Resolving the problem of multiple accessions of the same transcript deposited across various public databases.

abstract：:In recent years, high-throughput genomic technologies like chromatin immunoprecipitation sequencing (ChIp-seq) and transcriptome sequencing (RNA-seq) have been becoming both more refined and less expensive, making them more accessible. Many circular RNAs (circRNAs) that originate from back-spliced exons have been iden...

journal_title：Briefings in bioinformatics

authors： Tang Z,Li X,Zhao J,Qian F,Feng C,Li Y,Zhang J,Jiang Y,Yang Y,Wang Q,Li C

更新日期：2019-11-27 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：:Cell lines are widely used as in vitro models of tumorigenesis. However, an increasing number of researchers have found that cell lines differ from their sourced tumour samples after long-term cell culture. The application of unsuitable cell lines in experiments will affect the experimental accuracy and the treatment ...

journal_title：Briefings in bioinformatics

authors： Zhao N,Liu Y,Wei Y,Yan Z,Zhang Q,Wu C,Chang Z,Xu Y

更新日期：2017-05-01 00:00:00

abstract：:Patients with spinal muscular atrophy (SMA) are susceptible to the respiratory infections and might be at a heightened risk of poor clinical outcomes upon contracting coronavirus disease 2019 (COVID-19). In the face of the COVID-19 pandemic, the potential associations of SMA with the susceptibility to and prognosticat...

journal_title：Briefings in bioinformatics

authors： Li Z,Li X,Shen J,Tan H,Rong T,Lin Y,Feng E,Chen Z,Jiao Y,Liu G,Zhang L,Vai Chan MT,Kei Wu WK

更新日期：2020-11-14 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：:An initiative to increase biopharmaceutical research productivity by capturing, sharing and computationally integrating proprietary scientific discoveries with public knowledge is described. This initiative involves both organisational process change and multiple interoperating software systems. The software component...

journal_title：Briefings in bioinformatics

authors： Ficenec D,Osborne M,Pradines J,Richards D,Felciano R,Cho RJ,Chen RO,Liefeld T,Owen J,Ruttenberg A,Reich C,Horvath J,Clark T

更新日期：2003-09-01 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

authors： Bortolomeazzi M,Gaffo E,Bortoluzzi S

更新日期：2019-05-21 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

authors： Wang Z,Wang Y,Wang N,Wang J,Wang Z,Vallejos CE,Wu R

更新日期：2014-01-01 00:00:00

abstract：:Circular RNA (circRNA) is a group of RNA family generated by RNA circularization, which was discovered ubiquitously across different species and tissues. However, there is no global view of tissue specificity for circRNAs to date. Here we performed the comprehensive analysis to characterize the features of human and m...

journal_title：Briefings in bioinformatics

authors： Xia S,Feng J,Lei L,Hu J,Xia L,Wang J,Xiang Y,Liu L,Zhong S,Han L,He C

更新日期：2017-11-01 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

abstract：:With the availability of gene expression data by RNA-seq, powerful statistical approaches for grouping similar gene expression profiles across different environments have become increasingly important. We describe and assess a computational model for clustering genes into distinct groups based on the pattern of gene e...

journal_title：Briefings in bioinformatics

authors： Wang N,Wang Y,Hao H,Wang L,Wang Z,Wang J,Wu R

更新日期：2014-07-01 00:00:00

abstract：:Array-based gene expression studies frequently serve to identify genes that are expressed differently under two or more conditions. The actual analysis of the data, however, may be hampered by a number of technical and statistical problems. Possible remedies on the level of computational analysis lie in appropriate pr...

journal_title：Briefings in bioinformatics

authors： Steinhoff C,Vingron M

更新日期：2006-06-01 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：: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：:Since the completion of the Human Genome Project, it has been widely established that most DNA is not transcribed into proteins. These non-protein-coding regions are believed to be moderators within transcriptional and post-transcriptional processes, which play key roles in the onset of diseases. Long non-coding RNAs ...

journal_title：Briefings in bioinformatics

authors： Yotsukura S,duVerle D,Hancock T,Natsume-Kitatani Y,Mamitsuka H

更新日期：2017-01-01 00:00:00

abstract：:With the development of next-generation sequencing (NGS) technologies, a large amount of short read data has been generated. Assembly of these short reads can be challenging for genomes and metagenomes without template sequences, making alignment-based genome sequence comparison difficult. In addition, sequence reads ...

