Volume 18,
Number 1,
January 2002
Editorial
- Chris Sander:
The Journal Bioinformatics, key medium for computational biology.
1-2 BibTeX
Original Papers
- James K. Bonfield, Rodger Staden:
ZTR: a new format for DNA sequence trace data.
3-10 BibTeX
- Trond Hellem Bø, Inge Jonassen, Ingvar Eidhammer, Carsten Helgesen:
A fast top-down method for constructing reliable radiation hybrid frameworks.
11-18 BibTeX
- Vladimir Pavlovic, Ashutosh Garg, Simon Kasif:
A Bayesian framework for combining gene predictions.
19-27 BibTeX
- Jirí Macas, Tibor Mészáros, Marcela Nouzová:
PlantSat: a specialized database for plant satellite repeats.
28-35 BibTeX
- Bernhard Haubold, Thomas Wiehe:
Calculating the SNP-effective sample size from an alignment.
36-38 BibTeX
- Danh V. Nguyen, David M. Rocke:
Tumor classification by partial least squares using microarray gene expression data.
39-50 BibTeX
- Wolfram Liebermeister:
Linear modes of gene expression determined by independent component analysis.
51-60 BibTeX
- R. Sásik, N. Iranfar, Terence Hwa, W. F. Loomis:
Extracting transcriptional events from temporal gene expression patterns during Dictyostelium development.
61-66 BibTeX
- Christian Siehs, Rainer Oberbauer, Gert Mayer, Arno Lukas, Bernd Mayer:
Discrete simulation of regulatory homo- and heterodimerization in the apoptosis effector phase.
67-76 BibTeX
- Weizhong Li, Lukasz Jaroszewski, Adam Godzik:
Tolerating some redundancy significantly speeds up clustering of large protein databases.
77-82 BibTeX
- Philip J. Cotter, Daniel R. Caffrey, Denis C. Shields:
Improved database searches for orthologous sequences by conditioning on outgroup sequences.
83-91 BibTeX
- Christian E. V. Storm, Erik L. L. Sonnhammer:
Automated ortholog inference from phylogenetic trees and calculation of orthology reliability.
92-99 BibTeX
- Gary W. Stuart, Karen Moffett, Steve Baker:
Integrated gene and species phylogenies from unaligned whole genome protein sequences.
100-108 BibTeX
- Ursula Rost, Erich Bornberg-Bauer:
TreeWiz: interactive exploration of huge trees.
109-114 BibTeX
- 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 BibTeX
- Alexander Goesmann, Martin Haubrock, Folker Meyer, Jörn Kalinowski, Robert Giegerich:
PathFinder: reconstruction and dynamic visualization of metabolic pathways.
124-129 BibTeX
- Xi Chen, Yuhmei Lin, Ming Liu, Michael K. Gilson:
The Binding Database: data management and interface design.
130-139 BibTeX
- Hiroshi Nagata, Hiroshi Mizushima, Hiroshi Tanaka:
Concept and prototype of protein-ligand docking simulator with force feedback technology.
140-146 BibTeX
- Rachel Karchin, Kevin Karplus, David Haussler:
Classifying G-protein coupled receptors with support vector machines.
147-159 BibTeX
- Amanda Clare, Ross D. King:
Machine learning of functional class from phenotype data.
160-166 BibTeX
- Sabine Dietmann, Cornelius Frömmel:
Prediction of 3D neighbours of molecular surface patches in proteins by artificial neural networks.
167-174 BibTeX
- Lee C. Allcorn, Andrew C. R. Martin:
SACS-Self-maintaining database of antibody crystal structure information.
175-181 BibTeX
Discovery Notes
Applications Notes
- James K. Bonfield, Kathryn F. Beal, Matthew J. Betts, Rodger Staden:
Trev: a DNA trace editor and viewer.
194-195 BibTeX
- Biju Issac, Harpreet Singh, Harpreet Kaur, G. P. S. Raghava:
Locating probable genes using Fourier transform approach.
196-197 BibTeX
- 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 BibTeX
- 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 BibTeX
- Scott Chapman, Peer Schenk, Kemal Kazan, John Manners:
Using biplots to interpret gene expression patterns in plants.
202-204 BibTeX
- 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 BibTeX
- Alexander Sturn, John Quackenbush, Zlatko Trajanoski:
Genesis: cluster analysis of microarray data.
207-208 BibTeX
- A. Hofmann, A. Wlodawer:
PCSB-a program collection for structural biology and biophysical chemistry.
209-210 BibTeX
- A. Lobley, Lee Whitmore, B. A. Wallace:
DICHROWEB: an interactive website for the analysis of protein secondary structure from circular dichroism spectra.
211-212 BibTeX
- Christophe Combet, Martin Jambon, Gilbert Deléage, Christophe Geourjon:
Geno3D: automatic comparative molecular modelling of protein.
213-214 BibTeX
Letter
- D. R. Forsdyke:
Symmetry observations in long nucleotide sequences: a commentary on the Discovery Note of Qi and Cuticchia.
215-217 BibTeX
Erratum
Volume 18,
Number 2,
February 2002
Editorial
Original Papers
- Dirk Husmeier, Frank Wright:
A Bayesian approach to discriminate between alternative DNA sequence segmentations.
226-234 BibTeX
- Marc Sebban, I. Mokrousov, N. Rastogi, C. Sola:
A data-mining approach to spacer oligonucleotide typing of Mycobacterium tuberculosis.
