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Publications

**All work performed by the University of Rochester Genomics Research Center (GRC) should be acknowledged in scholarly publications, posters, and oral presentations. Proper recognition allows us to measure the impact of our work and supports our initiatives in obtaining sponsored funding. In addition, any GRC personnel who make a substantial intellectual or experimental contribution are deserving of further recognition as co-author on any published material at the discretion of the Director and Principal Investigator.  Please send citations of any published material to John Ashton or Michelle Zanche.**

We are proud to share the following publications supported by the Genomics Research Center:

 

2019

Transcriptomic analysis of cellular pathways in healing flexor tendons of plasminogen activator inhibitor 1 (PAI-1/Serpine1) null mice. Freeberg MAT, Easa A, Lillis JA, Benoit DSW, van Wijnen AJ, Awad HA. J Orthop Res. 2019 Aug 19. doi: 10.1002/jor.24448. [Epub ahead of print] PMID: 31424116

Early life exposures shape the CD4+ T cell transcriptome, influencing proliferation, differentiation, and mitochondrial dynamics later in life.  Burke CG, Myers JR, Boule LA, Post CM, Brookes PS, Lawrence BP.Sci Rep. 2019 Aug 7;9(1):11489. doi: 10.1038/s41598-019-47866-2.  PMID: 31391494

Wang W, Friedland SC, Guo B, O'Dell MR, Alexander WB, Whitney-Miller CL, Agostini-Vulaj D, Huber AR, Myers JR, Ashton JM, Dunne RF, Steiner LA, Hezel AF. ARID1A, a SWI/SNF subunit, is critical to acinar cell homeostasis and regeneration and is a barrier to transformation and epithelial-mesenchymal transition in the pancreas. Gut.2019 Jul;68(7):1245-1258. doi: 10.1136/gutjnl-2017-315541. Epub 2018 Sep 18. PubMed PMID: 30228219; PubMed Central PMCID: PMC6551318.

Genome-Wide Transcriptional Analysis Reveals Novel AhR Targets That Regulate Dendritic Cell Function during Influenza A Virus Infection. Franchini AM, Myers JR, Jin GB, Shepherd DM, Lawrence BP.  Immunohorizons. 2019 Jun 17;3(6):219-235. doi: 10.4049/immunohorizons.1900004.  PMID: 31356168.

Li D, Chiu G, Lipe B, Hopkins RA, Lillis J, Ashton JM, Paul S, Aljitawi OS. Decellularized Wharton jelly matrix: a biomimetic scaffold for ex vivo hematopoietic stem cell culture. Blood Adv. 2019 Apr 9;3(7):1011-1026. doi: 10.1182/bloodadvances.2018019315. PubMed PMID: 30940636; PubMed Central PMCID: PMC6457237.

Adane B, Ye H, Khan N, Pei S, Minhajuddin M, Stevens BM, Jones CL, D'Alessandro A, Reisz JA, Zaberezhnyy V, Gasparetto M, Ho TC, Kelly KK, Myers JR, Ashton JM, Siegenthaler J, Kume T, Campbell EL, Pollyea DA, Becker MW, Jordan CT. The Hematopoietic Oxidase NOX2 Regulates Self-Renewal of Leukemic Stem Cells. Cell Rep. 2019 Apr 2;27(1):238-254.e6. doi: 10.1016/j.celrep.2019.03.009. PubMed PMID: 30943405.

Frisch BJ, Hoffman CM, Latchney SE, LaMere MW, Myers J, Ashton J, Li AJ, Saunders J 2nd, Palis J, Perkins AS, McCabe A, Smith JN, McGrath KE, Rivera-Escalera F, McDavid A, Liesveld JL, Korshunov VA, Elliott MR, MacNamara KC, Becker MW, Calvi LM. Aged marrow macrophages expand platelet-biased hematopoietic stem cells via Interleukin1B. JCI Insight. 2019 Apr 18;5. doi: 10.1172/jci.insight.124213. PubMed PMID: 30998506; PubMed Central PMCID: PMC6542605.

