TrimNet: learning molecular representation from triplet messages for biomedicine.

abstract：:Numerous studies have shown that copy number variation (CNV) in lncRNA regions play critical roles in the initiation and progression of cancer. However, our knowledge about their functionalities is still limited. Here, we firstly provided a computational method to identify lncRNAs with copy number variation (lncRNAs-C...

journal_title：Briefings in bioinformatics

authors： Xu Y,Wu T,Li F,Dong Q,Wang J,Shang D,Xu Y,Zhang C,Dou Y,Hu C,Yang H,Zheng X,Zhang Y,Wang L,Li X

更新日期：2020-12-01 00:00:00

abstract：:Effective drug discovery contributes to the treatment of numerous diseases but is limited by high costs and long cycles. The Quantitative Structure-Activity Relationship (QSAR) method was introduced to evaluate the activity of a large number of compounds virtually, reducing the time and labor costs required for chemic...

journal_title：Briefings in bioinformatics

authors： Wang YL,Wang F,Shi XX,Jia CY,Wu FX,Hao GF,Yang GF

更新日期：2020-11-03 00:00:00

abstract：:The use of multiple testing procedures in the context of gene-set testing is an important but relatively underexposed topic. If a multiple testing method is used, this is usually a standard familywise error rate (FWER) or false discovery rate (FDR) controlling procedure in which the logical relationships that exist be...

journal_title：Briefings in bioinformatics

authors： Meijer RJ,Goeman JJ

更新日期：2016-09-01 00:00:00

abstract：:The modelling of biological systems is accompanied with epistemic uncertainties that range from structural uncertainty to parametric uncertainty due to such limitations as insufficient understanding of the underlying mechanism and incomplete measurement data of a system. Fuzzy logic approaches such as fuzzy Petri nets...

journal_title：Briefings in bioinformatics

authors： Liu F,Heiner M,Gilbert D

更新日期：2018-12-27 00:00:00

abstract：:Next generation sequencers have greatly improved our ability to mine polymorphisms and mutations out of entire (or portions of) genomes. The reliability of their outputs, though, showed to be very related to the sequencing chemistry and to deeply affect the quality of the downstream analyses. We focus here on the two-...

journal_title：Briefings in bioinformatics

authors： Castellana S,Romani M,Valente EM,Mazza T

更新日期：2013-11-01 00:00:00

abstract：:The cell-free DNA (cfDNA) methylation profile in liquid biopsy has been utilized to diagnose early-stage disease and estimate therapy response. However, typical clinical procedures are capable of purifying only very small amounts of cfDNA. Whole-genome bisulfite sequencing (WGBS) is the gold standard for measuring DNA...

journal_title：Briefings in bioinformatics

authors： Yin Y,Li J,Li J,Lee M,Zhao S,Guo L,Li J,Zhang M,Huang Y,Li XN,Deng Z,Sun D

更新日期：2020-12-15 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：:A key challenge of the post-genomic era is the identification of the function(s) of all the molecules in a given organism. Here, we review the status of sequence and structure-based approaches to protein function inference and ligand screening that can provide functional insights for a significant fraction of the appr...

journal_title：Briefings in bioinformatics

authors： Skolnick J,Brylinski M

更新日期：2009-07-01 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：: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：: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：OBJECTIVE:Development of novel informatics methods focused on improving pregnancy outcomes remains an active area of research. The purpose of this study is to systematically review the ways that artificial intelligence (AI) and machine learning (ML), including deep learning (DL), methodologies can inform patient care d...

journal_title：Briefings in bioinformatics

authors： Davidson L,Boland MR

更新日期：2021-01-06 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：: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：:Understanding the genetic basis of human traits/diseases and the underlying mechanisms of how these traits/diseases are affected by genetic variations is critical for public health. Current genome-wide functional genomics data uncovered a large number of functional elements in the noncoding regions of human genome, pr...

journal_title：Briefings in bioinformatics

authors： Li MJ,Yan B,Sham PC,Wang J

更新日期：2015-05-01 00:00:00

abstract：:In drug development, preclinical safety and pharmacokinetics assessments of candidate drugs to ensure the safety profile are a must. While in vivo and in vitro tests are traditionally used, experimental determinations have disadvantages, as they are usually time-consuming and costly. In silico predictions of these pre...

journal_title：Briefings in bioinformatics

authors： Hsiao Y,Su BH,Tseng YJ

更新日期：2020-08-07 00:00:00

abstract：:The presence of different transcripts of a gene across samples can be analysed by whole-transcriptome microarrays. Reproducing results from published microarray data represents a challenge owing to the vast amounts of data and the large variety of preprocessing and filtering steps used before the actual analysis is ca...

