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  1. Content type: Review

    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

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  2. Content type: Research

    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

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  3. Content type: Review

    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

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  4. Content type: Research

    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

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  5. Content type: Research

    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

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  6. Content type: Research

    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

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  7. Content type: Hypothesis

    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

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  8. Content type: Research

    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

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  9. Content type: Research

    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

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  10. Content type: Research

    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

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  11. Content type: APPLICATION NOTE

    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

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  12. Content type: Research

    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

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  13. Content type: Research

    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

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  14. Content type: Research

    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

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  15. Content type: Research

    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

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  16. Content type: Research

    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

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  17. Content type: Research

    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

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  18. Content type: Comment

    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

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  19. Content type: Discovery notes

    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

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  20. Content type: Research

    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

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  21. Content type: Hypothesis

    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

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  22. Content type: Research

    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

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  23. Content type: Research

    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

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  24. Content type: Review

    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

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  25. Content type: Research

    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

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  26. Content type: Research

    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

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  27. Content type: Discovery notes

    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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  28. Content type: Research

    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

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  29. Content type: Discovery notes

    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

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  30. Content type: Discovery notes

    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

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