Research

Janet Higgins

Computational Biologist

Biography.

Contact details:

+44 (0) 1603 450 092

janet.higgins@earlham.ac.uk

Janet Higgins is a postdoctoral research scientist in the De Vega group, she is currently part of the Agricultural Diversity Research Program of the GROW Colombia Project, where she aims at “Building Genetic resources to accelerate the breeding of crops relevant for Colombia”. Janet previously worked in the Core Genomics team and has a wide experience of bioinformatics. Within the De Vega group, Janet has been able to develop her interest in plant genomics. Her previous project explored signatures of selection and novel diversity in over 650 native rice genomes during the breeding of rice within Vietnam.

Janet has a wide interest in Natural History and is a Fellow of the Linnean Society and an active member of the Botanical Society of Britain & Ireland and Norfolk Wildlife Trust for which she participates in botanical surveys.

Projects.

Sustaining and improving rice in the face of climate change

Improving tolerance in tropical forage crops

Publications.

Exploring gene networks in two sunflower lines with contrasting leaf senescence phenotype using a system biology approach.

Oct 2019

Moschen S., Marino J., Nicosia S., Higgins J., Alseekh S., Astigueta F., Bengoa Luoni S., Rivarola M., Fernie A. R., Blanchet N., Langlade N. B., Paniego N., Fernández P., Heinz R. A.

Exploring gene networks in two sunflower lines with contrasting leaf senescence phenotype using a system biology approach.

BMC Plant Biology

Publishers version: doi:10.1186/s12870-019-2021-6

Genome-Wide Transcription During Early Wheat Meiosis Is Independent of Synapsis, Ploidy Level, and the Ph1 Locus.

Dec 2018

Martin A. C., Borrill P., Higgins J., Alabdullah A., Ramirez-Gonzalez R. H., Swarbreck D., Uauy C., Shaw P., Moore G.

Genome-Wide Transcription During Early Wheat Meiosis Is Independent of Synapsis, Ploidy Level, and the Ph1 Locus.

Frontiers in plant science

Publishers version: doi:10.3389/fpls.2018.01791

microRNAs associated with early neural crest development in Xenopus laevis.

Jan 2018

Ward N. J., Green D., Higgins J., Dalmay T., Münsterberg A., Moxon S., Wheeler G. N.

microRNAs associated with early neural crest development in Xenopus laevis.

BMC Genomics

Publishers version: doi:10.1186/s12864-018-4436-0

Exploiting the ZIP4 homologue within the wheat Ph1 locus has identified two lines exhibiting homoeologous crossoverin wheat-wild relative hybrids

Jul 2017

Rey M. D., Martin A., Higgins J., Swarbreck D., Uauy C., Shaw P., Moore G.

Exploiting the ZIP4 homologue within the wheat Ph1 locus has identified two lines exhibiting homoeologous crossoverin wheat-wild relative hybrids

Molecular Breeding

Publishers version: doi:10.1007/s11032-017-0700-2

Integration of transcriptomic and metabolic data reveals hub transcription factors involved in drought stress response in sunflower (Helianthus annuus L.).

Jul 2017

Moschen S., Di Rienzo J. A., Higgins J., Tohge T., Watanabe M., González S., Rivarola M., García-García F., Dopazo J., Hopp H. E., Hoefgen R., Fernie A. R., Paniego N., Fernández P., Heinz R. A.

Integration of transcriptomic and metabolic data reveals hub transcription factors involved in drought stress response in sunflower (Helianthus annuus L.).

Plant molecular biology

Publishers version: doi:10.1007/s11103-017-0625-5

Heterarchy of Transcription Factors Driving Basal and Luminal Cell Phenotypes in Human Urothelium Revealed by Open Chromatin Profiling

May 2017

Fishwick C., Higgins J., Percival-Alwyn L., Hustler A., Pearson J., Hinley J., Bastkowski S., Moxon S., Swarbreck D., Greenman C., Southgate J.

Heterarchy of Transcription Factors Driving Basal and Luminal Cell Phenotypes in Human Urothelium Revealed by Open Chromatin Profiling

Cell Death and Differentiation

Publishers version: doi:10.1038/cdd.2017.10

Network and biosignature analysis for the integration of transcriptomic and metabolomic data to characterize leaf senescence process in sunflower.

