Abstract:
:Protein remote homology detection is one of the most fundamental and central problems for the studies of protein structures and functions, aiming to detect the distantly evolutionary relationships among proteins via computational methods. During the past decades, many computational approaches have been proposed to solve this important task. These methods have made a substantial contribution to protein remote homology detection. Therefore, it is necessary to give a comprehensive review and comparison on these computational methods. In this article, we divide these computational approaches into three categories, including alignment methods, discriminative methods and ranking methods. Their advantages and disadvantages are discussed in a comprehensive perspective, and their performance is compared on widely used benchmark data sets. Finally, some open questions in this field are further explored and discussed.
journal_name
Brief Bioinformjournal_title
Briefings in bioinformaticsauthors
Chen J,Guo M,Wang X,Liu Bdoi
10.1093/bib/bbw108subject
Has Abstractpub_date
2018-03-01 00:00:00pages
231-244issue
2eissn
1467-5463issn
1477-4054pii
2562645journal_volume
19pub_type
杂志文章,评审abstract::Gene set analysis (GSA) is one of the methods of choice for analyzing the results of current omics studies; however, it has been mainly developed to analyze mRNA (microarray, RNA-Seq) data. The following review includes an update regarding general methods and resources for GSA and then emphasizes GSA methods and tools...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbz090
更新日期:2020-09-25 00:00:00
abstract::Posttranscriptional crosstalk and communication between RNAs yield large regulatory competing endogenous RNA (ceRNA) networks via shared microRNAs (miRNAs), as well as miRNA synergistic networks. The ceRNA crosstalk represents a novel layer of gene regulation that controls both physiological and pathological processes...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbx137
更新日期:2019-07-19 00:00:00
abstract::Understanding the functioning of biological systems depends on tackling complexity spanning spatial scales from genome to organ to whole organism. The basic unit of life, the cell, acts to co-ordinate information received across these scales and processes the myriad of signals to produce an integrated cellular respons...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章,评审
doi:10.1093/bib/bbp010
更新日期:2009-07-01 00:00:00
abstract::SARS-CoV-2 is an intensively investigated virus from the order Nidovirales (Coronaviridae family) that causes COVID-19 disease in humans. Through enormous scientific effort, thousands of viral strains have been sequenced to date, thereby creating a strong background for deep bioinformatics studies of the SARS-CoV-2 ge...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbaa385
更新日期:2020-12-21 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
pub_type: 杂志文章
doi:10.1093/bib/bbu037
更新日期:2015-07-01 00:00:00
abstract::In therapeutic research, the safety and efficacy of pharmaceutical products are necessarily tested on humans via clinical trials after an extensive and expensive preclinical development period. Methodologies such as computer modeling and clinical trial simulation (CTS) might represent a valuable option to reduce anima...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章,评审
doi:10.1093/bib/bbx055
更新日期:2018-11-27 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
pub_type: 杂志文章
doi:10.1093/bib/bbx097
更新日期:2019-01-18 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::Biological knowledge can be inferred from three major levels of information: molecules, organisms and ecologies. Bioinformatics is an established field that has made significant advances in the development of systems and techniques to organize contemporary molecular data; biodiversity informatics is an emerging discip...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章,评审
doi:10.1093/bib/bbm037
更新日期:2007-09-01 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
pub_type: 杂志文章,评审
doi:10.1093/bib/bby034
更新日期:2019-03-25 00:00:00
abstract::Identification of new drug-target interactions (DTIs) is an important but a time-consuming and costly step in drug discovery. In recent years, to mitigate these drawbacks, researchers have sought to identify DTIs using computational approaches. However, most existing methods construct drug networks and target networks...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbaa044
更新日期:2020-05-04 00:00:00
abstract::Aberrant DNA methylation is a fundamental characterization of epigenetics for carcinogenesis. Abnormality of DNA methylation-related functional elements (DMFEs) may lead to dysfunction of regulatory genes in the progression of cancers, contributing to prognosis of many cancers. There is an urgent need to construct a t...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbaa162
更新日期:2020-08-11 00:00:00
abstract::The formation of phenotypic traits, such as biomass production, tumor volume and viral abundance, undergoes a complex process in which interactions between genes and developmental stimuli take place at each level of biological organization from cells to organisms. Traditional studies emphasize the impact of genes by d...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbs049
更新日期:2014-01-01 00:00:00
abstract::Rapidly evolving sequencing technologies produce data on an unparalleled scale. A central challenge to the analysis of this data is sequence alignment, whereby sequence reads must be compared to a reference. A wide variety of alignment algorithms and software have been subsequently developed over the past two years. I...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章,评审
doi:10.1093/bib/bbq015
更新日期:2010-09-01 00:00:00
abstract::Exploring protein-ligand interactions is a subject of immense interest, as it provides deeper insights into molecular recognition, mechanism of interaction and subsequent functions. Predicting an accurate model for a protein-ligand interaction is a challenging task. Molecular docking is a computational method used for...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbaa279
更新日期:2020-10-26 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
pub_type: 杂志文章
doi:10.1093/bib/bbr076
更新日期:2012-09-01 00:00:00
abstract::Cells are compartmentalized by numerous membrane-bounded organelles and membraneless organelles (MLOs) to ensure temporal and spatial regulation of various biological processes. A number of MLOs, such as nucleoli, nuclear speckles and stress granules, exist as liquid droplets within the cells and arise from the conden...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbaa271
更新日期:2020-10-30 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
pub_type: 杂志文章
doi:10.1093/bib/bbq079
更新日期:2011-05-01 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::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
pub_type: 杂志文章
doi:10.1093/bib/bbt086
更新日期:2015-01-01 00:00:00
abstract::Integrated modelling of biological systems is challenged by composing components with sufficient kinetic data and components with insufficient kinetic data or components built only using experts' experience and knowledge. Fuzzy continuous Petri nets (FCPNs) combine continuous Petri nets with fuzzy inference systems, a...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbz114
更新日期:2021-01-18 00:00:00
abstract::Most of current gene expression signatures for cancer prognosis are based on risk scores, usually calculated as some summaries of expression levels of the signature genes, whose applications require presetting risk score thresholds and data normalization. In this study, we demonstrate the critical limitations of such ...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbv064
更新日期:2016-03-01 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
pub_type: 杂志文章
doi:10.1093/bib/bbaa169
更新日期:2020-08-14 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
pub_type: 杂志文章,评审
doi:10.1093/bib/bby028
更新日期:2019-03-25 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
pub_type: 杂志文章
doi:10.1093/bib/bbw017
更新日期:2017-03-01 00:00:00
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
pub_type: 杂志文章
doi:10.1093/bib/bbz113
更新日期:2020-12-01 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
pub_type: 杂志文章
doi:10.1093/bib/bby001
更新日期:2019-07-19 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
pub_type: 杂志文章
doi:10.1093/bib/bbaa425
更新日期:2021-01-30 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
pub_type: 杂志文章
doi:10.1093/bib/bbaa276
更新日期:2020-11-03 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