Volume 3, issue 1, December 2002
40 articles in this issue
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Species-specific protein sequence and fold optimizations
Authors
- Michel Dumontier
- Katerina Michalickova
- Christopher WV Hogue
- Content type: Research article
- Open Access
- Published: 17 December 2002
- Article: 39
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Quantifying robustness of biochemical network models
Authors
- Lan Ma
- Pablo A Iglesias
- Content type: Research article
- Open Access
- Published: 13 December 2002
- Article: 38
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Total sequence decomposition distinguishes functional modules, "molegos" in apurinic/apyrimidinic endonucleases
Authors (first, second and last of 4)
- Catherine H Schein
- Numan Özgün
- Werner Braun
- Content type: Research article
- Open Access
- Published: 25 November 2002
- Article: 37
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Clustering of the SOM easily reveals distinct gene expression patterns: results of a reanalysis of lymphoma study
Authors (first, second and last of 5)
- Junbai Wang
- Jan Delabie
- Ola Myklebost
- Content type: Research article
- Open Access
- Published: 24 November 2002
- Article: 36
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FunSpec: a web-based cluster interpreter for yeast
Authors (first, second and last of 4)
- Mark D Robinson
- Jörg Grigull
- Timothy R Hughes
- Content type: Methodology article
- Open Access
- Published: 13 November 2002
- Article: 35
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Automated modelling of signal transduction networks
Authors (first, second and last of 5)
- Martin Steffen
- Allegra Petti
- George Church
- Content type: Research article
- Open Access
- Published: 01 November 2002
- Article: 34
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Development and production of an oligonucleotide MuscleChip: use for validation of ambiguous ESTs
Authors (first, second and last of 7)
- Rehannah HA Borup
- Stefano Toppo
- Eric P Hoffman
- Content type: Research article
- Open Access
- Published: 29 October 2002
- Article: 33
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SeqHound: biological sequence and structure database as a platform for bioinformatics research
Authors (first, second and last of 7)
- Katerina Michalickova
- Gary D Bader
- Christopher WV Hogue
- Content type: Methodology article
- Open Access
- Published: 25 October 2002
- Article: 32
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Making sense of EST sequences by CLOBBing them
Authors
- John Parkinson
- David B Guiliano
- Mark Blaxter
- Content type: Research article
- Open Access
- Published: 25 October 2002
- Article: 31
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Computational detection of genomic cis- regulatory modules applied to body patterning in the early Drosophila embryo
Authors (first, second and last of 4)
- Nikolaus Rajewsky
- Massimo Vergassola
- Eric D Siggia
- Content type: Research article
- Open Access
- Published: 24 October 2002
- Article: 30
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Simulation of DNA array hybridization experiments and evaluation of critical parameters during subsequent image and data analysis
Authors (first, second and last of 8)
- Christoph K Wierling
- Matthias Steinfath
- Ralf Herwig
- Content type: Research article
- Open Access
- Published: 22 October 2002
- Article: 29
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Efficient Boolean implementation of universal sequence maps (bUSM)
Authors
- John Schwacke
- Jonas S Almeida
- Content type: Methodology article
- Open Access
- Published: 21 October 2002
- Article: 28
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Oliz, a suite of Perl scripts that assist in the design of microarrays using 50mer oligonucleotides from the 3' untranslated region
Authors
- Hao Chen
- Burt M Sharp
- Content type: Methodology article
- Open Access
- Published: 06 October 2002
- Article: 27
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Expression profiling of human renal carcinomas with functional taxonomic analysis
Authors (first, second and last of 6)
- Michael A Gieseg
- Theresa Cody
- Eric P Kaldjian
- Content type: Research article
- Open Access
- Published: 30 September 2002
- Article: 26
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Prediction of MHC class I binding peptides, using SVMHC
Authors
- Pierre Dönnes
- Arne Elofsson
- Content type: Research article
- Open Access
- Published: 11 September 2002
- Article: 25
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The functional importance of disease-associated mutation
Authors
- Sean D Mooney
- Teri E Klein
- Content type: Research article
- Open Access
- Published: 09 September 2002
- Article: 24
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Computational method for reducing variance with Affymetrix microarrays
Authors
- Stephen Welle
- Andrew I Brooks
- Charles A Thornton
- Content type: Research article
- Open Access
- Published: 30 August 2002
- Article: 23
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Microarray results: how accurate are they?
