{"id":100,"date":"2021-02-04T14:40:32","date_gmt":"2021-02-04T13:40:32","guid":{"rendered":"http:\/\/localhost\/mSzachniuk\/?page_id=100"},"modified":"2026-05-08T08:06:25","modified_gmt":"2026-05-08T06:06:25","slug":"research-grants","status":"publish","type":"page","link":"https:\/\/www.cs.put.poznan.pl\/mszachniuk\/site\/research-grants\/","title":{"rendered":"Research & Grants"},"content":{"rendered":"\n

Research interests<\/h1>\n\n\n\n

\nResearch interests include algorithms (theory and applications), mathematical modeling, combinatorial problems in life sciences, RNA structure (modeling, analysis, dynamics).\n<\/p>\n\n\n\n

Bioinformatics projects<\/h1>\n\n\n\n\n\n\n\n\n\n\n\n \n\n \n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n

RNApolis – a virtual laboratory of RNA bioinformatics<\/h4><\/td>\n<\/tr>\n

<\/td>under construction projects are marked with *<\/td>\n<\/tr>\n\n
@ GitHub<\/a><\/td>\nsome RNApolis projects available at GitHub \n<\/td>\n<\/tr>\n\n
GraphaFold*<\/a><\/td>\nGNN to predict non-canonical base pairs in RNA 2D structure \n<\/td>\n<\/tr>\n\n
GraphaRNA<\/a><\/td>\ngraph neural network and diffusion model for RNA 3D structure prediction [ref<\/a>]<\/td>\n<\/tr>\n\n
RNAComposer<\/a><\/td>\n fully automated RNA structure prediction server\n[ref<\/a>, ref<\/a>, ref<\/a>]\n<\/td>\n<\/tr>\n\n
RNAfitme<\/a><\/td>\nwebserver for modeling nucleobase and nucleoside residue conformation in fixed-backbone RNA structures\n[ref<\/a>]<\/td>\n<\/tr>\n\n
RNA FRABASE<\/a><\/td>\n RNA FRAgments dataBASE and search engine\n[ref<\/a>, ref<\/a>]\n<\/td>\n<\/tr>\n\n
RNAgrail*<\/td>\ngraph neural network and diffusion model for RNA 3D structure prediction<\/td>\n<\/tr>\n\n
RNAhugs<\/a><\/td>\nwebserver for RNA 3D structure alignment [ref<\/a>, ref<\/a>]<\/td>\n<\/tr>\n\n
RNAloops<\/a><\/td>\ndatabase of RNA multiloops [ref<\/a>]<\/td>\n<\/tr>\n\n
RNAlyzer<\/a><\/td>\nframework for quality analysis of RNA models\n[ref<\/a>]<\/td>\n<\/tr>\n\n
RNAmoley<\/a><\/td>\nweb application for local quality assessment and refinement of RNA 3D models<\/td>\n<\/tr>\n\n
RNApdbee<\/a><\/td>\nmultifunctional webserver tool for RNA structure annotation\n[ref<\/a>, ref<\/a>]<\/td>\n<\/tr>\n\n
RNAQUA<\/a><\/td>\ncomputational tool for RNA QUality Assessment\n[ref<\/a>]<\/td>\n<\/tr>\n\n
RNAspider<\/a>\n<\/td>\nwebserver to analyze entanglements in RNA 3D structures [ref<\/a>]<\/td>\n<\/tr>\n\n
RNAsolo<\/a>\n<\/td>\ndatabase of cleaned PDB-derived RNA 3D structures [ref<\/a>, ref<\/a>]<\/td>\n<\/tr>\n\n
RNAssess<\/a><\/td>\nwebserver for quality assessment of RNA 3D structures \n[ref<\/a>]<\/td>\n<\/tr>\n\n
RNAtango<\/a><\/td>\nwebserver to study RNA 3D structures through torsion angles [ref<\/a>]<\/td>\n<\/tr>\n\n
RNAthor<\/a><\/td>\nwebserver for the automatic normalization of RNA probing data\n[ref<\/a>]<\/td>\n<\/tr>\n\n
RNAtive<\/a><\/td>\nwebserver to rank RNA 3D models and infer the native [ref<\/a>]<\/td>\n<\/tr>\n\n
RNAvista<\/a><\/td>\nwebserver to assess RNA secondary structures with non-canonical base pairs\n[ref<\/a>]<\/td>\n<\/tr>\n\n
MCQ4Structures<\/a><\/td>\nstandalone app to compute torsion angle-based similarity of molecule structures\n[ref<\/a>]<\/td>\n<\/tr>\n\n

