Joel Rozowsky, PhD
Research Scientist in Molecular Biophysics and BiochemistryCards
About
Research
Publications
2026
Predicting disease-specific histone modifications and functional effects of non-coding variants by leveraging DNA language models
Wang X, Pan T, Chen S, Webb G, Jiang Y, Rozowsky J, Gerstein M, Song J. Predicting disease-specific histone modifications and functional effects of non-coding variants by leveraging DNA language models. Genome Biology 2026, 27: 97. PMID: 41691336, PMCID: PMC13011769, DOI: 10.1186/s13059-026-04003-3.Peer-Reviewed Original Research
2023
More than bad luck: Cancer and aging are linked to replication-driven changes to the epigenome
Minteer C, Thrush K, Gonzalez J, Niimi P, Rozenblit M, Rozowsky J, Liu J, Frank M, McCabe T, Sehgal R, Higgins-Chen A, Hofstatter E, Pusztai L, Beckman K, Gerstein M, Levine M. More than bad luck: Cancer and aging are linked to replication-driven changes to the epigenome. Science Advances 2023, 9: eadf4163. PMID: 37467337, PMCID: PMC10355820, DOI: 10.1126/sciadv.adf4163.Peer-Reviewed Original ResearchexRNA-eCLIP intersection analysis reveals a map of extracellular RNA binding proteins and associated RNAs across major human biofluids and carriers
LaPlante E, Stürchler A, Fullem R, Chen D, Starner A, Esquivel E, Alsop E, Jackson A, Ghiran I, Pereira G, Rozowsky J, Chang J, Gerstein M, Alexander R, Roth M, Franklin J, Coffey R, Raffai R, Mansuy I, Stavrakis S, deMello A, Laurent L, Wang Y, Tsai C, Liu T, Jones J, Van Keuren-Jensen K, Van Nostrand E, Mateescu B, Milosavljevic A. exRNA-eCLIP intersection analysis reveals a map of extracellular RNA binding proteins and associated RNAs across major human biofluids and carriers. Cell Genomics 2023, 3: 100303. PMID: 37228754, PMCID: PMC10203258, DOI: 10.1016/j.xgen.2023.100303.Peer-Reviewed Original ResearchThe EN-TEx resource of multi-tissue personal epigenomes & variant-impact models
Rozowsky J, Gao J, Borsari B, Yang Y, Galeev T, Gürsoy G, Epstein C, Xiong K, Xu J, Li T, Liu J, Yu K, Berthel A, Chen Z, Navarro F, Sun M, Wright J, Chang J, Cameron C, Shoresh N, Gaskell E, Drenkow J, Adrian J, Aganezov S, Aguet F, Balderrama-Gutierrez G, Banskota S, Corona G, Chee S, Chhetri S, Cortez Martins G, Danyko C, Davis C, Farid D, Farrell N, Gabdank I, Gofin Y, Gorkin D, Gu M, Hecht V, Hitz B, Issner R, Jiang Y, Kirsche M, Kong X, Lam B, Li S, Li B, Li X, Lin K, Luo R, Mackiewicz M, Meng R, Moore J, Mudge J, Nelson N, Nusbaum C, Popov I, Pratt H, Qiu Y, Ramakrishnan S, Raymond J, Salichos L, Scavelli A, Schreiber J, Sedlazeck F, See L, Sherman R, Shi X, Shi M, Sloan C, Strattan J, Tan Z, Tanaka F, Vlasova A, Wang J, Werner J, Williams B, Xu M, Yan C, Yu L, Zaleski C, Zhang J, Ardlie K, Cherry J, Mendenhall E, Noble W, Weng Z, Levine M, Dobin A, Wold B, Mortazavi A, Ren B, Gillis J, Myers R, Snyder M, Choudhary J, Milosavljevic A, Schatz M, Bernstein B, Guigó R, Gingeras T, Gerstein M. The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models. Cell 2023, 186: 1493-1511.e40. PMID: 37001506, PMCID: PMC10074325, DOI: 10.1016/j.cell.2023.02.018.Peer-Reviewed Original Research
2022
Phase 2 of extracellular RNA communication consortium charts next-generation approaches for extracellular RNA research
Mateescu B, Jones JC, Alexander RP, Alsop E, An JY, Asghari M, Boomgarden A, Bouchareychas L, Cayota A, Chang HC, Charest A, Chiu DT, Coffey RJ, Das S, De Hoff P, deMello A, D’Souza-Schorey C, Elashoff D, Eliato KR, Franklin JL, Galas DJ, Gerstein MB, Ghiran IH, Go DB, Gould S, Grogan TR, Higginbotham JN, Hladik F, Huang TJ, Huo X, Hutchins E, Jeppesen DK, Jovanovic-Talisman T, Kim BYS, Kim S, Kim KM, Kim Y, Kitchen RR, Knouse V, LaPlante EL, Lebrilla CB, Lee LJ, Lennon KM, Li G, Li F, Li T, Liu T, Liu Z, Maddox AL, McCarthy K, Meechoovet B, Maniya N, Meng Y, Milosavljevic A, Min BH, Morey A, Ng M, Nolan J, De Oliveira G, Paulaitis ME, Phu TA, Raffai RL, Reátegui E, Roth ME, Routenberg DA, Rozowsky J, Rufo J, Senapati S, Shachar S, Sharma H, Sood AK, Stavrakis S, Stürchler A, Tewari M, Tosar JP, Tucker-Schwartz AK, Turchinovich A, Valkov N, Van Keuren-Jensen K, Vickers KC, Vojtech L, Vreeland WN, Wang C, Wang K, Wang Z, Welsh JA, Witwer KW, Wong DTW, Xia J, Xie YH, Yang K, Zaborowski MP, Zhang C, Zhang Q, Zivkovic AM, Laurent LC. Phase 2 of extracellular RNA communication consortium charts next-generation approaches for extracellular RNA research. IScience 2022, 25: 104653. PMID: 35958027, PMCID: PMC9358052, DOI: 10.1016/j.isci.2022.104653.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsAuthor Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes
