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  1. 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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  2. 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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  3. 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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  4. 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

  5. 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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  6. 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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  7. 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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  8. 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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  9. 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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  10. 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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  11. 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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  12. 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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  13. 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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  14. 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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  15. 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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  16. 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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  17. 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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  18. 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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  19. 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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  20. 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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  21. 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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  22. Content type: Discovery notes

    The recently discovered Pandoraviruses are by far the largest viruses known, with their 2 megabase genomes exceeding in size the genomes of numerous bacteria and archaea. Pandoraviruses show a distant relation...

    Authors: Natalya Yutin and Eugene V Koonin

    Citation: Biology Direct 2013 8:25

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  23. 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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  24. Content type: Discovery notes

    The bacterial SOS response is an elaborate program for DNA repair, cell cycle regulation and adaptive mutagenesis under stress conditions. Using sensitive sequence and structure analysis, combined with context...

    Authors: L Aravind, Swadha Anand and Lakshminarayan M Iyer

    Citation: Biology Direct 2013 8:20

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  25. 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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  26. 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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  27. 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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  28. 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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  29. 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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