Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome

DNA sequencing with chain-terminating inhibitors

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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

A global reference for human genetic variation

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Minimap2: Pairwise alignment for nucleotide sequences

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The sequence of the human genome

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BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

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A framework for variation discovery and genotyping using next-generation DNA sequencing data

DePristo, M. A., Banks, E., Poplin, R. E., Garimella, K. V., Maguire, J., Hartl, C., Philippakis, A., del Angel, G., Rivas, M. A., Hanna, M., et al. (2011) · Nature Genetics · doi:10.1038/ng.806 · Cited by 11,457

Analysis of the genome sequence of the flowering plant Arabidopsis thaliana

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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

Initial sequencing and comparative analysis of the mouse genome

Mouse Genome Sequencing Consortium (2002) · Nature · doi:10.1038/nature01262 · Cited by 7,187

Using long-read CAGE sequencing to profile cryptic-promoter-derived transcripts and their contribution to the immunopeptidomePreprint

Maeng, J. H., Jang, H. J., Du, A. Y., Tzeng, S., & Wang, T. (2023) · Genome Research · doi:10.1101/gr.277061.122 · Cited by 16

Highly accurate assembly polishing with DeepPolisherPreprint

Mastoras, M., Asri, M., Brambrink, L., Hebbar, P., Kolesnikov, A., Cook, D. E., Nattestad, M., Lucas, J., Won, S. T., Chang, P.-C., et al. (2025) · Genome Research · doi:10.1101/gr.280149.124 · Cited by 18

Accurate fusion transcript identification from long- and short-read isoform sequencing at bulk or single-cell resolutionPreprint

Qin, Q., Popic, V., Wienand, K., Yu, H., White, E., Khorgade, A., Shin, A., Georgescu, C., Campbell, C. D., Dondi, A., et al. (2025) · Genome Research · doi:10.1101/gr.279200.124 · Cited by 17

Optimizing microbiome reference databases with PacBio full-length 16S rRNA sequencing for enhanced taxonomic classification and biomarker discovery

Han, H., Choi, Y. H., Kim, S. Y., Park, J. H., Chung, J., & Na, H. S. (2024) · Frontiers in Microbiology · doi:10.3389/fmicb.2024.1485073 · Cited by 15

Comprehensive comparison of the third-generation sequencing tools for bacterial 6mA profiling

Lu, B., Guo, Z., Liu, X., Ni, Y., Xu, L., Huang, J., Li, T., Feng, T., Li, R., & Deng, X. (2025) · Nature Communications · doi:10.1038/s41467-025-59187-2 · Cited by 14

Genome sequence of the English grain aphid,Sitobion avenaeand its endosymbiontBuchnera aphidicola

Byrne, S. L., Schughart, M., Carolan, J. C., Gaffney, M. T., Thorpe, P., Malloch, G. L., Wilkinson, T., & McNamara, L. (2021) · G3 Genes Genomes Genetics · doi:10.1093/g3journal/jkab418 · Cited by 17

Assembly of a Hybrid Formica aquilonia × F. polyctena Ant Genome From a Haploid Male

Nouhaud, P., Beresford, J., & Kulmuni, J. (2022) · Journal of Heredity · doi:10.1093/jhered/esac019 · Cited by 14

Chromosome‐level genome assembly for takin (Budorcas taxicolor) provides insights into its taxonomic status and genetic diversity

Li, A., Yang, Q., Li, R., Dai, X., Cai, K., Lei, Y., Jia, K., Jiang, Y., & Zan, L. (2022) · Molecular Ecology · doi:10.1111/mec.16483 · Cited by 15

Ancient trans-species polymorphism at the Major Histocompatibility Complex in primates

Fortier, A. L., & Pritchard, J. K. (2025) · eLife · doi:10.7554/elife.103547.3 · Cited by 14

Long amplicon HiFi sequencing for mitochondrial DNA genomes

Cai, Z., Hu, J., Yin, T., Wang, D., Shen, Q., Ma, C., Ou, D., Xu, M., Shi, X., Li, Q., et al. (2023) · Molecular Ecology Resources · doi:10.1111/1755-0998.13765 · Cited by 15