Moore J, Purcaro M, Pratt H, Epstein C, Shoresh N, Adrian J, Kawli T, Davis C, Dobin A, Kaul R, Halow J, Van Nostrand E, Freese P, Gorkin D, Shen Y, He Y, Mackiewicz M, Pauli-Behn F, Williams B, Mortazavi A, Keller C, Zhang X, Elhajjajy S, Huey J, Dickel D, Snetkova V, Wei X, Wang X, Rivera-Mulia J, Rozowsky J, Zhang J, Chhetri S, Zhang J, Victorsen A, White K, Visel A, Yeo G, Burge C, Lécuyer E, Gilbert D, Dekker J, Rinn J, Mendenhall E, Ecker J, Kellis M, Klein R, Noble W, Kundaje A, Guigó R, Farnham P, Cherry J, Myers R, Ren B, Graveley B, Gerstein M, Pennacchio L, Snyder M, Bernstein B, Wold B, Hardison R, Gingeras T, Stamatoyannopoulos J, Weng Z. Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature 2022, 605: e3-e3. PMID: 35474001, PMCID: PMC9095460, DOI: 10.1038/s41586-021-04226-3.Commentaries, Editorials and LettersA Novel Tissue Atlas and Online Tool for the Interrogation of Small RNA Expression in Human Tissues and Biofluids
Alsop E, Meechoovet B, Kitchen R, Sweeney T, Beach T, Serrano G, Hutchins E, Ghiran I, Reiman R, Syring M, Hsieh M, Courtright-Lim A, Valkov N, Whitsett T, Rakela J, Pockros P, Rozowsky J, Gallego J, Huentelman M, Shah R, Nakaji P, Kalani M, Laurent L, Das S, Van Keuren-Jensen K. A Novel Tissue Atlas and Online Tool for the Interrogation of Small RNA Expression in Human Tissues and Biofluids. Frontiers In Cell And Developmental Biology 2022, 10: 804164. PMID: 35317387, PMCID: PMC8934391, DOI: 10.3389/fcell.2022.804164.Peer-Reviewed Original ResearchOpen Problems in Extracellular RNA Data Analysis: Insights From an ERCC Online Workshop
Alexander R, Kitchen R, Tosar J, Roth M, Mestdagh P, Max K, Rozowsky J, Kaczor-Urbanowicz K, Chang J, Balaj L, Losic B, Van Nostrand E, LaPlante E, Mateescu B, White B, Yu R, Milosavljevic A, Stolovitzky G, Spengler R. Open Problems in Extracellular RNA Data Analysis: Insights From an ERCC Online Workshop. Frontiers In Genetics 2022, 12: 778416. PMID: 35047007, PMCID: PMC8762274, DOI: 10.3389/fgene.2021.778416.Peer-Reviewed Original Research
2021
Whole-genome sequencing of phenotypically distinct inflammatory breast cancers reveals similar genomic alterations to non-inflammatory breast cancers
Li X, Kumar S, Harmanci A, Li S, Kitchen RR, Zhang Y, Wali VB, Reddy SM, Woodward WA, Reuben JM, Rozowsky J, Hatzis C, Ueno NT, Krishnamurthy S, Pusztai L, Gerstein M. Whole-genome sequencing of phenotypically distinct inflammatory breast cancers reveals similar genomic alterations to non-inflammatory breast cancers. Genome Medicine 2021, 13: 70. PMID: 33902690, PMCID: PMC8077918, DOI: 10.1186/s13073-021-00879-x.Peer-Reviewed Original Research
2020
Expanded encyclopaedias of DNA elements in the human and mouse genomes
Moore J, Purcaro M, Pratt H, Epstein C, Shoresh N, Adrian J, Kawli T, Davis C, Dobin A, Kaul R, Halow J, Van Nostrand E, Freese P, Gorkin D, Shen Y, He Y, Mackiewicz M, Pauli-Behn F, Williams B, Mortazavi A, Keller C, Zhang X, Elhajjajy S, Huey J, Dickel D, Snetkova V, Wei X, Wang X, Rivera-Mulia J, Rozowsky J, Zhang J, Chhetri S, Zhang J, Victorsen A, White K, Visel A, Yeo G, Burge C, Lécuyer E, Gilbert D, Dekker J, Rinn J, Mendenhall E, Ecker J, Kellis M, Klein R, Noble W, Kundaje A, Guigó R, Farnham P, Cherry J, Myers R, Ren B, Graveley B, Gerstein M, Pennacchio L, Snyder M, Bernstein B, Wold B, Hardison R, Gingeras T, Stamatoyannopoulos J, Weng Z. Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature 2020, 583: 699-710. PMID: 32728249, PMCID: PMC7410828, DOI: 10.1038/s41586-020-2493-4.Peer-Reviewed Original Research