Last Name


TitleAssociate Professor
InstitutionBaylor College of Medicine
DepartmentDepartment of Molecular Physiology & Biophysics
DivisionMolecular Physiology & Biophysics
AddressOne Baylor Plaza
Houston TX 77030
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    1996Phi Beta Kappa, University of Washington
    2004Postdoctoral Fellowship, Cancer Research Institute
    2007Poster Award, NE Soc. for Dev. Biol. Annual Meeting
    2007K99 Pathways to Independence Award, National Cancer Institute
    2010LC Sciences Award, AAAS Southwest Area Regional Meeting
    2010Career Development Award, BCM Leukemia/Lymphoma SPORE
    2004Sidney J. Raffel Award for Outstanding Accomplishment in Graduate Study, Stanford University School of Medicine Department of Microbiology and Immunology

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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Palmieri M, Pal R, Nelvagal HR, Lotfi P, Stinnett GR, Seymour ML, Chaudhury A, Bajaj L, Bondar VV, Bremner L, Saleem U, Tse DY, Sanagasetti D, Wu SM, Neilson JR, Pereira FA, Pautler RG, Rodney GG, Cooper JD, Sardiello M. Corrigendum: mTORC1-independent TFEB activation via Akt inhibition promotes cellular clearance in neurodegenerative storage diseases. Nat Commun. 2017 Jun 13; 8:15793. PMID: 28607479.
      View in: PubMed
    2. Yang J, Kongchan N, Primo Planta C, Neilson JR, Hirschi KD. The atypical genesis and bioavailability of the plant-based small RNA MIR2911: bulking up while breaking down. Mol Nutr Food Res. 2017 Mar 20. PMID: 28319645.
      View in: PubMed
    3. Palmieri M, Pal R, Nelvagal HR, Lotfi P, Stinnett GR, Seymour ML, Chaudhury A, Bajaj L, Bondar VV, Bremner L, Saleem U, Tse DY, Sanagasetti D, Wu SM, Neilson JR, Pereira FA, Pautler RG, Rodney GG, Cooper JD, Sardiello M. mTORC1-independent TFEB activation via Akt inhibition promotes cellular clearance in neurodegenerative storage diseases. Nat Commun. 2017 Feb 06; 8:14338. PMID: 28165011.
      View in: PubMed
    4. Chaudhury A, Cheema S, Fachini JM, Kongchan N, Lu G, Simon LM, Wang T, Mao S, Rosen DG, Ittmann MM, Hilsenbeck SG, Shaw CA, Neilson JR. CELF1 is a central node in post-transcriptional regulatory programmes underlying EMT. Nat Commun. 2016 Nov 21; 7:13362. PMID: 27869122.
      View in: PubMed
    5. Tajhya RB, Hu X, Tanner MR, Huq R, Kongchan N, Neilson JR, Rodney GG, Horrigan FT, Timchenko LT, Beeton C. Functional KCa1.1 channels are crucial for regulating the proliferation, migration and differentiation of human primary skeletal myoblasts. Cell Death Dis. 2016 Oct 20; 7(10):e2426. PMID: 27763639.
      View in: PubMed
    6. Xu Y, Chaudhury A, Zhang M, Savoldo B, Metelitsa LS, Rodgers J, Yustein JT, Neilson JR, Dotti G. Glycolysis determines dichotomous regulation of T cell subsets in hypoxia. J Clin Invest. 2016 Jul 1; 126(7):2678-88. PMID: 27294526; PMCID: PMC4922684 [Available on 10/01/16].
    7. Domingues RG, Lago-Baldaia I, Pereira-Castro I, Fachini JM, Oliveira L, Drpic D, Lopes N, Henriques T, Neilson JR, Carmo AM, Moreira A. CD5 expression is regulated during human T-cell activation by alternative polyadenylation, PTBP1, and miR-204. Eur J Immunol. 2016 Jun; 46(6):1490-503. PMID: 27005442.
