Publications

Find our publications on PubMed, Google Scholar, or ORCID.

  1. Campbell, Donald R. and Cezard, Timothee and Gundersen, Sveinung and Yates, Andrew D. and Davies, Robert M. and Marshall, John and Park, Sang-Hoon and Wagner, Alex H. and Love, Michael I. and Thomas, Reggan and Hofmann, Oliver and Sheffield, Nathan C..
    Taming the reference genome jungle: the refget sequence collection standard
    bioRxiv (2025) DOI: 10.1101/2025.10.06.680641
  2. LeRoy.
    Fast, memory-efficient genomic interval tokenizers for modern machine learning
    ArXiv.org (2025) DOI: 10.48550/arxiv.2511.01555
  3. Bingjie Xue and Silvia Medrano and Jason P Smith and Alexandre Martini and Omar Guessom and Maria Louisa Sequeira and Ariel Gomez and Nathan C Sheffield.
    Decoding cell identity with region accessibility embedding distances
    (2025)
  4. Nathan J LeRoy and Guangtao Zheng and Oleksandr Khoroshevskyi and Donald Campbell and Aidong Zhang and Nathan C Sheffield.
    Atacformer: A transformer-based foundation model for analysis and interpretation of ATAC-seq data
    (2025)
  5. Nathan C Sheffield.
    Model Context Protocol: the unexpected catalyst of a bioinformatics interoperability revolution
    (2025)
  6. John T Stubbs and Adam W Turner and Jason P Smith and Gaelle Auguste and Yipei Song and Mohammad D Khan and Emily Farber and Suna Onengut-Gumuscu and Clint L Miller and Nathan C Sheffield.
    Differential chromatin accessibility analysis elucidates mechanisms of coronary artery disease-associated genetic variation
    (2025)
  7. Clark, Timothy and Caufield, Harry and Parker, Jillian A. and Al Manir, Sadnan and Amorim, Edilberto and Eddy, James and Gim, Nayoon and Gow, Brian and Goar, Wesley and Haendel, Melissa and Hansen, Jan N. and Harris, Nomi and Hermjakob, Henning and Joachimiak, Marcin and Jordan, Gianna and Lee, In-Hee and K. McWeeney, Shannon and Nebeker, Camille and Nikolov, Milen and Shaffer, Jamie and Sheffield, Nathan C and Sheynkman, Gloria and Stevenson, James and Chen, Jake Y. and Mungall, Chris and Wagner, Alex and Kong, Sek Won and Ghosh, Satrajit S. and Patel, Bhavesh and Williams, Andrew and Munoz-Torres, Monica C..
    AI-readiness for Biomedical Data: Bridge2AI Recommendations
    (2024) DOI: 10.1101/2024.10.23.619844
  8. Gharavi, Erfaneh and LeRoy, Nathan J. and Zheng, Guangtao and Zhang, Aaron and Brown, Donald E. and Sheffield, Nathan C..
    Joint Representation Learning for Retrieval and Annotation of Genomic Interval Sets
    Bioengineering (2024) DOI: 10.3390/bioengineering11030263
  9. Nathan J LeRoy and Jason P Smith and Guangtao Zheng and Julia Rymuza and Erfaneh Gharavi and Donald E Brown and Aidong Zhang and Nathan C Sheffield.
    Fast clustering and cell-type annotation of scATAC data using pre-trained embeddings
    NAR Genomics and Bioinformatics (2024) DOI: 10.1093/nargab/lqae073
  10. Julia Rymuza and Yuchen Sun and Guangtao Zheng and Nathan J LeRoy and Maria Murach and Neil Phan and Aidong Zhang and Nathan C Sheffield.
