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L Smeds, K Kamali, KD Makova. Non-canonical DNA in human and other ape telomere-to-telomere genomes. BIORXIV, 2024.

D Yoo, A Rhie, P Hebbar, F Antonacci, GA Logsdon, SJ Solar, D Antipov, BD Pickett, Y Safonova, F Montinaro, Y Luo, J Malukiewicz, JM Storer, J Lin, AN Sequeira, RJ Mangan, G Hickey, GM Anez, P Balachandran, A Bankevich, CR Beck, A Biddanda, M Borchers, GG Bouffard, E Brannan, SY Brooks, L Carbone, L Carrel, AP Chan, J Crawford, M Diekhans, E Engelbrecht, C Feschotte, G Formenti, GH Garcia, L de Gennaro, D Gilbert, RE Green, A Guarracino, I Gupta, D Haddad, J Han, RS Harris, GA Hartley, WT Harvey, M Hiller, K Hoekzema, ML Houck, H Jeong, K Kamali, M Kellis, B Kille, C Lee, Y Lee, W Lees, AP Lewis, Q Li, M Loftus, YHE Loh, H Loucks, J Ma, Y Mao, JFI Martinez, P Masterson, RC McCoy, B McGrath, S McKinney, BS Meyer, KH Miga, SK Mohanty, KM Munson, K Pal, M Pennell, PA Pevzner, D Porubsky, T Potapova, FR Ringeling, JL Rocha, OA Ryder, S Sacco, S Saha, T Sasaki, MC Schatz, NJ Schork, C Shanks, L Smeds, DR Son, C Steiner, AP Sweeten, MG Tassia, F Thibaud-Nissen, E Torres-González, M Trivedi, W Wei, J Wertz, M Yang, P Zhang, S Zhang, Y Zhang, Z Zhang, SA Zhao, Y Zhu, ED Jarvis, JL Gerton, I Rivas-González, B Paten, ZA Szpiech, CD Huber, TL Lenz, MK Konkel, SV Yi, S Canzar, CT Watson, PH Sudmant, E Molloy, E Garrison, CB Lowe, M Ventura, RJ O’Neill, S Koren, KD Makova, AM Phillippy, EE Eichler. Complete sequencing of ape genomes. BIORXIV, 2024.

PDF Sex chromosome Video Paper Link

M Cechova, KD Makova. The ape Y chromosome evolves extremely rapidly, but the X chromosome is conserved. NATURE, 2024.

KD Makova, BD Pickett, RS Harris, GA Hartley, M Cechova, K Pal, S Nurk, D Yoo, Q Li, P Hebbar, BC McGrath, F Antonacci, M Aubel, A Biddanda, M Borchers, E Bomberg, GG Bouffard, SY Brooks, L Carbone, L Carrel, A Carroll, PC Chang, CS Chin, DE Cook, SJC Craig, L de Gennaro, M Diekhans, A Dutra, GH Garcia, PGS Grady, RE Green, D Haddad, P Hallast, WT Harvey, G Hickey, DA Hillis, SJ Hoyt, H Jeong, K Kamali, SL Kosakovsky Pond, TM LaPolice, C Lee, AP Lewis, YE Loh, P Masterson, RC McCoy, P Medvedev, KH Miga, KM Munson, E Pak, B Paten, BJ Pinto, T Potapova, A Rhie, JL Rocha, F Ryabov, OA Ryder, S Sacco, K Shafin, VA Shepelev, V Slon, SJ Solar, JM Storer, PH Sudmant, Sweetalana, A Sweeten, MG Tassia, F Thibaud-Nissen, M Ventura, MA Wilson, AC Young, H Zeng, X Zhang, ZA Szpiech, CD Huber, JL Gerton, SV Yi, MC Schatz, IA Alexandrov, S Koren, RJ O’Neill, E Eichler, AM Phillippy. The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes. NATURE, 2024.

Sex chromosome Video Paper Link Press release

D Lariviere, SJC Craig, IM Paul, E Hohman, JS Savage, RO Wright, F Chiaromonte, KD Makova, ML Reimherr. Methylation profiles at birth linked to early childhood obesity. J DEV ORIG HEALTH DIS, 2024.

A Greshnova, K Pal, JFI Martinez, S Canzar, KD Makova. Transcript Isoform Diversity of Y Chromosome Ampliconic Genes of Great Apes Uncovered Using Long Reads and Telomere-to-Telomere Reference Genome Assemblies. BIORXIV, 2024.

A Lahnsteiner, SJC Craig, K Kamali, B Weissensteiner, B McGrath, A Risch, KD Makova. In vivo detection of DNA secondary structures using Permanganate/S1 Footprinting with Direct Adapter Ligation and Sequencing (PDAL-Seq). METHODS IN ENZYMOLOGY, 2024.

M Tomaszkiewicz, K Sahlin, P Medvedev, KD Makova. Transcript Isoform Diversity of Ampliconic Genes on the Y Chromosome of Great Apes. GENOME BIOL EVOL, 2023.

