Publications
Adenosine deaminases that act on RNA induce reproducible changes in abundance and sequence of embryonic miRNAs. Genome Res. 2012 ;22(8):1468-76.
. Advanced methylome analysis after bisulfite deep sequencing: an example in Arabidopsis. PLoS One. 2012 ;7(7):e41528.
. Benefit-of-doubt (BOD) scoring: a sequencing-based method for SNP candidate assessment from high to medium read number data sets. Genomics. 2013 ;101(3):204-9.
. NextGenMap: fast and accurate read mapping in highly polymorphic genomes. Bioinformatics. 2013 ;29(21):2790-1.
. Updating benchtop sequencing performance comparison. Nat Biotechnol. 2013 ;31(4):294-6.
. ADAR2 induces reproducible changes in sequence and abundance of mature microRNAs in the mouse brain. Nucleic Acids Res. 2014 ;42(19):12155-68.
. The Candida albicans Histone Acetyltransferase Hat1 Regulates Stress Resistance and Virulence via Distinct Chromatin Assembly Pathways. PLoS Pathog. 2015 ;11(10):e1005218.
. Decreased expression of endogenous feline leukemia virus in cat lymphomas: a case control study. BMC Vet Res. 2015 ;11:90.
. Ectodysplasin signalling genes and phenotypic evolution in sculpins (Cottus). Proc Biol Sci. 2015 ;282(1815).
. The pineapple genome and the evolution of CAM photosynthesis. Nat Genet. 2015 ;47(12):1435-42.
. Teaser: Individualized benchmarking and optimization of read mapping results for NGS data. Genome Biol. 2015 ;16:235.
. Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding. PLoS Genet. 2016 ;12(4):e1005954.
. Correction: Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding. PLoS Genet. 2016 ;12(12):e1006500.
. The genomic basis of circadian and circalunar timing adaptations in a midge. Nature. 2016 ;540(7631):69-73.
. Phased diploid genome assembly with single-molecule real-time sequencing. Nat Methods. 2016 ;13(12):1050-1054.
. Copy number increases of transposable elements and protein-coding genes in an invasive fish of hybrid origin. Mol Ecol. 2017 ;26(18):4712-4724.
. DangerTrack: A scoring system to detect difficult-to-assess regions. F1000Res. 2017 ;6:443.
. GenomeScope: fast reference-free genome profiling from short reads. Bioinformatics. 2017 ;33(14):2202-2204.
. Tools for annotation and comparison of structural variation. F1000Res. 2017 ;6:1795.
. . Accurate detection of complex structural variations using single-molecule sequencing. Nat Methods. 2018 ;15(6):461-468.
. Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line. Genome Res. 2018 ;28(8):1126-1135.
. Piercing the dark matter: bioinformatics of long-range sequencing and mapping. Nat Rev Genet. 2018 ;19(6):329-346.
. Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome. Nat Biotechnol. 2019 ;37(10):1155-1162.
. Ancestral Admixture Is the Main Determinant of Global Biodiversity in Fission Yeast. Mol Biol Evol. 2019 ;36(9):1975-1989.
.