Characterizing the Major Structural Variant Alleles of the Human Genome

The Sequence Alignment/Map format and SAMtools

Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041 · see citing works

Fast and accurate short read alignment with Burrows-Wheeler transform

Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607 · see citing works

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M., et al. (2010) · Genome Research · doi:10.1101/gr.107524.110 · Cited by 27,895 · 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

A global reference for human genetic variation

The 1000 Genomes Project Consortium, authors, C., Auton, A., Abecasis, G. R., Steering committee, Altshuler, D. M., Durbin, R. M., Abecasis, G. R., Bentley, D. R., Chakravarti, A., et al. (2015) · Nature · doi:10.1038/nature15393 · Cited by 18,247 · see citing works

Analysis of protein-coding genetic variation in 60,706 humans

Exome Aggregation Consortium, Lek, M., Karczewski, K. J., Minikel, E. V., Samocha, K. E., Banks, E., Fennell, T., O’Donnell-Luria, A. H., Ware, J. S., Hill, A. J., et al. (2016) · Nature · doi:10.1038/nature19057 · Cited by 9,587 · 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

An integrated map of genetic variation from 1,092 human genomes

The 1000 Genomes Project Consortium (2012) · Nature · doi:10.1038/nature11632 · Cited by 7,711 · see citing works

dbSNP: the NCBI database of genetic variation

Sherry, S. T. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.1.308 · Cited by 7,502 · see citing works

Canu: scalable and accurate long-read assembly via adaptive k -mer weighting and repeat separationPreprint

Koren, S., Walenz, B. P., Berlin, K., Miller, J. R., Bergman, N. H., & Phillippy, A. M. (2017) · Genome Research · doi:10.1101/gr.215087.116 · Cited by 7,340 · see citing works

Finishing the euchromatic sequence of the human genome

International Human Genome Sequencing Consortium (2004) · Nature · doi:10.1038/nature03001 · Cited by 4,971 · see citing works

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

Chin, C., Alexander, D., Marks, P., Klammer, A., Drake, J., Heiner, C., Clum, A., Copeland, A., Huddleston, J., Eichler, E., et al. (2013) · Nature Methods · doi:10.1038/nmeth.2474 · Cited by 4,008 · see citing works

Detection of large-scale variation in the human genome

Iafrate, A. J., Feuk, L., Rivera, M. N., Listewnik, M. L., Donahoe, P. K., Qi, Y., Scherer, S. W., & Lee, C. (2004) · Nature Genetics · doi:10.1038/ng1416 · Cited by 2,892 · see citing works

Large-scale copy number polymorphism in the human genome

Sebat, J., Lakshmi, B., Troge, J., Alexander, J., Young, J., Lundin, P., Månér, S., Massa, H., Walker, M., Chi, M., et al. (2004) · Science · doi:10.1126/science.1098918 · Cited by 2,557 · see citing works

Initial sequence of the chimpanzee genome and comparison with the human genome

The Chimpanzee Sequencing and Analysis Consortium (2005) · Nature · doi:10.1038/nature04072 · Cited by 2,459 · see citing works

An integrated map of structural variation in 2,504 human genomes

Sudmant, P. H., Rausch, T., Gardner, E. J., Handsaker, R. E., Abyzov, A., Huddleston, J., Zhang, Y., Ye, K., Jun, G., Hsi-Yang Fritz, M., et al. (2015) · Nature · doi:10.1038/nature15394 · Cited by 2,354 · see citing works

Transcriptome and genome sequencing uncovers functional variation in humans

The Geuvadis Consortium, Lappalainen, T., Sammeth, M., Friedländer, M. R., ‘t Hoen, P. A. C., Monlong, J., Rivas, M. A., Gonzàlez-Porta, M., Kurbatova, N., Griebel, T., et al. (2013) · Nature · doi:10.1038/nature12531 · Cited by 1,888 · 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

Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly

Schneider, V. A., Graves-Lindsay, T., Howe, K., Bouk, N., Chen, H.-C., Kitts, P. A., Murphy, T. D., Pruitt, K. D., Thibaud-Nissen, F., Albracht, D., et al. (2017) · Genome Research · doi:10.1101/gr.213611.116 · Cited by 1,193 · see citing works

Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory

Chaisson, M., & Tesler, G. (2012) · BMC Bioinformatics · doi:10.1186/1471-2105-13-238 · Cited by 1,183 · see citing works

Mapping copy number variation by population-scale genome sequencing

1000 Genomes Project, Mills, R. E., Walter, K., Stewart, C., Handsaker, R. E., Chen, K., Alkan, C., Abyzov, A., Yoon, S. C., Ye, K., et al. (2011) · Nature · doi:10.1038/nature09708 · Cited by 1,140 · 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

Fine-scale structural variation of the human genome

Tüzün, E., Sharp, A. J., Bailey, J. A., Kaul, R., Morrison, V., Pertz, L. M., Haugen, E., Hayden, H. S., Albertson, D. G., Pinkel, D., et al. (2005) · Nature Genetics · doi:10.1038/ng1562 · Cited by 991 · see citing works

Assembling large genomes with single-molecule sequencing and locality-sensitive hashing

Berlin, K., Koren, S., Chin, C.-S., Drake, J. P., Landolin, J. M., & Phillippy, A. M. (2015) · Nature Biotechnology · doi:10.1038/nbt.3238 · Cited by 928 · 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

Variation graph toolkit improves read mapping by representing genetic variation in the reference

Garrison, E., Sirén, J., Novak, A. M., Hickey, G., Eizenga, J. M., Dawson, E. T., Jones, W., Garg, S., Markello, C., Lin, M. F., et al. (2018) · Nature Biotechnology · doi:10.1038/nbt.4227 · Cited by 821 · see citing works

L1 retrotransposition in human neural progenitor cells

Coufal, N. G., Garcia-Perez, J. L., Peng, G. E., Yeo, G. W., Mu, Y., Lovci, M. T., Morell, M., O’Shea, K. S., Moran, J. V., & Gage, F. H. (2009) · Nature · doi:10.1038/nature08248 · Cited by 814 · see citing works

Diseases of Unstable Repeat Expansion: Mechanisms and Common Principles

Gatchel, J. R., & Zoghbi, H. Y. (2005) · Nature Reviews Genetics · doi:10.1038/nrg1691 · Cited by 784 · 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

