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  1. The learning of global genetic regulatory networks from expression data is a severely under-constrained problem that is aided by reducing the dimensionality of the search space by means of clustering genes int...

    Authors: David J Reiss, Nitin S Baliga and Richard Bonneau
    Citation: BMC Bioinformatics 2006 7:280
    Content type: Methodology article Published on:

  5. Agile is an iterative approach to software development that relies on strong collaboration and automation to keep pace with dynamic environments. We have successfully used agile development approaches to creat...

    Authors: David W Kane, Moses M Hohman, Ethan G Cerami, Michael W McCormick, Karl F Kuhlmman and Jeff A Byrd
    Citation: BMC Bioinformatics 2006 7:273
    Content type: Correspondence Published on:

  6. Pseudomonas aeruginosa, an opportunistic pathogen, is often encountered in chronic lung diseases such as cystic fibrosis or chronic obstructive pneumonia, as well as acute settings like mechanical ventilation acq...

    Authors: Didier Filopon, Annabelle Mérieau, Gilles Bernot, Jean-Paul Comet, Rozenne LeBerre, Benoit Guery, Benoit Polack and Janine Guespin-Michel
    Citation: BMC Bioinformatics 2006 7:272
    Content type: Research article Published on:

  8. Orthologs (genes that have diverged after a speciation event) tend to have similar function, and so their prediction has become an important component of comparative genomics and genome annotation. The gold st...

    Authors: Debra L Fulton, Yvonne Y Li, Matthew R Laird, Benjamin GS Horsman, Fiona M Roche and Fiona SL Brinkman
    Citation: BMC Bioinformatics 2006 7:270
    Content type: Methodology article Published on:

  10. The automation of many common molecular biology techniques has resulted in the accumulation of vast quantities of experimental data. One of the major challenges now facing researchers is how to process this da...

    Authors: Jianghui Xiong, Simon Rayner, Kunyi Luo, Yinghui Li and Shanguang Chen
    Citation: BMC Bioinformatics 2006 7:268
    Content type: Research article Published on:

  11. Incorporation of ontologies into annotations has enabled 'semantic integration' of complex data, making explicit the knowledge within a certain field. One of the major bottlenecks in developing bio-ontologies ...

    Authors: Alexander Garcia Castro, Philippe Rocca-Serra, Robert Stevens, Chris Taylor, Karim Nashar, Mark A Ragan and Susanna-Assunta Sansone
    Citation: BMC Bioinformatics 2006 7:267
    Content type: Methodology article Published on:

  12. Algorithms that locate evolutionarily conserved sequences have become powerful tools for finding functional DNA elements, including transcription factor binding sites; however, most methods do not take advanta...

    Authors: Jason Gertz, Justin C Fay and Barak A Cohen
    Citation: BMC Bioinformatics 2006 7:266
    Content type: Research article Published on:

  13. Jumping alignments have recently been proposed as a strategy to search a given multiple sequence alignment A against a database. Instead of comparing a database sequence S to the multiple alignment or profile as ...

    Authors: Anne-Kathrin Schultz, Ming Zhang, Thomas Leitner, Carla Kuiken, Bette Korber, Burkhard Morgenstern and Mario Stanke
    Citation: BMC Bioinformatics 2006 7:265
    Content type: Methodology article Published on:

  14. Array-based comparative genomic hybridization (array-CGH) is a recently developed technique for analyzing changes in DNA copy number. As in all microarray analyses, normalization is required to correct for exp...

    Authors: Pierre Neuvial, Philippe Hupé, Isabel Brito, Stéphane Liva, Élodie Manié, Caroline Brennetot, François Radvanyi, Alain Aurias and Emmanuel Barillot
    Citation: BMC Bioinformatics 2006 7:264
    Content type: Research article Published on:

  15. The number of sequenced eukaryotic genomes is rapidly increasing. This means that over time it will be hard to keep supplying customised gene finders for each genome. This calls for procedures to automatically...

    Authors: Kasper Munch and Anders Krogh
    Citation: BMC Bioinformatics 2006 7:263
    Content type: Methodology article Published on:

  16. Understanding the molecular details of protein-DNA interactions is critical for deciphering the mechanisms of gene regulation. We present a machine learning approach for the identification of amino acid residu...

