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ORCIDBioinformatics, Volume 18
Volume 18, Number 1, January 2002
- Chris Sander:
The Journal Bioinformatics, key medium for computational biology. 1-2
- James K. Bonfield, Rodger Staden:
ZTR: a new format for DNA sequence trace data. 3-10 - Trond Hellem Bø, Inge Jonassen
, Ingvar Eidhammer, Carsten Helgesen:
A fast top-down method for constructing reliable radiation hybrid frameworks. 11-18 - Vladimir Pavlovic, Ashutosh Garg, Simon Kasif:
A Bayesian framework for combining gene predictions. 19-27 - Jirí Macas, Tibor Mészáros, Marcela Nouzová:
PlantSat: a specialized database for plant satellite repeats. 28-35 - Bernhard Haubold, Thomas Wiehe:
Calculating the SNP-effective sample size from an alignment. 36-38 - Danh V. Nguyen, David M. Rocke:
Tumor classification by partial least squares using microarray gene expression data. 39-50 - Wolfram Liebermeister:
Linear modes of gene expression determined by independent component analysis. 51-60 - Roman Sásik, N. Iranfar, Terence Hwa, W. F. Loomis:
Extracting transcriptional events from temporal gene expression patterns during Dictyostelium development. 61-66 - Christian Siehs, Rainer Oberbauer, Gert Mayer, Arno Lukas, Bernd Mayer:
Discrete simulation of regulatory homo- and heterodimerization in the apoptosis effector phase. 67-76 - Weizhong Li, Lukasz Jaroszewski, Adam Godzik:
Tolerating some redundancy significantly speeds up clustering of large protein databases. 77-82 - Philip J. Cotter, Daniel R. Caffrey, Denis C. Shields:
Improved database searches for orthologous sequences by conditioning on outgroup sequences. 83-91 - Christian E. V. Storm, Erik L. L. Sonnhammer:
Automated ortholog inference from phylogenetic trees and calculation of orthology reliability. 92-99 - Gary W. Stuart, Karen Moffett, Steve Baker:
Integrated gene and species phylogenies from unaligned whole genome protein sequences. 100-108 - Ursula Rost, Erich Bornberg-Bauer:
TreeWiz: interactive exploration of huge trees. 109-114 - Tae-Kun Seo, Jeffrey L. Thorne, Masami Hasegawa, Hirohisa Kishino:
A viral sampling design for testing the molecular clock and for estimating evolutionary rates and divergence times. 115-123 - Alexander Goesmann, Martin Haubrock, Folker Meyer, Jörn Kalinowski, Robert Giegerich:
PathFinder: reconstruction and dynamic visualization of metabolic pathways. 124-129 - Xi Chen, Yuhmei Lin, Ming Liu, Michael K. Gilson:
The Binding Database: data management and interface design. 130-139 - Hiroshi Nagata, Hiroshi Mizushima, Hiroshi Tanaka:
Concept and prototype of protein-ligand docking simulator with force feedback technology. 140-146 - Rachel Karchin, Kevin Karplus, David Haussler:
Classifying G-protein coupled receptors with support vector machines. 147-159 - Amanda Clare, Ross D. King:
Machine learning of functional class from phenotype data. 160-166 - Sabine Dietmann, Cornelius Frömmel:
Prediction of 3D neighbours of molecular surface patches in proteins by artificial neural networks. 167-174 - Lee C. Allcorn, Andrew C. R. Martin:
SACS-Self-maintaining database of antibody crystal structure information. 175-181
- Darrell Conklin, Inge Jonassen, Rein Aasland, William R. Taylor:
Association of nucleotide patterns with gene function classes: application to human 3' untranslated sequences. 182-189 - Edouard Yeramian, Serge Bonnefoy, Gordon Langsley:
Physics-based gene identification: proof of concept for Plasmodium falciparum. 190-193
- James K. Bonfield, Kathryn F. Beal, Matthew J. Betts, Rodger Staden:
Trev: a DNA trace editor and viewer. 194-195 - Biju Issac, Harpreet Singh, Harpreet Kaur, G. P. S. Raghava:
Locating probable genes using Fourier transform approach. 196-197 - Vladimir B. Bajic, Seng Hong Seah, Allen Chong, Guanglan Zhang, Judice L. Y. Koh, Vladimir Brusic:
Dragon Promoter Finder: recognition of vertebrate RNA polymerase II promoters. 198-199 - Ashley C. Stuart, Valentin A. Ilyin, Andrej Sali:
LigBase: a database of families of aligned ligand binding sites in known protein sequences and structures. 200-201 - Scott C. Chapman, Peer Schenk, Kemal Kazan, John Manners:
