Volume 5; Issue 1

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BMC Bioinformatics
Volume 5; Issue 1

BMC Bioinformatics

Volume 5; Issue 1

1

Spotting effect in microarray experiments

Tristan Mary-Huard, Jean-Jacques Daudin, Stéphane Robin, Frédérique Bitton, Eric Cabannes, Pierre Hilson

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 1.09 MB

english, 2004

2

Aggregation of topological motifs in theEscherichia colitranscriptional regulatory network

Radu Dobrin, Qasim K Beg, Albert-László Barabási, Zoltán N Oltvai

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 582 KB

english, 2004

3

Graph-based iterative Group Analysis enhances microarray interpretation

Rainer Breitling, Anna Amtmann, Pawel Herzyk

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 303 KB

english, 2004

4

Structural characterization of genomes by large scale sequence-structure threading: application of reliability analysis in structural genomics

Artem Cherkasov, Shannan J Ho Sui, Robert C Brunham, Steven JM Jones

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 320 KB

english, 2004

5

A computer simulation analysis of the accuracy of partial genome sequencing and restriction fragment analysis in estimating genetic relationships: an application to papillomavirus DNA sequences

Baozhen Qiao, Ronald M Weigel

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 284 KB

english, 2004

6

Improving the scaling normalization for high-density oligonucleotide GeneChip expression microarrays

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 363 KB

english, 2004

7

Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics

Jens Reeder, Robert Giegerich

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 345 KB

english, 2004

8

Evaluation of the suitability of free-energy minimization using nearest-neighbor energy parameters for RNA secondary structure prediction

Kishore J Doshi, Jamie J Cannone, Christian W Cobaugh, Robin R Gutell

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 1.33 MB

english, 2004

9

Estimates of statistical significance for comparison of individual positions in multiple sequence alignments

Ruslan I Sadreyev, Nick V Grishin

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 1.05 MB

english, 2004

10

STING Millennium Suite: integrated software for extensive analyses of 3d structures of proteins and their complexes

Roberto H Higa, Roberto C Togawa, Arnaldo J Montagner, Juliana CF Palandrani, Igor KS Okimoto, Paula R Kuser, Michel EB Yamagishi, Adauto L Mancini, Goran Neshich

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 889 KB

english, 2004

11

Linear fuzzy gene network models obtained from microarray data by exhaustive search

Bahrad A Sokhansanj, J Patrick Fitch, Judy N Quong, Andrew A Quong

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 477 KB

english, 2004

12

The Hotdog fold: wrapping up a superfamily of thioesterases and dehydratases

Shane C Dillon, Alex Bateman

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 659 KB

english, 2004

13

MuTrack: a genome analysis system for large-scale mutagenesis in the mouse

Erich J Baker, Leslie Galloway, Barbara Jackson, Denise Schmoyer, Jay Snoddy

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 936 KB

english, 2004

14

Tests for finding complex patterns of differential expression in cancers: towards individualized medicine

James Lyons-Weiler, Satish Patel, Michael J Becich, Tony E Godfrey

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 446 KB

english, 2004

15

Alternative mapping of probes to genes forAffymetrixchips

Laurent Gautier, Morten Møller, Lennart Friis-Hansen, Steen Knudsen

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 518 KB

english, 2004

16

IdentiCS – Identification of coding sequence andin silicoreconstruction of the metabolic network directly from unannotated low-coverage bacterial genome sequence

Jibin Sun, An-Ping Zeng

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 378 KB

english, 2004

17

MUSCLE: a multiple sequence alignment method with reduced time and space complexity

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 658 KB

english, 2004

18

Influence of microarrays experiments missing values on the stability of gene groups by hierarchical clustering

Alexandre G de Brevern, Serge Hazout, Alain Malpertuy

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 888 KB

english, 2004

19

An imaging system for standardized quantitative analysis ofC. elegansbehavior

Zhaoyang Feng, Christopher J Cronin, John H Wittig, Paul W Sternberg, William R Schafer

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 297 KB

english, 2004

20

Applying Support Vector Machines for Gene ontology based gene function prediction

Arunachalam Vinayagam, Rainer König, Jutta Moormann, Falk Schubert, Roland Eils, Karl-Heinz Glatting, Sándor Suhai

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 1.10 MB

english, 2004

21

XHM: A system for detection of potential cross hybridizations in DNA microarrays

Kristian Flikka, Fekadu Yadetie, Astrid Laegreid, Inge Jonassen

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 582 KB

english, 2004

22

Estimating mutual information using B-spline functions – an improved similarity measure for analysing gene expression data

Carsten O Daub, Ralf Steuer, Joachim Selbig, Sebastian Kloska

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 438 KB

english, 2004

23

Bayesian model accounting for within-class biological variability in Serial Analysis of Gene Expression (SAGE)

Ricardo ZN Vêncio, Helena Brentani, Diogo FC Patrão, Carlos AB Pereira

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 768 KB

english, 2004

24

Array-A-Lizer: A serial DNA microarray quality analyzer

Andreas Petri, Jan Fleckner, Mads Wichmann Matthiessen

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 484 KB

english, 2004

25

Artificial neural network approach for selection of susceptible single nucleotide polymorphisms and construction of prediction model on childhood allergic asthma

Yasuyuki Tomita, Shuta Tomida, Yuko Hasegawa, Yoichi Suzuki, Taro Shirakawa, Takeshi Kobayashi, Hiroyuki Honda

