Identifying and Characterizing Regulatory Sequences in the Human Genome with Chromatin Accessibility Assays

by Terrence S. Furey, Nathan C. Sheffield
Published 2012-10-01

Seqpare: a novel metric of similarity between genomic interval sets [version 2; peer review: 2 approved]

by Selena C. Feng, Nathan C. Sheffield, Jianglin Feng
Published 2021-01-01

Bedshift: perturbation of genomic interval sets

by Aaron Gu, Hyun Jae Cho, Nathan C. Sheffield
Published 2021-08-01

COCOA: coordinate covariation analysis of epigenetic heterogeneity

by John T. Lawson, Jason P. Smith, Stefan Bekiranov, Francine E. Garrett-Bakelman, Nathan C. Sheffield
Published 2020-09-01

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

by Matthias Farlik, Nathan C. Sheffield, Angelo Nuzzo, Paul Datlinger, Andreas Schönegger, Johanna Klughammer, Christoph Bock
Published 2015-03-01

PEPPRO: quality control and processing of nascent RNA profiling data

by Jason P. Smith, Arun B. Dutta, Kizhakke Mattada Sathyan, Michael J. Guertin, Nathan C. Sheffield
Published 2021-05-01

Differential DNA Methylation Analysis without a Reference Genome

by Johanna Klughammer, Paul Datlinger, Dieter Printz, Nathan C. Sheffield, Matthias Farlik, Johanna Hadler, Gerhard Fritsch, Christoph Bock
Published 2015-12-01

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

by Eleni M. Tomazou, Nathan C. Sheffield, Christian Schmidl, Michael Schuster, Andreas Schönegger, Paul Datlinger, Stefan Kubicek, Christoph Bock, Heinrich Kovar
Published 2015-02-01

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

by Yoichiro Shibata, Nathan C Sheffield, Olivier Fedrigo, Courtney C Babbitt, Matthew Wortham, Alok K Tewari, Darin London, Lingyun Song, Bum-Kyu Lee, Vishwanath R Iyer, Stephen C J Parker, Elliott H Margulies, Gregory A Wray, Terrence S Furey, Gregory E Crawford
Published 2012-06-01

Multimodal analysis of cell-free DNA whole-genome sequencing for pediatric cancers with low mutational burden

by Peter Peneder, Adrian M. Stütz, Didier Surdez, Manuela Krumbholz, Sabine Semper, Mathieu Chicard, Nathan C. Sheffield, Gaelle Pierron, Eve Lapouble, Marcus Tötzl, Bekir Ergüner, Daniele Barreca, André F. Rendeiro, Abbas Agaimy, Heidrun Boztug, Gernot Engstler, Michael Dworzak, Marie Bernkopf, Sabine Taschner-Mandl, Inge M. Ambros, Ola Myklebost, Perrine Marec-Bérard, Susan Ann Burchill, Bernadette Brennan, Sandra J. Strauss, Jeremy Whelan, Gudrun Schleiermacher, Christiane Schaefer, Uta Dirksen, Caroline Hutter, Kjetil Boye, Peter F. Ambros, Olivier Delattre, Markus Metzler, Christoph Bock, Eleni M. Tomazou
Published 2021-05-01