The DOI matches its Crossref record; 220 of the 220 references it cites were found in a registry or an index.
Haplotype-resolved diverse human genomes and integrated analysis of structural variation
Open accessPublished version of a preprint
Abstract
Resolving genomic structural variation: Many human genomes have been reported using short-read technology, but it is difficult to resolve structural variants (SVs) using these data. These genomes thus lack comprehensive comparisons among individuals and populations. Ebert et al. used long-read structural variation calling across 64 human genomes representing diverse populations and developed new methods for variant discovery. This approach allowed the authors to increase the number of confirmed SVs and to describe the patterns of variation across populations. From this dataset, they identified quantitative trait loci affected by these SVs and determined how they may affect gene expression and potentially explain genome-wide association study hits. This information provides insights into patterns of normal human genetic variation and generates reference genomes that better represent the diversity of our species. Science , this issue p. eabf7117
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The cited source doesn’t support the claim as written.
In the citing paper
“Either the graphs needed to be constructed from variant calls against a reference 3,6,32 and, therefore, unable to properly represent nested variation while still suffering from some reference bias, or they were limited to only SVs 16 and unable to effectively be used for short-read mapping with current tools 6 .”
From Pangenome graph construction from genome alignments with Minigraph-Cactus (2024) · cites this paper as [32]
Checked by a reasoning model — may be wrong.
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“Previous studies have identified tens of megabases of sequence contained within structural variants (SVs) that are polymorphic within the population5.”
From A draft human pangenome reference. (2023) · cites this paper as [5]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“This provides a large set of fully phased human genome assemblies and outperforms earlier efforts on many levels of assembly quality5,16,60.”
From A draft human pangenome reference. (2023) · cites this paper as [5]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“In line with previous results5,54, we obtained high genotype concordance across all variant types and genomic contexts (Extended Data Fig. 9).”
From A draft human pangenome reference. (2023) · cites this paper as [5]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“Ebert et al.5 showed that using PanGenie, a pangenomic approach, with 32 samples, a subset of these variants could be genotyped in short-read genomes (about 13,000 genotyped on average, ranging from 12,000 to 15,000 per sample).”
From A draft human pangenome reference. (2023) · cites this paper as [5]
Experimental — accuracy not yet measured
The source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“The HGSVC and HPRC call sets are based on variant calls produced from haplotype-resolved assemblies of 32 and 44 samples, respectively5.”
From A draft human pangenome reference. (2023) · cites this paper as [5]
Experimental — accuracy not yet measuredThe cited source says what the claim attributes to it.
In the citing paper
“For example, compared with Ebert et al.5, the average median base level accuracy is nearly an order of magnitude higher, the N50 contiguity is nearly double and the structural accuracy is higher33.”
From A draft human pangenome reference. (2023) · cites this paper as [5]
The cited source says what the claim attributes to it.
In the citing paper
“This result confirms that short-read-based SV discovery relative to a linear reference genome misses a large proportion of SVs5,6,8.”
From A draft human pangenome reference. (2023) · cites this paper as [5]
The cited source says what the claim attributes to it.
In the citing paper
“This result confirms that SV callers based on short reads alone miss a large proportion of SVs located in regions inaccessible by short-read alignments, which has been previously reposed by several studies5,8.”
From A draft human pangenome reference. (2023) · cites this paper as [5]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing
Benjamini, Y., & Hochberg, Y. (1995) · Journal of the Royal Statistical Society Series B: Statistical Methodology · doi:10.1111/j.2517-6161.1995.tb02031.x · Cited by 109,482
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
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
STAR: ultrafast universal RNA-seq aligner
Dobin, A., Davis, C. A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., & Gingeras, T. R. (2013) · Bioinformatics · doi:10.1093/bioinformatics/bts635 · Cited by 51,709
Self-citationMAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
Katoh, K., & Standley, D. M. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst010 · Cited by 46,209
MUSCLE: multiple sequence alignment with high accuracy and high throughput
Edgar, R. C. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh340 · Cited by 44,662
Robinson, M. D., McCarthy, D. J., & Smyth, G. K. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btp616 · Cited by 41,364
PLINK: a tool set for whole-genome association and population-based linkage analyses.
Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A. R., Bender, D., Maller, J., Sklar, P., de Bakker, P. I. W., Daly, M. J., et al. (2007) · The American Journal of Human Genetics · doi:10.1086/519795 · Cited by 34,089
Cutadapt removes adapter sequences from high-throughput sequencing reads
Martin, M. (2011) · EMBnet.journal · doi:10.14806/ej.17.1.200 · Cited by 33,889
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
Research works printed but not linked: 3
- 10.1038/s41587-020-0719-5 · DOI · Paper page
- G. Ke et al . in Advances in Neural Information Processing Systems 30 I. Guyon U. V. Luxburg S. Bengio H. Wallach R. Fergus S. Vishwanathan R. Garnett Eds. (Curran Associates Inc. 2017) pp. 3146–3154.
