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  1. High-throughput short read sequencing is revolutionizing genomics and systems biology research by enabling cost-effective deep coverage sequencing of genomes and transcriptomes. Error detection and correction ...

    Authors: Xiao Yang, Srinivas Aluru and Karin S Dorman
    Citation: BMC Bioinformatics 2011 12(Suppl 1):S52
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 1

  2. To understand the gene regulatory system that governs the self-renewal and pluripotency of embryonic stem cells (ESCs) is an important step for promoting regenerative medicine. In it, the role of several core ...

    Authors: Sung-Joon Park and Kenta Nakai
    Citation: BMC Bioinformatics 2011 12(Suppl 1):S50
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 1

  3. Protein quantification is an essential step in many proteomics experiments. A number of labeling approaches have been proposed and adopted in mass spectrometry (MS) based relative quantification. The mTRAQ, on...

    Authors: Joo Young Yoon, Jeonghun Yeom, Heebum Lee, Kyutae Kim, Seungjin Na, Kunsoo Park, Eunok Paek and Cheolju Lee
    Citation: BMC Bioinformatics 2011 12(Suppl 1):S46
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 1

  4. Human immunodeficiency virus type one (HIV-1) is the major pathogen that causes the acquired immune deficiency syndrome (AIDS). With the availability of large-scale protein-protein interaction (PPI) measuremen...

    Authors: Xiaoning Qian and Byung-Jun Yoon
    Citation: BMC Bioinformatics 2011 12(Suppl 1):S19
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 1

  5. The abundance of new genomic data provides the opportunity to map the location of gene duplication and loss events on a species phylogeny. The first methods for mapping gene duplications and losses were based ...

    Authors: Pawel Górecki, Gordon J Burleigh and Oliver Eulenstein
    Citation: BMC Bioinformatics 2011 12(Suppl 1):S15
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 1

  6. The identification of genes responsible for human inherited diseases is one of the most challenging tasks in human genetics. Recent studies based on phenotype similarity and gene proximity have demonstrated gr...

    Authors: Wangshu Zhang, Fengzhu Sun and Rui Jiang
    Citation: BMC Bioinformatics 2011 12(Suppl 1):S11
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 1

  7. Protein is an important molecule that performs a wide range of functions in biological systems. Recently, the protein folding attracts much more attention since the function of protein can be generally derived...

    Authors: Fei Xia, Yong Dou, Guoqing Lei and Yusong Tan
    Citation: BMC Bioinformatics 2011 12(Suppl 1):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 1

  8. Guanine protein-coupled receptors (GPCRs) constitute a eukaryotic transmembrane protein family and function as “molecular switches” in the second messenger cascades and are found in all organisms between yeast...

    Authors: Anita Sarkar, Sonu Kumar and Durai Sundar
    Citation: BMC Bioinformatics 2011 12(Suppl 1):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 1

  9. Reconstruction of biological pathways is typically done through mapping well-characterized pathways of model organisms to a target genome, through orthologous gene mapping. A limitation of such pathway-mapping...

    Authors: Yong Chen, Fenglou Mao, Guojun Li and Ying Xu
    Citation: BMC Bioinformatics 2011 12(Suppl 1):S1
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 1

  10. Tumor cells are considered to have an aberrant cell state, and some evidence indicates different development states appearing in the tumorigenesis. Embryonic development and stem cell differentiation are order...

    Authors: Bo Zhang, Beibei Chen, Tao Wu, Zhenyu Xuan, Xiaopeng Zhu and Runsheng Chen
    Citation: BMC Bioinformatics 2011 12:53
    Content type: Methodology article Published on:

  11. The Gene Ontology (GO) Consortium organizes genes into hierarchical categories based on biological process, molecular function and subcellular localization. Tools such as GoMiner can leverage GO to perform ont...

    Authors: Barry R Zeeberg, Hongfang Liu, Ari B Kahn, Martin Ehler, Vinodh N Rajapakse, Robert F Bonner, Jacob D Brown, Brian P Brooks, Vladimir L Larionov, William Reinhold, John N Weinstein and Yves G Pommier
    Citation: BMC Bioinformatics 2011 12:52
    Content type: Software Published on:

  12. Large databases of genetic data are often biased in their representation. Thus, selection of genetic data with desired properties, such as evolutionary representation or shared genotypes, is problematic. Selec...

    Authors: Mohan Krishnamoorthy, Pragneshkumar Patel, Mira Dimitrijevic, Jonathan Dietrich, Margaret Green and Catherine Macken
    Citation: BMC Bioinformatics 2011 12:51
    Content type: Software Published on:

  15. The analysis of protein structures provides fundamental insight into most biochemical functions and consequently into the cause and possible treatment of diseases. As the structures of most known proteins cann...

