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  1. Substantial amounts of data on cell signaling, metabolic, gene regulatory and other biological pathways have been accumulated in literature and electronic databases. Conventionally, this information is stored ...

    Authors: Michael Hsing, Joel L Bellenson, Conor Shankey and Artem Cherkasov
    Citation: BMC Bioinformatics 2004 5:156
  2. Identifying protein-protein interactions is fundamental for understanding the molecular machinery of the cell. Proteome-wide studies of protein-protein interactions are of significant value, but the high-throu...

    Authors: Nan Lin, Baolin Wu, Ronald Jansen, Mark Gerstein and Hongyu Zhao
    Citation: BMC Bioinformatics 2004 5:154
  3. Microarray-based comparative genome hybridization experiments generate data that can be mapped onto the genome. These data are interpreted more easily when represented graphically in a genomic context.

    Authors: Ihab AB Awad, Christian A Rees, Tina Hernandez-Boussard, Catherine A Ball and Gavin Sherlock
    Citation: BMC Bioinformatics 2004 5:151
  4. The rapidly increasing number of completely sequenced genomes led to the establishment of the COG-database which, based on sequence homologies, assigns similar proteins from different organisms to clusters of ...

    Authors: Florian Meereis and Michael Kaufmann
    Citation: BMC Bioinformatics 2004 5:150
  5. The hit criterion is a key component of heuristic local alignment algorithms. It specifies a class of patterns assumed to witness a potential similarity, and this choice is decisive for the selectivity and sen...

    Authors: Laurent Noé and Gregory Kucherov
    Citation: BMC Bioinformatics 2004 5:149
  6. A key step in the analysis of microarray expression profiling data is the identification of genes that display statistically significant changes in expression signals between two biological conditions.

    Authors: Dietmar E Martin, Philippe Demougin, Michael N Hall and Michel Bellis
    Citation: BMC Bioinformatics 2004 5:148
  7. Researchers who use MEDLINE for text mining, information extraction, or natural language processing may benefit from having a copy of MEDLINE that they can manage locally. The National Library of Medicine (NLM...

    Authors: Diane E Oliver, Gaurav Bhalotia, Ariel S Schwartz, Russ B Altman and Marti A Hearst
    Citation: BMC Bioinformatics 2004 5:146
  8. Serial Analysis of Gene Expression (SAGE) is a method of large-scale gene expression analysis that has the potential to generate the full list of mRNAs present within a cell population at a given time and thei...

    Authors: Céline Keime, Francesca Damiola, Dominique Mouchiroud, Laurent Duret and Olivier Gandrillon
    Citation: BMC Bioinformatics 2004 5:143
  9. Microarray is a high-throughput technology to study expression of thousands of genes in parallel. A critical aspect of microarray production is the design aimed at space optimization while maximizing the numbe...

    Authors: Anu Sharma, Gyan Prakash Srivastava, Vineet K Sharma and Srinivasan Ramachandran
    Citation: BMC Bioinformatics 2004 5:142
  10. When publishing large-scale microarray datasets, it is of great value to create supplemental websites where either the full data, or selected subsets corresponding to figures within the paper, can be browsed. ...

    Authors: Christian A Rees, Janos Demeter, John C Matese, David Botstein and Gavin Sherlock
    Citation: BMC Bioinformatics 2004 5:141
  11. MicroRNAs are ~17–24 nt. noncoding RNAs found in all eukaryotes that degrade messenger RNAs via RNA interference (if they bind in a perfect or near-perfect complementarity to the target mRNA), or arrest transl...

    Authors: Neil R Smalheiser and Vetle I Torvik
    Citation: BMC Bioinformatics 2004 5:139
  12. The insect exoskeleton or cuticle is a bi-partite composite of proteins and chitin that provides protective, skeletal and structural functions. Little information is available about the molecular structure of ...

