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  1. We report a comprehensive computational dissection of the domain architecture of the SAMD9 family proteins that are involved in antivirus and antitumor response in humans. We show that the SAMD9 protein family...

    Authors: Sergei L. Mekhedov, Kira S. Makarova and Eugene V. Koonin
    Citation: Biology Direct 2017 12:13
  2. The protein Gcn1 (General control non-derepressible 1) is found in virtually all eukaryotes, and is a key component of the general amino acid control signal transduction pathway. This pathway is best known for...

    Authors: Ramachandran Rakesh, Rangachari Krishnan, Evelyn Sattlegger and Narayanaswamy Srinivasan
    Citation: Biology Direct 2017 12:12
  3. TRIF is a key protein in antiviral innate immunity, operating downstream of TLRs. TRIF activation leads to the production of interferon-β and pro-inflammatory cytokines. There is evidence from experiments to s...

    Authors: Jarjapu Mahita and Ramanathan Sowdhamini
    Citation: Biology Direct 2017 12:9
  4. The transition between epithelial and mesenchymal phenotypes (EMT) occurs in a variety of contexts. It is critical for mammalian development and it is also involved in tumor initiation and progression. Master ...

    Authors: Yoana Dimitrova, Andreas J. Gruber, Nitish Mittal, Souvik Ghosh, Beatrice Dimitriades, Daniel Mathow, William Aaron Grandy, Gerhard Christofori and Mihaela Zavolan
    Citation: Biology Direct 2017 12:8
  5. Mutations in the gene encoding for the E3 ubiquitin ligase Parkin are associated to a rare form of familiar autosomal recessive Parkinsonism. Despite decades of research on the Parkin protein, whose structure ...

    Authors: Joy Chakraborty, Valentina Basso and Elena Ziviani
    Citation: Biology Direct 2017 12:6
  6. Recent developments of high throughput sequencing technologies allow the characterization of the microbial communities inhabiting our world. Various metagenomic studies have suggested using microbial taxa as p...

    Authors: Mustafa Alshawaqfeh, Ahmad Bashaireh, Erchin Serpedin and Jan Suchodolski
    Citation: Biology Direct 2017 12:4
  7. The past decade has seen dramatic progress in our understanding of membrane contact sites (MCS). Important examples of these are endoplasmic reticulum (ER)-mitochondria contact sites. ER-mitochondria contacts ...

    Authors: Maria Sol Herrera-Cruz and Thomas Simmen
    Citation: Biology Direct 2017 12:3
  8. Molecular phenomena driving pathological aggregation in neurodegenerative diseases are not completely understood yet. Peculiar is the case of Spinocerebellar Ataxia 3 (SCA3) where the conformational properties...

    Authors: Gianvito Grasso, Jack A. Tuszynski, Umberto Morbiducci, Ginevra Licandro, Andrea Danani and Marco A. Deriu
    Citation: Biology Direct 2017 12:2
  9. 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 ...

    Authors: 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
    Citation: Biology Direct 2016 11:69
  10. It is believed that all cancers occur due to the mutation or change in one or more genes. In order to investigate the significance of the biological pathways which are interrupted by these genetic mutations, w...

    Authors: Sinjini Sikdar, Somnath Datta and Susmita Datta
    Citation: Biology Direct 2016 11:65
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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

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