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  1. In recent years, the genome biology community has expended considerable effort to confront the challenges of managing heterogeneous data in a structured and organized way and developed laboratory information m...

    Authors: Gernot Stocker, Maria Fischer, Dietmar Rieder, Gabriela Bindea, Simon Kainz, Michael Oberstolz, James G McNally and Zlatko Trajanoski
    Citation: BMC Bioinformatics 2009 10:390
    Content type: Software Published on:

  2. Large discrepancies in signature composition and outcome concordance have been observed between different microarray breast cancer expression profiling studies. This is often ascribed to differences in array p...

    Authors: Herman MJ Sontrop, Perry D Moerland, René van den Ham, Marcel JT Reinders and Wim FJ Verhaegh
    Citation: BMC Bioinformatics 2009 10:389
    Content type: Research article Published on:

  3. The accurate determination of transcription factor binding affinities is an important problem in biology and key to understanding the gene regulation process. Position weight matrices are commonly used to repr...

    Authors: Isabelle da Piedade, Man-Hung Eric Tang and Olivier Elemento
    Citation: BMC Bioinformatics 2009 10:388
    Content type: Methodology article Published on:

  4. The efficiency of lymph nodes depends on tissue structure and organization, which allow the coordination of lymphocyte traffic. Despite their essential role, our understanding of lymph node specific mechanisms...

    Authors: Valentina Baldazzi, Paola Paci, Massimo Bernaschi and Filippo Castiglione
    Citation: BMC Bioinformatics 2009 10:387
    Content type: Methodology article Published on:

  5. Optimization methods allow designing changes in a system so that specific goals are attained. These techniques are fundamental for metabolic engineering. However, they are not directly applicable for investiga...

    Authors: Gonzalo Guillén-Gosálbez and Albert Sorribas
    Citation: BMC Bioinformatics 2009 10:386
    Content type: Research article Published on:

  7. Graphical Gaussian models are popular tools for the estimation of (undirected) gene association networks from microarray data. A key issue when the number of variables greatly exceeds the number of samples is ...

    Authors: Nicole Krämer, Juliane Schäfer and Anne-Laure Boulesteix
    Citation: BMC Bioinformatics 2009 10:384
    Content type: Research article Published on:

  8. Phylogenetic profiling encompasses an important set of methodologies for in silico high throughput inference of functional relationships between genes. The simplest profiles represent the distribution of gene pre...

    Authors: Valentín Ruano-Rubio, Olivier Poch and Julie D Thompson
    Citation: BMC Bioinformatics 2009 10:383
    Content type: Research article Published on:

  9. Non-random patterns of genetic variation exist among individuals in a population owing to a variety of evolutionary factors. Therefore, populations are structured into genetically distinct subpopulations. As g...

    Authors: Apichart Intarapanich, Philip J Shaw, Anunchai Assawamakin, Pongsakorn Wangkumhang, Chumpol Ngamphiw, Kridsadakorn Chaichoompu, Jittima Piriyapongsa and Sissades Tongsima
    Citation: BMC Bioinformatics 2009 10:382
    Content type: Methodology article Published on:

  10. Predicting the binding sites between two interacting proteins provides important clues to the function of a protein. Recent research on protein binding site prediction has been mainly based on widely known mac...

    Authors: Bin Liu, Xiaolong Wang, Lei Lin, Buzhou Tang, Qiwen Dong and Xuan Wang
    Citation: BMC Bioinformatics 2009 10:381
    Content type: Research article Published on:

  11. Comparative genomic hybridization microarrays for the detection of constitutional chromosomal aberrations is the application of microarray technology coming fastest into routine clinical application. Through g...

    Authors: Joke Allemeersch, Steven Van Vooren, Femke Hannes, Bart De Moor, Joris Robert Vermeesch and Yves Moreau
    Citation: BMC Bioinformatics 2009 10:380
    Content type: Methodology article Published on:

  12. The rate of protein structures being deposited in the Protein Data Bank surpasses the capacity to experimentally characterise them and therefore computational methods to analyse these structures have become in...

    Authors: Tracey Bray, Pedro Chan, Salim Bougouffa, Richard Greaves, Andrew J Doig and Jim Warwicker
    Citation: BMC Bioinformatics 2009 10:379
    Content type: Software Published on:

  14. Biological sequences play a major role in molecular and computational biology. They are studied as information-bearing entities that make up DNA, RNA or proteins. The Sequence Ontology, which is part of the OB...

    Authors: Robert Hoehndorf, Janet Kelso and Heinrich Herre
    Citation: BMC Bioinformatics 2009 10:377
    Content type: Methodology article Published on:

  16. Biological networks are widely used to represent processes in biological systems and to capture interactions and dependencies between biological entities. Their size and complexity is steadily increasing due t...

