Soobeom Lee

Excited to share our latest work. Applying advanced single-molecule and single-cell DNA sequencing methods, we uncover an extraordinary landscape of somatic mutations in immune checkpoint genes in autoimmune lymphocytes. [1/n] rdcu.be/fdqbr

Excited to share our new paper in @NatureGenet led by the incredible @6jinLee! We uncover how cohesin loss impairs postmitotic refolding of 3D chromatin topology with limited context-specific effects on gene activation—especially during differentiation. nature.com/articles/s4158…

We’re unwrapping a new method today @MSKCancerCenter! Led by @SydneyBlattman, @NabihMaslah, @AustinAVarela, Ronan Chaligne and @dana_peer, plus colleagues at @10xGenomics, we’re delighted to share Genotyping In Fixed Transcriptomes (GIFT): biorxiv.org/content/10.648… 1/n

Pleased to share the beta release of Signac v2 today. This release makes some important changes, including support for BPCells matrices for large-scale analysis. Documentation can be found here: stuartlab.org/signac2/

⚠️ If you’re reading this, you’ve been infected* ⚠️ *~95% the human population has been infected by the Epstein-Barr Virus (EBV). Today in @Nature with @nyeo_sherry, @EMC22381830, @RyanDhindsa @SlavePetrovski, we shed some light on what happens next. nature.com/articles/s4158…

@CalebLareau @Nature @nyeo_sherry @EMC22381830 @RyanDhindsa @SlavePetrovski Huge congrats man! I and my colleagues was talking about how much harder it is to actually discover something than to build a new tool or generate data. It’s really impressive that every paper from you and your team brings new biological discoveries and has such eminent impacts!

How STABLE is chromosomal INSTABILITY? We followed copy numbers over years in colorectal cancer patients. Chromosomal instability is high at single cell level, but does not manifest macroscopically, suggesting negative selection of karyotypes: doi.org/10.1158/2159-8…

Spatial 5mC-seq profiling of embryos and decidua after implantation in mammal biorxiv.org/content/10.648… #biorxiv_genomic

How does the evolution of the cancer epigenome contribute to immune evasion? We investigated this in colorectal cancer, where we found that immune evasion follows a ‘Big Bang’ evolutionary pattern, initiated right at transformation: nature.com/articles/s4158…

.@NatureGenet paper by @BizarMd @columbiacancer Cellular states associated with metastatic organotropism & survival in patients with #PancreaticCancer “pre-existing cellular states within primary tumors appear to guide organ-specific metastatic relapse” nature.com/articles/s4158…

Super excited re: first Shendure/Baker Lab collaboration & preprint on a multiplex sequencing-based strategy for screening de novo proteome editors in mammalian cells. Kudos to brilliant Chase Suiter & @Green_Ahn @UWproteindesign on the work! Preprint: biorxiv.org/content/10.110…

Out today the last piece of work that Maria Guillamot did in our lab in a collaboration with @AWeinstock and @DrShrutiNaik (who lead the study) showing type I interferon (IFN)-mediated activation of hematopoietic stem/progenitor cells resulting in profound changes to systemic host responses...such studies could impact the way that we connect inflammation, autoimmunity to hematopoietic stem cell biology, differentiation and dysfunction... academic.oup.com/jimmunol/artic…

Big, beautiful trees!! SMART-PTA for whole-genome+transcriptome on thousand of single cells from the normal human esophagus 🤯 Massively scaling up the power of scWGS to build deep phylogenies and chart somatic evolution from birth throughout life. biorxiv.org/content/10.110…

1/ 🧵Happy to share our preprint from @WJGreenleaf’s Lab: beCasKAS, our method to directly detect #CRISPR base editor off-targets in primary cells. We additionally show how non-coding edits can be triaged for epigenetic dysregulation using deep learning. biorxiv.org/content/10.110…

We’re back! Registration is NOW OPEN for the 6th Annual Meeting on Advances in Nuclear Topology & 3D Chromatin Architecture in Cancer. Don’t miss insights from leading experts in the field. Join us online on Nov 25, 2025—register for free: #chromatin2025" target="_blank" rel="nofollow noopener">bit.ly/chromatin-2025…

Highly accurate sequencing OR high throughput? We refuse to choose. Introducing paired plus-minus sequencing (ppmSeq), a method built to deliver both. Our latest paper with @UltimaGenomics 👀👀👀 See ⬇️ for a primer on the next frontier of genomics biorxiv.org/content/10.110…

🧨Exciting new pre-print! Introducing ppmSeq - cost effective, scalable dual-strand 🧬 sequencing. Scalability & ultra-low error in one! A game changer for somatic genome discovery science and cfDNA clinical apps. Check out thread for deets! @AlexandrePCheng @UltimaGenomics

The IICD SRP is wrapping up soon! Yesterday, our interns presented their research at the Columbia CUPP Symposium. Huge thanks for organizing an incredible event! cc: @shi_lingting @elhamazizi @mssanjavickovic @khanh_n_dinh @DarcyPeterka @Genevera_Allen @joselmcfaline @soobeomlee

I'm excited to share work on a research direction my team has been advancing: connecting machine learning derived genetic variant embeddings to downstream tasks in human genetics. This work was led by the amazing @divyanshi91! biorxiv.org/content/10.110…

@ewang2323 @Cuijuan3 Congrats Eric!

🧵1/ Thrilled to share our lab’s first paper, just out in @BloodCancerDisc led by the talented @Cuijuan3 We uncovered an isoform-specific RUNX1C–BTG2 axis that drives chemoresistance in AML. 👉 aacrjournals.org/bloodcancerdis…