Segmental duplications and their variation in a complete human genome

Basic local alignment search tool

Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669 · see citing works

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

Stamatakis, A. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu033 · Cited by 32,291 · see citing works

BEDTools: a flexible suite of utilities for comparing genomic features

Quinlan, A. R., & Hall, I. M. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq033 · Cited by 27,437 · see citing works

Initial sequencing and analysis of the human genome

International Human Genome Sequencing Consortium, Whitehead Institute for Biomedical Research, C. F. G. R., Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J., Devon, K., Dewar, K., et al. (2001) · Nature · doi:10.1038/35057062 · Cited by 24,216 · see citing works

Welcome to the tidyverse

Wickham, H., Averick, M., Bryan, J., Chang, W., McGowan, L., François, R., Grolemund, G., Hayes, A., Henry, L., Hester, J., et al. (2019) · Journal of Open Source Software · doi:10.21105/joss.01686 · Cited by 22,138 · see citing works

MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform

Katoh, K. (2002) · Nucleic Acids Research · doi:10.1093/nar/gkf436 · Cited by 17,027 · see citing works

Minimap2: Pairwise alignment for nucleotide sequences

Li, H. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty191 · Cited by 14,807 · see citing works

The sequence of the human genome

Venter, J. C., Adams, M. D., Myers, E. W., Li, P. W., Mural, R. J., Sutton, G. G., Smith, H. O., Yandell, M., Evans, C. A., Holt, R. A., et al. (2001) · Science · doi:10.1126/science.1058040 · Cited by 13,909 · see citing works

Tandem repeats finder: a program to analyze DNA sequences

Benson, G. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.2.573 · Cited by 9,374 · see citing works

Evolution by Gene Duplication

Ohno, S. (1970) · doi:10.1007/978-3-642-86659-3 · Cited by 7,833 · see citing works

Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm

Cheng, H., Concepcion, G. T., Feng, X., Zhang, H., & Li, H. (2021) · Nature Methods · doi:10.1038/s41592-020-01056-5 · Cited by 5,859 · see citing works

Software for Computing and Annotating Genomic Ranges

Lawrence, M. F., Huber, W. K., Pagès, H., Aboyoun, P., Carlson, M. R. J., Gentleman, R. C., Morgan, M. T., & Carey, V. J. (2013) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003118 · Cited by 4,438 · see citing works

A draft sequence of the Neandertal genome

Green, R. E., Krause, J., Briggs, A. W., Maricic, T., Stenzel, U., Kircher, M., Patterson, N., Li, H., Zhai, W., Fritz, M. H.-Y., et al. (2010) · Science · doi:10.1126/science.1188021 · Cited by 4,318 · see citing works

circlize implements and enhances circular visualization in R

Gu, Z., Gu, L., Eils, R., Schlesner, M., & Brors, B. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu393 · Cited by 4,290 · see citing works

Genetic effects on gene expression across human tissues

GTEx Consortium (2017) · Nature · doi:10.1038/nature24277 · Cited by 4,036 · see citing works

The complete sequence of a human genome

Nurk, S., Koren, S., Rhie, A., Rautiainen, M., Bzikadze, A. V., Mikheenko, A., Vollger, M. R., Altemose, N., Uralsky, L., Gershman, A., et al. (2022) · Science · doi:10.1126/science.abj6987 · Cited by 3,136 · see citing works

Snakemake—a scalable bioinformatics workflow engine

Köster, J., & Rahmann, S. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts480 · Cited by 2,780 · see citing works

Genetic Variants Associated with Lp(a) Lipoprotein Level and Coronary Disease

Clarke, R., Peden, J. F., Hopewell, J. C., Kyriakou, T., Goel, A., Heath, S. C., Parish, S., Barlera, S., Franzosi, M. G., Rust, S., et al. (2009) · New England Journal of Medicine · doi:10.1056/nejmoa0902604 · Cited by 1,671 · see citing works

The Simons Genome Diversity Project: 300 genomes from 142 diverse populations

Mallick, S., Li, H., Lipson, M., Mathieson, I., Gymrek, M., Racimo, F., Zhao, M., Chennagiri, N., Nordenfelt, S., Tandon, A., et al. (2016) · Nature · doi:10.1038/nature18964 · Cited by 1,584 · see citing works

Real-time, portable genome sequencing for Ebola surveillance

Quick, J., Loman, N. J., Duraffour, S., Simpson, J. T., Severi, E., Cowley, L. A., Boré, J. A., Koundouno, F. R., Dudas, G., Mikhail, A. F. W., et al. (2016) · Nature · doi:10.1038/nature16996 · Cited by 1,450 · see citing works

A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters

Saxonov, S., Berg, P., & Brutlag, D. L. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0510310103 · Cited by 1,401 · see citing works

Recent Segmental Duplications in the Human Genome

Bailey, J. A., Gu, Z., Clark, R. A., Reinert, K., Samonte, R. V., Schwartz, S., Adams, M. D., Myers, E. W., Li, P. W., & Eichler, E. E. (2002) · Science · doi:10.1126/science.1072047 · Cited by 1,355 · see citing works

A copy number variation morbidity map of developmental delay

Cooper, G. M., Coe, B. P., Girirajan, S., Rosenfeld, J. A., Vu, T. H., Baker, C., Williams, C., Stalker, H., Hamid, R., Hannig, V., et al. (2011) · Nature Genetics · doi:10.1038/ng.909 · Cited by 1,351 · see citing works

A complete bacterial genome assembled de novo using only nanopore sequencing data

Loman, N., Quick, J., & Simpson, J. (2015) · Nature Methods · doi:10.1038/nmeth.3444 · Cited by 1,248 · see citing works

GFF Utilities: GffRead and GffCompare

Pertea, G., & Pertea, M. (2020) · F1000Research · doi:10.12688/f1000research.23297.2 · Cited by 1,152 · see citing works

Mapping and sequencing of structural variation from eight human genomes

Kidd, J. M., Cooper, G. M., Donahue, W. F., Hayden, H. S., Sampas, N., Graves, T., Hansen, N., Teague, B., Alkan, C., Antonacci, F., et al. (2008) · Nature · doi:10.1038/nature06862 · Cited by 1,119 · see citing works

Detecting DNA cytosine methylation using nanopore sequencing

Simpson, J. T., Workman, R. E., Zuzarte, P. C., David, M., Dursi, L. J., & Timp, W. (2017) · Nature Methods · doi:10.1038/nmeth.4184 · Cited by 1,109 · see citing works

Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells

Ball, M. P., Li, J. B., Gao, Y., Lee, J., LeProust, E. M., Park, I., Xie, B., Daley, G. Q., & Church, G. M. (2009) · Nature Biotechnology · doi:10.1038/nbt.1533 · Cited by 1,087 · see citing works

Liftoff: accurate mapping of gene annotations

Shumate, A., & Salzberg, S. L. (2020) · Bioinformatics · doi:10.1093/bioinformatics/btaa1016 · Cited by 991 · see citing works

Multi-platform discovery of haplotype-resolved structural variation in human genomes

Chaisson, M. J. P., Sanders, A. D., Zhao, X., Malhotra, A., Porubsky, D., Rausch, T., Gardner, E. J., Rodriguez, O. L., Guo, L., Collins, R. L., et al. (2019) · Nature Communications · doi:10.1038/s41467-018-08148-z · Cited by 891 · see citing works

Sustainable data analysis with Snakemake

Mölder, F., Jablonski, K. P., Letcher, B., Hall, M. B., Tomkins-Tinch, C. H., Sochat, V., Forster, J., Lee, S., Twardziok, S. O., Kanitz, A., et al. (2021) · F1000Research · doi:10.12688/f1000research.29032.1 · Cited by 786 · see citing works

Resolving the complexity of the human genome using single-molecule sequencing

Chaisson, M., Huddleston, J., Dennis, M. Y., Sudmant, P. H., Malig, M., Hormozdiari, F., Antonacci, F., Surti, U., Sandstrom, R. S., Boitano, M., et al. (2014) · Nature · doi:10.1038/nature13907 · Cited by 783 · see citing works

karyoploteR: an R/Bioconductor package to plot customizable genomes displaying arbitrary data

Gel, B., & Serra, E. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btx346 · Cited by 775 · see citing works

Telomere-to-telomere assembly of a complete human X chromosome

Miga, K. H., Koren, S., Rhie, A., Vollger, M. R., Gershman, A., Bzikadze, A., Brooks, S., Howe, E., Porubsky, D., Logsdon, G. A., et al. (2020) · Nature · doi:10.1038/s41586-020-2547-7 · Cited by 765 · see citing works

