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Siyuan (Steven) Wang

@sstevenwang.bsky.social
43 followers 16 following 31 posts

Image-based spatial multi-omics. Associate Professor at Yale. NIH Director's New Innovator Awardee. MIT Technology Review 35 Innovators Under 35.

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Siyuan (Steven) Wang @sstevenwang.bsky.social · 25/09/2026
Thank you Professor Anna Woloszynska and colleagues at @roswellpark.bsky.social Roswell Park Comprehensive Cancer Center for inviting me to give a keynote lecture in the 6th Translational Genomics and Epigenomics Symposium!
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Siyuan (Steven) Wang @sstevenwang.bsky.social · 24/07/2026
Glad to share our latest publication in Science! This work reports: 🧬 the first single-cell 3D genome atlas of human tonsil and B cell immunity, 🧬 a new function for cohesin loop extrusion, and 🧬 a novel chromatin "curl" structure. www.science.org/doi/10.1126/...
science.org
A 3D genome atlas of human tonsil and the role of loop extrusion in B cell somatic hypermutation
B cell maturation within the germinal center tissue microenvironment involves immunoglobulin gene diversification by somatic hypermutation (SHM). How three-dimensional (3D) genome architecture influen...
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Siyuan (Steven) Wang @sstevenwang.bsky.social · 15/01/2026
Thank you the student union of the biochemistry department and Professor Ahilya Sawh @hilsawh.bsky.social of the University of Toronto for inviting me to present in the George Connell Lecture Series! It was so wonderful to meet and discuss science with colleagues and students in the esteemed UofT.
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Siyuan (Steven) Wang @sstevenwang.bsky.social · 02/12/2025
Thank you for offering this wonderful piece of News&Views introducing our work!
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Reposted by Siyuan (Steven) Wang
Guido Barzaghi @guidobarzaghi.bsky.social · 28/11/2025
Read our @natgenet.nature.com News&Views on the impressive work by @muzumdarlab.bsky.social and @sstevenwang.bsky.social. How does the 3D genome guide Kras-driven cancers evolution? Find out with single-cell genome-wide chromatin tracing! 📖https://rdcu.be/eShAY
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Siyuan (Steven) Wang @sstevenwang.bsky.social · 13/11/2025
Thank you Dian and Xuebing for inviting me to visit the Department of Systems Biology at Columbia. Such engaging and inspiring audience at the talk. It felt like everyone had asked at least one question by the end. Thank you all for having me and for this invigorating day of scientific exchanges!
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Siyuan (Steven) Wang @sstevenwang.bsky.social · 04/11/2025
Thank you!
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Siyuan (Steven) Wang @sstevenwang.bsky.social · 08/10/2025
Link to Yale News article about this work: news.yale.edu/2025/10/02/n...
news.yale.edu
New technique offers bigger and better window into RNA activity in complex tissue
Yale researchers have created a new tool that will enable researchers to better view how RNA molecules function in tissue space.
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Siyuan (Steven) Wang @sstevenwang.bsky.social · 08/10/2025
Check out our new RAEFISH spatial transcriptomics technology published in Cell! This work represents the first time that transcripts from more than 20,000 genes were directly imaged in situ with any technology, and the first time numerous gRNAs were directly probed in an image-based CRISPR screen.
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GenomeTDCC @genometdcc.org · 01/10/2025
New highlight video! 🧪🧬💻 RAEFISH from Steven Wang at Yale unlocks whole-transcriptome imaging at single-molecule resolution. See 20,000+ RNAs light up in cells and tissues. Plus get direct gRNA detection in high-content CRISPR screens. Spatial biology just leveled up www.youtube.com/watch?v=P2j6...
youtube.com
Sequencing-free whole-genome spatial transcriptomics at single-molecule resolution
YouTube video by GenomeTDCC
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Nature Genetics @natgenet.nature.com · 27/08/2025
🎉PUBLISHED @natgenet.nature.com 📰Tracing the evolution of single-cell 3D genomes in Kras-driven #cancers. By Miao Liu, @muzumdarlab.bsky.social, @sstevenwang.bsky.social and colleagues. ⬇️ www.nature.com/articles/s41...
nature.com
Tracing the evolution of single-cell 3D genomes in Kras-driven cancers - Nature Genetics
This study uses chromatin tracing to identify alterations in single-cell 3D genome conformation during the progression of Kras-driven mouse lung adenocarcinoma and pancreatic ductal adenocarcinoma, an...
