Davis McCarthy
@davisjmcc.bsky.social
Head, Bioinformatics and Cellular Genomics Lab,
St Vincent's Institute of Medical Research, Melbourne. Stats, AI/ML, bioinformatics, genomics, single-cell.
https://www.svi.edu.au/researchers/dr-davis-mccarthy/
St Vincent's Institute of Medical Research, Melbourne. Stats, AI/ML, bioinformatics, genomics, single-cell.
https://www.svi.edu.au/researchers/dr-davis-mccarthy/
This is an amazing story
Recommended reading for anyone with even a passing interest in genetics, rare diseases, gene therapy, development...humans, biology, anything really!
It's been cool to watch as the picture has come together over the last year or so
Recommended reading for anyone with even a passing interest in genetics, rare diseases, gene therapy, development...humans, biology, anything really!
It's been cool to watch as the picture has come together over the last year or so
🧵 Our latest preprint is available.
It describes an extraordinary case of a boy with two very rare genetic conditions: Fanconi anaemia (FANCB, with a deep intronic pathogenic variant) and embryonic triploid–diploid mosaicism.
Read more here 👉 www.medrxiv.org/content/10.1...
It describes an extraordinary case of a boy with two very rare genetic conditions: Fanconi anaemia (FANCB, with a deep intronic pathogenic variant) and embryonic triploid–diploid mosaicism.
Read more here 👉 www.medrxiv.org/content/10.1...
Multi-lineage natural gene therapy mediated by embryonic triploid mosaicism in the context of Fanconi anaemia
Fanconi anemia is a rare inherited bone marrow failure syndrome caused by inactivation of genes in the Fanconi anemia/BRCA DNA repair pathway. We report a patient with X-linked Fanconi anemia, and aty...
www.medrxiv.org
November 7, 2025 at 2:10 AM
This is an amazing story
Recommended reading for anyone with even a passing interest in genetics, rare diseases, gene therapy, development...humans, biology, anything really!
It's been cool to watch as the picture has come together over the last year or so
Recommended reading for anyone with even a passing interest in genetics, rare diseases, gene therapy, development...humans, biology, anything really!
It's been cool to watch as the picture has come together over the last year or so
Reposted by Davis McCarthy
🧵 Our latest preprint is available.
It describes an extraordinary case of a boy with two very rare genetic conditions: Fanconi anaemia (FANCB, with a deep intronic pathogenic variant) and embryonic triploid–diploid mosaicism.
Read more here 👉 www.medrxiv.org/content/10.1...
It describes an extraordinary case of a boy with two very rare genetic conditions: Fanconi anaemia (FANCB, with a deep intronic pathogenic variant) and embryonic triploid–diploid mosaicism.
Read more here 👉 www.medrxiv.org/content/10.1...
Multi-lineage natural gene therapy mediated by embryonic triploid mosaicism in the context of Fanconi anaemia
Fanconi anemia is a rare inherited bone marrow failure syndrome caused by inactivation of genes in the Fanconi anemia/BRCA DNA repair pathway. We report a patient with X-linked Fanconi anemia, and aty...
www.medrxiv.org
November 7, 2025 at 1:54 AM
🧵 Our latest preprint is available.
It describes an extraordinary case of a boy with two very rare genetic conditions: Fanconi anaemia (FANCB, with a deep intronic pathogenic variant) and embryonic triploid–diploid mosaicism.
Read more here 👉 www.medrxiv.org/content/10.1...
It describes an extraordinary case of a boy with two very rare genetic conditions: Fanconi anaemia (FANCB, with a deep intronic pathogenic variant) and embryonic triploid–diploid mosaicism.
Read more here 👉 www.medrxiv.org/content/10.1...
Reposted by Davis McCarthy
This is absolutely the most obvious thing to do. The govt should be shoveling all the funding it can at getting all the researches in the US who have been cut by Trump.
