CV

Education

• Ph.D in Version Control Theory, GitHub University, 2018 (expected)
• M.S. in Jekyll, GitHub University, 2014
• B.S. in GitHub, GitHub University, 2012

Work experience

• Spring 2024: Academic Pages Collaborator
  • Github University
  • Duties includes: Updates and improvements to template
  • Supervisor: The Users
• Fall 2015: Research Assistant
  • Github University
  • Duties included: Merging pull requests
  • Supervisor: Professor Hub
• Summer 2015: Research Assistant
  • Github University
  • Duties included: Tagging issues
  • Supervisor: Professor Git

Skills

• Skill 1
• Skill 2
  • Sub-skill 2.1
  • Sub-skill 2.2
  • Sub-skill 2.3
• Skill 3

Publications

Genotyping sequence-resolved copy number variation using pangenomes reveals paralog-specific global diversity and expression divergence of duplicated genes. Permalink

Long-read sequencing identifies FGF14 repeat expansions in Parkinson’s disease. Permalink

Complex genetic variation in nearly complete human genomes. Permalink

Identification of GGC Repeat Expansions in ZFHX3 among Chilean Movement Disorder Patients. Permalink

Analysis and benchmarking of small and large genomic variants across tandem repeats. Permalink

An integrative TAD catalog in lymphoblastoid cell lines discloses the functional impact of deletions and insertions in human genomes. Permalink

Long-read sequencing of hundreds of diverse brains provides insight into the impact of structural variation on gene expression and DNA methylation. Permalink

VISTA: an integrated framework for structural variant discovery. Permalink

Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy. Permalink

A High-Quality Blue Whale Genome, Segmental Duplications, and Historical Demography. Permalink

Chromosome level genome assembly of the Etruscan shrew Suncus etruscus. Permalink

Advances in the discovery and analyses of human tandem repeats. Permalink

HQAlign: aligning nanopore reads for SV detection using current-level modeling. Permalink

Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation. Permalink

vamos: variable-number tandem repeats annotation using efficient motif sets. Permalink

A draft human pangenome reference. Permalink

Inversion polymorphism in a complete human genome assembly. Permalink

The motif composition of variable number tandem repeats impacts gene expression. Permalink

Gaps and complex structurally variant loci in phased genome assemblies. Permalink

Structural variation across 138,134 samples in the TOPMed consortium. Permalink

Recurrent inversion polymorphisms in humans associate with genetic instability and genomic disorders. Permalink

TT-Mars: structural variants assessment based on haplotype-resolved assemblies. Permalink

The Human Pangenome Project: a global resource to map genomic diversity. Permalink

Segmental duplications and their variation in a complete human genome. Permalink

Profiling variable-number tandem repeat variation across populations using repeat-pangenome graphs. Permalink

lra: A long read aligner for sequences and contigs. Permalink

Haplotype-resolved diverse human genomes and integrated analysis of structural variation. Permalink

A robust benchmark for detection of germline large deletions and insertions. Permalink

Human-specific tandem repeat expansion and differential gene expression during primate evolution. Permalink

Multi-platform discovery of haplotype-resolved structural variation in human genomes. Permalink

Long-read sequence and assembly of segmental duplications. Permalink

Deleterious mitochondrial DNA point mutations are overrepresented in Drosophila expressing a proofreading-defective DNA polymerase gamma. Permalink

High-resolution comparative analysis of great ape genomes. Permalink

Resolving multicopy duplications de novo using polyploid phasing. Permalink

HySA: a Hybrid Structural variant Assembly approach using next-generation and single-molecule sequencing technologies. Permalink

Assembly of long error-prone reads using de Bruijn graphs. Permalink

Long-read sequence assembly of the gorilla genome. Permalink

Genetic variation and the de novo assembly of human genomes. Permalink

An integrated map of structural variation in 2,504 human genomes. Permalink

Resolving the complexity of the human genome using single-molecule sequencing. Permalink

Reconstructing complex regions of genomes using long-read sequencing technology. Permalink

STAR: ultrafast universal RNA-seq aligner. Permalink

Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory. Permalink

Paired de bruijn graphs: a novel approach for incorporating mate pair information into genome assemblers. Permalink

De novo fragment assembly with short mate-paired reads: Does the read length matter? Permalink

Short read fragment assembly of bacterial genomes. Permalink

Microinversions in mammalian evolution. Permalink

Fragment assembly with short reads. Permalink

Talks

Teaching

Service and leadership

• Currently signed in to 43 different slack teams