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It's Phylomania Month!
by Michael Charleston 01 Nov '24

01 Nov '24

Forget the US Election (unless you have to vote there and haven't) — November is all about Phylomania. This is our 16th Season! If you haven't yet registered<http://www.maths.utas.edu.au/phylomania/phylomania2024.html> for our world famous conference on theoretical phylogenetics, there's still time! Face to face attendance is great, but if you can only register for online attendance, that's free! — So if your university is typical just now and tightening belts, you can always rock up from the comfort of your own home/office via Zoom. Join us, won't you? Oh — here's the conference page: http://www.maths.utas.edu.au/phylomania/phylomania2024.html (Don't be alarmed that it's only http, not https — registration and payments are secure.) Michael Charleston [cid:047c6aeb-4f47-4fd4-a4d5-15e209b6e666] Phylomania 2024: November 27-29<http://www.maths.utas.edu.au/phylomania/phylomania2024.html> Funded PhD project available in machine learning<https://www.utas.edu.au/research/degrees/available-projects/projects/mathem…> Specialty Chief Editor in Frontiers in Ecology and Evolution - Coevolution Mathematical Biology Group Professor in Bioinformatics School of Natural Sciences University of Tasmania AUSTRALIA Phone: +61 3 6226 2444 This email is confidential, and is for the intended recipient only. Access, disclosure, copying, distribution, or reliance on any of it by anyone outside the intended recipient organisation is prohibited and may be a criminal offence. Please delete if obtained in error and email confirmation to the sender. The views expressed in this email are not necessarily the views of the University of Tasmania, unless clearly intended otherwise.

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Postdoc position at the Menzies
by Bennet McComish 31 Oct '24

31 Oct '24

Hi all, I'm looking to recruit a postdoc to investigate the evolution of multiple sclerosis risk. The Postdoctoral Research Fellow will be involved in NHMRC and MS Australia funded research. This work uses population genomics to identify functional variation under selection at loci associated with multiple sclerosis risk, improving our understanding of the mechanisms underlying the disease. You will apply statistical and genomics expertise to develop pipelines to detect balancing selection in the major histocompatibility (MHC) region of the genome using large population datasets. This position will offer the opportunity for you to further develop leadership skills through planning and leading statistical genomics research and support the training and development of junior research staff and students. What we're looking for: + A PhD or equivalent in statistical genetics, genetic epidemiology, or a related field. + Experience in the analysis of genomic data including practical experience with the use of high performance computing for the analysis of genome sequence data, and ideally with a focus on analysing immune system genes in the MHC region. + Demonstrated skills in bioinformatics relevant programming languages such as python, R, or perl. + A good record of, and continuing commitment to, research that has achieved national recognition and made worthwhile contributions to the field of statistical genetics, demonstrated by a record of quality publications, presentations at conferences and preferably success in securing external competitive and other funding relative to career stage and opportunity. + A record of contributing to building and maintaining effective and productive links locally and nationally with the discipline, profession, industry (where relevant) and wider community. + Demonstrated ability to work autonomously, as well as to collaborate successfully with other researchers/clinicians and be able to prioritise tasks and meet deadlines. This is a full time, 1 year Fixed-Term position based in Hobart, Tasmania, with part-time hours considered for the right candidate. Details at: https://careers.utas.edu.au/cw/en/job/500426/postdoctoral-research-fellow-s… Applications close Monday, 25 November 2024, 11.55pm AEDT Please share with any potential candidates, and contact me for further information. Regards, Bennet Dr Bennet McComish Senior Research Fellow - Bioinformatics and Human Genetics Menzies Institute for Medical Research | University of Tasmania Private Bag 23, Hobart TAS 7000 +61 3 6226 4285 | bennet.mccomish(a)utas.edu.au<mailto:Bennet.McComish@utas.edu.au> I acknowledge and pay respect to the Tasmanian Aboriginal community as the traditional and original owners and continuing custodians of the land on which I work. This email is confidential, and is for the intended recipient only. Access, disclosure, copying, distribution, or reliance on any of it by anyone outside the intended recipient organisation is prohibited and may be a criminal offence. Please delete if obtained in error and email confirmation to the sender. The views expressed in this email are not necessarily the views of the University of Tasmania, unless clearly intended otherwise.

