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Haplotype-resolved diverse human genomes and integrated analysis of structural variation
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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
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“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]
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“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]
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“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]
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“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]
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“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]
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“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]
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“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]
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“This result confirms that short-read-based SV discovery relative to a linear reference genome misses a large proportion of SVs5,6,8.”
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“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]
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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
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
Self-citationIQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies
Nguyen, L.-T., Schmidt, H. A., von Haeseler, A., & Minh, B. Q. (2015) · Molecular Biology and Evolution · doi:10.1093/molbev/msu300 · Cited by 26,046
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
Self-citationA 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
Self-citationMinimap2: Pairwise alignment for nucleotide sequences
Li, H. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty191 · Cited by 14,807
APE: analyses of phylogenetics and evolution in R language
Paradis, E., Claude, J., & Strimmer, K. (2004) · Bioinformatics · doi:10.1093/bioinformatics/btg412 · Cited by 11,335
The Human Genome Browser at UCSC
Kent, W. J., Sugnet, C. W., Furey, T. S., Roskin, K. M., Pringle, T. H., Zahler, A. M., & Haussler, A. D. (2002) · Genome Research · doi:10.1101/gr.229102 · Cited by 10,400
Jalview Version 2—a multiple sequence alignment editor and analysis workbench
Waterhouse, A. M., Procter, J. B., Martin, D. M. A., Clamp, M. E., & Barton, G. J. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp033 · Cited by 10,349
Fast model-based estimation of ancestry in unrelated individuals
Alexander, D. H., Novembre, J., & Lange, K. (2009) · Genome Research · doi:10.1101/gr.094052.109 · Cited by 9,898
Statistical significance for genomewide studies
Storey, J. D., & Tibshirani, R. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1530509100 · Cited by 9,692
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
GCTA: a tool for genome-wide complex trait analysis
Yang, J., Lee, S. H., Goddard, M. E., & Visscher, P. M. (2011) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2010.11.011 · Cited by 8,279
A map of human genome variation from population-scale sequencing.
The 1000 Genomes Project Consortium (2010) · Nature · doi:10.1038/nature09534 · Cited by 7,877
UniProt: the Universal Protein knowledgebase
Apweiler, R. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkh131 · Cited by 7,593
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 7,260
Li, H. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr509 · Cited by 6,454
Assembly of long, error-prone reads using repeat graphs
Kolmogorov, M., Yuan, J., Lin, Y., & Pevzner, P. A. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0072-8 · Cited by 5,986
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
The GTEx Consortium atlas of genetic regulatory effects across human tissues
The GTEx Consortium, Aguet, F., Anand, S., Ardlie, K. G., Gabriel, S., Getz, G. A., Graubert, A., Hadley, K., Handsaker, R. E., Huang, K. H., et al. (2020) · Science · doi:10.1126/science.aaz1776 · Cited by 5,547
Self-citationUniProt: the universal protein knowledgebase
The UniProt Consortium (2017) · Nucleic Acids Research · doi:10.1093/nar/gkw1099 · Cited by 4,436
Buniello, A., MacArthur, J. A. L., Cerezo, M., Harris, L. W., Hayhurst, J., Malangone, C., McMahon, A., Morales, J., Mountjoy, E., Sollis, E., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gky1120 · Cited by 4,000
Self-citationphangorn: phylogenetic analysis in R
Schliep, K. P. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq706 · Cited by 3,826
Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets
Zhu, Z., Zhang, F., Hu, H., Bakshi, A., Robinson, M. R., Powell, J. E., Montgomery, G. W., Goddard, M. E., Wray, N. R., Visscher, P. M., et al. (2016) · Nature Genetics · doi:10.1038/ng.3538 · Cited by 3,352
The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote
Liao, Y., Smyth, G. K., & Shi, W. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt214 · Cited by 3,064
Pan-cancer analysis of whole genomes
The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium, Aaltonen, L. A., Abascal, F., Abeshouse, A., Aburatani, H., Adams, D. J., Agrawal, N., Ahn, K. S., Ahn, S.-M., Aikata, H., et al. (2020) · Nature · doi:10.1038/s41586-020-1969-6 · Cited by 3,064
GENCODE reference annotation for the human and mouse genomes
Frankish, A., Diekhans, M., Ferreira, A.-M., Johnson, R., Jungreis, I., Loveland, J. E., Mudge, J. M., Sisu, C., Wright, J. C., Armstrong, J. C., et al. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky955 · Cited by 3,006
Self-citationMUMmer4: A fast and versatile genome alignment system
Marçais, G., Delcher, A. L., Phillippy, A. M., Coston, R., Salzberg, S. L., & Zimin, A. (2018) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1005944 · Cited by 2,484
