wiki:publications

Publications

Peer-reviewed

  • 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. (ed). 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

Talks

Seminars

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

Conferences

  • 26th Conference on Intelligent Systems for Molecular Biology (ISMB 2018), 3DSIG COSI track: Where the context-free grammar meets the contact map: a probabilistic model of protein sequences aware of contacts between amino acids (Chicago, IL, United States, 6-10/07/2018)
  • Wroclaw Biofilm Symposium: In search of grammars for amyloid motifs (Wrocław, Poland, 10/10/2017)
  • 13th International Conference on Grammatical Inference (ICGI 2016): How to Measure the Topological Quality of Protein Grammars? (Delft, The Netherlands, 5-7/10/2016)
  • X Symposium of the Polish Bioinformatics Society (PTBi 2015): Deciphering the language of fungal pathogen recognition receptors (Lublin, 17-19/09/2015)
  • III Sympozjum “Współczesna myśl techniczna w naukach medycznych i biologicznych”: Metoda walidacji modeli strukturalnych kanału białkowego w oparciu o charakterystykę przepływu jonów (Wrocław, Poland, 25-26/05/2012)
  • 9th Workshop on Bioinformatics (PTBi 2011): Using functional characteristics for validation of predicted protein channel structures (Kraków, Poland, 30/09-2/10/2011)
  • 8th Workshop on Bioinformatics (PTBi 2010): Towards 3D modeling of interacting TM helix pairs based on classification of helix pair sequence (Ustroń, Poland, 1-3/10/2010)
  • 5th IAPR International Conference on Pattern Recognition in Bioinformatics (PRIB 2010): Towards 3D modeling of interacting TM helix pairs based on classification of helix pair sequence (Nijmegen, The Netherlands, 22-24/09/2010)
  • XVI Krajowa Konferencja Biocybernetyki i Inżynierii Biomedycznej: Modelowanie interakcji helis transmembranowych (Warsaw, Poland, 28/04/2010)
wiki/publications.txt · Last modified: 2018/07/17 19:01 by wdyrka

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