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BMC Bioinformatics, Volume 4
Volume 4, 2003
- Zhenjun Hu, Martin C. Frith
, Tianhua Niu, Zhiping Weng:
SeqVISTA: a graphical tool for sequence feature visualization and comparison. 1 - Gary D. Bader
An automated method for finding molecular complexes in large protein interaction networks. 2 - Peisen Zhang, Huitao Sheng, Alfredo Morabia, T. Conrad Gilliam:
Optimal Step Length EM Algorithm (OSLEM) for the estimation of haplotype frequency and its application in lipoprotein lipase genotyping. 3 - Jutta Bradtke, Harald Balz, Christa Fonatsch, Barbara Heinze, Anna Jauch, Brigitte Mohr, Claudia Schoch, Harald Rieder:
Computer aided analysis of additional chromosome aberrations in Philadelphia chromosome positive acute lymphoblastic leukaemia using a simplified computer readable cytogenetic notation. 4 - Francisco Azuaje:
Genomic data sampling and its effect on classification performance assessment. 5 - Nelson D. Young, John Healy:
GapCoder automates the use of indel characters in phylogenetic analysis. 6 - Yan Hong
A format for databasing and comparison of AFLP fingerprint profiles. 7 - Marco Berrera, Henriette Molinari, Federico Fogolari
Amino acid empirical contact energy definitions for fold recognition in the space of contact maps. 8 - Michal A. Kurowski, Joanna M. Sasin, Marcin Feder, Janusz Debski, Janusz M. Bujnicki:
Characterization of the cofactor-binding site in the SPOUT-fold methyltransferases by computational docking of S-adenosylmethionine to three crystal structures. 9 - Korbinian Strimmer:
Modeling gene expression measurement error: a quasi-likelihood approach. 10 - Ian M. Donaldson, Joel D. Martin, Berry de Bruijn, Cheryl Wolting, Vicki Lay, Brigitte Tuekam, Shudong Zhang, Berivan Baskin, Gary D. Bader
PreBIND and Textomy - mining the biomedical literature for protein-protein interactions using a support vector machine. 11 - Charles C. Kim
Significance analysis of lexical bias in microarray data. 12 - Michael C. O'Neill, Li Song:
Neural network analysis of lymphoma microarray data: prognosis and diagnosis near-perfect. 13 - Josephine Hoh, Fumihiko Matsuda, Xu Peng, Daniela Markovic, Mark G. Lathrop, Jürg Ott:
SNP haplotype tagging from DNA pools of two individuals. 14 - Jacques Rougemont, Pascal Hingamp
DNA microarray data and contextual analysis of correlation graphs. 15 - Kevin Truong, Mitsuhiko Ikura
Domain fusion analysis by applying relational algebra to protein sequence and domain databases. 16 - David J. Studholme
A comparison of Pfam and MEROPS: Two databases, one comprehensive, and one specialised. 17 - Michael M. Mwangi, Eric D. Siggia:
Genome wide identification of regulatory motifs in Bacillus subtilis. 18 - Hemant J. Purohit, Dhananjay V. Raje, A. Kapley:
Identification of signature and primers specific to genus Pseudomonas using mismatched patterns of 16S rDNA sequences. 19 - Parantu K. Shah, Carolina Perez-Iratxeta, Peer Bork
Information extraction from full text scientific articles: Where are the keywords? 20 - Thomas Schou Larsen, Anders Krogh
EasyGene - a prokaryotic gene finder that ranks ORFs by statistical significance. 21 - Jeff W. Bizzaro, Kenneth A. Marx:
Poly: a quantitative analysis tool for simple sequence repeat (SSR) tracts in DNA. 22 - Gautam Aggarwal, E. A. Worthey, Paul D. McDonagh, Peter J. Myler
Importing statistical measures into Artemis enhances gene identification in the Leishmania genome project. 23 - James M. Sorace, Min Zhan:
A data review and re-assessment of ovarian cancer serum proteomic profiling. 24 - Ramana V. Davuluri, Hao Sun
AGRIS: Arabidopsis Gene Regulatory Information Server, an information resource of Arabidopsis cis-regulatory elements and transcription factors. 25 - Xuejun Peng, Constance L. Wood, Eric M. Blalock, Kuey Chu Chen, Philip W. Landfield, Arnold J. Stromberg:
Statistical implications of pooling RNA samples for microarray experiments. 26 - Ashish Nimgaonkar, Despina Sanoudou
Reproducibility of gene expression across generations of Affymetrix microarrays. 27 - Marylyn D. Ritchie, Bill C. White, Joel S. Parker, Lance W. Hahn, Jason H. Moore
Optimizationof neural network architecture using genetic programming improvesdetection and modeling of gene-gene interactions in studies of humandiseases. 28 - James J. Campanella
MatGAT: An application that generates similarity/identity matrices using protein or DNA sequences. 29 - Robert M. Hubley, Eckart Zitzler, Jared C. Roach:
Evolutionary algorithms for the selection of single nucleotide polymorphisms. 30 - S. Blair Hedges, Prachi Shah:
Comparison of mode estimation methods and application in molecular clock analysis. 31 - Patrick J. Killion, Gavin Sherlock
