Lightnews — Scholar-powered news

Reposted by Elham Azizi

Irving Institute for Cancer Dynamics @cancerdynamics.bsky.social · 22h

We are highlighting the work of IICD scientists advancing our understanding of breast cancer. Their research, along with collaborative efforts across Columbia, continues to drive progress toward more precise and effective breast cancer treatments: bit.ly/4pHt8MD
#BreastCancerAwareness

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Elham Azizi @elhamazizi.bsky.social · 10d

The #AMICI 🤝 tutorial is out! Bringing #attention to #cellcellcommunication 🚨👉 amici-st.readthedocs.io/en/latest/
#spatialtranscriptomics #compbio #machinelearning

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Reposted by Elham Azizi

Allen Institute @alleninstitute.org · 12d

How do sex hormones influence organ development?

ADIs Mijo Simunovic, @elhamazizi.bsky.social, and José L. McFaline-Figueroa are searching for the answers by making an in-vitro platform that combines stem cells, genome editing, and AI. #FrontierScience

🔗 alleninstitute.org/division/fro...

Sex hormone morphogenesis: a new frontier in studying organ development

In this project, researchers will develop an in vitro platform that combines stem cell models of human development, high-throughput genome editing at the single cell level, and novel machine learning ...

alleninstitute.org

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Reposted by Elham Azizi

Khushi Desai @khushipde.bsky.social · 14d

14/ To put a cherry on top, AMICI discovered a spatial population of CD8 T cells influencing Invasive tumor cells towards ER-dependence (beyond known intrinsic cell cycles ‼️), explaining worse prognosis for immune-infiltrated ER+ tumors.

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Reposted by Elham Azizi

Khushi Desai @khushipde.bsky.social · 14d

11/ When we brought even more complexity with a Xenium breast cancer sample, AMICI presented a complex story 📖of CD4 T cell-driven activation of CD8 T cells as well as M1 → M2 macrophage polarization driven by Invasive tumor cells 💥.

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Elham Azizi @elhamazizi.bsky.social · 13d

Extremely proud of @justjhong.bsky.social @khushipde.bsky.social for bringing this innovation to life! #AMICI🤝 redefines #attention for cell–cell interaction inference from #spatial #transcriptomics going beyond proximity to capture who talks to whom, at what distance and w/ what downstream impact!

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Elham Azizi @elhamazizi.bsky.social · 22d

We are #hiring for an exciting campus-wide collaborative effort! 📢 See the first position below for large-scale #CRISPR perturbation screens! #cancerresearch @cancerdynamics.bsky.social @columbiaseas.bsky.social

José L. McFaline-Figueroa @jlmcfalinefigueroa.bsky.social · 22d

Please share!

The Irving Institute for Cancer Dynamics and the Fu Foundation School of Engineering & Applied Science at Columbia are seeking an Associate Research Scientist to design & execute pooled CRISPR and Perturb-seq screens. Apply here: apply.interfolio.com/172825

Apply - Interfolio {{$ctrl.$state.data.pageTitle}} - Apply - Interfolio

apply.interfolio.com

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Reposted by Elham Azizi

José L. McFaline-Figueroa @jlmcfalinefigueroa.bsky.social · 22d

Please share!

The Irving Institute for Cancer Dynamics and the Fu Foundation School of Engineering & Applied Science at Columbia are seeking an Associate Research Scientist to design & execute pooled CRISPR and Perturb-seq screens. Apply here: apply.interfolio.com/172825

Apply - Interfolio {{$ctrl.$state.data.pageTitle}} - Apply - Interfolio

apply.interfolio.com

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Reposted by Elham Azizi

Nature Portfolio @natureportfolio.nature.com · 28d

Attention early-career researchers focusing on GI & inflammatory diseases, #neuroscience or oncology: apply by Sept 16 for the Takeda Innovators in Science Award with Nature and join the previous winners. #Academicsky #GISky #medsky go.nature.com/4jBp3oM

Shruti Naik, PhD, Icahn School of Medicine at Mount Sinai
Recognized for helping advance therapeutic
strategies for ailments such as psoriasis,
chronic wounds, and cancer.

