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  1. In the post-genomic era where sequences are being determined at a rapid rate, we are highly reliant on computational methods for their tentative biochemical characterization. The Pfam database currently contai...

    Authors: Richa Mudgal, Sankaran Sandhya, Nagasuma Chandra and Narayanaswamy Srinivasan

    Citation: Biology Direct 2015 10:38

    Content type: Research

    Published on:

  2. Mounting evidence indicates that our planet might experience runaway effects associated to rising temperatures and ecosystem overexploitation, leading to catastrophic shifts on short time scales. Remediation s...

    Authors: Ricard V. Solé, Raúl Montañez and Salva Duran-Nebreda

    Citation: Biology Direct 2015 10:37

    Content type: Hypothesis

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  5. “Which came first, the Chicken or the Egg?” We suggest this question is not a paradox. The Modern Synthesis envisions speciation through genetic changes in germ cells via random mutations, an “Egg first” scena...

    Authors: Yitzhak Pilpel and Oded Rechavi

    Citation: Biology Direct 2015 10:34

    Content type: Comment

    Published on:

  6. Origin of life research has been slow to advance not only because of its complex evolutionary nature (Franklin Harold: In Search of Cell History, 2014) but also because of the lack of agreement on fundamental ...

    Authors: Jan Spitzer, Gary J. Pielak and Bert Poolman

    Citation: Biology Direct 2015 10:33

    Content type: Review

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  7. The ever-increasing expanse of online bioinformatics data is enabling new ways to, not only explore the visualization of these data, but also to apply novel mathematical methods to extract meaningful informati...

    Authors: Sebastian Benzekry, Jack A. Tuszynski, Edward A. Rietman and Giannoula Lakka Klement

    Citation: Biology Direct 2015 10:32

    Content type: Research

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  8. Transmembrane proteins have important roles in cells, as they are involved in energy production, signal transduction, cell-cell interaction, cell-cell communication and more. In human cells, they are frequentl...

    Authors: László Dobson, István Reményi and Gábor E. Tusnády

    Citation: Biology Direct 2015 10:31

    Content type: Research

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  10. Binding of cytochrome c, released from the damaged mitochondria, to the apoptotic protease activating factor 1 (Apaf-1) is a key event in the apoptotic signaling cascade. The binding triggers a major domain rearr...

    Authors: Daria N. Shalaeva, Daria V. Dibrova, Michael Y. Galperin and Armen Y. Mulkidjanian

    Citation: Biology Direct 2015 10:29

    Content type: Research

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  11. In this study, we identified 19 intron losses, including 11 precise intron losses (PILs), six imprecise intron losses (IILs), one de-exonization, and one exon deletion in tomato and potato, and 17 IILs in Arabido...

    Authors: Ming-Yue Ma, Tao Zhu, Xue-Nan Li, Xin-Ran Lan, Heng-Yuan Liu, Yu-Fei Yang and Deng-Ke Niu

    Citation: Biology Direct 2015 10:24

    Content type: Discovery notes

    Published on:

  12. Lignin plays an important role in plant structural support and water transport, and is considered one of the hallmarks of land plants. The recent discovery of lignin or its precursors in various algae has rais...

    Authors: Leen Labeeuw, Patrick T Martone, Yan Boucher and Rebecca J Case

    Citation: Biology Direct 2015 10:23

    Content type: Research

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  14. Deciphering the origin of uniquely eukaryotic features of sub-cellular systems, such as the translation apparatus, is critical in reconstructing eukaryogenesis. One such feature is the highly conserved, but po...

    Authors: A Maxwell Burroughs, Dapeng Zhang and L Aravind

    Citation: Biology Direct 2015 10:21

    Content type: Discovery notes

    Published on:

  16. Search of metagenomics sequence databases for homologs of virophage capsid proteins resulted in the discovery of a new family of virophages in the sheep rumen metagenome. The genomes of the rumen virophages (R...

    Authors: Natalya Yutin, Vladimir V Kapitonov and Eugene V Koonin

    Citation: Biology Direct 2015 10:19

    Content type: Discovery notes

    Published on:

  17. Co-regulation of gene expression has been known for many years, and studied widely both globally and for individual genes. Nevertheless, most analyses concerned transcriptional control, which in case of physic...

    Authors: Marlena Siwiak and Piotr Zielenkiewicz

    Citation: Biology Direct 2015 10:18

    Content type: Research

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  18. RNA viruses rapidly accumulate genetic variation, which can give rise to synthetic lethal (SL) and deleterious (SD) mutations. Synthetic lethal mutations (non-lethal when alone but lethal when combined in one ...

    Authors: Michel Petitjean, Anne Badel, Reiner A Veitia and Anne Vanet

    Citation: Biology Direct 2015 10:17

    Content type: Research

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  19. Members of the alphavirus supergroup include human pathogens such as chikungunya virus, hepatitis E virus and rubella virus. They encode a capping enzyme with methyltransferase-guanylyltransferase (MTase-GTase...

    Authors: Tero Ahola and David G Karlin

    Citation: Biology Direct 2015 10:16

    Content type: Research

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  20. Non-small cell lung cancer (NSCLC) is the predominant histological type of lung cancer, accounting for up to 85% of cases. Disease stage is commonly used to determine adjuvant treatment eligibility of NSCLC pa...

    Authors: Suyan Tian, Chi Wang and Ming-Wen An

    Citation: Biology Direct 2015 10:15

    Content type: Research

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  21. CD4+ T cells are key regulators of the adaptive immune system and can be divided into T helper (Th) cells and regulatory T (Treg) cells. During an immune response Th cells mature from a naive state into one of se...

    Authors: Michael JT Stubbington, Bidesh Mahata, Valentine Svensson, Andrew Deonarine, Jesper K Nissen, Alexander G Betz and Sarah A Teichmann

    Citation: Biology Direct 2015 10:14

    Content type: Research

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  22. 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

    Content type: Research

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  23. 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

    Content type: Discovery notes

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  24. 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

    Content type: Erratum

    Published on:

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

  25. 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

    Content type: Research

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  26. 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

    Content type: Research

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  27. 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

    Content type: Research

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  28. 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

    Content type: Reviewer acknowledgement

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  30. 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

    Content type: Research

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  33. 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

    Content type: Research

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  34. 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

    Content type: Research

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  36. 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

    Content type: Research

    Published on:

  37. 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

    Content type: Research

    Published on:

  38. 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

    Content type: Hypothesis

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  39. 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

    Content type: Comment

    Published on:

  40. 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

    Content type: Comment

    Published on:

  42. 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

    Content type: Research

    Published on:

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

  43. 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

    Content type: Research

    Published on:

  44. 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

    Content type: Discovery notes

    Published on:

  46. 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

    Content type: Research

    Published on:

  47. 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

    Content type: Research

    Published on:

  48. 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

    Content type: Review

    Published on:

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