URMC / Research / Rochester Genomics Center / Publications

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 Elizabeth Pritchett.**
GRC RRID: SCR_012359

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

2024

Srivastava Y, Akinyemi O, Rohe TC, Pritchett EM, Baker CD, Sharma A, Jenkins JJ, Mathews DH, Wedekind JE. Two riboswitch classes that share a common ligand-binding fold show major differences in the ability to accommodate mutations. Nucleic Acids Research, Volume 52, Issue 21, 27 November 2024, Pages 13152–13173, https://doi.org/10.1093/nar/gkae886

Knudsen-Clark AM, Mwangi D, Cazarin J, Morris K, Baker CD, Hablitz LM, McCall MN, Kim M, Altman BJ. Circadian rhythms of macrophages are altered by the acidic tumor microenvironment. EMBO Rep. 2024 Nov;25(11):5080-5112. doi: 10.1038/s44319-024-00288-2. Epub 2024 Oct 16. PMID: 39415049

Hughson AL, Hannon G, Salama NA, Vrooman TG, Stockwell CA, Mills BN, Garrett-Larsen J, Qui H, Katerji R, Benoodt L, Johnston CJ, Murphy JD, Kruger E, Ye J, Gavras NW, Keeley DC, Qin SS, Lesch ML, Muhitch JB, Love TMT, Calvi LM, Lord EM, Luheshi N, Elyes J, Linehan DC, Gerber SA. Integrating IL-12 mRNA nanotechnology with SBRT eliminates T cell exhaustion in preclinical models of pancreatic cancer. Mol Ther Nucleic Acids. 2024 Sep 30;35(4):102350. doi: 10.1016/j.omtn.2024.102350

Li C, Ture SK, Nieves-Lopez B, Blick-Nitko SK, Maurya P, Livada AC, Stahl TJ, Kim M, Pietropaoli AP, Morrell CN. Thrombocytopenia Independently Leads to Changes in Monocyte Immune Function. Circ Res. 2024 Apr 12;134(8):970-986.doi: 10.1161/CIRCRESAHA.123.323662. Epub 2024 Mar 8 PMID: 38456277

Asantewaa G, Tuttle ET, Ward NP, Kang YP, Kim Y, Kavanagh ME, Girnius N, Chen Y, Rodriguez K, Hecht F, Zocchi M, Smorodintsev-Schiller L, Scales TQ, Taylor K, Alimohammadi F, Duncan RP, Sechrist ZR, Agostini-Vulaj D, Schafer XL, Chang H, Smith ZR, O'Connor TN, Whelan S, Selfors LM, Crowdis J, Gray GK, Bronson RT, Brenner D, Rufini A, Dirksen RT, Hezel AF, Huber AR, Munger J, Cravatt BF, Vasiliou V, Cole CL, DeNicola GM, Harris IS. Glutathione synthesis in the mouse liver supports lipid abundance through NRF2 repression. Nat Commun. 2024;15(1):6152. PMCID: PMC11271484.

Lin MH, Jensen MK, Elrod ND, Chu HF, Haseley M, Beam AC, Huang KL, Chiang W, Russell WK, Williams K, Proschel C, Wagner EJ, Tong L. Cytoplasmic binding partners of the Integrator endonuclease INTS11 and its paralog CPSF73 are required for their nuclear function. Mol Cell. 2024;. PMCID: PMC11316654.

Sahasrabudhe DM, Liesveld JL, Minhajuddin M, Singh NA, Nath S, Kumar VM, Balys M, Evans AG, Azadniv M, Hansen JN, Becker MW, Sharon A, Thomas VK, Moore RG, Khera MK, Jordan CT, Singh RK. In silico predicted compound targeting the IQGAP1-GRD domain selectively inhibits growth of human acute myeloid leukemia. Sci Rep. 2024;14(1):12868. PMCID: PMC11150481.

Ciesla J, Huang KL, Wagner EJ, Munger J. A UL26-PIAS1 complex antagonizes anti-viral gene expression during Human Cytomegalovirus infection. PLoS Pathog. 2024;20(5):e1012058. PMCID: PMC11142722.

Rambout X, Maquat LE. Nuclear mRNA decay: regulatory networks that control gene expression. Nat Rev Genet. 2024;. PMCID: PMC11408106.

