Paweł Górecki - publications

JarosĹaw Paszek and PaweĹ GĂłrecki, Efficient Algorithms for Genomic Duplication Models, (APBC 2017), to appear in IEEE TCBB, 2017
Agnieszka Mykowiecka, PaweĹ SzczÄsny and PaweĹ GĂłrecki, Inferring gene-species assignments in the presence of horizontal gene transfer, (APBC 2017), to appear in IEEE TCBB, 2017
Agnieszka Mykowiecka and PaweĹ GĂłrecki Bootstrapping Algorithms for Gene Duplication and Speciation Events (AlCoB 2016) LNCS 9702, 106-118, 2016 DOI
PaweĹ GĂłrecki, JarosĹaw Paszek, Agnieszka Mykowiecka Mean Values of Gene Duplication and Loss Cost Functions (ISBRA 2016) LNCS 9683, 189-199, 2016 DOI
PaweĹ GĂłrecki, JarosĹaw Paszek, Oliver Eulenstein Unconstrained Diameters for Deep Coalescence accepted to IEEE/ACM TCBB
JarosĹaw Paszek, PaweĹ GĂłrecki, Genomic Duplication Problems for Unrooted Gene Trees, (APBC 2016), BMC Genomics 17(Suppl. 1):15, DOI
Arkadiusz Betkier, PaweĹ SzczÄsny and PaweĹ GĂłrecki, Fast Algorithms for Inferring Gene-Species Associations, (ISBRA 2015) LNCS 9096, 36-47, 2015
PaweĹ GĂłrecki, Oliver Eulenstein, Gene Tree Diameter for Deep Coalescence, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 12 no 1, 155-165, 2015, DOI
PaweĹ GĂłrecki, Oliver Eulenstein Refining Discordant Gene Trees, BMC Bioinformatics 15(Suppl 13):S3, 2014 DOI
PaweĹ GĂłrecki, JarosĹaw Paszek, Oliver Eulenstein, Unconstrained Gene Tree Diameters for Deep Coalescence, ACM BCB 2014 (Best Paper Award!) DOI
PaweĹ GĂłrecki, JarosĹaw Paszek, Oliver Eulenstein, Duplication Cost Diameters, LNCS, ISBRA 2014, LNCS 8492, 212-223 DOI
PaweĹ GĂłrecki, Oliver Eulenstein, Maximizing Deep Coalescence Cost, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 11 no. 1, 231-242, 2014, DOI.
PaweĹ GĂłrecki, Oliver Eulenstein, DrML: probabilistic modeling of gene duplications, Journal of Computational Biology, 2014, 21(1): 89-98, DOI,
Wen-Chieh Chang, PaweĹ GĂłrecki, Oliver Eulenstein, Exact solutions for species tree inference from discordant gene trees, Journal of Bioinformatics and Computational Biology 11(5):1342005, 2013, DOI
PaweĹ GĂłrecki, Oliver Eulenstein, Algorithms for Unrooted Gene Trees with Polytomies, ISBRA 2013, PDF
PaweĹ GĂłrecki, Oliver Eulenstein, Jerzy Tiuryn, Unrooted Tree Reconciliation: A Unified Approach, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 10 no. 2, 522-536, 2013, DOI
Wen-Chieh Chang, Andre Wehe, PaweĹ GĂłrecki, Oliver Eulenstein, Exact Solutions for Classical Gene Tree Parsimony Problems, BICoB 2013, PDF
PaweĹ GĂłrecki and Oliver Eulenstein Deep Coalescence Reconciliation with Unrooted Gene Trees: Linear Time Algorithms, LNCS, COCOON 2012, Vol. 7434, 531-542
Dimitrios Floudas, Manfred Binder, Robert Riley, Kerrie Barry, Robert A. Blanchette, Bernard Henrissat, Angel T. MartĂnez, Robert Otillar, Joseph W. Spatafora, Jagjit S. Yadav, Andrea Aerts, Isabelle Benoit, Alex Boyd, Alexis Carlson, Alex Copeland, Pedro M. Coutinho, Ronald P. de Vries, Patricia Ferreira, Keisha Findley, Brian Foster, Jill Gaskell, Dylan Glotzer, PaweĹ GĂłrecki, Joseph Heitman, Cedar Hesse, Chiaki Hori, Kiyohiko Igarashi, Joel A. Jurgens, Nathan Kallen, Phil Kersten, Annegret Kohler, Ursula KĂźes, T. K. Arun Kumar, Alan Kuo, Kurt LaButti, Luis F. Larrondo, Erika Lindquist, Albee Ling, Vincent Lombard, Susan Lucas, Taina Lundell, Rachael Martin, David J. McLaughlin, Ingo Morgenstern, Emanuelle Morin, Claude Murat, Laszlo G. Nagy, Matt Nolan, Robin A. Ohm, Aleksandrina Patyshakuliyeva, Antonis Rokas, Francisco J. Ruiz-Duenas, Grzegorz Sabat, Asaf Salamov, Masahiro Samejima, Jeremy Schmutz, Jason C. Slot, Franz St. John, Jan Stenlid, Hui Sun, Sheng Sun, Khajamohiddin Syed, Adrian Tsang, Ad Wiebenga, Darcy Young, Antonio Pisabarro, Daniel C. Eastwood, Francis Martin, Dan Cullen, Igor V. Grigoriev, and David S. Hibbett The Paleozoic Origin of Enzymatic Lignin Decomposition Reconstructed from 31 Fungal Genomes Science, 29 June 2012: Vol. 336 no. 6089, 1715-1719 Supplementary PDF
