Publications

Paweł Górecki

Number of publications: 66

2024

• Sanket Wagle, Alexey Markin, Paweł Górecki , Tavis K. Anderson, Oliver Eulenstein, Asymmetric Cluster-Based Measures for Comparative Phylogenetics, Journal of Computational Biology, 31 (4) 2024, p. 312-327. See in PBN
• Jerzy Tiuryn , Natalia Rutecka, Paweł Górecki , Phylogenetic network-assisted rooting of unrooted gene trees, Journal of Combinatorial Optimization, 47 (5) 2024, p. 1-27. See in PBN
• Paweł Górecki , Natalia Rutecka, Agnieszka Mykowiecka, Jarosław Paszek , Unifying duplication episode clustering and gene-species mapping inference, Algorithms for Molecular Biology, 19 (1) 2024, p. 1-20. See in PBN

2023

• Jelle J Goeman, Paweł Górecki , Ramin Monajemi, Xu Chen, Thomas E Nichols, Wouter Weeda, Cluster extent inference revisited: quantification and localisation of brain activity, JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY, 85 (4) 2023, p. 1128-1153. See in PBN
• Paweł Górecki , Natalia Rutecka, Agnieszka Mykowiecka, Jarosław Paszek , Simultaneous Reconstruction of Duplication Episodes and Gene-Species Mappings, Workshop on Algorithms in Bioinformatics 2023, Houston, the United States of America, 4 September 2023 - 6 September 2023. See in PBN

2022

• Marcin Wawerka, Dawid Dąbkowski, Natalia Rutecka, Agnieszka Mykowiecka, Paweł Górecki , Embedding gene trees into phylogenetic networks by conflict resolution algorithms, Algorithms for Molecular Biology, 17 (1) 2022, p. 11: 1-23. See in PBN
• Jerzy Tiuryn , Natalia Rutecka, Paweł Górecki , Rooting Gene Trees via Phylogenetic Networks, Lecture Notes in Computer Science, The 28th International Computing and Combinatorics Conference, Shenzen, China, 22 October 2022 - 24 October 2022, 13595 2022. See in PBN
• Alvin Chon, Paweł Górecki , Oliver Eulenstein, Xiaoqiu Huang, Ali Jannesari, Scalable and Extensible Robinson-Foulds for Comparative Phylogenetics, IEEE International Parallel and Distributed Processing Symposium Workshops, Lyon, France, 30 May 2022 - 3 June 2022. See in PBN

2021

• Marcin Wawerka, Dawid Dąbkowski, Natalia Rutecka, Agnieszka Mykowiecka, Paweł Górecki , Conflict Resolution Algorithms for Deep Coalescence Phylogenetic Networks, 21st International Workshop on Algorithms in Bioinformatics, Virtual, the United States of America, 2 August 2021 - 4 October 2021. See in PBN
• Jarosław Paszek , Oliver Eulenstein, Paweł Górecki , Novel genomic duplication models through integer linear programming, 12th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, Virtual on-line, the United States of America, 1 August 2021 - 4 August 2021. See in PBN
• Jarosław Paszek , Alexey Markin, Oliver Eulenstein, Paweł Górecki , Taming the Duplication-Loss-Coalescence Model with Integer Linear Programming, Journal of Computational Biology, 28 (8) 2021, p. 758-773. See in PBN
• Jerzy Tiuryn , Paweł Górecki , Oliver Eulenstein, The Unconstrained Diameters of the Duplication-Loss Cost and the Loss Cost, IEEE-ACM Transactions on Computational Biology and Bioinformatics, 18 (6) 2021, p. 2125-2135. See in PBN

2020

• Paweł Górecki , Alexey Markin, Oliver Eulenstein, Exact median-tree inference for unrooted reconciliation costs, BMC Evolutionary Biology, 20 (S1) 2020, p. 136: 1-15. See in PBN
• Jarosław Paszek , Jerzy Tiuryn , Paweł Górecki , Minimizing genomic duplication episodes, Computational Biology and Chemistry, 89 2020, p. 107260. See in PBN

