BMC Bioinformatics, Volume 3

Volume 3, 2002

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