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

ανά Sheffield, Nathan C., Furey, Terrence S.
Έκδοση 2012

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

ανά Sheffield, Nathan C., Bock, Christoph
Τόπος έκδοσης Bioinformatics (2016)

Analytical Approaches for ATAC-seq Data Analysis

ανά Smith, Jason P., Sheffield, Nathan C.
Τόπος έκδοσης Curr Protoc Hum Genet (2020)

Multi-Omics of Single Cells: Strategies and Applications

ανά Bock, Christoph, Farlik, Matthias, Sheffield, Nathan C.
Τόπος έκδοσης Trends Biotechnol (2016)

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

ανά Feng, Jianglin, Ratan, Aakrosh, Sheffield, Nathan C
Τόπος έκδοσης Bioinformatics (2019)

Identity and compatibility of reference genome resources

ανά Stolarczyk, Michał, Xue, Bingjie, Sheffield, Nathan C
Τόπος έκδοσης NAR Genom Bioinform (2021)

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

ανά Stacey, Andrew, Sheffield, Nathan C, Crandall, Keith A
Έκδοση 2008

Seqpare: a novel metric of similarity between genomic interval sets

ανά Feng, Selena C., Sheffield, Nathan C., Feng, Jianglin
Τόπος έκδοσης F1000Res (2021)

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

ανά Nagraj, V P, Magee, Neal E, Sheffield, Nathan C
Τόπος έκδοσης Nucleic Acids Res (2018)

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

ανά Schmidl, Christian, Rendeiro, André F., Sheffield, Nathan C., Bock, Christoph
Τόπος έκδοσης Nat Methods (2015)

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

ανά Lawson, John T, Tomazou, Eleni M, Bock, Christoph, Sheffield, Nathan C
Τόπος έκδοσης Bioinformatics (2018)

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

ανά Natarajan, Anirudh, Yardımcı, Galip Gürkan, Sheffield, Nathan C., Crawford, Gregory E., Ohler, Uwe
Έκδοση 2012

Refgenie: a reference genome resource manager

ανά Stolarczyk, Michał, Reuter, Vincent P, Smith, Jason P, Magee, Neal E, Sheffield, Nathan C
Τόπος έκδοσης Gigascience (2020)

COCOA: coordinate covariation analysis of epigenetic heterogeneity

ανά Lawson, John T., Smith, Jason P., Bekiranov, Stefan, Garrett-Bakelman, Francine E., Sheffield, Nathan C.
Τόπος έκδοσης Genome Biol (2020)

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

ανά Farlik, Matthias, Sheffield, Nathan C., Nuzzo, Angelo, Datlinger, Paul, Schönegger, Andreas, Klughammer, Johanna, Bock, Christoph
Τόπος έκδοσης Cell Rep (2015)

BART: a transcription factor prediction tool with query gene sets or epigenomic profiles

ανά Wang, Zhenjia, Civelek, Mete, Miller, Clint L, Sheffield, Nathan C, Guertin, Michael J, Zang, Chongzhi
Τόπος έκδοσης Bioinformatics (2018)

PEPPRO: quality control and processing of nascent RNA profiling data

ανά Smith, Jason P., Dutta, Arun B., Sathyan, Kizhakke Mattada, Guertin, Michael J., Sheffield, Nathan C.
Τόπος έκδοσης Genome Biol (2021)

Differential DNA Methylation Analysis without a Reference Genome

ανά Klughammer, Johanna, Datlinger, Paul, Printz, Dieter, Sheffield, Nathan C., Farlik, Matthias, Hadler, Johanna, Fritsch, Gerhard, Bock, Christoph
Τόπος έκδοσης Cell Rep (2015)

Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions

ανά Sheffield, Nathan C., Thurman, Robert E., Song, Lingyun, Safi, Alexias, Stamatoyannopoulos, John A., Lenhard, Boris, Crawford, Gregory E., Furey, Terrence S.
Έκδοση 2013

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

ανά Tomazou, Eleni M., Sheffield, Nathan C., Schmidl, Christian, Schuster, Michael, Schönegger, Andreas, Datlinger, Paul, Kubicek, Stefan, Bock, Christoph, Kovar, Heinrich
Τόπος έκδοσης Cell Rep (2015)