Authors (first, second and last of 4)
- Ravi Kothapalli
- Sean J Yoder
- Thomas P Loughran Jr
- Content type: Research article
- Open Access
- Published: 23 August 2002
- Article: 22
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The SGS3 protein involved in PTGS finds a family
Authors
- Alex Bateman
- Content type: Research article
- Open Access
- Published: 05 August 2002
- Article: 21
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Kangaroo – A pattern-matching program for biological sequences
Authors
- Doron Betel
- Christopher WV Hogue
- Content type: Methodology article
- Open Access
- Published: 31 July 2002
- Article: 20
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Visualizing the genome: techniques for presenting human genome data and annotations
Authors
- Ann E Loraine
- Gregg A Helt
- Content type: Methodology article
- Open Access
- Published: 30 July 2002
- Article: 19
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A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure
Authors
- Sean R Eddy
- Content type: Research article
- Open Access
- Published: 02 July 2002
- Article: 18
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The limit fold change model: A practical approach for selecting differentially expressed genes from microarray data
Authors (first, second and last of 5)
- David M Mutch
- Alvin Berger
- Matthew-Alan Roberts
- Content type: Methodology article
- Published: 21 June 2002
- Article: 17
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Identifying functional relationships among human genes by systematic analysis of biological literature
Authors
- Yong-Chuan Tao
- Rudolph L Leibel
- Content type: Research article
- Published: 07 June 2002
- Article: 16
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Erratum to: The Comparative RNA Web (CRW) Site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs: Correction
Authors (first, second and last of 14)
- Jamie J Cannone
- Sankar Subramanian
- Robin R Gutell
- Content type: Erratum
- Published: 31 May 2002
- Article: 15
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RIO: Analyzing proteomes by automated phylogenomics using resampled inference of orthologs
Authors
- Christian M Zmasek
- Sean R Eddy
- Content type: Methodology article
- Published: 16 May 2002
- Article: 14
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NBLAST: a cluster variant of BLAST for NxN comparisons
Authors
- Michel Dumontier
- Christopher WV Hogue
- Content type: Methodology article
- Published: 08 May 2002
- Article: 13
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CoreGenes: A computational tool for identifying and cataloging "core" genes in a set of small genomes
Authors
- Nikhat Zafar
- Raja Mazumder
- Donald Seto
- Content type: Methodology article
- Published: 24 April 2002
- Article: 12
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Homology Induction: the use of machine learning to improve sequence similarity searches
Authors
- Andreas Karwath
- Ross D King
- Content type: Methodology article
- Published: 23 April 2002
- Article: 11
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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
Authors
- Janusz M Bujnicki
- Leszek Rychlewski
- Content type: Research article
- Published: 03 April 2002
- Article: 10
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An algorithm and program for finding sequence specific oligo-nucleotide probes for species identification
Authors
- Alexander E Pozhitkov
- Diethard Tautz
- Content type: Research article
- Published: 06 March 2002
- Article: 9
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tacg – a grep for DNA
Authors
- Harry J Mangalam
- Content type: Methodology article
- Published: 06 March 2002
- Article: 8
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Correlating overrepresented upstream motifs to gene expression: a computational approach to regulatory element discovery in eukaryotes
Authors
- Michele Caselle
- Ferdinando Di Cunto
- Paolo Provero
- Content type: Methodology article
- Published: 14 February 2002
- Article: 7
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Universal sequence map (USM) of arbitrary discrete sequences
Authors
- Jonas S Almeida
- Susana Vinga
- Content type: Methodology article
- Published: 05 February 2002
- Article: 6
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Re-annotation of genome microbial CoDing-Sequences: finding new genes and inaccurately annotated genes
Authors
- Stéphanie Bocs
- Antoine Danchin
- Claudine Médigue
- Content type: Research article
- Published: 05 February 2002
- Article: 5
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Sources of variability and effect of experimental approach on expression profiling data interpretation
Authors (first, second and last of 6)
- Marina Bakay
- Yi-Wen Chen
- Eric P Hoffman
- Content type: Research article
- Published: 31 January 2002
- Article: 4
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Match-Only Integral Distribution (MOID) Algorithm for high-density oligonucleotide array analysis
Authors
- Yingyao Zhou
- Ruben Abagyan
- Content type: Research article
- Published: 22 January 2002
- Article: 3
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The Comparative RNA Web (CRW) Site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs
Authors (first, second and last of 14)
- Jamie J Cannone
- Sankar Subramanian
- Robin R Gutell
- Content type: Research article
- Published: 17 January 2002
- Article: 2
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Identification and characterization of subfamily-specific signatures in a large protein superfamily by a hidden Markov model approach
Authors
- Kevin Truong
- Mitsuhiko Ikura
- Content type: Methodology article
- Published: 10 January 2002
- Article: 1