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Telomere-to-telomere assembly of diploid chromosomes with Verkko

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Towards population-scale long-read sequencing

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Haplotype-aware variant calling with PEPPER-Margin-DeepVariant enables high accuracy in nanopore long-reads

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

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GraphAligner: rapid and versatile sequence-to-graph alignment

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Genome assembly in the telomere-to-telomere era

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Nanopore Technology and Its Applications in Gene Sequencing

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Generating lineage-resolved, complete metagenome-assembled genomes from complex microbial communities

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Semi-automated assembly of high-quality diploid human reference genomes

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Benchmarking challenging small variants with linked and long reads

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Advancements in long-read genome sequencing technologies and algorithms

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Chromosome-scale, haplotype-resolved assembly of human genomes

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Extended haplotype-phasing of long-read de novo genome assemblies using Hi-C

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

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Complex genetic variation in nearly complete human genomes

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Genomics in the long-read sequencing era

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

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Genome architecture and tetrasomic inheritance of autotetraploid potato

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Computational methods for chromosome-scale haplotype reconstruction

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lra: A long read aligner for sequences and contigs

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Increased mutation and gene conversion within human segmental duplications

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Dynamic, adaptive sampling during nanopore sequencing using Bayesian experimental design

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Applications of long-read sequencing to Mendelian genetics

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LongPhase: an ultra-fast chromosome-scale phasing algorithm for small and large variants

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

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Genome structural variation in human evolution

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A high-quality bonobo genome refines the analysis of hominid evolution

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Structural variant-based pangenome construction has low sensitivity to variability of haplotype-resolved bovine assemblies

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Profiling variable-number tandem repeat variation across populations using repeat-pangenome graphs

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Physical separation of haplotypes in dikaryons allows benchmarking of phasing accuracy in Nanopore and HiFi assemblies with Hi-C data

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Pushing the limits of HiFi assemblies reveals centromere diversity between two Arabidopsis thaliana genomes

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Strainberry: automated strain separation in low-complexity metagenomes using long reads

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Gaps and complex structurally variant loci in phased genome assemblies

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A Draft Human Pangenome ReferencePreprint

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The haplotype-resolved chromosome pairs of a heterozygous diploid African cassava cultivar reveal novel pan-genome and allele-specific transcriptome features

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Long-read whole-genome analysis of human single cells

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Merqury: reference-free quality, completeness, and phasing assessment for genome assembliesPreprint

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Gapless assembly of complete human and plant chromosomes using only nanopore sequencingPreprint

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

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A chromosome‐scale assembly of the bilberry genome identifies a complex locus controlling berry anthocyanin composition

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A chromosome-level phased genome enabling allele-level studies in sweet orange: a case study on citrus Huanglongbing tolerance

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

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An integrated personal and population-based Egyptian genome reference

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Whole-genome long-read sequencing downsampling and its effect on variant-calling precision and recallPreprint

Harvey, W. T., Ebert, P., Ebler, J., Audano, P. A., Munson, K. M., Hoekzema, K., Porubskỳ, D., Beck, C. R., Marschall, T., Garimella, K. V., et al. (2023) · Genome Research · doi:10.1101/gr.278070.123 · Cited by 43

State-of-the-art genome inference in the human MHC

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De novo diploid genome assembly using long noisy reads

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Parent-of-origin detection and chromosome-scale haplotyping using long-read DNA methylation sequencing and Strand-seq

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Fc gamma receptors: Their evolution, genomic architecture, genetic variation, and impact on human disease

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Inversion polymorphism in a complete human genome assembly

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Construction of Strand-seq libraries in open nanoliter arrays

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Haplotype-resolved assembly of a tetraploid potato genome using long reads and low-depth offspring data

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Phase Resolution of Heterozygous Sites in Diploid Genomes is Important to Phylogenomic Analysis under the Multispecies Coalescent Model

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A hidden layer of structural variation in transposable elements reveals potential genetic modifiers in human disease-risk lociPreprint

van Bree, E. J., Guimarães, R. L. F. P., Lundberg, M., Blujdea, E. R., Rosenkrantz, J. L., White, F. T. G., Poppinga, J., Ferrer‐Raventós, P., Schneider, A.-F. E., Clayton, I., et al. (2022) · Genome Research · doi:10.1101/gr.275515.121 · Cited by 30