    Authors: Falk Schreiber, Tim Dwyer, Kim Marriott and Michael Wybrow
    Citation: BMC Bioinformatics 2009 10:375
    Content type: Research article Published on:

  17. The rapid growth of the amount of publicly available reports on biomedical experimental results has recently caused a boost of text mining approaches for protein interaction extraction. Most approaches rely im...

    Authors: Timur Fayruzov, Martine De Cock, Chris Cornelis and Veronique Hoste
    Citation: BMC Bioinformatics 2009 10:374
    Content type: Research article Published on:

  19. Illumina Sentrix-6 Whole-Genome Expression BeadChips are relatively new microarray platforms which have been used in many microarray studies in the past few years. These Chips have a unique design in which eac...

    Authors: Wei Shi, Ashish Banerjee, Matthew E Ritchie, Steve Gerondakis and Gordon K Smyth
    Citation: BMC Bioinformatics 2009 10:372
    Content type: Methodology article Published on:

  20. DNA barcoding aims to assign individuals to given species according to their sequence at a small locus, generally part of the CO1 mitochondrial gene. Amongst other issues, this raises the question of how to de...

    Authors: Frederic Austerlitz, Olivier David, Brigitte Schaeffer, Kevin Bleakley, Madalina Olteanu, Raphael Leblois, Michel Veuille and Catherine Laredo
    Citation: BMC Bioinformatics 2009 10(Suppl 14):S10
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 14

  21. In this work we consider barcode DNA analysis problems and address them using alternative, alignment-free methods and representations which model sequences as collections of short sequence fragments (features). T...

    Authors: Pavel Kuksa and Vladimir Pavlovic
    Citation: BMC Bioinformatics 2009 10(Suppl 14):S9
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 14

  22. Sequence alignment is the rate-limiting step in constructing profile trees for DNA barcoding purposes. We recently demonstrated the feasibility of using unaligned rRNA sequences as barcodes based on a composit...

    Authors: Ka Hou Chu, Minli Xu and Chi Pang Li
    Citation: BMC Bioinformatics 2009 10(Suppl 14):S8
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 14

  23. According to many field experts, specimens classification based on morphological keys needs to be supported with automated techniques based on the analysis of DNA fragments. The most successful results in this...

    Authors: Paola Bertolazzi, Giovanni Felici and Emanuel Weitschek
    Citation: BMC Bioinformatics 2009 10(Suppl 14):S7
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 14

  24. Natural History science is characterised by a single immense goal (to document, describe and synthesise all facets pertaining to the diversity of life) that can only be addressed through a seemingly infinite s...

    Authors: Vincent S Smith, Simon D Rycroft, Kehan T Harman, Ben Scott and David Roberts
    Citation: BMC Bioinformatics 2009 10(Suppl 14):S6
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 14

  25. Linking together the data of interest to biodiversity researchers (including specimen records, images, taxonomic names, and DNA sequences) requires services that can mint, resolve, and discover globally unique...

    Authors: Roderic DM Page
    Citation: BMC Bioinformatics 2009 10(Suppl 14):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 14

  26. New web-based technologies provide an excellent opportunity for sharing and accessing information and using web as a platform for interaction and collaboration. Although several specialized tools are available...

    Authors: Mehrdad Hajibabaei and Gregory AC Singer
    Citation: BMC Bioinformatics 2009 10(Suppl 14):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 14

  27. Increasing the quantity and quality of data is a key goal of biodiversity informatics, leading to increased fitness for use in scientific research and beyond. This goal is impeded by a legacy of geographic loc...

    Authors: Andrew W Hill, Robert Guralnick, Paul Flemons, Reed Beaman, John Wieczorek, Ajay Ranipeta, Vishwas Chavan and David Remsen
    Citation: BMC Bioinformatics 2009 10(Suppl 14):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 14

  28. Currently primary scientific data, especially that dealing with biodiversity, is neither easily discoverable nor accessible. Amongst several impediments, one is a lack of professional recognition of scientific...

    Authors: Vishwas S Chavan and Peter Ingwersen
    Citation: BMC Bioinformatics 2009 10(Suppl 14):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 14

  32. Difficult problems in structural bioinformatics are often studied in simple exact models to gain insights and to derive general principles. Protein folding, for example, has long been studied in the lattice mo...

    Authors: Joel Gillespie, Martin Mayne and Minghui Jiang
    Citation: BMC Bioinformatics 2009 10:369
    Content type: Research article Published on:

  33. We present a biosegmentation benchmark that includes infrastructure, datasets with associated ground truth, and validation methods for biological image analysis. The primary motivation for creating this resource ...

    Authors: Elisa Drelie Gelasca, Boguslaw Obara, Dmitry Fedorov, Kristian Kvilekval and BS Manjunath
    Citation: BMC Bioinformatics 2009 10:368
    Content type: Database Published on:

  34. A number of tools for the examination of linkage disequilibrium (LD) patterns between nearby alleles exist, but none are available for quickly and easily investigating LD at longer ranges (>500 kb). We have de...

