diverse genomic data using information fusion.423-429
• 
  Aditya Vailaya,Peter Bluvas,Robert Kincaid,Allan Kuchinsky,Michael L. Creech,Annette Adler:
  An architecture for biological information extraction and representation.430-438
• 
  Daisuke Komura,Hiroshi Nakamura,Shuichi Tsutsumi,Hiroyuki Aburatani,Sigeo Ihara:
  Multidimensional support vector machines for visualization of gene expression data.439-444
• 
  Osman Abul,Reda Alhajj,Faruk Polat,Ken Barker:
  Finding differentially expressed genes for pattern generation.445-450
• 
  Nadia Bolshakova,Francisco Azuaje,Padraig Cunningham:
  An integrated tool for microarray data clustering and cluster validity assessment .451-455
• 
  Alexandros Stamatakis,Thomas Ludwig,Harald Meier:
  RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees.456-463

Genome Analysis

• 
  Tarjei S. Mikkelsen,James E. Galagan,Jill P. Mesirov:
  Improving genome annotations using phylogenetic profile anomaly detection.464-470

Sequence Analysis

• 
  Te-Ming Chen,Chung-Chin Lu,Wen-Hsiung Li:
  Prediction of splice sites with dependency graphs and their expanded bayesian networks.471-482
• 
  Gaurav Sachdeva,Kaushal Kumar,Preti Jain,Srinivasan Ramachandran:
  SPAAN: a software program for prediction of adhesins and adhesin-like proteins using neural networks.483-491

Gene Expression

• 
  Veronica Vinciotti,Raya Khanin,Davide D'Alimonte,Xiaohui Liu,N. Cattini,G. Hotchkiss,Giselda Bucca,O. de Jesus,J. Rasaiyaah,Colin P. Smith,Paul Kellam,Ernst Wit:
  An experimental evaluation of a loop versus a reference design for two-channel microarrays.492-501
• 
  Paul Delmar,Stéphane Robin,Jean-Jacques Daudin:
  VarMixt: efficient variance modelling for the differential analysis of replicated gene expression data.502-508
• 
  Liping Ji,Kian-Lee Tan:
  Identifying time-lagged gene clusters using gene expression data.509-516
• 
  Byung Soo Kim,Inyoung Kim,Sunho Lee,Sangcheol Kim,Sun Young Rha,Hyun Cheol Chung:
  Statistical methods of translating microarray data into clinically relevant diagnostic information in colorectal cancer.517-528
• 
  Zhong Guan,Hongyu Zhao:
  A semiparametric approach for marker gene selection based on gene expression data.529-536

Genome Analysis

• 
  Paul Stothard,David S. Wishart:
  Circular genome visualization and exploration using CGView.537-539

Sequence Analysis

• 
  Martín Sarachu,Marc Colet:
  wEMBOSS: a web interface for EMBOSS.540-541
• 
  Derek Kisman,Ming Li,Bin Ma,Li Wang:
  tPatternHunter: gapped, fast and sensitive translated homology search .542-544
• 
  D. Charif,Jean Thioulouse,J. R. Lobry,Guy Perrière:
  Online synonymous codon usage analyses with the ade4 and seqinR packages.545-547
• 
  Jinsoo Kim,Jungmin Seo,Young Seek Lee,Sangsoo Kim:
  TFExplorer: integrated analysis database for predicted transcription regulatory elements.548-550

Structural Bioinformatics

• 
  Allegra Via,Andreas Zanzoni,Manuela Helmer-Citterich:
  Seq2Struct: a resource for establishing sequence-structure links.551-553

Gene Expression

• 
  Andreas Buness,Wolfgang Huber,Klaus Steiner,Holger Sültmann,Annemarie Poustka:
  arrayMagic: two-colour cDNA microarray quality control, preprocessing.554-556

Genetics And Population Analysis

• 
  X. Kong,Tara Cox Matise:
  MAP-O-MAT: internet-based linkage mapping.557-559

Systems Biology

• 
  Brett G. Olivier,Johann M. Rohwer,Jan-Hendrik S. Hofmeyr:
  Modelling cellular systems with PySCeS.560-561

Volume 21, Number 5, March 2005

Genome Analysis

• 
  Bo Yan,Chongle Pan,Victor Olman,Robert L. Hettich,Ying Xu:
  A graph-theoretic approach for the separation of b and y ions in tandem mass spectra.563-574
• 
  Yu Chen,Dong Xu:
  Understanding protein dispensability through machine-learning analysis of high-throughput data.575-581

Sequence Analysis

• 
  Davide Campagna,Chiara Romualdi,Nicola Vitulo,Micky Del Favero,Matej Lexa,Nicola Cannata,Giorgio Valle:
  RAP: a new computer program for de novo identification of repeated sequences in whole genomes.582-588
• 
  Jinko Graham,Brad McNeney,Françoise Seillier-Moiseiwitsch:
  Stepwise detection of recombination breakpoints in sequence alignments.589-595
• 
  Yoseph Barash,Gal Elidan,Tommy Kaplan,Nir Friedman:
  CIS: compound importance sampling method for protein-DNA binding site p-value estimation.596-600
• 
  S. Burden,Yan-Xia Lin,R. Zhang:
  Improving promoter prediction Improving promoter prediction for the NNPP2.2 algorithm: a case study using Escherichia coli DNA sequences.601-607
• 
  Luciano da Fontoura Costa:
  Biological sequence analysis through the one-dimensional percolation transform and its enhanced version.608-616
• 
  Jennifer L. Gardy,Matthew R. Laird,Fei Chen,Sébastien Rey,C. J. Walsh,Martin Ester,Fiona S. L. Brinkman:
  PSORTb v.2.0: Expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis.617-623

Structural Bioinformatics

• 
  Ming Zhang,R. Allen White,Liqun Wang,Ronald N. Goldman,Lydia E. Kavraki,Brendan Hassett:
  Improving conformational searches by geometric screening.624-630

Gene Expression

• 
  Alexander R. Statnikov,Constantin F. Aliferis,Ioannis Tsamardinos,Douglas P. Hardin,Shawn Levy:
  A comprehensive evaluation of multicategory classification methods for microarray gene expression cancer diagnosis.631-643
• 
  Musa H. Asyali,Musa Alci:
  Reliability analysis of microarray data using fuzzy c-means and normal mixture modeling based classification methods.644-649
• 
  Itai Yanai,Hila Benjamin-Rodrig,Michael Shmoish,Vered Chalifa-Caspi,Maxim Shklar,Ron Ophir,Arren Bar-Even,Shirley Horn-Saban,Marilyn Safran,Eytan Domany,Doron Lancet,Orit Shmueli:
  Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification.650-659
• 
  Cyril Dalmasso,Philippe Broët,Thierry Moreau:
  A simple procedure for estimating the false discovery rate.660-668

Genome Analysis

• 
  Yecheng Huang,Janie Pumphrey,Alan R. Gingle:
  ESTminer: a Web interface for mining EST contig and cluster databases.669-670

Sequence Analysis

• 
  Huiqing Liu,Hao Han,Jinyan Li,Limsoon Wong:
  DNAFSMiner: a web-based software toolbox to recognize two types of functional sites in DNA sequences.671-673
• 
  Robert J. Beynon:
  A simple tool for drawing proteolytic peptide maps.674-675

Phylogenetics

• 
  Sergei L. Kosakovsky Pond,Simon D. W. Frost,Spencer V. Muse:
  HyPhy: hypothesis testing using phylogenies.676-679

Structural Bioinformatics

• 
  Norma H. Pawley,Jason D. Gans,Ryszard Michalczyk:
  APART: Automated Preprocessing for NMR Assignments with Reduced Tedium.680-682
• 
  Frank Zöllner,Steffen Neumann,Franz Kummert,Gerhard Sagerer:
  Database driven test case generation for protein?Cprotein docking.683-684
• 
  Doreen Pahlke,Dietmar Leitner,Urs Wiedemann,Dirk Labudde:
  COPS - Cis/trans peptide bond conformation prediction of amino acids on the basis of secondary structure information.685-686

Gene Expression

• 
  Henrik Bjørn Nielsen,Laurent Gautier,Steen Knudsen:
  Implementation of a gene expression index calculation method based on the PDNN model.687-688
• 
  Johnson Kian-Kok Ng,Wen-Tso Liu:
  LabArray: real-time imaging and analytical tool for microarrays.689-690

Genetics And Population Analysis

• 
  Rex T. Nelson,David M. Grant,Randy C. Shoemaker:
  ESTminer: a suite of programs for gene and allele identification.691-693

Data And Text Mining

• 
  Jing Ding,Daniel Berleant:
  MedKit: a helper toolkit for automatic mining of MEDLINE/PubMed citations.694-695

Databases And Ontologies:

• 
  Marius Felder,Karol Szafranski,Rüdiger Lehmann,Ludwig Eichinger,Angelika A. Noegel,Matthias Platzer,Gernot Glöckner:
  DictyMOLD - a Dictyostelium discoideum genome browser database.696-697

Volume 21, Number 6, March 2005

Sequence Analysis

• 
  Isabelle Callebaut,Jean Paul Mornon:
  OCRE: a novel domain made of imperfect, aromatic-rich octamer repeats.699-702

Genome Analysis

• 
  Xiangqun H. Zheng,Fu Lu,Zhen-Yuan Wang,Fei Zhong,Jeffrey Hoover,Richard J. Mural:
  Using shared genomic synteny and shared protein functions to enhance the identification of orthologous gene pairs.703-710

Structural Bioinformatics

• 
  Alejandro Panjkovich,Francisco Melo:
  Comparison of different melting temperature calculation methods for short DNA sequences .711-722

Gene Expression

• 
  David J. Bakewell,Ernst Wit:
  Weighted analysis of microarray gene expression using maximum-likelihood.723-729
• 
  Y-h. Taguchi,Y. Oono:
  Relational patterns of gene expression via non-metric multidimensional scaling analysis.730-740

Systems Biology

• 
  Peter J. Woolf,Wendy Prudhomme,Laurence Daheron,George Q. Daley,Douglas A. Lauffenburger:
  Bayesian analysis of signaling networks governing embryonic stem cell fate decisions.741-753
• 
  Juliane Schäfer,Korbinian Strimmer:
  An empirical Bayes approach to inferring large-scale gene association networks.754-764
• 
  John Jeremy Rice,Yuhai Tu,Gustavo Stolovitzky:
  Reconstructing biological networks using conditional correlation analysis.765-773
• 
  Chin-Rang Yang,Bruce E. Shapiro,Eric Mjolsness,G. Wesley Hatfield:
  An enzyme mechanism language for the mathematical modeling of metabolic pathways.774-780

Data And Text Mining

• 
  D. Y. Lin:
  An efficient Monte Carlo approach to assessing statistical significance in genomic studies.781-787
• 
  Dilip Rajagopalan,Pankaj Agarwal:
  Inferring pathways from gene lists using a literature-derived network of biological relationships.788-793

Databases And Ontologies

• 
  Yong Meng Teo,Xianbing Wang,Yew Kwong Ng:
  GLAD: a system for developing and deploying large-scale bioinformatics grid.794-802
• 
  Steve W. Cole,Weihong Yan,Zoran Galic,Jesusa Arevalo,Jerome A. Zack:
  Expression-based monitoring of transcription factor activity: the TELiS database.803-810
• 
  T. Boby,A.-M. Patch,S. J. Aves:
  TRbase: a database relating tandem repeats to disease genes for the human genome.811-816

Genome Analysis

• 
  István Miklós,Péter Ittzés,Jotun Hein:
  ParIS Genome Rearrangement server.817-820

Genetics And Population Analysis

• 
  Ole Christian Lingjærde,Lars O. Baumbusch,Knut Liestøl,Ingrid Kristine Glad,Anne-Lise Børresen-Dale:
  CGH-Explorer: a program for analysis of array-CGH data.821-822

Systems Biology

• 
  Cameron Wellock,Vijay Chickarmane,Herbert M. Sauro:
  The SBW-CMATLAB interface.823-824

Databases And Ontologies

• 
  J. Stuart Aitken,Roman Korf,Bonnie L. Webber,Jonathan Bard:
  COBrA: a bio-ontology editor.825-826
• 
  Thijs Beuming,Lucy Skrabanek,Masha Y. Niv,Piali Mukherjee,Harel Weinstein:
  PDZBase: a protein?Cprotein interaction database for PDZ-domains.827-828
• 
  Yu Rang Park,Chan Hee Park,Ju Han Kim:
  GOChase: correcting errors from Gene Ontology-based annotations for gene products.829-831
• 
  Philipp Pagel,Stefan Kovac,Matthias Oesterheld,Barbara Brauner,Irmtraud Dunger-Kaltenbach,Goar Frishman,Corinna Montrone,Pekka Mark,Volker Stümpflen,Hans-Werner Mewes,Andreas Ruepp,Dmitrij Frishman:
  The MIPS mammalian protein?Cprotein interaction database.832-834
• 
  Saranyan K. Palaniswamy,Victor X. Jin,Hao Sun,Ramana V. Davuluri:
  OMGProm: a database of orthologous mammalian gene promoters.835-836

Volume 21, Number 7, April 2005

Genome Analysis

• 
  Alexey V. Kochetov:
  AUG codons at the beginning of protein coding sequences are frequent in eukaryotic mRNAs with a suboptimal start codon context.837-840

Sequence Analysis

• 
  Matthieu Legendre,André Lambert,Daniel Gautheret:
  Profile-based detection of microRNA precursors in animal genomes.841-845

Genome Analysis

• 
  Vladimir Paar,Nenad Pavin,Marija Rosandic,Matko Gluncic,Ivan Basar,Robert Pezer,Sonja Durajlija Zinic:
  ColorHOR-novel graphical algorithm for fast scan of alpha satellite higher-order repeats and HOR annotation for GenBank sequence of human genome.846-852
• 
  Daniela Bartels,Sebastian Kespohl,Stefan P. Albaum,Tanja Drüke,Alexander Goesmann,Julia Herold,Olaf Kaiser,Alfred Pühler,Friedhelm Pfeiffer,Günter Raddatz,Jens Stoye,Folker Meyer,Stephan C. Schuster:
  BACCardI-a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison.853-859
• 
  Roger M. Jarvis,Royston Goodacre:
  Genetic algorithm optimization for pre-processing and variable selection of spectroscopic data.860-868
• 
  Peng Yin,Alexander J. Hartemink:
  Theoretical and practical advances in genome halving.869-879
• 
  Benjamin P. Westover,Jeremy D. Buhler,Justin L. Sonnenburg,Jeffrey I. Gordon:
  Operon prediction without a training set.880-888
• 
  Shahid H. Bokhari,Jon R. Sauer:
  A parallel graph decomposition algorithm for DNA sequencing with nanopores.889-896
• 
  Gideon Dror,Rotem Sorek,Ron Shamir:
  Accurate identification of alternatively spliced exons using support vector machine.897-901

Sequence Analysis

• 
  Yi-Kuo Yu,Stephen F. Altschul:
  The construction of amino acid substitution matrices for the comparison of proteins with non-standard compositions.902-911
• 
  Masumi Itoh,Susumu Goto,Tatsuya Akutsu,Minoru Kanehisa:
  Fast and accurate database homology search using upper bounds of local alignment scores.912-921
• 
  Chiara Sabatti,Lars Rohlin,Kenneth Lange,James C. Liao:
  Vocabulon: a dictionary model approach for reconstruction and localization of transcription factor binding sites.922-931
• 
  January 3rd Weiner,Geraint Thomas,Erich Bornberg-Bauer:
  Rapid motif-based prediction of circular permutations in multi-domain proteins.932-937
• 
  Wei-Mou Zheng:
  Relation between weight matrix and substitution matrix: motif search by similarity.938-943
• 
  Kuo-Chen Chou,Yu-Dong Cai:
  Predicting protein localization in budding Yeast.944-950
• 
  Johannes Söding:
  Protein homology detection by HMM?CHMM comparison.951-960
• 
  M. Michael Gromiha,Makiko Suwa:
  A simple statistical method for discriminating outer membrane proteins with better accuracy.961-968

Phylogenetics

• 
  Thomas M. Keane,Thomas J. Naughton,Simon A. A. Travers,James O. McInerney,Grace P. McCormack:
  DPRml: distributed phylogeny reconstruction by maximum likelihood.969-974
• 
  Gavin E. Crooks,Steven E. Brenner:
  An alternative model of amino acid replacement.975-980

Structural Bioinformatics

• 
  Dominik Gront,Andrzej Kolinski:
  A new approach to prediction of short-range conformational propensities in proteins.981-987
• 
  John D. Westbrook,Nobutoshi Ito,Haruki Nakamura,Kim Henrick,Helen M. Berman:
  PDBML: the representation of archival macromolecular structure data in XML.988-992
• 
  Tom M. W. Nye,Carlo Berzuini,Walter R. Gilks,M. Madan Babu,Sarah A. Teichmann:
  Statistical analysis of domains in interacting protein pairs.993-1001
• 
  Erik Sandelin:
  Extracting multiple structural alignments from pairwise alignments: a comparison of a rigorous and a heuristic approach.1002-1009
• 
  Xin Yuan,Christopher Bystroff:
  Non-sequential structure-based alignments reveal topology-independent core packing arrangements in proteins.1010-1019
• 
  Ilona Kifer,Ori Sasson,Michal Linial:
  Predicting fold novelty based on ProtoNet hierarchical classification.1020-1027
• 
  Carleton Kingsford,Bernard Chazelle,Mona Singh:
  Solving and analyzing side-chain positioning problems using linear and integer programming.1028-1039

