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Ewa Szczurek

Number of publications: 42

2023

Paulina Szymczak, Ewa Szczurek , Artificial intelligence-driven antimicrobial peptide discovery, CURRENT OPINION IN STRUCTURAL BIOLOGY, 83 2023, p. 102733. See in PBN
Agnieszka Geras, Shadi Darvish Shafighi , Konrad Domżał, IWONA FILIPIUK, Łukasz Rączkowski, Paulina Szymczak, Hosein Toosi, LESZEK KACZMAREK, Łukasz Koperski, Jens Lagergren, Dominika Nowis, Ewa Szczurek , Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data, GENOME BIOLOGY, 24 (1) 2023, p. 120: 1-36. See in PBN
Magda Markowska, Magdalena A. Budzinska, Anna Coenen-Stass, Senbai Kang, Ewa Kizling, Krzysztof Kolmus, Krzysztof Koras, Eike Staub, Ewa Szczurek , Synthetic lethality prediction in DNA damage repair, chromatin remodeling and the cell cycle using multi-omics data from cell lines and patients., Scientific Reports, 13 (1) 2023, p. 1-16. See in PBN

2022

Krzysztof Koras, Marcin Możejko, Paulina Szymczak, Adam Izdebski, Eike Staub, Ewa Szczurek , A generative recommender system with GMM prior for cancer drug generation and sensitivity prediction, Machine Learning in Computational Biology 2022, Washington, the United States of America, 21 November 2022 - 22 November 2022. See in PBN
Magda Markowska, Tomasz Cąkała, Bogac Aybey, Dilafruz Juraeva, Johanna Mazur, Edith Ross, Eike Staub, Ewa Szczurek , Błażej Miasojedow , CONET: copy number event tree model of evolutionary tumor history for single-cell data, GENOME BIOLOGY, 23 (1) 2022. See in PBN
Krzysztof Gogolewski , Błażej Miasojedow , Małgorzata Sadkowska-Todys, Małgorzata Stępień, Urszula Demkow, Agnieszka Lech, Ewa Szczurek , Daniel Rabczenko, Magdalena Rosińska, Anna Gambin , Data-driven case fatality rate estimation for the primary lineage of SARS-CoV-2 in Poland, Methods, 203 2022, p. 584-593. See in PBN
Senbai Kang, Nico Borgsmüller, Monica Valecha, Jack Kuipers, Joao M. Alves, Sonia Prado-López, Débora Chantada, Niko Beerenwinkel, David Posada, Ewa Szczurek , SIEVE: joint inference of single-nucleotide variants and cell phylogeny from single-cell DNA sequencing data, GENOME BIOLOGY, 23 (1) 2022. See in PBN
Thomas Czypionka, Emil N. Iftekhar, Barbara Prainsack, Viola Priesemann, Simon Bauer, André Calero Valdez, Sarah Cuschieri, Enrico Glaab, Eva Grill, Jenny Krutzinna, Christos Lionis, Helena Machado, Carlos Martins, George N. Pavlakis, Matjaž Perc, Elena Petelos, Martyn Pickersgill, Alexander Skupin, Eva Schernhammer, Ewa Szczurek , Sotirios Tsiodras, Peter Willeit, Paul Wilmes, The benefits, costs and feasibility of a low incidence COVID-19 strategy, Lancet Regional Health-Europe, 13 2022, p. 100294: 1-7. See in PBN