- 10.1038/s41586-020-2287-8 · DOI · Paper page
Cited by
Sorted by citations
Items 301–400 of 724
Ghorbani, M., Moosa, S., Siddig, Z., Farhad, R., Naeem, H., Harvey, W. T., Mastrorosa, F. K., Munson, K. M., Razali, R., ALIYEV, E. E., et al. (2025) · Nature Genetics · doi:10.1038/s41588-025-02173-7 · Cited by 13
Self-citationGenome-wide recombination map construction from single sperm sequencing in cattle
Yang, L., Gao, Y., Li, M., Park, K., Liu, S., Kang, X., Liu, M., Oswalt, A., Fang, L., Telugu, B. P. V. L., et al. (2022) · BMC Genomics · doi:10.1186/s12864-022-08415-w · Cited by 11
Self-citationNatural and Experimental Rewiring of Gene Regulatory Regions
Downes, D. J., & Hughes, J. R. (2022) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-112921-010715 · Cited by 12
Identification of a familial complex chromosomal rearrangement by optical genome mapping
Yang, Y., & Wang, H. (2022) · Molecular Cytogenetics · doi:10.1186/s13039-022-00619-9 · Cited by 11
GAVISUNK: genome assembly validation via inter-SUNK distances in Oxford Nanopore reads
Dishuck, P. C., Rozanski, A. N., Logsdon, G. A., Porubskỳ, D., & Eichler, E. E. (2022) · Bioinformatics · doi:10.1093/bioinformatics/btac714 · Cited by 11
Self-citationSmall polymorphisms are a source of ancestral bias in structural variant breakpoint placementPreprint
Audano, P. A., & Beck, C. R. (2024) · Genome Research · doi:10.1101/gr.278203.123 · Cited by 13
Self-citationTowards an unbiased characterization of genetic polymorphism: a comparison of 27 A. thaliana genomesPreprint
Igolkina, A. A., Vorbrugg, S., Rabanal, F. A., Liu, H., Ashkenazy, H., Kornienko, A. E., Fitz, J., Collenberg, M., Kubica, C., Morales, A. M., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.05.30.596703 · Cited by 11
Evolutionary insights from profiling LINE-1 activity at allelic resolution in a single human genome
Yang, L., Metzger, G. A., Valle, R. P. D., Rubalcaba, D. D., & McLaughlin, R. N. (2023) · The EMBO Journal · doi:10.1038/s44318-023-00007-y · Cited by 11
Liu, S., Shi, C., Chen, C., Tan, Y., Tian, Y., Macqueen, D. J., & Li, Q. (2025) · Cell Reports · doi:10.1016/j.celrep.2025.115697 · Cited by 14
Switch-like gene expression modulates disease risk
Aqil, A., Li, Y., Wang, Z., Islam, S., Russell, M., Kallak, T. K., Saitou, M., Gökçümen, Ö., & Masuda, N. (2025) · Nature Communications · doi:10.1038/s41467-025-60513-x · Cited by 10
Self-citationInitial Analysis of Structural Variation Detections in Cattle Using Long-Read Sequencing Methods
Gao, Y., Ma, L., & Liu, G. E. (2022) · Genes · doi:10.3390/genes13050828 · Cited by 10
PGG.SV: a whole-genome-sequencing-based structural variant resource and data analysis platform
Wang, Y., Ling, Y., Gong, J., Zhao, X., Zhou, H., Xie, B., Lou, H., Zhuang, X., Li, J., Initiative, T. H., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac905 · Cited by 10
Self-citationRetrotransposon insertions associated with risk of neurologic and psychiatric diseases
Ahn, H. W., Worman, Z., Lechsinska, A., Payer, L. M., Wang, T., Malik, N., Li, W., Burns, K. H., Nath, A., & Levin, H. L. (2022) · EMBO Reports · doi:10.15252/embr.202255197 · Cited by 10
DeepOM: single-molecule optical genome mapping via deep learning
Nogin, Y., Zur, T. D., Margalit, S., Barzilai, I., Alalouf, O., Ebenstein, Y., & Shechtman, Y. (2023) · Bioinformatics · doi:10.1093/bioinformatics/btad137 · Cited by 10
Yilmaz, F., Umamaheswaran, G., Mosley, T. J., Hallast, P., Kim, K., Mostovoy, Y., Purcell, R. H., Shaikh, T. H., Zwick, M. E., Kwok, P., et al. (2023) · Genome Medicine · doi:10.1186/s13073-023-01184-5 · Cited by 9
Self-citationAutomatic detection of complex structural genome variation across world populationsPreprint
Zhou, B., Arthur, J. G., Guo, H., Hughes, C., Kim, T., Huang, Y., Pattni, R., Lee, H., Ji, H. P., Song, G., et al. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/200170 · Cited by 10