Gene Expression

• 
  Francisco R. Pinto,L. Ashley Cowart,Yusuf A. Hannun,Bärbel Rohrer,Jonas S. Almeida:
  Local correlation of expression profiles with gene annotations-proof of concept for a general conciliatory method.1037-1045
• 
  Chao Sima,Ulisses M. Braga-Neto,Edward R. Dougherty:
  Superior feature-set ranking for small samples using bolstered error estimation.1046-1054
• 
  Yuan Ji,Kam-Wah Tsui,KyungMann Kim:
  A novel means of using gene clusters in a two-step empirical Bayes method for predicting classes of samples.1055-1061
• 
  Hisanori Kiryu,Taku Oshima,Kiyoshi Asai:
  Extracting relations between promoter sequences and their strengths from microarray data.1062-1068
• 
  Rajarajeswari Balasubramaniyan,Eyke Hüllermeier,Nils Weskamp,Jörg Kämper:
  Clustering of gene expression data using a local shape-based similarity measure.1069-1077
• 
  Jeanette E. Eckel,C. Gennings,Terry M. Therneau,L. D. Burgoon,D. R. Boverhof,Timothy R. Zacharewski:
  Normalization of two-channel microarray experiments: a semiparametric approach.1078-1083
• 
  Yee Hwa Yang,Yuanyuan Xiao,Mark R. Segal:
  Identifying differentially expressed genes from microarray experiments via statistic synthesis.1084-1093
• 
  Sébastien Rimour,David R. C. Hill,Cécile Militon,Pierre Peyret:
  GoArrays: highly dynamic and efficient microarray probe design.1094-1103
• 
  Gersende Fort,Sophie Lambert-Lacroix:
  Classification using partial least squares with penalized logistic regression.1104-1111
• 
  Antonio Reverter,Wes Barris,Sean McWilliam,Keren A. Byrne,Yong H. Wang,Siok-Hwee Tan,Nicholas J. Hudson,Brian P. Dalrymple:
  Validation of alternative methods of data normalization in gene co-expression studies.1112-1120
• 
  David R. Bickel:
  Probabilities of spurious connections in gene networks: application to expression time series.1121-1128
• 
  Yoram Ben-Shaul,Hagai Bergman,Hermona Soreq:
  Identifying subtle interrelated changes in functional gene categories using continuous measures of gene expression.1129-1137

Genetics And Population Analysis

• 
  Sven Bilke,Qing-Rong Chen,Craig C. Whiteford,Javed I. Khan:
  Detection of low level genomic alterations by comparative genomic hybridization based on cDNA micro-arrays.1138-1145
• 
  Paul H. C. Eilers,Renée X. de Menezes:
  Quantile smoothing of array CGH data.1146-1153

Systems Biology

• 
  Shuhei Kimura,Kaori Ide,Aiko Kashihara,Makoto Kano,Mariko Hatakeyama,Ryoji Masui,Noriko Nakagawa,Shigeyuki Yokoyama,Seiki Kuramitsu,Akihiko Konagaya:
  Inference of S-system models of genetic networks using a cooperative coevolutionary algorithm.1154-1163
• 
  Ulrik de Lichtenberg,Lars Juhl Jensen,Anders Fausbøll,Thomas Skøt Jensen,Peer Bork,Søren Brunak:
  Comparison of computational methods for the identification of cell cycle-regulated genes.1164-1171
• 
  M. Kloster,Chao Tang,Ned S. Wingreen:
  Finding regulatory modules through large-scale gene-expression data analysis.1172-1179
• 
  Kuan-Yao Tsai,Feng-Sheng Wang:
  Evolutionary optimization with data collocation for reverse engineering of biological networks.1180-1188
• 
  Syed Asad Rahman,P. Advani,R. Schunk,Rainer Schrader,Dietmar Schomburg:
  Metabolic pathway analysis web service (Pathway Hunter Tool at CUBIC).1189-1193
• 
  Gang Liu,Mark T. Swihart,Sriram Neelamegham:
  Sensitivity, principal component and flux analysis applied to signal transduction: the case of epidermal growth factor mediated signaling.1194-1202
• 
  Robert Urbanczik,C. Wagner:
  An improved algorithm for stoichiometric network analysis: theory and applications.1203-1210
• 
  Ranadip Pal,Aniruddha Datta,Michael L. Bittner,Edward R. Dougherty:
  Intervention in context-sensitive probabilistic Boolean networks.1211-1218
• 
  Ina Koch,Björn H. Junker,Monika Heiner:
  Application of Petri net theory for modelling and validation of the sucrose breakdown pathway in the potato tuber.1219-1226

Data And Text Mining

• 
  Asako Koike,Yoshiki Niwa,Toshihisa Takagi:
  Automatic extraction of gene/protein biological functions from biomedical text.1227-1236

Databases And Ontologies

• 
  Yingyao Zhou,Jason A. Young,Andrey Santrosyan,Kaisheng Chen,S. Frank Yan,Elizabeth A. Winzeler:
  In silico gene function prediction using ontology-based pattern identification.1237-1245
• 
  Julie Chabalier,Cécile Capponi,Yves Quentin,Gwennaele Fichant:
  ISYMOD: a knowledge warehouse for the identification, assembly and analysis of bacterial integrated systems.1246-1256
• 
  Georgios V. Gkoutos,Eain C. J. Green,Simon Greenaway,Andrew Blake,Ann-Marie Mallon,John M. Hancock:
  CRAVE: a database, middleware and visualization system for phenotype ontologies.1257-1262

Genome Analysis

• 
  Michael D. Gadberry,Simon T. Malcomber,Andrew N. Doust,Elizabeth A. Kellogg:
  Primaclade - a flexible tool to find conserved PCR primers across multiple species.1263-1264
• 
  Jian Xu,Jeffrey I. Gordon:
  MapLinker: a software tool that aids physical map-linked whole genome shotgun assembly.1265-1266

Sequence Analysis

• 
  Ivo Van Walle,Ignace Lasters,Lode Wyns:
  SABmark- a benchmark for sequence alignment that covers the entire known fold space.1267-1268
• 
  Lars Kiemer,Jannick Dyrløv Bendtsen,Nikolaj Blom:
  NetAcet: prediction of N-terminal acetylation sites.1269-1270
• 
  Burkhard Morgenstern,Nadine Werner,Sonja J. Prohaska,Rasmus Steinkamp,Isabelle Schneider,Amarendran Ramaswami Subramanian,Peter F. Stadler,Jan Weyer-Menkhoff:
  Multiple sequence alignment with user-defined constraints at GOBICS.1271-1273

Phylogenetics

• 
  Dimitris Paraskevis,Koen Deforche,Philippe Lemey,Gkikas Magiorkinis,Angelos Hatzakis,Anne-Mieke Vandamme:
  SlidingBayes: exploring recombination using a sliding window approach based on Bayesian phylogenetic inference.1274-1275

Structural Bioinformatics

• 
  Gábor E. Tusnády,Zsuzsanna Dosztányi,István Simon:
  TMDET: web server for detecting transmembrane regions of proteins by using their 3D coordinates.1276-1277

Gene Expression

• 
  Victor E. Gerth,Peter D. Vize:
  A Java tool for dynamic web-based 3D visualization of anatomy and overlapping gene or protein expression patterns.1278-1279
• 
  Gilles Caraux,Sylvie Pinloche:
  PermutMatrix: a graphical environment to arrange gene expression profiles in optimal linear order.1280-1281

Genetics And Population Analysis

• 
  Bernhard Hiller,Jutta Bradtke,Harald Balz,Harald Rieder:
  CyDAS: a cytogenetic data analysis system.1282-1283

Systems Biology

• 
  Pawan Dhar,Tan Chee Meng,Sandeep Somani,Li Ye,Kishore R. Sakharkar,Arun Krishnan,Azmi B. M. Ridwan,Sebastian Ho Kok Wah,Mandar A. Chitre,Hao Zhu:
  Grid Cellware: the first grid-enabled tool for modelling and simulating cellular processes.1284-1287

Databases And Ontologies

• 
  Chung-Yen Lin,Chia-Ling Chen,Chi-Shiang Cho,Li-Ming Wang,Chia-Ming Chang,Pao-Yang Chen,Chen-Zen Lo,Chao A. Hsiung:
  hp-DPI: Helicobacter pylori Database of Protein Interactomes-embracing experimental and inferred interactions.1288-1290
• 
  Joachim Reichelt,Guido Dieterich,Marsel Kvesic,Dietmar Schomburg,Dirk W. Heinz:
  BRAGI: linking and visualization of database information in a 3D viewer and modeling tool.1291-1293

Volume 21, Number 8, April 2005

Sequence Analysis

• 
  Naum I. Gershenzon,Ilya P. Ioshikhes:
  Synergy of human Pol II core promoter elements revealed by statistical sequence analysis.1295-1300
• 
  Alex Bateman,Matthew T. G. Holden,Corin Yeats:
  The G5 domain: a potential N-acetylglucosamine recognition domain involved in biofilm formation.1301-1303
• 
  Francesca D. Ciccarelli,Peer Bork:
  The WHy domain mediates the response to desiccation in plants and bacteria.1304-1307

Structural Bioinformatics

• 
  S. Sri Krishna,Nick V. Grishin:
  Structural drift: a possible path to protein fold change.1308-1310

Systems Biology

• 
  Antonio del Sol,Hirotomo Fujihashi,Paul O'Meara:
  Topology of small-world networks of protein?Cprotein complex structures.1311-1315

Genome Analysis

• 
  Tomoyuki Yamada,Shinichi Morishita:
  Accelerated off-target search algorithm for siRNA.1316-1324
• 
  Melissa D. Krebs,Robert D. Tingley,Julie E. Zeskind,Joung-Mo Kang,Maria E. Holmboe,Cristina E. Davis:
  Autoregressive modeling of analytical sensor data can yield classifiers in the predictor coefficient parameter space.1325-1331
• 
  Sven Degroeve,Yvan Saeys,Bernard De Baets,Pierre Rouzé,Yves Van de Peer:
  SpliceMachine: predicting splice sites from high-dimensional local context representations.1332-1338
• 
  Steven E. Hampson,Brandon S. Gaut,Pierre Baldi:
  Statistical detection of chromosomal homology using shared-gene density alone.1339-1348
• 
  John R. Rose,William H. Turkett Jr.,Iulia C. Oroian,William W. Laegreid,John W. Keele:
  Correlation of amino acid preference and mammalian viral genome type.1349-1357
• 
  Yun Lian,Harold R. Garner:
  Evidence for the regulation of alternative splicing via complementary DNA sequence repeats.1358-1364
• 
  Eric K. Nordberg:
  YODA: selecting signature oligonucleotides.1365-1370
• 
  Ketil Malde,Eivind Coward,Inge Jonassen:
  A graph based algorithm for generating EST consensus sequences.1371-1375
• 
  Javier Santoyo,Juan M. Vaquerizas,Joaquín Dopazo:
  Highly specific and accurate selection of siRNAs for high-throughput functional assays.1376-1382
• 
  Caroline C. Friedel,Katharina H. V. Jahn,Selina Sommer,Stephen Rudd,Hans-Werner Mewes,Igor V. Tetko:
  Support vector machines for separation of mixed plant?Cpathogen EST collections based on codon usage.1383-1388
• 
  Matthias B. Wahl,Ulrich Heinzmann,Kenji Imai:
  LongSAGE analysis revealed the presence of a large number of novel antisense genes in the mouse genome.1389-1392
• 
  Matthias B. Wahl,Ulrich Heinzmann,Kenji Imai:
  LongSAGE analysis significantly improves genome annotation: identifications of novel genes and alternative transcripts in the mouse.1393-1400
• 
  Xiaochen Bo,Shengqi Wang:
  TargetFinder: a software for antisense oligonucleotide target site selection based on MAST and secondary structures of target mRNA.1401-1402

Sequence Analysis

• 
  Elizabeth Jacob,Roschen Sasikumar,K. N. Ramachandran Nair:
  A fuzzy guided genetic algorithm for operon prediction.1403-1407
• 
  Iain M. Wallace,Orla O'Sullivan,Desmond G. Higgins:
  Evaluation of iterative alignment algorithms for multiple alignment.1408-1414
• 
  East Zhao,Hsuan-Liang Liu,Chi-Hung Tsai,Huai-Kuang Tsai,Chen-hsiung Chan,Cheng-Yan Kao:
  Cysteine separations profiles on protein sequences infer disulfide connectivity.1415-1420
• 
  Yasuyuki Nozaki,Matthew I. Bellgard:
  Statistical evaluation and comparison of a pairwise alignment algorithm that a priori assigns the number of gaps rather than employing gap penalties.1421-1428
• 
  Volkan Atalay,Rengül Çetin-Atalay:
  Implicit motif distribution based hybrid computational kernel for sequence classification.1429-1436
• 
  Veronique Prigent,Jean-Claude Thierry,Olivier Poch,Frédéric Plewniak:
  DbW: automatic update of a functional family-specific multiple alignment.1437-1442
• 
  Antonio Cavallo,Andrew C. R. Martin:
  Mapping SNPs to protein sequence and structure data.1443-1450
• 
  Maricel G. Kann,Paul A. Thiessen,Anna R. Panchenko,Alejandro A. Schäffer,Stephen F. Altschul,Stephen H. Bryant:
  A structure-based method for protein sequence alignment.1451-1456

Structural Bioinformatics

• 
  Kiyoko F. Aoki,Hiroshi Mamitsuka,Tatsuya Akutsu,Minoru Kanehisa:
  A score matrix to reveal the hidden links in glycans.1457-1463
• 
  Julian Gough:
  Convergent evolution of domain architectures (is rare).1464-1471
• 
  Brian G. Pierce,Weiwei Tong,Zhiping Weng:
  M-ZDOCK: a grid-based approach for C_n symmetric multimer docking.1472-1478
• 
  Hyun S. Moon,Jonghwa Bhak,Kwang Hyung Lee,Doheon Lee:
  Architecture of basic building blocks in protein and domain structural interaction networks.1479-1486
• 
  James R. Bradford,David R. Westhead:
  Improved prediction of protein-Cprotein binding sites using a support vector machines approach.1487-1494

Gene Expression

• 
  Ugis Sarkans,Helen E. Parkinson,Gonzalo Garcia Lara,Ahmet Oezcimen,Anjan Sharma,Niran Abeygunawardena,Sergio Contrino,Ele Holloway,Philippe Rocca-Serra,Gaurab Mukherjee,Mohammadreza Shojatalab,Misha Kapushesky,Susanna-Assunta Sansone,Anna Farne,Tim F. Rayner,Alvis Brazma:
  The ArrayExpress gene expression database: a software engineering and implementation perspective.1495-1501
• 
  Chen-An Tsai,Sue-Jane Wang,Dung-Tsa Chen,James J. Chen:
  Sample size for gene expression microarray experiments.1502-1508
• 
  Jianping Hua,Zixiang Xiong,James Lowey,Edward Suh,Edward R. Dougherty:
  Optimal number of features as a function of sample size for various classification rules.1509-1515
• 
  Rongwei Fu,Dipak K. Dey,Kent E. Holsinger:
  Bayesian models for the analysis of genetic structure when populations are correlated.1516-1529
• 
  Yuhang Wang,Fillia Makedon,James C. Ford,Justin D. Pearlman:
  HykGene: a hybrid approach for selecting marker genes for phenotype classification using microarray gene expression data.1530-1537
• 
  Qinghua Cui,Bing Liu,Tianzi Jiang,Songde Ma:
  Characterizing the dynamic connectivity between genes by variable parameter regression and Kalman filtering based on temporal gene expression data.1538-1541
• 
  Ranadip Pal,Aniruddha Datta,Albert J. Fornace Jr.,Michael L. Bittner,Edward R. Dougherty:
  Boolean relationships among genes responsive to ionizing radiation in the NCI 60 ACDS.1542-1549
• 
  Céline Lefebvre,Jean-Christophe Aude,Eric Glémet,Christian Néri:
  Balancing protein similarity and gene co-expression reveals new links between genetic conservation and developmental diversity in invertebrates.1550-1558
• 
  Xin Zhou,Ke Zhi Mao:
  LS Bound based gene selection for DNA microarray data.1559-1564
• 
  Baolin Wu:
  Differential gene expression detection using penalized linear regression models: the improved SAM statistics.1565-1571
• 
  Ursula Sauer,Claudia Preininger,Robert Hany-Schmatzberger:
  Quick and simple: quality control of microarray data.1572-1578

Genetics And Population Analysis

• 
  Charles F. Crane,Yan M. Crane:
  A nearest-neighboring-end algorithm for genetic mapping.1579-1591
• 
  Hans A. Kestler,André Müller,Thomas M. Gress,Malte Buchholz:
  Generalized Venn diagrams: a new method of visualizing complex genetic set relations.1592-1595

Systems Biology

• 
  Matthew Holford,Naixin Li,Prakash M. Nadkarni,Hongyu Zhao:
  VitaPad: visualization tools for the analysis of pathway data.1596-1602
• 
  Vassily Hatzimanikatis,Chunhui Li,Justin A. Ionita,Christopher S. Henry,Matthew D. Jankowski,Linda J. Broadbelt:
  Exploring the diversity of complex metabolic networks.1603-1609
• 
  Andreas Beyer,Thomas Wilhelm:
  Dynamic simulation of protein complex formation on a genomic scale.1610-1616
• 
  Marc Daniel Haunschild,Bernd Freisleben,Ralf Takors,Wolfgang Wiechert:
  Investigating the dynamic behavior of biochemical networks using model families.1617-1625
• 
  Reinhard Guthke,Ulrich Möller,Martin Hoffmann,Frank Thies,Susanne Töpfer:
  Dynamic network reconstruction from gene expression data applied to immune response during bacterial infection.1626-1634
• 
  Joachim Kopka,Nicolas Schauer,Stephan Krueger,Claudia Birkemeyer,Björn Usadel,Eveline Bergmüller,Peter Dörmann,Wolfram Weckwerth,Yves Gibon,Mark Stitt,Lothar Willmitzer,Alisdair R. Fernie,Dirk Steinhauser:
  GMD@CSB.DB: the Golm Metabolome Database.1635-1638
• 
  Paolo Tieri,Silvana Valensin,Vito Latora,Gastone C. Castellani,Massimo Marchiori,Daniel Remondini,Claudio Franceschi:
  Quantifying the relevance of different mediators in the human immune cell network.1639-1643