Annotation-free quantification of RNA splicing using LeafCutter

Li, Y. I., Knowles, D. A., Humphrey, J., Barbeira, A. N., Dickinson, S. P., Im, H. K., & Pritchard, J. K. (2018) · Nature Genetics · doi:10.1038/s41588-017-0004-9 · Cited by 765 · see citing works

De novo assembly and genotyping of variants using colored de Bruijn graphs

Iqbal, Z., Cáccamo, M., Turner, I., Flicek, P., & McVean, G. (2012) · Nature Genetics · doi:10.1038/ng.1028 · Cited by 695 · see citing works

RNA splicing is a primary link between genetic variation and disease

Li, Y. I., van de Geijn, B., Raj, A., Knowles, D. A., Petti, A. A., Golan, D., Gilad, Y., & Pritchard, J. K. (2016) · Science · doi:10.1126/science.aad9417 · Cited by 660 · see citing works

Whole-genome sequence variation, population structure and demographic history of the Dutch population

Francioli, L. C., Menelaou, A., Pulit, S. L., Elbers, C. C., Kloosterman, W. P., van Setten, J., Nijman, I. J., Renkens, I., de Bakker, P. I. W., van Dijk, F., et al. (2014) · Nature Genetics · doi:10.1038/ng.3021 · Cited by 642 · see citing works

LINE-1 Retrotransposition Activity in Human Genomes

Beck, C. R., Collier, P., Macfarlane, C., Malig, M., Kidd, J. M., Eichler, E. E., Badge, R. M., & Moran, J. V. (2010) · Cell · doi:10.1016/j.cell.2010.05.021 · Cited by 632 · see citing works

Fine-scale recombination rate differences between sexes, populations and individuals

Kong, A., Þorleifsson, G., Gudbjartsson, D. F., Másson, G., Sigurðsson, Á., Jónasdóttir, Á., Walters, G. B., Jónasdóttir, A., Gylfason, A., Kristinsson, K. T., et al. (2010) · Nature · doi:10.1038/nature09525 · Cited by 582 · see citing works

Fast and efficient QTL mapper for thousands of molecular phenotypes

Ongen, H., Buil, A., Brown, A. A., Dermitzakis, E. T., & Delaneau, O. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv722 · Cited by 571 · see citing works

Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data.

Degner, J. F., Marioni, J. C., Pai, A. A., Pickrell, J. K., Nkadori, E., Gilad, Y., & Pritchard, J. K. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp579 · Cited by 502 · see citing works

Assembly and diploid architecture of an individual human genome via single-molecule technologies

Pendleton, M., Sebra, R., Pang, A. W. C., Ummat, A., Franzén, O., Rausch, T., Stütz, A. M., Stedman, W., Anantharaman, T., Hastie, A. R., et al. (2015) · Nature Methods · doi:10.1038/nmeth.3454 · Cited by 474 · see citing works

Human subtelomeres are hot spots of interchromosomal recombination and segmental duplication

Linardopoulou, E. V., Williams, E. M., Fan, Y., Friedman, C. L., Young, J. M., & Trask, B. J. (2005) · Nature · doi:10.1038/nature04029 · Cited by 448 · see citing works

Genome-wide patterns and properties of de novo mutations in humans

Francioli, L. C., Polak, P. P., Koren, A., Menelaou, A., Chun, S., Renkens, I., van Duijn, C. M., Swertz, M. A., Wijmenga, C., van Ommen, G. B., et al. (2015) · Nature Genetics · doi:10.1038/ng.3292 · Cited by 381 · see citing works

Discovery and genotyping of structural variation from long-read haploid genome sequence dataPreprint

Huddleston, J., Chaisson, M., Steinberg, K. M., Warren, W., Hoekzema, K., Gordon, D., Graves-Lindsay, T. A., Munson, K. M., Kronenberg, Z. N., Vives, L., et al. (2016) · Genome Research · doi:10.1101/gr.214007.116 · Cited by 376 · see citing works

Genome graphs and the evolution of genome inference

Paten, B., Novak, A. M., Eizenga, J. M., & Garrison, E. (2017) · Genome Research · doi:10.1101/gr.214155.116 · Cited by 351 · 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

Genetic variation and the de novo assembly of human genomes

Chaisson, M., Wilson, R. K., & Eichler, E. E. (2015) · Nature Reviews Genetics · doi:10.1038/nrg3933 · Cited by 337 · see citing works

Long-read sequence assembly of the gorilla genome

Gordon, D., Huddleston, J., Chaisson, M. J. P., Hill, C. M., Kronenberg, Z. N., Munson, K. M., Malig, M., Raja, A., Fiddes, I., Hillier, L. W., et al. (2016) · Science · doi:10.1126/science.aae0344 · Cited by 333 · see citing works

Genomic Patterns of De Novo Mutation in Simplex Autism

Turner, T. N., Coe, B. P., Dickel, D. E., Hoekzema, K., Nelson, B. J., Zody, M. C., Kronenberg, Z. N., Hormozdiari, F., Raja, A. N., Pennacchio, L. A., et al. (2017) · Cell · doi:10.1016/j.cell.2017.08.047 · Cited by 330 · see citing works

De novo assembly and phasing of a Korean human genome

Seo, J.-S., Rhie, A., Kim, J., Lee, S.-J., Sohn, M.-H., Kim, C.-U., Hastie, A., Cao, H., Yun, J.-Y., Kim, J., et al. (2016) · Nature · doi:10.1038/nature20098 · Cited by 312 · see citing works

dbVar and DGVa: public archives for genomic structural variation

Lappalainen, I., Lopez, J. R., Skipper, L. M., Hefferon, T. W., Spalding, D., Garner, J., Chen, C., Maguire, M., Corbett, M., Zhou, G., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1213 · Cited by 310 · see citing works

A Human Genome Structural Variation Sequencing Resource Reveals Insights into Mutational Mechanisms

Kidd, J. M., Graves, T., Newman, T. L., Fulton, R. S., Hayden, H. S., Malig, M., Kallicki, J., Kaul, R., Wilson, R. K., & Eichler, E. E. (2010) · Cell · doi:10.1016/j.cell.2010.10.027 · Cited by 304 · see citing works

