- bioinformatics-list - lists2.utas.edu.au

Phylomania #17
by Michael Charleston 11 Mar '25

11 Mar '25

Dear previous attendees, friends of Phylomania etc., We are tentatively putting November 19th - 21st in our diaries for Phylomania 2025. Please do let us know if there's some big clash that we haven't thought of, so we can firm up the date and get ready (ahead of time!). And let us know if you'd love to come but that date is dreadful because of X. AND let us know if you'd like to come along and the date is good! Best wishes, Michael, Jeremy, Barbara and Peter Michael Charleston [cid:e66ba413-19c0-4daf-a4c5-7e9fca3d4a5e] Funded PhD project available in machine learning<https://www.utas.edu.au/research/degrees/available-projects/projects/mathem…> Tentative date for Phylomania #17: November 19-21, 2025 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 in WA
by Nicholas Blackburn 13 Jan '25

13 Jan '25

Hi all, Just sharing information from a colleague about a potential bioinformatics postdoc 1 year opportunity. Info below. Regards, Nick Postdoctoral Research Associate – Bioinformatics (Evolutionary/Conservation) Employer: University of Western Australia Duration: 1yr Brief Position Description: We are looking at the evolutionary genomics of fragmented populations of lizards in relation to phenotype, habitat change and population structure. We have whole genome sequences for ~300 lizards across a spread of discrete populations and we are looking for a bioinformatician with skill strengths in estimating mutation load (SnpEff). The successful candidate will work under the supervision of Dr Natasha LeBas, Prof Leigh Simmons (Centre for Evolutionary Biology) and Professor Dave Edwards (Applied Bioinformatics Group). Remote working may be considered. We are keen to fill and commence soon, please contact for further information. Bioinformaticians working in other disciplines welcome to apply. Key Responsibilities: Estimate genomic parameters of interest (mutation load, GWAS, GEA) from whole genome sequences and prepare data for analysis, analyse data and contribute to manuscript preparation. Contact name: Natasha LeBas Contact email: natasha.lebas(a)uwa.edu.au<mailto:natasha.lebas@uwa.edu.au> 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 - last chance!
by Michael Charleston 15 Nov '24

15 Nov '24

Please ignore this message if you're not coming - but if you have been putting off registering for Phylomania #16, please go to the registration page asap! To prove you are a human, you have to solve the puzzle of locating where in this email is the relevant link 😉 Best wishes, MC Michael Charleston [cid:070bd014-fdc8-4570-93c6-77ae68c464d8] 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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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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Fw: EXTERNAL: Position advertised - Data systems scientist 12 months
by Michael Charleston 15 Sep '23

15 Sep '23

Forwarding this advertisement to the bioinformatics list: anyone want some good work up in Darwin? From: Caroline Chong <Caroline.Chong(a)nt.gov.au<mailto:Caroline.Chong@nt.gov.au>> Sent: Thursday, 14 September 2023 5:51 PM To: DEPWS FloraFauna ALL <DEPWSFloraFaunaALL(a)nt.gov.au<mailto:DEPWSFloraFaunaALL@nt.gov.au>> Subject: EXTERNAL: Position advertised - Data systems scientist 12 months Good afternoon, We are seeking to recruit to our Data Systems Scientist 12 month position in Darwin. This is an excellent opportunity to apply your expertise and join our team. Closing date is 26 September 2023 - apply online at https://jobs.nt.gov.au/<https://protect-au.mimecast.com/s/LzLyCK1qMkf2pNWMpTMQFvG?domain=jobs.nt.go…>. Please distribute to your relevant networks and potential candidates. Thanks, Caroline. Dr Caroline Chong A/Director – Species Management Flora and Fauna Division Department of Environment, Parks and Water Security Northern Territory Government CSIRO Complex, 564 Vanderlin Drive, Berrimah PO Box 496, Palmerston, NT 0831 P: +61 8 8999 4592 E: caroline.chong(a)nt.gov.au<mailto:caroline.chong@nt.gov.au> 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!
by Michael Charleston 17 Aug '23