The Longhorn Array Database (LAD): An Open-Source, MIAME compliant implementation of the Stanford Microarray Database (SMD). 32 - Taesung Park, Sung-Gon Yi, Sung-Hyun Kang, Seung Yeoun Lee, Yong-Sung Lee, Richard Simon:
Evaluation of normalization methods for microarray data. 33 - Boris E. Shakhnovich, John M. Harvey, Steve Comeau, David Lorenz
ELISA: Structure-Function Inferences based on statistically significant and evolutionarily inspired observations. 34 - Steven B. Cannon, Nevin D. Young
OrthoParaMap: Distinguishing orthologs from paralogs by integrating comparative genome data and gene phylogenies. 35 - Mark Smolkin, Debashis Ghosh:
Cluster stability scores for microarray data in cancer studies. 36 - Hanga C. Galfalvy
Sex genes for genomic analysis in human brain: internal controls for comparison of probe level data extraction. 37 - Sashidhar Gadiraju, Carrie A. Vyhlidal, J. Steven Leeder, Peter K. Rogan
Genome-wide prediction, display and refinement of binding sites with information theory-based models. 38 - Coral del Val
cDNA2Genome: A tool for mapping and annotating cDNAs. 39 - Sven Bilke, Thomas Breslin
Probabilistic estimation of microarray data reliability and underlying gene expression. 40 - Roman L. Tatusov, Natalie D. Fedorova, John D. Jackson, Aviva R. Jacobs, Boris Kiryutin, Eugene V. Koonin, Dmitri M. Krylov, Raja Mazumder
The COG database: an updated version includes eukaryotes. 41 - Soren Prag, Josephine C. Adams
Molecular phylogeny of the kelch-repeat superfamily reveals an expansion of BTB/kelch proteins in animals. 42 - Yee Leng Yap, Xue Wu Zhang, Antoine Danchin
Relationship of SARS-CoV to other pathogenic RNA viruses explored by tetranucleotide usage profiling. 43 - Robert J. Klein, Sean R. Eddy
RSEARCH: Finding homologs of single structured RNA sequences. 44 - Dan M. Bolser
Visualisation and graph-theoretic analysis of a large-scale protein structural interactome. 45 - Marcin Grynberg
Domain analysis of the tubulin cofactor system: a model for tubulin folding and dimerization. 46 - G. P. S. Raghava
OXBench: A benchmark for evaluation of protein multiple sequence alignment accuracy. 47 - Samuel Kaski, Janne Nikkilä, Merja Oja, Jarkko Venna, Petri Törönen, Eero Castrén
Trustworthiness and metrics in visualizing similarity of gene expression. 48 - Alex Bateman
The TROVE module: A common element in Telomerase, Ro and Vault ribonucleoproteins. 49 - Evan Keibler, Michael R. Brent:
Eval: A software package for analysis of genome annotations. 50 - Scott D. Zuyderduyn, Steven J. M. Jones:
A knowledge discovery object model API for Java. 51 - Michael J. Wise
LEAping to conclusions: A computational reanalysis of late embryogenesis abundant proteins and their possible roles. 52 - Georgios S. Vernikos, Christos G. Gkogkas
GeneViTo: Visualizing gene-product functional and structural features in genomic datasets. 53 - Cesare Furlanello
Entropy-based gene ranking without selection bias for the predictive classification of microarray data. 54 - Stefan Washietl, Frank Eisenhaber
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. 55 - Deyun Pan, Ning Sun, Kei-Hoi Cheung, Zhong Guan, Ligeng Ma, Matthew Holford, Xingwang Deng, Hongyu Zhao
PathMAPA: a tool for displaying gene expression and performing statistical tests on metabolic pathways at multiple levels for Arabidopsis. 56 - Eldon Emberly, Nikolaus Rajewsky
Conservation of regulatory elements between two species of Drosophila. 57 - Thorsten Pöschel
Online tool for the discrimination of equi-distributions. 58 - Aedín C. Culhane
Cross-platform comparison and visualisation of gene expression data using co-inertia analysis. 59 - Junbai Wang, Trond Hellem Bø, Inge Jonassen
Tumor classification and marker gene prediction by feature selection and fuzzy c-means clustering using microarray data. 60 - Kevin G. Becker
PubMatrix: a tool for multiplex literature mining. 61 - Mark A. Levenstien, Yaning Yang, Jürg Ott:
Statistical significance for hierarchical clustering in genetic association and microarray expression studies. 62 - Elarbi Badidi
AnaBench: a Web/CORBA-based workbench for biomolecular sequence analysis. 63 - Francesca D. Ciccarelli
The PAM domain, a multi-protein complex-associated module with an all-alpha-helix fold. 64 - Anna G. Nazina, Dmitri A. Papatsenko:
Statistical extraction of Drosophila cis-regulatory modules using exhaustive assessment of local word frequency. 65 - Michael Brudno, Michael Chapman, Berthold Göttgens
Fast and sensitive multiple alignment of large genomic sequences. 66
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