DELLY: structural variant discovery by integrated paired-end and split-read analysis
Rausch, T., Zichner, T., Schlattl, A., Stütz, A. M., Beneš, V., & Korbel, J. O. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts378 · Cited by 2,438
Self-citationExpanded encyclopaedias of DNA elements in the human and mouse genomes
The ENCODE Project Consortium, Abascal, F., Acosta, R., Addleman, N. J., Adrian, J., Afzal, V., Ai, R., Aken, B., Akiyama, J. A., Jammal, O. A., et al. (2020) · Nature · doi:10.1038/s41586-020-2493-4 · Cited by 2,378
Self-citationAn 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
Self-citationThe UCSC Table Browser data retrieval tool
Karolchik, D. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkh103 · Cited by 2,314
BUSCO: Assessing Genome Assembly and Annotation Completeness
Seppey, M., Manni, M., & Zdobnov, E. M. (2019) · Methods in molecular biology · doi:10.1007/978-1-4939-9173-0_14 · Cited by 2,242
PhenoScanner V2: an expanded tool for searching human genotype–phenotype associations
Kamat, M., Blackshaw, J., Young, R., Surendran, P., Burgess, S., Danesh, J., Butterworth, A. S., & Staley, J. R. (2019) · Bioinformatics · doi:10.1093/bioinformatics/btz469 · Cited by 2,140
Scaling accurate genetic variant discovery to tens of thousands of samplesPreprint
Poplin, R. E., Ruano-Rubio, V., DePristo, M. A., Fennell, T. J., Carneiro, M. O., der Auwera, G. A. V., Kling, D. E., Gauthier, L. D., Levy‐Moonshine, A., Roazen, D., et al. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/201178 · Cited by 1,977
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
Self-citationA linear complexity phasing method for thousands of genomes
Delaneau, O., Marchini, J., & Zagury, J.-F. (2012) · Nature Methods · doi:10.1038/nmeth.1785 · Cited by 1,850
Wenger, A. M., Peluso, P., Rowell, W. J., Chang, P.-C., Hall, R. J., Concepcion, G. T., Ebler, J., Fungtammasan, A., Kolesnikov, A., Olson, N. D., et al. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0217-9 · Cited by 1,841
Self-citationA universal SNP and small-indel variant caller using deep neural networks
Poplin, R., Chang, P.-C., Alexander, D., Schwartz, S., Colthurst, T., Ku, A., Newburger, D., Dijamco, J., Nguyen, N., Afshar, P. T., et al. (2018) · Nature Biotechnology · doi:10.1038/nbt.4235 · Cited by 1,840
Reference-based phasing using the Haplotype Reference Consortium panel
Loh, P.-R., Danecek, P., Palamara, P. F., Fuchsberger, C., A Reshef, Y., K Finucane, H., Schoenherr, S., Forer, L., McCarthy, S., Abecasis, G. R., et al. (2016) · Nature Genetics · doi:10.1038/ng.3679 · Cited by 1,723
The impact of retrotransposons on human genome evolution
Cordaux, R., & Batzer, M. A. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2640 · Cited by 1,692
Abyzov, A., Urban, A. E., Snyder, M., & Gerstein, M. (2011) · Genome Research · doi:10.1101/gr.114876.110 · Cited by 1,658
Self-citationSequencing of 50 Human Exomes Reveals Adaptation to High Altitude
Yi, X., Liang, Y., Huerta-Sanchez, E., Jin, X., Cuo, Z. X. P., Pool, J. E., Xu, X., Jiang, H., Vinckenbosch, N., Korneliussen, T. S., et al. (2010) · Science · doi:10.1126/science.1190371 · Cited by 1,611 · cited 8×
“Restricting our analysis to SVs located within 5 kbp of genes and applying population branch statistics (PBS) (51), we identified 117 stratified SVs (PBS >3 standard deviations) (tables S34 and S35) and further characterize these by the number of base pairs deleted or inserted per locus (Fig.”
BackgroundMethodInfluentialSelf-citationThe 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
LUMPY: a probabilistic framework for structural variant discovery
Layer, R. M., Chiang, C., Quinlan, A. R., & Hall, I. M. (2014) · Genome biology · doi:10.1186/gb-2014-15-6-r84 · Cited by 1,544
Self-citationVersatile genome assembly evaluation with QUAST-LG
Mikheenko, A., Prjibelski, A. D., Saveliev, V., Antipov, D., & Gurevich, A. A. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty266 · Cited by 1,537
Alu repeats and human genomic diversity
Batzer, M., & Deininger, P. (2002) · Nature reviews genetics · doi:10.1038/nrg798 · Cited by 1,522
PhenoScanner: a database of human genotype-phenotype associations.
Staley, J. R., Blackshaw, J., Kamat, M. A., Ellis, S., Surendran, P., Sun, B. B., Paul, D. S., Freitag, D., Burgess, S., Danesh, J., et al. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw373 · Cited by 1,479
Human Demographic History Impacts Genetic Risk Prediction across Diverse Populations
Martin, A. R., Gignoux, C. R., Walters, R. K., Wojcik, G. L., Neale, B. M., Gravel, S., Daly, M. J., Bustamante, C. D., & Kenny, E. E. (2017) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2017.03.004 · Cited by 1,391
Fast and accurate long-read assembly with wtdbg2
Ruan, J., & Li, H. (2019) · Nature Methods · doi:10.1038/s41592-019-0669-3 · Cited by 1,352
BigWig and BigBed: enabling browsing of large distributed datasets
Kent, W. J., Zweig, A. S., Barber, G. P., Hinrichs, A. S., & Karolchik, D. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq351 · Cited by 1,268
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
Self-citationGenetic Signatures of Strong Recent Positive Selection at the Lactase Gene
Bersaglieri, T., Sabeti, P. C., Patterson, N. J., Vanderploeg, T. N., Schaffner, S. F., Drake, J. A., Rhodes, M. E., Reich, D., & Hirschhorn, J. N. (2004) · The American Journal of Human Genetics · doi:10.1086/421051 · Cited by 1,169
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 · cited 3×
“%) now assigned to homology-based (>50 bp) mu-tationmechanisms,includingHDR,NAHR,and VNTR. Breakpointcharacterizationwithshort-readdataapparentlybiasedearlyreportstowardspecificregions,concludingthat<30%ofSVs weredrivenbyhomology-basedmutational mechanisms( 25 – 27 ).”
