Publications

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. Dynamic evolution of great ape Y chromosomes. IN PRESS P NATL ACAD SCI USA, 2020.

Preprint Sex chromosome DOI

. Human L1 Transposition Dynamics Unraveled with Functional Data Analysis. MOL BIOL EVOL, 2020.

Regional variation DOI

. Age-related accumulation of de novo mitochondrial mutations in mammalian oocytes and somatic tissues. PLOS BIOL, 2020.

Mitochondrial DOI

. Ampliconic genes on the great ape Y chromosomes: Rapid evolution of copy number but conservation of expression levels. GENOME BIOL EVOL, 2020.

PDF Sex chromosome DOI

. Family reunion via error correction: an efficient analysis of duplex sequencing data. BMC BIOINFORMATICS, 2020.

Code Mitochondrial Microsatellite DOI

. Pronounced somatic bottleneck in mitochondrial DNA of human hair. PHILOS T R SOC B, 2019.

Code Mitochondrial DOI

. Bottleneck and selection in the germline and maternal age influence transmission of mitochondrial DNA in human pedigrees. P NATL ACAD SCI USA, 2019.

Mitochondrial DOI

. DiscoverY: a classifier for identifying Y chromosome sequences in male assemblies. BMC GENOMICS, 2019.

Sex chromosome DOI

. High Satellite Repeat Turnover in Great Apes Studied with Short- and Long-read Technologies. MOL BIOL EVOL, 2019.

Sex chromosome DOI

. Polygenic risk score based on weight gain trajectories is a strong predictor of childhood obesity. BIORXIV, 2019.

Childhood Obesity DOI

. Functional data analysis for computational biology. BIOINFORMATICS, 2019.

DOI

. Long-read sequencing technology indicates genome-wide effects of non-B DNA on polymerization speed and error rate. GENOME RES, 2018.

Regional variation DOI Press Release

. Deciphering highly similar multigene family transcripts from Iso-Seq data with IsoCon. NAT COMMUN, 2018.

Sex chromosome DOI

. Correcting palindromes in long reads after whole-genome amplification. BMC GENOMICS, 2018.

Sex chromosome DOI

. Child Weight Gain Trajectories Linked To Oral Microbiota Composition. SCI REP-UK, 2018.

Childhood Obesity DOI Press Release

. IWTomics: testing high-resolution sequence-based `Omics' data at multiple locations and scales. BIOINFORMATICS, 2018.

Microsatellite Regional variation DOI

. High Levels of Copy Number Variation of Ampliconic Genes across Major Human Y Haplogroups. GENOME BIOL EVOL, 2018.

Sex chromosome DOI

. RecoverY: k-mer-based read classification for Y-chromosome-specific sequencing and assembly. BIOINFORMATICS, 2018.

Sex chromosome DOI

. A Population Phylogenetic View of Mitochondrial Heteroplasmy. GENETICS, 2018.

Mitochondrial DOI

. Elevated mitochondrial genome variation after 50 generations of radiation exposure in a wild rodent. EVOL APPL, 2017.

Mitochondrial DOI

. Y and W Chromosome Assemblies: Approaches and Discoveries. TRENDS GENET, 2017.

Sex chromosome DOI

. Reverse Transcription Errors and RNA–DNA Differences at Short Tandem Repeats. MOL BIOL EVOL, 2016.

Microsatellite DOI

. Streamlined analysis of duplex sequencing data with Du Novo. GENOME BIOL, 2016.

Mitochondrial DOI

. A time- and cost-effective strategy to sequence mammalian Y Chromosomes: an application to the de novo assembly of gorilla Y. GENOME RES, 2016.

Sex chromosome DOI

. Accurate typing of short tandem repeats from genome-wide sequencing data and its applications. GENOME RES, 2015.

Microsatellite DOI

. Development and assessment of an optimized next-generation DNA sequencing approach for the mtgenome using the Illumina MiSeq. FORENSIC SCI INT-GEN, 2014.

Mitochondrial DOI

. Maternal age effect and severe germ-line bottleneck in the inheritance of human mitochondrial DNA. P NATL ACAD SCI USA, 2014.

Mitochondrial DOI

. The Intervention Nurses Start Infants Growing on Healthy Trajectories (INSIGHT) study. BMC PEDIATR, 2014.