Intercross population study reveals that co-mutation of mitfa genes in two subgenomes induces red skin color in common carp (Cyprinus carpio wuyuanensis)

Li, B., 厦门大学海洋与地球学院近海海洋环境科学国家重点实验室, 福. 厦., Chen, L., Yan, M., Zou, X., Bai, Y., Xue, Y., Zhou, J., Chen, B., Li, C., et al. (2023) · 动物学研究 · doi:10.24272/j.issn.2095-8137.2022.388 · Cited by 15

A landscape of complex tandem repeats within individual human genomes

Ichikawa, K., Kawahara, R., Asano, T., & Morishita, S. (2023) · Nature Communications · doi:10.1038/s41467-023-41262-1 · Cited by 14

Invited: Accelerating Genome Analysis via Algorithm-Architecture Co-Design

Mutlu, O., & Fırtına, C. (2023) · ACM/IEEE Design Automation Conference (DAC) · doi:10.1109/dac56929.2023.10247887 · Cited by 19

Integrated omic profiling of the medicinal mushroom Inonotus obliquus under submerged conditions

Hao, J., Wang, X., Shi, Y., Li, L., Chu, J., Li, J., Lin, W., Yu, T., & Hou, D. (2023) · BMC Genomics · doi:10.1186/s12864-023-09656-z · Cited by 16

Conservation genomics of an endangered montane amphibian reveals low population structure, low genomic diversity and selection pressure from disease

Trumbo, D. R., Hardy, B. M., Crockett, H. J., Muths, E., Forester, B. R., Cheek, R. G., Zimmerman, S. J., Corey-Rivas, S., Bailey, L. L., & Funk, W. C. (2023) · Molecular Ecology · doi:10.1111/mec.17175 · Cited by 14

Direct Comparative Analysis of a Pharmacogenomics Panel with PacBio Hifi® Long-Read and Illumina Short-Read Sequencing

Barthélémy, D., Belmonte, E., Pilla, L. D., Bardel, C., Duport, E., Gautier, V., & Payen, L. F. (2023) · Journal of Personalized Medicine · doi:10.3390/jpm13121655 · Cited by 15

Leveraging long-read sequencing technologies for pharmacogenomic testing: applications, analytical strategies, challenges, and future perspectives

Tafazoli, A., Hemmati, M., Rafigh, M., Alimardani, M., Khaghani, F., Korostyński, M., & Karnes, J. H. (2025) · Frontiers in Genetics · doi:10.3389/fgene.2025.1435416 · Cited by 18

Parallel String Graph Construction and Transitive Reduction for De Novo Genome Assembly

Guidi, G., Selvitopi, O., Ellis, M., Oliker, L., Yelick, K., & Buluç, A. (2021) · IEEE International Parallel and Distributed Processing Symposium (IPDPS) · doi:10.1109/ipdps49936.2021.00060 · Cited by 19

Low Threshold for Cutaneous Allergen Sensitization but No Spontaneous Dermatitis or Atopy in FLG-Deficient Mice

Muhandes, L., Chapsa, M., Pippel, M., Behrendt, R., Ge, Y., Dahl, A., Yi, B., Dalpke, A. H., Winkler, S., Hiller, M., et al. (2021) · Journal of Investigative Dermatology · doi:10.1016/j.jid.2021.02.763 · Cited by 15

Hearing Impairment with Monoallelic GJB2 Variants

Lin, Y., Wu, P., Tsai, C., Lin, Y.-H., Lo, M., Hsu, S.-J., Lin, P., Erdenechuluun, J., Wu, H., Hsu, C., et al. (2021) · Journal of Molecular Diagnostics · doi:10.1016/j.jmoldx.2021.07.007 · Cited by 15

Chromosome-level genome of the globe skimmer dragonfly (Pantala flavescens)

Liu, H., Jiang, F., Wang, S., Wang, H., Wang, A., Zhao, H., Xu, D., Yang, B., & Fan, W. (2022) · GigaScience · doi:10.1093/gigascience/giac009 · Cited by 15

mRatBN7.2: familiar and unfamiliar features of a new rat genome reference assembly

de Jong, T. V., Chen, H., Brashear, W. A., Kochan, K. J., Hillhouse, A., Zhu, Y., Dhande, I. S., Hudson, E., Sumlut, M. H., Smith, M. L., et al. (2022) · Physiological Genomics · doi:10.1152/physiolgenomics.00017.2022 · Cited by 16