BackgroundSelf-citationHuman L1 retrotransposon encodes a conserved endonuclease required for retrotransposition
Feng, Q., Moran, J. V., Kazazian, H. H., & Boeke, J. D. (1996) · Cell · doi:10.1016/s0092-8674(00)81997-2 · Cited by 1,139
DIP: the Database of Interacting Proteins
Xénarios, I. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.289 · Cited by 1,126
The genomic landscape of Neanderthal ancestry in present-day humans
Sankararaman, S., Mallick, S., Dannemann, M., Prüfer, K., Kelso, J., Pääbo, S., Patterson, N., & Reich, D. (2014) · Nature · doi:10.1038/nature12961 · Cited by 1,107
Byrska-Bishop, M., Evani, U. S., Zhao, X., Basile, A. O., Abel, H. J., Regier, A. A., Corvelo, A., Clarke, W. E., Musunuri, R., Nagulapalli, K., et al. (2022) · Cell · doi:10.1016/j.cell.2022.08.004 · Cited by 1,094
Self-citationHot L1s account for the bulk of retrotransposition in the human population
Brouha, B., Schustak, J., Badge, R. M., Lutz-Prigge, S., Farley, A. H., Moran, J. V., & Kazazian, H. H. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0831042100 · Cited by 1,073
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
Self-citationInterspersed repeats and other mementos of transposable elements in mammalian genomes
Smit, A. F. (1999) · Current Opinion in Genetics & Development · doi:10.1016/s0959-437x(99)00031-3 · Cited by 949
Somatic mosaicism in neuronal precursor cells mediated by L1 retrotransposition
Muotri, A. R., Chu, V. T., Marchetto, M. C. N., Deng, W., Moran, J. V., & Gage, F. H. (2005) · Nature · doi:10.1038/nature03663 · Cited by 942
RFMix: A Discriminative Modeling Approach for Rapid and Robust Local-Ancestry Inference
Maples, B. K., Gravel, S., Kenny, E. E., & Bustamante, C. D. (2013) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2013.06.020 · Cited by 900
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
Self-citationThe UCSC Genome Browser database: 2019 update
Haeussler, M., Zweig, A. S., Tyner, C., Speir, M. L., Rosenbloom, K. R., Raney, B. J., Lee, C. M., Lee, B. T., Hinrichs, A. S., Gonzalez, J. N., et al. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky1095 · Cited by 879
Self-citationExtensive sequencing of seven human genomes to characterize benchmark reference materials
Zook, J. M., Catoe, D., McDaniel, J., Vang, L., Spies, N., Sidow, A., Weng, Z., Liu, Y., Mason, C. E., Alexander, N., et al. (2016) · Scientific Data · doi:10.1038/sdata.2016.25 · Cited by 811
Self-citationResolving 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 786
Self-citationMechanisms underlying structural variant formation in genomic disorders
Carvalho, C. M. B., & Lupski, J. R. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2015.25 · Cited by 774
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
Self-citationTelomere-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
Self-citationEstimating the total number of phosphoproteins and phosphorylation sites in eukaryotic proteomes
Vlastaridis, P., Kyriakidou, P., Chaliotis, A., de Peer, Y. V., Oliver, S. G., & Amoutzias, G. D. (2017) · GigaScience · doi:10.1093/gigascience/giw015 · Cited by 746
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 723
Self-citationRoles for retrotransposon insertions in human disease
Hancks, D. C., & Kazazian, H. H. (2016) · Mobile DNA · doi:10.1186/s13100-016-0065-9 · Cited by 670
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
Self-citationHuman L1 Retrotransposition: cis Preference versus trans Complementation
Wei, W., Gilbert, N., Ooi, S. L., Lawler, J. F., Ostertag, E. M., Kazazian, H. H., Boeke, J. D., & Moran, J. V. (2001) · Molecular and Cellular Biology · doi:10.1128/mcb.21.4.1429-1439.2001 · Cited by 637
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
Self-citationdbSNP: a database of single nucleotide polymorphisms
Smigielski, E. M. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.352 · Cited by 630
A General Approach for Haplotype Phasing across the Full Spectrum of Relatedness
O'Connell, J., Gurdasani, D., Delaneau, O., Pirastu, N., Ulivi, S., Cocca, M., Traglia, M., Huang, J., Huffman, J. E., Rudan, I., et al. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004234 · Cited by 593
Active human retrotransposons: variation and disease
Hancks, D. C., & Kazazian, H. H. (2012) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2012.02.006 · Cited by 592
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 580
Sequence patterns indicate an enzymatic involvement in integration of mammalian retroposons
Jurka, J. (1997) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.94.5.1872 · Cited by 560
Partitioning Heritability of Regulatory and Cell-Type-Specific Variants across 11 Common Diseases
Gusev, A., Lee, S. H., Trynka, G., Finucane, H., Vilhjálmsson, B. J., Xu, H., Zang, C., Ripke, S., Bulik-Sullivan, B., Stahl, E., et al. (2014) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2014.10.004 · Cited by 544
Self-citationWhich transposable elements are active in the human genome?