17 Aug '23

Dear Phylomaniacs, We are delighted to announce that Phylomania 2023 - the 15th Annual Theoretical Phylogenetics at the University of Tasmania - will be going ahead again this year. Dates are set for the 22nd – 24th of November. Venue: Sandy Bay Campus of University of Tasmania (Hobart). The conference will be in hybrid mode again: online registration will be free, and we are working out the costing for attendance in person. We welcome abstract submissions from people wanting to present in person in Hobart as well as those who would prefer to present online. As per usual, although the conference title is phylocentric, we welcome talks on any mathematical, theoretical or applied aspects of evolutionary biology. The deadline for abstract submission is October 27th. Please see the conference website http://www.maths.utas.edu.au/phylomania/phylomania2023.html for more information! We hope to see you in Hobart in November! Stay tuned! Best wishes Mike, Barbara, Jeremy Michael Charleston [cid:da3731bc-18c2-42f0-bcef-ac31a3fd2075] 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: COMBINE survey 2023
by Michael Charleston 28 Mar '23

28 Mar '23

Hello Bioinformaticians! Here is a survey from COMBINE, the amazing student-run bioinformatics organization in Australia. They'd LOVE it if you would fill in this survey to help them plan events this year and next. Please can you help them out? Dear Bioinformatics community, Only 3 users have taken the below COMBINE survey! If you would like training workshops for bioinformatics / computational biology in Tasmania now is your opportunity to show the need! You do not need to be a COMBINE member to take the survey. Survey closes 31st March 2023 Supervisors – please encourage your students to complete this! You can complete it too. Regards, Nick [cid:b56fd09a-f6ae-4bc4-9398-190f6c1cf0a0] Hello, Bioinformatics community! We are planning bioinformatics events for 2023, and we want your input. Please take this survey to tell us about your needs. Take the survey now<https://docs.google.com/forms/d/e/1FAIpQLSdvlPu-jauTiMOxkrYf_hnkxPTrhTEiY39…>! [https://lh6.googleusercontent.com/USpUEyyTZ2R6yMsurZjVLu0Doaq2kB93El9pVjPWG…]<https://docs.google.com/forms/d/e/1FAIpQLSdvlPu-jauTiMOxkrYf_hnkxPTrhTEiY39…> COMBINE Survey 2023<https://docs.google.com/forms/d/e/1FAIpQLSdvlPu-jauTiMOxkrYf_hnkxPTrhTEiY39…> docs.google.com To value your time and to appreciate your contribution, we will be giving out a $25 Prezze gift voucher to two randomly chosen participants. Please add your email when prompted if you wish to enter the draw. Have you heard about COMBINE? COMBINE is a student-run Australian organisation for students in computational biology, bioinformatics, and related fields. COMBINE is the student subcommittee of The Australian Bioinformatics And Computational Biology Society (ABACBS). We aim to bring together students and early-career researchers from the computational and life sciences for networking, collaboration, and professional development. Australia has many research institutes, each with their own cohorts of students. Aside from conferences, there are few opportunities that bring these students together, allowing them to discover the different kinds of research going on at other institutes. COMBINE aims to bridge this institutional divide by organising seminars, workshops and social events, also as the yearly COMBINE Student Symposium. Together, these events allow students to connect with each other and build a network in a casual environment. Are you not a COMBINE member yet? Please join now<https://www.combine.org.au/>! Kind regards, Gayathry Krishnamurthy COMBINE Training and Events Officer (TAS) PhD Candidate (Medical Studies) Menzies Institute for Medical Research University of Tasmania menzies.utas.edu.au<https://menzies.utas.edu.au/> CRICOS 00586B University of Tasmania Electronic Communications Policy (December, 2014). 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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PhD scholarship to use machine learning to develop wildlife health intelligence system
by Andy Flies 16 Feb '23

