Publications

Holtgrefe, N. & Allman, E. & Baños, H. & van Iersel, L. & Moulton, V. & Rhodes, J. & Wicke, K. "Distinguishing Phylogenetic Level-2 Networks with Quartets and Inter-Taxon Quartet Distances" Bull Math Biol (2025) 87:168 https://doi.org/10.1007/s11538-025-01549-4

Allman, E. & Ané, C & Baños, H. & Rhodes, J. "Beyond Level-1: Identifiability of a Class of Galled Tree-Child Networks" Bull Math Biol (2025) 87, 166 https://doi.org/10.1007/s11538-025-01545-8

Allman, E. & Baños, H. & Rhodes, J. & Wicke, K. "NANUQ+: A divide-and-conquer approach to network estimation"  Algorithms Mol Biol (2025) 20, 14 https://doi.org/10.1186/s13015-025-00274-w

Williamson, K. & Eme, L. & Baños, H. & McCarthy, C. & Susko. E. & Kamikawa, R. & Orr, S. &  Muñoz-Gómez, S. & Bui, M. & Simpson, A. & Roger, A.  "A robustly rooted tree of eukaryotes reveals their excavate ancestry." Nature (2025). https://doi.org/10.1038/s41586-025-08709-5

Dinh, V. & Baños, H. "Misspecification Strikes: ASTRAL can Mislead in the Presence of Hybridization, even for Non-Anomalous Scenarios," Molecular Biology and Evolution (2025) https://doi.org/10.1093/molbev/msaf049

Rhodes, J. & Baños, H. & Xu, J. & Ané, C. "Identifying circular orders for blobs in phylogenetic networks," Advances in Applied Mathematics (2025) 163 part A https://doi.org/10.1016/j.aam.2024.102804

Allman, E. & Baños, H. & Mitchell, J. & Rhodes, J. "TINNiK: inference of the tree of blobs of a species network under the coalescent model,"  Algorithms Mol Biol (2024) 19, 23 https://doi.org/10.1186/s13015-024-00266-2

Pyron, A. & O’Connell, K. & Myers, E. & Beamer, D. & Baños, H. "Complex Hybridization in a Clade of Polytypic Salamanders (Plethodontidae: Desmognathus) Uncovered by Estimating Higher-Level Phylogenetic Networks", Systematic Biology (2024) https://doi.org/10.1093/sysbio/syae060

Baños, H. & Wong, T. & Daneau, J & Susko, E. & Minh, B. & Lanfear, R. & Brown, M. & Eme, L. & Roger, A. "GTRpmix: A linked general-time reversible model for profile mixture models," Molecular Biology and Evolution (2024) https://doi.org/10.1093/molbev/msae174

Allman, E & Baños, H. & Garrote-Lopez, M. & Rhodes, J. "Identifiability of Level-1 Species Networks from Gene Tree Quartets," Bull Math Biol 86, 110 (2024). https://doi.org/10.1007/s11538-024-01339-4

Ané, C. & Fogg, J. & Allman, E. & Baños, H. & Rhodes, J. "Anomalous networks under the multispecies coalescent: theory and prevalence" Journal of Mathematical Biology (2024) https://doi.org/10.1007/s00285-024-02050-7

Baños, H. & Susko, E. & Roger, A.J. "Is Over-parameterization a Problem for Profile Mixture Models?" Systematic Biology (2023) https://doi.org/10.1093/sysbio/syad063.

Allman, E. & Baños, H. & Mitchell J. & Rhodes, J. "The Tree of Blobs of a Species Network: Identifiability under the Coalescent,"  Journal of Mathematical Biology (2023) 86:10 https://doi.org/10.1007/s00285-022-01838-9

Allman, E. & Baños, H. & Rhodes, J. "Testing Multispecies Coalescent Simulators using Summary Statistics," IEEE/ACM Trans Comput Biol Bioinform (2022), doi: 10.1109/TCBB.2022.3177956

Allman, E. & Baños, H. & Rhodes, J. "Identifiability of species network topologies from genomic sequences using the logDet distance," Journal of Mathematical Biology (2022) 84:35 https://doi.org/10.1007/s00285-022-01734-2

Baños, H. & Bushek, N. & Davidson, R. & Gross, E. & Harris, P. & Krone, R. & Long, C. & Stweart, A. & Walker, R. "Phylogenetic trees," Journal of Software for Algebra and Geometry, Vol. 11 (2021), 1–7, DOI: 10.2140/jsag.2021.11.1

Rhodes J. & Baños, H. & Mitchell, J. & Allman, E. "MSCquartets 1.0: Quartet methods for species trees and networks under the multispecies coalescent model in R," Bioinformatics (2020), btaa868, https://doi.org/10.1093/bioinformatics/btaa868​​

Allman, E. & Baños, H. & Rhodes, J. "NANUQ: A method for inferring species networks from gene trees under the coalescent model," Algorithms for Molecular Biology volume 14, Article number: 24 (2019).  https://doi.org/10.1186/s13015-019-0159-2 

Baños, H. "Identifying Species Network Features from Gene Tree Quartets Under the Coalescent Model," Bull Math Biol (2019) 81: 494. https://doi.org/10.1007/s11538-018-0485-4

Allman, E. & Baños, H. & Evans, R. & Hosten, S.  & Kubjas, K. & Lemke, D. & Rhodes, J. & Zwiernik, P. "Maximum likelihood estimation of the Latent Class Model through model boundary decomposition," Journal of Algebraic Statistics. Vol 10 No 1 (2019): Issue in honor of S. E. Fienberg. https://ora.ox.ac.uk/objects/uuid:301ecb1e-2c67-458c-818f-6b689419e36c

Baños, H. & Bushek, N. & Davidson, R. & Gross, E. & Harris, P. & Krone, R. & Long, C. & Stweart, A. & Walker, R. "Dimensions of Group-Based Phylogenetic Mixtures," Bull Math Biol (2018) 81: 316. https://doi.org/10.1007/s11538-018-0489-0

Baños, H. & Oliveros, D. "A note on the intersection property for flat boxes and boxicity in ℝ^𝑑," Acta Math. Hungar. (2018) 155: 74. https://doi.org/10.1007/s10474-018-0817-8