Elham Azizi
@elhamazizi.bsky.social
Computational Cancer Biology azizilab.com
Irving Associate Professor @Columbia
#compbio #ml #genomics #singlecell #cancerimmunology
Irving Associate Professor @Columbia
#compbio #ml #genomics #singlecell #cancerimmunology
Reposted by Elham Azizi
#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
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
November 17, 2025 at 3:55 PM
#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
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
Reposted by Elham Azizi
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
Learn more: bit.ly/3WRPNsx
November 10, 2025 at 1:59 PM
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
Learn more: bit.ly/3WRPNsx
Reposted by Elham Azizi
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
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
November 6, 2025 at 3:59 PM
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
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
@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
October 24, 2025 at 2:37 PM
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
@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 👏👏👏
MrVI, based on deep generative modeling, is a unified framework for integrative, exploratory, and comparative analyses of large-scale (multi-sample) single-cell RNA-seq datasets. @justjhong.bsky.social @canergen.bsky.social @elhamazizi.bsky.social
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Deep generative modeling of sample-level heterogeneity in single-cell genomics - Nature Methods
MrVI, based on deep generative modelling, is a unified framework for integrative, exploratory and comparative analyses of large-scale (multi-sample) single-cell RNA-seq datasets.
www.nature.com
October 14, 2025 at 4:52 PM
Incredible work led by Pierre Boyeau and @justjhong.bsky.social 👏👏👏
Reposted by Elham Azizi
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
#BreastCancerAwareness
October 8, 2025 at 1:23 PM
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
#BreastCancerAwareness
The #AMICI 🤝 tutorial is out! Bringing #attention to #cellcellcommunication 🚨👉 amici-st.readthedocs.io/en/latest/
#spatialtranscriptomics #compbio #machinelearning
#spatialtranscriptomics #compbio #machinelearning
September 28, 2025 at 2:46 PM
The #AMICI 🤝 tutorial is out! Bringing #attention to #cellcellcommunication 🚨👉 amici-st.readthedocs.io/en/latest/
#spatialtranscriptomics #compbio #machinelearning
#spatialtranscriptomics #compbio #machinelearning
Reposted by Elham Azizi
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...
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
September 26, 2025 at 10:09 PM
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...
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...
Reposted by Elham Azizi
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.
September 25, 2025 at 2:06 AM
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.
Reposted by Elham Azizi
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 💥.
September 25, 2025 at 2:06 AM
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!
September 25, 2025 at 1:39 PM
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
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
September 16, 2025 at 4:48 PM
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
Reposted by Elham Azizi
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
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
September 16, 2025 at 3:02 PM
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
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
Reposted by Elham Azizi
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
September 10, 2025 at 5:21 PM
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
Reposted by Elham Azizi
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
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
September 10, 2025 at 10:27 AM
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
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
Reposted by Elham Azizi
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 (Azizi/Knowles): Inferring Cell Trajectory with Flow Matching
Excited for a semester of inspiring talks!
September 4, 2025 at 3:09 PM
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 (Azizi/Knowles): Inferring Cell Trajectory with Flow Matching
Excited for a semester of inspiring talks!
Reposted by Elham Azizi
🎉 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
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
August 2, 2025 at 3:00 PM
🎉 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
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
Reposted by Elham Azizi
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
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
August 28, 2025 at 3:04 PM
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
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
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
August 7, 2025 at 4:17 PM
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!
Reposted by Elham Azizi
🎥 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
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
August 7, 2025 at 3:58 PM
🎥 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
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
Reposted by Elham Azizi
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
📖 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
August 5, 2025 at 4:11 PM
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
📖 Read: bit.ly/4mufVnZ @columbiaseas.bsky.social @columbiacancer.bsky.social @mskcancercenter.bsky.social
Reposted by Elham Azizi
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!
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.
Multiplexed single-cell transcriptomics reveals diverse phenotypic outcomes for pathogenic SHP2 variants https://www.biorxiv.org/content/10.1101/2025.06.30.662374v1
July 10, 2025 at 4:51 PM
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!
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
July 8, 2025 at 3:48 PM
Thank you to all attendees, speakers, instructors, TAs and @cancerdynamics.bsky.social staff for another successful workshop!
Reposted by Elham Azizi
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
June 5, 2025 at 4:20 PM
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!
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!
May 29, 2025 at 6:18 PM
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!
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!