{"id":363,"date":"2020-07-09T16:51:59","date_gmt":"2020-07-09T16:51:59","guid":{"rendered":"http:\/\/sites.rutgers.edu\/bernstein-lab\/?page_id=363"},"modified":"2026-01-03T20:18:41","modified_gmt":"2026-01-03T20:18:41","slug":"publications","status":"publish","type":"page","link":"https:\/\/sites.rutgers.edu\/bernstein-lab\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"<h4 style=\"text-align: left\"><strong>2025<\/strong><\/h4>\n<h6 style=\"text-align: left\">\u203a\u00a0 Choza, J.I., Virani, M., Kuhn, N.C. et al. <strong>Parkinson\u2019s disease-associated alterations in DNA methylation and hydroxymethylation in human brain.<\/strong> npj Parkinsons Dis. 11, 363 (2025). doi: <a href=\"https:\/\/doi.org\/10.1038\/s41531-025-01209-3\">10.1038\/s41531-025-01209-3.<\/a> <a href=\"http:\/\/sites.rutgers.edu\/bernstein-lab\/wp-content\/uploads\/sites\/985\/2026\/01\/2025_Choza_npjPD.pdf\" target=\"_blank\" rel=\"noopener\">\ud83d\udd17<\/a><\/h6>\n<ul>\n<li><em>Preregistration DOI:\u00a0<\/em><a href=\"https:\/\/osf.io\/z4vbw\/overview\">10.17605\/OSF.IO\/Z4VBW<\/a><\/li>\n<li><em>Raw and processed data: <\/em><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/geo\/query\/acc.cgi?acc=GSE267937\">GEO (GSE267937)<\/a><\/li>\n<\/ul>\n<h4 style=\"text-align: left\"><strong>2024<\/strong><strong style=\"color: inherit;font-size: 1.44em\">\u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0<\/strong><\/h4>\n<h6 style=\"text-align: left\">\u203a\u00a0\u00a0<span dir=\"ltr\" role=\"presentation\">Kochmanski J, Virani M, Kuhn NC, <\/span><span dir=\"ltr\" role=\"presentation\">Boyd SL<\/span><span dir=\"ltr\" role=\"presentation\">, Becker K, Adams M, and <\/span><span dir=\"ltr\" role=\"presentation\">Bernstein AI<\/span><span dir=\"ltr\" role=\"presentation\">. <\/span><span dir=\"ltr\" role=\"presentation\">(2024) <strong>Developmental origins of Parkinson&#8217;s disease risk: perinatal exposure to the <\/strong><\/span><strong><span dir=\"ltr\" role=\"presentation\">organochlorine pesticide dieldrin leads to sex specific DNA modifications in critical <\/span><\/strong><span dir=\"ltr\" role=\"presentation\"><strong>neurodevelopmental pathways in the mouse midbrain<\/strong>. <\/span>Toxicological Sciences, kfae091, doi: <a href=\"https:\/\/doi.org\/10.1093\/toxsci\/kfae091\" target=\"_blank\" rel=\"noopener\">10.1093\/toxsci\/kfae091<\/a>.\u00a0<a href=\"http:\/\/sites.rutgers.edu\/bernstein-lab\/wp-content\/uploads\/sites\/985\/2024\/08\/2024_Kochmanski_ToxSci.pdf\" target=\"_blank\" rel=\"noopener\">\ud83d\udd17<\/a><\/h6>\n<ul>\n<li><em>Preregistration DOI: <\/em><a href=\"https:\/\/doi.org\/10.17605\/OSF.IO\/3QXFV\">10.17605\/OSF.IO\/3QXFV<\/a><\/li>\n<li><em>Dataset DOI:\u00a0<\/em><a class=\"link link-uri openInAnotherWindow\" href=\"https:\/\/doi.org\/10.5061\/dryad.ffbg79d30\" target=\"_blank\" rel=\"noopener\" data-google-interstitial=\"false\">10.5061\/dryad.ffbg79d30<\/a><\/li>\n<\/ul>\n<h6 style=\"text-align: left\">\u203a\u00a0 John T. Gionco, and Alison I. Bernstein. (2024) <strong>Emerging Role of Environmental Epitranscriptomics and RNA modifications in Parkinson\u2019s disease<\/strong>. Journal of Parkinson\u2019s disease. (In Press) doi:<a href=\"http:\/\/doi.org\/10.3233\/JPD-230457\" target=\"_blank\" rel=\"noopener\">10.3233\/JPD-230457<\/a>. <a href=\"http:\/\/sites.rutgers.edu\/bernstein-lab\/wp-content\/uploads\/sites\/985\/2024\/04\/2024_Gionco_JPD_Epitranscriptomics.pdf\" target=\"_blank\" rel=\"noopener\">\ud83d\udd17<\/a><\/h6>\n<h6 style=\"text-align: left\">\u203a\u00a0 Kochmanski and A.I. Bernstein (2024) <strong>Best practices for epigenome-wide DNA modifications data collection and analysis.