GREPore-Seq: A Robust Workflow to Detect Changes After Gene Editing Through Long-Range PCR and Nanopore Sequencing

Quan, Z.-J., Li, S.-A., Yang, Z.-X., Zhao, J.-J., Li, G., Zhang, F., Wen, W., Cheng, T., & Zhang, X. (2022) · Genomics Proteomics & Bioinformatics · doi:10.1016/j.gpb.2022.06.002 · Cited by 17

How Genomics Is Changing What We Know About the Evolution and Genome of Bordetella pertussis

Ring, N., Abrahams, J. S., Bagby, S., Preston, A., & MacArthur, I. (2019) · Advances in experimental medicine and biology · doi:10.1007/5584_2019_401 · Cited by 16

Directed evolution for high functional production and stability of a challenging G protein-coupled receptor

Waltenspühl, Y., Jeliazkov, J. R., Kummer, L., & Plückthun, A. (2021) · Scientific Reports · doi:10.1038/s41598-021-87793-9 · Cited by 13

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

High Coverage Highly Accurate Long-Read Sequencing of a Mouse Neuronal Cell Line Using the PacBio Revio SequencerPreprint

Manuel, J. G., Heins, H. B., Crocker, S., Neidich, J., Sadzewicz, L., Tallon, L. J., & Turner, T. N. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.06.06.543940 · Cited by 14

Unraveling the hidden complexity of cancer through long-read sequencingPreprint

Li, Q., Keşküş, A. G., Wagner, J., Izydorczyk, M., Timp, W., Sedlazeck, F. J., Klein, A. P., Zook, J. M., Kolmogorov, M., & Schatz, M. C. (2025) · Genome Research · doi:10.1101/gr.280041.124 · Cited by 15

Host-encoded DNA methyltransferases modify the epigenome and host tropism of invading phages

Takahashi, M., Hiraoka, S., Matsumoto, Y., Shibagaki, R., Ujihara, T., Maeda, H., Seo, S., Nagasaki, K., Takeuchi, H., & Matsuzaki, S. (2025) · iScience · doi:10.1016/j.isci.2025.112264 · Cited by 14

Why Are Long-Read Sequencing Methods Revolutionizing Microbiome Analysis?

González, A., Fullaondo, A., & Odriozola, A. (2025) · Microorganisms · doi:10.3390/microorganisms13081861 · Cited by 17

A novel 4.9 Kb deletion at beta-globin gene is identified by the third-generation sequencing: Case report from Baoan, China

Chen, X., Luo, M., Pan, L., Huang, Y.-T., Yan, Z., Shen, K., Mai, G., Liang, H. W., Li, J., Chen, Y., et al. (2022) · Clinica Chimica Acta · doi:10.1016/j.cca.2022.01.024 · Cited by 14

Full-Length Transcriptome Reconstruction Reveals the Genetic Mechanisms of Eyestalk Displacement and Its Potential Implications on the Interspecific Hybrid Crab (Scylla serrata ♀ × S. paramamosain ♂)

Ye, S., Yu, X., Chen, H., Zhang, Y., Wu, Q., Tan, H., Song, J. W., Saqib, H. S. A., Farhadi, A., Ikhwanuddin, M., et al. (2022) · Biology · doi:10.3390/biology11071026 · Cited by 14

Third‐Generation Sequencing of Epigenetic DNA

Searle, B., Müller, M., Carell, T., & Kellett, A. (2022) · Angewandte Chemie · doi:10.1002/ange.202215704 · Cited by 14

Identification of a novel 10.3 kb deletion causing α0-thalassemia by third-generation sequencing: Pedigree analysis and genetic diagnosis

Xu, R., Li, H., Song, Y., Du, J. C., Jin, J., Qin, Y., Jiang, Y., Gao, T., Zhang, C., Yi, M., et al. (2023) · Clinical Biochemistry · doi:10.1016/j.clinbiochem.2022.12.018 · Cited by 14

Comparative analysis of genome sequences of the two cultivated tetraploid cottons, Gossypium hirsutum (L.) and G. barbadense (L.)

