All posts by jameshane

Australasian Plant Pathology Society (APPS) Conference 2019 – Pathogen Bioinformatics Workshop 25th November, at AgriBio, La Trobe University

This year’s pathogen bioinformatics meeting will be held as a workshop of the APPS 2019 conference in Melbourne.  Please note that the workshop is held at the AgriBio building, La Trobe University.  For those of you staying near the MCEC where the main conference is being held, there will be a bus departing from MCEC at 8:30am going to AgriBio.  If you would like to catch this bus please contact or

Below is the program for the 2019 Pathogen Bioinformatics Meeting:

Time Start Time End Title Speaker Length Title
10:00 10:30 COFFEE 00:30
10:30 10:35 OPENING 00:05
10:35 11:05 TALK Jana Sperschneider 00:30
The chromosome-scale assembly of the flax rust fungus Melampsora lini: challenges of assembling a highly repetitive, dikaryotic fungal pathogen genome
11:05 11:25 TALK Belinda Fabian 00:20 Using genome-wide screening to identify genes important for bacterial colonisation of plant surfaces
11:25 11:55 MORNING TEA 00:30
11:55 12:25 TALK Rebekah Frampton 00:30 Genome of Bactericera cockerelli: Sequencing, assembly, and annotation
12:25 12:45 TALK Chala Turo 00:20 Assessing Recombination from Genome Sequences of Spot and Net form Barley Pathogens
12:45 13:45 LUNCH 01:00
13:45 14:05 TALK Lina Rozano 00:20 Structural prediction of ToxA-like and MAX effector proteins using threading and comparative modelling methods
14:05 14:25 TALK Janneke Aylward 00:20 Capnodiales genomes reveal aspects of mating type evolution
14:25 14:45
14:45 15:05 TALK Evan John 00:20
A novel method for analysis of RNAseq data guides identification of conserved promoter motifs associated with a key regulator of fungal virulence.
15:05 15:35 TALK Roberto Barrero 00:30 PathogenFinder – a bioinformatics tool to fast track plant viruses and viroids quarantine testing at the border
15:35 15:40 CLOSING 00:05



APPS Pathogen Bioinformatics special interest group meeting 2018 – update


Important Dates & Info:

Where: Agribio, La Trobe University, VIC
When: 28th November 10am – 4pm
Scope: genomics/bioinformatics of pathogen/pest host-interactions
Abstract submissions open: September 10th, 2018
Abstract submissions close: October 1st, 2018
Presentations & Bursaries announced: October 11th, 2018

Meeting Description & Scope:

The Victorian branch of the Australasian Plant Pathology Society is hosting a Pathogen Bioinformatics special interest group meeting on the 28th November. The scope of this meeting broadly encompasses the genomic and bioinformatic study of pathogen and pest interactions with their hosts. Similar meetings have been previously held under the name of the Australian Pathogen Bioinformatics Symposium, for more information go to

Registration is free for APPS members and $25 for non-members.

Students and ECRs are eligible to apply for travel bursaries from the Pathogen Bioinformatics group, if they:

  • submit an abstract
  • are up to 5 years post-PhD
  • include a signed letter of recommendation from their principal supervisor

We encourage you to submit abstracts and expression of interest for presentations to

For further updates, check


If you are attending either ABACBS (25th-30th, or the 6th annual Stromlo Molecular Pathology meeting (29-30th, this year, then this meeting may be compatible with your upcoming travel plans. The program will start at 10am to allow for people to travel from out of town and will finish at 4pm to allow those flying to Canberra. If you plan to do this also please let us know as group taxi arrangements can be made.

Australasian Plant Pathology Society (APPS) – Pathogen Bioinformatics Special Interest Group Meeting

The Victorian Branch of the Australasian Plant Pathology Society will be hosting a Pathogen Bioinformatics special interest group  meeting on the 28th November at AgriBio, La Trobe University, Melbourne.  The program will start at 10am to allow for people to travel from out of town and will finish at 4pm to allow those flying to Canberra for the 6th annual Stromlo Molecular Pathology meeting which starts on 29th  November (

 The scope of this meeting broadly encompasses the genomic and bioinformatic study of pathogen and pest interactions with their hosts.  Similar meetings have been previously held under the name of the Australian Pathogen Bioinformatics Symposium (

 Registration will be free for APPS members and $25 for non-members.

 Students and ECRs are eligible to apply for travel bursaries from the Pathogen Bioinformatics group, if they:

  • are <5 years post-Ph. D.
  • include signed letter of recommendation from their principal supervisor
  • submit an abstract 

We invite you to submit abstracts and expression of interest for presentations to   A registration website will open soon and further details will be posted here.

Pathogen Bioinformatics Workshop 2015 – de-brief

The Pathogen Bioinformatics Workshop (PathBio2015) held on Sunday 13th 2015, in Fremantle WA, featured a series of outstanding local, national and international presentations on ‘pathogenomics’ and bioinformatics.

This meeting was a satellite workshop to the Australasian Plant Pathology Conference 2015, which is happening right now (14th to the 16th September) in Fremantle, Western Australia.

Many thanks to all those who attended and presented, and a special thank you to Gagan Garg and Angela Williams of CSIRO Agriculture for helping out with meeting organisation.

Note: while  PathBio2015 was a follow-up to the 2014 Australian Pathogen Bioinformatics Symposium, it was financially supported by APPS in full and remaining funds that were provided for APBS2014 through the Australian Bioinformatics Network Connection Grants Scheme are still available for another pathogen bioinformatics meeting next year.  Suggestions of location, venue and guest speakers are welcome.