2021

Emil Nafis Iftekhar, Viola Priesemann, Rudi Balling, Simon Bauer, Philippe Beutels, André Calero Valdez, Sarah Cuschieri, Thomas Czypionka, Uga Dumpis, Enrico Glaab, Eva Grill, Claudia Hanson, Pirta Hotulainen, Peter Klimek, Mirjam Kretzschmar, Tyll Krüger, Jenny Krutzinna, Nicola Low, Helena Machado, Carlos Martins, Martin McKee, Sebastian Bernd Mohr, Armin Nassehi, Matjaž Perc, Elena Petelos, Martyn Pickersgill, Barbara Prainsack, Joacim Rocklöv, Eva Schernhammer, Anthony Staines, Ewa Szczurek , Sotirios Tsiodras, Steven Van Gucht, Peter Willeit, A look into the future of the COVID-19 pandemic in Europe: an expert consultation, Lancet Regional Health-Europe, 8 2021, p. 100185:1-14. See in PBN
Johannes Bracher, Daniel Wolffram, Jannik Deuschel, Konstantin Görgen, Jakob Ketterer, Alexander Ullrich, Sam Abbott, Maria Vittoria Barbarossa, Dimitris Bertsimas, Sangeeta Bhatia, MARCIN BODYCH, Nikos I. Bosse, Jan Pablo Burgard, Lauren Castro, Geoffrey Fairchild, Jan Fuhrmann, Sebastian Funk, Krzysztof Gogolewski , Quanquan Gu, Stefan Heyder, Thomas Hotz, Yuri Kheifetz, Holger Kirsten, Ekaterina Krymova, Michael Lingzhi Li, Jan H. Meinke, Isaac J. Michaud, Karol Niedzielewski, Tomasz Ożański, Franciszek Rakowski, Markus Scholz, Saksham Soni, Ajitesh Srivastava, Jakub Zieliński, Difan Zou, Tilmann Gneiting, Melanie Schienle, Hamza Tazi Bouardi, Omar Skali Lami, Łukasz Górski , Magdalena Gruziel-Słomka, Artur Kaczorek, Antoni Moszyński, Jedrzej Nowosielski, Maciej Radwan, Marcin Semeniuk, Rafał Bartczuk, Jan Kisielewski, Przemysław Biecek , VIKTOR BEZBORODOV, Dave A. Osthus, Anna Gambin , Błażej Miasojedow , Ewa Szczurek , Daniel Rabczenko, Magdalena Rosińska, Barbara Pabjan, EWARYST RAFAJŁOWICZ, EWA SKUBALSKA-RAFAJŁOWICZ, WOJCIECH RAFAJŁOWICZ, Agata Migalska, Antoine Flahault, Elisa Manetti, Christine Choirat, Benjamín Béjar Haro, Gavin Lee, Guillaume Obozinski, Tao Sun, Dorina Thanou, Pan Xu, Jinghui Chen, Lingxiao Wang, Weitong Zhang, Viktor K. Prasanna, Frost Tianjian Xu, MAREK BAWIEC, TYLL KRÜGER, A pre-registered short-term forecasting study of COVID-19 in Germany and Poland during the second wave, Nature Communications, vol. 12 (art. 5173) 2021, p. 1-16. See in PBN
Viola Priesemann, Rudi Balling, Melanie M Brinkmann, Sandra Ciesek, Thomas Czypionka, Isabella Eckerle, Giulia Giordano, Claudia Hanson, Zdenek Hel, Pirta Hotulainen, Peter Klimek, Armin Nassehi, Andreas Peichl, Matjaz Perc, Elena Petelos, Barbara Prainsack, Ewa Szczurek , An action plan for pan-European defence against new SARS-CoV-2 variants., The Lancet, 397 (10273) 2021, p. 469-470. See in PBN
Szymon M. Kiełbasa, Julieta Sepúlveda-Yáñez, Ramin Monajemi, Davy Cats, Hailiang Mei, Roberta Menafra, Susan Kloet, Hendrik Veelken, Cornelis A.M. van Bergen, Ewa Szczurek , Shadi Darvish Shafighi , CACTUS: integrating clonal architecture with genomic clustering and transcriptome profiling of single tumor cells, Genome Medicine, 13 (1) 2021, p. 1-16. See in PBN
Viola Priesemann, Melanie M Brinkmann, Sandra Ciesek, Sarah Cuschieri, Thomas Czypionka, Giulia Giordano, Deepti Gurdasani, Claudia Hanson, Niel Hens, Emil Iftekhar, Michelle Kelly-Irving, Peter Klimek, Mirjam Kretzschmar, Andreas Peichl, Matjaž Perc, Francesco Sannino, Eva Schernhammer, Alexander Schmidt, Anthony Staines, Ewa Szczurek , Calling for pan-European commitment for rapid and sustained reduction in SARS-CoV-2 infections, The Lancet, 397 (10269) 2021, p. 92-93. See in PBN
Krzysztof Koras, Ewa Kizling, Dilafruz Juraeva, Eike Staub, Ewa Szczurek , Interpretable deep recommender system model for prediction of kinase inhibitor efficacy across cancer cell lines., Scientific Reports, 11 (1) 2021, p. 1-16. See in PBN
Kieran Elmes, Fabian Schmich, Ewa Szczurek , Jeremy Jenkins, Niko Beerenwinkel, Alex Gavryushkin, Learning epistatic gene interactions from perturbation screens, PLoS ONE, 16 (7) 2021, p. e0254491:1-22. See in PBN
Viola Priesemann, Rudi Balling, Simon Bauer, Philippe Beutels, André Calero Valdez, Sarah Cuschieri, Thomas Czypionka, Uga Dumpis, Enrico Glaab, Eva Grill, Pirta Hotulainen, Emil N Iftekhar, Jenny Krutzinna, Christos Lionis, Helena Machado, Carlos Martins, Martin McKee, George N Pavlakis, Matjaž Perc, Elena Petelos, Martyn Pickersgill, Barbara Prainsack, Joacim Rocklöv, Eva Schernhammer, Ewa Szczurek , Sotirios Tsiodras, Steven Van Gucht, Peter Willeit, Towards a European strategy to address the COVID-19 pandemic, The Lancet, 398 (10303) 2021, p. 838-839. See in PBN