Data And Text Mining

• 
  Patrick Kemmeren,Thessa T. J. P. Kockelkorn,Theo Bijma,Rogier Donders,Frank C. P. Holstege:
  Predicting gene function through systematic analysis and quality assessment of high-throughput data.1644-1652
• 
  Carlos Santos,Daniela Eggle,David J. States:
  Wnt pathway curation using automated natural language processing: combining statistical methods with partial and full parse for knowledge extraction.1653-1658
• 
  Ying Tao,Carol Friedman,Yves A. Lussier:
  Visualizing information across multidimensional post-genomic structured and textual databases.1659-1667
• 
  Andrea L. Knorr,Ranjan Srivastava:
  Evaluation of HIV-1 kinetic models using quantitative discrimination analysis.1668-1677
• 
  Rasmus H. Fogh,Wayne Boucher,Wim F. Vranken,Anne Pajon,Tim J. Stevens,T. N. Bhat,John D. Westbrook,John M. C. Ionides,Ernest D. Laue:
  A framework for scientific data modeling and automated software development.1678-1684

Databases And Ontologies

• 
  Katy Wolstencroft,Robin McEntire,Robert Stevens,Lydia Tabernero,Andy Brass:
  Constructing ontology-driven protein family databases.1685-1692

Genome Analysis

• 
  Jin Billy Li,Miao Zhang,Susan K. Dutcher,Gary D. Stormo:
  Procom: a web-based tool to compare multiple eukaryotic proteomes.1693-1694
• 
  Weixi Li,Cathryn J. Rehmeyer,Chuck Staben,Mark L. Farman:
  TERMINUS - Telomeric End-Read Mining IN Unassembled Sequences.1695-1698
• 
  Tae-Hyung Kim,Yeo-Jin Jeon,Woo-Yeon Kim,Heui-Soo Kim:
  HESAS: HERVs Expression and Structure Analysis System.1699-1700
• 
  Lauris Kaplinski,Reidar Andreson,Tarmo Puurand,Maido Remm:
  MultiPLX: automatic grouping and evaluation of PCR primers.1701-1702
• 
  Simon de Givry,Martin Bouchez,Patrick Chabrier,Denis Milan,Thomas Schiex:
  CAR_H^TA GENE: multipopulation integrated genetic and radiation hybrid mapping.1703-1704

Sequence Analysis

• 
  Thomas M. Keane,Thomas J. Naughton:
  DSEARCH: sensitive database searching using distributed computing.1705-1706
• 
  Richard J. D. Rouse,Jesus M. Castagnetto,Roland H. Niedner:
  PatGen - a consolidated resource for searching genetic patent sequences.1707-1708

Phylogenetics

• 
  Kai M. A. Chan,Brian R. Moore:
  SYMMETREE: whole-tree analysis of differential diversification rates.1709-1710
• 
  Søren Besenbacher,Thomas Mailund,Lasse Westh-Nielsen,Christian N. S. Pedersen:
  RBT - a tool for building refined Buneman trees.1711-1712
• 
  Xun Gu,Wei Huang,Dongping Xu,Hongmei Zhang:
  GeneContent: software for whole-genome phylogenetic analysis.1713-1714

Structural Bioinformatics

• 
  Franck Dupuis,Jean-François Sadoc,Rémi Jullien,Borislav Angelov,Jean Paul Mornon:
  Voro3D: 3D Voronoi tessellations applied to protein structures.1715-1716
• 
  Norihiro Kikuchi,Akihiko Kameyama,Shuuichi Nakaya,Hiromi Ito,Takashi Sato,Toshihide Shikanai,Yoriko Takahashi,Hisashi Narimatsu:
  The carbohydrate sequence markup language (CabosML): an XML description of carbohydrate structures.1717-1718
• 
  Gianluca Pollastri,Aoife McLysaght:
  Porter: a new, accurate server for protein secondary structure prediction.1719-1720
• 
  Yuko Tsuchiya,Kengo Kinoshita,Haruki Nakamura:
  PreDs: a server for predicting dsDNA-binding site on protein molecular surfaces.1721-1723

Gene Expression

• 
  Matthias E. Futschik,Toni Crompton:
  OLIN: optimized normalization, visualization and quality testing of two-channel microarray data.1724-1726
• 
  Christian Schwager,Jonathon Blake:
  Bloader - a batch loader application for MIAMExpress.1727-1729

Genetics And Population Analysis

• 
  Holger Thiele,Peter J. Nürnberg:
  HaploPainter: a tool for drawing pedigrees with complex haplotypes.1730-1732
• 
  Christian N. K. Anderson,Uma Ramakrishnan,Yvonne L. Chan,Elizabeth A. Hadly:
  Serial SimCoal: A population genetics model for data from multiple populations and points in time.1733-1734
• 
  Sio Iong Ao,Kevin Y. Yip,Michael K. Ng,David Wai-Lok Cheung,Pui-Yee Fong,Ian Melhado,Pak Chung Sham:
  CLUSTAG: hierarchical clustering and graph methods for selecting tag SNPs.1735-1736
• 
  Pablo Serrano-Fernández,Saleh M. Ibrahim,Dirk Koczan,Uwe K. Zettl,Steffen Möller:
  In silico fine-mapping: narrowing disease-associated loci by intergenomics.1737-1738

Systems Biology

• 
  Steven L. Bell,Bernhard O. Palsson:
  expa: a program for calculating extreme pathways in biochemical reaction networks.1739-1740
• 
  Aaron N. Chang,Jason E. McDermott,Ram Samudrala:
  An enhanced Java graph applet interface for visualizing interactomes.1741-1742

Data And Text Mining

• 
  Violaine Pillet,Marc Zehnder,Alexander K. Seewald,Anne-Lise Veuthey,Johann Petrak:
  GPSDB: a new database for synonyms expansion of gene and protein names.1743-1744

Databases And Ontologies

• 
  Greg Finak,N. Godin,Michael T. Hallett,François Pepin,Z. Rajabi,V. Srivastava,Z. Tang:
  BIAS: Bioinformatics Integrated Application Software.1745-1746
• 
  Casey M. Bergman,Joseph W. Carlson,Susan E. Celniker:
  Drosophila DNase I footprint database: a systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila melanogaster.1747-1749

Volume 21, Number 9, May 1 2005

Databases And Ontologies

• 
  Andrean Goede,Mathias Dunkel,Nina Mester,Cornelius Frömmel,Robert Preissner:
  SuperDrug: a conformational drug database.1751-1753

Genome Analysis

• 
  Romesh Stanislaus,Chuming Chen,Jennifer Franklin,John M. Arthur,Jonas S. Almeida:
  AGML Central: web based gel proteomic infrastructure.1754-1757
• 
  Noriyuki Kitagawa,Takanori Washio,Shunichi Kosugi,Tomoya Yamashita,Kenji Higashi,Hiroshi Yanagawa,Kenichi Higo,Koji Satoh,Yasuhiro Ohtomo,Tomomi Sunako,Kazuo Murakami,Kenichi Matsubara,Jun Kawai,Piero Carninci,Yoshihide Hayashizaki,Shoshi Kikuchi,Masaru Tomita:
  Computational analysis suggests that alternative first exons are involved in tissue-specific transcription in rice (Oryza sativa).1758-1763
• 
  Jeffrey S. Morris,Kevin R. Coombes,John M. Koomen,Keith A. Baggerly,Ryuji Kobayashi:
  Feature extraction and quantification for mass spectrometry in biomedical applications using the mean spectrum.1764-1775
• 
  Darrell Conklin,Betty Haldeman,Zeren Gao:
  Gene finding for the helical cytokines.1776-1781
• 
  William H. Majoros,Mihaela Pertea,Sihaela Salzberg:
  Efficient implementation of a generalized pair hidden Markov model for comparative gene finding.1782-1788
• 
  Maria Stepanova,Tatiana Tiazhelova,Mikle Skoblov,Ancha V. Baranova:
  A comparative analysis of relative occurrence of transcription factor binding sites in vertebrate genomes and gene promoter areas.1789-1796

Sequence Analysis

• 
  Dirk Husmeier,Frank Wright,Iain Milne:
  Detecting interspecific recombination with a pruned probabilistic divergence measure.1797-1806
• 
  Shaun Mahony,David Hendrix,Aaron Golden,Terry J. Smith,Daniel S. Rokhsar:
  Transcription factor binding site identification using the self-organizing map.1807-1814
• 
  Jakob Hull Havgaard,Rune B. Lyngsø,Gary D. Stormo,Jan Gorodkin:
  Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%.1815-1824
• 
  J. M. Cameron,T. Hurd,B. H. Robinson:
  Computational identification of human mitochondrial proteins based on homology to yeast mitochondrially targeted proteins.1825-1830
• 
  Zheng Rong Yang:
  Prediction of caspase cleavage sites using Bayesian bio-basis function neural networks.1831-1837
• 
  Han-Lin Li,Chang-Jui Fu:
  A linear programming approach for identifying a consensus sequence on DNA sequences.1838-1845
• 
  Niklaus Fankhauser,Pascal Mäser:
  Identification of GPI anchor attachment signals by a Kohonen self-organizing map.1846-1852
• 
  Robel Y. Kahsay,Guang R. Gao,Li Liao:
  An improved hidden Markov model for transmembrane protein detection and topology prediction and its applications to complete genomes.1853-1858
• 
  Thomas D. Wu,Colin K. Watanabe:
  GMAP: a genomic mapping and alignment program for mRNA and EST sequence.1859-1875

Phylogenetics

• 
  Betty Lazareva-Ulitsky,Karen Diemer,Paul D. Thomas:
  On the quality of tree-based protein classification.1876-1890

Structural Bioinformatics

• 
  Karen Coeytaux,Anne Poupon:
  Prediction of unfolded segments in a protein sequence based on amino acid composition.1891-1900
• 
  Fred P. Davis,Andrej Sali:
  PIBASE: a comprehensive database of structurally defined protein interfaces.1901-1907
• 
  Alasdair T. R. Laurie,Richard M. Jackson:
  Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites.1908-1916

Gene Expression

• 
  Håvard Nesvold,Anja Bråthen Kristoffersen,Arne Holst-Jensen,Knut G. Berdal:
  Design of a DNA chip for detection of unknown genetically modified organisms (GMOs).1917-1926
• 
  Dae-Won Kim,Kwang Hyung Lee,Doheon Lee:
  Detecting clusters of different geometrical shapes in microarray gene expression data.1927-1934
• 
  Cristian Mircean,Ilya Shmulevich,David Cogdell,Woonyoung Choi,Yu Jia,Ioan Tabus,Stanley R. Hamilton,Wei Zhang:
  Robust estimation of protein expression ratios with lysate microarray technology.1935-1942
• 
  William T. Barry,Andrew B. Nobel,Fred A. Wright:
  Significance analysis of functional categories in gene expression studies: a structured permutation approach.1943-1949
• 
  Jelle J. Goeman,Jan Oosting,Anne-Marie Cleton-Jansen,Jakob K. Anninga,Hans C. van Houwelingen:
  Testing association of a pathway with survival using gene expression data.1950-1957
• 
  Xiaojun Di,Hajime Matsuzaki,Teresa A. Webster,Earl Hubbell,Guoying Liu,Shoulian Dong,Dan Bartell,Jing Huang,Richard Chiles,Geoffrey Yang,Mei-mei Shen,David Kulp,Giulia C. Kennedy,Rui Mei,Keith W. Jones,Simon Cawley:
  Dynamic model based algorithms for screening and genotyping over 100K SNPs on oligonucleotide microarrays.1958-1963
• 
  Staal Amund Vinterbo,Eun-Young Kim,Lucila Ohno-Machado:
  Small, fuzzy and interpretable gene expression based classifiers.1964-1970
• 
  Claudio Lottaz,Rainer Spang:
  Molecular decomposition of complex clinical phenotypes using biologically structured analysis of microarray data.1971-1978
• 
  Wenjiang J. Fu,Raymond J. Carroll,Suojin Wang:
  Estimating misclassification error with small samples via bootstrap cross-validation.1979-1986
• 
  Susmita Datta,Somnath Datta:
  Empirical Bayes screening of many p-values with applications to microarray studies.1987-1994
• 
  Marie-Laure Martin-Magniette,Julie Aubert,Eric Cabannes,Jean-Jacques Daudin:
  Evaluation of the gene-specific dye bias in cDNA microarray experiments.1995-2000

Genetics And Population Analysis

• 
  Shih-Chieh Su,C.-C. Jay Kuo,Ting Chen:
  Inference of missing SNPs and information quantity measurements for haplotype blocks.2001-2007

Systems Biology

• 
  Marcin Imielinski,Calin Belta,Ádám M. Halász,Harvey Rubin:
  Investigating metabolite essentiality through genome-scale analysis of Escherichia coli production capabilities.2008-2016
• 
  Ross D. King,Simon M. Garrett,George Macleod Coghill:
  On the use of qualitative reasoning to simulate and identify metabolic pathway.2017-2026
• 
  Sampsa Hautaniemi,Sourabh Kharait,Akihiro Iwabu,Alan Wells,Douglas A. Lauffenburger:
  Modeling of signal-response cascades using decision tree analysis.2027-2035
• 
  Weijiang Li,Hiroyuki Kurata:
  A grid layout algorithm for automatic drawing of biochemical networks.2036-2042
• 
  Kinya Okada,Shigehiko Kanaya,Kiyoshi Asai:
  Accurate extraction of functional associations between proteins based on common interaction partners and common domains.2043-2048

Data And Text Mining

• 
  Rob Jelier,Guido Jenster,Lambert C. J. Dorssers,C. Christiaan van der Eijk,Erik M. van Mulligen,Barend Mons,Jan A. Kors:
  Co-occurrence based meta-analysis of scientific texts: retrieving biological relationships between genes.2049-2058
• 
  Oliver Hofmann,Dietmar Schomburg:
  Concept-based annotation of enzyme classes.2059-2066

Databases And Ontologies

• 
  Gordon K. Smyth,Joëlle Michaud,Hamish S. Scott:
  Use of within-array replicate spots for assessing differential expression in microarray experiments.2067-2075
• 
  Kevin R. Brown,Igor Jurisica:
  Online Predicted Human Interaction Database.2076-2082

Genome Analysis

• 
  Jian Song,Yan Xu,P. Scott White,Kevin W. P. Miller,Murray Wolinsky:
  SNPsFinder - a web-based application for genome-wide discovery of single nucleotide polymorphisms in microbial genomes.2083-2084
• 
  Per Gärdén,Rikard Alm,Jari Häkkinen:
  PROTEIOS: an open source proteomics initiative.2085-2087
• 
  Jason W. H. Wong,Gerard Cagney,Hugh M. Cartwright:
  SpecAlign - processing and alignment of mass spectra datasets.2088-2090
• 
  Kuljeet S. Sandhu,Kshitish K. Acharya:
  ExPrimer: to design primers from exon-exon junctions.2091-2092

Sequence Analysis

• 
  Morris Michael,Christoph Dieterich,Martin Vingron:
  SITEBLAST-rapid and sensitive local alignment of genomic sequences employing motif anchors.2093-2094
• 
  Frédéric Chalmel,Aurélie Lardenois,Julie Dawn Thompson,Jean Muller,José-Alain Sahel,Thierry Léveillard,Olivier Poch:
  GOAnno: GO annotation based on multiple alignment.2095-2096
• 
  Weixi Li,Cathryn J. Rehmeyer,Chuck Staben,Mark L. Farman:
  TruMatch - a BLAST post-processor that identifies bona fide sequence matches to genome assemblies.2097-2098
• 
  Francisco Azuaje:
  Integrative data analysis for functional prediction: a multi-objective optimization approach.2099-2100

Phylogenetics

• 
  Adi Doron-Faigenboim,Adi Stern,Itay Mayrose,Eran Bacharach,Tal Pupko:
  Selecton: a server for detecting evolutionary forces at a single amino-acid site.2101-2103
• 
  Federico Abascal,Rafael Zardoya,David Posada:
  ProtTest: selection of best-fit models of protein evolution.2104-2105
• 
  Niko Beerenwinkel,Jörg Rahnenführer,Rolf Kaiser,Daniel Hoffmann,Joachim Selbig,Thomas Lengauer:
  Mtreemix: a software package for learning and using mixture models of mutagenetic trees.2106-2107
• 
  Joachim Friedrich,Thomas Dandekar,Matthias Wolf,Tobias Müller:
  ProfDist: a tool for the construction of large phylogenetic trees based on profile distances.2108-2109

Structural Bioinformatics

• 
  Andreas Möglich,Daniel Weinfurtner,Wolfram Gronwald,Till Maurer,Hans Robert Kalbitzer:
  PERMOL: restraint-based protein homology modeling using DYANA or CNS.2110-2111

Gene Expression

• 
  Joern Toedling,Sebastian Schmeier,Matthias Heinig,Benjamin Georgi,Stefan Roepcke:
  MACAT - microarray chromosome analysis tool.2112-2113
• 
  Laurie J. Heyer,D. Z. Moskowitz,J. A. Abele,P. Karnik,D. Choi,A. Malcolm Campbell,E. E. Oldham,B. K. Akin:
  MAGIC Tool: integrated microarray data analysis.2114-2115
• 
  Sek Won Kong,Kyu Baek Hwang,Richard D. Kim,Byoung-Tak Zhang,Steven A. Greenberg,Isaac S. Kohane,Peter J. Park:
  CrossChip: a system supporting comparative analysis of different generations of Affymetrix arrays.2116-2117
• 
  Yuan Ji,Chunlei Wu,Ping Liu,Jing Wang,Kevin R. Coombes:
  Applications of beta-mixture models in bioinformatics.2118-2122

