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  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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
  33. Current classification of protein folds are based, ultimately, on visual inspection of similarities. Previous attempts to use computerized structure comparison methods show only partial agreement with curated ...

    Authors: Vichetra Sam, Chin-Hsien Tai, Jean Garnier, Jean-Francois Gibrat, Byungkook Lee and Peter J Munson
    Citation: BMC Bioinformatics 2006 7:206
  34. Simulation of DNA-microarray data serves at least three purposes: (i) optimizing the design of an intended DNA microarray experiment, (ii) comparing existing pre-processing and processing methods for best anal...

    Authors: Casper J Albers, Ritsert C Jansen, Jan Kok, Oscar P Kuipers and Sacha AFT van Hijum
    Citation: BMC Bioinformatics 2006 7:205
  35. Trait heterogeneity, which exists when a trait has been defined with insufficient specificity such that it is actually two or more distinct traits, has been implicated as a confounding factor in traditional st...

    Authors: Tricia A Thornton-Wells, Jason H Moore and Jonathan L Haines
    Citation: BMC Bioinformatics 2006 7:204
  36. New analysis methods are being developed to integrate data from transcriptome, proteome, interactome, metabolome, and other investigative approaches. At the same time, existing methods are being modified to se...

    Authors: Pınar Pir, Betül Kırdar, Andrew Hayes, Z İlsen Önsan, Kutlu Ö Ülgen and Stephen G Oliver
    Citation: BMC Bioinformatics 2006 7:203
  37. Prostate cancer is one of the leading causes of cancer illness and death among men in the United States and world wide. There is an urgent need to discover good biomarkers for early clinical diagnosis and trea...

    Authors: Chaolin Zhang, Hai-Ri Li, Jian-Bing Fan, Jessica Wang-Rodriguez, Tracy Downs, Xiang-Dong Fu and Michael Q Zhang
    Citation: BMC Bioinformatics 2006 7:202
  38. Gene expression microarray technology permits the analysis of global gene expression profiles. The amount of sample needed limits the use of small excision biopsies and/or needle biopsies from human or animal ...

    Authors: Rachel IM van Haaften, Blanche Schroen, Ben JA Janssen, Arie van Erk, Jacques JM Debets, Hubert JM Smeets, Jos FM Smits, Arthur van den Wijngaard, Yigal M Pinto and Chris TA Evelo
    Citation: BMC Bioinformatics 2006 7:200
  39. Two-dimensional gel electrophoresis (2DE) is a powerful technique to examine post-translational modifications of complexly modulated proteins. Currently, spot detection is a necessary step to assess relations ...

    Authors: Werner Van Belle, Nina Ånensen, Ingvild Haaland, Øystein Bruserud, Kjell-Arild Høgda and Bjørn Tore Gjertsen
    Citation: BMC Bioinformatics 2006 7:198

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