Lucia Carbone, Ph.D.
- Professor of Medicine, School of Medicine
- Professor of Molecular and Medical Genetics, School of Medicine
- Henry T. Swigert Endowed Professor in Cardiovascular Medicine
- Director, Epigenetics Consortium
- Program in Molecular and Cellular Biosciences, School of Medicine
Biography
I am a Professor of Medicine at Oregon Health & Science University (OHSU) and Director of the KCVI Epigenetics Consortium. I am also a core scientist in the Division of Genetics at the Oregon National Primate Research Center (ONPRC). My research program focuses on understanding the mechanisms of genome instability during primate evolution as well as human development and disease.
I received my Master’s degree in Biology and PhD in Genetics and Molecular Evolution from the University of Bari (Italy), where I trained in the laboratory of Prof. Mariano Rocchi. There, I developed a strong foundation in chromosome biology that has guided my research career. I subsequently completed postdoctoral training at the Children’s Hospital Research Institute of Oakland (CHORI) in the laboratory of Dr. Pieter de Jong, a pioneer in high-throughput genomics. In 2010, I established my independent research program at OHSU and ONPRC. In 2016, I founded the KCVI Epigenetics Consortium, which provides shared infrastructure and expertise to support epigenetics research across OHSU and beyond.
My current research program integrates comparative genomics, epigenomics, and three-dimensional genome organization to investigate the molecular bases of congenital disorders and early embryonic development. By combining multi-omics datasets—including chromatin conformation, histone modifications, and transcriptomic profiles—with functional genomic tools such as CRISPR-based editing, we aim to uncover the mechanisms by which genome architecture regulates gene expression. Ultimately, my goal is to reveal fundamental principles of genome function and understand how structural variation drives both biological diversity and disease susceptibility.
Education and training
-
Degrees
- MSc, 2001, Universita' di Bari
- Ph.D., 2004, Universita' di Bari
Memberships and associations:
- American Heart Association (AHA)
Areas of interest
- Epigenetics
- Genomics
- Bioinformatics
- Evolution
Additional information
Honors and awards
- OHSU Senate’s 2021 Distinguished Faculty Collaboration Award
- Excellence in Research Award (Physiological Genomics Journal)
Publications
Selected publications
- Yoo, D., Rhie, A., Hebbar, P.et al. Complete sequencing of ape genomes (2025). Nature. 2025 May; 641(8062):401-418
- Hartley GA, Okhovat M, Hoyt SJ, Fuller E, Pauloski N, Alexandre N, Alexandrov I, Drennan R, Dubocanin D, Gilbert DM, Mao Y, McCann C, Neph S, Ryabov F, Sasaki T, Storer JM, Svendsen D, Troy W, Wells J, Core L, Stergachis A, Carbone L, O’Neill RJ Centromeric transposable elements and epigenetic status drive karyotypic variation in the eastern hoolock gibbon (2005) Cell Genomics, Apr 9;5(4):100808
- Lima AC, Okhovat M, Stendahl AM, VanCampen J, Nevonen KA, Herrera J, Li W, Harshman L, Yang R, Fedorov LM, Vigh-Conrad KA, Ahituv N, Conrad DF, Carbone L. Deletion of an evolutionarily conserved TAD boundary impacts spermatogenesis in mice (2025). Biol Reprod Apr 13;112(4):767-779.
- Makova KD, Pickett BD, Harris RS, Hartley GA, et al. The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes (2024). Nature. Jun;630(8016):401-411
- Layman CE, Ward S, Davis BA, Nevonen KA, Okhovat M, Rincon M, Valent A, Carbone L, Thornburg KL High-throughput methylome analysis reveals differential methylation for early and late onset preeclampsia for mothers and their children (2024) Physiol Genomics Mar 1;56(3):276-282.
- Yafei M, Harvey WT, Porubsky D, Munson KM, Hoekzema K, Lewis AP, Audano PA, Rozanski A, Yang X, Zhang S, Yoo DA, Gordon DS, Fair T, Wei X, Logsdon GA, Haukness M, Dishuck PC, Jeong H, Del Rosario R, Bauer VL, Fattor WT, Wilkerson GK, Mao Y, Shi Y, Sun Q, Lu Q, Paten B, Bakken TE, Pollen AA, Feng G, Sawyer SL, Warren WC, Carbone L, Eichler EE. Structurally divergent and recurrently mutated regions of primate genomes. (2024) Cell Feb 23:S0092-8674(24)00121-1)
- Okhovat M, VanCampen J, Lima AC, Nevonen KA, Layman CE, Ward S, Herrera J, Stendahl AM, Yang R, Harshman L, Li W, Sheng RR, Mao Y, Fedorov L, Ndjamen B, Vigh-Conrad KA, Matthews IR, Easow SA, Chan DK, Jan TA, Eichler EE, Rugonyi S, Conrad DF, Ahituv N, Carbone L. TAD Evolutionary and functional characterization reveals diversity in mammalian TAD boundary properties and function. (2023) Nature Communications 14, 8111
- Hartley G, Okhovat M, O’Neill RJ, Carbone L. (2021) Comparative analyses of gibbon centromeres reveal dynamic genus specific shifts in repeat composition. Molecular Biology and Evolution 38(9):3972-3992
- Okhovat M, Nevonen KA, Davis BA, Michener P, Ward S, Milhaven M, Harshman L, Sohota A, Fernandes JD, Salama SR, O’Neill RJ, Ahituv N, Veeramah KR, Carbone L. (2020) Co-option of the gibbon-specific LAVA retrotransposon. PNAS, 117 (32) 19328-19338
- Braun TP, Okhovat M, Coblentz C, Carratt SA, Foley A, Schonrock Z, Nevonen KA, Davis BA, Garcia B, LaTocha D, Jeng S, McWeeney S, Di Genua C, Drissen R, Nerlov C, Carbone L, Druker BJ, Maxson JE. (2019) Myeloid lineage enhancers drive oncogene synergy in CEBPA/CSF3R mutant acute myeloid leukemia. Nature Communications 10(1):5455
- Lazar NH, Nevonen KA, O'Connell B, McCann C., O’Neill RJ, Green RE, Meyer TJ, Okhovat M, and Carbone L. (2018) Epigenetic maintenance of topological domains in the rearranged gibbon genome. Genome Research 28(7):983-997
- Carbone L, Harris RA, Gnerre S, Veeramah KR, Lorente-Galdos B, Huddleston J, Meyer TJ, Herrero J, Roos C, Aken B, Anaclerio F, Archidiacono N, Baker C, Barrell D, Batzer MA, Beal K, Blancher A, Bohrson CL, Brameier M, Campbell MS, Capozzi O, Casola C, and the international consortium for the sequencing of the gibbon genome. (2014) Gibbon genome and the fast karyotype evolution of small apes. Nature. 2014 513(7517):195-201.
- Carbone L, Harris RA, Mootnick AR, Milosavljevic A, Martin DI, Rocchi M, Capozzi O, Archidiacono N, Konkel MK, Walker JA, Batzer MA, de Jong PJ. (2012) Centromere remodeling in Hoolock leuconedys (Hylobatidae) by a new transposable element unique to the gibbons. Genome Biology and Evolution 4(7):648-58