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  1. Gene duplication and gene loss during the evolution of eukaryotes have hindered attempts to estimate phylogenies and divergence times of species. Although current methods that identify clusters of orthologous ...

    Authors: Jaime E Blair, Prachi Shah and S Blair Hedges
    Citation: BMC Bioinformatics 2005 6:53
  2. High throughput microarray analyses result in many differentially expressed genes that are potentially responsible for the biological process of interest. In order to identify biological similarities between g...

    Authors: Blaise TF Alako, Antoine Veldhoven, Sjozef van Baal, Rob Jelier, Stefan Verhoeven, Ton Rullmann, Jan Polman and Guido Jenster
    Citation: BMC Bioinformatics 2005 6:51
  3. Proteochemometrics is a new methodology that allows prediction of protein function directly from real interaction measurement data without the need of 3D structure information. Several reported proteochemometr...

    Authors: Eva Freyhult, Peteris Prusis, Maris Lapinsh, Jarl ES Wikberg, Vincent Moulton and Mats G Gustafsson
    Citation: BMC Bioinformatics 2005 6:50
  4. Popular methods to reconstruct molecular phylogenies are based on multiple sequence alignments, in which addition or removal of data may change the resulting tree topology. We have sought a representation of h...

    Authors: Olivier Bastien, Philippe Ortet, Sylvaine Roy and Eric Maréchal
    Citation: BMC Bioinformatics 2005 6:49
  5. Many three-dimensional (3D) images are routinely collected in biomedical research and a number of digital atlases with associated anatomical and other information have been published. A number of tools are ava...

    Authors: Guangjie Feng, Nick Burton, Bill Hill, Duncan Davidson, Janet Kerwin, Mark Scott, Susan Lindsay and Richard Baldock
    Citation: BMC Bioinformatics 2005 6:47
  6. wFleaBase is a database with the necessary infrastructure to curate, archive and share genetic, molecular and functional genomic data and protocols for an emerging model organism, the microcrustacean Daphnia. Com...

    Authors: John K Colbourne, Vasanth R Singan and Don G Gilbert
    Citation: BMC Bioinformatics 2005 6:45
  7. Gene expression analysis based on comparison of electrophoretic patterns is strongly dependent on the accuracy of DNA fragment sizing. The current normalization strategy based on molecular weight markers has l...

    Authors: Koji Kadota, Ryutaro Fukumura, Joseph J Rodrigue, Ryoko Araki and Masumi Abe
    Citation: BMC Bioinformatics 2005 6:43
  8. Phages, viruses that infect prokaryotes, are the most abundant microbes in the world. A major limitation to studying these viruses is the difficulty of cultivating the appropriate prokaryotic hosts. One way ar...

    Authors: Florent Angly, Beltran Rodriguez-Brito, David Bangor, Pat McNairnie, Mya Breitbart, Peter Salamon, Ben Felts, James Nulton, Joseph Mahaffy and Forest Rohwer
    Citation: BMC Bioinformatics 2005 6:41
  9. Normalization is the process of removing non-biological sources of variation between array experiments. Recent investigations of data in gene expression databases for varying organisms and tissues have shown t...

    Authors: Tim Lu, Christine M Costello, Peter JP Croucher, Robert Häsler, Günther Deuschl and Stefan Schreiber
    Citation: BMC Bioinformatics 2005 6:37
  10. One important application of microarray experiments is to identify differentially expressed genes. Often, small and negative expression levels were clipped-off to be equal to an arbitrarily chosen cutoff value...

    Authors: Markus Neuhäuser, Tanja Boes and Karl-Heinz Jöckel
    Citation: BMC Bioinformatics 2005 6:35
  11. We present a biological data warehouse called Atlas that locally stores and integrates biological sequences, molecular interactions, homology information, functional annotations of genes, and biological ontolo...

    Authors: Sohrab P Shah, Yong Huang, Tao Xu, Macaire MS Yuen, John Ling and BF Francis Ouellette
    Citation: BMC Bioinformatics 2005 6:34
  12. Detection of DNA-binding sites in proteins is of enormous interest for technologies targeting gene regulation and manipulation. We have previously shown that a residue and its sequence neighbor information can...

    Authors: Shandar Ahmad and Akinori Sarai
    Citation: BMC Bioinformatics 2005 6:33
  13. Wise et al. introduced a rank-based statistical technique for meta-analysis of genome scans, the Genome Scan Meta-Analysis (GSMA) method. Levinson et al. recently described two generalizations of the GSMA stat...

    Authors: James A Koziol and Anne C Feng
    Citation: BMC Bioinformatics 2005 6:32
  14. Cellular processes require the interaction of many proteins across several cellular compartments. Determining the collective network of such interactions is an important aspect of understanding the role and re...

    Authors: Harold J Drabkin, Christopher Hollenbeck, David P Hill and Judith A Blake
    Citation: BMC Bioinformatics 2005 6:29
  15. Normalization is a critical step in analysis of gene expression profiles. For dual-labeled arrays, global normalization assumes that the majority of the genes on the array are non-differentially expressed betw...