      View in: PubMed
    8. Pal R, Bajaj L, Sharma J, Palmieri M, Di Ronza A, Lotfi P, Chaudhury A, Neilson J, Sardiello M, Rodney GG. NADPH oxidase promotes Parkinsonian phenotypes by impairing autophagic flux in an mTORC1-independent fashion in a cellular model of Parkinson's disease. Sci Rep. 2016; 6:22866. PMID: 26960433; PMCID: PMC4785399.
    9. Chaudhury A, Neilson JR. Use of the pBUTR Reporter System for Scalable Analysis of 3' UTR-Mediated Gene Regulation. Methods Mol Biol. 2016; 1358:109-28. PMID: 26463380.
      View in: PubMed
    10. Hsu TY, Simon LM, Neill NJ, Marcotte R, Sayad A, Bland CS, Echeverria GV, Sun T, Kurley SJ, Tyagi S, Karlin KL, Dominguez-Vidaña R, Hartman JD, Renwick A, Scorsone K, Bernardi RJ, Skinner SO, Jain A, Orellana M, Lagisetti C, Golding I, Jung SY, Neilson JR, Zhang XH, Cooper TA, Webb TR, Neel BG, Shaw CA, Westbrook TF. The spliceosome is a therapeutic vulnerability in MYC-driven cancer. Nature. 2015 Sep 17; 525(7569):384-8. PMID: 26331541.
      View in: PubMed
    11. Gennarino VA, Alcott CE, Chen CA, Chaudhury A, Gillentine MA, Rosenfeld JA, Parikh S, Wheless JW, Roeder ER, Horovitz DD, Roney EK, Smith JL, Cheung SW, Li W, Neilson JR, Schaaf CP, Zoghbi HY. NUDT21-spanning CNVs lead to neuropsychiatric disease and altered MeCP2 abundance via alternative polyadenylation. Elife. 2015; 4. PMID: 26312503.
      View in: PubMed
    12. Tan YD, Deng J, Neilson JR. RAX2: a genome-wide detection method of condition-associated transcription variation. Nucleic Acids Res. 2015 Sep 3; 43(15):e96. PMID: 25953852.
      View in: PubMed
    13. Tan YD, Chandler AM, Chaudhury A, Neilson JR. A powerful statistical approach for large-scale differential transcription analysis. PLoS One. 2015; 10(4):e0123658. PMID: 25894390; PMCID: PMC4404056.
    14. Xia Z, Donehower LA, Cooper TA, Neilson JR, Wheeler DA, Wagner EJ, Li W. Dynamic analyses of alternative polyadenylation from RNA-seq reveal a 3'-UTR landscape across seven tumour types. Nat Commun. 2014; 5:5274. PMID: 25409906; PMCID: PMC4467577.
    15. Chiang DY, Kongchan N, Beavers DL, Alsina KM, Voigt N, Neilson JR, Jakob H, Martin JF, Dobrev D, Wehrens XH, Li N. Loss of microRNA-106b-25 cluster promotes atrial fibrillation by enhancing ryanodine receptor type-2 expression and calcium release. Circ Arrhythm Electrophysiol. 2014 Dec; 7(6):1214-22. PMID: 25389315; PMCID: PMC4270890.
    16. Chaudhury A, Kongchan N, Gengler JP, Mohanty V, Christiansen AE, Fachini JM, Martin JF, Neilson JR. A piggyBac-based reporter system for scalable in vitro and in vivo analysis of 3' untranslated region-mediated gene regulation. Nucleic Acids Res. 2014 Jun; 42(10):e86. PMID: 24753411; PMCID: PMC4041432.
    17. Zhao P, Damerow MS, Stern P, Liu AH, Sweet-Cordero A, Siziopikou K, Neilson JR, Sharp PA, Cheng C. CD44 promotes Kras-dependent lung adenocarcinoma. Oncogene. 2013 Oct 24; 32(43):5186-90. PMID: 23208496; PMCID: PMC4227610.
