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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. 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

    Content type: Research

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  4. A few major discoveries have influenced how ecologists and evolutionists study microbes. Here, in the format of an interview, we answer questions that directly relate to how these discoveries are perceived in ...

    Authors: Rebecca J Case and Yan Boucher

    Citation: Biology Direct 2011 6:58

    Content type: Review

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  5. Sequence homology considerations widely used to transfer functional annotation to uncharacterized protein sequences require special precautions in the case of non-globular sequence segments including membrane-...

    Authors: Wing-Cheong Wong, Sebastian Maurer-Stroh and Frank Eisenhaber

    Citation: Biology Direct 2011 6:57

    Content type: Research

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  6. Mitochondria mediate most of the energy production that occurs in the majority of eukaryotic organisms. These subcellular organelles contain a genome that differs from the nuclear genome and is referred to as ...

    Authors: Eric Faure, Luis Delaye, Sandra Tribolo, Anthony Levasseur, Hervé Seligmann and Roxane-Marie Barthélémy

    Citation: Biology Direct 2011 6:56

    Content type: Hypothesis

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  8. The vertebrate globin gene repertoire consists of seven members that differ in terms of structure, function and phyletic distribution. While hemoglobin, myoglobin, cytoglobin, and neuroglobin are present in al...

    Authors: Jasmin Dröge and Wojciech Makałowski

    Citation: Biology Direct 2011 6:54

    Content type: Discovery notes

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  9. Identifying group-specific characteristics in metabolic networks can provide better insight into evolutionary developments. Here, we present an approach to classify the three domains of life using topological ...

    Authors: Laurin AJ Mueller, Karl G Kugler, Michael Netzer, Armin Graber and Matthias Dehmer

    Citation: Biology Direct 2011 6:53

    Content type: Research

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  10. Based on unique, coherent properties of phylogenetic analysis, key amino acid substitutions and structural modeling, we have identified a new class of unusual microbial rhodopsins related to the Anabaena senso...

    Authors: Juan A Ugalde, Sheila Podell, Priya Narasingarao and Eric E Allen

    Citation: Biology Direct 2011 6:52

    Content type: Discovery notes

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  12. Volutin granules appear to be universally distributed and are morphologically and chemically identical to acidocalcisomes, which are electron-dense granular organelles rich in calcium and phosphate, whose func...

    Authors: Manfredo J Seufferheld, Kyung Mo Kim, James Whitfield, Alejandro Valerio and Gustavo Caetano-Anollés

    Citation: Biology Direct 2011 6:50

    Content type: Research

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  13. Currently a huge amount of protein-protein interaction data is available therefore extracting meaningful ones are a challenging task. In a protein-protein interaction network, hubs are considered as key protei...

    Authors: Mouna Choura and Ahmed Rebaï

    Citation: Biology Direct 2011 6:49

    Content type: Research

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  14. Chromosomal orthologs can reveal the shared ancestral gene set and their evolutionary trends. Additionally, physico-chemical properties of encoded proteins could provide information about functional adaptation...

    Authors: Humberto Peralta, Gabriela Guerrero, Alejandro Aguilar and Jaime Mora

    Citation: Biology Direct 2011 6:48

    Content type: Research

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  16. Phylogenetic reconstruction using DNA and protein sequences has allowed the reconstruction of evolutionary histories encompassing all life. We present and discuss a means to incorporate much of this rich narra...

    Authors: David Williams, Gregory P Fournier, Pascal Lapierre, Kristen S Swithers, Anna G Green, Cheryl P Andam and J Peter Gogarten

    Citation: Biology Direct 2011 6:45

    Content type: Review

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  19. It is becoming increasingly difficult to reconcile the observed extent of horizontal gene transfers with the central metaphor of a great tree uniting all evolving entities on the planet. In this manuscript we ...

    Authors: James O McInerney, Davide Pisani, Eric Bapteste and Mary J O'Connell

    Citation: Biology Direct 2011 6:41

    Content type: Hypothesis

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  21. We introduce several forest-based and network-based methods for exploring microbial evolution, and apply them to the study of thousands of genes from 30 strains of E. coli. This case study illustrates how additio...

    Authors: Julie Beauregard-Racine, Cédric Bicep, Klaus Schliep, Philippe Lopez, François-Joseph Lapointe and Eric Bapteste

    Citation: Biology Direct 2011 6:39

    Content type: Research

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  22. The CRISPR-Cas adaptive immunity systems that are present in most Archaea and many Bacteria function by incorporating fragments of alien genomes into specific genomic loci, transcribing the inserts and using t...

    Authors: Kira S Makarova, L Aravind, Yuri I Wolf and Eugene V Koonin

    Citation: Biology Direct 2011 6:38

    Content type: Research

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  24. Life is a chemical reaction. Three major transitions in early evolution are considered without recourse to a tree of life. The origin of prokaryotes required a steady supply of energy and electrons, probably i...

    Authors: William F Martin

    Citation: Biology Direct 2011 6:36

    Content type: Review

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  26. Genome sequencing has revolutionized our view of the relationships among genomes, particularly in revealing the confounding effects of lateral genetic transfer (LGT). Phylogenomic techniques have been used to ...

