Publications

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. In vivo detection of DNA secondary structures using Permanganate/S1 Footprinting with Direct Adapter Ligation and Sequencing (PDAL-Seq). Methods in Enzymology, Volume 695, Chapter 8, 2024.

Non-B DNA & Microsatellite Paper Link

. Methylation profiles at birth linked to early childhood obesity. Accepted for publication by the Journal of Developmental origins of Health and Disease and is currently in press, 2024.

Childhood Obesity Paper Link

. The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes. BIORXIV, 2023.

Sex chromosome Paper Link

. Transcript Isoform Diversity of Ampliconic Genes on the Y Chromosome of Great Apes. GENOME BIOL EVOL, 2023.

Sex chromosome Paper Link

. The complete sequence of a human Y chromosome. Nature, 2023.

Sex chromosome Paper Link

. Accurate sequencing of DNA motifs able to form alternative (non-B) structures. GENOME RES, 2023.

Non-B DNA & Microsatellite Paper Link

. Constructing a polygenic risk score for childhood obesity using functional data analysis. Econom Stat, 2023.

Childhood Obesity Paper Link

. Whole-genome sequence and assembly of the Javan gibbon (Hylobates moloch). J HERED, 2022.

Sex chromosome Paper Link

. Variation in G-quadruplex Sequence and Topology Differentially Impacts Human DNA Polymerase Fidelity. DNA REPAIR, 2022.

Non-B DNA & Microsatellite Paper Link

. Advanced age increases frequencies of de novo mitochondrial mutations in macaque oocytes and somatic tissues. P NATL ACAD SCI USA, 2022.

Mitochondrial Paper Link

. Metabolomic profiling of stool of two-year old children from the INSIGHT study reveals links between butyrate and child weight outcomes. PED OBESITY, 2022.

Childhood Obesity Paper Link

. INSIGHT responsive parenting educational intervention for firstborns is associated with growth of secondborn siblings. OBESITY, 2022.

Childhood Obesity Paper Link

. Constructing a polygenic risk score for childhood obesity using functional data analysis. ECON STAT, 2021.

Childhood Obesity Paper Link

. Selection and thermostability suggest G-quadruplexes are novel functional elements of the human genome. GENOME RES, 2021.

Non-B DNA & Microsatellite Paper Link

. Towards complete and error-free genome assemblies of all vertebrate species. Nature, 2021.

Sex chromosome Paper Link

. Associations between stool micro-transcriptome, gut microbiota, and infant growth. J DEV ORIG HLTH DIS, 2021.

Childhood Obesity Paper Link

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

Sex chromosome Paper Link

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

Regional variation Paper Link

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

Mitochondrial Paper Link

. 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 Paper Link

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

Code Mitochondrial Non-B DNA & Microsatellite Paper Link

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

Code Mitochondrial Paper Link

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

Mitochondrial Paper Link

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

Sex chromosome Paper Link

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

Sex chromosome Paper Link

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

Childhood Obesity Paper Link

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

Paper Link

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

Regional variation Non-B DNA & Microsatellite Paper Link Press Release

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

Sex chromosome Paper Link

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

Childhood Obesity Paper Link Press Release

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

Sex chromosome Paper Link

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

Sex chromosome Paper Link

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

Mitochondrial Paper Link

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

Mitochondrial Paper Link

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

Sex chromosome Paper Link

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

Non-B DNA & Microsatellite Paper Link

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

Mitochondrial Paper Link

. 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 Paper Link

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

Non-B DNA & Microsatellite Paper Link

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

Mitochondrial Paper Link

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

Mitochondrial Paper Link

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

Childhood Obesity Paper Link

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

Regional variation Paper Link

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

Mitochondrial Paper Link

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

Regional variation Paper Link

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

Sex chromosome Paper Link

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

Non-B DNA & Microsatellite Paper Link

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

Non-B DNA & Microsatellite Paper Link

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

Non-B DNA & Microsatellite Paper Link

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

Regional variation Paper Link

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

Paper Link

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

Mitochondrial Paper Link

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

Mitochondrial Paper Link

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

Mitochondrial Paper Link

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

Paper Link

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

Sex chromosome Paper Link

. Molecular Clocks. eLS, 2008.

Regional variation Paper Link

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

Regional variation Paper Link

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

Regional variation Paper Link

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

Sex chromosome Paper Link

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

Paper Link

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

Sex chromosome Paper Link

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

Regional variation Paper Link

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

Regional variation Paper Link

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

Regional variation Sex chromosome Paper Link

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

Paper Link

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

Regional variation Sex chromosome Paper Link

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

Non-B DNA & Microsatellite Paper Link

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

Regional variation Paper Link

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

Regional variation Sex chromosome Paper Link