Dr Andrew Lonsdale
@lonsbio.bsky.social
Bioinformatics post-doc at @petermaccc.bsky.social in the @aliciao.bsky.social Lab. Keen believer in the benefit of side projects. He/Him. Work/Life: 💻💻💻💻💻 👨👩👧👧 👨👩👧👧
Reposted by Dr Andrew Lonsdale
Only 13 days, 12 hours, 45 minutes, and 5 seconds until #ABACBS2025!
Check out the full program and you can still register (dinner & workshops are almost sold out though!) www.abacbs.org/abacbs2025
Check out the full program and you can still register (dinner & workshops are almost sold out though!) www.abacbs.org/abacbs2025
ABACBS 2025 Conference
Adelaide, South Australia. Nov. 24-
www.abacbs.org
November 10, 2025 at 12:44 AM
Only 13 days, 12 hours, 45 minutes, and 5 seconds until #ABACBS2025!
Check out the full program and you can still register (dinner & workshops are almost sold out though!) www.abacbs.org/abacbs2025
Check out the full program and you can still register (dinner & workshops are almost sold out though!) www.abacbs.org/abacbs2025
Less than a month until #abacbs25 and I have a very important question for y'all in the Australian Bioinformatics and Computational Biology community - should we revive Conference Bingo?
October 29, 2025 at 12:15 PM
Less than a month until #abacbs25 and I have a very important question for y'all in the Australian Bioinformatics and Computational Biology community - should we revive Conference Bingo?
Reposted by Dr Andrew Lonsdale
My first CRAN package! 🤓
Two of my favourite UpSet plot packages have been caught out by recent ggplot2 updates. That has cascaded into some Bioconductor packages failing (mine + others), so I figured I'd add another UpSet plot option to the mix. Hopefully this can help stabilise things a bit.
Two of my favourite UpSet plot packages have been caught out by recent ggplot2 updates. That has cascaded into some Bioconductor packages failing (mine + others), so I figured I'd add another UpSet plot option to the mix. Hopefully this can help stabilise things a bit.
New on CRAN: SimpleUpset (0.1.2). View at https://CRAN.R-project.org/package=SimpleUpset
SimpleUpset: Create Upset Plots
Create Upset plots using a combination of 'ggplot2' and 'patchwork'.
CRAN.R-project.org
October 7, 2025 at 1:01 AM
My first CRAN package! 🤓
Two of my favourite UpSet plot packages have been caught out by recent ggplot2 updates. That has cascaded into some Bioconductor packages failing (mine + others), so I figured I'd add another UpSet plot option to the mix. Hopefully this can help stabilise things a bit.
Two of my favourite UpSet plot packages have been caught out by recent ggplot2 updates. That has cascaded into some Bioconductor packages failing (mine + others), so I figured I'd add another UpSet plot option to the mix. Hopefully this can help stabilise things a bit.
Reposted by Dr Andrew Lonsdale
barbieQ: An R software package for analysing barcode count data from clonal tracking experiments https://www.biorxiv.org/content/10.1101/2025.09.11.675529v1
September 15, 2025 at 2:48 AM
barbieQ: An R software package for analysing barcode count data from clonal tracking experiments https://www.biorxiv.org/content/10.1101/2025.09.11.675529v1
This year I came full circle to be the Faculty Advisor to COMBINE, the ISCB RSG for Australia (and @abacbs.bsky.social student subcommittee) — a group I was part of in the olden days.
It's mostly a hands-off role but my only (strong) advice so far? Get on BlueSky! So, welcome @combine1.bsky.social
It's mostly a hands-off role but my only (strong) advice so far? Get on BlueSky! So, welcome @combine1.bsky.social
August 28, 2025 at 12:25 AM
This year I came full circle to be the Faculty Advisor to COMBINE, the ISCB RSG for Australia (and @abacbs.bsky.social student subcommittee) — a group I was part of in the olden days.
It's mostly a hands-off role but my only (strong) advice so far? Get on BlueSky! So, welcome @combine1.bsky.social
It's mostly a hands-off role but my only (strong) advice so far? Get on BlueSky! So, welcome @combine1.bsky.social
Reposted by Dr Andrew Lonsdale
🚨 Abstract deadline extended! 🚨
You’ve now got until August 15 to submit for #ABACBS2025 — one-time extension only!
