Upcoming events hosted by or involving Genetics Otago will be listed here. Please check back regularly for updates. A calendar of events that may be of interest to our members can be found at the bottom of this page and in the sidebar of other pages on this site, please note that this includes events hosted outside of Genetics Otago.
- VISG Seminar Series
- Variant Analysis Hub Workshop
- Postgraduate Retreat
- GO Symposium
- Calendar of Events
VISG Seminar Series
The Virtual Institute of Statistical Genetics (VISG) Hub is a key part of Genetics Otago, providing a platform for researchers to collaborate and exchange knowledge and expertise in statistical genetics. The VISG Hub hosts seminars, workshops, and other events to promote statistical genetics research and foster collaboration between researchers.
We’re excited to announce our monthly genetics research seminars, aimed at connecting researchers in the field. The seminars will commence in May 2023 and will be hosted by GO’s Virtual Institute of Statistical Genetics (VISG) Hub along with the Department of Mathematics and Statistics at the University of Otago. These seminars will be available in person or via Zoom, and all are welcome.
Date: 3rd Thursday of the month
Time: 11:00 am – 12:00 pm
Schedule
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- May: Associate Professor Phil Wilcox, University of Otago
- June: Professor Mik Black, University of Otago
- July: Dr Ludovic Dutoit, University of Otago
– please note that this seminar will be held on the 27th of July rather than the 20th due to ICG.
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- August: Dr Setegn Alemu, AgResearch
- September: Ee Cheng Oi, Abacus Bio
- October: Franziska Weik, Beef + Lamb NZ Genetics
- November: Dr Jane Symonds and Dr Megan Scholtens, Cawthron
– please note that this seminar will be held on the 17th of November rather than the 16th due to the GO Annual Symposium.
Zoom Details
If you would like the Zoom details for this event, please contact us.
September Seminar
The seminar will be held on the 21st of September, 11 am in St David Complex Seminar Room A G.02 and will be given by Dr Ee Cheng Ooi, AbacusBio.
Title: Using SNP effects to understand the underlying biological mechanisms linking traits: a study of milk yield and fertility in dairy cattle
Abstract: Fertility in dairy cattle has declined as an unintended consequence of single trait selection for high milk yield. The antagonistic genetic correlation between milk yield and fertility is now well-documented, however, the underlying physiological mechanisms are still uncertain. To understand the relationship between these traits, we developed a method that clusters variants with similar patterns of effects and, after the integration of gene expression data, identifies the genes through which they are likely to act. Biological processes that are enriched in the genes of each cluster were then identified.
One of the clusters included variants that increase milk yield and decrease fertility, where the ‘archetypal’ variant (i.e., the one with the largest effect) was associated with the gene GC, while others were associated with TRIM32, LRRK2, and U6. These genes can be characterized by their effects on transcription and alternative splicing, suggesting that these processes are likely contributors to the antagonistic relationship between the two traits. Another cluster, with archetypal variant near DGAT1 and including variants associated with CDH2, BTRC, SFRP2, ZFHX3, and SLITRK5, affected milk yield but had little effect on fertility and are characterized by their effects on insulin, adipose tissue, and energy metabolism. A third cluster with archetypal variant near ZNF613 and including variants associated with ROBO1, EFNA5, PALLD, GPC6, and PTPRT affected fertility but not milk yield, and were characterized by their effects on GnRH neuronal migration, embryonic development, and/or ovarian function.
The use of archetypal clustering to group variants with similar patterns of effects may assist in identifying the biological processes underlying correlated traits. The method is hypothesis-generating and requires experimental confirmation. However, we have uncovered several novel mechanisms potentially affecting milk production and fertility such as GnRH neuronal migration. We anticipate our method to be a starting point for experimental research into novel pathways which have been previously unexplored within the context of dairy production.