    Methods for constructing and evaluating consensus genomic interval sets
    Nucleic Acids Research (2024) DOI: 10.1093/nar/gkae685
  11. Guangtao Zheng and Julia Rymuza and Erfaneh Gharavi and Nathan J LeRoy and Aidong Zhang and Nathan C Sheffield.
    Methods for evaluating unsupervised vector representations of genomic regions
    NAR Genomics and Bioinformatics (2024) DOI: 10.1093/nargab/lqae086
  12. Nathan J LeRoy and Oleksandr Khoroshevskyi and Aaron O’Brien and Rafał Stępień and Alip Arslan and Nathan C Sheffield.
    PEPhub: a database, web interface, and API for editing, sharing, and validating biological sample metadata
    GigaScience (2024) DOI: 10.1093/gigascience/giae033
  13. Smith, Jason P. and Paxton, Robert and Medrano, Silvia and Sheffield, Nathan C. and Sequeira-Lopez, Maria Luisa S. and Gomez, R. Ariel.
    Inhibition of Renin Expression Is Regulated by an Epigenetic Switch From an Active to a Poised State
    81: 1869–1882 (2024) DOI: 10.1161/hypertensionaha.124.22886
  14. Xiong, Guangzhi and LeRoy, Nathan J and Bekiranov, Stefan and Sheffield, Nathan C and Zhang, Aidong.
    DeepGSEA: explainable deep gene set enrichment analysis for single-cell transcriptomic data
    40 (2024) DOI: 10.1093/bioinformatics/btae434
  15. Bingjie Xue and Oleksandr Khoroshevskyi and R. Ariel Gomez and Nathan C. Sheffield.
    Opportunities and challenges in sharing and reusing genomic interval data
    Frontiers in Genetics 14: 1155809 (2023) DOI: 10.3389/fgene.2023.1155809
  16. Sheffield, Nathan C. and LeRoy, Nathan J. and Khoroshevskyi, Oleksandr.
    Challenges to sharing sample metadata in computational genomics
    Frontiers in Genetics (2023) DOI: 10.3389/fgene.2023.1154198
  17. Oleksandr Khoroshevskyi and Nathan J. LeRoy and Vincent P. Reuter and Nathan C. Sheffield.
    GEOfetch: A command-line tool for downloading data and standardized metadata from GEO and SRA
    Bioinformatics (2023) DOI: 10.1093/bioinformatics/btad069
  18. Karolina Sienkiewicz and Jinyu Chen and Ajay Chatrath and John T. Lawson and Nathan C. Sheffield and Louxin Zhang and Aakrosh Ratan.
    Detecting molecular subtypes from multi-omics datasets using {SUMO}
    Cell Reports Methods 2: 100152 (2022) DOI: 10.1016/j.crmeth.2021.100152
  19. Kristyna Kupkova and Jose Verdezoto Mosquera and Jason P. Smith and Micha{\l} Stolarczyk and Tessa L. Danehy and John T. Lawson and Bingjie Xue and John T. Stubbs and Nathan LeRoy and Nathan C. Sheffield.
    {GenomicDistributions}: fast analysis of genomic intervals with Bioconductor
    {BMC} Genomics 23 (2022) DOI: 10.1186/s12864-022-08467-y
  20. Nathan C. Sheffield and Vivien R. Bonazzi and Philip E. Bourne and Tony Burdett and Timothy Clark and Robert L. Grossman and Ola Spjuth and Andrew D. Yates.
    From biomedical cloud platforms to microservices: next steps in {FAIR} data and analysis
    Scientific Data 9: 553 (2022) DOI: 10.1038/s41597-022-01619-5
  21. Mikhail G. Dozmorov and Katarzyna M. Tyc and Nathan C. Sheffield and David C. Boyd and Amy L. Olex and Jason Reed and J. Chuck Harrell.
    Chromatin conformation capture (Hi-C) sequencing of patient-derived xenografts: analysis guidelines
    GigaScience (2021) DOI: 10.1093/gigascience/giab022
  22. Feng J, et al. IGD: high-performance search for large-scale genomic interval datasets. Bioinformatics. 2021 Jan;37(1):118-120..
