Jason Smith

@jpsmith5

Charlottesville, VA

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Publications

Smith JP, Paxton R, Medrano S, Sheffield NC, Sequeira-Lopez MLS, Gomez RA. Inhibition of Renin Expression Is Regulated by an Epigenetic Switch From an Active to a Poised State. Hypertension 2024 July. doi:10.1161/HYPERTENSIONAHA.124.22886.
LeRoy NJ, Smith JP, Zheng G, Rymuza J, Gharavi E, Brown DE, Zhang A, Sheffield NC. Fast clustering and cell-type annotation of scATAC data using pre-trained region embeddings. Nuceic Acids Research Genomics and Bioinformatics. Volume 6, Issue 3, September 2024, lqae073. doi: 10.1093/nargab/lqae073.
Martini AG, Smith JP, Medrano S, Finer G, Sheffield NC, Sequeira-Lopez MLS, Gomez RA. Renin Cell Development: Insights From Chromatin Accessibility and Single-Cell Transcriptomics. Circulation Research. 2023 3 Jul 2023. doi: 10.1161/CIRCRESAHA.123.322827.
Smith JP, Sequeira-Lopez MLS, Gomez RA. A novel role for the histone modifier PRDM6 and an opportunity to understand hypertension. Kidney Int. 2023 May 24:S0085-2538(23)00385-X. doi: 10.1016/j.kint.2023.05.012. Epub ahead of print. PMID: 37236422.
Martini AG, Smith JP, Medrano S, Sheffield NC, Sequeira-Lopez MLS, Gomez RA. Determinants of renin cell differentiation: a single cell epi-transcriptomics approach. bioRxiv Preprint. 2023 Jan 20:2023.01.18.524595. doi: 10.1101/2023.01.18.524595. PMID: 36711565; PMCID: PMC9882312.
Morris BB, Smith JP, Zhang Q, Jiang Z, Hampton OA, Churchman ML, Arnold SM, Owen DH, Gray JE, Dillon PM, Soliman HH, Stover DG, Colman H, Chakravarti A, Shain KH, Silva AS, Villano JL, Vogelbaum MA, Borges VF, Akerley WL, Gentzler RD, Hall RD, Matsen CB, Ulrich CM, Post AR, Nix DA, Singer EA, Larner JM, Stukenberg PT, Jones DR, Mayo MW. Replicative Instability Drives Cancer Progression. Biomolecules. 2022; 12(11):1570. https://doi.org/10.3390/biom12111570
Duvall E, Benitez CM, Tellez K, Enge M, Pauerstein PT, Li L, Baek S, Quake SR, Smith JP, Sheffield NC, Kim SK, Arda HE. Single-cell transcriptome and accessible chromatin dynamics during endocrine pancreas development. Proc Natl Acad Sci U S A. 2022 Jun 28;119(26):e2201267119. doi: 10.1073/pnas.2201267119. Epub 2022 Jun 22. PMID: 35733248.
Kupkova K, Mosquera JV, Smith JP, Stolarczyk M, Danehy TL, Lawson JT, Xue B, Stubbs JT 4th, LeRoy N, Sheffield NC. GenomicDistributions: fast analysis of genomic intervals with Bioconductor. BMC Genomics. 2022 Apr 12;23(1):299. doi: 10.1186/s12864-022-08467-y. PMID: 35413804; PMCID: PMC9003978.
Smith JP, Corces MR, Xu J, Reuter VP, Chang HY, Sheffield NC. PEPATAC: an optimized pipeline for ATAC-seq data analysis with serial alignments. NAR Genom Bioinform. 2021 Nov 23;3(4):lqab101. doi: 10.1093/nargab/lqab101. PMID: 34859208; PMCID: PMC8632735.
Gharavi E, Gu A, Zheng G, Smith JP, Cho HJ, Zhang A, Brown DE, Sheffield NC. Embeddings of genomic region sets capture rich biological associations in lower dimensions. Bioinformatics, 2021;, btab439, https://doi.org/10.1093/bioinformatics/btab439.
Smith JP, Dutta AB, Sathyan KM, Guertin MJ, Sheffield NC. PEPPRO: quality control and processing of nascent RNA profiling data. Genome Biol. 22, 155 (2021). https://doi.org/10.1186/s13059-021-02349-4.
Keppley LW, Walker S, Gademsey A, Smith JP, Keller S, Kester, M, Fox T. Nervonic acid limits weight gain in a mouse model of diet-induced obesity. The FASEB Journal 2020 September 22. doi:10.1096/fj.202000525R
Lawson JT, Smith JP, Bekiranov S, Garrett-Bakelman FE, Sheffield NC. COCOA: coordinate covariation analysis of epigenetic heterogeneity. Genome Biol. 2020;21(1):240. Published 2020 Sep 7. doi:10.1186/s13059-020-02139-4
Smith JP, Sheffield NC. Analytical approaches for ATAC-seq data analysis. Current Protocols in Human Genetics. 2020 June 15. doi: 10.1002/cphg.101
Stolarczyk M, Reuter VP, Smith JP, Magee NE, Sheffield NC. Refgenie: a reference genome resource manager. Gigascience. 2020 Feb 1;9(2):giz149. doi: 10.1093/gigascience/giz149. PMID: 31995185; PMCID: PMC6988606.