Biography: Ee Cheng Ooi is a cattle vet and consultant at AbacusBio, an agricultural science and technology company based in Dunedin. She is originally from Melbourne, Australia, but moved to New Zealand after completing her PhD in the genetic improvement of fertility in dairy cattle last year. After a decade of working for the Australian dairy industry, she decided to broaden her horizons by working across a variety of other countries and species, including beef and sheep. Her interests lie in agricultural extension, livestock production systems, veterinary epidemiology, and biostatistical analysis.
If you have any questions about this seminar series please contact us.
Variant Analysis Hub Workshop
This workshop, is being held in partnership with Genomics Aotearoa and NeSI and will be facilitated by Dr Chris Hakkaart (Sequera Labs).
Session 1 will start with an exploration of the core features of Nextflow and learning the fundamental commands and options for executing workflows. Next, we will learn the core features of nf-core and its tooling. This knowledge will then be applied as we learn the structure of an nf-core workflow and how customize its execution. Finally, we will learn about nf-core tooling for users and how it can help you execute your workflow.
The ideas and skills you learn during Session 1 will then be applied during Session 2 where we will explore the source code of the `nf-core/sarek` workflow. We will learn how to build a run command and then customize its execution. The session will finish by discussing how to execute Sarek at scale using full-size data.
Date: 11th and 12th October 2023
Time: 9:00 am – 12:00 pm
Venue: Online (Dunedin Hub for attendees is Hunter Centre Computer Lab 1.15)
Registration
Registration for this event is via Eventbrite, please use the button below to be redirected to the registration page.
Requirements
This workshop material will be run on the NeSI High Performance Computing (HPC) platforms – there is no need to install any software for this workshop. Instructions on how to access the NeSI HPC service will be sent out with the confirmation letter to registrants
Support
Genetics Otago would like to thank the below contributors to this event:
Postgraduate Retreat
The biennial Genetics Otago Postgraduate Retreat is happening in 2023! This event is open to all PGDipSci, Hons, MSc and PhD students who are using genetics as part of their research – you do not need to be enrolled as a GENE major.
Date: Friday 27th of October 2023
Time: 8:30 am – 4:30 pm
Location: Gallery Room, Staff Club
Details
The day will begin with tea and coffee before the formal programme begins at 9:00 am. They day will include sessions on science communication, Māori language, careers, wellbeing and ethics and will be fully catered. A full programme will be posted here once it is finalised.
Registration
Please register for this event using the button below
GO Symposium
The Genetics Otago Annual Symposium is expanding in 2023! We will be holding a three day event, with two days of Hub workshops followed by the full day symposium. Posters will be on display for the three days and we hope to get as many members as possible involved in this free event!
Date: 14th – 16th November 2023
Time: 9:00 am – 5:00 pm
Venue: St David Lecture Theatre Complex (and Genetics 300-level teaching Lab)
Workshops:
Genetics Otago Hubs will host workshops on the 14th and 15th of November. You will be able to register for these when you register for the main Symposium. Full details on these workshops are still to come but we plan to host the following:
- eDNA Hub: workshop to cover analysis and processing of environmental DNA data.
- CRISPR Hub: workshop to cover gRNA design and optimisation, CRISPR screens and data analysis.
- Oxford Nanopore Sequencing Hub: a combo wet lab/computational workshop covering nanopore sequencing and small group data analysis.
- Ethical Legal and Societal Considerations (ELSC) Hub: a panel-focused workshop to stimulate discussion around National Academies of Sciences, Engineering, and Medicine (NASEM) report
- Outreach Hub: media training plus tips for increasing visibility for your own research
- Outreach Hub: teacher training on newly developed resource kits.
- Variant Analysis Hub: nf-core pipeline data analysis workshop overflow (for those who missed out in October)
We will add more details as they come in, so stay tuned.
Symposium:
The main Symposium will take place on the 16th of November in the St David lecture theatre. This will feature invited speakers as well as selected abstracts. At the conclusion of the Symposium the 2023 GO Award winners will be announced (more details below).