235-243 BibTeX
- Zhengdong Zhang, Richard C. Willson, George E. Fox:
Identification of characteristic oligonucleotides in the bacterial 16S ribosomal RNA sequence dataset.
244-250 BibTeX
- A. Tsodikov, A. Szabo, D. Jones:
Adjustments and measures of differential expression for microarray data.
251-260 BibTeX
- Ilya Shmulevich, Edward R. Dougherty, Seungchan Kim, Wei Zhang:
Probabilistic Boolean networks: a rule-based uncertainty model for gene regulatory networks.
261-274 BibTeX
- Debashis Ghosh, Arul M. Chinnaiyan:
Mixture modelling of gene expression data from microarray experiments.
275-286 BibTeX
- Hiroyuki Toh, Katsuhisa Horimoto:
Inference of a genetic network by a combined approach of cluster analysis and graphical Gaussian modeling.
287-297 BibTeX
- Hideo Bannai, Yoshinori Tamada, Osamu Maruyama, Kenta Nakai, Satoru Miyano:
Extensive feature detection of N-terminal protein sorting signals.
298-305 BibTeX
- Melissa S. Cline, Richard Hughey, Kevin Karplus:
Predicting reliable regions in protein sequence alignments.
306-314 BibTeX
- Elmar Krieger, Gert Vriend:
Models@Home: distributed computing in bioinformatics using a screensaver based approach.
315-318 BibTeX
Applications Notes
- Francisco Azuaje:
A cluster validity framework for genome expression data.
319-320 BibTeX
- Henrik Bjørn Nielsen, Steen Knudsen:
Avoiding cross hybridization by choosing nonredundant targets on cDNA arrays.
321-322 BibTeX
- Christopher M. L. S. Bouton, Jonathan Pevsner:
DRAGON View: information visualization for annotated microarray data.
323-324 BibTeX
- Li Wuju, Momiao Xiong:
Tclass: tumor classification system based on gene expression profile.
325-326 BibTeX
- 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 BibTeX
- A. Collette, A. Six:
ISEApeaks: an Excel platform for GeneScan and Immunoscope data retrieval, management and analysis.
329-330 BibTeX
- 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 BibTeX
- 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 BibTeX
- A. Kozik, E. Kochetkova, R. Michelmore:
GenomePixelizer-a visualization program for comparative genomics within and between species.
335-336 BibTeX
- Richard R. Hudson:
Generating samples under a Wright-Fisher neutral model of genetic variation.
337-338 BibTeX
- 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 BibTeX
- J. Signorovitch, R. Nielsen:
PATRI-paternity inference using genetic data.
341-342 BibTeX
- Alexander Kanapin, Rolf Apweiler, Margaret Biswas, Wolfgang Fleischmann, Youla Karavidopoulou, Paul 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 BibTeX
GCB2000 Papers
- Artemis G. Hatzigeorgiou:
Translation initiation start prediction in human cDNAs with high accuracy.
343-350 BibTeX
- 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 BibTeX
- Inge Jonassen, Ingvar Eidhammer, Darrell Conklin, William R. Taylor:
Structure motif discovery and mining the PDB.
362-367 BibTeX
- Evgeni M. Zdobnov, Rodrigo Lopez, Rolf Apweiler, Thure Etzold:
The EBI SRS server-recent developments.
368-373 BibTeX
Volume 18,
Number 3,
March 2002
Editorial
Original Papers
- Martti T. Tammi, Erik Arner, Tom Britton, Björn Andersson:
Separation of nearly identical repeats in shotgun assemblies using defined nucleotide positions, DNPs.
379-388 BibTeX
- 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 BibTeX
- Graham R. Ball, Shahid Mian, F. Holding, R. O. Allibone, J. Lowe, S. Ali, G. Li, S. McCardle, I. 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 BibTeX
- 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 BibTeX
- Geoffrey J. McLachlan, Richard Bean, David Peel:
A mixture model-based approach to the clustering of microarray expression data.
413-422 BibTeX
- 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 BibTeX
- Martin J. Blythe, Irini A. Doytchinova, Darren R. Flower:
JenPep: a database of quantitative functional peptide data for immunology.
434-439 BibTeX
- Bin Ma, John Tromp, Ming Li:
PatternHunter: faster and more sensitive homology search.
440-445 BibTeX
- Pierre Vincens, Anne Badel-Chagnon, Cécile André, Serge A. Hazout:
D-ASSIRC: distributed program for finding sequence similarities in genomes.
446-451 BibTeX
- Christopher Lee, Catherine Grasso, Mark F. Sharlow:
Multiple sequence alignment using partial order graphs.
452-464 BibTeX
- Mark Ettinger:
The complexity of comparing reaction systems.
465-469 BibTeX
- Andrzej M. Kierzek:
STOCKS: STOChastic Kinetic Simulations of biochemical systems with Gillespie algorithm.
470-481 BibTeX
Discovery Notes
Applications Notes
- S. R. Ness, W. Terpstra, Martin Krzywinski, Marco A. Marra, Steven J. M. Jones:
Assembly of fingerprint contigs: parallelized FPC.
484-485 BibTeX
- Jean-Marie Rouillard, Christopher J. Herbert, Michael Zuker:
OligoArray: genome-scale oligonucleotide design for microarrays.