Mills, R. E., Bennett, E. A., Iskow, R. C., & Devine, S. E. (2007) · Trends in Genetics · doi:10.1016/j.tig.2007.02.006 · Cited by 541
Self-citationThe International Genome Sample Resource (IGSR) collection of open human genomic variation resources
Fairley, S., Lowy, E., Perry, E. H., & Flicek, P. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz836 · Cited by 514
Self-citationRecent Evidence for Evolution of the Genetic Code
Jukes, T. H., & Osawa, S. (1991) · Springer eBooks · doi:10.1007/978-4-431-68302-5_6 · Cited by 506
The impact of structural variation on human gene expression
GTEx Consortium, Chiang, C., Scott, A. J., Davis, J. R., Tsang, E. K., Li, X., Kim, Y., Hadzic, T., Damani, F. N., Ganel, L., et al. (2017) · Nature Genetics · doi:10.1038/ng.3834 · Cited by 495
Self-citationCharacterizing the Major Structural Variant Alleles of the Human Genome
Audano, P. A., Sulovari, A., Graves-Lindsay, T. A., Cantsilieris, S., Sorensen, M., Welch, A. E., Dougherty, M. L., Nelson, B. J., Shah, A., Dutcher, S. K., et al. (2019) · Cell · doi:10.1016/j.cell.2018.12.019 · Cited by 492
Self-citationJun, G., Flickinger, M., Hetrick, K. N., Romm, J. M., Doheny, K. F., Abecasis, G. R., Boehnke, M., & Kang, H. M. (2012) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2012.09.004 · Cited by 484
A method for genome-wide genealogy estimation for thousands of samples
Speidel, L., Forest, M., Shi, S., & Myers, S. R. (2019) · Nature Genetics · doi:10.1038/s41588-019-0484-x · Cited by 480
WhatsHap: fast and accurate read-based phasingPreprint
Martin, M., Patterson, M., Garg, S., Fischer, S. O., Pisanti, N., Klau, G. W., Schönhuth, A., & Marschall, T. (2016) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/085050 · Cited by 464
Self-citationLOLA: enrichment analysis for genomic region sets and regulatory elements in R and Bioconductor
Sheffield, N. C., & Bock, C. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv612 · Cited by 456
Klambauer, G., Schwarzbauer, K., Mayr, A., Clevert, D.-A., Mitterecker, A., Bodenhofer, U., & Hochreiter, S. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks003 · Cited by 454
W hats H ap : Weighted Haplotype Assembly for Future-Generation Sequencing Reads
Patterson, M., Marschall, T., Pisanti, N., van Iersel, L., Stougie, L., Klau, G. W., & Schönhuth, A. (2015) · Journal of Computational Biology · doi:10.1089/cmb.2014.0157 · Cited by 453
Self-citationRodriguez-Martin, B., Alvarez, E. G., Baez-Ortega, A., Zamora, J., Supek, F., Demeulemeester, J., Santamarina, M., Ju, Y. S., Temes, J., Garcia-Souto, D., et al. (2020) · Nature Genetics · doi:10.1038/s41588-019-0562-0 · Cited by 451
Self-citationZerbino, D. R., Wilder, S. P., Johnson, N., Juettemann, T., & Flicek, P. R. (2015) · Genome Biology · doi:10.1186/s13059-015-0621-5 · Cited by 429
Self-citationA 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
Self-citationExtensive transduction of nonrepetitive DNA mediated by L1 retrotransposition in cancer genomes
Tubio, J. M. C., Li, Y., Ju, Y. S., Martincorena, I., Cooke, S. L., Tojo, M., Gundem, G., Pipinikas, C. P., Zamora, J., Raine, K., et al. (2014) · Science · doi:10.1126/science.1251343 · Cited by 412
Self-citationAbundant contribution of short tandem repeats to gene expression variation in humans
Gymrek, M., Willems, T., Guilmatre, A., Zeng, H., Markus, B., Georgiev, S., Daly, M. J., Price, A. L., Pritchard, J. K., Sharp, A. J., et al. (2016) · Nature Genetics · doi:10.1038/ng.3461 · Cited by 410
An open resource for accurately benchmarking small variant and reference calls
Zook, J. M., McDaniel, J., Olson, N. D., Wagner, J., Parikh, H. M., Heaton, H., Irvine, S. A., Trigg, L., Truty, R., McLean, C. Y., et al. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0074-6 · Cited by 404
Non-AUG translation: a new start for protein synthesis in eukaryotesPreprint
Kearse, M. G., & Wilusz, J. E. (2017) · Genes & Development · doi:10.1101/gad.305250.117 · Cited by 398
Large multiallelic copy number variations in humans
Handsaker, R. E., Doren, V. V., Berman, J. R., Genovese, G., Kashin, S., Boettger, L. M., & McCarroll, S. A. (2015) · Nature Genetics · doi:10.1038/ng.3200 · Cited by 388
SVA Elements: A Hominid-specific Retroposon Family
Wang, H., Xing, J., Grover, D., Hedges, D. J., Han, K., Walker, J. A., & Batzer, M. A. (2005) · Journal of Molecular Biology · doi:10.1016/j.jmb.2005.09.085 · Cited by 386
Global reference mapping of human transcription factor footprints
Vierstra, J., Lazar, J., Sandstrom, R., Halow, J., Lee, K., Bates, D., Diegel, M., Dunn, D., Neri, F., Haugen, E., et al. (2020) · Nature · doi:10.1038/s41586-020-2528-x · Cited by 386