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 480 KB

english, 2004

26

SED, a normalization free method for DNA microarray data analysis

Huajun Wang, Hui Huang

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 278 KB

english, 2004

27

Automatic annotation of protein motif function with Gene Ontology terms

Xinghua Lu, Chengxiang Zhai, Vanathi Gopalakrishnan, Bruce G Buchanan

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 367 KB

english, 2004

28

GASP: Gapped Ancestral Sequence Prediction for proteins

Richard J Edwards, Denis C Shields

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 1.81 MB

english, 2004

29

Handling multiple testing while interpreting microarrays with the Gene Ontology Database

Michael V Osier, Hongyu Zhao, Kei-Hoi Cheung

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 908 KB

english, 2004

30

Determination of the differentially expressed genes in microarray experiments using local FDR

J Aubert, A Bar-Hen, J-J Daudin, S Robin

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 462 KB

english, 2004

31

Iterative class discovery and feature selection using Minimal Spanning Trees

Sudhir Varma, Richard Simon

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 293 KB

english, 2004

32

Functionally specified protein signatures distinctive for each of the different blue copper proteins

Anuradha Vivekanandan Giri, Sharmila Anishetty, Pennathur Gautam

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 300 KB

english, 2004

33

DIALIGN P: Fast pair-wise and multiple sequence alignment using parallel processors

Martin Schmollinger, Kay Nieselt, Michael Kaufmann, Burkhard Morgenstern

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 313 KB

english, 2004

34

Cross-species comparison significantly improves genome-wide prediction of cis-regulatory modules in Drosophila

Saurabh Sinha, Mark D Schroeder, Ulrich Unnerstall, Ulrike Gaul, Eric D Siggia

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 412 KB

english, 2004

35

SeeGH – A software tool for visualization of whole genome array comparative genomic hybridization data

Bryan Chi, Ronald J deLeeuw, Bradley P Coe, Calum MacAulay, Wan L Lam

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 448 KB

english, 2004

36

GDR (GenomeDatabase forRosaceae): integrated web resources for Rosaceae genomics and genetics research

Sook Jung, Christopher Jesudurai, Margaret Staton, Zhidian Du, Stephen Ficklin, Ilhyung Cho, Albert Abbott, Jeffrey Tomkins, Dorrie Main

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 335 KB

english, 2004

37

What can we learn from noncoding regions of similarity between genomes?

Thomas A Down, Tim JP Hubbard

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 390 KB

english, 2004

38

Simple statistical models predict C-to-U edited sites in plant mitochondrial RNA

Michael P Cummings, Daniel S Myers

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 271 KB

english, 2004

39

Allermatch™, a webtool for the prediction of potential allergenicity according to current FAO/WHO Codex alimentarius guidelines

Mark WEJ Fiers, Gijs A Kleter, Herman Nijland, Ad ACM Peijnenburg, Jan Peter Nap, Roeland CHJ van Ham

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 344 KB

english, 2004

40

PATTERNFINDER: combined analysis of DNA regulatory sequences and double-helix stability

Yanlin Huang, David Kowalski

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 275 KB

english, 2004

41

Profiled support vector machines for antisense oligonucleotide efficacy prediction

Gustavo Camps-Valls, Alistair M Chalk, Antonio J Serrano-López, José D Martín-Guerrero, Erik LL Sonnhammer

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 307 KB

english, 2004

42

A combinational feature selection and ensemble neural network method for classification of gene expression data

Bing Liu, Qinghua Cui, Tianzi Jiang, Songde Ma

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 980 KB

english, 2004

43

Few amino acid positions inrpoBare associated with most of the rifampin resistance inMycobacterium tuberculosis

Michael P Cummings, Mark R Segal

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 252 KB

english, 2004

44

cuticleDB: a relational database of Arthropod cuticular proteins

Christiana K Magkrioti, Ioannis C Spyropoulos, Vassiliki A Iconomidou, Judith H Willis, Stavros J Hamodrakas

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 400 KB

english, 2004

45

A population-based statistical approach identifies parameters characteristic of human microRNA-mRNA interactions

Neil R Smalheiser, Vetle I Torvik

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 284 KB

english, 2004

46

Comparison of computational methods for identifying translation initiation sites in EST data

Afshin Nadershahi, Scott C Fahrenkrug, Lynda BM Ellis

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 490 KB

english, 2004

47

A comprehensive comparison of comparative RNA structure prediction approaches

Paul P Gardner, Robert Giegerich

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 457 KB

english, 2004

48

GeneXplorer: an interactive web application for microarray data visualization and analysis

Christian A Rees, Janos Demeter, John C Matese, David Botstein, Gavin Sherlock

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 1.10 MB

english, 2004

49

ArrayD: A general purpose software for Microarray design

Anu Sharma, Gyan Prakash Srivastava, Vineet K Sharma, Srinivasan Ramachandran

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 351 KB

english, 2004

50

Identitag, a relational database for SAGE tag identification and interspecies comparison of SAGE libraries

Céline Keime, Francesca Damiola, Dominique Mouchiroud, Laurent Duret, Olivier Gandrillon

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 425 KB

english, 2004

51

Overdispersed logistic regression for SAGE: Modelling multiple groups and covariates

Keith A Baggerly, Li Deng, Jeffrey S Morris, C Marcelo Aldaz

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 329 KB

english, 2004

52

Extending the mutual information measure to rank inferred literature relationships

