Researcher Profile

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

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

Arbeithuber, B, Hester, J, Cremona, MA, Stoler, N, Zaidi, A, Higgins, B, Anthony, K, Chiaromonte, F, Diaz, FJ & Makova, KD 2020, 'Age-related accumulation of de novo mitochondrial mutations in mammalian oocytes and somatic tissues', PLoS biology, vol. 18, no. 7, 3000745. https://doi.org/10.1371/journal.pbio.3000745

Vegesna, R, Tomaszkiewicz, M, Ryder, OA, Campos-Sanchez, R, Medvedev, P, DeGiorgio, M & Makova, KD 2020, 'Ampliconic genes on the great ape y chromosomes: Rapid evolution of copy number but conservation of expression levels', Genome biology and evolution, vol. 12, no. 6, pp. 842-859. https://doi.org/10.1093/GBE/EVAA088

Cechova, M, Vegesna, R, Tomaszkiewicz, M, Harris, RS, Chen, D, Rangavittal, S, Medvedev, P & Makova, KD 2020, 'Dynamic evolution of great ape Y chromosomes', Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 42, pp. 26273-26280. https://doi.org/10.1073/pnas.2001749117

Stoler, N, Arbeithuber, B, Povysil, G, Heinzl, M, Salazar, R, Makova, KD, Tiemann-Boege, I & Nekrutenko, A 2020, 'Family reunion via error correction: An efficient analysis of duplex sequencing data', BMC bioinformatics, vol. 21, no. 1, 96. https://doi.org/10.1186/s12859-020-3419-8

Chen, D, Cremona, MA, Qi, Z, Mitra, RD, Chiaromonte, F & Makova, KD 2020, 'Human L1 transposition dynamics unraveled with functional data analysis', Molecular biology and evolution, vol. 37, no. 12, pp. 3576-3600. https://doi.org/10.1093/molbev/msaa194

Barrett, A, Arbeithuber, B, Zaidi, A, Wilton, P, Paul, IM, Nielsen, R & Makova, KD 2020, 'Pronounced somatic bottleneck in mitochondrial DNA of human hair', Philosophical Transactions of the Royal Society B: Biological Sciences, vol. 375, no. 1790, 20190175. https://doi.org/10.1098/rstb.2019.0175

Zaidi, AA, Wilton, PR, Su, MSW, Paul, IM, Arbeithuber, B, Anthony, K, Nekrutenko, A, Nielsen, R & Makova, KD 2019, 'Bottleneck and selection in the germline and maternal age influence transmission of mitochondrial DNA in human pedigrees', Proceedings of the National Academy of Sciences of the United States of America, vol. 116, no. 50, pp. 25172-25178. https://doi.org/10.1073/pnas.1906331116

Rangavittal, S, Stopa, N, Tomaszkiewicz, M, Sahlin, K, Makova, KD & Medvedev, P 2019, 'DiscoverY: A classifier for identifying y chromosome sequences in male assemblies', BMC genomics, vol. 20, no. 1, 641. https://doi.org/10.1186/s12864-019-5996-3

Vegesna, R, Tomaszkiewicz, M, Medvedev, P & Makova, KD 2019, 'Dosage regulation, and variation in gene expression and copy number of human Y chromosome ampliconic genes', PLoS genetics, vol. 15, no. 9, e1008369. https://doi.org/10.1371/journal.pgen.1008369

Cremona, MA, Xu, H, Makova, KD, Reimherr, M, Chiaromonte, F & Madrigal, P 2019, 'Functional data analysis for computational biology', Bioinformatics, vol. 35, no. 17, pp. 3211-3213. https://doi.org/10.1093/bioinformatics/btz045

Cechova, M, Harris, RS, Tomaszkiewicz, M, Arbeithuber, B, Chiaromonte, F & Makova, KD 2019, 'High Satellite Repeat Turnover in Great Apes Studied with Short- And Long-Read Technologies', Molecular biology and evolution, vol. 36, no. 11, pp. 2415-2431. https://doi.org/10.1093/molbev/msz156

Zaidi, AA & Makova, KD 2019, 'Investigating mitonuclear interactions in human admixed populations', Nature Ecology and Evolution, vol. 3, no. 2, pp. 213-222. https://doi.org/10.1038/s41559-018-0766-1

Harris, RS, Cechova, M & Makova, KD 2019, 'Noise-cancelling repeat finder: Uncovering tandem repeats in error-prone long-read sequencing data', Bioinformatics, vol. 35, no. 22, pp. 4809-4811. https://doi.org/10.1093/bioinformatics/btz484