Recombination initiation maps of individual human genomes

Pratto, F., Brick, K., Khil, P., Smagulova, F., Petukhova, G. V., & Camerini-Otero, R. D. (2014) · Science · doi:10.1126/science.1256442 · Cited by 295 · see citing works

Covariation of Synaptonemal Complex Length and Mammalian Meiotic Exchange Rates

Lynn, A., Koehler, K. E., Judis, L. M., Chan, E. R., Cherry, J. P., Schwartz, S., Seftel, A. D., Hunt, P. A., & Hassold, T. J. (2002) · Science · doi:10.1126/science.1071220 · Cited by 288 · see citing works

Long-read sequencing and de novo assembly of a Chinese genome

Shi, L., Guo, Y., Dong, C., Huddleston, J., Yang, H., Han, X., Fu, A., Li, Q., Li, N., Gong, S., et al. (2016) · Nature Communications · doi:10.1038/ncomms12065 · Cited by 257 · see citing works

Complete Haplotype Sequence of the Human Immunoglobulin Heavy-Chain Variable, Diversity, and Joining Genes and Characterization of Allelic and Copy-Number Variation

Watson, C. T., Steinberg, K. M., Huddleston, J., Warren, R. M., Malig, M., Schein, J. E., Willsey, A. J., Joy, J. B., Scott, J. K., Graves, T., et al. (2013) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2013.03.004 · Cited by 225 · see citing works

Long-read sequence and assembly of segmental duplications

Vollger, M. R., Dishuck, P. C., Sorensen, M., Welch, A. E., Dang, V., Dougherty, M. L., Graves-Lindsay, T. A., Wilson, R. K., Chaisson, M., & Eichler, E. E. (2018) · Nature Methods · doi:10.1038/s41592-018-0236-3 · Cited by 204 · see citing works

An assessment of the sequence gaps: Unfinished business in a finished human genome

Eichler, E. E., Clark, R. A., & She, X. (2004) · Nature Reviews Genetics · doi:10.1038/nrg1322 · Cited by 184 · see citing works

Mapping Bias Overestimates Reference Allele Frequencies at the HLA Genes in the 1000 Genomes Project Phase I Data

Brandt, D. Y. C., Aguiar, V. R. C., Bitarello, B. D., Nunes, K., Goudet, J., & Meyer, D. (2015) · G3 Genes Genomes Genetics · doi:10.1534/g3.114.015784 · Cited by 177 · see citing works

Adenosine-to-inosine RNA editing shapes transcriptome diversity in primates

Paz-Yaacov, N., Levanon, E. Y., Nevo, E., Kinar, Y., Harmelin, A., Jacob‐Hirsch, J., Amariglio, N., Eisenberg, E., & Rechavi, G. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1006183107 · Cited by 169 · see citing works

Large-Scale Variation Among Human and Great Ape Genomes Determined by Array Comparative Genomic HybridizationPreprint

Locke, D. P., Segraves, R., Carbone, L., Archidiacono, N., Albertson, D. G., Pinkel, D., & Eichler, E. E. (2003) · Genome Research · doi:10.1101/gr.1003303 · Cited by 161 · see citing works

Poxviruses as possible vectors for horizontal transfer of retroposons from reptiles to mammals

Piskurek, O., & Okada, N. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0700531104 · Cited by 149 · see citing works

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

Chaisson, M., Sanders, A. D., Zhao, X., Malhotra, A., Porubskỳ, D., Rausch, T., Gardner, E. J., Rodriguez, O. L., Guo, L., Collins, R. L., et al. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/193144 · Cited by 145 · 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

FoxO6 regulates memory consolidation and synaptic functionPreprint

Salih, D. A. M., Rashid, A. J., Colas, D., de la Torre-Ubieta, L., Zhu, R. P., Morgan, A. A., Santo, E. E., Ucar, D., Devarajan, K., Cole, C. J., et al. (2012) · Genes & Development · doi:10.1101/gad.208926.112 · Cited by 136 · see citing works

Single haplotype assembly of the human genome from a hydatidiform molePreprint

Steinberg, K. M., Schneider, V., Graves-Lindsay, T. A., Fulton, R. S., Agarwala, R., Huddleston, J., Shiryev, S. A., Morgulis, A. O., Surti, U., Warren, W. C., et al. (2014) · Genome Research · doi:10.1101/gr.180893.114 · Cited by 130 · see citing works

A unique chromatin complex occupies young α-satellite arrays of human centromeres

Henikoff, J. G., Thakur, J., Kasinathan, S., & Henikoff, S. (2015) · Science Advances · doi:10.1126/sciadv.1400234 · Cited by 91 · see citing works

Building a Pan-Genome Reference for a Population

Nguyen, N. K., Hickey, G., Zerbino, D. R., Raney, B. J., Earl, D. A., Armstrong, J. C., Kent, W. J., Haussler, D. H., & Paten, B. (2015) · Journal of Computational Biology · doi:10.1089/cmb.2014.0146 · Cited by 54 · see citing works

Paternal Origins of Complete Hydatidiform Moles Proven by Whole Genome Single-Nucleotide Polymorphism Haplotyping

Fan, J., Surti, U., Taillon‐Miller, P., Hsie, L., Kennedy, G. C., Hoffner, L., Ryder, T. B., Mutch, D. G., & Kwok, P. (2002) · Genomics · doi:10.1006/geno.2001.6676 · Cited by 45 · see citing works

Genome GraphsPreprint

Novak, A. M., Hickey, G., Garrison, E. P., Blum, S., Connelly, A., Dilthey, A., Eizenga, J. M., Elmohamed, M. A. S., Guthrie, S., Kahles, A., et al. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/101378 · Cited by 34 · see citing works

Identification of Multiple Forms of 180-kDa Ribosome Receptor in Human Cells

Langley, R. J., Leung, E. Y., Morris, C. M., Berg, R., McDonald, M., Weaver, A., Parry, D. A. D., Ni, J., Su, J. Y., Gentz, R., et al. (1998) · DNA and Cell Biology · doi:10.1089/dna.1998.17.449 · Cited by 25 · see citing works

Corrigendum: Discovery and genotyping of structural variation from long-read haploid genome sequence dataPreprint

