Recent Selected Publications

See my
cv or Google author profile for a full list

Leng, N.*, Chu, L-F., Barry, C., Li., Y.*, Choi, J.*, Li., X.*, Jiang, P., Stewart, R.M., Thomson, J.A., and
Kendziorski, C. Oscope identifies oscillatory genes in unsynchronized single-cell RNA-Seq experiments, Nature Methods, 12 (10): 947-950, 2015.

Leng, N.*, Li, Y., McIntosh, B.E., Nguyen, B.K., Duffin, B., Tian, S., Thomson, J.A., Dewey, C., Stewart, R., and
Kendziorski, C. EBSeq-HMM: A Bayesian approach for identifying gene-expression changes in ordered RNA-seq experiments, Bioinformatics, doi: 10.1093/bioinformatics/btv193, 2015.

Tran, K.A., Jackson, S.A., Olufs, Z.P.G., Leng, N.*,
Kendziorski, C., Roy, S., and R. Sridharan. Collaborative rewiring of the pluripotency network by chromatin and signaling modulating pathways, Nature Communications, 6(6188): doi:10.1038/ncomms7188, 2015.

Bartlett, R.S., Gaston, J.D., Yen, T.Y.,
Kendziorski, C., and Thibeault, S.L. Biomechanical screening of cell therapies for vocal fold scar. Tissue Engineering Part A, 21 (17-18), 2437-2447, 2015.

Korthauer, K.*, and
C. Kendziorski. MADGiC: a model-based approach for identifying driver genes in cancer, Bioinformatics, 31(10): 1526-1535, 2015.

Welham, N.V., Ling, C., Dawson, J.A.*,
Kendziorski, C., Thibeault, S.L., and Yamashita, M. Microarray-based characterization of differential gene expression during vocal fold wound healing, Disease Models and Mechanisms, 8(3): 311-321, 2015.

Marty, A.J., Broman, A.T.*,
Kendziorski, C., Zarnowski, R. Dwyer, T., Bond, L.M., Ntambi, J.M., Lounes-Hadj Sahraoui, A., Fontaine, J., and Gauthier, G.M. Fungal morphology, iron homeostasis, and lipid metabolism regulated by a GATA transcription factor in Blastomyces dermatitidis, PLoS Pathogens, 11(6):e1004959, 2015.

Bradley, W.H., Eng, K.*, Mutch, D.G., MacKinnon, C.,
Kendziorski, C., and Rader, J. Comparing gene expression data from FFPE tissue and qPCR with that from snap-frozen tissue and microarrays for modeling outcomes of patients with ovarian carcinoma, BMC Clinical Pathology 15 (1), 17, 2015.

Broman, K.W., Keller, M.P., Broman, A.T.,
Kendziorski, C., Yandell, B.S., Sen, S., and Attie, A.D. Identification and correction of sample mix-ups in expression genetic data: A case study, Genetics, to appear, 2015.

Tian, J., Keller, M.P., Oler, A., Rabagalia, M., Schueler, K., Stapleton, D., Broman, A.T., Zhao, W.,
Kendziorski, C., Yandell, B.S., Hagenbuch, B., Broman, K.W., and Attie, A.D. Identification of SlcoIa6 as a candidate gene that broadly affects gene expression in mouse pancreatic islets, Genetics, to appear, 2015.

Iruretagoyena J.I., Davis, W., Bird, C., Olsen, J., Radue, R., Broman, A.T.*,
Kendziorski, C., Bondurant, S.S., Golos, T., Bird, I., and Shah, D. Differential Changes in Gene Expression in Human Heart during Late First Trimester and Early Second Trimester of Pregnancy. Prenatal Diagnosis 34 (5), 431-437, 2014.

Kennedy-Darling, J., Guillen-Ahlers, H., Shortreed, M.R., Scalf, M., Knoener, R., Frey, B.L.,
Kendziorski, C., Olivier, M., Gasch, A.P., and Smith, L.M. Discovery of chromatin-associated proteins via sequence-specific capture and mass spectrometric protein identification in Saccharomyces cerevisiae, Journal of Proteome Research 13(8): 3810–3825, 2014.

Iruretagoyena J.I., Davis, W., Bird, C., Olsen, J., Radue, R., Broman, A.T.*,
Kendziorski, C., Bondurant, S.S., Golos, T., Bird, I., and Shah, D. Metabolic gene profile in early human fetal heart development. Molecular Human Reproduction 20(7): 690-700, 2014.