16 Feb '23

Hello everyone, We are looking for a PhD student to help develop a wildlife health intelligence system! This machine learning project but will include regular interactions with Tasmanian devils in captivity and some fieldwork. Contact me at andy.flies(a)utas.edu.au<mailto:andy.flies@utas.edu.au> for more info. Please share this message with any people or lists that might be interested https://www.utas.edu.au/research/degrees/available-projects/projects/menzie… Selection criteria Basic to advanced computer programming skills Prior experience in machine learning algorithms Ability to work with a diverse academic and industry team Interested people can see a bit more about our research program on this recent ABC 7:30 program video. https://www.abc.net.au/news/2023-01-16/hopes-for-new-vaccine-for-tasmanian-… Kind regards, Andy -- Andrew S. Flies, PhD Senior Research Fellow Chair - UTAS Institutional Biosafety Committee Menzies Institute for Medical Research University of Tasmania t: +61 3 6226 4614 | e: Andy.Flies(a)utas.edu.au<mailto:Andy.Flies@utas.edu.au> Website: WildImmunity.com<https://wildimmunity.com/> | Facebook: WildImmunity<https://www.facebook.com/WildImmunity/> Twitter: @WildImmunity<https://twitter.com/WildImmunity> | Youtube: @WildImmunity<https://www.youtube.com/@WildImmunity> | Instagram: WildImmunity<https://www.instagram.com/wildimmunity/> Wild and Comparative Immunology Consortium<https://www.wacimmuno.com/> Recent publication: Class II transactivator induces expression of MHC-I and MHC-II in transmissible Tasmanian devil facial tumours<https://doi.org/10.1098/rsob.220208> (Open Biology) Recent publication: A human adenovirus encoding IFN-γ can transduce Tasmanian devil facial tumour cells and upregulate MHC-I<https://doi.org/JGV-D-22-00136> (Journal of General Virology) Recent publication: Fluorescent Adaptable Simple Theranostic (FAST) proteins for single-step testing of recombinant proteins<https://doi.org/10.1126/sciadv.aba5031> (Science Advances) menzies.utas.edu.au<https://menzies.utas.edu.au/> [cid:image001.png@01D9421C.4F50C070] CRICOS 00586B University of Tasmania Electronic Communications Policy (December, 2014). 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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Save the Date for ASPS2023 Plant Science Conference
by Frances Sussmilch 13 Jan '23

13 Jan '23

Hi All, We are organising a national plant science conference for the Australian Society of Plant Scientists (ASPS2023) to be held in Hobart later this year. If you are interested in attending and/or assisting with conference organisation, please fill out the short expression of interest form linked below and circulate with your students and colleagues. Apologies for any cross-posting. Cheers, Frances ________________________ Dr Frances Sussmilch Biological Sciences School of Natural Sciences University of Tasmania Private bag 55, Hobart 7001 Tasmania, Australia [https://www.asps.org.au/wp-content/uploads/aspsbanner.jpg] Save the Date for ASPS2023! We are planning an in-person plant science conference in Hobart from 28 Nov - 1 Dec 2023. Please add yourself to our mailing list and help us during the planning stages by filling out our EOI form: https://forms.gle/osUAvNEyn9jcwtw78<https://protect-au.mimecast.com/s/611EC81Zm7f67ZVyyInei27?domain=asps.org.au> We welcome you to circulate this widely among your networks. Looking forward to seeing you there, The ASPS 2023 Organising Committee [cid:image001.png@01D91609.21932B30] Copyright © Australian Society of Plant Scientists 2023 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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COMBINE!
by Michael Charleston 18 Nov '22

18 Nov '22

COMBINE is a wonderful student-run society of bioinformaticians in Australia. They have asked me to forward this advert along, so here it is! Are you a current student studying computational biology or bioinformatics? Are you interested in being part of a community that supports students by planning events, encouraging social interactions and promoting technical skills — then come and join the COMBINE committee! Applications will be open until 12th December 2022 and new committee members will be contacted in early January 2023. Detailed position descriptions are listed here<https://protect-au.mimecast.com/s/9-0uCq7BJXt8WjqyLfZBsXz?domain=combine.us…>. Nominate yourself or someone else to join via the Nomination Form<https://protect-au.mimecast.com/s/qvmBCr8DKNf89lgRwfzkJCJ?domain=combine.us…>. For more information please contact combine(a)combine.org.au<mailto:combine@combine.org.au> Michael Charleston [cid:dd7d9f31-2dff-47a9-bd90-20318825f55c] Phylomania 2022 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: Contract computation work ...
by Barbara Holland 11 Nov '22

11 Nov '22

fyi From: Alex Hewitt <alex.hewitt(a)utas.edu.au> Sent: Wednesday, 9 November 2022 8:01 PM To: Barbara Holland <barbara.holland(a)utas.edu.au> Subject: Contract computation work ... Hi Barbara, You wouldn't happen to know any local students/graduates who may be interested in some contract bioinformatics work? We have some NGS data which relate to viral quasispecies and we are keen to churn through some analyses etc. It would be good if they knew python and R ... Best wishes, Alex Hewitt m. 0407359824 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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AMSI BioInfoSummer 2022, 21-24 November, The University of Melbourne - register now
by Michael Charleston 08 Aug '22

