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Hope Tanudisastro

@htanudisastro.bsky.social
511 followers 148 following 28 posts

MD-PhD candidate at the University of Sydney & Garvan Institute. Studying tandem repeats in single-cell contexts w/ @dgmacarthur.bsky.social

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Reposted by Hope Tanudisastro
Jill Moore @moorejille.bsky.social · 07/01/2026
Our paper on the newest version of the Registry of candidate cis-Regulatory Elements (cCREs) is out 🧬 Huge thanks to the many collaborators, experimentalists, analysts and software developers who made this work possible — truly a team effort! A "meme-torial" of the science is coming soon 👀
nature.com
An expanded registry of candidate cis-regulatory elements - Nature
The existing ENCODE registry of candidate human and mouse cis-regulatory elements is expanded with the addition of new ENCODE data, integrating new functional data as well as new cell and tissue types...
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Hope Tanudisastro @htanudisastro.bsky.social · 08/01/2026
Surprise visit to @nickywhiffin.bsky.social’s lab! So nice catching up with old friends, meeting new ones, and a reminder that even though Sydney is home, Oxford can still feel like one too :) @ruebenadawes.bsky.social
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Christel Depienne @christeldepienne.bsky.social · 05/09/2025
After our study on RNU4-2 and RNU5B-1 published in May (Nava et al, Nature Genetics 2025), I am excited to share our new preprint reporting dominant and recessive variants in RNU2-2 as a frequent cause of developmental and epileptic encephalopathy (DEE). 📄 www.medrxiv.org/content/10.1...
medrxiv.org
Systematic analysis of snRNA genes reveals frequent RNU2-2 variants in dominant and recessive developmental and epileptic encephalopathies
Variants in spliceosomal small nuclear RNA (snRNA) genes RNU4-2 (ReNU syndrome), RNU5B-1 , and RNU2-2 have recently been linked to dominant neurodevelopmental disorders (NDDs), revealing a major, prev...
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Reposted by Hope Tanudisastro
Molly Przeworski @mollyprz.bsky.social · 02/09/2025
In these dark times, it comes as a rare pleasure to highlight @natanaels.bsky.social ‬ & @marcdemanuel.bsky.social's work on germline and somatic mutations in humans. 1/n www.biorxiv.org/cgi/content/...
biorxiv.org
Collateral mutagenesis funnels multiple sources of DNA damage into a ubiquitous mutational signature
Mutations reflect the net effects of myriad types of damage, replication errors, and repair mechanisms, and thus are expected to differ across cell types with distinct exposures to mutagens, division ...
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Reposted by Hope Tanudisastro
Peter Kraft @peter-kraft.bsky.social · 02/09/2025
Multi-ancestry GWAS can increase power and precision, but how should we analyze them? Pooled or stratified? We answer that question in a paper out today in AJHG, led by Julie Dias and Haoyu Zhang. 1/7 www.cell.com/ajhg/fulltex...
cell.com
Evaluating multi-ancestry genome-wide association methods: Statistical power, population structure, and practical implications
Multi-ancestry GWASs enhance discovery in diverse populations, but optimal methods remain debated. Using theory, simulations, and analyses from the UK Biobank and All of Us, we show that pooled analys...
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Hope Tanudisastro @htanudisastro.bsky.social · 01/09/2025
Check out a new preprint led by @alberthenry.bsky.social & Anne Senabouth exploring causal inference across 28 immune cell types in TenK10K!
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Hope Tanudisastro @htanudisastro.bsky.social · 01/09/2025
Check out a new preprint led by @anglixue.bsky.social exploring single-cell chromatin accessibility in TenK10K!
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Reposted by Hope Tanudisastro
Nicky Whiffin @nickywhiffin.bsky.social · 18/08/2025
🚨 New preprint led by amazing duo @rociorius.bsky.social and @alexblakes.bsky.social in collaboration with @cassimons.bsky.social, @dgmacarthur.bsky.social and many other amazing folks! ❤️ We describe the clinical phenotype of a recessive NDD associated with biallelic variants in RNU4-2 🧬 See 🧵👇
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Hope Tanudisastro @htanudisastro.bsky.social · 14/08/2025
Amazing talk on thinking about genetic ancestry and discussion of narrow vs broad sampling by @jnovembre.bsky.social at the #OurDNA symposium this morning!