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Phylomania 2024 is coming!
by Michael Charleston 18 Oct '24

18 Oct '24

Don't forget to register and come to the SIXTEENTH annual Phylogenetics meeting held here in beautiful Hobart! Please spread the word 😄 Conference information, registration and payment page from here: http://www.maths.utas.edu.au/phylomania/phylomania2024.html Michael Charleston [cid:2c2f5484-04ea-4581-96d8-2518c031c102] Phylomania 2024: November 27-29<http://www.maths.utas.edu.au/phylomania/phylomania2024.html> Funded PhD project available in machine learning<https://www.utas.edu.au/research/degrees/available-projects/projects/mathem…> Specialty Chief Editor in Frontiers in Ecology and Evolution - Coevolution Mathematical Biology Group Professor in Bioinformatics School of Natural Sciences University of Tasmania AUSTRALIA Phone: +61 3 6226 2444 This email is confidential, and is for the intended recipient only. Access, disclosure, copying, distribution, or reliance on any of it by anyone outside the intended recipient organisation is prohibited and may be a criminal offence. Please delete if obtained in error and email confirmation to the sender. The views expressed in this email are not necessarily the views of the University of Tasmania, unless clearly intended otherwise.

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Genetic outlier analysis workshop - Sydney edition 4-5 July
by Michael Charleston 24 May '24

24 May '24

The Genetic Outlier Analysis workshop<https://url.au.m.mimecastprotect.com/s/uVJOCq7BJXt8q5rwjiXJrOd?domain=bioco…> will run 4-5 July 2024 at the UNSW, Kensington Campus. It will introduce the basics of genetic selection analysis, and step through the process of identifying signals of selection using participants' own data (or an example genomic dataset) using the outlier analysis method. The two-day workshop will be led by Dr Katarina Stuart from the University of Auckland, thanks to a grant from the Genetics Society of AustralAsia. It is fully-subsidised for Australian researchers and/or members of the Genetics Society of AustralAsia (subject to selection). Apply now<https://url.au.m.mimecastprotect.com/s/uVJOCq7BJXt8q5rwjiXJrOd?domain=bioco…> or read what previous participants have said<https://url.au.m.mimecastprotect.com/s/pClnCr8DKNf8gvjJli4HKcU?domain=bioco…> about the workshop. -- [https://ci3.googleusercontent.com/mail-sig/AIorK4zRFxnSsH5ylYQ8Tz5e6EKV45kV…] This email is confidential, and is for the intended recipient only. Access, disclosure, copying, distribution, or reliance on any of it by anyone outside the intended recipient organisation is prohibited and may be a criminal offence. Please delete if obtained in error and email confirmation to the sender. The views expressed in this email are not necessarily the views of the University of Tasmania, unless clearly intended otherwise.

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The first Australian BioCommons workshop of 2024!
by Michael Charleston 17 Jan '24