The Mobile Element Locator Tool (MELT): population-scale mobile element discovery and biologyPreprint
Gardner, E. J., Lam, V. K. L., Harris, D., Chuang, N. T., Scott, E., Pittard, W. S., Mills, R. E., & Devine, S. E. (2017) · Genome Research · doi:10.1101/gr.218032.116 · Cited by 378
Self-citationDiscovery 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
Self-citationComputational pan-genomics: status, promises and challenges
Marschall, T., Marz, M., Abeel, T., Dijkstra, L., Dutilh, B. E., Ghaffaari, A., Kersey, P., Kloosterman, W. P., Mäkinen, V., Novak, A. M., et al. (2016) · Briefings in Bioinformatics · doi:10.1093/bib/bbw089 · Cited by 369
Self-citationSVA Elements Are Nonautonomous Retrotransposons that Cause Disease in Humans
Ostertag, E. M., Goodier, J. L., Zhang, Y., & Kazazian, H. H. (2003) · The American Journal of Human Genetics · doi:10.1086/380207 · Cited by 357
Recent evidence for evolution of the genetic code
Osawa, S., Jukes, T. H., Watanabe, K., & Muto, A. (1992) · Microbiological Reviews · doi:10.1128/mr.56.1.229-264.1992 · Cited by 357
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
High-resolution comparative analysis of great ape genomes
Kronenberg, Z. N., Fiddes, I. T., Gordon, D., Murali, S., Cantsilieris, S., Meyerson, O. S., Underwood, J. G., Nelson, B. J., Chaisson, M. J. P., Dougherty, M. L., et al. (2018) · Science · doi:10.1126/science.aar6343 · Cited by 350
Self-citationGlobal 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
Self-citationThe 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 335
Self-citationLong-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
Self-citationEizenga, 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
Self-citationApparent latent structure within the UK Biobank sample has implications for epidemiological analysis
Haworth, S., Mitchell, R., Corbin, L., Wade, K. H., Dudding, T., Budu-Aggrey, A., Carslake, D., Hemani, G., Paternoster, L., Smith, G. D., et al. (2019) · Nature Communications · doi:10.1038/s41467-018-08219-1 · Cited by 314
L1 (LINE-1) Retrotransposon Evolution and Amplification in Recent Human History
Boissinot, S., Chevret, P., & Furano, A. V. (2000) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a026372 · Cited by 312
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
Self-citationMapping 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
Self-citationUnit-Length Line-1 Transcripts in Human Teratocarcinoma Cells
Skowroński, J., Fanning, T. G., & Singer, M. (1988) · Molecular and Cellular Biology · doi:10.1128/mcb.8.4.1385 · Cited by 301
Ballif, B. C., Theisen, A. P., Coppinger, J., Gowans, G. C., Hersh, J. H., Madan‐Khetarpal, S., Schmidt, K. R., Tervo, R. C., Escobar, L., Friedrich, C. A., et al. (2008) · Molecular Cytogenetics · doi:10.1186/1755-8166-1-8 · Cited by 295
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
Self-citationActive Alu retrotransposons in the human genomePreprint
Bennett, E. A., Keller, H., Mills, R. E., Schmidt, S., Moran, J. V., Weichenrieder, O., & Devine, S. E. (2008) · Genome Research · doi:10.1101/gr.081737.108 · Cited by 274
Self-citationLighter: fast and memory-efficient sequencing error correction without counting
Song, L., Florea, L., & Langmead, B. (2014) · Genome biology · doi:10.1186/s13059-014-0509-9 · Cited by 261
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 259
Self-citationByrska‐Bishop, M. S., Evani, U. S., Zhao, X., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.02.06.430068 · Cited by 259
Self-citationMutation spectrum revealed by breakpoint sequencing of human germline CNVs
Conrad, D. F., Bird, C., Blackburne, B. P., Lindsay, S., Mamanova, L., Lee, C., Turner, D., & Hurles, M. E. (2010) · Nature Genetics · doi:10.1038/ng.564 · Cited by 258
Self-citationA synthetic-diploid benchmark for accurate variant-calling evaluation
Li, H., Bloom, J. M., Farjoun, Y., Fleharty, M., Gauthier, L., Neale, B., & MacArthur, D. (2018) · Nature Methods · doi:10.1038/s41592-018-0054-7 · Cited by 253
Edge, P., & Bansal, V. (2019) · Nature Communications · doi:10.1038/s41467-019-12493-y · Cited by 252
A molecular mechanism for choosing alcohol over an alternative reward
Augier, E., Barbier, E., Dulman, R. S., Licheri, V., Augier, G., Domi, E., Barchiesi, R., Farris, S., Nätt, D., Mayfield, R. D., et al. (2018) · Science · doi:10.1126/science.aao1157 · Cited by 241
Single-cell sequencing reveals karyotype heterogeneity in murine and human malignancies
Bakker, B., Taudt, A., Belderbos, M. E., Porubskỳ, D., Spierings, D. C. J., de Jong, T. V., Halsema, N., Kazemier, H. G., Hoekstra-Wakker, K., Bradley, A., et al. (2016) · Genome biology · doi:10.1186/s13059-016-0971-7 · Cited by 238
