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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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  16. Content type: Research

    The PIWI module, found in the PIWI/AGO superfamily of proteins, is a critical component of several cellular pathways including germline maintenance, chromatin organization, regulation of splicing, RNA interfer...

    Authors: A Maxwell Burroughs, Lakshminarayan M Iyer and L Aravind

    Citation: Biology Direct 2013 8:13

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  17. Content type: Research

    MicroRNAs (miRNAs) are non-uniformly distributed in genomes and ~30% of the miRNAs in the human genome are clustered. In this study we have focused on the imprinted miRNA cluster miR-379/miR-656 on 14q32.31 (h...

    Authors: Saurabh V Laddha, Subhashree Nayak, Deepanjan Paul, Rajasekhara Reddy, Charu Sharma, Prerana Jha, Manoj Hariharan, Anurag Agrawal, Shantanu Chowdhury, Chitra Sarkar and Arijit Mukhopadhyay

    Citation: Biology Direct 2013 8:10

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  18. Content type: Research

    A single cultured marine organism, Nanoarchaeum equitans, represents the Nanoarchaeota branch of symbiotic Archaea, with a highly reduced genome and unusual features such as multiple split genes.

    Authors: Mircea Podar, Kira S Makarova, David E Graham, Yuri I Wolf, Eugene V Koonin and Anna-Louise Reysenbach

    Citation: Biology Direct 2013 8:9

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  19. Content type: Review

    Invasive cell growth and migration is usually considered a specifically metazoan phenomenon. However, common features and mechanisms of cytoskeletal rearrangements, membrane trafficking and signalling processe...

    Authors: Katarína Vaškovičová, Viktor Žárský, Daniel Rösel, Margaret Nikolič, Roberto Buccione, Fatima Cvrčková and Jan Brábek

    Citation: Biology Direct 2013 8:8

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  20. Content type: Research

    The Michaelis-Menten equation, proposed a century ago, describes the kinetics of enzyme-catalyzed biochemical reactions. Since then, this equation has been used in countless, increasingly complex models of cel...

    Authors: Ed Reznik, Stefan Yohe and Daniel Segrè

    Citation: Biology Direct 2013 8:7

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  21. Content type: Comment

    Thanks to advances in next-generation technologies, genome sequences are now being generated at breadth (e.g. across environments) and depth (thousands of closely related strains, individuals or samples) unimagin...

    Authors: Cheong Xin Chan and Mark A Ragan

    Citation: Biology Direct 2013 8:3

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  22. Content type: Research

    Alvinella pompejana is an annelid worm that inhabits deep-sea hydrothermal vent sites in the Pacific Ocean. Living at a depth of approximately 2500 meters, these worms experience extreme environmental conditions,...

    Authors: Thomas Holder, Claire Basquin, Judith Ebert, Nadine Randel, Didier Jollivet, Elena Conti, Gáspár Jékely and Fulvia Bono

    Citation: Biology Direct 2013 8:2

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  23. Content type: Research

    Collections of Clusters of Orthologous Genes (COGs) provide indispensable tools for comparative genomic analysis, evolutionary reconstruction and functional annotation of new genomes. Initially, COGs were made...

    Authors: Yuri I Wolf, Kira S Makarova, Natalya Yutin and Eugene V Koonin

    Citation: Biology Direct 2012 7:46

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  24. Content type: Review

    High-dimensional gene expression data provide a rich source of information because they capture the expression level of genes in dynamic states that reflect the biological functioning of a cell. For this reaso...

    Authors: Frank Emmert-Streib, Shailesh Tripathi and Ricardo de Matos Simoes

    Citation: Biology Direct 2012 7:44

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  25. Content type: Review

    As advances in life sciences and information technology bring profound influences on bioinformatics due to its interdisciplinary nature, bioinformatics is experiencing a new leap-forward from in-house computin...

