Azizi Lab @ Columbia

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​COMPUTATIONAL CANCER BIOLOGY LABORATORY

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​Our vision is to combine rigorous machine learning, statistics, genomics, and bioengineering techniques to derive principles of cancer initiation, progression, and response or resistance to immunotherapies, directly from patient specimens. Our interdisciplinary research involves developing novel probabilistic and deep generative models and utilizing cutting-edge single-cell genomic and imaging technologies, to characterize complex populations of interacting cells in the tumor microenvironment, as well as their spatial and temporal dynamics and underlying circuitry.

Our lab is primarily affiliated with the Biomedical Engineering Department and the Irving Institute for Cancer Dynamics (IICD) at Columbia University. We are also affiliated with the Computer Science Department, Data Science Institute and the Herbert Irving Comprehensive Cancer Center.  Our work is supported by funding from the NIH National Human Genome Research Institute, the NIH National Cancer Institute, the NSF, and the Chan Zuckerberg Initiative.

News

2025
  • "Joint representation and visualization of derailed cell states with Decipher" led by Achille and Joy accepted for publication in Genome Biology.
  • Dr. Joy Fan and Dr. Cameron Park successfully defended their PhD dissertations! 
  • Elham receives the Vilcek Prize for Creative Promise in Biomedical Science
  • Cameron's paper "Coordinated immune networks in leukemia bone marrow microenvironments distinguish response to cellular therapy" in collaboration with Shouvik and the Wu Lab published in Science Immunology.
2024
  • Joy and Ming's preprint "Echidna: A Bayesian framework for quantifying gene dosage effect impacting phenotypic plasticity" in collaboration with Will, Josh, Isha and the Izar lab, posted in Biorxiv. 
  • Lingting's abstract selected for oral presentation at the American Society of Hematology Annual Meeting.
  • Siyu's paper "Squidiff: Predicting cellular development and perturbation response with diffusion model" posted on Biorxiv.
  • A revised preprint on Decipher by Achille and Joy "Joint representation and visualization of derailed cell states with Decipher" published in Biorxiv.
  • Extended version of Cameron and Shouvik's paper "A Bayesian framework for inferring dynamic intercellular interactions from time-series single-cell data" published in Genome Research and featured as the cover story!
  • Joy and Achille's comment piece on the promise of AI for cancer biology published in Nature Methods.
  • Lingting receives the HICCC Precision Oncology and Systems Biology (POSB) postdoctoral award. 
  • Achille and Justin's paper "Stable Differentiable Causal Discovery" in collaboration with Dave Blei, accepted in ICML 2024.  
  • Our paper "Starfysh integrates spatial transcriptomic and histologic data to reveal heterogeneous tumor-immune hubs", work led by Siyu, Yinuo, Achille and Lingting, published in Nature Biotechnology (press release).
  • Kevin receives the Best Poster award at the 2nd Fusion Conference on Probing Human Disease Using Single-Cell Technologies.
  • Joy receives the "Avanessians Doctoral Fellowship for Engineering Thought Leaders and Innovators in Data Science".
2023
  • Cameron and Shouvik's paper "DIISCO: A Bayesian framework for inferring dynamic intercellular interactions from time-series single-cell data" accepted in RECOMB 2024.
  • Yinuo's paper "CellStitch: 3D Cellular Anisotropic Image Segmentation via Optimal Transport" in collaboration with the Blumberg lab, published in BMC Bioinformatics.
  • Lingting receives an NCI Genome and Epigenome Integrity in Cancer (GEIC) T32 postdoctoral fellowship.
  • Elham named 2024 Early-Career Innovator in Science in Cancer Immunology by Takeda and the New York Academy of Sciences (press release, videos, Columbia Engineering article)
  • Elham named Allen Distinguished Investigator - awarded funding for a collaborative project with Simunovic and McFaline-Figueroa Labs.
  • Achille and Justin's preprint "Stable Differentiable Causal Discovery" in collaboration with Dave Blei, published in arXiv.  
