Publications
In silico genetics: identification of a functional element regulating H2-Ealpha gene expression. Science. 2004 ;306(5696):690-5.
. In silico tools for splicing defect prediction: a survey from the viewpoint of end users. Genet Med. 2014 ;16(7):497-503.
. Integrated and sequence-ordered BAC- and YAC-based physical maps for the rat genome. Genome Res. 2004 ;14(4):766-79.
. Keeping an eye on the fly genome. Dev Biol. 2005 ;282(2):285-93.
. A Landscape of Metabolic Variation across Tumor Types. Cell Syst. 2018 ;6(3):301-313.e3.
. Large-scale sequencing in human chromosome 12p13: experimental and computational gene structure determination. Genome Res. 1997 ;7(3):268-80.
. Lessons learned from additional research analyses of unsolved clinical exome cases. Genome Med. 2017 ;9(1):26.
. Leveraging splice-affecting variant predictors and a minigene validation system to identify Mendelian disease-causing variants among exon-captured variants of uncertain significance. Hum Mutat. 2017 ;38(11):1521-1533.
. A map of human genome variation from population-scale sequencing. Nature. 2010 ;467(7319):1061-73.
. Metagenomic pyrosequencing and microbial identification. Clin Chem. 2009 ;55(5):856-66.
. A multi-task convolutional deep neural network for variant calling in single molecule sequencing. Nat Commun. 2019 ;10(1):998.
. MuSE: accounting for tumor heterogeneity using a sample-specific error model improves sensitivity and specificity in mutation calling from sequencing data. Genome Biol. 2016 ;17(1):178.
. Mutational landscape of aggressive cutaneous squamous cell carcinoma. Clin Cancer Res. 2014 ;20(24):6582-92.
. Next generation sequencing-based molecular diagnosis of retinitis pigmentosa: identification of a novel genotype-phenotype correlation and clinical refinements. Hum Genet. 2014 ;133(3):331-45.
. Novel microRNA candidates and miRNA-mRNA pairs in embryonic stem (ES) cells. PLoS One. 2008 ;3(7):e2548.
. nWayComp: a genome-wide sequence comparison tool for multiple strains/species of phylogenetically related microorganisms. In Silico Biol. 2007 ;7(2):195-200.
. Pash 2.0: scaleable sequence anchoring for next-generation sequencing technologies. Pac Symp Biocomput. 2008 ;:102-13.
. Pash: efficient genome-scale sequence anchoring by Positional Hashing. Genome Res. 2004 ;14(4):672-8.
. Pathway and network analysis of more than 2500 whole cancer genomes. Nat Commun. 2020 ;11(1):729.
. PhaseME: Automatic rapid assessment of phasing quality and phasing improvement. Gigascience. 2020 ;9(7).
. PhenoDB, GeneMatcher and VariantMatcher, tools for analysis and sharing of sequence data. Orphanet J Rare Dis. 2021 ;16(1):365.
. Piercing the dark matter: bioinformatics of long-range sequencing and mapping. Nat Rev Genet. 2018 ;19(6):329-346.
. PipMaker--a web server for aligning two genomic DNA sequences. Genome Res. 2000 ;10(4):577-86.
. Pooled Genomic Indexing (PGI): analysis and design of experiments. J Comput Biol. 2004 ;11(5):1001-21.
. Primate phylogenomics uncovers multiple rapid radiations and ancient interspecific introgression. PLoS Biol. 2020 ;18(12):e3000954.
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