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Kateryna Makova, Ph.D. - Publications

Affiliations: 
Biology Pennsylvania State University, State College, PA, United States 
Area:
Molecular evolution, comparative genomics
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85/116 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Tomaszkiewicz M, Sahlin K, Medvedev P, Makova KD. Transcript Isoform Diversity of Ampliconic Genes on the Y Chromosome of Great Apes. Genome Biology and Evolution. 15. PMID 37967251 DOI: 10.1093/gbe/evad205  0.327
2023 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, ... ... Makova KD, et al. The complete sequence of a human Y chromosome. Nature. PMID 37612512 DOI: 10.1038/s41586-023-06457-y  0.786
2023 Tomaszkiewicz M, Sahlin K, Medvedev P, Makova KD. Transcript Isoform Diversity of Ampliconic Genes on the Y Chromosome of Great Apes. Biorxiv : the Preprint Server For Biology. PMID 36993458 DOI: 10.1101/2023.03.02.530874  0.308
2022 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. Whole-genome sequence and assembly of the Javan gibbon (Hylobates moloch). The Journal of Heredity. PMID 36146896 DOI: 10.1093/jhered/esac043  0.389
2021 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, ... ... Makova KD, et al. Towards complete and error-free genome assemblies of all vertebrate species. Nature. 592: 737-746. PMID 33911273 DOI: 10.1038/s41586-021-03451-0  0.788
2020 Cechova M, Vegesna R, Tomaszkiewicz M, Harris RS, Chen D, Rangavittal S, Medvedev P, Makova KD. Dynamic evolution of great ape Y chromosomes. Proceedings of the National Academy of Sciences of the United States of America. PMID 33020265 DOI: 10.1073/pnas.2001749117  0.353
2020 Vegesna R, Tomaszkiewicz M, Ryder OA, Campos-Sánchez R, Medvedev P, DeGiorgio M, Makova KD. Ampliconic genes on the great ape Y chromosomes: Rapid evolution of copy number but conservation of expression levels. Genome Biology and Evolution. PMID 32374870 DOI: 10.1093/gbe/evaa088  0.786
2020 Stoler N, Arbeithuber B, Povysil G, Heinzl M, Salazar R, Makova KD, Tiemann-Boege I, Nekrutenko A. Family reunion via error correction: an efficient analysis of duplex sequencing data. Bmc Bioinformatics. 21: 96. PMID 32131723 DOI: 10.1186/S12859-020-3419-8  0.662
2020 Barrett A, Arbeithuber B, Zaidi A, Wilton P, Paul IM, Nielsen R, Makova KD. Pronounced somatic bottleneck in mitochondrial DNA of human hair. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 375: 20190175. PMID 31787049 DOI: 10.1098/Rstb.2019.0175  0.478
2019 Zaidi AA, Wilton PR, Su MS, Paul IM, Arbeithuber B, Anthony K, Nekrutenko A, Nielsen R, Makova KD. 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. PMID 31757848 DOI: 10.1073/Pnas.1906331116  0.687
2019 Harris RS, Cechova M, Makova KD. Noise-Cancelling Repeat Finder: Uncovering tandem repeats in error-prone long-read sequencing data. Bioinformatics (Oxford, England). PMID 31290946 DOI: 10.1093/bioinformatics/btz484  0.304
2019 Cechova M, Harris RS, Tomaszkiewicz M, Arbeithuber B, Chiaromonte F, Makova KD. High satellite repeat turnover in great apes studied with short- and long-read technologies. Molecular Biology and Evolution. PMID 31273383 DOI: 10.1093/Molbev/Msz156  0.357
2019 Craig S, Blankenberg D, Parodi A, Paul I, Birch L, Savage J, Marini M, Stokes J, Nekrutenko A, Reimherr M, Chiaromonte F, Makova K. 172. Child Weight Gain Trajectories Associated With Oral Microbiota Composition Biological Psychiatry. 85: S71. DOI: 10.1016/J.Biopsych.2019.03.186  0.55