Huddleston, J., Chaisson, M., Steinberg, K. M., Warren, W., Hoekzema, K., Gordon, D., Graves-Lindsay, T. A., Munson, K. M., Kronenberg, Z. N., Vives, L., et al. (2018) · Genome Research · doi:10.1101/gr.233007.117 · Cited by 10 · see citing works

Building a Pangenome Reference for a Population

Nguyen, N. K., Hickey, G., Zerbino, D. R., Raney, B. J., Earl, D. A., Armstrong, J. C., Haussler, D. H., & Paten, B. (2014) · Lecture notes in computer science · doi:10.1007/978-3-319-05269-4_17 · Cited by 9 · see citing works

Complete Genome Sequence of the BeAn 58058 Virus Isolated from Oryzomys sp. Rodents in the Amazon Region of Brazil

Wanzeller, A. L. M., Souza, A. L. P., Azevedo, R. D. S. D. S., Júnior, E. C. S., Filho, L. C. F., de Oliveira, R. C., Lemos, P. S., Júnior, J. V. J. S., & Vasconcelos, P. F. D. C. (2017) · Genome Announcements · doi:10.1128/genomea.01575-16 · Cited by 8 · see citing works

Opportunities and challenges in long-read sequencing data analysis

Amarasinghe, S. L., Su, S., Dong, X., Zappia, L., Ritchie, M. E., & Gouil, Q. (2020) · Genome Biology · doi:10.1186/s13059-020-1935-5 · Cited by 2,530 · see citing works

Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program

Taliun, D., Harris, D. N., Kessler, M. D., Carlson, J., Szpiech, Z. A., Torres, R., Taliun, S. A. G., Corvelo, A., Gogarten, S. M., Kang, H. M., et al. (2021) · Nature · doi:10.1038/s41586-021-03205-y · Cited by 2,213 · see citing works

Long-read human genome sequencing and its applications

Logsdon, G. A., Vollger, M. R., & Eichler, E. E. (2020) · Nature Reviews Genetics · doi:10.1038/s41576-020-0236-x · Cited by 1,222 · see citing works

A draft human pangenome reference.

Liao, W.-W., Asri, M., Ebler, J., Doerr, D., Haukness, M., Hickey, G., Lu, S., Lucas, J. K., Monlong, J., Abel, H. J., et al. (2023) · Nature · doi:10.1038/s41586-023-05896-x · Cited by 1,129 · see citing works

SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies

Goel, M., Sun, H., Jiao, W., & Schneeberger, K. (2019) · Genome biology · doi:10.1186/s13059-019-1911-0 · Cited by 1,058 · see citing works

A structural variation reference for medical and population genetics

Collins, R. L., Brand, H., Karczewski, K. J., Zhao, X., Alföldi, J., Francioli, L. C., Khera, A. V., Lowther, C., Gauthier, L. D., Wang, H., et al. (2020) · Nature · doi:10.1038/s41586-020-2287-8 · Cited by 1,037 · see citing works

Pan-Genome of Wild and Cultivated Soybeans

Liu, Y., Du, H., Li, P., Shen, Y., Peng, H., Liu, S., Zhou, G., Zhang, H., Liu, Z., Shi, M., et al. (2020) · Cell · doi:10.1016/j.cell.2020.05.023 · Cited by 983 · see citing works

Structural variant calling: the long and the short of it

Mahmoud, M., Gobet, N., Cruz-Dávalos, D. I., Mounier, N., Dessimoz, C., & Sedlazeck, F. J. (2019) · Genome Biology · doi:10.1186/s13059-019-1828-7 · Cited by 725 · see citing works

Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato

Alonge, M., Wang, X., Benoit, M., Soyk, S., Pereira, L., Zhang, L., Suresh, H., Ramakrishnan, S., Maumus, F., Ciren, D., et al. (2020) · Cell · doi:10.1016/j.cell.2020.05.021 · Cited by 810 · 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

Structural variation in the sequencing era

Ho, S. S., Urban, A. E., & Mills, R. E. (2019) · Nature Reviews Genetics · doi:10.1038/s41576-019-0180-9 · Cited by 608 · see citing works

Pan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations

Qin, P., Lu, H., Du, H., Wang, H., Chen, W., Chen, Z., He, Q., Ou, S., Zhang, H., Li, X., et al. (2021) · Cell · doi:10.1016/j.cell.2021.04.046 · Cited by 578 · see citing works

Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes

Shafin, K., Pesout, T., Lorig-Roach, R., Haukness, M., Olsen, H. E., Bosworth, C., Armstrong, J., Tigyi, K., Maurer, N., Koren, S., et al. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0503-6 · Cited by 567 · 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

Targeted nanopore sequencing with Cas9-guided adapter ligation

Gilpatrick, T., Lee, I., Graham, J. E., Raimondeau, E., Bowen, R., Heron, A., Downs, B. M., Sukumar, S. V., Sedlazeck, F. J., & Timp, W. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0407-5 · Cited by 432 · 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

Pangenomics enables genotyping of known structural variants in 5202 diverse genomes

Sirén, J., Monlong, J., Chang, X., Novak, A. M., Eizenga, J. M., Markello, C., Sibbesen, J. A., Hickey, G., Chang, P.-C., Carroll, A., et al. (2021) · Science · doi:10.1126/science.abg8871 · Cited by 400 · see citing works

A robust benchmark for detection of germline large deletions and insertions

Zook, J. M., Hansen, N. F., Olson, N. D., Chapman, L., Mullikin, J. C., Xiao, C., Sherry, S., Koren, S., Phillippy, A. M., Boutros, P. C., et al. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0538-8 · Cited by 418 · see citing works

Best practices for variant calling in clinical sequencing

Koboldt, D. C. (2020) · Genome Medicine · doi:10.1186/s13073-020-00791-w · Cited by 387 · see citing works

Pangenome Graphs

Eizenga, J. M., Novak, A. M., Sibbesen, J. A., Heumos, S., Ghaffaari, A., Hickey, G., Chang, X., Seaman, J. D., Rounthwaite, R., Ebler, J., et al. (2020) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-120219-080406 · Cited by 320 · see citing works

Towards population-scale long-read sequencing

De Coster, W., Weissensteiner, M. H., & Sedlazeck, F. J. (2021) · Nature Reviews Genetics · doi:10.1038/s41576-021-00367-3 · Cited by 323 · see citing works

