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  4. 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:

  5. 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:

  7. 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:

  8. 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:

  9. 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:

  14. 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:

  15. 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:

  18. 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:

  19. 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:

  20. 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:

  23. 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:

  24. 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:

  25. 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:

  26. 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:

  29. 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:

  33. 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:

  37. Genome sequences vary strongly in their repetitiveness and the causes for this are still debated. Here we propose a novel measure of genome repetitiveness, the index of repetitiveness, Ir, which can be computed i...

    Authors: Bernhard Haubold and Thomas Wiehe
    Citation: BMC Bioinformatics 2006 7:541
    Content type: Research article Published on:

  38. Dynamic modeling of metabolic reaction networks under in vivo conditions is a crucial step in order to obtain a better understanding of the (dis)functioning of living cells. So far dynamic metabolic models genera...

    Authors: I Emrah Nikerel, Wouter A van Winden, Walter M van Gulik and Joseph J Heijnen
    Citation: BMC Bioinformatics 2006 7:540
    Content type: Research article Published on:

  39. The development of effective frameworks that permit an accurate diagnosis of tumors, especially in their early stages, remains a grand challenge in the field of bioinformatics. Our approach uses statistical le...

    Authors: Andreas Keller, Nicole Ludwig, Nicole Comtesse, Andreas Hildebrandt, Eckart Meese and Hans-Peter Lenhof
    Citation: BMC Bioinformatics 2006 7:539
    Content type: Research article Published on:

  40. The small sample sizes often used for microarray experiments result in poor estimates of variance if each gene is considered independently. Yet accurately estimating variability of gene expression measurements...

    Authors: Maureen A Sartor, Craig R Tomlinson, Scott C Wesselkamper, Siva Sivaganesan, George D Leikauf and Mario Medvedovic
    Citation: BMC Bioinformatics 2006 7:538
    Content type: Research article Published on:

  41. Phylogenetic analysis of large, multiple-gene datasets, assembled from public sequence databases, is rapidly becoming a popular way to approach difficult phylogenetic problems. Supermatrices (concatenated mult...

    Authors: Martin Jones and Mark Blaxter
    Citation: BMC Bioinformatics 2006 7:536
    Content type: Software Published on:

  42. Microarray technology has become a widely accepted and standardized tool in biology. The first microarray data analysis programs were developed to support pair-wise comparison. However, as microarray experimen...

    Authors: Björn Usadel, Axel Nagel, Dirk Steinhauser, Yves Gibon, Oliver E Bläsing, Henning Redestig, Nese Sreenivasulu, Leonard Krall, Matthew A Hannah, Fabien Poree, Alisdair R Fernie and Mark Stitt
    Citation: BMC Bioinformatics 2006 7:535
    Content type: Software Published on:

  43. Although short interfering RNA (siRNA) has been widely used for studying gene functions in mammalian cells, its gene silencing efficacy varies markedly and there are only a few consistencies among the recently...

    Authors: Shigeru Takasaki, Yoshihiro Kawamura and Akihiko Konagaya
    Citation: BMC Bioinformatics 2006 7(Suppl 5):S22
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 7 Supplement 5

  44. The number of k-words shared between two sequences is a simple and effcient alignment-free sequence comparison method. This statistic, D2, has been used for the clustering of EST sequences. Sequence comparison ba...

    Authors: Sylvain Forêt, Miriam R Kantorovitz and Conrad J Burden
    Citation: BMC Bioinformatics 2006 7(Suppl 5):S21
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 7 Supplement 5

  45. The accurate prediction of a comprehensive set of messenger RNAs (targets) regulated by animal microRNAs (miRNAs) remains an open problem. In particular, the prediction of targets that do not possess evolution...

    Authors: Rahul Thadani and Martti T Tammi
    Citation: BMC Bioinformatics 2006 7(Suppl 5):S20
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 7 Supplement 5

  46. Since proteins perform their functions by interacting with one another and with other biomolecules, reconstructing a map of the protein-protein interactions of a cell, experimentally or computationally, is an ...

    Authors: Xiaomei Wu, Lei Zhu, Jie Guo, Cong Fu, Hongjun Zhou, Dong Dong, Zhenbo Li, Da-Yong Zhang and Kui Lin
    Citation: BMC Bioinformatics 2006 7(Suppl 5):S16
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 7 Supplement 5

  48. A key post genomics challenge is to identify how genes in an organism come together and perform physiological functions. An important first step in this direction is to identify transcriptional units, operons ...

    Authors: Sarita Ranjan, Ranjit Kumar Gundu and Akash Ranjan
    Citation: BMC Bioinformatics 2006 7(Suppl 5):S9
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 7 Supplement 5

  49. Determination of the subcellular location of a protein is essential to understanding its biochemical function. This information can provide insight into the function of hypothetical or novel proteins. These da...

    Authors: Josefine Sprenger, J Lynn Fink and Rohan D Teasdale
    Citation: BMC Bioinformatics 2006 7(Suppl 5):S3
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 7 Supplement 5

  50. In 1998, the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation was set up to champion the advancement of bioinformatics in the Asia Pacific. By 2002, APBioNet was able t...

    Authors: Shoba Ranganathan, Martti Tammi, Michael Gribskov and Tin Wee Tan
    Citation: BMC Bioinformatics 2006 7(Suppl 5):S1
    Content type: Introduction Published on:

    This article is part of a Supplement: Volume 7 Supplement 5

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