SpaceTetrado – computational tools for quadruplexes<\/h4><\/td>\n<\/tr>\n\n

DrawTetrado<\/a><\/td>\nstandalone app to draw layer diagrams representing quadruplex structures [ref<\/a>]<\/td>\n<\/tr>\n\n
ElTetrado<\/a><\/td>\nstandalone app for identification and classification of tetrads and quadruplexes\n[ref<\/a>]<\/td>\n<\/tr>\n\n
G4Composer<\/a><\/td>\nwebserver for quadruplex structure modeling<\/td>\n<\/tr>\n\n
LinkTetrado<\/a><\/td>\nstandalone app to identify polynucleotide motifs (tetrads, pentads and beyond)\n[ref<\/a>]<\/td>\n<\/tr>\n\n
ONQUADRO<\/a><\/td>\ndatabase of tetrads, quadruplexes, and G4-helices\n[ref<\/a>]<\/td>\n<\/tr>\n\n
WebTetrado<\/a><\/td>\nwebserver to annotate and visualize quadruplexes in nucleic acid 3D structures [ref<\/a>]<\/td>\n<\/tr>\n\n

Other bioinformatics tools<\/h4><\/td>\n<\/tr>\n\n

BIOREDIS<\/a><\/td>\ncomputational platform for designing nucleic acid therapeutics [ref]<\/td>\n<\/tr>\n\n
miRarchitect<\/a><\/td>\nmachine learning-based tool for rational design of artificial miRNAs [ref]<\/td>\n<\/tr>\n\n
SMERFA<\/a>*<\/td>\nstructural, muscular and elastic RNA finder and aligner [ref]<\/td>\n<\/tr>\n\n
Virxicon<\/a><\/td>\na lexicon of viral sequences\n[ref<\/a>]<\/td>\n<\/tr>\n\n<\/tbody>\n<\/table>\n\n\n\n