A Rhie, S Nurk, M Cechova, SJ Hoyt, DJ Taylor, N Altemose, PW Hook, S Koren, M Rautiainen, IA Alexandrov, J Allen, M Asri, AV Bzikadze, N-C Chen, C-S Chin, M Diekhans, P Flicek, G Formenti, A Fungtammasan, CG Giron, E Garrison, A Gershman, JL Gerton, PGS Grady, A Guarracino, L Haggerty, R Halabian, NF Hansen, R Harris, GA Hartley, WT Harvey, M Haukness, J Heinz, T Hourlier, RM Hubley, SE Hunt, S Hwang, M Jain, RK Kesharwani, AP Lewis, H Li, GA Logsdon, JK Lucas, W Makalowski, C Markovic, FJ Martin, AM McCartney, RC McCoy, J McDaniel, BM McNulty, P Medvedev, A Mikheenko, KM Munson, TD Murphy, HE Olsen, ND Olson, LF Paulin, D Porubsky, T Potapova, F Ryabov, SL Salzberg, MEG Sauria, FJ Sedlazeck, K Shafin, VA Shepelev, A Shumate, JM Storer, L Surapaneni, AM Taravella Oill, F Thibaud-Nissen, W Timp, M Tomaszkiewicz, MR Vollger, BP Walenz, AC Watwood, MH Weissensteiner, AM Wenger, MA Wilson, S Zarate, Y Zhu, JM Zook, EE Eichler, RJ O’Neill, MC Schatz, KH Miga, KD Makova, AM Phillippy. The complete sequence of a human Y chromosome. NATURE, 2023.

M Weissensteiner, MA Cremona, WM Guiblet, N Stoler, RS Harris, M Cechova, KA Eckert, F Chiaromonte, YF Huang, KD Makova. Accurate sequencing of DNA motifs able to form alternative (non-B) structures. GENOME RES, 2023.

SJC Craig, AM Kenney, J Lin, IM Paul, LL Birch, JS Savage, ME Marini, F Chiaromonte, ML Reimherr, KD Makova. Constructing a polygenic risk score for childhood obesity using functional data analysis. ECONOM STAT, 2023.

KD Makova, M Weissensteiner. Noncanonical DNA structures are drivers of genome evolution. TRENDS GENET, 2023.

M Escalona, J VanCampen, NW Maurer, M Haukness, M Okhovat, RS Harris, A Watwood, GA Hartley, RJ O’Neill, P Medvedev, KD Makova, C Vollmers, L Carbone, RE Green. Whole-genome sequence and assembly of the Javan gibbon (Hylobates moloch). J HERED, 2022.

ME Stein, A Nusawardhana, M Weissensteiner, M Leed, S Zhang, E Kejnovsky, I Kejnovská, KD Makova, KA Eckert. Variation in G-quadruplex Sequence and Topology Differentially Impacts Human DNA Polymerase Fidelity. DNA REPAIR, 2022.

E Torres-González, KD Makova. Exploring the effects of mitonuclear interactions on mitochondrial DNA gene expression in humans. FRONT GENET, 2022.

B Arbeithuber, MA Cremona, J Hester, A Barrett, B Higgins, K Anthony, F Chiaromonte, FJ Diaz, KD Makova. Advanced age increases frequencies of de novo mitochondrial mutations in macaque oocytes and somatic tissues. P NATL ACAD SCI USA, 2022.

D Nandy, SJ Craig, J Cai, Y Tian, IM Paul, JS Savage, ME Marini, EE Hohman, ML Reimherr, AD Patterson, KD Makova, F Chiaromonte. Metabolomic profiling of stool of two-year old children from the INSIGHT study reveals links between butyrate and child weight outcomes. PED OBESITY, 2022.

JS Savage, AK Hochgraf, E Loken, ME Marini, SJ Craig, KD Makova, LL Birch, IM Paul. INSIGHT responsive parenting educational intervention for firstborns is associated with growth of secondborn siblings. OBESITY, 2022.

WM Guiblet, M DeGiorgio, X Cheng, F Chiaromonte, KA Eckert, YF Huang, KD Makova. Selection and thermostability suggest G-quadruplexes are novel functional elements of the human genome. GENOME RES, 2021.

A Rhie, SA McCarthy, O Fedrigo, J Damas, G Formenti, S Koren, M Uliano-Silva, W Chow, A Fungtammasan, GL Gedman, LJ Cantin, F Thibaud-Nissen, L Haggerty, C Lee, BJ Ko, J Kim, I Bista, M Smith, B Haase, J Mountcastle, S Winkler, S Paez, J Howard, SC Vernes, TM Lama, F Grutzner, WC Warren, C Balakrishnan, D Burt, JM George, M Biegler, D Iorns, A Digby, D Eason, T Edwards, M Wilkinson, G Turner, A Meyer, AF Kautt, P Franchini, HW Detrich III, H Svardal, M Wagner, GJP Naylor, M Pippel, M Malinsky, M Mooney, M Simbirsky, BT Hannigan, T Pesout, M Houck, A Misuraca, SB Kingan, R Hall, Z Kronenberg, J Korlach, I Sović, C Dunn, Z Ning, A Hastie, J Lee, S Selvaraj, RE Green, NH Putnam, J Ghurye, E Garrison, Y Sims, J Collins, S Pelan, J Torrance, A Tracey, J Wood, D Guan, SE London, DF Clayton, CV Mello, SR Friedrich, PV Lovell, E Osipova, FO Al-Ajli, S Secomandi, H Kim, C Theofanopoulou, Y Zhou, RS Harris, KD Makova, P Medvedev, J Hoffman, P Masterson, K Clark, F Martin, K Howe, P Flicek, BP Walenz, W Kwak, H Clawson, M Diekhans, L Nassar, B Paten, RHS Kraus, H Lewin, AJ Crawford, MTP Gilbert, G Zhang, B Venkatesh, RW Murphy, KP Koepfli, B Shapiro, WE Johnson, F Di Palma, T Margues-Bonet, EC Teeling, T Warnow, JM Graves, OA Ryder, D Hausler, SJ O’Brien, K Howe, EW Myers, R Durbin, AM Phillippy, ED Jarvis. Towards complete and error-free genome assemblies of all vertebrate species. NATURE, 2021.