The meeting started off with two great pathogenomics talks from Assoc. Prof. Rosie Bradshaw of Massey University (NZ) on Dothistroma and Prof. Kim Plummer of La Trobe University (VIC) on Venturia.  Next was a presentation on advances in machine-learning based discovery of effector genes by Jana Sperschneider of CSIRO Agriculture.  Then Gagan Garg of CSIRO Agriculture presented comparative genomics and transcriptomics of Rhizoctonia solani, followed by Angela Williams of CSIRO Agriculture presenting a comparative genomics analysis of legume-infecting Fusarium oxysporum formae speciales.  Grant Smith of New Zealand Plant and Food Research ended the session, presenting on bioinformatic challenges in developing clade-specific PCR assays for field detection of Candidatus liberibacter solanacearum.

The first afternoon session started with Agneiska Mudge of University of Queensland, who is embarking on a new transcriptomics study of the Ganoderma-Oil palm interaction.  Then CCDM PhD student Stefania Bertazzoni presented recent work on finishing the genome of Parastagonospora nodorum with PacBio long sequence reads.  Matthew Denton-Giles of the CCDM then presented on his previous PhD work at Massey University, on effector discovery and characterisation in Ciborinia camelliae.  Finally, Mark Derbyshire of the CCDM presented an overview of PacBio genome assembly and finishing techniques and their application to the genome of Sclerotinia sclerotiorum.

The final session of the day started with CCDM PhD student Alison Testa presenting her recent work on bioinformatically defining AT-rich regions in fungal genomes and the effects of RIP-driven AT-rich region formation on gene codon composition and its application in pathogenicity gene discovery.  This was followed by Paula Moolhuijzen of the CCDM who presented on the comparative genomics of Pyrenophora tritici-repentis, and highlighted a need for reproducible analysis pipelines.  The final talk of the day was Manuel Zander, recent PhD graduate of the Batley Lab at University of Queensland, presenting comparative pan-genome analysis of presence/absence across isolates of the Leptosphaeria maculans.

Tweets from #Pathbio2015

Photos from the workshop













Pathogen Bioinformatics Workshop 2015

This meeting showcases recent research in ‘pathogenomics’ and bioinformatics.

Satellite meeting to the Australasian Plant Pathology Society Conference 2015

Registration here (APPS2015 workshops only)

When: Sunday 13th September, 9:30AM – 4:00 PM

Where: Esplanade Hotel, Fremantle

The meeting will be held in the Esplanade’s Rottnest Room, to get there walk up the main staircase to the side of the Harbour Master restaurant, all the way through to the last room on the left (see Esplanade Hotel Floorplan).  There will be signs inside reading ‘Pathogen Bioinformatics Workshop‘ directing you to the Rottnest Room, or you can just ask the concierge located on the right as  you walk into the lobby.


Start End Speaker Title
9:00:00 9:30:00 N/A Tea and Coffee
9:30:00 9:40:00 Opening Remarks
9:40:00 10:00:00 Rosie Bradshaw Taming a gymnosperm pathogen: transcriptome of a forest fungus
10:00:00 10:20:00 Kim Plummer Effector hunting with comparative genomics/secretomics of scab fungi
10:20:00 10:50:00 MORNING TEA
10:50:00 11:10:00 Jana Sperschneider EffectorP: predicting fungal effector proteins using machine learning
11:10:00 11:20:00 Gagan Garg Studying Rhizoctonia solani broad host range interactions through RNA-Seq
11:20:00 11:40:00 Angela Williams Looking for effectors in legume infecting F. oxysporum ff. spp.
11:40:00 12:00:00 Grant Smith The bioinformatic challenge of identifying differential diagnostic loci in the fastidious pathogen Candidatus liberibacter solanacearum
12:00:00 13:00:00 LUNCH
13:00:00 13:10:00 Agnieska Mudge Investigating the oil palm – Ganoderma interaction using transcriptomics
13:10:00 13:30:00 Stefania Bertazzoni Improving Parastagonospora nodorum genome with PacBio sequencing technology
13:30:00 13:50:00 Mark Derbyshire Improvement of the reference genome of the fungus Sclerotinia sclerotiorum using PacBio and Illumina sequencing
13:50:00 14:10:00 Matthew Denton-Giles The identification and characterization of a family of small secreted fungal proteins.
14:10:00 14:40:00 AFTERNOON TEA
14:40:00 15:00:00 Alison Testa A Survey of Regional G:C Bias Across the Fungal Kingdom Highlights “Two-Speed” Genome Evolution
15:00:00 15:20:00 Paula Moolhuijzen Comparative Analysis of Pyrenophora tritici-repentis Isolates
15:20:00 15:40:00 Manuel Zander Understanding the structure and variation within the genome of the pathogenic ascomycete fungus Leptosphaeria maculans
15:40:00 15:45:00 Closing Remarks

The APPS Welcome Reception will be located at the WA Maritime Museum at 6pm to 7:30pm, only 10 minutes walk from the Esplanade (see below).  Note: if you want to attend this you will need to register for the main conference.

There are many restaurants, cafes and bars within walking distance of the venue, we recommend Little Creatures, a short walk across the park from the Esplanade:

Attendees of this workshop may also be interested in the Australasian Plant Virology Workshop on the 16th-18th September, also in the Esplanade Hotel.

Keynote Speakers
Dr Alexander Karasev, The University of Idaho, USA
Dr Lava Kumar, International Institute of Tropical Agriculture (IITA), Nigeria
Dr Arvind Varsani, University of Canterbury, New Zealand
Dr Laura Boykin, The University of Western Australia

More details and registration at: