• 9524 Citations
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19982020

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Article
2020

Ampliconic Genes on the Great Ape Y Chromosomes: Rapid Evolution of Copy Number but Conservation of Expression Levels

Vegesna, R., Tomaszkiewicz, M., Ryder, O. A., Campos-Sánchez, R., Medvedev, P., DeGiorgio, M. & Makova, K. D., Jun 1 2020, In : Genome biology and evolution. 12, 6, p. 842-859 18 p.

Research output: Contribution to journalArticle

Open Access

Family reunion via error correction: An efficient analysis of duplex sequencing data

Stoler, N., Arbeithuber, B., Povysil, G., Heinzl, M., Salazar, R., Makova, K. D., Tiemann-Boege, I. & Nekrutenko, A., Mar 4 2020, In : BMC bioinformatics. 21, 1, 96.

Research output: Contribution to journalArticle

Open Access

Pronounced somatic bottleneck in mitochondrial DNA of human hair

Barrett, A., Arbeithuber, B., Zaidi, A., Wilton, P., Paul, I. M., Nielsen, R. & Makova, K. D., Jan 1 2020, In : Philosophical Transactions of the Royal Society B: Biological Sciences. 375, 1790, 20190175.

Research output: Contribution to journalArticle

Open Access
2 Scopus citations
2019

Bottleneck and selection in the germline and maternal age influence transmission of mitochondrial DNA in human pedigrees

Zaidi, A. A., Wilton, P. R., Su, M. S. W., Paul, I. M., Arbeithuber, B., Anthony, K., Nekrutenko, A., Nielsen, R. & Makova, K. D., Dec 10 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 50, p. 25172-25178 7 p.

Research output: Contribution to journalArticle

Open Access

DiscoverY: A classifier for identifying y chromosome sequences in male assemblies

Rangavittal, S., Stopa, N., Tomaszkiewicz, M., Sahlin, K., Makova, K. D. & Medvedev, P., Aug 9 2019, In : BMC genomics. 20, 1, 641.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Dosage regulation, and variation in gene expression and copy number of human Y chromosome ampliconic genes

Vegesna, R., Tomaszkiewicz, M., Medvedev, P. & Makova, K. D., Jan 1 2019, In : PLoS genetics. 15, 9, e1008369.

Research output: Contribution to journalArticle

Open Access

Functional data analysis for computational biology

Cremona, M. A., Xu, H., Makova, K. D., Reimherr, M., Chiaromonte, F. & Madrigal, P., Sep 1 2019, In : Bioinformatics. 35, 17, p. 3211-3213 3 p.

Research output: Contribution to journalArticle

1 Scopus citations

High Satellite Repeat Turnover in Great Apes Studied with Short- And Long-Read Technologies

Cechova, M., Harris, R. S., Tomaszkiewicz, M., Arbeithuber, B., Chiaromonte, F. & Makova, K. D., Nov 1 2019, In : Molecular biology and evolution. 36, 11, p. 2415-2431 17 p.

Research output: Contribution to journalArticle

Open Access
3 Scopus citations

Investigating mitonuclear interactions in human admixed populations

Zaidi, A. A. & Makova, K. D., Feb 1 2019, In : Nature Ecology and Evolution. 3, 2, p. 213-222 10 p.

Research output: Contribution to journalArticle

14 Scopus citations

Noise-cancelling repeat finder: Uncovering tandem repeats in error-prone long-read sequencing data

Harris, R. S., Cechova, M., Makova, K. D. & Birol, I., Nov 1 2019, In : Bioinformatics. 35, 22, p. 4809-4811 3 p.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations
2018

A population phylogenetic view of mitochondrial heteroplasmy

Wilton, P. R., Zaidi, A., Makova, K. & Nielsen, R., Mar 2018, In : Genetics. 208, 3, p. 1261-1274 14 p.

Research output: Contribution to journalArticle

11 Scopus citations

Child Weight Gain Trajectories Linked To Oral Microbiota Composition

Craig, S. J. C., Blankenberg, D. J., Parodi, A. C. L., Paul, I. M., Birch, L. L., Savage, J. S., Marini, M. E., Stokes, J. L., Nekrutenko, A., Reimherr, M., Chiaromonte, F. & Makova, K. D., Dec 1 2018, In : Scientific reports. 8, 1, 14030.

Research output: Contribution to journalArticle

7 Scopus citations

Correcting palindromes in long reads after whole-genome amplification

Warris, S., Schijlen, E., Van De Geest, H., Vegesna, R., Hesselink, T., Te Lintel Hekkert, B., Sanchez Perez, G., Medvedev, P., Makova, K. D. & De Ridder, D., Nov 6 2018, In : BMC genomics. 19, 1, 798.

Research output: Contribution to journalArticle

2 Scopus citations

Deciphering highly similar multigene family transcripts from Iso-Seq data with IsoCon

Sahlin, K., Tomaszkiewicz, M., Makova, K. D. & Medvedev, P., Dec 1 2018, In : Nature communications. 9, 1, 4601.

Research output: Contribution to journalArticle

7 Scopus citations
10 Scopus citations

High levels of copy number variation of ampliconic genes across major human Y haplogroups

Ye, D., Zaidi, A. A., Tomaszkiewicz, M., Anthony, K., Liebowitz, C., DeGiorgio, M., Shriver, M. D. & Makova, K. D., May 1 2018, In : Genome biology and evolution. 10, 5, p. 1333-1350 18 p.

Research output: Contribution to journalArticle

5 Scopus citations

IWTomics: Testing high-resolution sequence-based 'Omics' data at multiple locations and scales

Cremona, M., Pini, A., Cumbo, F., Makova, K. D., Chiaromonte, F. & Vantini, S., Jul 1 2018, In : Bioinformatics. 34, 13, p. 2289-2291 3 p.

Research output: Contribution to journalArticle

2 Scopus citations

Long-read sequencing technology indicates genome-wide effects of non-B DNA on polymerization speed and error rate

Guiblet, W. M., Cremona, M. A., Cechova, M., Harris, R. S., Kejnovská, I., Kejnovsky, E., Eckert, K., Chiaromonte, F. & Makova, K. D., Dec 2018, In : Genome research. 28, 12, p. 1767-1778 12 p.

Research output: Contribution to journalArticle

6 Scopus citations

RecoverY: K-mer-based read classification for Y-chromosome-specific sequencing and assembly

Rangavittal, S., Harris, R. S., Cechova, M., Tomaszkiewicz, M., Chikhi, R., Makova, K. D. & Medvedev, P., Apr 1 2018, In : Bioinformatics. 34, 7, p. 1125-1131 7 p.

Research output: Contribution to journalArticle

5 Scopus citations
2017

Elevated mitochondrial genome variation after 50 generations of radiation exposure in a wild rodent

Baker, R. J., Dickins, B., Wickliffe, J. K., Khan, F. A. A., Gaschak, S., Makova, K. D. & Phillips, C. D., Sep 2017, In : Evolutionary Applications. 10, 8, p. 784-791 8 p.

Research output: Contribution to journalArticle

12 Scopus citations
2016
16 Scopus citations

A time- and cost-effective strategy to sequence mammalian Y chromosomes: An application to the de novo assembly of gorilla Y

Tomaszkiewicz, M., Rangavittal, S., Cechova, M., Sanchez, R. C., Fescemyer, H. W., Harris, R., Ye, D., O'Brien, P. C. M., Chikhi, R., Ryder, O. A., Ferguson-Smith, M. A., Medvedev, P. & Makova, K. D., Apr 2016, In : Genome research. 26, 4, p. 530-540 11 p.

Research output: Contribution to journalArticle

42 Scopus citations

Integration and Fixation Preferences of Human and Mouse Endogenous Retroviruses Uncovered with Functional Data Analysis

Campos-Sánchez, R., Cremona, M. A., Pini, A., Chiaromonte, F. & Makova, K. D., Jun 2016, In : PLoS computational biology. 12, 6, e1004956.

Research output: Contribution to journalArticle

13 Scopus citations

Reverse Transcription Errors and RNA-DNA Differences at Short Tandem Repeats

Fungtammasan, A., Tomaszkiewicz, M., Campos-Sánchez, R., Eckert, K. A., Degiorgio, M. & Makova, K. D., Oct 1 2016, In : Molecular biology and evolution. 33, 10, p. 2744-2758 15 p.

Research output: Contribution to journalArticle

3 Scopus citations

Streamlined analysis of duplex sequencing data with Du Novo

Stoler, N., Arbeithuber, B., Guiblet, W., Makova, K. D. & Nekrutenko, A., Aug 26 2016, In : Genome biology. 17, 1, 180.

Research output: Contribution to journalArticle

10 Scopus citations
2015

Accurate typing of short tandem repeats from genome-wide sequencing data and its applications

Fungtammasan, A., Ananda, G., Hile, S. E., Su, M. S. W., Sun, C., Harris, R., Medvedev, P., Eckert, K. & Makova, K. D., May 1 2015, In : Genome research. 125, 5, p. 736-749 14 p.

Research output: Contribution to journalArticle

36 Scopus citations
2014

Controlling for contamination in re-sequencing studies with a reproducible web-based phylogenetic approach

Dickins, B., Rebolledo-Jaramillo, B., Su, M. S. W., Paul, I. M., Blankenberg, D., Stoler, N., Makova, K. D. & Nekrutenko, A., Mar 2014, In : BioTechniques. 56, 3, p. 134-141 8 p.

