Prof. Marta Szachniuk, associate professor
Head of Department
mszachniuk@ibch.poznan.pl
tel. 61 6653030
Dr. Marcin Radom
adiunkt
Dr. Mariusz Popenda
starszy specjalista chemik
Molecular structures and macromolecule interactions, with particular reference to RNA and RNA-protein interactions.
Characterization of new bioinformatics issues related to study of biomolecule structures and their solution by means of new theoretical models definition and computational methods development.
Performing in silico experiments, optionally supported by biological and chemical experiments.
Development of the concept of virtual RNA bioinformatics laboratory and its implementation in RNApolis platform (http://rnapolis.pl/).
Development of computational systems addressing current problems of structural biology, i.a., RNA FRABASE, RNAComposer, RNApdbee, RNAvista, RNAtango.
Modeling of RNA secondary and tertiary structure
Refinement of coarse-grained RNA 3D structure
Analysis of macromolecular structure in torsion angle space
Annotation and classification of pseudoknots
A. Belter, M. Popenda, M. Sajek, T. Wozniak, M.Z. Naskret-Barciszewska, M. Szachniuk, S. Jurga, J. Barciszewski, A new molecular mechanism of RNA circularization and the microRNA sponge formation, Journal of Biomolecular Structure and Dynamics, 2021 (doi:10.1080/07391102.2020.1844802).
J. Miskiewicz, J. Sarzynska, M. Szachniuk, How bioinformatics resources work with G4 RNAs, Briefings in Bioinformatics, 2021 (doi:10.1093/bib/bbaa201).
T.P. Lehmann, J. Miskiewicz, N. Szostak, M. Szachniuk, S. Grodecka-Gazdecka, P.P. Jagodzinski, In vitro and in silico analysis of miR-125a with rs12976445 polymorphism in breast cancer patients, Applied Sciences 10(20), 2020, 7275 (doi:10.3390/app10207275).
J. Gumna, T. Zok, K. Figurski, K. Pachulska-Wieczorek, M. Szachniuk, RNAthor - fast, accurate normalization, visualization and statistical analysis of RNA probing data resolved by capillary electrophoresis, PLOS ONE 15(10), 2020, e0239287 (doi:10.1371/journal.pone.0239287).
M. Magnus, M. Antczak, T. Zok, J. Wiedemann, P. Lukasiak, Y. Cao, J.M. Bujnicki, E. Westhof, M. Szachniuk, Z. Miao, RNA-Puzzles toolkit: A computational resource of RNA 3D structure benchmark datasets, structure manipulation, and evaluation tools, Nucleic Acids Research 48(2), 2020, 576-588 (doi: 10.1093/nar/gkz1108)
M. Popenda, J. Miskiewicz, J. Sarzynska, T. Zok, M. Szachniuk, Topology-based classification of tetrads and quadruplex structures, Bioinformatics 36(4), 2020, 1129-1134 (doi:10.1093/bioinformatics/btz738)
T. Zok, M. Popenda, M. Szachniuk, ElTetrado: a tool for identification and classification of tetrads and quadruplexes, BMC Bioinformatics 21, 2020, 40 (doi:10.1186/s12859-020-3385-1)
Z. Miao, R.W. Adamiak, M. Antczak, M.J. Boniecki, J.M. Bujnicki, S-J. Chen, C.Y. Cheng, Y. Cheng, F-C. Chou, R. Das, N.V. Dokholyan, F. Ding, C. Geniesse, Y. Jiang, A. Joshi, A. Krokhotin, M. Magnus, O. Mailhot, F. Major, T.M. Mann, P. Piatkowski, R. Pluta, M. Popenda, J. Sarzynska, L. Sun, M. Szachniuk, S. Tian, J. Wang, A.M. Watkins, J. Wiedemann, X. Xu, J.D. Yesselman, D. Zhang, Z. Zhang, C. Zhao, P. Zhao, Y. Zhou, T. Zok, A. Zyla, A. Ren, R.T. Batey, B.L. Golden, L. Huang, D.M. Lilley, Y. Liu, D.J. Patel, E. Westhof, RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers, RNA 26, 2020, 982-995 (doi:10.1261/rna.075341.120)
M. Szachniuk, RNApolis: computational platform for RNA structure analysis, Foundations of Computing and Decision Sciences 44(2), 2019, 241-257 (doi:10.2478/fcds-2019-0012).
M. Antczak, M. Zablocki, T. Zok, A. Rybarczyk, J. Blazewicz, M. Szachniuk, RNAvista: a webserver to assess RNA secondary structures withnon-canonical base pairs, Bioinformatics 35(1), 2019, 152-155 (doi:10.1093/bioinformatics/bty609).
T. Zok, M. Antczak, M. Zurkowski, M. Popenda, J. Blazewicz, R.W. Adamiak, M. Szachniuk, RNApdbee 2.0: multifunctional tool for RNA structure annotation, Nucleic Acids Research 46(W1), 2018, W30-W35 (doi:10.1093/nar/gky314).
M. Antczak, T. Zok, M. Osowiecki, M. Popenda, R.W. Adamiak, M. Szachniuk, RNAfitme: a webserver for modeling nucleobase and nucleoside residue conformation in fixed-backbone RNA structures, BMC Bioinformatics 19(1),2018, 304 (doi:10.1186/s12859-018-2317-9).
J. Miskiewicz, M. Szachniuk, Discovering structural motifs in miRNAprecursors from Viridiplantae kingdom, Molecules 23(6), 2018, 1367 (doi:10.3390/molecules23061367).
M. Antczak, M. Popenda, T. Zok, M. Zurkowski, R.W. Adamiak, M. Szachniuk, New algorithms to represent complex pseudoknotted RNA structures indot-bracket notation, Bioinformatics 34(8), 2018, 1304-1312 (doi:10.1093/bioinformatics/btx783).
Strona zrobiona w kreatorze stron internetowych WebWave
Institute of Bioorganic Chemistry,
Polish Academy of Sciences
Z. Noskowskiego 12/14
61-704 Poznań
tel centrala: (+48) 61 852 85 03
fax: (+48) 61 852 05 32
e-mail: ibch@ibch.poznan.pl
Sekretariat Dyrektora, tel: 61 852 89 19