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Regionally specified human pluripotent stem cell-derived astrocytes exhibit different molecular signatures and functional properties.

Bradley RA, Shireman J, McFalls C, Choi J, Canfield SG, Dong Y, Liu K, Lisota B, Jones JR, Petersen A, Bhattacharyya A, Palecek SP, Shusta EV, Kendziorski C, Zhang SC.

Development. 2019 Jul 8;146(13). pii: dev170910. doi: 10.1242/dev.170910.


Reversal of Vocal Fold Mucosal Fibrosis Using siRNA against the Collagen-Specific Chaperone Serpinh1.

Kishimoto Y, Yamashita M, Wei A, Toya Y, Ye S, Kendziorski C, Welham NV.

Mol Ther Nucleic Acids. 2019 Jun 7;16:616-625. doi: 10.1016/j.omtn.2019.04.014. Epub 2019 Apr 22.


Tissue specific human fibroblast differential expression based on RNAsequencing analysis.

Foote AG, Wang Z, Kendziorski C, Thibeault SL.

BMC Genomics. 2019 Apr 23;20(1):308. doi: 10.1186/s12864-019-5682-5.


Discordance between histologic and visual assessment of tissue viability in excised burn wound tissue.

Karim AS, Yan A, Ocotl E, Bennett DD, Wang Z, Kendziorski C, Gibson ALF.

Wound Repair Regen. 2019 Mar;27(2):150-161. doi: 10.1111/wrr.12692. Epub 2018 Dec 26.


Mechanotransduction of vocal fold fibroblasts and mesenchymal stromal cells in the context of the vocal fold mechanome.

Bartlett RS, Gaston JD, Ye S, Kendziorski C, Thibeault SL.

J Biomech. 2019 Jan 23;83:227-234. doi: 10.1016/j.jbiomech.2018.11.050. Epub 2018 Dec 7.


Mutations in GFAP Disrupt the Distribution and Function of Organelles in Human Astrocytes.

Jones JR, Kong L, Hanna MG 4th, Hoffman B, Krencik R, Bradley R, Hagemann T, Choi J, Doers M, Dubovis M, Sherafat MA, Bhattacharyya A, Kendziorski C, Audhya A, Messing A, Zhang SC.

Cell Rep. 2018 Oct 23;25(4):947-958.e4. doi: 10.1016/j.celrep.2018.09.083.


Trendy: segmented regression analysis of expression dynamics in high-throughput ordered profiling experiments.

Bacher R, Leng N, Chu LF, Ni Z, Thomson JA, Kendziorski C, Stewart R.

BMC Bioinformatics. 2018 Oct 16;19(1):380. doi: 10.1186/s12859-018-2405-x.


Genetic Drivers of Pancreatic Islet Function.

Keller MP, Gatti DM, Schueler KL, Rabaglia ME, Stapleton DS, Simecek P, Vincent M, Allen S, Broman AT, Bacher R, Kendziorski C, Broman KW, Yandell BS, Churchill GA, Attie AD.

Genetics. 2018 May;209(1):335-356. doi: 10.1534/genetics.118.300864. Epub 2018 Mar 22.


Correction: Identification of a serum-induced transcriptional signature associated with metastatic cervical cancer.

Palatnik A, Ye S, Kendziorski C, Iden M, Zigman JS, Hessner MJ, Rader JS.

PLoS One. 2018 Feb 23;13(2):e0193687. doi: 10.1371/journal.pone.0193687. eCollection 2018.


Single-cell RNA sequencing reveals intrinsic and extrinsic regulatory heterogeneity in yeast responding to stress.

Gasch AP, Yu FB, Hose J, Escalante LE, Place M, Bacher R, Kanbar J, Ciobanu D, Sandor L, Grigoriev IV, Kendziorski C, Quake SR, McClean MN.

PLoS Biol. 2017 Dec 14;15(12):e2004050. doi: 10.1371/journal.pbio.2004050. eCollection 2017 Dec.