Regional variation Non-B DNA & Microsatellite Paper Link

WM Guiblet, MA Cremona, RS Harris, D Chen, KA Eckert, F Chiaromonte, Y Huang, KD Makova. Non-B DNA: A major contributor to small- and large-scale variation in nucleotide substitution frequencies across the genome. NUCLEIC ACIDS RES, 2021.

MC Carney, X Zhan, A Rangnekar, MZ Chroneos, SJ Craig, KD Makova, IM Paul, SD Hicks. Associations between stool micro-transcriptome, gut microbiota, and infant growth. J DEV ORIG HLTH DIS, 2021.

M Cechova, R Vegesna, M Tomaszkiewicz, RS Harris, D Chen, S Rangavittal, P Medvedev, KD Makova. Dynamic evolution of great ape Y chromosomes. P NATL ACAD SCI USA, 2020.

D Chen, MA Cremona, Z Qi, RD Mitra, F Chiaromonte, KD Makova. Human L1 Transposition Dynamics Unraveled with Functional Data Analysis. MOL BIOL EVOL, 2020.

B Arbeithuber, J Hester, MA Cremona, N Stoler, A Zaidi, B Higgins, K Anthony, F Chiaromonte, FJ Diaz, KD Makova. Age-related accumulation of de novo mitochondrial mutations in mammalian oocytes and somatic tissues. PLOS BIOL, 2020.

PDF Sex chromosome Paper Link

R Vegesna, M Tomaszkiewicz, OA Ryder, R Campos-Sánchez, P Medvedev, M DeGiorgio, KD Makova. Ampliconic genes on the great ape Y chromosomes: Rapid evolution of copy number but conservation of expression levels. GENOME BIOL EVOL, 2020.

N Stoler, B Arbeithuber, G Povysil, M Heinzl, R Salazar, KD Makova, I Tiemann-Boege, A Nekrutenko. Family reunion via error correction: an efficient analysis of duplex sequencing data. BMC BIOINFORMATICS, 2020.

Code Mitochondrial Non-B DNA & Microsatellite Paper Link

A Barrett, B Arbeithuber, A Zaidi, P Wilton, IM Paul, R Nielsen, KD Makova. Pronounced somatic bottleneck in mitochondrial DNA of human hair. PHILOS T R SOC B, 2019.

Code Mitochondrial Paper Link

A Zaidi, P Wilton, MS-W Su, IM Paul, B Arbeithuber, K Anthony, A Nekrutenko, R Nielsen, KD Makova. Bottleneck and selection in the germline and maternal age influence transmission of mitochondrial DNA in human pedigrees. P NATL ACAD SCI USA, 2019.

R Vegesna, M Tomaszkiewicz, P Medvedev, KD Makova. Dosage regulation, and variation in gene expression and copy number of human Y chromosome ampliconic genes. PLOS GENET, 2019.

S Rangavittal, N Stopa, M Tomaszkiewicz, K Sahlin, KD Makova, P Medvedev. DiscoverY: a classifier for identifying Y chromosome sequences in male assemblies. BMC GENOMICS, 2019.

Code Sex chromosome Paper Link

RS Harris, M Cechova, KD Makova. Noise-Cancelling Repeat Finder: Uncovering tandem repeats in error-prone long-read sequencing data. BIOINFORMATICS, 2019.

M Cechova, RS Harris, M Tomaszkiewicz, B Arbeithuber, F Chiaromonte, KD Makova. High Satellite Repeat Turnover in Great Apes Studied with Short- and Long-read Technologies. MOL BIOL EVOL, 2019.

SJC Craig, AM Kenney, J Lin, IM Paul, LL Birch, JS Savage, ME Marini, F Chiaromonte, M Reimherr, KD Makova. Polygenic risk score based on weight gain trajectories is a strong predictor of childhood obesity. BIORXIV, 2019.

MA Cremona, H Xu, KD Makova, M Reimherr, F Chiaromonte, P Madrigal. Functional data analysis for computational biology. BIOINFORMATICS, 2019.

Mitochondrial Paper Link Press Release

AA Zaidi, KD Makova. Investigating mitonuclear interactions in human admixed populations. NAT ECOL EVOL, 2019.

WM Guiblet, MA Cremona, M Cechova, RS Harris, I Kejnovská, E Kejnovsky, KA Eckert, F Chiaromonte, KD Makova. Long-read sequencing technology indicates genome-wide effects of non-B DNA on polymerization speed and error rate. GENOME RES, 2018.

Regional variation Non-B DNA & Microsatellite Paper Link Press Release

K Sahlin, M Tomaszkiewicz, KD Makova, P Medvedev. Deciphering highly similar multigene family transcripts from Iso-Seq data with IsoCon. NAT COMMUN, 2018.

S Warris, E Schijlen, H van de Geest, R Vegesna, T Hesselink, B te Lintel Hekkert, G Sanchez Perez, P Medvedev, KD Makova, D de Ridder. Correcting palindromes in long reads after whole-genome amplification. BMC GENOMICS, 2018.

Childhood Obesity Paper Link Press Release

SJC Craig, D Blankenberg, ACL Parodi, IM Paul, LL Birch, JS Savage, ME Marini, JL Stokes, A Nekrutenko, M Reimherr, F Chiaromonte, KD Makova. Child Weight Gain Trajectories Linked To Oral Microbiota Composition. SCI REP-UK, 2018.

