Alistair Legione
@alegione.bsky.social
Senior Lecturer in Veterinary Microbiology and Public Health at the University of Melbourne. Interested in genomics of bacteria and viruses in wildlife and domestic animals
Reposted by Alistair Legione
Okay, it's the start of the academic year and there have been further funny (and some frustrating) mix ups ... just a gentle reminder that there are two of us - try to make sure you have the right one ...
November 26, 2025 at 7:21 AM
Okay, it's the start of the academic year and there have been further funny (and some frustrating) mix ups ... just a gentle reminder that there are two of us - try to make sure you have the right one ...
Reposted by Alistair Legione
If you missed my talk but still want some tips for writing good code for scientists, my slides are here:
daxkellie.quarto.pub/a-guide-to-w...
All the links and references are there too in case you want to see more! 😀🧪🌏
#ESA2025 #rstats #quartopub
daxkellie.quarto.pub/a-guide-to-w...
All the links and references are there too in case you want to see more! 😀🧪🌏
#ESA2025 #rstats #quartopub
November 26, 2025 at 6:12 AM
If you missed my talk but still want some tips for writing good code for scientists, my slides are here:
daxkellie.quarto.pub/a-guide-to-w...
All the links and references are there too in case you want to see more! 😀🧪🌏
#ESA2025 #rstats #quartopub
daxkellie.quarto.pub/a-guide-to-w...
All the links and references are there too in case you want to see more! 😀🧪🌏
#ESA2025 #rstats #quartopub
A lot of human medical things funded, no animal health studies funded - please human health researchers stick to the millions in NHMRC and MRRF available to you that the rest of us can't apply for!
🚨 #DECRA #DE26 announcement:
❗️Outcomes announced publicly for Discovery Early Career Researcher Award 2026❗️
See ARC's RMS for list ➡️ https://rms.arc.gov.au/RMS/Report/Download/Report/a3f6be6e-33f7-4fb5-98a6-7526aaa184cf/285
/bot
❗️Outcomes announced publicly for Discovery Early Career Researcher Award 2026❗️
See ARC's RMS for list ➡️ https://rms.arc.gov.au/RMS/Report/Download/Report/a3f6be6e-33f7-4fb5-98a6-7526aaa184cf/285
/bot
November 25, 2025 at 12:54 AM
A lot of human medical things funded, no animal health studies funded - please human health researchers stick to the millions in NHMRC and MRRF available to you that the rest of us can't apply for!
Reposted by Alistair Legione
DECRA success rate is the lowest in 14 years, since 2012 (1st year the scheme ran).
What a pathetic system we have for supporting new ideas, new people…
DE26: 13.1%
25: 17.9
24: 19.6
23: 15.0
22: 19.7
21: 17.1
20: 16.0
19: 17.2
18: 16.3
17: 16.7
16: 16.4
15: 14.3
14: 13.6
13: 15.6
12: 12.8
What a pathetic system we have for supporting new ideas, new people…
DE26: 13.1%
25: 17.9
24: 19.6
23: 15.0
22: 19.7
21: 17.1
20: 16.0
19: 17.2
18: 16.3
17: 16.7
16: 16.4
15: 14.3
14: 13.6
13: 15.6
12: 12.8
🚨 #DECRA #DE26 announcement:
❗️Outcomes announced publicly for Discovery Early Career Researcher Award 2026❗️
See ARC's RMS for list ➡️ https://rms.arc.gov.au/RMS/Report/Download/Report/a3f6be6e-33f7-4fb5-98a6-7526aaa184cf/285
/bot
❗️Outcomes announced publicly for Discovery Early Career Researcher Award 2026❗️
See ARC's RMS for list ➡️ https://rms.arc.gov.au/RMS/Report/Download/Report/a3f6be6e-33f7-4fb5-98a6-7526aaa184cf/285
/bot
November 25, 2025 at 12:34 AM
DECRA success rate is the lowest in 14 years, since 2012 (1st year the scheme ran).
What a pathetic system we have for supporting new ideas, new people…
DE26: 13.1%
25: 17.9
24: 19.6
23: 15.0
22: 19.7
21: 17.1
20: 16.0
19: 17.2
18: 16.3
17: 16.7
16: 16.4
15: 14.3
14: 13.6
13: 15.6
12: 12.8
What a pathetic system we have for supporting new ideas, new people…
DE26: 13.1%
25: 17.9
24: 19.6
23: 15.0
22: 19.7
21: 17.1
20: 16.0
19: 17.2
18: 16.3
17: 16.7
16: 16.4
15: 14.3
14: 13.6
13: 15.6
12: 12.8
Reposted by Alistair Legione
ARC says they’ll announce DECRA and LIEF outcomes tomorrow (Tuesday 25th Nov).