IPI59: An Actionable Biomarker to Improve Treatment Response in Serous Ovarian Carcinoma Patients.

Choi J, Ye S, Eng KH, Korthauer K, Bradley WH, Rader JS, Kendziorski C.

Stat Biosci. 2017 Jun;9(1):1-12. doi: 10.1007/s12561-016-9144-1. Epub 2016 Mar 29.


Identification of a serum-induced transcriptional signature associated with metastatic cervical cancer.

Palatnik A, Ye S, Kendziorski C, Iden M, Zigman JS, Hessner MJ, Rader JS.

PLoS One. 2017 Aug 30;12(8):e0181242. doi: 10.1371/journal.pone.0181242. eCollection 2017. Erratum in: PLoS One. 2018 Feb 23;13(2):e0193687.


Statistical Methods for Latent Class Quantitative Trait Loci Mapping.

Ye S, Bacher R, Keller MP, Attie AD, Kendziorski C.

Genetics. 2017 Jul;206(3):1309-1317. doi: 10.1534/genetics.117.203885. Epub 2017 May 26.


SCnorm: robust normalization of single-cell RNA-seq data.

Bacher R, Chu LF, Leng N, Gasch AP, Thomson JA, Stewart RM, Newton M, Kendziorski C.

Nat Methods. 2017 Jun;14(6):584-586. doi: 10.1038/nmeth.4263. Epub 2017 Apr 17.


The Transcription Factor Nfatc2 Regulates β-Cell Proliferation and Genes Associated with Type 2 Diabetes in Mouse and Human Islets.

Keller MP, Paul PK, Rabaglia ME, Stapleton DS, Schueler KL, Broman AT, Ye SI, Leng N, Brandon CJ, Neto EC, Plaisier CL, Simonett SP, Kebede MA, Sheynkman GM, Klein MA, Baliga NS, Smith LM, Broman KW, Yandell BS, Kendziorski C, Attie AD.

PLoS Genet. 2016 Dec 9;12(12):e1006466. doi: 10.1371/journal.pgen.1006466. eCollection 2016 Dec.


A statistical approach for identifying differential distributions in single-cell RNA-seq experiments.

Korthauer KD, Chu LF, Newton MA, Li Y, Thomson J, Stewart R, Kendziorski C.

Genome Biol. 2016 Oct 25;17(1):222.


Histone chaperone ASF1B promotes human β-cell proliferation via recruitment of histone H3.3.

Paul PK, Rabaglia ME, Wang CY, Stapleton DS, Leng N, Kendziorski C, Lewis PW, Keller MP, Attie AD.

Cell Cycle. 2016 Dec;15(23):3191-3202. Epub 2016 Oct 18.


Single-cell RNA-seq reveals novel regulators of human embryonic stem cell differentiation to definitive endoderm.

Chu LF, Leng N, Zhang J, Hou Z, Mamott D, Vereide DT, Choi J, Kendziorski C, Stewart R, Thomson JA.

Genome Biol. 2016 Aug 17;17(1):173. doi: 10.1186/s13059-016-1033-x.


Modeling fibrosis using fibroblasts isolated from scarred rat vocal folds.

Kishimoto Y, Kishimoto AO, Ye S, Kendziorski C, Welham NV.

Lab Invest. 2016 Jul;96(7):807-16. doi: 10.1038/labinvest.2016.43. Epub 2016 Apr 25.


Design and computational analysis of single-cell RNA-sequencing experiments.

Bacher R, Kendziorski C.

Genome Biol. 2016 Apr 7;17:63. doi: 10.1186/s13059-016-0927-y. Review.


The Dissection of Expression Quantitative Trait Locus Hotspots.

Tian J, Keller MP, Broman AT, Kendziorski C, Yandell BS, Attie AD, Broman KW.

