Preprints and ongoing work

  • W.Dyrka, M.Gąsior-Głogowska, M.Szefczyk: Searching for universal model of functional amyloid motifs using probabilistic context-free grammars (submitted).
  • R.Kowalski, M.Pyzik, W.Dyrka: Towards Improved Evolutionary Learning of Probabilistic Context-Free Grammars for Protein Sequences. In: Late-Breaking Abstracts of EVO* 2019, A.M.Mora, A.I.Esparcia-Alcázar (eds). arXiv 2019, 1907.12698:10-11.


  • W.Dyrka, V.Coustou, A.Daskalov, A.Lends, T.Bardin, M.Berbon, B.Kauffmann, C.Blanchard, B.Salin, A.Loquet, S.J.Saupe, Identification of NLR-associated amyloid signaling motifs in bacterial genomes, Journal of Molecular Biology 2020, 432(23):6005-6027
  • A.Daskalov, W.Dyrka, S.J.Saupe, NLR Function in Fungi as Revealed by the Study of Self/Non-self Recognition Systems. In: Benz J.P., Schipper K. (eds) Genetics and Biotechnology. The Mycota (A Comprehensive Treatise on Fungi as Experimental Systems for Basic and Applied Research), vol 2. Springer, Cham. 2020.
  • O.Unold, M.Gabor, W.Dyrka, Unsupervised Grammar Induction for Revealing the Internal Structure of Protein Sequence Motifs. In: Michalowski M., Moskovitch R. (eds) Artificial Intelligence in Medicine. AIME 2020. Lecture Notes in Computer Science (Lecture Notes in Artificial Intelligence) 12299:299-309, Springer, Cham. 2020.
  • W.Dyrka, M.Pyzik, F.Coste, H.Talibart, Estimating probabilistic context-free grammars for proteins using contact map constraints. PeerJ 2019, 7:e6559.
  • M.Pyzik, F.Coste, W.Dyrka. How to measure the topological quality of protein parse trees? In: The 14th International Conference on Grammatical Inference, O.Unold et al. (eds) Proceedings of Machine Learning Research 2019, 93:118–138.
  • M.Hatt, B.Laurent, A.Ouahabi, H.Fayad, S.Tan, L.Li, W.Lu, V.Jaouen, C.Tauber, J.Czakon, F.Drapejkowski, W.Dyrka, S.Camarasu-Pop, F.Cervenansky, P.Girard, T.Glatard, M.Kain, Y.Yao, C.Barillot, A.Kirov, D.Visvikis, The first MICCAI challenge on PET tumor segmentation. Medical Image Analysis 2018, 44:177–195.
  • B.M.Konopka*, M.Marciniak, W.Dyrka*, Quantiprot - a Python package for quantitative analysis of protein sequences. BMC Bioinformatics 2017, 18:339.
  • M.Lamacchia, W.Dyrka, A.Breton, S.J.Saupe, M.Paoletti, Overlapping Podospora anserina transcriptional responses to bacterial and fungal non self indicate a multilayered innate immune response. Frontiers in Microbiology 2016, 7:471.
  • W.Dyrka, M.Kurczyńska, B.M.Konopka, M.Kotulska, Fast assessment of structural models of ion channels based on their predicted current–voltage characteristics. Proteins 2016, 84:217–231.
  • A.Daskalov*, W.Dyrka*, S.J.Saupe, Theme and variations: evolutionary diversification of the HET-s functional amyloid motif, Scientific Reports 2015, 5:12494.
  • W.Dyrka, M.Lamacchia, P.Durrens, B.Kobe, A.Daskalov, M.Paoletti, D.J.Sherman, S.J.Saupe, Diversity and variability of NOD-like receptors in fungi, Genome Biology and Evolution 2014, 6:3137-3158.
  • W.Dyrka, J.-C.Nebel, M.Kotulska, Probabilistic grammatical model for helix-helix contact site classification, Algorithms for Molecular Biology 2013, 8:31.
  • W.Dyrka, M.M.Baruzel, M. Kotulska, Optimization of 3D Poisson-Nernst-Planck model for fast evaluation of diverse protein channels, Proteins 2013, 81:1802-22.
  • W.Dyrka, J.-C.Nebel, M.Kotulska, Towards 3D modeling of interacting TM helix pairs based on classification of helix pair sequence. In: Pattern Recognition in Bioinformatics, T.M.H. Dijkstra et al. (eds) Lecture Notes in Computer Science (Lecture Notes in Bioinformatics) 6282:62-73, Springer 2010.
  • M.Kotulska, W.Dyrka, P.Sadowski, Fluorescent methods in evaluation of nanopore conductivity - computational validation. In: Advanced electroporation techniques in biology and medicine, A.G.Pakhomov et al. (ed.) CRC Press 2010.
  • W.Dyrka, J.-C.Nebel, A Stochastic Context Free Grammar based Framework for Analysis of Protein Sequences, BMC Bioinformatics 2009, 10:323.
  • B.Konopka, W.Dyrka, J.-C.Nebel, M.Kotulska, Accuracy in predicting secondary structure of ionic channels. In: New challenges in computational collective intelligence. N.T.Nguyen et al. (ed). Studies in Computational Intelligence 244:315-326. Springer 2009.
  • W.Dyrka, A.Augousti, M.Kotulska, Ion flux through membrane channels – an enhanced algorithm for the Poisson-Nernst-Planck model, Journal of Computational Chemistry 2008, 29:1876-88.

