Benjamen White
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View article: De novo annotation of the wheat pan-genome reveals complexity and diversity of the hexaploid wheat pan-transcriptome
De novo annotation of the wheat pan-genome reveals complexity and diversity of the hexaploid wheat pan-transcriptome Open
Wheat is the most widely cultivated crop in the world with over 215 million hectares grown annually. However, to meet the demands of a growing global population, breeders face the challenge of increasing wheat production by approximately 6…
View article: Circadian regulation of the transcriptome in a complex polyploid crop
Circadian regulation of the transcriptome in a complex polyploid crop Open
The circadian clock is a finely balanced timekeeping mechanism that coordinates programmes of gene expression. It is currently unknown how the clock regulates expression of homoeologous genes in polyploids. Here, we generate a high-resolut…
View article: Whole genome sequencing of a wild yam species <i>Dioscorea tokoro</i> reveals a genomic region associated with sex
Whole genome sequencing of a wild yam species <i>Dioscorea tokoro</i> reveals a genomic region associated with sex Open
Dioscorea tokoro is a wild species distributed in East Asia including Japan. Typical of the genus Dioscorea, D. tokoro is dioecious with male and female flowers borne on separate individuals. To understand its sex determination system and …
View article: Circadian regulation of the transcriptome in a complex polyploid crop
Circadian regulation of the transcriptome in a complex polyploid crop Open
The circadian clock is a finely balanced time-keeping mechanism that coordinates programmes of gene expression. It is currently unknown how the clock regulates expression of homoeologous genes in polyploids. Here, we generate a high-resolu…
View article: Genome analyses reveal the hybrid origin of the staple crop white Guinea yam ( <i>Dioscorea rotundata</i> )
Genome analyses reveal the hybrid origin of the staple crop white Guinea yam ( <i>Dioscorea rotundata</i> ) Open
Significance Guinea yam is an important staple tuber crop in West Africa, where it contributes to the sustenance and sociocultural lives of millions of people. Understanding the genetic diversity of Guinea yam and its relationships with wi…
View article: Genome analyses reveal the hybrid origin of the staple food crop white Guinea yam
Genome analyses reveal the hybrid origin of the staple food crop white Guinea yam Open
White Guinea yam ( Dioscorea rotundata ) is an important staple tuber crop of West Africa. However, its origin remains unclear. In this study, we re-sequenced 336 accessions of white Guinea yam and compared them with the sequences of the w…
View article: Research Libraries: How You Can Support Text and Data Mining
Research Libraries: How You Can Support Text and Data Mining Open
Europe’s incoming Directive on Copyright in the Digital Single Market contains two new exceptions allowing text and data mining (TDM). The Directive is currently being implemented by all member states and must come into force no later than…
View article: Additional file 11: Supplemental dataset S9. of Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination
Additional file 11: Supplemental dataset S9. of Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination Open
Top 50 highest expressed genes observed to be enriched in tuber. (XLSX 59 kb)
View article: Additional file 1: Tables S1â S20. of Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination
Additional file 1: Tables S1â S20. of Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination Open
Supplementary data including world yam production statistics [94] (Table S1), summary of genome sequence reads (Table S2), summary of genome assembly (Table S3), CEGMA result [95] (Table S4), BUSCO result (Table S5), summary of chloroplast…
View article: Additional file 4: Supplemental dataset S2. of Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination
Additional file 4: Supplemental dataset S2. of Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination Open
Gene orthology between four angiosperms showing presence, absence, and duplication between species. (XLSX 1250 kb)
View article: Additional file 9: Supplemental dataset S7. of Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination
Additional file 9: Supplemental dataset S7. of Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination Open
Non-redundant Gene Ontology terms for 2795 genes significantly (after FDR correction) enriched in D. rotundata with orthologous genes identified in A. thaliana, B. distachyon, O. sativa, E. guineensis, P. dactylifera, and M. acuminata. (XL…
View article: Additional file 8: Supplemental dataset S6. of Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination
Additional file 8: Supplemental dataset S6. of Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination Open
Functional annotation of D. rotundata genes with no orthologous genes found in A. thaliana, B. distachyon, O. sativa, E. guineensis, P. dactylifera, and M. acuminata. (XLSX 720 kb)
View article: Additional file 3: Supplemental dataset S1. of Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination
Additional file 3: Supplemental dataset S1. of Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination Open
List of the 26,198 protein coding genes predicted in the D. rotundata genome. (XLSX 1480 kb)
View article: Additional file 10: Supplemental dataset S8. of Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination
Additional file 10: Supplemental dataset S8. of Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination Open
Non-redundant Gene Ontology terms for 11,348 genes significantly (after FDR correction) enriched in D. rotundata with no orthologous genes identfied in A. thaliana, B. distachyon, O. sativa, E. guineensis, P. dactylifera, and M. acuminata.…
View article: Additional file 5: Supplemental dataset S3. of Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination
Additional file 5: Supplemental dataset S3. of Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination Open
Functional annotation of D. rotundata genes conserved between D. rotundata and at least one other angiosperm (A. thaliana, B. distachyon, and O. sativa). (XLSX 639 kb)
View article: Additional file 7: Supplemental dataset S5. of Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination
Additional file 7: Supplemental dataset S5. of Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination Open
Functional annotation of D. rotundata genes conserved between D. rotundata and at least one other angiosperm (A. thaliana, B. distachyon, O. sativa, E. guineensis, P. dactylifera, and M. acuminata). (XLSX 356 kb)
View article: Additional file 12: Supplemental dataset S10. of Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination
Additional file 12: Supplemental dataset S10. of Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination Open
List of genes predicted within the female-specific (W-linked) region on pseudo-chromosome 11 identified by QTL-seq. (XLSX 464 kb)
View article: Additional file 13: Supplemental dataset S11. of Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination
Additional file 13: Supplemental dataset S11. of Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination Open
New SSR markers developed from D. rotundata genome sequence. (XLSX 126 kb)
View article: Additional file 6: Supplemental dataset S4. of Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination
Additional file 6: Supplemental dataset S4. of Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination Open
Gene orthology between seven angiosperms showing presence, absence, and duplication between species. (XLSX 2360 kb)
View article: ISCB-Student Council Narratives: Strategical development of the ISCB-Regional Student Groups in 2016
ISCB-Student Council Narratives: Strategical development of the ISCB-Regional Student Groups in 2016 Open
Regional Student Groups are groups established and managed by the ISCB-Student Council in different regions of the world. The article highlights some of the initiatives and management lessons from our 'top-performing' Spotlight Regional St…
View article: Highlights of the 2nd Bioinformatics Student Symposium by ISCB RSG-UK
Highlights of the 2nd Bioinformatics Student Symposium by ISCB RSG-UK Open
Following the success of the 1st Student Symposium by ISCB RSG-UK, a 2nd Student Symposium took place on 7th October 2015 at The Genome Analysis Centre, Norwich, UK. This short report summarizes the main highlights from the 2nd Bioinformat…
View article: BioJS2Galaxy - A step by step guide
BioJS2Galaxy - A step by step guide Open
By Benedikt Rauscher, Benjamen White – 12/07/2015. To encourage the use of BioJavaScript (BioJS) visualisations in Galaxy we decided to create this simple step by step guide on how to use @MrGreenify’s application, biojs2galaxy, which he i…