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  1. Defining blocks forming the global protein structure on the basis of local structural regularity is a very fruitful idea, extensively used in description, and prediction of structure from only sequence informa...

    Authors: Dariusz Plewczynski, Leszek Rychlewski, Yuzhen Ye, Lukasz Jaroszewski and Adam Godzik
    Citation: BMC Bioinformatics 2004 5:98
  2. Transposable elements (TE) are mobile genetic entities present in nearly all genomes. Previous work has shown that TEs tend to have a different nucleotide composition than the host genes, either considering co...

    Authors: Olivier Andrieu, Anna-Sophie Fiston, Dominique Anxolabéhère and Hadi Quesneville
    Citation: BMC Bioinformatics 2004 5:94
  3. The Split ends (Spen) family are large proteins characterised by N-terminal RNA recognition motifs (RRMs) and a conserved SPOC (Spen paralog and ortholog C-terminal) domain. The aim of this study is to charact...

    Authors: Luis Sánchez-Pulido, Ana M Rojas, Karel H van Wely, Carlos Martinez-A and Alfonso Valencia
    Citation: BMC Bioinformatics 2004 5:91
  4. Oligonucleotide frequencies were shown to be conserved signatures for bacterial genomes, however, the underlying constraints have yet not been resolved in detail. In this paper we analyzed oligonucleotide usag...

    Authors: Oleg N Reva and Burkhard Tümmler
    Citation: BMC Bioinformatics 2004 5:90
  5. The proliferation of structural and functional studies of RNA has revealed an increasing range of RNA's structural repertoire. Toward the objective of systematic cataloguing of RNA's structural repertoire, we ...

    Authors: Daniela Fera, Namhee Kim, Nahum Shiffeldrim, Julie Zorn, Uri Laserson, Hin Hark Gan and Tamar Schlick
    Citation: BMC Bioinformatics 2004 5:88
  6. Identification and characterization of novel Plasmodium gene families is necessary for developing new anti-malarial therapeutics. The products of the Plasmodium falciparum gene, MB2, were shown previously to have...

    Authors: Lisa C Romero, Thanh V Nguyen, Benoit Deville, Oluwasanmi Ogunjumo and Anthony A James
    Citation: BMC Bioinformatics 2004 5:83
  7. Due to the high cost and low reproducibility of many microarray experiments, it is not surprising to find a limited number of patient samples in each study, and very few common identified marker genes among di...

    Authors: Hongying Jiang, Youping Deng, Huann-Sheng Chen, Lin Tao, Qiuying Sha, Jun Chen, Chung-Jui Tsai and Shuanglin Zhang
    Citation: BMC Bioinformatics 2004 5:81
  8. Post-translational phosphorylation is one of the most common protein modifications. Phosphoserine, threonine and tyrosine residues play critical roles in the regulation of many cellular processes. The fast gro...

    Authors: Francesca Diella, Scott Cameron, Christine Gemünd, Rune Linding, Allegra Via, Bernhard Kuster, Thomas Sicheritz-Pontén, Nikolaj Blom and Toby J Gibson
    Citation: BMC Bioinformatics 2004 5:79
  9. When DNA microarray data are used for gene clustering, genotype/phenotype correlation studies, or tissue classification the signal intensities are usually transformed and normalized in several steps in order t...

    Authors: Helene H Thygesen and Aeilko H Zwinderman
    Citation: BMC Bioinformatics 2004 5:77
  10. The increasing number of protein sequences and 3D structure obtained from genomic initiatives is leading many of us to focus on proteomics, and to dedicate our experimental and computational efforts on the cre...

    Authors: Drew Lett, Michael Hsing and Frederic Pio
    Citation: BMC Bioinformatics 2004 5:75
  11. Microarray-based comparative genomic hybridisation (array CGH) is a technique by which variation in relative copy numbers between two genomes can be analysed by competitive hybridisation to DNA microarrays. Th...

    Authors: Junbai Wang, Leonardo A Meza-Zepeda, Stine H Kresse and Ola Myklebost
    Citation: BMC Bioinformatics 2004 5:74
  12. A routine goal in the analysis of microarray data is to identify genes with expression levels that correlate with known classes of experiments. In a growing number of array data sets, it has been shown that th...

