Fan Zhang, PhD
@fanzhangphd.bsky.social
Principal Investigator, Assistant Professor | #CUAnschutz Medical Campus
#ComputationalBiology #SingleCell #ML #AI #Autoimmune
Zhang Lab: fanzhanglab.org
Github: github.com/fanzhanglab
Linkedin: https://www.linkedin.com/in/fan-zhang-phd-2149306b/
#ComputationalBiology #SingleCell #ML #AI #Autoimmune
Zhang Lab: fanzhanglab.org
Github: github.com/fanzhanglab
Linkedin: https://www.linkedin.com/in/fan-zhang-phd-2149306b/
🚀 Excited to share our lab new paper published today in Briefings in Bioinformatics: "STEAM: Spatial Transcriptomics Evaluation Algorithm and Metric for clustering performance” academic.oup.com/bib/article/...
@cumedicalschool.bsky.social
@cumedicalschool.bsky.social
STEAM: Spatial Transcriptomics Evaluation Algorithm and Metric for clustering performance
Abstract. Spatial transcriptomic technologies allow researchers to explore the diversity and specificity of gene expression within an original tissue struc
academic.oup.com
October 31, 2025 at 5:53 PM
🚀 Excited to share our lab new paper published today in Briefings in Bioinformatics: "STEAM: Spatial Transcriptomics Evaluation Algorithm and Metric for clustering performance” academic.oup.com/bib/article/...
@cumedicalschool.bsky.social
@cumedicalschool.bsky.social
Excited 🎉 to share our work at #ACR25 at Chicago tomorrow 10:15! @juninamo.bsky.social from my lab will present a #Plenary talk on integrating #longitudinal #SingleCell and #MachineLearning to uncover #Predictive immune signatures preceding #RheumatoidArthritis onset! @curhuematology.bsky.social
October 25, 2025 at 4:39 PM
Excited 🎉 to share our work at #ACR25 at Chicago tomorrow 10:15! @juninamo.bsky.social from my lab will present a #Plenary talk on integrating #longitudinal #SingleCell and #MachineLearning to uncover #Predictive immune signatures preceding #RheumatoidArthritis onset! @curhuematology.bsky.social
Thank you for highlighting our recent work - we’re honored and excited to continue contributing to the field!
Fan Zhang, PhD, and the researchers in the Zhang Lab are helping lead the way toward potential new treatment options for rheumatoid arthritis and other autoimmune diseases. Learn more in part three of our research series: https://news.cuanschutz.edu/medicine/ai-single-cell-autoimmune-research-2025
Using Novel AI and Single-Cell Techniques to Advance Autoimmune Therapies
In the Zhang Lab at the CU Anschutz School of Medicine, researchers work to uncover pathways that could lead to targeted therapeutics for rheumatoid arthritis and other autoimmune conditions.
news.cuanschutz.edu
October 1, 2025 at 3:34 AM
Thank you for highlighting our recent work - we’re honored and excited to continue contributing to the field!
It was a great honor to be invited to give a talk at @kiroxford.bsky.social University of Oxford today. Many thanks to Dr. @y-luo.bsky.social for the kind invitation. I truly enjoyed the inspiring discussions with the brilliant scientists here!
September 26, 2025 at 9:39 PM
It was a great honor to be invited to give a talk at @kiroxford.bsky.social University of Oxford today. Many thanks to Dr. @y-luo.bsky.social for the kind invitation. I truly enjoyed the inspiring discussions with the brilliant scientists here!
Excited 🎉 to share our lab's new paper CellPhenoX, an #explainable #MachineLearning tool 🔨 for #SingleCell data, published advanced.onlinelibrary.wiley.com/doi/10.1002/...
⭐️ CellPhenoX detects both linear, nonlinear, and even subtle interaction effects underlying clinical single-cell datasets!
⭐️ CellPhenoX detects both linear, nonlinear, and even subtle interaction effects underlying clinical single-cell datasets!
CellPhenoX: An Explainable Machine Learning Method for Identifying Cell Phenotypes To Predict Clinical Outcomes from Single‐Cell Multi‐Omics
CellPhenoX is an explainable machine learning framework that identifies cell-specific phenotypes and interaction effects from single-cell omics data. By leveraging interpretable models, it enables ro...
advanced.onlinelibrary.wiley.com
September 23, 2025 at 6:01 PM
Excited 🎉 to share our lab's new paper CellPhenoX, an #explainable #MachineLearning tool 🔨 for #SingleCell data, published advanced.onlinelibrary.wiley.com/doi/10.1002/...
⭐️ CellPhenoX detects both linear, nonlinear, and even subtle interaction effects underlying clinical single-cell datasets!
⭐️ CellPhenoX detects both linear, nonlinear, and even subtle interaction effects underlying clinical single-cell datasets!
Reposted by Fan Zhang, PhD
More on the gut-joint connection.
Microbial threads in the tapestry of rheumatoid arthritis
In this Review, Jing Li & Kristine A. Kuhn discuss the bacterial microbiome’s role in RA pathogenesis and highlight microbiome-targeted interventions: buff.ly/Q1q10Ha
In this Review, Jing Li & Kristine A. Kuhn discuss the bacterial microbiome’s role in RA pathogenesis and highlight microbiome-targeted interventions: buff.ly/Q1q10Ha
September 17, 2025 at 10:40 PM
More on the gut-joint connection.
