Abstract:
:Understanding the pathogenesis of disease is instrumental in delineating its progression mechanisms and for envisioning ways to counteract it. In the process, animal models represent invaluable tools for identifying disease-related loci and their genetic components. Amongst them, the laboratory rat is used extensively in the study of many conditions and disorders. The Rat Genome Database (RGD-http://rgd.mcw.edu) has been established to house rat genetic, genomic and phenotypic data. Since its inception, it has continually expanded the depth and breadth of its content. Currently, in addition to rat genes, QTLs and strains, RGD houses mouse and human genes and QTLs and offers pertinent associated data, acquired through manual literature curation and imported via pipelines. A collection of controlled vocabularies and ontologies is employed for the standardized extraction and provision of biological data. The vocabularies/ontologies allow the capture of disease and phenotype associations of rat strains and QTLs, as well as disease and pathway associations of rat, human and mouse genes. A suite of tools enables the retrieval, manipulation, viewing and analysis of data. Genes associated with particular conditions or with altered networks underlying disease pathways can be retrieved. Genetic variants in humans or in sequenced rat strains can be searched and compared. Lists of rat strains and species-specific genes and QTLs can be generated for selected ontology terms and then analyzed, downloaded or sent to other tools. From many entry points, data can be accessed and results retrieved. To illustrate, diabetes is used as a case study to initiate and embark upon an exploratory journey.
journal_name
Comput Struct Biotechnol Jjournal_title
Computational and structural biotechnology journalauthors
Petri V,Hayman GT,Tutaj M,Smith JR,Laulederkind S,Wang SJ,Nigam R,De Pons J,Shimoyama M,Dwinell MRdoi
10.1016/j.csbj.2015.11.006subject
Has Abstractpub_date
2015-11-26 00:00:00pages
35-48issn
2001-0370pii
S2001-0370(15)00053-7journal_volume
14pub_type
杂志文章abstract::The fungi kingdom is composed of eukaryotic heterotrophs, which are responsible for balancing the ecosystem and play a major role as decomposers. They also produce a vast diversity of secondary metabolites, which have antibiotic or pharmacological properties. However, our lack of knowledge of gene function in fungi pr...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章
doi:10.1016/j.csbj.2020.11.019
更新日期:2020-11-20 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::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
pub_type: 杂志文章
doi:10.1016/j.csbj.2020.12.012
更新日期:2020-12-29 00:00:00
abstract::Membrane fatty acid desaturases are a diverse superfamily of enzymes that catalyze the introduction of double bonds into fatty acids. They are essential in a range of metabolic processes, such as the production of omega-3 fatty acids. However, our structure-function understanding of this superfamily is still developin...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章
doi:10.1016/j.csbj.2016.08.003
更新日期:2016-09-12 00:00:00
abstract::Huntington's disease is a progressive neurodegenerative disorder characterized by motor disturbances, cognitive decline, and neuropsychiatric symptoms. In this study, we utilized network-based analysis in an attempt to explore and understand the underlying molecular mechanism and to identify critical molecular players...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章
doi:10.1016/j.csbj.2016.02.001
更新日期:2016-02-10 00:00:00
abstract:Motivation:With Next Generation Sequencing becoming more affordable every year, NGS technologies asserted themselves as the fastest and most reliable way to detect Single Nucleotide Variants (SNV) and Copy Number Variations (CNV) in cancer patients. These technologies can be used to sequence DNA at very high depths thu...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章
doi:10.1016/j.csbj.2020.08.011
更新日期:2020-08-27 00:00:00
abstract::Bacteria sense temporal changes in extracellular stimuli via sensory signal transducers and move by rotating flagella towards into a favorable environment for their survival. Each flagellum is a supramolecular motility machine consisting of a bi-directional rotary motor, a universal joint and a helical propeller. The ...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章,评审
doi:10.1016/j.csbj.2019.07.020
更新日期:2019-07-31 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
abstract::Technical progress in the field of next-generation sequencing, mass spectrometry and bioinformatics facilitates the study of highly complex biological samples such as taxonomic and functional characterization of microbial communities that virtually colonize all present ecological niches. Compared to the structural inf...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章,评审
doi:10.1016/j.csbj.2014.12.005
更新日期:2014-12-24 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
pub_type: 杂志文章,评审
doi:10.5936/csbj.201210020
更新日期:2013-02-22 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::A fundamental question in biology is how complex structures are maintained after their initial specification. We address this question by reviewing the role of the Hox gene Abd-B in Drosophila testis organogenesis, which proceeds through embryonic, larval and pupal stages to reach maturation in adult stages. The data ...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章,评审