Monique Ryan urges Australia to fast track medical innovation funding as Trump guts research
www.theguardian.com/australia-ne...
www.theguardian.com/australia-ne...
Monique Ryan urges Australia to fast track medical innovation funding as Trump guts research
‘Releasing MRFF funds not only secures the future of Australia’s research sector; it delivers better health outcomes’, Kooyong MP says
www.theguardian.com
November 5, 2025 at 10:20 PM
This is absolutely the most obvious thing to do. The govt should be shoveling all the funding it can at getting all the researches in the US who have been cut by Trump.
Reposted by Davis McCarthy
Known as a “lip out” or the “golfer’s curse,” the sometimes strange behavior of golf balls has bedeviled players for centuries. Now, physicists have figured out how they happen. Just don't expect the discovery to improve your game... Fun story by @annademming.bsky.social for @science.org
Have physicists finally solved the ‘golfer’s curse’?
Team says it has hit on an explanation for heartbreaking “lip outs”
www.science.org
November 5, 2025 at 1:47 PM
Known as a “lip out” or the “golfer’s curse,” the sometimes strange behavior of golf balls has bedeviled players for centuries. Now, physicists have figured out how they happen. Just don't expect the discovery to improve your game... Fun story by @annademming.bsky.social for @science.org
Reposted by Davis McCarthy
Excited to share our latest preprint: LongBench—a cross-platform reference dataset profiling cancer cell lines with bulk and single-cell approaches.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Benchmarking long-read RNA-sequencing technologies with LongBench: a cross-platform reference dataset profiling cancer cell lines with bulk and single-cell approaches
Long-read RNA sequencing enables full-length transcript profiling and improved isoform resolution, but variable platforms and evolving chemistries demand careful benchmarking for reliable application....
www.biorxiv.org
September 15, 2025 at 5:22 AM
Excited to share our latest preprint: LongBench—a cross-platform reference dataset profiling cancer cell lines with bulk and single-cell approaches.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Davis McCarthy
I feel incredibly privileged to share this study on Fanconi anaemia, based on a small but important cohort. This work describes the genetics and clinical outcomes of patients in Australia and New Zealand with a diagnosis of FA.
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
Clinical and genetic spectrum of Fanconi anemia in Australia and New Zealand
Fanconi anemia (FA) is a rare genetic condition that predisposes to progressive bone marrow failure, a specific spectrum of malignancies, including he…
www.sciencedirect.com
September 11, 2025 at 3:50 AM
I feel incredibly privileged to share this study on Fanconi anaemia, based on a small but important cohort. This work describes the genetics and clinical outcomes of patients in Australia and New Zealand with a diagnosis of FA.
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
Reposted by Davis McCarthy
Thrilled to share our latest work on meiotic recombination, where we mapped rates and distributions by sequencing thousands of individual sperm. This study was led by Stevan Novakovic and @caitlinharris.bsky.social , in collaboration with @davisjmcc.bsky.social and Cynthia Liu.
September 5, 2025 at 3:49 AM
Thrilled to share our latest work on meiotic recombination, where we mapped rates and distributions by sequencing thousands of individual sperm. This study was led by Stevan Novakovic and @caitlinharris.bsky.social , in collaboration with @davisjmcc.bsky.social and Cynthia Liu.
Reposted by Davis McCarthy
Now that I've given my talk at today's excellent #ourdna symposium I can share this slide I put together for it. I knew these numbers, because I was the one paying for things, but still:
August 14, 2025 at 2:46 AM
Now that I've given my talk at today's excellent #ourdna symposium I can share this slide I put together for it. I knew these numbers, because I was the one paying for things, but still:
Reposted by Davis McCarthy
Valentine Svensson
Negative binomial regression and inference using a pre-trained transformer
https://arxiv.org/abs/2508.04111
Negative binomial regression and inference using a pre-trained transformer
https://arxiv.org/abs/2508.04111
August 7, 2025 at 4:16 AM
Valentine Svensson
Negative binomial regression and inference using a pre-trained transformer
https://arxiv.org/abs/2508.04111
Negative binomial regression and inference using a pre-trained transformer
https://arxiv.org/abs/2508.04111
When Jeffrey "graduated" from our lab to go to do a PhD at Cambridge I knew big things would come - and boy was I vindicated!