Elham Azizi, PhD, Columbia University
Recognized for cutting-edge work in applying AI to help unravel the complexities of the tumor microenvironment

Elaine Y. Hsiao, PhD, University of California, Los Angeles
Recognized for reshaping conventional thinking about the influence of the gut microbiome on the brain and behavior.

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Reposted by Elham Azizi

Fusion Conferences @fusionconf.bsky.social · 29d

Don't forget to secure your place at our new conference!
Cancer Immunology: Across Space & Time
📅Date: 10 Jul - 13 Jul 2026
🌏Location: Lisbon, Portugal
📢Early Bird & Talk Submission: 15th January 2026
Don't miss out, Register now: bit.ly/3IdEwii
#CancerImmuno #FusionImmunology #FusionCancerResearch

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Reposted by Elham Azizi

Irving Institute for Cancer Dynamics @cancerdynamics.bsky.social · Sep 4

Our first IICD Monthly Research Meeting of the semester was a success! 🔬Jun Won Park (Rane): Spatiodynamic Inference using Vision-Based Generative Modelling
🧬Aaron Zweig (Azizi/Knowles): Inferring Cell Trajectory with Flow Matching
Excited for a semester of inspiring talks!

Aaron Zweig speaking in front of an audience

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Reposted by Elham Azizi

scverse @scverse.bsky.social · Aug 2

🎉 scverse conference 2025 Registration & Call for Abstracts NOW OPEN! 🎉
We're excited to announce that registration and the call for abstracts are officially open for the scverse Conference 2025!
Details in thread!
🧵 1/3

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Reposted by Elham Azizi

scverse @scverse.bsky.social · Aug 28

Meet the keynote speakers for the 2025 scverse conference!

Elham Azizi, Associate Professor of Cancer Data Research and Biomedical Engineering at Columbia University
🧵

@elhamazizi.bsky.social
@columbiauniversity.bsky.social

#scverse #scverse2025 #machinelearning #genomics #cancerimmunology

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Elham Azizi @elhamazizi.bsky.social · Aug 7

The greatest joy of academia is the opportunity to work alongside phenomenally talented rising stars: @lingting-shi.bsky.social @mingxz.bsky.social Aaron Zweig and many more not pictured here ☺️ Thank you @cancerdynamics.bsky.social for supporting us!

Irving Institute for Cancer Dynamics @cancerdynamics.bsky.social · Aug 7

🎥 BTS from our #JSM2025 film shoot!
Yesterday we shared the final cut—today, we’re rewinding to those candid behind-the-scenes moments 🎬
Thank you to the @websedgescience.bsky.social sEdgeScience crew for capturing our work so thoughtfully!
#CancerGenomics #ScientificStorytelling

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Reposted by Elham Azizi

Irving Institute for Cancer Dynamics @cancerdynamics.bsky.social · Aug 7

🎥 BTS from our #JSM2025 film shoot!
Yesterday we shared the final cut—today, we’re rewinding to those candid behind-the-scenes moments 🎬
Thank you to the @websedgescience.bsky.social sEdgeScience crew for capturing our work so thoughtfully!
#CancerGenomics #ScientificStorytelling

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Reposted by Elham Azizi

Irving Institute for Cancer Dynamics @cancerdynamics.bsky.social · Aug 5

New paper from @elhamazizi.bsky.social, @bleilab.bsky.social & @danapeer.bsky.social labs: Decipher, a deep generative model to track disease trajectories in single-cell data.
📖 Read: bit.ly/4mufVnZ @columbiaseas.bsky.social @columbiacancer.bsky.social @mskcancercenter.bsky.social

Joint representation and visualization of derailed cell states with Decipher - Genome Biology

Biological insights often depend on comparing conditions such as disease and health. Yet, we lack effective computational tools for integrating single-cell genomics data across conditions or character...

bit.ly

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Reposted by Elham Azizi

José L. McFaline-Figueroa @jlmcfalinefigueroa.bsky.social · Jul 10

Wondeful collaboration! This study with the Shah lab (Columbia Chemistry), led by Anne Vlimmeren and Ross Giglio, profiled disease associated SHP2 variants, linking variant-specific changes in molecular programs with differences in structure and substrate specificity. Check it out!

