Mike Clark
Genetics, transcriptomics, RNA and neuroscience.
Lab head at the University of Melbourne, Australia.
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- 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. 🧪
- Reposted by Mike ClarkSo, 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
- 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.
- Reposted by Mike ClarkShare your stories here docs.google.com/forms/d/e/1F... #SaveOzScience
- Reposted by Mike ClarkIf 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 ClarkThe 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.
- Reposted by Mike ClarkBe kind to each other.. bad news for most coming in under embargo. We need more funding in the system...
- Reposted by Mike Clarkthis 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 🥼🧪🔬🧫 🇦🇺
- 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
- 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...
- 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....
- 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!
- Reposted by Mike ClarkPublicly 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
- @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
- @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
- 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.
- Reposted by Mike ClarkVery 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 Mike ClarkExcited to share matchbox. It’s super fast and versatile to search for patterns in reads, I’m curious to see all the uses it will find! Congrats to @jakobschuster.bsky.social , co-supervisors @michaelbclark.bsky.social @mritchieau.bsky.social and team! www.biorxiv.org/content/10.1...
- Reposted by Mike ClarkLooking for scientists working with long-read transcriptomics technologies to join a COST action proposal. Contact us!!! @nanoporetech.com @pacbio.bsky.social
- 🧪Happy to share our latest paper in Genome Biology. We profiled #RNA isoforms from 31 neuropsychiatric risk genes in the human brain using long-read sequencing. Unannotated isoforms commonly made up a significant proportion of a gene's expression. genomebiology.biomedcentral.com/articles/10....
- Overall we found more than 300 previously unreported RNA isoforms from 31 genes in brain. Some were highly abundant or even the dominant isoform, and we could show translation of novel RNAs into novel proteoforms, including new isoforms of the depression risk gene ITIH4 (see image).
- We developed a new analysis pipeline, IsoLamp, to discover and quantify isoforms from long-read amplicon sequencing. While much of the analysis and visualisation used IsoVis. IsoVis: isomix.org/isovis/ IsoLamp: github.com/ClarkLaborat...
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View full threadThis study reflects years of work, a big thanks to everyone involved, including Ricardo De Paoli-Iseppi who co-led the work and the many graduate and undergrad students who took on some of the genes for their projects or worked on IsoLamp including @josiegleeson.bsky.social & @youyupei.bsky.social
- Reposted by Mike ClarkLong-read transcriptomics is advancing quickly, we benchmarked leading bulk and single-cell protocols in this awesome collaborative effort! We hope it will be a valuable resource for the community. Congrats @youyupei.bsky.social @mritchieau.bsky.social @michaelbclark.bsky.social and all!
- 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...
- Reposted by Mike ClarkBioinformaticians / computational biologists take note - know where you should take your OS tool chain from and do not introduce backdoors.
- Reposted by Mike Clark🔹 What’s inside • Bulk, single-cell & single-nucleus RNA-seq from 8 lung-cancer cell lines spanning 3 cancer types for realistic DE analysis • Three long-read protocols (ONT PCR-cDNA, ONT direct RNA, PacBio Kinnex) and Illumina short-read sequencing • Synthetic spike-in controls for ground truth
- Reposted by Mike ClarkExcited 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...
- Our paper using Oxford #Nanopore direct RNA sequencing to identify m6A modifications on RNA isoforms in human brain is now out in Science Advances. 🧪 www.science.org/doi/10.1126/...
- We identified 57,000 m6A sites in 15,000 isoforms. Some of the key results were: - highest m6A levels in the cerebellum. - Pre-frontal cortex had the most unique m6A profile, associated with excitatory neurons and synaptic genes. - Some RNAs are hyper-modified. The lncRNA TUG1 had 37 m6A sites!
- - Different RNA isoforms from the same gene can have different modification rates at the same m6A site. Distance to a splice site, transcript 3' end, and the CDS versus UTR status of a nucleotide all exert influence.
- If you want to explore the data check out the Shiny App: clarklaboratory.shinyapps.io/human_brain_... Big thanks to Josie Gleeson and Ric De Paoli-Iseppi for leading this work.
- Reposted by Mike ClarkThe appearance of large language models caused a drastic shift in the vocabulary of academic writing, according to an analysis in #ScienceAdvances of more than 15 million biomedical abstracts published from 2010 to 2024. Learn more:
- Reposted by Mike ClarkNew pre-print from our wonderful collaborators at Roche, Genentech, and the University of Basel. A fun study investigating the molecular mechanisms of gymnosis (passive cellular uptake) of antisense oligonucleotides (ASOs). www.biorxiv.org/content/10.1...