Genetics And Population Analysis

• 
  Franz Rüschendorf,Peter J. Nürnberg:
  ALOHOMORA: a tool for linkage analysis using 10K SNP array data.2123-2125
• 
  Hongyu Yang,Hongyu Wang,Alan R. Gingle:
  IntegratedMap: a Web interface for integrating genetic map data.2126-2127
• 
  Kejun Liu,Spencer V. Muse:
  PowerMarker: an integrated analysis environment for genetic marker analysis.2128-2129
• 
  David Posada,Taylor J. Maxwell,Alan R. Templeton:
  TreeScan: a bioinformatic application to search for genotype/phenotype associations using haplotype trees.2130-2132
• 
  Chih-Yu (Carol) Chang,Joshua LaBaer:
  DNA polymorphism detector: an automated tool that searches for allelic matches in public databases for discrepancies found in clone or cDNA sequences.2133-2135

Systems Biology

• 
  Abhijit Chatterjee,Kapil Mayawala,Jeremy S. Edwards,Dionisios G. Vlachos:
  Time accelerated Monte Carlo simulations of biological networks using the binomial r-leap method.2136-2137

Data And Text Mining

• 
  Anna Divoli,Teresa K. Attwood:
  BioIE: extracting informative sentences from the biomedical literature.2138-2139

Databases And Ontologies

• 
  Pedro A. Reche,Hong Zhang,John-Paul Glutting,Ellis L. Reinherz:
  EPIMHC: a curated database of MHC-binding peptides for customized computational vaccinology.2140-2141
• 
  Pei Hao,Wei-Zhong He,Yin Huang,Liang-Xiao Ma,Ying Xu,Hong Xi,Chuan Wang,Boshu Liu,Jin-Miao Wang,Yi-Xue Li,Yang Zhong:
  MPSS: an integrated database system for surveying a set of proteins.2142-2143

Volume 21, Number 10, May 2005

Review - Structural Bioinformatics

• 
  Svava Ósk Jónsdóttir,Flemming Steen Jørgensen,Søren Brunak:
  Prediction methods and databases within chemoinformatics: emphasis on drugs and drug candidates.2145-2160

Discovery Notes - Sequence Analysis

• 
  Prachee Prakash,Sailu Yellaboina,Akash Ranjan,Seyed Ehetsham Hasnain:
  Computational prediction and experimental verification of novel IdeR binding sites in the upstream sequences of Mycobacterium tuberculosis open reading frames.2161-2166

Structural Bioinformatics

• 
  Akira R. Kinjo,Ken Nishikawa:
  Recoverable one-dimensional encoding of three-dimensional protein structures.2167-2170

Original Papers - Genome Analysis

• 
  C. Thach Nguyen,Y. C. Tay,Louxin Zhang:
  Divide-and-conquer approach for the exemplar breakpoint distance.2171-2176
• 
  Jayson Falkner,Philip C. Andrews:
  Fast tandem mass spectra-based protein identification regardless of the number of spectra or potential modifications examined.2177-2184
• 
  Lei Bao,Yan Cui:
  Prediction of the phenotypic effects of non-synonymous single nucleotide polymorphisms using structural and evolutionary information.2185-2190
• 
  Lee Lancashire,Oliver Schmid,Haroun Shah,Graham R. Ball:
  Classification of bacterial species from proteomic data using combinatorial approaches incorporating artificial neural networks, cluster analysis and principal components analysis.2191-2199
• 
  J. S. Yu,Stefano Ongarello,R. Fiedler,X. W. Chen,Gianna Toffolo,Claudio Cobelli,Zlatko Trajanoski:
  Ovarian cancer identification based on dimensionality reduction for high-throughput mass spectrometry data.2200-2209
• 
  Halima Bensmail,Jennifer Golek,Michelle M. Moody,O. John Semmes,Abdelali Haoudi:
  A novel approach for clustering proteomics data using Bayesian fast Fourier transform.2210-2224

Sequence Analysis

• 
  Valerio Freschi,Alessandro Bogliolo:
  Using sequence compression to speedup probabilistic profile matching.2225-2229
• 
  Robert G. Beiko,Cheong Xin Chan,Mark A. Ragan:
  A word-oriented approach to alignment validation.2230-2239
• 
  Alexander V. Favorov,Mikhail S. Gelfand,Anna V. Gerasimova,Dmitry A. Ravcheev,Andrey A. Mironov,Vsevolod J. Makeev:
  A Gibbs sampler for identification of symmetrically structured, spaced DNA motifs with improved estimation of the signal length.2240-2245
• 
  David H. Mathews:
  Predicting a set of minimal free energy RNA secondary structures common to two sequences.2246-2253
• 
  Ruadhan A. O'Flanagan,Guillaume Paillard,Richard Lavery,Anirvan M. Sengupta:
  Non-additivity in protein-DNA binding.2254-2263
• 
  Kyounghwa Bae,Bani K. Mallick,Christine G. Elsik:
  Prediction of protein interdomain linker regions by a hidden Markov model.2264-2270
• 
  Ho-Leung Chan,Tak Wah Lam,Wing-Kin Sung,Prudence W. H. Wong,Siu-Ming Yiu,X. Fan:
  The mutated subsequence problem and locating conserved genes.2271-2278
• 
  Mikael Bodén,John Hawkins:
  Prediction of subcellular localization using sequence-biased recurrent networks.2279-2286
• 
  Robel Y. Kahsay,Guoli Wang,Guang R. Gao,Li Liao,Roland L. Dunbrack Jr.:
  Quasi-consensus-based comparison of profile hidden Markov models for protein sequences.2287-2293

Phylogenetics

• 
  Ian H. Holmes:
  Using evolutionary Expectation Maximization to estimate indel rates.2294-2300
• 
  Dan Tsafrir,Ilan Tsafrir,Liat Ein-Dor,Or Zuk,Daniel A. Notterman,Eytan Domany:
  Sorting points into neighborhoods (SPIN): data analysis and visualization by ordering distance matrices.2301-2308
• 
  George M. Garrity,Timothy G. Lilburn:
  Self-organizing and self-correcting classifications of biological data.2309-2314
• 
  Andrew J. Bordner,Ruben Abagyan:
  REVCOM: a robust Bayesian method for evolutionary rate estimation.2315-2321
• 
  Peter F. Arndt,Terence Hwa:
  Identification and measurement of neighbor-dependent nucleotide substitution processes.2322-2328

Structural Bioinformatics

• 
  Stefan R. Henz,Daniel H. Huson,Alexander F. Auch,Kay Nieselt-Struwe,Stephan C. Schuster:
  Whole-genome prokaryotic phylogeny.2329-2335
• 
  Fabrizio Ferrè,Peter Clote:
  Disulfide connectivity prediction using secondary structure information and diresidue frequencies.2336-2346
• 
  Richard J. Morris,Rafael Najmanovich,Abdullah Kahraman,Janet M. Thornton:
  Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons.2347-2355
• 
  Jacek Blazewicz,Marta Szachniuk,Adam Wójtowicz:
  RNA tertiary structure determination: NOE pathways construction by tabu search.2356-2361
• 
  Yuzhen Ye,Adam Godzik:
  Multiple flexible structure alignment using partial order graphs.2362-2369
• 
  Qidong Zhang,Sukjoon Yoon,William J. Welsh:
  Improved method for predicting ?-turn using support vector machine.2370-2374
• 
  Markus Leber,Lars Kaderali,Alexander Schönhuth,Rainer Schrader:
  A fractional programming approach to efficient DNA melting temperature calculation.2375-2382

Gene Expression

• 
  Örjan Carlborg,D. J. De Koning,Kenneth F. Manly,Elissa J. Chesler,Robert W. Williams,Chris S. Haley:
  Methodological aspects of the genetic dissection of gene expression.2383-2393
• 
  Ka Yee Yeung,Roger Eugene Bumgarner,Adrian E. Raftery:
  Bayesian model averaging: development of an improved multi-class, gene selection and classification tool for microarray data.2394-2402
• 
  Hongzhe Li,Yihui Luan:
  Boosting proportional hazards models using smoothing splines, with applications to high-dimensional microarray data.2403-2409
• 
  Wotao Yin,Terrence Chen,Xiang Sean Zhou,Amit Chakraborty:
  Background correction for cDNA microarray images using the TV+L¹ model.2410-2416
• 
  Muhammad Shoaib B. Sehgal,Iqbal Gondal,Laurence Dooley:
  Collateral missing value imputation: a new robust missing value estimation algorithm for microarray data.2417-2423
• 
  Christian H. Busold,Stefan Winter,Nicole C. Hauser,Andrea Bauer,Jürgen Dippon,Jörg D. Hoheisel,Kurt Fellenberg:
  Integration of GO annotations in Correspondence Analysis: facilitating the interpretation of microarray data.2424-2429
• 
  K. K. Dobbin,Ernest S. Kawasaki,D. W. Petersen,R. M. Simon:
  Characterizing dye bias in microarray experiments.2430-2437

Genetics and Population Analysis

• 
  Jörg Rahnenführer,Niko Beerenwinkel,Wolfgang A. Schulz,Christian Hartmann,Andreas von Deimling,Bernd Wullich,Thomas Lengauer:
  Estimating cancer survival and clinical outcome based on genetic tumor progression scores.2438-2446
• 
  Yuehua Cui,Rongling Wu:
  Mapping genome-genome epistasis: a high-dimensional model.2447-2455
• 
  Rui-Sheng Wang,Ling-Yun Wu,Zhen-Ping Li,Xiang-Sun Zhang:
  Haplotype reconstruction from SNP fragments by minimum error correction.2456-2462
• 
  Dmitry A. Konovalov,Bruce E. Litow,Nigel Bajema:
  Partition-distance via the assignment problem.2463-2468
• 
  Wei Zhao,Ying Q. Chen,George Casella,James M. Cheverud,Rongling Wu:
  A non-stationary model for functional mapping of complex traits.2469-2477

Systems Biology

• 
  Nobukazu Ohki,Masatoshi Hagiwara:
  Bio-Object, a stochastic simulator for post-transcriptional regulation.2478-2487
• 
  Tsuyoshi Kato,Koji Tsuda,Kiyoshi Asai:
  Selective integration of multiple biological data for supervised network inference.2488-2495
• 
  I. Res,I. Mihalek,Olivier Lichtarge:
  An evolution based classifier for prediction of protein interfaces without using protein structures.2496-2501

Databases and Ontologies

• 
  Daniel Shegogue,W. Jim Zheng:
  Object-oriented biological system integration: a SARS coronavirus example.2502-2509

Applications Note - Genome Analysis

• 
  Feng-Chi Chen,Trees-Juen Chuang:
  ESTviewer: a web interface for visualizing mouse, rat, cattle, pig and chicken conserved ESTs in human genes and human alternatively spliced variants.2510-2513
• 
  Kwangmin Choi,Yu Ma,Jeong-Hyeon Choi,Sun Kim:
  PLATCOM: a Platform for Computational Comparative Genomics.2514-2516
• 
  Fengkai Zhang,Zhongming Zhao:
  SNPNB: analyzing neighboring-nucleotide biases on single nucleotide polymorphisms (SNPs).2517-2519
• 
  Igor V. Tetko,Barbara Brauner,Irmtraud Dunger-Kaltenbach,Goar Frishman,Corinna Montrone,Gisela Fobo,Andreas Ruepp,Alexey V. Antonov,Dimitrij Surmeli,Hans-Werner Mewes:
  MIPS bacterial genomes functional annotation benchmark dataset.2520-2521

Sequence Analysis

• 
  Manoj Bhasin,Aarti Garg,G. P. S. Raghava:
  PSLpred: prediction of subcellular localization of bacterial proteins.2522-2524
• 
  Dariusz Plewczynski,Adrian Tkacz,Lucjan Stanislaw Wyrwicz,Leszek Rychlewski:
  AutoMotif server: prediction of single residue post-translational modifications in proteins.2525-2527
• 
  Per Unneberg,Michael Strömberg,Fredrik Sterky:
  SNP discovery using advanced algorithms and neural networks.2528-2530

Phylogenetics

• 
  Sergei L. Kosakovsky Pond,Simon D. W. Frost:
  Datamonkey: rapid detection of selective pressure on individual sites of codon alignments.2531-2533

Structural Bioinformatics

• 
  Carlos J. Camacho,Chao Zhang:
  FastContact: rapid estimate of contact and binding free energies.2534-2536
• 
  Gilleain M. Torrance,David R. Gilbert,Ioannis Michalopoulos,David R. Westhead:
  Protein structure topological comparison, discovery and matching service.2537-2538
• 
  Jason E. Donald,Isaac A. Hubner,Veronica Rotemberg,Eugene I. Shakhnovich,Leonid A. Mirny:
  CoC: a database of universally conserved residues in protein folds.2539-2540
• 
  Sungsam Gong,Giseok Yoon,Insoo Jang,Dan M. Bolser,Panos Dafas,Michael Schroeder,Hansol Choi,Yoobok Cho,Kyungsook Han,Sunghoon Lee,Hwanho Choi,Michael Lappe,Liisa Holm,Sangsoo Kim,Donghoon Oh,Jonghwa Bhak:
  PSIbase: a database of Protein Structural Interactome map (PSIMAP).2541-2543

Gene Expression

• 
  Ivan G. Costa,Alexander Schönhuth,Alexander Schliep:
  The Graphical Query Language: a tool for analysis of gene expression time-courses.2544-2545
• 
  Nadia Bolshakova,Francisco Azuaje,Padraig Cunningham:
  A knowledge-driven approach to cluster validity assessment.2546-2547
• 
  Alexei A. Sharov,Dawood B. Dudekula,Minoru S. H. Ko:
  A web-based tool for principal component and significance analysis of microarray data.2548-2549
• 
  John Boyle:
  Gene-Expression Omnibus integration and clustering Tools in SeqExpress.2550-2551
• 
  Hui Sun Leong,Tim Yates,Claire L. Wilson,Crispin J. Miller:
  ADAPT: a database of affymetrix probesets and transcripts.2552-2553

Genetics and Population Analysis

• 
  Su Young Kim,Suk Woo Nam,Sug Hyung Lee,Won Sang Park,Nam Jin Yoo,Jung Young Lee,Yeun-Jun Chung:
  ArrayCyGHt: a web application for analysis and visualization of array-CGH data.2554-2555
• 
  Nandita Mukhopadhyay,Lee Almasy,Mark Schroeder,William P. Mulvihill,Daniel E. Weeks:
  Mega2: data-handling for facilitating genetic linkage and association analyses.2556-2557

Data amd Text Mining

• 
  Shailesh V. Date,Edward M. Marcotte:
  Protein function prediction using the Protein Link EXplorer (PLEX).2558-2559
• 
  Jing Ding,Karthikeyan Viswanathan,Daniel Berleant,Laron M. Hughes,Eve Syrkin Wurtele,Daniel A. Ashlock,Julie A. Dickerson,Andy W. Fulmer,Patrick S. Schnable:
  Using the biological taxonomy to access biological literature with PathBinderH.2560-2562

Databases and Ontologies

• 
  Pierre-Étienne Jacques,Alain L. Gervais,Mathieu Cantin,Jean-François Lucier,Guillaume Dallaire,Geneviève Drouin,Luc Gaudreau,Jean Goulet,Ryszard Brzezinski:
  MtbRegList, a database dedicated to the analysis of transcriptional regulation in Mycobacterium tuberculosis.2563-2565
• 
  Ana Tereza Ribeiro de Vasconcelos,Ana Carolina R. Guimarães,Carlos Henrique M. Castelletti,Célia S. Caruso,Cristina Ribeiro,Fabiano Yokaichiya,Geraldo R. G. Armôa,Gislaine da Silva P. Pereira,Israel T. da Silva,Carlos G. Schrago,Adélia L. V. Fernandes,Aline R. da Silveira,André G. Carneiro,Bruno M. Carvalho,Carlos Juliano M. Viana,Daniel Gramkow,Franklin J. Lima,Luiz G. G. Corrêa,Maurício de Alvarenga Mudado,Pablo Nehab-Hess,Rangel de Souza,Régis L. Corrêa,Claudia A. M. Russo:
  MamMiBase: a mitochondrial genome database for mammalian phylogenetic studies.2566-2567
• 
  Anyuan Guo,Kun He,Di Liu,Shunong Bai,Xiaocheng Gu,Liping Wei,Jingchu Luo:
  DATF: a database of Arabidopsis transcription factors.2568-2569
• 
  Tariq Riaz,Hen Ley Hor,Arun Krishnan,Francis Tang,Kuo-Bin Li:
  WebAllergen: a web server for predicting allergenic proteins.2570-2571

Volume 21, Number 11, June 2005

Original Papers - Genome Analysis

• 
  Teemu Kivioja,Mikko Arvas,Markku Saloheimo,Merja Penttilä,Esko Ukkonen:
  Optimization of cDNA-AFLP experiments using genomic sequence data.2573-2579
• 
  Yan Zhang,Vadim N. Gladyshev:
  An algorithm for identification of bacterial selenocysteine insertion sequence elements and selenoprotein genes.2580-2589
• 
  Daniel R. Clutterbuck,A. Leroy,Mary Anne O'Connell,C. A. M. Semple:
  A bioinformatic screen for novel A-I RNA editing sites reveals recoding editing in BC10.2590-2595