Alexander WB, Wang W, Hill MA, O'Dell MR, Ruffolo LI, Guo B, Jackson KM, Ullman N, Friedland SC, McCall MN, Patel A, Figueroa-Guilliani N, Georger M, Belt BA, Whitney-Miller CL, Linehan DC, Murphy PJ, Hezel AF. Smad4 restricts injury-provoked biliary proliferation and carcinogenesis. Dis Model Mech. 2024;17(6). PMCID: PMC10924230.

Loh KP, Wang Y, Sanapala C, Gilmore N, Netherby-Winslow C, Mendler JH, Liesveld J, Huselton E, Williams AM, Klepin HD, Jensen-Battaglia M, Mustian K, Vertino P, Susiarjo M, Janelsins MC. Exercise and inflammatory cytokine regulation among older adults with myeloid malignancies. Exp Gerontol. 2024;:112364. PMCID: PMC10923152.

Halblander FN, Meng FW, Murphy PJ. Anp32e protects against accumulation of H2A.Z at Sox motif containing promoters during zebrafish gastrulation. Dev Biol. 2024;. PMCID: PMC10922954.

Raymonda MH, Rodriguez-Sanchez I, Schafer XL, Smorodintsev-Schiller L, Harris IS, Munger J. Cytomegalovirus-induced inactivation of TSC2 disrupts the coupling of fatty acid biosynthesis to glucose availability resulting in a vulnerability to glucose starvation. mBio. 2024;:e0303123. PMCID: PMC10790783.

2023

Kenney MH, Rangel-Moreno J, Peng Y, Chen KL, Bruno J, Embong A, Pritchett EM, Fox JI, Becerril-Villanueva E, Gamboa-Dominguez A, Quataert S, Muthukrishnan G, Wood RW, Korman BD, Anolik JH, Xing L, Ritchlin CT, Schwarz EM, Wu CL. Multi-omics analysis identifies IgG2b class-switching with ALCAM-CD6 co-stimulation in joint-draining lymph nodes during advanced inflammatory-erosive arthritis. Front Immunol. 2023 Aug:25:14:1237498. doi: 10.3389/fimmu.2023.1237498. eCollection 2023.

Alkhars N, Gaca A, Zeng Y, Al-Jallad N, Rustchenko E, Wu TT, Eliav E, Xiao J. Antifungal Susceptibility of Oral Candida Isolates from Mother-Infant Dyads to Nystatin, Fluconazole, and Caspofungin. J Fungi (Basel). 2023 May 17;9(5):580. doi: 10.3390/jof9050580. PMID: 37233291

Schroeder GM, Akinyemi O, Malik J, Focht CM, Pritchett EM, Baker CD, McSally JP, Jenkins JJ, Mathews DH, Wedekind JE. A riboswitch separated from its ribosome-binding site still regulates translation. Nucleic Acids Res. 2023 Mar 21;51(5):2464-2484. doi: 10.1093/nar/gkad056. PMID: 36762498

Liu X, Burke RM, Lighthouse JK, Baker CD, Dirkx RA Jr, Kang B, Chakraborty Y, Mickelsen DM, Twardowski JJ, Mello SS, Ashton JM, Small EM. p53 Regulates the Extent of Fibroblast Proliferation and Fibrosis in Left Ventricle Pressure Overload. Circ Res. 2023;133(3):271-287. PMCID: PMC10361635.

Meng FW, Murphy KE, Makowski CE, Delatte B, Murphy PJ. Competition for H2A.Z underlies the developmental impacts of repetitive element de-repression. Development. 2023;150(21). PMCID: PMC10651094.

Dudgeon C, Casabianca A, Harris C, Ogier C, Bellina M, Fiore S, Bernet A, Ducarouoge B, Goldschneider D, Su X, Pitarresi J, Hezel A, De S, Narrow W, Soliman F, Shields C, Vendramini-Costa DB, Prela O, Wang L, Astsaturov I, Mehlen P, Carpizo DR. Netrin-1 feedforward mechanism promotes pancreatic cancer liver metastasis via hepatic stellate cell activation, retinoid, and ELF3 signaling. Cell Rep. 2023;42(11):113369.