Jun 2016

Moschen S., Higgins J., Di Rienzo J. A., Heinz R. A., Paniego N., Fernandez P.

Network and biosignature analysis for the integration of transcriptomic and metabolomic data to characterize leaf senescence process in sunflower.

BMC Bioinformatics

Publishers version: doi:10.1186/s12859-016-1045-2

Seedling development traits in Brassica napus examined by gene expression analysis and association mapping.

Jun 2015

Körber N., Bus A., Li J., Higgins J., Bancroft I., Higgins E. E., Papworth Parkin I. A., Salazar-Colqui B., Snowdon R. J., Stich B.

Seedling development traits in Brassica napus examined by gene expression analysis and association mapping.

BMC Plant Biology

Publishers version: doi:10.1186/s12870-015-0496-3

Jun 2012

Higgins J. A., Magusin A., Trick M., Fraser F., Bancroft I.

Use of mRNA-Seq to discriminate contributions to the transcriptome from the constituent genomes of the polyploid crop species Brassica napus.

BMC Genomics

Publishers version: doi:10.1186/1471-2164-13-247

Dissecting the genome of the polyploid crop oilseed rape by transcriptome sequencing.

Aug 2011

Bancroft I., Morgan C., Fraser F., Higgins J., Wells R., Clissold L., Baker D., Long Y., Meng J., Wang X., Liu S., Trick M.

Dissecting the genome of the polyploid crop oilseed rape by transcriptome sequencing.

Nature Biotechnology

Publishers version: doi:10.1038/nbt.1926

Apr 2010

Higgins J. A., Bailey P. C., Laurie D. A.

Comparative genomics of flowering time pathways using Brachypodium distachyon as a model for the temperate grasses

PLoS ONE

Publishers version: doi:10.1371/journal.pone.0010065

Feb 2010

Wright J. M., Febrer M., McKenzie N., Byrne M. E., Walsh S., Higgins J., Bevan M. W.

Genome sequencing and analysis of the model grass Brachypodium distachyon

Nature

Publishers version: doi:10.1038/nature08747

Jun 2008

Tsesmetzis N., Couchman M., Higgins J., Smith A., Doonan J. H., Seifert G. J., Schmidt E. E., Vastrik I., Birney E., Wu G., D'Eustachio P., Stein L. D., Morris R. J., Bevan M. W., Walsh S. V.

Arabidopsis reactome: a foundation knowledgebase for plant systems biology.

Plant Cell

Publishers version: doi:10.1105/tpc.108.057976

May 2007

Faure S., Higgins J., Turner A., Laurie D. A.

The Flowering Locus T-like gene family in barley (Hordeum vulgare)

Genetics

Publishers version: doi:10.1534/genetics.106.069500

A draft genome sequence of grass pea (Lathyrus sativus), a resilient diploid legume

Apr 2020

Emmrich P. M. F., Sarkar A., Njaci I., Kaithakottil G. G., Ellis T. H. N., Moore C., Edwards A., Heavens D., Waite D., Cheema J., Trick M., Moore J., Webb A., Calazzo R., Thomas J., Higgins J., Swarbreck D., Kumar S., Mundree S., Loose M., Yant L., Martin C., Wang T. L.

A draft genome sequence of grass pea (Lathyrus sativus), a resilient diploid legume

https://biorxiv.org/cgi/content/short/2020.04.24.058164v1

Publishers version: doi:10.1101/2020.04.24.0581

Evidence of selection, adaptation and untapped diversity in Vietnamese rice landraces

Jul 2020

Higgins J,Bruno Santos,Tran Dang,Khuat Huu,Tran Duy,Nguyen Thi,Nguyen Truong,Dang Thi,Nguyen Thuy,Kieu Thi,Cong Nguyen,Tran Thi,Nguyen Thanh,Hoang Dung,Nguyen Thanh,Hoang Thi,Ta Kim,Cuong Duy,Son Vi,La Tuan,Nguyen Van,Tran Dang,Anthony Hall,Sarah Dyer,Le Huy,Mario Caccamo,Jose De

Evidence of selection, adaptation and untapped diversity in Vietnamese rice landraces

https://www.biorxiv.org/content/10.1101/2020.07.07.191981v1

Publishers version: doi:10.1101/2020.07.07.191981

Resequencing of 672 Native Rice Accessions to Explore Genetic Diversity and Trait Associations in Vietnam.