A survey of current methods to detect and genotype inversions

Hanlon, V. C. T., Lansdorp, P. M., & Guryev, V. (2022) · Human Mutation · doi:10.1002/humu.24458 · Cited by 29

FixItFelix: improving genomic analysis by fixing reference errors

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Probably Correct: Rescuing Repeats with Short and Long Reads

Čechová, M. (2020) · Genes · doi:10.3390/genes12010048 · Cited by 27

Improving variant calling using population data and deep learning

Chen, N.-C., Kolesnikov, A., Goel, S., Yun, T., Chang, P.-C., & Carroll, A. W. (2023) · BMC Bioinformatics · doi:10.1186/s12859-023-05294-0 · Cited by 27

Advances in the discovery and analyses of human tandem repeats

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Construction and analysis of the chromosome-level haplotype-resolved genomes of two Crassostrea oyster congeners: Crassostrea angulata and Crassostrea gigas

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The role of structural variations in Alzheimer’s disease and other neurodegenerative diseases

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Evidence for opposing selective forces operating on human-specific duplicated TCAF genes in Neanderthals and humans

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Comprehensive and deep evaluation of structural variation detection pipelines with third-generation sequencing data

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

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

What a finding of gene copy number variation can add to the diagnosis of developmental neuropsychiatric disorders

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Robust haplotype-resolved assembly of diploid individuals without parental dataPreprint

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Haplotype-resolved Chinese male genome assembly based on high-fidelity sequencing

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Decoding sex: Elucidating sex determination and how high-quality genome assemblies are untangling the evolutionary dynamics of sex chromosomes

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BubbleGun: enumerating bubbles and superbubbles in genome graphs

Dabbaghie, F., Ebler, J., & Marschall, T. (2022) · Bioinformatics · doi:10.1093/bioinformatics/btac448 · Cited by 17

Detection of trait-associated structural variations using short-read sequencing

Kosugi, S., Kamatani, Y., Harada, K., Tomizuka, K., Momozawa, Y., Morisaki, T., & Terao, C. (2023) · Cell Genomics · doi:10.1016/j.xgen.2023.100328 · Cited by 19

Targeted adaptive long-read sequencing for discovery of complex phased variants in inherited retinal disease patients

Nakamichi, K., Gelder, R. N. V., Chao, J. R., & Mustafi, D. (2023) · Scientific Reports · doi:10.1038/s41598-023-35791-4 · Cited by 18

A deep dive into genome assemblies of non-vertebrate animals

Guiglielmoni, N., Rivera‐Vicéns, R. E., Koszul, R., & Flot, J. (2022) · Peer Community Journal · doi:10.24072/pcjournal.128 · Cited by 16

NanoSNP: a progressive and haplotype-aware SNP caller on low-coverage nanopore sequencing data

Huang, N., Xu, M., Nie, F., Ni, P., Xiao, C., Luo, F., & Wang, J. (2022) · Bioinformatics · doi:10.1093/bioinformatics/btac824 · Cited by 15

Profiling genes encoding the adaptive immune receptor repertoire with gAIRR Suite

Lin, M.-J., Lin, Y.-C., Chen, N.-C., Luo, A. C., Lai, S.-K., Hsu, C., Hsu, J. S., Chen, C., Yang, W., & Chen, P. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.922513 · Cited by 17

Dominance vs epistasis: the biophysical origins and plasticity of genetic interactions within and between alleles

Xie, X., Sun, X., Wang, Y., Lehner, B., & Li, X. (2023) · Nature Communications · doi:10.1038/s41467-023-41188-8 · Cited by 14

Haplotype Shuffling and Dimorphic Transposable Elements in the Human Extended Major Histocompatibility Complex Class II Region

Kulski, J. K., Suzuki, S., & Shiina, T. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.665899 · Cited by 15

Generation of lineage-resolved complete metagenome-assembled genomes by precision phasingPreprint

Bickhart, D. M., Kolmogorov, M., Tseng, E., Portik, D. M., Korobeynikov, A., Tolstoganov, I., Uritskiy, G., Liachko, I., Sullivan, S. T., Shin, S. B., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.05.04.442591 · Cited by 15

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

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

A telomere-to-telomere phased genome of an octoploid strawberry reveals a receptor kinase conferring anthracnose resistance

