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  1. Accumulating evidence suggests that the human microbiome impacts individual and public health. City subway systems are human-dense environments, where passengers often exchange microbes. The MetaSUB project pa...

    Authors: Chengsheng Zhu, Maximilian Miller, Nick Lusskin, Yannick Mahlich, Yanran Wang, Zishuo Zeng and Yana Bromberg

    Citation: Biology Direct 2019 14:19

    Content type: Research

    Published on:

  3. Determining the factors involved in the likelihood of a gene being under adaptive selection is still a challenging goal in Evolutionary Biology. Here, we perform an evolutionary analysis of the human metabolic...

    Authors: Begoña Dobon, Ludovica Montanucci, Juli Peretó, Jaume Bertranpetit and Hafid Laayouni

    Citation: Biology Direct 2019 14:17

    Content type: Research

    Published on:

  4. Neuroblastoma is one of the most common types of pediatric cancer. In current neuroblastoma prognosis, patients can be stratified into high- and low-risk groups. Generally, more than 90% of the patients in the...

    Authors: Yatong Han, Xiufen Ye, Chao Wang, Yusong Liu, Siyuan Zhang, Weixing Feng, Kun Huang and Jie Zhang

    Citation: Biology Direct 2019 14:16

    Content type: Research

    Published on:

  5. The availability of hundreds of city microbiome profiles allows the development of increasingly accurate predictors of the origin of a sample based on its microbiota composition. Typical microbiome studies inv...

    Authors: Carlos S. Casimiro-Soriguer, Carlos Loucera, Javier Perez Florido, Daniel López-López and Joaquin Dopazo

    Citation: Biology Direct 2019 14:15

    Content type: Research

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  11. CB2 (cannabinoid receptor 2) agonists have been shown to exert anti-tumor activities in different tumor types. However, there is no study exploring the role of MDA19 (a novel CB2 agonist) in tumors. In this study...

    Authors: Mei Rao, Dongfeng Chen, Peng Zhan and Jianqing Jiang

    Citation: Biology Direct 2019 14:9

    Content type: Research

    Published on:

  12. Integrating the rich information from multi-omics data has been a popular approach to survival prediction and bio-marker identification for several cancer studies. To facilitate the integrative analysis of mul...

    Authors: So Yeon Kim, Hyun-Hwan Jeong, Jaesik Kim, Jeong-Hyeon Moon and Kyung-Ah Sohn

    Citation: Biology Direct 2019 14:8

    Content type: Research

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  13. Rubber tree (Hevea brasiliensis) acts as an important tropic economic crop and rubber tree anthracnose, mainly caused by Colletotrichum gloeosporioides, is one of the most common fungal disease, which leads to se...

    Authors: Hongyan Yin, Xiaodong Zhang, Bei Zhang, Hongli Luo and Chaozu He

    Citation: Biology Direct 2019 14:7

    Content type: Research

    Published on:

  14. Splice sites prediction has been a long-standing problem in bioinformatics. Although many computational approaches developed for splice site prediction have achieved satisfactory accuracy, further improvement ...

    Authors: Ying Zeng, Hongjie Yuan, Zheming Yuan and Yuan Chen

    Citation: Biology Direct 2019 14:6

    Content type: Research

    Published on:

  15. In the recent years, genomic and pan-genomic studies have become increasingly important. Culturomics allows to study human microbiota through the use of different culture conditions, coupled with a method of r...

    Authors: Aurélia Caputo, Pierre-Edouard Fournier and Didier Raoult

    Citation: Biology Direct 2019 14:5

    Content type: Review

    Published on:

  16. More than 90% of neuroblastoma patients are cured in the low-risk group while only less than 50% for those with high-risk disease can be cured. Since the high-risk patients still have poor outcomes, we need mo...

    Authors: Yatong Han, Xiufen Ye, Jun Cheng, Siyuan Zhang, Weixing Feng, Zhi Han, Jie Zhang and Kun Huang

    Citation: Biology Direct 2019 14:4

    Content type: Research

    Published on:

  17. Some tumor cells can evolve into transmissible parasites. Notable examples include the Tasmanian devil facial tumor disease, the canine transmissible venereal tumor and transmissible cancers of mollusks. We pr...

    Authors: A. Y. Panchin, V. V. Aleoshin and Y. V. Panchin

    Citation: Biology Direct 2019 14:3

    Content type: Hypothesis

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  19. Protein-protein interactions are crucial for normal biological processes and to regulate cellular reactions that affect gene expression and function. Several previous studies have emphasized the roles of resid...

    Authors: Srinivasan Jayashree, Pavalam Murugavel, Ramanathan Sowdhamini and Narayanaswamy Srinivasan

    Citation: Biology Direct 2019 14:1

    Content type: Research

    Published on:

  20. Genetic parasites are ubiquitous satellites of cellular life forms most of which host a variety of mobile genetic elements including transposons, plasmids and viruses. Theoretical considerations and computer s...

    Authors: Faina Berezovskaya, Georgy P. Karev, Mikhail I. Katsnelson, Yuri I. Wolf and Eugene V. Koonin

    Citation: Biology Direct 2018 13:27

    Content type: Research

    Published on:

  21. 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

    Content type: Commentary

    Published on:

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

  22. 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

    Content type: Research

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  23. 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

    Content type: Research

    Published on:

  24. 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

    Content type: Research

    Published on:

  26. 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

    Content type: Comment

    Published on:

    The Commentary to this article has been published in Biology Direct 2018 13:26

  28. 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

    Content type: Hypothesis

    Published on:

  29. 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

    Content type: Review

    Published on:

  30. 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

    Content type: Research

    Published on:

  31. 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

    Content type: Research

    Published on:

  32. 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

    Content type: Research

    Published on:

  33. 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

    Content type: Research

    Published on:

  34. 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

    Content type: Opinion

    Published on:

  35. 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

    Content type: Research

    Published on:

  38. 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

    Content type: Research

    Published on:

  39. 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

    Content type: Research

    Published on:

  40. 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

    Content type: Discovery notes

    Published on:

  41. 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

    Content type: Research

    Published on:

  42. 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

    Content type: Research

    Published on:

  43. 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

    Content type: Research

    Published on:

  44. 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

    Content type: Research

    Published on:

  45. 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

    Content type: Research

    Published on:

  47. 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

    Content type: Opinion

    Published on:

  49. 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

    Content type: Application note

    Published on:

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