Meng, Q., Gu, J., Xu, Z., Zhang, J., Tang, J., Wang, A., Wang, P., Liu, Z., Rong, Y., Xie, P., et al. (2023) · Industrial Crops and Products · doi:10.1016/j.indcrop.2023.116471 · Cited by 15

Mabs, a suite of tools for gene-informed genome assembly

Schelkunov, M. I. (2023) · BMC Bioinformatics · doi:10.1186/s12859-023-05499-3 · Cited by 14

A practical assembly guideline for genomes with various levels of heterozygosity

Mochizuki, T., Sakamoto, M., Tanizawa, Y., Nakayama, T., Tanifuji, G., Kamikawa, R., & Nakamura, Y. (2023) · Briefings in Bioinformatics · doi:10.1093/bib/bbad337 · Cited by 14

HAT: de novo variant calling for highly accurate short-read and long-read sequencing data

Ng, J. K., & Turner, T. N. (2024) · Bioinformatics · doi:10.1093/bioinformatics/btad775 · Cited by 12

Linear DNA-driven recombination in mammalian mitochondria

Fragkoulis, G., Hangas, A., Fekete, Z., Michell, C., Moraes, C. T., Willcox, S., Griffith, J. D., Goffart, S., & Pohjoismäki, J. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae040 · Cited by 16

Chasing Sequencing Perfection: Marching Toward Higher Accuracy and Lower Costs

Jia, H., Tan, S., & Zhang, Y. E. (2024) · Genomics Proteomics & Bioinformatics · doi:10.1093/gpbjnl/qzae024 · Cited by 14

Advanced sequencing-based high-throughput and long-read single-cell transcriptome analysis

Huang, S., Shi, W., Li, S., Fan, Q., Yang, C. J., Cao, J., & Wu, L. (2024) · Lab on a Chip · doi:10.1039/d4lc00105b · Cited by 14

Pervasive relaxed selection in termite genomes

Ewart, K. M., Ho, S. Y. W., Chowdhury, A.-A., Jaya, F. R., Kinjo, Y., Bennett, J., Bourguignon, T., Rose, H. A., & Lo, N. C. (2024) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2023.2439 · Cited by 14

Comparative assessment of the intragenomic variations of dinoflagellate Tripos species through single-cell sequencing

Huang, X., Li, Y., Du, H., & Chen, N. (2024) · Marine Pollution Bulletin · doi:10.1016/j.marpolbul.2024.116690 · Cited by 14

Targeted long-read sequencing to quantify methylation of the C9orf72 repeat expansion

Udine, E., Finch, N. A., DeJesus‐Hernandez, M., Jackson, J. L., Baker, M., Saravanaperumal, S. A., Wieben, E. D., Ebbert, M., Shah, J., Petrucelli, L., et al. (2024) · Molecular Neurodegeneration · doi:10.1186/s13024-024-00790-0 · Cited by 14

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

PhaseME: Automatic rapid assessment of phasing quality and phasing improvement

Majidian, S., & Sedlazeck, F. J. (2020) · GigaScience · doi:10.1093/gigascience/giaa078 · Cited by 13

Multiplexing mutation rate assessment: determining pathogenicity of Msh2 variants in Saccharomyces cerevisiae

Ollodart, A. R., Yeh, C.-L. C., Miller, A. W., Shirts, B. H., Gordon, A. S., & Dunham, M. J. (2021) · Genetics · doi:10.1093/genetics/iyab058 · Cited by 16

Functional Homology for Antibody-Dependent Phagocytosis Across Humans and Rhesus Macaques

Pollara, J., Tay, M. Z., Edwards, R. W., Goodman, D. D., Crowley, A. R., Edwards, R. J., Easterhoff, D., Conley, H. E., Hoxie, T., Gurley, T. C., et al. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.678511 · Cited by 14

PacBio sequencing revealed variation in the microbiota diversity, species richness and composition between milk collected from healthy and mastitis cows