<\/strong> In: Translational and Applied Genomics, Rigor and Reproducibility in Genetics and Genomics. D. Dluzen and M. Schmidt, ed. Academic Press. pp. 261-294. doi:<a href=\"https:\/\/doi.org\/10.1016\/B978-0-12-817218-6.00006-1\" target=\"_blank\" rel=\"noopener\">10.1016\/B978-0-12-817218-6.00006-1<\/a>. <a href=\"http:\/\/sites.rutgers.edu\/bernstein-lab\/wp-content\/uploads\/sites\/985\/2024\/04\/2024_Rigor-and-Reproducibility-in-Genetics-and-Genomics-Chapter-12_removed.pdf\" target=\"_blank\" rel=\"noopener\">\ud83d\udd17<\/a><\/h6>\n<h4 style=\"text-align: left\"><strong>2023<\/strong><strong style=\"color: inherit;font-size: 1.44em\">\u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0<\/strong><\/h4>\n<h6 style=\"text-align: left\">\u203a Sierra L. Boyd, Nathan C. Kuhn, Joseph R. Patterson, Anna C. Stoll, Sydney A. Zimmerman, Mason R. Kolanowski, Joseph J. Neubecker, Kelvin C. Luk, Eric S. Ramsson, Caryl E. Sortwell, and Alison I. Bernstein (2023) <strong>Developmental exposure to the Parkinson\u2019s disease-associated organochlorine pesticide dieldrin alters dopamine neurotransmission in \u03b1- synuclein pre-formed fibril (PFF)-injected mice.<\/strong> Toxicological Sciences, kfad086, doi:<a href=\"https:\/\/doi.org\/10.1093\/toxsci\/kfad086\" target=\"_blank\" rel=\"noopener\">10.1093\/toxsci\/kfad086<\/a>. <a href=\"http:\/\/sites.rutgers.edu\/bernstein-lab\/wp-content\/uploads\/sites\/985\/2024\/04\/2023_Boyd_ToxSci.pdf\" target=\"_blank\" rel=\"noopener\">\ud83d\udd17<\/a><\/h6>\n<ul>\n<li><em>Preregistration DOI: <a href=\"https:\/\/doi.org\/10.17605\/OSF.IO\/QV4YA\" target=\"_blank\" rel=\"noopener\">10.17605\/OSF.IO\/QV4YA<\/a><\/em><\/li>\n<li><em>Dataset DOI: <a href=\"https:\/\/datadryad.org\/stash\/dataset\/doi:10.5061\/dryad.qz612jmmq\" target=\"_blank\" rel=\"noopener\">10.5061\/dryad.qz612jmmq<\/a><\/em><\/li>\n<\/ul>\n<h4 style=\"text-align: left\"><strong>2022<\/strong><\/h4>\n<h6>\u203a Kochmanski J, Kuhn NA, and Bernstein AI. (2022) <strong>Parkinson&#8217;s Disease-Associated, Sex-specific Changes in DNA Methylation at <em>PARK7<\/em> (DJ-1), <em>SLC17A6<\/em> (VGLUT2), <em>PTPRN2<\/em> (IA-2\u03b2), and <em>NR4A2<\/em> (NURR1) in Cortical Neurons. <\/strong>Nature Partner Journals: Parkinson\u2019s disease. 8 (120) doi:<a href=\"https:\/\/doi.org\/10.1038\/s41531-022-00355-2\" target=\"_blank\" rel=\"noopener\">10.1038\/s41531-022-00355-2<\/a>. <a href=\"http:\/\/sites.rutgers.edu\/bernstein-lab\/wp-content\/uploads\/sites\/985\/2023\/11\/2022_Kochmanksi_npjPD.pdf\" target=\"_blank\" rel=\"noopener\">\ud83d\udd17<\/a><\/h6>\n<ul>\n<li><em>Preregistration DOI: <a href=\"https:\/\/doi.org\/10.17605\/OSF.IO\/Z4VBW\" target=\"_blank\" rel=\"noopener\">10.17605\/osf.io\/z4vbw<\/a><\/em><\/li>\n<li><em>Dataset DOI: <a href=\"https:\/\/doi.org\/10.5061\/dryad.7d7wm37w0\" target=\"_blank\" rel=\"noopener\">10.5061\/dryad.7d7wm37w0<\/a><\/em><\/li>\n<\/ul>\n<h4><strong>2020<\/strong><\/h4>\n<h6>\u203a Gezer AO, Kochmanski J, VanOeveren SE, Cole-Strauss A, Kemp CJ, Patterson JR, Miller KM, Kuhn NC, Herman DE, McIntire A, Lipton JW, Luk KC, Fleming SM, Sortwell CE, Bernstein AI. (2020) <strong>Developmental exposure to the organochlorine pesticide dieldrin causes male-specific exacerbation of \u03b1-synuclein-preformed fibril-induced toxicity and motor deficits.