    Authors: Robert G Beiko

    Citation: Biology Direct 2011 6:34

    Content type: Research

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  30. The chloroplast-localized ribulose-1, 5-biphosphate carboxylase/oxygenase (Rubisco), the primary enzyme responsible for autotrophy, is instrumental in the continual adaptation of plants to variations in the co...

    Authors: Lin Sen, Mario A Fares, Bo Liang, Lei Gao, Bo Wang, Ting Wang and Ying-Juan Su

    Citation: Biology Direct 2011 6:29

    Content type: Research

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  32. Accurate estimation of the divergence time of the extant eukaryotes is a fundamentally important but extremely difficult problem owing primarily to gross violations of the molecular clock at long evolutionary ...

    Authors: Diana Chernikova, Sam Motamedi, Miklós Csürös, Eugene V Koonin and Igor B Rogozin

    Citation: Biology Direct 2011 6:26

    Content type: Research

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  33. GWAS owe their popularity to the expectation that they will make a major impact on diagnosis, prognosis and management of disease by uncovering genetics underlying clinical phenotypes. The dominant paradigm in...

    Authors: Alexander V Alekseyenko, Nikita I Lytkin, Jizhou Ai, Bo Ding, Leonid Padyukov, Constantin F Aliferis and Alexander Statnikov

    Citation: Biology Direct 2011 6:25

    Content type: Research

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  34. The costs and benefits of spliceosomal introns in eukaryotes have not been established. One recognized effect of intron splicing is its known enhancement of gene expression. However, the mechanism regulating s...

    Authors: Deng-Ke Niu and Yu-Fei Yang

    Citation: Biology Direct 2011 6:24

    Content type: Hypothesis

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  35. MicroRNAs are small RNA species that regulate gene expression post-transcriptionally and are aberrantly expressed in many cancers including hematological malignancies. However, the role of microRNAs in the pat...

    Authors: Jianxiang Chi, Erica Ballabio, Xiao-He Chen, Rajko Kušec, Steve Taylor, Deborah Hay, Daniela Tramonti, Nigel J Saunders, Timothy Littlewood, Francesco Pezzella, Jacqueline Boultwood, James S Wainscoat, Christian SR Hatton and Charles H Lawrie

    Citation: Biology Direct 2011 6:23

    Content type: Research

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  36. Genetic plasticity may be understood as the ability of a functional gene network to tolerate alterations in its components or structure. Usually, the studies involving gene modifications in the course of the e...

    Authors: Rodrigo JS Dalmolin, Mauro AA Castro, José L Rybarczyk Filho, Luis HT Souza, Rita MC de Almeida and José CF Moreira

    Citation: Biology Direct 2011 6:22

    Content type: Research

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  41. Pathway databases are becoming increasingly important and almost omnipresent in most types of biological and translational research. However, little is known about the quality and completeness of pathways stor...

    Authors: Evgeny Shmelkov, Zuojian Tang, Iannis Aifantis and Alexander Statnikov

    Citation: Biology Direct 2011 6:15

    Content type: Research

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  42. Synthesis of proteins is based on the genetic code - a nearly universal assignment of codons to amino acids (aas). A major challenge to the understanding of the origins of this assignment is the archetypal "ke...

    Authors: Andrei S Rodin, Eörs Szathmáry and Sergei N Rodin

    Citation: Biology Direct 2011 6:14

    Content type: Research

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  43. Mammalian genome sequence data are being acquired in large quantities and at enormous speeds. We now have a tremendous opportunity to better understand which genes are the most variable or conserved, and what ...

    Authors: Dapeng Wang, Fei Liu, Lei Wang, Shi Huang and Jun Yu

    Citation: Biology Direct 2011 6:13

    Content type: Research

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  45. Understanding the evolutionary plasticity of the genome requires a global, comparative approach in which genetic events are considered both in a phylogenetic framework and with regard to population genetics an...

    Authors: Anthony Levasseur and Pierre Pontarotti

    Citation: Biology Direct 2011 6:11

    Content type: Review

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  46. Posttranslationally modified amino acids are chemically distinct types of amino acids and in terms of evolution they might behave differently from their non-modified counterparts. In order to check this possib...

    Authors: Yerbol Z Kurmangaliyev, Alexander Goland and Mikhail S Gelfand

    Citation: Biology Direct 2011 6:8

    Content type: Discovery notes

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  47. In genetics it is customary to refer to double-stranded DNA as containing a "Watson strand" and a "Crick strand." However, there seems to be no consensus in the literature on the exact meaning of these two ter...

    Authors: Reed A Cartwright and Dan Graur

    Citation: Biology Direct 2011 6:7

    Content type: Opinion

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  48. Genome degradation is an ongoing process in all members of the Rickettsiales order, which makes these bacterial species an excellent model for studying reductive evolution through interspecies variation in genome...

    Authors: Kalliopi Georgiades, Vicky Merhej, Khalid El Karkouri, Didier Raoult and Pierre Pontarotti

    Citation: Biology Direct 2011 6:6

    Content type: Research

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  49. Modeling of a complex biological process can explain the results of experimental studies and help predict its characteristics. Among such processes is transcription in the presence of competing RNA polymerases...

    Authors: Vassily A Lyubetsky, Oleg A Zverkov, Lev I Rubanov and Alexandr V Seliverstov

    Citation: Biology Direct 2011 6:3

    Content type: Research

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