In recent times these announcements have been around 11am Canberra time. With 2 schemes on the same day, I assume they’ll announce one of them later in the day (probably DECRA first).
In recent times these announcements have been around 11am Canberra time. With 2 schemes on the same day, I assume they’ll announce one of them later in the day (probably DECRA first).
November 23, 2025 at 11:40 PM
ARC says they’ll announce DECRA and LIEF outcomes tomorrow (Tuesday 25th Nov).
In recent times these announcements have been around 11am Canberra time. With 2 schemes on the same day, I assume they’ll announce one of them later in the day (probably DECRA first).
In recent times these announcements have been around 11am Canberra time. With 2 schemes on the same day, I assume they’ll announce one of them later in the day (probably DECRA first).
Reposted by Alistair Legione
Very excited to be in Adelaide to attend #ABACBS2025 . Australia is a powerhouse of microbial genomics, and indeed of bioinformatics, so am very much looking forward to meeting everyone, old friends and new, and speaking tomorrow!
November 24, 2025 at 12:11 AM
Very excited to be in Adelaide to attend #ABACBS2025 . Australia is a powerhouse of microbial genomics, and indeed of bioinformatics, so am very much looking forward to meeting everyone, old friends and new, and speaking tomorrow!
Reposted by Alistair Legione
Study after study shows that using LLMs is bad for cognition, bad for learning, bad for understanding, bad for mental health. So why are our schools and universities still relentlessly pushing them?
Relying on ChatGPT to teach you about a topic leaves you with shallower knowledge than Googling and reading about it, according to new research that compared what more than 10,000 people knew after using one method or the other.
Shared by @gizmodo.com: buff.ly/yAAHtHq
Shared by @gizmodo.com: buff.ly/yAAHtHq
November 21, 2025 at 2:52 PM
Study after study shows that using LLMs is bad for cognition, bad for learning, bad for understanding, bad for mental health. So why are our schools and universities still relentlessly pushing them?
How many submarines that we're never going to get does this equal? Thoughts with all research staff doing amazing work that are undervalued by a government with no competition and no ambition
November 18, 2025 at 5:45 AM
How many submarines that we're never going to get does this equal? Thoughts with all research staff doing amazing work that are undervalued by a government with no competition and no ambition
Reposted by Alistair Legione
It soothes my bitter heart to know that no matter how much money Elon Musk has, he will never, ever be funny
t.co/QhuKU9HCxA
t.co/QhuKU9HCxA
November 13, 2025 at 9:59 PM
It soothes my bitter heart to know that no matter how much money Elon Musk has, he will never, ever be funny
t.co/QhuKU9HCxA
t.co/QhuKU9HCxA
Reposted by Alistair Legione
every company in 2025
November 12, 2025 at 5:59 PM
every company in 2025
Reposted by Alistair Legione
Reposted by Alistair Legione
Finally got my hands on a rare find: Sonja Buckley’s autobiography. She was instrumental in the development of tissue culture techniques for virus isolation & study, which required CONSIDERABLE skill pre-gloves, BSCs, & mechanical pipettes - & was the first person to isolate Lassa virus.
November 2, 2025 at 5:24 PM
Finally got my hands on a rare find: Sonja Buckley’s autobiography. She was instrumental in the development of tissue culture techniques for virus isolation & study, which required CONSIDERABLE skill pre-gloves, BSCs, & mechanical pipettes - & was the first person to isolate Lassa virus.
Reposted by Alistair Legione
The organising committee are delighted to invite you to submit an abstract for the ASM VIC Meeting, taking place at the Melbourne Convention and Exhibition Centre from 15–18 June 2026. www.theasmmeeting.org.au/abstract-sub...
October 28, 2025 at 9:52 PM
The organising committee are delighted to invite you to submit an abstract for the ASM VIC Meeting, taking place at the Melbourne Convention and Exhibition Centre from 15–18 June 2026. www.theasmmeeting.org.au/abstract-sub...
Reposted by Alistair Legione
New pre-print: Plasmid dependent phage effectively eliminate AMR bacteria and block plasmid transmission in the chicken gut microbiome
Fun collaboration with Tao He lab (JAAS) and @brockhurstlab.bsky.social lab (Manchester)
#phagesky#microsky
www.biorxiv.org/content/10.1...
Fun collaboration with Tao He lab (JAAS) and @brockhurstlab.bsky.social lab (Manchester)
#phagesky#microsky
www.biorxiv.org/content/10.1...
