Agents in bioinformatics, computational and systems biology.

abstract：:This Briefing reviews the widely used, currently active, up-to-date databases derived from the worldwide Protein Data Bank (PDB) to facilitate browsing, finding and exploring its entries. These databases contain visualization and analysis tools tailored to specific kinds of molecules and interactions, often including ...

journal_title：Briefings in bioinformatics

authors： Abriata LA

更新日期：2017-07-01 00:00:00

abstract：:Genomic data hold salient information about the characteristics of a living organism. Throughout the past decade, pinnacle developments have given us more accurate and inexpensive methods to retrieve genome sequences of humans. However, with the advancement of genomic research, there is a growing privacy concern regar...

journal_title：Briefings in bioinformatics

authors： Aziz MMA,Sadat MN,Alhadidi D,Wang S,Jiang X,Brown CL,Mohammed N

更新日期：2019-05-21 00:00:00

abstract：:Despite The Central Dogma states the destiny of gene as 'DNA makes RNA and RNA makes protein', the nucleic acids not only store and transmit genetic information but also, surprisingly, join in intracellular vital movement as a regulator of gene expression. Bioinformatics has contributed to knowledge for a series of em...

journal_title：Briefings in bioinformatics

authors： Zhang S,Zhou Y,Wang Y,Wang Z,Xiao Q,Zhang Y,Lou Y,Qiu Y,Zhu F

更新日期：2020-04-06 00:00:00

abstract：:The bipartite network representation of the drug-target interactions (DTIs) in a biosystem enhances understanding of the drugs' multifaceted action modes, suggests therapeutic switching for approved drugs and unveils possible side effects. As experimental testing of DTIs is costly and time-consuming, computational pre...

journal_title：Briefings in bioinformatics

authors： Durán C,Daminelli S,Thomas JM,Haupt VJ,Schroeder M,Cannistraci CV

更新日期：2018-11-27 00:00:00

abstract：:In view of great difficulties in the pathogenesis analysis of Alzheimer's disease (AD) presently, profiling the modifiable risk factors is crucial for early detection and intervention of AD. However, the causal associations among them have yet to be identified, and the effective integration and application of these da...

journal_title：Briefings in bioinformatics

authors： Wang Z,Meng L,Liu H,Shen L,Ji HF

更新日期：2020-09-21 00:00:00

abstract：:Drug-drug interactions (DDIs) constitute an important concern in drug development and postmarketing pharmacovigilance. They are considered the cause of many adverse drug effects exposing patients to higher risks and increasing public health system costs. Methods to follow-up and discover possible DDIs causing harm to ...

journal_title：Briefings in bioinformatics

authors： Vilar S,Friedman C,Hripcsak G

更新日期：2018-09-28 00:00:00

abstract：:Prognostic tests using expression profiles of several dozen genes help provide treatment choices for prostate cancer (PCa). However, these tests require improvement to meet the clinical need for resolving overtreatment, which continues to be a pervasive problem in PCa management. Genomic selection (GS) methodology, wh...

journal_title：Briefings in bioinformatics

authors： Li R,Wang S,Cui Y,Qu H,Chater JM,Zhang L,Wei J,Wang M,Xu Y,Yu L,Lu J,Feng Y,Zhou R,Huang Y,Ma R,Zhu J,Zhong W,Jia Z

更新日期：2020-09-08 00:00:00

abstract：:As one of the most important fundamental problems in protein sequence analysis, protein remote homology detection is critical for both theoretical research (protein structure and function studies) and real world applications (drug design). Although several computational predictors have been proposed, their detection p...

journal_title：Briefings in bioinformatics

authors： Liu B,Jiang S,Zou Q

更新日期：2018-11-07 00:00:00

abstract：BACKGROUND:Whole genome sequencing (WGS) is increasingly used for Mycobacterium tuberculosis (Mtb) research. Countries with the highest tuberculosis (TB) burden face important challenges to integrate WGS into surveillance and research. METHODS:We assessed the global status of Mtb WGS and developed a 3-week training co...

journal_title：Briefings in bioinformatics

authors： Rivière E,Heupink TH,Ismail N,Dippenaar A,Clarke C,Abebe G,Heusden P,Warren R,Meehan CJ,Van Rie A

更新日期：2020-10-03 00:00:00

abstract：:As the number of completely sequenced genomes rapidly increases, including now the complete Human Genome sequence, the post-genomic problems of genome-scale protein structure determination and the issue of gene function identification become ever more pressing. In fact, these problems can be seen as interrelated in th...

