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 March 2013 - Sequencing error correction without a reference genome

The Phenomics and Bioinformatics Research Centre has recently published an article in the journal BMC Bioinformatics which has attracted wide interest. The article, ‘Sequencing error correction without a reference genome’, was authored by PBRC member Julie Sleep and collaborators at the Centre for Cancer Biology and Australian Centre for Plant Functional Genomics.

This research tackles the important problem of identifying sequencing errors in next generation sequencing data, in the difficult case where a reference genome is not available. Methods, such as the one developed, are a critical step in microRNA studies, unsequenced genomes, and variant detection in ultra-deep sequencing.

This ‘highly accessed’ paper was ranked the #1 most popular article in the BMC Bioinformatics in terms of accesses for approximately 5 weeks after publication, and has been widely shared on social media. It is an open access article, freely available at this location with the corresponding software available here.

September 2013 - Plant root transport

Kylie Foster, PhD Student and Professor Stan Miklavcic, both of the Phenomics and Bioinformatics Research Centre, have recently had 2 papers accepted in the prestigious Journal of Theoretical Biology. "Mathematical modelling of the uptake and transport of salt in plant roots", represents significant new work in the modelling of ion transport, taking account of local variations in ion and water permeabilities across tissue regions. The second paper, "On the competitive uptake and transport of ions through differentiated root tissues", builds upon this work by taking account of differences in root tissue permeability to solutes and water, resulting in further insights into how plants take up nutrients as well as toxic ions from the soil.

September 2013 - Continuing collaborations

Three researchers from the Phenomics and Bioinformatics Research Centre recently visited the Centre for Plant Integrative Biology at the University of Nottingham. As well as attending workshops, and participating in many research discussions, Dr Chris Brien presented the seminar “Accounting for variation in designing greenhouse experiments with special reference to greenhouses containing plants on conveyor systems”, Ms Kylie Foster presented her work on “Mathematical modelling of salt and water uptake and transport in plant roots” and Mr Josh Chopin presented a seminar on his work on “Mathematical and Computational Modelling for the Phenotypic Analysis in Plant Biology”. These visits continue the PBRC’s collaboration with CPIB initiated by Professor Miklavcic earlier in 2013.

December 2012 - GRDC Scholarship Success

Congratulations to PBRC PhD Students Kylie Foster and Josh Chopin who were each awarded a Grains Industry Research Scholarship from the Grains Research and Development Corporation (GRDC). These awards include a tax-free PhD top-up scholarship of $18,500 per annum and a $10,000 per annum project fund. Kylie's PhD project involves the mathematical modelling of salt and water uptake and transport in plants for improved understanding of plant salinity tolerance, and Josh's PhD project involves the mathematical and computational analysis of plant images and 3D reconstruction of plant shapes for application to plant phenotyping. Earlier this year, PBRC Honours student Marcela Cespedes was also successful in obtaining a Grains Industry Undergraduate Honours Scholarship.

December 2012 - Best Paper Award

PBRC researchers Dr Hamid Laga and Professor Stan Miklavcic, along with their collaborators, were awarded the best paper award at the recent Digital Image Computing: Techniques and Applications (DICTA 2012) conference. Their paper was entitled "A Riemannian elastic metric for shape-based plant leaf classification".



PBRC Seminar Series 2014

Formal seminars are held on the Mawson Lakes campus throughout the year. The seminar co-ordinator is Dr Hamid Laga. All are welcome to attend these events.



Seminar Title

Time & Location

14 April 2014 Professor Shaun Hendy, University of Auckland TBA Mawson Lakes
19 May 2014 Professor Graham Farquhar, Australian National University TBA Mawson Lakes
2014 Professor John Sader, University of Melbourne TBA Mawson Lakes

Areas of study and research

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