CyanoPATH: a knowledgebase of genome-scale functional repertoire for toxic cyanobacterial blooms.

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：:Precision and personalized medicine will be increasingly based on the integration of various type of information, particularly electronic health records and genome sequences. The availability of cheap genome sequencing services and the information interoperability will increase the role of online bioinformatics analys...

journal_title：Briefings in bioinformatics

authors： Bianchi L,Liò P

更新日期：2017-11-01 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：:If the completion of the first draft of the human genome represents the coming of age of bioinformatics, then the emergence of bioinformatics as a university degree subject represents its establishment. In this paper bioinformatics as a subject for formal study is discussed, rather than as a subject for research, and ...

journal_title：Briefings in bioinformatics

authors： Counsell D

更新日期：2003-03-01 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：: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：:Despite its central role in the adaptation and microevolution of traits, the genetic architecture of phenotypic plasticity, i.e. multiple phenotypes produced by a single genotype in changing environments, remains elusive. We know little about the genes that underlie the plastic response of traits to the environment, t...

journal_title：Briefings in bioinformatics

authors： Wang Z,Pang X,Lv Y,Xu F,Zhou T,Li X,Feng S,Li J,Li Z,Wu R

更新日期：2013-01-01 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：:Integrative analyses of genomic, epigenomic and transcriptomic features for human and various model organisms have revealed that many such features are nonrandomly distributed in the genome. Significant enrichment (or depletion) of genomic features is anticipated to be biologically important. Detection of genomic regi...

journal_title：Briefings in bioinformatics

authors： De S,Pedersen BS,Kechris K

更新日期：2014-11-01 00:00:00

abstract：:Scoring functions (SFs) based on complex machine learning (ML) algorithms have gradually emerged as a promising alternative to overcome the weaknesses of classical SFs. However, extensive efforts have been devoted to the development of SFs based on new protein-ligand interaction representations and advanced alternativ...

journal_title：Briefings in bioinformatics

authors： Xiong GL,Ye WL,Shen C,Lu AP,Hou TJ,Cao DS

更新日期：2020-06-04 00:00:00

abstract：:Whole-organism metabolic rate co-varies allometrically with body mass, and is also affected by temperature through different biochemical mechanisms. Here we implement a computational platform to map specific quantitative trait loci (QTLs) that govern the dependence of metabolic rate on size and temperature. The model ...

journal_title：Briefings in bioinformatics

authors： Yan Q,Zhu X,Jiang L,Ye M,Sun L,Terblanche JS,Wu R

更新日期：2017-01-01 00:00:00

abstract：:The structural description of peptide ligands bound to G protein-coupled receptors (GPCRs) is important for the discovery of new drugs and deeper understanding of the molecular mechanisms of life. Here we describe a three-stage protocol for the molecular docking of peptides to GPCRs using a set of different programs: ...

journal_title：Briefings in bioinformatics

authors： Badaczewska-Dawid AE,Kmiecik S,Koliński M

更新日期：2020-06-10 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：: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：MOTIVATION:Computational methods accelerate drug discovery and play an important role in biomedicine, such as molecular property prediction and compound-protein interaction (CPI) identification. A key challenge is to learn useful molecular representation. In the early years, molecular properties are mainly calculated b...

journal_title：Briefings in bioinformatics

authors： Li P,Li Y,Hsieh CY,Zhang S,Liu X,Liu H,Song S,Yao X

更新日期：2020-11-04 00:00:00

abstract：:Phenotypes have gained increased notoriety in the clinical and biological domain owing to their application in numerous areas such as the discovery of disease genes and drug targets, phylogenetics and pharmacogenomics. Phenotypes, defined as observable characteristics of organisms, can be seen as one of the bridges th...

journal_title：Briefings in bioinformatics

authors： Oellrich A,Collier N,Groza T,Rebholz-Schuhmann D,Shah N,Bodenreider O,Boland MR,Georgiev I,Liu H,Livingston K,Luna A,Mallon AM,Manda P,Robinson PN,Rustici G,Simon M,Wang L,Winnenburg R,Dumontier M

更新日期：2016-09-01 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：:The discipline of bioinformatics has developed rapidly since the complete sequencing of the first genomes in the 1990s. The development of many high-throughput techniques during the last decades has ensured that bioinformatics has grown into a discipline that overlaps with, and is required for, the modern practice of ...

journal_title：Briefings in bioinformatics

authors： Tastan Bishop Ö,Adebiyi EF,Alzohairy AM,Everett D,Ghedira K,Ghouila A,Kumuthini J,Mulder NJ,Panji S,Patterton HG,H3ABioNet Consortium.,H3Africa Consortium.

更新日期：2015-03-01 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：:Mediation analysis has been a useful tool for investigating the effect of mediators that lie in the path from the independent variable to the outcome. With the increasing dimensionality of mediators such as in (epi)genomics studies, high-dimensional mediation model is needed. In this work, we focus on epigenetic studi...

journal_title：Briefings in bioinformatics

authors： Fang R,Yang H,Gao Y,Cao H,Goode EL,Cui Y

更新日期：2020-07-01 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：:A number of supervised machine learning models have recently been introduced for the prediction of drug-target interactions based on chemical structure and genomic sequence information. Although these models could offer improved means for many network pharmacology applications, such as repositioning of drugs for new t...

journal_title：Briefings in bioinformatics

authors： Pahikkala T,Airola A,Pietilä S,Shakyawar S,Szwajda A,Tang J,Aittokallio T

更新日期：2015-03-01 00:00:00

abstract：:Systems pharmacology is an emerging field that integrates systems biology and pharmacology to advance the process of drug discovery, development and the understanding of therapeutic mechanisms. The aim of the present work is to highlight the role that the systems pharmacology plays across the traditional herbal medici...

journal_title：Briefings in bioinformatics

authors： Huang C,Zheng C,Li Y,Wang Y,Lu A,Yang L

更新日期：2014-09-01 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：:The residence of spliceosomal introns within protein-coding genes can fluctuate over time, with genes gaining, losing or conserving introns in a complex process that is not entirely understood. One approach for studying intron evolution is to compare introns with respect to position and type within closely related gen...

journal_title：Briefings in bioinformatics

authors： Wilkerson MD,Ru Y,Brendel VP

更新日期：2009-11-01 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：: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：:Mass spectrometry (MS)-based proteomics has undergone rapid advancements in recent years, creating challenging problems for bioinformatics. We focus on four aspects where bioinformatics plays a crucial role (and proteomics is needed for clinical application): peptide-spectra matching (PSM) based on the new data-indepe...

journal_title：Briefings in bioinformatics

authors： Goh WWB,Wong L

更新日期：2019-01-18 00:00:00

abstract：:Fibrosis is a key component in the pathogenic mechanism of a variety of diseases. These diseases involving fibrosis may share common mechanisms and therapeutic targets, and therefore common intervention strategies and medicines may be applicable for these diseases. For this reason, deliberately introducing anti-fibros...

journal_title：Briefings in bioinformatics

authors： Wu D,Gao W,Li X,Tian C,Jiao N,Fang S,Xiao J,Xu Z,Zhu L,Zhang G,Zhu R

更新日期：2020-06-22 00:00:00

abstract：:The iteratively reweighted least square (IRLS) method is mostly identical to maximum likelihood (ML) method in terms of parameter estimation and power of quantitative trait locus (QTL) detection. But the IRLS is greatly superior to ML in terms of computing speed and the robustness of parameter estimation. In conjuncti...

journal_title：Briefings in bioinformatics

authors： Liu Y,Yang T,Li H,Yang R

更新日期：2014-01-01 00:00:00