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  1. 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:

  3. 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:

  5. 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:

  6. 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:

  7. 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:

  8. 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:

  9. 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:

  12. 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:

  14. 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:

  15. 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:

  16. 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:

  17. 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:

  18. 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:

  20. 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:

  22. 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:

  24. 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:

  25. 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:

  26. In the genomic age, gene trees may contain large amounts of data making them hard to read and understand. Therefore, an automated simplification is important.

    Authors: Paul-Ludwig Lott, Marvin Mundry, Christoph Sassenberg, Stefan Lorkowski and Georg Fuellen
    Citation: BMC Bioinformatics 2006 7:231
    Content type: Software Published on:

  27. 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:

  29. 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:

  30. Various software tools are available for the display of pairwise linkage disequilibrium across multiple single nucleotide polymorphisms. The HapMap project also presents these graphics within their website. Ho...

    Authors: Tom R Gaunt, Santiago Rodriguez, Carlos Zapata and Ian NM Day
    Citation: BMC Bioinformatics 2006 7:227
    Content type: Software Published on:

  33. Adaptative immune repertoire diversity in vertebrate species is generated by recombination of variable (V), diversity (D) and joining (J) genes in the immunoglobulin (IG) loci of B lymphocytes and in the T cel...

    Authors: Thierry-Pascal Baum, Vivien Hierle, Nicolas Pasqual, Fatena Bellahcene, Denys Chaume, Marie-Paule Lefranc, Evelyne Jouvin-Marche, Patrice Noël Marche and Jacques Demongeot
    Citation: BMC Bioinformatics 2006 7:224
    Content type: Database Published on:

  34. Meiotic double-strand breaks occur at relatively high frequencies in some genomic regions (hotspots) and relatively low frequencies in others (coldspots). Hotspots and coldspots are receiving increasing attent...

    Authors: Tong Zhou, Jianhong Weng, Xiao Sun and Zuhong Lu
    Citation: BMC Bioinformatics 2006 7:223
    Content type: Methodology article Published on:

  35. Tandem mass spectrometry (MS/MS) is a powerful tool for protein identification. Although great efforts have been made in scoring the correlation between tandem mass spectra and an amino acid sequence database,...

    Authors: Zhuo Zhang, Shiwei Sun, Xiaopeng Zhu, Suhua Chang, Xiaofei Liu, Chungong Yu, Dongbo Bu and Runsheng Chen
    Citation: BMC Bioinformatics 2006 7:222
    Content type: Research article Published on:

  36. RNAMute is an interactive Java application that calculates the secondary structure of all single point mutations, given an RNA sequence, and organizes them into categories according to their similarity with re...

    Authors: Alexander Churkin and Danny Barash
    Citation: BMC Bioinformatics 2006 7:221
    Content type: Software Published on:

  37. Accuracy of document retrieval from MEDLINE for gene queries is crucially important for many applications in bioinformatics. We explore five information retrieval-based methods to rank documents retrieved by P...

    Authors: Aditya K Sehgal and Padmini Srinivasan
    Citation: BMC Bioinformatics 2006 7:220
    Content type: Research article Published on:

  38. The elucidation of whole-cell regulatory, metabolic, interaction and other biological networks generates the need for a meaningful ranking of network elements. Centrality analysis ranks network elements according...

    Authors: Björn H Junker, Dirk Koschützki and Falk Schreiber
    Citation: BMC Bioinformatics 2006 7:219
    Content type: Software Published on:

  39. Modeling of cis-elements or regulatory motifs in promoter (upstream) regions of genes is a challenging computational problem. In this work, set of regulatory motifs simultaneously present in the promoters of a se...

    Authors: Amrita Pati, Cecilia Vasquez-Robinet, Lenwood S Heath, Ruth Grene and TM Murali
    Citation: BMC Bioinformatics 2006 7:218
    Content type: Software Published on:

  40. There has been an explosion in the number of single nucleotide polymorphisms (SNPs) within public databases. In this study we focused on non-synonymous protein coding single nucleotide polymorphisms (nsSNPs), ...

