Understanding the unimodal distributions of cancer occurrence rates: it takes two factors for a cancer to occur.

abstract：MOTIVATION:Long noncoding RNAs (lncRNAs) correspond to a eukaryotic noncoding RNA class that gained great attention in the past years as a higher layer of regulation for gene expression in cells. There is, however, a lack of specific computational approaches to reliably predict lncRNA in plants, which contrast the vari...

journal_title：Briefings in bioinformatics

authors： Negri TDC,Alves WAL,Bugatti PH,Saito PTM,Domingues DS,Paschoal AR

更新日期：2019-03-25 00:00:00

abstract：:microRNAs (miRNAs) are small endogenous non-coding RNAs that function as the universal specificity factors in post-transcriptional gene silencing. Discovering miRNAs, identifying their targets and further inferring miRNA functions have been a critical strategy for understanding normal biological processes of miRNAs an...

journal_title：Briefings in bioinformatics

authors： Liu B,Li J,Cairns MJ

更新日期：2014-01-01 00:00:00

abstract：:Phase separation is an important mechanism that mediates the spatial distribution of proteins in different cellular compartments. While phase-separated proteins share certain sequence characteristics, including intrinsically disordered regions (IDRs) and prion-like domains, such characteristics are insufficient for ma...

journal_title：Briefings in bioinformatics

authors： Yu C,Shen B,You K,Huang Q,Shi M,Wu C,Chen Y,Zhang C,Li T

更新日期：2020-09-02 00:00:00

abstract：:In therapeutic research, the safety and efficacy of pharmaceutical products are necessarily tested on humans via clinical trials after an extensive and expensive preclinical development period. Methodologies such as computer modeling and clinical trial simulation (CTS) might represent a valuable option to reduce anima...

journal_title：Briefings in bioinformatics

authors： Gal J,Milano G,Ferrero JM,Saâda-Bouzid E,Viotti J,Chabaud S,Gougis P,Le Tourneau C,Schiappa R,Paquet A,Chamorey E

更新日期：2018-11-27 00:00:00

abstract：:Dissecting the genetic mechanism underlying a complex disease hinges on discovering gene-environment interactions (GXE). However, detecting GXE is a challenging problem especially when the genetic variants under study are rare. Haplotype-based tests have several advantages over the so-called collapsing tests for detec...

journal_title：Briefings in bioinformatics

authors： Papachristou C,Biswas S

更新日期：2020-05-21 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：: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：:While the number of sequenced genes is increasing dramatically, the number of different protein structural families is expected to be more limited. Changes in enzymatic activity or protein interactions can dramatically modify the role of homologous proteins in different organisms or mutants. However, experimental data...

journal_title：Briefings in bioinformatics

authors： Chatonnet A,Cousin X,Robinson A

更新日期：2001-03-01 00:00:00

abstract：:Programs for RNA mutational analysis that are structure-based and rely on secondary structure prediction have been developed and expanded in the past several years. They can be used for a variety of purposes, such as in suggesting point mutations that will alter RNA virus replication or translation initiation, investi...

journal_title：Briefings in bioinformatics

authors： Barash D,Churkin A

更新日期：2011-03-01 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

abstract：:We introduce the Beta Workbench (BWB), a scalable tool built on top of the newly defined BlenX language to model, simulate and analyse biological systems. We show the features and the incremental modelling process supported by the BWB on a running example based on the mitogen-activated kinase pathway. Finally, we prov...

journal_title：Briefings in bioinformatics

authors： Dematté L,Priami C,Romanel A

更新日期：2008-09-01 00:00:00

abstract：:High-throughput omics data are generated almost with no limit nowadays. It becomes increasingly important to integrate different omics data types to disentangle the molecular machinery of complex diseases with the hope for better disease prevention and treatment. Since the relationship among different omics data featu...

journal_title：Briefings in bioinformatics

authors： Yang H,Cao H,He T,Wang T,Cui Y

更新日期：2018-11-29 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：:As a group of important plant species in agriculture and biology, polyploids have been increasingly studied in terms of their genome structure and organization. There are two types of polyploids, allopolyploids and autopolyploids, each resulting from a different genetic origin, which undergo meiotic divisions of a dis...

journal_title：Briefings in bioinformatics

authors： Xu F,Tong C,Lyu Y,Bo W,Pang X,Wu R

更新日期：2015-01-01 00:00:00

abstract：UNLABELLED:So-called next-generation sequencing (NGS) has provided the ability to sequence on a massive scale at low cost, enabling biologists to perform powerful experiments and gain insight into biological processes. BamView has been developed to visualize and analyse sequence reads from NGS platforms, which have bee...

