• 05/2026 Congratulations to Chongyue Zhao and Tianhao Liu on the publication of their STARS study in Nature Communications, introducing a deep learning framework to reconstruct single-cell-level gene expression from spatial transcriptomics data across resolutions.
• 04/2026 Congratulations to Soyeon Kim on the publication of her study on causal mediation analyses of DNA methylation on gene expression through genetic anchors in asthma in Science Advances.
• 04/2026 Congratulations to Zhongli Xu and Shiyue Tao on the publication of their PBMC DOGMA-seq study in Nature Communications.
• 03/2026 Haoran Hu won the Best Oral Presentation Award in the Annual Biostatistics Research Day.
• 03/2026 Congratulations to Xiangyu Ye for publishing a collaborative paper on Cell.
• 12/2025 Dr. Chen and Molin, together with collaborators Dr. Juan C. Celedón, Dr. Erick Forno, Dr. Kathryn S. Torok, and Dr. Zhao Ren, received the ENAR Team Science Award for their integrative multi-omics and precision medicine research.
• 10/2025 Chen lab was congratulated by the Department of Pediatrics on the research of AI-guided research on scleroderma. News
• 09/2025 Dr. Chen received pediatric discovery award from the Department of Pediatrics for his outstanding publication in translational science.
• 09/2025 Chen Lab received an R01 from NIAMS with Dr. Torok to integrate spational transcriptomics with histology images for identifying scleroderma subgroups.
• 08/2025 Chen Lab received a DoD grant with Dr. Torok to study pediatric scleroderma using a multi-omics approach.
• 08/2025 Congratulations to Xiangyu Ye for receiving the highly competitive finalist for the ASHG trainee award, also with an oral talk at ASHG conference at Boston in Oct.
• 07/2025 Dr. Chen is appointed as a regular member of BDMA study section at NIH.
• 07/2025 Congratulations to Shivum Telang for receiving the student travel award from the ICIBM conference in Columbus, Ohio.
• 06/2025 Congratulations to Tianhao Liu for receiving the 2025 3CPR Junior Investigator Travel Grant from the American Heart Association.
• 01/2025 Congratulations to Molin Yue’s work on child asthma endotypes published in JAMA. News report: ABC, NBC, CBS, Washington Post, Post Gazatte, Pitt

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• A list of complete publications

• Zhao C, Liu T, Miller LM, Li H, Zhao H, Barnett D, Yuan R, Zhang H, Wang Q, Eddens T, Torok KS, Zhou AX, Dai Z, Alcorn JF, Huang H#, Chen W#. Decoding spatial transcriptomics across multicellular and subcellular resolutions. Nature Communications. May 2026.

• Kim S, Caldino Bohn RI, Sriram A, Park HJ, Huang Z, Chen W, Celedón JC. Estimating in silico causal effects of DNA methylation on gene expression through genetic anchors in airway epithelium in asthma Science Advances. 2026; Vol. 12, No. 17.

• Xu Z, Tao S, Feng S, Ye X, Wang T, Hu H, Heidrich-O’Hare E, Chen W#, Duerr RH#. Dissecting PGE2-driven inhibition of T cell activation using single-cell multi-omic and inflammatory bowel disease genetic association analysis. Nature Communications. April 2026.

• Yue M, Gaietto K, Han YY, Rosser F, Xu Z, Qoyawayma C, Acosta-Perez E, Canino G, Forno E, Chen W#, Juan Celedon#. Transcriptomic Profiles in Nasal Epithelium and Asthma Endotypes in Youth. JAMA. 2025 Jan 2. doi: 10.1001/jama.2024.22684. PMID: 39745770

• Hu H, Wang X, Feng S, Xu Z, Liu J, Heidrich-O’Hare E, Chen Y, Yue M, Zeng L, Rong Z, Chen T, Billiar T, Ding Y, Huang H, Duerr R, Chen W. A unified model-based framework for doublet or multiplet detection in single-cell multiomics data. Nature Communications. 2024 Jul 2;15(1):5562.

