Publications
Comprehensive analysis of structural variants in breast cancer genomes using single-molecule sequencing. Genome Res. 2020 ;30(9):1258-1273.
. Phased diploid genome assembly with single-molecule real-time sequencing. Nat Methods. 2016 ;13(12):1050-1054.
. Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line. Genome Res. 2018 ;28(8):1126-1135.
. Piercing the dark matter: bioinformatics of long-range sequencing and mapping. Nat Rev Genet. 2018 ;19(6):329-346.
. The complete sequence of a human Y chromosome. Nature. 2023 ;621(7978):344-354.
. The complete sequence of a human Y chromosome. Nature. 2023 ;621(7978):344-354.
. Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato. Cell. 2020 ;182(1):145-161.e23.
. Duplication of a domestication locus neutralized a cryptic variant that caused a breeding barrier in tomato. Nat Plants. 2019 ;5(5):471-479.
. RaGOO: fast and accurate reference-guided scaffolding of draft genomes. Genome Biol. 2019 ;20(1):224.
. RaGOO: fast and accurate reference-guided scaffolding of draft genomes. Genome Biol. 2019 ;20(1):224.
. Parliament2: Accurate structural variant calling at scale. Gigascience. 2020 ;9(12).
. A multi-task convolutional deep neural network for variant calling in single molecule sequencing. Nat Commun. 2019 ;10(1):998.
. Teaser: Individualized benchmarking and optimization of read mapping results for NGS data. Genome Biol. 2015 ;16:235.
. GenomeScope: fast reference-free genome profiling from short reads. Bioinformatics. 2017 ;33(14):2202-2204.
. Phased diploid genome assembly with single-molecule real-time sequencing. Nat Methods. 2016 ;13(12):1050-1054.
. Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome. Nat Biotechnol. 2019 ;37(10):1155-1162.
. A complete reference genome improves analysis of human genetic variation. Science. 2022 ;376(6588):eabl3533.
. A multi-task convolutional deep neural network for variant calling in single molecule sequencing. Nat Commun. 2019 ;10(1):998.
. The complete sequence of a human genome. Science. 2022 ;376(6588):44-53.
. GenomeScope: fast reference-free genome profiling from short reads. Bioinformatics. 2017 ;33(14):2202-2204.
. The complete sequence of a human Y chromosome. Nature. 2023 ;621(7978):344-354.
. A robust benchmark for detection of germline large deletions and insertions. Nat Biotechnol. 2020 ;38(11):1347-1355.
. Accurate detection of complex structural variations using single-molecule sequencing. Nat Methods. 2018 ;15(6):461-468.
. Optimized sample selection for cost-efficient long-read population sequencing. Genome Res. 2021 ;31(5):910-918.
. Parliament2: Accurate structural variant calling at scale. Gigascience. 2020 ;9(12).
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