No-Regret Boosting. - Anna Gambin; Ewa Szczurek (ICANNGA (1), 2007)

Efficient Seeding Techniques for Protein Similarity Search. - Mikhail A. Roytberg; Anna Gambin; Laurent Noé; Slawomir Lasota 001; Eugenia Furletova; Ewa Szczurek; Gregory Kucherov (BIRD, 2008)

Classification of peptide mass fingerprint data by novel no-regret boosting method. - Anna Gambin; Ewa Szczurek; Janusz Dutkowski; Magda Bakun; Michal Dadlez (Comput. Biol. Medicine, 2009)

On Subset Seeds for Protein Alignment. - Mikhail A. Roytberg; Anna Gambin; Laurent Noé; Slawomir Lasota 001; Eugenia Furletova; Ewa Szczurek; Gregory Kucherov (IEEE ACM Trans. Comput. Biol. Bioinform., 2009)

Introducing Knowledge into Differential Expression Analysis. - Ewa Szczurek; Przemyslaw Biecek; Jerzy Tiuryn; Martin Vingron (J. Comput. Biol., 2010)

Deregulation upon DNA damage revealed by joint analysis of context-specific perturbation data. - Ewa Szczurek; Florian Markowetz; Irit Gat-Viks; Przemyslaw Biecek; Jerzy Tiuryn; Martin Vingron (BMC Bioinform., 2011)

Modeling signal transduction pathways and their transcriptional response. - Ewa Szczurek (2011)

Inferring the paths of somatic evolution in cancer. - Navodit Misra; Ewa Szczurek; Martin Vingron (Bioinform., 2014)

Modeling Mutual Exclusivity of Cancer Mutations. - Ewa Szczurek; Niko Beerenwinkel (PLoS Comput. Biol., 2014)

TiMEx: a waiting time model for mutually exclusive cancer alterations. - Simona Constantinescu; Ewa Szczurek; Pejman Mohammadi 001; Jörg Rahnenführer; Niko Beerenwinkel (Bioinform., 2016)

Linear effects models of signaling pathways from combinatorial perturbation data. - Ewa Szczurek; Niko Beerenwinkel (Bioinform., 2016)

Epistasis in genomic and survival data of cancer patients. - Dariusz Matlak; Ewa Szczurek (PLoS Comput. Biol., 2017)

Learning signaling networks from combinatorial perturbations by exploiting siRNA off-target effects. - Jerzy Tiuryn; Ewa Szczurek (Bioinform., 2019)

12 Grand Challenges in Single-Cell Data Science. - David Laehnemann; Johannes Köster; Ewa Szczurek; Davis J. McCarthy; Stephanie C. Hicks; Mark D. Robinson; Catalina A. Vallejos; Niko Beerenwinkel; Kieran R. Campbell; Ahmed Mahfouz; Luca Pinello; Pavel Skums; et al. (PeerJ Prepr., 2019)

Correction: Epistasis in genomic and survival data of cancer patients. - Dariusz Matlak; Ewa Szczurek (PLoS Comput. Biol., 2019)

A mathematical model of the metastatic bottleneck predicts patient outcome and response to cancer treatment. - Ewa Szczurek; Tyll Krüger; Barbara Klink; Niko Beerenwinkel (PLoS Comput. Biol., 2020)

A generative recommender system with GMM prior for cancer drug generation and sensitivity prediction. - Krzysztof Koras; Marcin Mozejko; Paulina Szymczak; Adam Izdebski; Eike Staub; Ewa Szczurek (MLCB, 2022)

A generative recommender system with GMM prior for cancer drug generation and sensitivity prediction. - Krzysztof Koras; Marcin Mozejko; Paulina Szymczak; Eike Staub; Ewa Szczurek (CoRR, 2022)

Artificial intelligence-driven antimicrobial peptide discovery. - Paulina Szymczak; Ewa Szczurek (CoRR, 2023)

De Novo Drug Design with Joint Transformers. - Adam Izdebski; Ewelina Weglarz-Tomczak; Ewa Szczurek; Jakub M. Tomczak (CoRR, 2023)

Factor Analysis with Correlated Topic Model for Multi-Modal Data. - Malgorzata Lazecka; Ewa Szczurek (AISTATS, 2025)

Unified Molecule Generation and Property Prediction. - Adam Izdebski; Jan Olszewski; Pankhil Gawade; Krzysztof Koras; Serra Korkmaz; Valentin Rauscher; Jakub M. Tomczak; Ewa Szczurek (CoRR, 2025)

Targeted AMP generation through controlled diffusion with efficient embeddings. - Diogo Soares; Leon Hetzel; Paulina Szymczak; Fabian J. Theis; Stephan Günnemann; Ewa Szczurek (CoRR, 2025)

ProSpero: Active Learning for Robust Protein Design Beyond Wild-Type Neighborhoods. - Michal Kmicikiewicz; Vincent Fortuin; Ewa Szczurek (CoRR, 2025)

Mamba Goes HoME: Hierarchical Soft Mixture-of-Experts for 3D Medical Image Segmentation. - Szymon Plotka; Maciej Chrabaszcz; Gizem Mert; Ewa Szczurek; Arkadiusz Sitek (CoRR, 2025)