HpQTL: a geometric morphometric platform to compute the genetic architecture of heterophylly.

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 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：: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：:Deoxyribonucleic acid replication is one of the most crucial tasks taking place in the cell, and it has to be precisely regulated. This process is initiated in the replication origins (ORIs), and thus it is essential to identify such sites for a deeper understanding of the cellular processes and functions related to t...

journal_title：Briefings in bioinformatics

authors： Manavalan B,Basith S,Shin TH,Lee G

更新日期：2020-11-25 00:00:00

abstract：:Phylogenomic databases provide orthology predictions for species with fully sequenced genomes. Although the goal seems well-defined, the content of these databases differs greatly. Seven ortholog databases (Ensembl Compara, eggNOG, HOGENOM, InParanoid, OMA, OrthoDB, Panther) were compared on the basis of reference tre...

journal_title：Briefings in bioinformatics

authors： Boeckmann B,Robinson-Rechavi M,Xenarios I,Dessimoz C

更新日期：2011-09-01 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：: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：:Computational aspects of host-parasite phylogenies form part of a set of general associations between areas and organisms, hosts and parasites, and species and genes. The problem is not new and the commonalities of exploring vicariance biogeography (organisms tracking areas) and host-parasite co-speciation (parasites ...

journal_title：Briefings in bioinformatics

authors： Stevens J

更新日期：2004-12-01 00:00:00

abstract：:While leading to millions of people's deaths every year the treatment of viral infectious diseases remains a huge public health challenge.Therefore, an in-depth understanding of human-virus protein-protein interactions (PPIs) as the molecular interface between a virus and its host cell is of paramount importance to ob...

journal_title：Briefings in bioinformatics

authors： Yang X,Lian X,Fu C,Wuchty S,Yang S,Zhang Z

更新日期：2021-01-30 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：: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：: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：:Understanding biological complexity demands a combination of high-throughput data and interdisciplinary skills. One way to bring to bear the necessary combination of data types and expertise is by encapsulating domain knowledge in software and composing that software to create a customized data analysis environment. T...

journal_title：Briefings in bioinformatics

authors： Bare JC,Baliga NS

更新日期：2014-07-01 00:00:00

abstract：:The so-called 'omics' approaches used in modern biology aim at massively characterizing the molecular repertories of living systems at different levels. Metabolomics is one of the last additions to the 'omics' family and it deals with the characterization of the set of metabolites in a given biological system. As meta...

journal_title：Briefings in bioinformatics

authors： Chagoyen M,Pazos F

更新日期：2013-11-01 00:00:00

abstract：:In order to reach precision medicine and improve patients' quality of life, machine learning is increasingly used in medicine. Brain disorders are often complex and heterogeneous, and several modalities such as demographic, clinical, imaging, genetics and environmental data have been studied to improve their understan...

journal_title：Briefings in bioinformatics

authors： Burgos N,Bottani S,Faouzi J,Thibeau-Sutre E,Colliot O

更新日期：2020-12-15 00:00:00

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：:Information Integrator is an extension to IBM's relational database DB2, which uses data federation to provide benefits to molecular biology researchers through two unique capabilities: increased flexibility in combining data from disparate sources, and SQL access to non-SQL data, easing the task of automating data an...

journal_title：Briefings in bioinformatics

authors： Arenson AD

更新日期：2003-12-01 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：: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：: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：:The prevalence of dropout events is a serious problem for single-cell Hi-C (scHiC) data due to insufficient sequencing depth and data coverage, which brings difficulties in downstream studies such as clustering and structural analysis. Complicating things further is the fact that dropouts are confounded with structura...

journal_title：Briefings in bioinformatics

authors： Han C,Xie Q,Lin S

更新日期：2020-11-17 00:00:00

abstract：:Online sequence repositories are teeming with RNA sequencing (RNA-Seq) data from a wide range of eukaryotes. Although most of these data sets contain large numbers of organelle-derived reads, researchers tend to ignore these data, focusing instead on the nuclear-derived transcripts. Consequently, GenBank contains mass...

journal_title：Briefings in bioinformatics

authors： Smith DR,Sanitá Lima M

更新日期：2017-11-01 00:00:00

abstract：:The Gulbenkian Training Programme in Bioinformatics has been offering hands-on training courses in Oeiras, PT for more than a decade. This article is a review of its functional organization and evolution. We aim to share our experience with people considering setting-up similar training facilities elsewhere. More than...

journal_title：Briefings in bioinformatics

authors： Fernandes PL

更新日期：2010-11-01 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：:DNA methylation plays an essential role in cancer. Differential variability (DV) in cancer was recently observed that contributes to cancer heterogeneity and has been shown to be crucial in detecting epigenetic field defects, DNA methylation alterations happening early in carcinogenesis. As neighboring CpG sites are h...

journal_title：Briefings in bioinformatics

authors： Wang Y,Teschendorff AE,Widschwendter M,Wang S

更新日期：2019-01-18 00:00:00

abstract：:Access to gene expression data has become increasingly common in recent years; however, analysis has become more difficult as it is often desirable to integrate data from different platforms. Probe mapping across microarray platforms is the first and most crucial step for data integration. In this article, we systemat...

journal_title：Briefings in bioinformatics

authors： Allen JD,Wang S,Chen M,Girard L,Minna JD,Xie Y,Xiao G

更新日期：2012-09-01 00:00:00

abstract：:Effectively representing Medical Subject Headings (MeSH) headings (terms) such as disease and drug as discriminative vectors could greatly improve the performance of downstream computational prediction models. However, these terms are often abstract and difficult to quantify. In this paper, we converted the MeSH tree ...

journal_title：Briefings in bioinformatics

authors： Guo ZH,You ZH,Huang DS,Yi HC,Zheng K,Chen ZH,Wang YB

更新日期：2020-03-31 00:00:00

abstract：:Technical advances such as the development of molecular cloning, Sanger sequencing, PCR and oligonucleotide microarrays are key to our current capacity to sequence, annotate and study complete organismal genomes. Recent years have seen the development of a variety of so-called 'next-generation' sequencing platforms, w...

journal_title：Briefings in bioinformatics

authors： Horner DS,Pavesi G,Castrignanò T,De Meo PD,Liuni S,Sammeth M,Picardi E,Pesole G

更新日期：2010-03-01 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：: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