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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 4 |
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Methodology article
  
Fast and sensitive multiple alignment of large genomic sequences
Michael Brudno, Michael Chapman, Berthold G ttgens, Serafim Batzoglou, Burkhard Morgenstern
BMC Bioinformatics 2003, 4:66 (23December2003)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Statistical extraction of Drosophila cis-regulatory modules using exhaustive assessment of local word frequency
Anna G Nazina, Dmitri A Papatsenko
BMC Bioinformatics 2003, 4:65 (22December2003)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
The PAM domain, a multi-protein complex-associated module with an all-alpha-helix fold
Francesca D Ciccarelli, Elisa Izaurralde, Peer Bork
BMC Bioinformatics 2003, 4:64 (19December2003)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
AnaBench: a Web/CORBA-based workbench for biomolecular sequence analysis
Elarbi Badidi, Cristina De Sousa, B Franz Lang, Gertraud Burger
BMC Bioinformatics 2003, 4:63 (16December2003)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Statistical significance for hierarchical clustering in genetic association and microarray expression studies
Mark A Levenstien, Yaning Yang, J rg Ott
BMC Bioinformatics 2003, 4:62 (11December2003)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
PubMatrix: a tool for multiplex literature mining
Kevin G Becker, Douglas A Hosack, Glynn Dennis Jr, Richard A Lempicki, Tiffani J Bright, Chris Cheadle, Jim Engel
BMC Bioinformatics 2003, 4:61 (10December2003)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Tumor classification and marker gene prediction by feature selection and fuzzy c-means clustering using microarray data
Junbai Wang, Trond Hellem B , Inge Jonassen, Ola Myklebost, Eivind Hovig
BMC Bioinformatics 2003, 4:60 (2December2003)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Cross-platform comparison and visualisation of gene expression data using co-inertia analysis
Aed n C Culhane, Guy Perri re, Desmond G Higgins
BMC Bioinformatics 2003, 4:59 (21November2003)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Online tool for the discrimination of equi-distributions
Thorsten Pschel, Cornelius Frmmel, Christoph Gille
BMC Bioinformatics 2003, 4:58 (21November2003)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Conservation of regulatory elements between two species of Drosophila
Eldon Emberly, Nikolaus Rajewsky, Eric D Siggia
BMC Bioinformatics 2003, 4:57 (20November2003)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [F1000 Biology] [Cited on BioMed Central]
Software
PathMAPA: a tool for displaying gene expression and performing statistical tests on metabolic pathways at multiple levels for Arabidopsis
Deyun Pan, Ning Sun, Kei-Hoi Cheung, Zhong Guan, Ligeng Ma, Matthew Holford, Xingwang Deng, Hongyu Zhao
BMC Bioinformatics 2003, 4:56 (7November2003)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Reannotation of the CELO genome characterizes a set of previously unassigned open reading frames and points to novel modes of host interaction in avian adenoviruses
Stefan Washietl, Frank Eisenhaber
BMC Bioinformatics 2003, 4:55 (7November2003)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Entropy-based gene ranking without selection bias for the predictive classification of microarray data
Cesare Furlanello, Maria Serafini, Stefano Merler, Giuseppe Jurman
BMC Bioinformatics 2003, 4:54 (6November2003)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
GeneViTo: Visualizing gene-product functional and structural features in genomic datasets
Georgios S Vernikos, Christos G Gkogkas, Vasilis J Promponas, Stavros J Hamodrakas
BMC Bioinformatics 2003, 4:53 (31October2003)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