486-487 BibTeX
- 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 BibTeX
- Gilles Didier, Pierre Brézellec, Elisabeth Remy, Alain Hénaut:
GeneANOVA-gene expression analysis of variance.
490-491 BibTeX
- Glenn Tesler:
GRIMM: genome rearrangements web server.
492-493 BibTeX
- Raphaël Leplae, Tim J. P. Hubbard:
MaxBench: evaluation of sequence and structure comparison methods.
494-495 BibTeX
- 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 BibTeX
- Harpreet Kaur, G. P. S. Raghava:
BetaTPred: prediction of beta-TURNS in a protein using statistical algorithms.
498-499 BibTeX
- Xun Gu, Kent Vander Velden:
DIVERGE: phylogeny-based analysis for functional-structural divergence of a protein family.
500-501 BibTeX
- Heiko A. Schmidt, Korbinian Strimmer, Martin Vingron, Arndt von Haeseler:
TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing.
502-504 BibTeX
Volume 18,
Number 4,
April 2002
Editorial
Original Papers
- Mark Schreiber, Chris Brown:
Compensation for nucleotide bias in a genome by representation as a discrete channel with noise.
507-512 BibTeX
- Steven Hampson, Dennis F. Kibler, Pierre Baldi:
Distribution patterns of over-represented k-mers in non-coding yeast DNA.
513-528 BibTeX
- Charles J. Colbourn, Alan C. H. Ling, Martin Tompa:
Construction of optimal quality control for oligo arrays.
529-535 BibTeX
- Ying Xu, Victor Olman, Dong Xu:
Clustering gene expression data using a graph-theoretic approach: an application of minimum spanning trees.
536-545 BibTeX
- Wei Pan:
A comparative review of statistical methods for discovering differentially expressed genes in replicated microarray experiments.
546-554 BibTeX
- Ilya Shmulevich, Wei Zhang:
Binary analysis and optimization-based normalization of gene expression data.
555-565 BibTeX
- 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 BibTeX
- David C. Hoyle, Magnus Rattray, Ray Jupp, Andy Brass:
Making sense of microarray data distributions.
576-584 BibTeX
- 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 BibTeX
- Daniel Aguilar, Baldomero Oliva, Francesc X. Avilés, Enrique Querol:
TranScout: prediction of gene expression regulatory proteins from their sequences.
597-607 BibTeX
- 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 BibTeX
- Mauro Delorenzi, Terence P. Speed:
An HMM model for coiled-coil domains and a comparison with PSSM-based predictions.
617-625 BibTeX
Discovery Notes
Applications Notes
- Loïc Ponger, Dominique Mouchiroud:
CpGProD: identifying CpG islands associated with transcription start sites in large genomic mammalian sequences.
631-633 BibTeX
- Adalberto T. Castelo, Wellington Martins, Guang R. Gao:
TROLL-Tandem Repeat Occurrence Locator.
634-636 BibTeX
- Maria Elena Ochagavia, Jean Richelle, Shoshana J. Wodak:
Advanced pairwise structure alignments of proteins and analysis of conformational changes.
637-640 BibTeX
- M. Madan Babu, K. Sankaran:
DOLOP-database of bacterial lipoproteins.
641-643 BibTeX
- Filippo Rusconi, Maya Belghazi:
Desktop prediction/analysis of mass spectrometric data in proteomic projects by using massXpert.
644-645 BibTeX
- Coral del Val, Peter Ernst, Rüdiger Bräuning, Karl-Heinz Glatting, Sándor Suhai:
PATH: a task for the inference of phylogenies.
646-647 BibTeX
Volume 18,
Number 5,
May 2002
Editorial
Original Papers
- Jacek Blazewicz, Piotr Formanowicz, Frédéric Guinand, Marta Kasprzak:
A heuristic managing errors for DNA sequencing.
652-660 BibTeX
- Zhou Yu, Tao Li, Jindong Zhao, Jingchu Luo:
PGAAS: a prokaryotic genome assembly assistant system.
661-665 BibTeX
- Yu-hua Hao, Zheng Tan:
The generation of long telomere overhangs in human cells: a model and its implication.
666-671 BibTeX
- M. Mar Albà, Roman A. Laskowski, John M. Hancock:
Detecting cryptically simple protein sequences using the SIMPLE algorithm.
672-678 BibTeX
- Olga G. Troyanskaya, Ora Arbell, Yair Koren, Gad M. Landau, Alexander Bolshoy:
Sequence complexity profiles of prokaryotic genomic sequences: A fast algorithm for calculating linguistic complexity.
679-688 BibTeX
- Nela Zavaljevski, Fred J. Stevens, Jaques Reifman:
Support vector machines with selective kernel scaling for protein classification and identification of key amino acid positions.
689-696 BibTeX
- Ernesto Estrada:
Characterization of the folding degree of proteins.
697-704 BibTeX
- T. Oyama, K. Kitano, Kenji Satou, T. Ito:
Extraction of knowledge on protein-protein interaction by association rule discovery.
705-714 BibTeX
- Suzanne M. Paley, Peter D. Karp:
Evaluation of computational metabolic-pathway predictions for Helicobacter pylori.
715-724 BibTeX
- Jinyan Li, Limsoon Wong:
Identifying good diagnostic gene groups from gene expression profiles using the concept of emerging patterns.
