Researcher Profile

Arbeithuber, B, Anthony, K, Higgins, B, Oppelt, P, Shebl, O, Tiemann-Boege, I, Chiaromonte, F, Ebner, T & Makova, KD 2026, 'Allele Frequency Selection and No Age-Related Increase in Human Oocyte Mitochondrial Mutations', Obstetrical and Gynecological Survey, vol. 81, no. 1, pp. 25-26. https://doi.org/10.1097/OGX.0000000000001486

Torres-Gonzalez, E, Arbeithuber, B, Stoler, N, Cremona, MA, Shebl, O, Ebner, T, Tiemann-Boege, I, Diaz, FJ, Chiaromonte, F & Makova, KD 2026, 'Mammalian mitochondrial DNA accumulates insertions and deletions with age in energetically demanding tissues', Molecular biology and evolution, vol. 43, no. 3, msag035. https://doi.org/10.1093/molbev/msag035

Human Pangenome Reference Consortium 2026, 'SNP calling, haplotype phasing and allele-specific analysis with long RNA-seq reads', Nature methods. https://doi.org/10.1038/s41592-026-03045-6

Zhang, X, Mohanty, SK, Chiaromonte, F & Makova, KD 2026, 'Substitution Spectrum and Selection at G-quadruplexes in Great Ape Telomere-to-Telomere Genomes', Genome biology and evolution, vol. 18, no. 3. https://doi.org/10.1093/gbe/evag040

Human Pangenome Reference Consortium (HPRC) 2026, 'Using the linear references from the pangenome to discover missing autism variants', Nature communications, vol. 17, no. 1, 1681. https://doi.org/10.1038/s41467-026-68378-4

Arbeithuber, B, Anthony, K, Higgins, B, Oppelt, P, Shebl, O, Tiemann-Boege, I, Chiaromonte, F, Ebner, T & Makova, KD 2025, 'Allele frequency selection and no age-related increase in human oocyte mitochondrial mutations', Science Advances, vol. 11, no. 32, eadw4954. https://doi.org/10.1126/sciadv.adw4954

Yoo, DA, Rhie, A, Hebbar, P, Antonacci, F, Logsdon, GA, Solar, SJ, Antipov, D, Pickett, BD, Safonova, Y, Montinaro, F, Luo, Y, Malukiewicz, J, Storer, JM, Lin, J, Sequeira, AN, Mangan, RJ, Hickey, G, Monfort Anez, G, Balachandran, P, Bankevich, A, Beck, CR, Biddanda, A, Borchers, M, Bouffard, GG, Brannan, E, Brooks, SY, Carbone, L, Carrel, L, Chan, AP, Crawford, J, Diekhans, M, Engelbrecht, E, Feschotte, C, Formenti, G, Garcia, GH, de Gennaro, L, Gilbert, D, Green, RE, Guarracino, A, Gupta, I, Haddad, D, Han, J, Harris, RS, Hartley, GA, Harvey, WT, Hiller, M, Hoekzema, K, Houck, ML, Jeong, H, Kamali, K, Kellis, M, Kille, B, Lee, C, Lee, Y, Lees, W, Lewis, AP, Li, Q, Loftus, M, Loh, YHE, Loucks, H, Ma, J, Mao, Y, Martinez, JFI, Masterson, P, McCoy, RC, McGrath, B, McKinney, S, Meyer, BS, Miga, KH, Mohanty, SK, Munson, KM, Pal, K, Pennell, M, Pevzner, PA, Porubsky, D, Potapova, T, Ringeling, FR, Rocha, JL, Ryder, OA, Sacco, S, Saha, S, Sasaki, T, Schatz, MC, Schork, NJ, Shanks, C, Smeds, L, Son, DR, Steiner, C, Sweeten, AP, Tassia, MG, Thibaud-Nissen, F, Torres-González, E, Trivedi, M, Wei, W, Wertz, J, Yang, M, Zhang, P, Zhang, S, Zhang, Y, Zhang, Z, Zhao, SA, Zhu, Y, Jarvis, ED, Gerton, JL, Rivas-González, I, Paten, B, Szpiech, ZA, Huber, CD, Lenz, TL, Konkel, MK, Yi, SV, Canzar, S, Watson, CT, Sudmant, PH, Molloy, E, Garrison, E, Lowe, CB, Ventura, M, O’Neill, RJ, Koren, S, Makova, KD, Phillippy, AM & Eichler, EE 2025, 'Complete sequencing of ape genomes', Nature, vol. 641, no. 8062, pp. 401-418. https://doi.org/10.1038/s41586-025-08816-3

