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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

    Content type: Methodology article

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  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

    Content type: Research article

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  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

    Content type: Software

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  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

    Content type: Software

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  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

    Content type: Methodology article

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  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

    Content type: Methodology article

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  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

    Content type: Software

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  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

    Content type: Software

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  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

    Content type: Software

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  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

    Content type: Software

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  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

    Content type: Research article

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  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

    Content type: Database

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  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

    Content type: Research article

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  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

    Content type: Research article

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  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

    Content type: Research article

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  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

    Content type: Database

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  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

    Content type: Database

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  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

    Content type: Research article

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  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

    Content type: Methodology article

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  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

    Content type: Research article

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    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

    Content type: Software

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  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

    Content type: Methodology article

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  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

    Content type: Research article

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  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

    Content type: Methodology article

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  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

    Content type: Methodology article

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  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

    Content type: Methodology article

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  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

    Content type: Software

    Published on:

  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

    Content type: Research article

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  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

    Content type: Methodology article

    Published on:

  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

    Content type: Methodology article

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  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

    Content type: Methodology article

    Published on:

  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

    Content type: Methodology article

    Published on:

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