EVOLUTION FROM FISH TO MAMMALS BY GENE DUPLICATION

Ohno, S., Wolf, U., & Atkin, N. B. (2009) · Hereditas · doi:10.1111/j.1601-5223.1968.tb02169.x · Cited by 711 · see citing works

HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long readsPreprint

Nurk, S., Walenz, B. P., Rhie, A., Vollger, M. R., Logsdon, G. A., Grothe, R., Miga, K. H., Eichler, E. E., Phillippy, A. M., & Koren, S. (2020) · Genome Research · doi:10.1101/gr.263566.120 · Cited by 709 · see citing works

Segmental Duplications: Organization and Impact Within the Current Human Genome Project AssemblyPreprint

Bailey, J. A., Yavor, A. M., Massa, H. F., Trask, B. J., & Eichler, E. E. (2001) · Genome Research · doi:10.1101/gr.187101 · Cited by 708 · see citing works

Haplotype-resolved diverse human genomes and integrated analysis of structural variation

Ebert, P., Audano, P. A., Zhu, Q., Rodriguez-Martin, B., Porubsky, D., Bonder, M. J., Sulovari, A., Ebler, J., Zhou, W., Serra Mari, R., et al. (2021) · Science · doi:10.1126/science.abf7117 · Cited by 702 · see citing works

Diversity of Human Copy Number Variation and Multicopy Genes

Sudmant, P. H., Kitzman, J. O., Antonacci, F., Alkan, C., Malig, M., Tsalenko, A., Sampas, N., Bruhn, L., Shendure, J., 1000 Genomes Project, et al. (2010) · Science · doi:10.1126/science.1197005 · Cited by 667 · see citing works

Structure, function, and genetics of lipoprotein (a)

Schmidt, K., Noureen, A., Kronenberg, F., & Utermann, G. (2016) · Journal of Lipid Research · doi:10.1194/jlr.r067314 · Cited by 647 · see citing works

Inherited amplification of an active gene in the cytochrome P450 CYP2D locus as a cause of ultrarapid metabolism of debrisoquine.

Johansson, I., Lundqvist, E., Bertilsson, L., Dahl, M., Sjöqvist, F., & Ingelman‐Sundberg, M. (1993) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.90.24.11825 · Cited by 645 · see citing works

Human-Specific NOTCH2NL Genes Affect Notch Signaling and Cortical Neurogenesis

Fiddes, I. T., Lodewijk, G. A., Mooring, M., Bosworth, C. M., Ewing, A. D., Mantalas, G. L., Novak, A. M., van den Bout, A., Bishara, A., Rosenkrantz, J. L., et al. (2018) · Cell · doi:10.1016/j.cell.2018.03.051 · Cited by 595 · see citing works

Molecular genetics of CYP2D6: Clinical relevance with focus on psychotropic drugs

Bertilsson, L., Dahl, M., Dalén, P., & Al‐Shurbaji, A. (2002) · British Journal of Clinical Pharmacology · doi:10.1046/j.0306-5251.2001.01548.x · Cited by 579 · see citing works

Segmental Duplications: Organization and Impact Within the Current Human Genome Project AssemblyPreprint

Bailey, J. A. (2001) · Genome Research · doi:10.1101/gr.gr-1871r · Cited by 573 · see citing works

Lipoprotein(a): resurrected by genetics

Kronenberg, F., & Utermann, G. (2013) · Journal of Internal Medicine · doi:10.1111/j.1365-2796.2012.02592.x · Cited by 521 · see citing works

Human-Specific NOTCH2NL Genes Expand Cortical Neurogenesis through Delta/Notch Regulation

Suzuki, I. K., Gacquer, D., Van Heurck, R., Kumar, D., Wojno, M., Bilheu, A., Herpoel, A., Lambert, N., Cheron, J., Polleux, F., et al. (2018) · Cell · doi:10.1016/j.cell.2018.03.067 · Cited by 471 · see citing works

Origin and evolution of the genus Homo

Wood, B. (1992) · Nature · doi:10.1038/355783a0 · Cited by 462 · see citing works

The design and construction of reference pangenome graphs with minigraph

Li, H., Feng, X., & Chu, C. (2020) · Genome Biology · doi:10.1186/s13059-020-02168-z · Cited by 455 · see citing works

Evolution of human-specific neural SRGAP2 genes by incomplete segmental duplication

Dennis, M. Y., Nuttle, X., Sudmant, P. H., Antonacci, F., Graves, T. A., Nefedov, M., Rosenfeld, J. A., Sajjadian, S., Malig, M., Kotkiewicz, H., et al. (2012) · Cell · doi:10.1016/j.cell.2012.03.033 · Cited by 407 · see citing works

Steady-state plasma levels of nortriptyline in twins: Influence of genetic factors and drug therapy

Alexanderson, B., Evans, D. A. P., & Sjöqvist, F. (1969) · BMJ · doi:10.1136/bmj.4.5686.764 · Cited by 360 · see citing works

Molecular cloning of cDNAs derived from a novel human intestinal mucin gene

Gum, J. R., Hicks, J. W., Swallow, D. M., Lagace, R. L., Byrd, J. C., Lamport, D. T. A., Siddiki, B., & Kim, Y. S. (1990) · Biochemical and Biophysical Research Communications · doi:10.1016/0006-291x(90)91408-k · Cited by 360 · see citing works

The DNA sequence and comparative analysis of human chromosome 20

Deloukas, P., Matthews, L. H., Ashurst, J. L., Burton, J., Gilbert, J. G. R., Jones, M., Stavrides, G., Almeida, J. P., Babbage, A., Bagguley, C. L., et al. (2001) · Nature · doi:10.1038/414865a · Cited by 359 · see citing works

Global diversity, population stratification, and selection of human copy-number variation

Sudmant, P. H., Mallick, S., Nelson, B. J., Hormozdiari, F., Krumm, N., Huddleston, J., Coe, B. P., Baker, C., Nordenfelt, S., Bamshad, M., et al. (2015) · Science · doi:10.1126/science.aab3761 · Cited by 345 · see citing works

Fcγ receptor gene polymorphisms in Japanese patients with systemic lupus erythematosus: Contribution of FCGR2B to genetic susceptibility

Kyogoku, C., Dijstelbloem, H. M., Tsuchiya, N., Hatta, Y., Kato, H., Yamaguchi, A., Fukazawa, T., Jansen, M., Hashimoto, H., van de Winkel, J. G. J., et al. (2002) · Arthritis & Rheumatism · doi:10.1002/art.10257 · Cited by 333 · see citing works

The structure, function and evolution of a complete human chromosome 8

Logsdon, G. A., Vollger, M. R., Hsieh, P., Mao, Y., Liskovykh, M. A., Koren, S., Nurk, S., Mercuri, L., Dishuck, P. C., Rhie, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03420-7 · Cited by 326 · see citing works

Snakemake—a scalable bioinformatics workflow engine

Köster, J., & Rahmann, S. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty350 · Cited by 310 · see citing works

Epigenetic patterns in a complete human genome

Gershman, A., Sauria, M. E. G., Guitart, X., Vollger, M. R., Hook, P. W., Hoyt, S. J., Jain, M., Shumate, A., Razaghi, R., Koren, S., et al. (2022) · Science · doi:10.1126/science.abj5089 · Cited by 297 · see citing works

Positive selection of a gene family during the emergence of humans and African apes

Johnson, M. E., Viggiano, L., Bailey, J. A., Abdul-Rauf, M., Goodwin, G. H., Rocchi, M., & Eichler, E. E. (2001) · Nature · doi:10.1038/35097067 · Cited by 296 · see citing works

Pangenome-based genome inference allows efficient and accurate genotyping across a wide spectrum of variant classes

Ebler, J., Ebert, P., Clarke, W. E., Rausch, T., Audano, P. A., Houwaart, T., Mao, Y., Korbel, J. O., Eichler, E. E., Zody, M. C., et al. (2022) · Nature Genetics · doi:10.1038/s41588-022-01043-w · Cited by 277 · see citing works

Deletion of the entire cytochrome P450 CYP2D6 gene as a cause of impaired drug metabolism in poor metabolizers of the debrisoquine/sparteine polymorphism.