Research output: Contribution to journalArticle

7 Scopus citations

Development and assessment of an optimized next-generation DNA sequencing approach for the mtgenome using the Illumina MiSeq

McElhoe, J. A., Holland, M. M., Makova, K. D., Su, M. S. W., Paul, I. M., Baker, C. H., Faith, S. A. & Young, B., Nov 2014, In : Forensic Science International: Genetics. 13, p. 20-29 10 p.

Research output: Contribution to journalArticle

58 Scopus citations

Genomic landscape of human, bat, and ex vivo DNA transposon integrations

Campos-Sánchez, R., Kapusta, A., Feschotte, C., Chiaromonte, F. & Makova, K. D., Jul 2014, In : Molecular biology and evolution. 31, 7, p. 1816-1822 7 p.

Research output: Contribution to journalArticle

14 Scopus citations

Maternal age effect and severe germ-line bottleneck in the inheritance of human mitochondrial DNA

Rebolledo-Jaramillo, B., Su, M. S. W., Stoler, N., McElhoe, J. A., Dickins, B., Blankenberg, D., Korneliussen, T. S., Chiaromonte, F., Nielsen, R., Holland, M. M., Paul, I. M., Nekrutenko, A. & Makova, K. D., Oct 28 2014, In : Proceedings of the National Academy of Sciences of the United States of America. 111, 43, p. 15474-15479 6 p.

Research output: Contribution to journalArticle

95 Scopus citations

Microsatellite Interruptions Stabilize Primate Genomes and Exist as Population-Specific Single Nucleotide Polymorphisms within Individual Human Genomes

Ananda, G., Hile, S. E., Breski, A., Wang, Y., Kelkar, Y., Makova, K. D. & Eckert, K. A., Jul 2014, In : PLoS genetics. 10, 7, e1004498.

Research output: Contribution to journalArticle

16 Scopus citations

The Intervention Nurses Start Infants Growing on Healthy Trajectories (INSIGHT) study

Paul, I. M., Williams, J. S., Anzman-Frasca, S., Beiler, J. S., Makova, K. D., Marini, M. E., Hess, L. B., Rzucidlo, S. E., Verdiglione, N., Mindell, J. A. & Birch, L. L., Jul 18 2014, In : BMC pediatrics. 14, 1, 184.

Research output: Contribution to journalArticle

53 Scopus citations
2013

Distinct mutational behaviors differentiate short tandem repeats from micro satellites in the human genome

Ananda, G., Walsh, E., Jacob, K. D., Krasilnikova, M., Eckert, K. A., Chiaromonte, F. & Makova, K. D., Apr 29 2013, In : Genome biology and evolution. 5, 3, p. 606-620 15 p.

Research output: Contribution to journalArticle

30 Scopus citations

Gene survival and death on the human y chromosome

Wilson Sayres, M. A. & Makova, K. D., Apr 1 2013, In : Molecular biology and evolution. 30, 4, p. 781-787 7 p.

Research output: Contribution to journalArticle

27 Scopus citations

Mature microsatellites: Mechanisms underlying dinucleotide microsatellite mutational biases in human cells

Baptiste, B. A., Ananda, G., Strubczewski, N., Lutzkanin, A., Khoo, S. J., Srikanth, A., Kim, N., Makova, K. D., Krasilnikova, M. M. & Eckert, K. A., Mar 2013, In : G3: Genes, Genomes, Genetics. 3, 3, p. 451-463 13 p.

Research output: Contribution to journalArticle

13 Scopus citations

Segmenting the human genome based on states of neutral genetic divergence

Don, P. K., Ananda, G., Chiaromonte, F. & Makova, K. D., Sep 3 2013, In : Proceedings of the National Academy of Sciences of the United States of America. 110, 36, p. 14699-14704 6 p.

Research output: Contribution to journalArticle

6 Scopus citations

The origin, evolution, and functional impact of short insertion-deletion variants identified in 179 human genomes

Montgomery, S. B., Goode, D. L., Kvikstad, E., Albers, C. A., Zhang, Z. D., Mu, X. J., Ananda, G., Howie, B., Karczewski, K. J., Smith, K. S., Anaya, V., Richardson, R., Davis, J., MacArthur, D. G., Sidow, A., Duret, L., Gerstein, M., Makova, K. D., Marchini, J., McVean, G. & 1 others, Lunter, G., May 2013, In : Genome research. 23, 5, p. 749-761 13 p.

Research output: Contribution to journalArticle

111 Scopus citations
2012

A genome-wide analysis of common fragile sites: What features determine chromosomal instability in the human genome?

Fungtammasan, A., Walsh, E., Chiaromonte, F., Eckert, K. A. & Makova, K. D., Jun 1 2012, In : Genome research. 22, 6, p. 993-1005 13 p.

