📚 2025 March - Congrats Inamo, J., et al on our recent publication of Deep immunophenotyping reveals circulating activated lymphocytes in individuals at risk for rheumatoid arthritis, JCI (Journal of Clinical Investigation), 2025. This study was featured at CU DOM News: “Leveraging Data Science for Disease Prediction in the Fight Against Rheumatoid Arthritis” 🎉

💰 2025 March - Congrats Fan to receive the Arthritis Foundation grant 🎉 - check out the featured post of the grant.

📚 2025 Feb - Congrats Reynoso, S., et al on our recent manuscript STEAM: Spatial Transcriptomics Evaluation Algorithm and Metric for clustering performance at bioRxiv!

📚 2025 Jan - Congrats Young, J., et al on our recent manuscript CellPhenoX: An eXplainable Cell-specific machine learning method to predict clinical Phenotypes using single-cell multi-omics at bioRxiv!

👏🏻 2024 Dec - Congrats, Fan, on being namedone of the 2024 Next Generation Leaders by the Allen Institute 🎉

📚 2024 Dec - Congrats Hope et al on our paper of Evaluating Methods for Integrating Single-Cell Data and Genetics to Understand Inflammatory Disease Complexity published at Frontiers in Immunology!

🎤 2024 Nov - Our lab has 3 speakers, Jade, Hope, and Jun, presenting at ASHG (American Society of Human Genetics), Denver.

💰 2024 July - Congrats Fan on her award as the Sontag Foundation Fellow 🎉

💰 2024 June - Congrats Jun to receive the CCTSI CO-Pilot Mentored award 🎉

📚 2024 May - Congrats Nanxi et al on our paper STew (Spatial Transcriptomics multi-viEW) published at Bioinformatics Advances!

👏🏻 2024 May - Congrats, Jade, on the acceptance of her abstract by 2024 ISMB international conference!

📚 2024 April - A collaborative paper is out at Science Translational Medicine, featured as cover story too!

👏🏻 2024 April - Congrats Jade on her “NSF GRFP Honorable Mentions"!!!

👏🏻 2024 April - Fan is awarded as “Rising Stars Award“ of the University of Colorado Department of Medicine.

👏🏻 2024 April - Welcome Courtney and Lauren join the lab!!

🎤 2024 March - Fan presented our lab work at the La Jolla Institute for Immunology in San Diego.

👏🏻 2024 March - Welcome Jessica join the lab as a rotating student!

🎤 2024 Feb - Jun presented our single-cell work at the 2024 Keystone Systemic Autoimmune and Autoinflammatory Disease Symposia!

📚 2024 Jan - Horisberger, A., Griffith, A., Keegan, J., Arazi, A., Pulford, J., Murzin, E., Howard, K., Hancock, B., Fava, A., Sasaki, T., Ghosh, T., Inamo, J., Beuschel, R., …, AMP RA/SLE Network, Brenner, M.B., Anolik, J.H., Raychaudhuri, S., Hacohen, N., James, J.A., Davidson, A., Petri, M.A., Buyon, J.P., Diamond, B., Zhang, F.*, Lederer, J.A.*, Rao, D.A*. Blood immunophenotyping identifies distinct kidney histopathology and outcomes in patients with lupus nephritis. bioRxiv, in review, 2024. Co-senior

📚 2023 Nov - Our work is highlighted by the “Front Line Genomics” in the “Spatial and Single-Cell Analysis Playbook”!

👏🏻 2023 Nov - Congrats Jun received the "Emerging Investigator Excellence Award" and gave two wonderful talks at ACR 2023, San Diego!

📚 2023 Nov - Our recent work “Zhang*, Jonsson*, et al” is out at Nature! Check the report at the School of Medicine News! Featured at theNIH NIAMS News 🎉

💰 2023 Oct - Fan received the Orthopedics-DBMI Dyad grant. Looking forward to collaborating with the Colorado Program for Musculoskeletal Research team!

📚 2023 Oct - Congrats Nanxi, Juan, Douglas, and Revanth for our recent work “Uncover spatially informed shared variations for single-cell spatial transcriptomics with STew” - see preprint on bioRxiv, 2023

🎤 2023 Oct - Fan was interviewed by Oxford Global - check the dialogue/video!

👏🏻 2023 Sep - Congrats Jade received the NLM (National Library of Medicine) T15 award!

🎤 2023 Sep - Fan is invited to give a talk at the “Precision medicine in the era of high-resolution biology & artificial intelligence” organized by EMBL-EBI at Sanofi, Boston!