    Authors: Changhui Yan, Michael Terribilini, Feihong Wu, Robert L Jernigan, Drena Dobbs and Vasant Honavar
    Citation: BMC Bioinformatics 2006 7:262
    Content type: Research article Published on:

  17. Assessment of array quality is an essential step in the analysis of data from microarray experiments. Once detected, less reliable arrays are typically excluded or "filtered" from further analysis to avoid mis...

    Authors: Matthew E Ritchie, Dileepa Diyagama, Jody Neilson, Ryan van Laar, Alexander Dobrovic, Andrew Holloway and Gordon K Smyth
    Citation: BMC Bioinformatics 2006 7:261
    Content type: Methodology article Published on:

  21. Amino acids in proteins are not used equally. Some of the differences in the amino acid composition of proteins are between species (mainly due to nucleotide composition and lifestyle) and some are between pro...

    Authors: Alberto Pasamontes and Santiago Garcia-Vallve
    Citation: BMC Bioinformatics 2006 7:257
    Content type: Methodology article Published on:

  22. The Tissue Microarray (TMA) facilitates high-throughput analysis of hundreds of tissue specimens simultaneously. However, bottlenecks in the storage and manipulation of the data generated from TMA reviews have...

    Authors: Catherine M Conway, Deirdre O'Shea, Sallyann O'Brien, Darragh K Lawler, Graham D Dodrill, Anthony O'Grady, Helen Barrett, Christian Gulmann, Lorraine O'Driscoll, William M Gallagher, Elaine W Kay and Daniel G O'Shea
    Citation: BMC Bioinformatics 2006 7:256
    Content type: Research article Published on:

  24. The identification of statistically overrepresented sequences in the upstream regions of coregulated genes should theoretically permit the identification of potential cis-regulatory elements. However, in pract...

    Authors: Jonathan M Carlson, Arijit Chakravarty, Radhika S Khetani and Robert H Gross
    Citation: BMC Bioinformatics 2006 7:254
    Content type: Methodology article Published on:

  26. As phenotypic features derived from heritable characters, the topologies of metabolic pathways contain both phylogenetic and phenetic components. In the post-genomic era, it is possible to measure the "phyloph...

    Authors: Yong Zhang, Shaojuan Li, Geir Skogerbø, Zhihua Zhang, Xiaopeng Zhu, Zefeng Zhang, Shiwei Sun, Hongchao Lu, Baochen Shi and Runsheng Chen
    Citation: BMC Bioinformatics 2006 7:252
    Content type: Research article Published on:

  27. Gene expression microarray data is notoriously subject to high signal variability. Moreover, unavoidable variation in the concentration of transcripts applied to microarrays may result in poor scaling of the s...

    Authors: Martino Barenco, Jaroslav Stark, Daniel Brewer, Daniela Tomescu, Robin Callard and Michael Hubank
    Citation: BMC Bioinformatics 2006 7:251
    Content type: Methodology article Published on:

  28. The statistical modeling of biomedical corpora could yield integrated, coarse-to-fine views of biological phenomena that complement discoveries made from analysis of molecular sequence and profiling data. Here...

    Authors: DM Blei, K Franks, MI Jordan and IS Mian
    Citation: BMC Bioinformatics 2006 7:250
    Content type: Research article Published on:

  29. A central goal of molecular biology is to understand the regulatory mechanisms of gene transcription and protein synthesis. Because of their solid basis in statistics, allowing to deal with the stochastic aspe...

    Authors: Norbert Dojer, Anna Gambin, Andrzej Mizera, Bartek Wilczyński and Jerzy Tiuryn
    Citation: BMC Bioinformatics 2006 7:249
    Content type: Methodology article Published on:

  30. In our previous studies, we found that the sites in prokaryotic genomes which are most susceptible to duplex destabilization under the negative superhelical stresses that occur in vivo are statistically highly si...

    Authors: Huiquan Wang and Craig J Benham
    Citation: BMC Bioinformatics 2006 7:248
    Content type: Research article Published on:

  33. In gene networks, the timing of significant changes in the expression level of each gene may be the most critical information in time course expression profiles. With the same timing of the initial change, gen...

    Authors: Hao Li, Constance L Wood, Yushu Liu, Thomas V Getchell, Marilyn L Getchell and Arnold J Stromberg
    Citation: BMC Bioinformatics 2006 7:245
    Content type: Research article Published on:

  35. Chaos game representation of genome sequences has been used for visual representation of genome sequence patterns as well as alignment-free comparisons of sequences based on oligonucleotide frequencies. Howeve...

