| Current progress and open challenges for applying deep learning across the biosciences N Sapoval, A Aghazadeh, MG Nute, DA Antunes, A Balaji, R Baraniuk, ... Nature Communications 13 (1), 1728, 2022 | 267 | 2022 |
| Species Tree Inference Methods Intended to Deal with Incomplete Lineage Sorting Are Robust to the Presence of Paralogs Z Yan, ML Smith, P Du, MW Hahn, L Nakhleh Systematic Biology, 2022 | 72* | 2022 |
| Complexity of avian evolution revealed by family-level genomes J Stiller, S Feng, AA Chowdhury, I Rivas-González, DA Duchêne, Q Fang, ... Nature 629 (8013), 851-860, 2024 | 64 | 2024 |
| Practical aspects of phylogenetic network analysis using PhyloNet Z Cao, X Liu, HA Ogilvie, Z Yan, L Nakhleh BioRxiv 746362, 2019 | 40 | 2019 |
| Maximum parsimony inference of phylogenetic networks in the presence of polyploid complexes Z Yan, Z Cao, Y Liu, HA Ogilvie, L Nakhleh Systematic Biology 71 (3), 706-720, 2022 | 30 | 2022 |
| NestedBD: Bayesian inference of phylogenetic trees from single-cell copy number profiles under a birth-death model Y Liu, M Edrisi, Z Yan, H A Ogilvie, L Nakhleh Algorithms for Molecular Biology 19 (1), 18, 2024 | 3 | 2024 |
| “Correcting” gene trees to be more like species trees frequently increases topological error Z Yan, HA Ogilvie, L Nakhleh Genome Biology and Evolution 15 (6), evad094, 2023 | 3 | 2023 |
| Comparing Inference under the Multispecies Coalescent with and without Recombination Z Yan, HA Ogilvie, L Nakhleh Molecular Phylogenetics and Evolution 181, 107724, 2023 | 3 | 2023 |
| Species Tree Inference: A Guide to Methods and Applications PD Blischak, JM Brown, Z Cao, A Cloutier, K Cobb, AA DiGiacomo, ... Princeton University Press, 2023 | 2 | 2023 |
| Polyphest: fast polyploid phylogeny estimation Z Yan, Z Cao, L Nakhleh Bioinformatics 40 (Supplement_2), ii20-ii28, 2024 | | 2024 |