-
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.