MA Cremona, A Pini, F Cumbo, KD Makova, F Chiaromonte, S Vantini. IWTomics: testing high-resolution sequence-based `Omics' data at multiple locations and scales. BIOINFORMATICS, 2018.

Non-B DNA & Microsatellite Regional variation Paper Link

D Ye, AA Zaidi, M Tomaszkiewicz, K Anthony, C Liebowitz, M DeGiorgio, MD Shriver, KD Makova. High Levels of Copy Number Variation of Ampliconic Genes across Major Human Y Haplogroups. GENOME BIOL EVOL, 2018.

S Rangavittal, RS Harris, M Cechova, M Tomaszkiewicz, R Chikhi, KD Makova, P Medvedev. RecoverY: k-mer-based read classification for Y-chromosome-specific sequencing and assembly. BIOINFORMATICS, 2018.

PR Wilton, AA Zaidi, KD Makova, R Nielsen. A Population Phylogenetic View of Mitochondrial Heteroplasmy. GENETICS, 2018.

MM Holland, KD Makova, JA McElhoe. Deep-Coverage MPS Analysis of Heteroplasmic Variants within the mtGenome Allows for Frequent Differentiation of Maternal Relatives. GENES-BASEL, 2018.

RJ Baker, B Dickins, JK Wickliffe, FAA Khan, S Gaschak, KD Makova, CD Phillips. Elevated mitochondrial genome variation after 50 generations of radiation exposure in a wild rodent. EVOL APPL, 2017.

M Tomaszkiewicz, P Medvedev, KD Makova. Y and W Chromosome Assemblies: Approaches and Discoveries. TRENDS GENET, 2017.

B Arbeithuber, KD Makova, I Tiemann-Boege. Artifactual mutations resulting from DNA lesions limit detection levels in ultrasensitive sequencing applications. DNA RES, 2016.

A Fungtammasan, M Tomaszkiewicz, R Campos-Sánchez, KA Eckert, M DeGiorgio, KD Makova. Reverse Transcription Errors and RNA–DNA Differences at Short Tandem Repeats. MOL BIOL EVOL, 2016.

N Stoler, B Arbeithuber, WM Guiblet, KD Makova, A Nekrutenko. Streamlined analysis of duplex sequencing data with Du Novo. GENOME BIOL, 2016.

R Campos-Sánchez, MA Cremona, A Pini, F Chiaromonte, KD Makova. Integration and Fixation Preferences of Human and Mouse Endogenous Retroviruses Uncovered with Functional Data Analysis. PLOS COMPUT BIOL, 2016.

M Tomaszkiewicz, S Rangavittal, M Cechova, R Campos-Sánchez, HW Fescemyer, RS Harris, D Ye, PCM O’Brien, R Chikhi, OA Ryder, MA Ferguson-Smith, P Medvedev, KD Makova. A time- and cost-effective strategy to sequence mammalian Y Chromosomes: an application to the de novo assembly of gorilla Y. GENOME RES, 2016.

KD Makova, RC Hardison. The effects of chromatin organization on variation in mutation rates in the genome. NAT REV GENET, 2015.

F Chiaromonte, KD Makova. Using Statistics to Shed Light on the Dynamics of the Human Genome: A Review. CONTRIB STAT, 2015.

A Fungtammasan, G Ananda, SE Hile, MS-W Su, C Sun, RS Harris, P Medvedev, KA Eckert, KD Makova. Accurate typing of short tandem repeats from genome-wide sequencing data and its applications. GENOME RES, 2015.

JA McElhoe, MM Holland, KD Makova, MS-W Su, IM Paul, CH Baker, SA Faith, B Young. Development and assessment of an optimized next-generation DNA sequencing approach for the mtgenome using the Illumina MiSeq. FORENSIC SCI INT-GEN, 2014.

B Rebolledo-Jaramillo, MS-W Su, N Stoler, JA McElhoe, B Dickins, D Blankenberg, TS Korneliussen, F Chiaromonte, R Nielsen, MM Holland, IM Paul, A Nekrutenko, KD Makova. Maternal age effect and severe germ-line bottleneck in the inheritance of human mitochondrial DNA. P NATL ACAD SCI USA, 2014.

IM Paul, JS Williams, S Anzman-Frasca, JS Beiler, KD Makova, ME Marini, LB Hess, SE Rzucidlo, N Verdiglione, JA Mindell, LL Birch. The Intervention Nurses Start Infants Growing on Healthy Trajectories (INSIGHT) study. BMC PEDIATR, 2014.

G Ananda, SE Hile, A Breski, Y Wang, YD Kelkar, KD Makova, KA Eckert. Microsatellite Interruptions Stabilize Primate Genomes and Exist as Population-Specific Single Nucleotide Polymorphisms within Individual Human Genomes. PLOS GENET, 2014.

R Campos-Sánchez, A Kapusta, C Feschotte, F Chiaromonte, KD Makova. Genomic Landscape of Human, Bat, and Ex Vivo DNA Transposon Integrations. MOL BIOL EVOL, 2014.

B Dickins, B Rebolledo-Jaramillo, MS-W Su, IM Paul, D Blankenberg, N Stoler, KD Makova, A Nekrutenko. Controlling for contamination in re-sequencing studies with a reproducible web-based phylogenetic approach. BIOTECHNIQUES, 2014.

EM Kvikstad, KD Makova. Rapid Evolution of Genes on the Human X Chromosome. eLS, 2013.

P Kuruppumullage Don, G Ananda, F Chiaromonte, KD Makova. Segmenting the human genome based on states of neutral genetic divergence. P NATL ACAD SCI USA, 2013.