Structural variation across 138,134 samples in the TOPMed consortium
Jun, G., English, A., Metcalf, G., Yang, J., Chaisson, M., Pankratz, N., Menon, V., Salerno, W., Krasheninina, O., Smith, A., et al. (2023) · doi:10.21203/rs.3.rs-2515453/v1 · Cited by 24
Self-citationLuo, C., Liu, Y. H., & Zhou, X. (2024) · Nature Communications · doi:10.1038/s41467-024-51282-0 · Cited by 8
A Catalogue of Structural Variation across Ancestrally Diverse Asian Genomes
Tan, J. H. J., Li, Z., Gonzàlez-Porta, M., Rajaby, R., Lim, W. K., Tan, Y. A., Jimenez, R. T., Teo, R., Hebrard, M., Ow, J. L., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-53620-8 · Cited by 11
Self-citationZhang, S., Song, Q., Zhang, P., Wang, X., Guo, R., Li, Y., Liu, S., Yan, X., Zhang, J., Niu, Y., et al. (2024) · Cell Genomics · doi:10.1016/j.xgen.2024.100699 · Cited by 9
Self-citationYang, Q., Sun, J., Wang, X., Wang, J., Liu, Q., Ru, J., Zhang, X., Wang, S., Hao, R., Bian, P., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-57756-z · Cited by 9
The 1000 Chinese Pangenome empowers medical and population genetics
Wang, Y., Duan, Z., Chen, D., Shi, D., Ding, Y., Wang, Z., Li, B., Wang, Z., Guo, M., Yang, W., et al. (2026) · Nature · doi:10.1038/s41586-026-10315-y · Cited by 9
GreenHill: a de novo chromosome-level scaffolding and phasing tool using Hi-C
Ouchi, S., Kajitani, R., & Itoh, T. (2023) · Genome biology · doi:10.1186/s13059-023-03006-8 · Cited by 9
HQAlign: aligning nanopore reads for SV detection using current-level modeling
Joshi, D., Diggavi, S. N., Chaisson, M., & Kannan, S. (2023) · Bioinformatics · doi:10.1093/bioinformatics/btad580 · Cited by 9
Self-citationReview of Molecular Technologies for Investigating Canine Cancer
Kehl, A., Aupperle‐Lellbach, H., de Brot, S., & van der Weyden, L. (2024) · Animals · doi:10.3390/ani14050769 · Cited by 12
Multicolor Whole-Genome Mapping in Nanochannels for Genetic Analysis
Uppuluri, L., Jadhav, T., Wang, Y., & Xiao, M. (2021) · Analytical Chemistry · doi:10.1021/acs.analchem.1c01373 · Cited by 10
Mobile elements in human population-specific genome and phenotype divergencePreprint
Kojima, S., Koyama, S., Ka, M., Saito, Y., Parrish, E. H., Endo, M., Takata, S., Mizukoshi, M., Hikino, K., Takeda, A., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.03.25.485726 · Cited by 9
Transposable element-mediated rearrangements are prevalent in human genomesPreprint
Balachandran, P., Walawalkar, I. A., Flores, J. I., Dayton, J. N., Audano, P. A., & Beck, C. R. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.06.16.496479 · Cited by 9
Self-citationLiu, G. E. (2025) · Journal of Animal Science and Biotechnology · doi:10.1186/s40104-025-01294-7 · Cited by 8
Next-generation sequencing strategies in venous thromboembolism: in whom and for what purpose?
Trégouët, D., & Morange, P. (2024) · Journal of Thrombosis and Haemostasis · doi:10.1016/j.jtha.2024.04.004 · Cited by 8
Structural variants in linkage disequilibrium with GWAS-significant SNPs
Liang, H., Sedillo, J. C., Schrodi, S. J., & Ikeda, A. (2024) · Heliyon · doi:10.1016/j.heliyon.2024.e32053 · Cited by 10
Zhang, X., Kumar, A., Gong, X., Xing, C., & Mootha, V. V. (2024) · Ophthalmology Science · doi:10.1016/j.xops.2024.100611 · Cited by 8
Structural Variants Contribute to Phenotypic Variation in Maize
Catlin, N. S., Agha, H. I., Platts, A. E., Munasinghe, M., Hirsch, C. N., & Josephs, E. B. (2025) · Molecular Ecology · doi:10.1111/mec.17662 · Cited by 8
Accurate, Scalable Structural Variant Genotyping in Complex Genomes at Population Scales
Hu, M., Wan, P., Chen, C., Tang, S., Chen, J., Wang, L., Chakraborty, M., Zhou, Y., Chen, J., Gaut, B. S., et al. (2025) · Molecular Biology and Evolution · doi:10.1093/molbev/msaf180 · Cited by 9
Self-citationMontalvo, N., Requena, F., Capriotti, E., & Rausell, A. (2025) · Bioinformatics · doi:10.1093/bioinformatics/btaf523 · Cited by 11