LEAping to conclusions: A computational reanalysis of late embryogenesis abundant proteins and their possible roles
Michael J Wise
BMC Bioinformatics 2003, 4:52 (29October2003)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
A knowledge discovery object model API for Java
Scott D Zuyderduyn, Steven JM Jones
BMC Bioinformatics 2003, 4:51 (28October2003)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
Eval: A software package for analysis of genome annotations
Evan Keibler, Michael R Brent
BMC Bioinformatics 2003, 4:50 (17October2003)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
The TROVE module: A common element in Telomerase, Ro and Vault ribonucleoproteins
Alex Bateman, Valerie Kickhoefer
BMC Bioinformatics 2003, 4:49 (16October2003)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Trustworthiness and metrics in visualizing similarity of gene expression
Samuel Kaski, Janne Nikkil , Merja Oja, Jarkko Venna, Petri Trnen, Eero Castr n
BMC Bioinformatics 2003, 4:48 (13October2003)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
OXBench: A benchmark for evaluation of protein multiple sequence alignment accuracy
GPS Raghava, Stephen MJ Searle, Patrick C Audley, Jonathan D Barber, Geoffrey J Barton
BMC Bioinformatics 2003, 4:47 (10October2003)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Domain analysis of the tubulin cofactor system: a model for tubulin folding and dimerization
Marcin Grynberg, Lukasz Jaroszewski, Adam Godzik
BMC Bioinformatics 2003, 4:46 (10October2003)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Visualisation and graph-theoretic analysis of a large-scale protein structural interactome
Dan Bolser, Panos Dafas, Richard Harrington, Jong Park, Michael Schroeder
BMC Bioinformatics 2003, 4:45 (8October2003)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
RSEARCH: Finding homologs of single structured RNA sequences
Robert J Klein, Sean R Eddy
BMC Bioinformatics 2003, 4:44 (22September2003)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Relationship of SARS-CoV to other pathogenic RNA viruses explored by tetranucleotide usage profiling
Yee Leng Yap, Xue Wu Zhang, Antoine Danchin
BMC Bioinformatics 2003, 4:43 (20September2003)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Molecular phylogeny of the kelch-repeat superfamily reveals an expansion of BTB/kelch proteins in animals
Soren Prag, Josephine C Adams
BMC Bioinformatics 2003, 4:42 (17September2003)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
The COG database: an updated version includes eukaryotes
Roman L Tatusov, Natalie D Fedorova, John D Jackson, Aviva R Jacobs, Boris Kiryutin, Eugene V Koonin, Dmitri M Krylov, Raja Mazumder, Sergei L Mekhedov, Anastasia N Nikolskaya, B Sridhar Rao, Sergei Smirnov, Alexander V Sverdlov, Sona Vasudevan, Yuri I Wolf, Jodie J Yin, Darren A Natale
BMC Bioinformatics 2003, 4:41 (11September2003)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [F1000 Biology] [Cited on BioMed Central]
Methodology article
Probabilistic estimation of microarray data reliability and underlying gene expression
Sven Bilke, Thomas Breslin, Mikael Sigvardsson
BMC Bioinformatics 2003, 4:40 (10September2003)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
cDNA2Genome: A tool for mapping and annotating cDNAs
Coral del Val, Karl-Heinz Glatting, Sandor Suhai
BMC Bioinformatics 2003, 4:39 (10September2003)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
Genome-wide prediction, display and refinement of binding sites with information theory-based models
Sashidhar Gadiraju, Carrie A Vyhlidal, J Steven Leeder, Peter K Rogan
BMC Bioinformatics 2003, 4:38 (8September2003)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Sex genes for genomic analysis in human brain: internal controls for comparison of probe level data extraction.
