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  1. Content type: Research

    Only a small fraction of bacteria and archaea that are identifiable by metagenomics can be grown on standard media. Recent efforts on deep metagenomics sequencing, single-cell genomics and the use of specializ...

    Authors: Isabelle Pagnier, Natalya Yutin, Olivier Croce, Kira S Makarova, Yuri I Wolf, Samia Benamar, Didier Raoult, Eugene V Koonin and Bernard La Scola

    Citation: Biology Direct 2015 10:13

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  2. Content type: Discovery notes

    Plant viruses of the recently recognized family Amalgaviridae have monopartite double-stranded (ds) RNA genomes and encode two proteins: an RNA-dependent RNA polymerase (RdRp) and a putative capsid protein (CP). ...

    Authors: Mart Krupovic, Valerian V Dolja and Eugene V Koonin

    Citation: Biology Direct 2015 10:12

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  3. Content type: Erratum

    Following the publication of this article [1] it was noticed that, due to an error on the part of the publisher, the 2nd round of comments submitted by Reviewer 1, Dr. López-García, were unintentionally omitte...

    Authors: Scott L Hooper and Helaine J Burstein

    Citation: Biology Direct 2015 10:11

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    The original article was published in Biology Direct 2014 9:24

  4. Content type: Research

    Epidermal Growth Factor Receptor (EGFR) is a well-characterized cancer drug target. In the past, several QSAR models have been developed for predicting inhibition activity of molecules against EGFR. These mode...

    Authors: Harinder Singh, Sandeep Singh, Deepak Singla, Subhash M Agarwal and Gajendra P S Raghava

    Citation: Biology Direct 2015 10:10

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  5. Content type: Research

    Telocytes (TCs) is an interstitial cell with extremely long and thin telopodes (Tps) with thin segments (podomers) and dilations (podoms) to interact with neighboring cells. TCs have been found in different or...

    Authors: Jian Wang, Ling Ye, Meiling Jin and Xiangdong Wang

    Citation: Biology Direct 2015 10:9

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  6. Content type: Research

    Protein-RNA interactions perform diverse functions within the cell. Understanding the recognition mechanism of protein-RNA complexes has been a challenging task in molecular and computational biology. In earli...

    Authors: Raju Nagarajan, Sonia Pankaj Chothani, Chandrasekaran Ramakrishnan, Masakazu Sekijima and M Michael Gromiha

    Citation: Biology Direct 2015 10:8

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  7. Content type: Reviewer acknowledgement

    The editors of Biology Direct would like to thank all the reviewers who have contributed to the journal in Volume 9 (2014).

    Authors: Eugene V Koonin, Laura F Landweber and David Lipman

    Citation: Biology Direct 2015 10:7

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  8. Content type: Research

    Alterations in gut microbiota composition under antibiotic pressure have been widely studied, revealing a restricted diversity of gut flora, including colonization by organisms such as Enterococci, while their im...

    Authors: Aurélia Caputo, Grégory Dubourg, Olivier Croce, Sushim Gupta, Catherine Robert, Laurent Papazian, Jean-Marc Rolain and Didier Raoult

    Citation: Biology Direct 2015 10:5

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  9. Content type: Research

    About 5–6% of the European bison (Bison bonasus) males are affected by posthitis (necrotic inflammation of the prepuce) and die in the wild forest. Despite many years of study, pathogenesis of this disease has no...

    Authors: Kamil Oleński, Małgorzata Tokarska, Dorota Maria Hering, Paulina Puckowska, Anna Ruść, Cino Pertoldi and Stanisław Kamiński

    Citation: Biology Direct 2015 10:2

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  10. Content type: Research

    A key challenge in the field of HIV-1 protein evolution is the identification of coevolving amino acids at the molecular level. In the past decades, many sequence-based methods have been designed to detect pos...