725-734 BibTeX
- Frank De Smet, Janick Mathys, Kathleen Marchal, Gert Thijs, Bart De Moor, Yves Moreau:
Adaptive quality-based clustering of gene expression profiles.
735-746 BibTeX
- Daniel Bozinov, Jörg Rahnenführer:
Unsupervised technique for robust target separation and analysis of DNA microarray spots through adaptive pixel clustering.
747-756 BibTeX
- Wasco Wruck, Huw Griffiths, Matthias Steinfath, Hans Lehrach, Uwe Radelof, John O'Brien:
Xdigitise: visualization of hybridization experiments.
757-760 BibTeX
Applications Notes
- Wei Zhu, Volker Brendel:
Gene structure identification with MyGV using cDNA evidence and protein homologs to improve ab initio predictions.
761-762 BibTeX
- Vincent Lombard, E. B. Camon, Helen E. Parkinson, Pascal Hingamp, Guenter Stoesser, Nicole Redaschi:
EMBL-Align: a new public nucleotide and amino acid multiple sequence alignment database.
763-764 BibTeX
- Jeffrey D. Grant, Roland L. Dunbrack Jr., Frank J. Manion, Michael F. Ochs:
BeoBLAST: distributed BLAST and PSI-BLAST on a Beowulf cluster.
765-766 BibTeX
- Patrice Gouet, Emmanuel Courcelle:
ENDscript: a workflow to display sequence and structure information.
767-768 BibTeX
- Flavio Monigatti, Elisabeth Gasteiger, Amos Bairoch, Eva Jung:
The Sulfinator: predicting tyrosine sulfation sites in protein sequences.
769-770 BibTeX
- M. R. Fielden, R. G. Halgren, E. Dere, T. R. Zacharewski:
GP3: GenePix post-processing program for automated analysis of raw microarray data.
771-773 BibTeX
- Mary E. Edgerton, Ronald C. Taylor, John I. Powell, Lawrence Hunter, Richard Simon, Edison T. Liu:
A bioinformatics tool to select sequences for microarray studies of mouse models of oncogenesis.
774-775 BibTeX
Volume 18,
Number 6,
June 2002
Original Papers
- Burkhard Morgenstern, Oliver Rinner, Saïd Abdeddaïm, Dirk Haase, Klaus F. X. Mayer, Andreas W. M. Dress, Hans-Werner Mewes:
Exon discovery by genomic sequence alignment.
777-787 BibTeX
- A. Raval, Zoubin Ghahramani, David L. Wild:
A Bayesian network model for protein fold and remote homologue recognition.
788-801 BibTeX
- Ingolf Sommer, Alexander Zien, Niklas von Öhsen, Ralf Zimmer, Thomas Lengauer:
Confidence measures for protein fold recognition.
802-812 BibTeX
- A. C. M. Luyf, J. de Gast, Antoine H. C. van Kampen:
Visualizing metabolic activity on a genome-wide scale.
813-818 BibTeX
- Shandar Ahmad, M. Michael Gromiha:
NETASA: neural network based prediction of solvent accessibility.
819-824 BibTeX
- Mor Peleg, Iwei Yeh, Russ B. Altman:
Modelling biological processes using workflow and Petri Net models.
825-837 BibTeX
- A. M. Leontovich, L. I. Brodsky, V. A. Drachev, V. K. Nikolaev:
Adaptive algorithm of automated annotation.
838-844 BibTeX
- Maximilian Schlosshauer, Mattias Ohlsson:
A novel approach to local reliability of sequence alignments.
847-854 BibTeX
- Upinder S. Bhalla:
The chemical organization of signaling interactions.
855-863 BibTeX
- Yi-Kuo Yu, Ralf Bundschuh, Terence Hwa:
Hybrid alignment: high-performance with universal statistics.
864-872 BibTeX
- Eldar Giladi, Michael G. Walker, James Ze Wang, Wayne Volkmuth:
SST: an algorithm for finding near-exact sequence matches in time proportional to the logarithm of the database size.
873-877 BibTeX
Discovery Notes
- Ehud Gazit:
Global analysis of tandem aromatic octapeptide repeats: The significance of the aromatic-glycine motif.
880-883 BibTeX
Applications Notes
Volume 18,
Number 7,
July 2002
Structural Genomics
- Burkhard Rost, Barry Honig, Alfonso Valencia:
Bioinformatics in structural genomics - Editorial.
897 BibTeX
- Elon Portugaly, Ilona Kifer, Michal Linial:
Selecting targets for structural determination by navigating in a graph of protein families.
899-907 BibTeX
- Federico Abascal, Alfonso Valencia:
Clustering of proximal sequence space for the identification of protein families.
908-921 BibTeX
- Jinfeng Liu, Burkhard Rost:
Target space for structural genomics revisited.
922-933 BibTeX
- Manuel C. Peitsch:
About the use of protein models.
934-938 BibTeX
- Xavier Fradera, Xavier de la Cruz, Carlos H. T. P. Silva, Josep Lluis Gelpí, F. Javier Luque, Modesto Orozco:
Ligand-induced changes in the binding sites of proteins.
939-948 BibTeX
Original Papers
- G. Charles Ostermeier, David J. Dix, Stephen A. Krawetz:
A bioinformatic strategy to rapidly characterize cDNA libraries.
