Systems pharmacology in drug discovery and therapeutic insight for herbal medicines.

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：: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：: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：:Broader functional annotation of known as well as putative genetic variations is a valuable mean for prioritizing targets in disease studies and large-scale genotyping projects. In this article, we present a practical guide to SNPnexus, a web-based tool that provides an aggregate set of functional annotations for geno...

journal_title：Briefings in bioinformatics

authors： Dayem Ullah AZ,Lemoine NR,Chelala C

更新日期：2013-07-01 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

abstract：:The contribution of transposable elements (TEs) to genome structure and evolution as well as their impact on genome sequencing, assembly, annotation and alignment has generated increasing interest in developing new methods for their computational analysis. Here we review the diversity of innovative approaches to ident...

journal_title：Briefings in bioinformatics

authors： Bergman CM,Quesneville H

更新日期：2007-11-01 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：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：: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：:Computational detection methods have been widely used in studies on the biogenesis and the function of circular RNAs (circRNAs). However, all of the existing tools showed disadvantages on certain aspects of circRNA detection. Here, we propose an improved multithreading detection tool, CIRI2, which used an adapted maxi...

journal_title：Briefings in bioinformatics

authors： Gao Y,Zhang J,Zhao F

更新日期：2018-09-28 00:00:00

abstract：:RNA structures are widely distributed across all life forms. The global conformation of these structures is defined by a variety of constituent structural units such as helices, hairpin loops, kissing-loop motifs and pseudoknots, which often behave in a modular way. Their ubiquitous distribution is associated with a v...

journal_title：Briefings in bioinformatics

authors： Gupta A,Bansal M

更新日期：2020-07-15 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：: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：:Moonlighting proteins provide more options for cells to execute multiple functions without increasing the genome and transcriptome complexity. Although there have long been calls for computational methods for the prediction of moonlighting proteins, no method has been designed for determining moonlighting long noncodi...

journal_title：Briefings in bioinformatics

authors： Liu X,Xu Y,Wang R,Liu S,Wang J,Luo Y,Leung KS,Cheng L

更新日期：2021-01-18 00:00:00

abstract：:Daily work in molecular biology presently depends on a large number of computational tools. An in-depth, large-scale study of that 'ecosystem' of Web tools, its characteristics, interconnectivity, patterns of usage/citation, temporal evolution and rate of decay is crucial for understanding the forces that shape it and...

journal_title：Briefings in bioinformatics

authors： Pazos F,Chagoyen M

更新日期：2019-07-19 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 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：: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：:In the business and healthcare sectors data warehousing has provided effective solutions for information usage and knowledge discovery from databases. However, data warehousing applications in the biological research and development (R&D) sector are lagging far behind. The fuzziness and complexity of biological data r...

journal_title：Briefings in bioinformatics

authors： Schönbach C,Kowalski-Saunders P,Brusic V

更新日期：2000-05-01 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：: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：: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：: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：: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 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：: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：:Plant transcriptome encompasses numerous endogenous, regulatory non-coding RNAs (ncRNAs) that play a major biological role in regulating key physiological mechanisms. While studies have shown that ncRNAs are extremely diverse and ubiquitous, the functions of the vast majority of ncRNAs are still unknown. With ever-inc...

journal_title：Briefings in bioinformatics

authors： Vivek AT,Kumar S

更新日期：2020-12-18 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：: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：: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