Wang Q, Bhattacharya S, Mereness JA, Anderson C, Lillis JA, Misra RS, Romas S, Huyck H, Howell A, Bandyopadhyay G, Donlon K, Myers JR, Ashton J, Pryhuber GS, Mariani TJ. A novel in vitro model of primary human pediatric lung epithelial cells. Pediatr Res.2019 Feb 18;. doi: 10.1038/s41390-019-0340-9. [Epub ahead of print] PubMed PMID: 30776794; PubMed Central PMCID: PMC6698433.

Hernandez G, Mills TS, Rabe JL, Chavez JS, Kuldanek S, Kirkpatrick G, Noetzli L, Jubair WK, Zanche M, Meyers JR, Stevens BM, Fleenor CJ, Adane B, Dinarello CA, Ashton J, Jordan CT, Di Paola J, Hagman JR, Holers VM, Kuhn KA, Pietras EM. Pro-inflammatory cytokine blockade attenuates myeloid expansion in a murine model of rheumatoid arthritis. Haematologica. 2019 May 17;. doi: 10.3324/haematol.2018.197210. [Epub ahead of print] PubMed PMID: 31101752.Defining nonsense-mediated mRNA decay intermediates in human cells. Kurosaki T, Myers JR, Maquat LE.  Methods. 2019 Feb 15;155:68-76. doi: 10.1016/j.ymeth.2018.12.005. Epub 2018 Dec 19. Review. PMID: 30576707

2018

SENCR stabilizes vascular endothelial cell adherens junctions through interaction with CKAP4.  Lyu Q, Xu S, Lyu Y, Choi M, Christie CK, Slivano OJ, Rahman A, Jin ZG, Long X, Xu Y, Miano JM. Proc Natl Acad Sci U S A. 2019 Jan 8;116(2):546-555. doi: 10.1073/pnas.1810729116. Epub 2018 Dec 24. PMID: 30584103

Neonatal gut and respiratory microbiota: coordinated development through time and space.  Alex Grier, Andrew McDavid, Bokai Wang, Xing Qiu, James Java, Sanjukta Bandyopadhyay, Hongmei Yang, Jeanne Holden-Wiltse, Haeja A Kessler, Ann L Gill, Heidie Huyck, Ann R Falsey, David J Topham, Kristin M Scheible, Mary T Caserta, Gloria S Pryhuber, Steven R Gill.  Microbiome. 2018; 6: 193. Published online 2018 Oct 26. doi: 10.1186/s40168-018-0566-5.  PMCID: PMC6204011

Mechanosensitive Gene Regulation by Myocardin-Related Transcription Factors Is Required for Cardiomyocyte Integrity in Load-Induced Ventricular Hypertrophy. Trembley MA, Quijada P, Agullo-Pascual E, Tylock KM, Colpan M, Dirkx RA Jr, Myers JR, Mickelsen DM, de Mesy Bentley K, Rothenberg E, Moravec CS, Alexis JD, Gregorio CC, Dirksen RT, Delmar M, Small EM.Circulation. 2018 Oct 23;138(17):1864-1878. doi: 10.1161/CIRCULATIONAHA.117.031788.  PMID: 29716942

NMD-degradome sequencing reveals ribosome-bound intermediates with 3'-end non-templated nucleotides.  Kurosaki T, Miyoshi K, Myers JR, Maquat LE. Nat Struct Mol Biol. 2018 Oct;25(10):940-950. doi: 10.1038/s41594-018-0132-7. Epub 2018 Oct 1. Erratum in: Nat Struct Mol Biol. 2018 Nov;25(11):1059. PMID:30275517.

Ye H, Adane B, Khan N, Alexeev E, Nusbacher N, Minhajuddin M, Stevens BM, Winters AC, Lin X, Ashton JM, Purev E, Xing L, Pollyea DA, Lozupone CA, Serkova NJ, Colgan SP, Jordan CT. Subversion of Systemic Glucose Metabolism as a Mechanism to Support the Growth of Leukemia Cells. Cancer Cell. 2018 Oct 8;34(4):659-673.e6. doi: 10.1016/j.ccell.2018.08.016. Epub 2018 Sep 27. PubMed PMID: 30270124; PubMed Central PMCID: PMC6177322.