2019

• P. Tabaszewski, Paweł Górecki , Alexey Markin, Tavis Anderson, Oliver Eulenstein, Consensus of all Solutions for Intractable Phylogenetic Tree Inference, IEEE-ACM Transactions on Computational Biology and Bioinformatics, 18 (1) 2019, p. 149-161. See in PBN
• Agnieszka Mykowiecka, Paweł Górecki , Credibility of Evolutionary Events in Gene Trees, IEEE-ACM Transactions on Computational Biology and Bioinformatics, 16 (3) 2019, p. 713-726. See in PBN
• Paweł Górecki , Alexey Markin, Oliver Eulenstein, Feasibility Algorithms for the Duplication-Loss Cost, 25th International Computing and Combinatorics Conference, Xian, China, 29 July 2019 - 31 July 2019. See in PBN
• Cornelis A.M. van Bergen, Marvyn T. Koning, Edwin Quinten, Agnieszka Mykowiecka, Julieta Sepulveda, Ramin Monajemi, Ruben A.L. De Groen, Joost Vermaat, Susan L. Kloet, Szymon M. Kielbasa, Marcelo A. Navarrete, Paweł Górecki , Hendrik Veelken, High-Throughput BCR Sequencing and Single-Cell Transcriptomics Reveal Distinct Transcriptional Profiles Associated with Subclonal Evolution of Follicular Lymphoma, Blood, 134 (Supplement_1) 2019, p. 298-298. See in PBN
• Paweł Górecki , Agnieszka Mykowiecka, Jarosław Paszek , Oliver Eulenstein, Mathematical properties of the gene duplication cost, Discrete Applied Mathematics, 258 2019, p. 114-122. See in PBN

2018

• Paweł Górecki , Oliver Eulenstein, Bijective Diameters of Gene Tree Parsimony Costs, IEEE-ACM Transactions on Computational Biology and Bioinformatics, 15 (5) 2018, p. 1723-1727. See in PBN
• Paweł Górecki , Alexey Markin, Oliver Eulenstein, Cophenetic Distances: A Near-Linear Time Algorithmic Framework, 24th International Computing and Combinatorics Conference, Qingdao, China, 2 July 2018 - 4 July 2018. See in PBN
• Paweł Górecki , Jarosław Paszek , Efficient algorithms for genomic duplication models, IEEE-ACM Transactions on Computational Biology and Bioinformatics, 15 (5) 2018, p. 1515-1524. See in PBN
• Paweł Górecki , Jarosław Paszek , Inferring duplication episodes from unrooted gene trees, BMC Genomics, 19 (5) 2018, p. 71-95. See in PBN
• Paweł Górecki , Agnieszka Mykowiecka, Paweł Szczęsny, Inferring gene-species assignments in the presence of horizontal gene transfer, IEEE-ACM Transactions on Computational Biology and Bioinformatics, 2018. See in PBN
• Agnieszka Mykowiecka, Paweł Górecki , Anna Muszewska, Inferring time-consistent and well-supported horizontal gene transfers., IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Madryt, Spain, 2 December 2018 - 5 December 2018. See in PBN
• Michał Ciach, Anna Muszewska, Paweł Górecki , Locus-aware decomposition of gene trees with respect to polytomous species trees., Algorithms for Molecular Biology, 13 2018, p. 11. See in PBN
• Dawid Dąbkowski, Paweł Górecki , Minimising the Deep Coalescence, International Conference on Bioinformatics and Computational Biology, Las Vegas, the United States of America, 19 March 2018 - 21 March 2018. See in PBN
• Dawid Dąbkowski, Paweł Tabaszewski, Paweł Górecki , Minimizing the deep coalescence cost, Journal of Bioinformatics and Computational Biology, 16 (5) 2018, p. 1840021. See in PBN
• Oliver Eulenstein, Paweł Górecki , Paweł Tabaszewski, Phylogenetic Consensus for Exact Median Trees, The 9th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, Washington, D.C, the United States of America, 29 August 2018 - 1 September 2018. See in PBN

2017

• Michał Aleksander Ciach, Paweł Górecki , Anna Muszewska, Detecting locus acquisition events in gene trees., Leibniz International Proceedings in Informatics, LIPIcs, 17th International Workshop on Algoritms in Bioinformatics WABI , Boston, the United States of America, 20 August 2017 - 22 August 2017, 88 (brak) 2017, p. brak. See in PBN
• Paweł Górecki , Jarosław Paszek , New Algorithms for the Genomic Duplication Problem, Lecture Notes in Computer Science, RECOMB International Workshop on Comparative Genomics, Barcelona, Spain, 10562 2017, p. 101-115. See in PBN
• Paweł Górecki , Alexey Markin, Agnieszka Mykowiecka, Jarosław Paszek , Oliver Eulenstein, Phylogenetic Tree Reconciliation: Mean Values for Fixed Gene Trees, 13th International Symposium on Bioinformatics Research and Applications, Honolulu, the United States of America, 30 May 2017 - 2 June 2017. See in PBN
• Paweł Górecki , Jarosław Paszek , Oliver Eulenstein, Unconstrained Diameters for Deep Coalescence, IEEE-ACM Transactions on Computational Biology and Bioinformatics, 14 (5) 2017, p. 1002-1012. See in PBN