Jonathan D Wren

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 477 KB

english, 2004

53

Tools for loading MEDLINE into a local relational database

Diane E Oliver, Gaurav Bhalotia, Ariel S Schwartz, Russ B Altman, Marti A Hearst

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 284 KB

english, 2004

54

Content-rich biological network constructed by mining PubMed abstracts

Hao Chen, Burt M Sharp

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 346 KB

english, 2004

55

Rank Difference Analysis of Microarrays (RDAM), a novel approach to statistical analysis of microarray expression profiling data

Dietmar E Martin, Philippe Demougin, Michael N Hall, Michel Bellis

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 3.21 MB

english, 2004

56

Improved hit criteria for DNA local alignment

Laurent Noé, Gregory Kucherov

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 304 KB

english, 2004

57

Network analysis of metabolic enzyme evolution inEscherichia coli

Sara Light, Per Kraulis

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 371 KB

english, 2004

58

PCOGR: Phylogenetic COG ranking as an online tool to judge the specificity of COGs with respect to freely definable groups of organisms

Florian Meereis, Michael Kaufmann

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 810 KB

english, 2004

59

Caryoscope: An Open Source Java application for viewing microarray data in a genomic context

Ihab AB Awad, Christian A Rees, Tina Hernandez-Boussard, Catherine A Ball, Gavin Sherlock

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 1.84 MB

english, 2004

60

Incidence of "quasi-ditags" in catalogs generated by Serial Analysis of Gene Expression (SAGE)

Sergey V Anisimov, Alexei A Sharov

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 672 KB

english, 2004

61

Inter-residue distances derived from fold contact propensities correlate with evolutionary substitution costs

Gareth Williams, Patrick Doherty

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 370 KB

english, 2004

62

Information assessment on predicting protein-protein interactions

Nan Lin, Baolin Wu, Ronald Jansen, Mark Gerstein, Hongyu Zhao

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 285 KB

english, 2004

63

PASBio: predicate-argument structures for event extraction in molecular biology

Tuangthong Wattarujeekrit, Parantu K Shah, Nigel Collier

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 407 KB

english, 2004

64

Modeling of cell signaling pathways in macrophages by semantic networks

Michael Hsing, Joel L Bellenson, Conor Shankey, Artem Cherkasov

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 545 KB

english, 2004

65

Gapped alignment of protein sequence motifs through Monte Carlo optimization of a hidden Markov model

Andrew F Neuwald, Jun S Liu

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 3.37 MB

english, 2004

66

A computational approach for ordering signal transduction pathway components from genomics and proteomics Data

Yin Liu, Hongyu Zhao

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 233 KB

english, 2004

67

Combining gene expression data from different generations of oligonucleotide arrays

Kyu-Baek Hwang, Sek Won Kong, Steve A Greenberg, Peter J Park

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 612 KB

english, 2004

68

GOTree Machine (GOTM): a web-based platform for interpreting sets of interesting genes using Gene Ontology hierarchies

Bing Zhang, Denise Schmoyer, Stefan Kirov, Jay Snoddy

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 719 KB

english, 2004

69

Reuse of imputed data in microarray analysis increases imputation efficiency

Ki-Yeol Kim, Byoung-Jin Kim, Gwan-Su Yi

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 352 KB

english, 2004

70

Implications for domain fusion protein-protein interactions based on structural information

Jer-Ming Chia, Prasanna R Kolatkar

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 262 KB

english, 2004

71

Extractor for ESI quadrupole TOF tandem MS data enabled for high throughput batch processing

Andreas M Boehm, Robert P Galvin, Albert Sickmann

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 472 KB

english, 2004

72

TETRA: a web-service and a stand-alone program for the analysis and comparison of tetranucleotide usage patterns in DNA sequences

Hanno Teeling, Jost Waldmann, Thierry Lombardot, Margarete Bauer, Oliver Frank Glöckner

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 933 KB

english, 2004

73

Multivariate search for differentially expressed gene combinations

Yuanhui Xiao, Robert Frisina, Alexander Gordon, Lev Klebanov, Andrei Yakovlev

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 307 KB

english, 2004

74

Identification and utilization of inter-species conserved (ISC) probesets on Affymetrix human GeneChip®platforms for the optimization of the assessment of expression patterns in non human primate (NHP) samples

Zhining Wang, Mark G Lewis, Martin E Nau, Alma Arnold, Maryanne T Vahey

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 1.15 MB

english, 2004

75

A probabilistic model for the evolution of RNA structure

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 702 KB

english, 2004

76

Improvement of alignment accuracy utilizing sequentially conserved motifs

Saikat Chakrabarti, Nitin Bhardwaj, Prem A Anand, Ramanathan Sowdhamini

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 1.34 MB

english, 2004

77

d-matrix – database exploration, visualization and analysis

Dominik Seelow, Raffaello Galli, Siegrun Mebus, Hans-Peter Sperling, Hans Lehrach, Silke Sperling

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 1.58 MB

english, 2004

78

Oligo kernels for datamining on biological sequences: a case study on prokaryotic translation initiation sites

Peter Meinicke, Maike Tech, Burkhard Morgenstern, Rainer Merkl

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 338 KB

english, 2004

79

VisANT: an online visualization and analysis tool for biological interaction data