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Reposted by Hope Tanudisastro
Michael S. Balzer @balzer-lab.org · 08/08/2025
🔥 Huge congrats to @ksusztak.bsky.social & team on a landmark @natgenet.nature.com paper! 🚶‍♂️🐁🐀Cross-species 🫘kidney pathway dysregulation via #singlecell functional profiling of individual samples — opening new therapeutic avenues. 🔗 www.nature.com/articles/s41... 🧪 #NephSky #MedSky
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Hope Tanudisastro @htanudisastro.bsky.social · 13/08/2025
#HGSA2025 week kicks off with the OurDNA symposium tomorrow (with a preview of the OurDNA browser!) Register to attend online here👇
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Reposted by Hope Tanudisastro
Cedric Boeckx @cedricboeckx.bsky.social · 09/08/2025
“findings suggest the existence of tens of thousands of enhancers that remain undiscovered by currently available chromatin data” 🧪🧬
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Jeffrey Pullin @jeffreypullin.bsky.social · 22/07/2025
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...
medrxiv.org
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...
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Reposted by Hope Tanudisastro
Simon Fisher @profsimonfisher.bsky.social · 07/08/2025
In another milestone for human genetics, the world's largest set of whole-genome DNA sequences now encompasses data from nearly half a million people, described in this new @nature.com paper from @ukbiobank.bsky.social: 🧪👇
nature.com
Whole-genome sequencing of 490,640 UK Biobank participants - Nature
A study reports whole-genome sequences for 490,640 participants from the UK Biobank and combines these data with phenotypic data to provide new insights into the relationship between human variation a...
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Reposted by Hope Tanudisastro
Christy LaFlamme (she/her) @cwlaflamme.bsky.social · 01/08/2025
Such a wonderful experience at this year’s Leena Peltonen School for Human Genomics @ Wellcome Genome, UK. Thank you to the organizers for putting this together! Caught up with old friends and made so many new friends. Feeling immensely uplifted for the future of human genetics research! #lpshg2025
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Andrea Ganna @andganna.bsky.social · 30/07/2025
Leena Peltonen School of Human Genetics in full-swing! @gosiatrynka.bsky.social @dgmacarthur.bsky.social @bpasaniuc.bsky.social @tuuliel.bsky.social @hilarycmartin.bsky.social @sashagusevposts.bsky.social @zkutalik.bsky.social @mashaals.bsky.social @alemedinarivera.bsky.social
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Tobi Alegbe @tobioinformatics.bsky.social · 08/07/2025
🚨New preprint just dropped 🚨 medrxiv.org/content/10.1101/2025.06.24.25330216 The main output from my PhD is finally public and we’re SUPER excited about the findings! If you’re interested in what we learnt about IBD with a massive 700+ sample sc-eQTL dataset of the gut, read on!
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Gherman Novakovsky @gnovakovsky.bsky.social · 30/05/2025
Excited to share my first contribution here at Illumina! We developed PromoterAI, a deep neural network that accurately identifies non-coding promoter variants that disrupt gene expression.🧵 (1/)
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Reposted by Hope Tanudisastro
Charlie Pugh @cwjpugh.bsky.social · 26/05/2025
New preprint in collaboration with @paulinanunezv.bsky.social supervised by @jonnyfrazer.bsky.social and Mafalda Dias – we propose a simple approach to improving zero-shot variant effect prediction in pre-existing protein and genome language models: 🧶 1/n www.biorxiv.org/content/10.1...
biorxiv.org
From Likelihood to Fitness: Improving Variant Effect Prediction in Protein and Genome Language Models
Generative models trained on natural sequences are increasingly used to predict the effects of genetic variation, enabling progress in therapeutic design, disease risk prediction, and synthetic biolog...
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Reposted by Hope Tanudisastro
Zornitza Stark @zornitza.bsky.social · 23/05/2025
🤗 Hugely excited to share our work on automating iterative reanalysis in #raredisease, preprint out: www.medrxiv.org/content/10.1... 🤖🧬 github.com/populationge... A superb collaboration with @dgmacarthur.bsky.social @cassimons.bsky.social @heidirehm.bsky.social @ksamocha.bsky.social and many more!
medrxiv.org
Scalable automated reanalysis of genomic data in research and clinical rare disease cohorts
Reanalysis of genomic data in rare disease is highly effective in increasing diagnostic yields but remains limited by manual approaches. Automation and optimization for high specificity will be necess...
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Reposted by Hope Tanudisastro
Oz Single Cell @ozsinglecell.bsky.social · 21/05/2025
Joseph Powell welcomes everyone to the start of #ozsinglecell2025!
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Hope Tanudisastro @htanudisastro.bsky.social · 20/05/2025
Looking forward to attending #ozsinglecell2025. I’ll be sharing some findings on tandem repeats #TRs in single cell contexts using TenK10K Phase 1 on Thursday at 11:55.
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Doug Fowler @dougfowler.bsky.social · 15/05/2025
Our "Atlas of Variant Effects 2030 Roadmap" is live: zenodo.org/records/1542... 1/n
zenodo.org
Atlas of Variant Effects 2030 Roadmap: resolving human variants of uncertain significance
At the Clinical Atlas of Variant Effects meeting (CLAVE meeting, July 2024, Pittsburgh USA), we developed recommendations for a draft atlas that can be realized by 2030, with a focus on empowering gen...