Research grants<\/h1>\n\n\n\n\n \n\n\n \n \n\n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n
2025-2028<\/td>\n –<\/td>\n
Grant No 2024\/53\/B\/ST6\/02789 (OPUS 27) from the National Science Centre (NCN, Poland), Modelowanie struktury RNA ukierunkowane na motywy funkcjonalne (Functional motif-targeted RNA structure modeling)<\/em> – principal investigator<\/strong><\/div><\/span><\/td>\n <\/tr>\n
2024-2026<\/td>\n –<\/td>\n
Bilateral Research and Mobility Project under the scientific cooperation between the Polish Academy of Sciences (PAS) and the Czech Academy of Sciences (CAS), Zaawansowane algorytmy wspomagaj\u0105ce predykcj\u0119 wysokiej jako\u015bci modeli 3D RNA (Advanced algorithms to support prediction of high quality 3D RNA models)<\/em> – principal investigator<\/strong><\/div><\/span><\/td>\n <\/tr>\n
2024-2027<\/td>\n –<\/td>\n
Grant No 2023\/51\/D\/ST6\/01207 (SONATA 19) from the National Science Centre (NCN, Poland), Eksploracja motyw\u00f3w p\u0119tli wielokrotnych w strukturach RNA (Exploring multiple loop motifs in RNA structures)<\/em> – executor<\/div><\/span><\/td>\n <\/tr>\n
2021-2027<\/td>\n –<\/td>\n
Grant No 2021\/ABM\/05\/00004 from the Medical Research Agency (ABM, Poland), Stworzenie uniwersalnej platformy szybkiego reagowania, bazuj\u0105cej na technologii RNA, zapewniaj\u0105cej bezpiecze\u0144stwo lekowe i epidemiologiczne kraju (Development of a universal fast-response platform, based on RNA technology, ensuring the national drug and epidemiological safety)<\/em> – task manager, team leader<\/div><\/span><\/td>\n <\/tr>\n
2021-2026<\/td>\n –<\/td>\n
Grant No 2020\/39\/O\/ST6\/01488 (PRELUDIUM BIS 2) from the National Science Centre (NCN, Poland), Przewidywanie struktur 3D RNA z wykorzystaniem generatywnych sieci przestawnych (Predicting 3D RNA structures using Generative Adversarial Networks)<\/em> – principal investigator<\/strong><\/div><\/span><\/td>\n <\/tr>\n
2020-2023<\/td>\n –<\/td>\n
Grant No 2019\/35\/B\/ST6\/03074 (OPUS 18) from the National Science Centre (NCN, Poland), Eksploracja cech i modelowanie struktury kwadrupleks\u00f3w (Feature exploration and modelling of quadruplex structures)<\/em> – principal investigator<\/strong><\/div><\/span><\/td>\n <\/tr>\n
2017-2020<\/td>\n –<\/td>\n
Grant No 2016\/23\/B\/ST6\/03931 (OPUS 12) from the National Science Centre (NCN, Poland), RNApolis \u2013 metody i algorytmy do modelowania i analizy struktury RNA (RNApolis – methods and algorithms to model and analyze the RNA structure)<\/em> – principal investigator<\/strong><\/div><\/span><\/td>\n <\/tr>\n
2017-2018<\/td>\n –<\/td>\n
Grant No 2016\/23\/N\/ST6\/03779 (PRELUDIUM 12) from the National Science Centre (NCN, Poland), Rozw\u00f3j bioinformatycznych modeli do analizy struktur 3D RNA w przestrzeni k\u0105towej (Development of bioinformatics models to analyze 3D RNA structures in torsion angle space)<\/em> – supervisor<\/div><\/span><\/td>\n <\/tr>\n
2016-2018<\/td>\n –<\/td>\n
Bilateral Research and Mobility Project Canaletto under the scientific cooperation between the Polish Academy of Sciences (PAS) and the Consiglio Nazionale delle Ricerche (CNR; Italy), Zaprojektowanie i implementacja metod do integracji danych z \neksperyment\u00f3w analizy zmienno\u015bci liczby kopii (CNV) z ekspresj\u0105 gen\u00f3w (GE) oraz sieciami interakcji bia\u0142ko-bia\u0142ko (PPI) (Design and implementation of methods to integrate the analysis of Copy Number Variation (CNV) experiments with Gene Expression (GE) and Protein-Protein Interaction (PPI))<\/em> – principal investigator<\/strong><\/div><\/span><\/td>\n <\/tr>\n
2013-2015<\/td>\n –<\/td>\n
Grant No 2012\/05\/B\/ST6\/03026 (OPUS 3) from the National Science Centre (NCN, Poland), Informatyczne modele i metody w biologii kom\u00f3rkowej (Computational models and methods in cell biology)<\/em> – main executor<\/div><\/span><\/td>\n <\/tr>\n
2013-2015<\/td>\n –<\/td>\n
Grant No 2012\/06\/A\/ST6\/00384 (MAESTRO 3) from the National Science Centre (NCN, Poland), Automatyczne, wysokoprzepustowe modelowanie struktur przestrzennych RNA (Automated, high-throughput modeling of RNA three-dimensional structures)<\/em> – executor<\/div><\/span><\/td>\n <\/tr> \n
2010-2012<\/td>\n –<\/td>\n
POIG.02.02-30-009\/09, Rozw\u00f3j Infrastruktury Europejskiego Centrum Bioinformatyki i Genomiki (A development of the European Centre for Bioinformatics and Genomics infrastructure)<\/em> – administrative specialist<\/div><\/span><\/td>\n <\/tr>\n
2010-2012<\/td>\n –<\/td>\n
Bilateral Research and Mobility Project under the scientific cooperation between the Polish Academy of Sciences (PAS) and the Consiglio Nazionale delle Ricerche (CNR; Italy), Advanced bioinformatic algorithms in molecular biology (Zaawansowane algorytmy bioinformatyczne w biologii molekularnej)<\/em> – project participant<\/div><\/span><\/td>\n <\/tr>\n
2008-2011<\/td>\n –<\/td>\n
Grant No NN519314635 from the Ministry of Science and Higher Education (MNiSW, Poland), Pierwszorz\u0119dowa i przestrzenna struktura kwas\u00f3w nukleinowych i bia\u0142ek – analiza i algorytmy (Primary and tertiary structure of nucleic acids and proteins – analysis and algorithms)<\/em> – executor<\/div><\/span><\/td>\n <\/tr>\n
2005-2009<\/td>\n –<\/td>\n
EU FP6 project BIOPTRAIN (Grant agreement ID: 7597) from the European Commission, Bioinformatics Optimisation Training (Optymalizacja w bioinformatyce)<\/em> – project manager<\/div><\/span><\/td>\n <\/tr> \n
2005-2009<\/td>\n –<\/td>\n
EU FP6 project COMPUVAC (Grant agreement ID: 5246) from the European Commission, Rational design and standardized evaluation of novel genetic vaccines (Racjonalne projektowanie oraz standaryzowana ewaluacja nowych szczepionek genetycznych)<\/em> – executor<\/div><\/span><\/td>\n <\/tr>\n
2005-2008<\/td>\n –<\/td>\n
2004-2007<\/td>\n –<\/td>\n
Grant No 3T11F00227 from the State Committee for Scientific Research (KBN, Poland), Informatyczne aspekty analizy strukturalnej biomoleku\u0142 (Computational aspects of biomolecule structure analysis)<\/em> – executor<\/div><\/span><\/td>\n <\/tr>\n
2002-2004<\/td>\n –<\/td>\n
MPI-PUT ESR Training Project – ESR<\/div><\/span><\/td>\n <\/tr>\n
2001-2003<\/td>\n –<\/td>\n
Grant No 7T11F02621 from the State Committee for Scientific Research (KBN, Poland), Algorytmy wspomagaj\u0105ce analiz\u0119 liniowej i przestrzennej struktury kwas\u00f3w nukleinowych i bia\u0142ek (Algorithms for an analysis of primary and tertiary structure of proteins and nucleic acids)<\/em> – executor<\/div><\/span><\/td>\n <\/tr>\n<\/tbody><\/table>\n\n\n\n

