Kaja Gutowska (Chmielewska) | Scientific Achievements



Articles

Gutowska K, Kogut D., Kardyńska M., Formanowicz P., Śmieja J., Puszyński K.: Petri nets and ODEs as complementary methods for comprehensive analysis on an example of the ATM–p53–NF-κB signaling pathways, Scientific Reports, 2022, 12(1), 1-13, https://doi.org/10.1038/s41598-022-04849-0.

Gutowska K, Formanowicz, D., Formanowicz, P.: Interrelations between Iron and Vitamin A—Studied Using Systems Approach, International Journal of Molecular Sciences, 2022, 23(3), 1189, https://doi.org/10.3390/ijms23031189.

Formanowicz D., Gutowska K., Szawulak B., Formanowicz P.: The crosstalk between SARS-CoV-2 infection and RAA system in essential hypertension - analyses using systems approach, International Journal of Molecular Science, 2021, 22(19), 10518, https://doi.org/10.3390/ijms221910518.

Villmann T., Kaden M., Bohnsack K. S., Weber M., Kudła M., Gutowska K., Błażewicz J.: Learning vector quantization as an interpretable classifier for the detection of SARS-CoV-2 types based on their RNA sequences, Neural Comput & Applic., 2021, 1-12, https://link.springer.com/article/10.1007%2Fs00521-021-06018-2.

Gutowski Ł., Gutowska K., Brożek, A., Nowicki, M., Formanowicz, D.: ABG Assistant—Towards an Understanding of Complex Acid-Base Disorders. Journal of Clinical Medicine, 2021, 10(7), 1516, https://doi.org/10.3390/jcm10071516 .

Kudła M., Gutowska K., Synak J., Weber M., Bohnsack K.S., Łukasiak P., Villmann T., Błażewicz J., Szachniuk M.: Virxicon: a lexicon of viral sequences, Bioinformatics, 2020, 36(22-23), 5507-5513, https://doi.org/10.1093/bioinformatics/btaa1066.

Villmann T., Kaden M., Bohnsack K. S., Weber M., Kudła M., Gutowska K., Błażewicz J.: Analysis of SARS-CoV-2 RNA-Sequences by Interpretable Machine Learning Models. BioRxiv, 2020, https://doi.org/10.1101/2020.05.15.097741.

Gutowski Ł., Gutowska K., Pioruńska-Stolzmann M., Formanowicz P., Formanowicz D.: Systems Approach to Study Associations between OxLDL and Abdominal Aortic Aneurysms. International Journal of Molecular Sciences, 2019, 20(16), 3909, https://doi.org/10.3390/ijms20163909.

Gutowska K., Formanowicz D., Formanowicz P.: Selected Aspects of Tobacco-Induced Prothrombotic State, Inflammation and Oxidative Stress: Modeled and Analyzed Using Petri Nets. Interdisciplinary Sciences: Computational Life Sciences, 2019, 11(3), 373-386, https://doi.org/10.1007/s12539-018-0310-7.

Formanowicz D., Gutowska K., Formanowicz P.: Theoretical Studies on the Engagement of Interleukin 18 in the Immuno-Inflammatory Processes Underlying Atherosclerosis. International Journal of Molecular Sciences, 2018, 19(11), 3476, https://doi.org/10.3390/ijms19113476.

Chmielewska K., Formanowicz D., Formanowicz P.: The effect of cigarette smoking on endothelial damage and atherosclerosis development – modeled and analyzed using Petri nets. Archives of Control Sciences, 2017, 27(2), 211-228, http://dx.doi.org/10.1515/acsc-2017-0013.



Chapters in a monograph

Gutowska K., Formanowicz D., Formanowicz P.: Systems Approach Based on Petri Nets as a Method for Modeling and Analysis of Complex Biological Systems Presented on the Example of Atherosclerosis Development Process. In Advanced, Contemporary Control, Springer, Cham, 2020, 579-586, https://link.springer.com/chapter/10.1007%2F978-3-030-50936-1_49.

Villmann T., Kaden M., Wąsik S., Kudła M., Gutowska K., Villmann A., Błażewicz J.: Searching for the Origins of Life – Detecting RNA Life Signatures Using Learning Vector Quantization. In: Advances in Self-Organizing Maps, Learning Vector Quantization, Clustering and Data Visualization: Proceedings of the 13th International Workshop, WSOM+ 2019, Barcelona, Spain, June 26-28, 2019. ed. Alfredo Vellido: Springer International Publishing, 2020, 324-333, https://link.springer.com/chapter/10.1007/978-3-030-19642-4_32.

Kogut D., Gutowska K., Poterała-Hejmo A., Śmieja J., Formanowicz D., Formanowicz P.: Petri nets and ODE as complementary tools in analysis of signaling pathways. In: Proceedings of 11th International Conference on Bioinformatics and Computational Biology. ed. Oliver Eulenstein, Hisham Al-Mubaid, Qin Ding - [Manchester], United Kingdom: EasyChair, 2019, 150-160, https://doi.org/10.29007/542h.