Gaedigk, A., Blum, M., Gaedigk, R., Eichelbaum, M. F., & Meyer, U. (1991) · Europe PMC (PubMed Central) · Cited by 274 · see citing works

mrsFAST: a cache-oblivious algorithm for short-read mapping

Hach, F., Hormozdiari, F., Alkan, C., Hormozdiari, F., Birol, İ., Eichler, E. E., & Şahinalp, S. C. (2010) · Nature Methods · doi:10.1038/nmeth0810-576 · Cited by 274 · see citing works

Plasma levels of monomethylated tricyclic antidepressants during treatment with imipramine-like compounds

Hammer, W., & Sjöqvist, F. (1967) · Life Sciences · doi:10.1016/0024-3205(67)90218-4 · Cited by 263 · see citing works

Single-molecule regulatory architectures captured by chromatin fiber sequencing

Stergachis, A. B., Debo, B. M., Haugen, E., Churchman, L. S., & Stamatoyannopoulos, J. A. (2020) · Science · doi:10.1126/science.aaz1646 · Cited by 257 · see citing works

Shotgun sequence assembly and recent segmental duplications within the human genome

She, X., Jiang, Z., Clark, R. A., Liu, G., Cheng, Z., Tüzün, E., Church, D. M., Sutton, G., Halpern, A. L., & Eichler, E. E. (2004) · Nature · doi:10.1038/nature03062 · Cited by 256 · see citing works

Complex SNP-related sequence variation in segmental genome duplications

Fredman, D., White, S. J., Potter, S., Eichler, E. E., den Dunnen, J. T., & Brookes, A. J. (2004) · Nature Genetics · doi:10.1038/ng1401 · Cited by 232 · see citing works

Human Genetics and the Causal Role of Lipoprotein(a) for Various Diseases

Kronenberg, F. (2016) · Cardiovascular Drugs and Therapy · doi:10.1007/s10557-016-6648-3 · Cited by 227 · see citing works

Ancestral reconstruction of segmental duplications reveals punctuated cores of human genome evolution

Jiang, Z., Tang, H., Ventura, M., Cardone, M. F., Marquès‐Bonet, T., She, X., Pevzner, P. A., & Eichler, E. E. (2007) · Nature Genetics · doi:10.1038/ng.2007.9 · Cited by 212 · see citing works

Complete Sequence of the 43-kb Human Ribosomal DNA Repeat: Analysis of the Intergenic Spacer

Gonzalez, I. L., & Sylvester, J. E. (1995) · Genomics · doi:10.1006/geno.1995.1049 · Cited by 205 · see citing works

Weighted minimizer sampling improves long read mapping

Jain, C., Rhie, A., Zhang, H., Chu, C., Walenz, B. P., Koren, S., & Phillippy, A. M. (2020) · Bioinformatics · doi:10.1093/bioinformatics/btaa435 · Cited by 205 · see citing works

Evolution and cell-type specificity of human-specific genes preferentially expressed in progenitors of fetal neocortex

Florio, M., Heide, M., Pinson, A., Brandl, H., Albert, M., Winkler, S., Wimberger, P., Huttner, W. Β., & Hiller, M. (2018) · eLife · doi:10.7554/elife.32332 · Cited by 196 · see citing works

Two mutant alleles of the human cytochrome P-450db1 gene (P450C2D1) associated with genetically deficient metabolism of debrisoquine and other drugs.

Skoda, R. C., Gonzalez, F. J., Demierre, A., & Meyer, U. (1988) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.85.14.5240 · Cited by 195 · see citing works

Copy Number Variations in the Survival Motor Neuron Genes: Implications for Spinal Muscular Atrophy and Other Neurodegenerative Diseases

Butchbach, M. E. R. (2016) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2016.00007 · Cited by 193 · see citing works

A defunctioning polymorphism in FCGR2B is associated with protection against malaria but susceptibility to systemic lupus erythematosus

Willcocks, L. C., Carr, E. J., Niederer, H. A., Rayner, T. F., Williams, T. N., Yang, W., Scott, J. A. G., Urban, B. C., Peshu, N., Vyse, T. J., et al. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0915133107 · Cited by 189 · see citing works

Analysis of the CYP2D6 gene in relation to debrisoquin and desipramine hydroxylation in a Swedish population

Dahl, M., Johansson, I., Porsmyr‐Palmertz, M., Ingelman‐Sundberg, M., & Sjöqvist, F. (1992) · Clinical Pharmacology & Therapeutics · doi:10.1038/clpt.1992.2 · Cited by 186 · see citing works

The hominoid-specific gene TBC1D3 promotes generation of basal neural progenitors and induces cortical folding in mice

Ju, X.-C., Hou, Q.-Q., Sheng, A.-L., Wu, K.-Y., Zhou, Y., Jin, Y., Wen, T., Yang, Z., Wang, X., & Luo, Z. (2016) · eLife · doi:10.7554/elife.18197 · Cited by 170 · see citing works

The complete sequence of a human genomePreprint

Nurk, S., Koren, S., Rhie, A., Rautiainen, M., Bzikadze, A. V., Mikheenko, A., Vollger, M. R., Altemose, N., Uralsky, L. I., Gershman, A., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.05.26.445798 · Cited by 169 · see citing works

Chromosomal polymorphisms of 1, 9, 16, and Y in 4 major ethnic groups: A large prenatal study

Hsu, L. Y. F., Benn, P. A., Tannenbaum, H. L., Perlis, T. E., Carlson, A. D., Opitz, J. M., & Reynolds, J. F. (1987) · American Journal of Medical Genetics · doi:10.1002/ajmg.1320260116 · Cited by 168 · see citing works

Polymorphic variants on chromosomes probably play a significant role in infertility

Madon, P. F., Athalye, A. S., & Parikh, F. R. (2005) · Reproductive BioMedicine Online · doi:10.1016/s1472-6483(10)61691-4 · Cited by 168 · see citing works

The Tre2 ( USP6 ) oncogene is a hominoid-specific gene

Paulding, C., Ruvolo, M., & Haber, D. A. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0437015100 · Cited by 146 · see citing works

Miropeats: graphical DNA sequence comparisons

Parsons, J. D. (1995) · Computer applications in the biosciences · doi:10.1093/bioinformatics/11.6.615 · Cited by 141 · see citing works

Optimal alignment between groups of sequences and its application to multiple sequence alignment

Gotoh, O. (1993) · Computer applications in the biosciences · doi:10.1093/bioinformatics/9.3.361 · Cited by 127 · see citing works

Single-cell template strand sequencing by Strand-seq enables the characterization of individual homologs

Sanders, A. D., Falconer, E., Hills, M., Spierings, D. C. J., & Lansdorp, P. M. (2017) · Nature Protocols · doi:10.1038/nprot.2017.029 · Cited by 125 · see citing works

A case-control study identifying chromosomal polymorphic variations as forms of epigenetic alterations associated with the infertility phenotype

Minocherhomji, S., Athalye, A. S., Madon, P. F., Kulkarni, D., Uttamchandani, S. A., & Parikh, F. R. (2008) · Fertility and Sterility · doi:10.1016/j.fertnstert.2008.05.071 · Cited by 123 · see citing works

Massively multiplex single-molecule oligonucleosome footprinting

Abdulhay, N. J., McNally, C. P., Hsieh, L. J., Kasinathan, S., Keith, A., Estes, L. S., Karimzadeh, M., Underwood, J. G., Goodarzi, H., Narlikar, G. J., et al. (2020) · eLife · doi:10.7554/elife.59404 · Cited by 108 · see citing works

The DNA sequence and comparative analysis of human chromosome 5

Schmutz, J., Martin, J., Terry, A. Y., Couronne, O., Grimwood, J., Lowry, S., Gordon, L. A., Scott, D., Xie, G. G., Huang, W., et al. (2004) · Nature · doi:10.1038/nature02919 · Cited by 104 · see citing works

Multiple Transcripts of MUC3: Evidence for Two Genes, MUC3A and MUC3B

Pratt, W. S., Crawley, S., Hicks, J., Ho, J., Nash, M., Kim, Y. S., Gum, J. R., & Swallow, D. M. (2000) · Biochemical and Biophysical Research Communications · doi:10.1006/bbrc.2000.3406 · Cited by 101 · see citing works

BAC microarray analysis of 15q11–q13 rearrangements and the impact of segmental duplications

Locke, D. P., Segraves, R., Nicholls, R. D., Schwartz, S., Pinkel, D., Albertson, D. G., & Eichler, E. E. (2004) · Journal of Medical Genetics · doi:10.1136/jmg.2003.013813 · Cited by 101 · see citing works

A novel randomized iterative strategy for aligning multiple protein sequences

Berger, M. P., & Munson, P. J. (1991) · Computer applications in the biosciences · doi:10.1093/bioinformatics/7.4.479 · Cited by 100 · see citing works

Associations of distinct variants of the intestinal mucin gene MUC3A with ulcerative colitis and Crohn's disease

Kyo, K., Muto, T., Nagawa, H., Lathrop, M. G., & Nakamura, Y. (2001) · Journal of Human Genetics · doi:10.1007/s100380170118 · Cited by 98 · see citing works

Do polymorphic variants of chromosomes affect the outcome of in vitro fertilization and embryo transfer treatment?