Mohanty, SK, Chiaromonte, F & Makova, KD 2025, 'Evolutionary dynamics of predicted G-quadruplexes in human and other great apes', Genome biology, vol. 26, no. 1, 161. https://doi.org/10.1186/s13059-025-03635-1

Human Pangenome Reference Consortium 2025, 'Highly accurate assembly polishing with DeepPolisher', Genome Research, vol. 35, no. 7, pp. 1595-1608. https://doi.org/10.1101/gr.280149.124

Smeds, L, Kamali, K, Kejnovská, I, Kejnovský, E, Chiaromonte, F & Makova, KD 2025, 'Non-canonical DNA in human and other ape telomere-to-telomere genomes', Nucleic acids research, vol. 53, no. 7, gkaf298. https://doi.org/10.1093/nar/gkaf298

Hile, SE, Weissensteiner, MH, Pytko, KG, Dahl, J, Kejnovsky, E, Kejnovská, I, Hedglin, M, Georgakopoulos-Soares, I, Makova, KD & Eckert, KA 2025, 'Replicative DNA polymerase epsilon and delta holoenzymes show wide-ranging inhibition at G-quadruplexes in the human genome', Nucleic acids research, vol. 53, no. 8, gkaf352. https://doi.org/10.1093/nar/gkaf352

Lariviere, D, Craig, SJC, Paul, IM, Hohman, EE, Savage, JS, Wright, RO, Chiaromonte, F, Makova, KD & Reimherr, ML 2024, 'Methylation profiles at birth linked to early childhood obesity', Journal of Developmental Origins of Health and Disease, vol. 15, e7. https://doi.org/10.1017/S2040174424000060

Makova, KD, Pickett, BD, Harris, RS, Hartley, GA, Cechova, M, Pal, K, Nurk, S, Yoo, DA, Li, Q, Hebbar, P, McGrath, BC, Antonacci, F, Aubel, M, Biddanda, A, Borchers, M, Bornberg-Bauer, E, Bouffard, GG, Brooks, SY, Carbone, L, Carrel, L, Carroll, A, Chang, PC, Chin, CS, Cook, DE, Craig, SJC, de Gennaro, L, Diekhans, M, Dutra, A, Garcia, GH, Grady, PGS, Green, RE, Haddad, D, Hallast, P, Harvey, WT, Hickey, G, Hillis, DA, Hoyt, SJ, Jeong, H, Kamali, K, Pond, SLK, LaPolice, TM, Lee, C, Lewis, AP, Loh, YHE, Masterson, P, McGarvey, KM, McCoy, RC, Medvedev, P, Miga, KH, Munson, KM, Pak, E, Paten, B, Pinto, BJ, Potapova, T, Rhie, A, Rocha, JL, Ryabov, F, Ryder, OA, Sacco, S, Shafin, K, Shepelev, VA, Slon, V, Solar, SJ, Storer, JM, Sudmant, PH, Sweetalana, Sweeten, A, Tassia, MG, Thibaud-Nissen, F, Ventura, M, Wilson, MA, Young, AC, Zeng, H, Zhang, X, Szpiech, ZA, Huber, CD, Gerton, JL, Yi, SV, Schatz, MC, Alexandrov, IA, Koren, S, O’Neill, RJ, Eichler, EE & Phillippy, AM 2024, 'The complete sequence and comparative analysis of ape sex chromosomes', Nature, vol. 630, no. 8016, pp. 401-411. https://doi.org/10.1038/s41586-024-07473-2

Weissensteiner, MH, Cremona, MA, Guiblet, WM, Stoler, N, Harris, RS, Cechova, M, Eckert, KA, Chiaromonte, F, Huang, YF & Makova, KD 2023, 'Accurate sequencing of DNA motifs able to form alternative (non-B) structures', Genome Research, vol. 33, no. 6, pp. 907-923. https://doi.org/10.1101/gr.277490.122

Makova, KD & Weissensteiner, MH 2023, 'Noncanonical DNA structures are drivers of genome evolution', Trends in Genetics, vol. 39, no. 2, pp. 109-124. https://doi.org/10.1016/j.tig.2022.11.005

