Publications by authors named "Richard Sandstrom"

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Publisher Correction: The ENCODE Imputation Challenge: a critical assessment of methods for cross-cell type imputation of epigenomic profiles.
Jacob Matthew Schreiber, Carles A Boix, Jin Wook Lee, Hongyang Li, Yuanfang Guan, Richard S Sandstrom

Genome Biol· February 2025

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The ENCODE Uniform Analysis Pipelines.
Benjamin C Hitz, Jin-Wook Lee, Otto Jolanki, Meenakshi S Kagda, Keenan Graham, Richard Sandstrom

Res Sq· July 2023

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The ENCODE Uniform Analysis Pipelines.
Benjamin C Hitz, Lee Jin-Wook, Otto Jolanki, Meenakshi S Kagda, Keenan Graham, Richard Sandstrom

bioRxiv· April 2023

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Inaccessible LCG Promoters Act as Safeguards to Restrict T Cell Development to Appropriate Notch Signaling Environments.
Suzanne Furuyama, Qian Vicky Wu, Barbara Varnum-Finney, Richard Sandstrom, Wouter Meuleman

Stem Cell Reports· April 2021

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Index and biological spectrum of human DNase I hypersensitive sites.
Wouter Meuleman, Alexander Muratov, Eric Rynes, Jessica Halow, Kristen Lee, Richard Sandstrom

Nature· August 2020

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Global reference mapping of human transcription factor footprints.
Jeff Vierstra, John Lazar, Richard Sandstrom, Jessica Halow, Kristen Lee

Nature· July 2020

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Global Regulatory DNA Potentiation by SMARCA4 Propagates to Selective Gene Expression Programs via Domain-Level Remodeling.
John E Lazar, Sandra Stehling-Sun, Vivek Nandakumar, Hao Wang, Daniel R Chee, Richard Sandstrom

Cell Rep· June 2020

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Global Regulatory DNA Potentiation by SMARCA4 Propagates to Selective Gene Expression Programs via Domain-Level Remodeling.
John E Lazar, Sandra Stehling-Sun, Vivek Nandakumar, Hao Wang, Daniel R Chee, Richard Sandstrom

Cell Rep· May 2020

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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

Front Plant Sci· November 2019

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Integrated Functional Genomic Analysis Enables Annotation of Kidney Genome-Wide Association Study Loci.
Karsten B Sieber, Anna Batorsky, Kyle Siebenthall, Kelly L Hudkins, Jeff D Vierstra, Richard Sandstrom

J Am Soc Nephrol· March 2019

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Integrated epigenomic profiling reveals endogenous retrovirus reactivation in renal cell carcinoma.
Kyle T Siebenthall, Chris P Miller, Jeff D Vierstra, Julie Mathieu, Maria Tretiakova, Richard Sandstrom

EBioMedicine· March 2019

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The birth of a human-specific neural gene by incomplete duplication and gene fusion.
Max L Dougherty, Xander Nuttle, Osnat Penn, Bradley J Nelson, John Huddleston, Richard Sandstrom

Genome Biol· March 2017

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Cross-species Analyses Unravel the Complexity of H3K27me3 and H4K20me3 in the Context of Neural Stem Progenitor Cells.
Christopher T Rhodes, Richard S Sandstrom, Shu-Wei Angela Huang, Yufeng Wang, Gunnar Schotta

Neuroepigenetics· June 2016

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Corrigendum: Domains of genome-wide gene expression dysregulation in Down's syndrome.
Audrey Letourneau, Federico A Santoni, Ximena Bonilla, M Reza Sailani, David Gonzalez, Richard S Sandstrom

Nature· March 2016

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Erratum: Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo.
Matthew T Maurano, Eric Haugen, Richard Sandstrom, Jeff Vierstra, Anthony Shafer

Nat Genet· January 2016

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Genome Sequencing of Autism-Affected Families Reveals Disruption of Putative Noncoding Regulatory DNA.
Tychele N Turner, Fereydoun Hormozdiari, Michael H Duyzend, Sarah A McClymont, Paul W Hook, Richard Sandstrom

Am J Hum Genet· January 2016

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Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo.
Matthew T Maurano, Eric Haugen, Richard Sandstrom, Jeff Vierstra, Anthony Shafer

Nat Genet· December 2015

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DNase I hypersensitivity analysis of the mouse brain and retina identifies region-specific regulatory elements.
Matthew S Wilken, Joseph A Brzezinski, Anna La Torre, Kyle Siebenthall, Robert Thurman, Richard S Sandstrom

Epigenetics Chromatin· May 2015

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Native elongating transcript sequencing reveals human transcriptional activity at nucleotide resolution.
Andreas Mayer, Julia di Iulio, Seth Maleri, Umut Eser, Jeff Vierstra, Richard Sandstrom

Cell· April 2015

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Integrative analysis of 111 reference human epigenomes.

Nature· February 2015

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Cell-of-origin chromatin organization shapes the mutational landscape of cancer.
Paz Polak, Rosa Karlić, Amnon Koren, Robert Thurman, Richard Sandstrom

Nature· February 2015

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Genome-wide comparative analysis reveals human-mouse regulatory landscape and evolution.
Olgert Denas, Richard Sandstrom, Yong Cheng, Kathryn Beal, Javier Herrero

BMC Genomics· February 2015

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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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Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution.
Jeff Vierstra, Eric Rynes, Richard Sandstrom, Miaohua Zhang, Theresa Canfield

Science· November 2014

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