Christopherson, M.R. Dawson, J.A.*, Stevenson, D., Cunningham, A., Bramhacharya, S., Weimer, P.J.,
Kendziorski, C., and G. Suen. Unique aspects of fiber degradation by the ruminal ethanologen Ruminococcus albus 7 revealed by physiological and transcriptomic analysis. BMC genomics 15(1): 1066, 2014.

Hines, E.A., Szakaly, R.J., Leng, N.*, Webster, A.T., Verheyden, J.M., Lashua, A.J.
Kendziorski, C., Rosenthal, L.A., Gern, J.E., Sorkness, R.L., Sun, X., and R.F. Lemanske Jr. Comparison of Temporal Transcriptomic Profiles from Immature Lungs of Two Rat Strains Reveals a Viral Response Signature Associated with Chronic Lung Dysfunction. PLoS One 9(12): e112997, 2014.

St. John, H.C, Bishop, K.A., Meyer, M.B. Benkusky, N.A., Leng, N.*,
Kendziorski, C., Bonewald, L.F., and J.W. Pike. The osteoblast to osteocyte transition: epigenetic changes and response to the vitamin D3 hormone. Molecular Endocrinology 28(7):1150-65, 2014.

Song, C., Chung, L., Xiaokang, P., Zhanjun, L., Ding, Y., Sachdev, M., Muthusami, S., Gowda, C.S., Ge, Z., Steffens, S., Tan, B-H.,
Kendziorski, C., Newton, M.A., and S. Dovat. Chromatin State Shaping the Gene Expression Profiling in the Inducible Differentiation of Promyelocytic Leukemia Cells. Blood 124(21), 2014.

Ye, S.*, Dawson, J.A.*, and
Kendziorski, C. Extending information retrieval methods to personalized genomic based studies of disease, Cancer Informatics, 13(7): 85-95, 2014.

Eng, K.E.*, S. Wang, W.H. Bradley, J.S. Rader, and
Kendziorski, C. Pathway-Index Models for Construction of Patient-Specific Risk Profiles, Statistics in Medicine, 32(9): 1524-1535, 2013.

Anderson, S.A., Nizzi, C., Chang, Y.I., Deck, K.M., Schmidt, P., Galy, B. Broman, A.T.,
Kendziorski, C., Hentze, M.W., Fleming, M.D., Zhang, J., and Eisenstein, R.S. The IRP1-HIF-2α axis coordinates iron and oxygen sensing with erythropoiesis and iron absorption, Cell Metabolism, 17(2):282-90. doi: 10.1016, 2013.

Smits, B., Haag, J.D., Rissman, A.I., Sharman, D., Tran, A., Schoenborn, A., Baird, R., Peiffer, D., Leinweber, M., Muelbl, M., Meilahn, A., Eichelberg, M.R., Leng, N.*,
Kendziorski, C., Manorama, J., Powers, P., Alexander, C., and Gould, M.N.. The Gene Desert Mammary Carcinoma Susceptibility Locus Mcs1a Regulates Nr2f1 Modifying Mammary Epithelial Cell Differentiation and Proliferation. PLoS Genetics 9(6): e1003549. doi:10.1371/journal.pgen.1003549, 2013.

Ray, M., Goldstein, S., Zhou, S., Potamousis, K., Sarkar, D., Newton, M. A., Esterberg, E.*,
Kendziorski, C., Bogler, O., and Schwartz, D. C. Discovery of structural alterations in solid tumor oligodendroglioma by single molecule analysis. BMC genomics, 14(1), 505, 2013.

Jiang, Y.Z., Wang, K., Li, Y., Dai, C.F., Wang, P*.,
Kendziorski, C., Chen, D.B., and Zheng, J. Transcriptional and Functional Adaptations of Human Endothelial Cells to Physiological Chronic Low Oxygen. Biology of Reproduction 88(5), 2013.

Leng, N.*, J.A. Dawson*, R. M. Stewart, V. Ruotti, A. Rissman, B. Smits, J. Haag, M.N. Gould, J.A. Thomson, and
Kendziorski, C. EBSeq: An empirical Bayes hierarchical model for inference in RNA-seq experiments, Bioinformatics 29(8): 1035-1043, 2013.

*Denotes CK student or postdoc