Insights into natural neocentromere evolution from a cattle T2T X chromosome
Pineda, P. S., MacPhillamy, C., Ren, Y. X., Chen, T., Zhong, L., Adelson, D. L., Dessaix, C., Pérez-Silva, J. G., Haggerty, L. S., Martin, F. J., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-65778-w · Cited by 12
Phasing of de novo mutations using a scaled‐up multiple amplicon long‐read sequencing approach
Holt, G. S., Batty, L. E., Alobaidi, B., Smith, H., Oud, M. S., Ramos, L., Xavier, M. J., & Veltman, J. A. (2022) · Human Mutation · doi:10.1002/humu.24450 · Cited by 7
Natural Selection Signatures in the Hondo and Ryukyu Japanese Subpopulations
Liu, X., Matsunami, M., Horikoshi, M., Ito, S., Ishikawa, Y., Suzuki, K., Momozawa, Y., Niida, S., Kimura, R., Ozaki, K., et al. (2023) · Molecular Biology and Evolution · doi:10.1093/molbev/msad231 · Cited by 8
Pangenomic genotyping with the marker array
Mun, T., Vaddadi, K., & Langmead, B. (2023) · Algorithms for Molecular Biology · doi:10.1186/s13015-023-00225-3 · Cited by 8
A high-resolution map of small-scale inversions in the gibbon genomePreprint
Mercuri, L., Palmisano, D., L’Abbate, A., D’Addabbo, P., Montinaro, F., Catacchio, C. R., Hasenfeld, P., Ventura, M., Korbel, J. O., Sanders, A. D., et al. (2022) · Genome Research · doi:10.1101/gr.276960.122 · Cited by 7
Self-citationAmelHap: Leveraging drone whole-genome sequence data to create a honey bee HapMap
Parejo, M., Talenti, A., Richardson, M., Alain Vignal, A., Barnett, M. W., & Wragg, D. (2023) · Scientific Data · doi:10.1038/s41597-023-02097-z · Cited by 8
Locityper: targeted genotyping of complex polymorphic genesPreprint
Prodanov, T., Plender, E. G., Seebohm, G., Meuth, S. G., Eichler, E. E., & Marschall, T. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.05.03.592358 · Cited by 8
Self-citationLiang, S.-A., Ren, T., Zhang, J., He, J., Wang, X., Jiang, X., He, Y., McCoy, R. C., Fu, Q., Akey, J. M., et al. (2025) · Genome Biology · doi:10.1186/s13059-025-03502-z · Cited by 8
Gao, Y., Yang, L., Kuhn, K. L., Li, W., Zanton, G. I., Bowman, M., Zhao, P., Zhou, Y., Fang, L., Cole, J. B., et al. (2025) · Journal of Advanced Research · doi:10.1016/j.jare.2025.04.014 · Cited by 8
Self-citationGu, L., Chen, P., Chen, A., Chen, K., Zheng, X., Yu, D., Wang, Z., Fang, L., Liu, G. E., & Zhao, P. (2025) · iMetaOmics. · doi:10.1002/imo2.70027 · Cited by 8
Get ready for short tandem repeats analysis using long reads-the challenges and the state of the art
Chaushevska, M., Alapont-Celaya, K., Schack, A. K., Krych, Ł., Garrido-Navas, M. C., Krithara, A., & Madjarov, G. (2025) · Frontiers in Genetics · doi:10.3389/fgene.2025.1610026 · Cited by 8
A personalized multi‐platform assessment of somatic mosaicism in the human frontal cortex
Zhou, W., Mumm, C., Gan, Y., Switzenberg, J. A., Wang, J., Oliveira, P. D., Kathuria, K., Losh, S. J., McDonald, T. L., Bessell, B., et al. (2025) · Alzheimer s & Dementia · doi:10.1002/alz70855_103962 · Cited by 8
Self-citationLong-read genome sequencing enhances diagnostics of pediatric neurological disorders
Ek, M., Kvarnung, M., de Boer, E. T. B., Fleur, L. L., Ljöstad, L., Lyander, A., Faergeman, S. L., Drue, S. O., Thonberg, H., Nordgren, A., et al. (2026) · Genome Medicine · doi:10.1186/s13073-025-01596-5 · Cited by 7
Using the linear references from the pangenome to discover missing autism variants
Sui, Y., Lin, J., Noyes, M. D., Kwon, Y., Wong, I., Koundinya, N., Harvey, W. T., Wu, M., Hoekzema, K., Munson, K. M., et al. (2026) · Nature Communications · doi:10.1038/s41467-026-68378-4 · Cited by 8
Self-citationConcurrent L1 retrotransposition events promote reciprocal translocations in human tumorigenesis
Zumalave, S., Santamarina, M., Espasandín, N. P., Zamora, J., García‐Souto, D., Temes, J., Baker, T. M., Rodríguez‐Castro, J., Otero, P., Pequeño‐Valtierra, A., et al. (2026) · Science · doi:10.1126/science.aee4513 · Cited by 13