Gutowska K., Formanowicz P.: Algorytm przeszukiwania tabu dla problemu znajdowania podzbiorów kluczowych tranzycji w modelach biologicznych opartych na sieciach Petriego (eng. A tabu search algorithm for the problem of finding subsets of crucial transitions in Petri net based models of biological systems). [In]: Automatyzacja procesów dyskretnych. Teoria i zastosowania. Vol II. Eds.: Andrzeja Świerniaka i Jolanty Krystek, Wydawnictwo Politechniki Śląskiej, Gliwice, 2018, 67-74, http://kkapd.pl/new/index.php/pliki-do-pobrania/category/6-tom-ii-2018?download=132.

Chmielewska K., Formanowicz D., Formanowicz P.: Modelowanie i analiza uszkodzeń śródbłonka za pomocą sieci Petriego (eng. Modeling and analysis of endothelial damage using Petri nets). [In]: Automatyzacja procesów dyskretnych. Teoria i zastosowania. Vol II. Eds.: Andrzeja Świerniaka i Jolanty Krystek, Wydawnictwo Pracowni Komputerowej Jacka Skalmierskiego, Gliwice, 2016, 41-56, http://kkapd.pl/new/index.php/pliki-do-pobrania/category/3-tom-ii-2016?download=61.


Conferences and Seminars

2021

BIML: 5th Workshop BioInformatics meets Machine Learning, Mittweida, Germany (1-2.12.2021). Talk: "Systems approach to study relations between SARS-CoV-2 infection and RAA system in essential hypertension" (Gutowska K., Formanowicz D., Szawulak B., Formanowicz P.)

Seminar of the Institute of Computing Science, Institute of Computing Science, Poznan University of Technology, Poznań, Poland (26.10.2021). Talk: "Podejście systemowe do badania zależności między układem RAA a infekcją SARS-CoV-2" (Gutowska K., Formanowicz D., Szawulak B., Formanowicz P.)

PTBI 2021: Symposium of Polish Bioinformatics Society, online, Poland (15-17.09.2021). Talk: "Systems approach to study relations between SARS-CoV-2 infection and essential hypertension" (Gutowska K., Formanowicz D., Szawulak B., Formanowicz P.)

RNA goes viral, Poznań, Poland (01-02.07.2021). Talk: "Virxicon - a database for RNA and DNA virus sequences" (Gutowska K., Kudła M., Synak J., Weber M., Bohnsack K.S., Łukasiak P., Villmann T., Błażewicz J., Szachniuk M.)

ECCO: The 34th Conference of the European Chapter on Combinatorial Optimization, Madrid, Spain (10-11.06.2021). Talk: "Problems of searching for certain subsets of transitions as an essential stage in an analysis of models of complex biological systems" (Gutowska K., Formanowicz P.)

Seminar, Institute of Automatic Control, Silesian University of Technology, Gliwice, Poland (27.01.2021). Talk: "Sieci Petriego i ODE jako uzupełniające się metody analiz ścieżek sygnałowych - badania na przykładzie modelu opartego o szlaki ATM--p53--NF-κB" (Gutowska K., Kogut D., Kardyńska M., Formanowicz P., Śmieja J., Puszyński K.)

2020

ABLS: Applied Bioinformatics in Life Sciences, Leuven, Belgium (13-14.12.2020). Poster: "Comprehensive analysis of the mechanism of the DNA damage response system based on the ATM/p53/NF-κB pathways - Petri nets and ODEs as complementary methods" (Gutowska K., Kogut D., Kardyńska M., Formanowicz P., Puszyński K.)

2019

KIA: Seminar of Information Technology and Automation Committee of the Polish Academy of Sciences, Poznań, Poland (29.11.2019). Talk: "Wykorzystanie podejścia systemowego opartego o sieci Petriego do modelowania i analizy rozwoju tętniaka aorty brzusznej" (Gutowska K., Gutowski Ł., Pioruńska-Stolzmann M., Formanowicz P., Formanowicz D.)

GSN: The 23rd Gliwice Scientific Meetings, Gliwice, Poland (22-23.11.2019). Poster: "Petri nets vs ODE - competition or cooperation? Systems approach to modeling and analysis of the crosstalk between ATM, p53, and NF-κB" (Gutowska K., Kogut D., Kardyńska M., Formanowicz P., Puszyński K.)

Seminar, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland (14.10.2019). Talk: "Badanie wpływu oxLDL na powiększanie i pękanie tętniaka aorty brzusznej – podejście systemowe" (Gutowska K., Gutowski Ł., Pioruńska-Stolzmann M., Formanowicz P., Formanowicz D.)