2020

Ewa Szczurek , Tyll Krüger, Barbara Klink, Niko Beerenwinkel, A mathematical model of the metastatic bottleneck predicts patient outcome and response to cancer treatment, PLoS Computational Biology, 16 (10) 2020, p. e1008056. See in PBN
David Lähnemann, Johannes Köster, Ewa Szczurek , Davis J. McCarthy, Stephanie C. Hicks, Mark D. Robinson, Catalina A. Vallejos, Kieran R. Campbell, Niko Beerenwinkel, Ahmed Mahfouz, Luca Pinello, Pavel Skums, Alexandros Stamatakis, Camille Stephan-Otto Attolini, Samuel Aparicio, Jasmijn Baaijens, Marleen Balvert, Buys de Barbanson, Antonio Cappuccio, Giacomo Corleone, Bas E. Dutilh, Maria Florescu, Victor Guryev, Rens Holmer, Katharina Jahn, Thamar Jessurun Lobo, Emma M. Keizer, Indu Khatri, Szymon M. Kielbasa, Jan O. Korbel, Alexey M. Kozlov, Tzu-Hao Kuo, Boudewijn P.F. Lelieveldt, Ion I. Mandoiu, John C. Marioni, Tobias Marschall, Felix Mölder, Amir Niknejad, Lukasz Raczkowski, Marcel Reinders, Jeroen de Ridder, Antoine-Emmanuel Saliba, Antonios Somarakis, Oliver Stegle, Fabian J. Theis, Huan Yang, Alex Zelikovsky, Alice C. McHardy, Benjamin J. Raphael, Sohrab P. Shah, Alexander Schönhuth, Eleven grand challenges in single-cell data science, GENOME BIOLOGY, 21 (1) 2020. See in PBN
Krzysztof Koras, Dilafruz Juraeva, Julian Kreis, Johanna Mazur, Eike Staub, Eike Staub, Ewa Szczurek , Feature selection strategies for drug sensitivity prediction, Scientific Reports, 10 (1) 2020. See in PBN

2019

Łukasz Rączkowski, Marcin Możejko, Ewa Szczurek , Joanna Zambonelli, ARA: accurate, reliable and active histopathological image classification framework with Bayesian deep learning, Scientific Reports, 9 (1) 2019, p. 1-12. See in PBN
Ewa Szczurek , Jerzy Tiuryn , Learning signaling networks from combinatorial perturbations by exploiting siRNA off-target effects, Bioinformatics, 35 (14) 2019, p. i605-i614. See in PBN

2017

Dariusz Matlak, Ewa Szczurek , Epistasis in genomic and survival data of cancer patients, PLoS Computational Biology, 13 (7) 2017, p. 1-16. See in PBN
Kee Pang Soh, Ewa Szczurek , Thomas Sakoparnig, Niko Beerenwinkel, Predicting cancer type from tumour DNA signatures, Genome Medicine, 9 (104) 2017, p. 1-11. See in PBN

2016

Niko Beerenwinkel, Ewa Szczurek , Linear effects models of signaling pathways from combinatorial perturbation data., Bioinformatics, 2016. See in PBN

2015

Daniel Andritschke, Niko Beerenwinkel, Alain Casanova, Raquel Conde-Alvarez, Christoph Dehio, Sabrina Dilling, Simone Eicher, Mario Emmenlauer, Wolf-Dietrich Hardt, Saskia Kreibich, Shyan Huey Low, Simone Muntweiler, Pauli Rämö, Fabian Schmich, Ewa Szczurek , Christian von Mering, gespeR: a statistical model for deconvoluting off-target-confounded RNA interference screens, GENOME BIOLOGY, 2015. See in PBN
Niko Beerenwinkel, Simona Constantinescu, Pejman Mohammadi1, Jörg Rahnenführer, Ewa Szczurek , TiMEx: a waiting time model for mutually exclusive cancer alterations, Bioinformatics, 2015. See in PBN