949-952 BibTeX
- J. M. Dodson, P. T. Charles, D. A. Stenger, J. J. Pancrazio:
Quantitative assessment of filter-based cDNA microarrays: gene expression profiles of human T-lymphoma cell lines.
953-960 BibTeX
- Adam B. Olshen, Ajay N. Jain:
Deriving quantitative conclusions from microarray expression data.
961-970 BibTeX
- Fabrizio Lillo, Salvatore Basile, Rosario N. Mantegna:
Comparative genomics study of inverted repeats in bacteria.
971-979 BibTeX
- Alessandro Pintar, Oliviero Carugo, Sándor Pongor:
CX, an algorithm that identifies protruding atoms in proteins.
980-984 BibTeX
- Jerry Tsai, Mark Gerstein:
Calculations of protein volumes: sensitivity analysis and parameter database.
985-995 BibTeX
- Emek Demir, Ozgun Babur, Ugur Dogrusöz, Attila Gürsoy, Gurkan Nisanci, Rengül Çetin-Atalay, Mehmet Ozturk:
PATIKA: an integrated visual environment for collaborative construction and analysis of cellular pathways.
996-1003 BibTeX
- Jan-Jaap Wesselink, Beatriz de la Iglesia, Stephen A. James, Jo L. Dicks, Ian N. Roberts, Victor J. Rayward-Smith:
Determining a unique defining DNA sequence for yeast species using hashing techniques.
1004-1010 BibTeX
Applications Notes
Volume 18,
Number 8,
August 2002
Original Papers
- Pierre-François Baisnée, Steven Hampson, Pierre Baldi:
Why are complementary DNA strands symmetric?
1021-1033 BibTeX
- Sanja Rogic, B. F. Francis Ouellette, Alan K. Mackworth:
Improving gene recognition accuracy by combining predictions from two gene-finding programs.
1034-1045 BibTeX
- Atul A. Shah, Michael C. Giddings, Jasmin B. Parvaz, Raymond F. Gesteland, John F. Atkins, Ivaylo P. Ivanov:
Computational identification of putative programmed translational frameshift sites.
1046-1053 BibTeX
- Gregory Stephanopoulos, Daehee Hwang, William A. Schmitt, Jatin Misra, George Stephanopoulos:
Mapping physiological states from microarray expression measurements.
1054-1063 BibTeX
- Brad Love, David R. Rank, Sharron G. Penn, David A. Jenkins, Russell S. Thomas:
A conditional density error model for the statistical analysis of microarray data.
1064-1072 BibTeX
- Shuta Tomida, Taizo Hanai, Hiroyuki Honda, Takeshi Kobayashi:
Analysis of expression profile using fuzzy adaptive resonance theory.
1073-1083 BibTeX
- Bill C. H. Chang, Saman K. Halgamuge:
Protein motif extraction with neuro-fuzzy optimization.
1084-1090 BibTeX
- Pedro Gonnet, Frédérique Lisacek:
Probabilistic alignment of motifs with sequences.
1091-1101 BibTeX
- Nicola Cannata, Stefano Toppo, Chiara Romualdi, Giorgio Valle:
Simplifying amino acid alphabets by means of a branch and bound algorithm and substitution matrices.
1102-1108 BibTeX
- Zheng Yuan, Rohan D. Teasdale:
Prediction of Golgi Type II membrane proteins based on their transmembrane domains.
1109-1115 BibTeX
- Tal Pupko, Itsik Pe'er, Masami Hasegawa, Dan Graur, Nir Friedman:
A branch-and-bound algorithm for the inference of ancestral amino-acid sequences when the replacement rate varies among sites: Application to the evolution of five gene families.
1116-1123 BibTeX
- Lorraine K. Tanabe, W. John Wilbur:
Tagging gene and protein names in biomedical text.
1124-1132 BibTeX
Applications Notes
- Jeppe S. Spicker, Friedrik Wikman, Ming-Lan Lu, Carlos Cordon-Cardo, Christopher T. Workman, Torben F. Ørntoft, Søren Brunak, Steen Knudsen:
Neural network predicts sequence of TP53 gene based on DNA chip.
1133-1134 BibTeX
- Boris Lenhard, Wyeth W. Wasserman:
TFBS: Computational framework for transcription factor binding site analysis.
1135-1136 BibTeX
- Eyal Seroussi, Micha Ron, Darek Kedra:
ShiftDetector: detection of shift mutations.
1137-1138 BibTeX
- Junbai Wang, Vigdis Nygaard, Birgitte Smith-Sørensen, Eivind Hovig, Ola Myklebost:
MArray: analysing single, replicated or reversed microarray experiments.
1139-1140 BibTeX
- Bruno Contreras-Moreira, Paul A. Bates:
Domain Fishing: a first step in protein comparative modelling.
1141-1142 BibTeX
- Farid Chetouani, Philippe Glaser, Frank Kunst:
DiffTool: building, visualizing and querying protein clusters.
1143-1144 BibTeX
- Yuh-Jyh Hu:
The NCTU BioInfo Archive of biological data sets for bioinformatics research and experimentation.
1145-1146 BibTeX
- Lichun Wang, Jean-Jack M. Riethoven, Alan J. Robinson:
XEMBL: distributing EMBL data in XML format.
1147-1148 BibTeX
- Evgeni M. Zdobnov, Rodrigo Lopez, Rolf Apweiler, Thure Etzold:
The EBI SRS server-new features.