    18. Neilson JR, Sandberg R. Heterogeneity in mammalian RNA 3' end formation. Exp Cell Res. 2010 May 1; 316(8):1357-64. PMID: 20211174; PMCID: PMC2866830.
    19. Edbauer D, Neilson JR, Foster KA, Wang CF, Seeburg DP, Batterton MN, Tada T, Dolan BM, Sharp PA, Sheng M. Regulation of synaptic structure and function by FMRP-associated microRNAs miR-125b and miR-132. Neuron. 2010 Feb 11; 65(3):373-84. PMID: 20159450.
      View in: PubMed
    20. Wu H, Neilson J, Manjunath N. MicroRNA cloning from cells of the immune system. Methods Mol Biol. 2010; 667:67-77. PMID: 20827527.
      View in: PubMed
    21. Jones MR, Quinton LJ, Blahna MT, Neilson JR, Fu S, Ivanov AR, Wolf DA, Mizgerd JP. Zcchc11-dependent uridylation of microRNA directs cytokine expression. Nat Cell Biol. 2009 Sep; 11(9):1157-63. PMID: 19701194; PMCID: PMC2759306.
    22. Neilson JR, Sharp PA. Small RNA regulators of gene expression. Cell. 2008 Sep 19; 134(6):899-902. PMID: 18805079.
      View in: PubMed
    23. Sandberg R, Neilson JR, Sarma A, Sharp PA, Burge CB. Proliferating cells express mRNAs with shortened 3' untranslated regions and fewer microRNA target sites. Science. 2008 Jun 20; 320(5883):1643-7. PMID: 18566288; PMCID: PMC2587246.
    24. Gallo EM, Winslow MM, Canté-Barrett K, Radermacher AN, Ho L, McGinnis L, Iritani B, Neilson JR, Crabtree GR. Calcineurin sets the bandwidth for discrimination of signals during thymocyte development. Nature. 2007 Nov 29; 450(7170):731-5. PMID: 18046413.
      View in: PubMed
    25. Wu H, Neilson JR, Kumar P, Manocha M, Shankar P, Sharp PA, Manjunath N. miRNA profiling of naïve, effector and memory CD8 T cells. PLoS One. 2007; 2(10):e1020. PMID: 17925868; PMCID: PMC2000354.
    26. Ebert MS, Neilson JR, Sharp PA. MicroRNA sponges: competitive inhibitors of small RNAs in mammalian cells. Nat Methods. 2007 Sep; 4(9):721-6. PMID: 17694064; PMCID: PMC3857099.
    27. Neilson JR, Zheng GX, Burge CB, Sharp PA. Dynamic regulation of miRNA expression in ordered stages of cellular development. Genes Dev. 2007 Mar 1; 21(5):578-89. PMID: 17344418; PMCID: PMC1820899.
    28. Heit JJ, Apelqvist AA, Gu X, Winslow MM, Neilson JR, Crabtree GR, Kim SK. Calcineurin/NFAT signalling regulates pancreatic beta-cell growth and function. Nature. 2006 Sep 21; 443(7109):345-9. PMID: 16988714.
      View in: PubMed
    29. Davé V, Childs T, Xu Y, Ikegami M, Besnard V, Maeda Y, Wert SE, Neilson JR, Crabtree GR, Whitsett JA. Calcineurin/Nfat signaling is required for perinatal lung maturation and function. J Clin Invest. 2006 Oct; 116(10):2597-609. PMID: 16998587; PMCID: PMC1570374.
    30. Arron JR, Winslow MM, Polleri A, Chang CP, Wu H, Gao X, Neilson JR, Chen L, Heit JJ, Kim SK, Yamasaki N, Miyakawa T, Francke U, Graef IA, Crabtree GR. NFAT dysregulation by increased dosage of DSCR1 and DYRK1A on chromosome 21. Nature. 2006 Jun 1; 441(7093):595-600. PMID: 16554754.