journal_title：Briefings in bioinformatics

authors： Jones DT

更新日期：2001-05-01 00:00:00

abstract：:Since the 1st discovery of transcriptional enhancers in 1981, their textbook definition has remained largely unchanged in the past 37 years. With the emergence of high-throughput assays and genome editing, which are switching the paradigm from bottom-up discovery and testing of individual enhancers to top-down profili...

journal_title：Briefings in bioinformatics

authors： Ho EY,Cao Q,Gu M,Chan RW,Wu Q,Gerstein M,Yip KY

更新日期：2020-05-21 00:00:00

abstract：:A class-imbalanced classifier is a decision rule to predict the class membership of new samples from an available data set where the class sizes differ considerably. When the class sizes are very different, most standard classification algorithms may favor the larger (majority) class resulting in poor accuracy in the ...

journal_title：Briefings in bioinformatics

authors： Lin WJ,Chen JJ

更新日期：2013-01-01 00:00:00

abstract：:Identification of new drug-target interactions (DTIs) is an important but a time-consuming and costly step in drug discovery. In recent years, to mitigate these drawbacks, researchers have sought to identify DTIs using computational approaches. However, most existing methods construct drug networks and target networks...

journal_title：Briefings in bioinformatics

authors： Zhao T,Hu Y,Valsdottir LR,Zang T,Peng J

更新日期：2020-05-04 00:00:00

abstract：:Protein dynamics is central to all biological processes, including signal transduction, cellular regulation and biological catalysis. Among them, in-depth exploration of ligand-driven protein dynamics contributes to an optimal understanding of protein function, which is particularly relevant to drug discovery. Hence, ...

journal_title：Briefings in bioinformatics

authors： Yang JF,Wang F,Chen YZ,Hao GF,Yang GF

更新日期：2020-12-01 00:00:00

abstract：:Nucleosomes contribute to compacting the genome into the nucleus and regulate the physical access of regulatory proteins to DNA either directly or through the epigenetic modifications of the histone tails. Precise mapping of nucleosome positioning across the genome is, therefore, essential to understanding the genome ...

journal_title：Briefings in bioinformatics

authors： Quintales L,Vázquez E,Antequera F

更新日期：2015-07-01 00:00:00

abstract：:Biologists very often use enrichment methods based on statistical hypothesis tests to identify gene properties that are significantly over-represented in a given set of genes of interest, by comparison with a 'background' set of genes. These enrichment methods, although based on rigorous statistical foundations, are n...

journal_title：Briefings in bioinformatics

authors： Fabris F,Palmer D,de Magalhães JP,Freitas AA

更新日期：2020-05-21 00:00:00

abstract：:SARS-CoV-2 is an intensively investigated virus from the order Nidovirales (Coronaviridae family) that causes COVID-19 disease in humans. Through enormous scientific effort, thousands of viral strains have been sequenced to date, thereby creating a strong background for deep bioinformatics studies of the SARS-CoV-2 ge...

journal_title：Briefings in bioinformatics

authors： Goswami P,Bartas M,Lexa M,Bohálová N,Volná A,Červeň J,Červeňová V,Pečinka P,Špunda V,Fojta M,Brázda V

更新日期：2020-12-21 00:00:00

abstract：:The number of bioinformatics tools and resources that support molecular and cell biology approaches is continuously expanding. Moreover, systems and network biology analyses are accompanied more and more by integrated bioinformatics methods. Traditional information-centered university teaching methods often fail, as (...

journal_title：Briefings in bioinformatics

authors： Korcsmaros T,Dunai ZA,Vellai T,Csermely P

更新日期：2013-09-01 00:00:00

abstract：:Gene expression data have played an essential role in many biomedical studies. When the number of genes is large and sample size is limited, there is a 'lack of information' problem, leading to low-quality findings. To tackle this problem, both horizontal and vertical data integrations have been developed, where verti...

journal_title：Briefings in bioinformatics

authors： Wu M,Yi H,Ma S

更新日期：2020-08-14 00:00:00

abstract：:The contribution of transposable elements (TEs) to genome structure and evolution as well as their impact on genome sequencing, assembly, annotation and alignment has generated increasing interest in developing new methods for their computational analysis. Here we review the diversity of innovative approaches to ident...

