Vinay Kartha
@vkartha.bsky.social
Senior Comp Bio Scientist @ www.gordian.bio | Single-cell genomics and data viz enthusiast | Former Postdoc @ Harvard SCRB / Broad Institute w/ Buenrostro Lab
New preprint from Shendure Lab on Locus-Scale aka Long-@$$ MPRAs led by the amazing Abby McGee & @carinabiar.bsky.social Most MPRAs test ~300 bp fragments next to a promoter. But real enhancers are bigger, act combinatorially and from a distance. 1/n www.biorxiv.org/content/10.6...
Epigenetic diagnosis of acute leukemia within two hours from sample receipt 🚀 Very happy to share the results of a great collaboration between @hovestadt.bsky.social and Griffin Labs, I co-led with @sbenfatto.bsky.social, published today in @natgenet.nature.com 📄 www.nature.com/articles/s41... 🧵1/n
Rapid epigenomic classification of acute leukemia - Nature Genetics
The authors present a molecular classification of acute leukemia using 5-methylcytosine signatures, together with a neural network-based classifier for clinical use.
nature.com
Excited to share my postdoc work, out on bioRxiv today! Histones package DNA into nucleosomes to form the building blocks of chromatin, but how modular and programmable is this system? 1/9
With funding cuts and whatnot going on… I want to say that my experience on the @ucsandiego.bsky.social T32 for Genetics with @bahome.bsky.social was VERY influential in my growth as a scientist 🧪🧬💻 and keeping me in bioinformatics during the early pandemic 🦠 (versus pivoting to Big Tech ✨👩🏽💻)
EJVallender@ejvallender.bsky.social · last yr.Here are the T32 curves.
Had a super week filled with great science, curiosity and discussions at this year's Gordon Research Conference on Human genetics and genomics. Also fun when you get to give a talk the same day as your postdoc advisor @jbuenrostro.bsky.social
Vinay Kartha@vkartha.bsky.social · last yr.Excited to be attending this year's Human genetics and genomics Gordon Research Conference in Portland, ME, where I'll be presenting work from @gordianbio.bsky.social related to our in vivo mosaic screening platform applied to accelerate patient-relevant target discovery in complex diseases!
Excited to be attending this year's Human genetics and genomics Gordon Research Conference in Portland, ME, where I'll be presenting work from @gordianbio.bsky.social related to our in vivo mosaic screening platform applied to accelerate patient-relevant target discovery in complex diseases!
How do non-coding variants in enhancers lead to disease? Happy to share our recent work, led by @ewholling.bsky.social, in which we discovered that poised chromatin sensitizes enhancers to aberrant activation by non-coding mutations, contributing to disease. www.biorxiv.org/content/10.1... 1/
Terminal Genome Viewer (tgv), written in Rust github.com/zeqianli/tgv
Zero-shot evaluation reveals limitations of single-cell foundation models genomebiology.biomedcentral.com/articles/10.... 🧬🖥️🧪 github.com/microsoft/ze...
@thejohnnyyu.bsky.social, @therealnima.bsky.social, and I, are excited to tell you about Tahoe-100M! The largest publicly available single-cell dataset that measures the effect of 1200 genes on 50 cell line models. The Vevo team has outdone itself. #Tahoe100M www.biorxiv.org/content/10.1...
Tahoe-100M: A Giga-Scale Single-Cell Perturbation Atlas for Context-Dependent Gene Function and Cellular Modeling
Building predictive models of the cell requires systematically mapping how perturbations reshape each cell's state, function, and behavior. Here, we present Tahoe-100M, a giga-scale single-cell atlas ...
biorxiv.org
New to bluesky, but I’m excited to share my work over the last few years with @jbuenrostro.bsky.social! Chronic inflammation creates an epigenetic memory in colonic stem cells, priming them for tumor growth: tinyurl.com/ColitisNagar.... Here’s a walkthrough of what we found (🧵)
It's great to see the heatmap icon I contributed to bioicons.com has been used in papers. Bioicons is a open-source repository for vector graphs. There are many very nice icons on there. Please do check it out.
Gonzalo Benegas@gonzalobenegas.bsky.social · last yr.Can DNA sequence models predict mutations affecting human traits? We introduce TraitGym, a curated benchmark of causal regulatory variants for 113 Mendelian & 83 complex traits, and evaluate functional genomics and DNA language models. Joint work w/ Gökcen Eraslan and @yun-s-song.bsky.social 🧵👇
Despite the trying times, thrilled to share our @natprot.bsky.social Nature Protocols on massively parallel in vivo Perturb-seq: www.nature.com/articles/s41... Grateful for the excellent primer by Christopher Bock and Eugenia Pankevich: www.nature.com/articles/s41...
Massively parallel in vivo Perturb-seq screening - Nature Protocols
This protocol leverages tailored adeno-associated virus vectors for effective delivery of pooled CRISPR-based genetic perturbations in live animals combined with single-cell gene expression readout of...
nature.com
It’s been a tough few weeks. My 10yo daughter was diagnosed with a very rare, aggressive cancer called interdigitating dendritic cell sarcoma (IDCS). I’m reaching out to identify clinicians/patients who have encountered pediatric IDCS or other (non-LCH) dendritic or histiocytic sarcomas cases.
