My lab focuses on developing statistical and computational methods for the analysis of large-scale biomedical data and applying them to study complex diseases. Collaborating with our colleagues, we use cutting-edge technologies including DNA-seq, RNA-seq, methylation, ATAC-seq and single cell sequencing to study human diseases such as childhood asthma and age-related macular degeneration. Chen lab welcomes collaborators and trainees to move science forward. Our lab is generously supported by National Institute of Health, National Science Foundation, University of Pittsburgh and UPMC.
Xu Z, Heidrich-O’Hare E, Chen W, Duerr R. Comprehensive benchmarking of CITE-seq versus DOGMA-seq single cell multimodal omics. .
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. .
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.
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. .
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. .
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. .
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. .
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. .
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. .
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. .
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. .