MA Wilson Sayres, KD Makova. Gene Survival and Death on the Human Y Chromosome. MOL BIOL EVOL, 2013.

BA Baptiste, G Ananda, N Strubczewski, A Lutzkanin, SJ Khoo, A Srikanth, N Kim, KD Makova, MM Krasilnikova, KA Eckert. Mature Microsatellites: Mechanisms Underlying Dinucleotide Microsatellite Mutational Biases in Human Cells. G3-GENES GENOM GENET, 2013.

CC Steiner, KD Makova, OA Ryder. Mitochondrial Genome: Clues about the Evolution of Extant Equids and Genomic Diversity of Horse Breeds. EQUINE GENOMICS, 2013.

SB Montgomery, DL Goode, EM Kvikstad, CA Albers, ZD Zhang, XJ Mu, G Ananda, B Howie, KJ Karczewski, KS Smith, V Anaya, R Richardson, J Davis, The 1000 Genomes Project Consortium, DG MacArthur, A Sidow, L Duret, M Gerstein, KD Makova, J Marchini, G McVean, G Lunter. The origin, evolution, and functional impact of short insertion–deletion variants identified in 179 human genomes. GENOME RES, 2013.

G Ananda, E Walsh, KD Jacob, MM Krasilnikova, KA Eckert, F Chiaromonte, KD Makova. Distinct Mutational Behaviors Differentiate Short Tandem Repeats from Microsatellites in the Human Genome. GENOME BIOL EVOL, 2013.

BJ Wagstaff, DJ Hedges, RS Derbes, R Campos-Sánchez, F Chiaromonte, KD Makova, AM Roy-Engel. Rescuing Alu: Recovery of New Inserts Shows LINE-1 Preserves Alu Activity through A-Tail Expansion. PLOS GENET, 2012.

K Wolfe, ML Wayne, KD Makova, TY Steen, M Uyenoyama, N Takahata. SMBE Proposal to the Government of Japan. MOL BIOL EVOL, 2012.

Non-B DNA & Microsatellite Regional variation Paper Link

A Fungtammasan, E Walsh, F Chiaromonte, KA Eckert, KD Makova. A genome-wide analysis of common fragile sites: What features determine chromosomal instability in the human genome?. GENOME RES, 2012.

MA Wilson Sayres, KD Makova. Genome analyses substantiate male mutation bias in many species. BIOESSAYS, 2011.

E Afgan, D Baker, N Coraor, H Goto, IM Paul, KD Makova, A Nekrutenko, J Taylor. Harnessing cloud computing with Galaxy Cloud. NAT BIOTECHNOL, 2011.

MA Wilson Sayres, C Venditti, M Pagel, KD Makova. DO VARIATIONS IN SUBSTITUTION RATES AND MALE MUTATION BIAS CORRELATE WITH LIFE-HISTORY TRAITS? A STUDY OF 32 MAMMALIAN GENOMES. EVOLUTION, 2011.

H Goto, B Dickins, E Afgan, IM Paul, J Taylor, KD Makova, A Nekrutenko. Dynamics of mitochondrial heteroplasmy in three families investigated via a repeatable re-sequencing study. GENOME BIOL, 2011.

Z Lombard, C Park, KD Makova, M Ramsay. A computational approach to candidate gene prioritization for X-linked mental retardation using annotation-based binary filtering and motif-based linear discriminatory analysis. BIOL DIRECT, 2011.

G Ananda, F Chiaromonte, KD Makova. A genome-wide view of mutation rate co-variation using multivariate analyses. GENOME BIOL, 2011.

YD Kelkar, KA Eckert, F Chiaromonte, KD Makova. A matter of life or death: How microsatellites emerge in and vanish from the human genome. GENOME RES, 2011.

H Goto, OA Ryder, AR Fisher, B Schultz, SL Kosakovsky Pond, A Nekrutenko, KD Makova. A Massively Parallel Sequencing Approach Uncovers Ancient Origins and High Genetic Variability of Endangered Przewalski's Horses. GENOME BIOL EVOL, 2011.

C Park, L Carrel, KD Makova. Strong Purifying Selection at Genes Escaping X Chromosome Inactivation. MOL BIOL EVOL, 2010.

SC Schuster, W Miller, A Ratan, LP Tomsho, B Giardine, LR Kasson, RS Harris, DC Petersen, F Zhao, J Qi, C Alkan, JM Kidd, Y Sun, DI Drautz, P Bouffard, DM Muzny, JG Reid, LV Nazareth, Q Wang, RC Burhans, C Riemer, NE Wittekindt, P Moorjani, EA Tindall, CG Danko, WS Teo, AM Buboltz, Z Zhang, Q Ma, A Oosthuysen, AW Steenkamp, H Oostuisen, P Venter, J Gajewski, Y Zhang, BF Pugh, KD Makova, A Nekrutenko, ER Mardis, N Patterson, TH Pringle, F Chiaromonte, JC Mullikin, EE Eichler, RC Hardison, RA Gibbs, TT Harkins, VM Hayes. Complete Khoisan and Bantu genomes from southern Africa. NATURE, 2010.

YD Kelkar, N Strubczewski, SE Hile, F Chiaromonte, KA Eckert, KD Makova. What Is a Microsatellite: A Computational and Experimental Definition Based upon Repeat Mutational Behavior at A/T and GT/AC Repeats. GENOME BIOL EVOL, 2010.

EM Kvikstad, KD Makova. The (r)evolution of SINE versus LINE distributions in primate genomes: Sex chromosomes are important. GENOME RES, 2010.