Mislati R, Uccello TP, Lin Z, Iliza KT, Toussaint KC, Gerber SA, Doyley MM. Shear wave elastography can stratify rectal cancer response to short-course radiation therapy. Sci Rep. 2023;13(1):16149. PMCID: PMC10522682.

Lv X, Murphy K, Murphy Z, Getman MR, Rahman NF, Nakamura Y, Blanc L, Gallagher PG, Palis J, Mohandas N, Steiner LA. HEXIM1 is an Essential Transcription Regulator During Human Erythropoiesis. Blood. 2023;. PMCID: PMC10733840.

Takasugi M, Ohtani N, Takemura K, Emmrich S, Zakusilo FT, Yoshida Y, Kutsukake N, Mariani JN, Windrem MS, Chandler-Militello D, Goldman SA, Satoh J, Ito S, Seluanov A, Gorbunova V. CD44 correlates with longevity and enhances basal ATF6 activity and ER stress resistance. Cell Rep. 2023;42(9):113130. PMCID: PMC10591879.

Cazarin J, DeRollo RE, Shahidan SNABA, Burchett JB, Mwangi D, Krishnaiah S, Hsieh AL, Walton ZE, Brooks R, Mello SS, Weljie AM, Dang CV, Altman BJ. MYC disrupts transcriptional and metabolic circadian oscillations in cancer and promotes enhanced biosynthesis. PLoS Genet. 2023;19(8):e1010904. PMCID: PMC10491404.

Zhang Z, Tian X, Lu JY, Boit K, Ablaeva J, Zakusilo FT, Emmrich S, Firsanov D, Rydkina E, Biashad SA, Lu Q, Tyshkovskiy A, Gladyshev VN, Horvath S, Seluanov A, Gorbunova V. Increased hyaluronan by naked mole-rat Has2 improves healthspan in mice. Nature. 2023;621(7977):196-205. PMCID: PMC10666664.

Wu J, Subbaiah KCV, Hedaya O, Chen S, Munger J, Tang WHW, Yan C, Yao P. FAM210A regulates mitochondrial translation and maintains cardiac mitochondrial homeostasis. Cardiovasc Res. 2023;. PMCID: PMC10651191.

Uccello TP, Lesch ML, Kintzel SA, Gradzewicz LB, Lamrous L, Murphy SP, Fleming FJ, Mills BN, Murphy JD, Hughson A, Hannon G, Garrett-Larsen J, Qiu H, Drage MG, Ye J, Gavras NW, Keeley DC, Love TMT, Repasky EA, Lord EM, Linehan DC, Gerber SA. New insights into the responder/nonresponder divide in rectal cancer: Damage-induced Type I IFNs dictate treatment efficacy and can be targeted to enhance radiotherapy. Cell Death Dis. 2023;14(7):470. PMCID: PMC10372053.

Quarato ER, Salama NA, Li AJ, Smith CO, Zhang J, Kawano Y, McArthur M, Liesveld JL, Becker MW, Elliott MR, Eliseev RA, Calvi LM. Efferocytosis by bone marrow mesenchymal stromal cells disrupts osteoblastic differentiation via mitochondrial remodeling. Cell Death Dis. 2023;14(7):428. PMCID: PMC10349065.

Sailer CJ, Hong Y, Dahal A, Ryan AT, Mir S, Gerber SA, Reagan PM, Kim M. PD-1(Hi) CAR-T cells provide superior protection against solid tumors. Front Immunol. 2023;14:1187850. PMCID: PMC10303811.

Ye J, Gavras NW, Keeley DC, Hughson AL, Hannon G, Vrooman TG, Lesch ML, Johnston CJ, Lord EM, Belt BA, Linehan DC, Eyles J, Gerber SA. CD73 and PD-L1 dual blockade amplifies antitumor efficacy of SBRT in murine PDAC models. J Immunother Cancer. 2023;11(5). PMCID: PMC10163599.

Gerber S, Uccello T, Lesch M, Kintzel S, Gradzewicz L, Lamrous L, Murphy S, Fleming F, Mills B, Murphy J, Hughson A, Garrett-Larsen J, Qiu H, Drage M, Ye J, Gavras N, Keeley D, Love T, Repasky E, Lord E, Linehan D. New insights into the responder/nonresponder divide in rectal cancer: Damage-induced Type I IFNs dictate treatment efficacy and can be targeted to enhance radiotherapy. Res Sq. 2023;. PMCID: PMC10120761.

