Skip to main content

Articles

Page 6 of 18

  1. The microbial communities populating human and natural environments have been extensively characterized with shotgun metagenomics, which provides an in-depth representation of the microbial diversity within a ...

    Authors: Moreno Zolfo, Francesco Asnicar, Paolo Manghi, Edoardo Pasolli, Adrian Tett and Nicola Segata
    Citation: Biology Direct 2018 13:9
  2. We report a protein sequence analysis of the cell cycle regulatory protease, separase. The sequence and structural conservation of the C-terminal protease domain has long been recognized, whereas the N-termina...

    Authors: Michael Melesse, Joshua N. Bembenek and Igor B. Zhulin
    Citation: Biology Direct 2018 13:7
  3. There are numerous computational tools for taxonomic or functional analysis of microbiome samples, optimized to run on hundreds of millions of short, high quality sequencing reads. Programs such as MEGAN allow...

    Authors: Daniel H. Huson, Benjamin Albrecht, Caner Bağcı, Irina Bessarab, Anna Górska, Dino Jolic and Rohan B. H. Williams
    Citation: Biology Direct 2018 13:6
  4. High-throughput methodologies such as microarrays and next-generation sequencing are routinely used in cancer research, generating complex data at different omics layers. The effective integration of omics data c...

    Authors: Margherita Francescatto, Marco Chierici, Setareh Rezvan Dezfooli, Alessandro Zandonà, Giuseppe Jurman and Cesare Furlanello
    Citation: Biology Direct 2018 13:5
  5. Natural selection is possible only because all species produce more offsprings than what is needed to maintain the population. Still, the lifetime number of offspring varies widely across species. One may expe...

    Authors: Aleksandra V. Bezmenova, Georgii A. Bazykin and Alexey S. Kondrashov
    Citation: Biology Direct 2018 13:4
  6. The experience with running various types of classification on the CAMDA neuroblastoma dataset have led us to the conclusion that the results are not always obvious and may differ depending on type of analysis...

    Authors: Anna Leśniewska, Joanna Zyprych-Walczak, Alicja Szabelska-Beręsewicz and Michal J. Okoniewski
    Citation: Biology Direct 2018 13:3
  7. Though earlier works on modelling transcript abundance from vertebrates to lower eukaroytes have specifically singled out the Zip’s law, the observed distributions often deviate from a single power-law slope. ...

    Authors: Wing-Cheong Wong, Hong-kiat Ng, Erwin Tantoso, Richie Soong and Frank Eisenhaber
    Citation: Biology Direct 2018 13:2
  8. Genetic parasites, including viruses and mobile genetic elements, are ubiquitous among cellular life forms, and moreover, are the most abundant biological entities on earth that harbor the bulk of the genetic ...

    Authors: Eugene V. Koonin, Yuri I. Wolf and Mikhail I. Katsnelson
    Citation: Biology Direct 2017 12:31
  9. The Clusters of Orthologous Groups (COGs) of proteins systematize evolutionary related proteins into specific groups with similar functions. However, the available databases do not provide means to assess the ...

    Authors: Daria V. Dibrova, Kirill A. Konovalov, Vadim V. Perekhvatov, Konstantin V. Skulachev and Armen Y. Mulkidjanian
    Citation: Biology Direct 2017 12:29
  10. Weaning stress affects the small intestine of piglets. MiR-146b is differentially expressed in suckling and weaned piglets. In this study, we evaluated the effects of miR-146b on cell viability, proliferation,...

    Authors: Xin Tao, Shujie Liu, Xiaoming Men and Ziwei Xu
    Citation: Biology Direct 2017 12:27
  11. In prokaryotic genomes, functionally coupled genes can be organized in conserved gene clusters enabling their coordinated regulation. Such clusters could contain one or several operons, which are groups of co-...

    Authors: Olesya I. Klimchuk, Kirill A. Konovalov, Vadim V. Perekhvatov, Konstantin V. Skulachev, Daria V. Dibrova and Armen Y. Mulkidjanian
    Citation: Biology Direct 2017 12:26
  12. Programmed ribosomal frameshifting (PRF) is a gene expression mechanism which enables the translation of two N-terminally coincident, C-terminally distinct protein products from a single mRNA. Many viruses uti...

    Authors: Adam M. Dinan, John F. Atkins and Andrew E. Firth
    Citation: Biology Direct 2017 12:24
  13. High-level debates in evolutionary biology often treat the Modern Synthesis as a framework of population genetics, or as an intellectual lineage with a changing distribution of beliefs. Unfortunately, these fl...

    Authors: Arlin Stoltzfus
    Citation: Biology Direct 2017 12:23
  14. Bacterial species present in multispecies microbial communities often react to the same chemical signal but at vastly different concentrations. The existence of different response thresholds with respect to th...

    Authors: János Juhász, Dóra Bihary, Attila Jády, Sándor Pongor and Balázs Ligeti
    Citation: Biology Direct 2017 12:22
  15. Oil palm is an important source of edible oil. The importance of the crop, as well as its long breeding cycle (10-12 years) has led to the sequencing of its genome in 2013 to pave the way for genomics-guided b...

    Authors: Kuang-Lim Chan, Tatiana V. Tatarinova, Rozana Rosli, Nadzirah Amiruddin, Norazah Azizi, Mohd Amin Ab Halim, Nik Shazana Nik Mohd Sanusi, Nagappan Jayanthi, Petr Ponomarenko, Martin Triska, Victor Solovyev, Mohd Firdaus-Raih, Ravigadevi Sambanthamurthi, Denis Murphy and Eng-Ti Leslie Low
    Citation: Biology Direct 2017 12:21
  16. Much effort is underway to build and upgrade databases and tools related to occurrence, diversity, and characterization of CRISPR-Cas systems. As microbial communities and their genome complements are unearthe...

    Authors: Alice Toms and Rodolphe Barrangou
    Citation: Biology Direct 2017 12:20
  17. Cancer cell invasion, dissemination, and metastasis have been linked to an epithelial-mesenchymal transition (EMT) of individual tumour cells. During EMT, adhesion molecules like E-cadherin are downregulated a...

    Authors: David Reher, Barbara Klink, Andreas Deutsch and Anja Voss-Böhme
    Citation: Biology Direct 2017 12:18
  18. During the generation and evolution of the eukaryotic cell, a proteobacterial endosymbiont was re-fashioned into the mitochondrion, an organelle that appears to have been present in the ancestor of all present...

    Authors: Güleycan Lutfullahoğlu-Bal, Abdurrahman Keskin, Ayşe Bengisu Seferoğlu and Cory D. Dunn
    Citation: Biology Direct 2017 12:16
  19. A basic tenet of protein science is that all information about the spatial structure of proteins is present in their sequences. Nonetheless, many proteins fail to attain native structure upon experimental dena...

    Authors: Irina Sorokina and Arcady Mushegian
    Citation: Biology Direct 2017 12:14
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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

Annual Journal Metrics

  • 2022 Citation Impact
    5.5 - 2-year Impact Factor
    3.8 - 5-year Impact Factor
    0.893 - SNIP (Source Normalized Impact per Paper)
    1.117 - SJR (SCImago Journal Rank)

    2023 Speed
    8 days submission to first editorial decision for all manuscripts (Median)
    74 days submission to accept (Median)

    2023 Usage 
    587,431 downloads
    409 Altmetric mentions