Using biplots to interpret gene expression patterns in plants. 202-204 - Daniel R. Rhodes, Jeremy C. Miller, Brian B. Haab, Kyle A. Furge:
CIT: identification of differentially expressed clusters of genes from microarray data. 205-206 - Alexander Sturn, John Quackenbush, Zlatko Trajanoski:
Genesis: cluster analysis of microarray data. 207-208 - A. Hofmann, A. Wlodawer:
PCSB-a program collection for structural biology and biophysical chemistry. 209-210 - A. Lobley, Lee Whitmore, B. A. Wallace:
DICHROWEB: an interactive website for the analysis of protein secondary structure from circular dichroism spectra. 211-212 - Christophe Combet, Martin Jambon, Gilbert Deléage, Christophe Geourjon:
Geno3D: automatic comparative molecular modelling of protein. 213-214
- Donald R. Forsdyke:
Symmetry observations in long nucleotide sequences: a commentary on the Discovery Note of Qi and Cuticchia. 215-217
- Steffen Möller, Michael D. R. Croning, Rolf Apweiler:
Erratum: Evaluation of methods for the prediction of membrane spanning regions. 218
Volume 18, Number 2, February 2002
- Steven Henikoff:
Beyond the central dogma. 223-225
- Dirk Husmeier, Frank Wright:
A Bayesian approach to discriminate between alternative DNA sequence segmentations. 226-234 - Marc Sebban, Igor Mokrousov, Nalin Rastogi, Christophe Sola:
A data-mining approach to spacer oligonucleotide typing of Mycobacterium tuberculosis. 235-243 - Zhengdong Zhang, Richard C. Willson, George E. Fox:
Identification of characteristic oligonucleotides in the bacterial 16S ribosomal RNA sequence dataset. 244-250 - Alexander D. Tsodikov, Aniko Szabo, David Jones:
Adjustments and measures of differential expression for microarray data. 251-260 - Ilya Shmulevich, Edward R. Dougherty, Seungchan Kim, Wei Zhang:
Probabilistic Boolean networks: a rule-based uncertainty model for gene regulatory networks. 261-274 - Debashis Ghosh, Arul M. Chinnaiyan:
Mixture modelling of gene expression data from microarray experiments. 275-286 - Hiroyuki Toh, Katsuhisa Horimoto:
Inference of a genetic network by a combined approach of cluster analysis and graphical Gaussian modeling. 287-297 - Hideo Bannai, Yoshinori Tamada, Osamu Maruyama, Kenta Nakai, Satoru Miyano:
Extensive feature detection of N-terminal protein sorting signals. 298-305 - Melissa S. Cline, Richard Hughey, Kevin Karplus:
Predicting reliable regions in protein sequence alignments. 306-314 - Elmar Krieger, Gert Vriend:
Models@Home: distributed computing in bioinformatics using a screensaver based approach. 315-318
- Francisco Azuaje:
A cluster validity framework for genome expression data. 319-320 - Henrik Bjørn Nielsen, Steen Knudsen:
Avoiding cross hybridization by choosing nonredundant targets on cDNA arrays. 321-322 - Christopher M. L. S. Bouton, Jonathan Pevsner:
DRAGON View: information visualization for annotated microarray data. 323-324 - Li Wuju, Momiao Xiong:
Tclass: tumor classification system based on gene expression profile. 325-326 - Klaus Bumm, Mingzhong Zheng, Clyde Bailey, Fenghuang Zhan, M. Chiriva-Internati, Paul Eddlemon, Julian Terry, Bart Barlogie, John D. Shaughnessy Jr.:
CGO: utilizing and integrating gene expression microarray data in clinical research and data management. 327-328 - A. Collette, Adrien Six:
ISEApeaks: an Excel platform for GeneScan and Immunoscope data retrieval, management and analysis. 329-330 - Gert Thijs, Yves Moreau, Frank De Smet, Janick Mathys, Magali Lescot, Stephane Rombauts, Pierre Rouzé, Bart De Moor, Kathleen Marchal:
INCLUSive: INtegrated Clustering, Upstream sequence retrieval and motif Sampling. 331-332 - Xavier Messeguer, Ruth Escudero, Domènec Farré, Oscar Núñez, Javier Martínez, M. Mar Albà:
PROMO: detection of known transcription regulatory elements using species-tailored searches. 333-334 - Alex Kozik, Elena Kochetkova, Richard W. Michelmore:
GenomePixelizer-a visualization program for comparative genomics within and between species. 335-336 - Richard R. Hudson:
