• Publications
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Nanopore sequencing and assembly of a human genome with ultra-long reads
Nanopore sequencing is a promising technique for genome sequencing due to its portability, ability to sequence long reads from single molecules, and to simultaneously assay DNA methylation. HoweverExpand
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Genome-wide association study identifies multiple susceptibility loci for pulmonary fibrosis
We performed a genome-wide association study of non-Hispanic, white individuals with fibrotic idiopathic interstitial pneumonias (IIPs; n = 1,616) and controls (n = 4,683), with follow-up replicationExpand
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Nanopore sequencing and assembly of a human genome with ultra-long reads
We report the sequencing and assembly of a reference genome for the human GM12878 Utah/Ceph cell line using the MinION (Oxford Nanopore Technologies) nanopore sequencer. 91.2 Gb of sequence data,Expand
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Following Tetraploidy in Maize, a Short Deletion Mechanism Removed Genes Preferentially from One of the Two Homeologs
Following genome duplication and selfish DNA expansion, maize used a heretofore unknown mechanism to shed redundant genes and functionless DNA with bias toward one of the parental genomes.
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GOATOOLS: A Python library for Gene Ontology analyses
TLDR
The biological interpretation of gene lists with interesting shared properties, such as up- or down-regulation in a particular experiment, is typically accomplished using gene ontology enrichment analysis tools. Expand
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Mosdepth: quick coverage calculation for genomes and exomes
TLDR
Mosdepth is a new command‐line tool for rapidly calculating genome‐wide sequencing coverage. Expand
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Comb-p: software for combining, analyzing, grouping and correcting spatially correlated P-values
TLDR
SUMMARY comb-p is a command-line tool and a python library that manipulates BED files of possibly irregularly spaced P-values and (1) calculates auto-correlation, (2) combines adjacent P- values, (3) performs false discovery adjustment, (4) finds regions of enrichment (i.e. series of adjacent low P-value) and assigns significance to those regions. Expand
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Pybedtools: a flexible Python library for manipulating genomic datasets and annotations
Summary: pybedtools is a flexible Python software library for manipulating and exploring genomic datasets in many common formats. It provides an intuitive Python interface that extends upon theExpand
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Fast and accurate alignment of long bisulfite-seq reads
TLDR
We perform the first comparison using longer reads to determine which aligners were most accurate and efficient and to evaluate a novel software tool, bwa-meth, built on a traditional mapper. Expand
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Altered Patterns of Fractionation and Exon Deletions in Brassica rapa Support a Two-Step Model of Paleohexaploidy
The genome sequence of the paleohexaploid Brassica rapa shows that fractionation is biased among the three subgenomes and that the least fractionated subgenome has approximately twice as manyExpand
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