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 ✨👩🏽‍💻)

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

So great meeting and talking to you @mragsac.com ! And I know, small world, we should all hang if you're ever in the Bay area anytime!

Also looking forward to catching up with some old friends, and connecting with many new ones while I'm there!

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...

Thank you #MIT

💯💯💯

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 ...

@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...

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.

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...

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...

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.

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.

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...

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...

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...

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...

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...

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

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

Paired CRISPR screens to map gene regulation in cis and trans https://www.biorxiv.org/content/10.1101/2024.11.27.625752v1

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.

Nice work Maya Sheth, @613weilin.bsky.social and co, looking forward to reading in more detail

Speaking of ground truth data for GRN evaluation - this is obviously heavily context and platform dependent, but using multiple layers of such info (across contexts) helps vett various methods, highlighting their respective strengths and weaknesses in each case

Have to also really credit the amount of work that goes into these important benchmarks, from data curation/QC, to assessing different underlying assumptions each method comes with, to the evaluation of outcomes based on ground truth observations, to the data/ code/model sharing that goes with it

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

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...

#snPATHO…

www.nature.com/articles/s42...

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...

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...

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...

Single-molecule states link transcription factor binding to gene expression www.nature.com/articles/s41...