Generating samples under a Wright-Fisher neutral model of genetic variation. 337-338 - George Seaton, Chris S. Haley, Sara A. Knott, Mike Kearsey, Peter M. Visscher:
QTL Express: mapping quantitative trait loci in simple and complex pedigrees. 339-340 - J. Signorovitch, Rasmus Nielsen:
PATRI-paternity inference using genetic data. 341-342 - Alexander Kanapin, Rolf Apweiler, Margaret Biswas, Wolfgang Fleischmann, Youla Karavidopoulou, Paul J. Kersey, Evgenia V. Kriventseva, Virginie Mittard, Nicola J. Mulder, Thomas M. Oinn, Isabelle Phan, Florence Servant, Evgeni M. Zdobnov:
Interactive InterPro-based comparisons of proteins in whole genomes. 374-375
- Artemis G. Hatzigeorgiou:
Translation initiation start prediction in human cDNAs with high accuracy. 343-350 - Stefan Schuster, Thomas Pfeiffer, Ferdinand Moldenhauer, Ina Koch, Thomas Dandekar:
Exploring the pathway structure of metabolism: decomposition into subnetworks and application to Mycoplasma pneumoniae. 351-361 - Inge Jonassen, Ingvar Eidhammer, Darrell Conklin, William R. Taylor:
Structure motif discovery and mining the PDB. 362-367 - Evgeni M. Zdobnov, Rodrigo Lopez, Rolf Apweiler, Thure Etzold:
The EBI SRS server-recent developments. 368-373
Volume 18, Number 3, March 2002
- Christos A. Ouzounis:
Bioinformatics and the theoretical foundations of molecular biology. 377-378
- Martti T. Tammi, Erik Arner, Tom Britton, Björn Andersson:
Separation of nearly identical repeats in shotgun assemblies using defined nucleotide positions, DNPs. 379-388 - Mattias Wahde, Gregory T. Klus, Michael L. Bittner, Yidong Chen, Zoltan Szallasi:
Assessing the significance of consistently mis-regulated genes in cancer associated gene expression matrices. 389-394 - Graham R. Ball, Shahid Mian, F. Holding, R. O. Allibone, James Lowe, S. Ali, G. Li, S. McCardle, Ian O. Ellis, Colin Creaser, Robert C. Rees:
An integrated approach utilizing artificial neural networks and SELDI mass spectrometry for the classification of human tumours and rapid identification of potential biomarkers. 395-404 - Winston Patrick Kuo, Tor-Kristian Jenssen, Atul J. Butte, Lucila Ohno-Machado, Isaac S. Kohane:
Analysis of matched mRNA measurements from two different microarray technologies. 405-412 - Geoffrey J. McLachlan, Richard W. Bean, David Peel:
A mixture model-based approach to the clustering of microarray expression data. 413-422 - Kurt Fellenberg, Nicole C. Hauser, Benedikt Brors, Jörg D. Hoheisel, Martin Vingron:
Microarray data warehouse allowing for inclusion of experiment annotations in statistical analysis. 423-433 - Martin J. Blythe, Irini A. Doytchinova, Darren R. Flower:
JenPep: a database of quantitative functional peptide data for immunology. 434-439 - Bin Ma, John Tromp, Ming Li:
PatternHunter: faster and more sensitive homology search. 440-445 - Pierre Vincens, Anne Badel-Chagnon, Cécile André, Serge A. Hazout:
D-ASSIRC: distributed program for finding sequence similarities in genomes. 446-451 - Christopher J. Lee, Catherine S. Grasso, Mark F. Sharlow:
Multiple sequence alignment using partial order graphs. 452-464 - Mark Ettinger:
The complexity of comparing reaction systems. 465-469 - Andrzej M. Kierzek:
STOCKS: STOChastic Kinetic Simulations of biochemical systems with Gillespie algorithm. 470-481
- Heikki Mannila, Anne Patrikainen, Jouni K. Seppänen, Juha Kere:
Long-range control of expression in yeast. 482-483
- S. R. Ness, W. Terpstra, Martin Krzywinski, Marco A. Marra, Steven J. M. Jones:
Assembly of fingerprint contigs: parallelized FPC. 484-485 - Jean-Marie Rouillard, Christopher J. Herbert, Michael Zuker:
OligoArray: genome-scale oligonucleotide design for microarrays. 486-487 - Pinglang Wang, Fei Ding, Hsienyuan Chiang, Robert C. Thompson, Stanley J. Watson, Fan Meng:
ProbeMatchDB-a web database for finding equivalent probes across microarray platforms and species. 488-489 - Gilles Didier, Pierre Brézellec, Elisabeth Remy, Alain Hénaut:
GeneANOVA-gene expression analysis of variance. 490-491 - Glenn Tesler:
GRIMM: genome rearrangements web server. 492-493 - Raphaël Leplae, Tim J. P. Hubbard:
