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  1. There are many fewer genes in the human genome than there are expressed transcripts. Alternative splicing is the reason. Alternatively spliced transcripts are often specific to tissue type, developmental stage...

    Authors: Ari B Kahn, Michael C Ryan, Hongfang Liu, Barry R Zeeberg, D Curtis Jamison and John N Weinstein
    Citation: BMC Bioinformatics 2007 8:75
    Content type: Database Published on:

  2. A microarray study may select different differentially expressed gene sets because of different selection criteria. For example, the fold-change and p-value are two commonly known criteria to select differenti...

    Authors: James J Chen, Chen-An Tsai, ShengLi Tzeng and Chun-Houh Chen
    Citation: BMC Bioinformatics 2007 8:74
    Content type: Methodology article Published on:

  3. SPOUT methyltransferases (MTases) are a large class of S-adenosyl-L-methionine-dependent enzymes that exhibit an unusual alpha/beta fold with a very deep topological knot. In 2001, when no crystal structures w...

    Authors: Karolina L Tkaczuk, Stanislaw Dunin-Horkawicz, Elzbieta Purta and Janusz M Bujnicki
    Citation: BMC Bioinformatics 2007 8:73
    Content type: Research article Published on:

  4. Density plot visualizations (also referred to as heat maps or color maps) are widely used in different fields including large-scale omics studies in biological sciences. However, the current color-codings limi...

    Authors: Richard Baran, Martin Robert, Makoto Suematsu, Tomoyoshi Soga and Masaru Tomita
    Citation: BMC Bioinformatics 2007 8:72
    Content type: Methodology article Published on:

  5. S/MARs are regions of the DNA that are attached to the nuclear matrix. These regions are known to affect substantially the expression of genes. The computer prediction of S/MARs is a highly significant task wh...

    Authors: Kenneth Evans, Sascha Ott, Annika Hansen, Georgy Koentges and Lorenz Wernisch
    Citation: BMC Bioinformatics 2007 8:71
    Content type: Research article Published on:

  6. The question of how a circle or line segment becomes covered when random arcs are marked off has arisen repeatedly in bioinformatics. The number of uncovered gaps is of particular interest. Approximate distrib...

    Authors: John Moriarty, Julian R Marchesi and Anthony Metcalfe
    Citation: BMC Bioinformatics 2007 8:70
    Content type: Methodology article Published on:

  7. MicroRNAs have emerged as important regulatory genes in a variety of cellular processes and, in recent years, hundreds of such genes have been discovered in animals. In contrast, functional annotations are ava...

    Authors: Dimos Gaidatzis, Erik van Nimwegen, Jean Hausser and Mihaela Zavolan
    Citation: BMC Bioinformatics 2007 8:69
    Content type: Research article Published on:

    The Erratum to this article has been published in BMC Bioinformatics 2007 8:248

  8. False occurrences of functional motifs in protein sequences can be considered as random events due solely to the sequence composition of a proteome. Here we use a numerical approach to investigate the random a...

    Authors: Allegra Via, Pier Federico Gherardini, Enrico Ferraro, Gabriele Ausiello, Gianpaolo Scalia Tomba and Manuela Helmer-Citterich
    Citation: BMC Bioinformatics 2007 8:68
    Content type: Research article Published on:

  10. The significant advances in microarray and proteomics analyses have resulted in an exponential increase in potential new targets and have promised to shed light on the identification of disease markers and cel...

    Authors: Chun-Nan Hsu, Jin-Mei Lai, Chia-Hung Liu, Huei-Hun Tseng, Chih-Yun Lin, Kuan-Ting Lin, Hsu-Hua Yeh, Ting-Yi Sung, Wen-Lian Hsu, Li-Jen Su, Sheng-An Lee, Chang-Han Chen, Gen-Cher Lee, DT Lee, Yow-Ling Shiue, Chang-Wei Yeh…
    Citation: BMC Bioinformatics 2007 8:66
    Content type: Methodology article Published on:

  11. Protein aggregation correlates with the development of several debilitating human disorders of growing incidence, such as Alzheimer's and Parkinson's diseases. On the biotechnological side, protein production ...

    Authors: Oscar Conchillo-Solé, Natalia S de Groot, Francesc X Avilés, Josep Vendrell, Xavier Daura and Salvador Ventura
    Citation: BMC Bioinformatics 2007 8:65
    Content type: Software Published on:

  12. Genome assemblers have grown very large and complex in response to the need for algorithms to handle the challenges of large whole-genome sequencing projects. Many of the most common uses of assemblers, howeve...

