Publications by Marta Casanellas

• M. Casanellas, J. Fernández-Sánchez, Phylogenetic invariants: straightforward from the general Markov to equivariant models, arxiv.org/abs/2310.18053

• M. Casanellas, R. Homs-Pons, A. Torres, A novel algebraic approach to time-reversible evolutionary models, SIAM Journal on Applied Mathematics (2024), 84 (4), 1845-1867. pdf Supplementary Material  

• M. Casanellas, Phylogenetic reconstruction based on algebra, in Cutting-edge Mathematics (RSME 2022),  H.Herrero, M.C.Navarro, H.Serrano, eds., Springer, 2024, pp 26-44, pdf

• M. Casanellas, M. Garrote-López, P. Zwiernik, Identifiability in robust estimation of tree structured models, Bernoulli journal (2024), 30(1), 1-21.

• M. Casanellas, J. Fernández-Sánchez, M. Garrote-López, M. Sabaté-Vidales, Designing weights for quartet-based methods when data is heterogeneous across lineages, Bulletin of Mathematical Biology (2023), vol. 85, 68.

• M. Casanellas, J. Fernández-Sánchez, J. Roca-Lacostena, The embedding problem for Markov matrices, Publicacions Matemàtiques (2023) 67(1), 411-445.

• M. Casanellas, J. Fernández-Sánchez, M. Garrote-López, SAQ: semi-algebraic quartet reconstruction method, IEEE/ Transactions on Computational Biology and Bioinformatics (2021), 18 (6), 2855-2861.  https://arxiv.org/abs/2011.13968

• M. Casanellas, J. Fernández-Sánchez, Rank conditions on phylogenetic networks, in "Extended Abstracts GEOMVAP 2019", Trends in Mathematics Springer-Birkhäuser (2021), vol. 15, 65-69 https://arxiv.org/abs/2004.12988

• M. Casanellas, J. Fernández-Sánchez, M. Garrote-López, Distance to the stochastic part of phylogenetic varieties, Journal of Symbolic Computation (2021), vol. 104, 563-682, https://arxiv.org/abs/1912.02138

• M. Casanellas, J. Fernández-Sánchez, J. Roca-Lacostena, An open set of 4x4 embeddable matrices whose principal logarithm is not a Markov generator, Linear and Multilinear Algebra (2020), 1-12  http://arxiv.org/abs/2005.00821

• M. Casanellas, J. Fernández-Sánchez, J. Roca-Lacostena, Embeddability and rate identifiability of Kimura 2-parameter matrices, Journal of Mathematical Biology (2020), 80, 995-1019, https://arxiv.org/abs/1902.08555

• M. Casanellas, S. Petrovic, C. Uhler, Algebraic Statistics in Practice: Applications to Networks, Annual Review of Statistics and its Applications (2020), vol. 7, 227-250.

• M. Casanellas, J. Rhodes, Algebraic Methods in Pylogenetics, preface of the special issue "Algebraic methods in phylogenetics" of Bulletin of Mathematical Biology (2019), 81 (2), 313-315, guest editors M. Casanellas and J. Rhodes, https://doi.org/10.1007/s11538-018-00551-3.  

• M. Ruffini, M. Casanellas, R. Gavaldà, A new method of moments for latent variable models, Machine Learning (2018), 107:1431–1455, https://doi.org/10.1007/s10994-018-5706-4, https://arxiv.org/abs/1612.03409

• C. Améndola, M. Casanellas, L.D. García-Puente, Tapas of algebraic statistics, Notices of the AMS (2018), 65 (8), 936-938.

• M. Casanellas, El modelo evolutivo de Kimura, un enlace entre el álgebra, la biología i la estadística, La Gaceta de la RSME (2018) vol. 21 (2), 241-257.

• M. Casanellas, J. Fernández-Sánchez, M. Garrote-López, The inertia of the symmetric approximation for low rank matrices, Linear and Multilinear algebra (2018), 66 (11), 2349-2353, https://doi.org/10.1080/03081087.2017.1398710 download

• M. Casanellas, J. Fernández-Sánchez, M. Michalek, Local equations for equivariant evolutionary models, Advances in Mathematics (2017) , 315, 285-323, arxiv:1512.07174. 

• M. Casanellas, M. Steel, Phylogenetic mixtures and linear invariants for equal input models, Journal of Mathematical Biology (2017), 74(5), 1107-1138, doi:10.1007/s00285-016-1055-8, arXiv:1602.04671

• M. Casanellas (and M. Steel) Phylogenetic Mixtures and Linear Invariants for Evolutionary Models with Non-uniform Stationary Distribution, Oberwolfach reports 20 (2017), 1233-1234.

• J. Fernández-Sánchez, M. Casanellas, Invariant versus classical approach when evolution is heterogeneous across sites and lineages, Systematic Biology (2016), 65 (2), 280-291, doi 10.1093/sysbio/syv086.

• M. Casanellas, J. Fernández-Sánchez, M. Michalek, Low degree equations for phylogenetic group-based models, Collectanea Mathematica 66 (2015), 203-225, doi: 10.1007/s13348-014-0120-0.
  

• E. Ibañez, M. Casanellas, EMtree for phylogenetic topology reconstruction on nonhomogeneous data, BMC Evolutionary Biology (2014) 14:132.