Hong Y, Walling BL, Kim HR, Serratelli WS, Lozada JR, Sailer CJ, Amitrano AM, Lim K, Mongre RK, Kim KD, Capece T, Lomakina EB, Reilly NS, Vo K, Gerber SA, Fan TC, Yu AL, Oakes PW, Waugh RE, Jun CD, Reagan PM, Kim M. ST3GAL1 and Î²II-spectrin pathways control CAR T cell migration to target tumors. Nat Immunol. 2023;24(6):1007-1019. PMCID: PMC10515092.

Maurya P, Ture SK, Li C, Scheible KM, McGrath KE, Palis J, Morrell CN. Transfusion of Adult, but Not Neonatal, Platelets Promotes Monocyte Trafficking in Neonatal Mice. Arterioscler Thromb Vasc Biol. 2023;43(6):873-885. PMCID: PMC11419309.

Osborn RM, Leach J, Zanche M, Ashton JM, Chu C, Thakar J, Dewhurst S, Rosenberger S, Pavelka M, Pryhuber GS, Mariani TJ, Anderson CS. Preparation of noninfectious scRNAseq samples from SARS-CoV-2-infected epithelial cells. PLoS One. 2023;18(2):e0281898. PMCID: PMC9956660.

Groves AM, Misra R, Clair G, Hernady E, Olson H, Orton D, Finkelstein J, Marples B, Johnston CJ. Influence of the irradiated pulmonary microenvironment on macrophage and T cell dynamics. Radiother Oncol. 2023;183:109543. PMCID: PMC10238652.

de Prisco N, Ford C, Elrod ND, Lee W, Tang LC, Huang KL, Lin A, Ji P, Jonnakuti VS, Boyle L, Cabaj M, Botta S, Ã•unap K, Reinson K, Wojcik MH, Rosenfeld JA, Bi W, Tveten K, Prescott T, Gerstner T, Schroeder A, Fong CT, George-Abraham JK, Buchanan CA, Hanson-Khan A, Bernstein JA, Nella AA, Chung WK, Brandt V, Jovanovic M, Targoff KL, Yalamanchili HK, Wagner EJ, Gennarino VA. Alternative polyadenylation alters protein dosage by switching between intronic and 3'UTR sites. Sci Adv. 2023;9(7):eade4814. PMCID: PMC9937581.

Rambout X, Cho H, Blanc R, Lyu Q, Miano JM, Chakkalakal JV, Nelson GM, Yalamanchili HK, Adelman K, Maquat LE. PGC-1Î± senses the CBC of pre-mRNA to dictate the fate of promoter-proximally paused RNAPII. Mol Cell. 2023;83(2):186-202.e11. PMCID: PMC9951270.

Moreno I Jr, RodrÃguez-SÃ¡nchez I, Schafer X, Munger J. Human cytomegalovirus induces neuronal enolase to support virally mediated metabolic remodeling. Proc Natl Acad Sci U S A. 2022;119(49):e2205789119. PMCID: PMC9894225.

Groves AM, Paris N, Hernady E, Johnston CJ, Aljitawi O, Lee YF, Kerns SL, Marples B. Prevention of Radiation-Induced Bladder Injury: A Murine Study Using Captopril. Int J Radiat Oncol Biol Phys. 2023;115(4):972-982.

Kurosaki T, Mitsutomi S, Hewko A, Akimitsu N, Maquat LE. Integrative omics indicate FMRP sequesters mRNA from translation and deadenylation in human neuronal cells. Mol Cell. 2022;82(23):4564-4581.e11. PMCID: PMC9753132.

Uccello TP, Lesch ML, Ullman NA, Kintzel SA, Gradzewicz LB, Velagaleti T, Fleming FJ, Mills BN, Murphy JD, Garrett-Larsen J, Qiu H, Drage MG, Ye J, Gavras NW, Johnston CJ, Love TMT, Repasky EA, Linehan DC, Lord EM, Gerber SA. Radiation Therapy Exacerbates Tumor-Promoting Innervation and Nerve Signaling in Rectal Cancer. Int J Radiat Oncol Biol Phys. 2023;115(3):733-745. PMCID: PMC9898185.

