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  1. Content type: Commentary

    A recent paper by (Gerlitz et al., Biol Direct 13:21, 2018) questions the validity of the data underlying prior analyses on the bioenergetics capacities of cells, and continues to promote the idea that the mit...

    Authors: Michael Lynch and Georgi K. Marinov

    Citation: Biology Direct 2018 13:26

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    The Comment to this article has been published in Biology Direct 2018 13:21

  2. Content type: Research

    Reproducing cell processes using an in silico system is an essential tool for understanding the underlying mechanisms and emergent properties of this extraordinary complex biological machine. However, computat...

    Authors: Luis S. Mayorga, Ignacio Cebrian, Meghna Verma, Stefan Hoops and Josep Bassaganya-Riera

    Citation: Biology Direct 2018 13:25

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  3. Content type: Research

    The relatively fast selection of symbiotic bacteria within hosts and the potential transmission of these bacteria across generations of hosts raise the question of whether interactions between host and bacteri...

    Authors: Dino Osmanovic, David A. Kessler, Yitzhak Rabin and Yoav Soen

    Citation: Biology Direct 2018 13:24

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  4. Content type: Research

    It is widely accepted that the last eukaryotic common ancestor and early eukaryotes were intron-rich and intron loss dominated subsequent evolution, thus the presence of only very few introns in some modern eu...

    Authors: Min Xue, Bing Chen, Qingqing Ye, Jingru Shao, Zhangxia Lyu and Jianfan Wen

    Citation: Biology Direct 2018 13:23

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  5. Content type: Comment

    The origin of eukaryotic cells was an important transition in evolution. The factors underlying the origin and evolutionary success of the eukaryote lineage are still discussed. One camp argues that mitochondr...

    Authors: Marie Gerlitz, Michael Knopp, Nils Kapust, Joana C. Xavier and William F. Martin

    Citation: Biology Direct 2018 13:21

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  6. Content type: Hypothesis

    Mutations in the CLN3 gene lead to so far an incurable juvenile-onset neuronal ceroid lipofuscinosis (JNCL) or Batten disease that starts at the age of 4–6 years with a progressive retinopathy leading to blindnes...

    Authors: Elena K. Shematorova, Dmitry G. Shpakovski, Anna D. Chernysheva and George V. Shpakovski

    Citation: Biology Direct 2018 13:19

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  7. Content type: Review

    This essay highlights critical aspects of the plausibility of pre-Darwinian evolution. It is based on a critical review of some better-known open, far-from-equilibrium system-based scenarios supposed to explai...

    Authors: Marc Tessera

    Citation: Biology Direct 2018 13:18

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  8. Content type: Research

    Modern experimental techniques deliver data sets containing profiles of tens of thousands of potential molecular and genetic markers that can be used to improve medical diagnostics. Previous studies performed ...

    Authors: Aneta Polewko-Klim, Wojciech Lesiński, Krzysztof Mnich, Radosław Piliszek and Witold R. Rudnicki

    Citation: Biology Direct 2018 13:17

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  9. Content type: Research

    Many methods have been developed for metagenomic sequence classification, and most of them depend heavily on genome sequences of the known organisms. A large portion of sequencing sequences may be classified a...

    Authors: Yuyang Qiao, Ben Jia, Zhiqiang Hu, Chen Sun, Yijin Xiang and Chaochun Wei

    Citation: Biology Direct 2018 13:15

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  10. Content type: Research

    Despite the progress in neuroblastoma therapies the mortality of high-risk patients is still high (40–50%) and the molecular basis of the disease remains poorly known. Recently, a mathematical model was used t...

    Authors: Marta R. Hidalgo, Alicia Amadoz, Cankut Çubuk, José Carbonell-Caballero and Joaquín Dopazo

    Citation: Biology Direct 2018 13:16

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  11. Content type: Research

    Neuroblastoma is the most common pediatric malignancy with heterogeneous clinical behaviors, ranging from spontaneous regression to aggressive progression. Many studies have identified aberrations related to t...

    Authors: Chen Suo, Wenjiang Deng, Trung Nghia Vu, Mingrui Li, Leming Shi and Yudi Pawitan

    Citation: Biology Direct 2018 13:14

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  12. Content type: Opinion

    A half century of studying protein folding in vitro and modeling it in silico has not provided us with a reliable computational method to predict the native conformations of proteins de novo, let alone identif...

    Authors: Irina Sorokina and Arcady Mushegian

    Citation: Biology Direct 2018 13:13

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  13. Content type: Research

    One of the main current challenges in computational biology is to make sense of the huge amounts of multidimensional experimental data that are being produced. For instance, large cohorts of patients are often...

    Authors: Léon-Charles Tranchevent, Petr V. Nazarov, Tony Kaoma, Georges P. Schmartz, Arnaud Muller, Sang-Yoon Kim, Jagath C. Rajapakse and Francisco Azuaje

    Citation: Biology Direct 2018 13:12

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  14. Content type: Research

    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

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  15. Content type: Research

    Knowledge of the protein structure is a pre-requisite for improved understanding of molecular function. The gap in the sequence-structure space has increased in the post-genomic era. Grouping related protein s...

    Authors: Gayatri Kumar, Richa Mudgal, Narayanaswamy Srinivasan and Sankaran Sandhya

    Citation: Biology Direct 2018 13:8

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  16. Content type: Discovery notes

    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

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  17. Content type: Research

    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

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  18. Content type: Research

    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

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  19. Content type: Research

    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

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  20. Content type: Research

    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

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  21. Content type: Research

    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

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  22. Content type: Opinion

    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

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  23. Content type: Application note

    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

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  24. Content type: Research

    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

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  25. Content type: Application note

    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

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  26. Content type: Research

    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

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  27. Content type: Opinion

    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

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  28. Content type: Research

    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

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  29. Content type: Research

    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

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  30. Content type: Research

    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

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  31. Content type: Research

    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

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  32. Content type: Research

    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

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  33. Content type: Research

    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

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  34. Content type: Discovery notes

    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

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  35. Content type: Discovery notes

    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

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  36. Content type: Research

    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

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  37. Content type: Research

    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

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