Dominik J. Otto

Publications

Eighteen items: ten peer-reviewed articles, five preprints, two conference abstracts and the doctoral dissertation. For citation counts, see Google Scholar or ORCID.

D. J. Otto in bold; * equal contribution; + co-corresponding authors. A BibTeX file of this list is available.

Lead-author publications

  1. [1]
    AnnZarro: scalable, interactive exploration of cell-by-cell and gene-by-gene relationships in single-cell data Software: AnnZarro D. J. Otto+, S. Baasri, and M. Setty+ bioRxiv, Oct. 2026 doi:10.64898/2026.10.10.758158
  2. [2]
    Comparing phenotypic manifolds with Kompot: Cluster-free differential expression at single-cell resolution Software: Kompot D. J. Otto, E. Arriaga-Gomez, E. Thieme, R. Yang, S. C. Lee+, and M. Setty+ bioRxiv, June 2025, under review at Cell Systems doi:10.1101/2025.06.03.657769
  3. [3]
    Quantifying cell-state densities in single-cell phenotypic landscapes using Mellon Software: Mellon D. J. Otto, C. Jordan, B. Dury, C. Dien, and M. Setty Nature Methods, July 2024 doi:10.1038/s41592-024-02302-w
  4. [4]
    CUT&Tag2for1: a modified method for simultaneous profiling of the accessible and silenced regulome in single cells Software: 2for1separator D. H. Janssens*, D. J. Otto*, M. P. Meers, M. Setty, K. Ahmad, and S. Henikoff Genome Biology, Mar. 2022 doi:10.1186/s13059-022-02642-w
  5. [5]
    ProstaTrend—A Multivariable Prognostic RNA Expression Score for Aggressive Prostate Cancer ProstaTrend M. Kreuz*, D. J. Otto*, S. Fuessel*, C. Blumert, C. Bertram, S. Bartsch, D. Loeffler, S.-H. Puppel, M. Rade, T. Buschmann, S. Christ, K. Erdmann, M. Friedrich, M. Froehner, M. H. Muders, S. Schreiber, M. Specht, M. I. Toma, F. Benigni, M. Freschi, G. Gandaglia, A. Briganti, G. B. Baretton, M. Loeffler, J. Hackermüller, K. Reiche, M. Wirth, and F. Horn European Urology, Sept. 2020 doi:10.1016/j.eururo.2020.06.001