    IGD: high-performance search for large-scale genomic interval datasets
    Bioinformatics (2021) DOI: 10.1093/bioinformatics/btaa1062
  23. Nathan C Sheffield and Michał Stolarczyk and Vincent P Reuter and André F Rendeiro.
    Linking big biomedical datasets to modular analysis with Portable Encapsulated Projects
    GigaScience (2021) DOI: 10.1093/gigascience/giab077
  24. Nathan C. Sheffield and Michał Stolarczyk and Vincent P. Reuter and Andre F. Rendeiro.
    Supporting data for "Linking big biomedical datasets to modular analysis with Portable Encapsulated Projects"
    GigaScience Database (2021) DOI: 10.5524/100936
  25. Mohan C. Manjegowda and Jonathan Joy-Gaba and Eric Wengert and Anusha U. Saga and Daniel Warthen and Amelie Kuchler and Ronald Gaykema and Manoj K. Patel and Nathan C. Sheffield and Michael M. Scott.
    DNA Methyltransferase 1 and 3a Expression in the Frontal Cortex Regulates Palatable Food Consumption
    bioRxiv (2021) DOI: 10.1101/2021.05.23.445176
  26. Erfaneh Gharavi and Aaron Gu and Guangtao Zheng and Jason P Smith and Hyun Jae Cho and Aidong Zhang and Donald E Brown and Nathan C Sheffield.
    Embeddings of genomic region sets capture rich biological associations in lower dimensions
    Bioinformatics (2021) DOI: 10.1093/bioinformatics/btab439
  27. Jason P. Smith and Arun B. Dutta and Kizhakke Mattada Sathyan and Michael J. Guertin and Nathan C. Sheffield.
    PEPPRO: quality control and processing of nascent RNA profiling data
    Genome Biology 22 (2021) DOI: 10.1186/s13059-021-02349-4
  28. Aaron Gu and Hyun Jae Cho and Nathan C. Sheffield.
    Bedshift: perturbation of genomic interval sets
    Genome Biology 22 (2021) DOI: 10.1186/s13059-021-02440-w
  29. Jason P Smith and M Ryan Corces and Jin Xu and Vincent P Reuter and Howard Y Chang and Nathan C Sheffield.
    {PEPATAC}: an optimized pipeline for {ATAC}-seq data analysis with serial alignments
    {NAR} Genomics and Bioinformatics 3 (2021) DOI: 10.1093/nargab/lqab101
  30. Stolarczyk, Michal and Xue, Bingjie and Sheffield, Nathan C..
    Identity and compatibility of reference genome resources
    NAR Genomics and Bioinformatics 3: lqab036 (2021) DOI: 10.1093/nargab/lqab036
  31. Peter Peneder and Adrian M. Stütz and Didier Surdez and Manuela Krumbholz and Sabine Semper and Mathieu Chicard and Nathan C. Sheffield and Gaelle Pierron and Eve Lapouble and Marcus Tötzl and Bekir Ergüner and Daniele Barreca and André F. Rendeiro and Abbas Agaimy and Heidrun Boztug and Gernot Engstler and Michael Dworzak and Marie Bernkopf and Sabine Taschner-Mandl and Inge M. Ambros and Ola Myklebost and Perrine Marec-Bérard and Susan Ann Burchill and Bernadette Brennan and Sandra J. Strauss and Jeremy Whelan and Gudrun Schleiermacher and Christiane Schaefer and Uta Dirksen and Caroline Hutter and Kjetil Boye and Peter F. Ambros and Olivier Delattre and Markus Metzler and Christoph Bock and Eleni M. Tomazou.
    Multimodal analysis of cell-free DNA whole-genome sequencing for pediatric cancers with low mutational burden
    Nature Communications 12 (2021) DOI: 10.1038/s41467-021-23445-w
  32. Yates, Andrew and Adams, Jeremy and Chaturvedi, Somesh and Davies, Robert M. and Laird, Matthew R. and Leinonen, Rasko and Nag, Rishi and Sheffield, Nathan C. and Hofmann, Oliver and Keane, Thomas.