M. Ryan Corces, Jeffrey M. Granja, Shadi Shams, Bryan H. Louie, Jose A. Seoane, Wanding Zhou, Tiago C. Silva, Clarice Groeneveld, Christopher K. Wong, Seung Woo Cho, Ansuman T. Satpathy, Maxwell R. Mumbach, Katherine A. Hoadley, A. Gordon Robertson, Nathan C. Sheffield, Ina Felau, Mauro A. A. Castro, Benjamin P. Berman, Louis M. Staudt, Jean C. Zenklusen, Peter W. Laird, Christina Curtis, The Cancer Genome Atlas Analysis Network, William J. Greenleaf, Howard Y. Chang. The chromatin accessibility landscape of primary human cancers. Science 2018 Oct 26; 362.
Pope WH, Bowman CA, Russell DA, Jacobs-Sera D, Asai DJ, Cresawn SG, Jacobs WR, Hendrix RW, Lawrence JG, Hatfull GF; Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science; Phage Hunters Integrating Research and Education; Mycobacterial Genetics Course. Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity. eLife 2015 Apr 28;4.
Byrum CA, Smith J, Easterling MR, Bridges MC. Restricted expression of karyopherin alpha mRNA in the sea urchin suggests a role in neurogenesis. PLoS One. 2014 Sep 24;9(9):e108173.
Pelak K, Shianna KV, Ge D, Maia JM, Zhu M, Smith JP, Cirulli ET, Fellay J, Dickson SP, Gumbs CE, Heinzen EL, Need AC, Ruzzo EK, Singh A, Campbell CR, Hong LK, Lornsen KA, McKenzie AM, Sobreira NL, Hoover-Fong JE, Milner JD, Ottman R, Haynes BF, Goedert JJ, Goldstein DB. The characterization of twenty sequenced human genomes. PLoS Genet. 2010 Sep 9;6(9).
Sobreira NL, Cirulli ET, Avramopoulos D, Wohler E, Oswald GL, Stevens EL, Ge D, Shianna KV, Smith JP, Maia JM, Gumbs CE, Pevsner J, Thomas G, Valle D, Hoover-Fong JE, Goldstein DB. Whole-genome sequencing of a single proband together with linkage analysis identifies a Mendelian disease gene. PLoS Genet. 2010 Jun 17;6(6):e1000991.
Heinzen EL, Radtke RA, Urban TJ, Cavalleri GL, Depondt C, Need AC, Walley NM, Nicoletti P, Ge D, Catarino CB, Duncan JS, Kasperaviciūte D, Tate SK, Caboclo LO, Sander JW, Clayton L, Linney KN, Shianna KV, Gumbs CE, Smith J, Cronin KD, Maia JM, Doherty CP, Pandolfo M, Leppert D, Middleton LT, Gibson RA, Johnson MR, Matthews PM, Hosford D, Kälviäinen R, Eriksson K, Kantanen AM, Dorn T, Hansen J, Krämer G, Steinhoff BJ, Wieser HG, Zumsteg D, Ortega M, Wood NW, Huxley-Jones J, Mikati M, Gallentine WB, Husain AM, Buckley PG, Stallings RL, Podgoreanu MV, Delanty N, Sisodiya SM, Goldstein DB. Rare deletions at 16p13.11 predispose to a diverse spectrum of sporadic epilepsy syndromes. Am J Hum Genet. 2010 May 14;86(5):707-18.
Cirulli ET, Singh A, Shianna KV, Ge D, Smith JP, Maia JM, Heinzen EL, Goedert JJ, Goldstein DB; Center for HIV/AIDS Vaccine Immunology (CHAVI). Screening the human exome: a comparison of whole genome and whole transcriptome sequencing. Genome Biol. 2010;11(5):R57.
Fellay J, Ge D, Shianna KV, Colombo S, Ledergerber B, Cirulli ET, Urban TJ, Zhang K, Gumbs CE, Smith JP, Castagna A, Cozzi-Lepri A, De Luca A, Easterbrook P, Günthard HF, Mallal S, Mussini C, Dalmau J, Martinez-Picado J, Miro JM, Obel N, Wolinsky SM, Martinson JJ, Detels R, Margolick JB, Jacobson LP, Descombes P, Antonarakis SE, Beckmann JS, O’Brien SJ, Letvin NL, McMichael AJ, Haynes BF, Carrington M, Feng S, Telenti A, Goldstein DB; NIAID Center for HIV/AIDS Vaccine Immunology (CHAVI). Common genetic variation and the control of HIV-1 in humans. PLoS Genet. 2009 Dec;5(12):e1000791.
Fuhrman LE, Goel AK, Smith J, Shianna KV, Aballay A. Nucleolar proteins suppress Caenorhabditis elegans innate immunity by inhibiting p53/CEP-1. PLoS Genet. 2009 Sep;5(9):e1000657.
Fellay J, Shianna KV, Ge D, Colombo S, Ledergerber B, Weale M, Zhang K, Gumbs C, Castagna A, Cossarizza A, Cozzi-Lepri A, De Luca A, Easterbrook P, Francioli P, Mallal S, Martinez-Picado J, Miro JM, Obel N, Smith JP, Wyniger J, Descombes P, Antonarakis SE, Letvin NL, McMichael AJ, Haynes BF, Telenti A, Goldstein DB. A whole-genome association study of major determinants for host control of HIV-1. Science. 2007 Aug 17;317(5840):944-7.