Expansion of the eukaryotic proteome by alternative splicing

TW Nilsen, BR Graveley - Nature, 2010 - nature.com
The collection of components required to carry out the intricate processes involved in
generating and maintaining a living, breathing and, sometimes, thinking organism is …

RNA-seq: from technology to biology

S Marguerat, J Bähler - Cellular and molecular life sciences, 2010 - Springer
Next-generation sequencing technologies are now being exploited not only to analyse static
genomes, but also dynamic transcriptomes in an approach termed RNA-seq. Although these …

Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project

MB Gerstein, ZJ Lu, EL Van Nostrand, C Cheng… - Science, 2010 - science.org
We systematically generated large-scale data sets to improve genome annotation for the
nematode Caenorhabditis elegans, a key model organism. These data sets include …

Evolutionarily conserved principles predict 3D chromatin organization

MJ Rowley, MH Nichols, X Lyu, M Ando-Kuri… - Molecular cell, 2017 - cell.com
Topologically associating domains (TADs), CTCF loop domains, and A/B compartments
have been identified as important structural and functional components of 3D chromatin …

Formation, regulation and evolution of Caenorhabditis elegans 3′UTRs

CH Jan, RC Friedman, JG Ruby, DP Bartel - Nature, 2011 - nature.com
Post-transcriptional gene regulation frequently occurs through elements in mRNA 3′
untranslated regions (UTRs),. Although crucial roles for 3′ UTR-mediated gene regulation …

A Systematically Improved High Quality Genome and Transcriptome of the Human Blood Fluke Schistosoma mansoni

AV Protasio, IJ Tsai, A Babbage, S Nichol… - PLoS neglected …, 2012 - journals.plos.org
Schistosomiasis is one of the most prevalent parasitic diseases, affecting millions of people
in develo** countries. Amongst the human-infective species, Schistosoma mansoni is also …

Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome

G Zhang, G Guo, X Hu, Y Zhang, Q Li, R Li… - Genome …, 2010 - genome.cshlp.org
Understanding the dynamics of eukaryotic transcriptome is essential for studying the
complexity of transcriptional regulation and its impact on phenotype. However …

RNA‐Seq: a method for comprehensive transcriptome analysis

U Nagalakshmi, K Waern… - Current protocols in …, 2010 - Wiley Online Library
A recently developed technique called RNA Sequencing (RNA‐Seq) uses massively
parallel sequencing to allow transcriptome analyses of genomes at a far higher resolution …

Identification of fusion genes in breast cancer by paired-end RNA-sequencing

H Edgren, A Murumagi, S Kangaspeska, D Nicorici… - Genome biology, 2011 - Springer
Background Until recently, chromosomal translocations and fusion genes have been an
underappreciated class of mutations in solid tumors. Next-generation sequencing …

Balanced codon usage optimizes eukaryotic translational efficiency

W Qian, JR Yang, NM Pearson, C Maclean… - PLoS genetics, 2012 - journals.plos.org
Cellular efficiency in protein translation is an important fitness determinant in rapidly growing
organisms. It is widely believed that synonymous codons are translated with unequal …