    Authors: Christiana K Magkrioti, Ioannis C Spyropoulos, Vassiliki A Iconomidou, Judith H Willis and Stavros J Hamodrakas
    Citation: BMC Bioinformatics 2004 5:138
  13. Mutations in rpoB, the gene encoding the β subunit of DNA-dependent RNA polymerase, are associated with rifampin resistance in Mycobacterium tuberculosis. Several studies have been conducted where minimum inhibit...

    Authors: Michael P Cummings and Mark R Segal
    Citation: BMC Bioinformatics 2004 5:137
  14. Microarray experiments are becoming a powerful tool for clinical diagnosis, as they have the potential to discover gene expression patterns that are characteristic for a particular disease. To date, this probl...

    Authors: Bing Liu, Qinghua Cui, Tianzi Jiang and Songde Ma
    Citation: BMC Bioinformatics 2004 5:136
  15. This paper presents the use of Support Vector Machines (SVMs) for prediction and analysis of antisense oligonucleotide (AO) efficacy. The collected database comprises 315 AO molecules including 68 features eac...

    Authors: Gustavo Camps-Valls, Alistair M Chalk, Antonio J Serrano-López, José D Martín-Guerrero and Erik LL Sonnhammer
    Citation: BMC Bioinformatics 2004 5:135
  16. Novel proteins entering the food chain, for example by genetic modification of plants, have to be tested for allergenicity. Allermatch™ http://​allermatch.​org

    Authors: Mark WEJ Fiers, Gijs A Kleter, Herman Nijland, Ad ACM Peijnenburg, Jan Peter Nap and Roeland CHJ van Ham
    Citation: BMC Bioinformatics 2004 5:133
  17. Peach is being developed as a model organism for Rosaceae, an economically important family that includes fruits and ornamental plants such as apple, pear, strawberry, cherry, almond and rose. The genomics and...

    Authors: Sook Jung, Christopher Jesudurai, Margaret Staton, Zhidian Du, Stephen Ficklin, Ilhyung Cho, Albert Abbott, Jeffrey Tomkins and Dorrie Main
    Citation: BMC Bioinformatics 2004 5:130
  18. The discovery of cis-regulatory modules in metazoan genomes is crucial for understanding the connection between genes and organism diversity. It is important to quantify how comparative genomics can improve co...

    Authors: Saurabh Sinha, Mark D Schroeder, Ulrich Unnerstall, Ulrike Gaul and Eric D Siggia
    Citation: BMC Bioinformatics 2004 5:129
  19. Proteins having similar functions from different sources can be identified by the occurrence in their sequences, a conserved cluster of amino acids referred to as pattern, motif, signature or fingerprint. The ...

    Authors: Anuradha Vivekanandan Giri, Sharmila Anishetty and Pennathur Gautam
    Citation: BMC Bioinformatics 2004 5:127
  20. Thousands of genes in a genomewide data set are tested against some null hypothesis, for detecting differentially expressed genes in microarray experiments. The expected proportion of false positive genes in a...

    Authors: J Aubert, A Bar-Hen, J-J Daudin and S Robin
    Citation: BMC Bioinformatics 2004 5:125

    The Erratum to this article has been published in BMC Bioinformatics 2005 6:42

  21. The prediction of ancestral protein sequences from multiple sequence alignments is useful for many bioinformatics analyses. Predicting ancestral sequences is not a simple procedure and relies on accurate align...

    Authors: Richard J Edwards and Denis C Shields
    Citation: BMC Bioinformatics 2004 5:123
  22. Conserved protein sequence motifs are short stretches of amino acid sequence patterns that potentially encode the function of proteins. Several sequence pattern searching algorithms and programs exist forident...

    Authors: Xinghua Lu, Chengxiang Zhai, Vanathi Gopalakrishnan and Bruce G Buchanan
    Citation: BMC Bioinformatics 2004 5:122
  23. Screening of various gene markers such as single nucleotide polymorphism (SNP) and correlation between these markers and development of multifactorial disease have previously been studied. Here, we propose a s...