Zhenjun Hu, Joseph Mellor, Jie Wu, Charles DeLisi

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 571 KB

english, 2004

80

PhyME: A probabilistic algorithm for finding motifs in sets of orthologous sequences

Saurabh Sinha, Mathieu Blanchette, Martin Tompa

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 492 KB

english, 2004

81

SS-Wrapper: a package of wrapper applications for similarity searches on Linux clusters

Chunlin Wang, Elliot J Lefkowitz

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 301 KB

english, 2004

82

Incremental genetic K-means algorithm and its application in gene expression data analysis

Yi Lu, Shiyong Lu, Farshad Fotouhi, Youping Deng, Susan J Brown

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 296 KB

english, 2004

83

The InDeVal insertion/deletion evaluation tool: a program for finding target regions in DNA sequences and for aiding in sequence comparison

Sierra D Stoneberg Holt, Jason A Holt

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 282 KB

english, 2004

84

The Molecular Pages of the mesotelencephalic dopamine consortium (DopaNet)

Nicolas Le Novère, Marco Donizelli

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 277 KB

english, 2004

85

Computation of elementary modes: a unifying framework and the new binary approach

Julien Gagneur, Steffen Klamt

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 632 KB

english, 2004

86

ESTIMA, a tool for EST management in a multi-project environment

Charu G Kumar, Richard LeDuc, George Gong, Levan Roinishivili, Harris A Lewin, Lei Liu

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 1.14 MB

english, 2004

87

Calibration and assessment of channel-specific biases in microarray data with extended dynamical range

Henrik Bengtsson, Göran Jönsson, Johan Vallon-Christersson

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 2.49 MB

english, 2004

88

GOtcha: a new method for prediction of protein function assessed by the annotation of seven genomes

David MA Martin, Matthew Berriman, Geoffrey J Barton

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 457 KB

english, 2004

89

CLOE: Identification of putative functional relationships among genes by comparison of expression profiles between two species

Maurizio Pellegrino, Paolo Provero, Lorenzo Silengo, Ferdinando Di Cunto

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 326 KB

english, 2004

90

Quantifying the relationship between co-expression, co-regulation and gene function

Dominic J Allocco, Isaac S Kohane, Atul J Butte

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 405 KB

english, 2004

91

Performance of a genetic algorithm for mass spectrometry proteomics

Neal O Jeffries

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 301 KB

english, 2004

92

Discriminative topological features reveal biological network mechanisms

Manuel Middendorf, Etay Ziv, Carter Adams, Jen Hom, Robin Koytcheff, Chaya Levovitz, Gregory Woods, Linda Chen, Chris Wiggins

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 1.01 MB

english, 2004

93

A new mixture model approach to analyzing allelic-loss data using Bayes factors

Manisha Desai, Mary J Emond

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 306 KB

english, 2004

94

Protein family comparison using statistical models and predicted structural information

Richard Chung, Golan Yona

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 646 KB

english, 2004

95

Integrating partonomic hierarchies in anatomy ontologies

Albert Burger, Duncan Davidson, Yiya Yang, Richard Baldock

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 578 KB

english, 2004

96

Noise filtering and nonparametric analysis of microarray data underscores discriminating markers of oral, prostate, lung, ovarian and breast cancer

Virginie M Aris, Michael J Cody, Jeff Cheng, James J Dermody, Patricia Soteropoulos, Michael Recce, Peter P Tolias

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 362 KB

english, 2004

97

Constraint Logic Programming approach to protein structure prediction

Alessandro Dal Palù, Agostino Dovier, Federico Fogolari

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 359 KB

english, 2004

98

prot4EST: Translating Expressed Sequence Tags from neglected genomes

James D Wasmuth, Mark L Blaxter

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 832 KB

english, 2004

99

Haplotype frequency estimation error analysis in the presence of missing genotype data

Enda D Kelly, Fabian Sievers, Ross McManus

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 331 KB

english, 2004

100

DEDB: a database ofDrosophila melanogasterexons in splicing graph form

Bernett TK Lee, Tin Wee Tan, Shoba Ranganathan

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 865 KB

english, 2004

101

The tissue microarray data exchange specification: implementation by the Cooperative Prostate Cancer Tissue Resource

Jules J Berman, Milton Datta, Andre Kajdacsy-Balla, Jonathan Melamed, Jan Orenstein, Kevin Dobbin, Ashok Patel, Rajiv Dhir, Michael J Becich

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 1.11 MB

english, 2004

102

A two-way interface between limited Systems Biology Markup Language and R

Tomas Radivoyevitch

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 282 KB

english, 2004

103

Optimal cDNA microarray design using expressed sequence tags for organisms with limited genomic information

Yian A Chen, David J Mckillen, Shuyuan Wu, Matthew J Jenny, Robert Chapman, Paul S Gross, Gregory W Warr, Jonas S Almeida

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 382 KB

english, 2004

104

ABC: software for interactive browsing of genomic multiple sequence alignment data

Gregory M Cooper, Senthil AG Singaravelu, Arend Sidow

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 738 KB

english, 2004

105

Comparing functional annotation analyses with Catmap

Thomas Breslin, Patrik Edén, Morten Krogh

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 359 KB

english, 2004

106

Optimized LOWESS normalization parameter selection for DNA microarray data

John A Berger, Sampsa Hautaniemi, Anna-Kaarina Järvinen, Henrik Edgren, Sanjit K Mitra, Jaakko Astola