• Zhao C, Xu Z, Wang X, Tao S, MacDonald WA, He K, Poholek AC, Chen K, Huang H, Chen W. Innovative super-resolution in spatial transcriptomics: a transformer model exploiting histology images and spatial gene expression. Briefings in Bioinformatics. 2024 Jan 22;25(2):bbae052. PMID: 38436557. PMCID: PMC10939304

• Xu Z, Heidrich-O’Hare E, Chen W, Duerr R. Comprehensive benchmarking of CITE-seq versus DOGMA-seq single cell multimodal omics. Genome Biol 23, 135 (2022).

• Ganjdanesh A, Zhang J, Chew EY, Ding Y, Huang H, Chen W. LONGL-Net: temporal correlation structure guided deep learning model to predict longitudinal age-related macular degeneration severity. PNAS Nexus. 2022 Mar;1(1):pgab003.

• Zhang R, Ren Z, Celedón JC, Chen W. (2021) Inference of Large Modified Poisson-type Graphical Models: Application to RNA-seq Data in Childhood Atopic Asthma Studies. Annals of Applied Statistics. Vol.15, No. 2, June 2021

• Dai H, Lan P, Zhao D, Abou-Daya K, Liu W, Chen W, Friday AJ, Williams AL, Sun T, Chen J, Chen W, Mortin-Toth S, Danska JS, Wiebe C, Nickerson P, Li T, Mathews LR, Turnquist HR, Nicotra ML, Gingras S, Takayama E, Kubagawa H, Shlomchik MJ, Oberbarnscheidt MH, Li XC, Lakkis FG. PIRs mediate innate myeloid cell memory to nonself MHC molecules. Science. 2020 Jun 5;368(6495):1122-1127.

• Xin H, Lian Q, Jiang Y, Luo J, Wang X, Erb C, Xu Z, Zhang X, Heidrich-O’Hare E, Yan Q, Duerr RH, Chen K, Chen W. GMM-Demux: sample demultiplexing, multiplet detection, experiment planning, and novel cell-type verification in single cell sequencing. Genome Biol. 2020 Jul 30;21(1):188.

• Wang X, Sun Z, Zhang Y, Xu Z, Xin H, Huang H, Duerr RH, Chen K, Ding Y, Chen W. BREM-SC: a bayesian random effects mixture model for joint clustering single cell multi-omics data. Nucleic Acids Res. 2020 Jun 19;48(11):5814-5824.

• Yan Q, Weeks DE, Xin H, Swaroop A, Chew EY, Huang H, Ding Y, Chen W. Deep-learning-based Prediction of Late Age-Related Macular Degeneration Progression. Nature Machine Intelligence. 2020 Feb;2(2):141-150.

• Sun Z, Chen L, Xin H, Jiang Y, Huang Q, Cillo AR, Tabib T, Kolls JK, Bruno TC, Lafyatis R, Vignali DAA, Chen K, Ding Y, Hu M, Chen W. A Bayesian mixture model for clustering droplet-based single-cell transcriptomic data from population studies. Nature Communications. 2019;10(1):1649.

• Sawant DV, Yano H, Chikina M, Zhang Q, Liao M, Liu C, Callahan DJ, Sun Z, Sun T, Tabib T, Pennathur A, Corry DB, Luketich JD, Lafyatis R, Chen W, Poholek AC, Bruno TC, Workman CJ, Vignali DAA. Adaptive plasticity of IL-10(+) and IL-35(+) Treg cells cooperatively promotes tumor T cell exhaustion. Nature Immunology. 2019;20(6):724-35.

• Wei Y, Liu Y, Sun T, Chen W, Ding Y. Gene-based association analysis for bivariate time-to-event data through functional regression with copula models. Biometrics. 2019.

• Forno E, Wang T, Qi C, Yan Q, Xu CJ, Boutaoui N, Han YY, Weeks DE, Jiang Y, Rosser F, Vonk JM, Brouwer S, Acosta-Perez E, Colon-Semidey A, Alvarez M, Canino G, Koppelman GH, Chen W, Celedon JC. DNA methylation in nasal epithelium, atopy, and atopic asthma in children: a genome-wide study. The Lancet Respiratory medicine. 2019 Apr;7(4):336-346.

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