Childhood Obesity DOI

. Genomic Landscape of Human, Bat, and Ex Vivo DNA Transposon Integrations. MOL BIOL EVOL, 2014.

Regional variation DOI

. Controlling for contamination in re-sequencing studies with a reproducible web-based phylogenetic approach. BIOTECHNIQUES, 2014.

Mitochondrial DOI

. Segmenting the human genome based on states of neutral genetic divergence. P NATL ACAD SCI USA, 2013.

Regional variation DOI

. Gene Survival and Death on the Human Y Chromosome. MOL BIOL EVOL, 2013.

Sex chromosome DOI

. Mature Microsatellites: Mechanisms Underlying Dinucleotide Microsatellite Mutational Biases in Human Cells. G3-GENES GENOM GENET, 2013.

Microsatellite DOI

. The origin, evolution, and functional impact of short insertion–deletion variants identified in 179 human genomes. GENOME RES, 2013.

Microsatellite DOI

. Distinct Mutational Behaviors Differentiate Short Tandem Repeats from Microsatellites in the Human Genome. GENOME BIOL EVOL, 2013.

Microsatellite DOI

. Rescuing Alu: Recovery of New Inserts Shows LINE-1 Preserves Alu Activity through A-Tail Expansion. PLOS GENET, 2012.

Regional variation DOI

. SMBE Proposal to the Government of Japan. MOL BIOL EVOL, 2012.

DOI

. Harnessing cloud computing with Galaxy Cloud. NAT BIOTECHNOL, 2011.

Mitochondrial DOI

. Dynamics of mitochondrial heteroplasmy in three families investigated via a repeatable re-sequencing study. GENOME BIOL, 2011.

Mitochondrial DOI

. A Massively Parallel Sequencing Approach Uncovers Ancient Origins and High Genetic Variability of Endangered Przewalski's Horses. GENOME BIOL EVOL, 2011.

Mitochondrial DOI

. Complete Khoisan and Bantu genomes from southern Africa. NATURE, 2010.

DOI

. Genomic Analyses of Sex Chromosome Evolution. ANNU REV GENOM HUM G, 2009.

Sex chromosome DOI

. Molecular Clocks. eLS, 2008.

Regional variation DOI

. Human-macaque comparisons illuminate variation in neutral substitution rates. GENOME BIOL, 2008.

Regional variation DOI

. The genome-wide determinants of human and chimpanzee microsatellite evolution. GENOME RES, 2008.

Microsatellite DOI

. A Macaque's-Eye View of Human Insertions and Deletions: Differences in Mechanisms. PLOS COMPUT BIOL, 2007.

Regional variation DOI

. Evolutionary and Biomedical Insights from the Rhesus Macaque Genome. SCIENCE, 2007.

Sex chromosome DOI

. A framework for collaborative analysis of ENCODE data: Making large-scale analyses biologist-friendly. GENOME RES, 2007.

DOI

. Genomic Environment Predicts Expression Patterns on the Human Inactive X Chromosome. PLOS GENET, 2006.

Sex chromosome DOI

. Rapid and asymmetric divergence of duplicate genes in the human gene coexpression network. BMC BIOINFORMATICS, 2006.

Regional variation DOI

. Initial sequence of the chimpanzee genome and comparison with the human genome. NATURE, 2005.

Regional variation DOI

. Oscillating Evolution of a Mammalian Locus with Overlapping Reading Frames: An XLαs/ALEX Relay. PLOS GENET, 2005.

Regional variation DOI

. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. NATURE, 2004.

Regional variation Sex chromosome DOI

. COMPARATIVE GENOMICS. ANNU REV GENOM HUM G, 2004.

DOI

. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. NATURE, 2004.

Regional variation Sex chromosome DOI

. Tetranucleotide microsatellite markers for the Brown-headed Cowbird Molothrus ater. J AVIAN BIOL, 2003.

Microsatellite DOI

. Chromosome-wide SNPs reveal an ancient origin for Plasmodium falciparum. NATURE, 2002.

Regional variation DOI

. Male-driven evolution. CURR OPIN GENET DEV, 2002.

Regional variation Sex chromosome DOI

. Representational difference analysis to distinguish cryptic species. MOL ECOL, 1999.

Microsatellite DOI