Sequence Analysis

• 
  Jean-François Dufayard,Laurent Duret,Simon Penel,Manolo Gouy,François Rechenmann,Guy Perrière:
  Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases.2596-2603
• 
  Hadas Leonov,Isaiah T. Arkin:
  A periodicity analysis of transmembrane helices.2604-2610
• 
  Hiroshi Matsui,Kengo Sato,Yasubumi Sakakibara:
  Pair stochastic tree adjoining grammars for aligning and predicting pseudoknot RNA structures.2611-2617
• 
  Victor Kunin,Sarah A. Teichmann,Martijn A. Huynen,Christos A. Ouzounis:
  The properties of protein family space depend on experimental design.2618-2622
• 
  Rajesh Chowdhary,R. Ayesha Ali,Werner Albig,Detlef Doenecke,Vladimir B. Bajic:
  Promoter modeling: the case study of mammalian histone promoters.2623-2628
• 
  Jason E. Donald,Eugene I. Shakhnovich:
  Determining functional specificity from protein sequences.2629-2635
• 
  Pengyu Hong,Xiaole Shirley Liu,Qing Zhou,Xin Lu,Jun S. Liu,Wing Hung Wong:
  A boosting approach for motif modeling using ChIP-chip data.2636-2643
• 
  Zheng Rong Yang:
  Mining SARS-CoV protease cleavage data using non-orthogonal decision trees: a novel method for decisive template selection.2644-2650
• 
  Moti Zviling,Hadas Leonov,Isaiah T. Arkin:
  Genetic algorithm-based optimization of hydrophobicity tables.2651-2656
• 
  Irad E. Ben-Gal,Ayala Shani,André Gohr,Jan Grau,S. Arviv,Armin Shmilovici,Stefan Posch,Ivo Grosse:
  Identification of transcription factor binding sites with variable-order Bayesian networks.2657-2666

Structural Bioinformatics

• 
  Sangjo Han,Byung-chul Lee,Seung Taek Yu,Chan-seok Jeong,Soyoung Lee,Dongsup Kim:
  Fold recognition by combining profile-profile alignment and support vector machine.2667-2673

Gene Expression

• 
  A. L. Tarca,Janice E. K. Cooke:
  A robust neural networks approach for spatial and intensity-dependent normalization of cDNA microarray data.2674-2683
• 
  Gregory R. Grant,Junmin Liu,Christian J. Stoeckert Jr.:
  A practical false discovery rate approach to identifying patterns of differential expression in microarray data.2684-2690

Genetics and Populations Analysis

• 
  Jane Jijun Liu,Gene Cutler,Wuxiong Li,Zheng Pan,Sihua Peng,Timothy Hoey,Liangbiao Chen,Xuefeng Bruce Ling:
  Multiclass cancer classification and biomarker discovery using GA-based algorithms.2691-2697

Systems Biology

• 
  Bor-Sen Chen,Yu-Chao Wang,Wei-Sheng Wu,Wen-Hsiung Li:
  A new measure of the robustness of biochemical networks.2698-2705
• 
  Svetlana Bulashevska,Roland Eils:
  Inferring genetic regulatory logic from expression data.2706-2713
• 
  Thierry Emonet,Charles M. Macal,Michael J. North,Charles E. Wickersham,Philippe Cluzel:
  AgentCell: a digital single-cell assay for bacterial chemotaxis.2714-2721
• 
  Luonan Chen,Ruiqi Wang,Tianshou Zhou,Kazuyuki Aihara:
  Noise-induced cooperative behavior in a multicell system.2722-2729
• 
  Nitin Bhardwaj,Hui Lu:
  Correlation between gene expression profiles and protein-protein interactions within and across genomes.2730-2738
• 
  Phil Hyoun Lee,Doheon Lee:
  Modularized learning of genetic interaction networks from biological annotations and mRNA expression data.2739-2747

Data and Text Mining

• 
  Irena Spasic,Sophia Ananiadou,Jun'ichi Tsujii:
  MaSTerClass: a case-based reasoning system for the classification of biomedical terms.2748-2758
• 
  Zhang-Zhi Hu,Meenakshi Narayanaswamy,K. E. Ravikumar,K. Vijay-Shanker,Cathy H. Wu:
  Literature mining and database annotation of protein phosphorylation using a rule-based system.2759-2765
• 
  René Korn,Sascha Röhrig,Steffen Schulze-Kremer,Ulrich Brinkmann:
  Common denominator procedure: a novel approach to gene-expression data mining for identification of phenotype-specific genes.2766-2772

Databases and Ontologies

• 
  J. Stuart Aitken:
  Formalizing concepts of species, sex and developmental stage in anatomical ontologies.2773-2779

Application Notes - Genome Analysis

• 
  Chin Lung Lu,Tsui Ching Wang,Ying Chih Lin,Chuan Yi Tang:
  ROBIN: a tool for genome rearrangement of block-interchanges.2780-2782

Sequence Analysis

• 
  Vincent Miele,Pierre-Yves Bourguignon,David Robelin,Grégory Nuel,Hugues Richard:
  seq++: analyzing biological sequences with a range of Markov-related models.2783-2784

Structural Bioinformatics

• 
  Daniel Schober,Ulf Leser,Martin Zenke,Jens G. Reich:
  GandrKB--ontological microarray annotation and visualization.2785-2786
• 
  Taner Z. Sen,Robert L. Jernigan,Jean Garnier,Andrzej Kloczkowski:
  GOR V server for protein secondary structure prediction.2787-2788

Gene Expression

• 
  Aedín C. Culhane,Jean Thioulouse,Guy Perrière,Desmond G. Higgins:
  MADE4: an R package for multivariate analysis of gene expression data.2789-2790

Genetics and Population Analysis

• 
  Albert J. Vilella,Angel Blanco-Garcia,Stephan Hutter,Julio Rozas:
  VariScan: Analysis of evolutionary patterns from large-scale DNA sequence polymorphism data.2791-2793

Databases and Ontologies

• 
  Yu Song,Eunju Kim,Gary Geunbae Lee,Byoung-Kee Yi:
  POSBIOTM-NER: a trainable biomedical named-entity recognition system.2794-2796
• 
  Guillaume Koum,Augustin Yekel,Bengyella Ndifon,Frédéric Simard:
  Erratum.2797-2802

Volume 21, Supplement 1, June 2005

• 
  Proceedings Thirteenth International Conference on Intelligent Systems for Molecular Biology 2005, Detroit, MI, USA, 25-29 June 2005.2005[contents]

Volume 21, Number 12, June 2005

Letter to the Editor - Gene Expression

• 
  Kevin Dobbin,Joanna H. Shih,Richard Simon:
  Comment on 'Evaluation of the gene-specific dye bias in cDNA microarray experiments'.2803-2804

Discovery Note - Sequence Analysis

• 
  Vivek Anantharaman,L. Aravind:
  MEDS and PocR are novel domains with a predicted role in sensing simple hydrocarbon derivatives in prokaryotic signal transduction systems.2805-2811

Original Papers - Genome Analysis

• 
  Alan M. Durham,André Yoshiaki Kashiwabara,Fernando T. G. Matsunaga,Paulo H. Ahagon,Flávia Rainone,Leonardo Varuzza,Arthur Gruber:
  EGene: a configurable pipeline generation system for automated sequence analysis.2812-2813
• 
  Rachel Karchin,Mark Diekhans,Libusha Kelly,Daryl J. Thomas,Ursula Pieper,Narayanan Eswar,David Haussler,Andrej Sali:
  LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources.2814-2820

Sequence Analysis

• 
  B. Anand,V. S. Gowri,Narayanaswamy Srinivasan:
  Use of multiple profiles corresponding to a sequence alignment enables effective detection of remote homologues.2821-2826
• 
  Aleksandar Poleksic,Joseph F. Danzer,Kevin Hambly,Derek A. Debe:
  Convergent Island Statistics: a fast method for determining local alignment score significance.2827-2831

Structural Bioinformatics

• 
  Guoying Qi,Richard A. Lee,Steven Hayward:
  A comprehensive and non-redundant database of protein domain movements.2832-2838
• 
  Geraint Thomas,Richard B. Sessions,Martin J. Parker:
  Density guided importance sampling: application to a reduced model of protein folding.2839-2843
• 
  Jaehyun Sim,Seung-Yeon Kim,Julian Lee:
  Prediction of protein solvent accessibility using fuzzy k-nearest neighbor method.2844-2849
• 
  A. Selim Aytuna,Attila Gürsoy,Ozlem Keskin:
  Prediction of protein-protein interactions by combining structure and sequence conservation in protein interfaces.2850-2855
• 
  Daniele Varrazzo,Andrea Bernini,Ottavia Spiga,Arianna Ciutti,Stefano Chiellini,Vincenzo Venditti,Luisa Bracci,Neri Niccolai:
  Three-dimensional computation of atom depth in complex molecular structures.2856-2860

Gene Expression

• 
  Dung-Tsa Chen,James J. Chen,Seng-jaw Soong:
  Probe rank approaches for gene selection in oligonucleotide arrays with a small number of replicates.2861-2866
• 
  Albert M. Levin,Debashis Ghosh,Kathleen R. Cho,Sharon L. R. Kardia:
  A model-based scan statistic for identifying extreme chromosomal regions of gene expression in human tumors.2867-2874
• 
  Qunhua Li,Chris Fraley,Roger Eugene Bumgarner,Ka Yee Yeung,Adrian E. Raftery:
  Donuts, scratches and blanks: robust model-based segmentation of microarray images.2875-2882

Systems Biology

• 
  Kuang-Chi Chen,Tse-Yi Wang,Huei-Hun Tseng,Chi-Ying F. Huang,Cheng-Yan Kao:
  A stochastic differential equation model for quantifying transcriptional regulatory network inSaccharomyces cerevisiae.2883-2890
• 
  Francesco Pappalardo,Pierluigi Lollini,Filippo Castiglione,Santo Motta:
  Modeling and simulation of cancer immunoprevention vaccine.2891-2897
• 
  Lawrence Cabusora,Electra Sutton,Andy W. Fulmer,Christian V. Forst:
  Differential network expression during drug and stress response.2898-2905

Application Notes - Genome Analysis

• 
  Florence Armand,Philipp Bucher,C. Victor Jongeneel,Edward E. Farmer:
  Rapid and selective surveillance of Arabidopsis thaliana genome annotations with Centrifuge.2906-2908

Sequence Analysis

• 
  Dongsheng Che,Shane T. Jensen,Liming Cai,Jun S. Liu:
  BEST: Binding-site Estimation Suite of Tools.2909-2911
• 
  Benjamin Schuster-Böckler,Alex Bateman:
  Visualizing profile-profile alignment: pairwise HMM logos.2912-2913

Structural Bioinformatics

• 
  Adrian A. Canutescu,Roland L. Dunbrack Jr.:
  MollDE: a homology modeling framework you can click with.2914-2916
• 
  Harpreet Kaur Saini,Daniel Fischer:
  Meta-DP: domain prediction meta-server.2917-2920

Gene Expression

• 
  Stefanie Scheid,Rainer Spang:
  twilight; a Bioconductor package for estimating the local false discovery rate.2921-2922

Systems Biology

• 
  Johan Hattne,David Fange,Johan Elf:
  Stochastic reaction-diffusion simulation with MesoRD.2923-2924

Data and Text Mining

• 
  Yu Zheng,Daiwen Yang:
  STARS: statistics on inter-atomic distances and torsion angles in protein secondary structures.2925-2926

Databases and Ontologies

• 
  Chunhong Mao,Jing Qiu,Chunxia Wang,Trevor C. Charles,Bruno W. S. Sobral:
  NodMutDB: a database for genes and mutants involved in symbiosis.2927-2929
• 
  Eain C. J. Green,Georgios V. Gkoutos,Heena V. Lad,Andrew Blake,Joseph Weekes,John M. Hancock:
  EMPReSS: European Mouse Phenotyping Resource for Standardized Screens.2930-2931

Volume 21, Number 13, July 2005

Original Papers - Sequence Analysis

• 
  K. Cartharius,Kornelie Frech,Korbinian Grote,Bernward Klocke,Manuela Haltmeier,Andreas Klingenhoff,Matthias Frisch,M. Bayerlein,Thomas Werner:
  MatInspector and beyond: promoter analysis based on transcription factor binding sites.2933-2942
• 
  Giuseppe D'Avenio,Mauro Grigioni,G. Orefici,Roberta Creti:
  SWIFT (sequence-wide investigation with Fourier transform): a software tool for identifying proteins of a given class from the unannotated genome sequence.2943-2949
• 
  Milana Frenkel-Morgenstern,Hillary Voet,Shmuel Pietrokovski:
  Enhanced statistics for local alignment of multiple alignments improves prediction of protein function and structure.2950-2956
• 
  Mark DeLong,Guang Yao,Quanli Wang,Adrian Dobra,Esther P. Black,Jeffrey T. Chang,Andrea Bild,Mike West,Joseph Nevins,Holly Dressman:
  DIG - a system for gene annotation and functional discovery.2957-2959

Structural Bioinformatics

• 
  Marco Punta,Burkhard Rost:
  PROFcon: novel prediction of long-range contacts.2960-2968
• 
  Kai Wang,Ram Samudrala:
  FSSA: a novel method for identifying functional signatures from structural alignments.2969-2977
• 
  Lee-Wei Yang,Xiong Liu,Christopher Jon Jursa,Mark Holliman,A. J. Rader,Hassan A. Karimi,Ivet Bahar:
  iGNM: a database of protein functional motions based on Gaussian Network Model.2978-2987

Gene Expression

• 
  Fátima Al-Shahrour,Ramón Díaz-Uriarte,Joaquín Dopazo:
  Discovering molecular functions significantly related to phenotypes by combining gene expression data and biological information.2988-2993
• 
  Omer Demirkaya,Musa H. Asyali,Mohamed M. Shoukri:
  Segmentation of cDNA Microarray Spots Using Markov Random Field Modeling.2994-3000
• 
  Jiang Gui,Hongzhe Li:
  Penalized Cox regression analysis in the high-dimensional and low-sample size settings, with applications to microarray gene expression data.3001-3008
• 
  Yulan Liang,Bamidele Tayo,Xueya Cai,Arpad Kelemen:
  Differential and trajectory methods for time course gene expression data.3009-3016
• 
  Yudi Pawitan,Stefan Michiels,Serge Koscielny,Arief Gusnanto,Alexander Ploner:
  False discovery rate, sensitivity and sample size for microarray studies.3017-3024
• 
  Andrew E. Teschendorff,Yanzhong Wang,Nuno L. Barbosa-Morais,James D. Brenton,Carlos Caldas:
  A variational Bayesian mixture modelling framework for cluster analysis of gene-expression data.3025-3033

Genetics And Population Analysis

• 
  Vladimir N. Minin,Karin S. Dorman,Fang Fang,Marc A. Suchard:
  Dual multiple change-point model leads to more accurate recombination detection.3034-3042

Systems Biology

• 
  Age K. Smilde,Jeroen J. Jansen,Huub C. J. Hoefsloot,Robert-Jan A. N. Lamers,Jan van der Greef,Marieke E. Timmerman:
  ANOVA-simultaneous component analysis (ASCA): a new tool for analyzing designed metabolomics data.3043-3048

Applications Note - Genome Analysis

• 
  Dequan Li,Yan Fu,Ruixiang Sun,Charles X. Ling,Yonggang Wei,Hu Zhou,Rong Zeng,Qiang Yang,Simin He,Wen Gao:
  pFind: a novel database-searching software system for automated peptide and protein identification via tandem mass spectrometry.3049-3050

Sequence Analysis

• 
  Grégory Nuel:
  S-SPatt: simple statistics for patterns on Markov chains.3051-3052
• 
  M. W. J. van Passel,Angela C. M. Luyf,Antoine H. C. van Kampen,Aldert Bart,A. van der Ende:
  delta rho-Web, an online tool to assess composition similarity of individual nucleic acid sequences.3053-3055

Structural Bioinformatics

• 
  Jeng-Sheng Yeh,Ding-Yun Chen,Bing-Yu Chen,Ming Ouhyoung:
  A web-based three-dimensional protein retrieval system by matching visual similarity.3056-3057

Gene Expression

• 
  Ian John Donaldson,Michael Chapman,Berthold Göttgens:
  TFBScluster: a resource for the characterization of transcriptional regulatory networks.3058-3059

Genetics And Population Analysis

• 
  Emily L. Webb,Gabrielle S. Sellick,Richard S. Houlston:
  SNPLINK: multipoint linkage analysis of densely distributed SNP data incorporating automated linkage disequilibrium removal.3060-3061

Volume 21, Number 14, July 2005

Letter To The Editor

• 
  Marie-Laure Martin-Magniette,Julie Aubert,Eric Cabannes,Jean-Jacques Daudin:
  Answer to the comments of K. Dobbin, J. Shih and R. Simon on the paper 'Evaluation of the gene-specific dye-bias in cDNA microarray experiments'.3065-

Original Papers - Genome Analysis

• 
  Neal O. Jeffries:
  Algorithms for alignment of mass spectrometry proteomic data.3066-3073
• 
  Weixiong Zhang,Jianhua Ruan,Tuan-hua David Ho,Youngsook You,Taotao Yu,Ralph S. Quatrano:
  Cis-regulatory element based targeted gene finding: genome-wide identification of abscisic acid- and abiotic stress-responsive genes inArabidopsis thaliana.3074-3081

Sequence Analysis

• 
  Rainer Pudimat,Ernst Günter Schukat-Talamazzini,Rolf Backofen:
  A multiple-feature framework for modelling and predicting transcription factor binding sites.3082-3088

Structural Bioinformatics

• 
  Carol L. Ecale Zhou,Adam T. Zemla,Diana C. Roe,Malin M. Young,Marisa Lam,Joseph S. Schoeniger,Rod Balhorn:
  Computational approaches for identification of conserved/unique binding pockets in the A chain of ricin.3089-3096

Gene Expression

• 
  Sin-Ho Jung:
  Sample size for FDR-control in microarray data analysis.3097-3104
• 
  Yan Lu,Peng-Yuan Liu,Peng Xiao,Hong-Wen Deng:
  Hotelling'sT₂ multivariate profiling for detecting differential expression in microarrays.3105-3113
• 
  Peng Qiu,Z. Jane Wang,K. J. Ray Liu:
  Ensemble dependence model for classification and prediction of cancer and normal gene expression data.3114-3121