1149-1150 BibTeX
Volume 18,
Number 9,
September 2002
Original Papers
- Koichi Nishigaki, Ayumu Saito:
Genome structures embossed by oligonucleotide-stickiness.
1153-1161 BibTeX
- Allen J. Gavin, Todd E. Scheetz, Chad A. Roberts, Brian O'Leary, Terry A. Braun, Val C. Sheffield, Marcelo Bento Soares, John P. Robinson, Thomas L. Casavant:
Pooled library tissue tags for EST-based gene discovery.
1162-1166 BibTeX
- Sündüz Keles, Mark J. van der Laan, Michael B. Eisen:
Identification of regulatory elements using a feature selection method.
1167-1175 BibTeX
- S. A. Rifkin, J. Kim:
Geometry of gene expression dynamics.
1176-1183 BibTeX
- Daehee Hwang, William A. Schmitt, George Stephanopoulos, Gregory Stephanopoulos:
Determination of minimum sample size and discriminatory expression patterns in microarray data.
1184-1193 BibTeX
- Mario Medvedovic, Siva Sivaganesan:
Bayesian infinite mixture model based clustering of gene expression profiles.
1194-1206 BibTeX
- Yidong Chen, Vishnu Kamat, Edward R. Dougherty, Michael L. Bittner, Paul S. Meltzer, Jeffrey M. Trent:
Ratio statistics of gene expression levels and applications to microarray data analysis.
1207-1215 BibTeX
- Danh V. Nguyen, David M. Rocke:
Multi-class cancer classification via partial least squares with gene expression profiles.
1216-1226 BibTeX
- Robert F. Stengel, Raffaele M. Ghigliazza, Nilesh V. Kulkarni:
Optimal enhancement of immune response.
1227-1235 BibTeX
- Yonil Park, John L. Spouge:
The correlation error and finite-size correction in an ungapped sequence alignment.
1236-1242 BibTeX
- Sam Griffiths-Jones, Alex Bateman:
The use of structure information to increase alignment accuracy does not aid homologue detection with profile HMMs.
1243-1249 BibTeX
- Christophe G. Lambert, Nadia Léonard, Xavier De Bolle, Eric Depiereux:
ESyPred3D: Prediction of proteins 3D structures.
1250-1256 BibTeX
- Ville-Veikko Rantanen, Mats Gyllenberg, Timo Koski, Mark S. Johnson:
A dissimilarity matrix between protein atom classes based on Gaussian mixtures.
1257-1263 BibTeX
Applications Notes
- Nick Moseyko, Lewis J. Feldman:
VIZARD: analysis of Affymetrix Arabidopsis GeneChi® data.
1264-1265 BibTeX
- Meena K. Sakharkar, Pandjassarame Kangueane, Dmitri A. Petrov, Ashok S. Kolaskar, S. Subbiah:
SEGE: A database on 'intron less/single exonic' genes from eukaryotes.
1266-1267 BibTeX
- Yan Zhou, Guyang Matthew Huang, Liping Wei:
UniBLAST: a system to filter, cluster, and display BLAST results and assign unique gene annotation.
1268 BibTeX
- Jens Kleinjung, Nigel Douglas, Jaap Heringa:
Parallelized multiple alignment.
1270-1271 BibTeX
- Volker Hollich, Christian E. V. Storm, Erik L. L. Sonnhammer:
OrthoGUI: graphical presentation of Orthostrapper results.
1272-1273 BibTeX
- Oleksandr V. Buzko, Kevan M. Shokat:
A kinase sequence database: sequence alignments and family assignment.
1274-1275 BibTeX
- Iddo Friedberg, Hanah Margalit:
PeCoP: automatic determination of persistently conserved positions in protein families.
1276-1277 BibTeX
- Patrick McConnell, Kimberly F. Johnson, Simon M. Lin:
Applications of Tree-Maps to hierarchical biological data.
1278-1279 BibTeX
- Douglas S. Greer, John D. Westbrook, Philip E. Bourne:
An ontology driven architecture for derived representations of macromolecular structure.
1280-1281 BibTeX
Erratum
Volume 18,
Number 10,
October 2002
SAC 2002 Paper
Original Papers
- Irmtraud M. Meyer, Richard Durbin:
Comparative ab initio prediction of gene structures using pair HMMs.
1309-1318 BibTeX
- Ilya Shmulevich, Edward R. Dougherty, Wei Zhang:
ayesian automatic relevance determination algorithms for classifying gene expression data.
1332-1339 BibTeX
- Lars Kaderali, Alexander Schliep:
Selecting signature oligonucleotides to identify organisms using DNA arrays.
1340-1349 BibTeX
- Kuang Lin, Alex C. W. May, William R. Taylor:
Threading Using Neural nEtwork (TUNE): the measure of protein sequence-structure compatibility.
1350-1357 BibTeX
- Ovidiu Ivanciuc, Catherine H. Schein, Werner Braun:
Data mining of sequences and 3D structures of allergenic proteins.
1358-1364 BibTeX
- Brendan J. McConkey, Vladimir Sobolev, Marvin Edelman:
Quantification of protein surfaces, volumes and atom-atom contacts using a constrained Voronoi procedure.
1365-1373 BibTeX
- Uri Keich, Pavel A. Pevzner:
Finding motifs in the twilight zone.