2022

Ackerman JE, Best KT, Muscat SN, Pritchett EM, Nichols AE, Wu CL, Loiselle AE. Defining the spatial-molecular map of fibrotic tendon healing and the drivers of Scleraxis-lineage cell fate and function. Cell Rep. 2022 Nov; 41(8):111706. doi: 10.1016/j.celrep.2022.111706. PMID: 36417854

McMurray HR, Stern HA, Ambeskovic A, Land H, McCall MN. Protocol to use TopNet for gene regulatory network modeling using gene expression data from perturbation experiments. STAR Protoc. 2022;3(4):101737. PMCID: PMC9529586.

Guo B, Friedland SC, Alexander W, Myers JA, Wang W, O'Dell MR, Getman M, Whitney-Miller CL, Agostini-Vulaj D, Huber AR, Mello SS, Vertino PM, Land HK, Steiner LA, Hezel AF. Arid1a mutation suppresses TGF-Î² signaling and induces cholangiocarcinoma. Cell Rep. 2022;40(9):111253. PMCID: PMC9808599.

Trzeciak A, Mongre RK, Kim MR, Lim K, Madero RA, Parkhurst CN, Pietropaoli AP, Kim M. Neutrophil heterogeneity in complement C1q expression associated with sepsis mortality. Front Immunol. 2022;13:965305. PMCID: PMC9380571.

Battaglia NG, Murphy JD, Uccello TP, Hughson A, Gavras NW, Caldon JJ, Gerber SA, Lord EM. Combination of NKG2A and PD-1 Blockade Improves Radiotherapy Response in Radioresistant Tumors. J Immunol. 2022;209(3):629-640. PMCID: PMC9339479.

Ashton JM, Rehrauer H, Myers J, Myers J, Zanche M, Balys M, Foox J, Mason CE, Steen R, Kuentzel M, Aquino C, Garcia-Reyero N, Chittur SV. Comparative Analysis of Single-Cell RNA Sequencing Platforms and Methods. J Biomol Tech. 2021;32(4). PMCID: PMC9258609.

Ciesla J, Moreno I Jr, Munger J. TNFÎ±-induced metabolic reprogramming drives an intrinsic anti-viral state. PLoS Pathog. 2022;18(7):e1010722. PMCID: PMC9321404.

Manevski M, Devadoss D, Long C, Singh SP, Nasser MW, Borchert GM, Nair MN, Rahman I, Sopori M, Chand HS. Increased Expression of LASI lncRNA Regulates the Cigarette Smoke and COPD Associated Airway Inflammation and Mucous Cell Hyperplasia. Front Immunol. 2022;13:803362. PMCID: PMC9237255.

Emmrich S, Trapp A, Tolibzoda Zakusilo F, Straight ME, Ying AK, Tyshkovskiy A, Mariotti M, Gray S, Zhang Z, Drage MG, Takasugi M, Klusmann JH, Gladyshev VN, Seluanov A, Gorbunova V. Characterization of naked mole-rat hematopoiesis reveals unique stem and progenitor cell patterns and neotenic traits. EMBO J. 2022;41(15):e109694. PMCID: PMC9340489.

Yang J, Das BC, Aljitawi O, Kumar A, Das S, Van Veldhuizen P. Magmas Inhibition in Prostate Cancer: A Novel Target for Treatment-Resistant Disease. Cancers (Basel). 2022;14(11). PMCID: PMC9179500.

Sautchuk R, Kalicharan BH, Escalera-Rivera K, Jonason JH, Porter GA, Awad HA, Eliseev RA. Transcriptional regulation of cyclophilin D by BMP/Smad signaling and its role in osteogenic differentiation. Elife. 2022;11. PMCID: PMC9191891.

Kleckner AS, Kleckner IR, Culakova E, Wojtovich AP, Klinedinst NJ, Kerns SL, Hardy SJ, Inglis JE, Padula GDA, Mustian KM, Janelsins MC, Dorsey SG, Saligan LN, Peppone LJ. Exploratory Analysis of Associations Between Whole Blood Mitochondrial Gene Expression and Cancer-Related Fatigue Among Breast Cancer Survivors. Nurs Res. 2022;71(5):411-417. PMCID: PMC9420746.