* equal contributors



  • Witold Dyrka, Oprogramowanie wspomagające delineację guza na obrazie PET, Winter School 2017, BioNanopor / Students Science Club, Wroclaw University of Science and Technology, Szklarska Poręba, Poland, 7/01/2017
  • Witold Dyrka, Język(i) białek? – przesłanki, przyczynki i perspektywy, The Linguistic Engineering Group, Department of Artificial Intelligence, Institute of Computer Science, Polish Academy of Sciences, Warsaw, Poland, 22/02/2016
  • Witold Dyrka, A framework based on probabilistic context-free grammars and a genetic algorithm for analysis of protein sequences, Symbiose network, IRISA / Inria Rennes, France, 27/02/2014
  • Witold Dyrka, Structure prediction of a protein channel based on probabilistic formal grammars, Bioinformatics Graduate Students' Organization, George Mason University, Manassas, VA, United States, 20/07/2010
  • Witold Dyrka, Zastosowanie probabilistycznych gramatyk formalnych w modelowaniu interfejsów helisa-helisa w białkach kanałowych, Group of Computational Complexity and Algorithms, Institute of Computer Science, University of Wrocław, Poland, 19/11/2008


  • Witold Dyrka, Towards Improved Evolutionary Learning of Probabilistic Context-Free Grammars for Protein Sequences, Evostar 2019 Late-Breaking Abstracts, Lepzig, Germany, 24-26/04/2019
  • Witold Dyrka, Estimating probabilistic context-free grammars for proteins using contact map constraints, The 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2018), MetaBio2 workshop (re-scheduled to MABM 2018 workshop), Madrid, Spain, 3-6/12/2018
  • Mateusz Skrzypecki, Evaluation of residue-residue contact prediction in metamorphic proteins, XI Symposium of the Polish Bioinformatics Society (PTBi 2018), Wrocław, Poland, 5-7/09/2018
  • Mateusz Pyzik, How to measure the topological quality of protein parse trees?, 14th International Conference on Grammatical Inference (ICGI 2018), Wrocław, Poland, 5-7/09/2018
  • Witold Dyrka, Where the context-free grammar meets the contact map: a probabilistic model of protein sequences aware of contacts between amino acids, 26th Conference on Intelligent Systems for Molecular Biology (ISMB 2018), 3DSIG COSI track, Chicago, IL, United States, 6-10/07/2018
  • Witold Dyrka, In search of grammars for amyloid motifs, Wroclaw Biofilm Symposium, Wrocław, Poland, 10/10/2017
  • Witold Dyrka, How to Measure the Topological Quality of Protein Grammars?, 13th International Conference on Grammatical Inference (ICGI 2016), Delft, The Netherlands, 5-7/10/2016
  • Witold Dyrka, Deciphering the language of fungal pathogen recognition receptors, VIII Symposium of the Polish Bioinformatics Society (PTBi 2015), Lublin, Poland, 17-19/09/2015
  • Witold Dyrka, Metoda walidacji modeli strukturalnych kanału białkowego w oparciu o charakterystykę przepływu jonów, III Sympozjum “Współczesna myśl techniczna w naukach medycznych i biologicznych”, Wrocław, Poland, 25-26/05/2012
  • Witold Dyrka, Using functional characteristics for validation of predicted protein channel structures, 9th Workshop on Bioinformatics (PTBi 2011), Kraków, Poland, 30/09-2/10/2011
  • Witold Dyrka, Towards 3D modeling of interacting TM helix pairs based on classification of helix pair sequence, 8th Workshop on Bioinformatics (PTBi 2010), Ustroń, Poland, 1-3/10/2010
  • Witold Dyrka, Towards 3D modeling of interacting TM helix pairs based on classification of helix pair sequence, 5th IAPR International Conference on Pattern Recognition in Bioinformatics (PRIB 2010), Nijmegen, The Netherlands, 22-24/09/2010
  • Witold Dyrka, Modelowanie interakcji helis transmembranowych, XVI Krajowa Konferencja Biocybernetyki i Inżynierii Biomedycznej, Warsaw, Poland, 28/04/2010
wiki/publications.txt · Last modified: 2020/12/11 19:07 by wdyrka

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