17 Jan '24

Hello and welcome to 2024. Australian BioCommons has a number of exciting workshops planned for the year, the first of which is on the identification of genetic outliers, spread over two linked 5-hour online sessions. Here's the main page, which will allow you to register: https://www.biocommons.org.au/events/genetic-outlier<https://protect-au.mimecast.com/s/9kMmCvl0O7S71AyqVhQx2gF?domain=biocommons…> ... and here are a couple of relevant social media posts: https://twitter.com/AusBiocommons/status/1747059289611780383<https://protect-au.mimecast.com/s/tW2TCxnMQNt18xQDNIYqfXN?domain=twitter.com> https://www.linkedin.com/feed/update/urn:li:activity:7142700103013707778<https://protect-au.mimecast.com/s/aJ5fCyoNROTrDLyKVuRlMUV?domain=linkedin.c…> Enjoy, and share! Best wishes, Michael Charleston [cid:e1aa5815-487b-48c8-bbcd-a7617249f44d] Phylomania 2023: November 22-24<http://www.maths.utas.edu.au/phylomania/phylomania2023.html> Specialty Chief Editor in Frontiers in Ecology and Evolution - Coevolution Mathematical Biology Group Professor in Bioinformatics School of Natural Sciences University of Tasmania AUSTRALIA Phone: +61 3 6226 2444 This email is confidential, and is for the intended recipient only. Access, disclosure, copying, distribution, or reliance on any of it by anyone outside the intended recipient organisation is prohibited and may be a criminal offence. Please delete if obtained in error and email confirmation to the sender. The views expressed in this email are not necessarily the views of the University of Tasmania, unless clearly intended otherwise.

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a Bioinformatics Training Needs Survey!
by Michael Charleston 12 Dec '23

12 Dec '23

Dear bioinformaticians and bioinformatics-friendly folk! As part of the National Bioinformatics Training Cooperative we offer national training to uplift the skills of Australian biologists and bioinformaticians. We collaborate to ensure we can offer the best training opportunities in areas that are relevant. It is important for us to hear what training you need so that we can best support your research. We'd love to know what bioinformatics training you wish you could attend. The survey should take less than 10 minutes to complete. Please complete the Bioinformatics Training Needs survey: https://www.surveymonkey.com/r/bioinf-training-24<https://protect-au.mimecast.com/s/Xv43C81Zm7f6Gjjw7CnxVbi?domain=surveymonk…>. Michael Charleston [cid:06bd1ae3-e8d8-4bc5-ab3f-269e2e848d58] Phylomania 2023: November 22-24<http://www.maths.utas.edu.au/phylomania/phylomania2023.html> Specialty Chief Editor in Frontiers in Ecology and Evolution - Coevolution Mathematical Biology Group Professor in Bioinformatics School of Natural Sciences University of Tasmania AUSTRALIA Phone: +61 3 6226 2444 This email is confidential, and is for the intended recipient only. Access, disclosure, copying, distribution, or reliance on any of it by anyone outside the intended recipient organisation is prohibited and may be a criminal offence. Please delete if obtained in error and email confirmation to the sender. The views expressed in this email are not necessarily the views of the University of Tasmania, unless clearly intended otherwise.

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Cogent3 workshop on 21st November now accepting remote attendees
by Barbara Holland 13 Nov '23

13 Nov '23

Hi, The cogent3<https://protect-au.mimecast.com/s/Cv4BCNLwPnf0xNl69imeNoS?domain=cogent3.org> half-day Data Wrangling with Cogent3 Workshop (running the day before Phylomania) is now accepting remote attendees! We will be capping total attendance at a maximum of 30, so be quick and register here<https://protect-au.mimecast.com/s/b_EzCOMxQoFpXAROwuvfEyJ?domain=docs.googl…>! On behalf of the cogent3 developer team 👾, Gavin Huttley ________________________________ Professor Gavin Huttley, Research School of Biology, ANU College of Science, RN Robertson Building, 46 Sullivans Creek Road, The Australian National University Canberra ACT 2600 Australia +61 2 6125 5308 https://biology.anu.edu.au/research/groups/huttley-group-bioinformatics-mol…<https://protect-au.mimecast.com/s/gwi7CP7yRptKm4G6ZS19XNx?domain=biology.an…> CRICOS #00120C ________________________________ This email is confidential, and is for the intended recipient only. Access, disclosure, copying, distribution, or reliance on any of it by anyone outside the intended recipient organisation is prohibited and may be a criminal offence. Please delete if obtained in error and email confirmation to the sender. The views expressed in this email are not necessarily the views of the University of Tasmania, unless clearly intended otherwise.