    Authors: Eric di Luccio and Patrice Koehl
    Citation: BMC Bioinformatics 2011 12:48
    Content type: Research article Published on:

  16. Molecular database search tools need statistical models to assess the significance for the resulting hits. In the classical approach one asks the question how probable a certain score is observed by pure chanc...

    Authors: Stefan Wolfsheimer, Inke Herms, Sven Rahmann and Alexander K Hartmann
    Citation: BMC Bioinformatics 2011 12:47
    Content type: Research article Published on:

  17. DNA microarrays have become a nearly ubiquitous tool for the study of human disease, and nowhere is this more true than in cancer. With hundreds of studies and thousands of expression profiles representing the...

    Authors: Fenglong Liu, Joseph A White, Corina Antonescu, Daniel Gusenleitner and John Quackenbush
    Citation: BMC Bioinformatics 2011 12:46
    Content type: Database Published on:

  18. In rule-based modeling, graphs are used to represent molecules: a colored vertex represents a component of a molecule, a vertex attribute represents the internal state of a component, and an edge represents a ...

    Authors: Nathan W Lemons, Bin Hu and William S Hlavacek
    Citation: BMC Bioinformatics 2011 12:45
    Content type: Research article Published on:

  22. Computational analysis of metagenomes requires the taxonomical assignment of the genome contigs assembled from DNA reads of environmental samples. Because of the diverse nature of microbiomes, the length of th...

    Authors: Ozkan U Nalbantoglu, Samuel F Way, Steven H Hinrichs and Khalid Sayood
    Citation: BMC Bioinformatics 2011 12:41
    Content type: Research article Published on:

  23. The interest in non-coding RNAs (ncRNAs) constantly rose during the past few years because of the wide spectrum of biological processes in which they are involved. This led to the discovery of numerous ncRNA g...

    Authors: Alexander Herbig and Kay Nieselt
    Citation: BMC Bioinformatics 2011 12:40
    Content type: Research article Published on:

  24. The use of high-throughput sequencing in combination with chromatin immunoprecipitation (ChIP-seq) has enabled the study of genome-wide protein binding at high resolution. While the amount of data generated fr...

    Authors: Peter Humburg, Chris A Helliwell, David Bulger and Glenn Stone
    Citation: BMC Bioinformatics 2011 12:39
    Content type: Research article Published on:

  25. In many environmental genomics applications a homologous region of DNA from a diverse sample is first amplified by PCR and then sequenced. The next generation sequencing technology, 454 pyrosequencing, has all...

    Authors: Christopher Quince, Anders Lanzen, Russell J Davenport and Peter J Turnbaugh
    Citation: BMC Bioinformatics 2011 12:38
    Content type: Research article Published on:

  26. When investigating covariate interactions and group associations with standard regression analyses, the relationship between the response variable and exposure may be difficult to characterize. When the relati...

    Authors: John J Heine, Walker H Land and Kathleen M Egan
    Citation: BMC Bioinformatics 2011 12:37
    Content type: Research article Published on:

  29. The notion that genes are non-randomly organized within the chromosomes of eukaryotic organisms has recently received strong experimental support. Clusters of co-expressed and co-localized genes have been reco...

    Authors: Tania Dottorini, Nicola Senin, Giorgio Mazzoleni, Kalle Magnusson and Andrea Crisanti
    Citation: BMC Bioinformatics 2011 12:34
    Content type: Software Published on:

  30. The rapid identification of Bacillus spores and bacterial identification are paramount because of their implications in food poisoning, pathogenesis and their use as potential biowarfare agents. Many automated an...

    Authors: Elon Correa and Royston Goodacre
    Citation: BMC Bioinformatics 2011 12:33
    Content type: Methodology article Published on:

  31. Caenorhabditis elegans gene-based phenotype information dates back to the 1970's, beginning with Sydney Brenner and the characterization of behavioral and morphological mutant alleles via classical genetics in or...

    Authors: Gary Schindelman, Jolene S Fernandes, Carol A Bastiani, Karen Yook and Paul W Sternberg
    Citation: BMC Bioinformatics 2011 12:32
    Content type: Methodology article Published on:

  32. Genomic position (GP) files currently used in next-generation sequencing (NGS) studies are always difficult to manipulate due to their huge size and the lack of appropriate tools to properly manage them. The s...

