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A list of all the posts and pages found on the site. For you robots out there is an XML version available for digesting as well.
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Fragment assembly with short reads. Permalink
Published in Bioinformatics (Oxford, England), 2004
Microinversions in mammalian evolution. Permalink
Published in Proceedings of the National Academy of Sciences of the United States of America, 2006
Short read fragment assembly of bacterial genomes. Permalink
Published in Genome research, 2008
De novo fragment assembly with short mate-paired reads: Does the read length matter? Permalink
Published in Genome research, 2009
Paired de bruijn graphs: a novel approach for incorporating mate pair information into genome assemblers. Permalink
Published in Journal of computational biology : a journal of computational molecular cell biology, 2011
Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory. Permalink
Published in BMC bioinformatics, 2012
STAR: ultrafast universal RNA-seq aligner. Permalink
Published in Bioinformatics (Oxford, England), 2013
Reconstructing complex regions of genomes using long-read sequencing technology. Permalink
Published in Genome research, 2014
Resolving the complexity of the human genome using single-molecule sequencing. Permalink
Published in Nature, 2015
An integrated map of structural variation in 2,504 human genomes. Permalink
Published in Nature, 2015
Genetic variation and the de novo assembly of human genomes. Permalink
Published in Nature reviews. Genetics, 2015
Long-read sequence assembly of the gorilla genome. Permalink
Published in Science (New York, N.Y.), 2016
Assembly of long error-prone reads using de Bruijn graphs. Permalink
Published in Proceedings of the National Academy of Sciences of the United States of America, 2016
HySA: a Hybrid Structural variant Assembly approach using next-generation and single-molecule sequencing technologies. Permalink
Published in Genome research, 2017
Resolving multicopy duplications de novo using polyploid phasing. Permalink
Published in Research in computational molecular biology : ... Annual International Conference, RECOMB ... : proceedings. RECOMB (Conference : 2005- ), 2017
High-resolution comparative analysis of great ape genomes. Permalink
Published in Science (New York, N.Y.), 2018
Deleterious mitochondrial DNA point mutations are overrepresented in Drosophila expressing a proofreading-defective DNA polymerase gamma. Permalink
Published in PLoS genetics, 2018
Long-read sequence and assembly of segmental duplications. Permalink
Published in Nature methods, 2019
Multi-platform discovery of haplotype-resolved structural variation in human genomes. Permalink
Published in Nature communications, 2019
Human-specific tandem repeat expansion and differential gene expression during primate evolution. Permalink
Published in Proceedings of the National Academy of Sciences of the United States of America, 2019
A robust benchmark for detection of germline large deletions and insertions. Permalink
Published in Nature biotechnology, 2020
Haplotype-resolved diverse human genomes and integrated analysis of structural variation. Permalink
Published in Science (New York, N.Y.), 2021
lra: A long read aligner for sequences and contigs. Permalink
Published in PLoS computational biology, 2021
Profiling variable-number tandem repeat variation across populations using repeat-pangenome graphs. Permalink
Published in Nature communications, 2021
Segmental duplications and their variation in a complete human genome. Permalink
Published in Science (New York, N.Y.), 2022
The Human Pangenome Project: a global resource to map genomic diversity. Permalink
Published in Nature, 2022
TT-Mars: structural variants assessment based on haplotype-resolved assemblies. Permalink
Published in Genome biology, 2022
Recurrent inversion polymorphisms in humans associate with genetic instability and genomic disorders. Permalink
Published in Cell, 2022
Structural variation across 138,134 samples in the TOPMed consortium. Permalink
Published in Research square, 2023
Gaps and complex structurally variant loci in phased genome assemblies. Permalink
Published in Genome research, 2023
The motif composition of variable number tandem repeats impacts gene expression. Permalink
Published in Genome research, 2023
Inversion polymorphism in a complete human genome assembly. Permalink
Published in Genome biology, 2023
A draft human pangenome reference. Permalink
Published in Nature, 2023
vamos: variable-number tandem repeats annotation using efficient motif sets. Permalink
Published in Genome biology, 2023
Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation. Permalink
Published in Nature methods, 2023
HQAlign: aligning nanopore reads for SV detection using current-level modeling. Permalink
Published in Bioinformatics (Oxford, England), 2023
Advances in the discovery and analyses of human tandem repeats. Permalink
Published in Emerging topics in life sciences, 2023
Chromosome level genome assembly of the Etruscan shrew Suncus etruscus. Permalink
Published in Scientific data, 2024
A High-Quality Blue Whale Genome, Segmental Duplications, and Historical Demography. Permalink
Published in Molecular biology and evolution, 2024
Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy. Permalink
Published in Nature biotechnology, 2024
VISTA: an integrated framework for structural variant discovery. Permalink
Published in Briefings in bioinformatics, 2024
Long-read sequencing of hundreds of diverse brains provides insight into the impact of structural variation on gene expression and DNA methylation. Permalink
Published in bioRxiv : the preprint server for biology, 2024
An integrative TAD catalog in lymphoblastoid cell lines discloses the functional impact of deletions and insertions in human genomes. Permalink
Published in Genome research, 2024
Analysis and benchmarking of small and large genomic variants across tandem repeats. Permalink
Published in Nature biotechnology, 2025
Identification of GGC Repeat Expansions in ZFHX3 among Chilean Movement Disorder Patients. Permalink
Published in Movement disorders : official journal of the Movement Disorder Society, 2025
Complex genetic variation in nearly complete human genomes. Permalink
Published in Nature, 2025
Long-read sequencing identifies FGF14 repeat expansions in Parkinson’s disease. Permalink
Published in medRxiv : the preprint server for health sciences, 2025
Genotyping sequence-resolved copy number variation using pangenomes reveals paralog-specific global diversity and expression divergence of duplicated genes. Permalink
Published in Nature genetics, 2025