Join us in Adelaide for world-class #bioinformatics, workshops, student & EMCR events, and more.
🔗 www.abacbs.org/abacbs2025
You’ve now got until August 15 to submit for #ABACBS2025 — one-time extension only!
Join us in Adelaide for world-class #bioinformatics, workshops, student & EMCR events, and more.
🔗 www.abacbs.org/abacbs2025
ABACBS 2025 Conference
Adelaide, South Australia. Nov. 24-
www.abacbs.org
August 5, 2025 at 12:16 AM
🚨 Abstract deadline extended! 🚨
You’ve now got until August 15 to submit for #ABACBS2025 — one-time extension only!
Join us in Adelaide for world-class #bioinformatics, workshops, student & EMCR events, and more.
🔗 www.abacbs.org/abacbs2025
You’ve now got until August 15 to submit for #ABACBS2025 — one-time extension only!
Join us in Adelaide for world-class #bioinformatics, workshops, student & EMCR events, and more.
🔗 www.abacbs.org/abacbs2025
Every conference I have been involved with, I threaten that this will be the one where we do not extend abstracts.
Can you take that risk?
Can you take that risk?
⚠️ ONE HOUR TO GO ⚠️
2 Days left!! 🏃
It's time to get your abstracts reviewed and submitted! 🚀
Closing this Friday, 11th of April at 5:00PM AEST (or 3:00PM AWST 😛)
cancerbioinformatics.au/abstracts
It's time to get your abstracts reviewed and submitted! 🚀
Closing this Friday, 11th of April at 5:00PM AEST (or 3:00PM AWST 😛)
cancerbioinformatics.au/abstracts
April 11, 2025 at 5:57 AM
Every conference I have been involved with, I threaten that this will be the one where we do not extend abstracts.
Can you take that risk?
Can you take that risk?
Reposted by Dr Andrew Lonsdale
The strchive.org paper is out!!
The paper describes STRchive as a resource to improve the diagnosis of tandem repeat disorders, then goes beyond it to consider what can be learned about childhood onset and population prevalence of these diseases.
🖥️ 🧬
link.springer.com/article/10.1...
The paper describes STRchive as a resource to improve the diagnosis of tandem repeat disorders, then goes beyond it to consider what can be learned about childhood onset and population prevalence of these diseases.
🖥️ 🧬
link.springer.com/article/10.1...
STRchive: a dynamic resource detailing population-level and locus-specific insights at tandem repeat disease loci - Genome Medicine
Approximately 8% of the human genome consists of repetitive elements called tandem repeats (TRs): short tandem repeats (STRs) of 1–6 bp motifs and variable number tandem repeats (VNTRs) of 7 + bp moti...
link.springer.com
March 26, 2025 at 8:01 PM
The strchive.org paper is out!!
The paper describes STRchive as a resource to improve the diagnosis of tandem repeat disorders, then goes beyond it to consider what can be learned about childhood onset and population prevalence of these diseases.
🖥️ 🧬
link.springer.com/article/10.1...
The paper describes STRchive as a resource to improve the diagnosis of tandem repeat disorders, then goes beyond it to consider what can be learned about childhood onset and population prevalence of these diseases.
🖥️ 🧬
link.springer.com/article/10.1...
Reposted by Dr Andrew Lonsdale
Our paper benchmarking feature selection for scRNA-seq integration and reference usage is out now www.nature.com/articles/s41...!
Keep reading for more about how we did the study and what we found out 🧵 👇
1/16
Keep reading for more about how we did the study and what we found out 🧵 👇
1/16
https://www.nature.com/articles/s41592-025-02624-3🎉
March 18, 2025 at 3:40 PM
Our paper benchmarking feature selection for scRNA-seq integration and reference usage is out now www.nature.com/articles/s41...!
Keep reading for more about how we did the study and what we found out 🧵 👇
1/16
Keep reading for more about how we did the study and what we found out 🧵 👇
1/16
"The thing about Carlton is they always try to walk it in" #afl #AFLTigersBlues
March 13, 2025 at 10:46 PM
"The thing about Carlton is they always try to walk it in" #afl #AFLTigersBlues
Reposted by Dr Andrew Lonsdale
We are recruiting a group leader in laboratory research at Peter Mac Cancer Centre in
Melbourne, Australia 🔬🦘💥
Work in a cutting edge research environment in a vibrant world city!