journal_title：Briefings in bioinformatics

authors： Bergman CM,Quesneville H

更新日期：2007-11-01 00:00:00

abstract：:A proliferation of chemical, reaction and enzyme databases, new computational methods and software tools for data-driven rational biosynthesis design have emerged in recent years. With the coming of the era of big data, particularly in the bio-medical field, data-driven rational biosynthesis design could potentially b...

journal_title：Briefings in bioinformatics

authors： Chen F,Yuan L,Ding S,Tian Y,Hu QN

更新日期：2020-07-15 00:00:00

abstract：:The understanding of complex biological networks often relies on both a dedicated layout and a topology. Currently, there are three major competing layout-aware systems biology formats, but there are no software tools or software libraries supporting all of them. This complicates the management of molecular network la...

journal_title：Briefings in bioinformatics

authors： Hoksza D,Gawron P,Ostaszewski M,Hasenauer J,Schneider R

更新日期：2020-07-15 00:00:00

abstract：:The use of microarray technology to measure gene expression on a genome-wide scale has been well established for more than a decade. Methods to process and analyse the vast quantity of expression data generated by a typical microarray experiment are similarly well-established. The Affymetrix Exon 1.0 ST array is a rel...

journal_title：Briefings in bioinformatics

authors： Lockstone HE

更新日期：2011-11-01 00:00:00

abstract：MOTIVATION:The functional changes of the genes, RNAs and proteins will eventually be reflected in the metabolic level. Increasing number of researchers have researched mechanism, biomarkers and targeted drugs by metabolites. However, compared with our knowledge about genes, RNAs, and proteins, we still know few about d...

journal_title：Briefings in bioinformatics

authors： Zhao T,Hu Y,Cheng L

更新日期：2020-10-13 00:00:00

abstract：:Many bioinformatics problems, such as sequence alignment, gene prediction, phylogenetic tree estimation and RNA secondary structure prediction, are often affected by the 'uncertainty' of a solution, that is, the probability of the solution is extremely small. This situation arises for estimation problems on high-dimen...

journal_title：Briefings in bioinformatics

authors： Hamada M

更新日期：2014-09-01 00:00:00

abstract：:Short tandem repeats are highly polymorphic and associated with a wide range of phenotypic variation, some of which cause neurodegenerative disease in humans. With advances in high-throughput sequencing technologies, there are novel opportunities to study genetic variation. While available sequencing technologies and ...

journal_title：Briefings in bioinformatics

authors： Cao MD,Balasubramanian S,Bodén M

更新日期：2015-03-01 00:00:00

abstract：:Systematic sequencing of cancer genomes has revealed prevalent heterogeneity, with patients harboring various combinatorial patterns of genetic alteration. In particular, a phenomenon that a group of genes exhibits mutually exclusive patterns has been widespread across cancers, covering a broad spectrum of crucial can...

journal_title：Briefings in bioinformatics

authors： Deng Y,Luo S,Deng C,Luo T,Yin W,Zhang H,Zhang Y,Zhang X,Lan Y,Ping Y,Xiao Y,Li X

更新日期：2019-01-18 00:00:00

abstract：:RNA structures are widely distributed across all life forms. The global conformation of these structures is defined by a variety of constituent structural units such as helices, hairpin loops, kissing-loop motifs and pseudoknots, which often behave in a modular way. Their ubiquitous distribution is associated with a v...

journal_title：Briefings in bioinformatics

authors： Gupta A,Bansal M

更新日期：2020-07-15 00:00:00

abstract：:Gene expression profiling holds great potential as a new approach to histological diagnosis and precision medicine of cancers of unknown primary (CUP). Batch effects and different data types greatly decrease the predictive performance of biomarker-based algorithms, and few methods have been widely applied to identify ...

journal_title：Briefings in bioinformatics

authors： Shen Y,Chu Q,Yin X,He Y,Bai P,Wang Y,Fang W,Timko MP,Fan L,Jiang W

更新日期：2020-04-08 00:00:00

abstract：:Most of the microRNAs (miRNAs) play their regulatory roles through posttranscriptional target decay or translational inhibition. For both plants and animals, these regulatory events were previously considered to take place in cytoplasm, as mature miRNAs were observed to be exported to the cytoplasm for Argonaute (AGO)...

journal_title：Briefings in bioinformatics

authors： Yu D,Tang Z,Shao C,Ma X,Xiang T,Fan Z,Wang H,Meng Y

更新日期：2018-11-27 00:00:00