    Authors: Yingchun Liu and Markus Ringnér
    Citation: BMC Bioinformatics 2004 5:70
  13. Rhabdomyosarcoma is a relatively common tumour of the soft tissue, probably due to regulatory disruption of growth and differentiation of skeletal muscle stem cells. Identification of genes differentially expr...

    Authors: Andrea Bisognin, Stefania Bortoluzzi and Gian Antonio Danieli
    Citation: BMC Bioinformatics 2004 5:68
  14. We have compared 38 isolates of the SARS-CoV complete genome. The main goal was twofold: first, to analyze and compare nucleotide sequences and to identify positions of single nucleotide polymorphism (SNP), in...

    Authors: Gordana M Pavlović-Lažetić, Nenad S Mitić and Miloš V Beljanski
    Citation: BMC Bioinformatics 2004 5:65
  15. The identification of relevant biological features in large and complex datasets is an important step towards gaining insight in the processes underlying the data. Other advantages of feature selection include...

    Authors: Yvan Saeys, Sven Degroeve, Dirk Aeyels, Pierre Rouzé and Yves Van de Peer
    Citation: BMC Bioinformatics 2004 5:64
  16. Microarray data must be normalized because they suffer from multiple biases. We have identified a source of spatial experimental variability that significantly affects data obtained with Cy3/Cy5 spotted glass ...

    Authors: Tristan Mary-Huard, Jean-Jacques Daudin, Stéphane Robin, Frédérique Bitton, Eric Cabannes and Pierre Hilson
    Citation: BMC Bioinformatics 2004 5:63
  17. The usefulness of log2 transformation for cDNA microarray data has led to its widespread application to Affymetrix data. For Affymetrix data, where absolute intensities are indicative of number of transcripts, th...

    Authors: Kellie J Archer, Catherine I Dumur and Viswanathan Ramakrishnan
    Citation: BMC Bioinformatics 2004 5:60
  18. Computational gene prediction continues to be an important problem, especially for genomes with little experimental data.

    Authors: Ian Korf
    Citation: BMC Bioinformatics 2004 5:59
  19. Transcriptional regulation is a key mechanism in the functioning of the cell, and is mostly effected through transcription factors binding to specific recognition motifs located upstream of the coding region o...

    Authors: Davide Corà, Ferdinando Di Cunto, Paolo Provero, Lorenzo Silengo and Michele Caselle
    Citation: BMC Bioinformatics 2004 5:57
  20. It is well known that different species have different protein domain repertoires, and indeed that some protein domains are kingdom specific. This information has not yet been incorporated into statistical met...

    Authors: Lachlan Coin, Alex Bateman and Richard Durbin
    Citation: BMC Bioinformatics 2004 5:56
  21. The Distributed Annotation System (DAS) allows merging of DNA sequence annotations from multiple sources and provides a single annotation view. A straightforward way to establish a DAS annotation server is to ...

    Authors: Vincent Negre and Christoph Grunau
    Citation: BMC Bioinformatics 2004 5:55
  22. The detection of small yet statistically significant differences in gene expression in spotted DNA microarray studies is an ongoing challenge. Meeting this challenge requires careful examination of the perform...

    Authors: Jeffrey P Townsend
    Citation: BMC Bioinformatics 2004 5:54
  23. Several aspects of microarray data analysis are dependent on identification of genes expressed at or near the limits of detection. For example, regression-based normalization methods rely on the premise that m...

    Authors: Igor Dozmorov, Nicholas Knowlton, Yuhong Tang and Michael Centola
    Citation: BMC Bioinformatics 2004 5:53
  24. An increasing number of whole viral and bacterial genomes are being sequenced and deposited in public databases. In parallel to the mounting interest in whole genomes, the number of whole genome analyses softw...

    Authors: Srikanth Celamkoti, Sashidhara Kundeti, Anjan Purkayastha, Raja Mazumder, Charles Buck and Donald Seto
    Citation: BMC Bioinformatics 2004 5:52
  25. To examine interactions among the angiotensin converting enzyme (ACE) insertion/deletion, plasminogen activator inhibitor-1 (PAI-1) 4G/5G, and tissue plasminogen activator (t-PA) insertion/deletion gene polymorph...

    Authors: Christopher S Coffey, Patricia R Hebert, Marylyn D Ritchie, Harlan M Krumholz, J Michael Gaziano, Paul M Ridker, Nancy J Brown, Douglas E Vaughan and Jason H Moore
    Citation: BMC Bioinformatics 2004 5:49

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