2018 Guiblet W, Cremona M, Cechova M, Harris R, Kejnovska I, Kejnovsky E, Eckert KA, Chiaromonte F, Makova KD. Long-read sequencing technology indicates genome-wide effects of non-B DNA on polymerization speed and error rate. Genome Research. PMID 30401733 DOI: 10.1101/Gr.241257.118  0.353
2018 Warris S, Schijlen E, van de Geest H, Vegesna R, Hesselink T, Te Lintel Hekkert B, Sanchez Perez G, Medvedev P, Makova KD, de Ridder D. Correcting palindromes in long reads after whole-genome amplification. Bmc Genomics. 19: 798. PMID 30400848 DOI: 10.1186/s12864-018-5164-1  0.35
2018 Craig SJC, Blankenberg D, Parodi ACL, Paul IM, Birch LL, Savage JS, Marini ME, Stokes JL, Nekrutenko A, Reimherr M, Chiaromonte F, Makova KD. Child Weight Gain Trajectories Linked To Oral Microbiota Composition. Scientific Reports. 8: 14030. PMID 30232389 DOI: 10.1038/S41598-018-31866-9  0.531
2018 Ye D, Zaidi A, Tomaszkiewicz M, Anthony K, Liebowitz C, DeGiorgio M, Shriver MD, Makova KD. High levels of copy number variation of ampliconic genes across major human Y haplogroups. Genome Biology and Evolution. PMID 29718380 DOI: 10.1093/gbe/evy086  0.317
2018 Holland MM, Makova KD, McElhoe JA. Deep-Coverage MPS Analysis of Heteroplasmic Variants within the mtGenome Allows for Frequent Differentiation of Maternal Relatives. Genes. 9. PMID 29495418 DOI: 10.3390/genes9030124  0.328
2018 Wilton PR, Zaidi A, Makova K, Nielsen R. A Population Phylogenetic View of Mitochondrial Heteroplasmy. Genetics. PMID 29343499 DOI: 10.1534/Genetics.118.300711  0.532
2018 Tomaszkiewicz M, Makova K. Targeted sequencing of ampliconic gene transcripts from total human male testis RNA Protocol Exchange. DOI: 10.1038/Protex.2018.109  0.352
2017 Baker RJ, Dickins B, Wickliffe JK, Khan FAA, Gaschak S, Makova KD, Phillips CD. Elevated mitochondrial genome variation after 50 generations of radiation exposure in a wild rodent. Evolutionary Applications. 10: 784-791. PMID 29151870 DOI: 10.1111/Eva.12475  0.798
2017 Tomaszkiewicz M, Medvedev P, Makova KD. Y and W Chromosome Assemblies: Approaches and Discoveries. Trends in Genetics : Tig. PMID 28236503 DOI: 10.1016/j.tig.2017.01.008  0.353
2016 Fungtammasan A, Walsh E, Chiaromonte F, Eckert KA, Makova KD. Corrigendum: A genome-wide analysis of common fragile sites: What features determine chromosomal instability in the human genome? Genome Research. 26: 1451. PMID 27698254 DOI: 10.1101/gr.214460.116  0.777
2016 Stoler N, Arbeithuber B, Guiblet W, Makova KD, Nekrutenko A. Streamlined analysis of duplex sequencing data with Du Novo. Genome Biology. 17: 180. PMID 27566673 DOI: 10.1186/S13059-016-1039-4  0.649
2016 Fungtammasan A, Tomaszkiewicz M, Campos-Sanchez R, Eckert K, DeGiorgio M, Makova KD. Reverse Transcription Errors and RNA-DNA Differences at Short Tandem Repeats. Molecular Biology and Evolution. PMID 27413049 DOI: 10.1093/Molbev/Msw139  0.781
2016 Campos-Sánchez R, Cremona MA, Pini A, Chiaromonte F, Makova KD. Integration and Fixation Preferences of Human and Mouse Endogenous Retroviruses Uncovered with Functional Data Analysis. Plos Computational Biology. 12: e1004956. PMID 27309962 DOI: 10.1371/Journal.Pcbi.1004956  0.826
2016 Tomaszkiewicz M, Rangavittal S, Cechova M, Campos Sanchez R, Fescemyer HW, Harris R, Ye D, O'Brien PC, Chikhi R, Ryder OA, Ferguson-Smith MA, Medvedev P, Makova KD. A time- and cost-effective strategy to sequence mammalian Y Chromosomes: an application to the de novo assembly of gorilla Y. Genome Research. PMID 26934921 DOI: 10.1101/gr.199448.115  0.36
2016 Farkas CA, Fuentes F, Rebolledo B, Makova K, Nekrutenko A, Castro A, Pincheira R. Abstract B17: Role of Sall2 transcription factor under genotoxic stress: A transcriptomic approach Cancer Research. 76. DOI: 10.1158/1538-7445.Fbcr15-B17  0.572