Genetics And Population Analysis

• 
  Katechan Jampachaisri,Lea Valinsky,James Borneman,S. James Press:
  Classification of oligonucleotide fingerprints: application for microbial community and gene expression analyses.3122-3130

Systems Biology

• 
  Simon Rogers,Mark A. Girolami:
  A Bayesian regression approach to the inference of regulatory networks from gene expression data.3131-3137

Data And Text Mining

• 
  Pierre Geurts,Marianne Fillet,Dominique de Seny,Marie-Alice Meuwis,Michel Malaise,Marie-Paule Merville,Louis Wehenkel:
  Proteomic mass spectra classification using decision tree based ensemble methods.3138-3145
• 
  Tsutomu Matsunaga,Masaaki Muramatsu:
  Knowledge-based computational search for genes associated with the metabolic syndrome.3146-3154

Databases And Ontologies

• 
  Konstantinos Karasavvas,Richard A. Baldock,Albert Burger:
  A criticality-based framework for task composition in multi-agent bioinformatics integration systems.3155-3163

Applications Note - Sequence Analysis

• 
  D. Benjamin Gordon,Lena Nekludova,Scott McCallum,Ernest Fraenkel:
  TAMO: a flexible, object-oriented framework for analyzing transcriptional regulation using DNA-sequence motifs.3164-3165
• 
  Olivier Pible,Gilles Imbert,Jean-Luc Pellequer:
  INTERALIGN: interactive alignment editor for distantly related protein sequences.3166-3167
• 
  Sebastian Zöllner,Xiaoquan Wen,Jonathan K. Pritchard:
  Association mapping and fine mapping with TreeLD.3168-3170

Phylogenetics

• 
  Yoon-Seong Jeon,Hwanwon Chung,Sunyoung Park,Inae Hur,Jae-Hak Lee,Jongsik Chun:
  jPHYDIT: a JAVA-based integrated environment for molecular phylogeny of ribosomal RNA sequences.3171-3173

Structural Bioinformatics

• 
  C. Paul Barrett,Martin E. M. Noble:
  Dynamite extended: two new services to simplify protein dynamic analysis.3174-3175
• 
  Carles Ferrer-Costa,Josep Lluis Gelpí,Leire Zamakola,Ivan Parraga,Xavier de la Cruz,Modesto Orozco:
  PMUT: a web-based tool for the annotation of pathological mutations on proteins.3176-3178
• 
  Dominik Gront,Andrzej Kolinski:
  HCPM - program for hierarchical clustering of protein models.3179-3180
• 
  Sergi Vives,Bradford Loucas,Mariel Vázquez,David J. Brenner,Rainer K. Sachs,Lynn Hlatky,Michael Cornforth,Javier Arsuaga:
  SCHIP: statistics for chromosome interphase positioning based on interchange data.3181-3182

Gene Expression

• 
  M. Obreiter,C. Fischer,J. Chang-Claude,L. Beckmann:
  SDMinP: a program to control the family wise error rate using step-down minP adjustedP-values.3183-3184
• 
  Nathalie Pochet,Frizo A. L. Janssens,Frank De Smet,Kathleen Marchal,Johan A. K. Suykens,Bart De Moor:
  M@CBETH: a microarray classification benchmarking tool.3185-3186

Genetics And Population Analysi

• 
  Alun Thomas:
  GMCheck: Bayesian error checking for pedigreegenotypes and phenotypes.3187-3188

Data And Text Mining

• 
  Mingyi Liu,Andrei Grigoriev:
  Fast parsers for Entrez Gene.3189-3190
• 
  Burr Settles:
  ABNER: an open source tool for automatically tagging genes, proteins and other entity names in text.3191-3192
• 
  Mark A. van de Wiel,Serge J. Smeets,Ruud H. Brakenhoff,Bauke Ylstra:
  CGHMultiArray: exact P-values for multi-array comparative genomic hybridization data.3193-3194

Databases And Ontologies

• 
  Thorsten Henrich,Mirana Ramialison,Beate Wittbrodt,Beatrice Assouline,Franck Bourrat,Anja Berger,Heinz Himmelbauer,Takashi Sasaki,Nobuyoshi Shimizu,Monte Westerfield,Hisato Kondoh,Joachim Wittbrodt:
  MEPD: a resource for medaka gene expression patterns.3195-3197
• 
  Philip Jones,Nisha Vinod,Thomas A. Down,Andre Hackmann,Andreas Kähäri,Ernst Kretschmann,Antony F. Quinn,Daniela Wieser,Henning Hermjakob,Rolf Apweiler:
  Dasty and UniProt DAS: a perfect pair for protein feature visualization.3198-3199

Volume 21, Number 15, August 2005

Review - Data And Text Mining

• 
  Julia Handl,Joshua D. Knowles,Douglas B. Kell:
  Computational cluster validation in post-genomic data analysis.3201-3212

Discovery Note - Genome Analysis

• 
  Mingyi Liu,Shaoping Wu,Heiko Walch,Andrei Grigoriev:
  Exon-domain correlation and its corollaries.3213-3216

Original Paper - Genome Analysis

• 
  Jason E. McDermott,Roger Eugene Bumgarner,Ram Samudrala:
  Functional annotation from predicted protein interaction networks.3217-3226

Sequence Analysis

• 
  Hsin-Nan Lin,Jia-Ming Chang,Kuen-Pin Wu,Ting-Yi Sung,Wen-Lian Hsu:
  HYPROSP II-A knowledge-based hybrid method for protein secondary structure prediction based on local prediction confidence.3227-3233

Structural Bioinformatics

• 
  Daeui Park,Semin Lee,Dan M. Bolser,Michael Schroeder,Michael Lappe,Donghoon Oh,Jong Bhak:
  Comparative interactomics analysis of protein family interaction networks using PSIMAP (protein structural interactome map).3234-3240
• 
  Jason Weston,Christina S. Leslie,Eugene Ie,Dengyong Zhou,André Elisseeff,William Stafford Noble:
  Semi-supervised protein classification using cluster kernels.3241-3247
• 
  D. R. Goucher,S. M. Wincovitch,S. H. Garfield,K. M. Carbone,T. H. Malik:
  A quantitative determination of multi-protein interactions by the analysis of confocal images using a pixel-by-pixel assessment algorithm.3248-3254
• 
  Dmitry Lupyan,Alejandra Leo-Macias,Angel R. Ortiz:
  A new progressive-iterative algorithm for multiple structure alignment.3255-3263

Gene Expression

• 
  Jianhua Hu,Fei Zou,Fred A. Wright:
  Practical FDR-based sample size calculations in microarray experiments.3264-3272

Genetics And Population Analysis

• 
  Andrei S. Rodin,Eric Boerwinkle:
  Mining genetic epidemiology data with Bayesian networks I: Bayesian networks and example application (plasma apoE levels).3273-3278

Systems Biology

• 
  Yin Liu,Nianjun Liu,Hongyu Zhao:
  Inferring protein-protein interactions through high-throughput interaction data from diverse organisms.3279-3285

Data And Text Mining

• 
  Patrick Flaherty,Guri Giaever,Jochen Kumm,Michael I. Jordan,Adam P. Arkin:
  A latent variable model for chemogenomic profiling.3286-3293
• 
  Hao Yu,Xiaoyan Zhu,Minlie Huang,Ming Li:
  Discovering patterns to extract protein-protein interactions from the literature: Part II.3294-3300
• 
  Annette M. Molinaro,Richard Simon,Ruth M. Pfeiffer:
  Prediction error estimation: a comparison of resampling methods.3301-3307

Applications Note - Genome Analysis

• 
  Adam A. Margolin,Joel Greshock,Tara L. Naylor,Yael Mosse,John M. Maris,Graham Bignell,Alexander I. Saeed,John Quackenbush,Barbara L. Weber:
  CGHAnalyzer: a stand-alone software package for cancer genome analysis using array-based DNA copy number data.3308-3311

Sequence Analysis

• 
  Anke Busch,Sebastian Will,Rolf Backofen:
  SECISDesign: a server to design SECIS-elements within the coding sequence.3312-3313
• 
  Andrew E. Firth,Wayne M. Patrick:
  Statistics of protein library construction.3314-3315

Structural Bioinformatics

• 
  Swanand P. Gore,David F. Burke,Tom L. Blundell:
  PROVAT: a tool for Voronoi tessellation analysis of protein structures and complexes.3316-3317
• 
  Jason Vertrees,Phillip Barritt,Steve Whitten,Vincent J. Hilser:
  COREX/BEST server: a web browser-based program that calculates regional stability variations within protein structures.3318-3319
• 
  Fabrice Jossinet,Eric Westhof:
  Sequence to Structure (S2S): display, manipulate and interconnect RNA data from sequence to structure.3320-3321
• 
  Zoltán Gáspári,Kristian Vlahovicek,Sándor Pongor:
  Efficient recognition of folds in protein 3D structures by the improved PRIDE algorithm.3322-3323

Gene Expression

• 
  Amira Djebbari,Svetlana Karamycheva,Eleanor Howe,John Quackenbush:
  MeSHer: identifying biological concepts in microarray assays based on PubMed references and MeSH terms.3324-3326

Data And Text Mining

• 
  Liskin Swint-Kruse,Curties S. Brown:
  Resmap: automated representation of macromolecular interfaces as two-dimensional networks.3327-3328

Databases And Ontologies

• 
  Hongseok Yun,Dong-Yup Lee,Joonwoo Jeong,Seunghyun Lee,Sang Yup Lee:
  MFAML: a standard data structure for representing and exchanging metabolic flux models.3329-3330

Volume 21, Number 16, August 2005

Original Papers - Genome Analysis

• 
  Ryan T. Koehler,Nicolas Peyret:
  Thermodynamic properties of DNA sequences: characteristic values for the human genome.3333-3339
• 
  Sophia Yancopoulos,Oliver Attie,Richard Friedberg:
  Efficient sorting of genomic permutations by translocation, inversion and block interchange.3340-3346

Sequence Analysis

• 
  Daniel P. Aalberts,Eric G. Daub,Jesse W. Dill:
  Quantifying optimal accuracy of local primary sequence bioinformatics methods.3347-3351

Structural Bioinformatics

• 
  Sven Siebert,Rolf Backofen:
  MARNA: multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons.3352-3359
• 
  Jordi Espadaler,Oriol Romero-Isart,Richard M. Jackson,Baldo Oliva:
  Prediction of protein-protein interactions using distant conservation of sequence patterns and structure relationships.3360-3368
• 
  Zheng Rong Yang,Rebecca Thomson,Philip McNeil,Robert Esnouf:
  RONN: the bio-basis function neural network technique applied to the detection of natively disordered regions in proteins.3369-3376

Gene Expression

• 
  Huiqing Liu,Jinyan Li,Limsoon Wong:
  Use of extreme patient samples for outcome prediction from gene expression data.3377-3384
• 
  Wei Chu,Zoubin Ghahramani,Francesco Falciani,David L. Wild:
  Biomarker discovery in microarray gene expression data with Gaussian processes.3385-3393

Genetics And Population Analysis

• 
  Thomas B. Kepler,Min He,John K. Tomfohr,Blythe H. Devlin,Marcella Sarzotti,M. Louise Markert:
  Statistical analysis of antigen receptor spectratype data.3394-3400

Systems Biology

• 
  Ron Y. Pinter,Oleg Rokhlenko,Esti Yeger Lotem,Michal Ziv-Ukelson:
  Alignment of metabolic pathways.3401-3408
• 
  Jingchun Sun,Jinlin Xu,Zhen Liu,Qi Liu,Aimin Zhao,Tieliu Shi,Yi-Xue Li:
  Refined phylogenetic profiles method for predicting protein-protein interactions.3409-3415

Databases And Ontologies

• 
  Purvesh Khatri,Bogdan Done,Archana Rao,Arina Done,Sorin Draghici:
  A semantic analysis of the annotations of the human genome.3416-3421

Applications Note - Genome Analysis

• 
  Tim J. Carver,Kim Rutherford,Matthew Berriman,Marie-Adèle Rajandream,Bart Barrell,Julian Parkhill:
  ACT: the Artemis comparison tool.3422-3423
• 
  Bhaskar DasGupta,Kishori M. Konwar,Ion I. Mandoiu,Alexander A. Shvartsman:
  DNA-BAR: distinguisher selection for DNA barcoding.3424-3426

Sequence Analysis

• 
  Laurent Guéguen:
  Sarment: Python modules for HMM analysis and partitioning of sequences.3427-3428
• 
  Mike Smith,Victor Kunin,Leon Goldovsky,Anton J. Enright,Christos A. Ouzounis:
  MagicMatch - cross-referencing sequence identifiers across databases.3429-3430
• 
  Timothy F. Oliver,Bertil Schmidt,Darran Nathan,Ralf Clemens,Douglas L. Maskell:
  Using reconfigurable hardware to accelerate multiple sequence alignment with ClustalW.3431-3432

Structural Bioinformatics

• 
  Zsuzsanna Dosztányi,Veronika Csizmok,Peter Tompa,István Simon:
  IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content.3433-3434
• 
  Jaime Prilusky,Clifford E. Felder,Tzviya Zeev-Ben-Mordehai,Edwin H. Rydberg,Orna Man,Jacques S. Beckmann,Israel Silman,Joel L. Sussman:
  FoldIndex copyright: a simple tool to predict whether a given protein sequence is intrinsically unfolded.3435-3438

Gene Expression

• 
  Steffen Durinck,Yves Moreau,Arek Kasprzyk,Sean R. Davis,Bart De Moor,Alvis Brazma,Wolfgang Huber:
  BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis.3439-3440

Genetics And Population Analysis

• 
  Matthieu Falque:
  IRILmap: linkage map distance correction for intermated recombinant inbred lines/advanced recombinant inbred strains.3441-3442
• 
  Jin-Long Li,Miao-Xin Li,H.-Y. Deng,P. E. Duffy,Hong-Wen Deng:
  PhD: a web database application for phenotype data management.3443-3444
• 
  Janis E. Wigginton,Gonçalo R. Abecasis:
  PEDSTATS: descriptive statistics, graphics and quality assessment for gene mapping data.3445-3447

Systems Biology

• 
  Steven Maere,Karel Heymans,Martin Kuiper:
  BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks.3448-3449

Data And Text Mining

• 
  Guido Dieterich,Uwe Kärst,Jürgen Wehland,Lothar Jänsch:
  MineBlast: a literature presentation service supporting protein annotation by data mining of BLAST results.3450-3451
• 
  Weijian Xuan,Stanley J. Watson,Fan Meng:
  GeneInfoMiner - a web server for exploring biomedical literature using batch sequence ID.3452-3453

Databases And Ontologies

• 
  Markus Krummenacker,Suzanne M. Paley,Lukas A. Mueller,Thomas Yan,Peter D. Karp:
  Querying and computing with BioCyc databases.3454-3455
• 
  Piotr Kraj,Richard A. McIndoe:
  caBIONet - A .NET wrapper to access and process genomic data stored at the National Cancer Institute's Center for Bioinformatics databases.3456-3458

Volume 21, Number 17, September 2005

Editorials

• 
  Paul T. Spellman:
  A Status Report on Mage.3459-3460

Original Papers
Genome Analysis

• 
  Xiaokang Pan,Lincoln Stein,Volker Brendel:
  SynBrowse: a synteny browser for comparative sequence analysis.3461-3468
• 
  Kuo-Ho Yen,Chiang Lee,Hsiao-Sheng Liu,Chung-Liang Ho:
  A precise and scalable method for querying genes in chromosomal banding regions based on cytogenetic annotations.3469-3474

Sequence Analysis

• 
  Zhen-Ping Li,Wenfeng Zhou,Xiang-Sun Zhang,Luonan Chen:
  A parsimonious tree-grow method for haplotype inference.3475-3481
• 
  Tetsuya Sato,Yoshihiro Yamanishi,Minoru Kanehisa,Hiroyuki Toh:
  The inference of protein-protein interactions by co-evolutionary analysis is improved by excluding the information about the phylogenetic relationships.3482-3489
• 
  Didier Gonze,Sylvie Pinloche,Olivier Gascuel,Jacques van Helden:
  Discrimination of yeast genes involved in methionine and phosphate metabolism on the basis of upstream motifs.3490-3500

Structural Bioinformatics

• 
  Chun-Hsiang Huang,Chin Lung Lu,Hsien-Tai Chiu:
  A heuristic approach for detecting RNA H-type pseudoknots.3501-3508
• 
  Chris Steven Pettitt,Liam J. McGuffin,David T. Jones:
  Improving sequence-based fold recognition by using 3D model quality assessment.3509-3515
• 
  Jens Reeder,Robert Giegerich:
  Consensus shapes: an alternative to the Sankoff algorithm for RNA consensus structure prediction.3516-3523

Gene Expression

• 
  Jianhua Hu,Mini Kapoor,Wei Zhang,Stanley R. Hamilton,Kevin R. Coombes:
  Analysis of dose-response effects on gene expression data with comparison of two microarray platforms.3524-3529
• 
  Kenneth A. Krohn,Markus Eszlinger,R. Paschke,Ingo Roeder,Ernst Schuster:
  Increased power of microarray analysis by use of an algorithm based on a multivariate procedure.3530-3534

Genetics and Population Analysis

• 
  Richard E. Myers,Catherine V. Gale,A. Harrison,Yasu Takeuchi,Paul Kellam:
  A statistical model for HIV-1 sequence classification using the subtype analyser (STAR).3535-3540