Genetics. 2016 Apr;202(4):1563-74. doi: 10.1534/genetics.115.183624. Epub 2016 Feb 2.


OEFinder: a user interface to identify and visualize ordering effects in single-cell RNA-seq data.

Leng N, Choi J, Chu LF, Thomson JA, Kendziorski C, Stewart R.

Bioinformatics. 2016 May 1;32(9):1408-10. doi: 10.1093/bioinformatics/btw004. Epub 2016 Jan 6.


Comparing gene expression data from formalin-fixed, paraffin embedded tissues and qPCR with that from snap-frozen tissue and microarrays for modeling outcomes of patients with ovarian carcinoma.

Bradley WH, Eng K, Le M, Mackinnon AC, Kendziorski C, Rader JS.

BMC Clin Pathol. 2015 Sep 24;15:17. doi: 10.1186/s12907-015-0017-1. eCollection 2015.


Identification of the Bile Acid Transporter Slco1a6 as a Candidate Gene That Broadly Affects Gene Expression in Mouse Pancreatic Islets.

Tian J, Keller MP, Oler AT, Rabaglia ME, Schueler KL, Stapleton DS, Broman AT, Zhao W, Kendziorski C, Yandell BS, Hagenbuch B, Broman KW, Attie AD.

Genetics. 2015 Nov;201(3):1253-62. doi: 10.1534/genetics.115.179432. Epub 2015 Sep 18.


Oscope identifies oscillatory genes in unsynchronized single-cell RNA-seq experiments.

Leng N, Chu LF, Barry C, Li Y, Choi J, Li X, Jiang P, Stewart RM, Thomson JA, Kendziorski C.

Nat Methods. 2015 Oct;12(10):947-950. doi: 10.1038/nmeth.3549. Epub 2015 Aug 24.


Identification and Correction of Sample Mix-Ups in Expression Genetic Data: A Case Study.

Broman KW, Keller MP, Broman AT, Kendziorski C, Yandell BS, Sen Ś, Attie AD.

G3 (Bethesda). 2015 Aug 19;5(10):2177-86. doi: 10.1534/g3.115.019778.


Biomechanical Screening of Cell Therapies for Vocal Fold Scar.

Bartlett RS, Gaston JD, Yen TY, Ye S, Kendziorski C, Thibeault SL.

Tissue Eng Part A. 2015 Sep;21(17-18):2437-47. doi: 10.1089/ten.TEA.2015.0168. Epub 2015 Jul 22.


Fungal Morphology, Iron Homeostasis, and Lipid Metabolism Regulated by a GATA Transcription Factor in Blastomyces dermatitidis.

Marty AJ, Broman AT, Zarnowski R, Dwyer TG, Bond LM, Lounes-Hadj Sahraoui A, Fontaine J, Ntambi JM, Keleş S, Kendziorski C, Gauthier GM.

PLoS Pathog. 2015 Jun 26;11(6):e1004959. doi: 10.1371/journal.ppat.1004959. eCollection 2015 Jun.


EBSeq-HMM: a Bayesian approach for identifying gene-expression changes in ordered RNA-seq experiments.

Leng N, Li Y, McIntosh BE, Nguyen BK, Duffin B, Tian S, Thomson JA, Dewey CN, Stewart R, Kendziorski C.

Bioinformatics. 2015 Aug 15;31(16):2614-22. doi: 10.1093/bioinformatics/btv193. Epub 2015 Apr 5.


Collaborative rewiring of the pluripotency network by chromatin and signalling modulating pathways.

Tran KA, Jackson SA, Olufs ZP, Zaidan NZ, Leng N, Kendziorski C, Roy S, Sridharan R.

Nat Commun. 2015 Feb 4;6:6188. doi: 10.1038/ncomms7188.


Microarray-based characterization of differential gene expression during vocal fold wound healing in rats.

Welham NV, Ling C, Dawson JA, Kendziorski C, Thibeault SL, Yamashita M.