Compacting de Bruijn graphs from sequencing data quickly and in low memory
Chikhi, R., Limasset, A., & Medvedev, P. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw279 · Cited by 228
Evolutionary toggling of the MAPT 17q21.31 inversion region
Zody, M. C., Jiang, Z., Fung, H.-C., Antonacci, F., Hillier, L. W., Cardone, M. F., Graves, T. A., Kidd, J. M., Cheng, Z., Abouelleil, A., et al. (2008) · Nature Genetics · doi:10.1038/ng.193 · Cited by 227
Self-citationRegier, A., Farjoun, Y., Larson, D. E., Krasheninina, O. A., Kang, H. M., Howrigan, D. P., Chen, B.-J., Kher, M., Banks, E., Ames, D. C., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-06159-4 · Cited by 224
Self-citationCompleting the map of human genetic variation
The Human Genome Structural Variation Working Group, Eichler, E. E., Nickerson, D. A., Altshuler, D., Bowcock, A. M., Brooks, L., Carter, N. P., Church, D. M., Felsenfeld, A. L., Guyer, M. S., et al. (2007) · Nature · doi:10.1038/447161a · Cited by 213
Self-citationThe Diabetes Susceptibility Gene Clec16a Regulates Mitophagy
Soleimanpour, S. A., Gupta, A., Bakay, M., Ferrari, A. M., Groff, D. N., Fadista, J., Spruce, L. A., Kushner, J. A., Groop, L., Seeholzer, S. H., et al. (2014) · Cell · doi:10.1016/j.cell.2014.05.016 · Cited by 211
Bifrost: highly parallel construction and indexing of colored and compacted de Bruijn graphs
Holley, G., & Melsted, P. (2020) · Genome biology · doi:10.1186/s13059-020-02135-8 · Cited by 211
SVA retrotransposons: Evolution and genetic instability
Hancks, D. C., & Kazazian, H. H. (2010) · Seminars in Cancer Biology · doi:10.1016/j.semcancer.2010.04.001 · Cited by 208
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
Self-citationDNA template strand sequencing of single-cells maps genomic rearrangements at high resolution
Falconer, E., Hills, M., Naumann, U., Poon, S. S. S., Chavez, E. A., Sanders, A. D., Zhao, Y., Hirst, M., & Lansdorp, P. M. (2012) · Nature Methods · doi:10.1038/nmeth.2206 · Cited by 199
Self-citationParagraph: 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
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 195
Self-citationNucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library
Lam, H. Y. K., Mu, X. J., Stütz, A. M., Andrea Tanzer, A., Cayting, P. D., Snyder, M. P., Kim, P. M., Korbel, J. O., & Gerstein, M. (2009) · Nature Biotechnology · doi:10.1038/nbt.1600 · Cited by 193
Self-citationSVIM-asm: structural variant detection from haploid and diploid genome assemblies
Heller, D., & Vingron, M. (2020) · Bioinformatics · doi:10.1093/bioinformatics/btaa1034 · Cited by 191
Chromosome-scale, haplotype-resolved assembly of human genomes
Garg, S., Fungtammasan, A., Carroll, A. W., Chou, M., Schmitt, A. D., Zhou, X., Mac, S., Peluso, P. S., Hatas, E., Ghurye, J., et al. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0711-0 · Cited by 179
Self-citationEmergence of primate genes by retrotransposon-mediated sequence transduction
Xing, J., Wang, H., Belancio, V. P., Cordaux, R., Deininger, P. L., & Batzer, M. A. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0603224103 · Cited by 175
A continuum of admixture in the Western Hemisphere revealed by the African Diaspora genome
Mathias, R. A., Taub, M. A., Gignoux, C. R., Fu, W., Musharoff, S. A., O’Connor, T. D., Vergara, C., Torgerson, D. G., Pino-Yanes, M. D. M., Shringarpure, S., et al. (2016) · Nature Communications · doi:10.1038/ncomms12522 · Cited by 170
Active Alu Element “A-Tails”: Size Does MatterPreprint
Roy‐Engel, A. M., Salem, A. H., Oyeniran, O. O., Deininger, L., Hedges, D. J., Kilroy, G. E., Batzer, M. A., & Deininger, P. L. (2002) · Genome Research · doi:10.1101/gr.384802 · Cited by 167
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
Self-citationDarwinian and demographic forces affecting human protein coding genesPreprint
Nielsen, R., Hubisz, M. J., Hellmann, I., Torgerson, D. G., Andrés, A. M., Albrechtsen, A., Gutenkunst, R. N., Adams, M. D., Cargill, M., Boyko, A. R., et al. (2009) · Genome Research · doi:10.1101/gr.088336.108 · Cited by 158
Robust LOD scores for variance component-based linkage analysis
Blangero, J., Williams, J. T., & Almasy, L. A. (2000) · Genetic Epidemiology · doi:10.1002/1098-2272(2000)19:1+ · Cited by 153
Characterization of missing human genome sequences and copy-number polymorphic insertions
Kidd, J. M., Sampas, N., Antonacci, F., Graves, T., Fulton, R. S., Hayden, H. S., Alkan, C., Malig, M., Ventura, M., Giannuzzi, G., et al. (2010) · Nature Methods · doi:10.1038/nmeth.1451 · Cited by 150