    Authors: Yasuyuki Tomita, Shuta Tomida, Yuko Hasegawa, Yoichi Suzuki, Taro Shirakawa, Takeshi Kobayashi and Hiroyuki Honda
    Citation: BMC Bioinformatics 2004 5:120
  24. An important challenge for transcript counting methods such as Serial Analysis of Gene Expression (SAGE), "Digital Northern" or Massively Parallel Signature Sequencing (MPSS), is to carry out statistical analy...

    Authors: Ricardo ZN Vêncio, Helena Brentani, Diogo FC Patrão and Carlos AB Pereira
    Citation: BMC Bioinformatics 2004 5:119
  25. The information theoretic concept of mutual information provides a general framework to evaluate dependencies between variables. In the context of the clustering of genes with similar patterns of expression it...

    Authors: Carsten O Daub, Ralf Steuer, Joachim Selbig and Sebastian Kloska
    Citation: BMC Bioinformatics 2004 5:118
  26. The current progress in sequencing projects calls for rapid, reliable and accurate function assignments of gene products. A variety of methods has been designed to annotate sequences on a large scale. However,...

    Authors: Arunachalam Vinayagam, Rainer König, Jutta Moormann, Falk Schubert, Roland Eils, Karl-Heinz Glatting and Sándor Suhai
    Citation: BMC Bioinformatics 2004 5:116
  27. The nematode Caenorhabditis elegans is widely used for the genetic analysis of neuronal cell biology, development, and behavior. Because traditional methods for evaluating behavioral phenotypes are qualitative an...

    Authors: Zhaoyang Feng, Christopher J Cronin, John H Wittig Jr, Paul W Sternberg and William R Schafer
    Citation: BMC Bioinformatics 2004 5:115
  28. Microarray technologies produced large amount of data. The hierarchical clustering is commonly used to identify clusters of co-expressed genes. However, microarray datasets often contain missing values (MVs) r...

    Authors: Alexandre G de Brevern, Serge Hazout and Alain Malpertuy
    Citation: BMC Bioinformatics 2004 5:114
  29. A necessary step for a genome level analysis of the cellular metabolism is the in silico reconstruction of the metabolic network from genome sequences. The available methods are mainly based on the annotation of ...

    Authors: Jibin Sun and An-Ping Zeng
    Citation: BMC Bioinformatics 2004 5:112
  30. Short oligonucleotide arrays have several probes measuring the expression level of each target transcript. Therefore the selection of probes is a key component for the quality of measurements. However, once pr...

    Authors: Laurent Gautier, Morten Møller, Lennart Friis-Hansen and Steen Knudsen
    Citation: BMC Bioinformatics 2004 5:111
  31. Microarray studies in cancer compare expression levels between two or more sample groups on thousands of genes. Data analysis follows a population-level approach (e.g., comparison of sample means) to identify ...

    Authors: James Lyons-Weiler, Satish Patel, Michael J Becich and Tony E Godfrey
    Citation: BMC Bioinformatics 2004 5:110
  32. Recent technological advances in high-throughput data collection allow for experimental study of increasingly complex systems on the scale of the whole cellular genome and proteome. Gene network models are nee...

    Authors: Bahrad A Sokhansanj, Patrick J Fitch, Judy N Quong and Andrew A Quong
    Citation: BMC Bioinformatics 2004 5:108
  33. The integration of many aspects of protein/DNA structure analysis is an important requirement for software products in general area of structural bioinformatics. In fact, there are too few software packages on...

    Authors: Roberto H Higa, Roberto C Togawa, Arnaldo J Montagner, Juliana CF Palandrani, Igor KS Okimoto, Paula R Kuser, Michel EB Yamagishi, Adauto L Mancini and Goran Neshich
    Citation: BMC Bioinformatics 2004 5:107
  34. A detailed understanding of an RNA's correct secondary and tertiary structure is crucial to understanding its function and mechanism in the cell. Free energy minimization with energy parameters based on the ne...

    Authors: Kishore J Doshi, Jamie J Cannone, Christian W Cobaugh and Robin R Gutell
    Citation: BMC Bioinformatics 2004 5:105

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