Bioinformatics

ORIGINAL PAPERS:

Jinling Huang and Suchendra M. Bhandarkar

A comparison of physical mapping algorithms based on the maximum likelihood model
Bioinformatics 2003 19: 1303-1310; doi:10.1093/bioinformatics/btg166 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Pei-chin Chang and Konan Peck

Design and assessment of a fast algorithm for identifying specific probes for human and mouse genes
Bioinformatics 2003 19: 1311-1317; doi:10.1093/bioinformatics/btg162 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Todd E. Scheetz, Nishank Trivedi, Chad A. Roberts, Tamara Kucaba, Brian Berger, Natalie L. Robinson, Clayton L. Birkett, Allen J. Gavin, Brian O’Leary, Terry A. Braun, Maria F. Bonaldo, John P. Robinson, Val C. Sheffield, Marcelo B. Soares, and Thomas L. Casavant

ESTprep: preprocessing cDNA sequence reads
Bioinformatics 2003 19: 1318-1324; doi:10.1093/bioinformatics/btg159 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

D.L. Wilson, M.J. Buckley, C.A. Helliwell, and I.W. Wilson

New normalization methods for cDNA microarray data
Bioinformatics 2003 19: 1325-1332; doi:10.1093/bioinformatics/btg146 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Wei Pan

On the use of permutation in and the performance of a class of nonparametric methods to detect differential gene expression
Bioinformatics 2003 19: 1333-1340; doi:10.1093/bioinformatics/btg167 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Xujing Wang, Martin J. Hessner, Yan Wu, Nirupma Pati, and Soumitra Ghosh

Quantitative quality control in microarray experiments and the application in data filtering, normalization and false positive rate prediction
Bioinformatics 2003 19: 1341-1347; doi:10.1093/bioinformatics/btg154 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Sorin Draghici, Olga Kulaeva, Bruce Hoff, Anton Petrov, Soheil Shams, and Michael A. Tainsky

Noise sampling method: an ANOVA approach allowing robust selection of differentially regulated genes measured by DNA microarrays
Bioinformatics 2003 19: 1348-1359; doi:10.1093/bioinformatics/btg165 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Blythe Durbin and David M. Rocke

Estimation of transformation parameters for microarray data
Bioinformatics 2003 19: 1360-1367; doi:10.1093/bioinformatics/btg178 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

M. Spencer

Exact significance levels for the maximum ² method of detecting recombination
Bioinformatics 2003 19: 1368-1370; doi:10.1093/bioinformatics/btg171 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Misaki Sato, Hitomi Umeki, Rintaro Saito, Akio Kanai, and Masaru Tomita

Computational analysis of stop codon readthrough in D.melanogaster
Bioinformatics 2003 19: 1371-1380; doi:10.1093/bioinformatics/btg183 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Venkatarajan S. Mathura, Catherine H. Schein, and Werner Braun

Identifying property based sequence motifs in protein families and superfamilies: application to DNase-1 related endonucleases
Bioinformatics 2003 19: 1381-1390; doi:10.1093/bioinformatics/btg164 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Hongyu Zhang

Alignment of BLAST high-scoring segment pairs based on the longest increasing subsequence algorithm
Bioinformatics 2003 19: 1391-1396; doi:10.1093/bioinformatics/btg168 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Caleb Webber and Geoffrey J. Barton

Increased coverage obtained by combination of methods for protein sequence database searching
Bioinformatics 2003 19: 1397-1403; doi:10.1093/bioinformatics/btg156 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Robert C. Edgar and Kimmen Sjölander

SATCHMO: sequence alignment and tree construction using hidden Markov models
Bioinformatics 2003 19: 1404-1411; doi:10.1093/bioinformatics/btg158 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Victor Kunin and Christos A. Ouzounis

GeneTRACE–reconstruction of gene content of ancestral species
Bioinformatics 2003 19: 1412-1416; doi:10.1093/bioinformatics/btg174 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Jung-Hsien Chiang and Hsu-Chun Yu

MeKE: discovering the functions of gene products from biomedical literature via sentence alignment
Bioinformatics 2003 19: 1417-1422; doi:10.1093/bioinformatics/btg160 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Hong-Wu Ma and An-Ping Zeng

The connectivity structure, giant strong component and centrality of metabolic networks
Bioinformatics 2003 19: 1423-1430; doi:10.1093/bioinformatics/btg177 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Artem L. Ponomarev and Ronald L. Davis

An adjustable-threshold algorithm for the identification of objects in three-dimensional images
Bioinformatics 2003 19: 1431-1435; doi:10.1093/bioinformatics/btg176 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

APPLICATIONS NOTES:

Michael A. Banks, Will Eichert, and Jeffrey B. Olsen

Which genetic loci have greater population assignment power?
Bioinformatics 2003 19: 1436-1438; doi:10.1093/bioinformatics/btg172 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Perikles Simon

Q-Gene: processing quantitative real-time RT–PCR data
Bioinformatics 2003 19: 1439-1440; doi:10.1093/bioinformatics/btg157 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Yong Li, Mario G. Rosso, Nicolai Strizhov, Prisca Viehoever, and Bernd Weisshaar

GABI-Kat SimpleSearch: a flanking sequence tag (FST) database for the identification of T-DNA insertion mutants in Arabidopsis thaliana
Bioinformatics 2003 19: 1441-1442; doi:10.1093/bioinformatics/btg170 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

J. Lynn Fink, Scott Drewes, Hiren Patel, John B. Welsh, Daniel R. Masys, Jacques Corbeil, and Michael Gribskov

2HAPI: a microarray data analysis system
Bioinformatics 2003 19: 1443-1445; doi:10.1093/bioinformatics/btg169 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Catherine Grasso, Michael Quist, Kevin Ke, and Christopher Lee

POAVIZ: a Partial Order Multiple Sequence Alignment Visualizer
Bioinformatics 2003 19: 1446-1448; doi:10.1093/bioinformatics/btg175 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

René Gibson and Douglas R. Smith

Genome visualization made fast and simple
Bioinformatics 2003 19: 1449-1450; doi:10.1093/bioinformatics/btg152 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Paul Janssen, Anton J. Enright, Benjamin Audit, Ildefonso Cases, Leon Goldovsky, Nicola Harte, Victor Kunin, and Christos A. Ouzounis

COmplete GENome Tracking (COGENT): a flexible data environment for computational genomics
Bioinformatics 2003 19: 1451-1452; doi:10.1093/bioinformatics/btg161 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

T. B. Fischer, K. V. Arunachalam, D. Bailey, V. Mangual, S. Bakhru, R. Russo, D. Huang, M. Paczkowski, V. Lalchandani, C. Ramachandra, B. Ellison, S. Galer, J. Shapley, E. Fuentes, and J. Tsai

The binding interface database (BID): a compilation of amino acid hot spots in protein interfaces
Bioinformatics 2003 19: 1453-1454; doi:10.1093/bioinformatics/btg163 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

REPLY TO THE READER'S COMMENTS:

Triplet repeats in human genome: distribution and their association with genes and other genomic regions
Bioinformatics 2003 19: 1455; doi:10.1093/bioinformatics/btg322 [Print PDF][Screen PDF] [Request Permissions]  

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