Bandyopadhyay G, Huyck HL, Misra RS, Bhattacharya S, Wang Q, Mereness J, Lillis J, Myers JR, Ashton J, Bushnell T, Cochran M, Holden-Wiltse J, Katzman P, Deutsch G, Whitsett JA, Xu Y, Mariani TJ, Pryhuber GS. Dissociation, cellular isolation, and initial molecular characterization of neonatal and pediatric human lung tissues. Am J Physiol Lung Cell Mol Physiol. 2018 Oct 1;315(4):L576-L583. doi: 10.1152/ajplung.00041.2018. Epub 2018 Jul 5. PubMed PMID: 29975103; PubMed Central PMCID: PMC6230879.

Pei S, Minhajuddin M, Adane B, Khan N, Stevens BM, Mack SC, Lai S, Rich JN, Inguva A, Shannon KM, Kim H, Tan AC, Myers JR, Ashton JM, Neff T, Pollyea DA, Smith CA, Jordan CT. AMPK/FIS1-Mediated Mitophagy Is Required for Self-Renewal of Human AML Stem Cells. Cell Stem Cell. 2018 Jul 5;23(1):86-100.e6. doi: 10.1016/j.stem.2018.05.021. Epub 2018 Jun 14. PubMed PMID: 29910151; PubMed Central PMCID: PMC6035102.

Schott EM, Farnsworth CW, Grier A, Lillis JA, Soniwala S, Dadourian GH, Bell RD, Doolittle ML, Villani DA, Awad H, Ketz JP, Kamal F, Ackert-Bicknell C, Ashton JM, Gill SR, Mooney RA, Zuscik MJ. Targeting the gut microbiome to treat the osteoarthritis of obesity. JCI Insight. 2018 Apr 19;3(8). doi: 10.1172/jci.insight.95997. eCollection 2018 Apr 19. PubMed PMID: 29669931; PubMed Central PMCID: PMC5931133.

Wong, E.L., Lutz, N.M., Hogan, V.A., Lamantia, C.E., McMurray, H.R., Myers, J.R., Ashton, J.M., and Majewska, A.K. (2017). Developmental alcohol exposure impairs synaptic plasticity without overtly altering microglialfunction in mouse visual cortex. Brain BehavImmun.

2017

Wong, E.L., Lutz, N.M., Hogan, V.A., Lamantia, C.E., McMurray, H.R., Myers, J.R., Ashton, J.M., and Majewska, A.K. (2017). Developmental alcohol exposure impairs synaptic plasticity without overtly altering microglial function in mouse visual cortex. Brain Behav Immun.

Elbarbary, R.A., Miyoshi, K., Hedaya, O., Myers, J.R., and Maquat, L.E. (2017). UPF1 helicase promotes TSN-mediated miRNA decay. Genes Dev 31, 1483-1493.

Bhattacharya S, Rosenberg AF, Peterson DR, Grzesik K, Baran AM, Ashton JM, Gill SR, Corbett AM, Holden-Wiltse J, Topham DJ, Walsh EE, Mariani TJ, Falsey AR. "Transcriptomic Biomarkers to Discriminate Bacterial from Nonbacterial Infection in Adults Hospitalized with Respiratory Illness." Scientific reports. 2017 Jul 26; 7(1):6548. Epub 2017 Jul 26.

Martinson, E. O., Mrinalini, Kelkar, Y. D., Chang, C. H., & Werren, J. H. (2017). The Evolution of Venom by Co-option of Single-Copy Genes. Curr Biol, 27(13), 2007-2013 e2008. doi:10.1016/j.cub.2017.05.032.

Beach, T. A., C. J. Johnston, A. M. Groves, J. P. Williams and J. N. Finkelstein (2017). "Radiation induced pulmonary fibrosis as a model of progressive fibrosis: Contributions of DNA damage, inflammatory response and cellular senescence genes." Exp Lung Res 43(3): 134-149.

Elbarbary, R. A., K. Miyoshi, J. R. Myers, P. Du, J. M. Ashton, B. Tian and L. E. Maquat (2017). "Tudor-SN-mediated endonucleolytic decay of human cell microRNAs promotes G1/S phase transition." Science 356(6340): 859-862.

