Publications

Highlights

Bertram, D., Ophey, A., Röttgen, S., Kufer, K., Merten, N., Fink, G. R., Kalbe, E., Hansen, C., Maetzler, W., Kapsecker, M., Reimer, L. M., Jonas, S., Damgaard, A. T., Bertelsen, N. B., Skjaerbaek, C., Borghammer, P., Groenewald, K., Ratti, P.-L., Hu, M. T., … Bozek, K. (2026). ActiTect: A generalizable machine learning pipeline for REM sleep behavior disorder screening through standardized actigraphy. npj Digital Medicine. https://doi.org/10.1038/s41746-026-02738-8

Rose, F., Michaluk, M., Blindauer, T., Ignatowska-Jankowska, B. M., O’shaughnessy, L., Stephens, G. J., Pereira, T. D., Uusisaari, M. Y., & Bozek, K. (2026). Deep Imputation for Skeleton data (DISK) for behavioral science. In NATURE METHODS (Bd. 23, Nummer 1). NATURE PORTFOLIO. https://doi.org/10.1038/s41592-025-02893-y

Pisula, J. I., Helbig, D., Sancéré, L., Persa, O.-D., Bürger, C., Fröhlich, A., Lorenz, C., Bingmann, S., Niebel, D., Drexler, K., Landsberg, J., Thomas, R., Bozek, K., & Brägelmann, J. (2025). Explainable, federated deep learning model predicts disease progression risk of cutaneous squamous cell carcinoma. npj Precision Oncology, 9(1), 205. https://doi.org/10.1038/s41698-025-00997-4

2026

Popp, F., Zander, T., Schmidt, T., Bozek, K., Quaas, A., Hellmich, M., Schiller, P., Spanuth, I., Knipper, K., & Bruns, C. (2026). AI-CROSS study protocol: AI-based identification of responders to CROSS neoadjuvant chemoradiotherapy in esophageal cancer. In ONCOLOGY RESEARCH AND TREATMENT (Bd. 49, Nummer 1, S. 273). KARGER.

Sancéré, L., Lorenz, C., Helbig, D., Persa, O.-D., Dengler, S., Kreuter, A., Laimer, M., Lang, R., Fröhlich, A., Landsberg, J., Brägelmann, J., & Bozek, K. (2026). Histo-Miner: Deep learning based tissue features extraction pipeline from H&E whole slide images of cutaneous squamous cell carcinoma. PLoS Computational Biology, 22(1), e1013907. https://doi.org/10.1371/journal.pcbi.1013907

Sancéré, L., Moreau, N., & Bozek, K. (2026). Context-aware Skin Cancer Epithelial Cell Classification with Scalable Graph Transformers. arXiv e-prints, arXiv:2602.15783. https://doi.org/10.48550/arXiv.2602.15783

2025

Bachurski, D., Gholamipoorfard, R., Bu, Y. J., Holker, P., Wessendorf, L., Jestrabek, H., Stahl, D., Godel, P., Gaedke, F., Ranjbari, E., Seyhan, S., Resch, U., Schmidt, L. M., Tertel, T., Rose, F., Pinheiro, C., Corona, M. L., Vom Stein, A. F., Nguyen, P. H., … Abedpour, N. (2025). High-dimensional single-cell profling of extracellular vesicle recipients by tellurium-based labeling of the extracellular vesicle proteome (TeLEV) reveals EV-driven remodeling of the immune microenvironment in chronic lymphocytic leukemia. In ONCOLOGY RESEARCH AND TREATMENT (Bd. 48, Nummer SUPPL 2, 2). KARGER.

Butt, L., Unnersj -Jess, D., H hne, M., Reilly, D., Hahnfeldt, R., Bozek, K., Schermer, B., & Benzing, T. (2025). Phosphorylative State of Podocin Affects Podocyte Morphology and Function. JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY, 36(10). (WOS:001693041204011). https://doi.org/10.1681/ASN.2025pg9k5dhz

Deserno, M., & Bozek, K. (2025). Unsupervised Representation Learning of C. elegans Poses and Behavior Sequences From Microscope Video Recordings. https://doi.org/10.7554/elife.106593.1

