Public data and open source tools for multi-assay genomic investigation of disease.

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：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：:It is easy for today's students and researchers to believe that modern bioinformatics emerged recently to assist next-generation sequencing data analysis. However, the very beginnings of bioinformatics occurred more than 50 years ago, when desktop computers were still a hypothesis and DNA could not yet be sequenced. T...

journal_title：Briefings in bioinformatics

authors： Gauthier J,Vincent AT,Charette SJ,Derome N

更新日期：2019-11-27 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：:Maintaining the consistency of genomic annotations is an increasingly complex task because of the iterative and dynamic nature of assembly and annotation, growing numbers of biological databases and insufficient integration of annotations across databases. As information exchange among databases is poor, a 'novel' seq...

journal_title：Briefings in bioinformatics

authors： Weirick T,John D,Uchida S

更新日期：2017-03-01 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 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：: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：: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：: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：: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：: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：: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：: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：: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：: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：: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：:Precision medicine promises to revolutionize treatment, shifting therapeutic approaches from the classical one-size-fits-all to those more tailored to the patient's individual genomic profile, lifestyle and environmental exposures. Yet, to advance precision medicine's main objective-ensuring the optimum diagnosis, tre...

journal_title：Briefings in bioinformatics

authors： Gutiérrez-Sacristán A,De Niz C,Kothari C,Kong SW,Mandl KD,Avillach P

更新日期：2021-01-18 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：:Mathematical models can serve as a tool to formalize biological knowledge from diverse sources, to investigate biological questions in a formal way, to test experimental hypotheses, to predict the effect of perturbations and to identify underlying mechanisms. We present a pipeline of computational tools that performs ...

journal_title：Briefings in bioinformatics

authors： Montagud A,Traynard P,Martignetti L,Bonnet E,Barillot E,Zinovyev A,Calzone L

更新日期：2019-07-19 00:00:00

abstract：:RNA-sequencing (RNA-seq) has rapidly become a popular tool to characterize transcriptomes. A fundamental research problem in many RNA-seq studies is the identification of reliable molecular markers that show differential expression between distinct sample groups. Together with the growing popularity of RNA-seq, a numb...

journal_title：Briefings in bioinformatics

authors： Seyednasrollah F,Laiho A,Elo LL

更新日期：2015-01-01 00:00:00

abstract：:P53 is the 'guardian of the genome' and is responsible for regulating cell cycle and apoptosis. The genomic p53 binding regions, where activating transcriptional factors and cofactors like p300 simultaneously bind, are called 'p53-dependent enhancers', which play an important role in tumorigenesis. Current experimenta...

journal_title：Briefings in bioinformatics

authors： Niu X,Deng K,Liu L,Yang K,Hu X

更新日期：2020-05-11 00:00:00

abstract：:Lipidomics, the systematic study of the lipid composition of a cell or tissue, is an invaluable complement to knowledge gained by genomics and proteomics research. Mass spectrometry provides a means to detect hundreds of lipids in parallel, and this includes low abundance species of lipids. Nevertheless, frequently oc...

journal_title：Briefings in bioinformatics

authors： Hartler J,Tharakan R,Köfeler HC,Graham DR,Thallinger GG

更新日期：2013-05-01 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：: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：:Alternative polyadenylation (APA) in breast tumor samples results in the removal/addition of cis-regulatory elements such as microRNA (miRNA) target sites in the 3'-untranslated region (3'-UTRs) of genes. Although previous computational APA studies focused on a subset of genes strongly affected by APA (APA genes), we ...

journal_title：Briefings in bioinformatics

authors： Kim S,Bai Y,Fan Z,Diergaarde B,Tseng GC,Park HJ

更新日期：2020-08-26 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：: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：: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：BACKGROUND:The most frequently mutated gene pairs in pancreatic adenocarcinoma (PAAD) are KRAS and TP53, and our goal is to illustrate the multiomics and molecular dynamics landscapes of KRAS/TP53 mutation and also to obtain prospective novel drugs for KRAS- and TP53-mutated PAAD patients. Moreover, we also made an att...

journal_title：Briefings in bioinformatics

authors： Kaushik AC,Wang YJ,Wang X,Wei DQ

更新日期：2020-07-31 00:00:00