MA Wilson, KD Makova. Genomic Analyses of Sex Chromosome Evolution. ANNU REV GENOM HUM G, 2009.

MA Wilson, KD Makova. Evolution and Survival on Eutherian Sex Chromosomes. PLOS GENET, 2009.

H Goto, L Peng, KD Makova. Evolution of X-Degenerate Y Chromosome Genes in Greater Apes: Conservation of Gene Content in Human and Gorilla, But Not Chimpanzee. J MOL EVOL, 2009.

C Park, KD Makova. Coding region structural heterogeneity and turnover of transcription start sites contribute to divergence in expression between duplicate genes. GENOME BIOL, 2009.

EM Kvikstad, F Chiaromonte, KD Makova. Ride the wavelet: A multiscale analysis of genomic contexts flanking small insertions and deletions. GENOME RES, 2009.

AN Lau, L Peng, H Goto, L Chemnick, OA Ryder, KD Makova. Horse Domestication and Conservation Genetics of Przewalski's Horse Inferred from Sex Chromosomal and Autosomal Sequences. MOL BIOL EVOL, 2009.

W-H Li, KD Makova. Molecular Clocks. ELS, 2008.

S Tyekucheva, KD Makova, JE Karro, RC Hardison, W Miller, F Chiaromonte. Human-macaque comparisons illuminate variation in neutral substitution rates. GENOME BIOL, 2008.

YD Kelkar, S Tyekucheva, F Chiaromonte, KD Makova. The genome-wide determinants of human and chimpanzee microsatellite evolution. GENOME RES, 2008.

EM Kvikstad, S Tyekucheva, F Chiaromonte, KD Makova. A Macaque's-Eye View of Human Insertions and Deletions: Differences in Mechanisms. PLOS COMPUT BIOL, 2007.

RA Gibbs, J Rogers, MG Katze, R Bumgarner, GM Weinstock, ER Mardis, KA Remington, RL Strausberg, JC Venter, RK Wilson, MA Batzer, CD Bustamante, EE Eichler, MW Hahn, RC Hardison, KD Makova, W Miller, A Milosavljevic, RE Palermo, A Siepel, JM Sikela, T Attaway, S Bell, KE Bernard, CJ Buhay, MN Chandrabose, M Dao, C Davis, KD Delehaunty, Y Ding, HH Dinh, S Dugan-Rocha, LA Fulton, RA Gabisi, TT Garner, J Godfrey, AC Hawes, J Hernandez, S Hines, M Holder, J Hume, SN Jhangiani, V Joshi, ZM Khan, EF Kirkness, A Cree, RG Fowler, S Lee, LR Lewis, Z Li, Y-S Liu, SM Moore, DM Muzny, LV Nazareth, DN Ngo, GO Okwuonu, G Pai, D Parker, HA Paul, CM Pfannkoch, CS Pohl, Y-H Rogers, SJ Ruiz, A Sabo, J Santibanez, BW Schneider, SM Smith, EJ Sodergren, AF Svatek, TR Utterback, S Vattathil, W Warren, CS White, AT Chinwalla, Y Feng, AL Halpern, LW Hillier, X Huang, P Minx, JO Nelson, KH Pepin, X Qin, GG Sutton, E Venter, BP Walenz, JW Wallis, KC Worley, S-P Yang, SM Jones, MA Marra, M Rocchi, JE Schein, R Baertsch, L Clarke, M Csürös, J Glasscock, RA Harris, PH Havlak, AR Jackson, H Jiang, Y Liu, DN Messina, Y Shen, HX-Z Song, T Wylie, L Zhang, E Birney, K Han, MK Konkel, J Lee, AFA Smit, B Ullmer, H Wang, J Xing, RC Burhans, Z Cheng, JE Karro, J Ma, B Raney, X She, MJ Cox, JP Demuth, LJ Dumas, S-G Han, J Hopkins, A Karimpour-Fard, YH Kim, JR Pollack, T Vinar, C Addo-Quaye, J Degenhardt, A Denby, MJ Hubisz, A Indap, C Kosiol, BT Lahn, HA Lawson, A Marklein, R Nielsen, EJ Vallender, AG Clark, B Ferguson, RD Hernandez, K Hirani, H Kehrer-Sawatzki, J Kolb, S Patil, L-L Pu, Y Ren, DG Smith, DA Wheeler, I Schenck, EV Ball, R Chen, DN Cooper, B Giardine, F Hsu, WJ Kent, A Lesk, DL Nelson, WE O’Brien, K Prüfer, PD Stenson, JC Wallace, H Ke, X-M Liu, P Wang, AP Xiang, F Yang, GP Barber, D Haussler, D Karolchik, AD Kern, RM Kuhn, KE Smith, AS Zwieg. Evolutionary and Biomedical Insights from the Rhesus Macaque Genome. SCIENCE, 2007.

D Blankenberg, J Taylor, I Schenck, J He, Y Zhang, M Ghent, N Veeraraghavan, I Albert, W Miller, KD Makova, RC Hardison, A Nekrutenko. A framework for collaborative analysis of ENCODE data: Making large-scale analyses biologist-friendly. GENOME RES, 2007.

MP Goetting-Minesky, KD Makova. Mammalian Male Mutation Bias: Impacts of Generation Time and Regional Variation in Substitution Rates. J MOL EVOL, 2006.

L Carrel, C Park, S Tyekucheva, J Dunn, F Chiaromonte, KD Makova. Genomic Environment Predicts Expression Patterns on the Human Inactive X Chromosome. PLOS GENET, 2006.