Self-citationComparative genome analysis using sample-specific string detection in accurate long reads
Khorsand, P., Denti, L., Bonizzoni, P., Chikhi, R., & Hormozdiari, F. (2021) · Bioinformatics Advances · doi:10.1093/bioadv/vbab005 · Cited by 9
Wilson, T. E., Ahmed, S. I., Higgins, J., Salk, J. J., & Glover, T. W. (2022) · NAR Genomics and Bioinformatics · doi:10.1093/nargab/lqad042 · Cited by 6
Design of optimal labeling patterns for optical genome mapping via information theory
Nogin, Y., Bar-Lev, D., Hanania, D., Zur, T. D., Ebenstein, Y., Yaakobi, E., Weinberger, N., & Shechtman, Y. (2023) · Bioinformatics · doi:10.1093/bioinformatics/btad601 · Cited by 7
Linderman, M. D., Wallace, J., van der Heyde, A., Wieman, E., Brey, D., Shi, Y., Hansen, P., Shamsi, Z., Liu, J. Z., Gelb, B. D., et al. (2024) · Bioinformatics · doi:10.1093/bioinformatics/btae129 · Cited by 8
Hu, H. K., Gao, R., Gao, W., Gao, B., Jiang, Z., Zhou, M., Wang, G., & Jiang, T. (2024) · Briefings in Bioinformatics · doi:10.1093/bib/bbae336 · Cited by 9
A Map of 3′ DNA Transduction Variants Mediated by Non-LTR Retroelements on 3202 Human Genomes
Halabian, R., & Makałowski, W. (2022) · Biology · doi:10.3390/biology11071032 · Cited by 6
Chromosome-Length Haplotypes with StrandPhaseR and Strand-seq
Hanlon, V. C. T., Porubskỳ, D., & Lansdorp, P. M. (2022) · Methods in molecular biology · doi:10.1007/978-1-0716-2819-5_12 · Cited by 7
The big challenge for livestock genomics is to make sequence data pay
Johnsson, M. (2023) · Peer Community Journal · doi:10.24072/pcjournal.300 · Cited by 7
Devine, S. E. (2023) · Genes · doi:10.3390/genes14101923 · Cited by 8
Self-citationPanSVR: Pan-Genome Augmented Short Read Realignment for Sensitive Detection of Structural Variations
Li, G., Jiang, T., Li, J., & Wang, Y. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.731515 · Cited by 7
Dhande, I. S., Braun, M., & Doris, P. A. (2021) · Hypertension · doi:10.1161/hypertensionaha.121.18112 · Cited by 7
Combining dense and sparse labeling in optical DNA mapping
Torstensson, E., Goyal, G., Johnning, A., Westerlund, F., & Ambjörnsson, T. (2021) · PLoS ONE · doi:10.1371/journal.pone.0260489 · Cited by 7
Multiplex structural variant detection by whole-genome mapping and nanopore sequencing
Uppuluri, L., Wang, Y., YOUNG, E. A., Wong, J. S., Abid, H. Z., & Xiao, M. (2022) · Scientific Reports · doi:10.1038/s41598-022-10483-7 · Cited by 8
LJA: Assembling Long and Accurate Reads Using Multiplex de Bruijn GraphsPreprint
Bankevich, A., Bzikadze, A. V., Kolmogorov, M., Antipov, D., & Pevzner, P. A. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.12.10.420448 · Cited by 7
Reference genomes of 545 silkworms enable high-throughput exploring genotype-phenotype relationshipsPreprint
Tong, X., Han, M., Lu, K., Tai, S., Liang, S., Liu, Y., Hu, H., Shen, J., Long, A., Zhan, C., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.09.28.462073 · Cited by 7
Self-citationRausch, T., Snajder, R., Léger, A., Simovic-Lorenz, M., Stegle, O., Birney, E., Bonder, M. J., Ernst, A., & Korbel, J. O. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.02.20.480758 · Cited by 7
Self-citationThousands of human mutation clusters are explained by short-range template switchingPreprint
Löytynoja, A. (2022) · Genome Research · doi:10.1101/gr.276478.121 · Cited by 6
Nakamura, W., Hirata, M., Oda, S., Chiba, K., Okada, A., Mateos, R. N., Sugawa, M., Iida, N., Ushiama, M., Tanabe, N., et al. (2023) · medRxiv · doi:10.1101/2023.05.30.23289318 · Cited by 7
A Draft Arab Pangenome ReferencePreprint
Nassir, N., Almarri, M. A., Kumail, M., Mohamed, N., Balan, B., Hanif, S., AlObathani, M., Jamalalail, B. A., ElSokary, H. A., Kondaramage, D., et al. (2024) · SSRN Electronic Journal · doi:10.2139/ssrn.4891977 · Cited by 7
Synchronous L1 retrotransposition events promote chromosomal crossover early in human tumorigenesisPreprint