2015 Fungtammasan A, Ananda G, Hile SE, Su MS, Sun C, Harris R, Medvedev P, Eckert K, Makova KD. Accurate typing of short tandem repeats from genome-wide sequencing data and its applications. Genome Research. 25: 736-49. PMID 25823460 DOI: 10.1101/Gr.185892.114  0.825
2015 Makova KD, Hardison RC. The effects of chromatin organization on variation in mutation rates in the genome. Nature Reviews. Genetics. 16: 213-23. PMID 25732611 DOI: 10.1038/Nrg3890  0.302
2014 Rebolledo-Jaramillo B, Su MS, Stoler N, McElhoe JA, Dickins B, Blankenberg D, Korneliussen TS, Chiaromonte F, Nielsen R, Holland MM, Paul IM, Nekrutenko A, Makova KD. Maternal age effect and severe germ-line bottleneck in the inheritance of human mitochondrial DNA. Proceedings of the National Academy of Sciences of the United States of America. 111: 15474-9. PMID 25313049 DOI: 10.1073/Pnas.1409328111  0.776
2014 McElhoe JA, Holland MM, Makova KD, Su MS, Paul IM, Baker CH, Faith SA, Young B. Development and assessment of an optimized next-generation DNA sequencing approach for the mtgenome using the Illumina MiSeq. Forensic Science International. Genetics. 13: 20-9. PMID 25051226 DOI: 10.1016/J.Fsigen.2014.05.007  0.342
2014 Ananda G, Hile SE, Breski A, Wang Y, Kelkar Y, Makova KD, Eckert KA. Microsatellite interruptions stabilize primate genomes and exist as population-specific single nucleotide polymorphisms within individual human genomes. Plos Genetics. 10: e1004498. PMID 25033203 DOI: 10.1371/Journal.Pgen.1004498  0.837
2014 Campos-Sánchez R, Kapusta A, Feschotte C, Chiaromonte F, Makova KD. Genomic landscape of human, bat, and ex vivo DNA transposon integrations. Molecular Biology and Evolution. 31: 1816-32. PMID 24809961 DOI: 10.1093/Molbev/Msu138  0.805
2014 Dickins B, Rebolledo-Jaramillo B, Su MS, Paul IM, Blankenberg D, Stoler N, Makova KD, Nekrutenko A. Controlling for contamination in re-sequencing studies with a reproducible web-based phylogenetic approach. Biotechniques. 56: 134-6, 138-41. PMID 24641477 DOI: 10.2144/000114146  0.779
2013 Kuruppumullage Don P, Ananda G, Chiaromonte F, Makova KD. Segmenting the human genome based on states of neutral genetic divergence. Proceedings of the National Academy of Sciences of the United States of America. 110: 14699-704. PMID 23959903 DOI: 10.1073/Pnas.1221792110  0.76
2013 Montgomery SB, Goode DL, Kvikstad E, Albers CA, Zhang ZD, Mu XJ, Ananda G, Howie B, Karczewski KJ, Smith KS, Anaya V, Richardson R, Davis J, MacArthur DG, ... ... Makova KD, et al. The origin, evolution, and functional impact of short insertion-deletion variants identified in 179 human genomes. Genome Research. 23: 749-61. PMID 23478400 DOI: 10.1101/Gr.148718.112  0.829
2013 Baptiste BA, Ananda G, Strubczewski N, Lutzkanin A, Khoo SJ, Srikanth A, Kim N, Makova KD, Krasilnikova MM, Eckert KA. Mature microsatellites: mechanisms underlying dinucleotide microsatellite mutational biases in human cells. G3 (Bethesda, Md.). 3: 451-63. PMID 23450065 DOI: 10.1534/G3.112.005173  0.73
2013 Ananda G, Walsh E, Jacob KD, Krasilnikova M, Eckert KA, Chiaromonte F, Makova KD. Distinct mutational behaviors differentiate short tandem repeats from microsatellites in the human genome. Genome Biology and Evolution. 5: 606-20. PMID 23241442 DOI: 10.1093/Gbe/Evs116  0.746
2013 Wilson Sayres MA, Makova KD. Gene survival and death on the human Y chromosome. Molecular Biology and Evolution. 30: 781-7. PMID 23223713 DOI: 10.1093/molbev/mss267  0.723
2013 Steiner CC, Ryder OA, Makova KD. Mitochondrial Genome: Clues about the Evolution of Extant Equids and Genomic Diversity of Horse Breeds Equine Genomics. 311-321. DOI: 10.1002/9781118522158.ch19  0.345
