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Author Details

Nathan Sheffield (CM4AI)
University of Virginia
0000-0001-5643-4068
2007
81
30
Standards
PMIDPaper TitleJournal TitlePublished Year
37067481excluderanges: exclusion sets for T2T-CHM13, GRCm39, and other genome assemblies.Bioinformatics2023
35211690Detecting molecular subtypes from multi-omics datasets using SUMO.Cell Rep Methods2022
35733248Single-cell transcriptome and accessible chromatin dynamics during endocrine pancreas development.Proc Natl Acad Sci U S A2022
35669346Expanding the Galaxy's reference data.Bioinform Adv2022
33367484IGD: high-performance search for large-scale genomic interval datasets.Bioinformatics2021
33880552Chromatin conformation capture (Hi-C) sequencing of patient-derived xenografts: analysis guidelines.Gigascience2021
34890448Linking big biomedical datasets to modular analysis with Portable Encapsulated Projects.Gigascience2021
34416909Bedshift: perturbation of genomic interval sets.Genome Biol2021
34017945Identity and compatibility of reference genome resources.NAR Genom Bioinform2021
33992117PEPPRO: quality control and processing of nascent RNA profiling data.Genome Biol2021
34260694Refget: standardized access to reference sequences.Bioinformatics2021
34050156Multimodal analysis of cell-free DNA whole-genome sequencing for pediatric cancers with low mutational burden.Nat Commun2021
32543102Analytical Approaches for ATAC-seq Data Analysis.Curr Protoc Hum Genet2020
32894181COCOA: coordinate covariation analysis of epigenetic heterogeneity.Genome Biol2020
31150060Augmented Interval List: a novel data structure for efficient genomic interval search.Bioinformatics2019
29506020MIRA: an R package for DNA methylation-based inference of regulatory activity.Bioinformatics2018
30150718The DNA methylation landscape of glioblastoma disease progression shows extensive heterogeneity in time and space.Nat Med2018
29878235LOLAweb: a containerized web server for interactive genomic locus overlap enrichment analysis.Nucleic Acids Res2018
29873782Coloc-stats: a unified web interface to perform colocalization analysis of genomic features.Nucleic Acids Res2018
30361341The chromatin accessibility landscape of primary human cancers.Science2018
29608647BART: a transcription factor prediction tool with query gene sets or epigenomic profiles.Bioinformatics2018
28118844Single-cell epigenomic variability reveals functional cancer heterogeneity.Genome Biol2017
28134926DNA methylation heterogeneity defines a disease spectrum in Ewing sarcoma.Nat Med2017
26802024The second European interdisciplinary Ewing sarcoma research summit--A joint effort to deconstructing the multiple layers of a complex disease.Oncotarget2016
26508757LOLA: enrichment analysis for genomic region sets and regulatory elements in R and Bioconductor.Bioinformatics2016
27212022Multi-Omics of Single Cells: Strategies and Applications.Trends Biotechnol2016
25732828Single-cell DNA methylome sequencing and bioinformatic inference of epigenomic cell-state dynamics.Cell Rep2015
26280331ChIPmentation: fast, robust, low-input ChIP-seq for histones and transcription factors.Nat Methods2015
26673328Differential DNA Methylation Analysis without a Reference Genome.Cell Rep2015
25704812Epigenome mapping reveals distinct modes of gene regulation and widespread enhancer reprogramming by the oncogenic fusion protein EWS-FLI1.Cell Rep2015
23482648Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions.Genome Res2013
22761590Extensive evolutionary changes in regulatory element activity during human origins are associated with altered gene expression and positive selection.PLoS Genet2012
24705081Identifying and characterizing regulatory sequences in the human genome with chromatin accessibility assays.Genes (Basel)2012
23034120Chromatin accessibility reveals insights into androgen receptor activation and transcriptional specificity.Genome Biol2012
22955983Predicting cell-type-specific gene expression from regions of open chromatin.Genome Res2012
22955617The accessible chromatin landscape of the human genome.Nature2012
21750106Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity.Genome Res2011
20795780Mitochondrial genomics in Orthoptera using MOSAS.Mitochondrial DNA2010
20525592Nonstationary evolution and compositional heterogeneity in beetle mitochondrial phylogenomics.Syst Biol2009
18928554Calculating expected DNA remnants from ancient founding events in human population genetics.BMC Genet2008
18779259A comparative analysis of mitochondrial genomes in Coleoptera (Arthropoda: Insecta) and genome descriptions of six new beetles.Mol Biol Evol2008
3170715Cost containment of formalin-preserved stool specimens for ova and parasites from outpatients.J Clin Microbiol1988
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Collaborators

Christoph Bock
CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences
Co-authored papers 11
Terrence S Furey
University of North Carolina at Chapel Hill
Co-authored papers 6
Gregory E Crawford
Center for Genomic & Computational Biology, Duke University
Co-authored papers 6
Lingyun Song
Center for Genomic & Computational Biology, Duke University
Co-authored papers 5
Paul Datlinger
CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences
Co-authored papers 5
Johanna Klughammer
CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences
Co-authored papers 4
Eleni M Tomazou
St. Anna Children's Cancer Research Institute (CCRI)
Co-authored papers 4
Bum-Kyu Lee
Cancer Research Center, University at Albany, State University of New York
Co-authored papers 3
Heinrich Kovar
St. Anna Children's Cancer Research Institute (CCRI), Medical University Vienna
Co-authored papers 3
Vishwanath R Iyer
Indian Institute of Technology Bombay
Co-authored papers 3
Uta Dirksen
University Hospital Essen, West German Cancer Center
Co-authored papers 3
Darin London
Co-authored papers 3
Micha?? Stolarczyk
University of Virginia
Co-authored papers 3
John T Lawson
Center for Public Health Genomics, University of Virginia
Co-authored papers 3
Andreas Sch??negger
CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences
Co-authored papers 3
Yoichiro Shibata
Center for Genomic and Computational Biology, Duke University.
Co-authored papers 3
Andr?? F Rendeiro
CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences
Co-authored papers 3
Matthias Farlik
CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences
Co-authored papers 3
Olivier Delattre
PSL Research University, Institut Curie Research Center, INSERM U, Institut Curie
Co-authored papers 3
Hojun Song
Texas A&M University, College Station
Co-authored papers 3
Michael F Whiting
Brigham Young University
Co-authored papers 3
Aakrosh Ratan
Center for Public Health Genomics, University of Virginia
Co-authored papers 2
Robert E Thurman
University of Washington
Co-authored papers 2
Bekir Erg??ner
CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences
Co-authored papers 2
Markus Metzler
University Hospital Erlangen
Co-authored papers 2
Alexias Safi
Center for Genomic and Computational Biology, Duke University Medical Center
Co-authored papers 2
Zhancheng Zhang
Co-authored papers 2
Didier Surdez
Balgrist University Hospital, University of Zurich (UZH)
Co-authored papers 2
John A Stamatoyannopoulos
Altius Institute for Biomedical Sciences
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Jeremy M Simon
University of North Carolina
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Release 1.2