Drug response in association with pharmacogenomics and pharmacomicrobiomics: towards a better personalized medicine.

abstract：:Glycosylation of proteins is involved in immune defense, cell-cell adhesion, cellular recognition and pathogen binding and is one of the most common and complex post-translational modifications. Science is still struggling to assign detailed mechanisms and functions to this form of conjugation. Even the structural ana...

journal_title：Briefings in bioinformatics

authors： Dallas DC,Martin WF,Hua S,German JB

更新日期：2013-05-01 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：: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：: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：: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：: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：: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：:Cell-penetrating peptides (CPPs) facilitate the delivery of therapeutically relevant molecules, including DNA, proteins and oligonucleotides, into cells both in vitro and in vivo. This unique ability explores the possibility of CPPs as therapeutic delivery and its potential applications in clinical therapy. Over the l...

journal_title：Briefings in bioinformatics

authors： Su R,Hu J,Zou Q,Manavalan B,Wei L

更新日期：2020-03-23 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：: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：: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：:Systems pharmacology is an emerging field that integrates systems biology and pharmacology to advance the process of drug discovery, development and the understanding of therapeutic mechanisms. The aim of the present work is to highlight the role that the systems pharmacology plays across the traditional herbal medici...

journal_title：Briefings in bioinformatics

authors： Huang C,Zheng C,Li Y,Wang Y,Lu A,Yang L

更新日期：2014-09-01 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：: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：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：:SARS-CoV-2 is an intensively investigated virus from the order Nidovirales (Coronaviridae family) that causes COVID-19 disease in humans. Through enormous scientific effort, thousands of viral strains have been sequenced to date, thereby creating a strong background for deep bioinformatics studies of the SARS-CoV-2 ge...

journal_title：Briefings in bioinformatics

authors： Goswami P,Bartas M,Lexa M,Bohálová N,Volná A,Červeň J,Červeňová V,Pečinka P,Špunda V,Fojta M,Brázda V

更新日期：2020-12-21 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：: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：: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：: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：:Online sequence repositories are teeming with RNA sequencing (RNA-Seq) data from a wide range of eukaryotes. Although most of these data sets contain large numbers of organelle-derived reads, researchers tend to ignore these data, focusing instead on the nuclear-derived transcripts. Consequently, GenBank contains mass...

journal_title：Briefings in bioinformatics

authors： Smith DR,Sanitá Lima M

更新日期：2017-11-01 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：MOTIVATION:Long noncoding RNAs (lncRNAs) correspond to a eukaryotic noncoding RNA class that gained great attention in the past years as a higher layer of regulation for gene expression in cells. There is, however, a lack of specific computational approaches to reliably predict lncRNA in plants, which contrast the vari...

journal_title：Briefings in bioinformatics

authors： Negri TDC,Alves WAL,Bugatti PH,Saito PTM,Domingues DS,Paschoal AR

更新日期：2019-03-25 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：: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：: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：: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：: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：:A class-imbalanced classifier is a decision rule to predict the class membership of new samples from an available data set where the class sizes differ considerably. When the class sizes are very different, most standard classification algorithms may favor the larger (majority) class resulting in poor accuracy in the ...

journal_title：Briefings in bioinformatics

authors： Lin WJ,Chen JJ

更新日期：2013-01-01 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