Jun 2021

Higgins J,Santos B,Khanh TD,Trung KH,Duong TD,Doai NTP,Khoa NT,Ha DTT,Diep NT,Dung KT,Phi CN,Thuy TT,Tuan NT,Tran HD,Trung NT,Giang HT,Nhung TK,Tran CD,Lang SV,Nghia T,Van Giang,Xuan TD,Hall A,Dyer S,Ham LH,Caccamo M,De Vega

Resequencing of 672 Native Rice Accessions to Explore Genetic Diversity and Trait Associations in Vietnam.

Rice (New York, N.Y.)

Publishers version: doi:10.1186/s12284-021-00481-0

Aug 2021

Higgins J.,Santos B.,Khanh T.D.,Trung K.H.,Duong T.D.,Doai N.T.P.,Hall A.,Dyer S.,Caccamo M.,De Vega J

Identifying genomic regions and candidate genes selected during the breeding of rice in Vietnam

bioRxiv

Publishers version: doi:0.1101/2021.08.04.455072

Jul 2021

Higgins J.,Tomaszewska P.,Pellny T.,Castiblanco V.,Arango J.,Tohme J.,Schwarzacher T.,Mitchell R.,Heslop-Harrison J.,De Vega J

The five Urochloa spp. used in development of tropical forage cultivars originate from defined subpopulations with differentiated gene pools

bioRxiv

Publishers version: doi:10.1101/2021.07.21.453213

Awards.

Daphne Jackson Fellowship 2004-2006

Janet Higgins

Biography.

Projects.

Sustaining and improving rice in the face of climate change

Improving tolerance in tropical forage crops

Publications.

Exploring gene networks in two sunflower lines with contrasting leaf senescence phenotype using a system biology approach.

Genome-Wide Transcription During Early Wheat Meiosis Is Independent of Synapsis, Ploidy Level, and the Ph1 Locus.

microRNAs associated with early neural crest development in Xenopus laevis.

Exploiting the ZIP4 homologue within the wheat Ph1 locus has identified two lines exhibiting homoeologous crossoverin wheat-wild relative hybrids

Integration of transcriptomic and metabolic data reveals hub transcription factors involved in drought stress response in sunflower (Helianthus annuus L.).

Heterarchy of Transcription Factors Driving Basal and Luminal Cell Phenotypes in Human Urothelium Revealed by Open Chromatin Profiling

Network and biosignature analysis for the integration of transcriptomic and metabolomic data to characterize leaf senescence process in sunflower.

Seedling development traits in Brassica napus examined by gene expression analysis and association mapping.

Use of mRNA-Seq to discriminate contributions to the transcriptome from the constituent genomes of the polyploid crop species Brassica napus.

Dissecting the genome of the polyploid crop oilseed rape by transcriptome sequencing.

Comparative genomics of flowering time pathways using Brachypodium distachyon as a model for the temperate grasses

Genome sequencing and analysis of the model grass Brachypodium distachyon

Arabidopsis reactome: a foundation knowledgebase for plant systems biology.

The Flowering Locus T-like gene family in barley (Hordeum vulgare)

A draft genome sequence of grass pea (Lathyrus sativus), a resilient diploid legume

Evidence of selection, adaptation and untapped diversity in Vietnamese rice landraces

Resequencing of 672 Native Rice Accessions to Explore Genetic Diversity and Trait Associations in Vietnam.

Identifying genomic regions and candidate genes selected during the breeding of rice in Vietnam

The five Urochloa spp. used in development of tropical forage cultivars originate from defined subpopulations with differentiated gene pools

Awards.

Related reading.

How bioinformatics can crack the complex case of protist biodiversity

The dramatic effects genomics will have on our future world

The inextricable link between climate change and biodiversity.

Hidden Biodiversity: How genomics can save nature’s secrets before they’re lost forever

Can we reach net zero & climate resilience? Here are 6 ways Earlham scientists are getting us there

Hybrid Wheat Initiative: the ‘holy grail’ of wheat breeding

From bloom to bust: Algae, the bountiful scum of the Earth

The blood boneyard: determining the fate of blood stem cells

N is for nitrogen: how can we make our crops sustainable?

How single-cell genomics can foil drug-resistant cancer

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