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Reposted by Hope Tanudisastro
Peter C Allen @petercallen.bsky.social · 23/04/2025
🧬Oz Single Cell Hackathon 2025🧬Join us at the Garvan Institute 19-21 May before the Oz Single Cell conference! Tackle challenges in scMultiomics integration, viz & predictive modeling. Details 👉 petercallen.github.io/2025-OSC-hac... #OzSingleCell #ozsinglecell25 @ozsinglecell.bsky.social
petercallen.github.io
Home | 2025 Oz Single Cell Hackathon
2025 Oz Single Cell Hackathon
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Cas Simons @cassimons.bsky.social · 11/04/2025
Are you an experienced Bioinformatician looking to make a real-world impact for families living with rare disease? Love team science and working at scale? Remote-first (NSW, VIC or QLD). Join me, @dgmacarthur.bsky.social, and the CPG Rare Disease Program: career10.successfactors.com/career?caree...
career10.successfactors.com
Career Opportunities: Rare Disease Bioinformatician (42637)
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Reposted by Hope Tanudisastro
Daniel MacArthur @dgmacarthur.bsky.social · 05/04/2025
Reckon we still have a while before ChatGPT replaces genetic counselors
ChatGPT chat interface. The prompt is “draw a pedigree illustrating second cousins” and the response is a nonsensical pedigree including sibling consanguinity between a pair of brothers
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Hope Tanudisastro @htanudisastro.bsky.social · 24/03/2025
The TenK10K Phase 1 dataset is out! A mammoth effort to generate and analyze paired WGS + scRNA-seq at scale - already yielding exciting insights, with many more to come.
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Reposted by Hope Tanudisastro
Anshul Kundaje @anshulkundaje.bsky.social · 07/01/2025
Very excited to announce that the single cell/nuc. RNA/ATAC/multi-ome resource from ENCODE4 is now officially public. This includes raw data, processed data, annotations and pseudobulk products. Covers many human & mouse tissues. 1/ www.encodeproject.org/single-cell/...
encodeproject.org
Single cell – ENCODEHomo sapiens clickable body map
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Reposted by Hope Tanudisastro
Harriet Dashnow @hdashnow.bsky.social · 12/12/2024
I am excited to present STRchive.org v2! A resource for tandem repeats associated with Mendelian disease. We have resigned the website, added new loci, streamlined our data for easier reuse, added more detailed citations, presented population frequency data and more!
strchive.org
STRchive
An archive of STRs associated with human diseases
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Hope Tanudisastro @htanudisastro.bsky.social · 04/12/2024
Massive congrats @laurayeates1.bsky.social 🎉
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Reposted by Hope Tanudisastro
Mike Schatz @mikeschatz.bsky.social · 25/11/2024
Sometimes you just have to persevere through negative reviews. Reviewers, please be kind :) #methodsmatter bit.ly/gs2-scholar
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Hope Tanudisastro @htanudisastro.bsky.social · 21/11/2024
Spent the afternoon listening to @itaiyanai.bsky.social break down developmental constraints in #cancer, connecting AMR principles to cancer drug resistance. Brilliant science aside, it was a masterclass in how to convey complex ideas incredibly clearly. Thanks for the amazing talk in Boston! 🧬
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Hope Tanudisastro @htanudisastro.bsky.social · 21/11/2024
Wonderful talk on the dissection of genetic contributions to different T2D phenotypes...looking forward to reading the preprint when it comes out!
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Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 14/11/2024
Evo: A genomic language model of prokaryote genomes generates functional cas9 proteins and transposons. @brianhiestand.bsky.social www.science.org/doi/10.1126/...
Evo, a 7-billion-parameter genomic foundation model, learns biological complexity from individual nucleotides to whole genomes.
Pretraining a genomic foundation model across prokaryotic life.Fine-tuning on CRISPR-Cas sequences enables generative design of protein-RNA complexes.Fig. 4. Fine-tuning on IS200/IS605 sequences enables generative design of transposable biological systems.