Self-citationComputational Pan-Genomics: Status, Promises and ChallengesPreprint
Marschall, T., Marz, M., Abeel, T., Dijkstra, L., Dutilh, B. E., Ghaffaari, A., Kersey, P. J., Kloosterman, W. P., Mäkinen, V., Novak, A. M., et al. (2016) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/043430 · Cited by 147
Self-citationTan, L. L., Oswald, M. J., Heinl, C., Romero, O. A. R., Kaushalya, S. K., Monyer, H., & Kuner, R. (2019) · Nature Communications · doi:10.1038/s41467-019-08873-z · Cited by 144
Wham: Identifying Structural Variants of Biological Consequence
Kronenberg, Z. N., Osborne, E. J., Cone, K. R., Kennedy, B., Domyan, E. T., Shapiro, M. D., Elde, N. C., & Yandell, M. D. (2015) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1004572 · Cited by 139
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 134
Self-citationTracy: basecalling, alignment, assembly and deconvolution of sanger chromatogram trace files
Rausch, T., Fritz, M. H.-Y., Untergasser, A., & Benes, V. (2020) · BMC Genomics · doi:10.1186/s12864-020-6635-8 · Cited by 130
Self-citationSanders, A. D., Falconer, E., Hills, M., Spierings, D. C. J., & Lansdorp, P. M. (2017) · Nature Protocols · doi:10.1038/nprot.2017.029 · Cited by 129
Self-citationGenome-wide de novo L1 Retrotransposition Connects Endonuclease Activity with Replication
Flasch, D. A., Macia, Á., Sánchez, L., Ljungman, M., Heras, S. R., García-Pérez, J. L., Wilson, T. E., & Moran, J. V. (2019) · Cell · doi:10.1016/j.cell.2019.02.050 · Cited by 127
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 123
Self-citationEvolutionary changes in the genetic code
Jukes, T. H., & Osawa, S. (1993) · Comparative Biochemistry and Physiology Part B Comparative Biochemistry · doi:10.1016/0305-0491(93)90122-l · Cited by 122
5′-Transducing SVA retrotransposon groups spread efficiently throughout the human genomePreprint
Damert, A., Raiz, J., Horn, A. V., Löwer, J., Wang, H., Xing, J., Batzer, M. A., Löwer, R., & Schumann, G. G. (2009) · Genome Research · doi:10.1101/gr.093435.109 · Cited by 117
Efficient set tests for the genetic analysis of correlated traits
Casale, F. P., Rakitsch, B., Lippert, C., & Stegle, O. (2015) · Nature Methods · doi:10.1038/nmeth.3439 · Cited by 116
Self-citationlra: A long read aligner for sequences and contigs
Ren, J., & Chaisson, M. (2021) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1009078 · Cited by 110
Self-citationZhou, 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 98
Self-citationThe Role of Somatic L1 Retrotransposition in Human Cancers
Scott, E., & Devine, S. E. (2017) · Viruses · doi:10.3390/v9060131 · Cited by 95
Self-citationDense and accurate whole-chromosome haplotyping of individual genomes
Porubskỳ, D., Garg, S., Sanders, A. D., Korbel, J. O., Guryev, V., Lansdorp, P. M., & Marschall, T. (2017) · Nature Communications · doi:10.1038/s41467-017-01389-4 · Cited by 95
Self-citationSingle-cell analysis of structural variations and complex rearrangements with tri-channel processing
Sanders, A. D., Meiers, S., Ghareghani, M., Porubskỳ, D., Jeong, H., Vliet, A. V., Rausch, T., Richter‐Pechańska, P., Kunz, J. B., Jenni, S., et al. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0366-x · Cited by 95
Self-citationHuman Genome Assembly in 100 MinutesPreprint
Chin, C.-S., & Khalak, A. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/705616 · Cited by 91
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 89
Self-citationHsieh, 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 86
Self-citationBecker, T., Lee, W., Leone, J., Zhu, Q., Zhang, C., Liu, S., Sargent, J., Shanker, K., Mil-Homens, A., Cerveira, E., et al. (2018) · Genome biology · doi:10.1186/s13059-018-1404-6 · Cited by 76
Self-citationRecurrent 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
Self-citationsvtools: population-scale analysis of structural variation
Larson, D. E., Abel, H., Chiang, C., Badve, A., Das, I., Eldred, J. M., Layer, R. M., & Hall, I. M. (2019) · Bioinformatics · doi:10.1093/bioinformatics/btz492 · Cited by 71
Self-citationLong-read genome sequencing for the molecular diagnosis of neurodevelopmental disorders
Hiatt, S. M., Lawlor, J. M. J., Handley, L. H., Ramaker, R. C., Rogers, B. B., Partridge, E. C., Boston, L. B., Williams, M. E., Plott, C., Jenkins, J. W., et al. (2021) · Human Genetics and Genomics Advances · doi:10.1016/j.xhgg.2021.100023 · Cited by 70
Bonder, M. J., Smail, C., Gloudemans, M. J., Frésard, L., Jakubosky, D. A., D’Antonio, M., Li, X., Ferraro, N. M., Carcamo‐Orive, I., Mirauta, B. A., et al. (2021) · Nature Genetics · doi:10.1038/s41588-021-00800-7 · Cited by 69