ICOLE 2019: International Colloquium Lessach, Lessach, Austria (23-29.09.2019). Talk: "An extension of classical analysis of Petri net-based models on example of enlargement and rupture of abdominal aortic aneurysm" (Gutowska K., Gutowski Ł., Pioruńska-Stolzmann M., Formanowicz P., Formanowicz D.)

PTBI 2019: XII Symposium of Polish Bioinformatics Society, Kraków, Poland (19-21.09.2019). Poster and flash talk: "Studies on oxLDL influence on enlargement and rupture of abdominal aortic aneurysm through comparison of two Petri nets based models" (Gutowska K., Gutowski Ł., Pioruńska-Stolzmann M., Formanowicz P., Formanowicz D.)

Seminar, Institute of Automatic Control, Silesian University of Technology, Gliwice, Poland (08.05.2019). Talk: "Teoretyczne badania wpływu IL-18 na immunologiczne procesy zapalne leżące u podstaw miażdżycy - model i analiza oparte na sieciach Petriego" (Gutowska K., Formanowicz D., Formanowicz P.)

2018

KKAPD: XXI National Conference of Discrete Processes Automation, Zakopane, Poland (26-29.09.2018). Talk: "A tabu search algorithm for the problem of finding subsets of crucial transitions in Petri net based models of biological systems." (Gutowska K., Formanowicz P.)

PTBI 2018: XI Convention of the Polish Bioinformatics Society, Wrocław, Poland (05-07.09.2018). Talk: "Aortic aneurysm formation and progression analyzed using Petri net-based approach." (Chmielewska K., Formanowicz D., Formanowicz P.)

BIT18: Bioinformatics in Toruń, Toruń, Poland (28-30.06.2018). Poster: "A systems biology approach to study of different pathways of interleukin 18 synthesis." (Chmielewska K., Formanowicz D., Formanowicz P.)

ECCO XXXI - CO: Joint conference of the European Chapter on Combinatorial optimization (ECCO) and the International Symposium on Combinatorial optimization (CO), Fribourg, Switzerland (14-16.06.2018). Talk: "A heuristic for finding some sets of transitions of Petri net-based models of complex biological systems." (Chmielewska K., Formanowicz P.)

RECOMB: Computational Cancer Biology, Paris, France (19-20.04.2018). Poster: "A systems biology approach to study interactions between interleukin 18 and different types of macrophages." (Chmielewska K., Formanowicz D., Formanowicz P.)

2017

Seminar, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland (27.11.2017). Talk: "Zastosowanie sieci Petriego do modelowania i analizy wpływu interleukiny 18 na miażdżycę." (Chmielewska K., Formanowicz D., Formanowicz P.)

ICOLE 2017: International Colloquium Lessach, Lessach, Austria (01-07.10.2017). Talk: "Modeling and analysis of interleukin 18 influence on cardiovascular system using Petri nets." (Chmielewska K., Formanowicz D., Formanowicz P.)

PTBI 2017: X Convention of the Polish Bioinformatics Society, Uniejów, Poland (27-29.09.2017). Poster: "Interleukin 18 influence on the cardiovascular system modeled and analyzed using Petri net-based approach." (Chmielewska K., Formanowicz D., Formanowicz P.)

PIC17: 3rd Meeting of Polish Iron Club, Gdańsk, Poland (15-16.09.2017). Talk: "Interrelations between vitamin A and iron - modeled and analysed using Petri nets." (Chmielewska K., Formanowicz D., Formanowicz P.)

OR17: International Conference on Operations Research, Berlin, Germany (06-08.09.2017). Talk: "Atherosclerosis development as a complex biological phenomenon studied using Petri nets." (Chmielewska K., Formanowicz D., Formanowicz P.)

BIT17: Bioinformatics in Torun, Toruń, Poland (22-24.06.2017). Poster: "Modeling and analysis of disorders in prothrombotic states as reason of atherosclerosis development using Petri net-based approch." (Chmielewska K., Formanowicz D., Formanowicz P.)

2016

Seminar of the Laboratory of Algorithm Design and Programming Systems, Institute of Computing Science, Poznan University of Technology, Poland (22.11.2016). Talk: "Modeling of interactions of various factors in atherosclerosis." (Chmielewska K., Formanowicz D., Formanowicz P.)

PTBI 2016: IX Convention of the Polish Bioinformatics Society, Białystok, Poland (28-30.09.2016). Talk: "From tobacco smoke throught prothrombotic state to atherosclerosis - a systems approach." (Chmielewska K., Formanowicz D., Formanowicz P.)

KKAPD: XX National Conference of Discrete Processes Automation, Zakopane, Poland (21-24.09.2016). Talk: "Modeling and analysis of endothelial damage using Petri nets." (Chmielewska K., Formanowicz D., Formanowicz P.)

BIT16: Bioinformatics in Torun, Toruń, Poland (16-18.06.2016). Poster: "Selected aspects of the participation of tobacco smoke in the development of atherosclerosis modeled and analyzed using Petri nets." (Chmielewska K., Formanowicz D., Formanowicz P.)