% Publications of Dominik J. Otto, for the website.
% Source of truth: Applications 2027/_baseline/cv_2027.tex (order, author marks, status strings).
% The publications page is generated from this file:  python3 tools/build_publications.py
%
% Non-standard fields read by the generator (ignored by BibTeX):
%   x_group          lead | other           (section on the page, as in the CV)
%   x_equal          surnames with equal contribution, separated by ";"   (rendered *)
%   x_corresponding  surnames of co-corresponding authors, separated by ";" (rendered +)
%   x_status         status after the venue, e.g. "under review at Cell Systems"
%   x_kind           preprint | conference abstract | doctoral dissertation | erratum
%   x_highlight      software page anchor or short label shown as a tag
% Keep status strings identical to the CV; when a paper moves, change it here and in the CV together.

@article{annzarro2026,
  title = {AnnZarro: scalable, interactive exploration of cell-by-cell and gene-by-gene relationships in single-cell data},
  author = {D. J. Otto and S. Baasri and M. Setty},
  journal = {bioRxiv},
  year = {2026}, month = oct,
  doi = {10.64898/2026.10.10.758158},
  x_group = {lead}, x_corresponding = {Otto; Setty}, x_kind = {preprint}, x_highlight = {AnnZarro}
}

@article{kompot2025,
  title = {Comparing phenotypic manifolds with Kompot: Cluster-free differential expression at single-cell resolution},
  author = {D. J. Otto and E. Arriaga-Gomez and E. Thieme and R. Yang and S. C. Lee and M. Setty},
  journal = {bioRxiv},
  year = {2025}, month = jun,
  doi = {10.1101/2025.06.03.657769},
  x_group = {lead}, x_corresponding = {Lee; Setty}, x_status = {under review at Cell Systems}, x_kind = {preprint}, x_highlight = {Kompot}
}

@article{mellon2024,
  title = {Quantifying cell-state densities in single-cell phenotypic landscapes using Mellon},
  author = {D. J. Otto and C. Jordan and B. Dury and C. Dien and M. Setty},
  journal = {Nature Methods},
  year = {2024}, month = jul,
  doi = {10.1038/s41592-024-02302-w},
  x_group = {lead}, x_highlight = {Mellon}
}

@article{cuttag2for1_2022,
  title = {CUT\&Tag2for1: a modified method for simultaneous profiling of the accessible and silenced regulome in single cells},
  author = {D. H. Janssens and D. J. Otto and M. P. Meers and M. Setty and K. Ahmad and S. Henikoff},
  journal = {Genome Biology},
  year = {2022}, month = mar,
  doi = {10.1186/s13059-022-02642-w},
  x_group = {lead}, x_equal = {Janssens; Otto}, x_highlight = {2for1separator}
}

@article{prostatrend2020,
  title = {ProstaTrend—A Multivariable Prognostic RNA Expression Score for Aggressive Prostate Cancer},
  author = {M. Kreuz and D. J. Otto and S. Fuessel and C. Blumert and C. Bertram and S. Bartsch and D. Loeffler and S.-H. Puppel and M. Rade and T. Buschmann and S. Christ and K. Erdmann and M. Friedrich and M. Froehner and M. H. Muders and S. Schreiber and M. Specht and M. I. Toma and F. Benigni and M. Freschi and G. Gandaglia and A. Briganti and G. B. Baretton and M. Loeffler and J. Hackermüller and K. Reiche and M. Wirth and F. Horn},
  journal = {European Urology},
  year = {2020}, month = sep,
  doi = {10.1016/j.eururo.2020.06.001},
  x_group = {lead}, x_equal = {Kreuz; Otto; Fuessel}, x_highlight = {ProstaTrend}
}

@article{mills2026,
  title = {Dysregulation of epithelial differentiation architecture underlies field cancerization in head and neck cancer},
  author = {C. Mills and Y. Huang and C. M. Lee and C. Finkbeiner and R. K. Lex and D. J. Otto and R. Yang and H. West-Foyle and D. Jones and A. Long and S. Minot and E. Nguyen and P. Itagi and S. Schuster and A. Elz and L. Schroeder and N. Futran and E. Marchiano and R. Ferrandino and R. A. Risques and G. Ha and A. Bandhlish and B. Barber and M. Setty and S. Beronja},
  journal = {bioRxiv},
  year = {2026}, month = oct,
  doi = {10.64898/2026.10.12.757511},
  x_group = {other}, x_equal = {Huang; Lee}, x_corresponding = {Setty; Beronja}, x_status = {under review at Nature}, x_kind = {preprint}
}

@article{echo2026,
  title = {Echo characterizes the desynchronization of gene expression and chromatin accessibility during cell-state transitions},
  author = {C. Finkbeiner and D. J. Otto and M. Setty},
  journal = {bioRxiv},
  year = {2026}, month = may,
  doi = {10.64898/2026.05.20.726634},
  x_group = {other}, x_kind = {preprint}
}

@article{polii2026,
  title = {Sequential RNA polymerase II activation drives human hematopoiesis},
  author = {D. H. Janssens and C. A. Codomo and D. J. Otto and L. Silberstein and K. Ahmad and S. Henikoff},
  journal = {Cell Reports},
  year = {2026}, month = jan,
  doi = {10.1016/j.celrep.2025.116802},
  x_group = {other}
}

@article{jordan2025blood,
  title = {Detecting lineage-specific regulatory activity and stemness retention in single-cell multiomics of human hematopoiesis},
  author = {C. Jordan and D. J. Otto and J. Greene and S. Henikoff and M. Setty},
  journal = {Blood},
  volume = {146}, note = {Supplement 1},
  year = {2025}, month = nov,
  doi = {10.1182/blood-2025-6119},
  x_group = {other}, x_kind = {conference abstract}
}

