Cloud 3D-QSAR: a web tool for the development of quantitative structure-activity relationship models in drug discovery.

abstract：:Gene expression profiling holds great potential as a new approach to histological diagnosis and precision medicine of cancers of unknown primary (CUP). Batch effects and different data types greatly decrease the predictive performance of biomarker-based algorithms, and few methods have been widely applied to identify ...

journal_title：Briefings in bioinformatics

authors： Shen Y,Chu Q,Yin X,He Y,Bai P,Wang Y,Fang W,Timko MP,Fan L,Jiang W

更新日期：2020-04-08 00:00:00

abstract：:Genomic data hold salient information about the characteristics of a living organism. Throughout the past decade, pinnacle developments have given us more accurate and inexpensive methods to retrieve genome sequences of humans. However, with the advancement of genomic research, there is a growing privacy concern regar...

journal_title：Briefings in bioinformatics

authors： Aziz MMA,Sadat MN,Alhadidi D,Wang S,Jiang X,Brown CL,Mohammed N

更新日期：2019-05-21 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：: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：: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：:The outbreak caused by the novel coronavirus SARS-CoV-2 has been declared a global health emergency. G-quadruplex structures in genomes have long been considered essential for regulating a number of biological processes in a plethora of organisms. We have analyzed and identified 25 four contiguous GG runs (G2NxG2NyG2N...

journal_title：Briefings in bioinformatics

authors： Ji D,Juhas M,Tsang CM,Kwok CK,Li Y,Zhang Y

更新日期：2020-06-01 00:00:00

abstract：:Effectively representing Medical Subject Headings (MeSH) headings (terms) such as disease and drug as discriminative vectors could greatly improve the performance of downstream computational prediction models. However, these terms are often abstract and difficult to quantify. In this paper, we converted the MeSH tree ...

journal_title：Briefings in bioinformatics

authors： Guo ZH,You ZH,Huang DS,Yi HC,Zheng K,Chen ZH,Wang YB

更新日期：2020-03-31 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

authors： Sarkar IN

更新日期：2007-09-01 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：:Drug-drug interactions (DDIs) constitute an important concern in drug development and postmarketing pharmacovigilance. They are considered the cause of many adverse drug effects exposing patients to higher risks and increasing public health system costs. Methods to follow-up and discover possible DDIs causing harm to ...

journal_title：Briefings in bioinformatics

authors： Vilar S,Friedman C,Hripcsak G

更新日期：2018-09-28 00:00:00

abstract：:The discipline of bioinformatics has developed rapidly since the complete sequencing of the first genomes in the 1990s. The development of many high-throughput techniques during the last decades has ensured that bioinformatics has grown into a discipline that overlaps with, and is required for, the modern practice of ...

journal_title：Briefings in bioinformatics

authors： Tastan Bishop Ö,Adebiyi EF,Alzohairy AM,Everett D,Ghedira K,Ghouila A,Kumuthini J,Mulder NJ,Panji S,Patterton HG,H3ABioNet Consortium.,H3Africa Consortium.

更新日期：2015-03-01 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：:The use of microarray technology to measure gene expression on a genome-wide scale has been well established for more than a decade. Methods to process and analyse the vast quantity of expression data generated by a typical microarray experiment are similarly well-established. The Affymetrix Exon 1.0 ST array is a rel...

journal_title：Briefings in bioinformatics

authors： Lockstone HE

更新日期：2011-11-01 00:00:00

abstract：:Despite The Central Dogma states the destiny of gene as 'DNA makes RNA and RNA makes protein', the nucleic acids not only store and transmit genetic information but also, surprisingly, join in intracellular vital movement as a regulator of gene expression. Bioinformatics has contributed to knowledge for a series of em...

journal_title：Briefings in bioinformatics

authors： Zhang S,Zhou Y,Wang Y,Wang Z,Xiao Q,Zhang Y,Lou Y,Qiu Y,Zhu F

更新日期：2020-04-06 00:00:00

abstract：:Understanding biological complexity demands a combination of high-throughput data and interdisciplinary skills. One way to bring to bear the necessary combination of data types and expertise is by encapsulating domain knowledge in software and composing that software to create a customized data analysis environment. T...

journal_title：Briefings in bioinformatics

authors： Bare JC,Baliga NS

更新日期：2014-07-01 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：: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：MOTIVATION:Computational methods accelerate drug discovery and play an important role in biomedicine, such as molecular property prediction and compound-protein interaction (CPI) identification. A key challenge is to learn useful molecular representation. In the early years, molecular properties are mainly calculated b...

journal_title：Briefings in bioinformatics

authors： Li P,Li Y,Hsieh CY,Zhang S,Liu X,Liu H,Song S,Yao X

更新日期：2020-11-04 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：: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：: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：:Phylogenomic databases provide orthology predictions for species with fully sequenced genomes. Although the goal seems well-defined, the content of these databases differs greatly. Seven ortholog databases (Ensembl Compara, eggNOG, HOGENOM, InParanoid, OMA, OrthoDB, Panther) were compared on the basis of reference tre...

journal_title：Briefings in bioinformatics

authors： Boeckmann B,Robinson-Rechavi M,Xenarios I,Dessimoz C

更新日期：2011-09-01 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

authors： Song J,Wang Y,Li F,Akutsu T,Rawlings ND,Webb GI,Chou KC

更新日期：2019-03-25 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

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：:The combination of DNA bisulfite treatment with high-throughput sequencing technologies has enabled investigation of genome-wide DNA methylation beyond CpG sites and CpG islands. These technologies have opened new avenues to understand the interplay between epigenetic events, chromatin plasticity and gene regulation. ...

journal_title：Briefings in bioinformatics

authors： Adusumalli S,Mohd Omar MF,Soong R,Benoukraf T

更新日期：2015-05-01 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：:The adoption of agent technologies and multi-agent systems constitutes an emerging area in bioinformatics. In this article, we report on the activity of the Working Group on Agents in Bioinformatics (BIOAGENTS) founded during the first AgentLink III Technical Forum meeting on the 2nd of July, 2004, in Rome. The meetin...

journal_title：Briefings in bioinformatics

authors： Merelli E,Armano G,Cannata N,Corradini F,d'Inverno M,Doms A,Lord P,Martin A,Milanesi L,Möller S,Schroeder M,Luck M

更新日期：2007-01-01 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

authors： Allen JD,Wang S,Chen M,Girard L,Minna JD,Xie Y,Xiao G

更新日期：2012-09-01 00:00:00

abstract：OBJECTIVE:Development of novel informatics methods focused on improving pregnancy outcomes remains an active area of research. The purpose of this study is to systematically review the ways that artificial intelligence (AI) and machine learning (ML), including deep learning (DL), methodologies can inform patient care d...

journal_title：Briefings in bioinformatics

authors： Davidson L,Boland MR

更新日期：2021-01-06 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