Postal address:
Center for Integrative Bioinformatics Vienna (CIBIV)
Max Perutz Labs
Dr. Bohr Gasse 9
A-1030 Wien, Austria
Research interests
Single-cell Sequencing
Microscope Image Processing
Education
Oct 2018 - Jan 2021: M.Sc. in Mathematics, University of Göttingen, Germany
Oct 2015 - Oct 2018: B.Sc. in Mathematics, University of Göttingen, Germany
Professional Experience
Feb 2021 - present: Ph.D. student, Center for Integrative Bioinformatics Vienna (CIBIV), University of Vienna, Austria
Publications
in press
J. Naase, M. Balmanae, L. Holcik, M. Novatchkova, L. Dobnikar, T. Krausgruber, S. Ladstatter, C. Bock, A. von Haeseler, C. Esk, and J.A. Knoblich
(in press) Quantitative profiling of human brain organoid cell diversity across four protocols and multiple cell lines. Cell Rep., 44, 116168, in press (DOI: 10.1016/j.celrep.2025.116168,
PMID: 40864552)
e contributed equally
2025
J. Naas, A. von Haeseler, C. Elgert
(2025) Rethinking scRNA-seq Trajectories in Phylogenetic Paradigms: Overcoming Challenges of Missing Ancestral Information. bioRxiv, 2025.07.22.664676 (DOI: 10.1101/2025.07.22.664676)
2024
D. Lindenhofere, S. Haendelere, C. Eske, J.B. Littleboye, C. Brunet Avalos, J. Naas, F.G. Pflug, E.G.P. van de Ven, D. Reumann, A.D. Baffet, A. von Haeseler, and J.A. Knoblich
(2024) Cerebral organoids display dynamic clonal growth and tunable tissue replenishment. Nat. Cell Biol., 26, 710-718. (DOI: 10.1038/s41556-024-01412-z,
PMID: 38714853)
e contributed equally
J. Naase, M. Balmanae, L. Holcik, M. Novatchkova, L. Dobnikar, T. Krausgruber, S. Ladstatter, C. Bock, A. von Haeseler, C. Esk, and J.A. Knoblich
(2024) Reconstitution of Human Brain Cell Diversity in Organoids via Four Protocols. bioRxiv, 2024.11.15.623576 (DOI: 10.1101/2024.11.15.623576)
e contributed equally
J. Naas, G. Nies, H. Li, S. Stoldt, B. Schmitzer, S. Jakobs, and A. Munk
(2024) MultiMatch: Geometry-Informed Colocalization in Multi-Color Super-Resolution Microscopy. Commun. Biol., 7, 1139. (DOI: 10.1038/s42003-024-06772-8,
PMID: 39271907)
2023
S. Grampp, R. Krüger, V. Lauer, S. Uebel, K.X. Knaup, J. Naas, V. Höffken, T. Weide, N. Schiffer, S. Naas, and J. Schödel
(2023) Hypoxia hits APOL1 in the kidney. Kidney Int., 104, 53-60. (DOI: 10.1016/j.kint.2023.03.035,
PMID: 37098381)
S. Naas, R. Krüger, K.X. Knaup, J. Naas, S. Grampp, N. Schiffer, M. Wiesener, and J. Schödel
(2023) Hypoxia controls expression of kidney-pathogenic MUC1 variants. Life Sci. Alliance, 6, e202302078. (DOI: 10.26508/lsa.202302078,
PMID: 37316299,
PMCID: PMC10267510)
2022
S. Tiedeck, M.B. Heindl, P. Kramlinger, J. Naas, F. Brütting, N. Kirkwood, P. Mulvaney, and G. Herink
(2022) Single-Pixel Fluorescence Spectroscopy Using Near-Field Dispersion for Single-Photon Counting and Single-Shot Acquisition. ACS Photonic, 9, 2931–2937. (DOI: 10.1021/acsphotonics.2c00710)
Á. Vértesy, O.L. Eichmueller, J. Naas, M. Novatchkova, C. Esk, M. Balmaña, S. Ladstaetter, C. Bock, A. von Haeseler, and J.A. Knoblich
(2022) Gruffi: an algorithm for computational removal of stressed cells from brain organoid transcriptomic datasets. EMBO J., 41, e111118. (DOI: 10.15252/embj.2022111118,
PMID: 35919947,
software)
