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  1. An important challenge for transcript counting methods such as Serial Analysis of Gene Expression (SAGE), "Digital Northern" or Massively Parallel Signature Sequencing (MPSS), is to carry out statistical analy...

    Authors: Ricardo ZN Vêncio, Helena Brentani, Diogo FC Patrão and Carlos AB Pereira
    Citation: BMC Bioinformatics 2004 5:119
    Content type: Methodology article Published on:

  3. The current progress in sequencing projects calls for rapid, reliable and accurate function assignments of gene products. A variety of methods has been designed to annotate sequences on a large scale. However,...

    Authors: Arunachalam Vinayagam, Rainer König, Jutta Moormann, Falk Schubert, Roland Eils, Karl-Heinz Glatting and Sándor Suhai
    Citation: BMC Bioinformatics 2004 5:116
    Content type: Methodology article Published on:

  4. The nematode Caenorhabditis elegans is widely used for the genetic analysis of neuronal cell biology, development, and behavior. Because traditional methods for evaluating behavioral phenotypes are qualitative an...

    Authors: Zhaoyang Feng, Christopher J Cronin, John H Wittig Jr, Paul W Sternberg and William R Schafer
    Citation: BMC Bioinformatics 2004 5:115
    Content type: Software Published on:

  5. Microarray technologies produced large amount of data. The hierarchical clustering is commonly used to identify clusters of co-expressed genes. However, microarray datasets often contain missing values (MVs) r...

    Authors: Alexandre G de Brevern, Serge Hazout and Alain Malpertuy
    Citation: BMC Bioinformatics 2004 5:114
    Content type: Research article Published on:

  7. A necessary step for a genome level analysis of the cellular metabolism is the in silico reconstruction of the metabolic network from genome sequences. The available methods are mainly based on the annotation of ...

    Authors: Jibin Sun and An-Ping Zeng
    Citation: BMC Bioinformatics 2004 5:112
    Content type: Methodology article Published on:

  8. Short oligonucleotide arrays have several probes measuring the expression level of each target transcript. Therefore the selection of probes is a key component for the quality of measurements. However, once pr...

    Authors: Laurent Gautier, Morten Møller, Lennart Friis-Hansen and Steen Knudsen
    Citation: BMC Bioinformatics 2004 5:111
    Content type: Methodology article Published on:

  9. Microarray studies in cancer compare expression levels between two or more sample groups on thousands of genes. Data analysis follows a population-level approach (e.g., comparison of sample means) to identify ...

    Authors: James Lyons-Weiler, Satish Patel, Michael J Becich and Tony E Godfrey
    Citation: BMC Bioinformatics 2004 5:110
    Content type: Methodology article Published on:

  11. Recent technological advances in high-throughput data collection allow for experimental study of increasingly complex systems on the scale of the whole cellular genome and proteome. Gene network models are nee...

    Authors: Bahrad A Sokhansanj, Patrick J Fitch, Judy N Quong and Andrew A Quong
    Citation: BMC Bioinformatics 2004 5:108
    Content type: Methodology article Published on:

  12. The integration of many aspects of protein/DNA structure analysis is an important requirement for software products in general area of structural bioinformatics. In fact, there are too few software packages on...

    Authors: Roberto H Higa, Roberto C Togawa, Arnaldo J Montagner, Juliana CF Palandrani, Igor KS Okimoto, Paula R Kuser, Michel EB Yamagishi, Adauto L Mancini and Goran Neshich
    Citation: BMC Bioinformatics 2004 5:107
    Content type: Software Published on:

  14. A detailed understanding of an RNA's correct secondary and tertiary structure is crucial to understanding its function and mechanism in the cell. Free energy minimization with energy parameters based on the ne...

    Authors: Kishore J Doshi, Jamie J Cannone, Christian W Cobaugh and Robin R Gutell
    Citation: BMC Bioinformatics 2004 5:105
    Content type: Research article Published on:

  17. Determination of genetic relatedness among microorganisms provides information necessary for making inferences regarding phylogeny. However, there is little information available on how well the genetic relati...

    Authors: Baozhen Qiao and Ronald M Weigel
    Citation: BMC Bioinformatics 2004 5:102
    Content type: Methodology article Published on:

  18. We establish that the occurrence of protein folds among genomes can be accurately described with a Weibull function. Systems which exhibit Weibull character can be interpreted with reliability theory commonly ...

    Authors: Artem Cherkasov, Shannan J Ho Sui, Robert C Brunham and Steven JM Jones
    Citation: BMC Bioinformatics 2004 5:101
    Content type: Research article Published on:

  20. cDNA microarrays are a powerful means to screen for biologically relevant gene expression changes, but are often limited by their ability to detect small changes accurately due to "noise" from random and syste...

    Authors: Bin Yao, Sanjay N Rakhade, Qunfang Li, Sharlin Ahmed, Raul Krauss, Sorin Draghici and Jeffrey A Loeb
    Citation: BMC Bioinformatics 2004 5:99
    Content type: Research article Published on:

  21. 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
    Content type: Software Published on:

  25. 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
    Content type: Methodology article Published on:

  28. 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
    Content type: Research article Published on:

  29. 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
    Content type: Research article Published on:

  31. 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
    Content type: Database Published on:

  36. 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
    Content type: Research article Published on:

  38. 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
    Content type: Methodology article Published on:

  40. 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
    Content type: Database Published on:

  42. 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
    Content type: Methodology article Published on:

  44. 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
    Content type: Research article Published on:

  45. 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
    Content type: Software Published on:

  49. 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
    Content type: Software Published on:

  50. Carbohydrates are involved in a variety of fundamental biological processes and pathological situations. They therefore have a large pharmaceutical and diagnostic potential. Knowledge of the 3D structure of gl...

    Authors: Thomas Lütteke and Claus-W von der Lieth
    Citation: BMC Bioinformatics 2004 5:69
    Content type: Software Published on:

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