    Authors: Daniel D Sommer, Arthur L Delcher, Steven L Salzberg and Mihai Pop
    Citation: BMC Bioinformatics 2007 8:64
    Content type: Software Published on:

  13. When aligning several hundreds or thousands of sequences, such as epidemic virus sequences or homologous/orthologous sequences of some big gene families, to reconstruct the epidemiological history or their phy...

    Authors: Arthur Chun-Chieh Shih, DT Lee, Chin-Lin Peng and Yu-Wei Wu
    Citation: BMC Bioinformatics 2007 8:63
    Content type: Software Published on:

  14. The post-genomic era is characterised by a torrent of biological information flooding the public databases. As a direct consequence, similarity searches starting with a single query sequence frequently lead to...

    Authors: Anne Friedrich, Raymond Ripp, Nicolas Garnier, Emmanuel Bettler, Gilbert Deléage, Olivier Poch and Luc Moulinier
    Citation: BMC Bioinformatics 2007 8:62
    Content type: Methodology article Published on:

  17. There is a need for software applications that provide users with a complete and extensible toolkit for chemo- and bioinformatics accessible from a single workbench. Commercial packages are expensive and close...

    Authors: Ola Spjuth, Tobias Helmus, Egon L Willighagen, Stefan Kuhn, Martin Eklund, Johannes Wagener, Peter Murray-Rust, Christoph Steinbeck and Jarl ES Wikberg
    Citation: BMC Bioinformatics 2007 8:59
    Content type: Software Published on:

  18. Backtranslation is the process of decoding a sequence of amino acids into the corresponding codons. All synthetic gene design systems include a backtranslation module. The degeneracy of the genetic code makes ...

    Authors: Alfredo Ferro, Rosalba Giugno, Giuseppe Pigola, Alfredo Pulvirenti, Cinzia Di Pietro, Michele Purrello and Marco Ragusa
    Citation: BMC Bioinformatics 2007 8:58
    Content type: Software Published on:

  19. The bio-ontology community falls into two camps: first we have biology domain experts, who actually hold the knowledge we wish to capture in ontologies; second, we have ontology specialists, who hold knowledge...

    Authors: Mikel Egaña Aranguren, Sean Bechhofer, Phillip Lord, Ulrike Sattler and Robert Stevens
    Citation: BMC Bioinformatics 2007 8:57
    Content type: Commentary Published on:

  20. Computational analysis of gene regulatory regions is important for prediction of functions of many uncharacterized genes. With this in mind, search of the target genes for interferon (IFN) induction appears of...

    Authors: Elena A Ananko, Yury V Kondrakhin, Tatiana I Merkulova and Nikolay A Kolchanov
    Citation: BMC Bioinformatics 2007 8:56
    Content type: Research article Published on:

  24. One of the crucial aspects of day-to-day laboratory information management is collection, storage and retrieval of information about research subjects and biomedical samples. An efficient link between sample d...

    Authors: Juris Viksna, Edgars Celms, Martins Opmanis, Karlis Podnieks, Peteris Rucevskis, Andris Zarins, Amy Barrett, Sudeshna Guha Neogi, Maria Krestyaninova, Mark I McCarthy, Alvis Brazma and Ugis Sarkans
    Citation: BMC Bioinformatics 2007 8:52
    Content type: Software Published on:

  25. In proteomics experiments, database-search programs are the method of choice for protein identification from tandem mass spectra. As amino acid sequence databases grow however, computing resources required for...

    Authors: Jason WH Wong, Matthew J Sullivan, Hugh M Cartwright and Gerard Cagney
    Citation: BMC Bioinformatics 2007 8:51
    Content type: Methodology article Published on:

  26. Lately, there has been a great interest in the application of information extraction methods to the biomedical domain, in particular, to the extraction of relationships of genes, proteins, and RNA from scienti...

    Authors: Sampo Pyysalo, Filip Ginter, Juho Heimonen, Jari Björne, Jorma Boberg, Jouni Järvinen and Tapio Salakoski
    Citation: BMC Bioinformatics 2007 8:50
    Content type: Research article Published on:

  27. Integration of multiple results from Quantitative Trait Loci (QTL) studies is a key point to understand the genetic determinism of complex traits. Up to now many efforts have been made by public database devel...

    Authors: Jean-Baptiste Veyrieras, Bruno Goffinet and Alain Charcosset
    Citation: BMC Bioinformatics 2007 8:49
    Content type: Methodology article Published on:

  29. Computational prediction methods are currently used to identify genes in prokaryote genomes. However, identification of the correct translation initiation sites remains a difficult task. Accurate translation i...

    Authors: Yuko Makita, Michiel JL de Hoon and Antoine Danchin
    Citation: BMC Bioinformatics 2007 8:47
    Content type: Methodology article Published on:

  31. The mechanisms underlying protein function and associated conformational change are dominated by a series of local entropy fluctuations affecting the global structure yet are mediated by only a few key residue...

