The era of big data: Genome-scale modelling meets machine learning.

abstract：:Bacteria can migrate towards more suitable environments by rotating flagella that are under the control of sensory signal transduction networks. The bacterial flagellum is composed of the long helical filament functioning as a propeller, the flexible hook as a universal joint and the basal body as a rotary motor power...

journal_title：Computational and structural biotechnology journal

authors： Terahara N,Namba K,Minamino T

更新日期：2020-10-15 00:00:00

abstract：:Taxonomic differentiation among morphologically identical Ascaris species is a debatable scientific issue in the context of Ascariasis epidemiology. To explain the disease epidemiology and also the taxonomic position of different Ascaris species, genome information of infecting strains from endemic areas throughout th...

journal_title：Computational and structural biotechnology journal

authors： Das K,Chowdhury P,Ganguly S

更新日期：2015-09-04 00:00:00

abstract：:The wide application of new DNA sequencing technologies is generating vast quantities of genetic variation data at unprecedented speed. Developing methodologies to decode the pathogenicity of the variants is imperatively demanding. We hypothesized that as deleterious variants may function through disturbing structural...

journal_title：Computational and structural biotechnology journal

authors： Tam B,Sinha S,Wang SM

更新日期：2020-12-02 00:00:00

abstract：:The long noncoding RNAs (lncRNAs) are ubiquitous in organisms and play crucial role in a variety of biological processes and complex diseases. Emerging evidences suggest that lncRNAs interact with corresponding proteins to perform their regulatory functions. Therefore, identifying interacting lncRNA-protein pairs is t...

journal_title：Computational and structural biotechnology journal

authors： Yi HC,You ZH,Cheng L,Zhou X,Jiang TH,Li X,Wang YB

更新日期：2019-11-30 00:00:00

abstract：:Microbial communities organize into spatial patterns that are largely governed by interspecies interactions. This phenomenon is an important metric for understanding community functional dynamics, yet the use of spatial patterns for predicting microbial interactions is currently lacking. Here we propose supervised dee...

journal_title：Computational and structural biotechnology journal

authors： Lee JY,Sadler NC,Egbert RG,Anderton CR,Hofmockel KS,Jansson JK,Song HS

更新日期：2020-05-29 00:00:00

abstract：:BOG (Bacterium and virus analysis of Orthologous Groups) is a package for identifying groups of differentially regulated genes in the light of gene functions for various virus and bacteria genomes. It is designed to identify Clusters of Orthologous Groups (COGs) that are enriched among genes that have gone through sig...

journal_title：Computational and structural biotechnology journal

authors： Park J,Taslim C,Lin S

更新日期：2015-05-21 00:00:00

abstract：Purpose:Visceral fat is an independent risk factor for metabolic and cardiovascular disease. The study aimed to investigate the associations between gut microbiome and visceral fat. Methods:We recruited 32 obese adults and 30 healthy controls at baseline. Among the obese subjects, 14 subjects underwent laparoscopic sl...

journal_title：Computational and structural biotechnology journal

authors： Nie X,Chen J,Ma X,Ni Y,Shen Y,Yu H,Panagiotou G,Bao Y

更新日期：2020-09-20 00:00:00

abstract：:The field of machine learning has allowed researchers to generate and analyse vast amounts of data using a wide variety of methodologies. Artificial Neural Networks (ANN) are some of the most commonly used statistical models and have been successful in biomarker discovery studies in multiple disease types. This review...

journal_title：Computational and structural biotechnology journal

authors： Zafeiris D,Rutella S,Ball GR

更新日期：2018-02-21 00:00:00

abstract：:Metabonomics/metabolomics is an important science for the understanding of biological systems and the prediction of their behaviour, through the profiling of metabolites. Two technologies are routinely used in order to analyse metabolite profiles in biological fluids: nuclear magnetic resonance (NMR) spectroscopy and ...

journal_title：Computational and structural biotechnology journal

authors： Dona AC,Kyriakides M,Scott F,Shephard EA,Varshavi D,Veselkov K,Everett JR

更新日期：2016-03-09 00:00:00

abstract：:Polyketides are an important group of secondary metabolites, many of which have important industrial applications in the food and pharmaceutical industries. Polyketides are synthesized from one of three classes of enzymes differentiated by their biochemical features and product structure: type I, type II or type III p...

journal_title：Computational and structural biotechnology journal

authors： Lussier FX,Colatriano D,Wiltshire Z,Page JE,Martin VJ

更新日期：2013-02-22 00:00:00

abstract：:Buried active sites of enzymes are connected to the bulk solvent through a network of hydrophobic channels. We developed a discretized model that can accurately predict ligand transport along hydrophobic channels up to six orders of magnitude faster than any other existing method. The non-dimensional nature of the mod...

