Kendziorski Lab

Developing statistical methods for genomics and computational biology

Recent Selected Publications

See my cv or Google scholar profile for a full list

Lungova, V., Chen, X., Wang, Z.*, Kendziorski, C., and Thibeault, S.L. Human induced pluripotent stem cell-derived vocal fold mucosa mimics development and responses to smoke exposure. Nature Communications, 10(1): 1-16, 2019.

Bradley, R.A., Shireman, J., McFalls, C., Choi, J.*, Canfield, S.G., Dong, Y., Liu, K., Lisota, B., Jones. J.R., Peterson, A., Bhattacharyya, A., Palecek, S.P., Shusta, E.V., Kendziorski, C., and Zhang, S-C. Regionally specified human pluripotent stem cell-derived astrocytes exhibit different molecular signatures and functional properties. Development 170910, 2019.

Bartlett, R.S. Gaston, J.D., Ye, S*., Kendziorski, C., and Thibeault, S. Mechanotransduction of vocal fold fibroblasts and mesenchymal stromal cells in the context of the vocal fold mechanome. Journal of Biomechanics 83: 227-234, 2019.

Karim, A.S., Yan, A., Ocotl, E., Bennett, D.D., Wang, Z*., Kendziorski, C., and Gibson, A.L.F. Discordance between histologic and visual assessment of tissue viability in excised burn wound tissue. Wound Repair and Regeneration 27(2):150-161, 2019.

Foote, A.G., Wang, Z.*, Kendziorski, C., and Thibeault, S.L. Tissue specific human fibroblast differential expression based on RNA-sequencing analysis. BMC Genomics 20(1): 308, 2019.

Kishimoto, Y., Yamashita, M., Wei, A., Toya, Y., Ye, S.*, Kendziorski, C., and Welham, N.V. Reversal of vocal fold mucosal fibrosis using siRNA against the collagen-specific chaperone Serpinh1. Molecular Therapy-Nucleic Acids 16: 616-625, 2019.

Keller, M.P., Rabaglia, M.E., Schueler, K.L., Stapleton, D.S., Gatti, D.M., Vincent, M., Mitok, K.A., Wang, Z.*, Ishimura, T., Simonett, S.P., Emfinger, C.H., Das, R., Beck, T., Kendziorski, C., Broman, K.W., Yandell, B.S., Churchill, G.A., and Attie, A.D. Gene loci associated with insulin secretion in islets of nondiabetic mice. Journal of Clinical Investigation 129(10): 4419-4432, 2019.

Chu, L-F., Mamott, D., Ni, Z.*, Bacher, R.*, Liu, C., Swanson, S., Kendziorski, C., Stewart, R., and Thomson, J.A. An In Vitro Segmentation Clock Model Derived From Embryonic Stem Cells. Cell Reports 28(9): 2247-2255, 2019.

Karim, A.S., Wang, Z.*, Glover, C.R., Kendziorski, C., and Gibson, A.L.F. 40 M2 Macrophages May Mitigate Burn Inflammation and Promote Wound Healing. Journal of Burn Care & Research 40: S29-30, 2019.

Blitzer, G.C., Wang, A., Brown, J.*, Burr, A., Matkowskyj, K.A., Schuppener, L., Kovacs, K., Witt, J.S., Kendziorski, C., Iyer, G., and Baschnagel, A.M. Tumor Lymphocyte, Macrophage, and GITR Changes in Tissue Microarray and RNA Sequencing of Patients with and without Neoadjuvant Radiation Therapy for Pancreatic Cancer. International Journal of Radiation Oncology 105(1): S207, 2019.

Ma, X., Korthauer, K., Kendziorski, C., and Newton, M.A. A compositional model to assess expression changes from single-cell RNA-seq data. bioRxiv 655795, 2019.

Seirup, M., Chu, L-F., Sengupta, S., Leng, N.*, Shafer, C.M., Duffin, B., Elwell, A.L. Bolin, J.M, Swanson, S., Stewart, R., Kendziorski, C., Thomson, J.A., and Bacher, R.* Tradeoff between more cells and higher read depth for single-cell RNA-seq spatial ordering analysis of the liver lobule. bioRxiv 764191, 2019.

Fogg, K., Miller, A.E. , Li, Y.*, Flanigan, W., Walker, A., O’Shea, A., Kendziorski, C., Kreeger, P. Ovarian Cancer Cells Direct Monocyte Differentiation Through a Non-Canonical Pathway. BMC Cancer 20(1):1008, 2020.

Seirup, M., Chu, L-F., Sengupta, S., Leng, N.*, H. Browder, Shafer, C.M., Duffin, B., Elwell, A.L. Bolin, J.M, Swanson, S., Stewart, R., Kendziorski, C., Thomson, J.A., and Bacher, R.* Reproducibility across single-cell RNA-seq protocols for spatial ordering analysis. PLoS One 15(9): e0239711, 2020.

Ni, Z.*, Chen, S.*, Brown, J.*, and Kendziorski, C. CB2 distinguishes cells from background barcodes in 10x Genomics data. Genome Biology 21:137, 2020.

Barry, C., Schmitz, M.T., Argus, C., Bolin, J.M., Probasco, M.D., Leng, N.*, Duffin, B.M., Steill, J., Swanson, S., McIntosh, B.E., Stewart, R., Kendziorski, C., Thomson, J.A., and Bacher, R*. Automated minute scale RNA-seq of pluripotent stem cell differentiation reveals early divergence of human and mouse gene expression kinetics. PLoS Computational Biology 15(12): 2020.

Ma, X., C. Kendziorski, and M.A. Newton. 2020. “EBSeq: Improving Mixing Computations for Multi-Group Differential Expression Analysis.” bioRxiv, 2020.

Ma, X., Korthauer, K.*, Kendziorski, C., and Newton, M.A. A compositional model to assess expression changes from single-cell RNA-seq data. Annals of Applied Statistics, to appear, 2020.

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, invited revision, 2020.

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, 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, 2021.

Brown, J.*, Z. Ni*, C. Mohanty*, R. Bacher*, and C. Kendziorski. 2020. Normalization by Distributional Resampling of High Throughput Single-Cell RNA-Sequencing Data. Bioinformatics, 2021.




*Denotes CK student or postdoc