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  1. There has been considerable effort focused on developing efficient programs for tagging single-nucleotide polymorphisms (SNPs). Many of these programs do not account for potential reduced genomic coverage resu...

    Authors: Christopher K Edlund, Won H Lee, Dalin Li, David J Van Den Berg and David V Conti
    Citation: BMC Bioinformatics 2008 9:174
    Content type: Software Published on:

  3. Systematic approaches for identifying proteins involved in different types of cancer are needed. Experimental techniques such as microarrays are being used to characterize cancer, but validating their results ...

    Authors: Ramon Aragues, Chris Sander and Baldo Oliva
    Citation: BMC Bioinformatics 2008 9:172
    Content type: Research article Published on:

  5. The conservation of gene order among prokaryotic genomes can provide valuable insight into gene function, protein interactions, or events by which genomes have evolved. Although some tools are available for vi...

    Authors: Christine Fong, Laurence Rohmer, Matthew Radey, Michael Wasnick and Mitchell J Brittnacher
    Citation: BMC Bioinformatics 2008 9:170
    Content type: Software Published on:

  6. Large-scale, comprehensive and standardized high-throughput mouse phenotyping has been established as a tool of functional genome research by the German Mouse Clinic and others. In all these projects, vast amo...

    Authors: Holger Maier, Christoph Lengger, Bruno Simic, Helmut Fuchs, Valérie Gailus-Durner and Martin Hrabé de Angelis
    Citation: BMC Bioinformatics 2008 9:169
    Content type: Software Published on:

  7. Comparative genomics has become a significant research area in recent years, following the availability of a number of sequenced genomes. The comparison of genomes is of great importance in the analysis of fun...

    Authors: Sridevi Nagarajan, Willem Rens, James Stalker, Tony Cox and Malcolm A Ferguson-Smith
    Citation: BMC Bioinformatics 2008 9:168
    Content type: Software Published on:

  8. Analysis of sequence composition is a routine task in genome research. Organisms are characterized by their base composition, dinucleotide relative abundance, codon usage, and so on. Unique subsequences are ma...

    Authors: Julia Herold, Stefan Kurtz and Robert Giegerich
    Citation: BMC Bioinformatics 2008 9:167
    Content type: Methodology article Published on:

  10. Mixture models of mutagenetic trees are evolutionary models that capture several pathways of ordered accumulation of genetic events observed in different subsets of patients. They were used to model HIV progre...

    Authors: Jasmina Bogojeska, Thomas Lengauer and Jörg Rahnenführer
    Citation: BMC Bioinformatics 2008 9:165
    Content type: Research article Published on:

  12. Mass spectrometry is an essential analytical technique for high-throughput analysis in proteomics and metabolomics. The development of new separation techniques, precise mass analyzers and experimental protoco...

    Authors: Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert and Oliver Kohlbacher
    Citation: BMC Bioinformatics 2008 9:163
    Content type: Software Published on:

  14. In plant mitochondria, the post-transcriptional RNA editing process converts C to U at a number of specific sites of the mRNA sequence and usually restores phylogenetically conserved codons and the encoded ami...

    Authors: Ernesto Picardi and Carla Quagliariello
    Citation: BMC Bioinformatics 2008 9(Suppl 2):S14
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 2

  15. Recent progresses in genotyping technologies allow the generation high-density genetic maps using hundreds of thousands of genetic markers for each DNA sample. The availability of this large amount of genotypi...

    Authors: Alessandro Orro, Guia Guffanti, Erika Salvi, Fabio Macciardi and Luciano Milanesi
    Citation: BMC Bioinformatics 2008 9(Suppl 2):S13
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 2

  16. Microarray experiments enable simultaneous measurement of the expression levels of virtually all transcripts present in cells, thereby providing a ‘molecular picture’ of the cell state. On the other hand, the ...

    Authors: Margherita Mutarelli, Luigi Cicatiello, Lorenzo Ferraro, Olì MV Grober, Maria Ravo, Angelo M Facchiano, Claudia Angelini and Alessandro Weisz
    Citation: BMC Bioinformatics 2008 9(Suppl 2):S12
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 2

  17. Protein-protein interactions are at the basis of most cellular processes and crucial for many bio-technological applications. During the last few years the development of high-throughput technologies has produ...

    Authors: Paolo Marcatili, Giovanni Bussotti and Anna Tramontano
    Citation: BMC Bioinformatics 2008 9(Suppl 2):S11
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 2

  18. Searching for similarities in protein and DNA databases has become a routine procedure in Molecular Biology. The Smith-Waterman algorithm has been available for more than 25 years. It is based on a dynamic pro...

