Cancer transcriptome profiling at the juncture of clinical translation
Methodological breakthroughs over the past four decades have repeatedly revolutionized
transcriptome profiling. Using RNA sequencing (RNA-seq), it has now become possible to …
transcriptome profiling. Using RNA sequencing (RNA-seq), it has now become possible to …
dbSNP—database for single nucleotide polymorphisms and other classes of minor genetic variation
ST Sherry, M Ward, K Sirotkin - Genome research, 1999 - genome.cshlp.org
Akey aspect of research in genetics is associating sequence variations with heritable
phenotypes. The most common variations are single nucleotide polymorphisms (SNPs) …
phenotypes. The most common variations are single nucleotide polymorphisms (SNPs) …
MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects
Background Second-generation sequencing technologies are precipitating major shifts with
regards to what kinds of genomes are being sequenced and how they are annotated. While …
regards to what kinds of genomes are being sequenced and how they are annotated. While …
Gaining comprehensive biological insight into the transcriptome by performing a broad-spectrum RNA-seq analysis
Abstract RNA-sequencing (RNA-seq) is an essential technique for transcriptome studies,
hundreds of analysis tools have been developed since it was debuted. Although recent …
hundreds of analysis tools have been developed since it was debuted. Although recent …
tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence
We describe a program, tRNAscan-SE, which identifies 99–100% of transfer RNA genes in
DNA sequence while giving less than one false positive per 15 gigabases. Two previously …
DNA sequence while giving less than one false positive per 15 gigabases. Two previously …
Genome-wide classification and expression analysis of MYB transcription factor families in rice and Arabidopsis
Background The MYB gene family comprises one of the richest groups of transcription
factors in plants. Plant MYB proteins are characterized by a highly conserved MYB DNA …
factors in plants. Plant MYB proteins are characterized by a highly conserved MYB DNA …
GenBank
DA Benson, M Cavanaugh, K Clark… - Nucleic acids …, 2012 - academic.oup.com
Abstract GenBank®(http://www. ncbi. nlm. nih. gov) is a comprehensive database that
contains publicly available nucleotide sequences for almost 260 000 formally described …
contains publicly available nucleotide sequences for almost 260 000 formally described …
Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays
Oligonucleotide arrays can provide a broad picture of the state of the cell, by monitoring the
expression level of thousands of genes at the same time. It is of interest to develop …
expression level of thousands of genes at the same time. It is of interest to develop …
GenBank
DA Benson, K Clark, I Karsch-Mizrachi… - Nucleic acids …, 2013 - pmc.ncbi.nlm.nih.gov
GenBank® is a comprehensive database that contains publicly available nucleotide
sequences for over 280 000 formally described species. These sequences are obtained …
sequences for over 280 000 formally described species. These sequences are obtained …
A quantitative atlas of polyadenylation in five mammals
A Derti, P Garrett-Engele, KD MacIsaac… - Genome …, 2012 - genome.cshlp.org
We developed PolyA-seq, a strand-specific and quantitative method for high-throughput
sequencing of 3′ ends of polyadenylated transcripts, and used it to globally map …
sequencing of 3′ ends of polyadenylated transcripts, and used it to globally map …