Plasmid dependent phage eliminate pathogenic bacteria and antibiotic resistance plasmids from the chicken gut microbiome
Conjugative plasmids are a key reservoir of antimicrobial resistance (AMR) in commensal and pathogenic bacteria within the gut microbiome. Plasmid-dependent phage (PDPs) are a promising therapeutic op...
www.biorxiv.org
October 27, 2025 at 8:19 AM
New pre-print: Plasmid dependent phage effectively eliminate AMR bacteria and block plasmid transmission in the chicken gut microbiome
Fun collaboration with Tao He lab (JAAS) and @brockhurstlab.bsky.social lab (Manchester)
#phagesky#microsky
www.biorxiv.org/content/10.1...
Fun collaboration with Tao He lab (JAAS) and @brockhurstlab.bsky.social lab (Manchester)
#phagesky#microsky
www.biorxiv.org/content/10.1...
Reposted by Alistair Legione
the fact that a company doesnt wanna drop the dopest of video game in which you're a FREED SLAVE killing KKK WHITE SUPREMACISTS because theyre worried about the FUCKING BACKLASH tells you all you need to know about the current state of america
October 9, 2025 at 12:07 AM
the fact that a company doesnt wanna drop the dopest of video game in which you're a FREED SLAVE killing KKK WHITE SUPREMACISTS because theyre worried about the FUCKING BACKLASH tells you all you need to know about the current state of america
Reposted by Alistair Legione
Unbelievable, Bakta reached its 1,000th citation!
A huge shout out and thank you to all Bakta users, bug reporters, those sharing ideas and suggesting features...
...just the entire incredibly supporting binfie community!
Without you, Bakta wouldn't be the same.
Thank you!
A huge shout out and thank you to all Bakta users, bug reporters, those sharing ideas and suggesting features...
...just the entire incredibly supporting binfie community!
Without you, Bakta wouldn't be the same.
Thank you!
October 6, 2025 at 8:11 AM
Unbelievable, Bakta reached its 1,000th citation!
A huge shout out and thank you to all Bakta users, bug reporters, those sharing ideas and suggesting features...
...just the entire incredibly supporting binfie community!
Without you, Bakta wouldn't be the same.
Thank you!
A huge shout out and thank you to all Bakta users, bug reporters, those sharing ideas and suggesting features...
...just the entire incredibly supporting binfie community!
Without you, Bakta wouldn't be the same.
Thank you!
Reposted by Alistair Legione
Dear community, Bakta needs your help!
To further improve the functional annotation of "hypothetical" CDS, me and @gbouras13.bsky.social, we are looking for the worst Bakta-annotated bacterial genomes ;-)
(1/2)
To further improve the functional annotation of "hypothetical" CDS, me and @gbouras13.bsky.social, we are looking for the worst Bakta-annotated bacterial genomes ;-)
(1/2)
October 6, 2025 at 7:27 AM
Dear community, Bakta needs your help!
To further improve the functional annotation of "hypothetical" CDS, me and @gbouras13.bsky.social, we are looking for the worst Bakta-annotated bacterial genomes ;-)
(1/2)
To further improve the functional annotation of "hypothetical" CDS, me and @gbouras13.bsky.social, we are looking for the worst Bakta-annotated bacterial genomes ;-)
(1/2)
Reposted by Alistair Legione
Longer descriptive thread:
In the US, you can see that women born before 1979 have had >2 children per woman by the time they reached age 45.
Also, women born before 1984 have had >2 children per woman by the time they reached age 40.
In the US, you can see that women born before 1979 have had >2 children per woman by the time they reached age 45.
Also, women born before 1984 have had >2 children per woman by the time they reached age 40.
Most graphs of the fertility rate depict the 'period fertility rate', which is based on a single year's data and doesn't necessarily reflect how many children women actually have across their lifetimes.
I've used data from the Human Fertility Database to show the cumulative number instead:
I've used data from the Human Fertility Database to show the cumulative number instead:
October 1, 2025 at 10:56 AM
Longer descriptive thread:
In the US, you can see that women born before 1979 have had >2 children per woman by the time they reached age 45.
Also, women born before 1984 have had >2 children per woman by the time they reached age 40.
In the US, you can see that women born before 1979 have had >2 children per woman by the time they reached age 45.
Also, women born before 1984 have had >2 children per woman by the time they reached age 40.
Reposted by Alistair Legione
AI is the asbestos we are shoveling into the walls of our society and our descendants will be digging it out for generations”
Doctorow on the impending economic collapse when the AI bubble bursts. pluralistic.net/2025/09/27/e...
Pluralistic: The real (economic) AI apocalypse is nigh (27 Sep 2025) – Pluralistic: Daily links from Cory Doctorow
pluralistic.net
September 28, 2025 at 10:59 PM
AI is the asbestos we are shoveling into the walls of our society and our descendants will be digging it out for generations”
Imagine the conservative outrage if asylum seekers were given a million dollars each? Why are we ok keeping our fellow humans in these camps and paying profit driven entities 8x that to enforce our evil?