2016

• Paweł Górecki , Agnieszka Mykowiecka, Bootstrapping Algorithms for Gene Duplication and Speciation Events, Lecture Notes in Computer Science, Algorithms for Computational Biology, Trujillo, Spain, 21 June 2016 - 22 June 2016. See in PBN
• Paweł Górecki , Jarosław Paszek , Genomic duplication problems for unrooted gene trees, BMC Genomics, 2016. See in PBN
• Paweł Górecki , Jarosław Paszek , Agnieszka Mykowiecka, Mean Values of Gene Duplication and Loss Cost Functions, Lecture Notes in Computer Science, International Symposium on Bioinformatics Research and Applications, 5 June 2016 - 8 June 2016. See in PBN

2015

• Arkadiusz Betkier, Paweł Górecki , Paweł Szczęsny, Fast Algorithms for Inferring Gene-Species Associations, Lecture Notes in Computer Science, International Symposium on Bioinformatics Research and Applications, Norfolk, the United States of America, 7 June 2015 - 10 June 2015. See in PBN
• Oliver Eulenstein, Paweł Górecki , Gene Tree Diameter for Deep Coalescence, IEEE-ACM Transactions on Computational Biology and Bioinformatics, 2015. See in PBN

2014

• Oliver Eulenstein, Paweł Górecki , DrML: Probabilistic Modeling of Gene Duplications, Journal of Computational Biology, 2014. See in PBN
• Paweł Górecki , Jarosław Paszek , Eulenstein Oliver, Duplication Cost Diameters, Lecture Notes in Computer Science, International Symposium on Bioinformatics Research and Applications, China, 2014. See in PBN
• Oliver Eulenstein, Paweł Górecki , Maximizing Deep Coalescence Cost, IEEE-ACM Transactions on Computational Biology and Bioinformatics, 2014. See in PBN
• Oliver Eulenstein, Paweł Górecki , Refining Discordant Gene Trees, BMC Bioinformatics, 2014. See in PBN
• Paweł Górecki , Jarosław Paszek , Oliver Eulenstein, Unconstrained Gene Tree Diameters for Deep Coalescence, ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, the United States of America, 2014. See in PBN

2013

• Oliver Eulentsein, Paweł Górecki , Algorithms for Unrooted Gene Trees with Polytomies, 2013. See in PBN
• Wen-Chieh Chang, Ande Wehe, Paweł Górecki , Oliver Eulenstein, Exact Solutions for Classical Gene Tree Parsimony Problems, 2013. See in PBN
• Oliver Eulenstein, Paweł Górecki , Chang Wen-Chien, Exact Solutions for Species Tree Inference from Discordant Gene Trees, Journal of Bioinformatics and Computational Biology, 2013. See in PBN
• Oliver Eulenstein, Paweł Górecki , Jerzy Tiuryn , Unrooted Tree Reconciliation: A Unified Approach, IEEE-ACM Transactions on Computational Biology and Bioinformatics, 2013. See in PBN