Systems Biology

• 
  Niels Grabe,Karsten Neuber:
  A multicellular systems biology model predicts epidermal morphology, kinetics and Ca²⁺ flow.3541-3547
• 
  Denise Scholtens,Marc Vidal,Robert Gentleman:
  Local modeling of global interactome networks.3548-3557
• 
  Vitaly A. Selivanov,Ludmilla E. Meshalkina,Olga N. Solovjeva,Philip W. Kuchel,Antonio Ramos-Montoya,German A. Kochetov,Paul W.-N. Lee,Marta Cascante:
  Rapid simulation and analysis of isotopomer distributions using constraints based on enzyme mechanisms: an example from HT29 cancer cells.3558-3564

Applications Note
Genome Analysis

• 
  Katrin Hoffmann,Tom H. Lindner:
  easyLINKAGE-Plus--automated linkage analyses using large-scale SNP data.3565-3567

Sequence Analysis

• 
  Maike Tech,Nico Pfeifer,Burkhard Morgenstern,Peter Meinicke:
  TICO: a tool for improving predictions of prokaryotic translation initiation sites.3568-3569

Structural Bioinformatics

• 
  Kengo Kinoshita,Motonori Ota:
  P-cats: prediction of catalytic residues in proteins from their tertiary structures.3570-3571
• 
  Falk Schreiber,Henning Schwöbbermeyer:
  MAVisto: a tool for the exploration of network motifs.3572-3574

Gene Expression

• 
  Gunnar Wrobel,Frédéric Chalmel,Michael Primig:
  goCluster integrates statistical analysis and functional interpretation of microarray expression data.3575-3577
• 
  Amanda M. White,Don Simone Daly,Alan R. Willse,Miroslava Protic,Darrell P. Chandler:
  Automated Microarray Image Analysis Toolbox for MATLAB.3578-3579

Data and Text Mining

• 
  Ungsik Yu,Yoon Jeong Choi,Jung Kyoon Choi,Sangsoo Kim:
  TO-GO: a Java-based Gene Ontology navigation environment.3580-3581
• 
  Núria Domedel-Puig,Lorenz Wernisch:
  Applying GIFT, a Gene Interactions Finder in Text, to fly literature.3582-3583

Databases and Ontologies

• 
  Lennart Martens,Joël Vandekerckhove,Kris Gevaert:
  DBToolkit: processing protein databases for peptide-centric proteomics.3584-3585

Volume 21, Number 18, September 2005

Review - Databases and Ontologies

• 
  Purvesh Khatri,Sorin Draghici:
  Ontological analysis of gene expression data: current tools, limitations, and open problems.3587-3595

Sequence Analysis

• 
  Jonathan E. Allen,Steven Salzberg:
  JIGSAW: integration of multiple sources of evidence for gene prediction.3596-3603
• 
  Robert Petryszak,Ernst Kretschmann,Daniela Wieser,Rolf Apweiler:
  The predictive power of the CluSTr database.3604-3609
• 
  Xiaowo Wang,Jing Zhang,Fei Li,Jin Gu,Tao He,Xuegong Zhang,Yanda Li:
  MicroRNA identification based on sequence and structure alignment.3610-3614
• 
  Hongyi Zhou,Yaoqi Zhou:
  SPEM: improving multiple sequence alignment with sequence profiles and predicted secondary structures.3615-3621

Structural Bioinformatics

• 
  Ashish V. Tendulkar,Milind A. Sohoni,Babatunde Ogunnaike,Pramod P. Wangikar:
  A geometric invariant-based framework for the analysis of protein conformational space.3622-3628

Gene Expression

• 
  Hongkai Ji,Wing Hung Wong:
  TileMap: create chromosomal map of tiling array hybridizations.3629-3636
• 
  Xuejun Liu,Marta Milo,Neil D. Lawrence,Magnus Rattray:
  A tractable probabilistic model for Affymetrix probe-level analysis across multiple chips.3637-3644
• 
  Yuting Yang,Levent Engin,Eve Syrkin Wurtele,Carolina Cruz-Neira,Julie A. Dickerson:
  Integration of metabolic networks and gene expression in virtual reality.3645-3650

Systems Biology

• 
  Tianwei Yu,Wei Sun,Shinsheng Yuan,Ker-Chau Li:
  Study of coordinative gene expression at the biological process level.3651-3657

Data and Text Mining

• 
  Sylvain Gaudan,Harald Kirsch,Dietrich Rebholz-Schuhmann:
  Resolving abbreviations to their senses in Medline.3658-3664

Applications Note - Genome Analysis

• 
  J. C. Abbott,David M. Aanensen,Kim Rutherford,Sarah A. Butcher,Brian G. Spratt:
  WebACT - an online companion for the Artemis Comparison Tool.3665-3666
• 
  Marcus J. Claesson,Douwe van Sinderen:
  BlastXtract - a new way of exploring translated searches.3667-3668
• 
  Alessandro Romualdi,Roman Siddiqui,Gernot Glöckner,Rüdiger Lehmann,Jürgen Sühnel:
  GenColors: accelerated comparative analysis and annotation of prokaryotic genomes at various stages of completeness.3669-3671
• 
  Elias Zintzaras,John P. A. Ioannidis:
  HEGESMA: genome search meta-analysis and heterogeneity testing.3672-3673

Sequence Analysis

• 
  Ana Conesa,Stefan Götz,Juan Miguel García-Gómez,Javier Terol,Manuel Talón,Montserrat Robles:
  Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research.3674-3676

Structural Bioinformatics

• 
  Alexej Abyzov,Mounir Errami,Chesley M. Leslin,Valentin A. Ilyin:
  Friend, an integrated analytical front-end application for bioinformatics.3677-3678
• 
  Carles Ferrer-Costa,Hugh P. Shanahan,Susan Jones,Janet M. Thornton:
  HTHquery: a method for detecting DNA-binding proteins with a helix-turn-helix structural motif.3679-3680

Gene Expression

• 
  Ted Liefeld,Michael Reich,Joshua Gould,Peili Zhang,Pablo Tamayo,Jill P. Mesirov:
  GeneCruiser: a web service for the annotation of microarray data.3681-3682
• 
  Claire L. Wilson,Crispin J. Miller:
  Simpleaffy: a BioConductor package for Affymetrix Quality Control and data analysis.3683-3685

Genetics and Population Analysis

• 
  Bo Peng,Marek Kimmel:
  simuPOP: a forward-time population genetics simulation environment.3686-3687

Systems Biology

• 
  Vijay Chickarmane,Sri R. Paladugu,Frank T. Bergmann,Herbert M. Sauro:
  Bifurcation discovery tool.3688-3690

Databases and Ontologies

• 
  J. Michael Brockman,Priyam Singh,Donglin Liu,Sean Quinlan,Jesse Salisbury,Joel H. Graber:
  PACdb: PolyA Cleavage Site and 3'-UTR Database.3691-3693
• 
  Quan-Yuan He,Jing Cao,Xiang-Hua Liu,Miao-Xin Li,Yi-Song Liu,Jin-Yun Xie,Song-Ping Liang:
  DEPD: a novel database for differentially expressed proteins.3694-3696
• 
  Min He,John K. Tomfohr,Blythe H. Devlin,Marcella Sarzotti,M. Louise Markert,Thomas B. Kepler:
  SpA: web-accessible spectratype analysis: data management, statistical analysis and visualization.3697-3699
• 
  Erratum.3700

Volume 21, Supplement 2, September 2005

• 
  ECCB/JBI'05 Proceedings, Fourth European Conference on Computational Biology/Sixth Meeting of the Spanish Bioinformatics Network (Jornadas de BioInformática), Palacio de Congresos, Madrid, Spain, September 28 - October 1, 2005.2005[contents]

Volume 21, Number 19, October 2005

Discovery Note Genome Analysis

• 
  Yi Xing,Christopher J. Lee:
  Assessing the application of Ka/Ks ratio test to alternatively spliced exons.3701-3703

Sequence Analysis

• 
  Gavin E. Crooks,Richard E. Green,Steven E. Brenner:
  Pairwise alignment incorporating dipeptide covariation.3704-3710

Structural Bioinformatics

• 
  Rui Kuang,Jason Weston,William Stafford Noble,Christina S. Leslie:
  Motif-based protein ranking by network propagation.3711-3718
• 
  Rinaldo W. Montalvão,Richard E. Smith,Simon C. Lovell,Tom L. Blundell:
  CHORAL: a differential geometry approach to the prediction of the cores of protein structures.3719-3725
• 
  Gelio Alves,Yi-Kuo Yu:
  Robust accurate identification of peptides (RAId): deciphering MS² data using a structured library search withde novo based statistics.3726-3732

Gene Expression

• 
  Imola K. Fodor,David O. Nelson,Michelle Alegria-Hartman,Kristin Robbins,Richard G. Langlois,Kenneth W. Turteltaub,Todd H. Corzett,Sandra L. McCutchen-Maloney:
  Statistical challenges in the analysis of two-dimensional difference gel electrophoresis experiments using DeCyder^TM.3733-3740
• 
  Fan Li,Yiming Yang:
  Analysis of recursive gene selection approaches from microarray data.3741-3747
• 
  Guido Sanguinetti,Marta Milo,Magnus Rattray,Neil D. Lawrence:
  Accounting for probe-level noise in principal component analysis of microarray data.3748-3754
• 
  Lodewyk F. A. Wessels,Marcel J. T. Reinders,Augustinus A. M. Hart,Cor J. Veenman,Hongyue Dai,Yudong D. He,Laura J. van't Veer:
  A protocol for building and evaluating predictors of disease state based on microarray data.3755-3762

Genetics and Population Analysis

• 
  Weil R. Lai,Mark D. Johnson,Raju Kucherlapati,Peter J. Park:
  Comparative analysis of algorithms for identifying amplifications and deletions in array CGH data.3763-3770
• 
  Sonja Zehetmayer,Peter Bauer,Martin Posch:
  Two-stage designs for experiments with a large number of hypotheses.3771-3777

Systems Biology

• 
  Peter M. Kasson,Johannes B. Huppa,Mark M. Davis,Axel T. Brünger:
  A hybrid machine-learning approach for segmentation of protein localization data.3778-3786

Databases and Ontologies

• 
  Xizeng Mao,Tao Cai,John G. Olyarchuk,Liping Wei:
  Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary.3787-3793

Applications Note Phylogenetics

• 
  Bui Quang Minh,Le Sy Vinh,Arndt von Haeseler,Heiko A. Schmidt:
  pIQPNNI: parallel reconstruction of large maximum likelihood phylogenies.3794-3796
• 
  Tulio de Oliveira,Koen Deforche,Sharon Cassol,Mika Salminen,Dimitris Paraskevis,Chris Seebregts,Joke Snoeck,Estrelita J. Janse van Rensburg,Annemarie M. J. Wensing,David A. van de Vijver,Charles A. Boucher,Ricardo Camacho,Anne-Mieke Vandamme:
  An automated genotyping system for analysis of HIV-1 and other microbial sequences.3797-3800
• 
  Geert Trooskens,David De Beule,Frederik Decouttere,Wim Van Criekinge:
  Phylogenetic trees: visualizing, customizing and detecting incongruence.3801-3802

Structural Bioinformaics

• 
  Wei Li,Junwen Wang,Jin-An Feng:
  NdPASA: a pairwise sequence alignment server for distantly related proteins.3803-3805

Databases and Ontologies

• 
  Leon Goldovsky,Paul J. Janssen,Dag G. Ahrén,Benjamin Audit,Ildefonso Cases,Nikos Darzentas,Anton J. Enright,Núria López-Bigas,José M. Peregrín-Alvarez,Mike Smith,Sophia Tsoka,Victor Kunin,Christos A. Ouzounis:
  CoGenT++: an extensive and extensible data environment for computational genomics.3806-3810

Volume 21, Number 20, October 2005

Genome Analysis

• 
  Tao Huang,Baolin Wu,Paul Lizardi,Hongyu Zhao:
  Detection of DNA copy number alterations using penalized least squares regression.3811-3817

Sequence Analysis

• 
  Onkar C. Kulkarni,R. Vigneshwar,Valadi K. Jayaraman,Bhaskar D. Kulkarni:
  Identification of coding and non-coding sequences using local Hölder exponent formalism.3818-3823
• 
  Gavin A. Price,Gavin E. Crooks,Richard E. Green,Steven E. Brenner:
  Statistical evaluation of pairwise protein sequence comparison with the Bayesian bootstrap.3824-3831

Phylogenetics

• 
  Shane T. Jensen,Lei Shen,Jun S. Liu:
  Combining phylogenetic motif discovery and motif clustering to predict co-regulated genes.3832-3839

Gene Expression

• 
  Jesús S. Aguilar-Ruiz:
  Shifting and scaling patterns from gene expression data.3840-3845
• 
  Luis Diambra,Luciano da Fontoura Costa:
  Complex networks approach to gene expression driven phenotype imaging.3846-3851
• 
  Xinping Cui,Jin Xu,Rehana Asghar,Pascal Condamine,Jan T. Svensson,Steve Wanamaker,Nils Stein,Mikeal Roose,Timothy J. Close:
  Detecting single-feature polymorphisms using oligonucleotide arrays and robustified projection pursuit.3852-3858
• 
  Karen Willbrand,François Radvanyi,Jean-Pierre Nadal,Jean-Paul Thiery,Thomas M. A. Fink:
  Identifying genes from up-down properties of microarray expression series.3859-3864
• 
  Yudi Pawitan,Karuturi R. Krishna Murthy,Stefan Michiels,Alexander Ploner:
  Bias in the estimation of false discovery rate in microarray studies.3865-3872
• 
  Kavitha Bhasi,Alan Forrest,Murali Ramanathan:
  SPLINDID: a semi-parametric, model-based method for obtaining transcription rates and gene regulation parameters from genomic and proteomic expression profiles.3873-3879
• 
  David Meintrup,Ellen Reisinger:
  A statistical model providing comprehensive predictions for the mRNA differential display.3880-3886
• 
  Matthias Scholz,Fatma Kaplan,Charles L. Guy,Joachim Kopka,Joachim Selbig:
  Non-linear PCA: a missing data approach.3887-3895
• 
  Aik Choon Tan,Daniel Q. Naiman,Lei Xu,Raimond L. Winslow,Donald Geman:
  Simple decision rules for classifying human cancers from gene expression profiles.3896-3904
• 
  Lei Xu,Aik Choon Tan,Daniel Q. Naiman,Donald Geman,Raimond L. Winslow:
  Robust prostate cancer marker genes emerge from direct integration of inter-study microarray data.3905-3911

Genetics And Population Analysis

• 
  Dmitry A. Konovalov,Nigel Bajema,Bruce E. Litow:
  Modified SIMPSONO(n³) algorithm for the full sibship reconstruction problem.3912-3917

Data and Text Mining

• 
  Sreenivas Chavali,Anubha Mahajan,Rubina Tabassum,Souvik Maiti,Dwaipayan Bharadwaj:
  Oligonucleotide properties determination and primer designing: a critical examination of predictions.3918-3925

Applications Note Structural Bioinformatics

• 
  Chi Yu Chan,Charles E. Lawrence,Ye Ding:
  Structure clustering features on the Sfold Web server.3926-3928
• 
  Martin Jambon,Olivier Andrieu,Christophe Combet,Gilbert Deléage,François Delfaud,Christophe Geourjon:
  The SuMo server: 3D search for protein functional sites.3929-3930
• 
  Nir Kalisman,Ami Levi,Tetyana Maximova,Dan Reshef,Sharon Zafriri-Lynn,Yan Gleyzer,Chen Keasar:
  MESHI: a new library of Java classes for molecular modeling.3931-3932

Gene Expression

• 
  Shyamal D. Peddada,Shawn F. Harris,J. Zajd,E. Harvey:
  ORIOGEN: order restricted inference for ordered gene expression data.3933-3934

Genetics and Population Analysis

• 
  Derek Gordon,Chad Haynes,Jon Blumenfeld,Stephen J. Finch:
  PAWE-3D: visualizing power for association with error in case-control genetic studies of complex traits.3935-3937
• 
  Sheng Gu,Andrew J. Pakstis,Kenneth K. Kidd:
  HAPLOT: a graphical comparison of haplotype blocks, tagSNP sets and SNP variation for multiple populations.3938-3939

Data and Text Mining

• 
  Tobias Sing,Oliver Sander,Niko Beerenwinkel,Thomas Lengauer:
  ROCR: visualizing classifier performance in R.3940-3941

Volume 21, Number 21, November 2005

Review - Data and Text Mining

• 
  Niko Beerenwinkel,Tobias Sing,Thomas Lengauer,Jörg Rahnenführer,Kirsten Roomp,Igor Savenkov,Roman Fischer,Daniel Hoffmann,Joachim Selbig,Klaus Korn,Hauke Walter,Thomas Berg,Patrick Braun,Gerd Fätkenheuer,Mark Oette,Jürgen K. Rockstroh,Bernd Kupfer,Rolf Kaiser,Martin Däumer:
  Computational methods for the design of effective therapies against drug resistant HIV strains.3943-3950

Discovery Notes - Genome Analysis

• 
  Liang Chen,Hongyu Zhao:
  Negative correlation between compositional symmetries and local recombination rates.3951-3958

Structural Bioinformatics

• 
  Iwona A. Cymerman,Gregor Meiss,Janusz M. Bujnicki:
  DNase II is a member of the phospholipase D superfamily.3959-3962

Sequence Analysis

• 
  Chittibabu Guda,Shankar Subramaniam:
  TARGET: a new method for predicting protein subcellular localization in eukaryotes.3963-3969