MaxBench: evaluation of sequence and structure comparison methods. 494-495 - Robel Y. Kahsay, Guoli Wang, Nataraj Dongre, Guang R. Gao, Roland L. Dunbrack Jr.:
CASA: a server for the critical assessment of protein sequence alignment accuracy. 496-497 - Harpreet Kaur, G. P. S. Raghava:
BetaTPred: prediction of beta-TURNS in a protein using statistical algorithms. 498-499 - Xun Gu, Kent Vander Velden:
DIVERGE: phylogeny-based analysis for functional-structural divergence of a protein family. 500-501 - Heiko A. Schmidt, Korbinian Strimmer, Martin Vingron, Arndt von Haeseler:
TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. 502-504
Volume 18, Number 4, April 2002
- Rainer Fuchs:
From Sequence to Biology: The Impact on Bioinformatics. 505-506
- Mark J. Schreiber, Chris M. Brown:
Compensation for nucleotide bias in a genome by representation as a discrete channel with noise. 507-512 - Steven Hampson, Dennis F. Kibler, Pierre Baldi:
Distribution patterns of over-represented k-mers in non-coding yeast DNA. 513-528 - Charles J. Colbourn, Alan C. H. Ling, Martin Tompa:
Construction of optimal quality control for oligo arrays. 529-535 - Ying Xu, Victor Olman, Dong Xu:
Clustering gene expression data using a graph-theoretic approach: an application of minimum spanning trees. 536-545 - Wei Pan:
A comparative review of statistical methods for discovering differentially expressed genes in replicated microarray experiments. 546-554 - Ilya Shmulevich, Wei Zhang:
Binary analysis and optimization-based normalization of gene expression data. 555-565 - Thomas D. Moloshok, R. R. Klevecz, Jeffrey D. Grant, Frank J. Manion, W. F. Speier IV, Michael F. Ochs:
Application of Bayesian Decomposition for analysing microarray data. 566-575 - David C. Hoyle, Magnus Rattray, Ray Jupp, Andy Brass:
Making sense of microarray data distributions. 576-584 - Dov Greenbaum, Ronald Jansen, Mark Gerstein:
Analysis of mRNA expression and protein abundance data: an approach for the comparison of the enrichment of features in the cellular population of proteins and transcripts. 585-596 - Daniel Aguilar, Baldomero Oliva, Francesc X. Avilés, Enrique Querol:
TranScout: prediction of gene expression regulatory proteins from their sequences. 597-607 - Shigeki Mitaku, Takatsugu Hirokawa, Toshiyuki Tsuji:
Amphiphilicity index of polar amino acids as an aid in the characterization of amino acid preference at membrane-water interfaces. 608-616 - Mauro Delorenzi, Terence P. Speed:
An HMM model for coiled-coil domains and a comparison with PSSM-based predictions. 617-625
- Riccardo Bennett-Lovsey, Sarah E. Hart, Hiroki Shirai, Kenji Mizuguchi:
The SWIB and the MDM2 domains are homologous and share a common fold. 626-630
- Loïc Ponger, Dominique Mouchiroud:
CpGProD: identifying CpG islands associated with transcription start sites in large genomic mammalian sequences. 631-633 - Adalberto T. Castelo, Wellington Santos Martins, Guang R. Gao:
TROLL-Tandem Repeat Occurrence Locator. 634-636 - Maria Elena Ochagavía, Jean Richelle, Shoshana J. Wodak:
Advanced pairwise structure alignments of proteins and analysis of conformational changes. 637-640 - M. Madan Babu, K. Sankaran:
DOLOP-database of bacterial lipoproteins. 641-643 - Filippo Rusconi, Maya Belghazi:
Desktop prediction/analysis of mass spectrometric data in proteomic projects by using massXpert. 644-645 - Coral del Val, Peter Ernst, Rüdiger Bräuning, Karl-Heinz Glatting, Sándor Suhai:
PATH: a task for the inference of phylogenies. 646-647
Volume 18, Number 5, May 2002
- Ken Nishikawa:
Information Concept in Biology. 649-651
- Jacek Blazewicz, Piotr Formanowicz, Frédéric Guinand, Marta Kasprzak:
A heuristic managing errors for DNA sequencing. 652-660 - Zhou Yu, Tao Li, Jindong Zhao, Jingchu Luo:
PGAAS: a prokaryotic genome assembly assistant system. 661-665 - Yu-hua Hao, Zheng Tan:
The generation of long telomere overhangs in human cells: a model and its implication. 666-671 - M. Mar Albà, Roman A. Laskowski, John M. Hancock:
Detecting cryptically simple protein sequences using the SIMPLE algorithm. 672-678