journal_title：Computational and structural biotechnology journal

authors： Escalante DE,Aksan A

更新日期：2019-06-11 00:00:00

abstract：:Coronaviruses are a group of enveloped RNA viruses that are diversely found in humans and now declared a global pandemic by the World Health Organization in March 2020. The population's susceptibility to these highly pathogenic coronaviruses has contributed to large outbreaks, evolved into public health events, and ra...

journal_title：Computational and structural biotechnology journal

authors： Singh DD,Han I,Choi EH,Yadav DK

更新日期：2020-01-01 00:00:00

abstract：:An increasing number of ABC membrane protein structures are determined by cryo-electron microscopy and X-ray crystallography, consequently identifying differences between their conformations has become an arising issue. Therefore, we propose to define standardized measures for ABC Type I exporter structure characteriz...

journal_title：Computational and structural biotechnology journal

authors： Csizmadia G,Farkas B,Spagina Z,Tordai H,Hegedűs T

更新日期：2018-10-18 00:00:00

abstract：:Lung cancer is the leading worldwide cause of cancer mortality, however, neither curative treatments nor substantial prolonged survival has been achieved, highlighting the need for investigating new proteins responsible for its development and progression. IKKα is an essential protein for cell survival and differentia...

journal_title：Computational and structural biotechnology journal

authors： Page A,Ortega A,Alameda JP,Navarro M,Paramio JM,Saiz-Pardo M,Almeida EI,Hernández P,Fernández-Aceñero MJ,García-Fernández RA,Casanova ML

更新日期：2019-02-07 00:00:00

abstract：:Although the potential advantages of clinical germline genome editing (GGE) over currently available methods are limited, the implementation of GGE in the clinic has been proposed and discussed. Ethical issues related to such an application have been extensively debated, meanwhile, seemingly less attention has been pa...

journal_title：Computational and structural biotechnology journal

authors： Niemiec E,Howard HC

更新日期：2020-03-21 00:00:00

abstract：:Traditional Chinese Medicine (TCM) has a long history of widespread clinical applications, especially in East Asia, and is becoming frequently used in Western countries. However, owing to extreme complicacy in both chemical ingredients and mechanism of action, a deep understanding of TCM is still difficult. To acceler...

journal_title：Computational and structural biotechnology journal

authors： Li B,Ma C,Zhao X,Hu Z,Du T,Xu X,Wang Z,Lin J

更新日期：2018-11-23 00:00:00

abstract：:Autism spectrum disorder (ASD) is a neurodevelopmental condition for which early identification and intervention is crucial for optimum prognosis. Our previous work showed gut Immunoglobulin A (IgA) to be significantly elevated in the gut lumen of children with ASD compared to typically developing (TD) children. Gut m...

journal_title：Computational and structural biotechnology journal

authors： Wang M,Doenyas C,Wan J,Zeng S,Cai C,Zhou J,Liu Y,Yin Z,Zhou W

更新日期：2020-12-29 00:00:00

abstract：:DNA methyltransferase 1 (DNMT1), a large multidomain enzyme, is believed to be involved in the passive transmission of genomic methylation patterns via methylation maintenance. Yet, the molecular mechanism of interaction networks underlying DNMT1 structures, dynamics, and its biological significance has yet to be full...

journal_title：Computational and structural biotechnology journal

authors： Liang Z,Zhu Y,Long J,Ye F,Hu G

更新日期：2020-03-23 00:00:00

abstract：:Neglected infectious diseases (NIDs) are a persistent cause of death and disability in low-income countries. Currently available drugs and vaccines are often ineffective, costly or associated with severe side-effects. Although the scale of research on NIDs does not reflect their disease burden, there are encouraging s...

journal_title：Computational and structural biotechnology journal

authors： Olesen OF,Ackermann M

更新日期：2017-01-19 00:00:00

abstract：:Murine models with modified gene function as a result of N-ethyl-N-nitrosourea (ENU) mutagenesis have been used to study phenotypes resulting from genetic change. This study investigated genetic factors associated with red blood cell (RBC) physiology and structural integrity that may impact on blood component storage ...

journal_title：Computational and structural biotechnology journal

authors： Kildey K,Flower RL,Tran TV,Tunningley R,Harris J,Dean MM

更新日期：2013-09-23 00:00:00

abstract：:New variants of β-1,4-galactanase from the mesophilic organism Aspergillus aculeatus were designed using the structure of β-1,4-galactanase from the thermophile organism Myceliophthora thermophila as a template. Some of the variants were generated using PROPKA 3.0, a validated pKa prediction tool, to test its usefulne...