    Refget: standardized access to reference sequences
    Bioinformatics 38: 299-300 (2021) DOI: 10.1093/bioinformatics/btab524
  33. Selena C Feng and Nathan C. Sheffield and Jianglin Feng.
    Seqpare: a novel metric of similarity between genomic interval sets
    F1000Research 9: 581 (2020) DOI: 10.1101/2020.04.05.026732
  34. Jason P. Smith and Nathan C. Sheffield.
    Analytical Approaches for {ATAC}-seq Data Analysis
    Current Protocols in Human Genetics 106 (2020) DOI: 10.1002/cphg.101
  35. John T. Lawson and Jason P. Smith and Stefan Bekiranov and Francine E. Garrett-Bakelman and Nathan C. Sheffield.
    {COCOA}: coordinate covariation analysis of epigenetic heterogeneity
    Genome Biology 21 (2020) DOI: 10.1186/s13059-020-02139-4
  36. Stolarczyk, Michal and Reuter, Vincent P. and Smith, Jason P. and Magee, Neal E. and Sheffield, Nathan C..
    Refgenie: a reference genome resource manager
    GigaScience 9: giz149 (2020) DOI: 10.1093/gigascience/giz149
  37. Feng J, et al. Augmented Interval List: a novel data structure for efficient genomic interval search. Bioinformatics. 2019 Dec;35(23):4907-4911..
    Augmented Interval List: a novel data structure for efficient genomic interval search
    Bioinformatics (2019) DOI: 10.1093/bioinformatics/btz407
  38. Nathan C. Sheffield.
    Bulker: a multi-container environment manager
    OSF Preprints (2019) DOI: 10.31219/osf.io/natsj
  39. Johanna Klughammer and Barbara Kiesel and Thomas Roetzer and Nikolaus Fortelny and Amelie Nemc and Karl-Heinz Nenning and Julia Furtner and Nathan C. Sheffield and Paul Datlinger and Nadine Peter and Martha Nowosielski and Marco Augustin and Mario Mischkulnig and Thomas Ströbel and Donat Alpar and Bekir Ergüner and Martin Senekowitsch and Patrizia Moser and Christian F. Freyschlag and Johannes Kerschbaumer and Claudius Thomé and Astrid E. Grams and Günther Stockhammer and Melitta Kitzwoegerer and Stefan Oberndorfer and Franz Marhold and Serge Weis and Johannes Trenkler and Johanna Buchroithner and Josef Pichler and Johannes Haybaeck and Stefanie Krassnig and Kariem Mahdy Ali and Gord von Campe and Franz Payer and Camillo Sherif and Julius Preiser and Thomas Hauser and Peter A. Winkler and Waltraud Kleindienst and Franz Würtz and Tanisa Brandner-Kokalj and Martin Stultschnig and Stefan Schweiger and Karin Dieckmann and Matthias Preusser and Georg Langs and Bernhard Baumann and Engelbert Knosp and Georg Widhalm and Christine Marosi and Johannes A. Hainfellner and Adelheid Woehrer and Christoph Bock.
    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
  40. Nathan C. Sheffield and VP Nagraj and Vince P. Reuter.
    {simpleCache}: {R} caching for reproducible, distributed, large-scale projects
    The Journal of Open Source Software 3: 463 (2018) DOI: 10.21105/joss.00463 (corresponding author)
  41. Boris Simovski and Chakravarthi Kanduri and Sveinung Gundersen and Dmytro Titov and Diana Domanska and Christoph Bock and Lara Bossini-Castillo and Maria Chikina and Alexander Favorov and Ryan M Layer and Andrey A Mironov and Aaron R Quinlan and Nathan C Sheffield and Gosia Trynka and Geir K Sandve.
