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  1. The set of forces and sequence of events that govern the transition from an unfolded polypeptide chain to a functional protein with correct spatial structure remain incompletely known, despite the importance o...

    Authors: Irina Sorokina and Arcady Mushegian

    Citation: Biology Direct 2016 11:64

    Content type: Hypothesis

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  2. While the local-mode HMMER3 is notable for its massive speed improvement, the slower glocal-mode HMMER2 is more exact for domain annotation by enforcing full domain-to-sequence alignments. Since a unit of doma...

    Authors: Choon-Kong Yap, Birgit Eisenhaber, Frank Eisenhaber and Wing-Cheong Wong

    Citation: Biology Direct 2016 11:63

    Content type: Research

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  3. Most of the eukaryotic genome is transcribed, yielding a complex network of transcripts including thousands of lncRNAs that generally lack protein coding potential. However, only a small percentage of these mo...

    Authors: Herah Hansji, Euphemia Y. Leung, Bruce C. Baguley, Graeme J. Finlay, David Cameron-Smith, Vandre C. Figueiredo and Marjan E. Askarian-Amiri

    Citation: Biology Direct 2016 11:62

    Content type: Research

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  4. Importins and exportins influence gene expression by enabling nucleocytoplasmic shuttling of transcription factors. A key transcription factor of innate immunity, NF-κB, is sequestered in the cytoplasm by its ...

    Authors: Zbigniew Korwek, Karolina Tudelska, Paweł Nałęcz-Jawecki, Maciej Czerkies, Wiktor Prus, Joanna Markiewicz, Marek Kochańczyk and Tomasz Lipniacki

    Citation: Biology Direct 2016 11:61

    Content type: Research

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  5. Transcriptome data from the gene knockout experiment in mouse is widely used to investigate functions of genes and relationship to phenotypes. When a gene is knocked out, it is important to identify which gene...

    Authors: Benjamin Hur, Sangsoo Lim, Heejoon Chae, Seokjun Seo, Sunwon Lee, Jaewoo Kang and Sun Kim

    Citation: Biology Direct 2016 11:57

    Content type: APPLICATION NOTE

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  6. Accurate estimation of the isoelectric point (pI) based on the amino acid sequence is useful for many analytical biochemistry and proteomics techniques such as 2-D polyacrylamide gel electrophoresis, or capillary...

    Authors: Lukasz P. Kozlowski

    Citation: Biology Direct 2016 11:55

    Content type: Research

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  7. The Tim17 family of proteins plays a fundamental role in the biogenesis of mitochondria. Three Tim17 family proteins, Tim17, Tim22, and Tim23, are the central components of the widely conserved multi-subunit p...

    Authors: Vojtěch Žárský and Pavel Doležal

    Citation: Biology Direct 2016 11:54

    Content type: Research

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  8. Evolutionary game theory (EGT) has been widely used to simulate tumour processes. In almost all studies on EGT models analysis is limited to two or three phenotypes. Our model contains four main phenotypes. Mo...

    Authors: Andrzej Świerniak and Michał Krześlak

    Citation: Biology Direct 2016 11:53

    Content type: Research

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  9. Gene covariation networks are commonly used to study biological processes. The inference of gene covariation networks from observational data can be challenging, especially considering the large number of play...

    Authors: Anatoly Yambartsev, Michael A. Perlin, Yevgeniy Kovchegov, Natalia Shulzhenko, Karina L. Mine, Xiaoxi Dong and Andrey Morgun

    Citation: Biology Direct 2016 11:52

    Content type: Research

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  10. Leukemias are malignant proliferative disorders of the blood forming system. Sequencing studies demonstrate that the leukemic cell population consists of multiple clones. The genetic relationship between the d...

    Authors: Thomas Stiehl, Christoph Lutz and Anna Marciniak-Czochra

    Citation: Biology Direct 2016 11:51

    Content type: Research

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  11. It has been demonstrated that a pathway-based feature selection method that incorporates biological information within pathways during the process of feature selection usually outperforms a gene-based feature ...

