Dual RNA-seq of pathogen and host
AJ Westermann, SA Gorski, J Vogel - Nature Reviews Microbiology, 2012 - nature.com
A comprehensive understanding of host–pathogen interactions requires a knowledge of the
associated gene expression changes in both the pathogen and the host. Traditional, probe …
associated gene expression changes in both the pathogen and the host. Traditional, probe …
Analysing and interpreting DNA methylation data
C Bock - Nature Reviews Genetics, 2012 - nature.com
DNA methylation is an epigenetic mark that has suspected regulatory roles in a broad range
of biological processes and diseases. The technology is now available for studying DNA …
of biological processes and diseases. The technology is now available for studying DNA …
MYC regulates the antitumor immune response through CD47 and PD-L1
SC Casey, L Tong, Y Li, R Do, S Walz, KN Fitzgerald… - Science, 2016 - science.org
The MYC oncogene codes for a transcription factor that is overexpressed in many human
cancers. Here we show that MYC regulates the expression of two immune checkpoint …
cancers. Here we show that MYC regulates the expression of two immune checkpoint …
JBrowse: a dynamic web platform for genome visualization and analysis
Background JBrowse is a fast and full-featured genome browser built with JavaScript and
HTML5. It is easily embedded into websites or apps but can also be served as a standalone …
HTML5. It is easily embedded into websites or apps but can also be served as a standalone …
HBV DNA integration and clonal hepatocyte expansion in chronic hepatitis B patients considered immune tolerant
WS Mason, US Gill, S Litwin, Y Zhou, S Peri, O Pop… - Gastroenterology, 2016 - Elsevier
Background & Aims Chronic infection with hepatitis B virus (HBV) progresses through
different phases. The first, called the immune-tolerant phase, has been associated with a …
different phases. The first, called the immune-tolerant phase, has been associated with a …
Dual RNA-seq unveils noncoding RNA functions in host–pathogen interactions
Bacteria express many small RNAs for which the regulatory roles in pathogenesis have
remained poorly understood due to a paucity of robust phenotypes in standard virulence …
remained poorly understood due to a paucity of robust phenotypes in standard virulence …
RNA methylomes reveal the m6A-mediated regulation of DNA demethylase gene SlDML2 in tomato fruit ripening
L Zhou, S Tian, G Qin - Genome biology, 2019 - Springer
Background Methylation of nucleotides, notably in the forms of 5-methylcytosine (5mC) in
DNA and N 6-methyladenosine (m 6 A) in mRNA, carries important information for gene …
DNA and N 6-methyladenosine (m 6 A) in mRNA, carries important information for gene …
Identifying ChIP-seq enrichment using MACS
Abstract Model-based analysis of ChIP-seq (MACS) is a computational algorithm that
identifies genome-wide locations of transcription/chromatin factor binding or histone …
identifies genome-wide locations of transcription/chromatin factor binding or histone …
The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools
P Lamesch, TZ Berardini, D Li, D Swarbreck… - Nucleic acids …, 2012 - academic.oup.com
Abstract The Arabidopsis Information Resource (TAIR, http://arabidopsis. org) is a genome
database for Arabidopsis thaliana, an important reference organism for many fundamental …
database for Arabidopsis thaliana, an important reference organism for many fundamental …
Integrated genome browser: visual analytics platform for genomics
NH Freese, DC Norris, AE Loraine - Bioinformatics, 2016 - academic.oup.com
Motivation: Genome browsers that support fast navigation through vast datasets and provide
interactive visual analytics functions can help scientists achieve deeper insight into …
interactive visual analytics functions can help scientists achieve deeper insight into …