Pan-genomics in the human genome era

Sherman, R. M., & Salzberg, S. L. (2020) · Nature Reviews Genetics · doi:10.1038/s41576-020-0210-7 · Cited by 364 · see citing works

A roadmap for understanding the evolutionary significance of structural genomic variation

Mérot, C., Oomen, R. A., Tigano, A., & Wellenreuther, M. (2020) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2020.03.002 · Cited by 357 · see citing works

The population genetics of structural variants in grapevine domestication

Zhou, Y., Minio, A., Massonnet, M., Solares, E., Lv, Y., Beridze, T., Cantu, D., & Gaut, B. S. (2019) · Nature Plants · doi:10.1038/s41477-019-0507-8 · Cited by 339 · see citing works

Genotyping structural variants in pangenome graphs using the vg toolkit

Hickey, G., Heller, D., Monlong, J., Sibbesen, J. A., Sirén, J., Eizenga, J., Dawson, E. T., Garrison, E., Novak, A. M., & Paten, B. (2020) · Genome Biology · doi:10.1186/s13059-020-1941-7 · Cited by 319 · see citing works

Genomic Analysis in the Age of Human Genome Sequencing

Lappalainen, T., Scott, A. J., Brandt, M. K., & Hall, I. M. (2019) · Cell · doi:10.1016/j.cell.2019.02.032 · Cited by 298 · see citing works

Long-read sequencing of 3,622 Icelanders provides insight into the role of structural variants in human diseases and other traits

Beyter, D., Ingimundardóttir, H., Oddsson, Á., Eggertsson, H. P., Björnsson, E., Jónsson, H., Atlason, B. A., Kristmundsdóttir, S., Mehringer, S., Hardarson, M. T., et al. (2021) · Nature Genetics · doi:10.1038/s41588-021-00865-4 · Cited by 265 · see citing works

Long-read mapping to repetitive reference sequences using Winnowmap2

Jain, C., Rhie, A., Hansen, N. F., Koren, S., & Phillippy, A. M. (2022) · Nature Methods · doi:10.1038/s41592-022-01457-8 · Cited by 266 · see citing works

Genomic frontiers in congenital heart disease

Morton, S. U., Quiat, D., Seidman, J. G., & Seidman, C. E. (2021) · Nature Reviews Cardiology · doi:10.1038/s41569-021-00587-4 · Cited by 239 · see citing works

Pathogenic Mechanisms of Somatic Mutation and Genome Mosaicism in Aging

Vijg, J., & Dong, X. (2020) · Cell · doi:10.1016/j.cell.2020.06.024 · Cited by 230 · see citing works

Truvari: refined structural variant comparison preserves allelic diversity

English, A. C., Menon, V. K., Gibbs, R. A., Metcalf, G. A., & Sedlazeck, F. J. (2022) · Genome Biology · doi:10.1186/s13059-022-02840-6 · Cited by 236 · see citing works

Retention of duplicated genes in evolution

Kuzmin, E., Taylor, J. S., & Boone, C. M. (2021) · Trends in Genetics · doi:10.1016/j.tig.2021.06.016 · Cited by 227 · see citing works

Third-Generation Sequencing: The Spearhead towards the Radical Transformation of Modern Genomics

Athanasopoulou, K., Boti, M. A., Adamopoulos, P. G., Skourou, P. C., & Scorilas, A. (2021) · Life · doi:10.3390/life12010030 · Cited by 234 · see citing works

Targeted long-read sequencing identifies missing disease-causing variation

Miller, D. E., Sulovari, A., Wang, T., Loucks, H., Hoekzema, K., Munson, K. M., Lewis, A. P., Fuerte, E. P. A., Paschal, C. R., Walsh, T., et al. (2021) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2021.06.006 · Cited by 226 · see citing works

Paragraph: a graph-based structural variant genotyper for short-read sequence data

Chen, S., Krusche, P., Dolzhenko, E., Sherman, R. M., Petrovski, R., Schlesinger, F., Kirsche, M., Bentley, D. R., Schatz, M. C., Sedlazeck, F. J., et al. (2019) · Genome Biology · doi:10.1186/s13059-019-1909-7 · Cited by 196 · see citing works

Is it time to change the reference genome?

Ballouz, S., Dobin, A., & Gillis, J. (2019) · Genome Biology · doi:10.1186/s13059-019-1774-4 · Cited by 175 · see citing works

Accurate long-read de novo assembly evaluation with Inspector

Chen, Y., Zhang, Y., Wang, A. Y., Gao, M., & Chong, Z. (2021) · Genome biology · doi:10.1186/s13059-021-02527-4 · Cited by 207 · see citing works

Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads

Human Genome Structural Variation Consortium, Porubsky, D., Ebert, P., Audano, P. A., Vollger, M. R., Harvey, W. T., Marijon, P., Ebler, J., Munson, K. M., Sorensen, M., et al. (2021) · Nature Biotechnology · doi:10.1038/s41587-020-0719-5 · Cited by 203 · see citing works

Genetic Variation, Comparative Genomics, and the Diagnosis of Disease

Eichler, E. E. (2019) · New England Journal of Medicine · doi:10.1056/nejmra1809315 · Cited by 181 · see citing works

Protein-coding repeat polymorphisms strongly shape diverse human phenotypes

Mukamel, R. E., Handsaker, R. E., Sherman, M. A., Barton, A. R., Zheng, Y., McCarroll, S. A., & Loh, P.-R. (2021) · Science · doi:10.1126/science.abg8289 · Cited by 178 · see citing works

A pangenome reference of 36 Chinese populations

Gao, Y., Yang, X., Chen, H., Tan, X., Yang, Z., Deng, L., Wang, B., Kong, S., Li, S., Cui, Y., et al. (2023) · Nature · doi:10.1038/s41586-023-06173-7 · Cited by 177 · see citing works

High-quality genome assembly and resequencing of modern cotton cultivars provide resources for crop improvement

Ma, Z.-Y., Zhang, Y., Wu, L.-Q., Zhang, G.-Y., Sun, Z.-W., Li, Z.-K., Jiang, Y., Ke, H., Chen, B., Liu, Z.-W., et al. (2021) · Nature Genetics · doi:10.1038/s41588-021-00910-2 · Cited by 139 · see citing works