📚 2023 Aug - A collaborative work “Bai, et al, Machine Learning Reveals Synovial Fibroblast Genes Associated with Pain Affect Sensory Nerve Growth in Rheumatoid Arthritis“ - see preprint on medRxiv, 2023

📚 2023 July - Congrats to Jun on our recent work “Inamo, et al , Deep immunophenotyping reveals circulating activated lymphocytes in individuals at risk for rheumatoid arthritis“ at bioRxiv!

👏🏻 2023 July - Welcome Jade Young from the CPBS program to join the lab!

💰 2023 July - Fan received the award from the 2023 Arthritis National Research Foundation (ANRF) grant!!

💰 2023 June - Fan is one of the seven faculties across the School of Medicine who received the 2023 Translational Research Scholars Program grant from the CU School of Medicine!

📚 2023May - A collaborative work “Thomas, et al, A longitudinal single-cell therapeutic atlas of anti-tumour necrosis factor treatment in inflammatory bowel disease“ - see preprint on bioRxiv, 2023

📚 2023 Apr - A collaborative work “Iijima, H., Zhang, F., Ambrosio, F., Matsui, Y., Network-based cytokine inference implicates Oncostatin M as a driver for inflammation phenotype of knee osteoarthritis“ - see preprint onbioRxiv, 2023

📚 2023 Apr - A collaborative work “Weinand, K., et al, The Chromatin Landscape of Pathogenic Transcriptional Cell States in Rheumatoid Arthritis” - see preprint on bioRxiv, 2023

📚 2023 Mar - A collaborative work “Kang, J.B., et al, Mapping the dynamic genetic regulatory architecture of HLA genes at single-cell resolution” - see preprint on medRxiv, 2023

📚 2023 Mar - A collaborative work “Dunlap, G.S., et al, Clonal associations of lymphocyte subsets and functional states revealed by single cell antigen receptor profiling of T and B cells in rheumatoid arthritis synovium” - see preprint on bioRxiv, 2023

🎤 2023 Mar - Fan gave a Keynote Speak at OARSI (Osteoarthritis Research Society International) in Denver!

👏🏻 2023 Mar - Welcome Revanth Krishna to join the lab as our Software Engineer/Bioinformatician! Revanth is co-supervised with Dr. Chuangqi Wang’s lab.

💰 2023 Mar - (co-I) Received a co-I NIDDK R01 grant through collaboration with Dr. Joshua Thurman!

👏🏻 2023 Mar - Welcome Kewalin Samart to join the lab for research rotation!

👏🏻 2023 Jan - Welcome Nicholas Cordaro to join the lab for research rotation!

👏🏻 2023 Jan - Welcome Jade Young to join the lab for research rotation!

👏🏻 2023 Jan - Welcome Hope Townsend join the lab for research rotation!

📚 2023 Jan - Congrats to Doug and Jun on our paper at Frontiers in Immunology!

2022

🎤 2022 Dec - Fan gave a Talk on “A robust computational method for spatiotemporal trajectory association analysis in single-cell spatial transcriptomics” at the 2022 Rocky Mountain Bioinformatics Conference! The work is led by Juan and Douglas from our lab!

🎤 2022 Nov - Fan gave a Talk on “Deciphering Complement System-Dependent Cellular Pathways in Human Rheumatoid Arthritis Synovial Tissues Using Single-Cell Computational Omics” at the “Genetics, Genomics and Proteomics “ Session at ACR (American College of Rheumatology) Convergence 2022 in Philadelphia.

🎤 2022 Nov - Fan is invited to give a Talk on “Integration of Genetics into MultiomicsDiscovery in Rheumatology using Single-cell Computational Omics for Precision Medicine” at the ACR (American College of Rheumatology) Convergence 2022 in Philadelphia.

🎤 2022 Oct - Our Abstract “Vargas, J., Fritz, D., Zhang, F. A robust computational framework to benchmark spatiotemporal trajectory association analysis in single-cell spatial transcriptomics” is accepted as a poster talk by The 14th annual RECOMB/ISCB Conference on Regulatory & Systems Genomics with DREAM Challenges (RSGDREAM)

👏🏻 2022 Oct - Congrats to Jun on his JSPS (Japan Society for the Promotion of Science) grant! Well deserved!

👏🏻 2022 Oct - Welcome, JunInamo, MD/PhD, joining the lab as a Postdoc Fellow!

🎤 2022 Sep - Fan gave a talk to the PhD students from the Interdisciplinary Quantitative Biology (IQBio) program at BioFrontiers at CU Boulder!