1374-1381 BibTeX
- Uri Keich, Pavel A. Pevzner:
U Subtle motifs: defining the limits of motif finding algorithms.
1382-1390 BibTeX
Discovery Notes
Application Notes
Corrigendum
- Jinyan Li, Limsoon Wong:
Identifying good diagnostic gene groups from gene expression profiles using the concept of emerging patterns .
1406-1407 BibTeX
Volume 18,
Number 11,
November 2002
Editorial
- Catherine A. Ball, Gavin Sherlock, Helen E. Parkinson, Philippe Rocca-Serra, Catherine Brooksbank, Helen C. Causton, Duccio Cavalieri, Terry Gaasterland, Pascal Hingamp, Frank Holstege, Martin Ringwald, Paul T. Spellman, Christian J. Stoeckert Jr., Jason E. Stewart, Ronald Taylor, Alvis Brazma, John Quackenbush:
An open letter to the scientific journals.
1409 BibTeX
Original Papers
- Amit V. Kulkarni, Noelle Sevilir Williams, Yun Lian, Jonathan D. Wren, David Mittelman, Alexander Pertsemlidis, Harold R. Garner:
ARROGANT: an application to manipulate large gene collections.
1410-1417 BibTeX
- Nikola Stojanovic, Jean L. Chang, Jessica Lehoczky, Michael C. Zody, Ken Dewar:
Identification of mixups among DNA sequencing plates.
1418-1426 BibTeX
- Long-Cheng Li, Rajvir Dahiya:
MethPrimer: designing primers for methylation PCRs.
1427-1431 BibTeX
- Dong Xu, Guangshan Li, Liyou Wu, Jizhong Zhou, Ying Xu:
PRIMEGENS: robust and efficient design of gene-specific probes for microarray analysis.
1432-1437 BibTeX
- Kevin Dobbin, Richard Simon:
Comparison of microarray designs for class comparison and class discovery.
1438-1445 BibTeX
- Seferina Mavroudi, Stergios Papadimitriou, Anastasios Bezerianos:
Gene expression data analysis with a dynamically extended self-organized map that exploits class information.
1446-1453 BibTeX
- Olga G. Troyanskaya, Mitchell E. Garber, Patrick O. Brown, David Botstein, Russ B. Altman:
Nonparametric methods for identifying differentially expressed genes in microarray data.
1454-1461 BibTeX
- Lisa M. McShane, Michael D. Radmacher, Boris Freidlin, Ren Yu, Ming-Chung Li, Richard Simon:
Methods for assessing reproducibility of clustering patterns observed in analyses of microarray data.
1462-1469 BibTeX
- William J. Lemon, Jeffrey J. T. Palatini, Ralf Krahe, Fred A. Wright:
Theoretical and experimental comparisons of gene expression indexes for oligonucleotide arrays.
1470-1476 BibTeX
- Michiel J. L. de Hoon, Seiya Imoto, Satoru Miyano:
Statistical analysis of a small set of time-ordered gene expression data using linear splines.
1477-1485 BibTeX
- Ashish Bhan, David J. Galas, T. Gregory Dewey:
A duplication growth model of gene expression networks.
1486-1493 BibTeX
- Jonathan M. Keith, Peter Adams, Darryn E. Bryant, Dirk P. Kroese, Keith R. Mitchelson, Duncan A. E. Cochran, Gita H. Lala:
A simulated annealing algorithm for finding consensus sequences.
1494-1499 BibTeX
- J. T. Reese, William R. Pearson:
Empirical determination of effective gap penalties for sequence comparison.
1500-1507 BibTeX
- Harpreet Kaur, G. P. S. Raghava:
An evaluation of ß-turn prediction methods.
1508-1514 BibTeX
- Julie E. Leonard, Jeffrey B. Colombe, Joshua L. Levy:
Finding relevant references to genes and proteins in Medline using a Bayesian approach.
1515-1522 BibTeX
- Vyacheslav N. Grishin, Nick V. Grishin:
Euclidian space and grouping of biological objects.
1523-1534 BibTeX
Discovery Notes
- Stefan Janecek:
A motif of a microbial starch-binding domain found in human genethonin.
1534-1537 BibTeX
Applications Notes
- Sheldon J. McKay, Steven J. M. Jones:
AcePrimer: automation of PCR primer design based on gene structure.
1538-1539 BibTeX
- Carlo Colantuoni, George Henry, Scott Zeger, Jonathan Pevsner:
SNOMAD (Standardization and NOrmalization of MicroArray Data): web-accessible gene expression data analysis.
1540-1541 BibTeX
- Marilyn Safran, Irina Solomon, Orit Shmueli, Michal Lapidot, Shai Shen-Orr, Avital Adato, Uri Ben-Dor, Nir Esterman, Naomi Rosen, Inga Peter, Tsviya Olender, Vered Chalifa-Caspi, Doron Lancet:
GeneCardsTM 2002: towards a complete, object-oriented, human gene compendium.
1542-1543 BibTeX
- Angelika Ehlers, John Osborne, Stephanie Slack, Rachel L. Roper, Chris Upton:
Poxvirus Orthologous Clusters (POCs).
1544-1545 BibTeX
- Kevin L. Howe, Alex Bateman, Richard Durbin:
QuickTree: building huge Neighbour-Joining trees of protein sequences.
1546-1547 BibTeX
- S. S. Sheik, Prasanna Sundararajan, A. S. Z. Hussain, Krishna Sekar:
Ramachandran plot on the web.
