Abstract:
:In clinical cancer treatment, genomic alterations would often affect the response of patients to anticancer drugs. Studies have shown that molecular features of tumors could be biomarkers predictive of sensitivity or resistance to anticancer agents, but the identification of actionable mutations are often constrained by the incomplete understanding of cancer genomes. Recent progresses of next-generation sequencing technology greatly facilitate the extensive molecular characterization of tumors and promote precision medicine in cancers. More and more clinical studies, cancer cell lines studies, CRISPR screening studies as well as patient-derived model studies were performed to identify potential actionable mutations predictive of drug response, which provide rich resources of molecularly and pharmacologically profiled cancer samples at different levels. Such abundance of data also enables the development of various computational models and algorithms to solve the problem of drug sensitivity prediction, biomarker identification and in silico drug prioritization by the integration of multiomics data. Here, we review the recent development of methods and resources that identifies mutation-dependent effects for cancer treatment in clinical studies, functional genomics studies and computational studies and discuss the remaining gaps and future directions in this area.
journal_name
Brief Bioinformjournal_title
Briefings in bioinformaticsauthors
Yao H,Liang Q,Qian X,Wang J,Sham PC,Li MJdoi
10.1093/bib/bbz109subject
Has Abstractpub_date
2020-12-01 00:00:00pages
1886-1903issue
6eissn
1467-5463issn
1477-4054pii
5626330journal_volume
21pub_type
杂志文章abstract::Ontologies are now pervasive in biomedicine, where they serve as a means to standardize terminology, to enable access to domain knowledge, to verify data consistency and to facilitate integrative analyses over heterogeneous biomedical data. For this purpose, research on biomedical ontologies applies theories and metho...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbs053
更新日期:2013-11-01 00:00:00
abstract::Since the small RNA-sequencing (sRNA-seq) technology became available, it allowed the discovery of thousands new microRNAs (miRNAs) in humans and many other species, providing new data on these small RNAs (sRNAs) of high biological and translational relevance. MiRNA discovery has not yet reached saturation, even in th...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbx148
更新日期:2019-05-21 00:00:00
abstract::RNA editing is a widespread co/posttranscriptional mechanism affecting primary RNAs by specific nucleotide modifications, which plays relevant roles in molecular processes including regulation of gene expression and/or the processing of noncoding RNAs. In recent years, the detection of editing sites has been improved ...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章,评审
doi:10.1093/bib/bbx129
更新日期:2019-03-22 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
pub_type: 杂志文章
doi:10.1093/bib/bbaa037
更新日期:2020-03-31 00:00:00
abstract::Small noncoding RNAs (sRNA/sncRNAs) are generated from different genomic loci and play important roles in biological processes, such as cell proliferation and the regulation of gene expression. Next-generation sequencing (NGS) has provided an unprecedented opportunity to discover and quantify diverse kinds of sncRNA, ...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbz151
更新日期:2021-01-18 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
pub_type: 杂志文章
doi:10.1093/bib/bbt075
更新日期:2015-01-01 00:00:00
abstract:MOTIVATION:With the recent advances in DNA sequencing technologies, the study of the genetic composition of living organisms has become more accessible for researchers. Several advances have been achieved because of it, especially in the health sciences. However, many challenges which emerge from the complexity of sequ...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章,评审
doi:10.1093/bib/bby072
更新日期:2019-11-27 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
pub_type: 杂志文章
doi:10.1093/bib/bby118
更新日期:2018-12-27 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
pub_type: 杂志文章
doi:10.1093/bib/bbaa322
更新日期:2020-12-18 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
pub_type: 杂志文章
doi:10.1093/bib/bby115
更新日期:2018-11-29 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
pub_type: 杂志文章
doi:10.1093/bib/bbq063
更新日期:2010-11-01 00:00:00
abstract::Gene expression profiling holds great potential as a new approach to histological diagnosis and precision medicine of cancers of unknown primary (CUP). Batch effects and different data types greatly decrease the predictive performance of biomarker-based algorithms, and few methods have been widely applied to identify ...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbaa031
更新日期:2020-04-08 00:00:00
abstract::Protein phosphorylation is a reversible and ubiquitous post-translational modification that primarily occurs at serine, threonine and tyrosine residues and regulates a variety of biological processes. In this paper, we first briefly summarized the current progresses in computational prediction of eukaryotic protein ph...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bby122
更新日期:2020-03-23 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
pub_type: 杂志文章
doi:10.1093/bib/bbaa033
更新日期:2021-01-18 00:00:00
abstract::Research into genome assembly algorithms has experienced a resurgence due to new challenges created by the development of next generation sequencing technologies. Several genome assemblers have been published in recent years specifically targeted at the new sequence data; however, the ever-changing technological lands...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbp026
更新日期:2009-07-01 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
pub_type: 杂志文章,评审
doi:10.1093/bib/bbs006
更新日期:2013-01-01 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
pub_type: 杂志文章
doi:10.1093/bib/bbn023
更新日期:2008-09-01 00:00:00
abstract::Biologists very often use enrichment methods based on statistical hypothesis tests to identify gene properties that are significantly over-represented in a given set of genes of interest, by comparison with a 'background' set of genes. These enrichment methods, although based on rigorous statistical foundations, are n...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbz028
更新日期:2020-05-21 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
pub_type: 杂志文章
doi:10.1093/bib/bbw049
更新日期:2017-07-01 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
pub_type: 杂志文章
doi:10.1093/bib/bbaa048
更新日期:2020-05-04 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
pub_type: 杂志文章,评审
doi:10.1093/bib/bbp046
更新日期:2010-03-01 00:00:00
abstract::Accurately identifying the interactions between genomic factors and the response of cancer drugs plays important roles in drug discovery, drug repositioning and cancer treatment. A number of studies revealed that interactions between genes and drugs were 'many-genes-to-many drugs' interactions, i.e. common modules, op...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbaa087
更新日期:2020-06-26 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
pub_type: 杂志文章
doi:10.1093/bib/bbaa310
更新日期:2020-12-15 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
pub_type: 历史文章,杂志文章
doi:10.1093/bib/bbu022
更新日期:2015-03-01 00:00:00
abstract::Transposable elements (TEs) are an important source of human genetic variation with demonstrable effects on phenotype. Recently, a number of computational methods for the detection of polymorphic TE (polyTE) insertion sites from next-generation sequence data have been developed. The use of such tools will become incre...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbw072
更新日期:2017-11-01 00:00:00
abstract::Systematic sequencing of cancer genomes has revealed prevalent heterogeneity, with patients harboring various combinatorial patterns of genetic alteration. In particular, a phenomenon that a group of genes exhibits mutually exclusive patterns has been widespread across cancers, covering a broad spectrum of crucial can...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbx109
更新日期:2019-01-18 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
pub_type: 杂志文章
doi:10.1093/bib/bbs062
更新日期:2014-01-01 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
pub_type: 杂志文章
doi:10.1093/bib/bby124
更新日期:2020-03-23 00:00:00
abstract::Despite gene expression programs being notoriously complex, RNA abundance is usually assumed as a proxy for transcriptional activity. Recently developed approaches, able to disentangle transcriptional and post-transcriptional regulatory processes, have revealed a more complex scenario. It is now possible to work out h...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbaa389
更新日期:2020-12-22 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
pub_type: 杂志文章
doi:10.1093/bib/bbaa266
更新日期:2020-11-04 00:00:00