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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 - Jamie J. Cannone, Sankar Subramanian
The Comparative RNA Web (CRW) Site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. 2 - Yingyao Zhou, Ruben Abagyan:
Match-Only Integral Distribution (MOID) Algorithm for high-density oligonucleotide array analysis. 3 - 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 - Stéphanie Bocs, Antoine Danchin
Re-annotation of genome microbial CoDing-Sequences: finding new genes and inaccurately annotated genes. 5 - Jonas S. Almeida, Susana Vinga
Universal sequence map (USM) of arbitrary discrete sequences. 6 - Michele Caselle
Correlating overrepresented upstream motifs to gene expression: a computational approach to regulatory element discovery in eukaryotes. 7 - Harry Mangalam:
tacg - a grep for DNA. 8 - Alexander E. Pozhitkov
An algorithm and program for finding sequence specific oligo-nucleotide probes for species identification. 9 - 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 - Andreas Karwath
Homology Induction: the use of machine learning to improve sequence similarity searches. 11 - Nikhat Zafar, Raja Mazumder
CoreGenes: A computational tool for identifying and cataloging "core" genes in a set of small genomes. 12 - Michel Dumontier
NBLAST: a cluster variant of BLAST for NxN comparisons. 13 - Christian M. Zmasek, Sean R. Eddy
RIO: Analyzing proteomes by automated phylogenomics using resampled inference of orthologs. 14 - Jamie J. Cannone, Sankar Subramanian
The Comparative RNA Web (CRW) Site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs: Correction. 15 - Yong-Chuan Tao, Rudolph L. Leibel:
Identifying functional relationships among human genes by systematic analysis of biological literature. 16 - David M. Mutch
The limit fold change model: A practical approach for selecting differentially expressed genes from microarray data. 17 - Sean R. Eddy
A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure. 18 - Ann E. Loraine, Gregg A. Helt:
Visualizing the genome: techniques for presenting human genome data and annotations. 19 - Doron Betel
Kangaroo - A pattern-matching program for biological sequences. 20 - Alex Bateman
The SGS3 protein involved in PTGS finds a family. 21 - Ravi Kothapalli, Sean J. Yoder, Shrikant M. Mane, Thomas P. Loughran Jr.:
Microarray results: how accurate are they? 22 - Stephen Welle, Andrew I. Brooks, Charles A. Thornton:
Computational method for reducing variance with Affymetrix microarrays. 23 - Sean D. Mooney
The functional importance of disease-associated mutation. 24 - Pierre Dönnes
Prediction of MHC class I binding peptides, using SVMHC. 25 - Michael A. Gieseg, Theresa Cody, Michael Z. Man, Steven J. Madore, Mark A. Rubin
Expression profiling of human renal carcinomas with functional taxonomic analysis. 26 - 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 - John Schwacke, Jonas S. Almeida:
Efficient Boolean implementation of universal sequence maps (bUSM). 28 - Christoph K. Wierling
Simulation of DNA array hybridization experiments and evaluation of critical parameters during subsequent image and data analysis. 29 - Nikolaus Rajewsky
Computational detection of genomic cis-regulatory modules applied to body patterning in the early Drosophila embryo. 30 - John Parkinson
Making sense of EST sequences by CLOBBing them. 31 - Katerina Michalickova, Gary D. Bader
SeqHound: biological sequence and structure database as a platform for bioinformatics research. 32 - Rehannah H. A. Borup, Stefano Toppo
Development and production of an oligonucleotide MuscleChip: use for validation of ambiguous ESTs. 33 - Martin Steffen
Automated modelling of signal transduction networks. 34 - Mark D. Robinson
FunSpec: a web-based cluster interpreter for yeast. 35 - Junbai Wang, Jan Delabie
Clustering of the SOM easily reveals distinct gene expression patterns: results of a reanalysis of lymphoma study. 36 - Catherine H. Schein
Total sequence decomposition distinguishes functional modules, "molegos" in apurinic/apyrimidinic endonucleases. 37 - Lan Ma, Pablo A. Iglesias
Quantifying robustness of biochemical network models. 38 - Michel Dumontier
Species-specific protein sequence and fold optimizations. 39 - Konrad Büssow
ORFer - retrieval of protein sequences and open reading frames from GenBank and storage into relational databases or text files. 40
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