Publications

Nikos Karaiskos

Senior scientist

About	Research	Publications	Software	Teaching	IP

List of publications on Google Scholar.

[32] Scalable image-based visualization and alignment of spatial transcriptomics datasets

S Preibisch†, M Innerberger, D León-Periñán, N Karaiskos†, N Rajewsky†

Cell Systems (2025)

[31] Combining spatial transcriptomics and ECM imaging in 3D for mapping cellular interactions in the tumor microenvironment

TM Pentimalli, S Schallenberg, D León-Periñán, I Legnini, I Theurillat, G Thomas, A Boltengagen, S Fritzsche, J Nimo, L Ruff, G Dernbach, P Jurmeister, S Murphy, MT Gregory, Y Liang, M Cordenonsi, S Piccolo, F Coscia, A Woehler, N Karaiskos, F Klauschen, N Rajewsky†

Cell Systems (2025)

[30] Interleukin-12 signaling drives Alzheimer’s disease pathology through disrupting neuronal and oligodendrocyte homeostasis

S Schneeberger*, SJ Kim*, MN Geesdorf*, E Friebel, P Eede, M Jendrach, A Boltengagen, C Braeuning, T Ruhwedel, AJ Hülsmeier, N Gimber, M Foerster, J Obst, M Andreadou, S Mundt, J Schmoranzer, S Prokop, W Kessler, T Kuhlmann, W Möbius, K-A Nave, T Hornemann, B Becher, JM Edgar, N Karaiskos, C Kocks, N Rajewsky†, FL Heppner†

Nature Aging (2025)

[29] Protocol for high-resolution 3D spatial transcriptomics using Open-ST

M Schott, D León-Periñán, E Splendiani, E Ferretti, G Macino†, N Karaiskos†, N Rajewsky†

STAR Protocols (2024)

[28] Challenges and opportunities in the clinical translation of high-resolution spatial transcriptomics

TM Pentimalli†, N Karaiskos†, N Rajewsky†

Annual Reviews of Pathology (2024)

[27] Open-ST: High-resolution spatial transcriptomics in 3D

M Schott, D León-Periñán, E Splendiani, L Strenger, JR Licha, TM Pentimalli, S Schallenberg, J Alles, S Samut Tagliaferro, A Boltengagen, S Ehrig, S Abbiati, S Dommerich, M Pagani, E Ferretti, G Macino†, N Karaiskos†, N Rajewsky†

Cell (2024)

[26] Optocoder: computational decoding of spatially indexed bead arrays

E Senel, N Rajewsky†, N Karaiskos†

NAR Genomics and Bioinformatics (2022)

[25] Single-cell transcriptomics reveals common epithelial response patterns in human acute kidney injury

C Hinze, C Kocks, J Leiz, N Karaiskos, A Boltengagen, S Cao, CM Skopnik, J Klocke, J-H Hardenberg, H Stockmann, I Gotthardt, B Obermayer, L Haghverdi, E Wyler, M Landthaler, S Bachmann, AC Hocke, V Corman, J Busch, W Schneider, N Himmerkus, M Bleich, K-U Eckardt†, P Enghard†, N Rajewsky†, KM Schmidt-Ott†

Genome Medicine (2022)

[24] Spacemake: processing and analysis of large-scale spatial transcriptomics

TR Sztanka-Toth, M Jens, N Karaiskos†, N Rajewsky†

GigaScience (2022)

[23] NovoSpaRc: flexible spatial reconstruction of single-cell gene expression with optimal transport

N Moriel*, E Senel*, N Friedman, N Rajewsky, N Karaiskos†, M Nitzan†

Nature Protocols (2021)

[22] Defective metabolic programming impairs early neuronal morphogenesis in neural cultures and an organoid model of Leigh syndrome

G Inak, A Rybak-Wolf, P Lisowski, TM Pentimalli, R Jüttner, P Glažar, K Uppal, E Bottani, D Brunetti, C Secker, A Zink, D Meierhofer, MT Henke, M Dey, U Ciptasari, B Mlody, T Hahn, M Berruezo-Llacuna, N Karaiskos, M Di Virgilio, JA Mayr, SB Wortmann, J Priller, M Gotthardt, DP Jones, E Mayatepek, W Stenzel, S Diecke, R Kühn, EE Wanker, N Rajewsky†, M Schuelke†, A Prigione†

Nature Communications (2021)

[21] Kidney single-cell transcriptomes predict spatial corticomedullary gene expression and tissue osmolality gradients

C Hinze, N Karaiskos, A Boltengagen, K Walentin, K Redo, N Himmerkus, M Bleich, SS Potter, AS Potter, KU Eckardt, C Kocks, N Rajewsky, KM Schmidt-Ott†

JASN (2021)

[20] Gene selection for optimal prediction of cell position in tissues from single-cell transcriptomics data

J Tanevski*, T Nguyen*, B Truong*, N Karaiskos, ME Ahsen, X Zhang, C Shu, K Xu, X Liang, Y Hu, HVV Pham, L Xiaomei, TD Le, AL Tarca, G Bhatti, R Romero, N Karathanasis, P Loher, Y Chen, Z Ouyang, D Mao, Y Zhang, M Zand, J Ruan, C Hafemeister, P Qiu, D Tran, T Nguyen, A Gabor, T Yu, J Guinney, E Glaab, R Krause, P Banda, G Stolovitzky, N Rajewsky†, J Saez-Rodriguez†, P Meyer†

Life Science Alliance (2020)

[19] Human muscle-derived CLEC14A-positive cells regenerate muscle independent of PAX7

A Marg, H Escobar, N Karaiskos, SA Grunwald, E Metzler, J Kieshauer, S Sauer, D Pasemann, E Malfatti, D Mompoint, S Quijano-Roy, A Boltengagen, J Schneider, M Schülke, S Kunz, R Carlier, C Birchmeier, H Amthor, A Spuler, C Kocks, N Rajewsky, S Spuler†

Nature Communications (2020)

[18] Gene expression cartography

M Nitzan*, N Karaiskos*, N Friedman†, N Rajewsky†

Nature (2019)

[17] FLAM-seq: full-length mRNA sequencing reveals principles of poly (A) tail length control

I Legnini*, J Alles*, N Karaiskos, S Ayoub, N Rajewsky†

Nature Metdods (2019)

[16] A single-cell transcriptome atlas of the mouse glomerulus

N Karaiskos*, M Rahmatollahi*, A Boltengagen, H Liu, M Hoehne, M Rinschen, B Schermer, T Benzing, N Rajewsky, C Kocks, M Kann†, R-U Müller†

JASN (2018)

[15] The Drosophila embryo at single-cell transcriptome resolution

N Karaiskos*, P Wahle*, J Alles, A Boltengagen, S Ayoub, C Kipar, C Kocks, N Rajewsky†, RP Zinzen†

Science (2017)

[14] Cell fixation and preservation for droplet-based single-cell transcriptomics

J Alles*, N Karaiskos*, SD Praktiknjo*, S Grosswendt, P Wahle, P-L Ruffault, S Ayoub, L Schreyer, A Boltengagen, C Birchmeier, R Zinzen, C Kocks†, N Rajewsky†

BMC Biology (2017)