@article{clec2a2025,
  title = {Multi-omics analysis reveals CLEC2A is a leukemia-restricted CART target in KMT2A-rearranged Acute Myeloid Leukemia},
  author = {D. Kirkey and D. H. Janssens and M. Hines and S. Shin and G. Hawkins and M. Blankenfeld and N. Panahi and I. Lira and T. Hylkema and L. Robinson and B. Liu and R. Ries and J. Peplinski and L. Wallace and C. Nourigat and L. Perkins and L. Pardo and M. Makatsa and M. R. Loken and D. J. Otto and K. Ikegami and B. Hadland and B. de Angelis and C. Quintarelli and S. Furlan and K. Tarlock and S. Henikoff and B. Huang and F. Locatelli and W. Li and S. Meshinchi},
  journal = {Research Square},
  year = {2025}, month = oct,
  doi = {10.21203/rs.3.rs-7768680/v1},
  x_group = {other}, x_kind = {preprint, under review}
}

@article{bencomo2025jid,
  title = {Spatial transcriptomics analysis of Merkel cell carcinoma reveals novel immune cell subsets and hypoxia as correlates of immunotherapy response},
  author = {T. Bencomo and C. Morningstar and H. J. Rodriguez Chevez and D. J. Otto and M. Smith and E. Newell and M. Setty and P. Nghiem},
  journal = {Journal of Investigative Dermatology},
  volume = {145}, number = {8}, pages = {S219},
  year = {2025}, month = aug,
  doi = {10.1016/j.jid.2025.06.1542},
  x_group = {other}, x_kind = {conference abstract}
}

@article{openproblems2025,
  title = {Defining and benchmarking open problems in single-cell analysis},
  author = {M. D. Luecken and S. Gigante and D. B. Burkhardt and R. Cannoodt and D. C. Strobl and N. S. Markov and L. Zappia and G. Palla and W. Lewis and D. Dimitrov and M. E. Vinyard and D. S. Magruder and M. F. Mueller and A. Andersson and E. Dann and Q. Qin and D. J. Otto and M. Klein and O. B. Botvinnik and L. Deconinck and K. Waldrant and S. N. Yasa and A. Szałata and A. Benz and Z. Li and {Open Problems Jamboree Members} and J. M. Bloom and A. O. Pisco and J. Saez-Rodriguez and D. Wulsin and L. Pinello and Y. Saeys and F. J. Theis and S. Krishnaswamy},
  journal = {Nature Biotechnology},
  year = {2025}, month = jul,
  doi = {10.1038/s41587-025-02694-w},
  x_group = {other}
}

@article{mll2024,
  title = {MLL oncoprotein levels influence leukemia lineage identities},
  author = {D. H. Janssens and M. Duran and D. J. Otto and W. Wu and Y. Xu and D. Kirkey and C. G. Mullighan and J. S. Yi and S. Meshinchi and J. F. Sarthy and K. Ahmad and S. Henikoff},
  journal = {Nature Communications},
  year = {2024}, month = oct,
  doi = {10.1038/s41467-024-53399-8},
  x_group = {other}
}

@article{dream2024,
  title = {Community assessment of methods to deconvolve cellular composition from bulk gene expression},
  author = {B. S. White and A. de Reyniès and A. M. Newman and others and {Tumor Deconvolution DREAM Challenge consortium (D. J. Otto, consortium member)} and J. Saez-Rodriguez and L. M. Heiser and J. Guinney and A. J. Gentles},
  journal = {Nature Communications},
  year = {2024}, month = aug,
  doi = {10.1038/s41467-024-50618-0},
  x_group = {other}
}

@article{rade2024,
  title = {A reliable transcriptomic risk-score applicable to formalin-fixed paraffin-embedded biopsies improves outcome prediction in localized prostate cancer},
  author = {M. Rade and M. Kreuz and A. Borkowetz and U. Sommer and C. Blumert and S. Füssel and C. Bertram and D. Löffler and D. J. Otto and L. A. Wöller and C. Schimmelpfennig and U. Köhl and A.-C. Gottschling and P. Hönscheid and G. B. Baretton and M. Wirth and C. Thomas and F. Horn and K. Reiche},
  journal = {Molecular Medicine},
  year = {2024}, month = feb,
  doi = {10.1186/s10020-024-00789-9},
  x_group = {other}
}

@article{schimmelpfennig2023,
  title = {Characterization and evaluation of gene fusions as a measure of genetic instability and disease prognosis in prostate cancer},
  author = {C. Schimmelpfennig and M. Rade and S. Füssel and D. Löffler and C. Blumert and C. Bertram and A. Borkowetz and D. J. Otto and S.-H. Puppel and P. Hönscheid and U. Sommer and G. B. Baretton and U. Köhl and M. Wirth and C. Thomas and F. Horn and M. Kreuz and K. Reiche},
  journal = {BMC Cancer},
  year = {2023}, month = jun,
  doi = {10.1186/s12885-023-11019-6},
  x_group = {other}
}

@phdthesis{otto2021thesis,
  title = {Computational Gene Expression Deconvolution},
  author = {D. J. Otto},
  school = {Universität Leipzig},
  year = {2021}, month = aug,
  url = {https://nbn-resolving.org/urn:nbn:de:bsz:15-qucosa2-757637},
  x_group = {other}, x_kind = {doctoral dissertation}
}

@inproceedings{bauer2021,
  title = {Histological grading of the prostate carcinoma using deep learning: an unsupervised approach},
  author = {M. Bauer and S. Zürner and M. Kreuz and D. J. Otto and G. Popp and U.-D. Braumann},
  booktitle = {Medical Imaging 2021: Digital Pathology, SPIE},
  year = {2021}, month = feb,
  doi = {10.1117/12.2581043},
  x_group = {other}
}