    Authors: Svetlin A Manavski and Giorgio Valle
    Citation: BMC Bioinformatics 2008 9(Suppl 2):S10
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 2

  19. The ESTree database (db) is a collection of Prunus persica and Prunus dulcis EST sequences that in its current version encompasses 75,404 sequences from 3 almond and 19 peach libraries. Nine peach genotypes and f...

    Authors: Barbara Lazzari, Andrea Caprera, Alberto Vecchietti, Ivan Merelli, Francesca Barale, Luciano Milanesi, Alessandra Stella and Carlo Pozzi
    Citation: BMC Bioinformatics 2008 9(Suppl 2):S9
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 2

  20. Urokinase, its receptor and the integrins are functionally associated and involved in regulation of cell signaling, migration, adhesion and proliferation. No structural information is available on this potenti...

    Authors: Bernard Degryse, Juan Fernandez-Recio, Valentina Citro, Francescol Blasi and Maria Vittoria Cubellis
    Citation: BMC Bioinformatics 2008 9(Suppl 2):S8
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 2

  21. Present-day ‘-omics’ technologies produce overwhelming amounts of data which include genome sequences, information on gene expression (transcripts and proteins) and on cell metabolic status. These data represent ...

    Authors: Maria Luisa Chiusano, Nunzio D'Agostino, Alessandra Traini, Concetta Licciardello, Enrico Raimondo, Mario Aversano, Luigi Frusciante and Luigi Monti
    Citation: BMC Bioinformatics 2008 9(Suppl 2):S7
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 2

  22. A basic question of protein structural studies is to which extent mutations affect the stability. This question may be addressed starting from sequence and/or from structure. In proteomics and genomics studies...

    Authors: Emidio Capriotti, Piero Fariselli, Ivan Rossi and Rita Casadio
    Citation: BMC Bioinformatics 2008 9(Suppl 2):S6
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 2

  23. Baculovirus-expressed HIV-1 Pr55gag Virus-Like Particles (HIV-VLPs) induce maturation and activation of monocyte-derived dendritic cells (MDDCs) with a production of Th1- and Th2-specific cytokines.

    Authors: Luigi Buonaguro, Alessandro Monaco, Eleonora Aricò, Ena Wang, Maria Lina Tornesello, George K Lewis, Franco M Marincola and Franco M Buonaguro
    Citation: BMC Bioinformatics 2008 9(Suppl 2):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 2

  24. The unsupervised discovery of structures (i.e. clusterings) underlying data is a central issue in several branches of bioinformatics. Methods based on the concept of stability have been recently proposed to as...

    Authors: Alberto Bertoni and Giorgio Valentini
    Citation: BMC Bioinformatics 2008 9(Suppl 2):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 2

  25. Brain, heart and skeletal muscle share similar properties of excitable tissue, featuring both discrete behavior (all-or-nothing response to electrical activation) and continuous behavior (recovery to rest foll...

    Authors: Ezio Bartocci, Flavio Corradini, Emilia Entcheva, Radu Grosu and Scott A Smolka
    Citation: BMC Bioinformatics 2008 9(Suppl 2):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 2

  26. The occurrence of very similar structural motifs brought about by different parts of non homologous proteins is often indicative of a common function. Indeed, relatively small local structures can mediate bind...

    Authors: Gabriele Ausiello, Pier Federico Gherardini, Paolo Marcatili, Anna Tramontano, Allegra Via and Manuela Helmer-Citterich
    Citation: BMC Bioinformatics 2008 9(Suppl 2):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 2

  29. Protein structure comparison is a key problem in bioinformatics. There exist several methods for doing protein comparison, being the solution of the Maximum Contact Map Overlap problem (MAX-CMO) one of the alt...

    Authors: David A Pelta, Juan R González and Marcos Moreno Vega
    Citation: BMC Bioinformatics 2008 9:161
    Content type: Methodology article Published on:

  30. Accurate annotation of translation initiation sites (TISs) is essential for understanding the translation initiation mechanism. However, the reliability of TIS annotation in widely used databases such as RefSe...

    Authors: Gang-Qing Hu, Xiaobin Zheng, Li-Ning Ju, Huaiqiu Zhu and Zhen-Su She
    Citation: BMC Bioinformatics 2008 9:160
    Content type: Methodology article Published on:

  35. The hierarchical clustering tree (HCT) with a dendrogram [1] and the singular value decomposition (SVD) with a dimension-reduced representative map [2] are popular methods for two-way sorting the gene-by-array ma...

