The amount of available biological data, originating from various experimental procedures (genome and transcriptome sequencing, structure determination, functional assays), is vast. In our group, we employ computational techniques, such as machine learning, molecular dynamics simulations, and sequence analysis to make use of this data. We are particularly interested in understanding how protein folds have emerged and how protein structures and functions are encoded by the alphabet of 20 amino acids.
For the description of the current projects see our web page
phone: +48 22 55 43767
room: 02.111
Education and degrees:
2011; Ph.D. in Biology, Faculty of Biology, University of Tübingen, Germany
2007; M.Sc. in Biology, Faculty of Biology, University of Warsaw, Poland
Positions:
since 2018; Group leader in the Centre of New Technologies, University of Warsaw, Poland
2016 – 2018; Project leader in the Centre of New Technologies, University of Warsaw, Poland
2011 – 2016; Postdoc in the Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Warsaw, Poland
2010 – 2011; Postdoc in the Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
2007 – 2010; Ph.D. student in the Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
Research grants and fellowships:
2019 – 2022; Foundation of Polish Science, First Team research grant
2016 – 2019; Polish National Science Centre, SONATA BIS research grant
2013 – 2015; Polish Ministry of Science and Higher Education, Fellowship for outstanding young scientists
2014; German Academic Exchange Service (DAAD), Short–term research grant
2012 – 2015; Polish National Science Centre, SONATA research grant
2012 – 2013; Foundation of Polish Science, START fellowship
2011 – 2013; Polish Ministry of Science and Higher Education, Iuventus Plus research grant
Selected publications:
Szczepaniak K, Ludwiczak J, Winski A, Dunin-Horkawicz S. Variability of the core geometry in parallel coiled-coil bundles. J Struct Biol. 2018 Oct;204(1):117-124.
Ludwiczak J, Jarmula A, Dunin–Horkawicz S. Combining Rosetta with molecular dynamics (MD): A benchmark of the MD–based ensemble protein design. J Struct Biol. 2018 Jul;203(1):54–61.
Lupas AN, Bassler J, Dunin–Horkawicz S. The Structure and Topology of α–Helical Coiled Coils. Subcell Biochem. 2017;82:95–129.
Matelska D, Kurkowska M, Purta E, Bujnicki JM, Dunin–Horkawicz S. Loss of Conserved Noncoding RNAs in Genomes of Bacterial Endosymbionts. Genome Biol Evol. 2016 Jan 18;8(2):426–38.
Bocian-Ostrzycka KM, Łasica AM, Dunin-Horkawicz S, Grzeszczuk MJ, Drabik K, Dobosz AM, Godlewska R, Nowak E, Collet JF, Jagusztyn-Krynicka EK. Functional and evolutionary analyses of Helicobacter pylori HP0231 (DsbK) protein with strong oxidative and chaperone activity characterized by a highly diverged dimerization domain. Front Microbiol. 2015 Oct 8;6:1065.
Blatter M, Dunin–Horkawicz S, Grishina I, Maris C, Thore S, Maier T, Bindereif A, Bujnicki JM, Allain FH. The Signature of the Five–Stranded vRRM Fold Defined by Functional, Structural and Computational Analysis of the hnRNP L Protein. J Mol Biol. 2015 Sep 25;427(19):3001–22.
Dunin–Horkawicz S, Kopec KO, Lupas AN. Prokaryotic ancestry of eukaryotic protein networks mediating innate immunity and apoptosis. J Mol Biol. 2014 Apr 3;426(7):1568–82.
Matelska D, Purta E, Panek S, Boniecki MJ, Bujnicki JM, Dunin–Horkawicz S. S6:S18 ribosomal protein complex interacts with a structural motif present in its own mRNA. RNA. 2013 Oct;19(10):1341–8.
Hartmann MD, Grin I, Dunin–Horkawicz S, Deiss S, Linke D, Lupas AN, Hernandez Alvarez B. Complete fiber structures of complex trimeric autotransporter adhesins conserved in enterobacteria. Proc Natl Acad Sci U S A. 2012 Dec 18;109(51):20907–12.
Ferris HU, Dunin–Horkawicz S, Mondéjar LG, Hulko M, Hantke K, Martin J, Schultz JE, Zeth K, Lupas AN, Coles M. The mechanisms of HAMP–mediated signaling in transmembrane receptors. Structure. 2011 Mar 9;19(3):378–85.
Dunin–Horkawicz S, Lupas AN. Measuring the conformational space of square four–helical bundles with the program samCC. J Struct Biol. 2010 May;170(2):226–35.
Dunin–Horkawicz S, Lupas AN. Comprehensive analysis of HAMP domains: Implications for transmembrane signal transduction J Mol Biol. 2010 Apr 16;397(5):1156–74.