Joza, S., Pelletier, A., Gagnon, J.-F., Montplaisir, J. Y., Bertram, D., Bozek, K., Postuma, R. B., & Sommerauer, M. (2025). Validation of RBDtector: An Open-Source Automated Software for Scoring REM Sleep Without Atonia. Journal of Sleep Research, e70037. https://doi.org/10.1111/jsr.70037

Lorenz, C., Sancere, L., Helbig, D., Persa, O. D., Dengler, S., Kreuter, A., Laimer, M., Froehlich, A., Landsberg, J., Bozek, K., & Braegelmann, J. (2025). Predicting response of cutaneous scquamous cell carcinomas to immune checkpoint blockade (ICB) using a novel deep learning histology pipeline. In JOURNAL DER DEUTSCHEN DERMATOLOGISCHEN GESELLSCHAFT (Bd. 23, Nummern S6, SI, S. 14). WILEY.

Naji, H., Hahn, P., Pisula, J. I., Ugliano, S., Simon, A., Büttner, R., & Bozek, K. (2025). Deep learning-based interpretable prediction of recurrence of diffuse large B-cell lymphoma. BJC Reports, 3(1), 34. https://doi.org/10.1038/s44276-025-00147-0

Pisula, J., Helbig, D., Lorenz, C., Sancere, L., Persa, O. D., Buerger, C., Froehlich, A., Bingmann, S., Niebel, D., Drexler, K., Landsberg, J., Thomas, R., Bozek, K., & Braegelmann, J. (2025). Predicting disease progression risk of cutaneous squamous cell carcinoma using an explainable, federated deep learning model. In JOURNAL DER DEUTSCHEN DERMATOLOGISCHEN GESELLSCHAFT (Bd. 23, Nummern S6, SI, S. 139–140). WILEY.

Pisula, J. I., & Bozek, K. (2025a). Efficient WSI classification with sequence reduction and transformers pretrained on text. Scientific Reports, 15(1), 5612. https://doi.org/10.1038/s41598-025-88139-5

Pisula, J. I., & Bozek, K. (2025b). Fine-Tuning a Multiple Instance Learning Feature Extractor with Masked Context Modelling and Knowledge Distillation. In A. Del Bue, C. Canton, J. Pont-Tuset, & T. Tommasi (Hrsg.), Computer Vision – ECCV 2024 Workshops (S. 1–15). Springer Nature Switzerland.

Rose, F., Ibruli, O., Lichius, L., Kiljan, M., Gozum, G., Caiaffa, M. I., Cai, J., Niu, L.-N., Herter, J. M., Grüll, H., Büttner, R., Beleggia, F., Bosco, G., George, J., Herter-Sprie, G. S., Reinhardt, H. C., & Bozek, K. (2025). Imaging mass cytometry dataset of small-cell lung cancer tumors and tumor microenvironments. BMC Research Notes, 18(1), 385. https://doi.org/10.1186/s13104-025-07460-4

Stahl, D., Gödel, P., Balke-Want, H., Gholamipoorfard, R., Segbers, P., Tetenborg, L., Koker, M., Dörr, J., Gregor, L., Bachurski, D., Rose, F., Simon, A. G., Good, Z., Jakob, J., Häupl, B., Nill, M., Flümann, R., Riet, T., Lange, D., … Ullrich, R. T. (2025). CSF1R(+) myeloid-monocytic cells drive CAR-T cell resistance in aggressive B cell lymphoma. Cancer Cell, 43(8), 1476-1494.e10. https://doi.org/10.1016/j.ccell.2025.05.013

Vali, M., Arabi, H., Bozek, K., & IEEE. (2025). Active Learning with Uncertainty-Guided Sample Selection for PET/CT Tumor Segmentation. University of Cologne. (WOS:001661275600016). 2025 IEEE INTERNATIONAL CONFERENCE ON IMAGING SYSTEMS AND TECHNIQUES, IST. https://doi.org/10.1109/IST66504.2025.11268389

2024

Ibruli O, Rose F, Beleggia F, Schmitt A, Cartolano M, Fernandez LT, Saggau J, Bonasera D, Kiljan M, Gozum G, Lichius L, Cai J, Niu LN, Caiaffa MI, Herter JM, Walczak H, Liccardi G, Grüll H, Büttner R, Bosco G, George J, Thomas RK, Bozek K, Reinhardt HC, Herter-Sprie GS. A novel mouse model recapitulating the MMR-defective SCLC subtype uncovers an actionable sensitivity to immune checkpoint blockade. J Cancer Res Clin Oncol. 2024 Nov 14;150(11):496. https://doi.org/10.1007/s00432-024-05942-9