Jasmine and Iris: population-scale structural variant comparison and analysis

Kirsche, M., Prabhu, G., Sherman, R. M., Ni, B., Battle, A. J., Aganezov, S. S., & Schatz, M. C. (2023) · Nature Methods · doi:10.1038/s41592-022-01753-3 · Cited by 159 · see citing works

The Arms Race Between KRAB–Zinc Finger Proteins and Endogenous Retroelements and Its Impact on Mammals

Bruno, M., Mahgoub, M., & Macfarlan, T. S. (2019) · Annual Review of Genetics · doi:10.1146/annurev-genet-112618-043717 · Cited by 155 · 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

High-resolution silkworm pan-genome provides genetic insights into artificial selection and ecological adaptation

Tong, X., Han, M., Lu, K., Tai, S., Liang, S., Liu, Y., Hu, H., Shen, J., Long, A., Zhan, C., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-33366-x · Cited by 165 · see citing works

StainedGlass: interactive visualization of massive tandem repeat structures with identity heatmaps

Vollger, M. R., Kerpedjiev, P., Phillippy, A. M., & Eichler, E. E. (2022) · Bioinformatics · doi:10.1093/bioinformatics/btac018 · Cited by 161 · 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

Recurrent inversion polymorphisms in humans associate with genetic instability and genomic disorders

Porubskỳ, D., Höps, W., Ashraf, H., Hsieh, P., Rodríguez–Martín, B., Yilmaz, F., Ebler, J., Hallast, P., Maggiolini, F. A. M., Harvey, W. T., et al. (2022) · Cell · doi:10.1016/j.cell.2022.04.017 · Cited by 159 · see citing works

From cytogenetics to cytogenomics: whole-genome sequencing as a first-line test comprehensively captures the diverse spectrum of disease-causing genetic variation underlying intellectual disability

Lindstrand, A., Eisfeldt, J., Pettersson, M., Carvalho, C. M. B., Kvarnung, M., Grigelioniené, G., Anderlid, B., Bjerin, O., Gustavsson, P., Hammarsjö, A., et al. (2019) · Genome Medicine · doi:10.1186/s13073-019-0675-1 · Cited by 142 · see citing works

Next-generation sequencing for constitutional variants in the clinical laboratory, 2021 revision: a technical standard of the American College of Medical Genetics and Genomics (ACMG)

Rehder, C. W., Bean, L. J., Bick, D. P., Chao, E., Chung, W. K., Das, S., O’Daniel, J. M., Rehm, H. L., Shashi, V., & Vincent, L. M. (2021) · Genetics in Medicine · doi:10.1038/s41436-021-01139-4 · Cited by 149 · see citing works

Human-specific tandem repeat expansion and differential gene expression during primate evolution

Sulovari, A., Li, R., Audano, P. A., Porubskỳ, D., Vollger, M. R., Logsdon, G. A., Warren, W. C., Pollen, A. A., Chaisson, M., Eichler, E. E., et al. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1912175116 · Cited by 131 · see citing works

The pan-genome and local adaptation of Arabidopsis thaliana

Kang, M., Wu, H., Liu, H., Liu, W., Zhu, M., Han, Y., Liu, W., Chen, C., Song, Y., Tan, L., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-42029-4 · Cited by 139 · see citing works

Expectations and blind spots for structural variation detection from long-read assemblies and short-read genome sequencing technologies

Zhao, X., Collins, R. L., Lee, W.-P., Weber, A. M., Jun, Y., Zhu, Q., Weisburd, B., Huang, Y., Audano, P. A., Wang, H., et al. (2021) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2021.03.014 · Cited by 132 · see citing works

Telomere-to-telomere assemblies of 142 strains characterize the genome structural landscape in Saccharomyces cerevisiae

O’Donnell, S., Yue, J., Saada, O. A., Agier, N., Caradec, C., Cokelaer, T., Chiara, M. D., Delmas, S., Dutreux, F., Fournier, T., et al. (2023) · Nature Genetics · doi:10.1038/s41588-023-01459-y · Cited by 132 · see citing works

Population-scale long-read sequencing uncovers transposable elements associated with gene expression variation and adaptive signatures in Drosophila

Rech, G. E., Radío, S., Guirao‐Rico, S., Aguilera, L., Horváth, V., Green, L., Lindstadt, H., Jamilloux, V., Quesneville, H., & González, J. (2022) · Nature Communications · doi:10.1038/s41467-022-29518-8 · Cited by 120 · see citing works

NanoVar: accurate characterization of patients’ genomic structural variants using low-depth nanopore sequencing

Tham, C. Y., Tirado-Magallanes, R., Goh, Y., Fullwood, M. J., Koh, B. T. H., Wang, W., Ng, C. H., Chng, W. J., Thiéry, A. H., Tenen, D. G., et al. (2020) · Genome biology · doi:10.1186/s13059-020-01968-7 · Cited by 126 · see citing works

Improved assembly and variant detection of a haploid human genome using single‐molecule, high‐fidelity long reads

Vollger, M. R., Logsdon, G. A., Audano, P. A., Sulovari, A., Porubskỳ, D., Peluso, P. S., Wenger, A. M., Concepcion, G. T., Kronenberg, Z. N., Munson, K. M., et al. (2019) · Annals of Human Genetics · doi:10.1111/ahg.12364 · Cited by 122 · see citing works

A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypesPreprint

Li, R., Gong, M., Zhang, X., Wang, F., Liu, Z., Zhang, L., Yang, Q., Xu, Y., Xu, M., Zhang, H., et al. (2023) · Genome Research · doi:10.1101/gr.277372.122 · Cited by 122 · see citing works

Beyond the exome: What’s next in diagnostic testing for Mendelian conditions

Wojcik, M. H., Reuter, C. M., Marwaha, S., Mahmoud, M., Duyzend, M., Barseghyan, H., Yuan, B., Boone, P. M., Groopman, E., Délot, E. C., et al. (2023) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2023.06.009 · Cited by 134 · 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

The Need for a Human Pangenome Reference Sequence

Miga, K. H., & Wang, T. (2021) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-120120-081921 · Cited by 120 · see citing works

