Single-Cell DNA Methylome Sequencing and Bioinformatic Inference of Epigenomic Cell-State Dynamics
Farlik, Matthias, Sheffield, Nathan C., Nuzzo, Angelo, Datlinger, Paul, Schönegger, Andreas, Klughammer, Johanna, Bock, Christoph
Published in Cell reports (Cambridge) (03.03.2015)
Published in Cell reports (Cambridge) (03.03.2015)
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Journal Article
ChIPmentation: fast, robust, low-input ChIP-seq for histones and transcription factors
Schmidl, Christian, Rendeiro, André F, Sheffield, Nathan C, Bock, Christoph
Published in Nature methods (01.10.2015)
Published in Nature methods (01.10.2015)
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Journal Article
Epigenome Mapping Reveals Distinct Modes of Gene Regulation and Widespread Enhancer Reprogramming by the Oncogenic Fusion Protein EWS-FLI1
Tomazou, Eleni M., Sheffield, Nathan C., Schmidl, Christian, Schuster, Michael, Schönegger, Andreas, Datlinger, Paul, Kubicek, Stefan, Bock, Christoph, Kovar, Heinrich
Published in Cell reports (Cambridge) (24.02.2015)
Published in Cell reports (Cambridge) (24.02.2015)
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Journal Article
Predicting cell-type-specific gene expression from regions of open chromatin
Natarajan, Anirudh, Yardimci, Galip Gürkan, Sheffield, Nathan C, Crawford, Gregory E, Ohler, Uwe
Published in Genome research (01.09.2012)
Published in Genome research (01.09.2012)
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Journal Article
Methods for constructing and evaluating consensus genomic interval sets
Rymuza, Julia, Sun, Yuchen, Zheng, Guangtao, LeRoy, Nathan J, Murach, Maria, Phan, Neil, Zhang, Aidong, Sheffield, Nathan C
Published in Nucleic acids research (23.09.2024)
Published in Nucleic acids research (23.09.2024)
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Journal Article
Single-cell transcriptome and accessible chromatin dynamics during endocrine pancreas development
Duvall, Eliza, Benitez, Cecil M, Tellez, Krissie, Enge, Martin, Pauerstein, Philip T, Li, Lingyu, Baek, Songjoon, Quake, Stephen R, Smith, Jason P, Sheffield, Nathan C, Kim, Seung K, Arda, H Efsun
Published in Proceedings of the National Academy of Sciences - PNAS (28.06.2022)
Published in Proceedings of the National Academy of Sciences - PNAS (28.06.2022)
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Journal Article
Opportunities and challenges in sharing and reusing genomic interval data
Xue, Bingjie, Khoroshevskyi, Oleksandr, Gomez, R Ariel, Sheffield, Nathan C
Published in Frontiers in genetics (20.03.2023)
Published in Frontiers in genetics (20.03.2023)
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Journal Article
PEPPRO: quality control and processing of nascent RNA profiling data
Smith, Jason P, Dutta, Arun B, Sathyan, Kizhakke Mattada, Guertin, Michael J, Sheffield, Nathan C
Published in Genome Biology (15.05.2021)
Published in Genome Biology (15.05.2021)
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Journal Article
Challenges to sharing sample metadata in computational genomics
Sheffield, Nathan C, LeRoy, Nathan J, Khoroshevskyi, Oleksandr
Published in Frontiers in genetics (23.05.2023)
Published in Frontiers in genetics (23.05.2023)
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Journal Article
MIRA: an R package for DNA methylation-based inference of regulatory activity
Lawson, John T, Tomazou, Eleni M, Bock, Christoph, Sheffield, Nathan C
Published in Bioinformatics (01.08.2018)
Published in Bioinformatics (01.08.2018)
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Journal Article
Nonstationary Evolution and Compositional Heterogeneity in Beetle Mitochondrial Phylogenomics
Sheffield, Nathan C., Song, Hojun, Cameron, Stephen L., Whiting, Michael F.
Published in Systematic biology (01.08.2009)
Published in Systematic biology (01.08.2009)
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Journal Article
Differential DNA Methylation Analysis without a Reference Genome
Klughammer, Johanna, Datlinger, Paul, Printz, Dieter, Sheffield, Nathan C., Farlik, Matthias, Hadler, Johanna, Fritsch, Gerhard, Bock, Christoph
Published in Cell reports (Cambridge) (22.12.2015)
Published in Cell reports (Cambridge) (22.12.2015)
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Journal Article
GenomicDistributions: fast analysis of genomic intervals with Bioconductor
Kupkova, Kristyna, Mosquera, Jose Verdezoto, Smith, Jason P, Stolarczyk, Michał, Danehy, Tessa L, Lawson, John T, Xue, Bingjie, Stubbs, 4th, John T, LeRoy, Nathan, Sheffield, Nathan C
Published in BMC genomics (12.04.2022)
Published in BMC genomics (12.04.2022)
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Journal Article
COCOA: coordinate covariation analysis of epigenetic heterogeneity
Lawson, John T., Smith, Jason P., Bekiranov, Stefan, Garrett-Bakelman, Francine E., Sheffield, Nathan C.
Published in Genome Biology (07.09.2020)
Published in Genome Biology (07.09.2020)
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Journal Article
Methods for evaluating unsupervised vector representations of genomic regions
Zheng, Guangtao, Rymuza, Julia, Gharavi, Erfaneh, LeRoy, Nathan J, Zhang, Aidong, Sheffield, Nathan C
Published in NAR genomics and bioinformatics (01.09.2024)
Published in NAR genomics and bioinformatics (01.09.2024)
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Journal Article
Integrative single-cell meta-analysis reveals disease-relevant vascular cell states and markers in human atherosclerosis
Mosquera, Jose Verdezoto, Auguste, Gaëlle, Wong, Doris, Turner, Adam W., Hodonsky, Chani J., Alvarez-Yela, Astrid Catalina, Song, Yipei, Cheng, Qi, Lino Cardenas, Christian L., Theofilatos, Konstantinos, Bos, Maxime, Kavousi, Maryam, Peyser, Patricia A., Mayr, Manuel, Kovacic, Jason C., Björkegren, Johan L.M., Malhotra, Rajeev, Stukenberg, P. Todd, Finn, Aloke V., van der Laan, Sander W., Zang, Chongzhi, Sheffield, Nathan C., Miller, Clint L.
Published in Cell reports (Cambridge) (28.11.2023)
Published in Cell reports (Cambridge) (28.11.2023)
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Journal Article
When phylogenetic assumptions are violated: base compositional heterogeneity and among-site rate variation in beetle mitochondrial phylogenomics
SONG, HOJUN, SHEFFIELD, NATHAN C., CAMERON, STEPHEN L., MILLER, KELLY B., WHITING, MICHAEL F.
Published in Systematic entomology (01.07.2010)
Published in Systematic entomology (01.07.2010)
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Journal Article
Joint Representation Learning for Retrieval and Annotation of Genomic Interval Sets
Gharavi, Erfaneh, LeRoy, Nathan J, Zheng, Guangtao, Zhang, Aidong, Brown, Donald E, Sheffield, Nathan C
Published in Bioengineering (Basel) (01.03.2024)
Published in Bioengineering (Basel) (01.03.2024)
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