Ya Yang

发表

Analysis of Paralogs in Target Enrichment Data Pinpoints Multiple Ancient Polyploidy Events in Alchemilla s.l. (Rosaceae)

Diego F. Morales-Briones, David C. Tank, Hong Ma, 2020, bioRxiv.

Orthology Inference in Nonmodel Organisms Using Transcriptomes and Low-Coverage Genomes: Improving Accuracy and Matrix Occupancy for Phylogenomics

Stephen A. Smith, Ya Yang, 2014, Molecular biology and evolution.

Optimizing de novo assembly of short-read RNA-seq data for phylogenomics

Stephen A. Smith, Ya Yang, 2013, BMC Genomics.

Back to the future: Reintegrating biology to understand how past eco-evolutionary change can predict future outcomes.

M. Alberti, Ya Yang, Sahas Barve, 2021, Integrative and comparative biology.

Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants

Stephen A. Smith, Ya Yang, Joseph W. Brown, 2015, BMC Evolutionary Biology.

Disentangling Sources of Gene Tree Discordance in Phylogenomic Data Sets: Testing Ancient Hybridizations in Amaranthaceae s.l

Diego F. Morales-Briones, Stephen A. Smith, W. C. Yim, 2020, Systematic biology.

Disentangling Sources of Gene Tree Discordance in Phylogenomic Datasets: Testing Ancient Hybridizations in Amaranthaceae s.l

Diego F. Morales-Briones, Stephen A. Smith, W. C. Yim, 2020 .

Evolution of Portulacineae marked by gene tree conflict and gene family expansion associated with adaptation to harsh environments

Stephen A. Smith, Tao Feng, U. Eggli, 2018, bioRxiv.

Evolution of Portulacineae marked by gene tree conflict and gene family expansion associated with adaptation to harsh environments

Stephen A. Smith, Tao Feng, U. Eggli, 2018, bioRxiv.

Improved transcriptome sampling pinpoints 26 ancient and more recent polyploidy events in Caryophyllales, including two allopolyploidy events.

Stephen A. Smith, Ya Yang, S. Brockington, 2018, The New phytologist.

Improved transcriptome sampling pinpoints 26 paleopolyploidy events in Caryophyllales, including two paleo-allopolyploidy events

Stephen A. