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  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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

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

  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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

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

  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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
  36. 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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