2012 Wagstaff BJ, Hedges DJ, Derbes RS, Campos Sanchez R, Chiaromonte F, Makova KD, Roy-Engel AM. Rescuing Alu: recovery of new inserts shows LINE-1 preserves Alu activity through A-tail expansion. Plos Genetics. 8: e1002842. PMID 22912586 DOI: 10.1371/Journal.Pgen.1002842  0.325
2012 Fungtammasan A, Walsh E, Chiaromonte F, Eckert KA, Makova KD. A genome-wide analysis of common fragile sites: what features determine chromosomal instability in the human genome? Genome Research. 22: 993-1005. PMID 22456607 DOI: 10.1101/Gr.134395.111  0.781
2011 Afgan E, Baker D, Coraor N, Goto H, Paul IM, Makova KD, Nekrutenko A, Taylor J. Harnessing cloud computing with Galaxy Cloud. Nature Biotechnology. 29: 972-4. PMID 22068528 DOI: 10.1038/Nbt.2028  0.68
2011 Wilson Sayres MA, Makova KD. Genome analyses substantiate male mutation bias in many species. Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. 33: 938-45. PMID 22006834 DOI: 10.1002/bies.201100091  0.755
2011 Kelkar YD, Eckert KA, Chiaromonte F, Makova KD. A matter of life or death: how microsatellites emerge in and vanish from the human genome. Genome Research. 21: 2038-48. PMID 21994250 DOI: 10.1101/Gr.122937.111  0.784
2011 Wilson Sayres MA, Venditti C, Pagel M, Makova KD. Do variations in substitution rates and male mutation bias correlate with life-history traits? A study of 32 mammalian genomes. Evolution; International Journal of Organic Evolution. 65: 2800-15. PMID 21967423 DOI: 10.1111/J.1558-5646.2011.01337.X  0.748
2011 Goto H, Ryder OA, Fisher AR, Schultz B, Kosakovsky Pond SL, Nekrutenko A, Makova KD. A massively parallel sequencing approach uncovers ancient origins and high genetic variability of endangered Przewalski's horses. Genome Biology and Evolution. 3: 1096-106. PMID 21803766 DOI: 10.1093/Gbe/Evr067  0.759
2011 Goto H, Dickins B, Afgan E, Paul IM, Taylor J, Makova KD, Nekrutenko A. Dynamics of mitochondrial heteroplasmy in three families investigated via a repeatable re-sequencing study. Genome Biology. 12: R59. PMID 21699709 DOI: 10.1186/Gb-2011-12-6-R59  0.803
2011 Lombard Z, Park C, Makova KD, Ramsay M. A computational approach to candidate gene prioritization for X-linked mental retardation using annotation-based binary filtering and motif-based linear discriminatory analysis. Biology Direct. 6: 30. PMID 21668950 DOI: 10.1186/1745-6150-6-30  0.651
2011 Ananda G, Chiaromonte F, Makova KD. A genome-wide view of mutation rate co-variation using multivariate analyses. Genome Biology. 12: R27. PMID 21426544 DOI: 10.1186/Gb-2011-12-3-R27  0.758
2010 Kelkar YD, Strubczewski N, Hile SE, Chiaromonte F, Eckert KA, Makova KD. What is a microsatellite: a computational and experimental definition based upon repeat mutational behavior at A/T and GT/AC repeats. Genome Biology and Evolution. 2: 620-35. PMID 20668018 DOI: 10.1093/Gbe/Evq046  0.782
2010 Park C, Carrel L, Makova KD. Strong purifying selection at genes escaping X chromosome inactivation. Molecular Biology and Evolution. 27: 2446-50. PMID 20534706 DOI: 10.1093/Molbev/Msq143  0.619
2010 Kvikstad EM, Makova KD. The (r)evolution of SINE versus LINE distributions in primate genomes: sex chromosomes are important. Genome Research. 20: 600-13. PMID 20219940 DOI: 10.1101/Gr.099044.109  0.773
2010 Schuster SC, Miller W, Ratan A, Tomsho LP, Giardine B, Kasson LR, Harris RS, Petersen DC, Zhao F, Qi J, Alkan C, Kidd JM, Sun Y, Drautz DI, Bouffard P, ... ... Makova KD, et al. Complete Khoisan and Bantu genomes from southern Africa. Nature. 463: 943-7. PMID 20164927 DOI: 10.1038/Nature08795  0.705
