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/ My Citations | ORCID.
  1. 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)

  2. 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 Biology (2017)

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

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

  5. 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)

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

  7. 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 Rep (2015)

  8. 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 Rep (2015)

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

  10. 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 Research (2013)

  11. 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 Biology (2012)

  12. Bernstein BE, Birney E, Dunham I, Green ED, Gunter C, Snyder M, Kundaje A, Aldred SF et al.
    An integrated encyclopedia of DNA elements in the human genome.
    Nature (2012)

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

  14. 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)

  15. 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 Genetics (2012)

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

  17. 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 Research (2011)

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

  19. 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.
    Systematic Entomology (2010)

  20. Sheffield NC, Song H, Cameron SL, and Whiting MF
    Nonstationary evolution and compositional heterogeneity in beetle mitochondrial phylogenomics.
    Systematic biology (2009)

  21. 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.
    Molecular biology and evolution (2008)

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

Historic list

Historic list of publications (no longer maintained) * = equal contributors

    2015

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

    Featured in a press release at Center for Molecular Medicine. Article in GenomeWeb, and Epigenie.
  2. Farlik M*, Sheffield NC*, Nuzzo A, Datlinger P, Schönegger A, Klughammer J, Bock C.
    Single-cell DNA methylome sequencing and bioinformatic inference of epigenomic cell-state dynamics.
    Cell Reports (2015) 10: 8: 1386-1397

    Cover article, and featured at news.cell.com blog, and in the cell.com header slider. Highlighted in Nature Methods Methods-in-Brief.
  3. Tomazou EM*, Sheffield NC*, Schmidl C, Schuster M, Schönegger A, Datlinger P, Kubicek S, Bock C, Kovar H.
    Epigenome mapping reveals distinct modes of gene regulation and widespread enhancer reprogramming by the oncogenic fusion protein EWS-FLI1.
    Cell Reports (2015) 10: 7: 1082-1095
    Featured in a press release at St. Anna's Children's Cancer Research Institute. Article in main Austrian newspaper Der Standard
  4. 2013

  5. 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 Research (2013) 23: 777-788
  6. Sheffield, NC
    The interaction between base compositional heterogeneity and among-site rate variation in models of molecular evolution.
    IRSN Evolutionary Biology (2013)
  7. 2012

  8. Sheffield, NC and Furey, TS
    Identifying and characterizing regulatory sequences in the human genome with chromatin accessibility assays.
    Genes (2012) 3: 651-670
  9. Tewari, AK, Yardimci, GG, Shibata, Y, Sheffield, NC, Song, L, Taylor, BS, Georgiev, SG, Ohler, U, Coetzee, GA, Furey, TS, Crawford, GE, and Febbo, PG.
    Chromatin accessibility reveals insight into androgen receptor activation and transcriptional specificity.
    Genome Biology (2012) 13:R88
  10. Thurman, RE, Rynes, E, Humbert, R, Vierstra, J, Maurano, MT, Haugen, E, Sheffield, NC, et al.
    The accessible chromatin landscape of the human genome.
    Nature (2012) 489: 75-82
  11. Natarajan, A, Yardimci, G, Sheffield, NC, Crawford, G, Ohler, U.
    Predicting cell-type specific gene expression using DNaseI hypersensitivity data.
    Genome Research (2012) 22: 1711-1722
  12. Shibata,YS*, Sheffield, NC*, Fedrigo, O, Babbitt CC, Wortham M, Tewari, AK, London, D, Song, L, Lee, B, Iyer, VR, Parker, SCJ, Margulies, E, Wray, G, Furey, TS, Crawford, GE.
    Extensive evolutionary changes in regulatory element activity during human origins are associated with altered gene expression and positive selection.
    PLoS Genetics (2012) 8: e1002789
    - Highlighted in Nature Genetics
  13. ENCODE Consortium.
    An integrated encyclopedia of DNA elements in the human genome.
    Nature (2012) 489: 57-74
  14. 2011

  15. ENCODE Consortium.
    A User's Guide to the Encyclopedia of DNA Elements (ENCODE).
    PLoS Biology (2011) 9: e1001046.
  16. Song L*, Zhang Z*, Grasfeder LL*, Boyle AP*, Giresi PG*, Lee BK*, Sheffield, NC*, Graf S, Huss M, Keefe D, Liu Z, London D, McDaniell RM, Shibata Y, Showers KA, Simon JM, Vales T, Wang T, Winter D, Zhang Z, Clarke ND, Birney E, Iyer VR, Crawford GE, Lieb JD, Furey TS.
    Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity.
    Genome Research (2011) 21: 1757-1767
  17. 2010

  18. Sheffield, NC*, Hiatt, KD*, Valentine, MC, Song, H, and Whiting, MF.
    Mitochondrial genomics in Orthoptera using MOSAS.
    Mitochondrial DNA (2010) 21:87-104.
    - Top 5 Most-Read Article, Oct 2010
  19. Song, H, Sheffield, NC, Cameron, SL, Miller, KB, & Whiting, MF.
    When phylogenetic assumptions are violated: base compositional heterogeneity and among-site rate variation in beetle mitochondrial phylogenomics.
    Systematic Entomology (2010) 35: 429-448.
  20. 2009

  21. Sheffield, NC*, Song, H*, Cameron, SL, & Whiting, MF.
    Nonstationary Evolution and Compositional Heterogeneity in Beetle Mitochondrial Phylogenomics.
    Systematic Biology (2009) 58:381-394.
  22. 2008

  23. Sheffield, NC, Song, H, Cameron, SL, & Whiting, MF.
    A comparative analysis of mitochondrial genomes in Coleoptera (Arthropoda: Insecta) and genome descriptions of six new beetles.
    Molecular Biology and Evolution (2008) 25: 2499-509.
  24. Stacey, A*, Sheffield, NC*, & Crandall, KA.
    Calculating expected DNA remnants from ancient founding events in human population genetics.
    BMC Genetics (2008) 9: 66.
    -