Abstract:
:Relative changes in mRNA as well as protein levels induced by sublethal doses of antibiotics on bacteria are measured and results visualised in the context of metabolic pathway diagrams. The mRNA levels present at a given time point after the addition of the antibiotic are measured using microarrays from Affymetrix. Additionally, the relative amount of each protein synthesised during 3 minute intervals sampled at the given times is measured using radio-labelling followed by two-dimensional polyacrylamide gel electrophoresis and the subsequent analysis of the images produced by exposure to a phosphorimager. Metabolic pathway diagrams are both constructed in-house and imported from KEGG (Kyoto Encyclopedia of Genes and Genomes). Both protein and mRNA expression data can be displayed in the pathway diagrams such that the colour of the vectors or enzyme identifiers indicate the relative change in expression level and reproducibility.
journal_name
Brief Bioinformjournal_title
Briefings in bioinformaticsauthors
Wolf D,Gray CP,de Saizieu Adoi
10.1093/bib/1.3.297keywords:
subject
Has Abstractpub_date
2000-09-01 00:00:00pages
297-304issue
3eissn
1467-5463issn
1477-4054journal_volume
1pub_type
杂志文章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
pub_type: 杂志文章,评审
doi:10.1093/bib/bby038
更新日期:2019-09-27 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 However, most of the existing approaches use the outdated pathway information and neglect the complex gene interactions in pathway.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
pub_type: 杂志文章
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更新日期:2019-01-18 00:00:00
abstract::Biologists very often use enrichment methods based on statistical hypothesis tests to identify gene properties that are significantly over-represented in a given set of genes of interest, by comparison with a 'background' set of genes. These enrichment methods, although based on rigorous statistical foundations, are n...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
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更新日期:2020-05-21 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
pub_type: 杂志文章,评审
doi:10.1093/bib/5.4.339
更新日期:2004-12-01 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
pub_type: 杂志文章
doi:10.1093/bib/bbaa332
更新日期:2020-12-15 00:00:00
abstract::Functional annotation of protein sequence with high accuracy has become one of the most important issues in modern biomedical studies, and computational approaches of significantly accelerated analysis process and enhanced accuracy are greatly desired. Although a variety of methods have been developed to elevate prote...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbz081
更新日期:2020-07-15 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
pub_type: 杂志文章
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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
pub_type: 杂志文章
doi:10.1093/bib/bbx011
更新日期:2018-07-20 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
pub_type: 杂志文章
doi:10.1093/bib/bbaa191
更新日期:2020-08-26 00:00:00
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journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bby122
更新日期:2020-03-23 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
pub_type: 杂志文章
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更新日期:2020-12-30 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
pub_type: 历史文章,杂志文章
doi:10.1093/bib/bbu022
更新日期:2015-03-01 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
pub_type: 杂志文章
doi:10.1093/bib/bbr073
更新日期:2013-03-01 00:00:00
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journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/4.3.260
更新日期:2003-09-01 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
pub_type: 杂志文章
doi:10.1093/bib/bbz090
更新日期:2020-09-25 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
pub_type: 历史文章,杂志文章,评审
doi:10.1093/bib/bby063
更新日期:2019-11-27 00:00:00
abstract::The so-called 'omics' approaches used in modern biology aim at massively characterizing the molecular repertories of living systems at different levels. Metabolomics is one of the last additions to the 'omics' family and it deals with the characterization of the set of metabolites in a given biological system. As meta...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbs055
更新日期:2013-11-01 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
pub_type: 杂志文章,评审
doi:10.1093/bib/bbx139
更新日期:2019-05-21 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
pub_type: 杂志文章
doi:10.1093/bib/bbv109
更新日期:2016-11-01 00:00:00
abstract::We introduce the Beta Workbench (BWB), a scalable tool built on top of the newly defined BlenX language to model, simulate and analyse biological systems. We show the features and the incremental modelling process supported by the BWB on a running example based on the mitogen-activated kinase pathway. Finally, we prov...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbn023
更新日期:2008-09-01 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
pub_type: 杂志文章
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更新日期:2020-12-21 00:00:00
abstract::As the number of completely sequenced genomes rapidly increases, including now the complete Human Genome sequence, the post-genomic problems of genome-scale protein structure determination and the issue of gene function identification become ever more pressing. In fact, these problems can be seen as interrelated in th...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章,评审
doi:10.1093/bib/2.2.111
更新日期:2001-05-01 00:00:00
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pub_type: 杂志文章
doi:10.1093/bib/bbr030
更新日期:2011-09-01 00:00:00
abstract::The prevalence of dropout events is a serious problem for single-cell Hi-C (scHiC) data due to insufficient sequencing depth and data coverage, which brings difficulties in downstream studies such as clustering and structural analysis. Complicating things further is the fact that dropouts are confounded with structura...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbaa289
更新日期:2020-11-17 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
pub_type: 杂志文章,评审
doi:10.1093/bib/bby028
更新日期:2019-03-25 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
pub_type: 杂志文章
doi:10.1093/bib/bbp051
更新日期:2009-11-01 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
pub_type: 杂志文章
doi:10.1093/bib/bbaa246
更新日期:2020-10-03 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
pub_type: 杂志文章,评审
doi:10.1093/bib/bbm037
更新日期:2007-09-01 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
pub_type: 杂志文章,评审
doi:10.1093/bib/bbp046
更新日期:2010-03-01 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
pub_type: 杂志文章
doi:10.1093/bib/bbv091
更新日期:2016-09-01 00:00:00