    Coloc-stats: a unified web interface to perform colocalization analysis of genomic features
    Nucleic Acids Research 46: W186–W193 (2018) DOI: 10.1093/nar/gky474
  42. John Lawson and Eleni Tomazou and Christoph Bock and Nathan C. Sheffield.
    MIRA: An {R} package for {DNA} methylation-based inference of regulatory activity
    Bioinformatics bty083 (2018) DOI: 10.1093/bioinformatics/bty083
  43. VP Nagraj and Neal Magee and Nathan C. Sheffield.
    LOLAweb: a containerized web server for interactive genomic locus overlap enrichment analysis
    Nucleic Acids Research (2018) DOI: 10.1093/nar/gky464
  44. Zhenjia Wang and Mete Civelek and Clint L Miller and Nathan C Sheffield and Michael J Guertin and Chongzhi Zang.
    {BART}: a transcription factor prediction tool with query gene sets or epigenomic profiles
    Bioinformatics (2018) DOI: 10.1093/bioinformatics/bty194
  45. M. Ryan Corces and Jeffrey M. Granja and Shadi Shams and Bryan H. Louie and Jose A. Seoane and Wanding Zhou and Tiago C. Silva and Clarice Groeneveld and Christopher K. Wong and Seung Woo Cho and Ansuman T. Satpathy and Maxwell R. Mumbach and Katherine A. Hoadley and A. Gordon Robertson and Nathan C. Sheffield and Ina Felau and Mauro A. A. Castro and Benjamin P. Berman and Louis M. Staudt and Jean C. Zenklusen and Peter W. Laird and Christina Curtis and William J. Greenleaf and Howard Y. Chang and Rehan Akbani and Christopher C. Benz and Evan A. Boyle and Bradley M. Broom and Andrew D. Cherniack and Brian Craft and John A. Demchok and Ashley S. Doane and Olivier Elemento and Martin L. Ferguson and Mary J. Goldman and D. Neil Hayes and Jing He and Toshinori Hinoue and Marcin Imielinski and Steven J. M. Jones and Anab Kemal and Theo A. Knijnenburg and Anil Korkut and De-Chen Lin and Yuexin Liu and Michael K. A. Mensah and Gordon B. Mills and Vincent P. Reuter and Andre Schultz and Hui Shen and Jason P. Smith and Roy Tarnuzzer and Sheyla Trefflich and Zhining Wang and John N. Weinstein and Lindsay C. Westlake and Jin Xu and Liming Yang and Christina Yau and Yang Zhao and Jingchun Zhu.
    The chromatin accessibility landscape of primary human cancers
    Science (2018) DOI: 10.1126/science.aav1898
  46. Ulrike M. Litzenburger and Jason D. Buenrostro and Beijing Wu and Ying Shen and Nathan C. Sheffield and Arwa Kathiria and William J. Greenleaf and Howard Y. Chang.
    Single-cell epigenomic variability reveals functional cancer heterogeneity
    Genome Biol. 18: 15 (2017) DOI: 10.1186/s13059-016-1133-7
  47. Nathan C Sheffield and Gaelle Pierron and Johanna Klughammer and Paul Datlinger and Andreas Schönegger and Michael Schuster and Johanna Hadler and Didier Surdez and Delphine Guillemot and Eve Lapouble and Paul Freneaux and Jacqueline Champigneulle and Raymonde Bouvier and Diana Walder and Ingeborg M Ambros and Caroline Hutter and Eva Sorz and Ana T Amaral and Enrique de {\'{A}}lava and Katharina Schallmoser and Dirk Strunk and Beate Rinner and Bernadette Liegl-Atzwanger and Berthold Huppertz and Andreas Leithner and Gonzague de Pinieux and Philippe Terrier and Val{\'{e}}rie Laurence and Jean Michon and Ruth Ladenstein and Wolfgang Holter and Reinhard Windhager and Uta Dirksen and Peter F Ambros and Olivier Delattre and Heinrich Kovar and Christoph Bock and Eleni M Tomazou.