    Authors: Robert Lawrence, Aaron G Day-Williams, Richard Mott, John Broxholme, Lon R Cardon and Eleftheria Zeggini
    Citation: BMC Bioinformatics 2009 10:367
    Content type: Database Published on:

  35. Template selection and target-template alignment are critical steps for template-based modeling (TBM) methods. To identify the template for the twilight zone of 15~25% sequence similarity between targets and t...

    Authors: Chih-Chieh Chen, Jenn-Kang Hwang and Jinn-Moon Yang
    Citation: BMC Bioinformatics 2009 10:366
    Content type: Methodology article Published on:

  36. Alanine scanning mutagenesis is a powerful experimental methodology for investigating the structural and energetic characteristics of protein complexes. Individual amino-acids are systematically mutated to ala...

    Authors: Stefano Lise, Cedric Archambeau, Massimiliano Pontil and David T Jones
    Citation: BMC Bioinformatics 2009 10:365
    Content type: Research article Published on:

  37. Efficient analysis of results from mass spectrometry-based proteomics experiments requires access to disparate data types, including native mass spectrometry files, output from algorithms that assign peptide s...

    Authors: Jignesh R Parikh, Manor Askenazi, Scott B Ficarro, Tanya Cashorali, James T Webber, Nathaniel C Blank, Yi Zhang and Jarrod A Marto
    Citation: BMC Bioinformatics 2009 10:364
    Content type: Software Published on:

  38. Analysis of the plethora of metabolites found in the NMR spectra of biological fluids or tissues requires data complexity to be simplified. We present a graphical user interface (GUI) for NMR-based metabonomic...

    Authors: Jose L Izquierdo-García, Ignacio Rodríguez, Angelos Kyriazis, Palmira Villa, Pilar Barreiro, Manuel Desco and Jesús Ruiz-Cabello
    Citation: BMC Bioinformatics 2009 10:363
    Content type: Software Published on:

  41. Analysis of within-patient HIV evolution under anti-HIV therapy is crucial to a better understanding the possible mechanisms of HIV drug-resistance acquisition. The high evolutionary rate of HIV allows us to t...

    Authors: Naoki Hasegawa, Wataru Sugiura, Junko Shibata, Masakazu Matsuda, Fengrong Ren and Hiroshi Tanaka
    Citation: BMC Bioinformatics 2009 10:360
    Content type: Methodology article Published on:

  43. Statistical analysis of DNA microarray data provides a valuable diagnostic tool for the investigation of genetic components of diseases. To take advantage of the multitude of available data sets and analysis m...

    Authors: Enrico Glaab, Jonathan M Garibaldi and Natalio Krasnogor
    Citation: BMC Bioinformatics 2009 10:358
    Content type: Software Published on:

  44. Large multigene sequence alignments have over recent years been increasingly employed for phylogenomic reconstruction of the eukaryote tree of life. Such supermatrices of sequence data are preferred over singl...

    Authors: Surendra Kumar, Åsmund Skjæveland, Russell JS Orr, Pål Enger, Torgeir Ruden, Bjørn-Helge Mevik, Fabien Burki, Andreas Botnen and Kamran Shalchian-Tabrizi
    Citation: BMC Bioinformatics 2009 10:357
    Content type: Software Published on:

  46. Previous methods of detecting the taxonomic origins of arbitrary sequence collections, with a significant impact to genome analysis and in particular metagenomics, have primarily focused on compositional featu...

    Authors: Shiri Freilich, Leon Goldovsky, Assaf Gottlieb, Eric Blanc, Sophia Tsoka and Christos A Ouzounis
    Citation: BMC Bioinformatics 2009 10:355
    Content type: Methodology article Published on:

  47. The microarray data analysis realm is ever growing through the development of various tools, open source and commercial. However there is absence of predefined rational algorithmic analysis workflows or batch ...

    Authors: Aristotelis Chatziioannou, Panagiotis Moulos and Fragiskos N Kolisis
    Citation: BMC Bioinformatics 2009 10:354
    Content type: Software Published on:

  49. The ChIP-chip technology has been used in a wide range of biomedical studies, such as identification of human transcription factor binding sites, investigation of DNA methylation, and investigation of histone ...

    Authors: Mingqi Wu, Faming Liang and Yanan Tian
    Citation: BMC Bioinformatics 2009 10:352
    Content type: Methodology article Published on:

  50. Many proteins are highly modular, being assembled from globular domains and segments of natively disordered polypeptides. Linear motifs, short sequence modules functioning independently of protein tertiary str...

    Authors: Allegra Via, Cathryn M Gould, Christine Gemünd, Toby J Gibson and Manuela Helmer-Citterich
    Citation: BMC Bioinformatics 2009 10:351
    Content type: Methodology article Published on:

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