We value research excellence, creativity and diversity.
Join us!
careers.petermac.org/job/MELBOURN...
Melbourne, Australia 🔬🦘💥
Work in a cutting edge research environment in a vibrant world city!
We value research excellence, creativity and diversity.
Join us!
careers.petermac.org/job/MELBOURN...
Group Leader
Group Leader
careers.petermac.org
March 5, 2025 at 8:04 AM
We are recruiting a group leader in laboratory research at Peter Mac Cancer Centre in
Melbourne, Australia 🔬🦘💥
Work in a cutting edge research environment in a vibrant world city!
We value research excellence, creativity and diversity.
Join us!
careers.petermac.org/job/MELBOURN...
Melbourne, Australia 🔬🦘💥
Work in a cutting edge research environment in a vibrant world city!
We value research excellence, creativity and diversity.
Join us!
careers.petermac.org/job/MELBOURN...
Reposted by Dr Andrew Lonsdale
Pleased to present our CITE-seq paper analysing 45 BAL samples from (un)treated children with CF and controls. BAL is a tricky tissue, 44 celltypes dominated by macrophages. Trailblazing analysis led by @jovmaksimovic.bsky.social @melanieneeland.bsky.social @shivanthans.bsky.social and collaborators
Single-cell atlas of BAL from preschool cystic fibrosis reveals key inflammatory pathways modified by the CFTR modulator ivacaftor in the early life lung. https://www.medrxiv.org/content/10.1101/2025.02.24.25322508v1
March 1, 2025 at 3:40 AM
Pleased to present our CITE-seq paper analysing 45 BAL samples from (un)treated children with CF and controls. BAL is a tricky tissue, 44 celltypes dominated by macrophages. Trailblazing analysis led by @jovmaksimovic.bsky.social @melanieneeland.bsky.social @shivanthans.bsky.social and collaborators
Question for @titus.idyll.org or 🧬 🖥️ if it triggers a recollection:
I've a vague memory of a (possibly) Titus blog/tweet/talk ~10yo of something like:
"Mucking around with computational infrastructure is great and all, but it isn't the *science*"
and can't find the source.
I've a vague memory of a (possibly) Titus blog/tweet/talk ~10yo of something like:
"Mucking around with computational infrastructure is great and all, but it isn't the *science*"
and can't find the source.
February 25, 2025 at 11:18 AM
Question for @titus.idyll.org or 🧬 🖥️ if it triggers a recollection:
I've a vague memory of a (possibly) Titus blog/tweet/talk ~10yo of something like:
"Mucking around with computational infrastructure is great and all, but it isn't the *science*"
and can't find the source.
I've a vague memory of a (possibly) Titus blog/tweet/talk ~10yo of something like:
"Mucking around with computational infrastructure is great and all, but it isn't the *science*"
and can't find the source.
Reposted by Dr Andrew Lonsdale
📣 Registrations and Abstract submissions are now open for Cancer Bioinformatics Australia 2025!
Abstracts, due 11th April: cancerbioinformatics.au/abstracts
Registration: cancerbioinformatics.au/register
Further info: cancerbioinformatics.au
See flyer for our amazing invited speakers!
Abstracts, due 11th April: cancerbioinformatics.au/abstracts
Registration: cancerbioinformatics.au/register
Further info: cancerbioinformatics.au
See flyer for our amazing invited speakers!
February 25, 2025 at 11:08 AM
📣 Registrations and Abstract submissions are now open for Cancer Bioinformatics Australia 2025!
Abstracts, due 11th April: cancerbioinformatics.au/abstracts
Registration: cancerbioinformatics.au/register
Further info: cancerbioinformatics.au
See flyer for our amazing invited speakers!
Abstracts, due 11th April: cancerbioinformatics.au/abstracts
Registration: cancerbioinformatics.au/register
Further info: cancerbioinformatics.au
See flyer for our amazing invited speakers!
Reposted by Dr Andrew Lonsdale
#Rstats bsky.app/profile/did:...
Nextflow bsky.app/profile/did:...
Genomics/bioinfo 🧬🖥️ bsky.app/profile/did:...