    Authors: Jenny Gu and Philip E Bourne
    Citation: BMC Bioinformatics 2007 8:45
    Content type: Research article Published on:

  32. Biological information is commonly used to cluster or classify entities of interest such as genes, conditions, species or samples. However, different sources of data can be used to classify the same set of ent...

    Authors: Francisco R Pinto, João A Carriço, Mário Ramirez and Jonas S Almeida
    Citation: BMC Bioinformatics 2007 8:44
    Content type: Methodology article Published on:

  33. One of the essential processing events during pre-mRNA maturation is the post-transcriptional addition of a polyadenine [poly(A)] tail. The 3'-end poly(A) track protects mRNA from unregulated degradation, and ...

    Authors: Guoli Ji, Jianti Zheng, Yingjia Shen, Xiaohui Wu, Ronghan Jiang, Yun Lin, Johnny C Loke, Kimberly M Davis, Greg J Reese and Qingshun Quinn Li
    Citation: BMC Bioinformatics 2007 8:43
    Content type: Research article Published on:

  34. Transcription factors (TFs) are key regulatory proteins that enhance or repress the transcriptional rate of their target genes by binding to specific promoter regions (i.e. cis-acting elements) upon activation or...

    Authors: Diego Mauricio Riaño-Pachón, Slobodan Ruzicic, Ingo Dreyer and Bernd Mueller-Roeber
    Citation: BMC Bioinformatics 2007 8:42
    Content type: Database Published on:

  35. Genome-wide expression, sequence and association studies typically yield large sets of gene candidates, which must then be further analysed and interpreted. Information about these genes is increasingly being ...

    Authors: Kay Prüfer, Bjoern Muetzel, Hong-Hai Do, Gunter Weiss, Philipp Khaitovich, Erhard Rahm, Svante Pääbo, Michael Lachmann and Wolfgang Enard
    Citation: BMC Bioinformatics 2007 8:41
    Content type: Software Published on:

  37. Metalloproteins are proteins capable of binding one or more metal ions, which may be required for their biological function, for regulation of their activities or for structural purposes. Metal-binding propert...

    Authors: Andrea Passerini, Claudia Andreini, Sauro Menchetti, Antonio Rosato and Paolo Frasconi
    Citation: BMC Bioinformatics 2007 8:39
    Content type: Research article Published on:

  38. In order to recapitulate tumor progression pathways using epigenetic data, we developed novel clustering and pathway reconstruction algorithms, collectively referred to as heritable clustering. This approach g...

    Authors: Zailong Wang, Pearlly Yan, Dustin Potter, Charis Eng, Tim H-M Huang and Shili Lin
    Citation: BMC Bioinformatics 2007 8:38
    Content type: Research article Published on:

  40. Genotype information generated by individual and international efforts carries the promise of revolutionizing disease studies and the association of phenotypes with alleles and haplotypes. Given the enormous a...

    Authors: Ofir Davidovich, Gad Kimmel and Ron Shamir
    Citation: BMC Bioinformatics 2007 8:36
    Content type: Software Published on:

  41. Microarrays have become extremely useful for analysing genetic phenomena, but establishing a relation between microarray analysis results (typically a list of genes) and their biological significance is often ...

    Authors: Franck Rapaport, Andrei Zinovyev, Marie Dutreix, Emmanuel Barillot and Jean-Philippe Vert
    Citation: BMC Bioinformatics 2007 8:35
    Content type: Research article Published on:

  46. The progress in the "-omic" sciences has allowed a deeper knowledge on many biological systems with industrial interest. This knowledge is still rarely used for advanced bioprocess monitoring and control at th...

    Authors: Ana P Teixeira, Carlos Alves, Paula M Alves, Manuel JT Carrondo and Rui Oliveira
    Citation: BMC Bioinformatics 2007 8:30
    Content type: Methodology article Published on:

  47. Clustering methods are widely used on gene expression data to categorize genes with similar expression profiles. Finding an appropriate (dis)similarity measure is critical to the analysis. In our study, we dev...

    Authors: Kyungpil Kim, Shibo Zhang, Keni Jiang, Li Cai, In-Beum Lee, Lewis J Feldman and Haiyan Huang
    Citation: BMC Bioinformatics 2007 8:29
    Content type: Research article Published on:

  49. The need for fast and accurate scoring functions has been driven by the increased use of in silico virtual screening twinned with high-throughput screening as a method to rapidly identify potential candidates in ...

    Authors: Chrysi Konstantinou-Kirtay, John BO Mitchell and James A Lumley
    Citation: BMC Bioinformatics 2007 8:27
    Content type: Research article Published on:

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