Stahl D, Gödel P, Balke-Want H, Segbers P, Tetenborg L, Gholamipoorfard R, Bachurski D, Rose F, Good Z, Simon AG, Nill M, Flümann R, Riet T, Dörr J, Blakemore SJ, Baurmann H, Voltin C-A, Potter N, Schlözer L, Wagener-Ryczek S, Iuga A-I, Heger J-M, Ludwig H, Schleifenbaum JK, Bröckelmann PJ, Jachimowicz RD, Knittel G, Borchmann S, Merkelbach-Bruse S, Pallasch C, Peifer M, Nitz M, Brägelmann J, Müller W, Persigehl T, Bozek K, Büttner R, Hallek MJ, Kobold S, Chmielewski M, Reinhardt HC, Mackall CL, Abedpour N, Borchmann P, Ullrich RT. Targeting Lymphoma Associated Myeloid-Monocytic Cells through CSF1R Blockade Enhances CAR-T Cell Response in Aggressive B Cell Lymphoma. Blood. 2024;144(Supplement 1):367. https://doi.org/10.1182/blood-2024-203291

Harder C, Pryalukhin A, Quaas A, Eich ML, Tretiakova M, Klein S, Seper A, Heidenreich A, Netto GJ, Hulla W, Büttner R, Bozek K, Tolkach Y. Enhancing Prostate Cancer Diagnosis: Artificial Intelligence-Driven Virtual Biopsy for Optimal Magnetic Resonance Imaging-Targeted Biopsy Approach and Gleason Grading Strategy. Mod Pathol. 2024 Oct;37(10):100564. https://doi.org/10.1016/j.modpat.2024.100564

Jung JO, Pisula JI, Beyerlein X, Lukomski L, Knipper K, Abu Hejleh AP, Fuchs HF, Tolkach Y, Chon SH, Nienhüser H, Büchler MW, Bruns CJ, Quaas A, Bozek K, Popp F, Schmidt T. Deep Learning Histology for Prediction of Lymph Node Metastases and Tumor Regression after Neoadjuvant FLOT Therapy of Gastroesophageal Adenocarcinoma. Cancers (Basel). 2024 Jul 3;16(13):2445. https://doi.org/10.3390/cancers16132445

Lukomski L, Pisula J, Wagner T, Sabov A, Große Hokamp N, Bozek K, Popp F, Kann M, Kurschat C, Becker JU, Bruns C, Thomas M, Stippel D. First experiences with machine learning predictions of accelerated declining eGFR slope of living kidney donors 3 years after donation. J Nephrol. 2024 Jul;37(6):1631-1642. https://doi.org/10.1007/s40620-024-01967-y

Naji H, Sancere L, Simon A, Büttner R, Eich ML, Lohneis P, Bozek K. HoLy-Net: Segmentation of histological images of diffuse large B-cell lymphoma. Comput Biol Med. 2024 Mar;170:107978. https://doi.org/10.1016/j.compbiomed.2024.107978

Moreau N, Shabani M, Schell C, Bozek K. GLOMNET: A Hover Deep Learning Model for Glomerulus Instance Segmentation. 2024 IEEE International Symposium on Biomedical Imaging (ISBI), Athens, Greece, 2024, pp. 1-5, doi: 10.1109/ISBI56570.2024.10635729

2023

Butt L, Unnersjö-Jess D, Reilly D, Hahnfeldt R, Rinschen MM, Bozek K, Schermer B, Benzing T, Höhne M. In vivo characterization of a podocyte-expressed short podocin isoform. BMC Nephrol. 2023 Dec 19;24(1):378. https://doi.org/10.1186/s12882-023-03420-x

Jung JO, Pisula JI, Bozek K, Popp F, Fuchs HF, Schröder W, Bruns CJ, Schmidt. Prediction of postoperative complications after oesophagectomy using machine-learning methods. Br J Surg. 2023 Sep 6;110(10):1361-1366. http://doi.org/10.1093/bjs/znad181