2009 Wilson MA, Makova KD. Genomic analyses of sex chromosome evolution. Annual Review of Genomics and Human Genetics. 10: 333-54. PMID 19630566 DOI: 10.1146/annurev-genom-082908-150105  0.357
2009 Kvikstad EM, Chiaromonte F, Makova KD. Ride the wavelet: A multiscale analysis of genomic contexts flanking small insertions and deletions. Genome Research. 19: 1153-64. PMID 19502380 DOI: 10.1101/Gr.088922.108  0.809
2009 Park C, Makova KD. Coding region structural heterogeneity and turnover of transcription start sites contribute to divergence in expression between duplicate genes. Genome Biology. 10: R10. PMID 19175934 DOI: 10.1186/Gb-2009-10-1-R10  0.655
2009 Goto H, Peng L, Makova KD. Evolution of X-degenerate Y chromosome genes in greater apes: conservation of gene content in human and gorilla, but not chimpanzee. Journal of Molecular Evolution. 68: 134-44. PMID 19142680 DOI: 10.1007/S00239-008-9189-Y  0.654
2009 Lau AN, Peng L, Goto H, Chemnick L, Ryder OA, Makova KD. Horse domestication and conservation genetics of Przewalski's horse inferred from sex chromosomal and autosomal sequences. Molecular Biology and Evolution. 26: 199-208. PMID 18931383 DOI: 10.1093/Molbev/Msn239  0.653
2008 Kelkar YD, Tyekucheva S, Chiaromonte F, Makova KD. The genome-wide determinants of human and chimpanzee microsatellite evolution. Genome Research. 18: 30-8. PMID 18032720 DOI: 10.1101/Gr.7113408  0.814
2007 Kvikstad EM, Tyekucheva S, Chiaromonte F, Makova KD. A macaque's-eye view of human insertions and deletions: differences in mechanisms. Plos Computational Biology. 3: 1772-82. PMID 17941704 DOI: 10.1371/Journal.Pcbi.0030176  0.817
2007 Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Research. 17: 960-4. PMID 17568012 DOI: 10.1101/Gr.5578007  0.651
2007 Gibbs RA, Rogers J, Katze MG, Bumgarner R, Weinstock GM, Mardis ER, Remington KA, Strausberg RL, Venter JC, Wilson RK, Batzer MA, Bustamante CD, Eichler EE, Hahn MW, ... ... Makova KD, et al. Evolutionary and biomedical insights from the rhesus macaque genome. Science (New York, N.Y.). 316: 222-34. PMID 17431167 DOI: 10.1126/Science.1139247  0.573
2006 Carrel L, Park C, Tyekucheva S, Dunn J, Chiaromonte F, Makova KD. Genomic environment predicts expression patterns on the human inactive X chromosome. Plos Genetics. 2: e151. PMID 17009873 DOI: 10.1371/Journal.Pgen.0020151  0.68
2006 Chung WY, Albert R, Albert I, Nekrutenko A, Makova KD. Rapid and asymmetric divergence of duplicate genes in the human gene coexpression network. Bmc Bioinformatics. 7: 46. PMID 16441884 DOI: 10.1186/1471-2105-7-46  0.579
2005 Nekrutenko A, Wadhawan S, Goetting-Minesky P, Makova KD. Oscillating evolution of a mammalian locus with overlapping reading frames: an XLalphas/ALEX relay. Plos Genetics. 1: e18. PMID 16110341 DOI: 10.1371/Journal.Pgen.0010018  0.592
2005 Makova K, Norton H. Worldwide polymorphism at the MC1R locus and normal pigmentation variation in humans. Peptides. 26: 1901-8. PMID 15979202 DOI: 10.1016/J.Peptides.2004.12.032  0.346
2004 Miller W, Makova KD, Nekrutenko A, Hardison RC. Comparative genomics. Annual Review of Genomics and Human Genetics. 5: 15-56. PMID 15485342 DOI: 10.1146/annurev.genom.5.061903.180057  0.687
2004 Makova KD, Yang S, Chiaromonte F. Insertions and deletions are male biased too: a whole-genome analysis in rodents. Genome Research. 14: 567-73. PMID 15059997 DOI: 10.1101/Gr.1971104  0.309
2004 Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, Sodergren EJ, Scherer S, Scott G, Steffen D, Worley KC, Burch PE, Okwuonu G, Hines S, Lewis L, DeRamo C, Delgado O, ... ... Makova K, et al. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature. 428: 493-521. PMID 15057822 DOI: 10.1038/Nature02426  0.828