Hong, Y., Zhou, Y., Tao, J., Wang, S. X., & Zhao, X. (2011) · Human Reproduction · doi:10.1093/humrep/deq333 · Cited by 95 · see citing works

Historical and Clinical Perspectives on Chromosomal Translocations

Wilch, E., & Morton, C. C. (2018) · Advances in experimental medicine and biology · doi:10.1007/978-981-13-0593-1_1 · Cited by 92 · see citing works

Characterizing polymorphic inversions in human genomes by single-cell sequencingPreprint

Sanders, A. D., Hills, M., Porubskỳ, D., Guryev, V., Falconer, E., & Lansdorp, P. M. (2016) · Genome Research · doi:10.1101/gr.201160.115 · Cited by 91 · see citing works

Fast characterization of segmental duplications in genome assemblies

Numanagić, I., Gökkaya, A. Ş., Zhang, L., Berger, B., Alkan, C., & Hach, F. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty586 · Cited by 91 · see citing works

Chromosome heteromorphisms: an impact on infertility

Şahin, F. İ., Yılmaz, Z., Yüreğir, Ö. Ö., Balcı, T. B., Özer, Ö., & Zeyneloğlu, H. B. (2008) · Journal of Assisted Reproduction and Genetics · doi:10.1007/s10815-008-9216-3 · Cited by 86 · see citing works

Variation in human chromosome 21 ribosomal RNA genes characterized by TAR cloning and long-read sequencing

Kim, J.-H., Dilthey, A. T., Nagaraja, R., Lee, H.-S., Koren, S., Dudekula, D., Wood III, W. H., Piao, Y., Ogurtsov, A. Y., Utani, K., et al. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky442 · Cited by 86 · see citing works

Adaptive archaic introgression of copy number variants and the discovery of previously unknown human genes

Hsieh, P., Vollger, M. R., Dang, V., Porubskỳ, D., Baker, C. A., Cantsilieris, S., Hoekzema, K., Lewis, A. P., Munson, K. M., Sorensen, M., et al. (2019) · Science · doi:10.1126/science.aax2083 · Cited by 81 · see citing works

The Evolution of Human Segmental Duplications and the Core Duplicon HypothesisPreprint

Marquès‐Bonet, T., & Eichler, E. E. (2009) · Cold Spring Harbor Symposia on Quantitative Biology · doi:10.1101/sqb.2009.74.011 · Cited by 76 · see citing works

Recurrent inversion toggling and great ape genome evolution

Porubsky, D., Sanders, A. D., Höps, W., Hsieh, P., Sulovari, A., Li, R., Mercuri, L., Sorensen, M., Murali, S. C., Gordon, D., et al. (2020) · Nature Genetics · doi:10.1038/s41588-020-0646-x · Cited by 72 · see citing works

Behaviour of human heterochromatic regions during the synapsis of homologous chromosomes

Codina-Pascual, M., Navarro, J., Oliver‐Bonet, M., KRAUS, J. A., Speicher, M. R., Arango, O., Egozcue, J., & Benet, J. (2006) · Human Reproduction · doi:10.1093/humrep/del028 · Cited by 69 · see citing works

The Hominoid-specific Oncogene TBC1D3 Activates Ras and Modulates Epidermal Growth Factor Receptor Signaling and Trafficking

Wainszelbaum, M. J., Charron, A. J., Chen, K., Kirkpatrick, D. S., Srikanth, P., Barbieri, M. A., Gygi, S. P., & Stahl, P. D. (2008) · Journal of Biological Chemistry · doi:10.1074/jbc.m800234200 · Cited by 64 · see citing works

Islands of euchromatin-like sequence and expressed polymorphic sequences within the short arm of human chromosome 21Preprint

Lyle, R., Prandini, P., Osoegawa, K., ten Hallers, B., Humphray, S., Zhu, B., Eyras, E., Castelo, R., Bird, C., Gagos, S., et al. (2007) · Genome Research · doi:10.1101/gr.6675307 · Cited by 62 · see citing works

Independent centromere formation in a capricious, gene-free domain of chromosome 13q21 in Old World monkeys and pigs

Cardone, M. F., Alonso, A., Pazienza, M., Ventura, M., Montemurro, G., Carbone, L., de Jong, P. J., Stanyon, R., D’Addabbo, P., Archidiacono, N., et al. (2006) · Genome biology · doi:10.1186/gb-2006-7-10-r91 · Cited by 62 · see citing works

Transcriptional fates of human-specific segmental duplications in brainPreprint

Dougherty, M. L., Underwood, J. G., Nelson, B. J., Tseng, E., Munson, K. M., Penn, O., Nowakowski, T. J., Pollen, A. A., & Eichler, E. E. (2018) · Genome Research · doi:10.1101/gr.237610.118 · Cited by 62 · see citing works

Duplications of proximal 16q flanked by heterochromatin are not euchromatic variants and show no evidence of heterochromatic position effect

Barber, J. C. K., Zhang, S., Friend, N., Collins, A., Maloney, V. K., Hastings, R., Farren, B., Barnicoat, A. J., Polityko, A. D., Rumyantseva, N., et al. (2006) · Cytogenetic and Genome Research · doi:10.1159/000094225 · Cited by 59 · see citing works

Splicing regulation of the Survival Motor Neuron genes and implications for treatment of spinal muscular atrophy

Thomas, W. B. (2010) · Frontiers in bioscience · doi:10.2741/3670 · Cited by 57 · see citing works

A comprehensive map of single-base polymorphisms in the hypervariable LPA kringle IV type 2 copy number variation region

Coassin, S., Schönherr, S., Weißensteiner, H., Erhart, G., Forer, L., Losso, J. L., Lamina, C., Haun, M., Utermann, G., Paulweber, B., et al. (2018) · Journal of Lipid Research · doi:10.1194/jlr.m090381 · Cited by 55 · see citing works

Analyzing Copy Number Variation with Droplet Digital PCR

Bell, A. D., Usher, C. L., & McCarroll, S. A. (2018) · Methods in molecular biology · doi:10.1007/978-1-4939-7778-9_9 · Cited by 54 · see citing works

DupMasker: A tool for annotating primate segmental duplicationsPreprint

Jiang, Z., Hubley, R. M., Smit, A. F. A., & Eichler, E. E. (2008) · Genome Research · doi:10.1101/gr.078477.108 · Cited by 48 · see citing works

Human Population Cytogenetics: A Review*

Bhasin, M. K. (2005) · International Journal of Human Genetics · doi:10.1080/09723757.2005.11885918 · Cited by 44 · see citing works

Molecular characterization of the secondary constriction region (qh) of human chromosome 9 with pericentric inversion

Luke, S., Verma, R. S., & Mathews, R. A. C. (1992) · Journal of Cell Science · doi:10.1242/jcs.103.4.919 · Cited by 41 · see citing works

An evolutionary driver of interspersed segmental duplications in primates

Cantsilieris, S., Sunkin, S. M., Johnson, M. E., Anaclerio, F., Huddleston, J., Baker, C. A., Dougherty, M. L., Underwood, J. G., Sulovari, A., Hsieh, P., et al. (2020) · Genome biology · doi:10.1186/s13059-020-02074-4 · Cited by 35 · see citing works

halSynteny: a fast, easy-to-use conserved synteny block construction method for multiple whole-genome alignments

Krasheninnikova, K., Diekhans, M., Armstrong, J., Dievskii, A., Paten, B., & O'Brien, S. (2020) · GigaScience · doi:10.1093/gigascience/giaa047 · Cited by 30 · see citing works

Are heterochromatin polymorphisms associated with recurrent miscarriage?

Çağlayan, A. O., Özyazgan, I., Demiryılmaz, F., & Özgün, M. T. (2010) · Journal of obstetrics and gynaecology research · doi:10.1111/j.1447-0756.2010.01207.x · Cited by 29 · see citing works

Pangenome-based genome inferencePreprint

Ebler, J., Clarke, W. E., Rausch, T., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.11.11.378133 · Cited by 25 · see citing works

Chromosomal Studies in Infertile Men

Kalantari, P., Sepehri, H., Behjati, F., Ashtiani, Z. O., & Akbari, M. T. (2003) · Russian Journal of Genetics · doi:10.1023/a:1023288020685 · Cited by 23 · see citing works

Euchromatic heteromorphism or duplication without phenotypic effect?

