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

    Genome-wide analysis reveals downregulation of miR-379/miR-656 cluster in human cancers

    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...

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

    Biology Direct 2013 8:10

    Published on: 24 April 2013

  2. Research

    Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park

    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.

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

    Biology Direct 2013 8:9

    Published on: 22 April 2013

  3. Review

    Invasive cells in animals and plants: searching for LECA machineries in later eukaryotic life

    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...

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

    Biology Direct 2013 8:8

    Published on: 4 April 2013

  4. Research

    Invariance and optimality in the regulation of an enzyme

    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...

    Ed Reznik, Stefan Yohe and Daniel Segrè

    Biology Direct 2013 8:7

    Published on: 22 March 2013

  5. Comment

    Next-generation phylogenomics

    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...

    Cheong Xin Chan and Mark A Ragan

    Biology Direct 2013 8:3

    Published on: 22 January 2013

  6. Research

    Deep transcriptome-sequencing and proteome analysis of the hydrothermal vent annelid Alvinella pompejana identifies the CvP-bias as a robust measure of eukaryotic thermostability

    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,...

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

    Biology Direct 2013 8:2

    Published on: 16 January 2013

  7. Review

    Bioinformatics clouds for big data manipulation

    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...

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

    Biology Direct 2012 7:43

    Published on: 28 November 2012

  8. Research

    Early evolution of efficient enzymes and genome organization

    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...

    András Szilágyi, Ádám Kun and Eörs Szathmáry

    Biology Direct 2012 7:38

    Published on: 31 October 2012

  9. Research

    Thousands of missed genes found in bacterial genomes and their analysis with COMBREX

    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...

    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

    Biology Direct 2012 7:37

    Published on: 30 October 2012

  10. Research

    Distinct groups of repetitive families preserved in mammals correspond to different periods of regulatory innovations in vertebrates

    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...

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

    Biology Direct 2012 7:36

    Published on: 25 October 2012

  11. Research

    Comparative genomic analysis of the DUF71/COG2102 family predicts roles in diphthamide biosynthesis and B12 salvage

    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...

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

    Biology Direct 2012 7:32

    Published on: 26 September 2012

  12. Research

    Stop codons in bacteria are not selectively equivalent

    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...

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

    Biology Direct 2012 7:30

    Published on: 13 September 2012

  13. Review

    Identifying the mechanisms of intron gain: progress and trends

    Continued improvements in Next-Generation DNA/RNA sequencing coupled with advances in gene annotation have provided researchers access to a plethora of annotated genomes. Subsequent analyses of orthologous gen...

    Paul Yenerall and Leming Zhou

    Biology Direct 2012 7:29

    Published on: 10 September 2012

  14. Opinion

    Does the central dogma still stand?

    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...

    Eugene V Koonin

    Biology Direct 2012 7:27

    Published on: 23 August 2012

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