2012

• Oliver Eulenstein, Paweł Górecki , A Robinson-Foulds Measure to Compare Unrooted Trees with Rooted Trees, Lecture Notes in Computer Science, 2012. See in PBN
• Oliver Eulenstein, Paweł Górecki , Algorithms: Simultaneous Error-Correction and Rooting for Gene Tree Reconciliation and the Gene Duplication Problem, BMC Bioinformatics, 2012. See in PBN
• Oliver Eulenstein, Paweł Górecki , Deep Coalescence Reconciliation with Unrooted Gene Trees: Linear Time Algorithms, Lecture Notes in Computer Science, 2012. See in PBN
• Gordon J. Burleigh, Oliver Eulenstein, Paweł Górecki , GTP Supertrees from Unrooted Gene Trees: Linear Time Algorithms for NNI Based Local Searches, Lecture Notes in Computer Science, 2012. See in PBN
• Paweł Górecki , Jerzy Tiuryn , Inferring Evolutionary Scenarios in the Duplication, Loss and Horizontal Gene Transfer Model, Lecture Notes in Computer Science, 2012. See in PBN
• Andrea Aerts, Kerrie Barry, Isabelle Benoit, Manfred Binder, Robert A. Blanchette, Alex Boyd, Alexis Carlson, Alex Copeland, Pedro M. Coutinho, Dan Cullen, Daniel C. Eastwood, Patricia Ferreira, Keisha Findley, Dimitrios Floudas, Brian Foster, Jill Gaskell, Dylan Glotzer, Igor V. Grigoriev, Paweł Górecki , Joseph Heitman, Bernard Henrissat, Cedar Hesse, David S. Hibbett, Chiaki Hori, Kiyohiko Igarashi, Joel A. Jurgens, Nathan Kallen, Phil Kersten, Annegret Kohler, T. K. Arun Kumar, Alan Kuo, Ursula Kües, Kurt LaButti, Luis F. Larrondo, Erika Lindquist, Albee Ling, Vincent Lombard, Susan Lucas, Taina Lundell, Francis Martin, Rachael Martin, Angel T. Martínez, David J. McLaughlin, Ingo Morgenstern, Emanuelle Morin, Claude Murat, Laszlo G. Nagy, Matt Nolan, Robin A. Ohm, Robert Otillar, Aleksandrina Patyshakuliyeva, Antonio Pisabarro, Robert Riley, Antonis Rokas, Francisco J. Ruiz-Dueñas, Grzegorz Sabat, Asaf Salamov, Masahiro Samejima, Jeremy Schmutz, Jason C. Slot, Joseph W. Spatafora, Franz St. John, Jan Stenlid, Hui Sun, Sheng Sun, Khajamohiddin Syed, Adrian Tsang, Ad Wiebenga, Jagjit S. Yadav, Darcy Young, Ronald P. de Vries, The Paleozoic Origin of Enzymatic Lignin Decomposition Reconstructed from 31 Fungal Genomes, Science, 2012. See in PBN

2011

• Oliver Eulenstein, Paweł Górecki , A linear time algorithm for error-corrected reconciliation of unrooted gene trees, Lecture Notes in Computer Science, 2011. See in PBN
• Gordon Burleigh, Oliver Eulenstein, Paweł Górecki , Maximum likelihood models and algorithms for gene tree evolution with duplications and losses, BMC Bioinformatics, 2011. See in PBN

2010

• Paweł Górecki , H-trees: a Model of Evolutionary Scenarios with Horizontal Gene Transfer, Fundamenta Informaticae, 2010. See in PBN

2007

• Paweł Górecki , Jerzy Tiuryn , Inferring phylogeny from whole genomes, Bioinformatics, 2007. See in PBN
• Paweł Górecki , Jerzy Tiuryn , URec: a system for unrooted reconciliation, Bioinformatics, 2007. See in PBN

2006

• Paweł Górecki , Jerzy Tiuryn , DLS-trees: a model of evolutionary scenarios, Theoretical Computer Science, 2006. See in PBN

2004

• Paweł Górecki , Jerzy Tiuryn , On the structure of reconciliations, Lecture Notes in Computer Science, 2004. See in PBN
• Paweł Górecki , Reconciliation problems for duplication, loss and horizontal gene transfer, 2004. See in PBN

2003

• Paweł Górecki , Maximum likelihood estimation for duplication, loss model, 2003. See in PBN
• Paweł Górecki , Single step reconciliation algorihm for duplication, loss and horizontal gene transfer model, 2003. See in PBN

Others

• Javad Ansarifar, Alexey Markin, Paweł Górecki , Oliver Eulenstein, Integer Linear Programming Formulation for the Unified Duplication-Loss-Coalescence Model, Bioinformatics Research and Applications: 16th International Symposium, ISBRA 2020, Moscow, Russia, December 1–4, 2020, Proceedings, , p. 229-242. See in PBN
• Jarosław Paszek , Paweł Górecki , New Algorithms for the Genomic Duplication Problem, Comparative Genomics: 15th International Workshop, RECOMB CG 2017, Barcelona, Spain, October 4-6, 2017, Proceedings, , p. 101-115. See in PBN
• Sanket Wagle, Alexey Markin, Paweł Górecki , Tavis Anderson, Oliver Eulenstein, The Asymmetric Cluster Affinity Cost, Comparative Genomics: 20th International Conference, RECOMB-CG 2023, Istanbul, Turkey, April 14–15, 2023, Proceedings, , p. 131-145. See in PBN