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Reposted by Siyuan (Steven) Wang
Yale Cancer Center @yalecancer.bsky.social · 19/08/2025
New @natgenet.nature.com study from @muzumdarlab.bsky.social + @sstevenwang.bsky.social maps 3D genomes in KRAS-driven lung & pancreatic #cancer, revealing stage-specific changes + potential biomarkers. ➡️ yalecancercenter.org/news-article...
yalecancercenter.org
Cancer's Progress Detailed by 3D Genomic Maps
Using new technology, Yale researchers examine cancer progression in single cells to visualize and understand its evolution from pre-cancerous to advanced
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Siyuan (Steven) Wang @sstevenwang.bsky.social · 19/08/2025
Such a pleasure collaborating with you and your lab too, Mandar! Cheers!
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Siyuan (Steven) Wang @sstevenwang.bsky.social · 19/08/2025
Link to YSM News article about this work: medicine.yale.edu/news-article... 12/12
medicine.yale.edu
Cancer's Progress Detailed by 3D Genomic Maps
Using new technology, Yale researchers examine cancer progression in single cells to visualize and understand its evolution from pre-cancerous to advanced
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Siyuan (Steven) Wang @sstevenwang.bsky.social · 19/08/2025
Link to paper: www.nature.com/articles/s41... 11/12
nature.com
Tracing the evolution of single-cell 3D genomes in Kras-driven cancers - Nature Genetics
This study uses chromatin tracing to identify alterations in single-cell 3D genome conformation during the progression of Kras-driven mouse lung adenocarcinoma and pancreatic ductal adenocarcinoma, an...
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Siyuan (Steven) Wang @sstevenwang.bsky.social · 19/08/2025
This work was done in collaboration with my @yaleschoolofmed.bsky.social colleague Professor Mandar Muzumdar @muzumdarlab.bsky.social and co-led by Drs. Miao Liu, Shengyan Jin, and Sherry Agabiti. Congrats to all authors! Also thank you National Cancer Institute for funding this work! 10/12
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Siyuan (Steven) Wang @sstevenwang.bsky.social · 19/08/2025
We expect that applying these approaches broadly will have an enormous impact on understanding the epigenetic basis of cancer in situ and will lead to the development of novel diagnostic, prognostic, and therapeutic biomarkers based on the 3D genome. 9/12
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Siyuan (Steven) Wang @sstevenwang.bsky.social · 19/08/2025
Our work also establishes a series of experimental and analytic methodologies (e.g., Trace2State, Trace2Biomarker, Trace2Regulator), allowing adaptation of these pipelines by the research community to study many other types of cancer and biological systems. 8/12
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Siyuan (Steven) Wang @sstevenwang.bsky.social · 19/08/2025
Overall, our work charts a comprehensive blueprint of 3D genome alterations during cancer progression in the native tissue context and systematically demonstrates how this rich resource can provide novel biological insights and potential biomarkers. 7/12
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Siyuan (Steven) Wang @sstevenwang.bsky.social · 19/08/2025
4) A new way to discover novel 3D genome regulatory genes in cancer, which can also serve as potential therapeutic targets. 6/12
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Siyuan (Steven) Wang @sstevenwang.bsky.social · 19/08/2025
3) A new 3D genome function, as our data reveal that cancer genes associated with 3D compartment changes are more stably regulated than non-compartment-regulated genes. 5/12
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Siyuan (Steven) Wang @sstevenwang.bsky.social · 19/08/2025
2) The utility of 3D genome mapping in better discovering prognostic and predictive biomarkers – uncovering novel candidate progression driver genes associated with patient survival as potential therapeutic targets. 4/12
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Siyuan (Steven) Wang @sstevenwang.bsky.social · 19/08/2025
1) Surprisingly nonmonotonic, stage-specific alterations in global 3D genome folding heterogeneity, compactness, and compartmentalization as cancers progress from normal to preinvasive to invasive tumors, elucidating an unexpected 3D genome structural bottleneck during early cancer progression. 3/12
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Siyuan (Steven) Wang @sstevenwang.bsky.social · 19/08/2025
Particularly, we further developed a single-cell, genome-wide chromatin tracing method for applications to lung, pancreas, and cancer tissues. We applied our method to faithful autochthonous murine models of lung and pancreatic cancers that mimic the cognate human cancers. Our data revealed: 2/12
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Siyuan (Steven) Wang @sstevenwang.bsky.social · 19/08/2025
Glad to share our latest publication in Nature Genetics: Tracing the evolution of single-cell 3D genomes in Kras-driven cancers. In this work, we generated the first single-cell 3D genome atlases of any cancer using any technique. 1/12
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Siyuan (Steven) Wang @sstevenwang.bsky.social · 09/08/2025
Check out this new video highlighting our lab :-) Thank you @yaleschoolofmed.bsky.social Video Team for the production! m.youtube.com/watch?v=p-hE...
