Mike Clark
@michaelbclark.bsky.social
Genetics, transcriptomics, RNA and neuroscience.
Lab head at the University of Melbourne, Australia.
View own.
Lab head at the University of Melbourne, Australia.
View own.
If you're studying #RNA transcript isoforms, check out IsoVis (the Isoform Visualiser webserver). isomix.org/isovis/
Recent updates now also allow visualisation of:
1. RNA modification sites and levels
2. Peptides mapping to open reading frames in isoforms and their abundances. 🧪
Recent updates now also allow visualisation of:
1. RNA modification sites and levels
2. Peptides mapping to open reading frames in isoforms and their abundances. 🧪
December 17, 2025 at 4:52 AM
If you're studying #RNA transcript isoforms, check out IsoVis (the Isoform Visualiser webserver). isomix.org/isovis/
Recent updates now also allow visualisation of:
1. RNA modification sites and levels
2. Peptides mapping to open reading frames in isoforms and their abundances. 🧪
Recent updates now also allow visualisation of:
1. RNA modification sites and levels
2. Peptides mapping to open reading frames in isoforms and their abundances. 🧪
Reposted by Mike Clark
So, who are the the Functional Genomics Working Group?
🎯Our goal is to understand how genes🧬, cells🦠and molecules💠contribute to psychiatric disorders🧠
We work with other PGC groups and different 'omics data (methylation, cytometry, single cell etc.) to do this🧪
🧵1/3
🎯Our goal is to understand how genes🧬, cells🦠and molecules💠contribute to psychiatric disorders🧠
We work with other PGC groups and different 'omics data (methylation, cytometry, single cell etc.) to do this🧪
🧵1/3
December 3, 2025 at 5:37 PM
So, who are the the Functional Genomics Working Group?
🎯Our goal is to understand how genes🧬, cells🦠and molecules💠contribute to psychiatric disorders🧠
We work with other PGC groups and different 'omics data (methylation, cytometry, single cell etc.) to do this🧪
🧵1/3
🎯Our goal is to understand how genes🧬, cells🦠and molecules💠contribute to psychiatric disorders🧠
We work with other PGC groups and different 'omics data (methylation, cytometry, single cell etc.) to do this🧪
🧵1/3
Reposted by Mike Clark
🌟...let's meet the next #earlycareerresearcher #ECR #postdoc with a big heart for functional genomics 🧬
🥁 ... Dr RICARDO DE PAOLI-ISEPPI from @unimelb.bsky.social #UniMelb will tell us how he uses #longreadsequencing to understand #RNAsplicing.
🥁 ... Dr RICARDO DE PAOLI-ISEPPI from @unimelb.bsky.social #UniMelb will tell us how he uses #longreadsequencing to understand #RNAsplicing.
December 10, 2025 at 9:38 AM
🌟...let's meet the next #earlycareerresearcher #ECR #postdoc with a big heart for functional genomics 🧬
🥁 ... Dr RICARDO DE PAOLI-ISEPPI from @unimelb.bsky.social #UniMelb will tell us how he uses #longreadsequencing to understand #RNAsplicing.
🥁 ... Dr RICARDO DE PAOLI-ISEPPI from @unimelb.bsky.social #UniMelb will tell us how he uses #longreadsequencing to understand #RNAsplicing.
December 15, 2025 at 11:22 AM
Reposted by Mike Clark
Share your stories here docs.google.com/forms/d/e/1F... #SaveOzScience
Australian Science & Biomedical Research in Crisis
Please use this form to share the impact of Australia's historically low success rates for major competitive research grants on your research, your team, and your mental health.
Researchers do researc...
docs.google.com
December 1, 2025 at 2:17 PM
Share your stories here docs.google.com/forms/d/e/1F... #SaveOzScience
Reposted by Mike Clark
If your #NHMRC ideas grant was unsuccessful and you have a story to share about the impact of this on your #biomedicalresearch, career, team - get in touch. Federal DOH have asked #NARF to collect stories of impact of low funding. #SaveOzScience #DiscoveriesNeedDollars #EMCRs
November 26, 2024 at 1:46 AM
If your #NHMRC ideas grant was unsuccessful and you have a story to share about the impact of this on your #biomedicalresearch, career, team - get in touch. Federal DOH have asked #NARF to collect stories of impact of low funding. #SaveOzScience #DiscoveriesNeedDollars #EMCRs
Reposted by Mike Clark
The success rate for NHMRC Ideas Grants announced yesterday was just over 8%. That means 11 of every 12 people who applied got rejected. This is a culture changing level of rejection and frankly a point of national shame. This is a crisis for research.
I will not rest until we see this resolved.
I will not rest until we see this resolved.
November 26, 2025 at 8:34 PM
The success rate for NHMRC Ideas Grants announced yesterday was just over 8%. That means 11 of every 12 people who applied got rejected. This is a culture changing level of rejection and frankly a point of national shame. This is a crisis for research.
I will not rest until we see this resolved.