Deserno M, Bozek K. WormSwin: Instance segmentation of C. elegans using vision transformer. Sci Rep. 2023 Jul 7;13(1):11021. http://doi.org/10.1038/s41598-023-38213-7

Unnersjö-Jess D, Butt L, Höhne M, Sergei G, Fatehi A, Witasp A, Wernerson A, Patrakka J, Hoyer PF, Blom H, Schermer B, Bozek K, Benzing T. Deep learning-based segmentation and quantification of podocyte foot process morphology suggests differential patterns of foot process effacement across kidney pathologies. Kidney Int. 2023 Jun;103(6):1120-1130. http://doi.org/10.1016/j.kint.2023.03.013

Vom Stein AF, Rebollido-Rios R, Lukas A, Koch M, von Lom A, Reinartz S, Bachurski D, Rose F, Bozek K, Abdallah AT, Kohlhas V, Saggau J, Zölzer R, Zhao Y, Bruns C, Bröckelmann PJ, Lohneis P, Büttner R, Häupl B, Oellerich T, Nguyen PH, Hallek M. LYN kinase programs stromal fibroblasts to facilitate leukemic survival via regulation of c-JUN and THBS1. Nat Commun. 2023 Mar 10;14(1):1330. http://doi.org/10.1038/s41467-023-36824-2

Pisula JI, Datta RR, Valdez LB, Avemarg JR, Jung JO, Plum P, Löser H, Lohneis P, Meuschke M, Dos Santos DP, Gebauer F, Quaas A, Walch A, Bruns CJ, Lawonn K, Popp FC, Bozek K. Predicting the HER2 status in oesophageal cancer from tissue microarrays using convolutional neural networks. Br J Cancer. 2023 Mar;128(7):1369-1376. http://doi.org/10.1038/s41416-023-02143-y

Naji H, Hahn L, Bozek K. Lymphoma Cell Nuclei Classification using Color and Morphology Features. Current Directions in Biomedical Engineering. 2023;9(1): 210-213. https://doi.org/10.1515/cdbme-2023-1053

2022

N Hanuscheck, C Thalman, M Domingues, S Schmaul, M Muthuraman, F Hetsch, M Ecker, H Endle, M Oshaghi, G Martino, T Kuhlmann, K Bozek, T van Beers, S Bittner, J von Engelhardt, J Vogt, CF Vogelaar, F Zipp. Interleukin-4 receptor signaling modulates neuronal network activity, J Exp Med (2022) 219 (6): e20211887. https://doi.org/10.1084/jem.20211887 2022

2021

K Bozek, L Hebert, Y Portugal, GJ Stephens. Markerless tracking of entire insect colony. Nat Commun 12, 1733. doi.org/10.1038/s41467-021-21769-1 2021

DMT Nguyen, ML Luzzolino, A Mankel, K Bozek, GJ Stephens, O Peleg. Flow-Mediated Olfactory Communication in Honey Bee Swarms. PNAS, March 30, 118 (13) e2011916118; 2021

L Butt, D Unnersjö-Jess, M Höhne, G Sergei, A Witasp, A Wernerson, J Patrakka, PF Hoyer, H Blom, B Schermer, K Bozek*, T Benzing*. Deep learning-based segmentation and quantification of podocyte foot process morphology (preprint)

2020

AFC Lopes, K Bozek, M Herholz, A Trifunovic, M Rieckher, B Schumacher | A C. elegans model for neurodegeneration in Cockayne Syndrome | Nucleic Acids Research, gkaa795, https://doi.org/10.1093/nar/gkaa795 2020

RNU Kok, L Hebert, G Huelsz-Prince, YJ Goos, X Zheng, K Bozek, GJ Stephens, SJ Tans, JS Van Zon | OrganoidTracker: efficient cell tracking using mashine learning and manual error correction | 15(10): e0240802. https://doi.org/10.1371/journal.pone.0240802 2020

2019

K Bozek, L Hebert, AS Mikheyev, GJ Stephens | Pixel personality for dense object tracking in a 2D honeybee hive | arxiv.org/abs/1812.11797

2018

K Bozek, J Rangel, J Arora, M Tin, E Crotteau, GM Loper, J Fewell, AS Mikheyev | Parallel genomic evolution of parasite tolerance in wild honey bee populations | https://www.biorxiv.org/content/10.1101/498436v1

