Wednesday, 22 April 2015

List of Publications

Jennifer Deegan was previously a research scientist at the Universities of Glasgow and Cambridge, the John Innes Centre and EMBL-EBI. She is now a stay-at-home Mum, and volunteers in independent plant science research at the Department of Plant Sciences at the University of Cambridge.

Equal Opportunities Biographies

Department of Plant Sciences, University of Cambridge

Royal Society

Research Grants

Biomaker Challenge 2017 - Winner of Biomaker Spirit Trophy 

This was a project to build a working focus stacking photography system to take photographs of gametophyte ferns at 10x magnification.

We built the system successfully and some good photographs, showing that the system worked.

The photos can be seen at

A write-up of the system, which is still developing, can be seen at

OpenPlant 2017

This was a further grant from the same organisation to enable us to extend the range of magnifications of the system. 

We also committed to creating teaching materials to explain how others could build simpler versions of the same system at secondary school and undergraduate level. We further committed to document how other labs could build exact copies of our professional system to take photos in their own labs. 

Working with collaborators at John Innes Centre and the Sainsbury Laboratories in Cambridge we would attempt to photograph Utricularia gibba traps and Arabidopsis thaliana trichomes. 

This work is currently in progress. 

Academic science - Plant Science 

Clark JI, Coen ES. The cycloidea gene can respond to a common dorsoventral prepattern in Antirrhinum. Plant J. 2002 Jun;30(6):639-48.

 Da Luo, Carpenter R, Copsey L, Vincent C, Clark JI, and Coen ES. Control of Organ Asymmetry in Flowers of Antirrhinum. Cell, Vol. 99, 367-376, November 12, 1999. 

Deegan, J. (2017). Photographing The Fern Gametophyte Developmental Series – The First Attempt. Pteridologist, 6 (4), 263-265.

Deegan, J. and Deegan, T. (2018) Macrophotography of fern gametophytes using a focus stacking system. Accepted for publication 2017.

Academic science - Bioinformatics 

First Author 

Deegan JI, Dimmer EC, Mungall CJ. Formalization of taxon-based constraints to detect inconsistencies in annotation and ontology development. BMC Bioinformatics. 2010; 11 : 530.

 Clark JI, Brooksbank C, Lomax J. It's all GO for plant scientists. Plant Physiol. 2005 Jul;138(3):1268-79.

Supervising Author 

Feltrin E, Campanaro S, Diehl AD, Ehler E, Faulkner G, Fordham J, Gardin C, Harris M, Hill D, Knoell R, Laveder P, Mittempergher L, Nori A, Reggiani C, Sorrentino V, Volpe P, Zara I, Valle G and Deegan née Clark J. Muscle Research and Gene Ontology: New standards for improved data integration. BMC Medical Genomics 2009, 2:6


Mungall CJ, Bada M, Berardini TZ, Deegan JI, Ireland A, Harris MA, Hill DP, Lomax J. Cross-Product Extensions of the Gene Ontology. J Biomed Inform. 2011 February ; 44(1): 80-86

Gene Ontology Consortium. The Gene Ontology (GO) database and informatics resource. Nucleic Acids Research, 2004, Vol. 32, Database issue

 Wortman JR, Gilsenan JM, Joardar V, Deegan JI, et al. The 2008 update of the Aspergillus nidulans genome annotation: a community effort. Fungal Genet Biol. 2009 March; 46(Suppl 1): S2 : 13.

The Gene Ontology Consortium. The Gene Ontology in 2010: extensions and refinements. Nucleic Acids Research, 2010, Vol. 38, Database issue.

Gene Ontology Consortium. The Gene Ontology (GO) project in 2006. D322-D326 Nucleic Acids Research, 2006, Vol. 34, Database issue Gene Ontology Consortium. "An Introduction to the Gene Ontology." (2004).

Day-Richter J, Harris MA, Haendel M, The Gene Ontology OBO-Edit Working Group, Lewis S. OBO-Edit - an ontology editor for biologists. Bioinformatics Applications Note. Vol. 23 no. 16 2007, pages 2198-2200

Harris MA, Deegan JI et al. The Gene Ontology project in 2008. D440-D444 Nucleic Acids Research, 2008, Vol. 36, Database issue.

Sacks, O., Barry, S.R., Fixing My Gaze: A Scientist's Journey into Seeing in Three Dimensions (2010), Basic Books; First Trade Paper Edition edition.

Popular Press: Garden Writing

Asystasia Chinese Violet Control: Information On Chinese Violet Growing Conditions, Gardening Know How, March 2013.

An Artists' Colony, Gardeners' World Magazine, October 2012.

Just like Topsy, Amateur Gardening, 22/29 December 2012.

Be careful what you wish for, Gardeners' World Magazine, July 2013.

Untitled comment, Gardeners' World Magazine, August 2013.

Technical writing for websites

MailOrderTrees: Quality British Grown Trees:

Plant descriptions:
Blog posts:

Current affairs 

Apply the bleeper to SNP's speeches, Financial Times, April 12 2013.

UK's future could rest on a single vote, Financial Times, August 11 2014

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