    Authors: Lin Dai, Xin Gao, Yan Guo, Jingfa Xiao and Zhang Zhang

    Citation: Biology Direct 2012 7:43

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  26. Content type: Hypothesis

    The virus-host arms race is a major theater for evolutionary innovation. Archaea and bacteria have evolved diverse, elaborate antivirus defense systems that function on two general principles: i) immune system...

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

    Citation: Biology Direct 2012 7:40

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  27. Content type: Research

    Cellular life with complex metabolism probably evolved during the reign of RNA, when it served as both information carrier and enzyme. Jensen proposed that enzymes of primordial cells possessed broad specifici...

    Authors: András Szilágyi, Ádám Kun and Eörs Szathmáry

    Citation: Biology Direct 2012 7:38

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  28. Content type: Research

    The dramatic reduction in the cost of sequencing has allowed many researchers to join in the effort of sequencing and annotating prokaryotic genomes. Annotation methods vary considerably and may fail to identi...

    Authors: Derrick E Wood, Henry Lin, Ami Levy-Moonshine, Rajiswari Swaminathan, Yi-Chien Chang, Brian P Anton, Lais Osmani, Martin Steffen, Simon Kasif and Steven L Salzberg

    Citation: Biology Direct 2012 7:37

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  29. Content type: Research

    Mammalian genomes are repositories of repetitive DNA sequences derived from transposable elements (TEs). Typically, TEs generate multiple, mostly inactive copies of themselves, commonly known as repetitive fam...

    Authors: Jerzy Jurka, Weidong Bao, Kenji K Kojima, Oleksiy Kohany and Matthew G Yurka

    Citation: Biology Direct 2012 7:36

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  30. Content type: Research

    The availability of over 3000 published genome sequences has enabled the use of comparative genomic approaches to drive the biological function discovery process. Classically, one used to link gene with functi...

    Authors: Valérie de Crécy-Lagard, Farhad Forouhar, Céline Brochier-Armanet, Liang Tong and John F Hunt

    Citation: Biology Direct 2012 7:32

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  31. Content type: Research

    The evolution and genomic stop codon frequencies have not been rigorously studied with the exception of coding of non-canonical amino acids. Here we study the rate of evolution and frequency distribution of st...

    Authors: Inna S Povolotskaya, Fyodor A Kondrashov, Alice Ledda and Peter K Vlasov

    Citation: Biology Direct 2012 7:30

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  32. Content type: Opinion

    Prions are agents of analog, protein conformation-based inheritance that can confer beneficial phenotypes to cells, especially under stress. Combined with genetic variation, prion-mediated inheritance can be c...

    Authors: Eugene V Koonin

    Citation: Biology Direct 2012 7:27

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  33. Content type: Research

    CRISPR (Clustered, Regularly, Interspaced, Short, Palindromic Repeats) loci provide prokaryotes with an adaptive immunity against viruses and other mobile genetic elements. CRISPR arrays can be transcribed and...

    Authors: Avital Brodt, Mor N Lurie-Weinberger and Uri Gophna

    Citation: Biology Direct 2011 6:65

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  34. Content type: Research

    The ability to perform de novo biosynthesis of purines is present in organisms in all three domains of life, reflecting the essentiality of these molecules to life. Although the pathway is quite similar in eukary...

    Authors: Anne M Brown, Samantha L Hoopes, Robert H White and Catherine A Sarisky

    Citation: Biology Direct 2011 6:63

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  35. Content type: Research

    Speciation corresponds to the progressive establishment of reproductive barriers between groups of individuals derived from an ancestral stock. Since Darwin did not believe that reproductive barriers could be ...

    Authors: Etienne Joly

    Citation: Biology Direct 2011 6:62

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  36. Content type: Research

    Transcription factors are thought to regulate the transcription of microRNA genes in a manner similar to that of protein-coding genes; that is, by binding to conventional transcription factor binding site DNA ...

    Authors: Jittima Piriyapongsa, I King Jordan, Andrew B Conley, Tom Ronan and Neil R Smalheiser

    Citation: Biology Direct 2011 6:61

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