    Authors: Guangdi Li, Kristof Theys, Jens Verheyen, Andrea-Clemencia Pineda-Peña, Ricardo Khouri, Supinya Piampongsant, Mónica Eusébio, Jan Ramon and Anne-Mieke Vandamme

    Citation: Biology Direct 2015 10:1

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  11. Content type: Research

    Mutations in nucleotide sequences provide a foundation for genetic variability, and selection is the driving force of the evolution and molecular adaptation. Despite considerable progress in the understanding ...

    Authors: Alexander Goncearenco and Igor N Berezovsky

    Citation: Biology Direct 2014 9:29

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  12. Content type: Research

    Moonlighting proteins perform two or more cellular functions, which are selected based on various contexts including the cell type they are expressed, their oligomerization status, and the binding of different...

    Authors: Ishita Khan, Yuqian Chen, Tiange Dong, Xioawei Hong, Rikiya Takeuchi, Hirotada Mori and Daisuke Kihara

    Citation: Biology Direct 2014 9:30

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  13. Content type: Hypothesis

    Fundamental problems faced by the protocells and their modern descendants include how to go from one phenotypic state to another; escape from a basin of attraction in the space of phenotypes; reconcile conflic...

    Authors: Vic Norris, Rosetta N Reusch, Kazuei Igarashi and Robert Root-Bernstein

    Citation: Biology Direct 2014 10:28

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  14. Content type: Comment

    When a field shares the consensus that a particular phenomenon does NOT occur, this may reflect extensive experimental investigations with negative outcomes, or may represent the “common sense” position based ...

    Authors: Neil R Smalheiser and Octavio L A Gomes

    Citation: Biology Direct 2014 10:27

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  15. Content type: Comment

    Our body harbors hundreds of microbial species and contains many more bacterial than human cells. These microbes are not passive riders but rather a vital component of the organism. The human microbiota affect...

    Authors: Petro Starokadomskyy

    Citation: Biology Direct 2014 10:25

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  16. Content type: Research

    Internalization-based hypotheses of eukaryotic origin require close physical association of host and symbiont. Prior hypotheses of how these associations arose include chance, specific metabolic couplings betw...

    Authors: Scott L Hooper and Helaine J Burstein

    Citation: Biology Direct 2014 9:24

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    The Erratum to this article has been published in Biology Direct 2015 10:11

  17. Content type: Research

    Long-lived marine megavertebrates (e.g. sharks, turtles, mammals, and seabirds) are inherently vulnerable to anthropogenic mortality. Although some mathematical models have been applied successfully to manage ...

    Authors: Easton R White, John D Nagy and Samuel H Gruber

    Citation: Biology Direct 2014 9:23

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  18. Content type: Discovery notes

    Through the course of their evolution, viruses with large genomes have acquired numerous host genes, most of which perform function in virus reproduction in a manner that is related to their original activitie...

    Authors: Natalya Yutin, Guilhem Faure, Eugene V Koonin and Arcady R Mushegian

    Citation: Biology Direct 2014 9:22

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  19. 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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  20. 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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  21. 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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  22. Content type: Research

    The stability of long intergenic non-coding RNAs (lincRNAs) that possess tissue/cell-specific expression, might be closely related to their physiological functions. However, the mechanism associated with stabi...

    Authors: Lei Wang, Dequan Zhou, Jing Tu, Yan Wang and Zuhong Lu

    Citation: Biology Direct 2014 9:15

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  23. Content type: Research

    Because amino acid activation is rate-limiting for uncatalyzed protein synthesis, it is a key puzzle in understanding the origin of the genetic code. Two unrelated classes (I and II) of contemporary aminoacyl-...

    Authors: Charles W Carter Jr, Li Li, Violetta Weinreb, Martha Collier, Katiria Gonzalez-Rivera, Mariel Jimenez-Rodriguez, Ozgün Erdogan, Brian Kuhlman, Xavier Ambroggio, Tishan Williams and S Niranj Chandrasekharan

    Citation: Biology Direct 2014 9:11

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  24. Content type: Review

    The emergence of Next Generation Sequencing generates an incredible amount of sequence and great potential for new enzyme discovery. Despite this huge amount of data and the profusion of bioinformatic methods ...

