New York Genome Center

Posting my talk tomorrow @nygenome.org (hosted by @gamzeandgursoy.bsky.social). lectures.gersteinlab.org/summary/AI-A... Doing genomics with AI & then seeing if AI can take over the whole thing (spoiler: not yet!). New slides on assessing agent models with externalized reasoning (vs. baselines)

@landau.bsky.social @rdrapkin8-penn.bsky.social Paul Mischel, and Adam Widman are searching for pre-cancerous signals of ovarian cancer in the blood, laying the foundation for non-invasive screening test. 🩸@tinaswish.bsky.social
@weillcornell.bsky.social @mskcancercenter.bsky.social

TDP43 dysfunction in ALS leads to transposon mayhem in the transcriptome. Nice work from @nygenome.org ‘s ALS consortium, lead by Hemali Phatnani, and @nyulangone.bsky.social ‘s @karthiknatarajan.bsky.social & @mollygale.bsky.social. Nice work guys!

www.biorxiv.org/content/10.6...

TDP-43 dysfunction leads to the accumulation of cryptic transposable element-derived exons, crypTEs, in iPSC derived neurons and ALS/FTD patient tissues TDP-43 is an RNA and DNA binding protein that plays major roles in regulating RNA processing. In particular, TDP-43 dysfunction leads to the accumulation of cryptic splice isoforms that result from im...

📣Excited to announce a new pre-print from the lab 📣

Led by my student @storiesofisobel.bsky.social in collab with Hemali Phatnani @nygenome.org
We discovered a novel class of TDP-43 dependent cryptic gene-TE spliced transcripts: crypTEs

#TEsky #RNAsky #ALS
doi.org/10.64898/2026.01.09.698641

Now online in Cancer Discovery @aacrjournals.bsky.social: Genotype-to-Phenotype Mapping of Somatic Clonal Mosaicism via Single-Cell Co-Capture of DNA Mutations & mRNA Transcripts by @dennisjyuan.bsky.social, @landau.bsky.social, et al. doi.org/10.1158/2159... @nygenome.org @weillcornell.bsky.social

A comprehensive spatial splicing analysis in the brain under normal and neoplastic conditions @natbiotech.nature.com @raulrabadan.bsky.social @columbiauniversity.bsky.social @davidaknowles.bsky.social @nygenome.org
www.nature.com/articles/s41...

Congratulations to NYGC Core Faculty Members, @nevillesanjana.bsky.social and Rahul Satija for their feature on the @clarivate.com #highlycited2025 list!
Learn more here:
www.nygenome.org/news-events/...

Don't forget to watch our new Faces of IICD Video Series featuring Beatrice Grauman, a PhD student in the Vicković Lab @nygenome.org. ⤵️

IICD Newsletter November 2025

The November newsletter is out now. Don’t miss our alumni spotlight, cutting-edge research on colon aging, a new K-12 partnership, and other exciting updates: cancerdynamics.columbia.edu/news/iicd-ne...
cc: @nygenome.org @brentstockwell.bsky.social

Tissue and cellular spatiotemporal dynamics in colon aging - Nature Biotechnology cSplotch compares spatial transcriptomics data across ages and regions of mouse colon tissue.

Tissue and cellular spatiotemporal dynamics in colon aging - @nygenome.org @flatironinstitute.org @broadinstitute.org @cancerdynamics.bsky.social go.nature.com/47I1RBF

Congrats to our lab's recent MD-PhD grad Rachel Yan (
@rachelyan.bsky.social) on the beautiful cover art accompanying her MultiPerturb-seq study!

New York Cures – NY-CURESNew York Cures Website NY-CURES is working to advance bold, state-backed investment in biomedical research—on the scale of successful initiatives in California and Texas—to grow New York’s leadership in science, innovation, and health.

From patient to scientist: Sergei German beat cancer thanks to clinical trials, inspiring him to leave his career in finance and drive research @nygenome.org

A NY statewide biomedical institute will make more incredible stories like his possible.

Help make this happen, sign up at www.nycures.org/

Meet Beatrice Grauman, PhD student in the Vicković Lab at @nygenome.org 🌟. Her research explores tumor–microenvironment interactions and cancer evolution.
🎥Find out what inspires her outside the lab in our latest Faces of IICD feature
🔗 bit.ly/3K0Xidr
#FacesOfIICD #PhDLife #WomenInSTEM

Massive team effort. A huge thank you to the Ultima Genomics team, our clinical collaborators and sequencing team @nygenome.org
Look at the author list, it's huge! Takes a village. Super proud of trainees Aaron, Sam and Sri

Photo collage of Joel Joseph

Our intern spotlight continues with Joel Joseph, a CS + Data Science senior @arizonastate.bsky.social. Mentored by Dr. Sanja Vicković @nygenome.org, his research focuses on using computational tools to study tumor interactions in colorectal cancer. bit.ly/SRPQA2025 @columbiauniversity.bsky.social

Collage of Daniel Alshansky. Left: Daniel in a lab coat working with lab equipment at his bench. Top right: Daniel and Cody Slater in lab coats examining a sample together. Bottom right: Daniel seated, engaged in conversation with Joel Joseph.