<\/strong> Neurobiology of Disease.141:104947. doi: <a href=\"https:\/\/doi.org\/10.1016\/j.nbd.2020.104947\" target=\"_blank\" rel=\"noopener\">10.1016\/j.nbd.2020.104947<\/a>. <a href=\"http:\/\/sites.rutgers.edu\/bernstein-lab\/wp-content\/uploads\/sites\/985\/2023\/11\/2020_Gezer_NBD.pdf\" target=\"_blank\" rel=\"noopener\">\ud83d\udd17<\/a><\/h6>\n<ul>\n<li><em>Preregistration DOI: <a href=\"https:\/\/doi.org\/10.17605\/OSF.IO\/H49XF\" target=\"_blank\" rel=\"noopener\">10.17605\/osf.io\/h49xf<\/a>, <a href=\"https:\/\/doi.org\/10.17605\/OSF.IO\/WPF6U\" target=\"_blank\" rel=\"noopener\">10.17605\/osf.io\/wpf6u<\/a><\/em><\/li>\n<li><em>Dataset DOI: <a href=\"https:\/\/data.mendeley.com\/datasets\/h2ptyjr2cf\/1\" target=\"_blank\" rel=\"noopener\">10.17632\/h2ptyjr2cf.1<\/a><\/em><\/li>\n<\/ul>\n<h6>\u203a Kochmanski, J. and Bernstein, A.I. (2020) <strong>The Impact of Environmental Health Factors on <\/strong><strong>5-Hydroxymethylcytosine <\/strong><strong>in the Brain.<\/strong> Current Environmental Health Reports. doi: <a href=\"https:\/\/doi.org\/10.1007\/s40572-020-00268-3\" target=\"_blank\" rel=\"noopener\">10.1007\/s40572-020-00268-3<\/a>. <a href=\"http:\/\/sites.rutgers.edu\/bernstein-lab\/wp-content\/uploads\/sites\/985\/2023\/11\/2020_Kochmanski_CEHR.pdf\" target=\"_blank\" rel=\"noopener\">\ud83d\udd17<\/a><\/h6>\n<h4><strong>2019<\/strong><\/h4>\n<h6>\u203a Kochmanski J, Savonen C, Bernstein AI (2019) <strong>A Novel Application of Mixed Effects Models for <\/strong><strong>Reconciling Base-Pair Resolution 5-methylcytosine and 5-hydroxymethylcytosine Data in <\/strong><strong>Neuroepigenetics.<\/strong> Frontiers in Genetics. doi: <a href=\"https:\/\/doi.org\/10.3389\/fgene.2019.00801\" target=\"_blank\" rel=\"noopener\">10.3389\/fgene.2019.00801<\/a>. <a href=\"http:\/\/sites.rutgers.edu\/bernstein-lab\/wp-content\/uploads\/sites\/985\/2023\/11\/2019_Kochmanski_FrontiersInGenetics.pdf\" target=\"_blank\" rel=\"noopener\">\ud83d\udd17<\/a><\/h6>\n<h6>\u203a Kochmanski J, VanOeveren SE, Patterson JR, Bernstein AI (2019) <strong>Developmental Dieldrin <\/strong><strong>Exposure Alters DNA Methylation at Genes Related to Dopaminergic Neuron Development <\/strong><strong>and Parkinson&#8217;s Disease in Mouse Midbrain.<\/strong> Toxicological Sciences. 169(2): 593-607. doi:<a href=\"https:\/\/doi.org\/10.1093\/toxsci\/kfz069\" target=\"_blank\" rel=\"noopener\">10.1093\/toxsci\/kfz069<\/a>. <a href=\"http:\/\/sites.rutgers.edu\/bernstein-lab\/wp-content\/uploads\/sites\/985\/2023\/11\/2019_Kochmanski_ToxSci.pdf\" target=\"_blank\" rel=\"noopener\">\ud83d\udd17<\/a><\/h6>\n<ul>\n<li><em>Dataset DOI: <a href=\"https:\/\/doi.org\/10.5061\/dryad.s3n76mr\" target=\"_blank\" rel=\"noopener\">10.5061\/dryad.s3n76mr<\/a><\/em><\/li>\n<\/ul>\n<p><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/sites\/myncbi\/1jYin8D-OS0\/bibliography\/40138190\/public\/?sort=date&amp;direction=ascending\" target=\"_blank\" rel=\"noopener\">View Alison Bernstein&#8217;s NCBI Bibliography<\/a><\/p>\n<p>PDFs available via link icons.