Self-citationNucDiff: in-depth characterization and annotation of differences between two sets of DNA sequences
Khelik, K., Lagesen, K., Sandve, G. K., Rognes, T., & Nederbragt, A. J. (2017) · BMC Bioinformatics · doi:10.1186/s12859-017-1748-z · Cited by 64
A CAG/CTG expansion in the normal population
Nakamoto, M., Takebayashi, H., Kawaguchi, Y., Narumiya, S., Taniwaki, M., Nakamura, Y., Ishikawa, Y., Akiguchi, I., Kimura, J., & Kakizuka, A. (1997) · Nature Genetics · doi:10.1038/ng1297-385 · Cited by 62
Immune signatures correlate with L1 retrotransposition in gastrointestinal cancersPreprint
Jung, H., Choi, J. K., & Lee, E. A. (2018) · Genome Research · doi:10.1101/gr.231837.117 · Cited by 62
Evolutionary changes in the genetic code
Osawa, S., Muto, A., Jukes, T. H., & Ohama, T. (1990) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.1990.0060 · Cited by 61
Profiling variable-number tandem repeat variation across populations using repeat-pangenome graphs
Lu, T.-Y. T., Munson, K. M., Lewis, A. P., Zhu, Q., Tallon, L. J., Devine, S. E., Lee, C., Eichler, E. E., & Chaisson, M. (2021) · Nature Communications · doi:10.1038/s41467-021-24378-0 · Cited by 60
Self-citationCotto, K. C., Feng, Y.-Y., Ramu, A., Richters, M. M., Freshour, S. L., Skidmore, Z. L., Xia, H., McMichael, J. F., Kunisaki, J., Campbell, K. M., et al. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/436634 · Cited by 59
Population-scale proteome variation in human induced pluripotent stem cells
(2020) · doi:10.7554/elife.57390 · Cited by 59
Self-citationThe structure, function, and evolution of a complete human chromosome 8Preprint
Logsdon, G. A., Vollger, M. R., Hsieh, P., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.09.08.285395 · Cited by 55
Self-citationAlteration of genome folding via contact domain boundary insertion
Zhang, D., Huang, P., Sharma, M., Keller, C. A., Giardine, B. M., Zhang, H., Gilgenast, T. G., Phillips‐Cremins, J. E., Hardison, R. C., & Blobel, G. A. (2020) · Nature Genetics · doi:10.1038/s41588-020-0680-8 · Cited by 48
breakpointR: an R/Bioconductor package to localize strand state changes in Strand-seq data
Porubskỳ, D., Sanders, A. D., Taudt, A., Colomé‐Tatché, M., Lansdorp, P. M., & Guryev, V. (2019) · Bioinformatics · doi:10.1093/bioinformatics/btz681 · Cited by 47
Self-citationLINE-1 preTa Elements in the Human Genome
Salem, A. H., Myers, J. S., Otieno, A. C., Watkins, W. S., Jorde, L. B., & Batzer, M. A. (2003) · Journal of Molecular Biology · doi:10.1016/s0022-2836(03)00032-9 · Cited by 43
Regier, A., Farjoun, Y., Larson, D. E., et al. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/269316 · Cited by 34
Self-citationZhao, X., Weber, A. M., & Mills, R. E. (2017) · GigaScience · doi:10.1093/gigascience/gix061 · Cited by 32
Self-citationAccurate chromosome-scale haplotype-resolved assembly of human genomesPreprint
Garg, S., Fungtammasan, A., Carroll, A. W., Chou, M., Schmitt, A., Zhou, X., Mac, S., Peluso, P., Hatas, E., Ghurye, J., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/810341 · Cited by 29
Self-citationStrand-seq enables reliable separation of long reads by chromosome via expectation maximization
Ghareghani, M., Porubskỳ, D., Sanders, A. D., Meiers, S., Eichler, E. E., Korbel, J. O., & Marschall, T. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty290 · Cited by 27
Self-citation
Flagged first, then by citations
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
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
“For PAV (v0.”
BackgroundMethodResultInfluentialSelf-citationByrska-Bishop, M., Evani, U. S., Zhao, X., Basile, A. O., Abel, H. J., Regier, A. A., Corvelo, A., Clarke, W. E., Musunuri, R., Nagulapalli, K., et al. (2022) · Cell · doi:10.1016/j.cell.2022.08.004 · Cited by 1,094
Self-citationFu, J. M., Satterstrom, F. K., Peng, M., Brand, H., Collins, R. L., Dong, S., Wamsley, B., Klei, L., Wang, L., Hao, S. P., et al. (2022) · Nature Genetics · doi:10.1038/s41588-022-01104-0 · Cited by 640
Self-citationDetection of mosaic and population-level structural variants with Sniffles2
Smolka, M., Paulin, L. F., Grochowski, C. M., Horner, D. W., Mahmoud, M., Behera, S., Kalef-Ezra, E., Gandhi, M., Hong, K., Pehli̇van, D., et al. (2024) · Nature Biotechnology · doi:10.1038/s41587-023-02024-y · Cited by 548
Graph pangenome captures missing heritability and empowers tomato breeding
Zhou, Y., Zhang, Z., Bao, Z., Li, H., Lyu, Y., Zan, Y., Wu, Y., Cheng, L. Z., Fang, Y., Wu, K., et al. (2022) · Nature · doi:10.1038/s41586-022-04808-9 · Cited by 542
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.
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