journal_title：Briefings in bioinformatics

authors： Rodrigo-Domingo M,Waagepetersen R,Bødker JS,Falgreen S,Kjeldsen MK,Johnsen HE,Dybkær K,Bøgsted M

更新日期：2014-07-01 00:00:00

abstract：:Relative changes in mRNA as well as protein levels induced by sublethal doses of antibiotics on bacteria are measured and results visualised in the context of metabolic pathway diagrams. The mRNA levels present at a given time point after the addition of the antibiotic are measured using microarrays from Affymetrix. A...

journal_title：Briefings in bioinformatics

authors： Wolf D,Gray CP,de Saizieu A

更新日期：2000-09-01 00:00:00

abstract：:Circular RNA (circRNA) is a group of RNA family generated by RNA circularization, which was discovered ubiquitously across different species and tissues. However, there is no global view of tissue specificity for circRNAs to date. Here we performed the comprehensive analysis to characterize the features of human and m...

journal_title：Briefings in bioinformatics

authors： Xia S,Feng J,Lei L,Hu J,Xia L,Wang J,Xiang Y,Liu L,Zhong S,Han L,He C

更新日期：2017-11-01 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：:DNA-binding hot spot residues of proteins are dominant and fundamental interface residues that contribute most of the binding free energy of protein-DNA interfaces. As experimental methods for identifying hot spots are expensive and time consuming, computational approaches are urgently required in predicting hot spots...

journal_title：Briefings in bioinformatics

authors： Zhang S,Zhao L,Zheng CH,Xia J

更新日期：2020-05-21 00:00:00

abstract：:Competitive endogenous RNA (ceRNA) represents a novel layer of gene regulation that controls both physiological and pathological processes. However, there is still lack of computational tools for quickly identifying ceRNA regulation. To address this problem, we presented an R-package, CeRNASeek, which allows identifyi...

journal_title：Briefings in bioinformatics

authors： Zhang M,Jin X,Li J,Tian Y,Wang Q,Li X,Xu J,Li Y,Li X

更新日期：2020-05-04 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：:Verification in phylogenetics represents an extremely difficult subject. Phylogenetic analysis deals with the reconstruction of evolutionary histories of species, and as long as mankind is not able to travel in time, it will not be possible to verify deep evolutionary histories reconstructed with modern computational ...

journal_title：Briefings in bioinformatics

authors： Stamatakis A,Izquierdo-Carrasco F

更新日期：2011-05-01 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：:With the development of next-generation sequencing (NGS) technologies, a large amount of short read data has been generated. Assembly of these short reads can be challenging for genomes and metagenomes without template sequences, making alignment-based genome sequence comparison difficult. In addition, sequence reads ...

journal_title：Briefings in bioinformatics

authors： Song K,Ren J,Reinert G,Deng M,Waterman MS,Sun F

更新日期：2014-05-01 00:00:00

abstract：:Cell-penetrating peptides (CPPs) facilitate the delivery of therapeutically relevant molecules, including DNA, proteins and oligonucleotides, into cells both in vitro and in vivo. This unique ability explores the possibility of CPPs as therapeutic delivery and its potential applications in clinical therapy. Over the l...

journal_title：Briefings in bioinformatics

authors： Su R,Hu J,Zou Q,Manavalan B,Wei L

更新日期：2020-03-23 00:00:00

abstract：:The explosion in genomic sequence available in public databases has resulted in an unprecedented opportunity for computational whole genome analyses. A number of promising comparative-based approaches have been developed for gene finding, regulatory element discovery and other purposes, and it is clear that these tool...

journal_title：Briefings in bioinformatics

authors： Dubchak I,Pachter L

更新日期：2002-03-01 00:00:00

abstract：:Regulation of proteolysis plays a critical role in a myriad of important cellular processes. The key to better understanding the mechanisms that control this process is to identify the specific substrates that each protease targets. To address this, we have developed iProt-Sub, a powerful bioinformatics tool for the a...

journal_title：Briefings in bioinformatics

authors： Song J,Wang Y,Li F,Akutsu T,Rawlings ND,Webb GI,Chou KC

更新日期：2019-03-25 00:00:00

abstract：:An initiative to increase biopharmaceutical research productivity by capturing, sharing and computationally integrating proprietary scientific discoveries with public knowledge is described. This initiative involves both organisational process change and multiple interoperating software systems. The software component...

journal_title：Briefings in bioinformatics

authors： Ficenec D,Osborne M,Pradines J,Richards D,Felciano R,Cho RJ,Chen RO,Liefeld T,Owen J,Ruttenberg A,Reich C,Horvath J,Clark T

更新日期：2003-09-01 00:00:00