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  1. Protein secretion is a cell translocation process of major biological and technological significance. The secretion and downstream processing of proteins by recombinant cells is of great commercial interest. T...

    Authors: Otávio JB Brustolini, Luciano G Fietto, Cosme D Cruz and Flávia ML Passos
    Citation: BMC Bioinformatics 2009 10:194
    Content type: Research article Published on:

  4. Prior to cluster analysis or genetic network analysis it is customary to filter, or remove genes considered to be irrelevant from the set of genes to be analyzed. Often genes whose variation across samples is ...

    Authors: David Tritchler, Elena Parkhomenko and Joseph Beyene
    Citation: BMC Bioinformatics 2009 10:193
    Content type: Methodology article Published on:

  5. The recent availability of an expanding collection of genome sequences driven by technological advances has facilitated comparative genomics and in particular the identification of synteny among multiple genom...

    Authors: Man-Ping Ng, Ismael A Vergara, Christian Frech, Qingkang Chen, Xinghuo Zeng, Jian Pei and Nansheng Chen
    Citation: BMC Bioinformatics 2009 10:192
    Content type: Database Published on:

  8. With the recent development of microarray technologies, the comparability of gene expression data obtained from different platforms poses an important problem. We evaluated two widely used platforms, Affymetri...

    Authors: Rose Du, Kelan Tantisira, Vincent Carey, Soumyaroop Bhattacharya, Stephanie Metje, Alvin T Kho, Barbara J Klanderman, Roger Gaedigk, Ross Lazarus, Thomas J Mariani, J Steven Leeder and Scott T Weiss
    Citation: BMC Bioinformatics 2009 10:189
    Content type: Research article Published on:

  9. High-dimensional biomolecular profiling of genetically different individuals in one or more environmental conditions is an increasingly popular strategy for exploring the functioning of complex biological syst...

    Authors: Yang Li, Morris A Swertz, Gonzalo Vera, Jingyuan Fu, Rainer Breitling and Ritsert C Jansen
    Citation: BMC Bioinformatics 2009 10:188
    Content type: Software Published on:

  10. Bioinformatics and medical informatics are two research fields that serve the needs of different but related communities. Both domains share the common goal of providing new algorithms, methods and technologic...

    Authors: Daniel Glez-Peña, Fernando Díaz, Jesús M Hernández, Juan M Corchado and Florentino Fdez-Riverola
    Citation: BMC Bioinformatics 2009 10:187
    Content type: Software Published on:

  11. The MAQC project demonstrated that microarrays with comparable content show inter- and intra-platform reproducibility. However, since the content of gene databases still increases, the development of new gener...

    Authors: Daniela Eggle, Svenja Debey-Pascher, Marc Beyer and Joachim L Schultze
    Citation: BMC Bioinformatics 2009 10:186
    Content type: Research article Published on:

  12. Discovery of new medicinal agents from natural sources has largely been an adventitious process based on screening of plant and microbial extracts combined with bioassay-guided identification and natural produ...

    Authors: Michael HT Li, Peter MU Ung, James Zajkowski, Sylvie Garneau-Tsodikova and David H Sherman
    Citation: BMC Bioinformatics 2009 10:185
    Content type: Software Published on:

  13. Flow cytometry technology is widely used in both health care and research. The rapid expansion of flow cytometry applications has outpaced the development of data storage and analysis tools. Collaborative effo...

    Authors: Yu Qian, Olga Tchuvatkina, Josef Spidlen, Peter Wilkinson, Maura Gasparetto, Andrew R Jones, Frank J Manion, Richard H Scheuermann, Rafick-Pierre Sekaly and Ryan R Brinkman
    Citation: BMC Bioinformatics 2009 10:184
    Content type: Correspondence Published on:

  14. Many studies report about detection and functional characterization of cis-regulatory motifs in untranslated regions (UTRs) of mRNAs but little is known about the nature and functional role of their distributi...

    Authors: Antonio Turi, Corrado Loglisci, Eliana Salvemini, Giorgio Grillo, Donato Malerba and Domenica D'Elia
    Citation: BMC Bioinformatics 2009 10(Suppl 6):S25
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 6

  15. Recent technological advances in DNA sequencing and genotyping have led to the accumulation of a remarkable quantity of data on genetic polymorphisms. However, the development of new statistical and computatio...

