Dr AFC: drug repositioning through anti-fibrosis characteristic.

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：: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：: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：: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：:CyanoPATH is a database that curates and analyzes the common genomic functional repertoire for cyanobacteria harmful algal blooms (CyanoHABs) in eutrophic waters. Based on the literature of empirical studies and genome/protein databases, it summarizes four types of information: common biological functions (pathways) d...

journal_title：Briefings in bioinformatics

authors： Du W,Li G,Ho N,Jenkins L,Hockaday D,Tan J,Cao H

更新日期：2020-12-16 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：: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：: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：: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：:Accurate inference of orthologous genes is a pre-requisite for most comparative genomics studies, and is also important for functional annotation of new genomes. Identification of orthologous gene sets typically involves phylogenetic tree analysis, heuristic algorithms based on sequence conservation, synteny analysis,...

journal_title：Briefings in bioinformatics

authors： Kristensen DM,Wolf YI,Mushegian AR,Koonin EV

更新日期：2011-09-01 00:00:00

abstract：:Alternative polyadenylation (APA) in breast tumor samples results in the removal/addition of cis-regulatory elements such as microRNA (miRNA) target sites in the 3'-untranslated region (3'-UTRs) of genes. Although previous computational APA studies focused on a subset of genes strongly affected by APA (APA genes), we ...

journal_title：Briefings in bioinformatics

authors： Kim S,Bai Y,Fan Z,Diergaarde B,Tseng GC,Park HJ

更新日期：2020-08-26 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：: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：MOTIVATION:Over the past decade, the field of next-generation sequencing (NGS) has seen dramatic advances in methods and a decrease in costs. Consequently, a large expansion of data has been generated by NGS, most of which have originated from RNA-sequencing (RNA-seq) experiments. Because mitochondrial genes are expres...

journal_title：Briefings in bioinformatics

authors： Nachtigall PG,Grazziotin FG,Junqueira-de-Azevedo ILM

更新日期：2021-01-30 00:00:00

abstract：MOTIVATION:With the recent advances in DNA sequencing technologies, the study of the genetic composition of living organisms has become more accessible for researchers. Several advances have been achieved because of it, especially in the health sciences. However, many challenges which emerge from the complexity of sequ...

journal_title：Briefings in bioinformatics

authors： Padovani de Souza K,Setubal JC,Ponce de Leon F de Carvalho AC,Oliveira G,Chateau A,Alves R

更新日期：2019-11-27 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：:Precision medicine promises to revolutionize treatment, shifting therapeutic approaches from the classical one-size-fits-all to those more tailored to the patient's individual genomic profile, lifestyle and environmental exposures. Yet, to advance precision medicine's main objective-ensuring the optimum diagnosis, tre...

journal_title：Briefings in bioinformatics

authors： Gutiérrez-Sacristán A,De Niz C,Kothari C,Kong SW,Mandl KD,Avillach P

更新日期：2021-01-18 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：:Cell lines are widely used as in vitro models of tumorigenesis. However, an increasing number of researchers have found that cell lines differ from their sourced tumour samples after long-term cell culture. The application of unsuitable cell lines in experiments will affect the experimental accuracy and the treatment ...

journal_title：Briefings in bioinformatics

authors： Zhao N,Liu Y,Wei Y,Yan Z,Zhang Q,Wu C,Chang Z,Xu Y

更新日期：2017-05-01 00:00:00

abstract：BACKGROUND:The most frequently mutated gene pairs in pancreatic adenocarcinoma (PAAD) are KRAS and TP53, and our goal is to illustrate the multiomics and molecular dynamics landscapes of KRAS/TP53 mutation and also to obtain prospective novel drugs for KRAS- and TP53-mutated PAAD patients. Moreover, we also made an att...

journal_title：Briefings in bioinformatics

authors： Kaushik AC,Wang YJ,Wang X,Wei DQ

更新日期：2020-07-31 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：: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 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：: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：:Gene expression data have played an essential role in many biomedical studies. When the number of genes is large and sample size is limited, there is a 'lack of information' problem, leading to low-quality findings. To tackle this problem, both horizontal and vertical data integrations have been developed, where verti...

journal_title：Briefings in bioinformatics

authors： Wu M,Yi H,Ma S

更新日期：2020-08-14 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：: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：:microRNAs (miRNAs) are small endogenous non-coding RNAs that function as the universal specificity factors in post-transcriptional gene silencing. Discovering miRNAs, identifying their targets and further inferring miRNA functions have been a critical strategy for understanding normal biological processes of miRNAs an...

journal_title：Briefings in bioinformatics

authors： Liu B,Li J,Cairns MJ

更新日期：2014-01-01 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：: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