08 Aug '22

[ Or stay in Tasmania for Phylomania #14, November 23-25! (Official announcement and registration page soon) (yes, sorry they clash) ] Registrations are now open for AMSI BioInfoSummer 2022<https://protect-au.mimecast.com/s/OyLsCnxyDVH7yBJBzsrxumv?domain=bis.amsi.o…>. The four-day bioinformatics conference will be hosted by Melbourne Integrative Genomics at The University of Melbourne from 21-24 November. The program includes specialist lectures, hands-on workshops, an interactive careers advice session, a public lecture and networking events. Delegates are strongly encouraged to attend in person to maximise their conference experience however virtual participation is also available. Conference themes: * High-resolution biology * Genome architecture * Whole-cell modelling * Populations As usual, we need your help to promote this program please. How you can help: 1. Forward the BioInfoSummer 2022 event emails through your networks as your receive them (attached is the latest one sent yesterday) 2. Display the attached digital posters on your electronic signage boards around your departments/organisations (please advise if you require different sizing) 3. Ask lecturers and tutors to promote in classes by including the attached posters in their slide deck 4. Encourage your students, ECRs and colleagues to register 5. Make your students aware of any travel funding they can access from their home departments to support their attendance AMSI BioInfoSummer 2022 21-24 November | The University of Melbourne bis.amsi.org.au<https://protect-au.mimecast.com/s/OyLsCnxyDVH7yBJBzsrxumv?domain=bis.amsi.o…> Audience: 3rd year undergraduates through to early career researchers, academics and industry professionals Registration fees: Discounted AMSI member four-day conference registration $160 student / $320 standard (day registration and virtual participation also available). Travel grants: Students can apply for a travel grant sponsored by Australian BioCommons to support in-person participation in Melbourne. Applications close midnight Monday 17 October. We have a limited grant budget so ask all applicants to explore what funding is available to them at their home universities to supplement AMSI support. Poster abstract submissions close Monday 31 October. A great opportunity for delegates to share their research with the bioinformatics community. Up to $800 in prizes in prizes for the best poster and best fast forward talks Kind regards Angela Angela Coughlin Program Manager, Research and Higher Education [cid:image001.png@01D8A812.310FB3E0] Australian Mathematical Sciences Institute Building 161, Monash Rd, c/- The University of Melbourne, Victoria 3010 Australia P: 03 8344 2103 | E: angela.coughlin(a)amsi.org.au<mailto:angela.coughlin@amsi.org.au> | W: amsi.org.au<https://protect-au.mimecast.com/s/n5LBCoVzE9HroW7WMC0QxxO?domain=amsi.org.a…> [cid:image002.png@01D8A812.310FB3E0]<https://protect-au.mimecast.com/s/Yl65Cp8AG6fnl6j6Gc6qCG8?domain=facebook.c…> [cid:image003.png@01D8A812.310FB3E0] <https://protect-au.mimecast.com/s/la9OCq7BJXt84wpwDu9Z2Id?domain=twitter.com> [cid:image004.png@01D8A812.310FB3E0] <https://protect-au.mimecast.com/s/e-shCr8DKNf8NJ5JpuO9lqi?domain=au.linkedi…> [cid:image005.png@01D8A812.310FB3E0]<https://protect-au.mimecast.com/s/OyLsCnxyDVH7yBJBzsrxumv?domain=bis.amsi.o…> 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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BioHackathon 2022
by Michael Charleston 25 Jul '22

25 Jul '22

This just in! (ok while I was on leave)... Help make the BioHackathon global Are you interested in joining us for the Australian Outpost of the BioHackathon Europe? This is a unique opportunity to participate in a significant global event and network with your international peers while working locally on practical coding challenges. BioCommons will cover flights and accommodation for the duration of ELIXIR’s BioHackathon, 7-11 November 2022. Expressions of interest due 1 Aug 2022. Find your project and express your interest<https://protect-au.mimecast.com/s/8aQjC3Q870Up8WAXATgM6NB?domain=biocommons…> Thanks very much! Michael Charleston [cid:53684f1d-32d2-4dea-840e-27d07d4a5634] 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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PhD scholarship at UTAS - Genetics of flowering in chickpea
by Jakob Butler 01 Jul '22

01 Jul '22

Hey bioinformatics-inclined people, We're on the hunt for a PhD student to join a project supervised by Jim Weller examining the genetics of flowering time in chickpeas. The prospective candidate will be using GWAS, bi-parental genetics and transcriptomics to exploring the architecture of phenology traits across the chickpea genome, with the aim of informing breeder decisions into the climate-addled future we're looking at. This project is under the banner of the GRDC, and comes with a guaranteed 3.5 year scholarship. We're hoping for someone who has completed Honours in molecular biology, bioinformatics, plant physiology or genetics (or anything else tangentially related). A background in plant science is not essential, but the project will involve a fair chunk of plant husbandry, so be prepared! Applications close on the 18th July (so about two weeks). https://www.utas.edu.au/research/degrees/available-projects/projects/biolog… Cheers, Jak --------------------------------------------------------------- Dr Jakob Butler | Postdoctoral research fellow University of Tasmania (UTAS) | School of Natural Sciences Rm372d, Life Sciences Building, Churchill Avenue, Hobart, TAS 7005, Australia M: +61 439 323 751 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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We are hiring! Don't forget to apply!
by Michael Charleston 20 Jun '22