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Phylomania 2023: Like and subscribe!!
by Michael Charleston 13 Oct '23

13 Oct '23

Dear all, The registration page, payment page and a cheeky announcement about a (free!) Cogent3 workshop are all live on the Phylomania 2023 web page! Here it is in case Google can't find it for you: http://www.maths.utas.edu.au/phylomania/phylomania2023.html Can't wait to see you all! Michael Charleston [cid:b3651a8f-8aa0-4f81-8f66-598bae99e09e] Phylomania 2023: November 22-24 Specialty Chief Editor in Frontiers in Ecology and Evolution - Coevolution Mathematical Biology Group Professor in Bioinformatics School of Natural Sciences University of Tasmania AUSTRALIA Phone: +61 3 6226 2444 This email is confidential, and is for the intended recipient only. Access, disclosure, copying, distribution, or reliance on any of it by anyone outside the intended recipient organisation is prohibited and may be a criminal offence. Please delete if obtained in error and email confirmation to the sender. The views expressed in this email are not necessarily the views of the University of Tasmania, unless clearly intended otherwise.

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Fw: Cogent3 workshop at Phylomania announcement
by Michael Charleston 03 Oct '23

03 Oct '23

From: Gavin A Huttley <Gavin.Huttley(a)anu.edu.au> Sent: Tuesday, 3 October 2023 2:54 PM To: Michael Charleston <michael.charleston(a)utas.edu.au> Subject: Cogent3 workshop at Phylomania announcement Hi 👋! The development team of cogent3<https://protect-au.mimecast.com/s/RVN3C3Q870UpzOogZigneHc?domain=cogent3.org> will run a half-day Data Wrangling with Cogent3 Workshop on the afternoon of 21st November 2023. This is before the start of Phylomania, and it's free 🎉! You can register here<https://protect-au.mimecast.com/s/IM2TC4QZgDUBKqE2rUxaS9_?domain=forms.gle>. Read on past the signature to see workshop details. We hope you can join us! On behalf of the cogent3 developer team, Gavin Huttley ________________________________ Data Wrangling with Cogent3 The workshop is geared towards developers who specialize in phylogenetic methods. Acquiring empirical data for evaluating the performance of a new method is challenging. Your choice of data has important ramifications for your evaluation of the performance of your method. While the standard strategy of recycling published data sets is convenient, this risks perpetuating biases embedded in those data sets. We will show how cogent3<https://protect-au.mimecast.com/s/RVN3C3Q870UpzOogZigneHc?domain=cogent3.org> and associated tools can greatly simplify getting public data for analyses, serving the needs of phylogenetic method developers. As there is an overlap with standard phylogenetic data pre-processing workflows, users of phylogenetic (or molecular evolutionary) methods can also benefit from attending this workshop. Workshop Content The topics we will cover are: * Factors for method developers to consider when designing experiments. * How to extract specific types of sequences (e.g. by homology type, sequence class, or level of divergence) from biological databases like Genbank and Ensembl. * Handling inconsistencies in biological data resources. * Multiple sequence alignment and subsequent quality control. Prerequisites All you need for this workshop is a laptop and some familiarity with command-line applications. Ideally, you should be able to install software on your machine (see Computer Setup<https://protect-au.mimecast.com/s/UJQ0C5QZjEUZL23PAcywB7p?domain=github.com> on the wiki). More workshop information Details regarding physical location and setting up your computer before the workshop will be posted to the Cogent3 Workshop Wiki<https://protect-au.mimecast.com/s/Wuq5C6X1k7CrYq76Xf51HA3?domain=github.com>. We look forward to seeing you there! 👾 cogent3's development team. ________________________________ Professor Gavin Huttley, Research School of Biology, ANU College of Science, RN Robertson Building, 46 Sullivans Creek Road, The Australian National University Canberra ACT 2600 Australia +61 2 6125 5308 https://biology.anu.edu.au/research/groups/huttley-group-bioinformatics-mol…<https://protect-au.mimecast.com/s/5QBFC71Zl7fA1w2XLcqzgE7?domain=biology.an…> CRICOS #00120C ________________________________ This email is confidential, and is for the intended recipient only. Access, disclosure, copying, distribution, or reliance on any of it by anyone outside the intended recipient organisation is prohibited and may be a criminal offence. Please delete if obtained in error and email confirmation to the sender. The views expressed in this email are not necessarily the views of the University of Tasmania, unless clearly intended otherwise.