I will not rest until we see this resolved.
Reposted by Mike Clark
Be kind to each other.. bad news for most coming in under embargo. We need more funding in the system...
November 26, 2025 at 4:40 AM
Be kind to each other.. bad news for most coming in under embargo. We need more funding in the system...
Hard to know for sure until NHMRC releases funding details. From the grants I reviewed I think requested funds have increased as cost of research has gone up. Clearly funding available hasn't kept pace to even maintain the poor success rate we previously had.
November 26, 2025 at 9:45 PM
Hard to know for sure until NHMRC releases funding details. From the grants I reviewed I think requested funds have increased as cost of research has gone up. Clearly funding available hasn't kept pace to even maintain the poor success rate we previously had.
Reposted by Mike Clark
this is unsustainable, the $600M underspend of the #MRFF could be funnelled, or at least partially funnelled, to supporting excellent #NHMRC applications that fall below the funding cut off because there is too little money in the pot #DiscoveriesNeedDollars #SaveOzScience
An abismal 8% success rate for this year’s #NHMRC #IdeasGrant scheme. Must be an all time low. Congratulations to those successful, you really earned it! Commiserations to the NINETY TWO percent of applicants who didn’t get it… #australianresearch #discoveriesneeddollars 🥼🧪🔬🧫 🇦🇺
November 26, 2025 at 10:28 AM
this is unsustainable, the $600M underspend of the #MRFF could be funnelled, or at least partially funnelled, to supporting excellent #NHMRC applications that fall below the funding cut off because there is too little money in the pot #DiscoveriesNeedDollars #SaveOzScience
It's an all time low in both the percentage and number of #NHMRC #IdeasGrant funded. Previous lowest percentage was 9.8% in the 2020. However 283 grants were funded that year, this year it's under 200.
November 26, 2025 at 10:50 AM
It's an all time low in both the percentage and number of #NHMRC #IdeasGrant funded. Previous lowest percentage was 9.8% in the 2020. However 283 grants were funded that year, this year it's under 200.
Individual outcomes aren't publicly released yet, but all applicants have been told if they were successful or not
November 26, 2025 at 10:41 AM
Individual outcomes aren't publicly released yet, but all applicants have been told if they were successful or not
Australian #NHMRC Ideas grants are out. 8.1% success rate. Lowest since the scheme began. Congrats to the successful few, as it looks like less than 200 were funded. 🧪
November 26, 2025 at 6:06 AM
Australian #NHMRC Ideas grants are out. 8.1% success rate. Lowest since the scheme began. Congrats to the successful few, as it looks like less than 200 were funded. 🧪
Chelsea Mayoh gave one of the most inspiring talks of the conference. Performing RNA-seq on kids with cancer in Australia has been highly successful in generating reportable findings, treatment recommendations, correcting diagnoses and mostly importantly, improving survival. #abacbs2025
November 26, 2025 at 4:48 AM
Chelsea Mayoh gave one of the most inspiring talks of the conference. Performing RNA-seq on kids with cancer in Australia has been highly successful in generating reportable findings, treatment recommendations, correcting diagnoses and mostly importantly, improving survival. #abacbs2025
This project was led by the talented @jakobschuster.bsky.social in colab with @qgouil.bsky.social & @mritchieau.bsky.social
As an example of the power of Matchbox, Jakob’s last tool was Restrander. A 17 line matchbox script achieved the same result as 1400 lines of C++ in Restrander!
As an example of the power of Matchbox, Jakob’s last tool was Restrander. A 17 line matchbox script achieved the same result as 1400 lines of C++ in Restrander!
November 26, 2025 at 2:03 AM
This project was led by the talented @jakobschuster.bsky.social in colab with @qgouil.bsky.social & @mritchieau.bsky.social
As an example of the power of Matchbox, Jakob’s last tool was Restrander. A 17 line matchbox script achieved the same result as 1400 lines of C++ in Restrander!
As an example of the power of Matchbox, Jakob’s last tool was Restrander. A 17 line matchbox script achieved the same result as 1400 lines of C++ in Restrander!
We’ve demonstrated Matchbox for demultiplexing long-read scRNA-seq data with 10X or SPLiT-seq barcodes; restranding RNA-seq reads; assessing CRISPR editing efficiency; and haplotyping repeat regions.
Matchbox is implemented in rust and available from github.com/jakob-schust....
Matchbox is implemented in rust and available from github.com/jakob-schust....
November 26, 2025 at 2:03 AM
We’ve demonstrated Matchbox for demultiplexing long-read scRNA-seq data with 10X or SPLiT-seq barcodes; restranding RNA-seq reads; assessing CRISPR editing efficiency; and haplotyping repeat regions.
Matchbox is implemented in rust and available from github.com/jakob-schust....
Matchbox is implemented in rust and available from github.com/jakob-schust....
Sequencing data requires read processing. Some tasks are common (trimming, de-multiplexing, filtering) & others bespoke, especially if you have non-standard read-structures.
