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
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• Gary D. Bader, Christopher W. V. Hogue:
  An automated method for finding molecular complexes in large protein interaction networks. 2
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• 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
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• 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
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• Francisco Azuaje:
  Genomic data sampling and its effect on classification performance assessment. 5
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• Nelson D. Young, John Healy:
  GapCoder automates the use of indel characters in phylogenetic analysis. 6
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• Yan Hong, Aaron Chuah:
  A format for databasing and comparison of AFLP fingerprint profiles. 7
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• Marco Berrera, Henriette Molinari, Federico Fogolari:
  Amino acid empirical contact energy definitions for fold recognition in the space of contact maps. 8
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• 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
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• Korbinian Strimmer:
  Modeling gene expression measurement error: a quasi-likelihood approach. 10
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• Ian Donaldson, Joel D. Martin, Berry de Bruijn, Cheryl Wolting, Vicki Lay, Brigitte Tuekam, Shudong Zhang, Berivan Baskin, Gary D. Bader, Katerina Michalickova, Tony Pawson, Christopher W. V. Hogue:
  PreBIND and Textomy - mining the biomedical literature for protein-protein interactions using a support vector machine. 11
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• Charles C. Kim, Stanley Falkow:
  Significance analysis of lexical bias in microarray data. 12
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• Michael C. O'Neill, Li Song:
  Neural network analysis of lymphoma microarray data: prognosis and diagnosis near-perfect. 13
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• Josephine Hoh, Fumihiko Matsuda, Xu Peng, Daniela Markovic, Mark G. Lathrop, Jürg Ott:
  SNP haplotype tagging from DNA pools of two individuals. 14
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• Jacques Rougemont, Pascal Hingamp:
  DNA microarray data and contextual analysis of correlation graphs. 15
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• Kevin Truong, Mitsuhiko Ikura:
  Domain fusion analysis by applying relational algebra to protein sequence and domain databases. 16
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• David J. Studholme, Neil D. Rawlings, Alan J. Barrett, Alex Bateman:
  A comparison of Pfam and MEROPS: Two databases, one comprehensive, and one specialised. 17
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• Michael M. Mwangi, Eric D. Siggia:
  Genome wide identification of regulatory motifs in Bacillus subtilis. 18
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• 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
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• Parantu K. Shah, Carolina Perez-Iratxeta, Peer Bork, Miguel A. Andrade:
  Information extraction from full text scientific articles: Where are the keywords? 20
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• Thomas Schou Larsen, Anders Krogh:
  EasyGene - a prokaryotic gene finder that ranks ORFs by statistical significance. 21
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• Jeff W. Bizzaro, Kenneth A. Marx:
  Poly: a quantitative analysis tool for simple sequence repeat (SSR) tracts in DNA. 22
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• 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
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• James M. Sorace, Min Zhan:
  A data review and re-assessment of ovarian cancer serum proteomic profiling. 24
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• Ramana V. Davuluri, Hao Sun, Saranyan K. Palaniswamy, Nicole Matthews, Carlos Molina, Mike Kurtz, Erich Grotewold:
  AGRIS: Arabidopsis Gene Regulatory Information Server, an information resource of Arabidopsis cis-regulatory elements and transcription factors. 25
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• 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
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• Ashish Nimgaonkar, Despina Sanoudou, Atul J. Butte, Judith N. Haslett, Louis M. Kunkel, Alan H. Beggs, Isaac S. Kohane:
  Reproducibility of gene expression across generations of Affymetrix microarrays. 27
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• 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
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• James J. Campanella, Ledion Bitincka, John Smalley:
  MatGAT: An application that generates similarity/identity matrices using protein or DNA sequences. 29
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• Robert M. Hubley, Eckart Zitzler, Jared C. Roach:
  Evolutionary algorithms for the selection of single nucleotide polymorphisms. 30
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• S. Blair Hedges, Prachi Shah:
  Comparison of mode estimation methods and application in molecular clock analysis. 31
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• Patrick J. Killion, Gavin Sherlock, Vishwanath R. Iyer:
  The Longhorn Array Database (LAD): An Open-Source, MIAME compliant implementation of the Stanford Microarray Database (SMD). 32
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• Taesung Park, Sung-Gon Yi, Sung-Hyun Kang, Seung Yeoun Lee, Yong-Sung Lee, Richard Simon:
  Evaluation of normalization methods for microarray data. 33
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• Boris E. Shakhnovich, John M. Harvey, Steve Comeau, David Lorenz, Charles DeLisi, Eugene I. Shakhnovich:
  ELISA: Structure-Function Inferences based on statistically significant and evolutionarily inspired observations. 34
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• Steven B. Cannon, Nevin D. Young:
