Recent Publications and Acknowledgements

The Research Computing (CiS) staff and infrastructure have been acknowledged in the below publications.

InstitutesYearAuthorsPaper Title & Link
EI2019Akay et al Identification of functional long non-coding RNAs in C. elegans
EI2019Paajanen et al A critical comparison of technologies for a plant genome sequencing project
JIC2019Arora et al Resistance gene cloning from a wild crop relative by sequence capture and association genetics
TSL2019Rallapalli et al Rapid fine mapping of causative mutations from sets of unordered, contig-sized fragments of genome sequence
JIC2019He et al Natural depletion of H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation
EI2018Johnson et al Adaptation and conservation insights from the koala genome
EI2018Cocker et al Primula vulgaris (primrose) genome assembly, annotation and gene expression, with comparative genomics on the heterostyly supergene
EI2018Venturini et al Leveraging multiple transcriptome assembly methods for improved gene structure annotation
EI2018Thanki et al GeneSeqToFamily: a Galaxy workflow to find gene families based on the Ensembl Compara GeneTrees pipeline
EI, JIC, QIB, TSL2018Jouet et al Albugo candida race diversity, ploidy and host-associated microbes revealed using DNA sequence capture on diseased plants in the field
EI, JIC, TSL2018Appels et al Shifting the limits in wheat research and breeding using a fully annotated reference genome
JIC2018Vior et al Discovery and Biosynthesis of the Antibiotic Bicyclomycin in Distantly Related Bacterial Classes
JIC2018Lewis et al Potential for re-emergence of wheat stem rust in the United Kingdom
JIC2018Horler et al SeedStor: A Germplasm Information Management System and Public Database.
JIC2018Tavares et al Selection and gene flow shape genomic islands that control floral guides
EI2017Leggett et al A world of opportunities with nanopore sequencing
EI2017Mapleson et al KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies
EI2017Clavijo et al W2RAP: a pipeline for high quality, robust assemblies of large complex genomes from short read data
EI, JIC2017Eckes et al Introducing the Brassica Information Portal: Towards integrating genotypic and phenotypic Brassica crop data
EI, JIC, TSL2017Krasileva et al Uncovering hidden variation in polyploid wheat
JIC, TSL2017Woolfenden et al A computational approach for inferring the cell wall properties that govern guard cell dynamics
EI2016Thanki et al Aequatus: An open-source homology browser
EI2016Islam et al Emergence of wheat blast in Bangladesh was caused by a South American lineage of Magnaporthe oryzae
JIC2016Hsieha et al Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues
JIC2016Park et al DNA demethylation is initiated in the central cells of Arabidopsis and rice
JIC2016Borrill et al expVIP: a Customizable RNA-seq Data Analysis and Visualization Platform
JIC2016Dobon et al The host-pathogen interaction between wheat and yellow rust induces temporally coordinated waves of gene expression
JIC, TSL2016Steuernagel et al Rapid cloning of disease-resistance genes in plants using mutagenesis and sequence capture
JIC2015Delauxa et al Algal ancestor of land plants was preadapted for symbiosis
JIC, TSL, QIB2015Rickett et al Incorporating prior knowledge improves detection of differences in bacterial growth rate

Acknowledging CiS in your work

We would appreciate the acknowledgement of the use of our services and infrastructure, by including the following statement in any resulting publication:

This research was supported in part by the NBI Computing infrastructure for Science (CiS) group through [list CiS resources]. [We specifically acknowledge the assistance of <relevant CiS staff members’ names>]

We would also appreciate the consistent use of the bold text above, followed by a list of the specific resources used and, if pertinent, the names of the CiS staff involved.