Huw A. Ogilvie

发表

Practical Aspects of Phylogenetic Network Analysis Using PhyloNet

Xinhao Liu, Zhi Yan, Zhen Cao, 2019, bioRxiv.

Unifying Gene Duplication, Loss, and Coalescence on Phylogenetic Networks

Peng Du, Luay Nakhleh, Huw A. Ogilvie, 2019, ISBRA.

A Divide-and-Conquer Method for Scalable Phylogenetic Network Inference from Multi-locus Data

Xinhao Liu, Jiafan Zhu, Luay Nakhleh, 2019 .

Practical Speedup of Bayesian Inference of Species Phylogenies by Restricting the Space of Gene Trees

Luay Nakhleh, Huw A. Ogilvie, Yaxuan Wang, 2019, bioRxiv.

Unifying Gene Duplication, Loss, and Coalescence on Phylogenetic Networks

Luay Nakhleh, Huw A. Ogilvie, Peng Du, 2019, bioRxiv.

BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis

Sebastián Duchêne, Graham Jones, Igor Siveroni, 2018, bioRxiv.

StarBEAST2 brings faster species tree inference and accurate estimates of substitution rates

Huw A. Ogilvie, Remco R. Bouckaert, Alexei J. Drummond, 2016 .

Supplementary Data Files

Huw A. Ogilvie, Alexei J. Drummond, Dong Xie, 2015 .

Inference of species histories in the presence of gene flow

Tanja Stadler, Huw A. Ogilvie, Alexei J. Drummond, 2018, bioRxiv.

Bayesian Inference of Species Networks from Multilocus Sequence Data

Tanja Stadler, Huw A. Ogilvie, Alexei J. Drummond, 2017 .

Computational Performance and Statistical Accuracy of *BEAST and Comparisons with Other Methods

Huw A. Ogilvie, Alexei J. Drummond, Dong Xie, 2015, Systematic biology.

Advances in Computational Methods for Phylogenetic Networks in the Presence of Hybridization

Huw A. Ogilvie, R.A.L. Elworth, H. A. Ogilvie, 2018, Bioinformatics and Phylogenetics.

SARS-CoV-2 genomic diversity and the implications for qRT-PCR diagnostics and transmission

Huw A. Ogilvie, C. Mason, T. Treangen, 2021, Genome research.

StarBEAST2 Brings Faster Species Tree Inference and Accurate Estimates of Substitution Rates

Huw A. Ogilvie, R. Bouckaert, A. Drummond, 2016, bioRxiv.

microRNA profiling of root tissues and root forming explant cultures in Medicago truncatula

Huw A. Ogilvie, Rodney P Eyles, Philip H. Williams, 2013, Planta.

Validation and description of two new north-western Australian Rainbow skinks with multispecies coalescent methods and morphology

Huw A. Ogilvie, C. Moritz, H. Ogilvie, 2017, PeerJ.

“Correcting” gene trees to be more like species trees increases topological error when incomplete lineage sorting is high

Huw A. Ogilvie, L. Nakhleh, H. Ogilvie, 2022, bioRxiv.

MaCroDNA: Accurate integration of single-cell DNA and RNA data for a deeper understanding of tumor heterogeneity

Huw A. Ogilvie, L. Nakhleh, H. Ogilvie, 2023, bioRxiv.

Novel Integrative Modeling of Molecules and Morphology across Evolutionary Timescales

Huw A. Ogilvie, A. Drummond, T. Vaughan, 2021, Systematic biology.

CEP–CEPR1 signalling inhibits the sucrose-dependent enhancement of lateral root growth

Huw A. Ogilvie, M. Djordjevic, H. Ogilvie, 2019, Journal of experimental botany.

Maximum Parsimony Inference of Phylogenetic Networks in the Presence of Polyploid Complexes

Huw A. Ogilvie, L. Nakhleh, H. Ogilvie, 2020, bioRxiv.

Phylovar: Towards scalable phylogeny-aware inference of single-nucleotide variations from single-cell DNA sequencing data

Huw A. Ogilvie, L. Nakhleh, D. Posada, 2022, bioRxiv.

Hidden genomic diversity of SARS-CoV-2: implications for qRT-PCR diagnostics and transmission

Huw A. Ogilvie, R. A. Leo Elworth, C. Mason, 2020, bioRxiv.