Barber, J. C. K. (1994) · Prenatal Diagnosis · doi:10.1002/pd.1970140418 · Cited by 9 · see citing works

The complete sequence of a human genome

Nurk, S., Koren, S., Rhie, A., Rautiainen, M., Bzikadze, A. V., Mikheenko, A., Vollger, M. R., Altemose, N., Uralsky, L., Gershman, A., et al. (2022) · Science · doi:10.1126/science.abj6987 · Cited by 3,136 · see citing works

Complete genomic and epigenetic maps of human centromeres

Altemose, N., Logsdon, G. A., Bzikadze, A. V., Sidhwani, P., Langley, S. A., Caldas, G. V., Hoyt, S. J., Uralsky, L., Ryabov, F. D., Shew, C. J., et al. (2022) · Science · doi:10.1126/science.abl4178 · Cited by 618 · see citing works

The Human Pangenome Project: a global resource to map genomic diversity

Wang, T., Antonacci-Fulton, L., Howe, K., Lawson, H. A., Lucas, J. K., Phillippy, A. M., Popejoy, A. B., Asri, M., Carson, C., Chaisson, M. J. P., et al. (2022) · Nature · doi:10.1038/s41586-022-04601-8 · Cited by 494 · see citing works

The complete sequence of a human Y chromosome

Rhie, A., Nurk, S., Cechova, M., Hoyt, S. J., Taylor, D. J., Altemose, N., Hook, P. W., Koren, S., Rautiainen, M., Alexandrov, I. A., et al. (2023) · Nature · doi:10.1038/s41586-023-06457-y · Cited by 471 · see citing works

A complete reference genome improves analysis of human genetic variation

Aganezov, S., Yan, S. M., Soto, D. C., Kirsche, M., Zarate, S., Avdeyev, P., Taylor, D. J., Shafin, K., Shumate, A., Xiao, C., et al. (2022) · Science · doi:10.1126/science.abl3533 · Cited by 441 · see citing works

NextDenovo: an efficient error correction and accurate assembly tool for noisy long reads

Hu, J. Y., Wang, Z., Sun, Z., Hu, B., Ayoola, A. O., Liang, F., Li, J., Sandoval, J. R., Cooper, D. N., Ye, K., et al. (2024) · Genome biology · doi:10.1186/s13059-024-03252-4 · Cited by 481 · see citing works

From telomere to telomere: The transcriptional and epigenetic state of human repeat elements

Hoyt, S. J., Storer, J. M., Hartley, G. A., Grady, P. G. S., Gershman, A., de Lima, L. G., Limouse, C., Halabian, R., Wojenski, L., Rodriguez, M., et al. (2022) · Science · doi:10.1126/science.abk3112 · Cited by 411 · see citing works

Epigenetic patterns in a complete human genome

Gershman, A., Sauria, M. E. G., Guitart, X., Vollger, M. R., Hook, P. W., Hoyt, S. J., Jain, M., Shumate, A., Razaghi, R., Koren, S., et al. (2022) · Science · doi:10.1126/science.abj5089 · Cited by 297 · see citing works

A systematic framework for understanding the microbiome in human health and disease: from basic principles to clinical translation

Ma, Z., Zuo, T., Frey, N., & Rangrez, A. Y. (2024) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-024-01946-6 · Cited by 297 · see citing works

The variation and evolution of complete human centromeres

Logsdon, G. A., Rozanski, A. N., Ryabov, F., Potapova, T., Shepelev, V. A., Catacchio, C. R., Porubskỳ, D., Mao, Y., Yoo, D., Rautiainen, M., et al. (2024) · Nature · doi:10.1038/s41586-024-07278-3 · Cited by 210 · see citing works

Benchmarking challenging small variants with linked and long reads

Wagner, J., Olson, N. D., Harris, L. N., McDaniel, J., Khan, Z., Farek, J., Mahmoud, M., Stankovic, A., Kovacevic, V., Yoo, B., et al. (2022) · Cell Genomics · doi:10.1016/j.xgen.2022.100128 · Cited by 200 · see citing works

Long-Read DNA Sequencing: Recent Advances and Remaining Challenges

Warburton, P. E., & Sebra, R. P. (2023) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-101722-103045 · Cited by 163 · see citing works

The complete sequence of a human genomePreprint

Nurk, S., Koren, S., Rhie, A., Rautiainen, M., Bzikadze, A. V., Mikheenko, A., Vollger, M. R., Altemose, N., Uralsky, L. I., Gershman, A., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.05.26.445798 · Cited by 169 · see citing works

Variant calling and benchmarking in an era of complete human genome sequences

Olson, N. D., Wagner, J., Dwarshuis, N. J., Miga, K. H., Sedlazeck, F. J., Salit, M., & Zook, J. M. (2023) · Nature Reviews Genetics · doi:10.1038/s41576-023-00590-0 · Cited by 154 · see citing works

Evolutionary analysis of a complete chicken genome

Huang, Z., Xu, Z.-X., Bai, H., Huang, Y., Kang, N., Ding, X.-T., Liu, J., Luo, H.-R., Yang, C., Chen, W., et al. (2023) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.2216641120 · Cited by 155 · see citing works

Complete sequencing of ape genomes

Yoo, D., Rhie, A., Hebbar, P., Antonacci, F., Logsdon, G. A., Solar, S. J., Antipov, D., Pickett, B. D., Safonova, Y., Montinaro, F., et al. (2025) · Nature · doi:10.1038/s41586-025-08816-3 · Cited by 157 · see citing works

Human-specific genetics: new tools to explore the molecular and cellular basis of human evolution

Pollen, A. A., Kilik, U., Lowe, C. B., & Camp, J. G. (2023) · Nature Reviews Genetics · doi:10.1038/s41576-022-00568-4 · Cited by 157 · see citing works

Complex genetic variation in nearly complete human genomes

Logsdon, G. A., Ebert, P., Audano, P. A., Loftus, M. G., Porubskỳ, D., Ebler, J., Yilmaz, F., Hallast, P., Prodanov, T., Yoo, D., et al. (2025) · Nature · doi:10.1038/s41586-025-09140-6 · Cited by 148 · see citing works

Genomics in the long-read sequencing era

van Dijk, E., Naquin, D., Gorrichon, K., Jaszczyszyn, Y., Ouazahrou, R., Thermes, C., & Hernandez, C. (2023) · Trends in Genetics · doi:10.1016/j.tig.2023.04.006 · Cited by 134 · see citing works

Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies

Cartney, A. M. M., Shafin, K., Alonge, M., Bzikadze, A. V., Formenti, G., Fungtammasan, A., Howe, K., Jain, C., Koren, S., Logsdon, G. A., et al. (2022) · Nature Methods · doi:10.1038/s41592-022-01440-3 · Cited by 124 · see citing works

Assembly of 43 human Y chromosomes reveals extensive complexity and variation

Hallast, P., Ebert, P., Loftus, M. G., Yilmaz, F., Audano, P. A., Logsdon, G. A., Bonder, M. J., Zhou, W., Höps, W., Kim, K., et al. (2023) · Nature · doi:10.1038/s41586-023-06425-6 · Cited by 123 · see citing works

Genome-wide detection of cytosine methylations in plant from Nanopore data using deep learning

Ni, P., Huang, N., Nie, F., Zhang, J., Zhang, Z., Wu, B. M., Bai, L., Liu, W., Xiao, C., Luo, F., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-26278-9 · Cited by 120 · see citing works

Co‐based Nanozymatic Profiling: Advances Spanning Chemistry, Biomedical, and Environmental Sciences

Li, J., Cai, X., Jiang, P., Wang, H., Zhang, S., Sun, T., Chen, C., & Fan, K. (2023) · Advanced Materials · doi:10.1002/adma.202307337 · Cited by 115 · see citing works

DNA 5-methylcytosine detection and methylation phasing using PacBio circular consensus sequencing

Ni, P., Nie, F., Zhong, Z., Xu, J., Huang, N., Zhang, J., Zhao, H., Zou, Y. F., Huang, Y., Li, J., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-39784-9 · Cited by 114 · see citing works

Human de novo mutation rates from a four-generation pedigree reference

Porubskỳ, D., Dashnow, H., Sasani, T. A., Logsdon, G. A., Hallast, P., Noyes, M. D., Kronenberg, Z. N., Mokveld, T., Koundinya, N., Nolan, C., et al. (2025) · Nature · doi:10.1038/s41586-025-08922-2 · Cited by 111 · see citing works

An efficient error correction and accurate assembly tool for noisy long readsPreprint

Hu, J. Y., Wang, Z., Sun, Z., Hu, B., Ayoola, A. O., Liang, F., Li, J., Sandoval, J. R., Cooper, D. N., Ye, K., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.03.09.531669 · Cited by 110 · see citing works