journal_title：Briefings in bioinformatics

authors： Carver T,Harris SR,Otto TD,Berriman M,Parkhill J,McQuillan JA

更新日期：2013-03-01 00:00:00

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：:Occurrence and development of cancers are governed by complex networks of interacting intercellular and intracellular signals. The technology of single-cell RNA sequencing (scRNA-seq) provides an unprecedented opportunity for dissecting the interplay between the cancer cells and the associated microenvironment. Here w...

journal_title：Briefings in bioinformatics

authors： Zhang J,Guan M,Wang Q,Zhang J,Zhou T,Sun X

更新日期：2020-05-21 00:00:00

abstract：:Broader functional annotation of known as well as putative genetic variations is a valuable mean for prioritizing targets in disease studies and large-scale genotyping projects. In this article, we present a practical guide to SNPnexus, a web-based tool that provides an aggregate set of functional annotations for geno...

journal_title：Briefings in bioinformatics

authors： Dayem Ullah AZ,Lemoine NR,Chelala C

更新日期：2013-07-01 00:00:00

abstract：:We discuss and review different ways to map cellular components and their temporal interaction with other such components to different non-spatially explicit mathematical models. The essential choices made in the literature are between discrete and continuous state spaces, between rule and event-based state updates an...

journal_title：Briefings in bioinformatics

authors： Kirkilionis M

更新日期：2010-01-01 00:00:00

abstract：:Daily work in molecular biology presently depends on a large number of computational tools. An in-depth, large-scale study of that 'ecosystem' of Web tools, its characteristics, interconnectivity, patterns of usage/citation, temporal evolution and rate of decay is crucial for understanding the forces that shape it and...

journal_title：Briefings in bioinformatics

authors： Pazos F,Chagoyen M

更新日期：2019-07-19 00:00:00

abstract：:The increasing ease with which massive genetic information can be obtained from patients or healthy individuals has stimulated the development of interpretive bioinformatics tools as aids in clinical practice. Most such tools analyze evolutionary information and simple physical-chemical properties to predict whether r...

journal_title：Briefings in bioinformatics

authors： Galano-Frutos JJ,García-Cebollada H,Sancho J

更新日期：2021-01-18 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：:The products of multi-exon genes are a mixture of alternatively spliced isoforms, from which the translated proteins can have similar, different or even opposing functions. It is therefore essential to differentiate and annotate functions for individual isoforms. Computational approaches provide an efficient complemen...

journal_title：Briefings in bioinformatics

authors： Li HD,Omenn GS,Guan Y

更新日期：2016-11-01 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：:Pathway enrichment analysis has been widely used to identify cancer risk pathways, and contributes to elucidating the mechanism of tumorigenesis. However, most of the existing approaches use the outdated pathway information and neglect the complex gene interactions in pathway. Here, we first reviewed the existing wide...

journal_title：Briefings in bioinformatics

authors： Yang Q,Wang S,Dai E,Zhou S,Liu D,Liu H,Meng Q,Jiang B,Jiang W

更新日期：2019-01-18 00:00:00

abstract：:Computational and mathematical modelling has become a valuable tool for investigating biological systems. Modelling enables prediction of how biological components interact to deliver system-level properties and extrapolation of biological system performance to contexts and experimental conditions where this is unknow...

journal_title：Briefings in bioinformatics

authors： Read MN,Alden K,Timmis J,Andrews PS

更新日期：2018-09-18 00:00:00

abstract：:Understanding the interconnections of microbial pathogenicity phenomena, such as biofilm formation, quorum sensing and antimicrobial resistance, is a tremendous open challenge for biomedical research. Progress made by wet-lab researchers and bioinformaticians in understanding the underlying regulatory phenomena has be...

journal_title：Briefings in bioinformatics

authors： Castelhano Santos N,Pereira MO,Lourenço A

更新日期：2015-01-01 00:00:00

abstract：:Synonymous mutations do not change the encoded amino acids but may alter the structure or function of an mRNA in ways that impact gene function. Advances in next generation sequencing technologies have detected numerous synonymous mutations in the human genome. Several computational models have been proposed to predic...

journal_title：Briefings in bioinformatics

authors： Cheng N,Li M,Zhao L,Zhang B,Yang Y,Zheng CH,Xia J

更新日期：2020-05-21 00:00:00

abstract：:Plant transcriptome encompasses numerous endogenous, regulatory non-coding RNAs (ncRNAs) that play a major biological role in regulating key physiological mechanisms. While studies have shown that ncRNAs are extremely diverse and ubiquitous, the functions of the vast majority of ncRNAs are still unknown. With ever-inc...

journal_title：Briefings in bioinformatics

authors： Vivek AT,Kumar S

更新日期：2020-12-18 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