PaweĹ GĂłrecki and Oliver Eulenstein, Algorithms: Simultaneous Error-Correction and Rooting for Gene Tree Reconciliation and the Gene Duplication Problem, BMC Bioinformatics 13(Suppl 10):S14, 2012
PaweĹ GĂłrecki, J. Gordon Burleigh and Oliver Eulenstein GTP supertrees from unrooted gene trees: linear time algorithms for NNI based local searches, (ISBRA 2012), LNCS 7292, 115-126, 2012
PaweĹ GĂłrecki and Oliver Eulenstein, A Robinson-Foulds measure to compare unrooted trees with rooted trees (ISBRA 2012), LNCS 7292, 102-114, 2012
PaweĹ GĂłrecki and Jerzy Tiuryn, Inferring evolutionary scenarios in the duplication, loss and horizontal gene transfer model, LNCS 7230, 83-105, 2012
PaweĹ GĂłrecki and Oliver Eulenstein, A linear time algorithm for error-corrected reconciliation of unrooted gene trees, 2011, LNBI, Vol.6674, 148-159 (ISBRA 2011) Supplementary data
PaweĹ GĂłrecki, Gordon J. Burleigh and Oliver Eulenstein, Maximum likelihood models and algorithms for gene tree evolution with duplications and losses BMC Bioinformatics 2011, 12(Suppl. 1):S15 PDF, Supplementary data and DrML (software).
PaweĹ GĂłrecki, H-trees: a model of evolutionary scenario with horizontal gene transfer, Fundamenta Informaticae, 103(1-4), 105-128, 2010
PaweĹ GĂłrecki and Jerzy Tiuryn, URec: a system for unrooted reconciliation, Bioinformatics 2007 23(4):511-512 Software (URec) and data
PaweĹ GĂłrecki and Jerzy Tiuryn, Inferring phylogeny from whole genomes, Bioinformatics 2007 23: e116-e122 (Proc. of ECCB 2006)
PaweĹ GĂłrecki and Jerzy Tiuryn, DLS-trees: a model of evolutionary scenarios, Theoretical Computer Science, Vol. 359, 2006, Pages 378-399
PaweĹ GĂłrecki, Detection of horizontal gene transfer, PhD thesis, Warsaw, January 2006
PaweĹ GĂłrecki and Jerzy Tiuryn, On the structure of reconciliations, 2005, LNCS, vol. 3388, pg. 42-54, (Proceedings of RCG 2004)
PaweĹ GĂłrecki, Reconciliation problems for duplication, loss and horizontal gene transfer, Proceedings of the Eighth Annual International Conference on Research in Computational Molecular Biology, RECOMB 2004, 2004, San Diego, USA
PaweĹ GĂłrecki, Single step reconciliation algorithm for duplication, loss and horizontal gene transfer model, Proceedings of the European Conference on Computational Biology, ECCB 2003, Sept. 27-30, 2003, Paris, France

Posters

Paweł Górecki, Oliver Eulenstein and Jerzy Tiuryn, Evolutionary costs in gene-species reconciliation, MCEB'2012, France (poster session)
Ilka M. Axmann, Paweł Górecki and Szymon M.Kiełbasa, Following the Evolution of Regulatory Elements in Marine Cyanobacteria, IBSB 2007, Tokyo, Japan (poster session)
Paweł Górecki and Jerzy Tiuryn, Reconciling gene and species evolution in the presence of horizontal gene transfer, ECCB 2005, Madrid (poster session)
Paweł Górecki, Maximum likelihood estimation for duplication-loss model, Currents in Computational Molecular Biology 2003, RECOMB 2003, Berlin (poster session)

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Last update 11/2014