Very exciting work - rigorous and insightful (exactly as I came to expect from Jeffrey) and immediately useful for a huge number of cool projects.
Awesome 🌟, well done!
Very exciting work - rigorous and insightful (exactly as I came to expect from Jeffrey) and immediately useful for a huge number of cool projects.
Awesome 🌟, well done!
Very excited to share new work from my PhD on a new software package for eQTL mapping: quasar. The quasar software package is a C++ program designed to provide a flexible and efficient eQTL mapping. www.medrxiv.org/content/10.1...
Flexible and efficient count-distribution and mixed-model methods for eQTL mapping with quasar
Identifying genetic variants that affect gene expression, expression quantitative trait loci (eQTLs), is a major focus of modern genomics. Today, various methods exist for eQTL mapping, each using dif...
www.medrxiv.org
July 23, 2025 at 4:55 AM
When Jeffrey "graduated" from our lab to go to do a PhD at Cambridge I knew big things would come - and boy was I vindicated!
Very exciting work - rigorous and insightful (exactly as I came to expect from Jeffrey) and immediately useful for a huge number of cool projects.
Awesome 🌟, well done!
Very exciting work - rigorous and insightful (exactly as I came to expect from Jeffrey) and immediately useful for a huge number of cool projects.
Awesome 🌟, well done!
Reposted by Davis McCarthy
people don't actually want to test point-nulls in NHST, they want to test interval nulls and they rely on the structure of the test to define the "interval null" (*waves hands vaguely*) for them, rather than explicitly defining an interval null and testing it.
July 23, 2025 at 4:38 AM
people don't actually want to test point-nulls in NHST, they want to test interval nulls and they rely on the structure of the test to define the "interval null" (*waves hands vaguely*) for them, rather than explicitly defining an interval null and testing it.
Reposted by Davis McCarthy
📢 Announcing the MOPITAS Autumn School on Spatial Transcriptomics Data Analysis – taking place November 12–14, in Munich. Don't miss this excellent opportunity to deepen your expertise in data science and multi-OMICS analysis - especially as a PhD student in the data science community.
July 4, 2025 at 7:20 PM
📢 Announcing the MOPITAS Autumn School on Spatial Transcriptomics Data Analysis – taking place November 12–14, in Munich. Don't miss this excellent opportunity to deepen your expertise in data science and multi-OMICS analysis - especially as a PhD student in the data science community.
Reposted by Davis McCarthy
The day is finally here! 🎉 We’re releasing the invited speaker line-up, key dates, and lots more info for ABACBS 2025.
Check it out and share widely: www.abacbs.org/abacbs2025
Registrations and abstract submissions open next week, with abstracts due in August!
Check it out and share widely: www.abacbs.org/abacbs2025
Registrations and abstract submissions open next week, with abstracts due in August!
ABACBS 2025 Conference
Adelaide, South Australia. Nov. 24-
www.abacbs.org
July 4, 2025 at 4:34 AM
The day is finally here! 🎉 We’re releasing the invited speaker line-up, key dates, and lots more info for ABACBS 2025.
Check it out and share widely: www.abacbs.org/abacbs2025
Registrations and abstract submissions open next week, with abstracts due in August!
Check it out and share widely: www.abacbs.org/abacbs2025
Registrations and abstract submissions open next week, with abstracts due in August!
Reposted by Davis McCarthy
Job alert: Join us for a postdoc in AI in genetics at @EMBL Heidelberg! Great collaboration with @Adrian Cortes @GSK, aiming to develop new tools to elucidate genetic effects using population-scale cohorts and single-cell readouts. Please share!
embl.wd103.myworkdayjobs.com/de-DE/EMBL/d...
embl.wd103.myworkdayjobs.com/de-DE/EMBL/d...