Farnsworth, C. W., E. M. Schott, S. E. Jensen, J. Zukoski, A. M. Benvie, M. A. Refaai, S. L. Kates, E. M. Schwarz, M. J. Zuscik, S. R. Gill and R. A. Mooney (2017). "Adaptive Upregulation of Clumping Factor A (ClfA) by Staphylococcus aureus in the Obese, Type 2 Diabetic Host Mediates Increased Virulence." Infect Immun 85(6).

Gasparetto, M., S. Pei, M. Minhajuddin, N. Khan, D. A. Pollyea, J. R. Myers, J. M. Ashton, M. W. Becker, V. Vasiliou, K. R. Humphries, C. T. Jordan and C. A. Smith (2017). "Targeted therapy for a subset of acute myeloid leukemias that lack expression of aldehyde dehydrogenase 1A1." Haematologica 102(6): 1054-1065.

Hilimire, T. A., J. M. Chamberlain, V. Anokhina, R. P. Bennett, O. Swart, J. R. Myers, J. M. Ashton, R. A. Stewart, A. L. Featherston, K. Gates, E. D. Helms, H. C. Smith, S. Dewhurst and B. L. Miller (2017). "HIV-1 Frameshift RNA-Targeted Triazoles Inhibit Propagation of Replication-Competent and Multi-Drug-Resistant HIV in Human Cells." ACS Chem Biol 12(6): 1674-1682.

Le Bleu, H. K., F. A. Kamal, M. Kelly, J. P. Ketz, M. J. Zuscik and R. A. Elbarbary (2017). "Extraction of high-quality RNA from human articular cartilage." Anal Biochem 518: 134-138.

Nakatsuji, T., T. H. Chen, S. Narala, K. A. Chun, A. M. Two, T. Yun, F. Shafiq, P. F. Kotol, A. Bouslimani, A. V. Melnik, H. Latif, J. N. Kim, A. Lockhart, K. Artis, G. David, P. Taylor, J. Streib, P. C. Dorrestein, A. Grier, S. R. Gill, K. Zengler, T. R. Hata, D. Y. Leung and R. L. Gallo (2017). "Antimicrobials from human skin commensal bacteria protect against Staphylococcus aureus and are deficient in atopic dermatitis." Sci Transl Med 9(378).

Shen, J., C. Wang, D. Li, T. Xu, J. Myers, J. M. Ashton, T. Wang, M. J. Zuscik, A. McAlinden and R. J. O'Keefe (2017). "DNA methyltransferase 3b regulates articular cartilage homeostasis by altering metabolism." JCI Insight 2(12).

Yang, F., L. Zhang, H. Wakabayashi, J. Myers, Y. Jiang, Y. Cao, C. Jimenez-Ortigosa, D. S. Perlin and E. Rustchenko (2017). "Tolerance to Caspofungin in Candida albicans Is Associated with at Least Three Distinctive Mechanisms That Govern Expression of FKS Genes and Cell Wall Remodeling." Antimicrob Agents Chemother 61(5).

2016

Berrondo, C., Flax, J., Kucherov, V., Siebert, A., Osinski, T., Rosenberg, A., Fucile, C., Richheimer, S., and Beckham, C.J. (2016). Expression of the Long Non-Coding RNA HOTAIR Correlates with Disease Progression in Bladder Cancer and Is Contained in Bladder Cancer Patient Urinary Exosomes. PLoS One 11, e0147236.

Chu, C. Y., X. Qiu, L. Wang, S. Bhattacharya, G. Lofthus, A. Corbett, J. Holden-Wiltse, A. Grier, B. Tesini, S. R. Gill, A. R. Falsey, M. T. Caserta, E. E. Walsh and T. J. Mariani (2016). "The Healthy Infant Nasal Transcriptome: A Benchmark Study." Sci Rep 6: 33994.

Ho, T. C., M. LaMere, B. M. Stevens, J. M. Ashton, J. R. Myers, K. M. O'Dwyer, J. L. Liesveld, J. H. Mendler, M. Guzman, J. D. Morrissette, J. Zhao, E. S. Wang, M. Wetzler, C. T. Jordan and M. W. Becker (2016). "Evolution of acute myelogenous leukemia stem cell properties after treatment and progression." Blood 128(13): 1671-1678.

Li, X., N. Chatterjee, K. Spirohn, M. Boutros and D. Bohmann (2016). "Cdk12 Is A Gene-Selective RNA Polymerase II Kinase That Regulates a Subset of the Transcriptome, Including Nrf2 Target Genes." Sci Rep 6: 21455.