This was the lead news item at The Guardian first thing this morning.
www.theguardian.com/world/2025/s...
www.theguardian.com/world/2025/s...
US private prisons operator to be paid $790m to hold 100 people on Nauru in quiet expansion of contract
A sixteenfold increase in the original contract without public notification raises allegations of ‘gross mismanagement’ and a process ‘run out of control’
www.theguardian.com
September 28, 2025 at 9:56 PM
Imagine the conservative outrage if asylum seekers were given a million dollars each? Why are we ok keeping our fellow humans in these camps and paying profit driven entities 8x that to enforce our evil?
System is broken if you can cheat someone out of 600k, still own the million dollar property, and only be fined 11k.
September 27, 2025 at 5:45 AM
System is broken if you can cheat someone out of 600k, still own the million dollar property, and only be fined 11k.
Reposted by Alistair Legione
I’ve set up a mailing list to send out an email when I have an article come out, instead of than hoping that an algorithm will serve it to you.
Subscribe here for free: camwilson.beehiiv.com/subscribe
Subscribe here for free: camwilson.beehiiv.com/subscribe
Cam Wilson's reporting
Join my mailing list so you get notified every time I publish an article or some reporting.
camwilson.beehiiv.com
September 23, 2025 at 11:50 PM
I’ve set up a mailing list to send out an email when I have an article come out, instead of than hoping that an algorithm will serve it to you.
Subscribe here for free: camwilson.beehiiv.com/subscribe
Subscribe here for free: camwilson.beehiiv.com/subscribe
Reposted by Alistair Legione
Highlight of my career writing a couple of these for the icon herself www.instagram.com/reel/DOdwrqz...
September 15, 2025 at 10:01 AM
Highlight of my career writing a couple of these for the icon herself www.instagram.com/reel/DOdwrqz...
Reposted by Alistair Legione
X-Mapper 🦠🧬🧪 - a sequence aligner developed for microbes, now on Bioconda! 🚀
• 11–24× fewer suboptimal alignments (same for human genome)
• 3–579× lower inconsistency
• improves on ~30% of reads aligned to non-target species
github.com/mathjeff/map...
bioconda.github.io/recipes/x-ma...
#microsky
• 11–24× fewer suboptimal alignments (same for human genome)
• 3–579× lower inconsistency
• improves on ~30% of reads aligned to non-target species
github.com/mathjeff/map...
bioconda.github.io/recipes/x-ma...
#microsky
September 15, 2025 at 2:32 AM
X-Mapper 🦠🧬🧪 - a sequence aligner developed for microbes, now on Bioconda! 🚀
• 11–24× fewer suboptimal alignments (same for human genome)
• 3–579× lower inconsistency
• improves on ~30% of reads aligned to non-target species
github.com/mathjeff/map...
bioconda.github.io/recipes/x-ma...
#microsky
• 11–24× fewer suboptimal alignments (same for human genome)
• 3–579× lower inconsistency
• improves on ~30% of reads aligned to non-target species
github.com/mathjeff/map...
bioconda.github.io/recipes/x-ma...
#microsky
Reposted by Alistair Legione
Preprint out for myloasm, our new nanopore / HiFi metagenome assembler!
Nanopore's getting accurate, but
1. Can this lead to better metagenome assemblies?
2. How, algorithmically, to leverage them?
with co-author Max Marin @mgmarin.bsky.social, supervised by Heng Li @lh3lh3.bsky.social
1 / N
Nanopore's getting accurate, but
1. Can this lead to better metagenome assemblies?
2. How, algorithmically, to leverage them?
with co-author Max Marin @mgmarin.bsky.social, supervised by Heng Li @lh3lh3.bsky.social
1 / N
High-resolution metagenome assembly for modern long reads with myloasm https://www.biorxiv.org/content/10.1101/2025.09.05.674543v1
September 7, 2025 at 11:35 PM
Preprint out for myloasm, our new nanopore / HiFi metagenome assembler!
Nanopore's getting accurate, but
1. Can this lead to better metagenome assemblies?
2. How, algorithmically, to leverage them?
with co-author Max Marin @mgmarin.bsky.social, supervised by Heng Li @lh3lh3.bsky.social
1 / N
Nanopore's getting accurate, but
1. Can this lead to better metagenome assemblies?
2. How, algorithmically, to leverage them?
with co-author Max Marin @mgmarin.bsky.social, supervised by Heng Li @lh3lh3.bsky.social
1 / N