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.
Dozmorov MG, Tyc KM, Sheffield NC, Boyd DC, Olex AL, Reed J, and Harrell JC. Chromatin conformation capture (Hi-C) sequencing of patient-derived xenografts: analysis guidelines GigaScience (2021)
DOI: /10.1093/gigascience/giab022
Sheffield NC, Stolarczyk M, Reuter VP, and Rendeiro A. Linking big biomedical datasets to modular analysis with Portable Encapsulated Projects bioRxiv (2021)
DOI: 10.1101/2020.10.08.331322
Gharavi E, Gu A, Zheng G, Smith JP, Zhang A, Brown DE, and Sheffield NC. Embeddings of genomic region sets capture rich biological associations in low dimensions Bioinformatics (2021)
DOI: 10.1093/bioinformatics/btab439
Stolarczyk M, Xue B, and Sheffield NC. Identity and compatibility of reference genome resources NAR Genomics and Bioinformatics (2021)
DOI: 10.1093/nargab/lqab036
Yates AD, Adams J, Chaturvedi S, Davies R, Laird M, Leinonen R, Nag R, Sheffield NC, Hofmann O, and Keane T. Refget: standardised access to reference sequences Bioinformatics (2021)
DOI: 10.1093/bioinformatics/btab524
Gu A, Cho HJ, and Sheffield NC. Bedshift: perturbation of genomic interval sets Genome Biology (2021)
DOI: 10.1186/s13059-021-02440-w
Manjegowda MC, Joy-Gaba J, Wengert E, Saga AU, Warthen D, Kuchler A, Gaykema R, Patel MK, Sheffield NC, and Scott MM. DNA Methyltransferase 1 and 3a Expression in the Frontal Cortex Regulates Palatable Food Consumption bioRxiv (2021)
DOI: 10.1101/2021.05.23.445176
Peneder P, Stütz AM, Surdez D, Krumbholz M, Semper S, Chicard M, Sheffield NC, Pierron G, Lapouble E, Tötzl M, Ergüner B, Barreca D, Rendeiro AF, Agaimy A, Boztug H, Engstler G, Dworzak M, Bernkopf M, Taschner-Mandl S, Ambros IM, Myklebost O, Marec-Bérard P, Burchill SA, Brennan B, Strauss SJ, Whelan J, Schleiermacher G, Schaefer C, Dirksen U, Hutter C, Boye K, Ambros PF, Delattre O, Metzler M, Bock C, and Tomazou EM. Multimodal analysis of cell-free DNA whole-genome sequencing for pediatric cancers with low mutational burden Nature Communications (2021)
DOI: 10.1038/s41467-021-23445-w
Smith JP, Dutta AB, Sathyan KM, Guertin MJ, and Sheffield NC. PEPPRO: quality control and processing of nascent RNA profiling data Genome Biology (2021)
DOI: 10.1186/s13059-021-02349-4
Feng J, and Sheffield NC. IGD: high-performance search for large-scale genomic interval datasets Bioinformatics (2020)
DOI: 10.1093/bioinformatics/btaa1062
Smith JP, Corces R, Xu J, Wei Y, Reuter VP, Chang HY, and Sheffield NC. PEPATAC: An optimized ATAC-seq pipeline with serial alignments bioRxiv (2020)
DOI: 10.1101/2020.10.21.347054
VijayKrishna N, Joshi J, Coraor N, Hillman-Jackson J, Bouvier D, van den Beek M, Eguinoa I, Coppens F, Golitsynskiy S, Stolarczyk M, Sheffield NC, Gladman S, Cuccuru G, Grüning B, Soranzo N, Rasche H, Langhorst BW, Bernt M, Fornika D, de Lima Morais DA, Barrette M, van Heusden P, Petrillo M, Puertas-Gallardo A, Patak A, Hotz H-R, and Blankenberg D. Expanding the Galaxy's reference data bioRxiv (2020)
DOI: 10.1101/2020.10.09.327114
Lawson JT, Smith JP, Bekiranov S, Garrett-Bakelman FE, and Sheffield NC. COCOA: coordinate covariation analysis of epigenetic heterogeneity Genome Biology (2020)
DOI: 10.1186/s13059-020-02139-4
Sienkiewicz K, Chen J, Chatrath A, Lawson JT, Sheffield NC, Zhang L, and Ratan A. Data Integration with SUMO Detects Latent Relationships Between Patients in Lower-Grade Gliomas bioRxiv (2020)
DOI: 10.1101/2020.08.10.244343
Smith JP, and Sheffield NC. Analytical Approaches for ATAC-seq Data Analysis Current Protocols in Human Genetics (2020)
DOI: 10.1002/cphg.101
Feng SC, Sheffield NC, and Feng J. Seqpare: a self-consistent metric of similarity between genomic interval sets F1000Research (2020)
DOI: 10.1101/2020.04.05.026732
Stolarczyk M, Reuter VP, Smith JP, Magee NE, and Sheffield NC. Refgenie: a reference genome resource manager GigaScience (2020)