<\/p>\n","protected":false},"excerpt":{"rendered":"

Research interests Research interests include algorithms (theory and applications), mathematical modeling, combinatorial problems in life sciences, RNA structure (modeling, analysis, dynamics). Bioinformatics projects RNApolis – a virtual laboratory of RNA bioinformatics under construction projects are marked with * @ GitHub some RNApolis projects available at GitHub GraphaFold* GNN to predict non-canonical base pairs in RNA […]<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-100","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/www.cs.put.poznan.pl\/mszachniuk\/site\/wp-json\/wp\/v2\/pages\/100","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.cs.put.poznan.pl\/mszachniuk\/site\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.cs.put.poznan.pl\/mszachniuk\/site\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.cs.put.poznan.pl\/mszachniuk\/site\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.cs.put.poznan.pl\/mszachniuk\/site\/wp-json\/wp\/v2\/comments?post=100"}],"version-history":[{"count":169,"href":"https:\/\/www.cs.put.poznan.pl\/mszachniuk\/site\/wp-json\/wp\/v2\/pages\/100\/revisions"}],"predecessor-version":[{"id":3111,"href":"https:\/\/www.cs.put.poznan.pl\/mszachniuk\/site\/wp-json\/wp\/v2\/pages\/100\/revisions\/3111"}],"wp:attachment":[{"href":"https:\/\/www.cs.put.poznan.pl\/mszachniuk\/site\/wp-json\/wp\/v2\/media?parent=100"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}