  • Cameron and Shouvik's preprint "DIISCO: A Bayesian framework for inferring dynamic intercellular interactions from time-series single-cell data" in collaboration with the Wu lab, published in Biorxiv.
  • Achille and Joy's preprint "Deep generative model deciphers derailed trajectories in acute myeloid leukemia" in collaboration with the Pe'er lab, published in Biorxiv.
  • Michael receives the "Outstanding Achievement Award in Biomedical Engineering Master’s Studies" 
  • Achille's papers "A large-scale observational study of the causal effects of a behavioral health nudge" and "Modeling personalized heart rate response to exercise and environmental factors with wearables data", in collaboration with Apple, published in Science Advances and npj Digial Medicine. 
  • The lab receives an R21 grant from NIH NHGRI
  • Yinuo's preprint "CellStitch: 3D Cellular Anisotropic Image Segmentation via Optimal Transport" in collaboration with the Blumberg lab, published in Biorxiv.
  • Four short papers accepted at the ICML 2023 Workshop on Computational Biology; posters presented by Lingting, Michael, Lia, Kevin and Justin.
  • Justin and Achille win the 1st prize award in the GSK.ai CausalBench Challenge (report)
  • Kevin receives an NSF Graduate Research Fellowship
  • The lab receives an R01 grant from NIH NHGRI
  • Joy's paper in collaboration with the Izar lab, "Multi-modal single-cell and whole-genome sequencing of small, frozen clinical specimens", published in Nature Genetics (press release)​. 
2022​
  • Our preprint "Starfysh reveals heterogeneous spatial dynamics in the breast tumor microenvironment", work led by Siyu, Yinuo, Achille and Lingting, published in Biorxiv (highlights, code)
  • The lab receives a Chan Zuckerberg Initiative Award 
  • Joy's abstract  “Mapping Genotype to Phenotype through Joint Probabilistic Modeling of Single-Cell Gene Expression and Chromosomal Copy Number Variation” selected for oral presentation at the​ 14th annual RECOMB/ISCB Conference on Regulatory & Systems Genomics.
  • Justin's preprint work with the Yosef lab, "Deep generative modeling for quantifying sample-level heterogeneity in single-cell omics" published in Biorxiv.
  • Achille receives a PhD fellowship from the Eric and Wendy Schmidt Center (EWSC) at the Broad Institute.
  • The lab receives a Columbia Cancer-Engineering Seed Grant in collaboration with Dr. Brent Stockwell
  • Achille and Joy's paper accepted at the Workshop on Computational Biology at ICML and receives best poster presentation award.
  • Cameron and Shouvik's poster accepted at the Workshop on Computational Biology at ICML and receives contributed talk award.
  • The lab receives an NSF CAREER Award 
  • Joy's preprint in collaboration with the Izar lab, "Multi-modal single-cell and whole-genome sequencing of minute, frozen specimens to propel clinical applications", published in Biorxiv. ​​
2021
  • Our paper "Mapping the evolution of T cell states during response and resistance to adoptive cellular therapy" is published in  Cell Reports .​  Highlighted in Theory Lab Podcast discussion led by American Cancer Society.
  • Yinuo receives the Presidential Distinguished Fellowship
  • The lab is featured in Columbia Engineering Magazine story on AI in Health and Medicine
  • Xueer, Joy, Cameron and Lauren's paper accepted at Workshop on Computational Biology at ICML
  • Azizi lab selected for funding in the Columbia Research Initiatives in Science & Engineering competition with Dr. Benjamin Izar and Dr. Richard Carvajal
2020
  • Yinuo and Alex's paper accepted at LMRL Workshop at NeurIPS
  • The lab awarded HICCC Intra/InterProgrammatic Pilot grant, with Dr. Ran Reshef 
  • The lab featured in Columbia Engineering Magazine Faculty Q&A  
  • Joy receives the Van C. Mow fellowship 
  • Cameron receives the Kaganov fellowship
  • Columbia University Herbert Irving Comprehensive Cancer Center features our research 
  • Columbia University Bio Bytes Podcast chat with Elham
  • The lab receives an R00 Pathway to Independence Award from NIH/NCI
  • Azizi lab awarded Data Science Institute Seed Grant in partnership with IICD, with Dr. Jellert Gaublomme and Dr. Brent Stockwell​​