Diversification of the C-TERMINALLY ENCODED PEPTIDE (CEP) gene family in angiosperms, and evolution of plant-family specific CEP genes

Huw A. Ogilvie, M. Djordjevic, H. Ogilvie, 2014, BMC Genomics.

The Impact of Model Misspecification on Phylogenetic Network Inference

Huw A. Ogilvie, L. Nakhleh, H. Ogilvie, 2022, bioRxiv.

NestedBD: Bayesian Inference of Phylogenetic Trees From Single-Cell DNA Copy Number Profile Data Under a Birth-Death Model

Huw A. Ogilvie, L. Nakhleh, H. Ogilvie, 2022, bioRxiv.

Bayesian Inference of Species Networks from Multilocus Sequence Data

Tanja Stadler, Huw A. Ogilvie, Alexei J Drummond, 2017, bioRxiv.

Phylogenomic assessment of the role of hybridization and introgression in trait evolution

Huw A. Ogilvie, L. Nakhleh, H. Ogilvie, 2020, bioRxiv.

MoTERNN: Classifying the Mode of Cancer Evolution Using Recursive Neural Networks

Huw A. Ogilvie, L. Nakhleh, H. Ogilvie, 2022, bioRxiv.

Fungal phytopathogens encode functional homologues of plant rapid alkalinization factor (RALF) peptides.

Huw A. Ogilvie, David A Jones, P. Solomon, 2017, Molecular plant pathology.

Joint inference of species histories and gene flow

Huw A. Ogilvie, Nicola F. Müller, A. Drummond, 2018 .

Inferring Species Trees Using Integrative Models of Species Evolution

Tanja Stadler, Huw A. Ogilvie, Alexei J. Drummond, 2018, bioRxiv.

A divide-and-conquer method for scalable phylogenetic network inference from multilocus data

Xinhao Liu, Jiafan Zhu, Huw A. Ogilvie, 2019, bioRxiv.

The peptide-encoding CEP1 gene modulates lateral root and nodule numbers in Medicago truncatula.

Huw A. Ogilvie, M. Djordjevic, H. Ogilvie, 2013, Journal of experimental botany.

Annotation-free delineation of prokaryotic homology groups

Huw A. Ogilvie, L. Nakhleh, H. Ogilvie, 2022, PLoS Comput. Biol..

Comparing Inference under the Multispecies Coalescent with and without Recombination.

Huw A. Ogilvie, L. Nakhleh, H. Ogilvie, 2023, Molecular phylogenetics and evolution.

Comparing Inference under the MSC versus the MSC-with-Recombination

Huw A. Ogilvie, L. Nakhleh, H. Ogilvie, 2022, bioRxiv.

“Correcting” Gene Trees to be More Like Species Trees Frequently Increases Topological Error

Huw A. Ogilvie, L. Nakhleh, Zhi Yan, 2023, Genome biology and evolution.

Phylogenetic Network Dissimilarity Measures That Take Branch Lengths Into Account

Huw A. Ogilvie, L. Nakhleh, Berk A. Yakici, 2022, bioRxiv.

Supporting per-locus substitution rates improves the accuracy of species networks and avoids spurious reticulations

Huw A. Ogilvie, L. Nakhleh, H. Ogilvie, 2022, bioRxiv.

The multispecies coalescent ( MSC ) reconstructs species trees from a set of genes , and fully

Huw A. Ogilvie, A. Drummond, 2016 .

Rosette core fungal resistance in Arabidopsis thaliana

Huw A. Ogilvie, L. M. Markillie, G. Orr, 2019, Planta.

Accurate integration of single-cell DNA and RNA for analyzing intratumor heterogeneity using MaCroDNA

Huw A. Ogilvie, L. Nakhleh, M. Edrisi, 2023, Nature communications.

Phylovar: toward scalable phylogeny-aware inference of single-nucleotide variations from single-cell DNA sequencing data

Huw A. Ogilvie, L. Nakhleh, M. Edrisi, 2022, Bioinformatics.

MaCroDNA: Accurate integration of single-cell DNA and RNA 1 data for a deeper understanding of tumor heterogeneity

Huw A. Ogilvie, L. Nakhleh, H. Ogilvie, 2022 .