I'm generally not a big fan of the vanity wall of publications concept, which is just another place to maintain; the best place to look for publications is at one of the providers below. But I figured out how to auto-populate this publication list from my bibtex database using JabRef, so it's no more work to have a list here, so here it is.



    List of publications on Pubmed | Google Scholar | ORCID.
  1. Feng J, and Sheffield NC
    IGD: high-performance search for large-scale genomic interval datasets.
    Bioinformatics (2020)

  2. Sheffield NC, Stolarczyk M, Reuter VP, and Rendeiro A
    Linking big biomedical datasets to modular analysis with Portable Encapsulated Projects.
    bioRxiv (2020)

  3. Smith JP, Corces R, Xu J, Wei Y, Reuter VP, Chang HY, and Sheffield NC
    PEPATAC: A portable, optimized ATAC-seq pipeline.
    bioRxiv (2020)

  4. Lawson JT, Smith JP, Bekiranov S, Garrett-Bakelman FE, and Sheffield NC
    COCOA: coordinate covariation analysis of epigenetic heterogeneity.
    Genome Biology (2020)

  5. Smith JP, and Sheffield NC
    Analytical Approaches for ATAC-seq Data Analysis.
    Current Protocols in Human Genetics (2020)

  6. Feng SC, Sheffield NC, and Feng J
    Seqpare: a self-consistent metric of similarity between genomic interval sets.
    F1000Research (2020)

  7. Smith JP, Dutta AB, Sathyan KM, Guertin MJ, and Sheffield NC
    Quality control and processing of nascent RNA profiling data.
    bioRxiv (2020)

  8. Stolarczyk M, Reuter VP, Smith JP, Magee NE, and Sheffield NC
    Refgenie: a reference genome resource manager.
    GigaScience (2020)

  9. Sheffield NC
    Bulker: a multi-container environment manager.
    OSF Preprints (2019)

  10. Stolarczyk M, Reuter VP, Smith JP, Magee NE, and Sheffield NC
    Supporting data for "Refgenie: a reference genome resource manager".
    GigaScience Database (2019)

  11. Feng J, Ratan A, and Sheffield NC
    Augmented Interval List: a novel data structure for efficient genomic interval search.
    Bioinformatics (2019)

  12. Lawson J, and Sheffield NC
    COCOA: Coordinate Covariation Analysis. R package version 1.0.1.
    Bioconductor (2019)

  13. Klughammer J, Kiesel B, Roetzer T, Fortelny N, Nemc A, Nenning K-H, Furtner J, Sheffield NC et al.
    The DNA methylation landscape of glioblastoma disease progression shows extensive heterogeneity in time and space.
    Nature Medicine (2018)

  14. Simovski B, Kanduri C, Gundersen S, Titov D, Domanska D, Bock C, Bossini-Castillo L, Chikina M et al.
    Coloc-stats: a unified web interface to perform colocalization analysis of genomic features.
    Nucleic Acids Research (2018)

  15. Lawson J, Tomazou E, Bock C, and Sheffield NC
    MIRA: An R package for DNA methylation-based inference of regulatory activity.
    Bioinformatics (2018)

  16. Wang Z, Civelek M, Miller CL, Sheffield NC, Guertin MJ, and Zang C
    BART: a transcription factor prediction tool with query gene sets or epigenomic profiles.
    Bioinformatics (2018)

  17. Sheffield NC, Nagraj V, and Reuter VP
    simpleCache: R caching for reproducible, distributed, large-scale projects.
    The Journal of Open Source Software (2018)

  18. Nagraj V, Magee N, and Sheffield NC
    LOLAweb: a containerized web server for interactive genomic locus overlap enrichment analysis.
    Nucleic Acids Research (2018)

  19. Litzenburger UM, Buenrostro JD, Wu B, Shen Y, Sheffield NC, Kathiria A, Greenleaf WJ, and Chang HY
    Single-cell epigenomic variability reveals functional cancer heterogeneity.
    Genome Biol (2017)

  20. Sheffield NC, Pierron G, Klughammer J, Datlinger P, Schönegger A, Schuster M, Hadler J, Surdez D et al.
    DNA methylation heterogeneity defines a disease spectrum in Ewing sarcoma.
    Nature Medicine (2017)

  21. Sheffield NC, and Bock C
    LOLA: enrichment analysis for genomic region sets and regulatory elements in R and Bioconductor.
    Bioinformatics (2016)

  22. Bock C, Farlik M, and Sheffield NC
    Multi-Omics of Single Cells: Strategies and Applications.
    Trends Biotechnol (2016)