Zumalave, S., Santamarina, M., Espasandín, N. P., García‐Souto, D., Temes, J., Baker, T. M., Pequeño‐Valtierra, A., Otero, I., Rodríguez‐Castro, J., Oitabén, A., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.08.27.596794 · Cited by 8
Self-citationJointly benchmarking small and structural variant calls with vcfdist
Dunn, T., Zook, J. M., Holt, J., & Narayanasamy, S. (2024) · Genome biology · doi:10.1186/s13059-024-03394-5 · Cited by 6
Wang, Y., Liang, N., & Gao, G. (2024) · Nature Communications · doi:10.1038/s41467-024-55392-7 · Cited by 7
Alternative splicing of transposable elements in human breast cancer
Nesta, A. V., Veiga, D. F. T., Banchereau, J., Anczuków, O., & Beck, C. R. (2025) · Mobile DNA · doi:10.1186/s13100-025-00341-4 · Cited by 8
Lakbir, S., de Wit, R., de Bruijn, I., Kundra, R., Madupuri, R., Gao, J., Schultz, N. D., Meijer, G. A., Heringa, J., Fijneman, R. J. A., et al. (2025) · npj Precision Oncology · doi:10.1038/s41698-025-00922-9 · Cited by 8
Population-level structural variant characterization using pangenome graphs
Wang, S., Xu, T., Zhang, P., & Ye, K. (2026) · Nature Genetics · doi:10.1038/s41588-026-02538-6 · Cited by 7
Self-citationUtility of Optical Genome Mapping in Repeat Disorders
Mutlu, M. B., Karakaya, T., Çelebi, H. B. G., Duymuş, F., Seyhan, S., Yılmaz, S., Yiş, U., Atık, T., Yetkin, M. F., & Gümüş, H. (2024) · Clinical Genetics · doi:10.1111/cge.14633 · Cited by 7
Phenotypic Expansion of Knobloch Syndrome Type 2 in an Individual With a De Novo PAK2 Variant
Werren, E. A., Kalsner, L., Ewald, J. M., Peracchio, M., King, C., Vats, P., Audano, P. A., Robinson, P. N., Adams, M. D., Kelly, M. A., et al. (2025) · American Journal of Medical Genetics Part A · doi:10.1002/ajmg.a.64006 · Cited by 6
Self-citationWalker, K., Kalra, D., Lowdon, R. F., Chen, G., Molik, D. C., Soto, D. C., Dabbaghie, F., Khleifat, A. A., Mahmoud, M., Paulin, L. F., et al. (2022) · F1000Research · doi:10.12688/f1000research.110194.1 · Cited by 7
Self-citationXiao, Y., Xiao, Z., Liu, L., Ma, Y., Zhao, H., Wu, Y., Huang, J., Xu, P., Liu, J., & Li, J. (2024) · GigaScience · doi:10.1093/gigascience/giae045 · Cited by 8
Mapping cis- and trans-regulatory target genes of human-specific deletions
Fair, T., Pavlovic, B. J., Swope, D., Castillo, O. E., Schaefer, N. K., & Pollen, A. A. (2025) · Nature Communications · doi:10.1038/s41467-025-67424-x · Cited by 8
Unified views on variant impact across many diseases
Kumar, S., & Gerstein, M. (2023) · Trends in Genetics · doi:10.1016/j.tig.2023.02.002 · Cited by 6
Self-citationRuggieri, A. A., Livraghi, L., Lewis, J. J., Evans, E., Cicconardi, F., Hebberecht, L., Montgomery, S. H., Ghezzi, A., Rodríguez‐Martínez, J. A., Jiggins, C. D., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.04.14.488334 · Cited by 5
Increased mutation rate and interlocus gene conversion within human segmental duplicationsPreprint
Vollger, M. R., DeWitt, W. S., Dishuck, P. C., Harvey, W. T., Guitart, X., Goldberg, M. E., Rozanski, A. N., Lucas, J., Asri, M., Munson, K. M., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.07.06.498021 · Cited by 7
Self-citationHuman pangenome supports analysis of complex genomic regions
Massarat, A. R., Gymrek, M., McStay, B., & Jónsson, H. (2023) · Nature · doi:10.1038/d41586-023-01490-3 · Cited by 6
Complete de novo assembly and re-annotation of the zebrafish genomePreprint
Okendo, J., Koren, S., Rhie, A., Torrado-Tapias, A., Pickett, B. D., Brooks, S. Y., Bouffard, G. G., Crawford, J., Sison, C., Joardar, V., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.11.17.688901 · Cited by 10
Association of human-specific expanded short tandem repeats with neuron-specific regulatory features
Liu, Q., & Tian, W. (2025) · Science Advances · doi:10.1126/sciadv.adp9707 · Cited by 6
A global map for introgressed structural variation and selection in humans