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 1.52 MB

english, 2004

107

GECKO: a complete large-scale gene expression analysis platform

Joachim Theilhaber, Anatoly Ulyanov, Anish Malanthara, Jack Cole, Dapeng Xu, Robert Nahf, Michael Heuer, Christoph Brockel, Steven Bushnell

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 507 KB

english, 2004

108

A functional hierarchical organization of the protein sequence space

Noam Kaplan, Moriah Friedlich, Menachem Fromer, Michal Linial

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 427 KB

english, 2004

109

SCOPmap: Automated assignment of protein structures to evolutionary superfamilies

Sara Cheek, Yuan Qi, S Sri Krishna, Lisa N Kinch, Nick V Grishin

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 4.24 MB

english, 2004

110

GenomeViz: visualizing microbial genomes

Rohit Ghai, Torsten Hain, Trinad Chakraborty

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 1.83 MB

english, 2004

111

Hierarchical structure and modules in theEscherichia colitranscriptional regulatory network revealed by a new top-down approach

Hong-Wu Ma, Jan Buer, An-Ping Zeng

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 644 KB

english, 2004

112

Using 3D Hidden Markov Models that explicitly represent spatial coordinates to model and compare protein structures

Vadim Alexandrov, Mark Gerstein

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 429 KB

english, 2004

113

MiCoViTo: a tool for gene-centric comparison and visualization of yeast transcriptome states

Gaëlle Lelandais, Philippe Marc, Pierre Vincens, Claude Jacq, Stéphane Vialette

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 429 KB

english, 2004

114

Analysis of superfamily specific profile-profile recognition accuracy

James A Casbon, Mansoor AS Saqi

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 268 KB

english, 2004

115

A novel Mixture Model Method for identification of differentially expressed genes from DNA microarray data

Kayvan Najarian, Maryam Zaheri, Ali A Rad, Siamak Najarian, Javad Dargahi

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 589 KB

english, 2004

116

Identifying spatially similar gene expression patterns in early stage fruit fly embryo images: binary feature versus invariant moment digital representations

Rajalakshmi Gurunathan, Bernard Van Emden, Sethuraman Panchanathan, Sudhir Kumar

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 1.32 MB

english, 2004

117

A power law global error model for the identification of differentially expressed genes in microarray data

Norman Pavelka, Mattia Pelizzola, Caterina Vizzardelli, Monica Capozzoli, Andrea Splendiani, Francesca Granucci, Paola Ricciardi-Castagnoli

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 1.62 MB

english, 2004

118

An SVD-based comparison of nine whole eukaryotic genomes supports a coelomate rather than ecdysozoan lineage

Gary W Stuart, Michael W Berry

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 443 KB

english, 2004

119

Predicting binding sites of hydrolase-inhibitor complexes by combining several methods

Taner Z Sen, Andrzej Kloczkowski, Robert L Jernigan, Changhui Yan, Vasant Honavar, Kai-Ming Ho, Cai-Zhuang Wang, Yungok Ihm, Haibo Cao, Xun Gu, Drena Dobbs

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 790 KB

english, 2004

120

An empirical analysis of training protocols for probabilistic gene finders

William H Majoros, Steven L Salzberg

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 341 KB

english, 2004

121

Clustering under the line graph transformation: application to reaction network

Jose C Nacher, Nobuhisa Ueda, Takuji Yamada, Minoru Kanehisa, Tatsuya Akutsu

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 837 KB

english, 2004

122

A database for G proteins and their interaction with GPCRs

Antigoni L Elefsinioti, Pantelis G Bagos, Ioannis C Spyropoulos, Stavros J Hamodrakas

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 1.22 MB

english, 2004

123

Analysis of oligonucleotide array experiments with repeated measures using mixed models

Hao Li, Constance L Wood, Thomas V Getchell, Marilyn L Getchell, Arnold J Stromberg

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 334 KB

english, 2004

124

Cancer characterization and feature set extraction by discriminative margin clustering

Kamesh Munagala, Robert Tibshirani, Patrick O Brown

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 1.65 MB

english, 2004

125

SIGI: score-based identification of genomic islands

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 588 KB

english, 2004

126

Gene prediction using the Self-Organizing Map: automatic generation of multiple gene models

Shaun Mahony, James O McInerney, Terry J Smith, Aaron Golden

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 432 KB

english, 2004

127

Biochemical Network Stochastic Simulator (BioNetS): software for stochastic modeling of biochemical networks

David Adalsteinsson, David McMillen, Timothy C Elston

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 1.01 MB

english, 2004

128

A web services choreography scenario for interoperating bioinformatics applications

Remko de Knikker, Youjun Guo, Jin-long Li, Albert KH Kwan, Kevin Y Yip, David W Cheung, Kei-Hoi Cheung

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 1.09 MB

english, 2004

129

Computational protein biomarker prediction: a case study for prostate cancer

Michael Wagner, Dayanand N Naik, Alex Pothen, Srinivas Kasukurti, Raghu Ram Devineni, Bao-Ling Adam, O John Semmes, George L Wright

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 349 KB

english, 2004

130

CisOrtho: A program pipeline for genome-wide identification of transcription factor target genes using phylogenetic footprinting