Postdoctoral Researcher in Computational Genetics
The research group of Oliver Stegle looks for a postdoctoral researcher to join a collaborative project with GSK with the goal to apply computational methods to investigate the effects of rare variant...
embl.wd103.myworkdayjobs.com
June 26, 2025 at 10:00 AM
Job alert: Join us for a postdoc in AI in genetics at @EMBL Heidelberg! Great collaboration with @Adrian Cortes @GSK, aiming to develop new tools to elucidate genetic effects using population-scale cohorts and single-cell readouts. Please share!
embl.wd103.myworkdayjobs.com/de-DE/EMBL/d...
embl.wd103.myworkdayjobs.com/de-DE/EMBL/d...
Applications for this position will close on Friday 30 June
So if you or anyone you know might be interested in applying, time to get your skates on!
So if you or anyone you know might be interested in applying, time to get your skates on!
📢 PostDoc opportunity in our Bioinformatics & Cellular Genomics lab at SVI! 🧬
You’d join a welcoming, supportive, and brilliant team.
Why not spend a few years in Melbourne and be part of something exciting?
Apply here: www.seek.com.au/job/84737876
#ScienceCareers #PostDoc #Bioinformatics
You’d join a welcoming, supportive, and brilliant team.
Why not spend a few years in Melbourne and be part of something exciting?
Apply here: www.seek.com.au/job/84737876
#ScienceCareers #PostDoc #Bioinformatics
Research Officer - Bioinformatics Job in Fitzroy, Melbourne VIC - SEEK
Seeking a Postdoc to develop computational toolkits to enable large-scale studies of single-cell and spatial 'omics and statistical genetics
www.seek.com.au
June 25, 2025 at 1:02 AM
Applications for this position will close on Friday 30 June
So if you or anyone you know might be interested in applying, time to get your skates on!
So if you or anyone you know might be interested in applying, time to get your skates on!
Reposted by Davis McCarthy
🚨 New paper published in @natmethods.nature.com!
We introduce SpotSweeper, the first spatially-aware QC methods for spatial transcriptomics.
📰 Paper : nature.com/articles/s41...
💻 Code: github.com/MicTott/Spot...
📈 Website: mictott.github.io/SpotSweeper/
🧵👇
We introduce SpotSweeper, the first spatially-aware QC methods for spatial transcriptomics.
📰 Paper : nature.com/articles/s41...
💻 Code: github.com/MicTott/Spot...
📈 Website: mictott.github.io/SpotSweeper/
🧵👇
SpotSweeper: spatially aware quality control for spatial transcriptomics - Nature Methods
SpotSweeper is a spatially aware method for quality control of spatially resolved transcriptomics data that corrects for spatial confounding missed by existing methods, including both local and region...
nature.com
June 6, 2025 at 12:03 PM
🚨 New paper published in @natmethods.nature.com!
We introduce SpotSweeper, the first spatially-aware QC methods for spatial transcriptomics.
📰 Paper : nature.com/articles/s41...
💻 Code: github.com/MicTott/Spot...
📈 Website: mictott.github.io/SpotSweeper/
🧵👇
We introduce SpotSweeper, the first spatially-aware QC methods for spatial transcriptomics.
📰 Paper : nature.com/articles/s41...
💻 Code: github.com/MicTott/Spot...
📈 Website: mictott.github.io/SpotSweeper/
🧵👇
Reposted by Davis McCarthy
Hey Australian genetics/genomics friends: the OurDNA Symposium will be in Sydney on 14 August, just before the HGSA meeting. Learn more about inclusive recruitment for genomics and get a preview of the OurDNA variant browser! events.humanitix.com/ourdna-sympo...