Hsieh, P., Soisangwan, N., Gordon, D., Javidh, A., Harvey, W. T., Porubskỳ, D., Hoekzema, K., Baker, C. A., Munson, K. M., Kinipi, C., et al. (2026) · Science · doi:10.1126/science.adz7518 · Cited by 7
Self-citationPooled, Long-read Sequencing for Structural Variant Characterization in Schistosome Populations
Nair, S., Li, X., Anderson, T., & Platt, R. N. (2025) · Genome Biology and Evolution · doi:10.1093/gbe/evaf127 · Cited by 6
Ma, W., & Chaisson, M. (2025) · Nature Genetics · doi:10.1038/s41588-025-02346-4 · Cited by 6
Self-citationPajic, P., & Gökçümen, Ö. (2025) · Genome Biology and Evolution · doi:10.1093/gbe/evaf250 · Cited by 5
Transient telomere uncapping triggers telomeric and subtelomeric rearrangements
Dudragne, L., Garrido, C., Ilioaia, O., Bernardes, J., & Xu, Z. (2026) · EMBO Reports · doi:10.1038/s44319-026-00717-4 · Cited by 6
Genetic diversity and regulatory features of human-specific NOTCH2NL duplications
Real, T. D., Hebbar, P., Yoo, D., Antonacci, F., Pačar, I., Dubocanin, D., Diekhans, M., Mikol, G. J., Popoola, O. G., Mallory, B. J., et al. (2026) · Cell Genomics · doi:10.1016/j.xgen.2026.101194 · Cited by 5
Self-citationCelus, C. S., Ahmad, S. F., Gangwar, M., Kumar, S., & Kumar, A. (2024) · Gene · doi:10.1016/j.gene.2024.149159 · Cited by 6
Self-citationJumping in the human brain: A review on somatic transposition
Zhang, Y., Guo, Y., Jia, H., Ma, H., Tan, S., & Zhang, Y. E. (2025) · Fundamental Research · doi:10.1016/j.fmre.2025.03.001 · Cited by 5
Molecular QTL are enriched for structural variants in a cattle long-read cohort
Mapel, X. M., Leonard, A. S., & Pausch, H. (2026) · Communications Biology · doi:10.1038/s42003-026-09596-w · Cited by 5
Peng, X. P., Al-Ddafari, M. S., Caballero-Oteyza, A., Mezouar, C. E., Mrovecova, P., Dib, S., Massen, Z., Smahi, M. C.-E., Faiza, A., Hassaïne, R. T., et al. (2023) · Clinical Immunology · doi:10.1016/j.clim.2023.109758 · Cited by 5
Said, I., Barbash, D. A., & Clark, A. G. (2024) · Genome Biology and Evolution · doi:10.1093/gbe/evae153 · Cited by 6
Copy-number variants differ in frequency across genetic ancestry groups
Schultz, L. M., Knighton, A., Huguet, G., Saci, Z., Jean‐Louis, M., Mollon, J., Knowles, E. E. M., Glahn, D. C., Jacquemont, S., & Almasy, L. A. (2024) · Human Genetics and Genomics Advances · doi:10.1016/j.xhgg.2024.100340 · Cited by 7
VISTA: an integrated framework for structural variant discovery
Sarwal, V., Lee, S., Yang, J., Sankararaman, S., Chaisson, M., Eskin, E., & Mangul, S. (2024) · Briefings in Bioinformatics · doi:10.1093/bib/bbae462 · Cited by 5
Self-citationMa, C., Shi, X., Li, X., Zhang, Y.-P., & Peng, M. (2024) · BMC Genomics · doi:10.1186/s12864-024-10875-1 · Cited by 5
Self-citation
Metadata
- Authors
- Ebert, P., Audano, P. A., Zhu, Q., Rodriguez-Martin, B., Porubsky, D., Bonder, M. J., Sulovari, A., Ebler, J., Zhou, W., Serra Mari, R., Yilmaz, F., Zhao, X., Hsieh, P., Lee, J., Kumar, S., Lin, J., Rausch, T., Chen, Y., Ren, J., Santamarina, M., Höps, W., Ashraf, H., Chuang, N. T., Yang, X., Munson, K. M., Lewis, A. P., Fairley, S., Tallon, L. J., Clarke, W. E., Basile, A. O., Byrska-Bishop, M., Corvelo, A., Evani, U. S., Lu, T.-Y., Chaisson, M. J. P., Chen, J., Li, C., Brand, H., Wenger, A. M., Ghareghani, M., Harvey, W. T., Raeder, B., Hasenfeld, P., Regier, A. A., Abel, H. J., Hall, I. M., Flicek, P., Stegle, O., Gerstein, M. B., Tubio, J. M. C., Mu, Z., Li, Y. I., Shi, X., Hastie, A. R., Ye, K., Chong, Z., Sanders, A. D., Zody, M. C., Talkowski, M. E., Mills, R. E., Devine, S. E., Lee, C., Korbel, J. O., Marschall, T., & Eichler, E. E.
- Affiliations
- Heinrich Heine University Düsseldorf (DE)
- University of Washington (US)
- The Jackson Laboratory for Genomic Medicine (US)
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany.
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15th Avenue NE, Seattle, WA 98195-5065, USA.
