Arthur Ko

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Arthur Ko

Arthur Ko

@arthur5ko

Human geneticist at Children’s National Hospital. NHGRI DATA Scholar.

Katılım Haziran 2012
750 Takip Edilen363 Takipçiler
Arthur Ko retweetledi
Tychele Turner
Tychele Turner@tycheleturner·
❄️ Introducing SNOW - the Second-pass de Novo variant Offspring Workflow. A Python toolkit for cleaning, merging, phasing, and annotating de novo variants from trio sequencing data for QC and downstream analysis. Works with short-read and long-read data, adds parent-of-origin annotation, and yes; there is a snowfall mode ☃️ github.com/tycheleturner/… #genomics #bioinformatics #denovo
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Sasha Gusev
Sasha Gusev@SashaGusevPosts·
I wrote about how genetic risk works in the context of embryo selection and how people often think about it all wrong. A short 🧵:
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Sasha Gusev
Sasha Gusev@SashaGusevPosts·
A few thoughts on Herasight, the new embryo selection company. First, the post below and the white paper imply that competitors like Nucleus have been marketing and selling grossly erroneous risk estimates. This is shocking if true! 🧵
Alex Strudwick Young@AlexTISYoung

At @herasight, we wanted to compare our genetic predictors (PGS) to those from @nucleusgenomics. However, in many cases, we couldn’t reconcile plausible performance of their PGSs with customer risk reports we saw — this may have misled customers about their disease risks.

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Anne Carpenter, PhD
Anne Carpenter, PhD@DrAnneCarpenter·
I’d love to hear biologists weigh in on the fundamental question: can you predict the impact of cell perturbations better by studying the natural variation in a population of healthy cells (more data), or by studying cells that have been perturbed genetically or chemically?
Adam Green@adamlewisgreen

virtual cells are currently bottlenecked by compute, not novel data: drug discovery is an iterative search process (design, test, analyze) through therapeutic design space guided by a dynamics model directly trawling this therapeutic space with large hypothesis-free perturbational screens is an incredibly inefficient, expensive means of doing this search. the combinatorial space of cell states x perturbations is too large to brute-force it is even more of a fool's errand to run these screens solely for the purpose of generating training data for the dynamics model (i.e. "virtual cell") we'll use to navigate therapeutic design space rather, a general cellular dynamics model (there will be one model to rule them all) is most cost- and time-efficiently pretrained on large, diverse observational datasets of majority healthy cells, not perturbational atlases of diseased cells. the icing and cherry on top are useless if you haven't baked the cake we have plenty (petabytes) of this observational data already and are currently FLOP-constrained, not novel biological data (bioFLOP) constrained. therefore, we'd be better served spending on pretraining compute, not assaying millions of single cells we are doubly FLOP-constrained because the future is scaling up inference-time compute running in silico experiments on our mechanistically interpretable virtual cell, in order to select the most promising targeted perturbational experiments to run in the wet lab the compute demands of this inference-time experimental search will far exceed those of pretraining the virtual cell this virtual hypothesis-driven approach will direct us toward the regions of cell state x therapeutic design space where collecting perturbational data has the highest return. rather than trawl, we will precision-guided spearfish this is the only way to efficiently search therapeutic design space, using FLOPs to better allocate bioFLOPs

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Sasha Gusev
Sasha Gusev@SashaGusevPosts·
People often intuitively interpret genetic ancestry PCA plots as simple genetic distances, but this is not always the case. Below are random pairs of individuals that are far apart in PCA space (lines) but actually have fewer total variant differences (numbers).
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Human Pangenome Reference Consortium
A more complete understanding of human genetics starts with accurate, high-quality reference genomes. HPRC is building a reference that reflects the breadth of human genetic variation, supporting better prediction, diagnosis, and treatment. Learn more: humanpangenome.org/samples/
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Ron Do
Ron Do@DoGenetics·
New perspective out now in @NatureGenet! nature.com/articles/s4158… We argue that current variant classifications oversimplify disease risk and propose an integrated Bayesian framework that unifies pathogenicity & penetrance.
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Arthur Ko
Arthur Ko@arthur5ko·
@jakphd Doesn’t it just mean Anne gets to take 23andme like she planned?
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Sasha Gusev
Sasha Gusev@SashaGusevPosts·
Racism twitter has taken to arguing that observed racial differences must be "in part" explained by genetic differences, though they demure on how much. Not only is this claim aggressively misleading, it is completely unsupported by data. A 🧵:
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Medhat Mahmoud
Medhat Mahmoud@MedhatMahmoud_·
1/ 🧬 A Hitchhiker’s Guide to Long-Read Genomic Analysis is out now @genomeresearch! This mini-review walks through the latest advances in long-read DNA sequencing — from assemblies to variant calling to epigenetics. Link 🔗 genome.cshlp.org/content/35/4/5… 🧵👇
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Sarah Marzi
Sarah Marzi@sj_marzi·
We're so thrilled to finally share with you the published version of our CUT&Tag optimization and benchmarking paper "CUT&Tag recovers up to half of ENCODE ChIP-seq histone acetylation peaks" - out in @NatureComms today: nature.com/articles/s4146…
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Alex Rosenberg
Alex Rosenberg@dna_rosenberg·
A big win for Parse, our customers, and the research community! Filing meritless lawsuits is not the way. Very proud of our team at Parse, and I’m looking forward to sharing more exciting science, partnerships, and product news over the coming weeks and months! parsebiosciences.com/news/parse-bio…
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Sasha Gusev
Sasha Gusev@SashaGusevPosts·
Thrilled to receive the Presidential Early Career Award for Scientists and Engineers (PECASE)! Could not have done this without my amazing lab members and mentors. whitehouse.gov/ostp/news-upda…
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Sasha Gusev
Sasha Gusev@SashaGusevPosts·
I wrote about the ongoing debates over genomic data sharing and the use of such data for "abhorrent science", including some perspective papers that came out last month. A few key points: 🧵
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Lappalainen Lab
Lappalainen Lab@tuuliel_lab·
🌟 Exciting news: The Leena Peltonen School of Human Genetics returns in 2025! We're excited to bring PhD students together with an all-star list of leaders in human genetics. 📅 July 27-31, 2025 📍 Wellcome Genome Campus, UK 📝 Apply by March 7 at lpshg.com
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