Henry R Bigelow, Adam S Wenick, Allan Wong, Oliver Hobert

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 518 KB

english, 2004

131

SUPFAM: A database of sequence superfamilies of protein domains

Shashi B Pandit, Rana Bhadra, VS Gowri, S Balaji, B Anand, N Srinivasan

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 241 KB

english, 2004

132

A Hidden Markov Model method, capable of predicting and discriminating β-barrel outer membrane proteins

Pantelis G Bagos, Theodore D Liakopoulos, Ioannis C Spyropoulos, Stavros J Hamodrakas

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 716 KB

english, 2004

133

VKCDB: Voltage-gated potassium channel database

Bin Li, Warren J Gallin

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 317 KB

english, 2004

134

Frequent occurrence of recognition Site-like sequences in the restriction endonucleases

Jan C Biro, Josephine MK Biro

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 1.47 MB

english, 2004

135

Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data

Feng Gao, Barrett C Foat, Harmen J Bussemaker

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 557 KB

english, 2004

136

Selection of informative clusters from hierarchical cluster tree with gene classes

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 722 KB

english, 2004

137

A SNP-centric database for the investigation of the human genome

Alberto Riva, Isaac S Kohane

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 307 KB

english, 2004

138

PASS2: an automated database of protein alignments organised as structural superfamilies

Anirban Bhaduri, Ganesan Pugalenthi, Ramanathan Sowdhamini

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 923 KB

english, 2004

139

Auto-validation of fluorescent primer extension genotyping assay using signal clustering and neural networks

Ching Yu Austin Huang, Joel Studebaker, Anton Yuryev, Jianping Huang, Kathryn E Scott, Jennifer Kuebler, Shobha Varde, Steven Alfisi, Craig A Gelfand, Mark Pohl, Michael T Boyce-Jacino

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 1.04 MB

english, 2004

140

Structural characterization of genomes by large scale sequence-structure threading

Artem Cherkasov, Steven JM Jones

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 1.03 MB

english, 2004

141

Predicting co-complexed protein pairs using genomic and proteomic data integration

Lan V Zhang, Sharyl L Wong, Oliver D King, Frederick P Roth

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 495 KB

english, 2004

142

MolTalk – a programming library for protein structures and structure analysis

Alexander V Diemand, Holger Scheib

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 351 KB

english, 2004

143

Identification of polymorphic tandem repeats by direct comparison of genome sequence from different bacterial strains : a web-based resource

France Denœud, Gilles Vergnaud

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 949 KB

english, 2004

144

Pegasys: software for executing and integrating analyses of biological sequences

Sohrab P Shah, David YM He, Jessica N Sawkins, Jeffrey C Druce, Gerald Quon, Drew Lett, Grace XY Zheng, Tao Xu, BF Francis Ouellette

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 589 KB

english, 2004

145

No statistical support for correlation between the positions of protein interaction sites and alternatively spliced regions

Marc N Offman, Ramil N Nurtdinov, Mikhail S Gelfand, Dmitrij Frishman

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 929 KB

english, 2004

146

Leveraging two-way probe-level block design for identifying differential gene expression with high-density oligonucleotide arrays

Leah Barrera, Chris Benner, Yong-Chuan Tao, Elizabeth Winzeler, Yingyao Zhou

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 1.79 MB

english, 2004

147

BioBuilder as a database development and functional annotation platform for proteins

J Daniel Navarro, Naveen Talreja, Suraj Peri, BM Vrushabendra, BP Rashmi, N Padma, Vineeth Surendranath, Chandra Kiran Jonnalagadda, PS Kousthub, Nandan Deshpande, K Shanker, Akhilesh Pandey

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 608 KB

english, 2004

148

Identification of regions in multiple sequence alignments thermodynamically suitable for targeting by consensus oligonucleotides: application to HIV genome

Olga V Matveeva, Brian T Foley, Vladimir A Nemtsov, Raymond F Gesteland, Senya Matsufuji, John F Atkins, Aleksey Y Ogurtsov, Svetlana A Shabalina

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 269 KB

english, 2004

149

A hybrid clustering approach to recognition of protein families in 114 microbial genomes

Timothy J Harlow, J Peter Gogarten, Mark A Ragan

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 443 KB

english, 2004

150

B.E.A.R. GeneInfo: A tool for identifying gene-related biomedical publications through user modifiable queries

Guohui Zhou, Xinyu Wen, Hang Liu, Michael J Schlicht, Martin J Hessner, Peter J Tonellato, Milton W Datta

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 424 KB

english, 2004

151

Hybrid clustering for microarray image analysis combining intensity and shape features

Jörg Rahnenführer, Daniel Bozinov

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 869 KB

english, 2004

152

Visualising very large phylogenetic trees in three dimensional hyperbolic space

Timothy Hughes, Young Hyun, David A Liberles

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 444 KB

english, 2004

153

An application of conditional logistic regression and multifactor dimensionality reduction for detecting gene-gene Interactions on risk of myocardial infarction: The importance of model validation

Christopher S Coffey, Patricia R Hebert, Marylyn D Ritchie, Harlan M Krumholz, J Michael Gaziano, Paul M Ridker, Nancy J Brown, Douglas E Vaughan, Jason H Moore

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 292 KB

english, 2004

154

Three-parameter lognormal distribution ubiquitously found in cDNA microarray data and its application to parametric data treatment

Tomokazu Konishi

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 2.63 MB

english, 2004

155

A structural study for the optimisation of functional motifs encoded in protein sequences