Hanga C Galfalvy, Loubna Erraji-Benchekroun, Peggy Smyrniotopoulos, Paul Pavlidis, Steven P Ellis, J John Mann, Etienne Sibille, Victoria Arango
BMC Bioinformatics 2003, 4:37 (8September2003)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Cluster stability scores for microarray data in cancer studies
Mark Smolkin, Debashis Ghosh
BMC Bioinformatics 2003, 4:36 (6September2003)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
OrthoParaMap: Distinguishing orthologs from paralogs by integrating comparative genome data and gene phylogenies
Steven B Cannon, Nevin D Young
BMC Bioinformatics 2003, 4:35 (2September2003)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Database
ELISA: Structure-Function Inferences based on statistically significant and evolutionarily inspired observations
Boris E Shakhnovich, John M Harvey, Steve Comeau, David Lorenz, Charles DeLisi, Eugene Shakhnovich
BMC Bioinformatics 2003, 4:34 (2September2003)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Evaluation of normalization methods for microarray data
Taesung Park, Sung-Gon Yi, Sung-Hyun Kang, SeungYeoun Lee, Yong-Sung Lee, Richard Simon
BMC Bioinformatics 2003, 4:33 (2September2003)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Database
The Longhorn Array Database (LAD): An Open-Source, MIAME compliant implementation of the Stanford Microarray Database (SMD)
Patrick J Killion, Gavin Sherlock, Vishwanath R Iyer
BMC Bioinformatics 2003, 4:32 (20August2003)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Comparison of mode estimation methods and application in molecular clock analysis
S Blair Hedges, Prachi Shah
BMC Bioinformatics 2003, 4:31 (31July2003)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Evolutionary algorithms for the selection of single nucleotide polymorphisms
Robert M Hubley, Eckart Zitzler, Jared C Roach
BMC Bioinformatics 2003, 4:30 (23July2003)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
MatGAT: An application that generates similarity/identity matrices using protein or DNA sequences
James J Campanella, Ledion Bitincka, John Smalley
BMC Bioinformatics 2003, 4:29 (10July2003)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Optimization
of neural network architecture using genetic programming improves
detection and modeling of gene-gene interactions in studies of human
diseases
Marylyn D Ritchie, Bill C White, Joel S Parker, Lance W Hahn, Jason H Moore
BMC Bioinformatics 2003, 4:28 (7July2003)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Reproducibility of gene expression across generations of Affymetrix microarrays
Ashish Nimgaonkar, Despina Sanoudou, Atul J Butte, Judith N Haslett, Louis M Kunkel, Alan H Beggs, Isaac S Kohane
BMC Bioinformatics 2003, 4:27 (25June2003)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Statistical implications of pooling RNA samples for microarray experiments
Xuejun Peng, Constance L Wood, Eric M Blalock, Kuey Chu Chen, Philip W Landfield, Arnold J Stromberg
BMC Bioinformatics 2003, 4:26 (24June2003)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
AGRIS: Arabidopsis Gene Regulatory Information Server, an information resource of Arabidopsis cis-regulatory elements and transcription factors
Ramana V Davuluri, Hao Sun, Saranyan K Palaniswamy, Nicole Matthews, Carlos Molina, Mike Kurtz, Erich Grotewold
BMC Bioinformatics 2003, 4:25 (23June2003)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
A data review and re-assessment of ovarian cancer serum proteomic profiling
James M Sorace, Min Zhan
BMC Bioinformatics 2003, 4:24 (9June2003)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] [1 comment]
Research article
Importing statistical measures into Artemis enhances gene identification in the Leishmania genome project
Gautam Aggarwal, EA Worthey, Paul D McDonagh, Peter J Myler
BMC Bioinformatics 2003, 4:23 (7June2003)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Poly: a quantitative analysis tool for simple sequence repeat (SSR) tracts in DNA
Jeff W Bizzaro, Kenneth A Marx
BMC Bioinformatics 2003, 4:22 (5June2003)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
EasyGene  a prokaryotic gene finder that ranks ORFs by statistical significance
Thomas Schou Larsen, Anders Krogh
BMC Bioinformatics 2003, 4:21 (3June2003)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Information extraction from full text scientific articles: Where are the keywords?
Parantu K Shah, Carolina Perez-Iratxeta, Peer Bork, Miguel A Andrade
BMC Bioinformatics 2003, 4:20 (29May2003)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Identification of signature and primers specific to genus Pseudomonas using mismatched patterns of 16S rDNA sequences
HJ Purohit, DV Raje, A Kapley
BMC Bioinformatics 2003, 4:19 (22May2003)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] [1 comment]
Research article
Genome wide identification of regulatory motifs in Bacillus subtilis
Michael M Mwangi, Eric D Siggia
BMC Bioinformatics 2003, 4:18 (16May2003)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
A comparison of Pfam and MEROPS: Two databases, one comprehensive, and one specialised.