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Hope Tanudisastro @htanudisastro.bsky.social · 04/11/2024
Excited to share more at #ASHG2024! I’ll be diving into these findings in my talk on Wed Nov 6 at 1:45pm in the ‘Decoding Gene Expression Cis and Trans’ session in Room 401. I’d love to connect and explore collaborations as we scale up to an even larger cohort very soon! 9/9
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Hope Tanudisastro @htanudisastro.bsky.social · 04/11/2024
Team effort by @annasecuomo.bsky.social, Ben Weisburd, @jeffreypullin.bsky.social, @hdashnow.bsky.social, Egor Dolzhenko, Melissa Gymrek, Ira Deveson, my advisors @dgmacarthur.bsky.social and Joseph Powell, and many others 🙌 8/9
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Hope Tanudisastro @htanudisastro.bsky.social · 04/11/2024
🔹Summary: TRs are powerful, context-specific regulators of cell type-specific expression, and represent an important complement to SNV-centric approaches for deciphering genetic regulation. 🚀 biorxiv.org/content/10.1... Dataset: zenodo.org/records/1401... 7/9
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Hope Tanudisastro @htanudisastro.bsky.social · 04/11/2024
🔹 RD example: The poly(GCA) 5’ UTR repeat in #GLS not only associates with GLS expression, but also inversely associates with an upstream lncRNA, highlighting the strength of our genome-wide approach and the potential for a TR to modulate the expression of multiple genes. 6/9
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Hope Tanudisastro @htanudisastro.bsky.social · 04/11/2024
🔹 Example: A 5'UTR poly(GCC) repeat in BCL2L11 significant in CD4 naive cells is likely driving a signal for inflammatory bowel disease, pointing to a role for TRs in T-cell regulation of #IBD. 5/9
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Hope Tanudisastro @htanudisastro.bsky.social · 04/11/2024
🔹 Complex traits and disease : We show through colocalization that TRs are likely drivers of over 2,000 GWAS loci associated with immune-mediated and hematological traits, and further identify novel TRs warranting investigation in rare disease cohorts. 💪🧬 4/9
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Hope Tanudisastro @htanudisastro.bsky.social · 04/11/2024
🔹 Causal insights: We found over 6,000 candidate causal sc-eTRs, influencing expression in as many as ~21% of genes tested. TRs are crucial, yet often overlooked, regulators of gene expression. 🔍 3/9
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Hope Tanudisastro @htanudisastro.bsky.social · 04/11/2024
🔹 Resource: We cataloged 2.6M polymorphic TRs and identified over 58,000 single-cell expression quantitative trait loci (sc-eTRs) in 28 immune cell types—many with cell-type-specific roles! 💥 Link: biorxiv.org/content/10.1... 2/9
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Hope Tanudisastro @htanudisastro.bsky.social · 04/11/2024
📢 New preprint alert: Excited to share our deep dive into the role of tandem repeats (TRs) in single-cell gene expression across the immune system, using WGS and scRNA-seq data from 1,790 individuals and over 5 million blood cells! 🧬 🧵👇 #repeats #SingleCell 1/9
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Hope Tanudisastro @htanudisastro.bsky.social · 04/11/2024
Excited to share more at #ASHG2024! I’ll be diving into these findings in my talk on Wed Nov 6 at 1:45pm in the ‘Decoding Gene Expression Cis and Trans’ session in Room 401. I’d love to connect and explore collaborations as we scale up to an even larger cohort very soon! 9/9
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Hope Tanudisastro @htanudisastro.bsky.social · 04/11/2024
A huge thank you to our amazing collaborators 🙌 @annasecuomo.bsky.social , @BenWeisburd, @hdashnow.bsky.social , @EgorDolzhenko, @MelissaGymrek, @jeffreypullin.bsky.social and my supervisors @dgmacarthur.bsky.social and @JosephPowell 8/9
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Hope Tanudisastro @htanudisastro.bsky.social · 04/11/2024
🔹 Summary: TRs are powerful, context-specific regulators of cell type-specific expression, and represent an important complement to SNV-centric approaches for deciphering genetic regulation. 🚀 Dive into the paper to explore more! www.biorxiv.org/content/10.1... 10.5281/zenodo.14010498
biorxiv.org
| bioRxiv
bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
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Hope Tanudisastro @htanudisastro.bsky.social · 04/11/2024
🔹 Rare disease insight: The poly(GCA) 5’ UTR repeat in #GLS not only associates with GLS expression, but also inversely associates with an upstream lncRNA, highlighting the strength of our genome-wide, unbiased approach and the potential for a TR to modulate the expression of multiple genes. 6/9
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Hope Tanudisastro @htanudisastro.bsky.social · 04/11/2024
🔹 Example: A 5'UTR poly(CGC) repeat in BCL2L11 significant in CD4 naive cells is likely driving a signal for inflammatory bowel disease, pointing to a role for TRs in T-cell regulation of #IBD. 5/9
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Hope Tanudisastro @htanudisastro.bsky.social · 04/11/2024
🔹 Complex Traits and Disease : We show through colocalization that TRs are likely drivers of over 2,000 GWAS loci associated with immune-mediated and hematological traits, and further identify novel TRs warranting investigation in rare disease cohorts 💪🧬 4/9
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Hope Tanudisastro @htanudisastro.bsky.social · 04/11/2024
🔹 Causal Insights: We found over 6,000 candidate causal sc-eTRs, influencing expression in as many as ~21% of genes tested. TRs are crucial, yet often overlooked, regulators of gene expression. 🔍 3/9
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