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  1. 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

    Published on:

  2. 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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  3. 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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  4. 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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  5. 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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  6. 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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  7. 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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  8. 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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  9. 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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  10. 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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  11. 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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  12. 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

    Published on:

  13. 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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  14. 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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  15. 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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  16. 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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  17. 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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  18. 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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  19. 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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  20. 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:

  21. 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

    Published on:

  22. The discovery of the viroid in 1971, which initiated the third major expansion of the biosphere towards smaller living entities—after discovery of the “subvisual” microorganisms in 1675 and that of the “submic...

    Authors: Theodor O. Diener

    Citation: Biology Direct 2016 11:15

    Content type: Hypothesis

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  23. 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

    Published on:

  24. Antiangiogenic agents have been recently added to the oncological armamentarium with bevacizumab probably being the most popular representative in current clinical practice. The elucidation of the mode of acti...

    Authors: Katerina D. Argyri, Dimitra D. Dionysiou, Fay D. Misichroni and Georgios S. Stamatakos

    Citation: Biology Direct 2016 11:12

    Content type: Research

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  25. CpG dinucleotides are extensively underrepresented in mammalian genomes. It is widely accepted that genome-wide CpG depletion is predominantly caused by an elevated CpG > TpG mutation rate due to frequent cyto...

    Authors: Alexander Y. Panchin, Vsevolod J. Makeev and Yulia A. Medvedeva

    Citation: Biology Direct 2016 11:11

    Content type: Research

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  26. Genotyping by re-sequencing has become a standard approach to estimate single nucleotide polymorphism (SNP) diversity, haplotype structure and the biodiversity and has been defined as an efficient approach to ...

    Authors: Salvatore Camiolo, Gaurav Sablok and Andrea Porceddu

    Citation: Biology Direct 2016 11:8

    Content type: Application note

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  27. Translation of nucleotides into a numeric form has been approached in many ways and has allowed researchers to investigate the properties of protein-coding sequences and noncoding sequences. Typically, more pr...

    Authors: Tonya Woods, Thanawadee Preeprem, Kichun Lee, Woojin Chang and Brani Vidakovic

    Citation: Biology Direct 2016 11:6

    Content type: Research

    Published on:

  28. The cilium (flagellum) is a complex cellular structure inherited from the last eukaryotic common ancestor (LECA). A large number of ciliary proteins have been characterized in a few model organisms, but their ...

    Authors: Marek Eliáš, Vladimír Klimeš, Romain Derelle, Romana Petrželková and Jan Tachezy

    Citation: Biology Direct 2016 11:5

    Content type: Research

    Published on:

  29. Next-generation sequencing (NGS) enables the recovery of pathogen genomes from clinical samples without the need for culturing. Depletion of host/microbiota components (e.g., ribosomal RNA and poly-A RNA) and ...

    Authors: Dingchen Li, Zongwei Li, Zhe Zhou, Zhen Li, Xinyan Qu, Peisong Xu, Pingkun Zhou, Xiaochen Bo and Ming Ni

    Citation: Biology Direct 2016 11:3

    Content type: Discovery notes

    Published on:

  30. The length of a protein sequence is largely determined by its function. In certain species, it may be also affected by additional factors, such as growth temperature or acidity. In 2002, it was shown that in t...

    Authors: Tatiana V. Tatarinova, Inna Lysnyansky, Yuri V. Nikolsky and Alexander Bolshoy

    Citation: Biology Direct 2016 11:2

    Content type: Research

    Published on:

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