    Authors: Vincenzo Lagani, Alberto Montesanto, Fausta Di Cianni, Victor Moreno, Stefano Landi, Domenico Conforti, Giuseppina Rose and Giuseppe Passarino
    Citation: BMC Bioinformatics 2009 10(Suppl 6):S24
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 6

  16. A fundamental activity in biomedical research is Knowledge Discovery which has the ability to search through large amounts of biomedical information such as documents and data. High performance computational i...

    Authors: Marcello Castellano, Giuseppe Mastronardi, Roberto Bellotti and Gianfranco Tarricone
    Citation: BMC Bioinformatics 2009 10(Suppl 6):S23
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 6

  17. The number of natural proteins represents a small fraction of all the possible protein sequences and there is an enormous number of proteins never sampled by nature, the so called "never born proteins" (NBPs)....

    Authors: Giovanni Minervini, Giuseppe Evangelista, Laura Villanova, Debora Slanzi, Davide De Lucrezia, Irene Poli, Pier Luigi Luisi and Fabio Polticelli
    Citation: BMC Bioinformatics 2009 10(Suppl 6):S22
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 6

  18. Grid technology is the computing model which allows users to share a wide pletora of distributed computational resources regardless of their geographical location. Up to now, the high security policy requested in...

    Authors: Roberto Barbera, Giacinto Donvito, Alberto Falzone, Giuseppe La Rocca, Luciano Milanesi, Giorgio Pietro Maggi and Saverio Vicario
    Citation: BMC Bioinformatics 2009 10(Suppl 6):S21
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 6

  19. microRNAs (miRNAs) are single-stranded RNA molecules of about 20–23 nucleotides length found in a wide variety of organisms. miRNAs regulate gene expression, by interacting with target mRNAs at specific sites ...

    Authors: Maria G Roubelakis, Pantelis Zotos, Georgios Papachristoudis, Ioannis Michalopoulos, Kalliopi I Pappa, Nicholas P Anagnou and Sophia Kossida
    Citation: BMC Bioinformatics 2009 10(Suppl 6):S20
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 6

  20. In the biological sciences, the need to analyse vast amounts of information has become commonplace. Such large-scale analyses often involve drawing together data from a variety of different databases, held rem...

    Authors: Steve Pettifer, David Thorne, Philip McDermott, James Marsh, Alice Villéger, Douglas B Kell and Teresa K Attwood
    Citation: BMC Bioinformatics 2009 10(Suppl 6):S19
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 6

  21. The Distributed Annotation System (DAS) is a widely used network protocol for sharing biological information. The distributed aspects of the protocol enable the use of various reference and annotation servers ...

    Authors: Álvaro Martínez Barrio, Erik Lagercrantz, Göran O Sperber, Jonas Blomberg and Erik Bongcam-Rudloff
    Citation: BMC Bioinformatics 2009 10(Suppl 6):S18
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 6

  22. As biological networks often show complex topological features, mathematical methods are required to extract meaningful information. Clustering methods are useful in this setting, as they allow the summary of ...

    Authors: Franck Picard, Vincent Miele, Jean-Jacques Daudin, Ludovic Cottret and Stéphane Robin
    Citation: BMC Bioinformatics 2009 10(Suppl 6):S17
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 6

  23. To allow the survival of the population in the absence of nitrogen, some cyanobacteria strains have developed the capability of differentiating into nitrogen fixing cells, forming a characteristic pattern. In ...

    Authors: Ziomara P Gerdtzen, J Cristian Salgado, Axel Osses, Juan A Asenjo, Ivan Rapaport and Barbara A Andrews
    Citation: BMC Bioinformatics 2009 10(Suppl 6):S16
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 6

  24. A standardized and cost-effective molecular identification system is now an urgent need for Fungi owing to their wide involvement in human life quality. In particular the potential use of mitochondrial DNA spe...

    Authors: Monica Santamaria, Saverio Vicario, Graziano Pappadà, Gaetano Scioscia, Claudio Scazzocchio and Cecilia Saccone
    Citation: BMC Bioinformatics 2009 10(Suppl 6):S15
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 6

  25. DNA sequences have become a primary source of information in biodiversity analysis. For example, short standardized species-specific genomic regions, DNA barcodes, are being used as a global standard for speci...

    Authors: Gregory AC Singer and Mehrdad Hajibabaei
    Citation: BMC Bioinformatics 2009 10(Suppl 6):S14
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 6

  26. Chemogenomics is an emerging inter-disciplinary approach to drug discovery that combines traditional ligand-based approaches with biological information on drug targets and lies at the interface of chemistry, ...