  23. Kovar H, Amatruda J, Brunet E, Burdach S, Cidre-Aranaz F, de Alva E, Dirksen U, van der Ent W et al.
    The second European interdisciplinary Ewing sarcoma research summit – A joint effort to deconstructing the multiple layers of a complex disease.
    Oncotarget (2016)

  24. Klughammer J, Datlinger P, Printz D, Sheffield NC, Farlik M, Hadler J, Fritsch G, and Bock C
    Differential DNA Methylation Analysis without a Reference Genome.
    Cell Reports (2015)

  25. Schmidl C, Rendeiro AF, Sheffield NC, and Bock C
    ChIPmentation: fast, robust, low-input ChIP-seq for histones and transcription factors.
    Nat. Methods (2015)

  26. Farlik M, Sheffield NC, Nuzzo A, Datlinger P, Schönegger A, Klughammer J, and Bock C
    Single-cell DNA methylome sequencing and bioinformatic inference of epigenomic cell-state dynamics.
    Cell Reports (2015)

  27. Tomazou EM, Sheffield NC, Schmidl C, Schuster M, Schönegger A, Datlinger P, Kubicek S, Bock C, and Kovar H
    Epigenome mapping reveals distinct modes of gene regulation and widespread enhancer reprogramming by the oncogenic fusion protein EWS-FLI1.
    Cell Reports (2015)

  28. Sheffield NC, Thurman RE, Song L, Safi A, Stamatoyannopoulos JA, Lenhard B, Crawford GE, and Furey TS
    Patterns of regulatory activity across diverse human cell-types predict tissue identity, transcription factor binding, and long-range interactions.
    Genome Res (2013)

  29. Sheffield NC
    The Interaction between Base Compositional Heterogeneity and Among-Site Rate Variation in Models of Molecular Evolution.
    ISRN Evolutionary Biology (2013)

  30. Tewari AK, Yardimci GG, Shibata Y, Sheffield NC, Song L, Taylor BS, Georgiev SG, Coetzee GA, Ohler U, Furey TS, Crawford GE, and Febbo PG
    Chromatin accessibility reveals insights into androgen receptor activation and transcriptional specificity.
    Genome Biol (2012)

  31. ENCODE Consortium
    An integrated encyclopedia of DNA elements in the human genome.
    Nature (2012)

  32. Natarajan A, Yardimci GG, Sheffield NC, Crawford GE, and Ohler U
    Predicting cell-type-specific gene expression from regions of open chromatin.
    Genome Res (2012)

  33. Thurman RE, Rynes E, Humbert R, Vierstra J, Matthew T, Haugen E, Sheffield NC, Stergachis AB et al.
    The accessible chromatin landscape of the human genome.
    Nature (2012)

  34. Shibata Y, Sheffield NC, Fedrigo O, Babbitt CC, Wortham M, Tewari AK, London D, Song L et al.
    Extensive Evolutionary Changes in Regulatory Element Activity during Human Origins Are Associated with Altered Gene Expression and Positive Selection.
    PLos Genet (2012)

  35. Sheffield NC, and Furey TS
    Identifying and characterizing regulatory sequences in the human genome with chromatin accessibility assays.
    Genes (2012)

  36. Song L, Zhang ZZ, Grasfeder LL, Boyle AP, Giresi PG, Lee B-K, Sheffield NC, Gräf S et al.
    Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity.
    Genome Res (2011)

  37. Myers RM, Stamatoyannopoulos J, Snyder M, Dunham I, Hardison RC, Bernstein BE, Gingeras TR, Kent WJ et al.
    A user's guide to the encyclopedia of DNA elements (ENCODE).
    PLoS Biol (2011)

  38. Sheffield NC, Hiatt KD, Valentine MC, Song H, and Whiting MF
    Mitochondrial genomics in Orthoptera using MOSAS.
    Mitochondrial DNA (2010)

  39. Song H, Sheffield NC, Cameron SL, Miller KB, and Whiting MF
    When phylogenetic assumptions are violated: base compositional heterogeneity and among-site rate variation in beetle mitochondrial phylogenomics.
    Syst. Entomol (2010)

  40. Sheffield NC, Song H, Cameron SL, and Whiting MF
    Nonstationary evolution and compositional heterogeneity in beetle mitochondrial phylogenomics.
    Syst. Biol (2009)

  41. Sheffield NC, Song H, Cameron SL, and Whiting MF
    A comparative analysis of mitochondrial genomes in Coleoptera (Arthropoda: Insecta) and genome descriptions of six new beetles.
    Mol. Biol. Evol (2008)

  42. Stacey A, Sheffield NC, and Crandall KA
    Calculating expected DNA remnants from ancient founding events in human population genetics.
    BMC Genet (2008)