Kendziorski Lab

Developing statistical methods for genomics and computational biology

Recent Selected Publications

See my Google scholar profile for a full list

Bernstein, M.N.*, Z. Ni*, M. Collins, M.E. Burkard, and C. Kendziorski, and R. Stewart. CHARTS: A Web Application for Characterizing and Comparing Tumor Subpopulations in Publicly Available Single-Cell RNA-Seq Datasets. BMC Bioinformatics 23;22(1):83, 2021.

Brown, J.*, C. Barry, M.T. Schmitz, C. Argus, J. M. Bolin, M. P. Schwartz, A. Van Aartsen, J. Steill, S.Swanson, R. Stewart, J.A. Thomson, and C. Kendziorski. Interspecies Chimeric Conditions Affect the Developmental Rate of Human Pluripotent Stem Cells. PLoS Computational Biology, 17(3):e1008778, 2021.

Ma, X., Korthauer, K.*, Kendziorski, C., and M.A. Newton. A compositional model to assess expression changes from single-cell RNA-seq data. Annals of Applied Statistics, 15(2): 880-901, 2021.

Nimkulrat, S.D., Bernstein, M.N.*, Ni., Z.*, Brown, J.* , Kendziorski, C., and B. Blum. The Anna Karenina model of β cell maturation in development and their dedifferentiation in type 1 and type 2 diabetes. Diabetes 70(9): 2058-2066, 2021.

Simonett, S.P., Shin, S., Herring, J.A., Bacher, R.*, Smith, L.A., Dong, C., Rabagliaa, M.E., Stapelton, D.S., Schueler, K.L., Choi, J.*, Bernstein, M.N., Turkewitz, D.R., Perez-Cervantes, C., Spaeth, J., Stein, R., Tessem, J.S., Kendziorski, C., Keles, S., Moskowitz, I.P., Keller, M.P., and A.D. Attie. Identification of direct transcriptional targets of NFATC2 that promote β-cell proliferation. Journal of Clinical Investigation, Epub ahead of print doi: 10.1172/JCI144833, 2021.

De, I., Maklakova, V., Litscher, S., Boyd, M.M., Klemm, L.C., Wang, Z.*, Kendziorski, C., and L.S. Collier. Microglial responses to CSF1 overexpression do not promote the expansion of other glial lineages. Journal of Neuroinflammation 18(1): 1-13, 2021.

Rydzewski, N.R., Buehler, D., Kendziorski, C., Iyer, G., Zhao, S.G. and A.M Baschnagel. Immune-Depleted Phenotype in Non-Small Cell Lung Cancer Brain Metastases Predicts for Worse Overall Survival. International Journal of Radiation Oncology, Biology, and Physics 111(3): S14, 2021.

Brown, J.*, Z. Ni*, C. Mohanty*, R. Bacher*, and C. Kendziorski. Normalization by Distributional Resampling of High Throughput Single-Cell RNA-Sequencing Data. Bioinformatics 37(22): 4123-4128, 2021.

Bacher, R.*, L.F. Chu, C. Argus, J.M. Bolin, P. Knight, J.A. Thomson, R. Stewart, and C. Kendziorski. Enhancing Biological Signals and Detection Rates in Single-Cell RNA-Seq Experiments with CDNA Library Equalization. Nucleic Acids Research 50(2): e12, 2022.

Ni, Z.*, Prasad, A., Chen, S., Halber, R.B., Arkin, L., Drolet, B., Newton, M.A., and C.Kendziorski. SpotClean adjusts for spot swapping in spatial transcriptomics data. Nature Communications 13(1): 2971, 2022.

Bernstein, M.N.*, Ni, Z.*, Prasad, A., Brown, J.*, Mohanty, C.*, Stewart, R., Newton, M.A., and C. Kendziorski. SpatialCorr identifies gene sets with spatially varying correlation structure. Cell Reports Methods 2(12): 100369, 2022.

Chen, X., Lungova, V., Zhang, H., Mohanty, C.*, Kendziorski, C., and S.L. Thibeault. Novel immortalized human vocal fold epithelial cell line: In vitro tool for mucosal biology. The FASEB Journal 35 (2), e21243, 2022.

Emfinger, C.H., de Klerk, E, Schueler, K.L., Rabaglia, M.E., Stapleton, D.S., Simonett, S.P., Mitok, K.A., Wang, Z.*, Liu, X., Paulo, J.A., Yu, Q., Cardone, R.L., Foster, H.R., Lewandowski, S.L., Perales, J.C., Kendziorski, C., Gygi, S.P., Kibbey, R.G., Keller, M.P., Hebrok, M., Merrins, M.J., and A.D. Attie. Beta cell-specific deletion of Zfp148 improves nutrient-stimulated beta cell Ca2+ responses. Journal of Clinical Investigation 7(10): e154198, 2022.

Wendt, K., Brown, J.* , Lungova, V., Mohad, V., Kendziorski, C., and S.L. Thibeault. Transcriptome dynamics in developing larynx, trachea, and esophagus. Frontiers in Cell and Developmental Biology 10: 942622, 2022.