Introducing Matchbox: a fast and incredibly versatile read processor that can do all this & more 🧪
doi.org/10.1101/2025...
Introducing Matchbox: a fast and incredibly versatile read processor that can do all this & more 🧪
doi.org/10.1101/2025...
November 26, 2025 at 2:03 AM
Sequencing data requires read processing. Some tasks are common (trimming, de-multiplexing, filtering) & others bespoke, especially if you have non-standard read-structures.
Introducing Matchbox: a fast and incredibly versatile read processor that can do all this & more 🧪
doi.org/10.1101/2025...
Introducing Matchbox: a fast and incredibly versatile read processor that can do all this & more 🧪
doi.org/10.1101/2025...
Reposted by Mike Clark
Publicly available, reference datasets are a bioinformatician's best friend! Find out more about the LongBench resource at poster 17 #abacbs2025 from @mritchieau.bsky.social @wehi-research.bsky.social
November 25, 2025 at 11:39 PM
Publicly available, reference datasets are a bioinformatician's best friend! Find out more about the LongBench resource at poster 17 #abacbs2025 from @mritchieau.bsky.social @wehi-research.bsky.social
Ami Bhatt taking us through the wild world of bacterial mobile elements. Jumping insertion sequences that can cause antibiotic resistance; DNA invertons that flip in orientation (including in coding seqs); and the huge abundance of phages integrated into bacterial genomes in our guts. #abacbs2025
November 25, 2025 at 11:29 PM
Ami Bhatt taking us through the wild world of bacterial mobile elements. Jumping insertion sequences that can cause antibiotic resistance; DNA invertons that flip in orientation (including in coding seqs); and the huge abundance of phages integrated into bacterial genomes in our guts. #abacbs2025
Agreed. And thanks for giving such a clear and engaging talk. Not my field but I definitely learnt a few things.
November 25, 2025 at 1:45 PM
Agreed. And thanks for giving such a clear and engaging talk. Not my field but I definitely learnt a few things.
@zaminiqbal.bsky.social sequencing 765 historical plasmids (Murray collection) vs modern plasmids. 3 outcomes. 1. plasmid survive in same/similar form. 2. Now found embedded in modern massive plasmids. 3. Go extinct. ~1/2 of the types remain only as small fragments in other plasmids. #abacbs2025
November 25, 2025 at 7:35 AM
@zaminiqbal.bsky.social sequencing 765 historical plasmids (Murray collection) vs modern plasmids. 3 outcomes. 1. plasmid survive in same/similar form. 2. Now found embedded in modern massive plasmids. 3. Go extinct. ~1/2 of the types remain only as small fragments in other plasmids. #abacbs2025
@zaminiqbal.bsky.social on studying the evolution of plasmids in bacteria. How do we model evolution and understand something that jumps around between cells and species? Totally different biological system and investigatory mindset to studying vertically inherited chromosomes. #abacbs2025
November 25, 2025 at 7:32 AM
@zaminiqbal.bsky.social on studying the evolution of plasmids in bacteria. How do we model evolution and understand something that jumps around between cells and species? Totally different biological system and investigatory mindset to studying vertically inherited chromosomes. #abacbs2025
@jovmaksimovic.bsky.social – On how to “easily“ detect fusions in single-cells. 1. Identify fusions with bulk RNA seq. 2. Use Flexify to design fusion detection probes for 10x Flex. 3. Detect fusions and their expression in each cell with scRNA-seq. #abacbs2025
November 25, 2025 at 6:34 AM
@jovmaksimovic.bsky.social – On how to “easily“ detect fusions in single-cells. 1. Identify fusions with bulk RNA seq. 2. Use Flexify to design fusion detection probes for 10x Flex. 3. Detect fusions and their expression in each cell with scRNA-seq. #abacbs2025
Ruining Dong from @unimelb.bsky.social explaining how the ability to detect methylation in circulating tumor DNA (ctDNA) improves ability to determine tumor tissue of origin. Matching methylation profiles of tissues to ctDNA sounds simple, but spoiler alert, it’s actually pretty complex. #abacbs2025
November 25, 2025 at 6:11 AM
Ruining Dong from @unimelb.bsky.social explaining how the ability to detect methylation in circulating tumor DNA (ctDNA) improves ability to determine tumor tissue of origin. Matching methylation profiles of tissues to ctDNA sounds simple, but spoiler alert, it’s actually pretty complex. #abacbs2025
First up in the #abacbs2025 Gene Regulation & Epigenetics session is Feng Yan from @nadia-davidson.bsky.social lab evaluating different long-read methods for de-novo transcriptome analysis. TLDR: Still a way to go to reduce false postives, but RNA-bloom2 generally works best.
November 25, 2025 at 5:43 AM
First up in the #abacbs2025 Gene Regulation & Epigenetics session is Feng Yan from @nadia-davidson.bsky.social lab evaluating different long-read methods for de-novo transcriptome analysis. TLDR: Still a way to go to reduce false postives, but RNA-bloom2 generally works best.