Increased mutation and gene conversion within human segmental duplications

Vollger, M. R., Dishuck, P. C., Harvey, W. T., DeWitt, W. S., Guitart, X., Goldberg, M. E., Rozanski, A. N., Lucas, J., Asri, M., Human Pangenome Reference Consortium, et al. (2023) · Nature · doi:10.1038/s41586-023-05895-y · Cited by 104 · see citing works

A survey of algorithms for the detection of genomic structural variants from long-read sequencing data

Ahsan, M. U., Liu, Q., Perdomo, J. E., Li, F., & Wang, K. (2023) · Nature Methods · doi:10.1038/s41592-023-01932-w · Cited by 97 · see citing works

Applications of long-read sequencing to Mendelian genetics

Mastrorosa, F. K., Miller, D. E., & Eichler, E. E. (2023) · Genome Medicine · doi:10.1186/s13073-023-01194-3 · Cited by 91 · see citing works

Comprehensive SMN1 and SMN2 profiling for spinal muscular atrophy analysis using long-read PacBio HiFi sequencing

Chen, X., Harting, J., Farrow, E., Thiffault, I., Kasperavičiūtė, D., Hoischen, A., Gilissen, C., Pastinen, T., & Eberle, M. A. (2023) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2023.01.001 · Cited by 89 · see citing works

The complete and fully-phased diploid genome of a male Han Chinese

Yang, C., Zhou, Y., Song, Y., Wu, D., Zeng, Y., Nie, L., Liu, P., Zhang, S., Chen, G., Xu, J., et al. (2023) · Cell Research · doi:10.1038/s41422-023-00849-5 · Cited by 81 · see citing works

Structurally divergent and recurrently mutated regions of primate genomes

(2024) · doi:10.1016/j.cell.2024.01.052 · Cited by 73 · see citing works

The GIAB genomic stratifications resource for human reference genomes

Dwarshuis, N. J., Kalra, D., McDaniel, J., Sanio, P., Jerez, P. Á., Jadhav, B., Huang, W., Mondal, R., Busby, B., Olson, N. D., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-53260-y · Cited by 73 · see citing works

Merfin: improved variant filtering, assembly evaluation and polishing via k-mer validation

Formenti, G., Rhie, A., Walenz, B. P., Thibaud‐Nissen, F., Shafin, K., Koren, S., Myers, E. W., Jarvis, E. D., & Phillippy, A. M. (2022) · Nature Methods · doi:10.1038/s41592-022-01445-y · Cited by 70 · see citing works

T2T-YAO: A Telomere-to-Telomere Assembled Diploid Reference Genome for Han Chinese

He, Y., Chu, Y., Guo, S., Hu, J. Y., Li, R., Zheng, Y., Ma, X., Du, Z., Zhao, L., Yu, W., et al. (2023) · Genomics Proteomics & Bioinformatics · doi:10.1016/j.gpb.2023.08.001 · Cited by 61 · see citing works

DNA mismatch and damage patterns revealed by single-molecule sequencing

Liu, M. H., Costa, B. M., Bianchini, E. C., Choi, U., Bandler, R. C., Lassen, E., Grońska-Pęski, M., Schwing, A., Murphy, Z. R., Rosenkjær, D., et al. (2024) · Nature · doi:10.1038/s41586-024-07532-8 · Cited by 59 · see citing works

Functional innovation through new genes as a general evolutionary process

Xia, S., Chen, J., Arsala, D., Emerson, J. J., & Long, M. (2025) · Nature Genetics · doi:10.1038/s41588-024-02059-0 · Cited by 61 · see citing works

Gaps and complex structurally variant loci in phased genome assemblies

Porubsky, D., Vollger, M. R., Harvey, W. T., Rozanski, A. N., Ebert, P., Hickey, G., Hasenfeld, P., Sanders, A. D., Stober, C., Human Pangenome Reference Consortium, et al. (2023) · Genome Research · doi:10.1101/gr.277334.122 · Cited by 58 · see citing works

The complete telomere-to-telomere sequence of a mouse genome

Liu, J., Li, Q., Hu, Y., Yu, Y., Zheng, K., Li, D., Qin, L., & Yu, X. (2024) · Science · doi:10.1126/science.adq8191 · Cited by 57 · see citing works

A GGC-repeat expansion in ZFHX3 encoding polyglycine causes spinocerebellar ataxia type 4 and impairs autophagy

Figueroa, K. P., Groß, C., Buena‐Atienza, E., Paul, S., Gandelman, M., Kakar, N., Sturm, M., Casadei, N., Admard, J., Park, J., et al. (2024) · Nature Genetics · doi:10.1038/s41588-024-01719-5 · Cited by 55 · see citing works

Genome-wide repeat landscapes in cancer and cell-free DNA

Annapragada, A. V., Niknafs, N., White, J. R., Bruhm, D. C., Cherry, C., Medina, J. E., Adleff, V., Hruban, C., Mathios, D., Foda, Z. H., et al. (2024) · Science Translational Medicine · doi:10.1126/scitranslmed.adj9283 · Cited by 54 · see citing works

Advancing long-read nanopore genome assembly and accurate variant calling for rare disease detection

Negi, S., Stenton, S. L., Berger, S., Canigiula, P., McNulty, B., Violich, I., Gardner, J. M. V., Hillaker, T. L., O’Rourke, S. M., O’Leary, M., et al. (2025) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2025.01.002 · Cited by 51 · see citing works

A complete, telomere-to-telomere human genome sequence presents new opportunities for evolutionary genomics

Mao, Y., & Zhang, G. (2022) · Nature Methods · doi:10.1038/s41592-022-01512-4 · Cited by 50 · see citing works

Beyond the Human Genome Project: The Age of Complete Human Genome Sequences and Pangenome References

Taylor, D. J., Eizenga, J. M., Li, Q., Das, A., Jenike, K. M., Kenny, E. E., Miga, K. H., Monlong, J., McCoy, R. C., Paten, B., et al. (2024) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-021623-081639 · Cited by 50 · see citing works

Integrated analysis of the complete sequence of a macaque genome

Zhang, S., Xu, N., Fu, L., Yang, X., Ma, K., Li, Y., Yang, Z., Li, Z., Feng, Y., Jiang, X., et al. (2025) · Nature · doi:10.1038/s41586-025-08596-w · Cited by 48 · see citing works

SVbyEye: a visual tool to characterize structural variation among whole-genome assemblies

Porubskỳ, D., Guitart, X., Yoo, D., Dishuck, P. C., Harvey, W. T., & Eichler, E. E. (2025) · Bioinformatics · doi:10.1093/bioinformatics/btaf332 · Cited by 48 · see citing works

A 25-year odyssey of genomic technology advances and structural variant discovery

Porubskỳ, D., & Eichler, E. E. (2024) · Cell · doi:10.1016/j.cell.2024.01.002 · Cited by 48 · see citing works

Telomere-to-telomere pear ( Pyrus pyrifolia ) reference genome reveals segmental and whole genome duplication driving genome evolution

Sun, M., Yao, C., Shu, Q., He, Y., Chen, G., Yang, G., Xu, S., Liu, Y., Xue, Z., & Wu, J. (2023) · Horticulture Research · doi:10.1093/hr/uhad201 · Cited by 45 · see citing works

Genome stability from the perspective of telomere length

Lu, X., & Liu, L. (2023) · Trends in Genetics · doi:10.1016/j.tig.2023.10.013 · Cited by 41 · see citing works

Structural polymorphism and diversity of human segmental duplications

Jeong, H., Dishuck, P. C., Yoo, D., Harvey, W. T., Munson, K. M., Lewis, A. P., Kordosky, J., Garcia, G. H., Yilmaz, F., Hallast, P., et al. (2025) · Nature Genetics · doi:10.1038/s41588-024-02051-8 · Cited by 42 · see citing works

Computational analysis of DNA methylation from long-read sequencing

Fu, Y., Timp, W., & Sedlazeck, F. J. (2025) · Nature Reviews Genetics · doi:10.1038/s41576-025-00822-5 · Cited by 42 · see citing works

A complete diploid human genome benchmark for personalized genomics

Hansen, N. F., Dwarshuis, N., Ji, H. J., Rhie, A., Loucks, H., Logsdon, G., Vollger, M., Storer, J. M., Kim, J., Adam, E., et al. (2026) · Cell · doi:10.1016/j.cell.2026.06.016 · Cited by 11 · see citing works

Telomere-to-telomere sheep genome assembly identifies variants associated with wool fineness