DOI: 10.1093/gigascience/giz149
Feng J, Ratan A, and Sheffield NC. Augmented Interval List: a novel data structure for efficient genomic interval search Bioinformatics (2019)
DOI: 10.1093/bioinformatics/btz407
Corces MR, Granja JM, Shams S, Louie BH, Seoane JA, Zhou W, Silva TC, Groeneveld C, Wong CK, Cho SW, Satpathy AT, Mumbach MR, Hoadley KA, Robertson AG, Sheffield NC, Felau I, Castro MAA, Berman BP, Staudt LM, Zenklusen JC, Laird PW, Curtis C, Greenleaf WJ, and Chang HY. The chromatin accessibility landscape of primary human cancers Science (2018)
DOI: 10.1126/science.aav1898
Klughammer J, Kiesel B, Roetzer T, Fortelny N, Nemc A, Nenning K-H, Furtner J, Sheffield NC, Datlinger P, Peter N, Nowosielski M, Augustin M, Mischkulnig M, Ströbel T, Alpar D, Ergüner B, Senekowitsch M, Moser P, Freyschlag CF, Kerschbaumer J, Thome C, Grams AE, Stockhammer G, Kitzwoegerer M, Oberndorfer S, Marhold F, Weis S, Trenkler J, Buchroithner J, Pichler J, Haybaeck J, Krassnig S, Ali KM, von Campe G, Payer F, Sherif C, Preiser J, Hauser T, Winkler PA, Kleindienst W, Würtz F, Brandner-Kokalj T, Stultschnig M, Schweiger S, Dieckmann K, Preusser M, Langs G, Baumann B, Knosp E, Widhalm G, Marosi C, Hainfellner JA, Woehrer A, and Bock C. The DNA methylation landscape of glioblastoma disease progression shows extensive heterogeneity in time and space Nature Medicine (2018)
DOI: 10.1038/s41591-018-0156-x
Simovski B, Kanduri C, Gundersen S, Titov D, Domanska D, Bock C, Bossini-Castillo L, Chikina M, Favorov A, Layer RM, Mironov AA, Quinlan AR, Sheffield NC, Trynka G, and Sandve GK. Coloc-stats: a unified web interface to perform colocalization analysis of genomic features Nucleic Acids Research (2018)
DOI: 10.1093/nar/gky474
Lawson J, Tomazou E, Bock C, and Sheffield NC. MIRA: An R package for DNA methylation-based inference of regulatory activity Bioinformatics (2018)
DOI: 10.1093/bioinformatics/bty083
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)
DOI: 10.1093/bioinformatics/bty194
Sheffield NC, Nagraj V, and Reuter VP. simpleCache: R caching for reproducible, distributed, large-scale projects The Journal of Open Source Software (2018)
DOI: 10.21105/joss.00463
Nagraj V, Magee N, and Sheffield NC. LOLAweb: a containerized web server for interactive genomic locus overlap enrichment analysis Nucleic Acids Research (2018)
DOI: 10.1093/nar/gky464
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)
DOI: 10.1186/s13059-016-1133-7
Sheffield NC, Pierron G, Klughammer J, Datlinger P, Schönegger A, Schuster M, Hadler J, Surdez D, Guillemot D, Lapouble E, Freneaux P, Champigneulle J, Bouvier R, Walder D, Ambros IM, Hutter C, Sorz E, Amaral AT, de Alava E, Schallmoser K, Strunk D, Rinner B, Liegl-Atzwanger B, Huppertz B, Leithner A, de Pinieux G, Terrier P, Laurence V, Michon J, Ladenstein R, Holter W, Windhager R, Dirksen U, Ambros PF, Delattre O, Kovar H, Bock C, and Tomazou EM. DNA methylation heterogeneity defines a disease spectrum in Ewing sarcoma Nature Medicine (2017)
DOI: 10.1038/nm.4273
Sheffield NC, and Bock C. LOLA: enrichment analysis for genomic region sets and regulatory elements in R and Bioconductor Bioinformatics (2016)
DOI: 10.1093/bioinformatics/btv612
Bock C, Farlik M, and Sheffield NC. Multi-Omics of Single Cells: Strategies and Applications Trends Biotechnol (2016)
DOI: 10.1016/j.tibtech.2016.04.004
Kovar H, Amatruda J, Brunet E, Burdach S, Cidre-Aranaz F, de Alva E, Dirksen U, van der Ent W, Grohar P, Grunewald TG, Helman L, Houghton P, Iljin K, Korsching E, Ladanyi M, Lawlor E, Lessnick S, Ludwig J, Meltzer P, Metzler M, Mora J, Moriggl R, Nakamura T, Papamarkou T, Sarikas BR, Redini F, Richter GH, Rossig C, Schadler K, Schafer BW, Scotlandi K, Sheffield NC, Shelat A, Snaar-Jagalska E, Sorensen P, Stegmaier K, Stewart E, Sweet-Cordero A, Szuhai K, Tirado OM, Tirode F, Toretsky J, Tsafou K, Uren A, Zinovyev A, and Delattre O. The second European interdisciplinary Ewing sarcoma research summit – A joint effort to deconstructing the multiple layers of a complex disease Oncotarget (2016)