    Authors: Jijoy Joseph and Roschen Sasikumar
    Citation: BMC Bioinformatics 2006 7:243
    Content type: Methodology article Published on:

  36. That the structure determines the function of proteins is a central paradigm in biology. However, protein functions are more directly related to cooperative effects at the residue and multi-residue scales. As ...

    Authors: Apostol Gramada and Philip E Bourne
    Citation: BMC Bioinformatics 2006 7:242
    Content type: Research article Published on:

  37. Large-scale genomic studies based on transcriptome technologies provide clusters of genes that need to be functionally annotated. The Gene Ontology (GO) implements a controlled vocabulary organised into three ...

    Authors: Marc Aubry, Annabelle Monnier, Celine Chicault, Marie de Tayrac, Marie-Dominique Galibert, Anita Burgun and Jean Mosser
    Citation: BMC Bioinformatics 2006 7:241
    Content type: Methodology article Published on:

  38. Availability of high-resolution RNA crystal structures for the 30S and 50S ribosomal subunits and the subsequent validation of comparative secondary structure models have prompted the biologists to use three-d...

    Authors: Yadhu Kumar, Ralf Westram, Peter Kipfer, Harald Meier and Wolfgang Ludwig
    Citation: BMC Bioinformatics 2006 7:240
    Content type: Software Published on:

  39. Genomic tiling micro arrays have great potential for identifying previously undiscovered coding as well as non-coding transcription. To-date, however, analyses of these data have been performed in an ad hoc fashi...

    Authors: Kasper Munch, Paul P Gardner, Peter Arctander and Anders Krogh
    Citation: BMC Bioinformatics 2006 7:239
    Content type: Methodology article Published on:

  41. Activation of naïve B lymphocytes by extracellular ligands, e.g. antigen, lipopolysaccharide (LPS) and CD40 ligand, induces a combination of common and ligand-specific phenotypic changes through complex signal...

    Authors: Jamie A Lee, Robert S Sinkovits, Dennis Mock, Eva L Rab, Jennifer Cai, Peng Yang, Brian Saunders, Robert C Hsueh, Sangdun Choi, Shankar Subramaniam and Richard H Scheuermann
    Citation: BMC Bioinformatics 2006 7:237
    Content type: Research article Published on:

  43. Gene selection is an important step when building predictors of disease state based on gene expression data. Gene selection generally improves performance and identifies a relevant subset of genes. Many univar...

    Authors: Carmen Lai, Marcel JT Reinders, Laura J van't Veer and Lodewyk FA Wessels
    Citation: BMC Bioinformatics 2006 7:235
    Content type: Research article Published on:

  45. Association mapping using abundant single nucleotide polymorphisms is a powerful tool for identifying disease susceptibility genes for complex traits and exploring possible genetic diversity. Genotyping large ...

    Authors: Hsin-Chou Yang, Chia-Ching Pan, Chin-Yu Lin and Cathy SJ Fann
    Citation: BMC Bioinformatics 2006 7:233
    Content type: Software Published on:

  46. Most virus detection methods are geared towards the detection of specific single viruses or just a few known targets, and lack the capability to uncover the novel viruses that cause emerging viral infections. ...

    Authors: Cheng-Chung Chou, Te-Tsui Lee, Chun-Houh Chen, Hsiang-Yun Hsiao, Yi-Ling Lin, Mei-Shang Ho, Pan-Chyr Yang and Konan Peck
    Citation: BMC Bioinformatics 2006 7:232
    Content type: Methodology article Published on:

  47. The modeling of dynamic systems requires estimating kinetic parameters from experimentally measured time-courses. Conventional global optimization methods used for parameter estimation, e.g. genetic algorithms...

    Authors: Yoshiya Matsubara, Shinichi Kikuchi, Masahiro Sugimoto and Masaru Tomita
    Citation: BMC Bioinformatics 2006 7:230
    Content type: Research article Published on:

  48. Microarray data analysis is notorious for involving a huge number of genes compared to a relatively small number of samples. Gene selection is to detect the most significantly differentially expressed genes un...

    Authors: Kun Yang, Zhipeng Cai, Jianzhong Li and Guohui Lin
    Citation: BMC Bioinformatics 2006 7:228
    Content type: Research article Published on:

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