2003 John PR, Makova K, Li WH, Jenkins T, Ramsay M. DNA polymorphism and selection at the melanocortin-1 receptor gene in normally pigmented southern African individuals. Annals of the New York Academy of Sciences. 994: 299-306. PMID 12851329 DOI: 10.1111/J.1749-6632.2003.Tb03193.X  0.575
2003 Makova KD, Li WH. Divergence in the spatial pattern of gene expression between human duplicate genes. Genome Research. 13: 1638-45. PMID 12840042 DOI: 10.1101/Gr.1133803  0.466
2002 Li WH, Yi S, Makova K. Male-driven evolution. Current Opinion in Genetics & Development. 12: 650-6. PMID 12433577 DOI: 10.1016/S0959-437X(02)00354-4  0.572
2002 Mu J, Duan J, Makova KD, Joy DA, Huynh CQ, Branch OH, Li WH, Su XZ. Chromosome-wide SNPs reveal an ancient origin for Plasmodium falciparum. Nature. 418: 323-6. PMID 12124624 DOI: 10.1038/Nature00836  0.49
2002 Makova KD, Li WH. Strong male-driven evolution of DNA sequences in humans and apes. Nature. 416: 624-6. PMID 11948348 DOI: 10.1038/416624A  0.486
2002 Nekrutenko A, Makova KD, Li WH. The K(A)/K(S) ratio test for assessing the protein-coding potential of genomic regions: an empirical and simulation study. Genome Research. 12: 198-202. PMID 11779845 DOI: 10.1101/Gr.200901  0.68
2002 Mu J, Duan J, Makova KD, Joy DA, Huynh CQ, Branch OH, Li W, Su X. Erratum: correction: Chromosome-wide SNPs reveal an ancient origin for Plasmodium falciparum Nature. 419: 487-487. DOI: 10.1038/Nature01168  0.436
2001 Makova KD, Ramsay M, Jenkins T, Li WH. Human DNA sequence variation in a 6.6-kb region containing the melanocortin 1 receptor promoter. Genetics. 158: 1253-68. PMID 11454772  0.349
2001 Liu JC, Makova KD, Adkins RM, Gibson S, Li WH. Episodic evolution of growth hormone in primates and emergence of the species specificity of human growth hormone receptor. Molecular Biology and Evolution. 18: 945-53. PMID 11371582 DOI: 10.1093/Oxfordjournals.Molbev.A003895  0.504
2000 Makova KD, Nekrutenko A, Baker RJ. Evolution of microsatellite alleles in four species of mice (genus Apodemus). Journal of Molecular Evolution. 51: 166-72. PMID 10948273 DOI: 10.1007/S002390010077  0.697
2000 Nekrutenko A, Makova KD, Baker RJ. Isolation of binary species-specific PCR-based markers and their value for diagnostic applications. Gene. 249: 47-51. PMID 10831837 DOI: 10.1016/S0378-1119(00)00168-2  0.697
1999 Baker RJ, Makova KD, Chesser RK. Microsatellites indicate a high frequency of multiple paternity in Apodemus (Rodentia). Molecular Ecology. 8: 107-11. PMID 12187947 DOI: 10.1046/J.1365-294X.1999.00541.X  0.418
1999 Nekrutenko A, Makova KD, Chesser RK, Baker RJ. Representational difference analysis to distinguish cryptic species. Molecular Ecology. 8: 1235-8. PMID 10447864 DOI: 10.1046/J.1365-294X.1999.00682_1.X  0.608
1998 Makova KD, Patton JC, Krysanov EYu, Chesser RK, Baker RJ. Microsatellite markers in wood mouse and striped field mouse (genus Apodemus). Molecular Ecology. 7: 247-9. PMID 9532763  0.361
Low-probability matches (unlikely to be authored by this person)
2020 Arbeithuber B, Hester J, Cremona MA, Stoler N, Zaidi A, Higgins B, Anthony K, Chiaromonte F, Diaz FJ, Makova KD. Age-related accumulation of de novo mitochondrial mutations in mammalian oocytes and somatic tissues. Plos Biology. 18: e3000745. PMID 32667908 DOI: 10.1371/Journal.Pbio.3000745  0.298
2018 Sahlin K, Tomaszkiewicz M, Makova KD, Medvedev P. Deciphering highly similar multigene family transcripts from Iso-Seq data with IsoCon. Nature Communications. 9: 4601. PMID 30389934 DOI: 10.1038/s41467-018-06910-x  0.297