• A. Kedzierska, M. Casanellas, Empar: EM-based algorithm for parameter estimation of Markov models on trees,  arxiv:1207.1236

• M. Casanellas, A. Kedzierska, Generating Markov evolutionary matrices for a given branch length, Linear Algebra and its Applications (2013), 438, 2484-2499.

• A. Kedzierska, M.Casanellas, GenNon-h: Generating multiple sequence alignments on nonhomogeneous phylogenetic trees, BMC Bioinformatics (2012) 13:216, doi:10.1186/1471-2105-13-216.
  

• M. Casanellas, J. Fernández-Sánchez, A. Kedzierska, The space of phylogenetic mixtures for equivariant models,arXiv:1110.0920, Algorithms for Molecular Biology 7:33, 2012, doi:10.1186/1748-7188-7-33.

• M. Casanellas, Algebraic tools for evolutionary biology, International Association for Mathematical Phyisics - News Bulletin, April 2013, p.22-36.

• M. Casanellas, Algebraic tools for evolutionary biology, EMS Newsletter , December 2012, p.12-18.

• M. Casanellas, Técnicas algebraicas para la evolución de las especies. Gaceta de la RSME (2012), 15 (3).

• A. Kedzierska, M.Drton, R. Guigó, M. Casanellas, SPIn: model selection for phylogenetic mixtures via
  linear invariants, Molecular Biology and Evolution 29 (2012), 929-937.

• M. Casanellas, J.Fernández-Sánchez, Relevant phylogenetic invariants of evolutionary models, J. Mathématiques Pures et Appliquées 96 (2011),  207-229.

• M. Casanellas, J. Fernández-Sánchez, Geometry of  the Kimura 3-parameter model, Advances in Applied Mathematics 41 (2008), 265-292. 

• M. Casanellas, J. Fernández-Sánchez, Performance of a new invariants method on homogeneous and non-homogeneous quartet trees, Molecular Biology and Evolution, 24(1):288-293, 2007, Supplementary Material.

• M. Casanellas, S. Sullivant, The strand symmetric model, in "Algebraic statistics for computational biology", ed. L. Pachter and B. Sturmfels, Cambridge University Press 2005. 

• M. Casanellas, L. Garcia, S. Sullivant, Catalog of small trees, in "Algebraic statistics for computational biology", ed. L. Pachter and B. Sturmfels, Cambridge University Press 2005. 

For non-specialized readers:

• M. Casanellas, Las matemáticas de la evolución y la biodiversidad, unidad didáctica dentro de Las matemáticas del Planeta Tierra (2014), FECYT.

• M. Casanellas, J. Fernández-Sánchez, Reconstrucción filogenética usando geometría algebraica, Arbor CLXXXXVI 746 (2010), 1023-1033, http://hdl.handle.net/2117/16852 .

• M. Casanellas, Models algebraics en filogenètica, Butlletí de la Societat Catalana de Matemàtiques, 21 (2006), 213-228, pdf.

• M. Casanellas, Genètica i geometria algebraica, Butlletí de la FME 2005.

• M. Casanellas, R. Hartshorne, Stable Ulrich bundles, International J. Mathematics, 23 (2012) 1250083-1250133.

• M. Casanellas, R. Hartshorne, ACM bundles on cubic surfaces, Journal of the European Mathematical Society 13 (2011), 709-731.

• M. Casanellas, The minimal resolution conjecture for points on the cubic surface, Canadian Journal of Mathematics 61 (2009), 29-49.  

• L. Bazzotti, M. Casanellas,  Separators of points on algebraic surfaces, J.  Pure and Appl. Alg 207 (2006), 319-326. 

• M. Casanellas, E. Drozd, R. Hartshorne, Gorenstein liaison and ACM sheaves,  J. für die reine und angewandte Mathematik 584 (2005), 149-171.

• M. Casanellas, R. Hartshorne, Gorenstein biliaison and ACM sheaves, J. Algebra, 278 (2004), 314-341.                   

• N. Budur, M. Casanellas, E. Gorla, Hilbert functions of irreducible arithmetically Gorenstein schemes, J. Algebra, 272 (2004), 292-310. 

• M. Casanellas, Uniqueness of varieties of minimal degree containing a given scheme, Trans. Amer. Math. Soc., 356 (2004), 1875-1888.   

• M. Casanellas, Gorenstein liaison of 0-dimensional schemes, Manuscripta Mathematica, 111 (2003), 265-275.   

• M. Casanellas, R.M. Miró-Roig, On the Lazarsfeld-Rao property for Gorenstein liaison classes, J.  Pure and Appl. Alg.179 (2003), 7-12. 

• M. Casanellas, R.M. Miró-Roig, Gorenstein liaison and special linear configurations, Illinois J. Math. 46 (2002) 129-143.

• M. Casanellas, R.M. Miró-Roig, Gorenstein liaison of divisors on standard determinantal schemes and on rational normal scrolls, J.  Pure and Appl. Alg. 164 (2001), 325-343

• M. Casanellas, Glicci versus glicog, Rend. Sem. Mat. Torino 59 (2001), 127-129. 

• M. Casanellas, R.M. Miró-Roig, Gorenstein liaison of curves in P^4, J. Algebra 230 (2000), 656-664. 

• M. Casanellas, Characterization of non-connected Buchsbaum curves in P^n, Le Mathematiche, vol. LIV (1999), 187-195.