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  1. Research

    Expansion of the molecular and morphological diversity of Acanthamoebidae (Centramoebida, Amoebozoa) and identification of a novel life cycle type within the group

    Acanthamoebidae is a “family” level amoebozoan group composed of the genera Acanthamoeba, Protacanthamoeba, and very recently Luapeleamoeba. This clade of amoebozoans has received considerable attention from the ...

    Alexander K. Tice, Lora L. Shadwick, Anna Maria Fiore-Donno, Stefan Geisen, Seungho Kang, Gabriel A. Schuler, Frederick W. Spiegel, Katherine A. Wilkinson, Michael Bonkowski, Kenneth Dumack, Daniel J. G. Lahr, Eckhard Voelcker, Steffen Clauß, Junling Zhang and Matthew W. Brown

    Biology Direct 2016 11:69

    Published on: 28 December 2016

  2. Hypothesis

    The role of the backbone torsion in protein folding

    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...

    Irina Sorokina and Arcady Mushegian

    Biology Direct 2016 11:64

    Published on: 1 December 2016

  3. Research

    xHMMER3x2: Utilizing HMMER3’s speed and HMMER2’s sensitivity and specificity in the glocal alignment mode for improved large-scale protein domain annotation

    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...

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

    Biology Direct 2016 11:63

    Published on: 29 November 2016

  4. Research

    ZFAS1: a long noncoding RNA associated with ribosomes in breast cancer cells

    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...

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

    Biology Direct 2016 11:62

    Published on: 21 November 2016

  5. Research

    Importins promote high-frequency NF-κB oscillations increasing information channel capacity

    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 ...

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

    Biology Direct 2016 11:61

    Published on: 11 November 2016

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

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