Allegra Via, Manuela Helmer-Citterich

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 849 KB

english, 2004

156

ASAView: Database and tool for solvent accessibility representation in proteins

Shandar Ahmad, Michael Gromiha, Hamed Fawareh, Akinori Sarai

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 442 KB

english, 2004

157

GeneOrder3.0: Software for comparing the order of genes in pairs of small bacterial genomes

Srikanth Celamkoti, Sashidhara Kundeti, Anjan Purkayastha, Raja Mazumder, Charles Buck, Donald Seto

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 278 KB

english, 2004

158

Statistical monitoring of weak spots for improvement of normalization and ratio estimates in microarrays

Igor Dozmorov, Nicholas Knowlton, Yuhong Tang, Michael Centola

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 728 KB

english, 2004

159

Resolution of large and small differences in gene expression using models for the Bayesian analysis of gene expression levels and spotted DNA microarrays

Jeffrey P Townsend

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 471 KB

english, 2004

160

eL-DASionator: an LDAS upload file generator

Vincent Negre, Christoph Grunau

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 198 KB

english, 2004

161

Enhanced protein domain discovery using taxonomy

Lachlan Coin, Alex Bateman, Richard Durbin

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 326 KB

english, 2004

162

Computational identification of transcription factor binding sites by functional analysis of sets of genes sharing overrep-resented upstream motifs

Davide Corà, Ferdinando Di Cunto, Paolo Provero, Lorenzo Silengo, Michele Caselle

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 316 KB

english, 2004

163

Use of a structural alphabet for analysis of short loops connecting repetitive structures

Laurent Fourrier, Cristina Benros, Alexandre G de Brevern

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 1.60 MB

english, 2004

164

Gene finding in novel genomes

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 536 KB

english, 2004

165

Benchmarking tools for the alignment of functional noncoding DNA

Daniel A Pollard, Casey M Bergman, Jens Stoye, Susan E Celniker, Michael B Eisen

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 576 KB

english, 2004

166

Graphical technique for identifying a monotonic variance stabilizing transformation for absolute gene intensity signals

Kellie J Archer, Catherine I Dumur, Viswanathan Ramakrishnan

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 385 KB

english, 2004

167

An approach to large scale identification of non-obvious structural similarities between proteins

Artem Cherkasov, Steven JM Jones

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 1.62 MB

english, 2004

168

A fast algorithm for determining the best combination of local alignments to a query sequence

Gavin C Conant, Andreas Wagner

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 330 KB

english, 2004

169

Feature selection for splice site prediction: A new method using EDA-based feature ranking

Yvan Saeys, Sven Degroeve, Dirk Aeyels, Pierre Rouzé, Yves Van de Peer

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 409 KB

english, 2004

170

Bioinformatics analysis of SARS coronavirus genome polymorphism

Gordana M Pavlović-Lažetić, Nenad S Mitić, Miloš V Beljanski

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 501 KB

english, 2004

171

Esub8: A novel tool to predict protein subcellular localizations in eukaryotic organisms

Qinghua Cui, Tianzi Jiang, Bing Liu, Songde Ma

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 280 KB

english, 2004

172

Genome SEGE: A database for 'intronless' genes in eukaryotic genomes

Meena Kishore Sakharkar, Pandjassarame Kangueane

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 455 KB

english, 2004

173

Detection of chromosomal regions showing differential gene expression in human skeletal muscle and in alveolar rhabdomyosarcoma

Andrea Bisognin, Stefania Bortoluzzi, Gian Antonio Danieli

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 323 KB

english, 2004

174

pdb-care (PDB CArbohydrate REsidue check): a program to support annotation of complex carbohydrate structures in PDB files

Thomas Lütteke, Claus-W von der Lieth

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 1.40 MB

english, 2004

175

HMM Logos for visualization of protein families

Benjamin Schuster-Böckler, Jörg Schultz, Sven Rahmann

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 493 KB

english, 2004

176

Multiclass discovery in array data

Yingchun Liu, Markus Ringnér

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 313 KB

english, 2004

177

Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction

Robin D Dowell, Sean R Eddy

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 402 KB

english, 2004

178

Coronavirus 3CLproproteinase cleavage sites: Possible relevance to SARS virus pathology

Lars Kiemer, Ole Lund, Søren Brunak, Nikolaj Blom

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 368 KB

english, 2004

179

Correction: Benchmarking tools for the alignment of functional noncoding DNA

DA Pollard, CM Bergman, J Stoye, SE Celniker, MB Eisen

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 350 KB

english, 2004

180

M-CGH: Analysing microarray-based CGH experiments

Junbai Wang, Leonardo A Meza-Zepeda, Stine H Kresse, Ola Myklebost

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 499 KB

english, 2004

181

Interaction profile-based protein classification of death domain

Drew Lett, Michael Hsing, Frederic Pio

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 464 KB

english, 2004

182

A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases

Michelle L Green, Peter D Karp

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 442 KB

english, 2004

183

Comparing transformation methods for DNA microarray data

Helene H Thygesen, Aeilko H Zwinderman

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 360 KB

english, 2004

184

Phospho.ELM: A database of experimentally verified phosphorylation sites in eukaryotic proteins

Francesca Diella, Scott Cameron, Christine Gemünd, Rune Linding, Allegra Via, Bernhard Kuster, Thomas Sicheritz-Pontén, Nikolaj Blom, Toby J Gibson