ICYMI, co-founders Francisco LePort and @martinbjensen.bsky.social were guests of Dr. Moira Gunn on the BioTech Nation podcast. It ran on our hometown NPR station KQED and about 200 other @npr.org affiliates.
I could not be more thrilled to announce the Nature Methods @naturemethods.bsky.social Method of the Year is Spatial Proteomics! Please see our editorial as a roadmap to the fantastic content in this special issue! www.nature.com/articles/s41...
Method of the Year 2024: spatial proteomics - Nature Methods
Approaches for profiling the spatial proteome in tissues are the basis of atlas-scale projects that are delivering on their promise for understanding biological complexity in health and disease.
nature.com
Now on biorxiv! The JUMP-Cell Painting Consortium’s paper: “Morphological map of under- and over-expression of genes in human cells” This is the genetic perturbation portion of the JUMP’s dataset; our chemical perturbation paper will come in a few months www.biorxiv.org/content/10.1...
Morphological map of under- and over-expression of genes in human cells
Cell Painting images offer valuable insights into the state of a cell and enable many biological applications, but publicly available arrayed datasets only include hundreds of genes perturbed. The JUM...
biorxiv.org
We are hiring an intern to work with our team at Genentech next summer, on exciting projects related to deep learning for DNA/RNA sequences. Please share and apply! roche.wd3.myworkdayjobs.com/ROG-A2O-GENE...
2025 Summer Intern - Biology Research | AI Development
2025 Summer Intern - Biology Research | AI Development Department Summary At Genentech Research & Early Development (gRED) we have initiated an exciting journey to bring together and further stren...
roche.wd3.myworkdayjobs.com
Excited to share our work @science.org. led by our incredible @tommyz626.bsky.social at @rockefelleruniv.bsky.social! By profiling 21 million single cells across life stages, we reveal aging as distinct, development-like transitions, with dramatic cell population changes in specific time windows!
A panoramic view of cell population dynamics in mammalian aging
To elucidate aging-associated cellular population dynamics, we present PanSci, a single-cell transcriptome atlas profiling over 20 million cells from 623 mouse tissues across different life stages, se...
tinyurl.com
This seems amazing, nice stuff @mitchguttman.bsky.social and co, looking forward to reading
Mitch Guttman@mitchguttman.bsky.social · 2y agoGene regulation involves thousands of proteins that bind DNA, yet comprehensively mapping these is challenging. Our paper in Nature Genetics describes ChIP-DIP, a method for genome-wide mapping of hundreds of DNA-protein interactions in a single experiment. www.nature.com/articles/s41...
Paired CRISPR screens to map gene regulation in cis and trans https://www.biorxiv.org/content/10.1101/2024.11.27.625752v1
Paired CRISPR screens to map gene regulation in cis and trans https://www.biorxiv.org/content/10.1101/2024.11.27.625752v1
Recent massively-parallel approaches to decipher gene regulatory circuits have focused on the discov
biorxiv.org
A pair of graphs I think about a lot. On the topic of pooled CRISPR screens, the left is "replicate correlation" when simply examining the abundance of guide RNAs, i.e. log-normalized read counts. On the right is taking those same data and subtracting from a common starting point, i.e. pDNA.
Systematic benchmarking of several enhancer-to-gene association methods that utilize single cell data (including one developed by us earlier), highlighting advantages of the proposed scE2G model over alternatives and SOA metrics
Wei-Lin Qiu@613weilin.bsky.social · 2y agoExcited to share our latest preprint on scE2G – a new model to link enhancers to target genes using single-cell data – with state-of-the-art performance across multiple perturbation benchmarks. biorxiv.org/cgi/content/... Read more below! 1/12
#snPATHO… www.nature.com/articles/s42...
snPATHO-seq, a versatile FFPE single-nucleus RNA sequencing method to unlock pathology archives - Communications Biology
A combination of an FFPE nuclei preparation protocol and a probe-based transcriptomic profiling technique enables snRNA-seq characterization of archival human FFPE tissues, holding promise for retrosp...
nature.com
Cool work by Saunders, Allen et al. Some neat enhancements and a nice application of imaging coupled with transcriptomics for pooled screening in vivo A platform for multimodal in vivo pooled genetic screens reveals regulators of liver function www.biorxiv.org/content/10.1...
A platform for multimodal in vivo pooled genetic screens reveals regulators of liver function
Organ function requires coordinated activities of thousands of genes in distinct, spatially organized cell types. Understanding the basis of emergent tissue function requires approaches to dissect the...
biorxiv.org
Single-molecule states link transcription factor binding to gene expression www.nature.com/articles/s41...
Single-molecule states link transcription factor binding to gene expression - Nature
A study uses single-molecule footprinting to measure protein occupancy at regulatory elements on individual molecules in human cells and describes how different properties of transcription factor bind...
nature.com
The success of AI applied to drug discovery is being decided by a number of clinical trials. So far, the results are lackluster. Why? For AI to have a transformational effect in drug discovery, training data must come from living mammals. (🧵1/9)
in case this is useful to someone in this massive platform migration: a starting pack for single-cell omics computational methods go.bsky.app/GmS1cH
single-cell computational methods
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