recent & upcoming INVITED Talks

  • Harvard Program in Quantitative Genomics Seminar Series, May 2025.
  • Stanford Center for Cancer Systems Biology Symposium, May 2025. 
  • MIT Whitehead Institute, AI: Advancing Foundational Biology, April 2025.
  • CMU-Pitt PhD Program in Computational Biology Seminar, March 2025.
  • AACR-JCA Joint Conference: From Cancer Discovery Science to Therapeutic Innovation | Maui, February 2025.
  • American Society of Hematology (ASH) Annual Meeting, San Diego, December 2024.
  • Stanford Cancer Biology Seminar Series, October 2024. 
  • Bertinoro Computational Biology (BCB) meeting: Cancer Heterogeneity and Immune Interactions, Italy, Sep 2024.
  • Cancer Immunotherapy: from bench to bedside and back Nature Conference, DFCI, June 2024.
  • NCI Data Science Seminar Series, May 2024.
  • NIH NCI Spring School on Algorithmic Cancer biology, March 2024.
  • Probing Human Disease Using Single-Cell Technologies Fusion Conference, Feb 2024.
  • American Society of Hematology (ASH) Annual Meeting, San Diego, December 2023.
  • ​The 18th Machine Learning in Computational Biology (MLCB2023), Seattle WA, December 2023 [Keynote].  
  • MD Anderson Cancer Center’s 2023 Leading Edge of Cancer Research Symposium, November 2023. 
  • JKTG Foundation Symposium on Metastasis, Spatial Analytics and Combination Therapies, Bethesda MD, October 2023.
  • American Cancer Society Comedy Against Cancer fundraising event, Stamford CT, September 2023.
  • Single Cell Mapping in Development & Cancer Symposium, NYU Langone Department of Pathology, September 2023
  • EMBL-EBI Precision medicine in the era of high-resolution biology & artificial intelligence, Cambridge MA, September 2023.
  • Lipari Summer School: Computational Single-Cell Analysis with application in Biology and Medicine, July 2023.
  • Cell Growth and Proliferation Gordon Research Conference, July 2023.
  • Tumor-Immune Systems Biology Symposium, MSKCC, May 2023.
  • MSKCC Computational Oncology Seminar Series, April 2023.
  • NCI Cancer AI Research: Computational Approaches Addressing Imperfect Data Workshop, April 2023.
  • CSHL Probabilistic Modeling in Genomics, March 2023.
  • Transplantation and Cellular Therapy meeting of ASTCT and CIMTBR, February 2023.
  • Weill Cornell Medicine ICB Seminar Series, October 2022.
  • JSM 2022 Special Session on Statistical methods for single cell genomics and spatial transcriptomics, August 2022.
  • Probing Human Disease Using Single-Cell Technologies Fusion Conference, May 2022
  • University of Pennsylvania Bioengineering Graduate Research Symposium, April 2022, [Keynote].  
  • Women in Science at Columbia (WISC) Graduate Research Symposium, April 2022, [Keynote].  
  • Dept. of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, March 2022.
  • NIAID Data Science Seminar, December 2021.
  • UNC Computational Medicine Seminar, November 2021.
  • Johns Hopkins Biomedical Engineering Seminar Series, November 2021.
  • Redirected Immune Cell Therapies Webinar, The New York Academy of Sciences, September 2021.
  • University of Washington Machine Learning in Computational Biology Seminar Series, May 2021. 
  • NYU Biomedical Engineering Colloquium, April 2021.
  • ENAR Invited session on Bulk deconvolution and single-cell data analysis, March 2021.
  • NYU Pathology Department Research Seminar Series, March 2021.​
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