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  1. Research

    Unexpected links reflect the noise in networks

    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...

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

    Biology Direct 2016 11:52

    Published on: 13 October 2016

  2. Research

    Cancer heterogeneity and multilayer spatial evolutionary games

    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...

    Andrzej Świerniak and Michał Krześlak

    Biology Direct 2016 11:53

    Published on: 13 October 2016

  3. Research

    Emergence of heterogeneity in acute leukemias

    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...

    Thomas Stiehl, Christoph Lutz and Anna Marciniak-Czochra

    Biology Direct 2016 11:51

    Published on: 12 October 2016

  4. Comment

    The essence of life

    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...

    Wentao Ma

    Biology Direct 2016 11:49

    Published on: 26 September 2016

  5. Research

    Cpf1 nucleases demonstrate robust activity to induce DNA modification by exploiting homology directed repair pathways in mammalian cells

    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 ...

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

    Biology Direct 2016 11:46

    Published on: 14 September 2016

  6. Review

    Optimal treatment and stochastic modeling of heterogeneous tumors

    In this work we review past articles that have mathematically studied cancer heterogeneity and the impact of this heterogeneity on the structure of optimal therapy. We look at past works on modeling how hetero...

    Hamidreza Badri and Kevin Leder

    Biology Direct 2016 11:40

    Published on: 23 August 2016

  7. Review

    Unity and disunity in evolutionary sciences: process-based analogies open common research avenues for biology and linguistics

    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...

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

    Biology Direct 2016 11:39

    Published on: 20 August 2016

  8. Research

    Compartmentalization in PVC super-phylum: evolution and impact

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

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

    Biology Direct 2016 11:38

    Published on: 9 August 2016

  9. Research

    Comparative genomic analysis of retrogene repertoire in two green algae Volvox carteri and Chlamydomonas reinhardtii

    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...

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

    Biology Direct 2016 11:35

    Published on: 4 August 2016

  10. Discovery notes

    Alpha proteobacterial ancestry of the [Fe-Fe]-hydrogenases in anaerobic eukaryotes

    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...

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

    Biology Direct 2016 11:34

    Published on: 30 July 2016

  11. Review

    Stem-like features of cancer cells on their way to metastasis

    More than 90 % of cancer-related deaths are due to the development of a systemic metastatic disease. Clearly, much remains to be understood about the biological principles that govern human cancer metastasis, ...

    Sofia Gkountela and Nicola Aceto

    Biology Direct 2016 11:33

    Published on: 26 July 2016

  12. Research

    Selection on metabolic pathway function in the presence of mutation-selection-drift balance leads to rate-limiting steps that are not evolutionarily stable

    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...

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

    Biology Direct 2016 11:31

    Published on: 8 July 2016

  13. Discovery notes

    Intrinsic protein disorder in histone lysine methylation

    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...

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

    Biology Direct 2016 11:30

    Published on: 30 June 2016

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