      View in: PubMed
    31. Winslow MM, Gallo EM, Neilson JR, Crabtree GR. The calcineurin phosphatase complex modulates immunogenic B cell responses. Immunity. 2006 Feb; 24(2):141-52. PMID: 16473827.
      View in: PubMed
    32. Mammucari C, Tommasi di Vignano A, Sharov AA, Neilson J, Havrda MC, Roop DR, Botchkarev VA, Crabtree GR, Dotto GP. Integration of Notch 1 and calcineurin/NFAT signaling pathways in keratinocyte growth and differentiation control. Dev Cell. 2005 May; 8(5):665-76. PMID: 15866158.
      View in: PubMed
    33. Neilson JR, Sharp PA. Herpesviruses throw a curve ball: new insights into microRNA biogenesis and evolution. Nat Methods. 2005 Apr; 2(4):252-4. PMID: 15782215.
      View in: PubMed
    34. Chang CP, Neilson JR, Bayle JH, Gestwicki JE, Kuo A, Stankunas K, Graef IA, Crabtree GR. A field of myocardial-endocardial NFAT signaling underlies heart valve morphogenesis. Cell. 2004 Sep 3; 118(5):649-63. PMID: 15339668.
      View in: PubMed
    35. Schaeffer PJ, Wende AR, Magee CJ, Neilson JR, Leone TC, Chen F, Kelly DP. Calcineurin and calcium/calmodulin-dependent protein kinase activate distinct metabolic gene regulatory programs in cardiac muscle. J Biol Chem. 2004 Sep 17; 279(38):39593-603. PMID: 15262994.
      View in: PubMed
    36. Parsons SA, Millay DP, Wilkins BJ, Bueno OF, Tsika GL, Neilson JR, Liberatore CM, Yutzey KE, Crabtree GR, Tsika RW, Molkentin JD. Genetic loss of calcineurin blocks mechanical overload-induced skeletal muscle fiber type switching but not hypertrophy. J Biol Chem. 2004 Jun 18; 279(25):26192-200. PMID: 15082723.
      View in: PubMed
    37. Chang CP, McDill BW, Neilson JR, Joist HE, Epstein JA, Crabtree GR, Chen F. Calcineurin is required in urinary tract mesenchyme for the development of the pyeloureteral peristaltic machinery. J Clin Invest. 2004 Apr; 113(7):1051-8. PMID: 15057312; PMCID: PMC379320.
    38. Winslow MM, Neilson JR, Crabtree GR. Calcium signalling in lymphocytes. Curr Opin Immunol. 2003 Jun; 15(3):299-307. PMID: 12787755.
      View in: PubMed
    39. Graef IA, Wang F, Charron F, Chen L, Neilson J, Tessier-Lavigne M, Crabtree GR. Neurotrophins and netrins require calcineurin/NFAT signaling to stimulate outgrowth of embryonic axons. Cell. 2003 May 30; 113(5):657-70. PMID: 12787506.
      View in: PubMed
    40. Graef IA, Mermelstein PG, Stankunas K, Neilson JR, Deisseroth K, Tsien RW, Crabtree GR. L-type calcium channels and GSK-3 regulate the activity of NF-ATc4 in hippocampal neurons. Nature. 1999 Oct 14; 401(6754):703-8. PMID: 10537109.
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    41. Neilson JR, John GC, Carr JK, Lewis P, Kreiss JK, Jackson S, Nduati RW, Mbori-Ngacha D, Panteleeff DD, Bodrug S, Giachetti C, Bott MA, Richardson BA, Bwayo J, Ndinya-Achola J, Overbaugh J. Subtypes of human immunodeficiency virus type 1 and disease stage among women in Nairobi, Kenya. J Virol. 1999 May; 73(5):4393-403. PMID: 10196337; PMCID: PMC104220.
    42. Stankunas K, Graef IA, Neilson JR, Park SH, Crabtree GR. Signaling through calcium, calcineurin, and NF-AT in lymphocyte activation and development. Cold Spring Harb Symp Quant Biol. 1999; 64:505-16. PMID: 11232327.
      View in: PubMed
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