Dis Model Mech. 2015 Mar;8(3):311-21. doi: 10.1242/dmm.018366. Epub 2015 Jan 15.


MADGiC: a model-based approach for identifying driver genes in cancer.

Korthauer KD, Kendziorski C.

Bioinformatics. 2015 May 15;31(10):1526-35. doi: 10.1093/bioinformatics/btu858. Epub 2015 Jan 7.


Unique aspects of fiber degradation by the ruminal ethanologen Ruminococcus albus 7 revealed by physiological and transcriptomic analysis.

Christopherson MR, Dawson JA, Stevenson DM, Cunningham AC, Bramhacharya S, Weimer PJ, Kendziorski C, Suen G.

BMC Genomics. 2014 Dec 4;15:1066. doi: 10.1186/1471-2164-15-1066.


Comparison of temporal transcriptomic profiles from immature lungs of two rat strains reveals a viral response signature associated with chronic lung dysfunction.

Hines EA, Szakaly RJ, Leng N, Webster AT, Verheyden JM, Lashua AJ, Kendziorski C, Rosenthal LA, Gern JE, Sorkness RL, Sun X, Lemanske RF Jr.

PLoS One. 2014 Dec 1;9(12):e112997. doi: 10.1371/journal.pone.0112997. eCollection 2014.


Discovery of Chromatin-Associated Proteins via Sequence-Specific Capture and Mass Spectrometric Protein Identification in Saccharomyces cerevisiae.

Kennedy-Darling J, Guillen-Ahlers H, Shortreed MR, Scalf M, Frey BL, Kendziorski C, Olivier M, Gasch AP, Smith LM.

J Proteome Res. 2014 Aug 1;13(8):3810-25. doi: 10.1021/pr5004938. Epub 2014 Jul 17.


The osteoblast to osteocyte transition: epigenetic changes and response to the vitamin D3 hormone.

St John HC, Bishop KA, Meyer MB, Benkusky NA, Leng N, Kendziorski C, Bonewald LF, Pike JW.

Mol Endocrinol. 2014 Jul;28(7):1150-65. doi: 10.1210/me.2014-1091. Epub 2014 May 30.


Metabolic gene profile in early human fetal heart development.

Iruretagoyena JI, Davis W, Bird C, Olsen J, Radue R, Teo Broman A, Kendziorski C, Splinter BonDurant S, Golos T, Bird I, Shah D.

Mol Hum Reprod. 2014 Jul;20(7):690-700. doi: 10.1093/molehr/gau026. Epub 2014 Mar 27.


Differential changes in gene expression in human brain during late first trimester and early second trimester of pregnancy.

Iruretagoyena JI, Davis W, Bird C, Olsen J, Radue R, Teo Broman A, Kendziorski C, Splinter BonDurant S, Golos T, Bird I, Shah D.

Prenat Diagn. 2014 May;34(5):431-7. doi: 10.1002/pd.4322. Epub 2014 Feb 5.


Extending information retrieval methods to personalized genomic-based studies of disease.

Ye S, Dawson JA, Kendziorski C.

Cancer Inform. 2015 Feb 10;13(Suppl 7):85-95. doi: 10.4137/CIN.S16354. eCollection 2014.


Enhanced cellular responses and distinct gene profiles in human fetoplacental artery endothelial cells under chronic low oxygen.

Jiang YZ, Wang K, Li Y, Dai CF, Wang P, Kendziorski C, Chen DB, Zheng J.

Biol Reprod. 2013 Dec 5;89(6):133. doi: 10.1095/biolreprod.113.110551. Print 2013 Dec.


Discovery of structural alterations in solid tumor oligodendroglioma by single molecule analysis.

Ray M, Goldstein S, Zhou S, Potamousis K, Sarkar D, Newton MA, Esterberg E, Kendziorski C, Bogler O, Schwartz DC.

BMC Genomics. 2013 Jul 26;14:505. doi: 10.1186/1471-2164-14-505.