Meet Daniel Alshansky, a rising junior studying Biology & Computer Science @hofstrau.bsky.social. At the @nygenome.org Vicković Lab, he’s developing new transcriptomic engineering tools to push the boundaries of genomic research. Read more: bit.ly/SRPQA2025

SRP and Alliance interns in front of the New York Genome Center sign

The SRP and Alliance interns had a great time touring the New York Genome Center this week! 🧬
Thanks to @nygenome.org for the warm welcome and an inside look at innovative research in action. #Genomics #SRP2025

NYGC Core Faculty Member @nevillesanjana.bsky.social presented at GEN bio’s “The State of CRISPR and Genome Editing” virtual summit. He spoke about CRISPR, the noncoding genome, & its potential to transform precision therapies.

For more on Dr. Sanjana’s work: bit.ly/43YshNC

Machine Learning in Computational Biology Youtube channel for the Machine Learning in Computational Biology conference.

Just under a week until the #MLCB2025 paper/abstract deadline on June 1st! In-person registration is full but you can join the wait list forms.gle/gnj6AAV7oWj6... or watch online at youtube.com/@mlcbconf. Sept 10-11 at @nygenome.org. Full deets at mlcb.org! Please RP.

Machine Learning in Computational Biology Youtube channel for the Machine Learning in Computational Biology conference: https://mlcb.github.io/

Free in-person registration is open for #MLCB2025! Sept 10-11 at @nygenome.org and online at youtube.com/@mlcbconf. Paper/abstract deadline is June 1, more deets including our fantastic invited speaker lineup at mlcb.org! Please RP.

Our next NYC Postdoc Night Science event will be June 2nd! We'll start off at @nygenome.org, then head to a bar to continue the conversation.
Register here to join us! docs.google.com/forms/d/1s9W...

Our new contribution to the quest to find causal GWAS genes! Sam Ghatan from my lab at @nygenome.org led a systematic comparison of eQTLs and CRISPRi+scRNA-seq screens. TL;DR: they provide highly complementary insights, with ortogonal pros and cons. 🧵👇
www.biorxiv.org/content/10.1...

Single Cell Genomics Day 2025 has begun! Join the live stream here: satijalab.org/scgd25

Join the Satija Lab for the seventh annual Single Cell Genomics Day on 4/25 — a free, one-day workshop featuring recent advances & practical insights in single cell genomics, designed for researchers at all levels.

All talks will be live-streamed via: satijalab.org/scgd25. Hope to see you there!

Error-corrected flow-based sequencing at whole-genome scale and its application to circulating cell-free DNA profiling - Nature Methods This work integrates duplex sequencing with cost-effective Ultima sequencing to enhance the accuracy of whole-genome circulating cell-free DNA profiling.

Adam Widman & collaborators at @nygenome.org led a study to evaluate a low-cost, error-corrected whole-genome sequencing method to detect cancer DNA & assess disease burden in individuals with melanoma and urothelial cancer. @mskcancercenter.bsky.social
www.nature.com/articles/s41...

New York Genome Center Receives $125 Million to Continue Operations Plus, the 1803 Fund pledged $75 million to Oregon groups that serve Black youths, and the Bezos Earth Fund and the Global Methane Hub will give $27.4 million to lower methane emissions through livesto...

The New York Genome Center will receive $125 million from Simons Foundation International and the Carson Family Charitable Trust to continue its operations through 2029.
phlnthrp.com/4jfRPfs

#grantsroundup

pC-SAC: A method for high-resolution 3D genome reconstruction from low-resolution Hi-C data Abstract. The three-dimensional (3D) organization of the genome is crucial for gene regulation, with disruptions linked to various diseases. High-throughpu

Super excited to share the first 3D genome paper from my lab @narjournal.bsky.social , led by my smart and hardworking student Carlos (joint with @LuLaboratory) with assists from a brilliant summer intern Narjis. (1/n) academic.oup.com/nar/article/...

Error-corrected flow-based sequencing at whole-genome scale and its application to circulating cell-free DNA profiling Nature Methods - This work integrates duplex sequencing with cost-effective Ultima sequencing to enhance the accuracy of whole-genome circulating cell-free DNA profiling.

What happens when sequencing costs go ⏬ ?
Imagination and new opportunities go ⏫
@landau.bsky.social

Let's look at what you can do when you perform deep WGS on cfDNA for cancer detection. Our recent work with the
@UltimaGenomics
platform 🧵👇
Lets goooo!!
rdcu.be/ehkUb

Our vision for Precision Omics Initiative Sweden (PROMISE) is now published in Nature Medicine! By boosting data-driven precision omics in Sweden, we can not only empower research but also integrate it with healthcare in a new way, with an impact in 🇸🇪 and 🌎. 🧵: rdcu.be/egmXY

A complex phylogeny of lineage plasticity in metastatic castration resistant prostate cancer - npj Precision Oncology npj Precision Oncology - A complex phylogeny of lineage plasticity in metastatic castration resistant prostate cancer

New publication from my @nygenome.org group, in close collaboration with @wcmenglanderipm.bsky.social colleagues Jones Nauseef, Juan-Miguel Mosquera!

A complex phylogeny of lineage plasticity in metastatic castration resistant prostate cancer

www.nature.com/articles/s41...