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  1. APPLICATION NOTE

    CLIP-GENE: a web service of the condition specific context-laid integrative analysis for gene prioritization in mouse TF knockout experiments

    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...

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

    Biology Direct 2016 11:57

    Published on: 24 October 2016

  2. Research

    IPC – Isoelectric Point Calculator

    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...

    Lukasz P. Kozlowski

    Biology Direct 2016 11:55

    Published on: 21 October 2016

  3. Research

    Evolution of the Tim17 protein family

    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...

    Vojtěch Žárský and Pavel Doležal

    Biology Direct 2016 11:54

    Published on: 19 October 2016

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

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