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  1. 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:

  2. 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:

  4. 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:

  5. 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:

  6. 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:

  7. 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:

  8. 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:

  10. 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:

  11. 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:

  13. 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:

  14. 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:

  19. 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:

  20. 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:

  22. 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:

  23. There are mechanisms, notably ozone degradation, that can damage a single channel of two-channel microarray experiments. Resulting analyses therefore often choose between the unacceptable inclusion of poor qua...

    Authors: Andy G Lynch, David E Neal, John D Kelly, Glyn J Burtt and Natalie P Thorne
    Citation: BMC Bioinformatics 2007 8:26
    Content type: Research article Published on:

  24. Variable importance measures for random forests have been receiving increased attention as a means of variable selection in many classification tasks in bioinformatics and related scientific fields, for instan...

    Authors: Carolin Strobl, Anne-Laure Boulesteix, Achim Zeileis and Torsten Hothorn
    Citation: BMC Bioinformatics 2007 8:25
    Content type: Methodology article Published on:

  29. Gene expression microarray and other multiplex data hold promise for addressing the challenges of cellular complexity, refined diagnoses and the discovery of well-targeted treatments. A new approach to the con...

    Authors: Abdallah Sayyed-Ahmad, Kagan Tuncay and Peter J Ortoleva
    Citation: BMC Bioinformatics 2007 8:20
    Content type: Research article Published on:

  30. It is becoming increasingly important for researchers to be able to scan through large genomic regions for transcription factor binding sites or clusters of binding sites forming cis-regulatory modules. Correspon...

    Authors: Dustin E Schones, Andrew D Smith and Michael Q Zhang
    Citation: BMC Bioinformatics 2007 8:19
    Content type: Methodology article Published on:

  33. RNA metabolism, through 'combinatorial splicing', can generate enormous structural diversity in the proteome. Alternative domains may interact, however, with unpredictable phenotypic consequences, necessitatin...

    Authors: Mark C Emerick, Giovanni Parmigiani and William S Agnew
    Citation: BMC Bioinformatics 2007 8:16
    Content type: Methodology article Published on:

  34. Comprehensive description of the behavior of cellular components in a quantitative manner is essential for systematic understanding of biological events. Recent LC-MS/MS (tandem mass spectrometry coupled with ...

    Authors: Ayumu Saito, Masao Nagasaki, Masaaki Oyama, Hiroko Kozuka-Hata, Kentaro Semba, Sumio Sugano, Tadashi Yamamoto and Satoru Miyano
    Citation: BMC Bioinformatics 2007 8:15
    Content type: Software Published on:

  35. High-throughput experiments, such as with DNA microarrays, typically result in hundreds of genes potentially relevant to the process under study, rendering the interpretation of these experiments problematic. ...

    Authors: Rob Jelier, Guido Jenster, Lambert CJ Dorssers, Bas J Wouters, Peter JM Hendriksen, Barend Mons, Ruud Delwel and Jan A Kors
    Citation: BMC Bioinformatics 2007 8:14
    Content type: Research article Published on:

  38. Peptide ligands have tremendous therapeutic potential as efficacious drugs. Currently, more than 40 peptides are available in the market for a drug. However, since costly and time-consuming synthesis procedure...

    Authors: Yukiko Yagi, Kotaro Terada, Takahisa Noma, Kazunori Ikebukuro and Koji Sode
    Citation: BMC Bioinformatics 2007 8:11
    Content type: Research article Published on:

  39. Thermal injury is among the most severe forms of trauma and its effects are both local and systemic. Response to thermal injury includes cellular protection mechanisms, inflammation, hypermetabolism, prolonged...

    Authors: Eric Yang, Timothy Maguire, Martin L Yarmush, Francois Berthiaume and Ioannis P Androulakis
    Citation: BMC Bioinformatics 2007 8:10
    Content type: Methodology article Published on:

  40. Researchers involved in the annotation of large numbers of gene, clone or protein identifiers are usually required to perform a one-by-one conversion for each identifier. When the field of research is one such...

    Authors: Andreu Alibés, Patricio Yankilevich, Andrés Cañada and Ramón Díaz-Uriarte
    Citation: BMC Bioinformatics 2007 8:9
    Content type: Software Published on:

  41. We consider the problem of identifying the dynamic interactions in biochemical networks from noisy experimental data. Typically, approaches for solving this problem make use of an estimation algorithm such as ...

    Authors: Jongrae Kim, Declan G Bates, Ian Postlethwaite, Pat Heslop-Harrison and Kwang-Hyun Cho
    Citation: BMC Bioinformatics 2007 8:8
    Content type: Methodology article Published on:

  44. The four heterogeneous childhood cancers, neuroblastoma, non-Hodgkin lymphoma, rhabdomyosarcoma, and Ewing sarcoma present a similar histology of small round blue cell tumor (SRBCT) and thus often leads to mis...

    Authors: Nikhil R Pal, Kripamoy Aguan, Animesh Sharma and Shun-ichi Amari
    Citation: BMC Bioinformatics 2007 8:5
    Content type: Research article Published on:

  48. In general, the construction of trees is based on sequence alignments. This procedure, however, leads to loss of informationwhen parts of sequence alignments (for instance ambiguous regions) are deleted before...

    Authors: Gilles Didier, Laurent Debomy, Maude Pupin, Ming Zhang, Alexander Grossmann, Claudine Devauchelle and Ivan Laprevotte
    Citation: BMC Bioinformatics 2007 8:1
    Content type: Research article Published on:

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