Ma, T., Shen, L., Wen, Q., Lv, R., Hou, Q., Kwok, L. Y., Sun, Z., & Zhang, H. (2021) · Microbiology · doi:10.1099/mic.0.000968 · Cited by 14

Long-read sequencing reveals the evolutionary drivers of intra-host diversity across natural RNA mycovirus infections

Leigh, D. M., Peranić, K., Prospero, S., Cornejo, C., Ćurković‐Perica, M., Kupper, Q., Nuskern, L., Rigling, D., & Ježić, M. (2021) · Virus Evolution · doi:10.1093/ve/veab101 · Cited by 14

The genomics of ornamental plants: current status and opportunities

Li, M., Wen, Z., Meng, J., Cheng, T., Zhang, Q., & Sun, L. (2022) · Ornamental Plant Research · doi:10.48130/opr-2022-0006 · Cited by 14

A High-Quality Genome Assembly of Striped Catfish (Pangasianodon hypophthalmus) Based on Highly Accurate Long-Read HiFi Sequencing Data

Hai, D. M., Yên, D. T., Liêm, P. T., Tâm, B. M., Huong, D. T. T., Hằng, B. T. B., Hieu, D. Q., Garigliany, M., Coppieters, W. R., Kestemont, P., et al. (2022) · Genes · doi:10.3390/genes13050923 · Cited by 15

Going broad and deep: sequencing‐driven insights into plant physiology, evolution, and crop domestication

Gui, S., Martínez-Rivas, F. J., Wen, W., Meng, M., Yan, J., Usadel, B., & Fernie, A. R. (2022) · The Plant Journal · doi:10.1111/tpj.16070 · Cited by 14

Visualization tools for human structural variations identified by whole-genome sequencing

Yokoyama, T., & Kasahara, M. (2019) · Journal of Human Genetics · doi:10.1038/s10038-019-0687-0 · Cited by 14

Long-read transcriptome and other genomic resources for the angiosperm Silene noctiflora

Williams, A. M., Itgen, M. W., Broz, A. K., Carter, O. G., & Sloan, D. B. (2021) · G3 Genes Genomes Genetics · doi:10.1093/g3journal/jkab189 · Cited by 13

Germline mosaicism of a missense variant in KCNC2 in a multiplex family with autism and epilepsy characterized by long‐read sequencing

Mehinovic, E., Gray, T., Campbell, M. C., Ekholm, J. M., Wenger, A. M., Rowell, W. J., Grudo, A., Grimwood, J., Korlach, J., Gurnett, C. A., et al. (2022) · American Journal of Medical Genetics Part A · doi:10.1002/ajmg.a.62743 · Cited by 14

SDip: A novel graph-based approach to haplotype-aware assembly based structural variant calling in targeted segmental duplications sequencingPreprint

Heller, D., Vingron, M., Church, G. M., Li, H., & Garg, S. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.02.25.964445 · Cited by 14

An unusual tandem kinase fusion protein confers leaf rust resistance in wheatPreprint

Wang, Y., Abrouk, M., Gourdoupis, S., Koo, D., Karafiátová, M., Molnár, I., Doležel, J., Athiyannan, N., Cavalet-Giorsa, E., Jaremko, Ł., et al. (2022) · Research Square · doi:10.21203/rs.3.rs-1807889/v1 · Cited by 14

Fast and accurate mapping of long reads to complete genome assemblies with VerityMapPreprint

Bzikadze, A. V., Mikheenko, A., & Pevzner, P. A. (2022) · Genome Research · doi:10.1101/gr.276871.122 · Cited by 14

Highly complete long-read genomes reveal pangenomic variation underlying yeast phenotypic diversityPreprint

Weller, C. A., Andreev, I., Chambers, M. J., Park, M., Program, N. C. S., Bloom, J. S., & Sadhu, M. J. (2023) · Genome Research · doi:10.1101/gr.277515.122 · Cited by 14

Haplotype-aware sequence alignment to pangenome graphsPreprint

Chandra, G., Gibney, D., & Jain, C. (2024) · Genome Research · doi:10.1101/gr.279143.124 · Cited by 18

Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair

McDaniel, J., Patel, V., Olson, N. D., He, H., He, Z., Cole, K. D., Gooden, A. A., Schmitt, A. D., Sikkink, K. L., Sedlazeck, F. J., et al. (2025) · Scientific Data · doi:10.1038/s41597-025-05438-2 · Cited by 14

Cytogenetics and Cytogenomics in Clinical Diagnostics: Genome Architecture, Structural Variants, and Translational Applications

Federico, C., Brancato, D., Bruno, F., Coniglio, E., Sturiale, V., & Saccone, S. (2025) · Genes · doi:10.3390/genes16070780 · Cited by 16

Toxic/Bioactive Peptide Synthesis Genes Rearranged by Insertion Sequence Elements Among the Bloom-Forming Cyanobacteria Planktothrix

Entfellner, E., Li, R., Jiang, Y., Ru, J., Blom, J., Deng, L., & Kurmayer, R. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.901762 · Cited by 13

Comprehensive variant discovery in the era of complete human reference genomes

Čechová, M., & Miga, K. H. (2023) · Nature Methods · doi:10.1038/s41592-022-01740-8 · Cited by 13

Benchmarking Oxford Nanopore read alignment‐based insertion and deletion detection in crop plant genomes

Yildiz, G., Zanini, S. F., Afsharyan, N. P., Obermeier, C., Snowdon, R. J., & Golicz, A. A. (2023) · The Plant Genome · doi:10.1002/tpg2.20314 · Cited by 13

A multitiered haplotype strategy to enhance phased assembly and fine mapping of a disease resistance locus

Zou, C., Sapkota, S., Figueroa-Balderas, R. E., Glaubitz, J. C., Cantù, D., Kingham, B. F., Sun, Q., & Cadle-Davidson, L. E. (2023) · PLANT PHYSIOLOGY · doi:10.1093/plphys/kiad494 · Cited by 13

A new Plasmodium vivax reference genome for South American isolates

Meulenaere, K. D., Cuypers, B., Gamboa, D., Laukens, K., & Rosanas‐Urgell, A. (2023) · BMC Genomics · doi:10.1186/s12864-023-09707-5 · Cited by 15

Low-input PacBio sequencing generates high-quality individual fly genomes and characterizes mutational processes

Jia, H., Tan, S., Cai, Y., Guo, Y., Shen, J., Zhang, Y., Ma, H., Zhang, Q., Chen, J., Qiao, G., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-49992-6 · Cited by 13

Disentangling river and swamp buffalo genetic diversity: initial insights from the 1000 Buffalo Genomes Project

Pineda, P. S., Flores, E. B., Villamor, L. P., Parac, C. J. M., Khatkar, M. S., To, T., Smith, T. P. L., Rosen, B. D., Ajmone‐Marsan, P., Colli, L., et al. (2024) · GigaScience · doi:10.1093/gigascience/giae053 · Cited by 13

Genomic Signatures of Domestication in a Fungus Obligately Farmed by Leafcutter Ants

Leal-Dutra, C. A., Vizueta, J., Baril, T., Kooij, P. W., Rødsgaard-Jørgensen, A., Conlon, B. H., Croll, D., & Shik, J. Z. (2024) · Molecular Biology and Evolution · doi:10.1093/molbev/msae197 · Cited by 13

Molecular classification of a complex structural rearrangement of the RB1 locus in an infant with sporadic, isolated, intracranial, sellar region retinoblastoma

Schieffer, K. M., Feldman, A. Z., Kautto, E. A., McGrath, S. D., Miller, A. R., Hernandez‐Gonzalez, M. E., LaHaye, S., Miller, K. E., Koboldt, D. C., Brennan, P. J., et al. (2021) · Acta Neuropathologica Communications · doi:10.1186/s40478-021-01164-z · Cited by 13

3D Printing-Enabled DNA Extraction for Long-Read Genomics

Agrawal, P., Reifenberger, J. G., & Dorfman, K. D. (2020) · ACS Omega · doi:10.1021/acsomega.0c01912 · Cited by 13

Building better genome annotations across the tree of lifePreprint

Freedman, A. H., & Sackton, T. B. (2025) · Genome Research · doi:10.1101/gr.280377.124 · Cited by 13

