Bioinformatics, Volume 21

Volume 21, Number 1, January 2005

Editorials

• 
  Alfonso Valencia, Alex Bateman:
  Increasing the Impact of Bioinformatics. 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 uses blast 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, C. 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 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 Anderssonn, 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, G. 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:
  Y. Barash, G. Elidan, T. Kaplan, , N. Friedman. 596-600
• 
  S. Burden, Y.-X. 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
•