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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.
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...
Biology Direct 2013 8:10
Published on: 24 April 2013
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.
Biology Direct 2013 8:9
Published on: 22 April 2013
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...
Biology Direct 2013 8:8
Published on: 4 April 2013
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...
Biology Direct 2013 8:7
Published on: 22 March 2013
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...
Biology Direct 2013 8:3
Published on: 22 January 2013
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,...
Biology Direct 2013 8:2
Published on: 16 January 2013
Review
Punctuational theories of evolution suggest that adaptive evolution proceeds mostly, or even entirely, in the distinct periods of existence of a particular species. The mechanisms of this punctuated nature of ...
Biology Direct 2013 8:1
Published on: 16 January 2013
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...
Biology Direct 2012 7:46
Published on: 14 December 2012
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...
Biology Direct 2012 7:44
Published on: 10 December 2012
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...
Biology Direct 2012 7:43
Published on: 28 November 2012
Research
Life depends on biopolymer sequences as catalysts and as genetic material. A key step in the Origin of Life is the emergence of an autocatalytic system of biopolymers. Here we study computational models that a...
Biology Direct 2012 7:42
Published on: 24 November 2012
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...
Biology Direct 2012 7:40
Published on: 14 November 2012
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...
Biology Direct 2012 7:38
Published on: 31 October 2012
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...
Biology Direct 2012 7:37
Published on: 30 October 2012
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...
Biology Direct 2012 7:36
Published on: 25 October 2012
Review
Constructive neutral evolution (CNE) suggests that neutral evolution may follow a stepwise path to extravagance. Whether or not CNE is common, the mere possibility raises provocative questions about causation:...
Biology Direct 2012 7:35
Published on: 13 October 2012
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...
Biology Direct 2012 7:32
Published on: 26 September 2012
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...
Biology Direct 2012 7:30
Published on: 13 September 2012
Review
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...
Biology Direct 2012 7:29
Published on: 10 September 2012
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...
Biology Direct 2012 7:27
Published on: 23 August 2012