Molecular Monitoring of Fungicide Resistance in Crop Phytopathogens

Zulak, K. G. (2025) · Molecular Plant-Microbe Interactions · doi:10.1094/mpmi-09-24-0105-fi · 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

EasyAmplicon 2: Expanding PacBio and Nanopore Long Amplicon Sequencing Analysis Pipeline for Microbiome

Luo, H., Bai, D., Zhu, Z., Yousuf, S., Yang, H., Xun, J., Zeng, M., Wang, Y., Gao, Y., Peng, K., et al. (2025) · Advanced Science · doi:10.1002/advs.202512447 · Cited by 12

Troubleshooting common errors in assemblies of long-read metagenomes

Trigodet, F., Sachdeva, R., Banfield, J. F., & Eren, A. M. (2026) · Nature Biotechnology · doi:10.1038/s41587-025-02971-8 · Cited by 28

Next-generation sequencing approaches for soil microbiome research

Reznikova, D. A., Barannikova, M. V., Shnakhova, L. M., Mitkin, N. A., & Vatlin, A. A. (2026) · Frontiers in Soil Science · doi:10.3389/fsoil.2025.1706999 · Cited by 14

Factors and Methods for the Detection of Gene Expression Regulation

Wang, M., Li, Q., & Liu, L. (2023) · Biomolecules · doi:10.3390/biom13020304 · Cited by 15

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

INSnet: a method for detecting insertions based on deep learning network

Gao, R., Luo, J., Ding, H., & Zhai, H. (2023) · BMC Bioinformatics · doi:10.1186/s12859-023-05216-0 · Cited by 13

The comprehensive analysis of thalassemia alleles (CATSA) based on single-molecule real-time technology (SMRT) is a more powerful strategy in the diagnosis of thalassemia caused by rare variants

Feng, J., Cui, D., Li, C., Yang, Y., Li, Q., Li, X., Tan, S., Li, X., Meng, W., Li, H., et al. (2023) · Clinica Chimica Acta · doi:10.1016/j.cca.2023.117619 · Cited by 12

Postmortem Muscle Proteome Characteristics of Silver Carp ( Hypophthalmichthys molitrix ): Insights from Full-Length Transcriptome and Deep 4D Label-Free Proteomic

Jiao, X., Li, X., Zhang, N., Zhang, W., Yan, B., Huang, J., Zhao, J., Zhang, H., Chen, W., & Fan, D. (2024) · Journal of Agricultural and Food Chemistry · doi:10.1021/acs.jafc.3c06902 · Cited by 12

Trans-activating mutations of the pseudokinase ERBB3

Koivu, M. K. A., Chakroborty, D., Airenne, T. T., Johnson, M. S., Kurppa, K. J., & Elenius, K. (2024) · Oncogene · doi:10.1038/s41388-024-03070-9 · Cited by 12

Advancements in the clinical application of gene methylation for early cancer detection

Xu, X., Guo, Y., Liu, M., Hu, Y., & Li, S. (2024) · Frontiers in Epigenetics and Epigenomics · doi:10.3389/freae.2024.1430294 · Cited by 12

ULTRA-effective labeling of tandem repeats in genomic sequence

Olson, D. R., & Wheeler, T. J. (2024) · Bioinformatics Advances · doi:10.1093/bioadv/vbae149 · Cited by 14

Haploid‐Phased Chromosomal Telomere‐to‐Telomere Genome Assembly of Medicinal Plant Uncaria rhynchophylla Dissects Genetic Controls on the Biosynthesis of Bioactive Alkaloids

Hu, T., Duan, L., Shangguan, L., Zhao, Q., Ye, H., Wang, X., Li, X., Yang, N., Yan, F., Lv, Q., et al. (2024) · Plant Cell & Environment · doi:10.1111/pce.15257 · Cited by 13

Unveiling the Future of Infective Endocarditis Diagnosis: The Transformative Role of Metagenomic Next-Generation Sequencing in Culture-Negative Cases

