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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. Content type: Research

    The microbial communities populating human and natural environments have been extensively characterized with shotgun metagenomics, which provides an in-depth representation of the microbial diversity within a ...

    Authors: Moreno Zolfo, Francesco Asnicar, Paolo Manghi, Edoardo Pasolli, Adrian Tett and Nicola Segata

    Citation: Biology Direct 2018 13:9

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  2. Content type: Discovery notes

    We report a protein sequence analysis of the cell cycle regulatory protease, separase. The sequence and structural conservation of the C-terminal protease domain has long been recognized, whereas the N-termina...

    Authors: Michael Melesse, Joshua N. Bembenek and Igor B. Zhulin

    Citation: Biology Direct 2018 13:7

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  3. Content type: Research

    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...

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

    Citation: Biology Direct 2016 11:35

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  4. Content type: Review

    In the recent years, sequence-specific nucleases such as ZFNs, TALENs, and CRISPR/Cas9 have revolutionzed the fields of animal genome editing and transgenesis. However, these new techniques require microinject...

    Authors: Masahiro Sato, Masato Ohtsuka, Satoshi Watanabe and Channabasavaiah B. Gurumurthy

    Citation: Biology Direct 2016 11:16

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  5. Content type: Research

    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...

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

    Citation: Biology Direct 2016 11:11

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  6. Content type: Research

    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 ...

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

    Citation: Biology Direct 2016 11:5

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  7. Content type: Discovery notes

    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 ...

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

    Citation: Biology Direct 2016 11:3

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  8. Content type: Research

    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...

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

    Citation: Biology Direct 2015 10:55

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  9. Content type: Research

    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...

    Authors: 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…

    Citation: Biology Direct 2014 9:20

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  10. Content type: Research

    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...

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

    Citation: Biology Direct 2014 9:19

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  11. Content type: Review

    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...

    Authors: Alexander Kraev

    Citation: Biology Direct 2014 9:18

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  12. Content type: Research

    Significant efforts have been made to address the problem of identifying short genes in prokaryotic genomes. However, most known methods are not effective in detecting short genes. Because of the limited infor...

    Authors: Sun Chen, Chun-ying Zhang and Kai Song

    Citation: Biology Direct 2013 8:23

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  13. Content type: Research

    It is commonly assumed that a heterotrophic ancestor of the supergroup Archaeplastida/Plantae engulfed a cyanobacterium that was transformed into a primary plastid; however, it is still unclear how nuclear-enc...

    Authors: Przemysław Gagat, Andrzej Bodył and Paweł Mackiewicz

    Citation: Biology Direct 2013 8:18

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  14. Content type: Research

    RNA-seq is a next generation sequencing method with a wide range of applications including single nucleotide polymorphism (SNP) detection, splice junction identification, and gene expression level measurement....

    Authors: Changhoon Lee, R Adron Harris, Jason K Wall, R Dayne Mayfield and Claus O Wilke

    Citation: Biology Direct 2013 8:16

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  15. Content type: Research

    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...

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

    Citation: Biology Direct 2013 8:15

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