Thrilled 🎉 to shared I received my R01 NoA today @NIH_NIAMS! We will continue pushing the frontiers of autoimmune research by developing novel #AI #MachineLearning for #SingleCell #SpatialTranscriptomics 🧬💻💊! @cuanschutz.bsky.social @cudeptofmedicine.bsky.social @cubiomedinfo.bsky.social
August 12, 2025 at 6:30 PM
Thrilled 🎉 to shared I received my R01 NoA today @NIH_NIAMS! We will continue pushing the frontiers of autoimmune research by developing novel #AI #MachineLearning for #SingleCell #SpatialTranscriptomics 🧬💻💊! @cuanschutz.bsky.social @cudeptofmedicine.bsky.social @cubiomedinfo.bsky.social
Reposted by Fan Zhang, PhD
Next week! Join us on Thursday, August 14 at 6PM ET in Cambridge, MA (or online) for a Broad Discovery Series talk with @soumya-boston.bsky.social, “Arthritis, autoimmunity, and how the genome works.” Register: broadinstitute.swoogo.com/DiscoverySeries25
August 7, 2025 at 5:03 PM
Next week! Join us on Thursday, August 14 at 6PM ET in Cambridge, MA (or online) for a Broad Discovery Series talk with @soumya-boston.bsky.social, “Arthritis, autoimmunity, and how the genome works.” Register: broadinstitute.swoogo.com/DiscoverySeries25
Reposted by Fan Zhang, PhD
An analysis shows that current deep learning models do not beat linear baselines in predicting gene perturbation effects, thus emphasizing the importance of further method development and evaluation. @const-ae.bsky.social @wkhuber.bsky.social @s-anders.bsky.social
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Deep-learning-based gene perturbation effect prediction does not yet outperform simple linear baselines - Nature Methods
The analysis presented in this Brief Communication shows that, despite their complexity, current deep learning models do not outperform linear baselines in predicting gene perturbation effects, thus e...
www.nature.com
August 4, 2025 at 4:07 PM
An analysis shows that current deep learning models do not beat linear baselines in predicting gene perturbation effects, thus emphasizing the importance of further method development and evaluation. @const-ae.bsky.social @wkhuber.bsky.social @s-anders.bsky.social
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Excited 🎉 to receive the grant from the "Leadership Scholars Program in Women’s Health, Autoimmune Diseases, and Immune-Mediated Diseases" supported by NIH Office of Research on Women's Health and AMP-AIM network: orwh.od.nih.gov/in-the-spotl....
We have openings for bioinformaticians and postdocs!
We have openings for bioinformaticians and postdocs!
ORWH: In the Spotlight
Leadership Scholars Program in Women’s Health, Autoimmune Diseases, and Immune-Mediated Diseases Names Three New Awardees
orwh.od.nih.gov
July 10, 2025 at 5:13 PM
Excited 🎉 to receive the grant from the "Leadership Scholars Program in Women’s Health, Autoimmune Diseases, and Immune-Mediated Diseases" supported by NIH Office of Research on Women's Health and AMP-AIM network: orwh.od.nih.gov/in-the-spotl....
We have openings for bioinformaticians and postdocs!
We have openings for bioinformaticians and postdocs!
Reposted by Fan Zhang, PhD
Distinguishing individuals at risk for rheumatoid arthritis from healthy controls!
@fanzhangphd.bsky.social, Deepak A. Rao & team define specific lymphocyte phenotypes during the preclinical stage of rheumatoid arthritis: buff.ly/WdjB8VD
@fanzhangphd.bsky.social, Deepak A. Rao & team define specific lymphocyte phenotypes during the preclinical stage of rheumatoid arthritis: buff.ly/WdjB8VD
March 27, 2025 at 1:20 PM
Distinguishing individuals at risk for rheumatoid arthritis from healthy controls!
@fanzhangphd.bsky.social, Deepak A. Rao & team define specific lymphocyte phenotypes during the preclinical stage of rheumatoid arthritis: buff.ly/WdjB8VD
@fanzhangphd.bsky.social, Deepak A. Rao & team define specific lymphocyte phenotypes during the preclinical stage of rheumatoid arthritis: buff.ly/WdjB8VD
Excited 🎉to share our work led by@juninamo.bsky.social out in JCI @jclinical-invest.bsky.social! Using cross-cohort #singlecell (CyTOF & CITE-seq), we found key T cell expansions in at-risk RA: CCR2+T with Th17/Th22 phenotype and Tph, for #RheumatoidArthritis prevention! www.jci.org/articles/vie...
JCI - Deep immunophenotyping reveals circulating activated lymphocytes in individuals at risk for rheumatoid arthritis
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www.jci.org
March 17, 2025 at 6:07 PM
Excited 🎉to share our work led by@juninamo.bsky.social out in JCI @jclinical-invest.bsky.social! Using cross-cohort #singlecell (CyTOF & CITE-seq), we found key T cell expansions in at-risk RA: CCR2+T with Th17/Th22 phenotype and Tph, for #RheumatoidArthritis prevention! www.jci.org/articles/vie...