journal_title：Computational and structural biotechnology journal

authors： Torpenholt S,De Maria L,Olsson MH,Christensen LH,Skjøt M,Westh P,Jensen JH,Lo Leggio L

更新日期：2015-04-09 00:00:00

abstract：:Recent years have witnessed a spurt of activities in the elucidation of the molecular function of a class of proteins with great potential in biomass degradation. GH61 proteins are of fungal origin and were originally classified in family 61 of the glycoside hydrolases. From the beginning they were strongly suspected ...

journal_title：Computational and structural biotechnology journal

authors： Lo Leggio L,Welner D,De Maria L

更新日期：2012-11-30 00:00:00

abstract：:Motility studies of cells often rely on computer software that analyzes time-lapse recorded movies and establishes cell trajectories fully automatically. This raises the question of reproducibility of results, since different programs could yield significantly different results of such automated analysis. The fact tha...

journal_title：Computational and structural biotechnology journal

authors： Grădinaru C,Lopacińska JM,Huth J,Kestler HA,Flyvbjerg H,Mølhave K

更新日期：2012-11-21 00:00:00

abstract：:We report a study of the interaction between internalin A (inlA) and human or murine E-cadherin (Ecad). inlA is used by Listeria monocytogenes to internalize itself into host cell, but the bacterium is unable to invade murine cells, which has been attributed to the difference in sequence between hEcad and mEcad. Using...

journal_title：Computational and structural biotechnology journal

authors： Genheden S,Eriksson LA

更新日期：2013-12-15 00:00:00

abstract：:The impacts of environmental chemicals on the decline of kidney function have been suggested by a limited number of statistical and animal studies. Thus, those exposures may be modifiable risk factors for chronic kidney disease. Some of the chemicals, such as Perfluoroalkyl acid (PFA), are pervasive throughout our env...

journal_title：Computational and structural biotechnology journal

authors： Zhao J,Hinton P,Chen J,Jiang J

更新日期：2019-12-17 00:00:00

abstract：:Recent years have witnessed the tendency of measuring a biological sample on multiple omics scales for a comprehensive understanding of how biological activities on varying levels are perturbed by genetic variants, environments, and their interactions. This new trend raises substantial challenges to data integration a...

journal_title：Computational and structural biotechnology journal

authors： Baldwin E,Han J,Luo W,Zhou J,An L,Liu J,Zhang HH,Li H

更新日期：2020-03-05 00:00:00

abstract：:Biomimetic design of new materials uses nature as antetype, learning from billions of years of evolution. This work emphasizes the mechanical and tribological properties of skin, combining both hardness and wear resistance of its surface (the stratum corneum) with high elasticity of the bulk (epidermis, dermis, hypode...

journal_title：Computational and structural biotechnology journal

authors： Lackner JM,Waldhauser W,Major L,Teichert C,Hartmann P

更新日期：2013-05-08 00:00:00

abstract：:Inflammation shifts the hemostatic mechanisms in favor of thrombosis. Upon tissue damage or infection, a sudden increase of extracellular ATP occurs, that might contribute to the crosstalk between inflammation and thrombosis. On platelets, P2X1 receptors act to amplify platelet activation and aggregation induced by ot...

journal_title：Computational and structural biotechnology journal

authors： Oury C,Lecut C,Hego A,Wéra O,Delierneux C

更新日期：2014-11-28 00:00:00

abstract：:ChIP-seq experiments identify genome-wide profiles of DNA-binding molecules including transcription factors, enzymes and epigenetic marks. Biological replicates are critical for reliable site discovery and are required for the deposition of data in the ENCODE and modENCODE projects. While early reports suggested two r...

journal_title：Computational and structural biotechnology journal

authors： Yang Y,Fear J,Hu J,Haecker I,Zhou L,Renne R,Bloom D,McIntyre LM

更新日期：2014-01-31 00:00:00

abstract：:Allosteric modulation provides an effective avenue for selective and potent enzyme inhibition. Here, we summarize and critically discuss recent advances on the mechanisms of allosteric partial agonists for three representative signalling enzymes activated by cyclic nucleotides: the cAMP-dependent protein kinase (PKA),...

journal_title：Computational and structural biotechnology journal

authors： Byun JA,VanSchouwen B,Akimoto M,Melacini G

更新日期：2020-11-11 00:00:00