    Authors: Suyan Tian, Howard H. Chang and Chi Wang

    Citation: Biology Direct 2016 11:50

    Content type: Research

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  12. Although biology has achieved great successes in recent years, we have not got a clear idea on “what is life?” Actually, as explained here, the main reason for this situation is that there are two completely d...

    Authors: Wentao Ma

    Citation: Biology Direct 2016 11:49

    Content type: Comment

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  13. Recent analyses of next-generation sequencing datasets have shown that cell-specific regulatory elements in stem cells are marked with distinguishable patterns of transcription factor (TF) binding and epigenet...

    Authors: Esra Kurum, Bérénice A. Benayoun, Ankit Malhotra, Joshy George and Duygu Ucar

    Citation: Biology Direct 2016 11:47

    Content type: Discovery notes

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  14. Cpf1 nucleases have recently been repurposed for site-specific genome modification. Two members of the Cpf1 family, the AsCpf1 from Acidaminococcus sp. and the LbCpf1 from Lachnospiraceae bacterium were shown to ...

    Authors: Eszter Tóth, Nóra Weinhardt, Petra Bencsura, Krisztina Huszár, Péter I. Kulcsár, András Tálas, Elfrieda Fodor and Ervin Welker

    Citation: Biology Direct 2016 11:46

    Content type: Research

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  15. Species-rich adaptive radiations arising from rare plant and animal colonizers are common on remote volcanic archipelagoes. However, they present a paradox. The severe genetic bottleneck of founder events and ...

    Authors: Elysse M. Craddock

    Citation: Biology Direct 2016 11:44

    Content type: Hypothesis

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  16. A thorough understanding of the ecological and evolutionary mechanisms that drive the phenotypic evolution of neoplastic cells is a timely and key challenge for the cancer research community. In this respect, ...

    Authors: Tommaso Lorenzi, Rebecca H. Chisholm and Jean Clairambault

    Citation: Biology Direct 2016 11:43

    Content type: Research

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  17. Colon and intestinal crypts serve as an important model system for adult stem cell proliferation and differentiation. We develop a spatial stochastic model to study the rate of somatic evolution in a normal cr...

    Authors: Leili Shahriyari, Natalia L. Komarova and Alexandra Jilkine

    Citation: Biology Direct 2016 11:42

    Content type: Research

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  18. For a long time biologists and linguists have been noticing surprising similarities between the evolution of life forms and languages. Most of the proposed analogies have been rejected. Some, however, have per...

    Authors: Johann-Mattis List, Jananan Sylvestre Pathmanathan, Philippe Lopez and Eric Bapteste

    Citation: Biology Direct 2016 11:39

    Content type: Review

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  19. The PVC super-phylum gathers bacteria from seven phyla (Planctomycetes, Verrucomicrobiae, Chlamydiae, Lentisphaera, Poribacteria, OP3, WWE2) presenting different lifestyles, cell plans and environments. Planctomy...

    Authors: Sandrine Pinos, Pierre Pontarotti, Didier Raoult, Jean Pierre Baudoin and Isabelle Pagnier

    Citation: Biology Direct 2016 11:38

    Content type: Research

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  20. Retroposition, one of the processes of copying the genetic material, is an important RNA-mediated mechanism leading to the emergence of new genes. Because the transcription controlling segments are usually not...

    Authors: Marcin Jąkalski, Kazutaka Takeshita, Mathieu Deblieck, Kanako O. Koyanagi, Izabela Makałowska, Hidemi Watanabe and Wojciech Makałowski

    Citation: Biology Direct 2016 11:35

    Content type: Research

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  21. Eukaryogenesis, a major transition in evolution of life, originated from the symbiogenic fusion of an archaea with a metabolically versatile bacterium. By general consensus, the latter organism belonged to α p...

    Authors: Mauro Degli Esposti, Diego Cortez, Luis Lozano, Simon Rasmussen, Henrik Bjørn Nielsen and Esperanza Martinez Romero

    Citation: Biology Direct 2016 11:34

    Content type: Discovery notes

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  22. While commonly assumed in the biochemistry community that the control of metabolic pathways is thought to be critical to cellular function, it is unclear if metabolic pathways generally have evolutionarily sta...