Papers w/ code bsky.app/profile/did:...
RNA-seq bsky.app/profile/did:...
Biosecurity bsky.app/profile/did:...
Consgen bsky.app/profile/did:...
Genesky bsky.app/profile/did:...
Nextflow bsky.app/profile/did:...
Genomics/bioinfo 🧬🖥️ bsky.app/profile/did:...
Papers w/ code bsky.app/profile/did:...
RNA-seq bsky.app/profile/did:...
Biosecurity bsky.app/profile/did:...
Consgen bsky.app/profile/did:...
Genesky bsky.app/profile/did:...
February 4, 2025 at 8:48 PM
#Rstats bsky.app/profile/did:...
Nextflow bsky.app/profile/did:...
Genomics/bioinfo 🧬🖥️ bsky.app/profile/did:...
Papers w/ code bsky.app/profile/did:...
RNA-seq bsky.app/profile/did:...
Biosecurity bsky.app/profile/did:...
Consgen bsky.app/profile/did:...
Genesky bsky.app/profile/did:...
Nextflow bsky.app/profile/did:...
Genomics/bioinfo 🧬🖥️ bsky.app/profile/did:...
Papers w/ code bsky.app/profile/did:...
RNA-seq bsky.app/profile/did:...
Biosecurity bsky.app/profile/did:...
Consgen bsky.app/profile/did:...
Genesky bsky.app/profile/did:...
(1/2)
In Australia, the end of year holiday period coincides with summer, several public holidays, and school holidays. Return date to work is best described as:
Dec 27: Keen. As. Mustard.
Jan 30: Might get bit of work done before New Year's Eve.
In Australia, the end of year holiday period coincides with summer, several public holidays, and school holidays. Return date to work is best described as:
Dec 27: Keen. As. Mustard.
Jan 30: Might get bit of work done before New Year's Eve.
January 8, 2025 at 4:00 AM
(1/2)
In Australia, the end of year holiday period coincides with summer, several public holidays, and school holidays. Return date to work is best described as:
Dec 27: Keen. As. Mustard.
Jan 30: Might get bit of work done before New Year's Eve.
In Australia, the end of year holiday period coincides with summer, several public holidays, and school holidays. Return date to work is best described as:
Dec 27: Keen. As. Mustard.
Jan 30: Might get bit of work done before New Year's Eve.
Reposted by Dr Andrew Lonsdale
officer/rvg are GREAT packages to export ggplot2 (R plots) to editable Powerpoint slides.
Saves me heaps time when I make plots for others: everybody wants to change a bunch of details. Now they do that themselves in Powerpoint with my 'base' plot.
www.pipinghotdata.com/posts/2020-0...
Saves me heaps time when I make plots for others: everybody wants to change a bunch of details. Now they do that themselves in Powerpoint with my 'base' plot.
www.pipinghotdata.com/posts/2020-0...
PIPING HOT DATA: Exporting editable ggplot graphics to PowerPoint with officer and purrr
What, why, how, when, and who
www.pipinghotdata.com
December 18, 2024 at 2:18 AM
officer/rvg are GREAT packages to export ggplot2 (R plots) to editable Powerpoint slides.
Saves me heaps time when I make plots for others: everybody wants to change a bunch of details. Now they do that themselves in Powerpoint with my 'base' plot.
www.pipinghotdata.com/posts/2020-0...
Saves me heaps time when I make plots for others: everybody wants to change a bunch of details. Now they do that themselves in Powerpoint with my 'base' plot.
www.pipinghotdata.com/posts/2020-0...
I will never cease trying to make #preprintmas happen, the happy time of year when great science gets pushed out the door to a preprint server before everyone takessome time off 🎁 📓
Last year I noticed that a lot of of great bioinformatics / comp bio papers ended up on biorxiv etc just before the end of year holidays... so if you see more this year, be sure to mention preprintmas to find them all! 🎁 📓
December 19, 2024 at 12:09 AM
I will never cease trying to make #preprintmas happen, the happy time of year when great science gets pushed out the door to a preprint server before everyone takessome time off 🎁 📓
Reposted by Dr Andrew Lonsdale
Save the Date for Cancer Bioinformatics Australia '25!
The 2nd CBA will be in Sydney on June 18th 2025.
