Abstract:
:Deep learning of artificial neural networks has become the de facto standard approach to solving data analysis problems in virtually all fields of science and engineering. Also in biology and medicine, deep learning technologies are fundamentally transforming how we acquire, process, analyze, and interpret data, with potentially far-reaching consequences for healthcare. In this mini-review, we take a bird's-eye view at the past, present, and future developments of deep learning, starting from science at large, to biomedical imaging, and bioimage analysis in particular.
journal_name
Comput Struct Biotechnol Jjournal_title
Computational and structural biotechnology journalauthors
Meijering Edoi
10.1016/j.csbj.2020.08.003subject
Has Abstractpub_date
2020-08-07 00:00:00pages
2312-2325issn
2001-0370pii
S2001-0370(20)30356-1journal_volume
18pub_type
杂志文章,评审abstract::Post-transcriptional RNA modification occurs on all types of RNA and plays a vital role in regulating every aspect of RNA function. Thanks to the development of high-throughput sequencing technologies, transcriptome-wide profiling of RNA modifications has been made possible. With the accumulation of a large number of ...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章,评审
doi:10.1016/j.csbj.2020.06.010
更新日期:2020-06-13 00:00:00
abstract::Metabolomics is a relatively new high-throughput technology that aims at measuring all endogenous metabolites within a biological sample in an unbiased fashion. The resulting metabolic profiles may be regarded as functional signatures of the physiological state, and have been shown to comprise effects of genetic regul...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章,评审
doi:10.5936/csbj.201301009
更新日期:2013-03-22 00:00:00
abstract::Biomedical research and clinical decision depend increasingly on scientific evidence realized by a number of authoritative databases, mostly public and continually enriched via peer scientific contributions. Given the dynamic nature of biomedical evidence data and their usage in the sensitive domain of biomedical scie...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章
doi:10.1016/j.csbj.2018.08.002
更新日期:2018-08-17 00:00:00
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
pub_type: 杂志文章,评审
doi:10.1016/j.csbj.2020.10.009
更新日期:2020-10-15 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
pub_type: 杂志文章
doi:10.1016/j.csbj.2019.02.003
更新日期:2019-02-07 00:00:00
abstract::Functional annotation transfer across multi-gene family orthologs can lead to functional misannotations. We hypothesised that co-expression network will help predict functional orthologs amongst complex homologous gene families. To explore the use of transcriptomic data available in public domain to identify functiona...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章
doi:10.1016/j.csbj.2017.08.002
更新日期:2017-08-26 00:00:00
abstract::With next generation sequencing thousands of virus and viral vector integration genome targets are now under investigation to uncover specific integration preferences and to define clusters of integration, termed common integration sites (CIS), that may allow to assess gene therapy safety or to detect disease related ...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章
doi:10.1016/j.csbj.2015.10.006
更新日期:2015-11-30 00:00:00
abstract::Target based chemical screens are a mainstay of modern drug discovery, but the effectiveness of this reductionist approach is being questioned in light of declines in pharmaceutical R & D efficiency. In recent years, phenotypic screens have gained increasing acceptance as a complementary/alternative approach to early ...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章,评审
doi:10.1016/j.csbj.2016.09.001
更新日期:2016-09-18 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
pub_type: 杂志文章,评审
doi:10.1016/j.csbj.2020.10.026
更新日期:2020-11-11 00:00:00
abstract::The human ATP-binding cassette B5 (ABCB5) transporter, a member of the ABC transporter superfamily, is linked to chemoresistance in tumour cells by drug effluxion. However, little is known about its structure and drug-binding sites. In this study, we generated an atomistic model of the full-length human ABCB5 transpor...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章
doi:10.1016/j.csbj.2020.12.042
更新日期:2020-12-30 00:00:00
abstract::RNA splicing may generate different kinds of splice junctions, such as linear, back-splice and fusion junctions. Only a limited number of programs are available for detection and quantification of splice junctions. Here, we present Assembling Splice Junctions Analysis (ASJA), a software package that identifies and cha...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章
doi:10.1016/j.csbj.2019.08.001
更新日期:2019-08-07 00:00:00
abstract::Homology modeling is a method for building protein 3D structures using protein primary sequence and utilizing prior knowledge gained from structural similarities with other proteins. The homology modeling process is done in sequential steps where sequence/structure alignment is optimized, then a backbone is built and ...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章,评审
doi:10.1016/j.csbj.2020.11.007
更新日期:2020-11-14 00:00:00
abstract:Purpose:The goal of this study is to set an empirical baseline to map the structure-function relation of the antigens from the commercialized vaccine products. Methods:To study the structural changes of protein antigens after adsorption several analytical tools including DLS, FTIR, Fluorescence, LD, and SEM have been ...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章
doi:10.1016/j.csbj.2018.11.006
更新日期:2018-11-29 00:00:00
abstract::RNA-Seq was used to examine the microbial, eukaryotic, and viral communities in water catchments ('tanks') formed by tropical bromeliads from Costa Rica. In total, transcripts with taxonomic affiliation to a wide array of bacteria, archaea, and eukaryotes, were observed, as well as RNA-viruses that appeared related to...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章