    Authors: Helena Strömbergsson and Gerard J Kleywegt
    Citation: BMC Bioinformatics 2009 10(Suppl 6):S13
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 6

  27. Liquid Chromatography-Mass Spectrometry (LC-MS) is a commonly used technique to resolve complex protein mixtures. Visualization of large data sets produced from LC-MS, namely the chromatogram and the mass spec...

    Authors: Dimosthenis Tsagkrasoulis, Panagiotis Zerefos, George Loudos, Antonia Vlahou, Marc Baumann and Sophia Kossida
    Citation: BMC Bioinformatics 2009 10(Suppl 6):S12
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 6

  28. During the last years, high throughput experimental methods have been developed which generate large datasets of protein – protein interactions (PPIs). However, due to the experimental methodologies these data...

    Authors: Charalampos N Moschopoulos, Georgios A Pavlopoulos, Reinhard Schneider, Spiridon D Likothanassis and Sophia Kossida
    Citation: BMC Bioinformatics 2009 10(Suppl 6):S11
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 6

  29. ESTs and full-length cDNAs represent an invaluable source of evidence for inferring reliable gene structures and discovering potential alternative splicing events. In newly sequenced genomes, these tasks may n...

    Authors: Ernesto Picardi, Flavio Mignone and Graziano Pesole
    Citation: BMC Bioinformatics 2009 10(Suppl 6):S10
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 6

  30. Time-course microarray experiments study the progress of gene expression along time across one or several experimental conditions. Most developed analysis methods focus on the clustering or the differential ex...

    Authors: María José Nueda, Patricia Sebastián, Sonia Tarazona, Francisco García-García, Joaquín Dopazo, Alberto Ferrer and Ana Conesa
    Citation: BMC Bioinformatics 2009 10(Suppl 6):S9
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 6

  31. Genome-wide duplication is ubiquitous during diversification of the angiosperms, and gene duplication is one of the most important mechanisms for evolutionary novelties. As an indicator of functional evolution...

    Authors: Zhe Li, He Zhang, Song Ge, Xiaocheng Gu, Ge Gao and Jingchu Luo
    Citation: BMC Bioinformatics 2009 10(Suppl 6):S8
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 6

  32. The mollicute Mycoplasma conjunctivae is the etiological agent leading to infectious keratoconjunctivitis (IKC) in domestic sheep and wild caprinae. Although this pathogen is relatively benign for domestic animal...

    Authors: Sandra P Calderon-Copete, George Wigger, Christof Wunderlin, Tobias Schmidheini, Joachim Frey, Michael A Quail and Laurent Falquet
    Citation: BMC Bioinformatics 2009 10(Suppl 6):S7
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 6

  33. The comparative genomic analysis of a large number of orthologous promoter regions of the chordate and plant genes from the DoOP databases shows thousands of conserved motifs. Most of these motifs differ from ...

    Authors: Endre Sebestyén, Tibor Nagy, Sándor Suhai and Endre Barta
    Citation: BMC Bioinformatics 2009 10(Suppl 6):S6
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 6

  34. One of the most frequent uses of bioinformatics tools concerns functional characterization of a newly produced nucleotide sequence (a query sequence) by applying Blast or FASTA against a set of sequences (the ...

    Authors: Francesco Rubino and Marcella Attimonelli
    Citation: BMC Bioinformatics 2009 10(Suppl 6):S5
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 6

  35. The rapid accumulation of genomic information in databases necessitates rapid and specific algorithms for extracting biologically meaningful information. More or less complete retroviral sequences, also called...

    Authors: Göran Sperber, Anders Lövgren, Nils-Einar Eriksson, Farid Benachenhou and Jonas Blomberg
    Citation: BMC Bioinformatics 2009 10(Suppl 6):S4
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 6

  36. Comparative genomics is a central step in many sequence analysis studies, from gene annotation and the identification of new functional regions in genomes, to the study of evolutionary processes at the molecul...

    Authors: Simon Penel, Anne-Muriel Arigon, Jean-François Dufayard, Anne-Sophie Sertier, Vincent Daubin, Laurent Duret, Manolo Gouy and Guy Perrière
    Citation: BMC Bioinformatics 2009 10(Suppl 6):S3
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 6

  37. The identification of protein coding elements in sets of mammalian conserved elements is one of the major challenges in the current molecular biology research. Many features have been proposed for automaticall...