👏🏻 2022 Sep - Welcome, Nanxi Guo, a PhD student at the Biostatistics & Informatics PhD program joining the lab as a Research Assistant!

👏🏻 2022 Aug - Fan joins the Immunology PhD program as a faculty!

📚 2022 Aug - Vagars, …, Zhang, “Deciphering Complement System-dependent Cellular Pathways in Human Rheumatoid Arthritis Synovial Tissues Using Single-cell Computational Omics” is selected for an Oral Presentation at ACR (American College of Rheumatology) at the “Genetics, Genomics and Proteomics” session this Nov at Philadelphia!

🎤 2022 July - Fan gave a lecture on “Single-cell Computational and Statistical Methods Shed Light on Translational Medicine“ to the Computational Bioscience (CPBS) and Biostatistics summer programs in a joint seminar.

👏🏻 2022 June - Thank the monthly CU School of Medicine "Faculty and Staff Newsletter" Research and Innovation for highlighting our recent publication of Jonsson, A.H.*, Zhang, F.*, et al, Science Translational Medicine!

📚 2022 June - Jonsson, A.H.*, Zhang, F.., et al, Granzyme K+ CD8 T cells form a core population in inflamed human tissue, is out at Science Translational Medicine as the cover article!

📚2022 June - Liu, S.*, Li, L.*, Zhang, F.*, …, Church, Iterative transcription factor screening enables rapid generation of microglia-like cells from human iPSC, bioRxiv, In review

👏🏻 2022 June - Welcome, Douglas Fritz, MD/PhD Student, joining the lab for the summer rotation project!

👏🏻 2022 June - Welcome, Helen Wolde and Yonatan Wolde, from the CPBS summer program joining the lab!

💰2022 June - (co-I) Received a grant from the Spondylitis Association of America (SAA) on using single-cell omics to study SpA through collaboration with Dr. Kristi Kuhn.

👏🏻 2022 June - Our PhRMA grant is featured in the School of Medicine News! Thanks Greg Glasgow for writing the article about our grant: use machine learning and large-scale single-cell omics to develop better detection and treatment for the condition.

💰2022 May - (PI) Received PhRMA Research Starter Grant in Translational Medicine on using Single-cell Omics to decipher shared inflammatory phenotypes between RA and RA-ILD!

📚 2022 May - Meednu, Rangel-Moreno, Zhang, … , Anolik, J.H., Cell Reports, 2022

👏🏻 2022 May - Welcome, Hannah Wang, joining the lab for summer research!

👏🏻 2022 May - Fan joins the MSTP MD/PhD program as a faculty!

🎤 2022 April - Fan gave a talk on “Single-cell Computational Omics Shed Light On Inflammatory Disease Pathogenesis” at the “Department of Immunology and Microbiology Seminar”. Thank Dr. Leslie Berge and Dr. Linda Dyk for the invitation!

🎤 2022 April - Fan gave a talk on “Single-cell Computational Omics Reveal Insights into Rheumatoid Arthritis-Interstitial Lung Disease (RA-ILD) ” at the “Excellence in Respiratory Seminar”. Thank Dr. Marc Moss and Dr. Eszter Vladar for the invitation from the Pulmonary Division.

🎤 2022 April - Fan gave a talk on “Single-cell Computational Omics Shed Light On Inflammatory Disease Pathogenesis” at the Workshop on "Computational Biology in clinical medicine" hosted by Peking University.

👏🏻 2022 April - Welcome, Dr. Tusharkanti Ghosh, joining the lab as Research Associate!

👏🏻 2022 March - Welcome, Juan Vargas, a Graduate student from the MPH Biostatistics, joining the lab!

💰2022 March - (subaward) Received NIH NIAMS subaward from Accelerating Medicines Partnership Autoimmune and Immune-Mediated Diseases (AMP-AIM): Disease Team for Rheumatoid Arthritis (UC2 AR081025). We are honored to be part of this NIH NIAMS consortium grant!

👏🏻 2022 Feb - Fan joins the CPBS PhD program as a faculty!

📚 2022 Feb - Zhang, F.*, Jonsson, A.H.*, Nathan, A.*, Wei, K.*, Millard, N.*, et al, Cellular deconstruction of inflamed synovium defines diverse inflammatory phenotypes in rheumatoid arthritis, bioRxiv, 2022

🎤 2022 Jan - Fan gave a talk about “Single-cell Computational Omics Shed Light On Inflammatory Disease Pathogenesis” at Computational Bioscience (CPBS) seminar.

👏🏻 2022 Jan - Launch the Lab!