Neel Shah @nshahlab.bsky.social · Jul 3

Check out our latest preprint, from Anne van Vlimmeren in my group and Ross Giglio in @jlmcfalinefigueroa.bsky.social's lab. We used single-cell transcriptomics, biochemistry, and structural analysis, to reveal how mechanistically distinct SHP2 disease mutations yield different cellular states.

bioRxiv Molecular Biology @biorxiv-molbio.bsky.social · Jul 3

Multiplexed single-cell transcriptomics reveals diverse phenotypic outcomes for pathogenic SHP2 variants https://www.biorxiv.org/content/10.1101/2025.06.30.662374v1

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Elham Azizi @elhamazizi.bsky.social · Jul 8

Thank you to all attendees, speakers, instructors, TAs and ‪@cancerdynamics.bsky.social staff for another successful workshop!

Irving Institute for Cancer Dynamics @cancerdynamics.bsky.social · Jul 2

That’s a wrap on the second 2025 IICD Intensive Workshop! Thank you to all our incredible participants, speakers, and organizers for a week full of learning, collaboration, and new ideas in probabilistic data integration, spatial technologies, & optimal transport. cc: @elhamazizi.bsky.social

Photo collage of the 2025 IICD Intensive Workshop

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Reposted by Elham Azizi

Irving Institute for Cancer Dynamics @cancerdynamics.bsky.social · Jun 5

Congrats to IICD postdoc Aaron Zweig (@elhamazizi.bsky.social and @davidaknowles.bsky.social groups), awarded the prestigious Damon Runyon Quantitative Biology Fellowship @damonrunyon.org—one of only five granted this year! 🔗 bit.ly/3TeK7GQ #CancerResearch #QuantBio

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Elham Azizi @elhamazizi.bsky.social · May 29

Thrilled to share our latest work led by brilliant @lingting-shi.bsky.social with Ajna, Kevin, Ran Reshef lab tinyurl.com/594nru9b
A spatiotemporal atlas of human alloreactive T cells during #GVHD + new 💻 tools revealed T cell clones shift phenotype as they migrate in tissue contributing to injury!

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Reposted by Elham Azizi

Lingting Shi @lingting-shi.bsky.social · May 29

I just presented my work at the @keystonesymposia.bsky.social Single Cell Biology-where we tracked how human T cells evolve across time and space during #GVHD. And it changes everything.
💡 It’s not just infiltration—T cells adapt and shift phenotype as they migrate through tissue.
bioarxiv link 👇

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Reposted by Elham Azizi

Irving Institute for Cancer Dynamics @cancerdynamics.bsky.social · May 28

🎓 Congrats to Dr. @jlfan.bsky.social (@elhamazizi.bsky.social group) on receiving the Yuen-huo and Chao-chin Huang Award in Biomedical Engineering from @columbiaseas.bsky.social! The award honors her leadership and research excellence. 👏
🔗 www.bme.columbia.edu/celebrating-...

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Reposted by Elham Azizi

The Data Science Institute at Columbia University @datascicolumbia.bsky.social · Apr 25

#ColumbiaAI update: @columbiauniversity.bsky.social Data Science Institute Member @elhamazizi.bsky.social spoke at a recent @whiteheadinstitute.bsky.social symposium about how AI is advancing biomedical discovery.

Read more about the event: wi.mit.edu/news/ai-adva...

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Reposted by Elham Azizi

Irving Institute for Cancer Dynamics @cancerdynamics.bsky.social · Apr 14

Say hello to our new Alliance Intern, Mathias Perez from @polytechniqueparis.bsky.social! 👋 Working with @elhamazizi.bsky.social, Mathias explores zero-shot methods for single-RNA sequencing analysis and has interests in medical imaging. Welcome to the team! 🧬
#ColumbiaUniversity #AIinBiology

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Reposted by Elham Azizi

Science Magazine @science.org · Apr 9

Exclusive: Weeks after President Donald Trump’s administration ordered NIH to pull $250 million in biomedical research grants to Columbia University, the agency is freezing all remaining grant money owed to the university until further notice. scim.ag/4if5Rg1

NIH freezes all research grants to Columbia University

Amid negotiations with Trump, the university could risk losing nearly $700 million

scim.ag

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