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
Single-cell genomics and data viz enthusiast | Former Postdoc @ Harvard SCRB / Broad Institute w/ Buenrostro Lab
Reposted by Vinay Kartha
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
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.
www.nature.com
September 22, 2025 at 8:41 PM
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
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
Reposted by Vinay Kartha
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
September 11, 2025 at 7:55 PM
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
Reposted by Vinay Kartha
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 ✨👩🏽💻)
Here are the T32 curves.
July 15, 2025 at 8:07 PM
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 ✨👩🏽💻)
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
July 10, 2025 at 8:40 PM
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
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!
July 6, 2025 at 6:45 PM
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!
Reposted by Vinay Kartha
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/
June 23, 2025 at 12:57 PM
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/
Reposted by Vinay Kartha
Terminal Genome Viewer (tgv), written in Rust github.com/zeqianli/tgv
May 27, 2025 at 5:37 PM
Terminal Genome Viewer (tgv), written in Rust github.com/zeqianli/tgv
Reposted by Vinay Kartha
Zero-shot evaluation reveals limitations of single-cell foundation models genomebiology.biomedcentral.com/articles/10.... 🧬🖥️🧪 github.com/microsoft/ze...
April 21, 2025 at 3:30 PM
Zero-shot evaluation reveals limitations of single-cell foundation models genomebiology.biomedcentral.com/articles/10.... 🧬🖥️🧪 github.com/microsoft/ze...
💯💯💯
April 15, 2025 at 4:40 AM
💯💯💯
Reposted by Vinay Kartha
@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 ...
www.biorxiv.org
February 25, 2025 at 1:25 PM
@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...
Reposted by Vinay Kartha
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 (🧵)
February 18, 2025 at 3:01 AM
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 (🧵)
Reposted by Vinay Kartha
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.
February 15, 2025 at 1:29 PM
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.
Reposted by Vinay Kartha
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...
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...
www.nature.com
February 12, 2025 at 10:09 PM
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...
Grateful for the excellent primer by Christopher Bock and Eugenia Pankevich: www.nature.com/articles/s41...
Reposted by Vinay Kartha
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.
February 8, 2025 at 9:21 PM
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.
Reposted by Vinay Kartha
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.
It ran on our hometown NPR station KQED and about 200 other @npr.org affiliates.
February 3, 2025 at 3:55 PM
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.
It ran on our hometown NPR station KQED and about 200 other @npr.org affiliates.
Reposted by Vinay Kartha
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.
www.nature.com
December 6, 2024 at 8:52 PM
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...
Reposted by Vinay Kartha
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”
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...
www.biorxiv.org
December 4, 2024 at 2:09 PM
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”
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...
Reposted by Vinay Kartha
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
December 5, 2024 at 4:18 AM
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...
Reposted by Vinay Kartha
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
November 29, 2024 at 4:17 PM
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!
This seems amazing, nice stuff @mitchguttman.bsky.social and co, looking forward to reading
Gene 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...
www.nature.com/articles/s41...
ChIP-DIP maps binding of hundreds of proteins to DNA simultaneously and identifies diverse gene regulatory elements - Nature Genetics
ChIP-DIP (ChIP done in parallel) is a highly multiplex assay for protein–DNA binding, scalable to hundreds of proteins including modified histones, chromatin regulators and transcription factors, offe...
www.nature.com
November 28, 2024 at 7:19 PM
This seems amazing, nice stuff @mitchguttman.bsky.social and co, looking forward to reading
Reposted by Vinay Kartha
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
www.biorxiv.org
November 28, 2024 at 2:33 AM
Paired CRISPR screens to map gene regulation in cis and trans https://www.biorxiv.org/content/10.1101/2024.11.27.625752v1
Reposted by Vinay Kartha
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.
November 26, 2024 at 3:31 PM
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
Excited 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
biorxiv.org/cgi/content/...
Read more below!
1/12
Mapping enhancer-gene regulatory interactions from single-cell data
Mapping enhancers and their target genes in specific cell types is crucial for understanding gene regulation and human disease genetics. However, accurately predicting enhancer-gene regulatory interac...
biorxiv.org
November 25, 2024 at 8:26 PM
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
Reposted by Vinay Kartha