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>2025 \u203a\u00a0 Choza, J.I., Virani, M., Kuhn, N.C. et al. Parkinson\u2019s disease-associated alterations in DNA methylation and hydroxymethylation in human brain. npj Parkinsons Dis. 11, 363 (2025). doi: 10.1038\/s41531-025-01209-3. \ud83d\udd17 &hellip; <a href=\"https:\/\/sites.rutgers.edu\/bernstein-lab\/publications\/\" class=\"\">Read More<\/a><\/p>\n","protected":false},"author":21,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"template-custom.php","meta":{"_acf_changed":false,"footnotes":""},"class_list":["post-363","page","type-page","status-publish","hentry"],"acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v23.5 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>Publications - Bernstein Lab<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/sites.rutgers.edu\/bernstein-lab\/publications\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Publications - Bernstein Lab\" \/>\n<meta property=\"og:description\" content=\"2025 \u203a\u00a0 Choza, J.I., Virani, M., Kuhn, N.C. et al. 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Parkinson\u2019s disease-associated alterations in DNA methylation and hydroxymethylation in human brain. npj Parkinsons Dis. 11, 363 (2025). doi: 10.1038\/s41531-025-01209-3. \ud83d\udd17 &hellip; Read More","og_url":"https:\/\/sites.rutgers.edu\/bernstein-lab\/publications\/","og_site_name":"Bernstein Lab","article_modified_time":"2026-01-03T20:18:41+00:00","twitter_card":"summary_large_image","twitter_misc":{"Est. reading time":"2 minutes"},"schema":{"@context":"https:\/\/schema.org","@graph":[{"@type":"WebPage","@id":"https:\/\/sites.rutgers.edu\/bernstein-lab\/publications\/","url":"https:\/\/sites.rutgers.edu\/bernstein-lab\/publications\/","name":"Publications - Bernstein Lab","isPartOf":{"@id":"https:\/\/sites.rutgers.edu\/bernstein-lab\/#website"},"datePublished":"2020-07-09T16:51:59+00:00","dateModified":"2026-01-03T20:18:41+00:00","breadcrumb":{"@id":"https:\/\/sites.rutgers.edu\/bernstein-lab\/publications\/#breadcrumb"},"inLanguage":"en-US","potentialAction":[{"@type":"ReadAction","target":["https:\/\/sites.rutgers.edu\/bernstein-lab\/publications\/"]}]},{"@type":"BreadcrumbList","@id":"https:\/\/sites.rutgers.edu\/bernstein-lab\/publications\/#breadcrumb","itemListElement":[{"@type":"ListItem","position":1,"name":"Home","item":"https:\/\/sites.rutgers.edu\/bernstein-lab\/"},{"@type":"ListItem","position":2,"name":"Publications"}]},{"@type":"WebSite","@id":"https:\/\/sites.rutgers.edu\/bernstein-lab\/#website","url":"https:\/\/sites.rutgers.edu\/bernstein-lab\/","name":"Bernstein Lab","description":"","potentialAction":[{"@type":"SearchAction","target":{"@type":"EntryPoint","urlTemplate":"https:\/\/sites.rutgers.edu\/bernstein-lab\/?s={search_term_string}"},"query-input":{"@type":"PropertyValueSpecification","valueRequired":true,"valueName":"search_term_string"}}],"inLanguage":"en-US"}]}},"_links":{"self":[{"href":"https:\/\/sites.rutgers.edu\/bernstein-lab\/wp-json\/wp\/v2\/pages\/363"}],"collection":[{"href":"https:\/\/sites.rutgers.edu\/bernstein-lab\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/sites.rutgers.edu\/bernstein-lab\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/sites.rutgers.edu\/bernstein-lab\/wp-json\/wp\/v2\/users\/21"}],"replies":[{"embeddable":true,"href":"https:\/\/sites.rutgers.edu\/bernstein-lab\/wp-json\/wp\/v2\/comments?post=363"}],"version-history":[{"count":55,"href":"https:\/\/sites.rutgers.edu\/bernstein-lab\/wp-json\/wp\/v2\/pages\/363\/revisions"}],"predecessor-version":[{"id":785,"href":"https:\/\/sites.rutgers.edu\/bernstein-lab\/wp-json\/wp\/v2\/pages\/363\/revisions\/785"}],"wp:attachment":[{"href":"https:\/\/sites.rutgers.edu\/bernstein-lab\/wp-json\/wp\/v2\/media?parent=363"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}