Utility of long-read sequencing for All of Us

Mahmoud, M., Huang, Y., Garimella, K. V., Audano, P. A., Wan, W., Prasad, N., Handsaker, R. E., Hall, S., Pionzio, A., Schatz, M. C., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-44804-3 · Cited by 115 · see citing works

Reference flow: reducing reference bias using multiple population genomes

Chen, N.-C., Solomon, B., Mun, T., Iyer, S., & Langmead, B. (2021) · Genome biology · doi:10.1186/s13059-020-02229-3 · Cited by 113 · see citing works

A new era of long-read sequencing for cancer genomics

Sakamoto, Y., Sereewattanawoot, S., & Suzuki, A. (2019) · Journal of Human Genetics · doi:10.1038/s10038-019-0658-5 · Cited by 115 · see citing works

Structural variations in cancer and the 3D genome

Dubois, F. P. B., Sidiropoulos, N., Weischenfeldt, J., & Beroukhim, R. (2022) · Nature reviews. Cancer · doi:10.1038/s41568-022-00488-9 · Cited by 110 · see citing works

Genome sequencing and implications for rare disorders

Posey, J. E. (2019) · Orphanet Journal of Rare Diseases · doi:10.1186/s13023-019-1127-0 · Cited by 108 · see citing works

Comprehensive identification of transposable element insertions using multiple sequencing technologies

Chu, C., Borges-Monroy, R., Viswanadham, V., Lee, S., Li, H., Lee, E. A., & Park, P. J. (2021) · Nature Communications · doi:10.1038/s41467-021-24041-8 · Cited by 106 · see citing works

lra: A long read aligner for sequences and contigs

Ren, J., & Chaisson, M. (2021) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1009078 · Cited by 105 · see citing works

Newest Methods for Detecting Structural Variations

Coster, W. D., & Broeckhoven, C. V. (2019) · Trends in biotechnology · doi:10.1016/j.tibtech.2019.02.003 · Cited by 104 · see citing works

A Novel Framework for Characterizing Genomic Haplotype Diversity in the Human Immunoglobulin Heavy Chain Locus

Rodriguez, O. L., Gibson, W. S., Parks, T., Emery, M., Powell, J., Strahl, M., Deikus, G. Y., Auckland, K., Eichler, E. E., Marasco, W. A., et al. (2020) · Frontiers in Immunology · doi:10.3389/fimmu.2020.02136 · Cited by 94 · see citing works

SVision: a deep learning approach to resolve complex structural variants

Lin, J., Wang, S., Audano, P. A., Meng, D., Flores, J. I., Kosters, W. A., Yang, X., Jia, P., Marschall, T., Beck, C. R., et al. (2022) · Nature Methods · doi:10.1038/s41592-022-01609-w · Cited by 99 · see citing works

A review of the pangenome: how it affects our understanding of genomic variation, selection and breeding in domestic animals?

Gong, Y., Li, Y., Liu, X., Ma, Y., & Jiang, L. (2023) · Journal of Animal Science and Biotechnology/Journal of animal science and biotechnology · doi:10.1186/s40104-023-00860-1 · Cited by 101 · see citing works

Comprehensive analysis of structural variants in breast cancer genomes using single-molecule sequencingPreprint

Aganezov, S. S., Goodwin, S., Sherman, R. M., Sedlazeck, F. J., Arun, G., Bhatia, S., Lee, I., Kirsche, M., Wappel, R. L., Kramer, M., et al. (2020) · Genome Research · doi:10.1101/gr.260497.119 · Cited by 101 · see citing works

Identification and characterization of occult human-specific LINE-1 insertions using long-read sequencing technology

Zhou, W., Emery, S. B., Flasch, D. A., Wang, Y., Kwan, K. Y., Kidd, J. M., Moran, J. V., & Mills, R. E. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz1173 · Cited by 93 · see citing works

Novel Functional Sequences Uncovered through a Bovine Multiassembly Graph

Crysnanto, D., Leonard, A. S., Fang, Z.-H., & Pausch, H. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2101056118 · Cited by 96 · see citing works

One reference genome is not enough

Yang, X., Lee, W., Ye, K., & Lee, C. (2019) · Genome biology · doi:10.1186/s13059-019-1717-0 · Cited by 93 · see citing works

Population Structure, Stratification, and Introgression of Human Structural Variation

Almarri, M. A., Bergström, A., Prado-Martinez, J., Yang, F., Fu, B., Dunham, A. S., Chen, Y., Hurles, M. E., Tyler‐Smith, C., & Xue, Y. (2020) · Cell · doi:10.1016/j.cell.2020.05.024 · Cited by 92 · see citing works

Centromeric Satellite DNAs: Hidden Sequence Variation in the Human Population

Miga, K. H. (2019) · Genes · doi:10.3390/genes10050352 · Cited by 93 · 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

Recurrent repeat expansions in human cancer genomes

Erwin, G. S., Gürsoy, G., Al-Abri, R., Suriyaprakash, A., Dolzhenko, E., Zhu, K., Hoerner, C. R., White, S. M., Ramirez, L., Vadlakonda, A., et al. (2022) · Nature · doi:10.1038/s41586-022-05515-1 · Cited by 85 · see citing works

High-coverage nanopore sequencing of samples from the 1000 Genomes Project to build a comprehensive catalog of human genetic variationPreprint

Gustafson, J. A., Gibson, S. B., Damaraju, N., Zalusky, M. P., Hoekzema, K., Twesigomwe, D., Yang, L., Snead, A. A., Richmond, P. A., Coster, W. D., et al. (2024) · Genome Research · doi:10.1101/gr.279273.124 · Cited by 90 · see citing works

Ratatosk: hybrid error correction of long reads enables accurate variant calling and assembly

Holley, G., Beyter, D., Ingimundardóttir, H., Møller, P. L., Kristmundsdóttir, S., Eggertsson, H. P., & Halldórsson, B. V. (2021) · Genome biology · doi:10.1186/s13059-020-02244-4 · Cited by 82 · see citing works

Whole-genome sequencing with long reads reveals complex structure and origin of structural variation in human genetic variations and somatic mutations in cancer