Malcolm, D. W., J. E. Sorrells, D. Van Twisk, J. Thakar and D. S. Benoit (2016). "Evaluating side effects of nanoparticle-mediated siRNA delivery to mesenchymal stem cells using next generation sequencing and enrichment analysis." Bioeng Transl Med 1(2): 193-206.

Misra, R. S., S. Bhattacharya, H. L. Huyck, J. C. Wang, C. G. Slaunwhite, S. L. Slaunwhite, T. R. Wightman, S. Secor-Socha, S. K. Misra, T. P. Bushnell, A. M. Reynolds, R. M. Ryan, S. A. Quataert, G. S. Pryhuber and T. J. Mariani (2016). "Flow-based sorting of neonatal lymphocyte populations for transcriptomics analysis." J Immunol Methods 437: 13-20.

Nedelkovska, H., A. F. Rosenberg, S. P. Hilchey, O. Hyrien, W. R. Burack, S. A. Quataert, C. M. Baker, M. Azadniv, S. L. Welle, S. M. Ansell, M. Kim and S. H. Bernstein (2016). "Follicular Lymphoma Tregs Have a Distinct Transcription Profile Impacting Their Migration and Retention in the Malignant Lymph Node." PLoS One 11(5): e0155347.

Pei, S., M. Minhajuddin, A. D'Alessandro, T. Nemkov, B. M. Stevens, B. Adane, N. Khan, F. K. Hagen, V. K. Yadav, S. De, J. M. Ashton, K. C. Hansen, J. A. Gutman, D. A. Pollyea, P. A. Crooks, C. Smith and C. T. Jordan (2016). "Rational design of a parthenolide-based drug regimen that selectively eradicates acute myelogenous leukemia stem cells." J Biol Chem 291(48): 25280.

Ye, H., B. Adane, N. Khan, T. Sullivan, M. Minhajuddin, M. Gasparetto, B. Stevens, S. Pei, M. Balys, J. M. Ashton, D. J. Klemm, C. M. Woolthuis, A. W. Stranahan, C. Y. Park and C. T. Jordan (2016). "Leukemic Stem Cells Evade Chemotherapy by Metabolic Adaptation to an Adipose Tissue Niche." Cell Stem Cell 19(1): 23-37.

2015

Baras, A. S., C. J. Mitchell, J. R. Myers, S. Gupta, L. C. Weng, J. M. Ashton, T. C. Cornish, A. Pandey and M. K. Halushka (2015). "miRge - A Multiplexed Method of Processing Small RNA-Seq Data to Determine MicroRNA Entropy." PLoS One 10(11): e0143066.

Garrigan, D., S. B. Kingan, A. J. Geneva, J. P. Vedanayagam and D. C. Presgraves (2015). "Genome Diversity and Divergence in Drosophila mauritiana: Multiple Signatures of Faster X Evolution." Genome Biol Evol 7(5): 1331.

Hansen, J., C. Snow, E. Tuttle, D. H. Ghoneim, C. S. Yang, A. Spencer, S. A. Gunter, C. D. Smyser, C. A. Gurnett, M. Shinawi, W. B. Dobyns, J. Wheless, M. W. Halterman, L. A. Jansen, B. M. Paschal and A. R. Paciorkowski (2015). "De novo mutations in SIK1 cause a spectrum of developmental epilepsies." Am J Hum Genet 96(4): 682-690.

Merkley, M. A., T. C. Bice, A. Grier, A. M. Strohl, L. X. Man and S. R. Gill (2015). "The effect of antibiotics on the microbiome in acute exacerbations of chronic rhinosinusitis." Int Forum Allergy Rhinol 5(10): 884-893.

Sharma-Kuinkel, B. K., E. F. Mongodin, J. R. Myers, K. L. Vore, G. S. Canfield, C. M. Fraser, T. H. Rude, V. G. Fowler, Jr. and S. R. Gill (2015). "Potential Influence of Staphylococcus aureus Clonal Complex 30 Genotype and Transcriptome on Hematogenous Infections." Open Forum Infect Dis 2(3): ofv093.

