Publications
xAtlas: scalable small variant calling across heterogeneous next-generation sequencing experiments. Gigascience. 2022 ;12.
. Working on the assembly line. Trends Biochem Sci. 1995 ;20(4):162-3.
. WGSA: an annotation pipeline for human genome sequencing studies. J Med Genet. 2016 ;53(2):111-2.
. Vulcan: Improved long-read mapping and structural variant calling via dual-mode alignment. Gigascience. 2021 ;10(9).
. A visual and curatorial approach to clinical variant prioritization and disease gene discovery in genome-wide diagnostics. Genome Med. 2016 ;8(1):13.
. VCPA: genomic variant calling pipeline and data management tool for Alzheimer's Disease Sequencing Project. Bioinformatics. 2019 ;35(10):1768-1770.
. 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.
. UALCAN: A Portal for Facilitating Tumor Subgroup Gene Expression and Survival Analyses. Neoplasia. 2017 ;19(8):649-658.
. The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms. F1000Res. 2022 ;11:530.
. Teaser: Individualized benchmarking and optimization of read mapping results for NGS data. Genome Biol. 2015 ;16:235.
. SVhound: detection of regions that harbor yet undetected structural variation. BMC Bioinformatics. 2023 ;24(1):23.
. Software for automated analysis of DNA fingerprinting gels. Genome Res. 2003 ;13(5):940-53.
. SNPdetector: a software tool for sensitive and accurate SNP detection. PLoS Comput Biol. 2005 ;1(5):e53.
. A SNP discovery method to assess variant allele probability from next-generation resequencing data. Genome Res. 2010 ;20(2):273-80.
. SeqCNV: a novel method for identification of copy number variations in targeted next-generation sequencing data. BMC Bioinformatics. 2017 ;18(1):147.
. Searching thousands of genomes to classify somatic and novel structural variants using STIX. Nat Methods. 2022 ;19(4):445-448.
. Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines. Cell Syst. 2018 ;6(3):271-281.e7.
. Robust, flexible, and scalable tests for Hardy-Weinberg equilibrium across diverse ancestries. Genetics. 2021 ;218(1).
. 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.
. ReadDepth: a parallel R package for detecting copy number alterations from short sequencing reads. PLoS One. 2011 ;6(1):e16327.
. RaGOO: fast and accurate reference-guided scaffolding of draft genomes. Genome Biol. 2019 ;20(1):224.
. PRINCESS: comprehensive detection of haplotype resolved SNVs, SVs, and methylation. Genome Biol. 2021 ;22(1):268.
. PrimerSNP: a web tool for whole-genome selection of allele-specific and common primers of phylogenetically-related bacterial genomic sequences. BMC Microbiol. 2008 ;8:185.
. PipMaker--a web server for aligning two genomic DNA sequences. Genome Res. 2000 ;10(4):577-86.
. PhenoDB, GeneMatcher and VariantMatcher, tools for analysis and sharing of sequence data. Orphanet J Rare Dis. 2021 ;16(1):365.
.