    Authors: Yin-Jing Tien, Yun-Shien Lee, Han-Ming Wu and Chun-Houh Chen
    Citation: BMC Bioinformatics 2008 9:155
    Content type: Methodology article Published on:

  36. With advances in DNA re-sequencing methods and Next-Generation parallel sequencing approaches, there has been a large increase in genomic efforts to define and analyze the sequence variability present among in...

    Authors: Hector Sanchez-Villeda, Steven Schroeder, Sherry Flint-Garcia, Katherine E Guill, Masanori Yamasaki and Michael D McMullen
    Citation: BMC Bioinformatics 2008 9:154
    Content type: Software Published on:

  37. Spatially mapped large scale gene expression databases enable quantitative comparison of data measurements across genes, anatomy, and phenotype. In most ongoing efforts to study gene expression in the mammalia...

    Authors: Christopher Lau, Lydia Ng, Carol Thompson, Sayan Pathak, Leonard Kuan, Allan Jones and Mike Hawrylycz
    Citation: BMC Bioinformatics 2008 9:153
    Content type: Software Published on:

  39. A multiple sequence alignment (MSA) generated for a protein can be used to characterise residues by means of a statistical analysis of single columns. In addition to the examination of individual positions, th...

    Authors: Rainer Merkl and Matthias Zwick
    Citation: BMC Bioinformatics 2008 9:151
    Content type: Methodology article Published on:

  40. We sketch our species identification tool for palm sized computers that helps knowledgeable observers with census activities. An algorithm turns an identification matrix into a minimal length series of questio...

    Authors: Aswath Manoharan, Jeannie Stamberger, YuanYuan Yu and Andreas Paepcke
    Citation: BMC Bioinformatics 2008 9:150
    Content type: Research article Published on:

  41. DNA microarray technology has emerged as a major tool for exploring cancer biology and solving clinical issues. Predicting a patient's response to chemotherapy is one such issue; successful prediction would ma...

    Authors: René Natowicz, Roberto Incitti, Euler Guimarães Horta, Benoît Charles, Philippe Guinot, Kai Yan, Charles Coutant, Fabrice Andre, Lajos Pusztai and Roman Rouzier
    Citation: BMC Bioinformatics 2008 9:149
    Content type: Methodology article Published on:

  42. Protein structure prediction and computational protein design require efficient yet sufficiently accurate descriptions of aqueous solvent. We continue to evaluate the performance of the Coulomb/Accessible Surf...

    Authors: Marcel Schmidt am Busch, Anne Lopes, Najette Amara, Christine Bathelt and Thomas Simonson
    Citation: BMC Bioinformatics 2008 9:148
    Content type: Research article Published on:

  43. Many microarray experiments produce temporal profiles in different biological conditions but common cluster techniques are not able to analyze the data conditional on the biological conditions.

    Authors: Ling Wang, Monty Montano, Matt Rarick and Paola Sebastiani
    Citation: BMC Bioinformatics 2008 9:147
    Content type: Methodology article Published on:

  44. The risk of common diseases is likely determined by the complex interplay between environmental and genetic factors, including single nucleotide polymorphisms (SNPs). Traditional methods of data analysis are p...

    Authors: Leah E Mechanic, Brian T Luke, Julie E Goodman, Stephen J Chanock and Curtis C Harris
    Citation: BMC Bioinformatics 2008 9:146
    Content type: Methodology article Published on:

  46. An important goal of whole-genome studies concerned with single nucleotide polymorphisms (SNPs) is the identification of SNPs associated with a covariate of interest such as the case-control status or the type...

    Authors: Holger Schwender and Katja Ickstadt
    Citation: BMC Bioinformatics 2008 9:144
    Content type: Methodology article Published on:

  47. Genes and gene products are frequently annotated with Gene Ontology concepts based on the evidence provided in genomics articles. Manually locating and curating information about a genomic entity from the biom...

    Authors: Ali Cakmak and Gultekin Ozsoyoglu
    Citation: BMC Bioinformatics 2008 9:143
    Content type: Research article Published on:

  48. Microarray technology provides an efficient means for globally exploring physiological processes governed by the coordinated expression of multiple genes. However, identification of genes differentially expres...

    Authors: Yuan-De Tan, Myriam Fornage and Hongyan Xu
    Citation: BMC Bioinformatics 2008 9:142
    Content type: Methodology article Published on:

  49. Modern proteomes evolved by modification of pre-existing ones. It is extremely important to comparative biology that related proteins be identified as members of the same cognate group, since a characterized p...

    Authors: Adriano Barbosa-Silva, Venkata P Satagopam, Reinhard Schneider and J Miguel Ortega
    Citation: BMC Bioinformatics 2008 9:141
    Content type: Software Published on:

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