    Authors: Richard J Dobson, Patricia B Munroe, Mark J Caulfield and Mansoor AS Saqi
    Citation: BMC Bioinformatics 2006 7:217
    Content type: Methodology article Published on:

  41. Expression array data are used to predict biological functions of uncharacterized genes by comparing their expression profiles to those of characterized genes. While biologically plausible, this is both statis...

    Authors: Rafal Kustra, Romy Shioda and Mu Zhu
    Citation: BMC Bioinformatics 2006 7:216
    Content type: Methodology article Published on:

  42. Analysis of DNA microarray data takes as input spot intensity measurements from scanner software and returns differential expression of genes between two conditions, together with a statistical significance as...

    Authors: Allan A Sioson, Shrinivasrao P Mane, Pinghua Li, Wei Sha, Lenwood S Heath, Hans J Bohnert and Ruth Grene
    Citation: BMC Bioinformatics 2006 7:215
    Content type: Research article Published on:

  44. The environmental sequencing of the Sargasso Sea has introduced a huge new resource of genomic information. Unlike the protein sequences held in the current searchable databases, the Sargasso Sea sequences ori...

    Authors: Michael L Tress, Domenico Cozzetto, Anna Tramontano and Alfonso Valencia
    Citation: BMC Bioinformatics 2006 7:213
    Content type: Research article Published on:

  45. Ontologies and taxonomies are among the most important computational resources for molecular biology and bioinformatics. A series of recent papers has shown that the Gene Ontology (GO), the most prominent taxo...

    Authors: Jacob Köhler, Katherine Munn, Alexander Rüegg, Andre Skusa and Barry Smith
    Citation: BMC Bioinformatics 2006 7:212
    Content type: Methodology article Published on:

  46. Gene expression microarray experiments are expensive to conduct and guidelines for acceptable quality control at intermediate steps before and after the samples are hybridised to chips are vague. We conducted ...

    Authors: Lesley Jones, Darlene R Goldstein, Gareth Hughes, Andrew D Strand, Francois Collin, Stephen B Dunnett, Charles Kooperberg, Aaron Aragaki, James M Olson, Sarah J Augood, Richard LM Faull, Ruth Luthi-Carter, Valentina Moskvina and Angela K Hodges
    Citation: BMC Bioinformatics 2006 7:211
    Content type: Methodology article Published on:

  47. Large-scale genetic mapping projects require data management systems that can handle complex phenotypes and detect and correct high-throughput genotyping errors, yet are easy to use.

    Authors: Simon Fiddy, David Cattermole, Dong Xie, Xiao Yuan Duan and Richard Mott
    Citation: BMC Bioinformatics 2006 7:210
    Content type: Database Published on:

  48. We present a general approach to perform association analyses in pedigrees of arbitrary size and structure, which also allows for a mixture of pedigree members and independent individuals to be analyzed togeth...

    Authors: Kristina Allen-Brady, Jathine Wong and Nicola J Camp
    Citation: BMC Bioinformatics 2006 7:209
    Content type: Software Published on:

  49. Due to the functional importance of intrinsically disordered proteins or protein regions, prediction of intrinsic protein disorder from amino acid sequence has become an area of active research as witnessed in...

    Authors: Kang Peng, Predrag Radivojac, Slobodan Vucetic, A Keith Dunker and Zoran Obradovic
    Citation: BMC Bioinformatics 2006 7:208
    Content type: Software Published on:

  50. After complete sequencing of a number of genomes the focus has now turned to proteomics. Advanced proteomics technologies such as two-hybrid assay, mass spectrometry etc. are producing huge data sets of protei...

    Authors: Md Altaf-Ul-Amin, Yoko Shinbo, Kenji Mihara, Ken Kurokawa and Shigehiko Kanaya
    Citation: BMC Bioinformatics 2006 7:207
    Content type: Methodology article Published on:

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