Gene Expression

• 
  Yuan Gao,George M. Church:
  Improving molecular cancer class discovery through sparse non-negative matrix factorization.3970-3975
• 
  Shin Kawano,Kosuke Hashimoto,Takashi Miyama,Susumu Goto,Minoru Kanehisa:
  Prediction of glycan structures from gene expression data based on glycosyltransferase reactions.3976-3982
• 
  Lei Zhou,David M. Rocke:
  An expression index for Affymetrix GeneChips based on the generalized logarithm.3983-3989
• 
  David M. Rocke,Zelanna Goldberg,Chad Schweitert,Alison Santana:
  A method for detection of differential gene expression in the presence of inter-individual variability in response.3990-3992
• 
  Aurora Torrente,Misha Kapushesky,Alvis Brazma:
  A new algorithm for comparing and visualizing relationships between hierarchical and flat gene expression data clusterings.3993-3999
• 
  Li-Yu Daisy Liu,Naisyin Wang,Joanne R. Lupton,Nancy D. Turner,Robert S. Chapkin,Laurie A. Davidson:
  A two-stage normalization method for partially degraded mRNA microarray data.4000-4006
• 
  Biao Xing,Mark J. van der Laan:
  A causal inference approach for constructing transcriptional regulatory networks.4007-4013
• 
  Dongxiao Zhu,Alfred O. Hero III,Hong Cheng,Ritu Khanna,Anand Swaroop:
  Network constrained clustering for gene microarray data.4014-4020

Systems Biology

• 
  Ranadip Pal,Ivan Ivanov,Aniruddha Datta,Michael L. Bittner,Edward R. Dougherty:
  Generating Boolean networks with a prescribed attractor structure.4021-4025
• 
  Florian Markowetz,Jacques Bloch,Rainer Spang:
  Non-transcriptional pathway features reconstructed from secondary effects of RNA interference.4026-4032
• 
  Tianwei Yu,Ker-Chau Li:
  Inference of transcriptional regulatory network by two-stage constrained space factor analysis.4033-4038

Data and Text Mining

• 
  Habtom W. Ressom,Rency S. Varghese,Mohamed Abdel-Hamid,Sohair Abdel-Latif Eissa,Daniel Saha,Lenka Goldman,Emanuel F. Petricoin,Thomas P. Conrads,Timothy D. Veenstra,Christopher A. Loffredo,Radoslav Goldman:
  Analysis of mass spectral serum profiles for biomarker selection.4039-4045
• 
  Jonathan D. Wren,William H. Hildebrand,Sreedevi Chandrasekaran,Ulrich Melcher:
  Markov model recognition and classification of DNA/protein sequences within large text databases.4046-4053
• 
  Xiang Zhang,John M. Asara,Jiri Adamec,Mourad Ouzzani,Ahmed K. Elmagarmid:
  Data pre-processing in liquid chromatography-mass spectrometry-based proteomics.4054-4059

Databases and Ontologies

• 
  Christian J. A. Sigrist,Edouard De Castro,Petra S. Langendijk-Genevaux,Virginie Le Saux,Amos Bairoch,Nicolas Hulo:
  ProRule: a new database containing functional and structural information on PROSITE profiles.4060-4066

Applications Note - Sequence Analysis

• 
  Christoph Bock,Sabine Reither,Thomas Mikeska,Martina Paulsen,Jörn Walter,Thomas Lengauer:
  BiQ Analyzer: visualization and quality control for DNA methylation data from bisulfite sequencing.4067-4068

Gene Expression

• 
  Peter Sykacek,R. A. Furlong,Gos Micklem:
  A friendly statistics package for microarray analysis.4069-4070

Volume 21, Number 22, November 2005

Editorials

• 
  Claire Saxby:
  TheBioinformatics Open Access option.4071-4072

Genome Analysis

• 
  Igor Zwir,Henry Huang,Eduardo A. Groisman:
  Analysis of differentially-regulated genes within a regulatory network by GPS genome navigation.4073-4083
• 
  Hanni Willenbrock,Jane Fridlyand:
  A comparison study: applying segmentation to array CGH data for downstream analyses.4084-4091

Sequence Analysis

• 
  Won-Hyong Chung,Sung-Keun Rhee,Xiu-Feng Wan,Jin-Woo Bae,Zhe-Xue Quan,Yong-Ha Park:
  Design of long oligonucleotide probes for functional gene detection in a microbial community.4092-4100
• 
  Nikolaos G. Sgourakis,Pantelis G. Bagos,Stavros J. Hamodrakas:
  Prediction of the coupling specificity of GPCRs to four families of G-proteins using hidden Markov models and artificial neural networks.4101-4106
• 
  Kevin Karplus,Rachel Karchin,George Shackelford,Richard Hughey:
  CalibratingE-values for hidden Markov models using reverse-sequence null models.4107-4115
• 
  L. C. Martin,Gregory B. Gloor,S. D. Dunn,Lindi M. Wahl:
  Using information theory to search for co-evolving residues in proteins.4116-4124
• 
  Tiee-Jian Wu,Ying-Hsueh Huang,Lung-An Li:
  Optimal word sizes for dissimilarity measures and estimation of the degree of dissimilarity between DNA sequences.4125-4132

Structural Bioinformatics

• 
  Jonathan H. Chen,Sanjay Joshua Swamidass,Yimeng Dou,Jocelyne Bruand,Pierre Baldi:
  ChemDB: a public database of small molecules and related chemoinformatics resources.4133-4139
• 
  Peter Clote,Jérôme Waldispühl,Behshad Behzadi,Jean-Marc Steyaert:
  Energy landscape ofk-point mutants of an RNA molecule.4140-4147

Gene Expression

• 
  Alan R. Dabney:
  Classification of microarrays to nearest centroids.4148-4154
• 
  Rebecka Jörnsten,Hui-Yu Wang,William J. Welsh,Ming Ouyang:
  DNA microarray data imputation and significance analysis of differential expression.4155-4161
• 
  Graham J. G. Upton,Julie C. Lloyd:
  Oligonucleotide arrays: information from replication and spatial structure.4162-4168
• 
  Wenxuan Zhong,Peng Zeng,Ping Ma,Jun S. Liu,Michael Yu Zhu:
  RSIR: regularized sliced inverse regression for motif discovery.4169-4175

Systems Biology

• 
  Robert Urbanczik,C. Wagner:
  Functional stoichiometric analysis of metabolic networks.4176-4180

Databases and Ontologies

• 
  Hong Xu,Simon G. Gregory,Elizabeth R. Hauser,Judith E. Stenger,Margaret A. Pericak-Vance,Jeffery M. Vance,Stephan Züchner,Michael A. Hauser:
  SNPselector: a web tool for selecting SNPs for genetic association studies.4181-4186

Applications Note - Genome Analysis

• 
  Richard Münch,Karsten Hiller,Andreas Grote,Maurice Scheer,Johannes Klein,Max Schobert,Dieter Jahn:
  Virtual Footprint and PRODORIC: an integrative framework for regulon prediction in prokaryotes.4187-4189

Sequence Analysis

• 
  Richard J. Edwards,Denis C. Shields:
  BADASP: predicting functional specificity in protein families using ancestral sequences.4190-4191

Gene Expression

• 
  Davide D'Alimonte,David Lowe,Ian T. Nabney,Vassilis Mersinias,Colin P. Smith:
  MILVA: An interactive tool for the exploration of multidimensional microarray data.4192-4193
• 
  Laurent Jourdren,Stéphane Le Crom:
  Doelan: a solution for quality control monitoring of microarray production.4194-4195

Data and Text Mining

• 
  Alex L. Mitchell,Anna Divoli,Jee-Hyub Kim,Melanie Hilario,I. Selimas,Teresa K. Attwood:
  METIS: multiple extraction techniques for informative sentences.4196-4197
• 
  Erratum.4198

Volume 21, Supplement 3, November 2005

The Fifth Georgia Tech - Oak Ridge National Lab International Conference in Bioinformatics:In Silico Biology, Computational Genomics and Evolutionary Biology, Atlanta, Georgia, USA, November 17-19, 2005

• 
  Mark Borodovsky,Andrey Rzhetsky,Dmitrij Frishman:
  The Fifth Georgia Tech - Oak Ridge National Laboratory International Conference in Bioinformatics:in silico Biology, Computational Genomics and Evolutionary Biology.1
• 
  Galina V. Glazko,Alexander Gordon,Arcady R. Mushegian:
  The choice of optimal distance measure in genome-wide datasets.11
• 
  Georgy P. Karev,Faina S. Berezovskaya,Eugene V. Koonin:
  Modeling genome evolution with a diffusion approximation of a birth-and-death process.19
• 
  Michael E. Sparks,Volker Brendel:
  Incorporation of splice site probability models for non-canonical introns improves gene structure prediction in plants.30
• 
  Reed A. Cartwright:
  DNA assembly with gaps (Dawg): simulating sequence evolution.38
• 
  Austin L. Hughes,Helen Piontkivska,Kendall C. Krebs,David H. O'Connor,David I. Watkins:
  Within-host evolution of CD8⁺-TL epitopes encoded by overlapping and non-overlapping reading frames of simian immunodeficiency virus.44
• 
  Luke E. Ulrich,Igor B. Zhulin:
  Four-helix bundle: a ubiquitous sensory module in prokaryotic signal transduction.48
• 
  Irena I. Artamonova,Goar Frishman,Mikhail S. Gelfand,Dmitrij Frishman:
  Mining sequence annotation databanks for association patterns.57

Volume 21, Number 23, December 2005

Letter to the Editor - Data and Text Mining

• 
  Christian Blaschke,Alexander S. Yeh,Evelyn Camon,Marc E. Colosimo,Rolf Apweiler,Lynette Hirschman,Alfonso Valencia:
  Do you do text?4199-4200

Discovery Note - Structural Bioinformatics

• 
  Ruta Furmonaviciene,Brian J. Sutton,Fabian Glaser,Charles A. Laughton,Nick Jones,Herb F. Sewell,Farouk Shakib:
  An attempt to define allergen-specific molecular surface features: a bioinformatic approach.4201-4204

Systems Biology

• 
  Shinichiro Wachi,Ken Yoneda,Reen Wu:
  Interactome-transcriptome analysis reveals the high centrality of genes differentially expressed in lung cancer tissues.4205-4208

Genome Analysis

• 
  Frédéric Boyer,Anne Morgat,Laurent Labarre,Joël Pothier,Alain Viari:
  Syntons, metabolons and interactons: an exact graph-theoretical approach for exploring neighbourhood between genomic and functional data.4209-4215

Sequence Analysis

• 
  Eddo Kim,Yossef Kliger:
  Discovering hidden viral piracy.4216-4222
• 
  Keun-Joon Park,M. Michael Gromiha,Paul Horton,Makiko Suwa:
  Discrimination of outer membrane proteins using support vector machines.4223-4229

Structural Bioinformatics

• 
  Robert W. Janes:
  Bioinformatics analyses of circular dichroism protein reference databases.4230-4238
• 
  Huzefa Rangwala,George Karypis:
  Profile-based direct kernels for remote homology detection and fold recognition.4239-4247
• 
  Björn Wallner,Arne Elofsson:
  Pcons5: combining consensus, structural evaluation and fold recognition scores.4248-4254

Gene Expression

• 
  Hassan M. Fathallah-Shaykh:
  Noise and rank-dependent geometrical filter improves sensitivity of highly specific discovery by microarrays.4255-4262
• 
  Stan Pounds,Cheng Cheng:
  Sample size determination for the false discovery rate.4263-4271
• 
  Ida Scheel,Magne Aldrin,Ingrid Kristine Glad,Ragnhild Sørum,Heidi Lyng,Arnoldo Frigessi:
  The influence of missing value imputation on detection of differentially expressed genes from microarray data.4272-4279
• 
  Yang Xie,Wei Pan,Arkady B. Khodursky:
  A note on using permutation-based false discovery rate estimates to compare different analysis methods for microarray data.4280-4288

Systems Biology

• 
  Maris Lapinsh,Peteris Prusis,Staffan Uhlén,Jarl E. S. Wikberg:
  Improved approach for proteochemometrics modeling: application to organic compound - amine G protein-coupled receptor interactions.4289-4296

Databases and Ontologies

• 
  Andrew C. R. Martin:
  Mapping PDB chains to UniProtKB entries.4297-4301

Applications Note Genome Analysis

• 
  Alberto M. R. Dávila,Daniel M. Lorenzini,Pablo N. Mendes,Thiago S. Satake,Gabriel R. Sousa,Linair Maria Campos,Camila J. Mazzoni,Glauber Wagner,Paulo F. Pires,Edmundo C. Grisard,Maria Cláudia Reis Cavalcanti,Maria Luiza Machado Campos:
  GARSA: genomic analysis resources for sequence annotation.4302-4303

Sequence Analysis

• 
  Tobias Hindemitt,Klaus F. X. Mayer:
  CREDO: a web-based tool for computational detection of conserved sequence motifs in noncoding sequences.4304-4306

Genetics and Population Analysis

• 
  Hongyu Yang,Alan R. Gingle:
  OxfordGrid: a web interface for pairwise comparative map views.4307-4308
• 
  Giovanni Montana:
  HapSim: a simulation tool for generating haplotype data with pre-specified allele frequencies and LD coefficients.4309-4311

Databases and Ontologies

• 
  Jun Cai,Jing Zhang,Ying Huang,Yanda Li:
  ATID: a web-oriented database for collection of publicly available alternative translational initiation events.4312-4314
• 
  Gemma L. Holliday,Gail J. Bartlett,Daniel E. Almonacid,Noel M. O'Boyle,Peter Murray-Rust,Janet M. Thornton,John B. O. Mitchell:
  MACiE: a database of enzyme reaction mechanisms.4315-4316
• 
  Erratum.4317
• 
  Erratum.4318

Volume 21, Number 24, December 2005

Editorials

• 
  Alex Bateman,Alfonso Valencia:
  An update from theBioinformatics Editors.4319

Letter to the Editor

• 
  Steven Salzberg,James A. Yorke:
  Beware of mis-assembled genomes.4320-4321

Genome Analysis

• 
  Pernille Nielsen,Anders Krogh:
  Large-scale prokaryotic gene prediction and comparison to genome annotation.4322-4329

Sequence Analysis

• 
  Yu-Cheng Huang,Chun-Fan Chang,Chen-hsiung Chan,Tze-Jung Yeh,Ya-Chun Chang,Chaur-Chin Chen,Cheng-Yan Kao:
  Integrated minimum-set primers and unique probe design algorithms for differential detection on symptom-related pathogens.4330-4337

Phylogenetics

• 
  Wim Hordijk,Olivier Gascuel:
  Improving the efficiency of SPR moves in phylogenetic tree search methods based on maximum likelihood.4338-4347

Gene Expression

• 
  Jung Kyoon Choi,Ungsik Yu,Ook Joon Yoo,Sangsoo Kim:
  Differential coexpression analysis using microarray data and its application to human cancer.4348-4355
• 
  Shuangge Ma,Jian Huang:
  Regularized ROC method for disease classification and biomarker selection with microarray data.4356-4362
• 
  Fumihito Miura,Chihiro Uematsu,Yoshiyuki Sakaki,Takashi Ito:
  A novel strategy to design highly specific PCR primers based on the stability and uniqueness of 3'-end subsequences.4363-4370
• 
  Ezgi O. Booth,Nancy Van Driessche,Olga Zhuchenko,Adam Kuspa,Gad Shaulsky:
  Microarray phenotyping inDictyostelium reveals a regulon of chemotaxis genes.4371-4377
• 
  Shu-Dong Zhang,Timothy W. Gant:
  Effect of pooling samples on the efficiency of comparative studies using microarrays.4378-4383

Genetics And Population Analysis

• 
  Jing Li,Tao Jiang:
  Haplotype-based linkage disequilibrium mapping via direct data mining.4384-4393

Systems Biology

• 
  Xue-wen Chen,Mei Liu:
  Prediction of protein-protein interactions using random decision forest framework.4394-4400

Databases and Ontologies

• 
  Lena Strömbäck,Patrick Lambrix:
  Representations of molecular pathways: an evaluation of SBML, PSI MI and BioPAX.4401-4407

Applications Note Genome Analysis

• 
  Jacques Nicolas,Patrick Durand,Grégory Ranchy,Sébastien Tempel,Anne-Sophie Valin:
  Suffix-tree analyser (STAN): looking for nucleotidic and peptidic patterns in chromosomes.4408-4410
• 
  Timothy R. O'Connor,Curtis E. Dyreson,John J. Wyrick:
  Athena: a resource for rapid visualization and systematic analysis ofArabidopsis promoter sequences.4411-4413

Sequence Analysis

• 
  Celine A. Hayden,Travis J. Wheeler,Richard A. Jorgensen:
  Evaluating and improving cDNA sequence quality with cQC.4414-4415
• 
  Chi-Hung Tsai,Bo-Juen Chen,Chen-hsiung Chan,Hsuan-Liang Liu,Cheng-Yan Kao:
  Improving disulfide connectivity prediction with sequential distance between oxidized cysteines.4416-4419
• 
  James A. Smagala,Erica D. Dawson,Martin Mehlmann,Michael B. Townsend,Robert D. Kuchta,Kathy L. Rowlen:
  ConFind: a robust tool for conserved sequence identification.4420-4422

Phylogenetics

• 
  Paul J. Planet,Indra Neil Sarkar:
  mILD: a tool for constructing and analyzing matrices of pairwise phylogenetic character incongruence tests.4423-4424

Structural Bioinformatics

• 
  Fabian Birzele,Jan E. Gewehr,Ralf Zimmer:
  QUASAR - scoring and ranking of sequence-structure alignments.4425-4426

Gene Expression

• 
  Rodrigo D. Drummond,A. Pinheiro,C. S. Rocha,Marcelo Menossi:
  ISER: selection of differentially expressed genes from DNA array data by non-linear data transformations and local fitting.4427-4429

Genetics and Population Analysis

• 
  Fabio Pardi,Douglas F. Levinson,Cathryn M. Lewis:
  GSMA: software implementation of the genome search meta-analysis method.4430-4431

Data and Text Mining

• 
  Sean D. Hooper,Peer Bork:
  Medusa: a simple tool for interaction graph analysis.4432-4433
• 
  Erratum.4434
• 
  Erratum.4435