K Bozek, L Hebert, AS Mikheyev, GJ Stephens | Towards dense object tracking in a 2D honeybee hive. | Computer Vision and Pattern Recognition 2018

EE Khrameeva, I Kurochkin, K Bozek, P Giavalisco, P Khaitovich | Lipidome Evolution in Mammalian Tissues. | Mol Biol Evol 2018

2017

K Bozek, EE Khrameeva, J Reznick, D Omerbašić, NC Bennett, GR Lewin, J Azpurua, V Gorbunova, A Seluanov, P Regnard, F Wanert, J Marchal, F Pifferi, F Aujard, Z Liu, P Shi, S Pääbo, F Schroeder, L Willmitzer, P Giavalisco, P Khaitovich | Lipidome determinants of maximal lifespan in mammals. | Sci Rep. 2017

Q Li*, K Bozek*, C Xu, Y Guo, J Sun, S Pääbo, CC Sherwood, PR Hof, JJ Ely, Y Li, L Willmitzer, P Giavalisco, P Khaitovich (*equal contribution) | Changes in lipidome composition during brain development in humans, chimpanzees and macaque monkeys. | Mol Biol Evol 2017

2015

K Bozek, Y Wei, Z Yan, X Liu, J Xiong, M Sugimoto, M Tomita, S Pääbo, CC Sherwood, PR Hof, JJ Ely, Y Li, D Steinhauser, L Willmitzer, P Giavalisco, P Khaitovich | Organization and evolution of brain lipidome revealed by large-scale analysis of human, chimpanzee, macaque and mouse tissues.| Neuron 2015

2014

K Bozek, Y Wei, Z Yan, X Liu, J Xiong, M Sugimoto, M Tomita, S Pääbo, R Pieszek, CC Sherwood, PR Hof, JJ Ely, D Steinhauser, L Willmitzer, J Bangsbo, O Hansson, J Call, P Giavalisco, P Khaitovich | Exceptional evolutionary divergence of human muscle and brain metabolomes parallels human cognitive and physical uniqueness. | PLoS Biol 2014

EE Khrameeva, K Bozek, L He, Z Yan, X Jiang, Y Wei, K Tang, MS Gelfand, K Prufer, J Kelso, S Pääbo, P Giavalisco, M Lachmann, P Khaitovich | Neanderthal ancestry drives evolution of lipid catabolism in contemporary Europeans. | Nat Commun 2014

2013

K Bozek, T Lengauer, S Sierra, R Kaiser, FS Domingues | Analysis of Physicochemical and Structural Properties Determining HIV-1 Coreceptor Usage. | PLoS Comp Bio. 2013

2012

K Bozek, M Eckhardt, S Sierra, M Anders, R Kaiser, HG Kräusslich, B Müller, T Lengauer | An expanded model of HIV cell entry phenotype based on multi-parameter single-cell data. | Retrovirology. 2012

K Bozek, EE Nakayama, K Kono, T Shioda | Electrostatic potential of human immunodeficiency virus type 2 and rhesus macaque simian immunodeficiency virus capsid proteins. | Front Microbiol. 2012

2010

K Bozek, T Lengauer | Positive selection of HIV host factors and the evolution of lentivirus genes. | BMC Evol Biol. 2010

K Bozek, AL Rosahl, S Gaub, S Lorenzen, H Herzel. | Circadian transcription in liver. | Biosystems. 2010

2009

A Kuroishi, K Bozek, T Shioda, EE Nakayama | A single aminoacid substitution of the human immunodeficiency virus type 1 capsid protein affects viral sensitivity to TRIM5alpha. | Retrovirology. 2009

K Bozek, A Thielen, S Sierra, R Kaiser, T Lengauer | V3 loop sequence space analysis suggests different evolutionary patterns of CCR5- and CXCR4-tropic HIV. | PLoS One. 2009

K Kono, K Bozek, FS Domingues, T Shioda, EE Nakayama | Impact of a single amino acid in the variable region 2 of the Old World monkey TRIM5alpha SPRY (B30.2) domain on anti-human immunodeficiency virus type 2 activity. | Virology. 2009

K Bozek, A Relogio, SM Kielbasa, M Heine, C Dame, A Kramer, H Herzel | Regulation of clock- controlled genes in mammals. | PLoS One. 2009