Publications by authors named "Shane Neph"

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CUT&TIME captures the history of open chromatin in developing neurons.
Kiara C Eldred, Matthew Wooten, Derek H Janssens, Joshua Hahn, Shane J Neph

bioRxiv· September 2025

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A haplotype-resolved view of human gene regulation.
Mitchell R Vollger, Elliott G Swanson, Shane J Neph, Jane Ranchalis, Katherine M Munson

bioRxiv· June 2025

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Centromeric transposable elements and epigenetic status drive karyotypic variation in the eastern hoolock gibbon.
Gabrielle A Hartley, Mariam Okhovat, Savannah J Hoyt, Emily Fuller, Nicole Pauloski, Shane Neph

Cell Genom· April 2025

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Integrating Single-Molecule Sequencing and Deep Learning to Predict Haplotype-Specific 3D Chromatin Organization in a Mendelian Condition.
Danilo Dubocanin, Anna Kalygina, J Matthew Franklin, Cy Chittenden, Mitchell R Vollger, Shane Neph

bioRxiv· March 2025

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Genetic diversity and regulatory features of human-specific duplications.
Taylor D Real, Prajna Hebbar, DongAhn Yoo, Francesca Antonacci, Ivana Pačar, Shane J Neph

bioRxiv· March 2025

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Centromeric transposable elements and epigenetic status drive karyotypic variation in the eastern hoolock gibbon.
Gabrielle A Hartley, Mariam Okhovat, Savannah J Hoyt, Emily Fuller, Nicole Pauloski, Shane Neph

bioRxiv· August 2024

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eFORGE v2.0: updated analysis of cell type-specific signal in epigenomic data.
Charles E Breeze, Alex P Reynolds, Jenny van Dongen, Ian Dunham, John Lazar, Shane Neph

Bioinformatics· November 2019

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Mapping and Dynamics of Regulatory DNA in Maturing Siliques.
Alessandra M Sullivan, Andrej A Arsovski, Agnieszka Thompson, Richard Sandstrom, Robert E Thurman, Shane Neph

Front Plant Sci· November 2019

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Operating on Genomic Ranges Using BEDOPS.
Shane Neph, Alex P Reynolds, M Scott Kuehn, John A Stamatoyannopoulos

Methods Mol Biol· December 2016

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52 Genetic Loci Influencing Myocardial Mass.
Pim van der Harst, Jessica van Setten, Niek Verweij, Georg Vogler, Lude Franke, Shane Neph

J Am Coll Cardiol· September 2016

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Integrative analysis of 111 reference human epigenomes.

Nature· February 2015

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A comparative encyclopedia of DNA elements in the mouse genome.
Feng Yue, Yong Cheng, Alessandra Breschi, Jeff Vierstra, Weisheng Wu, Shane Neph

Nature· November 2014

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Conservation of trans-acting circuitry during mammalian regulatory evolution.
Andrew B Stergachis, Shane Neph, Richard Sandstrom, Eric Haugen, Alex P Reynolds

Nature· November 2014

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Mapping and dynamics of regulatory DNA and transcription factor networks in A. thaliana.
Alessandra M Sullivan, Andrej A Arsovski, Janne Lempe, Kerry L Bubb, Matthew T Weirauch, Shane Neph

Cell Rep· September 2014

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DNase I-hypersensitive exons colocalize with promoters and distal regulatory elements.
Tim R Mercer, Stacey L Edwards, Michael B Clark, Shane J Neph, Hao Wang

Nat Genet· August 2013

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Developmental fate and cellular maturity encoded in human regulatory DNA landscapes.
Andrew B Stergachis, Shane Neph, Alex Reynolds, Richard Humbert, Brady Miller

Cell· August 2013

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The accessible chromatin landscape of the human genome.
Robert E Thurman, Eric Rynes, Richard Humbert, Jeff Vierstra, Matthew T Maurano, Shane Neph

Nature· September 2012

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An expansive human regulatory lexicon encoded in transcription factor footprints.
Shane Neph, Jeff Vierstra, Andrew B Stergachis, Alex P Reynolds, Eric Haugen

Nature· September 2012

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Systematic localization of common disease-associated variation in regulatory DNA.
Matthew T Maurano, Richard Humbert, Eric Rynes, Robert E Thurman, Eric Haugen, Shane Neph

Science· September 2012

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Personal and population genomics of human regulatory variation.
Benjamin Vernot, Andrew B Stergachis, Matthew T Maurano, Jeff Vierstra, Shane Neph

Genome Res· September 2012

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Circuitry and dynamics of human transcription factor regulatory networks.
Shane Neph, Andrew B Stergachis, Alex Reynolds, Richard Sandstrom, Elhanan Borenstein

Cell· September 2012

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Foxp3 exploits a pre-existent enhancer landscape for regulatory T cell lineage specification.
Robert M Samstein, Aaron Arvey, Steven Z Josefowicz, Xiao Peng, Alex Reynolds, Shane Neph

Cell· September 2012

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BEDOPS: high-performance genomic feature operations.
Shane Neph, M Scott Kuehn, Alex P Reynolds, Eric Haugen, Robert E Thurman

Bioinformatics· July 2012

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The human mitochondrial transcriptome.
Tim R Mercer, Shane Neph, Marcel E Dinger, Joanna Crawford, Martin A Smith

Cell· August 2011

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Global mapping of protein-DNA interactions in vivo by digital genomic footprinting.
Jay R Hesselberth, Xiaoyu Chen, Zhihong Zhang, Peter J Sabo, Richard Sandstrom, Shane Neph

Nat Methods· April 2009

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