    Authors: Alena Orlenko, Ashley I. Teufel, Peter B. Chi and David A. Liberles

    Citation: Biology Direct 2016 11:31

    Content type: Research

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  23. Histone lysine methyltransferases (HKMTs), catalyze mono-, di- and trimethylation of lysine residues, resulting in a regulatory pattern that controls gene expression. Their involvement in many different cellul...

    Authors: Tamas Lazar, Eva Schad, Beata Szabo, Tamas Horvath, Attila Meszaros, Peter Tompa and Agnes Tantos

    Citation: Biology Direct 2016 11:30

    Content type: Discovery notes

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  24. Evolutionary relationship between class III nucleotide cyclases and an uncharacterized set of bacterial proteins from Actinobacteria, Bacteroidetes and Proteobacteria has been recognized and analyzed. Detailed...

    Authors: Gayatri Ramakrishnan, Abha Jain, Nagasuma Chandra and Narayanaswamy Srinivasan

    Citation: Biology Direct 2016 11:27

    Content type: Discovery notes

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  25. Viruses are the simplest replicating units, characterized by a limited number of coding genes and an exceptionally high rate of overlapping genes. We sought a unified evolutionary explanation that accounts for...

    Authors: Nadav Brandes and Michal Linial

    Citation: Biology Direct 2016 11:26

    Content type: Research

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  26. Viral capsid assembly involves the oligomerization of the capsid nucleoprotein (NP), which is an essential step in viral replication and may represent a potential antiviral target. An in vitro transcription-tr...

    Authors: Sean Broce, Lisa Hensley, Tomoharu Sato, Joshua Lehrer-Graiwer, Christian Essrich, Katie J. Edwards, Jacqueline Pajda, Christopher J. Davis, Rami Bhadresh, Clarence R. Hurt, Beverly Freeman, Vishwanath R. Lingappa, Colm A. Kelleher and Marcela V. Karpuj

    Citation: Biology Direct 2016 11:25

    Content type: Research

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  27. Recent advances in sequencing technologies enable the large-scale identification of genes that are affected by various genetic alterations in cancer. However, understanding tumor development requires insights ...

    Authors: Bálint Mészáros, András Zeke, Attila Reményi, István Simon and Zsuzsanna Dosztányi

    Citation: Biology Direct 2016 11:23

    Content type: Research

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  28. The family of D cyclins has a fundamental role in cell cycle progression, but its members (D1, D2, D3) are believed to have redundant functions. However, there is some evidence that contradicts the notion of m...

    Authors: Miguel Chaves-Ferreira, Gerald Krenn, Florence Vasseur, Aleksandr Barinov, Pedro Gonçalves, Orly Azogui, Ana Cumano, Zhi Li, Sandra Pellegrini, Benedita Rocha and Diego Laderach

    Citation: Biology Direct 2016 11:21

    Content type: Research

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  29. Short leader genes usually do not encode stable proteins, although their importance in expression control of bacterial genomes is widely accepted. Such genes are often involved in the control of attenuation re...

    Authors: Semen A. Korolev, Oleg A. Zverkov, Alexandr V. Seliverstov and Vassily A. Lyubetsky

    Citation: Biology Direct 2016 11:20

    Content type: Discovery notes

    Published on:

  30. In the recent years, sequence-specific nucleases such as ZFNs, TALENs, and CRISPR/Cas9 have revolutionzed the fields of animal genome editing and transgenesis. However, these new techniques require microinject...

    Authors: Masahiro Sato, Masato Ohtsuka, Satoshi Watanabe and Channabasavaiah B. Gurumurthy

    Citation: Biology Direct 2016 11:16

    Content type: Review

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  31. The hypothalamic-pituitary-adrenal (HPA) axis is a neuroendocrine system that regulates numerous physiological processes. Disruptions in the activity of the HPA axis are correlated with stress-related diseases...

    Authors: Lae U. Kim, Maria R. D’Orsogna and Tom Chou

    Citation: Biology Direct 2016 11:13

    Content type: Research

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