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 243 KB

english, 2004

185

FRAGS: estimation of coding sequence substitution rates from fragmentary data

Estienne C Swart, Winston A Hide, Cathal Seoighe

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 691 KB

english, 2004

186

Mistaken Identifiers: Gene name errors can be introduced inadvertently when using Excel in bioinformatics

Barry R Zeeberg, Joseph Riss, David W Kane, Kimberly J Bussey, Edward Uchio, W Marston Linehan, J Carl Barrett, John N Weinstein

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 664 KB

english, 2004

187

Joint analysis of two microarray gene-expression data sets to select lung adenocarcinoma marker genes

Hongying Jiang, Youping Deng, Huann-Sheng Chen, Lin Tao, Qiuying Sha, Jun Chen, Chung-Jui Tsai, Shuanglin Zhang

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 1.49 MB

english, 2004

188

Correction: Three-parameter lognormal distribution ubiquitously found in cDNA microarray data and its application to parametric data treatment

Tomokazu Konishi

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 148 KB

english, 2004

189

TheMB2gene family ofPlasmodiumspecies has a unique combination of S1 and GTP-binding domains

Lisa C Romero, Thanh V Nguyen, Benoit Deville, Oluwasanmi Ogunjumo, Anthony A James

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 528 KB

english, 2004

190

Visualization and analysis of microarray and gene ontology data with treemaps

Eric H Baehrecke, Niem Dang, Ketan Babaria, Ben Shneiderman

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 2.81 MB

english, 2004

191

Asynchronous adaptive time step in quantitative cellular automata modeling

Hao Zhu, Peter YH Pang, Yan Sun, Pawan Dhar

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 408 KB

english, 2004

192

mlstdbNet – distributed multi-locus sequence typing (MLST) databases

Keith A Jolley, Man-Suen Chan, Martin CJ Maiden

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 571 KB

english, 2004

193

galaxieEST: addressing EST identity through automated phylogenetic analysis

R Henrik Nilsson, Balaji Rajashekar, Karl-Henrik Larsson, Björn M Ursing

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 203 KB

english, 2004

194

RAG: RNA-As-Graphs web resource

Daniela Fera, Namhee Kim, Nahum Shiffeldrim, Julie Zorn, Uri Laserson, Hin Hark Gan, Tamar Schlick

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 466 KB

english, 2004

195

A double classification tree search algorithm for index SNP selection

Peisen Zhang, Huitao Sheng, Ryuhei Uehara

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 239 KB

english, 2004

196

An XML standard for the dissemination of annotated 2D gel electrophoresis data complemented with mass spectrometry results

Romesh Stanislaus, Liu Hong Jiang, Martha Swartz, John Arthur, Jonas S Almeida

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 366 KB

english, 2004

197

Global features of sequences of bacterial chromosomes, plasmids and phages revealed by analysis of oligonucleotide usage patterns

Oleg N Reva, Burkhard Tümmler

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 467 KB

english, 2004

198

SPOC: A widely distributed domain associated with cancer, apoptosis and transcription

Luis Sánchez-Pulido, Ana M Rojas, Karel H van Wely, Carlos Martinez-A, Alfonso Valencia

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 836 KB

english, 2004

199

Target SNP selection in complex disease association studies

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 260 KB

english, 2004

200

Delayed impact: ISI's citation tracking choices are keeping scientists in the dark

Matthew J Cockerill

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 200 KB

english, 2004

201

Detection of transposable elements by their compositional bias

Olivier Andrieu, Anna-Sophie Fiston, Dominique Anxolabéhère, Hadi Quesneville

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 320 KB

english, 2004

202

Clustering proteins from interaction networks for the prediction of cellular functions

Christine Brun, Carl Herrmann, Alain Guénoche

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 307 KB

english, 2004

203

Base-By-Base: Single nucleotide-level analysis of whole viral genome alignments

Ryan Brodie, Alex J Smith, Rachel L Roper, Vasily Tcherepanov, Chris Upton

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 650 KB

english, 2004

204

Integrated web service for improving alignment quality based on segments comparison

Dariusz Plewczynski, Leszek Rychlewski, Yuzhen Ye, Lukasz Jaroszewski, Adam Godzik

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 402 KB

english, 2004

205

Accuracy of cDNA microarray methods to detect small gene expression changes induced by neuregulin on breast epithelial cells

Bin Yao, Sanjay N Rakhade, Qunfang Li, Sharlin Ahmed, Raul Krauss, Sorin Draghici, Jeffrey A Loeb

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 1.56 MB

english, 2004

206

PyEvolve: a toolkit for statistical modelling of molecular evolution

Andrew Butterfield, Vivek Vedagiri, Edward Lang, Cath Lawrence, Matthew J Wakefield, Alexander Isaev, Gavin A Huttley

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 332 KB

english, 2004

207

Iterative Group Analysis (iGA): A simple tool to enhance sensitivity and facilitate interpretation of microarray experiments

Rainer Breitling, Anna Amtmann, Pawel Herzyk

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 273 KB

english, 2004

208

Two-stage normalization using background intensities in cDNA microarray data

Dankyu Yoon, Sung-Gon Yi, Ju-Han Kim, Taesung Park

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 346 KB

english, 2004

209

Boosting accuracy of automated classification of fluorescence microscope images for location proteomics

Kai Huang, Robert F Murphy

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 1.39 MB

english, 2004