David J Studholme, Neil D Rawlings, Alan J Barrett, Alex Bateman
BMC Bioinformatics 2003, 4:17 (9May2003)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Domain fusion analysis by applying relational algebra to protein sequence and domain databases
Kevin Truong, Mitsuhiko Ikura
BMC Bioinformatics 2003, 4:16 (6May2003)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
DNA microarray data and contextual analysis of correlation graphs
Jacques Rougemont, Pascal Hingamp
BMC Bioinformatics 2003, 4:15 (29April2003)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
SNP haplotype tagging from DNA pools of two individuals
Josephine Hoh, Fumihiko Matsuda, Xu Peng, Daniela Markovic, Mark G Lathrop, Jurg Ott
BMC Bioinformatics 2003, 4:14 (22April2003)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Neural network analysis of lymphoma microarray data: prognosis and diagnosis near-perfect
Michael C O'Neill, Li Song
BMC Bioinformatics 2003, 4:13 (10April2003)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] [1 comment]
Methodology article
Significance analysis of lexical bias in microarray data
Charles C Kim, Stanley Falkow
BMC Bioinformatics 2003, 4:12 (3April2003)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
PreBIND and Textomy mining the biomedical literature for protein-protein interactions using a support vector machine
Ian Donaldson, Joel Martin, Berry de Bruijn, Cheryl Wolting, Vicki Lay, Brigitte Tuekam, Shudong Zhang, Berivan Baskin, Gary D Bader, Katerina Michalickova, Tony Pawson, Christopher WV Hogue
BMC Bioinformatics 2003, 4:11 (27March2003)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Modeling gene expression measurement error: a quasi-likelihood approach
Korbinian Strimmer
BMC Bioinformatics 2003, 4:10 (20March2003)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Characterization of the cofactor-binding site in the SPOUT-fold methyltransferases by computational docking of S-adenosylmethionine to three crystal structures
Michal A Kurowski, Joanna M Sasin, Marcin Feder, Janusz Debski, Janusz M Bujnicki
BMC Bioinformatics 2003, 4:9 (14March2003)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Amino acid empirical contact energy definitions for fold recognition in the space of contact maps
Marco Berrera, Henriette Molinari, Federico Fogolari
BMC Bioinformatics 2003, 4:8 (28February2003)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
A format for databasing and comparison of AFLP fingerprint profiles
Yan Hong, Aaron Chuah
BMC Bioinformatics 2003, 4:7 (25February2003)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
GapCoder automates the use of indel characters in phylogenetic analysis
Nelson D Young, John Healy
BMC Bioinformatics 2003, 4:6 (19February2003)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Genomic data sampling and its effect on classification performance assessment
Francisco Azuaje
BMC Bioinformatics 2003, 4:5 (28January2003)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Computer aided analysis of additional chromosome aberrations in Philadelphia chromosome positive acute lymphoblastic leukaemia using a simplified computer readable cytogenetic notation
Jutta Bradtke, Harald Balz, Christa Fonatsch, Barbara Heinze, Anna Jauch, Brigitte Mohr, Claudia Schoch, Harald Rieder
BMC Bioinformatics 2003, 4:4 (28January2003)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Optimal Step Length EM Algorithm (OSLEM) for the estimation of haplotype frequency and its application in lipoprotein lipase genotyping
Peisen Zhang, Huitao Sheng, Alfredo Morabia, T Conrad Gilliam
BMC Bioinformatics 2003, 4:3 (15January2003)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
An automated method for finding molecular complexes in large protein interaction networks
Gary D Bader, Christopher WV Hogue
BMC Bioinformatics 2003, 4:2 (13January2003)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
SeqVISTA: a graphical tool for sequence feature visualization and comparison
Zhenjun Hu, Martin Frith, Tianhua Niu, Zhiping Weng
BMC Bioinformatics 2003, 4:1 (4January2003)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
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