OurDNA Symposium 2025: Partnering for impact
The OurDNA Symposium brings stakeholders together for important conversations about building the foundation for equitable genomics in Australia.
events.humanitix.com
June 23, 2025 at 1:03 AM
Hey Australian genetics/genomics friends: the OurDNA Symposium will be in Sydney on 14 August, just before the HGSA meeting. Learn more about inclusive recruitment for genomics and get a preview of the OurDNA variant browser! events.humanitix.com/ourdna-sympo...
Reposted by Davis McCarthy
Semantic Encoding in Medical LLMs for Vocabulary Standardisation https://www.medrxiv.org/content/10.1101/2025.06.16.25329716v1
June 18, 2025 at 4:30 AM
Reposted by Davis McCarthy
I cannot recommend Davis’s group more highly! In addition to excellent research, he has been a great mentor!
📢 PostDoc opportunity in our Bioinformatics & Cellular Genomics lab at SVI! 🧬
You’d join a welcoming, supportive, and brilliant team.
Why not spend a few years in Melbourne and be part of something exciting?
Apply here: www.seek.com.au/job/84737876
#ScienceCareers #PostDoc #Bioinformatics
You’d join a welcoming, supportive, and brilliant team.
Why not spend a few years in Melbourne and be part of something exciting?
Apply here: www.seek.com.au/job/84737876
#ScienceCareers #PostDoc #Bioinformatics
Research Officer - Bioinformatics Job in Fitzroy, Melbourne VIC - SEEK
Seeking a Postdoc to develop computational toolkits to enable large-scale studies of single-cell and spatial 'omics and statistical genetics
www.seek.com.au
June 16, 2025 at 9:46 AM
I cannot recommend Davis’s group more highly! In addition to excellent research, he has been a great mentor!
📢 PostDoc opportunity in our Bioinformatics & Cellular Genomics lab at SVI! 🧬
You’d join a welcoming, supportive, and brilliant team.
Why not spend a few years in Melbourne and be part of something exciting?
Apply here: www.seek.com.au/job/84737876
#ScienceCareers #PostDoc #Bioinformatics
You’d join a welcoming, supportive, and brilliant team.
Why not spend a few years in Melbourne and be part of something exciting?
Apply here: www.seek.com.au/job/84737876
#ScienceCareers #PostDoc #Bioinformatics
Research Officer - Bioinformatics Job in Fitzroy, Melbourne VIC - SEEK
Seeking a Postdoc to develop computational toolkits to enable large-scale studies of single-cell and spatial 'omics and statistical genetics
www.seek.com.au
June 16, 2025 at 7:07 AM
📢 PostDoc opportunity in our Bioinformatics & Cellular Genomics lab at SVI! 🧬
You’d join a welcoming, supportive, and brilliant team.
Why not spend a few years in Melbourne and be part of something exciting?
Apply here: www.seek.com.au/job/84737876
#ScienceCareers #PostDoc #Bioinformatics
You’d join a welcoming, supportive, and brilliant team.
Why not spend a few years in Melbourne and be part of something exciting?
Apply here: www.seek.com.au/job/84737876
#ScienceCareers #PostDoc #Bioinformatics
Reposted by Davis McCarthy
Delighted that the 'flagship' manuscript on our @genesandhealth.bsky.social 44k exomes (British Pakistanis & Bangladeshis) is now preprinted. Great academic-industry collaboration. Lots of new associations (mostly additive, a few recessive) and new insights into homoz knockouts & drug discovery.
Preprint alert! 🚨
doi.org/10.1101/2025...
Our manuscript on Exome sequencing and analysis of 44,028 British South Asians, using @genesandhealth.bsky.social is now available at @medrxivpreprint.bsky.social!
We present several great results, and I’m thrilled to highlight the pieces I worked on:
doi.org/10.1101/2025...
Our manuscript on Exome sequencing and analysis of 44,028 British South Asians, using @genesandhealth.bsky.social is now available at @medrxivpreprint.bsky.social!