20 Jun '22

Dear bioinformatics folk, If anyone out there is interested in a challenging, exciting and all-over wonderful three-year full-time research position developing new bioinformatics tools to tackle some cool problems, please look at the link below! https://careers.utas.edu.au/en/job/497476/postdoctoral-research-fellow The position is funded by the ARC Center of Excellence for Plant Success in Nature and Agriculture. It will be based in Hobart, Tasmania. The successful applicant should have a PhD in bioinformatics, computational biology, biostatistics or similar. We want to find someone who will be able to think outside the box and create new approaches that, with the expertise in plant science in the Centre, will enable researchers to uncover novel, complex molecular interactions from multiple -omics data. Programming and mathematical skills are more important than biological background. Feel free to contact me, Jazmine Humphreys (jazmine.humphreys(a)utas.edu.au) or Steve Smith (steven.smith(a)utas.edu.au) for more details, but applications must be made via the link above: don't send them straight to me! If you are unsure whether you have all the boxes ticked, please do get in touch. We are particularly keen to have a diverse range of backgrounds and experience talk to us. Applications close on 29th June - you have a bit over a week! (Blurb from the ad below:) We are seeking to appoint a Postdoctoral Research Fellow in the field of bioinformatics, School of Natural Sciences (https://www.utas.edu.au/natural-sciences), part of the College of Sciences and Engineering (https://universitytasmania.sharepoint.com/sites/CoSE). This position will be located within the School of Natural Sciences. The Postdoctoral Research Fellow will undertake research as part of a project funded by the Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, at the University of Tasmania node. The candidate will contribute to a key project within the Centre led by Chief Investigator Prof. Steven Smith and Prof. Michael Charleston entitled ‘Integrating multi-omics data to reveal gene expression networks in plants.’ The project will involve collaboration with other nodes of the Centre of Excellence. The Postdoctoral Research Fellow will develop new computational tools to gain greater insight into gene regulation by integrating different -omics datasets and interrogating them in ways that will reveal previously inaccessible information and understanding. This will require extending existing software packages while laying the groundwork to develop new analysis pipelines and programs. The researcher should have recognised expertise in biostatistics / bioinformatics, and programming, e.g., using R, python or C++. The researcher will be actively engaged with experimental biologists from the outset to ensure synergy between experimental and computational biology. In addition, they will contribute substantially to interaction with collaborators, project integration and reporting, and the supervision of research students. The appointee will be expected to operate with a degree of independence following general direction from the project leaders, and to interact positively and productively with other researchers participating in the project. Michael Charleston [cid:9e911cb1-c07d-40c9-a5ef-2f508c3b06e4][cid:a80a6fbd-e9dd-4c10-aa30-b218620ba092] 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: Seminar today 3pm - Joshua Stevenson
by Jeremy Sumner 19 May '22

19 May '22

Dear all, Just a friendly reminder that we have an ANZIAM* seminar this afternoon given by Joshua Stevenson via ZOOM at 3pm. Please see details below. Meeting URL: https://utas.zoom.us/j/88961934178 Meeting ID: 889 6193 4178 Title: Algebraic Models of Circular Genome Rearrangement Abstract: Phylogenetics is the study of evolutionary relationships between present-day organisms. Evolution can occur via a number of mechanisms, and one such mechanism is the application of large-scale genome rearrangement events, in which sections of the genome are broken apart and reattached in a different order or orientation. By considering the possible combinations of rearrangements that could convert one genome into another, we can identify how closely related the organisms are. I will give an overview of genome rearrangement modelling as an applied combinatorial problem, and then present our algebraic framework for modelling genomes. I will discuss some of my recent work in characterising `biologically reasonable' rearrangements and determining how many of these there are for a given number of regions. *ANZIAM (Australia and New Zealand Industrial and Applied Mathematics) is a division of the Australian Mathematical Society Dr Courtney Quinn Lecturer (Mathematics) School of Natural Sciences College of Sciences and Engineering University of Tasmania E: courtney.quinn(a)utas.edu.au<mailto:courtney.quinn@utas.edu.au> 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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