    {DNA} methylation heterogeneity defines a disease spectrum in {Ewing} sarcoma
    Nature Medicine 23: 386–395 (2017) DOI: 10.1038/nm.4273
  48. Heinrich Kovar and James Amatruda and Erika Brunet and Stefan Burdach and Florencia Cidre-Aranaz and Enrique de Alva and Uta Dirksen and Wietske van der Ent and Patrick Grohar and Thomas G.P. Grunewald and Lee Helman and Peter Houghton and Kristiina Iljin and Eberhard Korsching and Marc Ladanyi and Elizabeth Lawlor and Stephen Lessnick and Joseph Ludwig and Paul Meltzer and Markus Metzler and Jaume Mora and Richard Moriggl and Takuro Nakamura and Theodore Papamarkou and Branka Radic Sarikas and Francoise Redini and Guenther H.S. Richter and Claudia Rossig and Keri Schadler and Beat W. Schafer and Katia Scotlandi and Nathan C. Sheffield and Anang Shelat and Ewa Snaar-Jagalska and Poul Sorensen and Kimberly Stegmaier and Elizabeth Stewart and Alejandro Sweet-Cordero and Karoly Szuhai and Oscar M. Tirado and Franck Tirode and Jeffrey Toretsky and Kalliopi Tsafou and Aykut Uren and Andrei Zinovyev and Olivier Delattre.
    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
  49. Christoph Bock and Matthias Farlik and Nathan C. Sheffield.
    Multi-Omics of Single Cells: Strategies and Applications.
    Trends Biotechnol. 34: 605–608 (2016) DOI: 10.1016/j.tibtech.2016.04.004
  50. Sheffield, Nathan C. and Bock, Christoph.
    LOLA: enrichment analysis for genomic region sets and regulatory elements in R and Bioconductor
    Bioinformatics 32: 587-589 (2016) DOI: 10.1093/bioinformatics/btv612 (co-corresponding author)
  51. Christian Schmidl and Andr{\'{e}} F Rendeiro and Nathan C Sheffield and Christoph Bock.
    {ChIPmentation}: fast, robust, low-input {ChIP}-seq for histones and transcription factors
    Nat. Methods 12: 963–965 (2015) DOI: 10.1038/nmeth.3542
  52. Farlik, Matthias and Sheffield, Nathan C. and Nuzzo, Angelo and Datlinger, Paul and Sch{\"{o}}negger, Andreas and Klughammer, Johanna and Bock, Christoph.
    Single-cell {DNA} methylome sequencing and bioinformatic inference of epigenomic cell-state dynamics.
    Cell Reports 10: 1386–1397 (2015) DOI: 10.1016/j.celrep.2015.02.001 (co-first author)
  53. Klughammer, Johanna and Datlinger, Paul and Printz, Dieter and Sheffield, Nathan C and Farlik, Matthias and Hadler, Johanna and Fritsch, Gerhard and Bock, Christoph.
    Differential {DNA} Methylation Analysis without a Reference Genome.
    Cell Reports 13: 2621–2633 (2015) DOI: 10.1016/j.celrep.2015.11.024
  54. Tomazou, Eleni M. and Sheffield, Nathan C. and Schmidl, Christian and Schuster, Michael and Sch{\"{o}}negger, Andreas and Datlinger, Paul and Kubicek, Stefan and Bock, Christoph and Kovar, Heinrich.
    Epigenome mapping reveals distinct modes of gene regulation and widespread enhancer reprogramming by the oncogenic fusion protein {EWS-FLI1}.
    Cell Reports 10: 1082–1095 (2015) DOI: 10.1016/j.celrep.2015.01.042 (co-first author)
  55. Sheffield, Nathan C. and Thurman, Robert E. and Song, Lingyun and Safi, Alexias and Stamatoyannopoulos, John A. and Lenhard, Boris and Crawford, Gregory E. and Furey, Terrence S..