2021 M Guiblet W, Cremona MA, Harris RS, Chen D, Eckert KA, Chiaromonte F, Huang YF, Makova KD. Non-B DNA: a major contributor to small- and large-scale variation in nucleotide substitution frequencies across the genome. Nucleic Acids Research. PMID 33450015 DOI: 10.1093/nar/gkaa1269  0.292
2023 Weissensteiner MH, Cremona MA, Guiblet WM, Stoler N, Harris RS, Cechova M, Eckert KA, Chiaromonte F, Huang YF, Makova KD. Accurate sequencing of DNA motifs able to form alternative (non-B) structures. Genome Research. PMID 37433640 DOI: 10.1101/gr.277490.122  0.289
2023 Makova KD, Weissensteiner MH. Noncanonical DNA structures are drivers of genome evolution. Trends in Genetics : Tig. 39: 109-124. PMID 36604282 DOI: 10.1016/j.tig.2022.11.005  0.286
2008 Tyekucheva S, Makova KD, Karro JE, Hardison RC, Miller W, Chiaromonte F. Human-macaque comparisons illuminate variation in neutral substitution rates. Genome Biology. 9: R76. PMID 18447906 DOI: 10.1186/Gb-2008-9-4-R76  0.286
2018 Cremona MA, Pini A, Cumbo F, Makova KD, Chiaromonte F, Vantini S. IWTomics: testing high-resolution sequence-based "Omics" data at multiple locations and scales. Bioinformatics (Oxford, England). PMID 29474526 DOI: 10.1093/Bioinformatics/Bty090  0.283
2020 Chen D, Cremona MA, Qi Z, Mitra RD, Chiaromonte F, Makova KD. Human L1 Transposition Dynamics Unraveled with Functional Data Analysis. Molecular Biology and Evolution. PMID 32722770 DOI: 10.1093/Molbev/Msaa194  0.282
2006 Goetting-Minesky MP, Makova KD. Mammalian male mutation bias: impacts of generation time and regional variation in substitution rates. Journal of Molecular Evolution. 63: 537-44. PMID 16955237 DOI: 10.1007/s00239-005-0308-8  0.274
2023 Makova KD, Pickett BD, Harris RS, Hartley GA, Cechova M, Pal K, Nurk S, Yoo D, Li Q, Hebbar P, McGrath BC, Antonacci F, Aubel M, Biddanda A, Borchers M, et al. The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes. Biorxiv : the Preprint Server For Biology. PMID 38077089 DOI: 10.1101/2023.11.30.569198  0.273
2019 Vegesna R, Tomaszkiewicz M, Medvedev P, Makova KD. Dosage regulation, and variation in gene expression and copy number of human Y chromosome ampliconic genes. Plos Genetics. 15: e1008369. PMID 31525193 DOI: 10.1371/journal.pgen.1008369  0.261
2006 Taylor J, Tyekucheva S, Zody M, Chiaromonte F, Makova KD. Strong and weak male mutation bias at different sites in the primate genomes: insights from the human-chimpanzee comparison. Molecular Biology and Evolution. 23: 565-73. PMID 16280537 DOI: 10.1093/Molbev/Msj060  0.245
2017 Rangavittal S, Harris RS, Cechova M, Tomaszkiewicz M, Chikhi R, Makova KD, Medvedev P. RecoverY: K-mer based read classification for Y-chromosome specific sequencing and assembly. Bioinformatics (Oxford, England). PMID 29194476 DOI: 10.1093/bioinformatics/btx771  0.243
2021 Guiblet WM, DeGiorgio M, Cheng X, Chiaromonte F, Eckert KA, Huang YF, Makova KD. Selection and thermostability suggest G-quadruplexes are novel functional elements of the human genome. Genome Research. PMID 34187812 DOI: 10.1101/gr.269589.120  0.243
2009 Wilson MA, Makova KD. Evolution and survival on eutherian sex chromosomes. Plos Genetics. 5: e1000568. PMID 19609352 DOI: 10.1371/journal.pgen.1000568  0.236
2022 Torres-Gonzalez E, Makova KD. Exploring the Effects of Mitonuclear Interactions on Mitochondrial DNA Gene Expression in Humans. Frontiers in Genetics. 13: 797129. PMID 35846132 DOI: 10.3389/fgene.2022.797129  0.235
2019 Rangavittal S, Stopa N, Tomaszkiewicz M, Sahlin K, Makova KD, Medvedev P. DiscoverY: a classifier for identifying Y chromosome sequences in male assemblies. Bmc Genomics. 20: 641. PMID 31399045 DOI: 10.1186/s12864-019-5996-3  0.233