journal_title：Briefings in bioinformatics

authors： Song K,Ren J,Reinert G,Deng M,Waterman MS,Sun F

更新日期：2014-05-01 00:00:00

abstract：BACKGROUND:Whole genome sequencing (WGS) is increasingly used for Mycobacterium tuberculosis (Mtb) research. Countries with the highest tuberculosis (TB) burden face important challenges to integrate WGS into surveillance and research. METHODS:We assessed the global status of Mtb WGS and developed a 3-week training co...

journal_title：Briefings in bioinformatics

authors： Rivière E,Heupink TH,Ismail N,Dippenaar A,Clarke C,Abebe G,Heusden P,Warren R,Meehan CJ,Van Rie A

更新日期：2020-10-03 00:00:00

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

authors： Mora A

更新日期：2020-09-25 00:00:00

abstract：:The understanding of complex biological networks often relies on both a dedicated layout and a topology. Currently, there are three major competing layout-aware systems biology formats, but there are no software tools or software libraries supporting all of them. This complicates the management of molecular network la...

journal_title：Briefings in bioinformatics

authors： Hoksza D,Gawron P,Ostaszewski M,Hasenauer J,Schneider R

更新日期：2020-07-15 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：:Atomic charges play a very important role in drug-target recognition. However, computation of atomic charges with high-level quantum mechanics (QM) calculations is very time-consuming. A number of machine learning (ML)-based atomic charge prediction methods have been proposed to speed up the calculation of high-accura...

journal_title：Briefings in bioinformatics

authors： Wang J,Cao D,Tang C,Xu L,He Q,Yang B,Chen X,Sun H,Hou T

更新日期：2020-08-25 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：:In view of great difficulties in the pathogenesis analysis of Alzheimer's disease (AD) presently, profiling the modifiable risk factors is crucial for early detection and intervention of AD. However, the causal associations among them have yet to be identified, and the effective integration and application of these da...

journal_title：Briefings in bioinformatics

authors： Wang Z,Meng L,Liu H,Shen L,Ji HF

更新日期：2020-09-21 00:00:00

abstract：:Precision medicine has changed thinking in cancer therapy, highlighting a better understanding of the individual clinical interventions. But what role do the drivers and pathways identified from pan-cancer genome analysis play in the tumor? In this letter, we will highlight the importance of in silico modeling in prec...

journal_title：Briefings in bioinformatics

authors： Kunz M,Jeromin J,Fuchs M,Christoph J,Veronesi G,Flentje M,Nietzer S,Dandekar G,Dandekar T

更新日期：2020-05-21 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：MOTIVATION:The functional changes of the genes, RNAs and proteins will eventually be reflected in the metabolic level. Increasing number of researchers have researched mechanism, biomarkers and targeted drugs by metabolites. However, compared with our knowledge about genes, RNAs, and proteins, we still know few about d...

journal_title：Briefings in bioinformatics

authors： Zhao T,Hu Y,Cheng L

更新日期：2020-10-13 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：:Most of the microRNAs (miRNAs) play their regulatory roles through posttranscriptional target decay or translational inhibition. For both plants and animals, these regulatory events were previously considered to take place in cytoplasm, as mature miRNAs were observed to be exported to the cytoplasm for Argonaute (AGO)...

journal_title：Briefings in bioinformatics

authors： Yu D,Tang Z,Shao C,Ma X,Xiang T,Fan Z,Wang H,Meng Y

更新日期：2018-11-27 00:00:00

abstract：:Molecular interrogation of a biological sample through DNA sequencing, RNA and microRNA profiling, proteomics and other assays, has the potential to provide a systems level approach to predicting treatment response and disease progression, and to developing precision therapies. Large publicly funded projects have gene...

journal_title：Briefings in bioinformatics

authors： Kannan L,Ramos M,Re A,El-Hachem N,Safikhani Z,Gendoo DM,Davis S,Gomez-Cabrero D,Castelo R,Hansen KD,Carey VJ,Morgan M,Culhane AC,Haibe-Kains B,Waldron L

更新日期：2016-07-01 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

authors： Walker DC,Southgate J

更新日期：2009-07-01 00:00:00