    Patterns of regulatory activity across diverse human cell-types predict tissue identity, transcription factor binding, and long-range interactions
    Genome Res. 23: 777–88 (2013) DOI: 10.1101/gr.152140.112
  56. Sheffield, Nathan C..
    The Interaction between Base Compositional Heterogeneity and Among-Site Rate Variation in Models of Molecular Evolution
    ISRN Evolutionary Biology 2013: 1–8 (2013) DOI: 10.5402/2013/391561
  57. ENCODE Project Consortium, Nature (2012).
    An integrated encyclopedia of DNA elements in the human genome
    Nature (2012) DOI: 10.1038/nature11247
  58. Natarajan, Anirudh and Yardimci, Galip G\"{u}rkan and Sheffield, Nathan C and Crawford, Gregory E and Ohler, Uwe.
    Predicting cell-type-specific gene expression from regions of open chromatin.
    Genome Res. 22: 1711–22 (2012) DOI: 10.1101/gr.135129.111
  59. Sheffield, Nathan C and Furey, Terrence S.
    Identifying and characterizing regulatory sequences in the human genome with chromatin accessibility assays.
    Genes 3: 651–70 (2012) DOI: 10.3390/genes3040651
  60. Shibata, Yoichiro and Sheffield, Nathan C. and Fedrigo, Olivier and Babbitt, Courtney C. and Wortham, Matthew and Tewari, Alok K. and London, Darin and Song, Lingyun and Lee, Bum-Kyu and Iyer, Vishwanath R. and Parker, Stephen C. J. and Margulies, Elliott H. and Wray, Gregory A. and Furey, Terrence S. and Crawford, Gregory E..
    Extensive Evolutionary Changes in Regulatory Element Activity during Human Origins Are Associated with Altered Gene Expression and Positive Selection
    PLos Genet. 8: e1002789 (2012) DOI: 10.1371/journal.pgen.1002789 (co-first author)
  61. Robert E. Thurman and Eric Rynes and Richard Humbert and Jeff Vierstra and Matthew T. Maurano and Eric Haugen and Nathan C. Sheffield and Andrew B. Stergachis and Hao Wang and Benjamin Vernot and Kavita Garg and Sam John and Richard Sandstrom and Daniel Bates and Lisa Boatman and Theresa K. Canfield and Morgan Diegel and Douglas Dunn and Abigail K. Ebersol and Tristan Frum and Erika Giste and Audra K. Johnson and Ericka M. Johnson and Tanya Kutyavin and Bryan Lajoie and Bum-Kyu Lee and Kristen Lee and Darin London and Dimitra Lotakis and Shane Neph and Fidencio Neri and Eric D. Nguyen and Hongzhu Qu and Alex P. Reynolds and Vaughn Roach and Alexias Safi and Minerva E. Sanchez and Amartya Sanyal and Anthony Shafer and Jeremy M. Simon and Lingyun Song and Shinny Vong and Molly Weaver and Yongqi Yan and Zhancheng Zhang and Zhuzhu Zhang and Boris Lenhard and Muneesh Tewari and Michael O. Dorschner and R. Scott Hansen and Patrick A. Navas and George Stamatoyannopoulos and Vishwanath R. Iyer and Jason D. Lieb and Shamil R. Sunyaev and Joshua M. Akey and Peter J. Sabo and Rajinder Kaul and Terrence S. Furey and Job Dekker and Gregory E. Crawford and John A. Stamatoyannopoulos.
    The accessible chromatin landscape of the human genome
    Nature (2012) DOI: 10.1038/nature11232
  62. Tewari, Alok K and Yardimci, Galip G\"{u}rkan and Shibata, Yoichiro and Sheffield, Nathan C and Song, Lingyun and Taylor, Barry S and Georgiev, Stoyan G and Coetzee, Gerhard A and Ohler, Uwe and Furey, Terrence S and Crawford, Gregory E and Febbo, Phillip G.
    Chromatin accessibility reveals insights into androgen receptor activation and transcriptional specificity.
    Genome Biol. 13: R88 (2012) DOI: 10.1186/gb-2012-13-10-r88
  63. Myers, Richard M and Stamatoyannopoulos, John and Snyder, Michael and Dunham, Ian and Hardison, Ross C and Bernstein, Bradley E and Gingeras, Thomas R and Kent, W James and Birney, Ewan and Wold, Barbara and Crawford, Gregory E and Encode, The and Consortium, Project.
