Researcher Profile

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, aae0344, pp. 401-418. https://doi.org/10.1038/s41586-025-08816-3

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

Carney, MC, Zhan, X, Rangnekar, A, Chroneos, MZ, Craig, SJC, Makova, KD, Paul, IM & Hicks, SD 2021, 'Associations between stool micro-transcriptome, gut microbiota, and infant growth', Journal of Developmental Origins of Health and Disease, vol. 12, no. 6, pp. 876-882. https://doi.org/10.1017/S2040174420001324

Craig, SJC, Kenney, AM, Lin, J, Paul, IM, Birch, LL, Savage, JS, Marini, ME, Chiaromonte, F, Reimherr, ML & Makova, KD 2023, 'Constructing a polygenic risk score for childhood obesity using functional data analysis', Econometrics and Statistics, vol. 25, pp. 66-86. https://doi.org/10.1016/j.ecosta.2021.10.014

Nandy, D, Craig, SJC, Cai, J, Tian, Y, Paul, IM, Savage, JS, Marini, ME, Hohman, EE, Reimherr, ML, Patterson, AD, Makova, KD & Chiaromonte, F 2022, 'Metabolomic profiling of stool of two-year old children from the INSIGHT study reveals links between butyrate and child weight outcomes', Pediatric Obesity, vol. 17, no. 1, e12833. https://doi.org/10.1111/ijpo.12833

Guiblet, WM, Cremona, MA, Harris, RS, Chen, D, Eckert, KA, Chiaromonte, F, Huang, YF & Makova, KD 2021, 'Non-B DNA: A major contributor to small-and large-scale variation in nucleotide substitution frequencies across the genome', Nucleic acids research, vol. 49, no. 3, pp. 1497-1516. https://doi.org/10.1093/nar/gkaa1269

Guiblet, WM, DeGiorgio, M, Cheng, X, Chiaromonte, F, Eckert, KA, Huang, YF & Makova, KD 2021, 'Selection and thermostability suggest G-quadruplexes are novel functional elements of the human genome', Genome research, vol. 31, no. 7, pp. 1136-1149. https://doi.org/10.1101/gr.269589.120

Rhie, A, McCarthy, SA, Fedrigo, O, Damas, J, Formenti, G, Koren, S, Uliano-Silva, M, Chow, W, Fungtammasan, A, Kim, J, Lee, C, Ko, BJ, Chaisson, M, Gedman, GL, Cantin, LJ, Thibaud-Nissen, F, Haggerty, L, Bista, I, Smith, M, Haase, B, Mountcastle, J, Winkler, S, Paez, S, Howard, J, Vernes, SC, Lama, TM, Grutzner, F, Warren, WC, Balakrishnan, CN, Burt, D, George, JM, Biegler, MT, Iorns, D, Digby, A, Eason, D, Robertson, B, Edwards, T, Wilkinson, M, Turner, G, Meyer, A, Kautt, AF, Franchini, P, Detrich, HW, Svardal, H, Wagner, M, Naylor, GJP, Pippel, M, Malinsky, M, Mooney, M, Simbirsky, M, Hannigan, BT, Pesout, T, Houck, M, Misuraca, A, Kingan, SB, Hall, R, Kronenberg, Z, Sović, I, Dunn, C, Ning, Z, Hastie, A, Lee, J, Selvaraj, S, Green, RE, Putnam, NH, Gut, I, Ghurye, J, Garrison, E, Sims, Y, Collins, J, Pelan, S, Torrance, J, Tracey, A, Wood, J, Dagnew, RE, Guan, D, London, SE, Clayton, DF, Mello, CV, Friedrich, SR, Lovell, PV, Osipova, E, Al-Ajli, FO, Secomandi, S, Kim, H, Theofanopoulou, C, Hiller, M, Zhou, Y, Harris, RS, Makova, KD, Medvedev, P, Hoffman, J, Masterson, P, Clark, K, Martin, F, Howe, K, Flicek, P, Walenz, BP, Kwak, W, Clawson, H, Diekhans, M, Nassar, L, Paten, B, Kraus, RHS, Crawford, AJ, Gilbert, MTP, Zhang, G, Venkatesh, B, Murphy, RW, Koepfli, KP, Shapiro, B, Johnson, WE, Di Palma, F, Marques-Bonet, T, Teeling, EC, Warnow, T, Graves, JM, Ryder, OA, Haussler, D, O’Brien, SJ, Korlach, J, Lewin, HA, Howe, K, Myers, EW, Durbin, R, Phillippy, AM & Jarvis, ED 2021, 'Towards complete and error-free genome assemblies of all vertebrate species', Nature, vol. 592, no. 7856, pp. 737-746. https://doi.org/10.1038/s41586-021-03451-0