  OrthoParaMap: Distinguishing orthologs from paralogs by integrating comparative genome data and gene phylogenies. 35
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• Mark Smolkin, Debashis Ghosh:
  Cluster stability scores for microarray data in cancer studies. 36
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• Hanga C. Galfalvy, Loubna Erraji-Benchekroun, Peggy Smyrniotopoulos, Paul Pavlidis, Steven P. Ellis, J. John Mann, Etienne Sibille, Victoria Arango:
  Sex genes for genomic analysis in human brain: internal controls for comparison of probe level data extraction. 37
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• 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
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• Coral del Val, Karl-Heinz Glatting, Sándor Suhai:
  cDNA2Genome: A tool for mapping and annotating cDNAs. 39
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• Sven Bilke, Thomas Breslin, Mikael Sigvardsson:
  Probabilistic estimation of microarray data reliability and underlying gene expression. 40
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• 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:
  The COG database: an updated version includes eukaryotes. 41
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• Soren Prag, Josephine C. Adams:
  Molecular phylogeny of the kelch-repeat superfamily reveals an expansion of BTB/kelch proteins in animals. 42
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• Yee Leng Yap, Xue Wu Zhang, Antoine Danchin:
  Relationship of SARS-CoV to other pathogenic RNA viruses explored by tetranucleotide usage profiling. 43
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• Robert J. Klein, Sean R. Eddy:
  RSEARCH: Finding homologs of single structured RNA sequences. 44
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• Dan M. Bolser, Panos Dafas, Richard Harrington, Jong Park, Michael Schroeder:
  Visualisation and graph-theoretic analysis of a large-scale protein structural interactome. 45
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• Marcin Grynberg, Lukasz Jaroszewski, Adam Godzik:
  Domain analysis of the tubulin cofactor system: a model for tubulin folding and dimerization. 46
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• G. P. S. Raghava, Stephen M. J. Searle, Patrick C. Audley, Jonathan D. Barber, Geoffrey J. Barton:
  OXBench: A benchmark for evaluation of protein multiple sequence alignment accuracy. 47
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• Samuel Kaski, Janne Nikkilä, Merja Oja, Jarkko Venna, Petri Törönen, Eero Castrén:
  Trustworthiness and metrics in visualizing similarity of gene expression. 48
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• Alex Bateman, Valerie A. Kickhoefer:
  The TROVE module: A common element in Telomerase, Ro and Vault ribonucleoproteins. 49
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• Evan Keibler, Michael R. Brent:
  Eval: A software package for analysis of genome annotations. 50
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• Scott D. Zuyderduyn, Steven J. M. Jones:
  A knowledge discovery object model API for Java. 51
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• Michael J. Wise:
  LEAping to conclusions: A computational reanalysis of late embryogenesis abundant proteins and their possible roles. 52
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• Georgios S. Vernikos, Christos G. Gkogkas, Vassilis J. Promponas, Stavros J. Hamodrakas:
  GeneViTo: Visualizing gene-product functional and structural features in genomic datasets. 53
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• Cesare Furlanello, Maria Serafini, Stefano Merler, Giuseppe Jurman:
  Entropy-based gene ranking without selection bias for the predictive classification of microarray data. 54
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• 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
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• 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
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• Eldon Emberly, Nikolaus Rajewsky, Eric D. Siggia:
  Conservation of regulatory elements between two species of Drosophila. 57
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• Thorsten Pöschel, Cornelius Frömmel, Christoph Gille:
  Online tool for the discrimination of equi-distributions. 58
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• Aedín C. Culhane, Guy Perrière, Desmond G. Higgins:
  Cross-platform comparison and visualisation of gene expression data using co-inertia analysis. 59
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• Junbai Wang, Trond Hellem Bø, Inge Jonassen, Ola Myklebost, Eivind Hovig:
  Tumor classification and marker gene prediction by feature selection and fuzzy c-means clustering using microarray data. 60
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• Kevin G. Becker, Douglas A. Hosack, Glynn Dennis Jr., Richard A. Lempicki, Tiffani J. Bright, Chris Cheadle, James Engel:
  PubMatrix: a tool for multiplex literature mining. 61
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• Mark A. Levenstien, Yaning Yang, Jürg Ott:
  Statistical significance for hierarchical clustering in genetic association and microarray expression studies. 62
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• Elarbi Badidi, Cristina deSousa, B. Franz Lang, Gertraud Burger:
  AnaBench: a Web/CORBA-based workbench for biomolecular sequence analysis. 63
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• Francesca Ciccarelli, Elisa Izaurralde, Peer Bork:
  The PAM domain, a multi-protein complex-associated module with an all-alpha-helix fold. 64
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• Anna G. Nazina, Dmitri A. Papatsenko:
  Statistical extraction of Drosophila cis-regulatory modules using exhaustive assessment of local word frequency. 65
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• Michael Brudno, Michael Chapman, Berthold Göttgens, Serafim Batzoglou, Burkhard Morgenstern:
  Fast and sensitive multiple alignment of large genomic sequences. 66
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