Basnet, S. †, Mohanty, C.†*, Bochkov, Y.A., Brockman-Schneider, R.A., Kendziorski, C., and J.E. Gern. Rhinovirus C Causes Heterogeneous Infection and Gene Expression in Airway Epithelial Cell Subsets. Mucosal Immunology 16(4): 386-398, 2023.

Wang, A.R., Baschnagel, A.M., Ni., Z.*, Brennan, S.R., Newton, H.K., Behler, D., Kendziorski, C., Kimple, R.J., and G. Iyer. Network analyses: Inhibition of androgen receptor signaling reduces inflammation in the lung through AR-MAF-IL6 signaling axes. Genes & Diseases 11(3): 101072, 2023.

Shireman, J.M., Cheng, L.*, Goel, A., Garcia, D.M., Partha, S., Quinones-Hinojosa, A., Kendziorski, C., and M. Dey. Spatial Transcriptomics in Glioblastoma: Is Knowing the Right Zip Code the Key to the Next Therapeutic Breakthrough? Frontiers in Immunology, 13: 1266397, 2023.

Rao, A., Ni., Z., Dhrthi, S., Mohanty, C.*, Wang, A., Lee, D., Nickel, K., Varambally, S., Kimple, R.J., Lambert, P.F., Kendziorski, C., and G. Iyer. Targeted inhibition of BET proteins in HPV-16 associated head and neck squamous cell carcinoma reveals heterogeneous transcription response. bioRxiv, submitted, 2023.

Shireman, J.M., White, Q.* , Ni, Z.* , Mohanty, C.*, Cai, Y.*, Zhao, L., Agrawal, N., Gonugunta, N., Wang, X., McCarthy, L., Kasulabada, V., Pattnaik, A., Ahmed, A.U., Miller, J., Kulwin, C., Cohen-Gadol, A., Payner, T., Lin, C-T., Savage, J.J., Lane, B., Shiue, K., Kamer, A., Shah, M., Iyer, G., Watson, G., Kendziorski, C., and M. Dey. Genomic analysis of human brain metastases treated with stereotactic radiosurgery reveals unique signature based on treatment failure. iScience 27(4), 2024.

Djeddi, S., Fermandez-Salinas, D., Huang, G., Aguiar, V., Mohanty, C.*, Kendziorski, C., Gazal, S., Boyce, J., Ober, C., Gern, J., Barrett, N., and Gutierrez-Arcelus, M. Rhinovirus infection of airway epithelial cells uncovers the non-ciliated subset as a likely driver of genetic susceptibility to childhood-onset asthma. Cell Genomics 4(9): 100636, 2024.

Ran, A., Ni, Z.*, Xie, E.*, Rey, F.E., Kendziorski, C., and S.L. Thibeault. Single-Cell view into the role of microbiota shaping host immunity in the larynx. iScience 27(6): 110156, 2024.

Shapiro, D.D., Lozar, T., Cheng, L.*, Xie, E.*, Laklouk, I., Lee, M.H., Huang, W., Jarrard, D.F., Allen, G.O., Hu, R., Kinoshita, T., Esbona, K., Lamber, P.F., Capitini, C.M., Kendziorski, C., and E.J. Abel. Non-metastatic clear cell renal cell carcinoma immune cell infiltration heterogeneity and prognostic ability in patients following surgery. Cancers 16(3): 478, 2024.

Damodran, S., Shireman, J.M., Xie, E.*, Distler, R., Kendziorski, C., and M. Dey. Transcriptomic and proteomic spatial profiling of pediatric and adult diffuse midline glioma H3 K27-Altered. Scientific Reports 14(1): 22668, 2024.

Mohanty, C.*, Prasad, A., Cheng, L.*, Arkin, L.M., Shields, B.E., Drolet, B., and C. Kendziorski. SpatialView: An interactive web application for visualization of multiple samples in spatial transcriptomics experiments. Bioinformatics 40(3): btae117, 2024.

Mohanty, C.*, Singh, C.K., Daccache, J.A., Damsky, W., Kendziorski, C., Yan, D., Prasad, A., Zhang, D., Keenan, T., Drolet, B., Ahmad, N., and B.E. Shields. Granuloma Annulare Exhibits Mixed Immune and Macrophage Polarization Profiles with Spatial Transcriptomics. Journal of Investigative Dermatology 145(1): 109-121, 2025.

Bretl, M., Cheng, L.*, Kendziorski, C., and S.L. Thibeault. RNA-sequencing demonstrates transcriptional differences between human vocal fold fibroblasts and myofibroblasts. BMC Genomics 26(1): 347, 2025.

Xie, E.*, Cheng, L.*, Shireman, J., Cai, Y.*, Liu, J.*, Mohanty, C.*, Dey, M., and C. Kendziorski. CASSIA allows for robust, automated cell annotation in single-cell RNA-sequencing data. Nature Communications, invited revision, 2025.



*Denotes CK student or postdoc