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  1. The sequencing of many genomes and tiling arrays consisting of millions of DNA segments spanning entire genomes have made high-resolution copy number analysis possible. Microarray-based comparative genomic hyb...

    Authors: Dmitriy Skvortsov, Diana Abdueva, Michael E Stitzer, Steven E Finkel and Simon Tavaré
    Citation: BMC Bioinformatics 2007 8:203
  2. The ability to obtain profiles of gene expressions, proteins and metabolites with the advent of high throughput technologies has advanced the study of pathway and network reconstruction. Genome-wide network re...

    Authors: Zheng Li, Shireesh Srivastava, Sheenu Mittal, Xuerui Yang, Lufang Sheng and Christina Chan
    Citation: BMC Bioinformatics 2007 8:202
  3. Genome-wide maps of linkage disequilibrium (LD) and haplotypes have been created for different populations. Substantial sharing of the boundaries and haplotypes among populations was observed, but haplotype va...

    Authors: Dai Osabe, Toshihito Tanahashi, Kyoko Nomura, Shuichi Shinohara, Naoto Nakamura, Toshikazu Yoshikawa, Hiroshi Shiota, Parvaneh Keshavarz, Yuka Yamaguchi, Kiyoshi Kunika, Maki Moritani, Hiroshi Inoue and Mitsuo Itakura
    Citation: BMC Bioinformatics 2007 8:200
  4. Whereas the molecular assembly of protein expression clones is readily automated and routinely accomplished in high throughput, sequence verification of these clones is still largely performed manually, an ard...

    Authors: Elena Taycher, Andreas Rolfs, Yanhui Hu, Dongmei Zuo, Stephanie E Mohr, Janice Williamson and Joshua LaBaer
    Citation: BMC Bioinformatics 2007 8:198
  5. The advancements of proteomics technologies have led to a rapid increase in the number, size and rate at which datasets are generated. Managing and extracting valuable information from such datasets requires t...

    Authors: Jürgen Hartler, Gerhard G Thallinger, Gernot Stocker, Alexander Sturn, Thomas R Burkard, Erik Körner, Robert Rader, Andreas Schmidt, Karl Mechtler and Zlatko Trajanoski
    Citation: BMC Bioinformatics 2007 8:197
  6. Quantifying cell division and death is central to many studies in the biological sciences. The fluorescent dye CFSE allows the tracking of cell division in vitro and in vivo and provides a rich source of informat...

    Authors: Andrew Yates, Cliburn Chan, Jessica Strid, Simon Moon, Robin Callard, Andrew JT George and Jaroslav Stark
    Citation: BMC Bioinformatics 2007 8:196
  7. The wide use of Affymetrix microarray in broadened fields of biological research has made the probeset annotation an important issue. Standard Affymetrix probeset annotation is at gene level, i.e. a probeset i...

    Authors: Hui Yu, Feng Wang, Kang Tu, Lu Xie, Yuan-Yuan Li and Yi-Xue Li
    Citation: BMC Bioinformatics 2007 8:194
  8. An important step in annotation of sequenced genomes is the identification of transcription factor binding sites. More than a hundred different computational methods have been proposed, and it is difficult to ...

    Authors: Geir Kjetil Sandve, Osman Abul, Vegard Walseng and Finn Drabløs
    Citation: BMC Bioinformatics 2007 8:193
  9. Microarray techniques survey gene expressions on a global scale. Extensive biomedical studies have been designed to discover subsets of genes that are associated with survival risks for diseases such as lympho...

    Authors: Shuangge Ma and Jian Huang
    Citation: BMC Bioinformatics 2007 8:192
  10. Evolutionary analysis provides a formal framework for comparative analysis of genomic and other data. In evolutionary analysis, observed data are treated as the terminal states of characters that have evolved ...

    Authors: Thomas Hladish, Vivek Gopalan, Chengzhi Liang, Weigang Qiu, Peter Yang and Arlin Stoltzfus
    Citation: BMC Bioinformatics 2007 8:191
  11. In ribonucleic acid (RNA) molecules whose function depends on their final, folded three-dimensional shape (such as those in ribosomes or spliceosome complexes), the secondary structure, defined by the set of i...

    Authors: Amelia B Bellamy-Royds and Marcel Turcotte
    Citation: BMC Bioinformatics 2007 8:190
  12. Sequence motifs representing transcription factor binding sites (TFBS) are commonly encoded as position frequency matrices (PFM) or degenerate consensus sequences (CS). These formats are used to represent the ...

    Authors: Matti Kankainen and Ari Löytynoja
    Citation: BMC Bioinformatics 2007 8:189
  13. Detection of adaptive amino acid changes in proteins under recent short-term selection is of great interest for researchers studying microevolutionary processes in microbial pathogens or any other biological s...

    Authors: Sujay Chattopadhyay, Daniel E Dykhuizen and Evgeni V Sokurenko
    Citation: BMC Bioinformatics 2007 8:187
  14. Tiling microarrays are becoming an essential technology in the functional genomics toolbox. They have been applied to the tasks of novel transcript identification, elucidation of transcription factor binding s...