Fujimoto, A., Wong, J. H., Yoshii, Y., Akiyama, S., Tanaka, A., Yagi, H., Shigemizu, D., Nakagawa, H., Mizokami, M., & Shimada, M. (2021) · Genome Medicine · doi:10.1186/s13073-021-00883-1 · Cited by 79 · see citing works

The changing face of genome assemblies: Guidance on achieving high‐quality reference genomes

Whibley, A. C., Kelley, J. L., & Narum, S. R. (2020) · Molecular Ecology Resources · doi:10.1111/1755-0998.13312 · Cited by 85 · see citing works

Structural variants in the Chinese population and their impact on phenotypes, diseases and population adaptation

Wu, Z., Jiang, Z., Li, T., Xie, C., Zhao, L., Ouyang, S., Ouyang, S., Liu, Y., Li, T., & Xie, Z. (2021) · Nature Communications · doi:10.1038/s41467-021-26856-x · Cited by 78 · 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

Construction and integration of three de novo Japanese human genome assemblies toward a population-specific reference

Takayama, J., Tadaka, S., Yano, K., Katsuoka, F., Gocho, C., Funayama, T., Makino, S., Okamura, Y., Kikuchi, A., Sugimoto, S., et al. (2021) · Nature Communications · doi:10.1038/s41467-020-20146-8 · Cited by 83 · see citing works

MUM&Co: accurate detection of all SV types through whole-genome alignment

O’Donnell, S., & Fischer, G. (2020) · Bioinformatics · doi:10.1093/bioinformatics/btaa115 · Cited by 80 · see citing works

Evolutionary and functional impact of common polymorphic inversions in the human genome

Giner-Delgado, C., Villatoro, S., Lerga-Jaso, J., Gayà‐Vidal, M., Oliva, M., Castellano, D., Pantano, L., Bitarello, B. D., Izquierdo, D., Noguera, I., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-12173-x · Cited by 74 · 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

Towards accurate and reliable resolution of structural variants for clinical diagnosis

Liu, Z., Roberts, R. A., Mercer, T. R., Xu, J., Sedlazeck, F. J., & Tong, W. (2022) · Genome biology · doi:10.1186/s13059-022-02636-8 · Cited by 78 · see citing works

Deciphering the exact breakpoints of structural variations using long sequencing reads with DeBreak

Chen, Y., Wang, A. Y., Barkley, C. A., Zhang, Y., Zhao, X., Gao, M., Edmonds, M. D., & Chong, Z. (2023) · Nature Communications · doi:10.1038/s41467-023-35996-1 · Cited by 76 · see citing works

The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models

Rozowsky, J. S., Gao, J., Borsari, B., Yang, Y., Galeev, T. R., Gürsoy, G., Epstein, C. B., Xiong, K., Xu, J., Li, T., et al. (2023) · Cell · doi:10.1016/j.cell.2023.02.018 · Cited by 77 · see citing works

Application and Challenge of 3rd Generation Sequencing for Clinical Bacterial Studies

Khedher, M. B., Ghedira, K., Rolain, J., Ruimy, R., & Croce, O. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23031395 · Cited by 76 · see citing works

Complex genomic rearrangements: an underestimated cause of rare diseases

Schuy, J., Grochowski, C. M., Carvalho, C. M. B., & Lindstrand, A. (2022) · Trends in Genetics · doi:10.1016/j.tig.2022.06.003 · Cited by 75 · see citing works

Recombination of repeat elements generates somatic complexity in human genomes

Pascarella, G., Hon, C. C., Hashimoto, K., Busch, A., Luginbühl, J., Parr, C., Hin Yip, W., Abe, K., Kratz, A., Bonetti, A., et al. (2022) · Cell · doi:10.1016/j.cell.2022.06.032 · Cited by 77 · see citing works

Resolution of structural variation in diverse mouse genomes reveals chromatin remodeling due to transposable elements

Ferraj, A., Audano, P. A., Balachandran, P., Czechanski, A., Flores, J. I., Radecki, A. A., Mosur, V., Gordon, D., Walawalkar, I. A., Eichler, E. E., et al. (2023) · Cell Genomics · doi:10.1016/j.xgen.2023.100291 · Cited by 78 · see citing works

Long-read assembly of the Chinese rhesus macaque genome and identification of ape-specific structural variants

He, Y.-X., Luo, X., Zhou, B., Hu, T., Meng, X., Audano, P., Kronenberg, Z., Eichler, E., Jin, J., Guo, Y., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-12174-w · Cited by 70 · see citing works

The regulation of cortical neurogenesis

Villalba, A., Götz, M., & Borrell, V. (2020) · Current topics in developmental biology/Current Topics in Developmental Biology · doi:10.1016/bs.ctdb.2020.10.003 · Cited by 74 · see citing works

Structural variation in 1,019 diverse humans based on long-read sequencing

Schloissnig, S., Pani, S., Ebler, J., Hain, C., Tsapalou, V., Söylev, A., Hüther, P., Ashraf, H., Prodanov, T., Asparuhova, M., et al. (2025) · Nature · doi:10.1038/s41586-025-09290-7 · Cited by 134 · see citing works

Mapping and characterization of structural variation in 17,795 deeply sequenced human genomesPreprint

Abel, H., Larson, D. E., Chiang, C., Das, I., Kanchi, K., Layer, R. M., Neale, B. M., Salerno, W. J., Reeves, C., Buyske, S. G., et al. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/508515 · Cited by 22 · see citing works

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

Chaisson, M., Sanders, A. D., Zhao, X., Malhotra, A., Porubskỳ, D., Rausch, T., Gardner, E. J., Rodriguez, O. L., Guo, L., Collins, R. L., et al. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/193144 · Cited by 145 · see citing works

Mapping and characterization of structural variation in 17,795 human genomes

Genomics, N. C. F. C. D., Abel, H. J., Larson, D. E., Regier, A. A., Chiang, C., Das, I., Kanchi, K. L., Layer, R. M., Neale, B. M., Salerno, W. J., et al. (2020) · Nature · doi:10.1038/s41586-020-2371-0 · Cited by 310 · see citing works

SVarp: pangenome-based structural variant discoveryPreprint

Söylev, A., Ebler, J., Pani, S., Rausch, T., Korbel, J. O., & Marschall, T. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.02.18.580171 · Cited by 8 · see citing works