- German Cancer Research Center (DE)
- University of Michigan (US)
- Heinrich Heine University, Medical Faculty, Institute for Medical Biometry and Bioinformatics, Moorenstraße 20, 40225 Düsseldorf, Germany.
- Broad Institute (US)
- BioNano Genomics (United States) (US)
- Yale University (US)
- Xi'an Jiaotong University (CN)
- European Molecular Biology Laboratory (DE)
- University of Alabama at Birmingham (US)
- University of Southern California (US)
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain.
- University of Maryland, Baltimore (US)
- European Bioinformatics Institute (GB)
- New York Genome Center (US)
- New York Genome Center, New York, NY 10013, USA.
- Temple University (US)
- Pacific Biosciences (United States) (US)
- Max Planck Institute for Informatics (DE)
- Washington University in St. Louis (US)
- University of Chicago (US)
- Ewha Womans University (KR)
- Howard Hughes Medical Institute (US)
- Corresponding author
- Lee, Charles
- Korbel, Jan O.
- Marschall, Tobias
- Eichler, Evan E.
- ORCID
- Ebert, Peter
- Audano, Peter A.
- Zhu, Qihui
- Rodriguez-Martin, Bernardo
- Porubsky, David
- Bonder, Marc Jan
- Sulovari, Arvis
- Ebler, Jana
- Zhou, Weichen
- Serra Mari, Rebecca
- Yilmaz, Feyza
- Zhao, Xuefang
- Hsieh, PingHsun
- Lee, Joyce
- Kumar, Sushant
- Lin, Jiadong
- Rausch, Tobias
- Chen, Yu
- Ren, Jingwen
- Höps, Wolfram
- Ashraf, Hufsah
- Chuang, Nelson T.
- Yang, Xiaofei
- Munson, Katherine M.
- Lewis, Alexandra P.
- Fairley, Susan
- Tallon, Luke J.
- Clarke, Wayne E.
- Basile, Anna O.
- Byrska-Bishop, Marta
- Corvelo, André
- Evani, Uday S.
- Lu, Tsung-Yu
- Chaisson, Mark J. P.
- Chen, Junjie
- Li, Chong
- Brand, Harrison
- Wenger, Aaron M.
- Ghareghani, Maryam
- Harvey, William T.
- Raeder, Benjamin
- Hasenfeld, Patrick
- Regier, Allison A.
- Abel, Haley J.
- Hall, Ira M.
- Flicek, Paul
- Stegle, Oliver
- Gerstein, Mark B.
- Tubio, Jose M. C.
- Mu, Zepeng
- Li, Yang I.
- Shi, Xinghua
- Hastie, Alex R.
- Ye, Kai
- Chong, Zechen
- Sanders, Ashley D.
- Zody, Michael C.
- Talkowski, Michael E.
- Mills, Ryan E.
- Devine, Scott E.
- Lee, Charles
- Korbel, Jan O.
- Marschall, Tobias
- Eichler, Evan E.
- Venue
- Science
- Published
- 2021-04-02
- Volume
- 372
- Issue
- 6537
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC8026704
- OpenAlex
- W3130788486
- Cited by
- 702
- References
- 212
- Citations by year
- 2026: 97 · 2025: 143 · 2024: 135 · 2023: 128 · 2022: 134 · 2021: 62
- FWCI
- 66.01
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Licence
- cc-by-nd
- Locations
- Science (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nd)
- PubMed (publishedVersion)
- University of Groningen research database (University of Groningen / Centre for Information Technology) (publishedVersion, other-oa)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- MDC Repository (Max-Delbrueck-Center for Molecular Medicine) (submittedVersion)
- The Mouseion at the JAXlibrary (Jackson Laboratory) (submittedVersion)
- Funders
- National Institutes of Health (U24HG007497, R01HG002898, R01HD081256, 1U01HG010973, R01HG002385, R15HG009565, 1R35GM138212, 1OT3HL147154, 1R01HG007068-01A1, R01MH115957, R01GM130738)
- National Human Genome Research Institute (3UM1HG008901-03S1, 3UM1HG008901-04S2, K99HG011041, UM1HG008901)
- National Science Foundation of China (32070663)
- Wellcome (WT104947/Z/14/Z)
- Bundesministerium für Bildung und Forschung (031L0184, 031L0181A)
- Deutsche Forschungsgemeinschaft (391137747, 395192176)
- European Research Council (773026, 716290)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genome Rearrangement Algorithms
- Keywords
- haplotype-resolved genome, structural variants, de novo genome assembly, long-read sequencing, strand-specific sequencing, transposable elements, expression quantitative trait loci, positive selection, human genetic variation
- MeSH terms
- Whole Genome Sequencing, Female, Genotype, Haplotypes, Humans, Male, Genetic Variation, Genome, Human, Sequence Analysis, DNA, Retroelements, Interspersed Repetitive Sequences, Quantitative Trait Loci, Population Groups, INDEL Mutation, Sequence Inversion, High-Throughput Nucleotide Sequencing
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
