Publications
OikoBase: a genomics and developmental transcriptomics resource for the urochordate Oikopleura dioica. Nucleic Acids Res. 2013 ;41(Database issue):D845-53.
. PacBio-LITS: a large-insert targeted sequencing method for characterization of human disease-associated chromosomal structural variations. BMC Genomics. 2015 ;16(1):214.
. Pan-Cancer Molecular Classes Transcending Tumor Lineage Across 32 Cancer Types, Multiple Data Platforms, and over 10,000 Cases. Clin Cancer Res. 2018 ;24(9):2182-2193.
. Pan-urologic cancer genomic subtypes that transcend tissue of origin. Nat Commun. 2017 ;8(1):199.
. Parent of origin, mosaicism, and recurrence risk: probabilistic modeling explains the broken symmetry of transmission genetics. Am J Hum Genet. 2014 ;95(4):345-59.
. Parental somatic mosaicism is underrecognized and influences recurrence risk of genomic disorders. Am J Hum Genet. 2014 ;95(2):173-82.
. Parliament2: Accurate structural variant calling at scale. Gigascience. 2020 ;9(12).
. PBHoney: identifying genomic variants via long-read discordance and interrupted mapping. BMC Bioinformatics. 2014 ;15:180.
. A pediatric brain tumor atlas of genes deregulated by somatic genomic rearrangement. Nat Commun. 2021 ;12(1):937.
. Pediatric Cancer Genetics Research and an Evolving Preventive Ethics Approach for Return of Results after Death of the Subject. J Law Med Ethics. 2015 ;43(3):529-37.
. Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics. Cell. 2018 ;173(2):305-320.e10.
. Phased diploid genome assembly with single-molecule real-time sequencing. Nat Methods. 2016 ;13(12):1050-1054.
. PhaseME: Automatic rapid assessment of phasing quality and phasing improvement. Gigascience. 2020 ;9(7).
. PhenoDB: a new web-based tool for the collection, storage, and analysis of phenotypic features. Hum Mutat. 2013 ;34(4):566-71.
. PhenoDB, GeneMatcher and VariantMatcher, tools for analysis and sharing of sequence data. Orphanet J Rare Dis. 2021 ;16(1):365.
. Phylogenomic analyses provide insights into primate evolution. Science. 2023 ;380(6648):913-924.
. Phylogenomic analysis reveals bees and wasps (Hymenoptera) at the base of the radiation of Holometabolous insects. Genome Res. 2006 ;16(11):1334-8.
. A physical map of the chicken genome. Nature. 2004 ;432(7018):761-4.
. Piercing the dark matter: bioinformatics of long-range sequencing and mapping. Nat Rev Genet. 2018 ;19(6):329-346.
. The pineapple genome and the evolution of CAM photosynthesis. Nat Genet. 2015 ;47(12):1435-42.
. Portals for Exploring Noncoding Variants in Pediatric Cancer. Trends Genet. 2021 ;37(4):297-298.
. Practical Approaches for Whole-Genome Sequence Analysis of Heart- and Blood-Related Traits. Am J Hum Genet. 2017 ;100(2):205-215.
. Primary immunodeficiency diseases: Genomic approaches delineate heterogeneous Mendelian disorders. J Allergy Clin Immunol. 2017 ;139(1):232-245.
. Progress and prospects in rat genetics: a community view. Nat Genet. 2008 ;40(5):516-22.
. RaGOO: fast and accurate reference-guided scaffolding of draft genomes. Genome Biol. 2019 ;20(1):224.
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