Publications
_{Structural Bioinformatics}

Coles, M.; Ewers, C.; Albrecht, R.; Martinez-Goikoetxea, M.; Orlowska, M.; Martin, J.; Lupas, A.; Hartmann, M.; Dunin-Horkawicz, S.: Conformational diversity in poly-HAMP arrays and its implications for signal transduction. Protein Science 35 (9), e70743 (2026)

Krakowski, K.; Orlowska, M.; Kaminski, M.; Bartosik, D.; Dunin-Horkawicz, S.: pLAST: a tool for rapid comparison and classification of bacterial plasmid sequences. Bioinformatics 42 (8), btag574 (2026)

Qiu, K.; Lupas, A.; Dunin-Horkawicz, S.: pLM-Repeat: Exploiting the sequence representations of protein language models for sensitive repeat detection. Protein Science 35 (5), e70541 (2026)

Obrebski, T.; Maleszewska, M.; Dunin-Horkawicz, S.; Malik, A.: TET2 in epigenetic control of immune cells: implications for inflammatory responses and age-related pathologies. The Journal of Biological Chemistry 302 (3), 111267 (2026)

Kanhema, T.; Parobczak, K.; Patil, S.; Holm-Kaczmarek, D.; Hallin, E.; Ludwiczak, J.; Szczepankiewicz, A.; Pauzin, F.; Mahboob, A.; Szum, A. et al.; Ishizuka, Y.; Dunin-Horkawicz, S.; Kursula, P.; Wilczynski, G.; Magalska, A.; Bramham, C.: Arc/Arg3.1 binds the nuclear polyadenylate-binding protein RRM and regulates neuronal activity-dependent formation of nuclear speckles. Cell Reports 44 (4), 115525 (2025)

Madaj, R.; Martinez-Goikoetxea, M.; Kaminski, K.; Ludwiczak, J.; Dunin-Horkawicz, S.: Applicability of AlphaFold2 in the modeling of dimeric, trimeric, and tetrameric coiled-coil domains. Protein Science 34 (1), e5244 (2025)

Tomecki, R.; Drazkowska, K.; Madaj, R.; Mamot, A.; Dunin-Horkawicz, S.; Sikorski, P.: Expanding the available RNA labeling toolbox with CutA nucleotidyltransferase for efficient transcript labeling with purine and pyrimidine nucleotide analogs. ChemBioChem 25 (15), e202400202 (2024)

Winski, A.; Ludwiczak, J.; Orlowska, M.; Madaj, R.; Kaminski, K.; Dunin-Horkawicz, S.: AlphaFold2 captures the conformational landscape of the HAMP signaling domain. Protein Science 33 (1), e4846 (2024)

Smug, B.; Szczepaniak, K.; Riocha, E.; Dunin-Horkawicz, S.; Mostowy, R.: Ongoing shuffling of protein fragments diversifies core viral functions linked to interactions with bacterial hosts. Nature Communications 14 (1), 7460 (2023)

Kaminski, K.; Ludwiczak, J.; Pawlicki, K.; Alva, V.; Dunin-Horkawicz, S.: pLM-BLAST: distant homology detection based on direct comparison of sequence representations from protein language models. Bioinformatics 39 (10), btad579 (2023)

Dunin-Horkawicz, S.: Coiled-coil domains hiding in the AlphaFold database. In 9th Alpbach Workshop on: Repeat Proteins – Biology & Design. 9th Alpbach Workshop: Repeat Proteins – Biology & Design, Alpbach, Austria, September 07, 2025 - September 11, 2025. (2025)

Dunin-Horkawicz, S.: What can we learn from incorrect AlphaFold2 models? (the case of signal transduction). In 76. Mosbacher Kolloquium "AI-driven (r)evolution in structural biology & protein design". 76. Mosbacher Kolloquium "AI-driven (r)evolution in structural biology & protein design", Mosbach, Germany, March 20, 2025 - March 23, 2025. (2025)

Smug, B.; Szczepaniak, K.; Dunin-Horkawicz, S.; Rocha, E.; Mostowy, R.: How phages play with LEGO: studying protein-level mosaicism in phages and its evolutionary implications. In The Local Pangenome, 40, p. 88. The Local Pangenome, Alicante, Spain, October 25, 2023 - October 28, 2023. (2023)

Madaj, R.; Orlowska, M.; Kaminski, K.; Pawlicki, K.; Dunin-Horkawicz, S.: Side mutants of connexin proteins as a cause of non-functional gap junction beta channels: a structural bioinformatics approach. In BioInformatics in Torun 2023 - BIT23, p. 16. BioInformatics in Torun 2023 (BIT23), Torun, Poland, June 29, 2023. (2023)

Orlowska, M.; Madaj, R.; Kubica, J.; Kaminski, K.; Dunin-Horkawicz, S.: Bioinformatics approach for programmed cell death receptor from Nostoc punctiforme. In BioInformatics in Torun 2023 - BIT23, p. 34. BioInformatics in Torun 2023 (BIT23), Torun, Poland, June 29, 2023. (2023)

Kubica, J.; Madaj, R.; Orlowska, M.; Krarkowski, K.; Gront, D.; Dunin-Horkawicz, S.: Modeling of a putative programmed cell death receptor from Nostoc punctiforme. In 10th Prof. Krzysztof W. Szewczyk Intercollegiate Biotechnology Symposium: SYMBIOZA, O-17, p. 52. 10th Prof. Krzysztof W. Szewczyk Intercollegiate Biotechnology Symposium: SYMBIOZA, Warsaw, Poland, May 12, 2023 - May 14, 2023. (2023)

Coles, M.; Dunin-Horkawicz, S.; Hartmann, M.; Lupas, A.: Revisiting HAMP in the AlphaFold age. In 8th Alpbach Workshop: Coiled Coil, Fibrous and Repeat Proteins, p. 12. 8th Alpbach Workshop: Coiled Coil, Fibrous and Repeat Proteins , Alpbach, Austria, September 04, 2022 - September 09, 2022. (2022)

Lupas, A.; Dunin-Horkawicz, S.; Martinez-Goikoetxea, M.; Hartmann, M.; Hernandez Alvarez, B.: The structural diversity of natural coiled coils. In 8th Alpbach Workshop: Coiled Coil, Fibrous and Repeat Proteins, p. 39. 8th Alpbach Workshop: Coiled Coil, Fibrous and Repeat Proteins , Alpbach, Austria, September 04, 2022 - September 09, 2022. (2022)

Madaj, R.; Kamiński, K.; Wiński, A.; Ludwiczak, J.; Dunin-Horkawicz, S.: Coiled-coil domains and AlphaFold2: friends or foes? In 8th Alpbach Workshop: Coiled Coil, Fibrous and Repeat Proteins, p. 21. 8th Alpbach Workshop: Coiled Coil, Fibrous and Repeat Proteins , Alpbach, Austria, September 04, 2022 - September 09, 2022. (2022)

Ptacek, J.; Albrecht, R.; Dunin-Horkawicz, S.; Schultz, J.; Coles, M.; Hartmann, M.; Lupas, A.: Archaeal receptor Af1503: an ideal model for structural and functional studies of transmembrane signaling. In 8th Alpbach Workshop: Coiled Coil, Fibrous and Repeat Proteins, p. 54. 8th Alpbach Workshop: Coiled Coil, Fibrous and Repeat Proteins , Alpbach, Austria, September 04, 2022 - September 09, 2022. (2022)