Han, H., Salinas, N., Barbey, C. R., Jang, Y., Fan, Z., Verma, S., Whitaker, V., & Lee, S. (2025) · GigaScience · doi:10.1093/gigascience/giaf005 · Cited by 14

Identification and Genotyping of Transposable Element Insertions From Genome Sequencing Data

Chu, C., Zhao, B., Park, P. J., & Lee, E. A. (2020) · Current Protocols in Human Genetics · doi:10.1002/cphg.102 · Cited by 15

Telomere-to-Telomere and Haplotype-Phased Genome Assemblies of the Heterozygous Octoploid ‘Florida Brilliance’ Strawberry (Fragaria × ananassa)Preprint

Han, H., Barbey, C. R., Fan, Z., Verma, S., Whitaker, V., & Lee, S. (2022) · bioRxiv · doi:10.1101/2022.10.05.509768 · Cited by 14

ASHLEYS: automated quality control for single-cell Strand-seq data

Gros, C., Sanders, A. D., Korbel, J. O., Marschall, T., & Ebert, P. (2021) · Bioinformatics · doi:10.1093/bioinformatics/btab221 · Cited by 12

Locityper enables targeted genotyping of complex polymorphic genes

Prodanov, T., Plender, E. G., Seebohm, G., Meuth, S. G., Eichler, E. E., & Marschall, T. (2025) · Nature Genetics · doi:10.1038/s41588-025-02362-4 · Cited by 22

MosaiCatcher v2: a single-cell structural variations detection and analysis reference framework based on Strand-seq

Weber, T., Cosenza, M. R., & Korbel, J. O. (2023) · Bioinformatics · doi:10.1093/bioinformatics/btad633 · Cited by 12

FiMAP: A fast identity-by-descent mapping test for biobank-scale cohorts

Chen, H., Naseri, A., & Zhi, D. (2023) · PLoS Genetics · doi:10.1371/journal.pgen.1011057 · Cited by 12

Impact and characterization of serial structural variations across humans and great apes

Höps, W., Rausch, T., Jendrusch, M., Ashraf, H., Audano, P. A., Austine, O., Basile, A. O., Beck, C. R., Bonder, M. J., Byrska-Bishop, M., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-52027-9 · Cited by 12

Focused Strategies for Defining the Genetic Architecture of Congenital Heart Defects

Martin, L. J., & Benson, D. W. (2021) · Genes · doi:10.3390/genes12060827 · Cited by 14

New algorithms for accurate and efficient de novo genome assembly from long DNA sequencing reads

González-García, L. N., Guevara-Barrientos, D., Lozano‐Arce, D., Gil, J., Díaz-Riaño, J., Duarte, E., Andrade, G. I., Bojacá, J. C., Sanchez, M. C. H., Chavarro, C., et al. (2023) · Life Science Alliance · doi:10.26508/lsa.202201719 · Cited by 13

Coverage-preserving sparsification of overlap graphs for long-read assembly

Jain, C. (2023) · Bioinformatics · doi:10.1093/bioinformatics/btad124 · Cited by 9

Haplotype-resolved assemblies and variant benchmark of a Chinese Quartet

Jia, P., Dong, L., Yang, X., Wang, B., Bush, S. J., Wang, T., Lin, J., Wang, S., Zhao, X., Xu, T., et al. (2023) · Genome biology · doi:10.1186/s13059-023-03116-3 · Cited by 11

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

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

Graphasing: phasing diploid genome assembly graphs with single-cell strand sequencing

Henglin, M., Ghareghani, M., Harvey, W. T., Porubskỳ, D., Koren, S., Eichler, E. E., Ebert, P., & Marschall, T. (2024) · Refubium (Universitätsbibliothek der Freien Universität Berlin) · doi:10.17169/refubium-45268

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

Fully Phased Sequence of a Diploid Human Genome Determined de Novo from the DNA of a Single Individual

Soifer, L., Fong, N. L., Yi, N., Ireland, A. T., Lam, I., Sooknah, M., Paw, J. S., Peluso, P. S., Concepcion, G. T., Rank, D. R., et al. (2020) · G3 Genes Genomes Genetics · doi:10.1534/g3.119.400995 · Cited by 10

Accurate 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