DOI: 10.18632/oncotarget.6937
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)
DOI: 10.1016/j.celrep.2015.11.024
Schmidl C, Rendeiro AF, Sheffield NC, and Bock C. ChIPmentation: fast, robust, low-input ChIP-seq for histones and transcription factors Nat. Methods (2015)
DOI: 10.1038/nmeth.3542
Farlik M, Sheffield NC, Nuzzo A, Datlinger P, Schonegger A, Klughammer J, and Bock C. Single-cell DNA methylome sequencing and bioinformatic inference of epigenomic cell-state dynamics Cell Reports (2015)
DOI: 10.1016/j.celrep.2015.02.001
Tomazou EM, Sheffield NC, Schmidl C, Schuster M, Schonegger 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)
DOI: 10.1016/j.celrep.2015.01.042
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)
DOI: 10.1101/gr.152140.112
Sheffield NC. The Interaction between Base Compositional Heterogeneity and Among-Site Rate Variation in Models of Molecular Evolution ISRN Evolutionary Biology (2013)
DOI: 10.5402/2013/391561
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)
DOI: 10.1186/gb-2012-13-10-r88
ENCODE Consortium. An integrated encyclopedia of DNA elements in the human genome Nature (2012)
DOI: 10.1038/nature11247
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)
DOI: 10.1101/gr.135129.111
Thurman RE, Rynes E, Humbert R, Vierstra J, Matthew T, Haugen E, Sheffield NC, Stergachis AB, Wang H, Vernot B, Garg K, Sandstrom R, Bates D, Canfield TK, Diegel M, Dunn D, Ebersol AK, Frum T, Giste E, Johnson AK, Johnson EM, Kutyavin T, Lajoie B, Lee K, Lee K, London D, Lotakis D, Neph S, Neri F, Nguyen D, Reynolds AP, Roach V, Safi A, Sanchez ME, Sanyal A, Shafer A, Simon JM, Song L, Vong S, Weaver M, Zhang Z, Zhang Z, Lenhard B, Tewari M, Dorschner MO, Hansen RS, Navas PA, Iyer VR, Lieb JD, and Sunyaev SR. The accessible chromatin landscape of the human genome Nature (2012)
DOI: 10.1038/nature11232
Shibata Y, Sheffield NC, Fedrigo O, Babbitt CC, Wortham M, Tewari AK, London D, Song L, Lee B-K, Iyer VR, Parker SCJ, Margulies EH, Wray GA, Furey TS, and Crawford GE. Extensive Evolutionary Changes in Regulatory Element Activity during Human Origins Are Associated with Altered Gene Expression and Positive Selection PLos Genet (2012)
DOI: 10.1371/journal.pgen.1002789
Sheffield NC, and Furey TS. Identifying and characterizing regulatory sequences in the human genome with chromatin accessibility assays Genes (2012)
DOI: 10.3390/genes3040651
Song L, Zhang ZZ, Grasfeder LL, Boyle AP, Giresi PG, Lee B-K, 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, Clarke ND, Birney E, Iyer VR, Crawford GE, Lieb JD, and Furey TS. Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity Genome Res (2011)
DOI: 10.1101/gr.121541.111
Myers RM, Stamatoyannopoulos J, Snyder M, Dunham I, Hardison RC, Bernstein BE, Gingeras TR, Kent WJ, Birney E, Wold B, Crawford GE, Encode T, and Consortium P. A user's guide to the encyclopedia of DNA elements (ENCODE) PLoS Biol (2011)
DOI: 10.1371/journal.pbio.1001046
Sheffield NC, Hiatt KD, Valentine MC, Song H, and Whiting MF. Mitochondrial genomics in Orthoptera using MOSAS Mitochondrial DNA (2010)
DOI: 10.3109/19401736.2010.500812
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)
DOI: 10.1111/j.1365-3113.2009.00517.x
Sheffield NC, Song H, Cameron SL, and Whiting MF. Nonstationary evolution and compositional heterogeneity in beetle mitochondrial phylogenomics Syst. Biol (2009)
DOI: 10.1093/sysbio/syp037
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)
DOI: 10.1093/molbev/msn198
Stacey A, Sheffield NC, and Crandall KA. Calculating expected DNA remnants from ancient founding events in human population genetics BMC Genet (2008)
DOI: 10.1186/1471-2156-9-66