Nathan C Sheffield

Nathan C Sheffield

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Nathan C Sheffield

Nathan C Sheffield

Publications by authors named "Nathan C Sheffield"

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Refgenie: a reference genome resource manager.

Gigascience 2020 Feb;9(2)

Center for Public Health Genomics, University of Virginia, PO Box 800717, Charlottesville, VA, 22908, USA.

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http://dx.doi.org/10.1093/gigascience/giz149DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6988606PMC
February 2020

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

Bioinformatics 2019 Dec;35(23):4907-4911

Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA.

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http://dx.doi.org/10.1093/bioinformatics/btz407DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6901075PMC
December 2019

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

Bioinformatics 2018 08;34(15):2649-2650

Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA.

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http://dx.doi.org/10.1093/bioinformatics/bty083DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6061852PMC
August 2018

LOLAweb: a containerized web server for interactive genomic locus overlap enrichment analysis.

Nucleic Acids Res 2018 07;46(W1):W194-W199

Center for Public Health Genomics, University of Virginia, USA.

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http://dx.doi.org/10.1093/nar/gky464DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6030814PMC
July 2018

Single-cell epigenomic variability reveals functional cancer heterogeneity.

Genome Biol 2017 01 24;18(1):15. Epub 2017 Jan 24.

Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, 94305, USA.

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http://dx.doi.org/10.1186/s13059-016-1133-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5259890PMC
January 2017

Multi-Omics of Single Cells: Strategies and Applications.

Trends Biotechnol 2016 08 20;34(8):605-608. Epub 2016 May 20.

CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.

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http://dx.doi.org/10.1016/j.tibtech.2016.04.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4959511PMC
August 2016

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

Bioinformatics 2016 Feb 27;32(4):587-9. Epub 2015 Oct 27.

CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Department of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria and Max Planck Institute for Informatics, 66123 Saarbrücken, Germany.

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http://bioinformatics.oxfordjournals.org/content/early/2015/
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http://pubman.mpdl.mpg.de/pubman/item/escidoc:2257668:2/comp
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http://bioinformatics.oxfordjournals.org/lookup/doi/10.1093/
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http://dx.doi.org/10.1093/bioinformatics/btv612DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4743627PMC
February 2016

Differential DNA Methylation Analysis without a Reference Genome.

Cell Rep 2015 Dec 8;13(11):2621-2633. Epub 2015 Dec 8.

CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria; Department of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria; Max Planck Institute for Informatics, 66123 Saarbrücken, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2015.11.024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4695333PMC
December 2015

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

Nat Methods 2015 Oct 17;12(10):963-965. Epub 2015 Aug 17.

CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.

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http://www.nature.com/articles/nmeth.3542
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http://dx.doi.org/10.1038/nmeth.3542DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4589892PMC
October 2015

Single-cell DNA methylome sequencing and bioinformatic inference of epigenomic cell-state dynamics.

Cell Rep 2015 Mar 26;10(8):1386-97. Epub 2015 Feb 26.

CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria; Department of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria; Max Planck Institute for Informatics, 66123 Saarbrücken, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2015.02.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542311PMC
March 2015

Epigenome mapping reveals distinct modes of gene regulation and widespread enhancer reprogramming by the oncogenic fusion protein EWS-FLI1.

Cell Rep 2015 Feb 19;10(7):1082-95. Epub 2015 Feb 19.

Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, 1090 Vienna, Austria; Department of Pediatrics, Medical University of Vienna, 1090 Vienna, Austria. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2015.01.042DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542316PMC
February 2015

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

Genes (Basel) 2012 Oct 15;3(4):651-70. Epub 2012 Oct 15.

Depts of Genetics and Biology, Carolina Center for Genome Sciences, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA.

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http://dx.doi.org/10.3390/genes3040651DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3899983PMC
October 2012

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

Genome Res 2012 Sep;22(9):1711-22

Program in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina 27708, USA.

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http://dx.doi.org/10.1101/gr.135129.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431488PMC
September 2012

Mitochondrial genomics in Orthoptera using MOSAS.

Mitochondrial DNA 2010 Jun;21(3-4):87-104

Department of Biology, Brigham Young University, Provo, UT, USA.

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http://dx.doi.org/10.3109/19401736.2010.500812DOI Listing
June 2010

Nonstationary evolution and compositional heterogeneity in beetle mitochondrial phylogenomics.

Syst Biol 2009 Aug 15;58(4):381-94. Epub 2009 Jul 15.

Department of Biology, Brigham Young University, Provo, UT 84602, USA.

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http://dx.doi.org/10.1093/sysbio/syp037DOI Listing
August 2009

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

BMC Genet 2008 Oct 17;9:66. Epub 2008 Oct 17.

Department of Statistics, Brigham Young University, Provo, UT 84602, USA.

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http://dx.doi.org/10.1186/1471-2156-9-66DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2588638PMC
October 2008