m.youtube.com
Genome Architectures & Spatial Transcriptomics - The Siyuan Wang Lab at Yale School of Medicine
YouTube video by Yale Medicine
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Siyuan (Steven) Wang @sstevenwang.bsky.social · 08/08/2025
Thank you @genometdcc.bsky.social and the National Human Genome Research Institute for inviting me to present this introductory lecture to the public at the Genomic Technologies Open Science Day 2025!
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GenomeTDCC @genometdcc.org · 30/07/2025
How does 6ft of #DNA fit inside a cell only 10 microns wide? @sstevenwang.bsky.social provides a brief history of contemporary 3D #genomics technologies. Learn how spatial organization of DNA plays a vital role in gene regulation, development, and disease. 🧬🖥️🧪 #STS www.youtube.com/watch?v=gXCO...
youtube.com
A Brief History of Contemporary 3D Genomics Technologies
YouTube video by GenomeTDCC
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Siyuan (Steven) Wang @sstevenwang.bsky.social · 26/06/2025
Introducing Epi-PHR, the first non-disruptive, high-genomic-resolution, image-based epigenetic profiling method. Allelic Epi-PHR generates the first single-cell phased examination of histone mark deposition and 3D genome architecture at an imprinted locus by any technique. 1/8
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Siyuan (Steven) Wang @sstevenwang.bsky.social · 26/06/2025
We expect Epi-PHR will find broad application in diverse biological and medical contexts. Link to our preprint: www.biorxiv.org/content/10.1... 8/8
biorxiv.org
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Siyuan (Steven) Wang @sstevenwang.bsky.social · 26/06/2025
Surprisingly, we found among the maternal copies of this locus, the relationship between the histone mark and a chromatin domain boundary is opposite to what one would expect. This surprising finding was uniquely enabled by Epi-PHR. 7/8
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Siyuan (Steven) Wang @sstevenwang.bsky.social · 26/06/2025
Finally, we developed allelic Epi-PHR and combined it with fine-scale chromatin tracing to simultaneously profile histone mark deposition and chromatin folding at an imprinted genomic locus with parent-of-origin specificity. 6/8
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Siyuan (Steven) Wang @sstevenwang.bsky.social · 26/06/2025
We first demonstrated Epi-PHR's sensitivity at small genomic targets of 2 kb. We further showcased multiplexed Epi-PHR to profile combinations of epigenetic marks at 200 genes in the same single cells in culture and tissue. 5/8
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Siyuan (Steven) Wang @sstevenwang.bsky.social · 26/06/2025
1) can simultaneously profile more than one histone modification and chromatin associated protein at numerous genomic loci with high genomic resolution, 2) is non-disruptive and retains 3D chromatin architecture, and 3) inherently provides single-cell and in situ information. 4/8
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Siyuan (Steven) Wang @sstevenwang.bsky.social · 26/06/2025
To address the limitations, we developed Epigenetic Proximity Hybridization Reaction (Epi-PHR), an imaging-based technology that represents the first epigenetic profiling method that: 3/8
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Siyuan (Steven) Wang @sstevenwang.bsky.social · 26/06/2025
In eukaryotes, epigenetic states and 3D chromatin folding are critical regulators of many genomic functions. While these mechanisms are known to be closely interlinked, studying their relationship remains challenging due to technical limitations. 2/8
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Siyuan (Steven) Wang @sstevenwang.bsky.social · 26/06/2025
Introducing Epi-PHR, the first non-disruptive, high-genomic-resolution, image-based epigenetic profiling method. Allelic Epi-PHR generates the first single-cell phased examination of histone mark deposition and 3D genome architecture at an imprinted locus by any technique. 1/8
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