Publications
_{Structural Bioinformatics}

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)

Bu, F.; Adam, Y.; Adamiak, R.; Antczak, M.; de Aquino, B.; Badepally, N.; Batey, R.; Baulin, E.; Boinski, P.; Boniecki, M. et al.; Bujnicki, J.; Carpenter, K.; Chacon, J.; Chen, S.-J.; Chiu, W.; Cordero, P.; Das, N.; Das, R.; Dawson, W.; DiMaio, F.; Ding, F.; Dock-Bregeon, A.-C.; Dokholyan, N.; Dror, R.; Dunin-Horkawicz, S.; Eismann, S.; Ennifar, E.; Esmaeeli , R.; Farsani, M.; Ferré-D'Amaré , A.; Geniesse, C.; Ghanim, G.; Guzman, H.; Hood, I.; Huang, L.; Jain, D.; Jaryani, F.; Jin, L.; Joshi, A.; Karelina, M.; Kieft, J.; Kladwang, W.; Kmiecik , S.; Koirala, D.; Kollmann, M.; Kretsch, R.; Kurciński, M.; Li, J.; Li, S.; Magnus, M.; Masquida, B.; Moafinejad, S.; Mondal, A.; Mukherjee, S.; Nguyen, T.; Nikolaev, G.; Nithin, C.; Nye, G.; Pandaranadar Jeyeram, I.; Perez, A.; Pham, P.; Piccirilli, J.; Pilla, S.; Pluta, R.; Poblete, S.; Ponce-Salvatierra, A.; Popenda, M.; Popenda, L.; Pucci, F.; Rangan, R.; Ray, A.; Ren, A.; Sarzynska, J.; Sha, C.; Stefaniak, F.; Su, Z.; Suddala, K.; Szachniuk, M.; Townshend, R.; Trachman 3rd , R.; Wang, J.; Wang, W.; Watkins, A.; Wirecki, T.; Xiao, Y.; Xiong, P.; Xiong, Y.; Yang, J.; Yesselman, J.; Zhang, J.; Zhang, Y.; Zhang, Z.; Zhou, Y.; Zok, T.; Zhang, D.; Zhang, S.; Żyła, A.; Westhof, E.; Miao, Z.: RNA-Puzzles Round V: blind predictions of 23 RNA structures. Nature Methods 22 (2), pp. 399 - 411 (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)

Berdyński , B.; Ludwiczak, J.; Barczak, A.; Barcikowska-Kotowicz, M.; Kuźma-Kozakiewicz, M.; Dunin-Horkawicz, S.; Żekanowski, C.; Borzemska, B.: TREM2 Gene Compound Heterozygosity in Neurodegenerative Disorders. Journal of Alzheimer's Disease 89 (4), pp. 1211 - 1219 (2022)

Ludwiczak, J.; Winski, A.; Dunin-Horkawicz, S.: localpdb: A Python package to manage protein structures and their annotations. Bioinformatics 38 (9), pp. 2633 - 2635 (2022)

Latoszek, E.; Wiweger, M.; Ludwiczak, J.; Dunin-Horkawicz, S.; Kuznicki, J.; Czeredys, M.: Siah-1-interacting protein regulates mutated huntingtin protein aggregation in Huntington's disease models. Cell & Bioscience 12 (1), 34 (2022)

Kamiński, K.; Ludwiczak, J.; Jasiński, M.; Bukala, A.; Madaj, R.; Szczepaniak, K.; Dunin-Horkawicz, S.: Rossmann-toolbox: a deep learning-based protocol for the prediction and design of cofactor specificity in Rossmann fold proteins. Briefings in Bioinformatics 23 (1), bbab371 (2022)

Banaś, A.; Bocian-Ostrzycka, K.; Dunin-Horkawicz, S.; Ludwiczak, J.; Wilk, P.; Orlikowska, M.; Wyszyńska, A.; Dąbrowska, M.; Plichta, M.; Spodzieja, M. et al.; Polańska , M.; Malinowska, A.; Jagusztyn-Krynicka, E.: Interplay between DsbA1, DsbA2 and C8J_1298 periplasmic oxidoreductases of Campylobacter jejuni and their impact on bacterial physiology and pathogenesis. International Journal of Molecular Sciences 22 (24), 13451 (2021)

Zayats, V.; Perlinska, A.; Jarmolinska, A.; Jastrzebski, B.; Dunin-Horkawicz, S.; Sulkowska, J.: Slipknotted and unknotted monovalent cation-proton antiporters evolved from a common ancestor. PLoS Computational Biology 17 (10), e1009502 (2021)

Adamczyk, M.; Lewicka, E.; Szatkowska, R.; Nieznanska, H.; Ludwiczak, J.; Jasiński, M.; Dunin-Horkawicz, S.; Sitkiewicz, E.; Swiderska, B.; Goch, G. et al.; Jagura-Burdzy , G.: Revealing biophysical properties of KfrA-type proteins as a novel class of cytoskeletal, coiled-coil plasmid-encoded proteins. BMC Microbiology 21 (1), 32 (2021)

Szczepaniak, K.; Bukala, A.; Marinho da Silva Neto, A.; Ludwiczak, J.; Dunin-Horkawicz, S.: A library of coiled-coil domains: from regular bundles to peculiar twists. Bioinformatics 36 (22-23), pp. 5368 - 5376 (2020)

Merski, M.; Młynarczyk, K.; Ludwiczak, J.; Skrzeczkowski, J.; Dunin-Horkawicz, S.; Górna, M.: Self-analysis of repeat proteins reveals evolutionarily conserved patterns. BMC Bioinformatics 21 (1), 179 (2020)

Banaś, A.; Szczepaniak , A.; Plichta, M.; Bocian-Ostrzycka, K.; Dunin-Horkawicz, S.; Ludwiczak, J.; Płaczkiewicz, J.; Jagusztyn-Krynicka, E.: C8J_1298, a bifunctional thiol oxidoreductase of Campylobacter jejuni, affects Dsb (disulfide bond) network functioning. PLoS One 15 (3), e0230366 (2020)

Jarmula, A.; Łusakowska, A.; Fichna, J.; Topolewska, M.; Macias, A.; Johnson, K.; Töpf , A.; Straub, V.; Rosiak, E.; Szczepaniak , K. et al.; Dunin-Horkawicz, S.; Maruszak, A.; Kaminska, A.; Redowicz, M.: ANO5 mutations in the Polish limb girdle muscular dystrophy patients: Effects on the protein structure. Scientific Reports 9 (1), 11533 (2019)

Ludwiczak, J.; Winski, A.; Szczepaniak , A.; Alva, V.; Dunin-Horkawicz, S.: DeepCoil: a fast and accurate prediction of coiled-coil domains in protein sequences. Bioinformatics 35 (16), pp. 2790 - 2795 (2019)

Ludwiczak, J.; Winski, A.; Marinho da Silva Neto, A.; Szczepaniak, K.; Alva, V.; Dunin-Horkawicz, S.: PiPred: a deep-learning method for prediction of π-helices in protein sequences. Scientific Reports 9, 6888 (2019)