LARMD: integration of bioinformatic resources to profile ligand-driven protein dynamics with a case on the activation of estrogen receptor.

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：: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

authors： Qi L,Chen L,Li Y,Qin Y,Pan R,Zhao W,Gu Y,Wang H,Wang R,Chen X,Guo Z

更新日期：2016-03-01 00:00:00

abstract：:Occurrence and development of cancers are governed by complex networks of interacting intercellular and intracellular signals. The technology of single-cell RNA sequencing (scRNA-seq) provides an unprecedented opportunity for dissecting the interplay between the cancer cells and the associated microenvironment. Here w...

journal_title：Briefings in bioinformatics

authors： Zhang J,Guan M,Wang Q,Zhang J,Zhou T,Sun X

更新日期：2020-05-21 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

authors： Li Y,Jin X,Wang Z,Li L,Chen H,Lin X,Yi S,Zhang Y,Xu J

更新日期：2019-07-19 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：:Researchers have long been presented with the challenge imposed by the role of genetic heterogeneity in drug response. For many years, Pharmacogenomics and pharmacomicrobiomics has been investigating the influence of an individual's genetic background to drug response and disposition. More recently, the human gut micr...

journal_title：Briefings in bioinformatics

authors： Hassan R,Allali I,Agamah FE,Elsheikh SSM,Thomford NE,Dandara C,Chimusa ER

更新日期：2020-12-01 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

authors： Wang YL,Wang F,Shi XX,Jia CY,Wu FX,Hao GF,Yang GF

更新日期：2020-11-03 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

authors： Liu F,Sun W,Heiner M,Gilbert D

更新日期：2021-01-18 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：: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

authors： Burgos N,Bottani S,Faouzi J,Thibeau-Sutre E,Colliot O

更新日期：2020-12-15 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：: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

authors： Yang X,Lian X,Fu C,Wuchty S,Yang S,Zhang Z

更新日期：2021-01-30 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

authors： Zhang C,Zhao N,Zhang X,Xiao J,Li J,Lv D,Zhou W,Li Y,Xu J,Li X

更新日期：2020-08-11 00:00:00

abstract：:Heterophylly, i.e. morphological changes in leaves along the axis of an individual plant, is regarded as a strategy used by plants to cope with environmental change. However, little is known of the extent to which heterophylly is controlled by genes and how each underlying gene exerts its effect on heterophyllous vari...

journal_title：Briefings in bioinformatics

authors： Sun L,Wang J,Zhu X,Jiang L,Gosik K,Sang M,Sun F,Cheng T,Zhang Q,Wu R

更新日期：2018-07-20 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

authors： Zhang M,Jin X,Li J,Tian Y,Wang Q,Li X,Xu J,Li Y,Li X

更新日期：2020-05-04 00:00:00

abstract：:We discuss and review different ways to map cellular components and their temporal interaction with other such components to different non-spatially explicit mathematical models. The essential choices made in the literature are between discrete and continuous state spaces, between rule and event-based state updates an...

journal_title：Briefings in bioinformatics

authors： Kirkilionis M

更新日期：2010-01-01 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：:With the increasing recognition of its role in trait and disease development, it is crucial to account for genetic imprinting to illustrate the genetic architecture of complex traits. Genetic mapping can be innovated to test and estimate effects of genetic imprinting in a segregating population derived from experiment...

journal_title：Briefings in bioinformatics

authors： Sun L,Zhu X,Bo W,Xu F,Cheng T,Zhang Q,Wu R

更新日期：2015-05-01 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：: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：: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

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：: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：:The cell-free DNA (cfDNA) methylation profile in liquid biopsy has been utilized to diagnose early-stage disease and estimate therapy response. However, typical clinical procedures are capable of purifying only very small amounts of cfDNA. Whole-genome bisulfite sequencing (WGBS) is the gold standard for measuring DNA...

journal_title：Briefings in bioinformatics

authors： Yin Y,Li J,Li J,Lee M,Zhao S,Guo L,Li J,Zhang M,Huang Y,Li XN,Deng Z,Sun D

更新日期：2020-12-15 00:00:00

abstract：:Data from the SEER reports reveal that the occurrence rate of a cancer type generally follows a unimodal distribution over age, peaking at an age that is cancer-type specific and ranges from 30+ through 70+. Previous studies attribute such bell-shaped distributions to the reduced proliferative potential in senior year...

journal_title：Briefings in bioinformatics

authors： Qiu S,An Z,Tan R,He PA,Jing J,Li H,Wu S,Xu Y

更新日期：2020-12-30 00:00:00

abstract：:Despite its central role in the adaptation and microevolution of traits, the genetic architecture of phenotypic plasticity, i.e. multiple phenotypes produced by a single genotype in changing environments, remains elusive. We know little about the genes that underlie the plastic response of traits to the environment, t...

journal_title：Briefings in bioinformatics

authors： Wang Z,Pang X,Lv Y,Xu F,Zhou T,Li X,Feng S,Li J,Li Z,Wu R

更新日期：2013-01-01 00:00:00

abstract：:Programs for RNA mutational analysis that are structure-based and rely on secondary structure prediction have been developed and expanded in the past several years. They can be used for a variety of purposes, such as in suggesting point mutations that will alter RNA virus replication or translation initiation, investi...

journal_title：Briefings in bioinformatics

authors： Barash D,Churkin A

更新日期：2011-03-01 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：:The products of multi-exon genes are a mixture of alternatively spliced isoforms, from which the translated proteins can have similar, different or even opposing functions. It is therefore essential to differentiate and annotate functions for individual isoforms. Computational approaches provide an efficient complemen...

journal_title：Briefings in bioinformatics

authors： Li HD,Omenn GS,Guan Y

更新日期：2016-11-01 00:00:00

abstract：UNLABELLED:So-called next-generation sequencing (NGS) has provided the ability to sequence on a massive scale at low cost, enabling biologists to perform powerful experiments and gain insight into biological processes. BamView has been developed to visualize and analyse sequence reads from NGS platforms, which have bee...

journal_title：Briefings in bioinformatics

authors： Carver T,Harris SR,Otto TD,Berriman M,Parkhill J,McQuillan JA

更新日期：2013-03-01 00:00:00