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Editor-in-Chief
Melissa Norton, MD Biology Editor
Penelope Webb, PhD In-house Editor
Tim Sands PhD
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| | BMC Bioinformatics, Volume 3 |
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Methodology article
 
ORFer  retrieval of protein sequences and open reading frames from GenBank and storage into relational databases or text files
Konrad B ssow, Steve Hoffmann, Volker Sievert
BMC Bioinformatics 2002, 3:40 (19December2002)
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Research article
Species-specific protein sequence and fold optimizations
Michel Dumontier, Katerina Michalickova, Christopher WV Hogue
BMC Bioinformatics 2002, 3:39 (17December2002)
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Research article
Quantifying robustness of biochemical network models
Lan Ma, Pablo A Iglesias
BMC Bioinformatics 2002, 3:38 (13December2002)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Total sequence decomposition distinguishes functional modules, "molegos" in apurinic/apyrimidinic endonucleases
Catherine H Schein, Numan  zgn, Tadahide Izumi, Werner Braun
BMC Bioinformatics 2002, 3:37 (25November2002)
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Research article
Clustering of the SOM easily reveals distinct gene expression patterns: results of a reanalysis of lymphoma study
Junbai Wang, Jan Delabie, Hans Christian Aasheim, Erlend Smeland, Ola Myklebost
BMC Bioinformatics 2002, 3:36 (24November2002)
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Methodology article
FunSpec: a web-based cluster interpreter for yeast
Mark D Robinson, J rg Grigull, Naveed Mohammad, Timothy R Hughes
BMC Bioinformatics 2002, 3:35 (13November2002)
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Research article
Automated modelling of signal transduction networks
Martin Steffen, Allegra Petti, John Aach, Patrik D'haeseleer, George Church
BMC Bioinformatics 2002, 3:34 (1November2002)
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Research article
Development and production of an oligonucleotide MuscleChip: use for validation of ambiguous ESTs
Rehannah HA Borup, Stefano Toppo, Yi-Wen Chen, Tanya M Teslovich, Gerolamo Lanfranchi, Giorgio Valle, Eric P Hoffman
BMC Bioinformatics 2002, 3:33 (29October2002)
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Methodology article
SeqHound: biological sequence and structure database as a platform for bioinformatics research
Katerina Michalickova, Gary D Bader, Michel Dumontier, Hao Lieu, Doron Betel, Ruth Isserlin, Christopher WV Hogue
BMC Bioinformatics 2002, 3:32 (25October2002)
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Research article
Making sense of EST sequences by CLOBBing them
John Parkinson, David B Guiliano, Mark Blaxter
BMC Bioinformatics 2002, 3:31 (25October2002)
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Research article
Computational detection of genomic cis-regulatory modules applied to body patterning in the early Drosophila embryo
Nikolaus Rajewsky, Massimo Vergassola, Ulrike Gaul, Eric D Siggia
BMC Bioinformatics 2002, 3:30 (24October2002)
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Research article
Simulation of DNA array hybridization experiments and evaluation of critical parameters during subsequent image and data analysis
Christoph K Wierling, Matthias Steinfath, Thorsten Elge, Steffen Schulze-Kremer, Pia Aanstad, Matthew Clark, Hans Lehrach, Ralf Herwig
BMC Bioinformatics 2002, 3:29 (22October2002)
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Methodology article
Efficient Boolean implementation of universal sequence maps (bUSM)
John Schwacke, Jonas S Almeida
BMC Bioinformatics 2002, 3:28 (21October2002)
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Methodology article
Oliz, a suite of Perl scripts that assist in the design of microarrays using 50mer oligonucleotides from the 3' untranslated region
Hao Chen, Burt M Sharp
BMC Bioinformatics 2002, 3:27 (6October2002)
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Research article
Expression profiling of human renal carcinomas with functional taxonomic analysis
Michael A Gieseg, Theresa Cody, Michael Z Man, Steven J Madore, Mark A Rubin, Eric P Kaldjian
BMC Bioinformatics 2002, 3:26 (30September2002)
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Research article
Prediction of MHC class I binding peptides, using SVMHC
Pierre Dnnes, Arne Elofsson
BMC Bioinformatics 2002, 3:25 (11September2002)
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Research article
The functional importance of disease-associated mutation
Sean D Mooney, Teri E Klein
BMC Bioinformatics 2002, 3:24 (9September2002)
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Research article
Computational method for reducing variance with Affymetrix microarrays
Stephen Welle, Andrew I Brooks, Charles A Thornton
BMC Bioinformatics 2002, 3:23 (30August2002)
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Research article
Microarray results: how accurate are they?
