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  1. Patients diagnosed as diffuse large B cell lymphoma (DLBCL) with CD5 positive normally have a worse outcome and poorly respond to the regulatory treatment strategy.

    Authors: Qingyuan Qu, Ying Li, Xiaosheng Fang, Lingyan Zhang, Chao Xue, Xueling Ge, Xin Wang and Yujie Jiang
    Citation: Biology Direct 2019 14:23
  2. Recently high-throughput technologies have been massively used alongside clinical tests to study various types of cancer. Data generated in such large-scale studies are heterogeneous, of different types and fo...

    Authors: Iliyan Mihaylov, Maciej Kańduła, Milko Krachunov and Dimitar Vassilev
    Citation: Biology Direct 2019 14:22
  3. Metaproteomics allows to decipher the structure and functionality of microbial communities. Despite its rapid development, crucial steps such as the creation of standardized protein search databases and reliab...

    Authors: Johannes Werner, Augustin Géron, Jules Kerssemakers and Sabine Matallana-Surget
    Citation: Biology Direct 2019 14:21
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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

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

  18. 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
  19. 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
  20. 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
  21. 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

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

  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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
  36. 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
  37. 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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