Other publications

  1. [6]
    Dysregulation of epithelial differentiation architecture underlies field cancerization in head and neck cancer C. Mills, Y. Huang*, C. M. Lee*, C. Finkbeiner, R. K. Lex, D. J. Otto, R. Yang, H. West-Foyle, D. Jones, A. Long, S. Minot, E. Nguyen, P. Itagi, S. Schuster, A. Elz, L. Schroeder, N. Futran, E. Marchiano, R. Ferrandino, R. A. Risques, G. Ha, A. Bandhlish, B. Barber, M. Setty+, and S. Beronja+ bioRxiv, Oct. 2026, under review at Nature doi:10.64898/2026.10.12.757511
  2. [7]
    Echo characterizes the desynchronization of gene expression and chromatin accessibility during cell-state transitions C. Finkbeiner, D. J. Otto, and M. Setty bioRxiv, May 2026 doi:10.64898/2026.05.20.726634
  3. [8]
    Sequential RNA polymerase II activation drives human hematopoiesis D. H. Janssens, C. A. Codomo, D. J. Otto, L. Silberstein, K. Ahmad, and S. Henikoff Cell Reports, Jan. 2026 doi:10.1016/j.celrep.2025.116802
  4. [9]
    Detecting lineage-specific regulatory activity and stemness retention in single-cell multiomics of human hematopoiesis C. Jordan, D. J. Otto, J. Greene, S. Henikoff, and M. Setty Blood, vol. 146, Supplement 1, Nov. 2025 (conference abstract) doi:10.1182/blood-2025-6119
  5. [10]
    Multi-omics analysis reveals CLEC2A is a leukemia-restricted CART target in KMT2A-rearranged Acute Myeloid Leukemia D. Kirkey, D. H. Janssens, M. Hines, S. Shin, G. Hawkins, M. Blankenfeld, N. Panahi, I. Lira, T. Hylkema, L. Robinson, B. Liu, R. Ries, J. Peplinski, L. Wallace, C. Nourigat, L. Perkins, L. Pardo, M. Makatsa, M. R. Loken, D. J. Otto, K. Ikegami, B. Hadland, B. de Angelis, C. Quintarelli, S. Furlan, K. Tarlock, S. Henikoff, B. Huang, F. Locatelli, W. Li, and S. Meshinchi Research Square, Oct. 2025 (preprint, under review) doi:10.21203/rs.3.rs-7768680/v1
  6. [11]
    Spatial transcriptomics analysis of Merkel cell carcinoma reveals novel immune cell subsets and hypoxia as correlates of immunotherapy response T. Bencomo, C. Morningstar, H. J. Rodriguez Chevez, D. J. Otto, M. Smith, E. Newell, M. Setty, and P. Nghiem Journal of Investigative Dermatology, vol. 145, p. S219, Aug. 2025 (conference abstract) doi:10.1016/j.jid.2025.06.1542
  7. [12]
    Defining and benchmarking open problems in single-cell analysis M. D. Luecken, S. Gigante, D. B. Burkhardt, R. Cannoodt, D. C. Strobl, N. S. Markov, L. Zappia, G. Palla, W. Lewis, D. Dimitrov, M. E. Vinyard, D. S. Magruder, M. F. Mueller, A. Andersson, E. Dann, Q. Qin, D. J. Otto, M. Klein, O. B. Botvinnik, L. Deconinck, K. Waldrant, S. N. Yasa, A. Szałata, A. Benz, Z. Li, Open Problems Jamboree Members, J. M. Bloom, A. O. Pisco, J. Saez-Rodriguez, D. Wulsin, L. Pinello, Y. Saeys, F. J. Theis, and S. Krishnaswamy Nature Biotechnology, July 2025 doi:10.1038/s41587-025-02694-w
  8. [13]
    MLL oncoprotein levels influence leukemia lineage identities D. H. Janssens, M. Duran, D. J. Otto, W. Wu, Y. Xu, D. Kirkey, C. G. Mullighan, J. S. Yi, S. Meshinchi, J. F. Sarthy, K. Ahmad, and S. Henikoff Nature Communications, Oct. 2024 doi:10.1038/s41467-024-53399-8
  9. [14]
    Community assessment of methods to deconvolve cellular composition from bulk gene expression B. S. White, A. de Reyniès, A. M. Newman, et al., Tumor Deconvolution DREAM Challenge consortium (D. J. Otto, consortium member), J. Saez-Rodriguez, L. M. Heiser, J. Guinney, and A. J. Gentles Nature Communications, Aug. 2024 doi:10.1038/s41467-024-50618-0
  10. [15]
    A reliable transcriptomic risk-score applicable to formalin-fixed paraffin-embedded biopsies improves outcome prediction in localized prostate cancer M. Rade, M. Kreuz, A. Borkowetz, U. Sommer, C. Blumert, S. Füssel, C. Bertram, D. Löffler, D. J. Otto, L. A. Wöller, C. Schimmelpfennig, U. Köhl, A.-C. Gottschling, P. Hönscheid, G. B. Baretton, M. Wirth, C. Thomas, F. Horn, and K. Reiche Molecular Medicine, Feb. 2024 doi:10.1186/s10020-024-00789-9
  11. [16]
    Characterization and evaluation of gene fusions as a measure of genetic instability and disease prognosis in prostate cancer C. Schimmelpfennig, M. Rade, S. Füssel, D. Löffler, C. Blumert, C. Bertram, A. Borkowetz, D. J. Otto, S.-H. Puppel, P. Hönscheid, U. Sommer, G. B. Baretton, U. Köhl, M. Wirth, C. Thomas, F. Horn, M. Kreuz, and K. Reiche BMC Cancer, June 2023 doi:10.1186/s12885-023-11019-6
  12. [17]
    Computational Gene Expression Deconvolution D. J. Otto Doctoral dissertation, Universität Leipzig, Aug. 2021 Full text
  13. [18]
    Histological grading of the prostate carcinoma using deep learning: an unsupervised approach M. Bauer, S. Zürner, M. Kreuz, D. J. Otto, G. Popp, and U.-D. Braumann Medical Imaging 2021: Digital Pathology, SPIE, Feb. 2021 doi:10.1117/12.2581043

Patent filings

Co-inventor on two patent filings from doctoral research at Universität Leipzig and the Fraunhofer-Gesellschaft. These are filings, not granted patents.

  • WO2024052258A1, Novel RNA-biomarkers for diagnosis of prostate cancer. Priority Sept. 2022; PCT published Mar. 2024.
  • WO2021213981A1, Multi-gene expression assay for prostate carcinoma. Priority Apr. 2020; PCT published Oct. 2021; pending in Europe (EP4139489A1) and the United States (US20230265522A1).