Proteome-scale analysis of phase-separated proteins in immunofluorescence images.

abstract：:Understanding the genetic basis of human traits/diseases and the underlying mechanisms of how these traits/diseases are affected by genetic variations is critical for public health. Current genome-wide functional genomics data uncovered a large number of functional elements in the noncoding regions of human genome, pr...

journal_title：Briefings in bioinformatics

authors： Li MJ,Yan B,Sham PC,Wang J

更新日期：2015-05-01 00:00:00

abstract：:A number of supervised machine learning models have recently been introduced for the prediction of drug-target interactions based on chemical structure and genomic sequence information. Although these models could offer improved means for many network pharmacology applications, such as repositioning of drugs for new t...

journal_title：Briefings in bioinformatics

authors： Pahikkala T,Airola A,Pietilä S,Shakyawar S,Szwajda A,Tang J,Aittokallio T

更新日期：2015-03-01 00:00:00

abstract：:Many bioinformatics problems, such as sequence alignment, gene prediction, phylogenetic tree estimation and RNA secondary structure prediction, are often affected by the 'uncertainty' of a solution, that is, the probability of the solution is extremely small. This situation arises for estimation problems on high-dimen...

journal_title：Briefings in bioinformatics

authors： Hamada M

更新日期：2014-09-01 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：: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：: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：:The residence of spliceosomal introns within protein-coding genes can fluctuate over time, with genes gaining, losing or conserving introns in a complex process that is not entirely understood. One approach for studying intron evolution is to compare introns with respect to position and type within closely related gen...

journal_title：Briefings in bioinformatics

authors： Wilkerson MD,Ru Y,Brendel VP

更新日期：2009-11-01 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

authors： Huang J,Chen J,Zhang B,Zhu L,Cai H

更新日期：2020-06-26 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

authors： Deng Y,Luo S,Deng C,Luo T,Yin W,Zhang H,Zhang Y,Zhang X,Lan Y,Ping Y,Xiao Y,Li X

更新日期：2019-01-18 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：:The explosion in genomic sequence available in public databases has resulted in an unprecedented opportunity for computational whole genome analyses. A number of promising comparative-based approaches have been developed for gene finding, regulatory element discovery and other purposes, and it is clear that these tool...

journal_title：Briefings in bioinformatics

authors： Dubchak I,Pachter L

更新日期：2002-03-01 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

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：:As one of the most important fundamental problems in protein sequence analysis, protein remote homology detection is critical for both theoretical research (protein structure and function studies) and real world applications (drug design). Although several computational predictors have been proposed, their detection p...

journal_title：Briefings in bioinformatics

authors： Liu B,Jiang S,Zou Q

更新日期：2018-11-07 00:00:00

abstract：:RNA-seq has been an increasingly popular high-throughput platform to identify differentially expressed (DE) genes, which is much more reproducible and accurate than the previous microarray technology. Yet, a number of statistical issues remain to be resolved in data analysis, largely due to the high-throughput data vo...

journal_title：Briefings in bioinformatics

authors： Gu X

更新日期：2016-03-01 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：:One of the most complex and computationally intensive tasks of genome sequence analysis is genome assembly. Even today, few centres have the resources, in both software and hardware, to assemble a genome from the thousands or millions of individual sequences generated in a whole-genome shotgun sequencing project. With...

journal_title：Briefings in bioinformatics

authors： Pop M,Phillippy A,Delcher AL,Salzberg SL

更新日期：2004-09-01 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：:Correlated reaction sets (Co-Sets) are mathematically defined modules in biochemical reaction networks which facilitate the study of biological processes by decomposing complex reaction networks into conceptually simple units. According to the degree of association, Co-Sets can be classified into three types: perfect,...

journal_title：Briefings in bioinformatics

authors： Xi Y,Chen YP,Qian C,Wang F

更新日期：2011-03-01 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

authors： Xu Y,Wu T,Li F,Dong Q,Wang J,Shang D,Xu Y,Zhang C,Dou Y,Hu C,Yang H,Zheng X,Zhang Y,Wang L,Li X

更新日期：2020-12-01 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

authors： Fabris F,Palmer D,de Magalhães JP,Freitas AA

更新日期：2020-05-21 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：:Precision and personalized medicine will be increasingly based on the integration of various type of information, particularly electronic health records and genome sequences. The availability of cheap genome sequencing services and the information interoperability will increase the role of online bioinformatics analys...

journal_title：Briefings in bioinformatics

authors： Bianchi L,Liò P

更新日期：2017-11-01 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：: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：:A proliferation of chemical, reaction and enzyme databases, new computational methods and software tools for data-driven rational biosynthesis design have emerged in recent years. With the coming of the era of big data, particularly in the bio-medical field, data-driven rational biosynthesis design could potentially b...

journal_title：Briefings in bioinformatics

authors： Chen F,Yuan L,Ding S,Tian Y,Hu QN

更新日期：2020-07-15 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：:Synonymous mutations do not change the encoded amino acids but may alter the structure or function of an mRNA in ways that impact gene function. Advances in next generation sequencing technologies have detected numerous synonymous mutations in the human genome. Several computational models have been proposed to predic...

journal_title：Briefings in bioinformatics

authors： Cheng N,Li M,Zhao L,Zhang B,Yang Y,Zheng CH,Xia J

更新日期：2020-05-21 00:00:00

abstract：:DNA-binding hot spot residues of proteins are dominant and fundamental interface residues that contribute most of the binding free energy of protein-DNA interfaces. As experimental methods for identifying hot spots are expensive and time consuming, computational approaches are urgently required in predicting hot spots...

journal_title：Briefings in bioinformatics

authors： Zhang S,Zhao L,Zheng CH,Xia J

更新日期：2020-05-21 00:00:00

abstract：:If the completion of the first draft of the human genome represents the coming of age of bioinformatics, then the emergence of bioinformatics as a university degree subject represents its establishment. In this paper bioinformatics as a subject for formal study is discussed, rather than as a subject for research, and ...

journal_title：Briefings in bioinformatics

authors： Counsell D

更新日期：2003-03-01 00:00:00