    Authors: Teresa M Creanza, David S Horner, Annarita D'Addabbo, Rosalia Maglietta, Flavio Mignone, Nicola Ancona and Graziano Pesole
    Citation: BMC Bioinformatics 2009 10(Suppl 6):S2
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 6

  38. The EMBnet Conference 2008, focusing on 'Leading Applications and Technologies in Bioinformatics', was organized by the European Molecular Biology network (EMBnet) to celebrate its 20th anniversary. Since its fou...

    Authors: Domenica D'Elia, Andreas Gisel, Nils-Einar Eriksson, Sophia Kossida, Kimmo Mattila, Lubos Klucar and Erik Bongcam-Rudloff
    Citation: BMC Bioinformatics 2009 10(Suppl 6):S1
    Content type: Introduction Published on:

    This article is part of a Supplement: Volume 10 Supplement 6

  40. The structural analysis of protein ligand binding sites can provide information relevant for assigning functions to unknown proteins, to guide the drug discovery process and to infer relations among distant pr...

    Authors: Gabriele Ausiello, Pier Federico Gherardini, Elena Gatti, Ottaviano Incani and Manuela Helmer-Citterich
    Citation: BMC Bioinformatics 2009 10:182
    Content type: Methodology article Published on:

  41. Interaction graphs (signed directed graphs) provide an important qualitative modeling approach for Systems Biology. They enable the analysis of causal relationships in cellular networks and can even be useful ...

    Authors: Steffen Klamt and Axel von Kamp
    Citation: BMC Bioinformatics 2009 10:181
    Content type: Methodology article Published on:

  42. In moderate-throughput SNP genotyping there was a gap in the workflow, between choosing a set of SNPs and submitting their sequences to proprietary assay design software, which was not met by existing software...

    Authors: Helen I Field, Serena A Scollen, Craig Luccarini, Caroline Baynes, Jonathan Morrison, Alison M Dunning, Douglas F Easton and Paul DP Pharoah
    Citation: BMC Bioinformatics 2009 10:180
    Content type: Software Published on:

  43. Proteomic protein identification results need to be compared across laboratories and platforms, and thus a reliable method is needed to estimate false discovery rates. The target-decoy strategy is a platform-i...

    Authors: Lau Sennels, Jimi-Carlo Bukowski-Wills and Juri Rappsilber
    Citation: BMC Bioinformatics 2009 10:179
    Content type: Research article Published on:

  45. The Enteropathogen Resource Integration Center (ERIC; http://​www.​ericbrc.​org) has a goal of providing bioinformatics support for the scientific communi...

    Authors: Sam Zaremba, Mila Ramos-Santacruz, Thomas Hampton, Panna Shetty, Joel Fedorko, Jon Whitmore, John M Greene, Nicole T Perna, Jeremy D Glasner, Guy Plunkett III, Matthew Shaker and David Pot
    Citation: BMC Bioinformatics 2009 10:177
    Content type: Database Published on:

  46. Analysis of allelic variation for relevant genes and monitoring chromosome segment transmission during selection are important approaches in plant breeding and ecology. To minimize the number of required molec...

    Authors: Ursula K Frei, Bernd Wollenweber and Thomas Lübberstedt
    Citation: BMC Bioinformatics 2009 10:176
    Content type: Software Published on:

  47. DNA sequence comparison is based on optimal local alignment of two sequences using a similarity score. However, some new DNA sequencing technologies do not directly measure the base sequence, but rather an enc...

    Authors: Nils Homer, Barry Merriman and Stanley F Nelson
    Citation: BMC Bioinformatics 2009 10:175
    Content type: Research article Published on:

  49. Microarray analysis of immunoprecipitated chromatin (ChIP-chip) has evolved from a novel technique to a standard approach for the systematic study of protein-DNA interactions. In ChIP-chip, sites of protein-DN...

    Authors: Wei Sun, Michael J Buck, Mukund Patel and Ian J Davis
    Citation: BMC Bioinformatics 2009 10:173
    Content type: Methodology article Published on:

  50. Copy number variations (CNVs) may play an important role in disease risk by altering dosage of genes and other regulatory elements, which may have functional and, ultimately, phenotypic consequences. Therefore...

    Authors: Juan R González, Isaac Subirana, Geòrgia Escaramís, Solymar Peraza, Alejandro Cáceres, Xavier Estivill and Lluís Armengol
    Citation: BMC Bioinformatics 2009 10:172
    Content type: Methodology article Published on:

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