Dunin–Horkawicz S, Feder M, Bujnicki JM. Phylogenomic analysis of the GIY–YIG nuclease superfamily. BMC Genomics. 2006 Apr 28;7:98.
Dunin–Horkawicz S, Czerwoniec A, Gajda MJ, Feder M, Grosjean H, Bujnicki JM. MODOMICS: a database of RNA modification pathways. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D145–9.
| Title | Project Leader | Project period | Project funding |
|---|---|---|---|
| Zastosowanie metod uczenia maszynowego do badania struktury i funkcji bakteryjnych systemów transdukcji sygnału | Aleksander Wiński | 2019 - 2023 | Diamentowy Grant, MNiSW |
| An evolutionary-based approach to design the substrate specificity of the Rossmann fold enzymes | Stanisław Dunin-Horkawicz | 2019 - 2022 | FIRST TEAM, FNP |
| Molecular mechanisms of the allosteric communication in thymidylate synthase | Jan Ludwiczak | 2018 - 2021 | PRELUDIUM 14, NCN |
Vasilina Zayats, Agata P. Perlińska, Aleksandra I. Jarmolińska, Borys Jastrzębski, Stanisław Dunin-Horkawicz, Joanna I. Sułkowska
PLoS Computational Biology, 17(10), e1009502.
Kamil Kamiński, Jan Ludwiczak, Maciej Jasiński, Adriana Bukala, Rafał Madaj, Krzysztof Szczepaniak, Stanisław Dunin-Horkawicz
Briefings in Bioinformatics, Volume 23, Issue 1, January 2022, bbab371,
M. Adamczyk, E. Lewicka, R. Szatkowska, H. Nieznanska, J. Ludwiczak, M. Jasiński, S. Dunin-Horkawicz, E. Sitkiewicz, B. Swiderska, G. Goch, G. Jagura-Burdzy
BMC Microbiology volume 21, Article number: 32 (2021)
Merski, M., Młynarczyk, K., Ludwiczak, J., Skrzeczkowski, J., Dunin-Horkawicz, S., & Górna, M. W.
BMC bioinformatics, 21, 1-17
Banaś, A. M., Bocian-Ostrzycka, K. M., Plichta, M., Dunin-Horkawicz, S., Ludwiczak, J., Płaczkiewicz, J., & Jagusztyn-Krynicka, E. K.
PloS one, 15(3), e0230366
Szczepaniak, K., Bukala, A., da Silva Neto, A. M., Ludwiczak, J., & Dunin-Horkawicz, S.
Bioinformatics
Nowacka, M., Boccaletto, P., Jankowska, E., Jarzynka, T., Bujnicki, J. M., & Dunin-Horkawicz, S. (2019).
Database, 2019
Ludwiczak, J., Winski, A., Szczepaniak, K., Alva, V., & Dunin-Horkawicz, S. (2019).
Bioinformatics
Ludwiczak, J., Winski, A., Neto, A. M., Szczepaniak, K., Alva, V., & Dunin-Horkawicz, S.
Scientific Reports, 9(1)
Jarmula, A., Łusakowska, A., Fichna, J. P., Topolewska, M., Macias, A., Johnson, K., ... & Dunin-Horkawicz, S.
Scientific reports, 9(1), 1-17.
Ludwiczak, J., Szczęsna, E., da Silva Neto, A. M., Cieplak, P., Kasprzak, A. A., & Jarmuła, A.
Biochemical Journal, 476(17), 2449-2462.
Grzeszczuk, M. J., Bąk, A., Banaś, A. M., Urbanowicz, P., Dunin-Horkawicz, S., Gieldon, A., . . . & Jagusztyn-Krynicka, E. K.
PLOS ONE, 13(4), e0195358
Ludwiczak, J., Jarmula, A., & Dunin-Horkawicz, S.
Journal of Structural Biology, 203(1), 54-61.
Szczepaniak, K., Ludwiczak, J., Winski, A., & Dunin-Horkawicz, S.
Journal of Structural Biology, 204(1), 117-124.
Lupas, A. N., Bassler, J., & Dunin-Horkawicz, S. (2017).
Fibrous Proteins: Structures and Mechanisms (pp. 95-129). Springer, Cham.
| Title | Deadline for applications |
|---|---|
| Postdoc in Laboratory of Structural Bioinformatics | 22/11/2021 |
| PhD Student | 30/09/2021 |
| Student | 15/09/2021 |
| Student in Laboratory of Structural Bioinformatics | 15/07/2019 |
| PhD student in Laboratory of Structural Bioinformatics | 15/07/2019 |
| Postdoc for the project on modern approaches for phylogenetic reconstruction | 18/01/2019 |
| Student for the project on deciphering protein evolution with the aid of machine learning | 18/01/2019 |
To see the list of group’s publications, please visit the following link.