Kenney HM, Wu CL, Loiselle AE, Xing L, Ritchlin CT, Schwarz EM. Single-cell transcriptomics of popliteal lymphatic vessels and peripheral veins reveals altered lymphatic muscle and immune cell populations in the TNF-Tg arthritis model. Arthritis Res Ther. 2022;24(1):64. PMCID: PMC8900348.

Zhang H, Li X, Liu J, Lin X, Pei L, Boyce BF, Xing L. Proteasome inhibition-enhanced fracture repair is associated with increased mesenchymal progenitor cells in mice. PLoS One. 2022;17(2):e0263839. PMCID: PMC8880819.

Owlett LD, Karaahmet B, Le L, Belcher EK, Dionisio-Santos D, Olschowka JA, Elliott MR, O'Banion MK. Gas6 induces inflammation and reduces plaque burden but worsens behavior in a sex-dependent manner in the APP/PS1 model of Alzheimer's disease. J Neuroinflammation. 2022;19(1):38. PMCID: PMC8822838.

Wang Y, Yang Z, Gu J, Zhang Y, Wang X, Teng Z, Wang D, Gao L, Li W, Yeh S, Han Z. Estrogen receptor beta increases clear cell renal cell carcinoma stem cell phenotype via altering the circPHACTR4/miR-34b-5p/c-Myc signaling. FASEB J. 2022;36(2):e22163.

Yee M, McDavid AN, Cohen ED, Huyck HL, Poole C, Altman BJ, Maniscalco WM, Deutsch GH, Pryhuber GS, O'Reilly MA. Neonatal Hyperoxia Activates Activating Transcription Factor 4 to Stimulate Folate Metabolism and Alveolar Epithelial Type 2 Cell Proliferation. Am J Respir Cell Mol Biol. 2022;66(4):402-414. PMCID: PMC8990118.

Kerepesi C, Meer MV, Ablaeva J, Amoroso VG, Lee SG, Zhang B, Gerashchenko MV, Trapp A, Yim SH, Lu AT, Levine ME, Seluanov A, Horvath S, Park TJ, Gorbunova V, Gladyshev VN. Epigenetic aging of the demographically non-aging naked mole-rat. Nat Commun. 2022;13(1):355. PMCID: PMC8763950.

Uccello TP, Kintzel SA, Mills BN, Murphy JD, Garrett-Larsen J, Battaglia NG, Rodriguez CJ, Drage MG, Ye J, Love TMT, Johnston CJ, Repasky EA, Qiu H, Linehan DC, Lord EM, Gerber SA. Development of an Orthotopic Murine Model of Rectal Cancer in Conjunction With Targeted Short-Course Radiation Therapy. Adv Radiat Oncol. 2022;7(2):100867. PMCID: PMC8749199.

Kallenbach JG, Bachman JF, Paris ND, Blanc RS, O'Connor T, Furati E, Williams JP, Chakkalakal JV. Muscle-specific functional deficits and lifelong fibrosis in response to paediatric radiotherapy and tumour elimination. J Cachexia Sarcopenia Muscle. 2022;13(1):296-310. PMCID: PMC8818600.

2021

Misra A, Baker C, Pritchett EM, Burgos Villar KN, Ashton JM, Small EM. Characterizing Neonatal Heart Maturation, Regeneration, and Scar Resolution Using Spatial Transcriptomics. J Cardiovasc Dev Dis. 2021 Dec; 9(1):1. doi: 10.3390/jcdd9010001. PMID: 35050211

Vallejo A, Erice O, Entrialgo-Cadierno R, Feliu I, Guruceaga E, Perugorria MJ, Olaizola P, Muggli A, Macaya I, O'Dell M, Ruiz-Fernandez de Cordoba B, Ortiz-Espinosa S, Hezel AF, Arozarena I, Lecanda F, Avila MA, Fernandez-Barrena MG, Evert M, Ponz-Sarvise M, Calvisi DF, Banales JM, Vicent S. FOSL1 promotes cholangiocarcinoma via transcriptional effectors that could be therapeutically targeted. J Hepatol. 2021 Aug;75(2):363-376. doi: 10.1016/j.jhep.2021.03.028. Epub 2021 Apr 20. PMID: 33887357.