W-H Li, KD Makova. Domain Duplication and Gene Elongation. eLS, 2006.

J Taylor, S Tyekucheva, M Zody, F Chiaromonte, KD Makova. Strong and Weak Male Mutation Bias at Different Sites in the Primate Genomes: Insights from the Human-Chimpanzee Comparison. MOL BIOL EVOL, 2006.

W-Y Chung, R Albert, I Albert, A Nekrutenko, KD Makova. Rapid and asymmetric divergence of duplicate genes in the human gene coexpression network. BMC BIOINFORMATICS, 2006.

KD Makova, H Norton. Worldwide polymorphism at the MC1R locus and normal pigmentation variation in humans. PEPTIDES, 2005.

A Nekrutenko, S Wadhawan, MP Goetting-Minesky, KD Makova. Oscillating Evolution of a Mammalian Locus with Overlapping Reading Frames: An XLαs/ALEX Relay. PLOS GENET, 2005.

International Chicken Genome Sequencing Consortium, LW Hillier, W Miller, E Birney, W Warren, RC Hardison, CP Ponting, P Bork, DW Burt, MAM Groenen, ME Delany, JB Dodgson, AT Chinwalla, PF Cliften, SW Clifton, KD Delehaunty, C Fronick, RS Fulton, TA Graves, C Kremitzki, D Layman, V Magrini, JD McPherson, TL Miner, P Minx, WE Nash, MN Nhan, JO Nelson, LG Oddy, CS Pohl, J Randall-Maher, SM Smith, JW Wallis, S-P Yang, MN Romanov, CM Rondelli, B Paton, J Smith, D Morrice, L Daniels, HG Tempest, L Robertson, JS Masabanda, DK Griffin, A Vignal, V Fillon, L Jacobbson, S Kerje, L Andersson, RPM Crooijmans, J Aerts, JJ van der Poel, H Ellegren, RB Caldwell, SJ Hubbard, DV Grafham, AM Kierzek, SR McLaren, IM Overton, H Arakawa, KJ Beattie, Y Bezzubov, PE Boardman, JK Bonfield, MDR Croning, RM Davies, MD Francis, SJ Humphray, CE Scott, RG Taylor, C Tickle, WRA Brown, J Rogers, J-M Buerstedde, SA Wilson, L Stubbs, I Ovcharenko, L Gordon, S Lucas, MM Miller, H Inoko, T Shiina, J Kaufman, J Salomonsen, K Skjoedt, GK-S Wong, J Wang, B Liu, J Wang, J Yu, H Yang, M Nefedov, M Koriabine, PJ deJong, L Goodstadt, C Webber, NJ Dickens, I Letunic, M Suyama, D Torrents, C von Mering, EM Zdobnov, KD Makova, A Nekrutenko, L Elnitski, P Eswara, DC King, S Yang, S Tyekucheva, A Radakrishnan, RS Harris, F Chiaromonte, J Taylor, J He, M Rijnkels, S Griffiths-Jones, A Ureta-Vidal, MM Hoffman, J Severin, SMJ Searle, AS Law, D Speed, D Waddington, Z Cheng, E Tuzun, EE Eichler, Z Bao, P Flicek, DD Shteynberg, MR Brent, JM Bye, EJ Huckle, S Chatterji, C Dewey, L Pachter, A Kouranov, Z Mourelatos, AG Hatzigeorgiou, AH Paterson, R Ivarie, M Brandstrom, E Axelsson, N Backstrom, S Berlin, MT Webster, O Pourquie, A Reymond, C Ucla, SE Antonarakis, M Long, JJ Emerson, E Betrán, I Dupanloup, H Kaessmann, AS Hinrichs, G Bejerano, TS Furey, RA Harte, B Raney, A Siepel, WJ Kent, D Haussler, E Eyras, R Castelo, JF Abril, S Castellano, F Camara, G Parra, R Guigo, G Bourque, G Tesler, PA Pevzner, AFA Smit, LA Fulton, ER Mardis, RK Wilson. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. NATURE, 2004.

W Miller, KD Makova, A Nekrutenko, RC Hardison. COMPARATIVE GENOMICS. ANNU REV GENOM HUM G, 2004.