Ravi Kothapalli, Sean J Yoder, Shrikant Mane, Thomas P Loughran Jr
BMC Bioinformatics 2002, 3:22 (23August2002)
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Research article
The SGS3 protein involved in PTGS finds a family
Alex Bateman
BMC Bioinformatics 2002, 3:21 (5August2002)
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Methodology article
Kangaroo A pattern-matching program for biological sequences
Doron Betel, Christopher WV Hogue
BMC Bioinformatics 2002, 3:20 (31July2002)
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Methodology article
Visualizing the genome: techniques for presenting human genome data and annotations
Ann E Loraine, Gregg A Helt
BMC Bioinformatics 2002, 3:19 (30July2002)
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Research article
A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure
Sean R Eddy
BMC Bioinformatics 2002, 3:18 (2July2002)
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Methodology article
The limit fold change model: A practical approach for selecting differentially expressed genes from microarray data
David M Mutch, Alvin Berger, Robert Mansourian, Andreas Rytz, Matthew-Alan Roberts
BMC Bioinformatics 2002, 3:17 (21June2002)
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Research article
Identifying functional relationships among human genes by systematic analysis of biological literature
Yong-Chuan Tao, Rudolph L Leibel
BMC Bioinformatics 2002, 3:16 (7June2002)
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Correction
The Comparative RNA Web (CRW) Site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs: Correction
Jamie J Cannone, Sankar Subramanian, Murray N Schnare, James R Collett, Lisa M D'Souza, Yushi Du, Brian Feng, Nan Lin, Lakshmi V Madabusi, Kirsten M Mller, Nupur Pande, Zhidi Shang, Nan Yu, Robin R Gutell
BMC Bioinformatics 2002, 3:15 (31May2002)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
RIO: Analyzing proteomes by automated phylogenomics using resampled inference of orthologs
Christian M Zmasek, Sean R Eddy
BMC Bioinformatics 2002, 3:14 (16May2002)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
NBLAST: a cluster variant of BLAST for NxN comparisons
Michel Dumontier, Christopher WV Hogue
BMC Bioinformatics 2002, 3:13 (8May2002)
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Methodology article
CoreGenes: A computational tool for identifying and cataloging "core" genes in a set of small genomes
Nikhat Zafar, Raja Mazumder, Donald Seto
BMC Bioinformatics 2002, 3:12 (24April2002)
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Methodology article
Homology Induction: the use of machine learning to improve sequence similarity searches
Andreas Karwath, Ross D King
BMC Bioinformatics 2002, 3:11 (23April2002)
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Research article
RNA:(guanine-N2) methyltransferases RsmC/RsmD and their homologs revisited bioinformatic analysis and prediction of the active site based on the uncharacterized Mj0882 protein structure
Janusz M Bujnicki, Leszek Rychlewski
BMC Bioinformatics 2002, 3:10 (3April2002)
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Research article
An algorithm and program for finding sequence specific oligo-nucleotide probes for species identification
Alexander E Pozhitkov, Diethard Tautz
BMC Bioinformatics 2002, 3:9 (6March2002)
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Methodology article
tacg a grep for DNA
Harry J Mangalam
BMC Bioinformatics 2002, 3:8 (6March2002)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Correlating overrepresented upstream motifs to gene expression: a computational approach to regulatory element discovery in eukaryotes
Michele Caselle, Ferdinando Di Cunto, Paolo Provero
BMC Bioinformatics 2002, 3:7 (14February2002)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Re-annotation of genome microbial CoDing-Sequences: finding new genes and inaccurately annotated genes
St phanie Bocs, Antoine Danchin, Claudine Mdigue
BMC Bioinformatics 2002, 3:5 (5February2002)
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Methodology article
Universal sequence map (USM) of arbitrary discrete sequences
Jonas S Almeida, Susana Vinga
BMC Bioinformatics 2002, 3:6 (5February2002)
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Research article
Sources of variability and effect of experimental approach on expression profiling data interpretation
Marina Bakay, Yi-Wen Chen, Rehannah Borup, Po Zhao, Kanneboyina Nagaraju, Eric P Hoffman
BMC Bioinformatics 2002, 3:4 (31January2002)
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Research article
Match-Only Integral Distribution (MOID) Algorithm for high-density oligonucleotide array analysis
Yingyao Zhou, Ruben Abagyan
BMC Bioinformatics 2002, 3:3 (22January2002)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
The Comparative RNA Web (CRW) Site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs
Jamie J Cannone, Sankar Subramanian, Murray N Schnare, James R Collett, Lisa M D'Souza, Yushi Du, Brian Feng, Nan Lin, Lakshmi V Madabusi, Kirsten M Mller, Nupur Pande, Zhidi Shang, Nan Yu, Robin R Gutell
BMC Bioinformatics 2002, 3:2 (17January2002)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Identification and characterization of subfamily-specific signatures in a large protein superfamily by a hidden Markov model approach
Kevin Truong, Mitsuhiko Ikura
BMC Bioinformatics 2002, 3:1 (10January2002)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
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