Genomics

Section edited by Tal Dagan and Martijn Huynen

The genomics section embraces studies of whole genome structure, function and evolution. This includes the genomic research of specific life forms as well as metaorganisms and particular habitats. Papers considered for publication include methodology contributions dealing with the sequencing, assembly and annotation of genomic data, studies of whole genome or metagenome composition, organization and function, as well as evolutionary genomics.

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  1. Research

    Comparative genomic analysis of retrogene repertoire in two green algae Volvox carteri and Chlamydomonas reinhardtii

    Retroposition, one of the processes of copying the genetic material, is an important RNA-mediated mechanism leading to the emergence of new genes. Because the transcription controlling segments are usually not...

    Marcin Jąkalski, Kazutaka Takeshita, Mathieu Deblieck, Kanako O. Koyanagi, Izabela Makałowska, Hidemi Watanabe and Wojciech Makałowski

    Biology Direct 2016 11:35

    Published on: 4 August 2016

  2. Research

    Conservation and divergence of the histone code in nucleomorphs

    Nucleomorphs, the remnant nuclei of photosynthetic algae that have become endosymbionts to other eukaryotes, represent a unique example of convergent reductive genome evolution in eukaryotes, having evolved in...

    Georgi K. Marinov and Michael Lynch

    Biology Direct 2016 11:18

    Published on: 5 April 2016

  3. Research

    Preservation of methylated CpG dinucleotides in human CpG islands

    CpG dinucleotides are extensively underrepresented in mammalian genomes. It is widely accepted that genome-wide CpG depletion is predominantly caused by an elevated CpG > TpG mutation rate due to frequent cyto...

    Alexander Y. Panchin, Vsevolod J. Makeev and Yulia A. Medvedeva

    Biology Direct 2016 11:11

    Published on: 22 March 2016

  4. Research

    A paneukaryotic genomic analysis of the small GTPase RABL2 underscores the significance of recurrent gene loss in eukaryote evolution

    The cilium (flagellum) is a complex cellular structure inherited from the last eukaryotic common ancestor (LECA). A large number of ciliary proteins have been characterized in a few model organisms, but their ...

    Marek Eliáš, Vladimír Klimeš, Romain Derelle, Romana Petrželková and Jan Tachezy

    Biology Direct 2016 11:5

    Published on: 2 February 2016

  5. Discovery notes

    Direct next-generation sequencing of virus-human mixed samples without pretreatment is favorable to recover virus genome

    Next-generation sequencing (NGS) enables the recovery of pathogen genomes from clinical samples without the need for culturing. Depletion of host/microbiota components (e.g., ribosomal RNA and poly-A RNA) and ...

    Dingchen Li, Zongwei Li, Zhe Zhou, Zhen Li, Xinyan Qu, Peisong Xu, Pingkun Zhou, Xiaochen Bo and Ming Ni

    Biology Direct 2016 11:3

    Published on: 12 January 2016

  6. Research

    Pan-genomic analysis to redefine species and subspecies based on quantum discontinuous variation: the Klebsiella paradigm

    Various methods are currently used to define species and are based on the phylogenetic marker 16S ribosomal RNA gene sequence, DNA-DNA hybridization and DNA GC content. However, these are restricted genetic to...

    Aurélia Caputo, Vicky Merhej, Kalliopi Georgiades, Pierre-Edouard Fournier, Olivier Croce, Catherine Robert and Didier Raoult

    Biology Direct 2015 10:55

    Published on: 30 September 2015

  7. Research

    A new rhesus macaque assembly and annotation for next-generation sequencing analyses

    The rhesus macaque (Macaca mulatta) is a key species for advancing biomedical research. Like all draft mammalian genomes, the draft rhesus assembly (rheMac2) has gaps, sequencing errors and misassemblies that hav...

    Aleksey V Zimin, Adam S Cornish, Mnirnal D Maudhoo, Robert M Gibbs, Xiongfei Zhang, Sanjit Pandey, Daniel T Meehan, Kristin Wipfler, Steven E Bosinger, Zachary P Johnson, Gregory K Tharp, Guillaume Marçais, Michael Roberts, Betsy Ferguson, Howard S Fox, Todd Treangen…

    Biology Direct 2014 9:20

    Published on: 14 October 2014

  8. Research

    Mycobacteriophage-drived diversification of Mycobacterium abscessus

    Mycobacterium abscessus is an emerging opportunistic pathogen which diversity was acknowledged by the recent description of two subspecies accommodating M. abscessus, Mycobacterium bolletii and Mycobacterium mass...

    Mohamed Sassi, Philippe Gouret, Olivier Chabrol, Pierre Pontarotti and Michel Drancourt

    Biology Direct 2014 9:19

    Published on: 15 September 2014

  9. Review

    Parallel universes of Black Six biology

    Creation of lethal and synthetic lethal mutations in an experimental organism is a cornerstone of genetic dissection of gene function, and is related to the concept of an essential gene. Common inbred mouse st...

    Alexander Kraev

    Biology Direct 2014 9:18

    Published on: 19 July 2014

  10. Research

    Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing

    The major role of enzymatic toxins that target nucleic acids in biological conflicts at all levels has become increasingly apparent thanks in large part to the advances of comparative genomics. Typically, toxi...

    Vivek Anantharaman, Kira S Makarova, A Maxwell Burroughs, Eugene V Koonin and L Aravind

    Biology Direct 2013 8:15

    Published on: 15 June 2013

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