doi:10.1016/j.csbj.2014.12.001
更新日期:2014-12-13 00:00:00
abstract::Microsatellite instability (MSI) is a genomic property of the cancers with defective DNA mismatch repair and is a useful marker for cancer diagnosis and treatment in diverse cancer types. In particular, MSI has been associated with the active immune checkpoint blockade therapy response in cancer. Most of computational...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章
doi:10.1016/j.csbj.2020.03.007
更新日期:2020-03-19 00:00:00
abstract::The high mutation rate in retroviruses is one of the leading causes of drug resistance. In human immunodeficiency virus type-1 (HIV-1), synergistic mutations in its protease and the protease substrate - the Group-specific antigen (Gag) polyprotein - work together to confer drug resistance against protease inhibitors a...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章
doi:10.1016/j.csbj.2020.12.022
更新日期:2020-12-23 00:00:00
abstract::Alternative splicing contributes to the majority of protein diversity in higher eukaryotes by allowing one gene to generate multiple distinct protein isoforms. It adds another regulation layer of gene expression. Up to 95% of human multi-exon genes undergo alternative splicing to encode proteins with different functio...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章,评审
doi:10.1016/j.csbj.2020.12.009
更新日期:2020-12-24 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
pub_type: 杂志文章
doi:10.1016/j.csbj.2019.11.004
更新日期:2019-11-30 00:00:00
abstract::Runs of Homozygosity (RoHs) are popular among geneticists as the footprint of demographic processes, evolutionary forces and inbreeding in shaping our genome, and are known to confer risk of Mendelian and complex diseases. Notwithstanding growing interest in their study, there is unmet need for reliable and rapid meth...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章
doi:10.1016/j.csbj.2020.07.003
更新日期:2020-07-14 00:00:00
abstract:Purpose:Mutation-induced variation of protein-ligand binding affinity is the key to many genetic diseases and the emergence of drug resistance, and therefore predicting such mutation impacts is of great importance. In this work, we aim to predict the mutation impacts on protein-ligand binding affinity using efficient s...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章
doi:10.1016/j.csbj.2020.02.007
更新日期:2020-02-20 00:00:00
abstract::Across the eubacteria, antigenic variation has emerged as a strategy to evade host immunity. However, phenotypic variation in some of these antigens also allows the bacteria to exploit variable host niches as well. The specific mechanisms are not shared-derived characters although there is considerable convergent evol...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章,评审
doi:10.1016/j.csbj.2015.07.002
更新日期:2015-07-26 00:00:00
abstract::Computationally driven engineering of proteins aims to allow them to withstand an extended range of conditions and to mediate modified or novel functions. Therefore, it is crucial to the biotechnological industry, to biomedicine and to afford new challenges in environmental sciences, such as biocatalysis for green che...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章,评审
doi:10.1016/j.csbj.2020.06.029
更新日期:2020-06-30 00:00:00
abstract::Rab5 is a small GTPase that plays a crucial role in oncogenic signal transduction, which was considered as an attractive target for cancer therapy. Rapid GDP/GTP exchange in the packet of Rab5 sustains its high activity for promoting cancer progression. However, Rab5 currently remains undruggable due to the lack of sp...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章
doi:10.1016/j.csbj.2020.11.033
更新日期:2020-11-30 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
pub_type: 杂志文章
doi:10.1016/j.csbj.2018.11.002
更新日期:2018-11-23 00:00:00
abstract::Tolypocladium guangdongense has a similar metabolite profile to Ophiocordyceps sinensis, a highly regarded fungus used for traditional Chinese medicine with high nutritional and medicinal value. Although the genome sequence of T. guangdongense has been reported, relatively little is known about the regulatory networks...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章
doi:10.1016/j.csbj.2020.07.014
更新日期:2020-07-25 00:00:00
abstract::One of the long-standing challenges in biology is to understand how non-synonymous single nucleotide polymorphisms (nsSNPs) change protein structure and further affect their function. While it is impractical to solve all the mutated protein structures experimentally, it is quite feasible to model the mutated structure...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章
doi:10.1016/j.csbj.2015.09.002
更新日期:2015-09-30 00:00:00
abstract::Infectious diseases, including vector-borne diseases transmitted by arthropods, are a leading cause of morbidity and mortality worldwide. In the era of big data, addressing broad-scale, fundamental questions regarding the complex dynamics of these diseases will increasingly require the integration of diverse datasets ...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章,评审
doi:10.1016/j.csbj.2020.06.031
更新日期:2020-06-25 00:00:00
abstract::The human nasal microbiome is characterized by biodiversity and undergoes changes during the span of life. In granulomatosis with polyangiitis (GPA), the persistent nasal colonization by Staphylococcus aureus (S. aureus) assessed by culture-based detection methods has been associated with increased relapse frequency. ...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章,评审
doi:10.1016/j.csbj.2020.12.031
更新日期:2020-12-27 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
pub_type: 杂志文章
doi:10.1016/j.csbj.2015.03.010
更新日期:2015-04-09 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
pub_type: 杂志文章,评审
doi:10.1016/j.csbj.2020.11.011
更新日期:2020-01-01 00:00:00