Luo, L.-Y., Wu, H., Zhao, L.-M., Zhang, Y.-H., Huang, J.-H., Liu, Q.-Y., Wang, H.-T., Mo, D., EEr, H.-H., Zhang, L.-Q., et al. (2025) · Nature Genetics · doi:10.1038/s41588-024-02037-6 · Cited by 39 · see citing works

Single-haplotype comparative genomics provides insights into lineage-specific structural variation during cat evolution

Bredemeyer, K. R., Hillier, L., Harris, A. J., Hughes, G. M., Foley, N. M., Lawless, C., Carroll, R. A., Storer, J. M., Batzer, M. A., Rice, E. S., et al. (2023) · Nature Genetics · doi:10.1038/s41588-023-01548-y · Cited by 37 · see citing works

Protein-altering variants at copy number-variable regions influence diverse human phenotypes

Hujoel, M. L. A., Handsaker, R. E., Sherman, M. A., Kamitaki, N., Barton, A. R., Mukamel, R. E., Terao, C. C., McCarroll, S. A., & Loh, P. (2024) · Nature Genetics · doi:10.1038/s41588-024-01684-z · Cited by 36 · see citing works

The efficient phasing and imputation pipeline of low‐coverage whole genome sequencing data using a high‐quality and publicly available reference panel in cattle

Zhang, Z., Wang, A., Hu, H., Wang, L., Gong, M., Yang, Q., Liu, A., Li, R., Zhang, H., Zhang, Q., et al. (2023) · Animal Research and One Health · doi:10.1002/aro2.8 · Cited by 35 · see citing works

Large-scale neurophysiology and single-cell profiling in human neuroscience

Lee, A. T., Chang, E. F., Paredes, M. F., & Nowakowski, T. J. (2024) · Nature · doi:10.1038/s41586-024-07405-0 · Cited by 33 · see citing works

Direct transposition of native DNA for sensitive multimodal single-molecule sequencing

Nanda, A. S., Wu, K., Irkliyenko, I., Woo, B., Ostrowski, M. S., Clugston, A. S., Sayles, L. C., Xu, L., Satpathy, A. T., Nguyen, H. G., et al. (2024) · Nature Genetics · doi:10.1038/s41588-024-01748-0 · Cited by 35 · see citing works

Leveraging the power of long reads for targeted sequencingPreprint

Iyer, S. V., Goodwin, S., & McCombie, W. R. (2024) · Genome Research · doi:10.1101/gr.279168.124 · Cited by 34 · see citing works

Inversion polymorphism in a complete human genome assembly

Porubskỳ, D., Harvey, W. T., Rozanski, A. N., Ebler, J., Höps, W., Ashraf, H., Hasenfeld, P., Paten, B., Sanders, A. D., Marschall, T., et al. (2023) · Genome biology · doi:10.1186/s13059-023-02919-8 · Cited by 32 · see citing works

The Ruminant Telomere-to-Telomere (RT2T) Consortium

Kalbfleisch, T., McKay, S., Murdoch, B. M., Adelson, D. L., Almansa-Villa, D., Becker, G. M., Beckett, L. M., Benítez-Galeano, M. J., Biase, F. H., Casey, T., et al. (2024) · Nature Genetics · doi:10.1038/s41588-024-01835-2 · Cited by 32 · see citing works

The Dynamic Structure and Rapid Evolution of Human Centromeric Satellite DNA

Logsdon, G. A., & Eichler, E. E. (2022) · Genes · doi:10.3390/genes14010092 · Cited by 27 · see citing works

Genome-wide identification and expression analyses of CYP450 genes in sweet potato (Ipomoea batatas L.)

Lin, X., Tang, B., Li, Z., Shi, L., & Zhu, H. (2024) · BMC Genomics · doi:10.1186/s12864-024-09965-x · Cited by 30 · see citing works

Somatic epimutations cap genetic determinism in the human diploid chromatin epigenomePreprint

Vollger, M. R., Swanson, E. G., Neph, S. J., Mallory, B. J., Dubocanin, D., Ho, C., Cheng, Y. H. H., Ranchalis, J. E., Munson, K. M., Sedeño-Cortés, A. E., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.06.14.599122 · Cited by 30 · see citing works

A survey of current methods to detect and genotype inversions

Hanlon, V. C. T., Lansdorp, P. M., & Guryev, V. (2022) · Human Mutation · doi:10.1002/humu.24458 · Cited by 27 · see citing works

FixItFelix: improving genomic analysis by fixing reference errors

Behera, S., LeFaive, J., Orchard, P., Mahmoud, M., Paulin, L. F., Farek, J., Soto, D. C., Parker, S. C. J., Smith, A. V., Dennis, M. Y., et al. (2023) · Genome Biology · doi:10.1186/s13059-023-02863-7 · Cited by 28 · see citing works

Earth Biogenome Project: present status and future plans

Gupta, P. K. (2022) · Trends in Genetics · doi:10.1016/j.tig.2022.04.008 · Cited by 27 · see citing works

Advances in the discovery and analyses of human tandem repeats

Chaisson, M., Sulovari, A., Valdmanis, P. N., Miller, D. E., & Eichler, E. E. (2023) · Emerging Topics in Life Sciences · doi:10.1042/etls20230074 · Cited by 27 · see citing works

Resolving haplotype variation and complex genetic architecture in the human immunoglobulin kappa chain locus in individuals of diverse ancestry

Engelbrecht, E., Rodriguez, O. L., Shields, K. M., Schultze, S., Tieri, D. A., Jana, U., Yaari, G., Lees, W., Smith, M. L., & Watson, C. T. (2024) · Genes and Immunity · doi:10.1038/s41435-024-00279-2 · Cited by 26 · see citing works

Telomere-to-telomere genome assembly of a male goat reveals variants associated with cashmere traits

Wu, H., Luo, L.-Y., Zhang, Y.-H., Zhang, C.-Y., Huang, J.-H., Mo, D., Zhao, L.-M., Wang, Z.-X., Wang, Y.-C., He-Hua, E., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-54188-z · Cited by 33 · see citing works

A next-generation human genome sequence

Church, D. M. (2022) · Science · doi:10.1126/science.abo5367 · Cited by 25 · see citing works

Human-specific gene expansions contribute to brain evolution

(2025) · doi:10.1016/j.cell.2025.06.037 · Cited by 25 · see citing works

Genomic structural variation: A complex but important driver of human evolution

Soto, D. C., Uribe‐Salazar, J. M., Shew, C. J., Sekar, A., McGinty, S. P., & Dennis, M. Y. (2023) · American Journal of Biological Anthropology · doi:10.1002/ajpa.24713 · Cited by 25 · see citing works

Chromosomal inversion polymorphisms shape human brain morphology

Wang, H., Makowski, C., Zhang, Y., Qi, A., Kaufmann, T., Smeland, O. B., Fiecas, M. J. A., Yang, J., Visscher, P. M., & Chen, C. (2023) · Cell Reports · doi:10.1016/j.celrep.2023.112896 · Cited by 24 · see citing works

A telomere-to-telomere genome assembly of Zhonghuang 13, a widely-grown soybean variety from the original center of Glycine max

Zhang, A., Kong, T., Sun, B., Qiu, S., Guo, J., Ruan, S., Guo, Y., Guo, J., Zhang, Z., Liu, Y., et al. (2023) · The Crop Journal · doi:10.1016/j.cj.2023.10.003 · Cited by 25 · see citing works

Long-read sequencing: An effective method for genetic analysis of CYP21A2 variation in congenital adrenal hyperplasia

Li, H., Zhu, X., Yang, Y., Wang, W., Mao, A., Li, J., Bao, S., & Li, J. (2023) · Clinica Chimica Acta · doi:10.1016/j.cca.2023.117419 · Cited by 23 · see citing works

The NCBI Comparative Genome Viewer (CGV) is an interactive visualization tool for the analysis of whole-genome eukaryotic alignments

Rangwala, S. H., Rudnev, D., Ananiev, V., Oh, D., Asztalos, A., Benica, B., Borodin, E. A., Bouk, N., Evgeniev, V. I., Kodali, V. K., et al. (2024) · PLoS Biology · doi:10.1371/journal.pbio.3002405 · Cited by 23 · see citing works

Investigating the Performance of Oxford Nanopore Long-Read Sequencing with Respect to Illumina Microarrays and Short-Read Sequencing

Santos, R., Lee, H. A., Williams, A., Baffour-Kyei, A., Lee, S. H., Troakes, C., Al‐Chalabi, A., Breen, G. D., & Iacoangeli, A. (2025) · International Journal of Molecular Sciences · doi:10.3390/ijms26104492 · Cited by 22 · see citing works