    A user's guide to the encyclopedia of {DNA} elements (ENCODE).
    PLoS Biol. 9: e1001046 (2011) DOI: 10.1371/journal.pbio.1001046
  64. Sheffield, Nathan C. and Hiatt, Kevin D. and Valentine, Mark C. and Song, Hojun and Whiting, Michael F..
    Mitochondrial genomics in Orthoptera using MOSAS
    Mitochondrial DNA 21: 87–104 (2010) DOI: 10.3109/19401736.2010.500812
  65. Song, Hojun and Sheffield, Nathan C. and Cameron, Stephen L. and Miller, Kelly B. and Whiting, Michael F..
    When phylogenetic assumptions are violated: base compositional heterogeneity and among-site rate variation in beetle mitochondrial phylogenomics
    Syst. Entomol. 35: 429–448 (2010) DOI: 10.1111/j.1365-3113.2009.00517.x
  66. Sheffield, Nathan C. and Song, Hojun and Cameron, Stephen L. and Whiting, Michael F..
    Nonstationary evolution and compositional heterogeneity in beetle mitochondrial phylogenomics.
    Syst. Biol. 58: 381–94 (2009) DOI: 10.1093/sysbio/syp037
  67. Sheffield, Nathan C. and Song, Hojun and Cameron, Stephen L. and Whiting, Michael F..
    A comparative analysis of mitochondrial genomes in Coleoptera (Arthropoda: Insecta) and genome descriptions of six new beetles.
    Mol. Biol. Evol. 25: 2499–509 (2008) DOI: 10.1093/molbev/msn198
  68. Stacey, Andrew and Sheffield, Nathan C and Crandall, Keith A.
    Calculating expected {DNA} remnants from ancient founding events in human population genetics.
    BMC Genet. 9: 66 (2008) DOI: 10.1186/1471-2156-9-66 (co-first author)
  69. Eliza Duvall and Cecil M. Benitez and Krissie Tellez and Martin Enge and Philip T. Pauerstein and Lingyu Li and Songjoon Baek and Stephen R. Quake and Jason P. Smith and Nathan C. Sheffield and Seung K. Kim and H. Efsun Arda.
    Single-cell transcriptome and accessible chromatin dynamics during endocrine pancreas development
    119 () DOI: 10.1073/pnas.2201267119
  70. Nagampalli VijayKrishna and Jayadev Joshi and Nate Coraor and Jennifer Hillman-Jackson and Dave Bouvier and Marius van den Beek and Ignacio Eguinoa and Frederik Coppens and John Davis and Micha{\l} Stolarczyk and Nathan C Sheffield and Simon Gladman and Gianmauro Cuccuru and Björn Grüning and Nicola Soranzo and Helena Rasche and Bradley W Langhorst and Matthias Bernt and Dan Fornika and David Anderson de Lima Morais and Michel Barrette and Peter van Heusden and Mauro Petrillo and Antonio Puertas-Gallardo and Alex Patak and Hans-Rudolf Hotz and Daniel Blankenberg.
    Expanding the Galaxy's reference data
    2 () DOI: 10.1093/bioadv/vbac030
  71. Jonathan D Ogata and Wancen Mu and Eric S Davis and Bingjie Xue and J Chuck Harrell and Nathan C Sheffield and Douglas H Phanstiel and Michael I Love and Mikhail G Dozmorov.
    excluderanges: exclusion sets for T2T-{CHM}13, {GRCm}39, and other genome assemblies
    39 () DOI: 10.1093/bioinformatics/btad198
  72. Alexandre G. Martini and Jason P. Smith and Silvia Medrano and Gal Finer and Nathan C. Sheffield and Maria Luisa S. Sequeira-Lopez and R. Ariel Gomez.
    Renin Cell Development: Insights From Chromatin Accessibility and Single-Cell Transcriptomics
    133: 369–371 () DOI: 10.1161/circresaha.123.322827
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