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ABACBS 2023, Brisbane, Dec 4-8
by Michael Charleston 19 Sep '23

19 Sep '23

Dear colleagues, On behalf of the organising committee, we would like to let you know that early bird registration has now opened for the 2023 Annual Australian Bioinformatics and Computational Biology Society (ABACBS) Conference, to be held in Brisbane on 4-8 Dec (https://2023.abacbs.org/<https://protect-au.mimecast.com/s/s1WrCyoNROTrVx5zzcZn8xU?domain=2023.abacb…>). ABACBS is Australia’s largest bioinformatics conference and represents a community of over 1100 members across the country. To maximise global outreach of Australian science to an international audience, for the first time in ABACBS history, the Brisbane 2023 edition will be held in collaboration with the International Society of Computational Biology (ISCB), the world's leading professional society in the discipline. In addition to the discounts we are offering through early bird registration rates, everyone who registers for ABACBS can also sign up for discounted ISCB membership! ABACBS 2023 will facilitate multidisciplinary crosstalk among researchers, academics, and professionals from Australia and abroad who are involved in both the generation and analysis of molecular data from a broad spectrum of life sciences research. As per tradition, our week starts with the student-led COMBINE symposium (4 Dec), followed by the annual conference (5-6 Dec), and concludes with two days of satellite events (workshops, symposia, etc.; 7-8 Dec). Our session themes include: 1. Machine Learning for Discovery 2. Epigenomics and Long Read Sequencing 3. Phylogenetics & Evolution 4. Agricultural and Environmental Omics 5. Human Health and Translation 6. Cutting Edge Omics Technologies and Analysis 7. Big data infrastructure If you’re interested in organising a workshop or symposia, please see the website for more info. Our call for abstracts is currently open and will close on 25 Sep. Early bird registration will close on 16 Oct so please register as soon as you can to avoid missing out! Best wishes, CX and Jess Co-Convenor, ABACBS 2023 ----------------------------------------------------- Cheong Xin (CX) Chan, Ph.D. (Queensland) Senior Research Fellow & Senior Lecturer, School of Chemistry and Molecular Biosciences Group Leader, Australian Centre for Ecogenomics Affiliate Research Fellow, Institute for Molecular Bioscience Co-Convenor, ABACBS 2023<https://protect-au.mimecast.com/s/s1WrCyoNROTrVx5zzcZn8xU?domain=2023.abacb…> The University of Queensland St Lucia, Brisbane, QLD 4072 Australia P: +61-7-33653829 F: +61-7-33654511 M: +61-416-310786 E: c.chan1(a)uq.edu.au W: https://cxchan.com/<https://protect-au.mimecast.com/s/f3LTCzvO0NfMV5oppsXaOgt?domain=cxchan.com/> (Forwarded with best wishes by...:) Michael Charleston [cid:4bd115cb-9e87-42f7-88d1-0d98bf0e1ab0] Phylomania 2023: November 22-24 Specialty Chief Editor in Frontiers in Ecology and Evolution - Coevolution Mathematical Biology Group Professor in Bioinformatics School of Natural Sciences University of Tasmania AUSTRALIA Phone: +61 3 6226 2444 This email is confidential, and is for the intended recipient only. Access, disclosure, copying, distribution, or reliance on any of it by anyone outside the intended recipient organisation is prohibited and may be a criminal offence. Please delete if obtained in error and email confirmation to the sender. The views expressed in this email are not necessarily the views of the University of Tasmania, unless clearly intended otherwise.

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