    Authors: Yingdong Zhao, Ming-Chung Li and Richard Simon
    Citation: BMC Bioinformatics 2005 6:28
  16. Microarray-CGH experiments are used to detect and map chromosomal imbalances, by hybridizing targets of genomic DNA from a test and a reference sample to sequences immobilized on a slide. These probes are geno...

    Authors: Franck Picard, Stephane Robin, Marc Lavielle, Christian Vaisse and Jean-Jacques Daudin
    Citation: BMC Bioinformatics 2005 6:27
  17. A critical step in processing oligonucleotide microarray data is combining the information in multiple probes to produce a single number that best captures the expression level of a RNA transcript. Several sys...

    Authors: Kerby Shedden, Wei Chen, Rork Kuick, Debashis Ghosh, James Macdonald, Kathleen R Cho, Thomas J Giordano, Stephen B Gruber, Eric R Fearon, Jeremy MG Taylor and Samir Hanash
    Citation: BMC Bioinformatics 2005 6:26
  18. Alternative splicing (AS) is now considered as a major actor in transcriptome/proteome diversity and it cannot be neglected in the annotation process of a new genome. Despite considerable progresses in term of...

    Authors: Sylvain Foissac and Thomas Schiex
    Citation: BMC Bioinformatics 2005 6:25
  19. Current protein clustering methods rely on either sequence or functional similarities between proteins, thereby limiting inferences to one of these areas.

    Authors: Victor Kunin and Christos A Ouzounis
    Citation: BMC Bioinformatics 2005 6:24
  20. Post-translational modification by Small Ubiquitin-like Modifiers (SUMO) has been implicated in protein targeting, in the maintenance of genomic integrity and in transcriptional control. But the specific molec...

    Authors: Maria Novatchkova, Andreas Bachmair, Birgit Eisenhaber and Frank Eisenhaber
    Citation: BMC Bioinformatics 2005 6:22
  21. The large amount of data that are currently produced in the biological sciences can no longer be explored and visualized efficiently with traditional, specialized software. Instead, new capabilities are needed...

    Authors: John L Moreland, Apostol Gramada, Oleksandr V Buzko, Qing Zhang and Philip E Bourne
    Citation: BMC Bioinformatics 2005 6:21
  22. The process of oxidative folding combines the formation of native disulfide bond with conformational folding resulting in the native three-dimensional fold. Oxidative folding pathways can be described in terms...

    Authors: Vilmos Ágoston, Masa Cemazar, László Kaján and Sándor Pongor
    Citation: BMC Bioinformatics 2005 6:19
  23. Detection of Loss of Heterozygosity (LOH) is one of the most common molecular applications in the study of human diseases, in particular cancer. The technique is commonly used to examine whether a known tumour...

    Authors: Rifat A Hamoudi, Amina El-Hamidi and Ming-Qing Du
    Citation: BMC Bioinformatics 2005 6:18
  24. Enzyme-linked immunosorbent assay (ELISA) is a standard immunoassay to estimate a protein's concentration in a sample. Deploying ELISA in a microarray format permits simultaneous estimation of the concentratio...

    Authors: Don Simone Daly, Amanda M White, Susan M Varnum, Kevin K Anderson and Richard C Zangar
    Citation: BMC Bioinformatics 2005 6:17
  25. Searching a biological sequence database with a query sequence looking for homologues has become a routine operation in computational biology. In spite of the high degree of sophistication of currently availab...

    Authors: Antje Krause, Jens Stoye and Martin Vingron
    Citation: BMC Bioinformatics 2005 6:15
  26. Recent analysis of the yeast gene network shows that most genes have few inputs, indicating that enumerative gene reconstruction methods are both useful and computationally feasible. A simple enumerative recon...

    Authors: Thomas MacCarthy, Andrew Pomiankowski and Robert Seymour
    Citation: BMC Bioinformatics 2005 6:11
  27. Prediction of the transmembrane strands and topology of β-barrel outer membrane proteins is of interest in current bioinformatics research. Several methods have been applied so far for this task, utilizing dif...

    Authors: Pantelis G Bagos, Theodore D Liakopoulos and Stavros J Hamodrakas
    Citation: BMC Bioinformatics 2005 6:7
  28. Complex biological database systems have become key computational tools used daily by scientists and researchers. Many of these systems must be capable of executing on multiple different hardware and software ...

    Authors: Marko Srdanovic, Ulf Schenk, Michael Schwieger and Fabien Campagne
    Citation: BMC Bioinformatics 2005 6:5
  29. Structure-dependent substitution matrices increase the accuracy of sequence alignments when the 3D structure of one sequence is known, and are successful e.g. in fold recognition. We propose a new automated me...

    Authors: Jean-Christophe Gelly, Laurent Chiche and Jérôme Gracy
    Citation: BMC Bioinformatics 2005 6:4

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