We present several great results, and I’m thrilled to highlight the pieces I worked on:
Exome sequencing and analysis of 44,028 British South Asians enriched for high autozygosity
Genes and Health (G&H) is a biomedical study of adult British-Pakistani and -Bangladeshi research volunteers enriched for autozygosity. We performed whole exome sequencing in 44,028 G&H participants, ...
doi.org
June 12, 2025 at 7:14 PM
Delighted that the 'flagship' manuscript on our @genesandhealth.bsky.social 44k exomes (British Pakistanis & Bangladeshis) is now preprinted. Great academic-industry collaboration. Lots of new associations (mostly additive, a few recessive) and new insights into homoz knockouts & drug discovery.
Reposted by Davis McCarthy
People always stop me in the street to ask: "Yoav, where are the disease-associated eQLTs? We found a lot in GTEx but we can't find anymore. Do you know where they are?"
(For the record, no one has ever asked me this, but it is a really good question!)
I think we know where they are.
(For the record, no one has ever asked me this, but it is a really good question!)
I think we know where they are.
June 10, 2025 at 2:20 PM
People always stop me in the street to ask: "Yoav, where are the disease-associated eQLTs? We found a lot in GTEx but we can't find anymore. Do you know where they are?"
(For the record, no one has ever asked me this, but it is a really good question!)
I think we know where they are.
(For the record, no one has ever asked me this, but it is a really good question!)
I think we know where they are.
Reposted by Davis McCarthy
My message to Trump’s NIH Director? No one in America wants us to do LESS cancer research.
No one is asking Trump to make it harder to cure Alzheimer's disease.
Yet Trump is cutting all of this NOW and demanding an $18 BILLION cut to NIH next year. Not on my watch.
No one is asking Trump to make it harder to cure Alzheimer's disease.
Yet Trump is cutting all of this NOW and demanding an $18 BILLION cut to NIH next year. Not on my watch.
June 10, 2025 at 6:53 PM
My message to Trump’s NIH Director? No one in America wants us to do LESS cancer research.
No one is asking Trump to make it harder to cure Alzheimer's disease.
Yet Trump is cutting all of this NOW and demanding an $18 BILLION cut to NIH next year. Not on my watch.
No one is asking Trump to make it harder to cure Alzheimer's disease.
Yet Trump is cutting all of this NOW and demanding an $18 BILLION cut to NIH next year. Not on my watch.
Reposted by Davis McCarthy
Excited to share my first PhD paper in the @sbmontgom.bsky.social lab with @tamigj.bsky.social (www.biorxiv.org/content/10.1...)! Standard QTL methods treat each gene independently. But what if a single variant regulates multiple nearby genes at once - what we call “allelic proxitropy”? 🧵 ⬇️
June 8, 2025 at 5:39 PM
Excited to share my first PhD paper in the @sbmontgom.bsky.social lab with @tamigj.bsky.social (www.biorxiv.org/content/10.1...)! Standard QTL methods treat each gene independently. But what if a single variant regulates multiple nearby genes at once - what we call “allelic proxitropy”? 🧵 ⬇️
Reposted by Davis McCarthy
I am so excited to share our most recent work & my first big project as a graduate student! We leveraged spatial transcriptomics to study the cell-cell communication involved in human lung development. Here’s the full study: www.biorxiv.org/content/10.1...
(1/17)
(1/17)
A spatial transcriptomic atlas of acute neonatal lung injury across development and disease severity
A molecular understanding of lung organogenesis requires delineation of the timing and regulation of the cellular transitions that ultimately form and support a surface capable of gas exchange. While ...
www.biorxiv.org
June 6, 2025 at 6:34 PM
I am so excited to share our most recent work & my first big project as a graduate student! We leveraged spatial transcriptomics to study the cell-cell communication involved in human lung development. Here’s the full study: www.biorxiv.org/content/10.1...
(1/17)
(1/17)