Our December newsletter is live! Dive into fresh research from the Dinh and Azizi groups, an opinion article by the Vickovic lab, introductions to new members, upcoming events, and more. Check it out: cancerdynamics.columbia.edu/news/iicd-ne...

#CancerImmuno speaker list is live!📢 Join us in sunny Lisbon, July 2026. Register now and submit your talk to share your research. Early Bird Deadline: 15 Jan 2026 👉 Click here to register: bit.ly/4qZVqmd #FusionImmunology #FusionCancerResearch

New paper out in @natmethods.nature.com from @elhamazizi.bsky.social, Kam Leong & @jameszou.bsky.social! The team developed Squidiff, a diffusion #AI model to predict cellular responses to environmental cues and accelerate #PrecisionMedicine. Learn more: bit.ly/3WRPNsx

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

Please share🔉 We’re #hiring #AI #Engineers @columbiaseas.bsky.social @cancerdynamics.bsky.social 🚀Join us to build foundation models that learn & reason about cancer systems, integrating #LLMs #causalAI and multi-modal #genomics. Shape the next-generation of cancer therapies! tinyurl.com/5n7wp8ck

Incredible work led by Pierre Boyeau and @justjhong.bsky.social 👏👏👏

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

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

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...

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.

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 💥.

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!

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

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

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

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

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!

🎉 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

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

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!

🎥 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

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

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!

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

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

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!

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 👇

🎓 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-...

#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...

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

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

This!!! I hope someone in Washington is listening www.wsj.com/tech/biotech...

🎓 Congrats to Dr. Cameron Park ( @elhamazizi.bsky.social Lab) on a successful defense! On March 31st, she presented her dissertation on ML + multi-omics for immunotherapy response modeling! 👏 cc: @columbiaseas.bsky.social #IICDNews #PhDDefense #ComputationalBiology #MachineLearning

📚The IICD Monthly Research Meeting was a success! Maithê de Barros (Tavaré lab) and @mingxz.bsky.social from @elhamazizi.bsky.social lab delivered fascinating talks on gastric epithelial cells and machine learning in cancer research.

Don’t miss out on this very timely webinar series!

Announcing the Computational Spatial Biology seminar! With Nathan Levy (Yosef Lab), we’re bringing together researchers at the intersection of AI & spatial biology to share their work. Kicking off April 9th with Yist Yu presenting LUNA! Explore the lineup here: csbseminar.github.io

Wow. "NIH" canceled my co-mentored (with Dave Sulzer) PhD student's F31 funding. His work is on understanding the genetics and neuroscience of language learning disorders. F31 provides no indirect $ to Columbia, just pays his salary. Not that it should matter, but he's an American citizen. W.T.F.

Friends, I am at a loss of words for how devastating it would be to lose the entire intramural #NIH program. Some of the biggest medical and scientific breakthroughs have come from scientists in the NIH Intramural program. #SaveTheNIH 🧬🧪 🖥️ 🧠 www.science.org/content/arti...

Studies show that funding from the National Institutes of Health (NIH) contributed to 354 of 356 drugs (99.4%) approved by the FDA from 2010 to 2019. Recklessly slashing NIH funding will mean that patients will be waiting much longer for life-saving treatments.

We have to stand up for science! Anyone who can join these rallies and believes that US science must be protected should come! @standupforscience.bsky.social

ATTENTION (PLEASE SHARE) If anyone has or knows of any positions that might be appropriate for the NIH staff members who were terminated, please post the information in this thread. There are lots of talented and accomplished people who may be looking for new opportunities.

American science is under attack Opinion piece by Dr Harold Varmus, Nobel Prize winner, former director of the #NIH and the #NCI 🧪 “Perhaps what’s most disheartening is what feels like the absence of widespread opposition to this unraveling” www.nytimes.com/2025/02/14/o...

Happy International Day of Women and Girls in Science! @elhamazizi.bsky.social, Marianne Bronner, and Maayan Levy were awarded the Vilcek Prizes in Biomedical for their breakthroughs in neural crest stem cell research and cancer and long COVID treatments. Read about their work: vilcek.co/40VBwfE

Thrilled to introduce #CORAL🪸—a deep probabilistic graphical model that integrates spatial multiomics data! 🔹Resolves spatial resolution discrepancies across modalities 🔹Deconvolutes low-res data to achieve single-cell granularity 🔹Enables parallel integrative analysis 1/🪸

A full attack on US science means the red & blue lines will soon cross. Scientists just want science to progress to help society. This administration - and "Pres Musk" - is telling us they don't need/want US science. We will see many of our great ideas and innovation will go to China and elsewhere

This will kill science in the US. This is how China wins. Why is this not on the news? Why are people not more upset about this? grants.nih.gov/grants/guide...

This is catastrophic for US research universities as it ignores the real cost of doing research. The US academic-gov’t partnership forged post-WWII is the greatest creator of knowledge in history and is critical to US economic and technological competitiveness.

[SAVE THE DATE] MLCB 2025 is happening Sept 10-11 at the NY Genome Center in NYC! Attend the premier conference at the intersection of ML & Bio, share your research and make lasting connections! Submission deadline: June 1 More details: mlcb.github.io Help spread the word—please RT! #MLCB2025

New: The largest medical A.I. randomized controlled trial yet performed, enrolling >100,000 women undergoing mammography screening The use of AI led to 29% higher detection of cancer, no increase of false positives, and reduced workload compared with radiologists w/o AI thelancet.com/journals/lan...

Congratulations to @elhamazizi.bsky.social , recipient of the 2025 Vilcek Prize for Creative Promise in Biomedical Science. The @vilcekfoundation.bsky.social Award celebrates the contributions of immigrant artists and scientists in the U.S. www.engineering.columbia.edu/about/news/e...