Rat Genome Sequencing Project Consortium, RA Gibbs, GM Weinstock, ML Metzker, DM Muzny, EJ Sodergren, S Scherer, G Scott, D Steffen, KC Worley, PE Burch, GO Okwuonu, S Hines, LR Lewis, C DeRamo, O Delgado, S Dugan-Rocha, G Miner, M Morgan, AC Hawes, R Gill, CRA Holt, MD Adams, PG Amanatides, H Baden-Tillson, M Barnstead, S Chin, CA Evans, S Ferriera, C Fosler, A Glodek, Z Gu, D Jennings, CL Kraft, T Nguyen, CM Pfannkoch, C Sitter, GG Sutton, JC Venter, T Woodage, D Smith, H-M Lee, E Gustafson, P Cahill, A Kana, L Doucette-Stamm, K Weinstock, K Fechtel, RB Weiss, DM Dunn, ED Green, RW Blakesley, GG Bouffard, PJ de Jong, K Osoegawa, B Zhu, MA Marra, JE Schein, I Bosdet, C Fjell, SM Jones, M Krzywinski, C Mathewson, A Siddiqui, N Wye, JD McPherson, S Zhao, CM Fraser, J Shetty, S Shatsman, K Geer, Y Chen, S Abramzon, WC Nierman, RA Gibbs, GM Weinstock, PH Havlak, R Chen, K James Durbin, A Egan, Y Ren, HX-Z Song, B Li, Y Liu, X Qin, S Cawley, GM Weinstock, KC Worley, AJ Cooney, RA Gibbs, LM D’Souza, K Martin, J Qian Wu, ML Gonzalez-Garay, AR Jackson, KJ Kalafus, MP McLeod, A Milosavljevic, D Virk, A Volkov, DA Wheeler, Z Zhang, JA Bailey, EE Eichler, E Tuzun, E Birney, E Mongin, A Ureta-Vidal, C Woodwark, EM Zdobnov, P Bork, M Suyama, D Torrents, M Alexandersson, BJ Trask, JM Young, D Smith, H Huang, K Fechtel, H Wang, H Xing, K Weinstock, S Daniels, D Gietzen, J Schmidt, K Stevens, U Vitt, J Wingrove, F Camara, M Mar Albà, JF Abril, R Guigo, AFA Smit, I Dubchak, EM Rubin, O Couronne, A Poliakov, N Hübner, D Ganten, C Goesele, O Hummel, T Kreitler, Y-A Lee, J Monti, H Schulz, H Zimdahl, H Himmelbauer, H Lehrach, HJ Jacob, S Bromberg, J Gullings-Handley, MI Jensen-Seaman, AE Kwitek, J Lazar, D Pasko, PJ Tonellato, S Twigger, CP Ponting, JM Duarte, S Rice, L Goodstadt, SA Beatson, RD Emes, EE Winter, C Webber, P Brandt, G Nyakatura, M Adetobi, F Chiaromonte, L Elnitski, P Eswara, RC Hardison, M Hou, D Kolbe, KD Makova, W Miller, A Nekrutenko, C Riemer, S Schwartz, J Taylor, S Yang, Y Zhang, K Lindpaintner, TD Andrews, M Caccamo, M Clamp, L Clarke, V Curwen, R Durbin, E Eyras, SMJ Searle, GM Cooper, S Batzoglou, M Brudno, A Sidow, EA Stone, J Craig Venter, BA Payseur, G Bourque, C López-Otín, XS Puente, K Chakrabarti, S Chatterji, C Dewey, L Pachter, N Bray, VB Yap, A Caspi, G Tesler, PA Pevzner, D Haussler, KM Roskin, R Baertsch, H Clawson, TS Furey, AS Hinrichs, D Karolchik, WJ Kent, KR Rosenbloom, H Trumbower, M Weirauch, DN Cooper, PD Stenson, B Ma, MR Brent, M Arumugam, DD Shteynberg, RR Copley, MS Taylor, H Riethman, U Mudunuri, J Peterson, M Guyer, A Felsenfeld, S Old, S Mockrin, F Collins. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. NATURE, 2004.

KD Makova, S Yang, F Chiaromonte. Insertions and Deletions Are Male Biased Too: A Whole-Genome Analysis in Rodents. GENOME RES, 2004.

PR John, KD Makova, W-H Li, T Jenkins, M Ramsay. DNA Polymorphism and Selection at the Melanocortin-1 Receptor Gene in Normally Pigmented Southern African Individuals. ANN NY ACAD SCI, 2003.

JL Longmire, JL Roach, M Maltbie, PS White, OL Tatum, KD Makova, DC Hahn. Tetranucleotide microsatellite markers for the Brown-headed Cowbird Molothrus ater. J AVIAN BIOL, 2003.

KD Makova, W-H Li. Divergence in the Spatial Pattern of Gene Expression Between Human Duplicate Genes. GENOME RES, 2003.

J Mu, J Duan, KD Makova, DA Joy, CQ Huynh, OH Branch, W-H Li, X-Z Su. Chromosome-wide SNPs reveal an ancient origin for Plasmodium falciparum. NATURE, 2002.

KD Makova, W-H Li. Strong male-driven evolution of DNA sequences in humans and apes. NATURE, 2002.

A Nekrutenko, KD Makova, W-H Li. The K A/K S Ratio Test for Assessing the Protein-Coding Potential of Genomic Regions: An Empirical and Simulation Study. GENOME RES, 2002.

W-H Li, S Yi, KD Makova. Male-driven evolution. CURR OPIN GENET DEV, 2002.

Regional variation Publication

KD Makova, M Ramsay, T Jenkins, W-H Li. Human DNA Sequence Variation in a 6.6-kb Region Containing the Melanocortin 1 Receptor Promoter. GENETICS, 2001.

J-C Liu, KD Makova, RM Adkins, S Gibson, W-H Li. Episodic Evolution of Growth Hormone in Primates and Emergence of the Species Specificity of Human Growth Hormone Receptor. MOL BIOL EVOL, 2001.

KD Makova, A Nekrutenko, RJ Baker. Evolution of Microsatellite Alleles in Four Species of Mice (Genus Apodemus). J MOL EVOL, 2000.

A Nekrutenko, KD Makova, RJ Baker. Isolation of binary species-specific PCR-based markers and their value for diagnostic applications. GENE, 2000.

A Nekrutenko, KD Makova, RK Chesser, RJ Baker. Representational difference analysis to distinguish cryptic species. MOL ECOL, 1999.

RJ Baker, KD Makova, RK Chesser. Microsatellites indicate a high frequency of multiple paternity in Apodemus (Rodentia). MOL ECOL, 1999.

KD Makova, JC Patton. Increased Yield of Tri- and Tetranucleotide Heterospecific Microsatellites from Unenriched Small-Insert Libraries. BIOTECHNIQUES, 1998.