Publications
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FAIR Header Reference genome: a TRUSTworthy standard. Brief Bioinform. 2024 ;25(3).
. HMZDupFinder: a robust computational approach for detecting intragenic homozygous duplications from exome sequencing data. Nucleic Acids Res. 2024 ;52(4):e18.
. Single-nucleotide variant calling in single-cell sequencing data with Monopogen. Nat Biotechnol. 2024 ;42(5):803-812.
. SVhound: detection of regions that harbor yet undetected structural variation. BMC Bioinformatics. 2023 ;24(1):23.
. Searching thousands of genomes to classify somatic and novel structural variants using STIX. Nat Methods. 2022 ;19(4):445-448.
. . . Neptune: an environment for the delivery of genomic medicine. Genet Med. 2021 ;23(10):1838-1846.
. PhenoDB, GeneMatcher and VariantMatcher, tools for analysis and sharing of sequence data. Orphanet J Rare Dis. 2021 ;16(1):365.
. PRINCESS: comprehensive detection of haplotype resolved SNVs, SVs, and methylation. Genome Biol. 2021 ;22(1):268.
. Robust, flexible, and scalable tests for Hardy-Weinberg equilibrium across diverse ancestries. Genetics. 2021 ;218(1).
. Vulcan: Improved long-read mapping and structural variant calling via dual-mode alignment. Gigascience. 2021 ;10(9).
. Mapping and characterization of structural variation in 17,795 human genomes. Nature. 2020 ;583(7814):83-89.
. Parliament2: Accurate structural variant calling at scale. Gigascience. 2020 ;9(12).
. PhaseME: Automatic rapid assessment of phasing quality and phasing improvement. Gigascience. 2020 ;9(7).
. REDBot: Natural language process methods for clinical copy number variation reporting in prenatal and products of conception diagnosis. Mol Genet Genomic Med. 2020 ;8(11):e1488.
. Variant Classification Concordance using the ACMG-AMP Variant Interpretation Guidelines across Nine Genomic Implementation Research Studies. Am J Hum Genet. 2020 ;107(5):932-941.
. Atlas-CNV: a validated approach to call single-exon CNVs in the eMERGESeq gene panel. Genet Med. 2019 ;21(9):2135-2144.
. Evaluation of computational genotyping of structural variation for clinical diagnoses. Gigascience. 2019 ;8(9).
. A multi-task convolutional deep neural network for variant calling in single molecule sequencing. Nat Commun. 2019 ;10(1):998.
. RaGOO: fast and accurate reference-guided scaffolding of draft genomes. Genome Biol. 2019 ;20(1):224.
. VCPA: genomic variant calling pipeline and data management tool for Alzheimer's Disease Sequencing Project. Bioinformatics. 2019 ;35(10):1768-1770.
. Allelic decomposition and exact genotyping of highly polymorphic and structurally variant genes. Nat Commun. 2018 ;9(1):828.
. Characterizing reduced coverage regions through comparison of exome and genome sequencing data across 10 centers. Genet Med. 2018 ;20(8):855-866.
. A Landscape of Metabolic Variation across Tumor Types. Cell Syst. 2018 ;6(3):301-313.e3.
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