Shinge, S. A. U., Zhang, B., Zheng, B., Qiang, Y., Ali, H. M., Melchiade, Y. T. V., Zhang, L., Gao, M., Feng, G., Zeng, K., et al. (2025) · Journal of Epidemiology and Global Health · doi:10.1007/s44197-025-00455-1 · Cited by 14

Biodiversity of magnetotactic bacteria in the tropical marine environment of Singapore revealed by metagenomic analysis

Tan, S. M., Ismail, M. H., & Cao, B. (2021) · Environmental Research · doi:10.1016/j.envres.2021.110714 · 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 13

Complete Genome Sequence of Herpes Simplex Virus 2 Strain G

Chang, W., Jiao, X., Sui, H., Goswami, S., Sherman, B. T., Fromont, C., Caravaca, J. M., Tran, B. Q., & Imamichi, T. (2022) · Viruses · doi:10.3390/v14030536 · Cited by 12

Single-molecule long-read sequencing analysis improves genome annotation and sheds new light on the transcripts and splice isoforms of Zoysia japonica

Guan, J., Yin, S., Yue, Y., Liu, L., Guo, Y., Zhang, H., Fan, X., & Teng, K. (2022) · BMC Plant Biology · doi:10.1186/s12870-022-03640-7 · Cited by 12

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

Comparison of mitochondrial DNA variants detection using short- and long-read sequencing

Alkanaq, A. N., Hamanaka, K., Sekiguchi, F., Taguri, M., Takata, A., Miyake, N., Miyatake, S., Mizuguchi, T., & Matsumoto, N. (2019) · Journal of Human Genetics · doi:10.1038/s10038-019-0654-9 · Cited by 12

Detection Methods Fit-for-Purpose in Enforcement Control of Genetically Modified Plants Produced with Novel Genomic Techniques (NGTs)

Ribarits, A., Narendja, F. M., Stepanek, W., & Hochegger, R. (2020) · Agronomy · doi:10.3390/agronomy11010061 · Cited by 12

Long‐read whole genome sequencing reveals HOXD13 alterations in synpolydactyly

Melas, M., Kautto, E. A., Franklin, S. J., Mori, M., McBride, K. L., Mosher, T. M., Pfau, R. B., Hernandez‐Gonzalez, M. E., McGrath, S. D., Magrini, V. J., et al. (2021) · Human Mutation · doi:10.1002/humu.24304 · Cited by 12

Prediction of Antibiotic Resistance Evolution by Growth Measurement of All Proximal Mutants of Beta-Lactamase

Feng, S., Wu, Z., Liang, W., Zhang, X., Cai, X., Li, J., Liang, L., Lin, D., Stoesser, N. E., Doi, Y., et al. (2022) · Molecular Biology and Evolution · doi:10.1093/molbev/msac086 · Cited by 11

Benchmarking small variant detection with ONT reveals high performance in challenging regionsPreprint

Møller, P. L., Holley, G., Beyter, D., Nyegaard, M., & Halldórsson, B. V. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.10.22.350009 · Cited by 12

Circular consensus sequencing with long reads

Tang, L. (2019) · Nature Methods · doi:10.1038/s41592-019-0605-6 · Cited by 14

Article Watch: March, 2020

(2020) · Journal of Biomolecular Techniques JBT · doi:10.7171/jbt.20-3101-005 · Cited by 2

DeepConsensus: Gap-Aware Sequence Transformers for Sequence CorrectionPreprint

Baid, G., Cook, D. E., Shafin, K., Yun, T., Llinares-López, F., Berthet, Q., Wenger, A., Rowell, W., Nattestad, M., Yang, H., et al. (2021) · bioRxiv · doi:10.1101/2021.08.31.458403 · Cited by 13

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

Vollger, M. R., Logsdon, G. A., Audano, P. A., Sulovari, A., Porubskỳ, D., Peluso, P. S., Wenger, A. M., Concepcion, G. T., Kronenberg, Z. N., Munson, K. M., et al. (2019) · Annals of Human Genetics · doi:10.1111/ahg.12364 · Cited by 123

Using high-fidelity long-read sequencing to better detect and understand short tandem repeat variation in humans

Lougheed, D. R. (2023) · eScholarship@McGill (McGill) · doi:10.82308/54708