Planning is well under way, with invited speakers including but not limited to @jwhwong.bsky.social and @nadia-davidson.bsky.social
See cancerbioinformatics.au for info and updates.
December 15, 2024 at 10:51 PM
Save the Date for Cancer Bioinformatics Australia '25!
The 2nd CBA will be in Sydney on June 18th 2025.
Planning is well under way, with invited speakers including but not limited to @jwhwong.bsky.social and @nadia-davidson.bsky.social
See cancerbioinformatics.au for info and updates.
Reposted by Dr Andrew Lonsdale
Happy to see our Damsel @bioconductor.bsky.social package published in Bioinformatics. Great work putting together this DamID sequencing and package from student Caitlin Page. Thanks to collaborators too @lonsbio.bsky.social
academic.oup.com/bioinformati...
academic.oup.com/bioinformati...
Damsel: analysis and visualisation of DamID sequencing in R
AbstractSummary. DamID sequencing is a technique to map the genome-wide interaction of a protein with DNA. Damsel is the first Bioconductor package to prov
academic.oup.com
November 29, 2024 at 2:11 AM
Happy to see our Damsel @bioconductor.bsky.social package published in Bioinformatics. Great work putting together this DamID sequencing and package from student Caitlin Page. Thanks to collaborators too @lonsbio.bsky.social
academic.oup.com/bioinformati...
academic.oup.com/bioinformati...
My #pyconau talk on those side project(s) that keep on giving is up!
As I (almost) end with, contributions to fastqe.com and biomojify are always welcome!
🥑 🧀 🍇 🍅 💀 💩 🚨 🙂 😍
www.youtube.com/watch?v=E3-A...
As I (almost) end with, contributions to fastqe.com and biomojify are always welcome!
🥑 🧀 🍇 🍅 💀 💩 🚨 🙂 😍
www.youtube.com/watch?v=E3-A...
How I Used Python to Stop Worrying & Love Emoji in Bioinformatics
YouTube video by PyCon AU
www.youtube.com
November 27, 2024 at 11:45 AM
My #pyconau talk on those side project(s) that keep on giving is up!
As I (almost) end with, contributions to fastqe.com and biomojify are always welcome!
🥑 🧀 🍇 🍅 💀 💩 🚨 🙂 😍
www.youtube.com/watch?v=E3-A...
As I (almost) end with, contributions to fastqe.com and biomojify are always welcome!
🥑 🧀 🍇 🍅 💀 💩 🚨 🙂 😍
www.youtube.com/watch?v=E3-A...
Hive mind of 🧬 🖥️ - I am looking for one or two small data sets/repo that has a nice collection of bioinformatics file formats, e.g. a sample FASTA, FASTQ, VCF , GFF etc. They can be related experiments/organisms or disparate.
November 18, 2024 at 4:27 AM
Hive mind of 🧬 🖥️ - I am looking for one or two small data sets/repo that has a nice collection of bioinformatics file formats, e.g. a sample FASTA, FASTQ, VCF , GFF etc. They can be related experiments/organisms or disparate.
Many (myself included) scoffed when @pacbio.bsky.social advertised on a tram during #ICG2023 but now... every time I see a pink tram in Melbourne, I think of PacBio.
Maybe it's Maybelline?
Maybe it's the innovative Onso benchtop short-read DNA sequencing platform.
Maybe it's Maybelline?
Maybe it's the innovative Onso benchtop short-read DNA sequencing platform.
November 14, 2024 at 11:39 AM
Many (myself included) scoffed when @pacbio.bsky.social advertised on a tram during #ICG2023 but now... every time I see a pink tram in Melbourne, I think of PacBio.
Maybe it's Maybelline?
Maybe it's the innovative Onso benchtop short-read DNA sequencing platform.
Maybe it's Maybelline?
Maybe it's the innovative Onso benchtop short-read DNA sequencing platform.
"The promise and reality of AI in medical research" national keynote from @skummerf.bsky.social has been the most informative AI talk I ever seen. #abacbs24
November 4, 2024 at 11:37 PM
"The promise and reality of AI in medical research" national keynote from @skummerf.bsky.social has been the most informative AI talk I ever seen. #abacbs24
November 4, 2024 at 10:24 PM