    Authors: Thomas E Royce, Nicholas J Carriero and Mark B Gerstein
    Citation: BMC Bioinformatics 2007 8:186
  15. Systematic, high-throughput studies of mouse phenotypes have been hampered by the inability to analyze individual animal data from a multitude of sources in an integrated manner. Studies generally make compari...

    Authors: R Brent Calder, Rudolf B Beems, Harry van Steeg, I Saira Mian, Paul HM Lohman and Jan Vijg
    Citation: BMC Bioinformatics 2007 8:183
  16. Microarray compendia profile the expression of genes in a number of experimental conditions. Such data compendia are useful not only to group genes and conditions based on their similarity in overall expressio...

    Authors: Katrijn Van Deun, Kathleen Marchal, Willem J Heiser, Kristof Engelen and Iven Van Mechelen
    Citation: BMC Bioinformatics 2007 8:181
  17. Most human genes produce several transcripts with different exon contents by using alternative promoters, alternative polyadenylation sites and alternative splice sites. Much effort has been devoted to describ...

    Authors: Pierre de la Grange, Martin Dutertre, Margot Correa and Didier Auboeuf
    Citation: BMC Bioinformatics 2007 8:180
  18. Regulation of gene expression is relevant to many areas of biology and medicine, in the study of treatments, diseases, and developmental stages. Microarrays can be used to measure the expression level of thous...

    Authors: Markus Weniger, Julia C Engelmann and Jörg Schultz
    Citation: BMC Bioinformatics 2007 8:179
  19. RNA interference has revolutionized our ability to study the effects of altering the expression of single genes in mammalian (and other) cells through targeted knockdown of gene expression. In this report we d...

    Authors: Jyoti K Shah, Harold R Garner, Michael A White, David S Shames and John D Minna
    Citation: BMC Bioinformatics 2007 8:178
  20. G Protein-Coupled Receptors (GPCRs) are a large and diverse family of membrane proteins whose members participate in the regulation of most cellular and physiological processes and therefore represent key phar...

    Authors: Lucy Skrabanek, Marta Murcia, Michel Bouvier, Lakshmi Devi, Susan R George, Martin J Lohse, Graeme Milligan, Richard Neubig, Krzysztof Palczewski, Marc Parmentier, Jean-Philippe Pin, Gerrit Vriend, Jonathan A Javitch, Fabien Campagne and Marta Filizola
    Citation: BMC Bioinformatics 2007 8:177
  21. The aim of this paper is to demonstrate the application of watermarks based on DNA sequences to identify the unauthorized use of genetically modified organisms (GMOs) protected by patents. Predicted mutations ...

    Authors: Dominik Heider and Angelika Barnekow
    Citation: BMC Bioinformatics 2007 8:176
  22. The fundamental role that intrinsic stochasticity plays in cellular functions has been shown via numerous computational and experimental studies. In the face of such evidence, it is important that intracellula...

    Authors: Asawari Samant, Babatunde A Ogunnaike and Dionisios G Vlachos
    Citation: BMC Bioinformatics 2007 8:175
  23. 3' untranslated regions (3' UTRs) contain binding sites for many regulatory elements, and in particular for microRNAs (miRNAs). The importance of miRNA-mediated post-transcriptional regulation has become incre...

    Authors: Davide Corà, Ferdinando Di Cunto, Michele Caselle and Paolo Provero
    Citation: BMC Bioinformatics 2007 8:174
  24. High quality multiple alignments are crucial in the transfer of annotation from one genome to another. Multiple alignment methods strive to achieve ever increasing levels of average accuracy on benchmark sets ...

    Authors: Timo Lassmann and Erik LL Sonnhammer
    Citation: BMC Bioinformatics 2007 8(Suppl 5):S9

    This article is part of a Supplement: Volume 8 Supplement 5

  25. Identification of protein interacting sites is an important task in computational molecular biology. As more and more protein sequences are deposited without available structural information, it is strongly de...

    Authors: Chen-Ming Hsu, Chien-Yu Chen, Baw-Jhiune Liu, Chih-Chang Huang, Min-Hung Laio, Chien-Chieh Lin and Tzung-Lin Wu
    Citation: BMC Bioinformatics 2007 8(Suppl 5):S8

    This article is part of a Supplement: Volume 8 Supplement 5

  26. Sequence comparison faces new challenges today, with many complete genomes and large libraries of transcripts known. Gene annotation pipelines match these sequences in order to identify genes and their alterna...

    Authors: Jürgen Kleffe, Friedrich Möller and Burghardt Wittig
    Citation: BMC Bioinformatics 2007 8(Suppl 5):S7

    This article is part of a Supplement: Volume 8 Supplement 5

  27. Accurate prediction of intra-protein residue contacts from sequence information will allow the prediction of protein structures. Basic predictions of such specific contacts can be further refined by jointly an...

