Nathan Sheffield

Work

University of Virginia
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Associate Professor

US

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University of Virginia
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Assistant Professor

US

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Education

Duke University
United States of America

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PhD Computational Biology and Bioinformatics

Brigham Young University
United States of America

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B.S. Bioinformatics

Publications

The interaction between base compositional heterogeneity and among-site rate variation in models of molecular evolution.

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journal-article

When phylogenetic assumptions are violated: base compositional heterogeneity and among-site rate variation in beetle mitochondrial phylogenomics.

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journal-article

A comparative analysis of mitochondrial genomes in Coleoptera (Arthropoda: Insecta) and genome descriptions of six new beetles.

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journal-article

Identifying and characterizing regulatory sequences in the human genome with chromatin accessibility assays

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journal-article

Inhibition of Renin Expression Is Regulated by an Epigenetic Switch From an Active to a Poised State

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Hypertension

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Methods for evaluating unsupervised vector representations of genomic regions

Published by

NAR Genomics and Bioinformatics

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DeepGSEA: explainable deep gene set enrichment analysis for single-cell transcriptomic data

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Bioinformatics

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Joint Representation Learning for Retrieval and Annotation of Genomic Interval Sets

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Bioengineering

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Fast clustering and cell-type annotation of scATAC data using pre-trained embeddings

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NAR Genomics and Bioinformatics

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PEPhub: a database, web interface, and API for editing, sharing, and validating biological sample metadata

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GigaScience

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journal-article

Methods for constructing and evaluating consensus genomic interval sets

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Nucleic Acids Research

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journal-article

Fast clustering and cell-type annotation of scATAC data using pre-trained embeddings

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preprint

Protein Kinase A Inhibition Epigenetically SilencesRen1

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preprint

Methods for evaluating unsupervised vector representations of genomic regions

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preprint

Joint representation learning for retrieval and annotation of genomic interval sets

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preprint

PEPhub: a database, web interface, and API for editing, sharing, and validating biological sample metadata

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preprint

Methods for constructing and evaluating consensus genomic interval sets

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preprint

Renin Cell Development: Insights From Chromatin Accessibility and Single-Cell Transcriptomics

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Circulation Research

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journal-article

GEOfetch: a command-line tool for downloading data and standardized metadata from GEO and SRA

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Bioinformatics

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From biomedical cloud platforms to microservices: next steps in FAIR data and analysis

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preprint

GenomicDistributions: fast analysis of genomic intervals with Bioconductor

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BMC Genomics

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journal-article

excluderanges: exclusion sets for T2T-CHM13, GRCm39, and other genome assemblies

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preprint

From biomedical cloud platforms to microservices: next steps in FAIR data and analysis

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Scientific Data

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journal-article

Detecting molecular subtypes from multi-omics datasets using SUMO

Published by

Cell Reports Methods

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Identity and compatibility of reference genome resources

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preprint

Embeddings of genomic region sets capture rich biological associations in lower dimensions

Published by

Bioinformatics

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Linking big biomedical datasets to modular analysis with Portable Encapsulated Projects

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GigaScience

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Bedshift: perturbation of genomic interval sets

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Genome Biology

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PEPPRO: quality control and processing of nascent RNA profiling data

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Genome Biology

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PEPATAC: an optimized pipeline for ATAC-seq data analysis with serial alignments

Published by

NAR Genomics and Bioinformatics

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journal-article

Embeddings of genomic region sets capture rich biological associations in lower dimensions

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preprint

Identity and compatibility of reference genome resources

Published by

NAR Genomics and Bioinformatics

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journal-article

Refget: standardised access to reference sequences

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preprint

Seqpare: a self-consistent metric of similarity between genomic interval sets

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COCOA: Coordinate covariation analysis of epigenetic heterogeneity

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IGD: high-performance search for large-scale genomic interval datasets.

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Bioinformatics (Oxford, England)

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journal-article

Bedshift: perturbation of genomic interval sets

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preprint

Chromatin conformation capture (Hi-C) sequencing of patient-derived xenografts: analysis guidelines

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preprint

Expanding the Galaxy’s reference data

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preprint

Linking big biomedical datasets to modular analysis with Portable Encapsulated Projects

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preprint

PEPATAC: An optimized ATAC-seq pipeline with serial alignments

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preprint

COCOA: coordinate covariation analysis of epigenetic heterogeneity.

Published by

Genome biology

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journal-article

COCOA: coordinate covariation analysis of epigenetic heterogeneity

Published by

Genome Biology

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journal-article

COCOA: Coordinate covariation analysis of epigenetic heterogeneity

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preprint

Data Integration with SUMO Detects Latent Relationships Between Patients in Lower-Grade Gliomas

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preprint

Data Integration with SUMO Detects Latent Relationships Between Patients in Lower-Grade Gliomas

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preprint

IGD: high-performance search for large-scale genomic interval datasets

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preprint

Analytical Approaches for ATAC-seq Data Analysis.

Published by

Current protocols in human genetics

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journal-article

Quality control and processing of nascent RNA profiling data

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preprint

Refgenie: a reference genome resource manager.

Published by

GigaScience

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journal-article

COCOA: Coordinate covariation analysis of epigenetic heterogeneity

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preprint

Augmented Interval List: a novel data structure for efficient genomic interval search

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preprint

Augmented Interval List: a novel data structure for efficient genomic interval search

Published by

Bioinformatics

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journal-article

Bulker: a multi-container environment manager

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preprint

Refgenie: a reference genome resource manager

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preprint

MIRA: an R package for DNA methylation-based inference of regulatory activity

Published by

Bioinformatics

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journal-article

simpleCache: R caching for reproducible, distributed, large-scale projects

Published by

The Journal of Open Source Software

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DNA methylation heterogeneity defines a disease spectrum in Ewing sarcoma.

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Nature medicine

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Single-cell epigenomic variability reveals functional cancer heterogeneity.

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Genome biology

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Multi-Omics of Single Cells: Strategies and Applications.

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Trends in biotechnology

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journal-article

LOLA: enrichment analysis for genomic region sets and regulatory elements in R and Bioconductor.

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Bioinformatics

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The second European interdisciplinary Ewing sarcoma research summit--A joint effort to deconstructing the multiple layers of a complex disease.

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Oncotarget

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journal-article

Differential DNA Methylation Analysis without a Reference Genome.

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Cell reports

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journal-article

ChIPmentation: fast, robust, low-input ChIP-seq for histones and transcription factors.

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Nature methods

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Single-Cell DNA Methylome Sequencing and Bioinformatic Inference of Epigenomic Cell-State Dynamics

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Cell Reports

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journal-article

Epigenome Mapping Reveals Distinct Modes of Gene Regulation and Widespread Enhancer Reprogramming by the Oncogenic Fusion Protein EWS-FLI1

Published by

Cell Reports

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Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions.

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Chromatin accessibility reveals insights into androgen receptor activation and transcriptional specificity.

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An integrated encyclopedia of DNA elements in the human genome.

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Predicting cell-type-specific gene expression from regions of open chromatin.

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The accessible chromatin landscape of the human genome.

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Extensive evolutionary changes in regulatory element activity during human origins are associated with altered gene expression and positive selection.

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Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity.

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A user's guide to the encyclopedia of DNA elements (ENCODE).

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Mitochondrial genomics in Orthoptera using MOSAS.

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Nonstationary evolution and compositional heterogeneity in beetle mitochondrial phylogenomics.

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Calculating expected DNA remnants from ancient founding events in human population genetics.

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