Publications
Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines. Cell Syst. 2018 ;6(3):271-281.e7.
. Analysis commons, a team approach to discovery in a big-data environment for genetic epidemiology. Nat Genet. 2017 ;49(11):1560-1563.
. Exome sequencing reveals novel genetic loci influencing obesity-related traits in Hispanic children. Obesity (Silver Spring). 2017 ;25(7):1270-1276.
. GenomeScope: fast reference-free genome profiling from short reads. Bioinformatics. 2017 ;33(14):2202-2204.
. SeqCNV: a novel method for identification of copy number variations in targeted next-generation sequencing data. BMC Bioinformatics. 2017 ;18(1):147.
. UALCAN: A Portal for Facilitating Tumor Subgroup Gene Expression and Survival Analyses. Neoplasia. 2017 ;19(8):649-658.
. Clinical Sequencing Exploratory Research Consortium: Accelerating Evidence-Based Practice of Genomic Medicine. Am J Hum Genet. 2016 ;98(6):1051-1066.
. DNAism: exploring genomic datasets on the web with Horizon Charts. BMC Bioinformatics. 2016 ;17:49.
. 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.
. A visual and curatorial approach to clinical variant prioritization and disease gene discovery in genome-wide diagnostics. Genome Med. 2016 ;8(1):13.
. WGSA: an annotation pipeline for human genome sequencing studies. J Med Genet. 2016 ;53(2):111-2.
. Assessing structural variation in a personal genome-towards a human reference diploid genome. BMC Genomics. 2015 ;16(1):286.
. Comparison and integration of deleteriousness prediction methods for nonsynonymous SNVs in whole exome sequencing studies. Hum Mol Genet. 2015 ;24(8):2125-37.
. FOXO1 is required for binding of PR on IRF4, novel transcriptional regulator of endometrial stromal decidualization. Mol Endocrinol. 2015 ;29(3):421-33.
. The Matchmaker Exchange: a platform for rare disease gene discovery. Hum Mutat. 2015 ;36(10):915-21.
. Teaser: Individualized benchmarking and optimization of read mapping results for NGS data. Genome Biol. 2015 ;16:235.
. In silico tools for splicing defect prediction: a survey from the viewpoint of end users. Genet Med. 2014 ;16(7):497-503.
. Launching genomics into the cloud: deployment of Mercury, a next generation sequence analysis pipeline. BMC Bioinformatics. 2014 ;15:30.
. PBHoney: identifying genomic variants via long-read discordance and interrupted mapping. BMC Bioinformatics. 2014 ;15:180.
. Analysis of rare, exonic variation amongst subjects with autism spectrum disorders and population controls. PLoS Genet. 2013 ;9(4):e1003443.
. dbNSFP v2.0: a database of human non-synonymous SNVs and their functional predictions and annotations. Hum Mutat. 2013 ;34(9):E2393-402.
. NextGenMap: fast and accurate read mapping in highly polymorphic genomes. Bioinformatics. 2013 ;29(21):2790-1.
. PhenoDB: a new web-based tool for the collection, storage, and analysis of phenotypic features. Hum Mutat. 2013 ;34(4):566-71.
. Atlas2 Cloud: a framework for personal genome analysis in the cloud. BMC Genomics. 2012 ;13 Suppl 6(Suppl 6):S19.
. An integrative variant analysis suite for whole exome next-generation sequencing data. BMC Bioinformatics. 2012 ;13:8.
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