Rhie, A, Nurk, S, Cechova, M, Hoyt, SJ, Taylor, DJ, Altemose, N, Hook, PW, Koren, S, Rautiainen, M, Alexandrov, IA, Allen, J, Asri, M, Bzikadze, AV, Chen, NC, Chin, CS, Diekhans, M, Flicek, P, Formenti, G, Fungtammasan, A, Garcia Giron, C, Garrison, E, Gershman, A, Gerton, JL, Grady, PGS, Guarracino, A, Haggerty, L, Halabian, R, Hansen, NF, Harris, R, Hartley, GA, Harvey, WT, Haukness, M, Heinz, J, Hourlier, T, Hubley, RM, Hunt, SE, Hwang, S, Jain, M, Kesharwani, RK, Lewis, AP, Li, H, Logsdon, GA, Lucas, JK, Makalowski, W, Markovic, C, Martin, FJ, Mc Cartney, AM, McCoy, RC, McDaniel, J, McNulty, BM, Medvedev, P, Mikheenko, A, Munson, KM, Murphy, TD, Olsen, HE, Olson, ND, Paulin, LF, Porubsky, D, Potapova, T, Ryabov, F, Salzberg, SL, Sauria, MEG, Sedlazeck, FJ, Shafin, K, Shepelev, VA, Shumate, A, Storer, JM, Surapaneni, L, Taravella Oill, AM, Thibaud-Nissen, F, Timp, W, Tomaszkiewicz, M, Vollger, MR, Walenz, BP, Watwood, AC, Weissensteiner, MH, Wenger, AM, Wilson, MA, Zarate, S, Zhu, Y, Zook, JM, Eichler, EE, O’Neill, RJ, Schatz, MC, Miga, KH, Makova, KD & Phillippy, AM 2023, 'The complete sequence of a human Y chromosome', Nature, vol. 621, no. 7978, pp. 344-354. https://doi.org/10.1038/s41586-023-06457-y

Tomaszkiewicz, M, Sahlin, K, Medvedev, P & Makova, KD 2023, 'Transcript Isoform Diversity of Ampliconic Genes on the Y Chromosome of Great Apes', Genome biology and evolution, vol. 15, no. 11, evad205. https://doi.org/10.1093/gbe/evad205

Escalona, M, Vancampen, J, Maurer, NW, Haukness, M, Okhovat, M, Harris, RS, Watwood, A, Hartley, GA, O'neill, RJ, Medvedev, P, Makova, KD, Vollmers, C, Carbone, L & Green, RE 2023, 'Whole-genome sequence and assembly of the Javan gibbon (Hylobates moloch)', Journal of Heredity, vol. 114, no. 1, pp. 35-43. https://doi.org/10.1093/jhered/esac043

Arbeithuber, B, Cremona, MA, Hester, J, Barrett, A, Higgins, B, Anthony, K, Chiaromonte, F, Diaz, FJ & Makova, KD 2022, 'Advanced age increases frequencies of de novo mitochondrial mutations in macaque oocytes and somatic tissues', Proceedings of the National Academy of Sciences of the United States of America, vol. 119, no. 15, e2118740119. https://doi.org/10.1073/pnas.2118740119

Torres-Gonzalez, E & Makova, KD 2022, 'Exploring the Effects of Mitonuclear Interactions on Mitochondrial DNA Gene Expression in Humans', Frontiers in Genetics, vol. 13, 797129. https://doi.org/10.3389/fgene.2022.797129

Savage, JS, Hochgraf, AK, Loken, E, Marini, ME, Craig, SJC, Makova, KD, Birch, LL & Paul, IM 2022, 'INSIGHT responsive parenting educational intervention for firstborns is associated with growth of second-born siblings', Obesity, vol. 30, no. 1, pp. 183-190. https://doi.org/10.1002/oby.23301

Stein, ME, Hile, SE, Weissensteiner, MH, Lee, M, Zhang, S, Kejnovský, E, Kejnovská, I, Makova, KD & Eckert, KA 2022, 'Variation in G-quadruplex sequence and topology differentially impacts human DNA polymerase fidelity', DNA Repair, vol. 119, 103402. https://doi.org/10.1016/j.dnarep.2022.103402