Characterization of large-scale genomic differences in the first complete human genome

Yang, X., Wang, X., Zou, Y., Zhang, S., Xia, M., Fu, L., Vollger, M. R., Chen, N.-C., Taylor, D. J., Harvey, W. T., et al. (2023) · Genome biology · doi:10.1186/s13059-023-02995-w · Cited by 22 · see citing works

A near‐complete assembly of asparagus bean provides insights into anthocyanin accumulation in pods

Yang, Y., Wu, Z., Wu, Z., Li, T., Shen, Z., Zhou, X., Wu, X., Li, G., & Zhang, Y. (2023) · Plant Biotechnology Journal · doi:10.1111/pbi.14142 · Cited by 22 · see citing works

Envisioning a new era: Complete genetic information from routine, telomere-to-telomere genomes

Miga, K. H., & Eichler, E. E. (2023) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2023.09.011 · Cited by 23 · see citing works

Bioinformatics of germline variant discovery for rare disease diagnostics: current approaches and remaining challenges

Barbitoff, Y. A., Ushakov, M. O., Lazareva, T. E., Nasykhova, Y. A., Glotov, A. S., & Predeus, A. V. (2023) · Briefings in Bioinformatics · doi:10.1093/bib/bbad508 · Cited by 26 · see citing works

Identification of allele-specific KIV-2 repeats and impact on Lp(a) measurements for cardiovascular disease risk

Behera, S., Belyeu, J. R., Chen, X., Paulin, L. F., Nguyen, N. Q., Newman, E., Mahmoud, M., Menon, V. K., Qi, Q., Joshi, P. H., et al. (2024) · BMC Medical Genomics · doi:10.1186/s12920-024-02024-0 · Cited by 19 · see citing works

When synthetic biology meets medicine

Feng, Y., Su, C., Mao, G., Sun, B., Cai, Y., Dai, J., & Ma, Y. (2024) · Life Medicine · doi:10.1093/lifemedi/lnae010 · Cited by 21 · see citing works

UniAligner: a parameter-free framework for fast sequence alignment

Bzikadze, A. V., & Pevzner, P. A. (2023) · Nature Methods · doi:10.1038/s41592-023-01970-4 · Cited by 19 · see citing works

Genome-wide profiling of highly similar paralogous genes using HiFi sequencing

Chen, X., Baker, D., Dolzhenko, E., Devaney, J. M., Noya, J., Berlyoung, A. S., Brandon, R. C., Hruska, K. S., Lochovsky, L., Kruszka, P. S., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-57505-2 · Cited by 18 · see citing works

Tracing the evolution of sequencing into the era of genomic medicine

Mardis, E. R., & Wilson, R. K. (2025) · Nature Reviews Genetics · doi:10.1038/s41576-025-00884-5 · Cited by 18 · see citing works

From the reference human genome to human pangenome: Premise, promise and challenge

Singh, V. K., Pandey, S., & Bhardwaj, A. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2022.1042550 · Cited by 19 · see citing works

Long-read sequencing and genome assembly of natural history collection samples and challenging specimens

Bein, B., Chrysostomakis, I., Arantes, L. S., Brown, T., Gerheim, C., Schell, T., Schneider, C., Leushkin, E. V., Chen, Z., Sigwart, J. D., et al. (2025) · Genome biology · doi:10.1186/s13059-025-03487-9 · Cited by 18 · see citing works

The complete diploid reference genome of RPE-1 identifies human phased epigenetic landscapesPreprint

Volpe, E., Corda, L., Tommaso, E. D., Pelliccia, F., Ottalevi, R., Licastro, D., Guarracino, A., Capulli, M., Formenti, G., Tassone, E., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.11.01.565049 · Cited by 18 · see citing works

Independent expansion, selection, and hypervariability of the <i>TBC1D3</i> gene family in humans

Guitart, X., Porubsky, D., Yoo, D., Dougherty, M. L., Dishuck, P. C., Munson, K. M., Lewis, A. P., Hoekzema, K., Knuth, J., Chang, S., et al. (2024) · Genome Research · doi:10.1101/gr.279299.124 · Cited by 14 · see citing works

The pleiotropic spectrum of proximal 16p11.2 CNVs

Auwerx, C., Kutalik, Z., & Reymond, A. (2024) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2024.08.015 · Cited by 18 · see citing works

How repeats rearrange chromosomes: The molecular basis of chromosomal inversions in deer mice

Gozashti, L., Harringmeyer, O. S., & Hoekstra, H. E. (2025) · Cell Reports · doi:10.1016/j.celrep.2025.115644 · Cited by 16 · see citing works

AlcoR: alignment-free simulation, mapping, and visualization of low-complexity regions in biological data

Silva, J. M., Qi, W., Pinho, A. J., & Pratas, D. (2022) · GigaScience · doi:10.1093/gigascience/giad101 · Cited by 13 · see citing works

Nanopore sequencing with unique molecular identifiers enables accurate mutation analysis and haplotyping in the complex lipoprotein(a) KIV-2 VNTR

Amstler, S., Streiter, G., Pfurtscheller, C., Forer, L., Maio, S. D., Weißensteiner, H., Paulweber, B., Schönherr, S., Kronenberg, F., & Coassin, S. (2024) · Genome Medicine · doi:10.1186/s13073-024-01391-8 · Cited by 12 · see citing works

Identification of allele-specific KIV-2 repeats and impact on Lp(a) measurements for cardiovascular disease risk

Behera, S., Belyeu, J. R., Chen, X., Paulin, L. F., Nguyen, N. Q. H., Newman, E., Mahmoud, M., Menon, V. K., Qi, Q., Joshi, P., et al. (2023) · doi:10.1101/2023.04.24.538128 · Cited by 21 · see citing works

Long-read sequencing identifies copy-specific markers of SMN gene conversion in spinal muscular atrophy

Zwartkruis, M. M., Elferink, M., Gommers, D., Signoria, I., Blasco-Pérez, L., Costa‐Roger, M., van der Sel, J., Renkens, I., Green, J. W., Kortooms, J. V., et al. (2025) · Genome Medicine · doi:10.1186/s13073-025-01448-2 · Cited by 14 · see citing works

Template switching between the leading and lagging strands at replication forks generates inverted copy number variants through hairpin-capped extrachromosomal DNA

Martin, R., Espinoza, C. Y., Large, C. R. L., Rosswork, J., Bruinisse, C. V., Miller, A. W., Sanchez, J. C., Miller, M., Paskvan, S., Alvino, G. M., et al. (2024) · PLoS Genetics · doi:10.1371/journal.pgen.1010850 · Cited by 15 · see citing works

Deciphering the role of structural variation in human evolution: a functional perspective

Karageorgiou, C., Gökçümen, Ö., & Dennis, M. Y. (2024) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2024.102240 · Cited by 14 · see citing works

Highly accurate Korean draft genomes reveal structural variation highlighting human telomere evolution

Kim, J., Park, J., Yang, J. O., Kim, S., Joe, S., Park, G., Hwang, T., Cho, M.-J., Lee, S. J., Lee, J.-E., et al. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkae1294 · Cited by 14 · see citing works

Structural polymorphism and diversity of human segmental duplications

Jeong, H., Dishuck, P. C., Yoo, D., Harvey, W. T., Munson, K. M., Lewis, A. P., Kordosky, J., Garcia, G. H., Yilmaz, F., Hallast, P., et al. (2025) · Nature Genetics · doi:10.1038/s41588-024-02051-8 · Cited by 42 · see citing works

The evolution and population diversity of human-specific segmental duplications

Dennis, M. Y., Harshman, L., Nelson, B. J., Penn, O., Cantsilieris, S., Huddleston, J., Antonacci, F., Penewit, K., Denman, L., Raja, A., et al. (2017) · Nature Ecology &amp; Evolution · doi:10.1038/s41559-016-0069 · Cited by 159 · see citing works

Segmental Duplications in the Human Genome

Lacroix, M.-H., Oparina, N. Y., & Mashkova, T. D. (2003) · Molecular Biology · doi:10.1023/a:1023333302552 · Cited by 4 · see citing works

Segmental Duplications: A Source of Diversity, Evolution and Disease

Catacchio, C. R., Chiatante, G., Anaclerio, F., & Ventura, M. (2015) · Encyclopedia of Life Sciences · doi:10.1002/9780470015902.a0020838.pub2

A genome-wide survey of segmental duplications that mediate common human genetic variation of chromosomal architecture

Mehan, M. R., Freimer, N. B., & Ophoff, R. A. (2004) · Human Genomics · doi:10.1186/1479-7364-1-5-335 · Cited by 121 · see citing works