Keynote Speakers
Invited Speakers
Confirmed invited speakers:
- Dr Nathan Kenny, Ngāi Tahu and Te Ātiawa (Department of Biochemistry)
- Associate Professor Sara Filoche (Department of Obstetrics, Gynaecology and Women’s Health – Wellington)
- Dr George Wiggins (Department of Pathology and Biomedical Science – Christchurch)
Awards
Genetics Otago presents annual awards as part of the Symposium programme. In 2023 we will be presenting awards in the following categories:
- The Genetics Otago Award
- Senior and Peer Mentor Awards
- Student Supervisor Award
- Student and ECR Publication Awards
- Student and ECR Poster Awards
- Science Communication Award
Nominations and entries for these awards are now open and will close at 5:00 pm on the 27th of October 2023. Full details of the awards and how to enter can be found here.
Programme
The programme of events will be posted here once finalised.
Registration
Registration for this event will open soon. Abstract submission will be part of the registration process, all abstracts must be submitted by no later than 5:00 pm on the 27th of October 2023.
Calendar of Events
The below is a calendar of events hosted by GO as well as events hosted by others that may be of interest to our members. If you have an event you would like us to include please contact us here.
Please note the change in time and venue for this seminar due to the Stop Work meeting being held from 12 – 2 pm on the 9th of May.
It’s a team game: a research journey in infection and immunity
About Professor James Ussher’s research
James is an immunologist and a clinical microbiologist (at Southern Community Laboratories) whose research programme is focussed on the immune response to infection and on antibiotic resistance.
His laboratory is investigating the role of innate-like T-cells in anti-bacterial immunity and how they might be harnessed to prevent infection. They also contribute to several vaccine development projects. In addition, his laboratory uses whole genome sequencing of antibiotic resistant bacteria to identify outbreaks and track transmission pathways to enable interventions.
He is involved in collaborative research projects in New Zealand, the Pacific, Asia, and the United Kingdom.
In response to the COVID-19 pandemic, he co-led the establishment of the Vaccine Alliance Aotearoa New Zealand – Ohu Kaupare Huaketo (VAANZ), a multi-institutional team of researchers and industry focused on building New Zealand’s capability and platforms for vaccine development. He was a member of the Government’s COVID-19 Vaccine Taskforce and is a member of the COVID-19 Vaccine Technical Advisory Group.
Streaming information for Professor James Ussher
This event will be live-streamed, from 5:25pm Thursday 25th May 2023, at the following web address:
This online workshop is delivered by Genomics Aotearoa and NeSI, and will be taught from 10:00am-4:00pm NZT on the Thursday 15th of June, 2023. It is for New Zealand researchers interested in RNA-seq data analysis.
The focus of this workshop is to analyse RNA-seq data with the aim to identify differentially expressed genes.
Some of the topics covered in the workshop are:
– Quality assessment
– Trimming and filtering
– Mapping and read counts
– Differential expression analysis
– Over-representation analysis
Who this workshop is for
This is a beginner-friendly workshop which assumes you are familiar with the basics of R ( e.g., you can copy basic functions like head, tail, or colSums, you are aware of how R stores files as Objects) and bash (e.g., can change directory with cd command, make a new folder with mkdir command, view contents using less command). If you would like a refresher on R you can find one here. If you would like a refresher on bash you can find one here.
Setup
This is a fully online, hands-on workshop. This workshop material will be run on the NeSI High Performance Computing (HPC) platforms – there is no need to install any software for this workshop. Instructions on how to access the NeSI HPC service will be sent out with the confirmation letter to registrants.
The material for this workshop can be previewed here: https://genomicsaotearoa.github.io/RNA-seq-workshop/
Participants must have their own laptops and plan to participate actively. You will require a working web browser.
If you have any questions about these workshops, including whether they are suitable for you, please contact tyler.mcinnes@otago.ac.nz.
Friends in Focus
Dr Nic Rawlence is the Director of the University of Otago’s Paleogenetics Laboratory. He spends his days excavating fossil sites and examining specimens in museum basements, all the while methodically analysing, researching and teaching on Aotearoa’s biggest and tiniest taoka.
