Identification and comprehensive characterization of lncRNAs with copy number variations and their driving transcriptional perturbed subpathways reveal functional significance for cancer.

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：:Understanding the interconnections of microbial pathogenicity phenomena, such as biofilm formation, quorum sensing and antimicrobial resistance, is a tremendous open challenge for biomedical research. Progress made by wet-lab researchers and bioinformaticians in understanding the underlying regulatory phenomena has be...

journal_title：Briefings in bioinformatics

authors： Castelhano Santos N,Pereira MO,Lourenço A

更新日期：2015-01-01 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：:The use of multiple testing procedures in the context of gene-set testing is an important but relatively underexposed topic. If a multiple testing method is used, this is usually a standard familywise error rate (FWER) or false discovery rate (FDR) controlling procedure in which the logical relationships that exist be...

journal_title：Briefings in bioinformatics

authors： Meijer RJ,Goeman JJ

更新日期：2016-09-01 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：: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：: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

authors： Diroma MA,Ciaccia L,Pesole G,Picardi E

更新日期：2019-03-22 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

authors： Li H,Homer N

更新日期：2010-09-01 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

authors： Furlan M,de Pretis S,Pelizzola M

更新日期：2020-12-22 00:00:00

abstract：:The increasing ease with which massive genetic information can be obtained from patients or healthy individuals has stimulated the development of interpretive bioinformatics tools as aids in clinical practice. Most such tools analyze evolutionary information and simple physical-chemical properties to predict whether r...

journal_title：Briefings in bioinformatics

authors： Galano-Frutos JJ,García-Cebollada H,Sancho J

更新日期：2021-01-18 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：: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：: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：: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

authors： Rishishwar L,Mariño-Ramírez L,Jordan IK

更新日期：2017-11-01 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：: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：: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

abstract：:Cooperative regulation among multiple microRNAs (miRNAs) is a complex type of posttranscriptional regulation in human; however, the global view of the system-level regulatory principles across cancers is still unclear. Here, we investigated miRNA-miRNA cooperative regulatory landscape across 18 cancer types and summar...

journal_title：Briefings in bioinformatics

authors： Shao T,Wang G,Chen H,Xie Y,Jin X,Bai J,Xu J,Li X,Huang J,Jin Y,Li Y

更新日期：2019-09-27 00:00:00

abstract：:Computational aspects of host-parasite phylogenies form part of a set of general associations between areas and organisms, hosts and parasites, and species and genes. The problem is not new and the commonalities of exploring vicariance biogeography (organisms tracking areas) and host-parasite co-speciation (parasites ...

journal_title：Briefings in bioinformatics

authors： Stevens J

更新日期：2004-12-01 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：: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：:As the number of completely sequenced genomes rapidly increases, including now the complete Human Genome sequence, the post-genomic problems of genome-scale protein structure determination and the issue of gene function identification become ever more pressing. In fact, these problems can be seen as interrelated in th...

journal_title：Briefings in bioinformatics

authors： Jones DT

更新日期：2001-05-01 00:00:00

abstract：:In early January 2020, the novel coronavirus (SARS-CoV-2) responsible for a pneumonia outbreak in Wuhan, China, was identified using next-generation sequencing (NGS) and readily available bioinformatics pipelines. In addition to virus discovery, these NGS technologies and bioinformatics resources are currently being e...

journal_title：Briefings in bioinformatics

authors： Hu T,Li J,Zhou H,Li C,Holmes EC,Shi W

更新日期：2021-01-08 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：: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：: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 sol...

journal_title：Briefings in bioinformatics

authors： Chen J,Guo M,Wang X,Liu B

更新日期：2018-03-01 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：: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：:For many complex diseases, an earlier and more reliable diagnosis is considered a key prerequisite for developing more effective therapies to prevent or delay disease progression. Classical statistical learning approaches for specimen classification using omics data, however, often cannot provide diagnostic models wit...

journal_title：Briefings in bioinformatics

authors： Glaab E

更新日期：2016-05-01 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