    Authors: Milana Frenkel-Morgenstern, Rachel Magid, Eran Eyal and Shmuel Pietrokovski
    Citation: BMC Bioinformatics 2007 8(Suppl 5):S6

    This article is part of a Supplement: Volume 8 Supplement 5

  28. Recent development of mass spectrometry technology enabled the analysis of complex peptide mixtures. A lot of effort is currently devoted to the identification of biomarkers in human body fluids like serum or ...

    Authors: Janusz Dutkowski and Anna Gambin
    Citation: BMC Bioinformatics 2007 8(Suppl 5):S5

    This article is part of a Supplement: Volume 8 Supplement 5

  29. Our goal is to develop a state-of-the-art protein secondary structure predictor, with an intuitive and biophysically-motivated energy model. We treat structure prediction as an optimization problem, using para...

    Authors: Blaise Gassend, Charles W O'Donnell, William Thies, Andrew Lee, Marten van Dijk and Srinivas Devadas
    Citation: BMC Bioinformatics 2007 8(Suppl 5):S3

    This article is part of a Supplement: Volume 8 Supplement 5

  30. Reverse engineering cellular networks is currently one of the most challenging problems in systems biology. Dynamic Bayesian networks (DBNs) seem to be particularly suitable for inferring relationships between...

    Authors: Fulvia Ferrazzi, Paola Sebastiani, Marco F Ramoni and Riccardo Bellazzi
    Citation: BMC Bioinformatics 2007 8(Suppl 5):S2

    This article is part of a Supplement: Volume 8 Supplement 5

  31. A widely-used approach for discovering functional and physical interactions among proteins involves phylogenetic profile comparisons (PPCs). Here, proteins with similar profiles are inferred to be functionally...

    Authors: Raja Jothi, Teresa M Przytycka and L Aravind
    Citation: BMC Bioinformatics 2007 8:173
  32. There exist many segmentation techniques for genomic sequences, and the segmentations can also be based on many different biological features. We show how to evaluate and compare the quality of segmentations o...

    Authors: Niina Haiminen, Heikki Mannila and Evimaria Terzi
    Citation: BMC Bioinformatics 2007 8:171
  33. One goal of gene expression profiling is to identify signature genes that robustly distinguish different types or grades of tumors. Several tumor classifiers based on expression profiling have been proposed us...

    Authors: Junior Barrera, Roberto M Cesar Jr, Carlos Humes Jr, David C Martins Jr, Diogo FC Patrão, Paulo JS Silva and Helena Brentani
    Citation: BMC Bioinformatics 2007 8:169
  34. Cellular processes depend on the function of intracellular molecular networks. The curation of the literature relevant to specific biological pathways is important for many theoretical and experimental researc...

    Authors: Ganesh A Viswanathan, German Nudelman, Sonali Patil and Stuart C Sealfon
    Citation: BMC Bioinformatics 2007 8:168
  35. Relating features of protein sequences to structural hinges is important for identifying domain boundaries, understanding structure-function relationships, and designing flexibility into proteins. Efforts in t...

    Authors: Samuel C Flores, Long J Lu, Julie Yang, Nicholas Carriero and Mark B Gerstein
    Citation: BMC Bioinformatics 2007 8:167
  36. With the increased availability of high throughput data, such as DNA microarray data, researchers are capable of producing large amounts of biological data. During the analysis of such data often there is the ...

    Authors: Holger Fröhlich, Nora Speer, Annemarie Poustka and Tim Beißbarth
    Citation: BMC Bioinformatics 2007 8:166
  37. Micro- and macroarray technologies help acquire thousands of gene expression patterns covering important biological processes during plant ontogeny. Particularly, faithful visualization methods are beneficial ...

    Authors: Marc Strickert, Nese Sreenivasulu, Björn Usadel and Udo Seiffert
    Citation: BMC Bioinformatics 2007 8:165
  38. An accurate description of protein shape derived from protein structure is necessary to establish an understanding of protein-ligand interactions, which in turn will lead to improved methods for protein-ligand...

    Authors: Lei Xie and Philip E Bourne
    Citation: BMC Bioinformatics 2007 8(Suppl 4):S9

    This article is part of a Supplement: Volume 8 Supplement 4

  39. Phylogenetic profiles record the occurrence of homologs of genes across fully sequenced organisms. Proteins with similar profiles are typically components of protein complexes or metabolic pathways. Various ex...

    Authors: Shawn Cokus, Sayaka Mizutani and Matteo Pellegrini
    Citation: BMC Bioinformatics 2007 8(Suppl 4):S7

    This article is part of a Supplement: Volume 8 Supplement 4

  40. Using a previously developed automated method for enzyme annotation, we report the re-annotation of the ENZYME database and the analysis of local error rates per class. In control experiments, we demonstrate t...

    Authors: Benjamin Audit, Emmanuel D Levy, Wally R Gilks, Leon Goldovsky and Christos A Ouzounis
    Citation: BMC Bioinformatics 2007 8(Suppl 4):S3

    This article is part of a Supplement: Volume 8 Supplement 4

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