With a research background in ancient DNA, the evolution of New Zealand’s extinct biodiversity, and the impacts climate change and humans have had on this prehistoric ecosystem, Dr Rawlence has plenty of insight into a world lost to time.
In this month’s edition of the Friends in Focus talk series, he will dive into what the latest discoveries using ancient DNA can tell us about the evolution of New Zealand’s taoka species and their future in a fast changing world.
Come along and hear from a leading New Zealand expert on this fascinating subject.
12.10pm, Tuesday 20 June
Barclay Theatre
Free – Koha Appreciated
Welcome to ResBaz Aotearoa 2023
40+ free and online digital research skills sessions
Designed for postgraduate students, researchers and those that support them in any discipline – all of the Aotearoa NZ research community
Register for taster and hands-on sessions across a week-long schedule
Look out for local meetups in your institution
Read more about ResBaz
Sessions are free but you must register your attendance via the sessions or schedule lists.
eResearch @ Otago Day
Tuesday 4 July, 9:30am–3:00pm
This eResearch-focused event is free for all University staff and postgraduate students. This year’s event will be held in Room 117 of the Commerce Building (Zoom link available) and will focus on research being undertaken at the University as well as an update on new/upcoming eResearch services:
Short presentations by University of Otago researchers, specialist support staff, and some of our Research IT partner organisations, who are using electronic tools to help solve a variety of research and data management challenges.
Network with University of Otago researchers, specialist support staff, and staff from some of our Research IT partner organisations (REANZ and NeSI).
Learn about some of the IT services available to Otago researchers ranging from: mid-tier compute, HPC on NeSI; the REANNZ network; High Capacity Storage (HCS); the data transfer service and Library data management services.
You are welcome to forward this invitation to colleagues and postgraduate students.
When and Where:
Tuesday 4 July, 9:30am–3:00pm
Room 117 Commerce Building
Zoom: https://otago.zoom.us/j/95977317038?pwd=RHJJbS9BZDQ1ZkI4Y3hkV3N1cEY1Zz09
Meeting ID: 959 7731 7038
Password: 827288
RSVP:
If you’re joining us in person, we’ll start the day with morning tea and a light lunch will also be provided.
Please use the following link to RSVP by 9am on Tuesday 20 June so we can cater for you (https://forms.office.com/r/cZBErnEiya). This is a hard deadline for catering.
If you will be joining us via Zoom only – please still register so we can let you know about any updates and future eResearch events.
If you’re unable to join us on the day, but would like a link to the recorded talks, please email Nicola Walmsley (nicola.walmsley@otago.ac.nz). These will be available for a week after the event.
Questions:
If you have any queries about the event please contact Darren Hart (Manager, Research and Teaching IT Support, darren.hart@otago.ac.nz).
Advanced workshop: human genome assembly using long-read sequencing platforms
Genomics Aotearoa, in collaboration with New Zealand eScience Infrastructure, is piloting an advanced workshop on human genome assembly using long-read sequencing platforms. This is an in-person workshop hosted at the University of Otago, starting in the afternoon of 4 July and ending in the afternoon of 6 July, 2023.
This workshop will be led by members of the Human Pangenome Reference Consortium (HPRC): Ann McCartney (Assistant Researcher, UCSC Genomics Institute) and Julian Lucas (Senior Bioinformatics Systems Analyst, UCSC Genomics Institute). The workshop’s main focus covers read handling, assembly generation, evaluation and curation. The workshop’s scope also includes comparisons between sequence platforms and popular long-read assemblers, examples of good and bad assemblies, and approaches to assembly phasing.
We are seeking your input, to ensure that this workshop is relevant to your research interests and analysis needs. We would like to hear your thoughts on how this workshop could benefit you and what content you would like to see included.
Please complete an expression of interest here to sign up to this workshop, and to share your experiences, feedback and suggestions.
Contact Jian Sheng Boey for further information.