    Authors: Daniel Glez-Peña, Gonzalo Gómez-López, Miguel Reboiro-Jato, Florentino Fdez-Riverola and David G Pisano
    Citation: BMC Bioinformatics 2011 12:31
    Content type: Software Published on:

  33. The increasing availability of molecular sequence data means that the accuracy of future phylogenetic studies is likely to by limited by systematic bias and taxon choice rather than by data. In order to take a...

    Authors: Martin O Jones, Georgios D Koutsovoulos and Mark L Blaxter
    Citation: BMC Bioinformatics 2011 12:30
    Content type: Software Published on:

  35. Flux-balance analysis based on linear optimization is widely used to compute metabolic fluxes in large metabolic networks and gains increasingly importance in network curation and structural analysis. Thus, a ...

    Authors: Andreas Hoppe, Sabrina Hoffmann, Andreas Gerasch, Christoph Gille and Hermann-Georg Holzhütter
    Citation: BMC Bioinformatics 2011 12:28
    Content type: Software Published on:

  36. During meiosis, homologous chromosomes exchange segments via the formation of crossovers. This phenomenon is highly regulated; in particular, crossovers are distributed heterogeneously along the physical map a...

    Authors: Franck Gauthier, Olivier C Martin and Matthieu Falque
    Citation: BMC Bioinformatics 2011 12:27
    Content type: Software Published on:

  38. High-throughput screening (HTS) is a key part of the drug discovery process during which thousands of chemical compounds are screened and their activity levels measured in order to identify potential drug cand...

    Authors: Plamen Dragiev, Robert Nadon and Vladimir Makarenkov
    Citation: BMC Bioinformatics 2011 12:25
    Content type: Methodology article Published on:

  40. The Distributed Annotation System (DAS) has proven to be a successful way to publish and share biological data. Although there are more than 750 active registered servers from around 50 organizations, setting ...

    Authors: Bernat Gel Moreno, Andrew M Jenkinson, Rafael C Jimenez, Xavier Messeguer Peypoch and Henning Hermjakob
    Citation: BMC Bioinformatics 2011 12:23
    Content type: Software Published on:

  41. Building repositories of computational models of biological systems ensures that published models are available for both education and further research, and can provide a source of smaller, previously verified...

    Authors: Andrew K Miller, Tommy Yu, Randall Britten, Mike T Cooling, James Lawson, Dougal Cowan, Alan Garny, Matt DB Halstead, Peter J Hunter, David P Nickerson, Geo Nunns, Sarala M Wimalaratne and Poul M F Nielsen
    Citation: BMC Bioinformatics 2011 12:22
    Content type: Research article Published on:

  42. Most predictive methods currently available for the identification of protein secretion mechanisms have focused on classically secreted proteins. In fact, only two methods have been reported for predicting non...

    Authors: Daniel Restrepo-Montoya, Camilo Pino, Luis F Nino, Manuel E Patarroyo and Manuel A Patarroyo
    Citation: BMC Bioinformatics 2011 12:21
    Content type: Research article Published on:

  46. Single Nucleotide Polymorphism (SNP) analysis only captures a small proportion of associated genetic variants in Genome-Wide Association Studies (GWAS) partly due to small marginal effects. Pathway level analy...

    Authors: Jingyuan Zhao, Simone Gupta, Mark Seielstad, Jianjun Liu and Anbupalam Thalamuthu
    Citation: BMC Bioinformatics 2011 12:17
    Content type: Research article Published on:

  47. Discovering the genetic basis of common genetic diseases in the human genome represents a public health issue. However, the dimensionality of the genetic data (up to 1 million genetic markers) and its complexi...

    Authors: Raphaël Mourad, Christine Sinoquet and Philippe Leray
    Citation: BMC Bioinformatics 2011 12:16
    Content type: Research article Published on:

  48. The identification of binding targets for proteins using ChIP-Seq has gained popularity as an alternative to ChIP-chip. Sequencing can, in principle, eliminate artifacts associated with microarrays, and cheap ...

    Authors: Valerie Hower, Steven N Evans and Lior Pachter
    Citation: BMC Bioinformatics 2011 12:15
    Content type: Methodology article Published on:

  49. The rapid accumulation of data on non-synonymous single nucleotide polymorphisms (nsSNPs, also called SAPs) should allow us to further our understanding of the underlying disease-associated mechanisms. Here, w...

    Authors: Yizhou Li, Zhining Wen, Jiamin Xiao, Hui Yin, Lezheng Yu, Li Yang and Menglong Li
    Citation: BMC Bioinformatics 2011 12:14
    Content type: Research article Published on:

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