Sivagnanalingam, U., M. Balys, A. Eberhardt, N. Wang, J. R. Myers, J. M. Ashton, M. W. Becker, L. M. Calvi and J. H. Mendler (2015). "Residual Disease in a Novel Xenograft Model of RUNX1-Mutated, Cytogenetically Normal Acute Myeloid Leukemia." PLoS One 10(7): e0132375.

Bennett, J. A., K. P. Singh, Z. Unnisa, S. L. Welle and T. A. Gasiewicz (2015). "Deficiency in Aryl Hydrocarbon Receptor (AHR) Expression throughout Aging Alters Gene Expression Profiles in Murine Long-Term Hematopoietic Stem Cells." PLoS One 10(7): e0133791.

2014

Dardas, M., S. R. Gill, A. Grier, G. S. Pryhuber, A. L. Gill, Y. H. Lee and R. Guillet (2014). "The impact of postnatal antibiotics on the preterm intestinal microbiome." Pediatr Res 76(2): 150-158.

Garrigan, D., S. B. Kingan, A. J. Geneva, J. P. Vedanayagam and D. C. Presgraves (2014). "Genome diversity and divergence in Drosophila mauritiana: multiple signatures of faster X evolution." Genome Biol Evol 6(9): 2444-2458.

Ghoneim, D. H., J. R. Myers, E. Tuttle and A. R. Paciorkowski (2014). "Comparison of insertion/deletion calling algorithms on human next-generation sequencing data." BMC Res Notes 7: 864.

Militello, K. T., L. M. Chen, S. E. Ackerman, A. H. Mandarano and E. L. Valentine (2014). "A map of 5-methylcytosine residues in Trypanosoma brucei tRNA revealed by sodium bisulfite sequencing." Mol Biochem Parasitol 193(2): 122-126.

Singh, K. P., J. A. Bennett, F. L. Casado, J. L. Walrath, S. L. Welle and T. A. Gasiewicz (2014). "Loss of aryl hydrocarbon receptor promotes gene changes associated with premature hematopoietic stem cell exhaustion and development of a myeloproliferative disorder in aging mice." Stem Cells Dev 23(2): 95-106.

2013

Edholm, E. S., L. M. Albertorio Saez, A. L. Gill, S. R. Gill, L. Grayfer, N. Haynes, J. R. Myers and J. Robert (2013). "Nonclassical MHC class I-dependent invariant T cells are evolutionarily conserved and prominent from early development in amphibians." Proc Natl Acad Sci U S A 110(35): 14342-14347.

Lagadinou, E. D., A. Sach, K. Callahan, R. M. Rossi, S. J. Neering, M. Minhajuddin, J. M. Ashton, S. Pei, V. Grose, K. M. O'Dwyer, J. L. Liesveld, P. S. Brookes, M. W. Becker and C. T. Jordan (2013). "BCL-2 inhibition targets oxidative phosphorylation and selectively eradicates quiescent human leukemia stem cells." Cell Stem Cell 12(3): 329-341.

Pei, S., M. Minhajuddin, K. P. Callahan, M. Balys, J. M. Ashton, S. J. Neering, E. D. Lagadinou, C. Corbett, H. Ye, J. L. Liesveld, K. M. O'Dwyer, Z. Li, L. Shi, P. Greninger, J. Settleman, C. Benes, F. K. Hagen, J. Munger, P. A. Crooks, M. W. Becker and C. T. Jordan (2013). "Targeting aberrant glutathione metabolism to eradicate human acute myelogenous leukemia cells." J Biol Chem 288(47): 33542-33558.

2012

Ashton, J. M., M. Balys, S. J. Neering, D. C. Hassane, G. Cowley, D. E. Root, P. G. Miller, B. L. Ebert, H. R. McMurray, H. Land and C. T. Jordan (2012). "Gene sets identified with oncogene cooperativity analysis regulate in vivo growth and survival of leukemia stem cells." Cell Stem Cell 11(3): 359-372.

2011

Casado, F. L., K. P. Singh and T. A. Gasiewicz (2011). "Aryl hydrocarbon receptor activation in hematopoietic stem/progenitor cells alters cell function and pathway-specific gene modulation reflecting changes in cellular trafficking and migration." Mol Pharmacol 80(4): 673-682.