doi:10.1016/j.csbj.2015.01.001
更新日期:2015-01-21 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
pub_type: 杂志文章
doi:10.1016/j.csbj.2020.11.041
更新日期:2020-12-02 00:00:00
abstract::Protein-protein interactions (PPIs) play a key role in numerous biological processes. Many efforts have been undertaken to develop PPI modulators for therapeutic applications; however, to date, most of the peptide binders designed to target PPIs are derived from native binding helices or using the native helix binding...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章
doi:10.1016/j.csbj.2019.11.001
更新日期:2019-11-11 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::MicroRNAs (miRNAs) are well-studied small noncoding RNAs involved in post-transcriptional gene regulation in a wide range of organisms, including mammals. Their function is mediated by base pairing with their target RNAs. Although many features required for miRNA-mediated repression have been described, the identifica...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章,评审
doi:10.1016/j.csbj.2020.02.019
更新日期:2020-03-05 00:00:00
abstract::The use of herbs to treat various human diseases has been recorded for thousands of years. In Asia's current medical system, numerous herbal formulas have been repeatedly verified to confirm their effectiveness in different periods, which is a great resource for drug innovation and discovery. Through the mining of the...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章
doi:10.1016/j.csbj.2020.11.036
更新日期:2020-12-04 00:00:00
abstract::The emergence of recent SARS-CoV-2 has become a global health issue. This single-stranded positive-sense RNA virus is continuously spreading with increasing morbidities and mortalities. The proteome of this virus contains four structural and sixteen nonstructural proteins that ensure the replication of the virus in th...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章
doi:10.1016/j.csbj.2020.08.006
更新日期:2020-01-01 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 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::As knowledge of the genetics behind inflammatory bowel disease (IBD) has continually improved, there has been a demand for methods that can use this data in a clinically significant way. Genome-wide association analyses for IBD have identified 232 risk genetic loci for the disorder. While identification of these risk ...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章
doi:10.1016/j.csbj.2019.01.001
更新日期:2019-01-07 00:00:00
abstract::This mini review addresses recent developments in computational enzyme design. Successful protocols as well as known issues and limitations are discussed from an energetic perspective. It will be argued that improved results can be obtained by including a dynamic treatment in the design protocol. Finally, a molecular ...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章,评审
doi:10.5936/csbj.201209009
更新日期:2012-10-23 00:00:00
abstract::Human bodies are colonized by trillions of microorganisms, which are often referred to as human microbiota and play important roles in human health. Next generation sequencing studies have established links between the genetic content of human microbiota and various human diseases. However, it remains largely unknown ...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章,评审
doi:10.1016/j.csbj.2019.09.010
更新日期:2019-10-25 00:00:00
abstract::Interactions between their transmembrane domains (TMDs) frequently support the assembly of single-pass membrane proteins to non-covalent complexes. Yet, the TMD-TMD interactome remains largely uncharted. With a view to predicting homotypic TMD-TMD interfaces from primary structure, we performed a systematic analysis o...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章
doi:10.1016/j.csbj.2020.09.035
更新日期:2020-10-07 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
pub_type: 杂志文章,评审
doi:10.5936/csbj.201209019
更新日期:2012-11-30 00:00:00
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::Basic chemometric methods for making empirical regression models for QSPR/QSAR are briefly described from a user's point of view. Emphasis is given to PLS regression, simple variable selection and a careful and cautious evaluation of the performance of PLS models by repeated double cross validation (rdCV). A demonstra...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章,评审
doi:10.5936/csbj.201302007
更新日期:2013-03-02 00:00:00
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 ...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章,评审
doi:10.1016/j.csbj.2020.08.003
更新日期:2020-08-07 00:00:00
abstract::The COVID-19 pandemic has substantially stressed health care systems globally, subsequently reducing cancer care services and delaying treatments. Pediatric populations infected by COVID-19 have shown mild clinical symptoms compared to adults, perhaps due to decreased susceptibility. Several scientific societies and g...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章,评审
doi:10.1016/j.csbj.2021.01.005
更新日期:2021-01-12 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