Using the linear references from the pangenome to discover missing autism variants
Yang Sui, Jiadong Lin, Michelle D. Noyes, Youngjun Kwon, Isaac Wong, Nidhi Koundinya, William T. Harvey, Mei Wu, Kendra Hoekzema, Katherine M. Munson, Gage H. Garcia, Jordan Knuth, Julie Wertz, Tianyun Wang, Kelsey Hennick, Druha Karunakaran, Rafael A. Polo Prieto, Rebecca Meyer-Schuman, Fisher Cher...,
Dec 2026,
In: Nature communications
Date: Dec 2026
Mammalian mitochondrial DNA accumulates insertions and deletions with age in energetically demanding tissues
Edmundo Torres-Gonzalez, Barbara Arbeithuber, Nicholas Stoler, Marzia A. Cremona, Omar Shebl, Thomas Ebner, Irene Tiemann-Boege, Francisco J. Diaz, Francesca Chiaromonte, Kateryna D. Makova,
Mar 1 2026,
In: Molecular biology and evolution
Date: Mar 1 2026
Substitution Spectrum and Selection at G-quadruplexes in Great Ape Telomere-to-Telomere Genomes
Xinru Zhang, Saswat K. Mohanty, Francesca Chiaromonte, Kateryna D. Makova,
Mar 2026,
In: Genome biology and evolution
Date: Mar 2026
Allele Frequency Selection and No Age-Related Increase in Human Oocyte Mitochondrial Mutations
Barbara Arbeithuber, Kate Anthony, Bonnie Higgins, Peter Oppelt, Omar Shebl, Irene Tiemann-Boege, Francesca Chiaromonte, Thomas Ebner, Kateryna D. Makova,
Jan 2026,
In: Obstetrical and Gynecological Survey
Date: Jan 2026
SNP calling, haplotype phasing and allele-specific analysis with long RNA-seq reads
Neng Huang, Heng Li, Giulia Zunino, Ivo Violich, Ying Zhou, Wenjin Zhang, Dong Ahn Yoo, Kai Ye, Zheng Xu, Zilan Xin, Conor V. Whelan, Aaron M. Wenger, Ting Wang, Lisa E. Wang, Charles Wang, Brian P. Walenz, Mitchell R. Vollger, Flavia Villani, Rahul Varki, Matteo Tommaso Ungaro, Mohammed Uddin, Fran...,
2026,
In: Nature methods
Date: 2026
Evolutionary dynamics of predicted G-quadruplexes in human and other great apes
Saswat K. Mohanty, Francesca Chiaromonte, Kateryna D. Makova,
Dec 2025,
In: Genome biology
Date: Dec 2025
Allele frequency selection and no age-related increase in human oocyte mitochondrial mutations
Barbara Arbeithuber, Kate Anthony, Bonnie Higgins, Peter Oppelt, Omar Shebl, Irene Tiemann-Boege, Francesca Chiaromonte, Thomas Ebner, Kateryna D. Makova,
Aug 2025,
In: Science Advances
Date: Aug 2025
Highly accurate assembly polishing with DeepPolisher
Mira Mastoras, Mobin Asri, Lucas Brambrink, Prajna Hebbar, Alexey Kolesnikov, Daniel E. Cook, Maria Nattestad, Julian Lucas, Taylor S. Won, Pi Chuan Chang, Andrew Carroll, Benedict Paten, Kishwar Shafin, Ahmad Abou Tayoun, Derek Albracht, Jamie Allen, Alawi A. Alsheikh-Ali, Casey Andrews, Dmitry Ant...,
Jul 2025,
In: Genome Research
Date: Jul 2025
Replicative DNA polymerase epsilon and delta holoenzymes show wide-ranging inhibition at G-quadruplexes in the human genome
Suzanne E. Hile, Matthias H. Weissensteiner, Kara G. Pytko, Joseph Dahl, Eduard Kejnovsky, Iva Kejnovská, Mark Hedglin, Ilias Georgakopoulos-Soares, Kateryna D. Makova, Kristin A. Eckert,
May 8 2025,
In: Nucleic acids research
Date: May 8 2025
Non-canonical DNA in human and other ape telomere-to-telomere genomes
Linnéa Smeds, Kaivan Kamali, Iva Kejnovská, Eduard Kejnovský, Francesca Chiaromonte, Kateryna D. Makova,
Apr 24 2025,
In: Nucleic acids research
Date: Apr 24 2025
Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution
Ladeana W. Hillier, Webb Miller, Ewan Birney, Wesley Warren, Ross C. Hardison, Chris P. Ponting, Peer Bork, David W. Burt, Martien A.M. Groenen, Mary E. Delany, Jerry B. Dodgson, Asif T. Chinwalla, Paul F. Cliften, Sandra W. Clifton, Kimberly D. Delehaunty, Catrina Fronick, Robert S. Fulton, Tina A....,
Dec 9 2004,
In: Nature
Citations: 2,366
Initial sequence of the chimpanzee genome and comparison with the human genome
Tarjei S. Mikkelsen, Ladeana W. Hillier, Evan E. Eichler, Michael C. Zody, David B. Jaffe, Shiaw Pyng Yang, Wolfgang Enard, Ines Hellmann, Kerstin Lindblad-Toh, Tasha K. Altheide, Nicoletta Archidiacono, Peer Bork, Jonathan Butler, Jean L. Chang, Ze Cheng, Asif T. Chinwalla, Pieter Dejong, Kimberley...,
Sep 1 2005,
In: Nature
Citations: 1,938
Towards complete and error-free genome assemblies of all vertebrate species
Arang Rhie, Shane A. McCarthy, Olivier Fedrigo, Joana Damas, Giulio Formenti, Sergey Koren, Marcela Uliano-Silva, William Chow, Arkarachai Fungtammasan, Juwan Kim, Chul Lee, Byung June Ko, Mark Chaisson, Gregory L. Gedman, Lindsey J. Cantin, Francoise Thibaud-Nissen, Leanne Haggerty, Iliana Bista, M...,
Apr 29 2021,
In: Nature
Citations: 1,925
Genome sequence of the Brown Norway rat yields insights into mammalian evolution
Richard A. Gibbs, George M. Weinstock, Michael L. Metzker, Donna M. Muzny, Erica J. Sodergren, Steven Scherer, Graham Scott, David Steffen, Kim C. Worley, Paula E. Burch, Geoffrey Okwuonu, Sandra Hines, Lora Lewis, Christine Deramo, Oliver Delgado, Shannon Dugan-Rocha, George Miner, Margaret Morgan,...,
Apr 1 2004,
In: Nature
Citations: 1,820
Evolutionary and biomedical insights from the rhesus macaque genome
Richard A. Gibbs, Jeffrey Rogers, Michael G. Katze, Roger Bumgarner, George M. Weinstock, Elaine R. Mardis, Karin A. Remington, Robert L. Strausberg, J. Craig Venter, Richard K. Wilson, Mark A. Batzer, Carlos D. Bustamante, Evan E. Eichler, Matthew W. Hahn, Ross C. Hardison, Kateryna D. Makova, Webb...,
Apr 13 2007,
In: Science
Citations: 1,180
The complete sequence of a human Y chromosome
Arang Rhie, Sergey Nurk, Monika Cechova, Savannah J. Hoyt, Dylan J. Taylor, Nicolas Altemose, Paul W. Hook, Sergey Koren, Mikko Rautiainen, Ivan A. Alexandrov, Jamie Allen, Mobin Asri, Andrey V. Bzikadze, Nae Chyun Chen, Chen Shan Chin, Mark Diekhans, Paul Flicek, Giulio Formenti, Arkarachai Fungtam...,
2023,
In: Nature
Citations: 328
Complete Khoisan and Bantu genomes from southern Africa
Stephan C. Schuster, Webb Miller, Aakrosh Ratan, Lynn P. Tomsho, Belinda Giardine, Lindsay R. Kasson, Robert S. Harris, Desiree C. Petersen, Fangqing Zhao, Ji Qi, Can Alkan, Jeffrey M. Kidd, Yazhou Sun, Daniela I. Drautz, Pascal Bouffard, Donna M. Muzny, Jeffrey G. Reid, Lynne V. Nazareth, Qingyu Wa...,
Feb 18 2010,
In: Nature
Citations: 326
The K<sub>A</sub>/K<sub>S</sub> ratio test for assessing the protein-coding potential of genomic regions
Anton Nekrutenko, Kateryna D. Makova, Wen Hsiung Li,
2002,
In: Genome Research
Citations: 268
The genome-wide determinants of human and chimpanzee microsatellite evolution
Yogeshwar D. Kelkar, Svitlana Tyekucheva, Francesca Chiaromonte, Kateryna D. Makova,
Jan 2008,
In: Genome Research
Citations: 210
Strong male-driven evolution of DNA sequences in humans and apes
Kateryna D. Makova, Wen Hsiung Li,
Apr 11 2002,
In: Nature
Citations: 205