2022 Arbeithuber B, Cremona MA, Hester J, Barrett A, Higgins B, Anthony K, Chiaromonte F, Diaz FJ, Makova KD. 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. 119: e2118740119. PMID 35394879 DOI: 10.1073/pnas.2118740119  0.228
2012 Wolfe K, Wayne ML, Makova K, Steen TY, Uyenoyama M, Takahata N. SMBE proposal to the government of Japan. Molecular Biology and Evolution. 29: 441. PMID 22080475 DOI: 10.1093/Molbev/Msr209  0.224
2016 Arbeithuber B, Makova KD, Tiemann-Boege I. Artifactual mutations resulting from DNA lesions limit detection levels in ultrasensitive sequencing applications. Dna Research : An International Journal For Rapid Publication of Reports On Genes and Genomes. PMID 27477585 DOI: 10.1093/Dnares/Dsw038  0.211
2019 Zaidi AA, Makova KD. Investigating mitonuclear interactions in human admixed populations. Nature Ecology & Evolution. PMID 30643241 DOI: 10.1038/s41559-018-0766-1  0.209
2022 Stein M, Hile SE, Weissensteiner MH, Lee M, Zhang S, Kejnovský E, Kejnovská I, Makova KD, Eckert KA. Variation in G-quadruplex sequence and topology differentially impacts human DNA polymerase fidelity. Dna Repair. 119: 103402. PMID 36116264 DOI: 10.1016/j.dnarep.2022.103402  0.201
2021 Craig SJC, Kenney AM, Lin J, Paul IM, Birch LL, Savage JS, Marini ME, Chiaromonte F, Reimherr ML, Makova KD. Constructing a polygenic risk score for childhood obesity using functional data analysis. Econometrics and Statistics. 25: 66-86. PMID 36620476 DOI: 10.1016/j.ecosta.2021.10.014  0.168
2024 Lariviere D, Craig SJC, Paul IM, Hohman EE, Savage JS, Wright RO, Chiaromonte F, Makova KD, Reimherr ML. Methylation profiles at birth linked to early childhood obesity. Medrxiv : the Preprint Server For Health Sciences. PMID 38260407 DOI: 10.1101/2024.01.12.24301172  0.163
1998 Makova KD, Patton JC. Increased yield of tri- and tetranucleotide heterospecific microsatellites from unenriched small-insert libraries. Biotechniques. 24: 38, 40, 42-3. PMID 9454948  0.121
2019 Cremona M, Xu H, Makova K, Reimherr M, Chiaromonte F, Madrigal P. Functional data analysis for computational biology. Bioinformatics (Oxford, England). PMID 30668667 DOI: 10.1093/Bioinformatics/Btz045  0.092
2001 Longmire JL, Roach JL, Maltbie M, White PS, Tatum OL, Makova KD, Caldwell Hahn D. Tetranucleotide microsatellite markers for the brown-headed Cowbird Molothrus ater Journal of Avian Biology. 32: 76-78.  0.081
2021 Carney MC, Zhan X, Rangnekar A, Chroneos MZ, Craig SJC, Makova KD, Paul IM, Hicks SD. Associations between stool micro-transcriptome, gut microbiota, and infant growth. Journal of Developmental Origins of Health and Disease. 1-7. PMID 33407969 DOI: 10.1017/S2040174420001324  0.077
2014 Paul IM, Williams JS, Anzman-Frasca S, Beiler JS, Makova KD, Marini ME, Hess LB, Rzucidlo SE, Verdiglione N, Mindell JA, Birch LL. The Intervention Nurses Start Infants Growing on Healthy Trajectories (INSIGHT) study. Bmc Pediatrics. 14: 184. PMID 25037579 DOI: 10.1186/1471-2431-14-184  0.066
2021 Nandy D, Craig SJC, Cai J, Tian Y, Paul IM, Savage JS, Marini ME, Hohman EE, Reimherr ML, Patterson AD, Makova KD, Chiaromonte F. Metabolomic profiling of stool of two-year old children from the INSIGHT study reveals links between butyrate and child weight outcomes. Pediatric Obesity. e12833. PMID 34327846 DOI: 10.1111/ijpo.12833  0.053
2022 Savage JS, Hochgraf AK, Loken E, Marini ME, Craig SJC, Makova KD, Birch LL, Paul IM. INSIGHT responsive parenting educational intervention for firstborns is associated with growth of second-born siblings. Obesity (Silver Spring, Md.). 30: 183-190. PMID 34932886 DOI: 10.1002/oby.23301  0.044
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