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Comparative genomics

Section edited by Graziano Pesole

This section incorporates all aspects of comparative genomic analysis including but not limited to: methods and applications for the analysis of comparative phylogenetic and genomic data.

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  1. Content type: Research Article

    Random forests have often been claimed to uncover interaction effects. However, if and how interaction effects can be differentiated from marginal effects remains unclear. In extensive simulation studies, we i...

    Authors: Marvin N. Wright, Andreas Ziegler and Inke R. König

    Citation: BMC Bioinformatics 2016 17:145

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  2. Content type: Methodology Article

    Gene set analysis (GSA) aims to evaluate the association between the expression of biological pathways, or a priori defined gene sets, and a particular phenotype. Numerous GSA methods have been proposed to ass...

    Authors: Huey-Miin Hsueh and Chen-An Tsai

    Citation: BMC Bioinformatics 2016 17:74

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  3. Content type: Methodology article

    Success in genome-wide association studies and marker-assisted selection depends on good phenotypic and genotypic data. The more complete this data is, the more powerful will be the results of analysis. Nevert...

    Authors: A. Xavier, William M. Muir and Katy M. Rainey

    Citation: BMC Bioinformatics 2016 17:55

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  4. Content type: Research article

    One of the main aims of phylogenomics is the reconstruction of objects defined in the leaves along the whole phylogenetic tree to minimize the specified functional, which may also include the phylogenetic tree...

    Authors: Vassily Lyubetsky, Roman Gershgorin, Alexander Seliverstov and Konstantin Gorbunov

    Citation: BMC Bioinformatics 2016 17:40

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  5. Content type: Methodology Article

    In recent years, many studies focused on the description and comparison of large sets of related bacteriophage genomes. Due to the peculiar mosaic structure of these genomes, few informative approaches for com...

    Authors: Sèverine Bérard, Annie Chateau, Nicolas Pompidor, Paul Guertin, Anne Bergeron and Krister M. Swenson

    Citation: BMC Bioinformatics 2016 17:30

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  6. Content type: Research Article

    Branch lengths are an important attribute of phylogenetic trees, providing essential information for many studies in evolutionary biology. Yet, part of the current methodology to reconstruct a phylogeny from g...

    Authors: Manuel Binet, Olivier Gascuel, Celine Scornavacca, Emmanuel J. P. Douzery and Fabio Pardi

    Citation: BMC Bioinformatics 2016 17:23

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  7. Content type: Methodology Article

    In genome-wide association studies (GWAS) for complex diseases, the association between a SNP and each phenotype is usually weak. Combining multiple related phenotypic traits can increase the power of gene sea...

    Authors: James J. Yang, Jia Li, L. Keoki Williams and Anne Buu

    Citation: BMC Bioinformatics 2016 17:19

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  8. Content type: Research Article

    Given a gene and a species tree, reconciliation methods attempt to retrieve the macro-evolutionary events that best explain the discrepancies between the two tree topologies. The DTL parsimonious approach sear...

    Authors: Thu-Hien To, Edwin Jacox, Vincent Ranwez and Celine Scornavacca

    Citation: BMC Bioinformatics 2015 16:384

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  9. Content type: Software

    Some of the current software tools for comparative metagenomics provide ecologists with the ability to investigate and explore bacterial communities using α– & β–diversity. Feature subset selection – a sub-field ...

    Authors: Gregory Ditzler, J. Calvin Morrison, Yemin Lan and Gail L. Rosen

    Citation: BMC Bioinformatics 2015 16:358

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  10. Content type: Software

    Identification of biological specimens is a requirement for a range of applications. Reference-free methods analyse unprocessed sequencing data without relying on prior knowledge, but generally do not scale to...

    Authors: Saulo Alves Aflitos, Edouard Severing, Gabino Sanchez-Perez, Sander Peters, Hans de Jong and Dick de Ridder

    Citation: BMC Bioinformatics 2015 16:352

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  11. Content type: Research article

    GmrSD is a modification-dependent restriction endonuclease that specifically targets and cleaves glucosylated hydroxymethylcytosine (glc-HMC) modified DNA. It is encoded either as two separate single-domain Gm...

    Authors: Magdalena A. Machnicka, Katarzyna H. Kaminska, Stanislaw Dunin-Horkawicz and Janusz M. Bujnicki

    Citation: BMC Bioinformatics 2015 16:336

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  12. Content type: Methodology article

    Cellular organelles with genomes of their own (e.g. plastids and mitochondria) can pass genetic sequences to other organellar genomes within the cell in many species across the eukaryote phylogeny. The extent ...

    Authors: Jose Alfredo Samaniego Castruita, Marie Lisandra Zepeda Mendoza, Ross Barnett, Nathan Wales and M Thomas P. Gilbert

    Citation: BMC Bioinformatics 2015 16:232

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2016 Journal Metrics

  • Citation Impact
    2.448 - 2-year Impact Factor
    3.450 - 5-year Impact Factor
    0.946 - Source Normalized Impact per Paper (SNIP)
    1.467 - SCImago Journal Rank (SJR)

    1405 Usage Factor

    Social Media Impact
    816 mentions