McCall MN, Chu CY, Wang L, Benoodt L, Thakar J, Corbett A, Holden-Wiltse J, Slaunwhite C, Grier A, Gill SR, Falsey AR, Topham DJ, Caserta MT, Walsh EE, Qui X, Mariani TJ. A systems genomics approach uncovers molecular associates of RSV severity. PLoS Comput Biol. 2021 Dec 28; 17(12):e1009617. doi: 10.1371/journal.pcbi.1009617. PMID: 34962914

Quijada P, Trembley MA, Misra A, Myers JA, Baker CD, Pérez-Hernández M, Myers JR, Dirkx RA Jr, Cohen ED, Delmar M, Ashton JM, Small EM.Coordination of endothelial cell positioning and fate specification by the epicardium. Nat Commun. 2021 Jul 6;12(1):4155. doi: 10.1038/s41467-021-24414-z. PubMed PMID: 34230480; PubMed Central PMCID: PMC8260743.

Pecora N, Holzbauer S, Wang X, Gu Y, Taffner S, Hatwar T, Hardy D, Dziejman M, D'Heilly P, Pung K, Guh A, Qiu X, Gill S, Dumyati G. Genomic analysis of Clostridioides difficile in two regions of the United States reveals a diversity of strains and limited transmission. J Infect Dis. 2021 Jun 9:jiab294. doi: 10.1093/infdis/jiab294. Epub ahead of print. PMID: 34107037.

Chavez JS, Rabe JL, Loeffler D, Higa KC, Hernandez G, Mills TS, Ahmed N, Gessner RL, Ke Z, Idler BM, Niño KE, Kim H, Myers JR, Stevens BM, Davizon-Castillo P, Jordan CT, Nakajima H, Ashton J, Welner RS, Schroeder T, DeGregori J, Pietras EM. PU.1 enforces quiescence and limits hematopoietic stem cell expansion during inflammatory stress. J Exp Med. 2021 Jun 7;218(6). doi: 10.1084/jem.20201169. PubMed PMID: 33857288; PubMed Central PMCID: PMC8056754.

Cole CL, Bachman JF, Ye J, Murphy J, Gerber SA, Beck CA, Boyce BF, Muthukrishnan G, Chakkalakal JV, Schwarz EM, Linehan D. Increased myocellular lipid and IGFBP-3 expression in a pre-clinical model of pancreatic cancer-related skeletal muscle wasting. J Cachexia Sarcopenia Muscle. 2021 Jun;12(3):731-745. doi: 10.1002/jcsm.12699. Epub 2021 May 7. PMID: 33960737; PMCID: PMC8200439.

Rowswell-Turner RB, Singh RK, Urh A, Yano N, Kim KK, Khazan N, Pandita R, Sivagnanalingam U, Hovanesian V, James NE, Ribeiro JR, Kadambi S, Linehan DC, Moore RG. HE4 Overexpression by Ovarian Cancer Promotes a Suppressive Tumor Immune Microenvironment and Enhanced Tumor and Macrophage PD-L1 Expression. J Immunol. 2021 May 15;206(10):2478-2488. doi: 10.4049/jimmunol.2000281. Epub 2021 Apr 26. PMID: 33903172.

Astapova O, Seger C, Hammes SR. Ligand Binding Prolongs Androgen Receptor Protein Half-Life by Reducing its Degradation. J Endocr Soc. 2021 Mar 5;5(5):bvab035. doi: 10.1210/jendso/bvab035. PMID: 33869982; PMCID: PMC8043068.

Burke RM, Dirkx RA Jr, Quijada P, Lighthouse JK, Mohan A, O'Brien M, Wojciechowski W, Woeller CF, Phipps RP, Alexis JD, Ashton JM, Small EM.Prevention of Fibrosis and Pathological Cardiac Remodeling by Salinomycin. Circ Res. 2021 May 28;128(11):1663-1678. doi: 10.1161/CIRCRESAHA.120.317791. Epub 2021 Apr 7. PubMed PMID: 33825488; PubMed Central PMCID: PMC8159905.

