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Bioinformatics, Volume 21
Volume 21, Number 1, January 2005
- Alfonso Valencia, Alex Bateman
:
Increasing the Impact of Bioinformatics. 1-1
- Albert D. G. de Roos
:
Origins of introns based on the definition of exon modules and their conserved interfaces. 2-9
- 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
- Luonan Chen, Tianshou Zhou, Yun Tang:
Protein structure alignment by deterministic annealing. 51-62
- 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
- Kui Zhang, Fengzhu Sun, Hongyu Zhao
:
HAPLORE: a program for haplotype reconstruction in general pedigrees without recombination. 90-103
- Ramin Homayouni, Kevin Heinrich, Lai Wei, Michael W. Berry
:
Gene clustering by Latent Semantic Indexing of MEDLINE abstracts. 104-115
- 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
- Robert Belshaw, Aris Katzourakis
:
BlastAlign: a program that uses blast to align problematic nucleotide sequences. 122-123
- 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
- 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
- Vincent J. Carey, Jeff Gentry, Elizabeth Whalen, Robert Gentleman:
Network structures and algorithms in Bioconductor. 135-136
- 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
- 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
- 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
- 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
- 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
- Lifeng Chen, Hongfang Liu, Carol Friedman:
Gene name ambiguity of eukaryotic nomenclatures. 248-256
- Sam Griffiths-Jones
:
RALEE--RNA ALignment Editor in Emacs. 257-259
- Darren P. Martin, Carolyn Williamson, David Posada
:
RDP2: recombination detection and analysis from sequence alignments. 260-262
- 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
- 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
- Andrew Young
, Nathan Whitehouse, J. Cho, Chad A. Shaw
:
OntologyTraverser: an R package for GO analysis. 275-276
Volume 21, Number 3, February 2005
- Protein Refinement: A New Challenge For Casp In Its 10th Anniversary. 277
- 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
- Dustin E. Schones, Pavel Sumazin, Michael Q. Zhang:
Similarity of position frequency matrices for transcription factor binding sites. 307-313
- Haiquan Li
, Jinyan Li:
Discovery of stable and significant binding motif pairs from PDB complexes and protein interaction datasets. 314-324
- Anders F. Andersson
, Rolf Bernander, Peter Nilsson
:
Dual-genome primer design for construction of DNA microarrays. 325-332
- Juan M. Gonzalez
, Johannes Zimmermann
, Cesareo Saiz-Jimenez:
Evaluating putative chimeric sequences from PCR-amplified products. 333-337
- 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
- Carla Kuiken, Karina Yusim, Laura Boykin
, Russell Richardson:
The Los Alamos hepatitis C sequence database. 379-384
- 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
- C. J. Creevey, James O. McInerney:
Clann: investigating phylogenetic information through supertree analyses. 390-392
- Paolo Fontana, Eckart Bindewald, Stefano Toppo
, Riccardo Velasco
, Giorgio Valle
, Silvio C. E. Tosatto
:
The SSEA server for protein secondary structure alignment. 393-395
- 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
- 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
- Robert D. Finn
, Mhairi Marshall, Alex Bateman
:
iPfam: visualization of protein?Cprotein interactions in PDB at domain and amino acid resolutions. 410-412
- Gregor Leban, Ivan Bratko, Uros Petrovic
, Tomaz Curk
, Blaz Zupan
:
VizRank: finding informative data projections in functional genomics by machine learning. 413-414
- 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
- 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
- Tarjei S. Mikkelsen, James E. Galagan
, Jill P. Mesirov:
Improving genome annotations using phylogenetic profile anomaly detection. 464-470
- 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
- 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
- Paul Stothard, David S. Wishart
:
Circular genome visualization and exploration using CGView. 537-539
- 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
- Allegra Via, Andreas Zanzoni
, Manuela Helmer-Citterich
:
Seq2Struct: a resource for establishing sequence-structure links. 551-553
- Andreas Buness, Wolfgang Huber
, Klaus Steiner, Holger Sültmann
, Annemarie Poustka:
arrayMagic: two-colour cDNA microarray quality control, preprocessing. 554-556
- X. Kong, Tara Cox Matise:
MAP-O-MAT: internet-based linkage mapping. 557-559
- Brett G. Olivier
, Johann M. Rohwer
, Jan-Hendrik S. Hofmeyr:
Modelling cellular systems with PySCeS. 560-561
Volume 21, Number 5, March 2005
- 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
- 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
- Ming Zhang, R. Allen White, Liqun Wang, Ronald N. Goldman, Lydia E. Kavraki
, Brendan Hassett:
Improving conformational searches by geometric screening. 624-630
- 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
- Yecheng Huang, Janie Pumphrey, Alan R. Gingle:
ESTminer: a Web interface for mining EST contig and cluster databases. 669-670
- 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
- Sergei L. Kosakovsky Pond, Simon D. W. Frost, Spencer V. Muse:
HyPhy: hypothesis testing using phylogenies. 676-679
- 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
- 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
- Rex T. Nelson, David M. Grant, Randy C. Shoemaker:
ESTminer: a suite of programs for gene and allele identification. 691-693
- Jing Ding, Daniel Berleant:
MedKit: a helper toolkit for automatic mining of MEDLINE/PubMed citations. 694-695
- 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
- Isabelle Callebaut
, Jean Paul Mornon:
OCRE: a novel domain made of imperfect, aromatic-rich octamer repeats. 699-702
- 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