The gene desert mammary carcinoma susceptibility locus Mcs1a regulates Nr2f1 modifying mammary epithelial cell differentiation and proliferation.

Smits BM, Haag JD, Rissman AI, Sharma D, Tran A, Schoenborn AA, Baird RC, Peiffer DS, Leinweber DQ, Muelbl MJ, Meilahn AL, Eichelberg MR, Leng N, Kendziorski C, John MC, Powers PA, Alexander CM, Gould MN.

PLoS Genet. 2013 Jun;9(6):e1003549. doi: 10.1371/journal.pgen.1003549. Epub 2013 Jun 13.


Transcriptional and functional adaptations of human endothelial cells to physiological chronic low oxygen.

Jiang YZ, Wang K, Li Y, Dai CF, Wang P, Kendziorski C, Chen DB, Zheng J.

Biol Reprod. 2013 May 9;88(5):114. doi: 10.1095/biolreprod.113.108225. Print 2013 May.


EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments.

Leng N, Dawson JA, Thomson JA, Ruotti V, Rissman AI, Smits BM, Haag JD, Gould MN, Stewart RM, Kendziorski C.

Bioinformatics. 2013 Apr 15;29(8):1035-43. doi: 10.1093/bioinformatics/btt087. Epub 2013 Feb 21. Erratum in: Bioinformatics. 2013 Aug 15;29(16):2073.


The IRP1-HIF-2α axis coordinates iron and oxygen sensing with erythropoiesis and iron absorption.

Anderson SA, Nizzi CP, Chang YI, Deck KM, Schmidt PJ, Galy B, Damnernsawad A, Broman AT, Kendziorski C, Hentze MW, Fleming MD, Zhang J, Eisenstein RS.

Cell Metab. 2013 Feb 5;17(2):282-90. doi: 10.1016/j.cmet.2013.01.007.


Integrative analysis of a cross-loci regulation network identifies App as a gene regulating insulin secretion from pancreatic islets.

Tu Z, Keller MP, Zhang C, Rabaglia ME, Greenawalt DM, Yang X, Wang IM, Dai H, Bruss MD, Lum PY, Zhou YP, Kemp DM, Kendziorski C, Yandell BS, Attie AD, Schadt EE, Zhu J.

PLoS Genet. 2012;8(12):e1003107. doi: 10.1371/journal.pgen.1003107. Epub 2012 Dec 6.


A dominantly acting murine allele of Mcm4 causes chromosomal abnormalities and promotes tumorigenesis.

Bagley BN, Keane TM, Maklakova VI, Marshall JG, Lester RA, Cancel MM, Paulsen AR, Bendzick LE, Been RA, Kogan SC, Cormier RT, Kendziorski C, Adams DJ, Collier LS.

PLoS Genet. 2012;8(11):e1003034. doi: 10.1371/journal.pgen.1003034. Epub 2012 Nov 1.


Pathway index models for construction of patient-specific risk profiles.

Eng KH, Wang S, Bradley WH, Rader JS, Kendziorski C.

Stat Med. 2013 Apr 30;32(9):1524-35. doi: 10.1002/sim.5641. Epub 2012 Oct 16.


Tsc2, a positional candidate gene underlying a quantitative trait locus for hepatic steatosis.

Wang CY, Stapleton DS, Schueler KL, Rabaglia ME, Oler AT, Keller MP, Kendziorski CM, Broman KW, Yandell BS, Schadt EE, Attie AD.

J Lipid Res. 2012 Aug;53(8):1493-501. doi: 10.1194/jlr.M025239. Epub 2012 May 23.


R/EBcoexpress: an empirical Bayesian framework for discovering differential co-expression.

Dawson JA, Ye S, Kendziorski C.

Bioinformatics. 2012 Jul 15;28(14):1939-40. doi: 10.1093/bioinformatics/bts268. Epub 2012 May 16.

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