    Authors: Maria Sorokina, Mark Stam, Claudine Médigue, Olivier Lespinet and David Vallenet

    Citation: Biology Direct 2014 9:10

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  25. Content type: Research

    We have previously suggested a method for proteome wide analysis of variation at functional residues wherein we identified the set of all human genes with nonsynonymous single nucleotide variation (nsSNV) in t...

    Authors: Hayley Dingerdissen, Daniel S Weaver, Peter D Karp, Yang Pan, Vahan Simonyan and Raja Mazumder

    Citation: Biology Direct 2014 9:9

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  26. Content type: Discovery notes

    Pannexin1 is ubiquitously expressed in vertebrate tissues, but the role it plays in vascular tone regulation remains unclear. We found that Pannexin1 expression level is much higher in the endothelium relative...

    Authors: Dina Gaynullina, Olga S Tarasova, Oxana O Kiryukhina, Valery I Shestopalov and Yuri Panchin

    Citation: Biology Direct 2014 9:8

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  27. Content type: Discovery notes

    Cryptomonads, are a lineage of unicellular and mostly photosynthetic algae, that acquired their plastids through the “secondary” endosymbiosis of a red alga — and still retain the nuclear genome (nucleomorph) ...

    Authors: David R Smith, Serge N Vinogradov and David Hoogewijs

    Citation: Biology Direct 2014 9:7

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  28. Content type: Research

    H. sapiens-M. tuberculosis H37Rv protein-protein interaction (PPI) data are essential for understanding the infection mechanism of the formidable pathogen M. tuberculosis H37Rv. Computational prediction is an imp...

    Authors: Hufeng Zhou, Shangzhi Gao, Nam Ninh Nguyen, Mengyuan Fan, Jingjing Jin, Bing Liu, Liang Zhao, Geng Xiong, Min Tan, Shijun Li and Limsoon Wong

    Citation: Biology Direct 2014 9:5

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  29. Content type: Research

    For the anucleate platelet it has been unclear how well platelet transcriptomes correlate among different donors or across different RNA profiling platforms, and what the transcriptomes’ relationship is with t...

    Authors: Eric R Londin, Eleftheria Hatzimichael, Phillipe Loher, Leonard Edelstein, Chad Shaw, Kathleen Delgrosso, Paolo Fortina, Paul F Bray, Steven E McKenzie and Isidore Rigoutsos

    Citation: Biology Direct 2014 9:3

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  30. Content type: Research

    A recent study argued, based on data on functional genome size of major phyla, that there is evidence life may have originated significantly prior to the formation of the Earth.

    Authors: Caren Marzban, Raju Viswanathan and Ulvi Yurtsever

    Citation: Biology Direct 2014 9:1

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  31. Content type: Research

    The problem of probabilistic inference of gene content in the last common ancestor of several extant species with completely sequenced genomes is: for each gene that is conserved in all or some of the genomes,...

    Authors: Lavanya Kannan, Hua Li, Boris Rubinstein and Arcady Mushegian

    Citation: Biology Direct 2013 8:32

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  32. Content type: Research

    The generation of interferon-gamma (IFN-γ) by MHC class II activated CD4+ T helper cells play a substantial contribution in the control of infections such as caused by Mycobacterium tuberculosis. In the past, num...

    Authors: Sandeep Kumar Dhanda, Pooja Vir and Gajendra PS Raghava

    Citation: Biology Direct 2013 8:30

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  33. Content type: Discovery notes

    Translation elongation factors eEF1A1 and eEF1A2 are 92% identical but exhibit non-overlapping expression patterns. While the two proteins are predicted to have similar tertiary structures, it is notable that ...

    Authors: Dinesh C Soares and Catherine M Abbott

    Citation: Biology Direct 2013 8:29

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  34. Content type: Research

    In the past, numerous methods have been developed for predicting antigenic regions or B-cell epitopes that can induce B-cell response. To the best of authors’ knowledge, no method has been developed for predic...

    Authors: Sudheer Gupta, Hifzur Rahman Ansari, Ankur Gautam and Gajendra PS Raghava

    Citation: Biology Direct 2013 8:27

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