Ho TC, Kim HS, Chen Y, Li Y, LaMere MW, Chen C, Wang H, Gong J, Palumbo CD, Ashton JM, Kim HW, Xu Q, Becker MW, Leong KW. Scaffold-mediated CRISPR-Cas9 delivery system for acute myeloid leukemia therapy. Sci Adv. 2021 May;7(21). doi: 10.1126/sciadv.abg3217. Print 2021 May. PubMed PMID: 34138728; PubMed Central PMCID: PMC8133753.

Tian H, Chou FJ, Tian J, Zhang Y, You B, Huang CP, Yeh S, Niu Y, Chang C. ASC-J9® suppresses prostate cancer cell proliferation and invasion via altering the ATF3-PTK2 signaling. J Exp Clin Cancer Res. 2021 Jan 4;40(1):3. doi: 10.1186/s13046-020-01760-2. PMID: 33390173; PMCID: PMC7780640.

Kurosaki T, Imamachi N, Pröschel C, Mitsutomi S, Nagao R, Akimitsu N, Maquat LE. Loss of the fragile X syndrome protein FMRP results in misregulation of nonsense-mediated mRNA decay. Nat Cell Biol. 2021 Jan;23(1):40-48. doi: 10.1038/s41556-020-00618-1. Epub 2021 Jan 8. PMID: 33420492; PMCID: PMC8273690.

2020

Schroeder GM, Dutta D, Cavender CE, Jenkins JL, Pritchett EM, Baker CD, Ashton JM, Mathews DH, Wedekind JE. Analysis of a preQ1-I riboswitch in effector-free and bound states reveals a metabolite-programmed nucleobase-stacking spine that controls gene regulation. Nucleic Acids Res.2020 Aug 20;48(14):8146-8164. doi: 10.1093/nar/gkaa546. PubMed PMID: 32597951; PubMed Central PMCID: PMC7641330.

Herbert ZT, Thimmapuram J, Xie S, Kershner JP, Kolling FW, Ringelberg CS, LeClerc A, Alekseyev YO, Fan J, Podnar JW, Stevenson HS, Sommerville G, Gupta S, Berkeley M, Koeman J, Perera A, Scott AR, Grenier JK, Malik J, Ashton JM, Pivarski KL, Wang X, Kuffel G, Mesa TE, Smith AT, Shen J, Takata Y, Volkert TL, Love JA, Zhang Y, Wang J, Xuei X, Adams M, Levine SS. Multisite Evaluation of Next-Generation Methods for Small RNA Quantification. J Biomol Tech. 2020 Jul;31(2):47-56. doi: 10.7171/jbt.20-3102-001. PubMed PMID: 31966025; PubMed Central PMCID: PMC6953595.

Mische SM, Fisher NC, Meyn SM, Sol-Church K, Hegstad-Davies RL, Weis-Garcia F, Adams M, Ashton JM, Delventhal KM, Dragon JA, Holmes L, Jagtap P, Kubow KE, Mason CE, Palmblad M, Searle BC, Turck CW, Knudtson KL. A Review of the Scientific Rigor, Reproducibility, and Transparency Studies Conducted by the ABRF Research Groups. J Biomol Tech. 2020 Apr;31(1):11-26. doi: 10.7171/jbt.20-3101-003. Review. PubMed PMID: 31969795; PubMed Central PMCID: PMC6959150.

Pei S, Pollyea DA, Gustafson A, Stevens BM, Minhajuddin M, Fu R, Riemondy KA, Gillen AE, Sheridan RM, Kim J, Costello JC, Amaya ML, Inguva A, Winters A, Ye H, Krug A, Jones CL, Adane B, Khan N, Ponder J, Schowinsky J, Abbott D, Hammes A, Myers JR, Ashton JM, Nemkov T, D'Alessandro A, Gutman JA, Ramsey HE, Savona MR, Smith CA, Jordan CT. Monocytic Subclones Confer Resistance to Venetoclax-Based Therapy in Patients with Acute Myeloid Leukemia. Cancer Discov. 2020 Apr;10(4):536-551. doi: 10.1158/2159-8290.CD-19-0710. Epub 2020 Jan 23. PubMed PMID: 31974170; PubMed Central PMCID: PMC7124979.

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.