2014

Navodit Misra, Ewa Szczurek , Martin Vingron, Inferring the paths of somatic evolution in cancer, Bioinformatics, 2014. See in PBN
Niko Beerenwinkel, Ewa Szczurek , Modeling mutual exclusivity of cancer mutations, PLoS Computational Biology, 2014. See in PBN
Cécile Arrieumerlou, Niko Beerenwinkel, Houchaima Ben-Tekaya, Peter Bühlmann, Bettina Cardel, Alain Casanova, Raquel Conde-Alvarez, Pascale Cossart, Gábor Csúcs, Christoph Dehio, Anna Drewek, Simone Eicher, Mario Emmenlauer, Urs Greber, Wolf-Dietrich Hardt, Ari Helenius, Christoph Kasper, Andreas Kaufmann, Saskia Kreibich, Peter Kunszt, Andreas Kühbacher, Shyan Huey Low, Jason Mercer, Daria Mudrak, Simone Muntwiler, Lucas Pelkmans, Javier Pizarro-Cerdá, Michael Podvinec, Eva Pujadas, Bernd Rinn, Vincent Rouilly, Pauli Rämö, Fabian Schmich, Juliane Siebourg-Polster, Berend Snijder, Michael Stebler, Gabriel Studer, Ewa Szczurek , Matthias Truttmann, Andreas Vonderheit, Artur Yakimovich, Christian von Mering, Simultaneous analysis of large-scale RNAi screens for pathogen entry, BMC Genomics, 2014. See in PBN

2013

Aleksander Jankowski , Ewa Szczurek , Ralf Jauch, Jerzy Tiuryn , Shyam Prabhakar, Comprehensive prediction in 78 human cell lines reveals rigidity and compactness of transcription factor dimers, Genome Research, 23 (8) 2013, p. 1307-1318. See in PBN
P. Meyer, H. Klein, S. M. Kielbasa, J. Knisley, N. Chawla, A. K. Rider, F. Mordelet, A. Tan, A. Hartemink, R. S. Pinapati, L. Pinello, S. Emrich, K. Engelen, K. Marchal, G. Stolovitzky, Y. Huang, M. S. Esfahani, R. Dreos, P. Bucher, M. J. Chen, C. Y. Chen, J. M. Knight, S. M. Sahraeian, M. T. Ferdig, Y. A. Tung, Y. S. Chen, G. C. Yuan, Ewa Szczurek , A. Mysickova, M. Vingron, M. B. Kursa, J. Yeung, E. Maier, Y. Saeys, D. Zeevi, P. Meysman, E. Sharon, A. S. Rodriguez, R. Norel, E. Segal, J. Bonnell, D. Knisley, M. Bhattacharjee, G. Siwo, M. J. Sillanpaa, Witold Rudnicki, Inferring gene expression from ribosomal promoter sequences, a crowdsourcing approach, Genome Research, 2013. See in PBN
Navodit Misra, Ewa Szczurek , Martin Vingron, Synthetic sickness or lethality points at candidate combination therapy targets in glioblastoma, International Journal of Cancer, 2013. See in PBN

2012

Przemysław Biecek , Ewa Szczurek , Jerzy Tiuryn , Martin Vingron, The R Package bgmm: Mixture Modeling with Uncertain Knowledge, Journal of Statistical Software, 2012. See in PBN

2011

Przemysław Biecek , Irit Gat-Viks, Florian Markowetz, Ewa Szczurek , Jerzy Tiuryn , Martin Vingron, Deregulation upon DNA damage revealed by joint analysis of context-specific perturbation data, BMC Bioinformatics, 2011. See in PBN

2010

Przemysław Biecek , Ewa Szczurek , Jerzy Tiuryn , Martin Vingron, Introducing Knowledge into Differential Expression Analysis, Journal of Computational Biology, 2010. See in PBN

2009

Anna Gambin , Janusz Dutkowski, Michał Dadlez, Ewa Szczurek , Magdalena Bakun, Classification of peptide mass fingerprint data by novel no-regret boosting method, Computers in Biology and Medicine, 2009. See in PBN
Irit Gat-Viks, Ewa Szczurek , Jerzy Tiuryn , Martin Vingron, Elucidating regulatory mechanisms downstream of a signaling pathway using informative experiments, Molecular Systems Biology, 2009. See in PBN
Eugenia Furletova, Anna Gambin , Gregory Kucherov, Sławomir Lasota , Laurent Noé, Mikhail A. Roytberg, Ewa Szczurek , On Subset Seeds for Protein Alignment, IEEE-ACM Transactions on Computational Biology and Bioinformatics, 2009. See in PBN

2008

Eugenia Furletova, Anna Gambin , Gregory Kucherov, Sławomir Lasota , Laurent Noé, Mikhail A. Roytberg, Ewa Szczurek , Efficient Seeding Techniques for Protein Similarity Search, 2008. See in PBN