LOLA: enrichment analysis for genomic region sets and regulatory elements in R and Bioconductor von Sheffield, Nathan C, Bock, Christoph

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Single-Cell DNA Methylome Sequencing and Bioinformatic Inference of Epigenomic Cell-State Dynamics von Farlik, Matthias, Sheffield, Nathan C., Nuzzo, Angelo, Datlinger, Paul, Schönegger, Andreas, Klughammer, Johanna, Bock, Christoph

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ChIPmentation: fast, robust, low-input ChIP-seq for histones and transcription factors von Schmidl, Christian, Rendeiro, André F, Sheffield, Nathan C, Bock, Christoph

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Epigenome Mapping Reveals Distinct Modes of Gene Regulation and Widespread Enhancer Reprogramming by the Oncogenic Fusion Protein EWS-FLI1 von Tomazou, Eleni M., Sheffield, Nathan C., Schmidl, Christian, Schuster, Michael, Schönegger, Andreas, Datlinger, Paul, Kubicek, Stefan, Bock, Christoph, Kovar, Heinrich

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Bedshift: perturbation of genomic interval sets von Gu, Aaron, Cho, Hyun Jae, Sheffield, Nathan C

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Predicting cell-type-specific gene expression from regions of open chromatin von Natarajan, Anirudh, Yardimci, Galip Gürkan, Sheffield, Nathan C, Crawford, Gregory E, Ohler, Uwe

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Methods for constructing and evaluating consensus genomic interval sets von Rymuza, Julia, Sun, Yuchen, Zheng, Guangtao, LeRoy, Nathan J, Murach, Maria, Phan, Neil, Zhang, Aidong, Sheffield, Nathan C

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Opportunities and challenges in sharing and reusing genomic interval data von Xue, Bingjie, Khoroshevskyi, Oleksandr, Gomez, R Ariel, Sheffield, Nathan C

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Single-cell transcriptome and accessible chromatin dynamics during endocrine pancreas development von 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

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Challenges to sharing sample metadata in computational genomics von Sheffield, Nathan C, LeRoy, Nathan J, Khoroshevskyi, Oleksandr

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PEPPRO: quality control and processing of nascent RNA profiling data von Smith, Jason P, Dutta, Arun B, Sathyan, Kizhakke Mattada, Guertin, Michael J, Sheffield, Nathan C

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Multi-Omics of Single Cells: Strategies and Applications von Bock, Christoph, Farlik, Matthias, Sheffield, Nathan C

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MIRA: an R package for DNA methylation-based inference of regulatory activity von Lawson, John T, Tomazou, Eleni M, Bock, Christoph, Sheffield, Nathan C

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Differential DNA Methylation Analysis without a Reference Genome von Klughammer, Johanna, Datlinger, Paul, Printz, Dieter, Sheffield, Nathan C., Farlik, Matthias, Hadler, Johanna, Fritsch, Gerhard, Bock, Christoph

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Nonstationary Evolution and Compositional Heterogeneity in Beetle Mitochondrial Phylogenomics von Sheffield, Nathan C., Song, Hojun, Cameron, Stephen L., Whiting, Michael F.

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GenomicDistributions: fast analysis of genomic intervals with Bioconductor von 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

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COCOA: coordinate covariation analysis of epigenetic heterogeneity von Lawson, John T., Smith, Jason P., Bekiranov, Stefan, Garrett-Bakelman, Francine E., Sheffield, Nathan C.

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Integrative single-cell meta-analysis reveals disease-relevant vascular cell states and markers in human atherosclerosis von 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.

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Methods for evaluating unsupervised vector representations of genomic regions von Zheng, Guangtao, Rymuza, Julia, Gharavi, Erfaneh, LeRoy, Nathan J, Zhang, Aidong, Sheffield, Nathan C

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Joint Representation Learning for Retrieval and Annotation of Genomic Interval Sets von Gharavi, Erfaneh, LeRoy, Nathan J, Zheng, Guangtao, Zhang, Aidong, Brown, Donald E, Sheffield, Nathan C

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