Research output: Contribution to journalArticle

88 Scopus citations

Rescuing Alu: Recovery of New Inserts Shows LINE-1 Preserves Alu Activity through A-Tail Expansion

Wagstaff, B. J., Hedges, D. J., Derbes, R. S., Campos Sanchez, R., Chiaromonte, F., Makova, K. D. & Roy-Engel, A. M., Aug 2012, In : PLoS genetics. 8, 8, e1002842.

Research output: Contribution to journalArticle

25 Scopus citations
2011
11 Scopus citations

A genome-wide view of mutation rate co-variation using multivariate analyses

Ananda, G., Chiaromonte, F. & Makova, K. D., Mar 22 2011, In : Genome biology. 12, 3, R27.

Research output: Contribution to journalArticle

22 Scopus citations

A massively parallel sequencing approach uncovers ancient origins and high genetic variability of endangered Przewalski's horses

Goto, H., Ryder, O. A., Fisher, A. R., Schultz, B., Pond, S. L. K., Nekrutenko, A. & Makova, K. D., Dec 1 2011, In : Genome biology and evolution. 3, 1, p. 1096-1106 11 p.

Research output: Contribution to journalArticle

42 Scopus citations

A matter of life or death: How microsatellites emerge in and vanish from the human genome

Kelkar, Y. D., Eckert, K. A., Chiaromonte, F. & Makova, K. D., Dec 2011, In : Genome research. 21, 12, p. 2038-2048 11 p.

Research output: Contribution to journalArticle

45 Scopus citations

Do variations in substitution rates and male mutation bias correlate with life-history traits? a study of 32 mammalian genomes

Sayres, M. A. W., Venditti, C., Pagel, M. & Makova, K. D., Oct 1 2011, In : Evolution. 65, 10, p. 2800-2815 16 p.

Research output: Contribution to journalArticle

50 Scopus citations

Dynamics of mitochondrial heteroplasmy in three families investigated via a repeatable re-sequencing study

Goto, H., Dickins, B., Afgan, E., Paul, I. M., Taylor, J., Makova, K. D. & Nekrutenko, A., Jun 23 2011, In : Genome biology. 12, 6, R59.

Research output: Contribution to journalArticle

76 Scopus citations

Genome analyses substantiate male mutation bias in many species

Wilson Sayres, M. A. & Makova, K. D., Dec 1 2011, In : BioEssays. 33, 12, p. 938-945 8 p.

Research output: Contribution to journalArticle

42 Scopus citations
2010

Complete Khoisan and Bantu genomes from southern Africa

Schuster, S. C., Miller, W., Ratan, A., Tomsho, L. P., Giardine, B., Kasson, L. R., Harris, R. S., Petersen, D. C., Zhao, F., Qi, J., Alkan, C., Kidd, J. M., Sun, Y., Drautz, D. I., Bouffard, P., Muzny, D. M., Reid, J. G., Nazareth, L. V., Wang, Q., Burhans, R. & 28 others, Riemer, C., Wittekindt, N. E., Moorjani, P., Tindall, E. A., Danko, C. G., Teo, W. S., Buboltz, A. M., Zhang, Z., Ma, Q., Oosthuysen, A., Steenkamp, A. W., Oostuisen, H., Venter, P., Gajewski, J., Zhang, Y., Pugh, B. F., Makova, K. D., Nekrutenko, A., Mardis, E. R., Patterson, N., Pringle, T. H., Chiaromonte, F., Mullikin, J. C., Eichler, E. E., Hardison, R. C., Gibbs, R. A., Harkins, T. T. & Hayes, V. M., Feb 18 2010, In : Nature. 463, 7283, p. 943-947 5 p.

Research output: Contribution to journalArticle

262 Scopus citations

Strong purifying selection at genes escaping X chromosome inactivation

Park, C., Carrel, L. & Makova, K. D., Nov 2010, In : Molecular biology and evolution. 27, 11, p. 2446-2450 5 p.

Research output: Contribution to journalArticle

24 Scopus citations

The (r)evolution of SINE versus LINE distributions in primate genomes: Sex chromosomes are important

Kvikstad, E. M. & Makova, K. D., May 1 2010, In : Genome research. 20, 5, p. 600-613 14 p.

Research output: Contribution to journalArticle

31 Scopus citations

What is a microsatellite: A computational and experimental definition based upon repeat mutational behavior at A/T and GT/AC repeats

Kelkar, Y. D., Strubczewski, N., Hile, S. E., Chiaromonte, F., Eckert, K. A. & Makova, K. D., 2010, In : Genome biology and evolution. 2, 1, p. 620-635 16 p.

Research output: Contribution to journalArticle

75 Scopus citations