1548-1549 BibTeX
Volume 18,
Number 12,
December 2002
Editorial
Reviews
Discovery Notes
Original Papers
- Alistair M. Chalk, Erik L. L. Sonnhammer:
Computational antisense oligo prediction with a neural network model.
1567-1575 BibTeX
- Peter J. Park, Atul J. Butte, Isaac S. Kohane:
Comparing expression profiles of genes with similar promoter regions.
1576-1584 BibTeX
- Earl Hubbell, Wei-Min Liu, Rui Mei:
Robust estimators for expression analysis.
1585-1592 BibTeX
- Wei-Min Liu, Rui Mei, Xiaojun Di, Thomas B. Ryder, Earl Hubbell, S. Dee, Teresa A. Webster, C. A. Harrington, Ming-Hsiu Ho, J. Baid, S. P. Smeekens:
Analysis of high density expression microarrays with signed-rank call algorithms.
1593-1599 BibTeX
- Aedín C. Culhane, Guy Perrière, Elizabeth C. Considine, Thomas G. Cotter, Desmond G. Higgins:
Between-group analysis of microarray data.
1600-1608 BibTeX
- Michael A. Black, R. W. Doerge:
Calculation of the minimum number of replicate spots required for detection of significant gene expression fold change in microarray experiments.
1609-1616 BibTeX
- Ann-Marie Martoglio, James W. Miskin, Stephen K. Smith, David J. C. MacKay:
A decomposition model to track gene expression signatures: preview on observer-independent classification of ovarian cancer.
1617-1624 BibTeX
- Danh V. Nguyen, David M. Rocke:
Partial least squares proportional hazard regression for application to DNA microarray survival data.
1625-1632 BibTeX
- R. Sásik, E. Calvo, Jacques Corbeil:
Statistical analysis of high-density oligonucleotide arrays: a multiplicative noise model.
1633-1640 BibTeX
- Walter R. Gilks, Benjamin Audit, Daniela De Angelis, Sophia Tsoka, Christos A. Ouzounis:
Modeling the percolation of annotation errors in a database of protein sequences.
1641-1649 BibTeX
- An-Suei Yang, Lu-Yong Wang:
Local structure-based sequence profile database for local and global protein structure predictions.
1650-1657 BibTeX
- An-Suei Yang:
Structure-dependent sequence alignment for remotely related proteins.
1658-1665 BibTeX
- Adrian J. Shepherd, Nigel J. Martin, Roger G. Johnson, Paul Kellam, Christine A. Orengo:
PFDB: a generic protein family database integrating the CATH domain structure database with sequence based protein family resources.
1666-1672 BibTeX
- Mikhail A. Roytberg, Aleksey Y. Ogurtsov, Svetlana A. Shabalina, Alexey S. Kondrashov:
A hierarchical approach to aligning collinear regions of genomes.
1673-1680 BibTeX
- Alberto Riva, Isaac S. Kohane:
SNPper: retrieval and analysis of human SNPs.
1681-1685 BibTeX
Applications Notes
- Ralf Mrowka, Johannes Schuchhardt, Christoph Gille:
Oligodb-interactive design of oligo DNA for transcription profiling of human genes.
1686-1687 BibTeX
- Xiayi Ke, Andrew Collins, Shu Ye:
PCR designer for restriction analysis of various types of sequence mutation.
1688-1689 BibTeX
- Jianghui Hou:
Design of endonuclease restriction sites into primers for PCR cloning.
1690-1691 BibTeX
- R. Everitt, S. E. Minnema, M. A. Wride, C. S. Koster, J. E. Hance, F. C. Mansergh, D. E. Rancourt:
RED: the analysis, management and dissemination of expressed sequence tags.
1692-1693 BibTeX
- Jing Hua Zhao, Sebastien Lissarrague, Laurent Essioux, Pak Chung Sham:
GENECOUNTING: haplotype analysis with missing genotypes.
1694-1695 BibTeX
- Xin Chen, Ming Li, Bin Ma, John Tromp:
DNACompress: fast and effective DNA sequence compression.
1696-1698 BibTeX
- Li Zhi Sun, Zhi Liang Ji, Xin Chen, J. F. Wang, Yu Zong Chen:
ADME-AP: a database of ADME associated proteins.
1699-1700 BibTeX
- Jean Marc Kwasigroch, Dimitri Gilis, Yves Dehouck, Marianne Rooman:
PoPMuSiC, rationally designing point mutations in protein structures.
1701-1702 BibTeX
- Aleksey Y. Ogurtsov, Mikhail A. Roytberg, Svetlana A. Shabalina, Alexey S. Kondrashov:
OWEN: aligning long collinear regions of genomes.
1703-1704 BibTeX
- Junko Tanoue, Masatoshi Yoshikawa, Shunsuke Uemura:
The GeneAround GO viewer.
1705-1706 BibTeX
Supplements
Proceedings of the Tenth International Conference on Intelligent Systems for Molecular Biology, August 3-7, 2002, Edmondon, Alberta, Canada.
2002
Contents BibTeX
Proceedings of the European Conference on Computational Biology (ECCB 2002), October 6-9, 2002, Saarbrücken, Germnany.
2002
Contents BibTeX
Copyright © Sat May 16 23:51:27 2009
by Michael Ley (ley@uni-trier.de)
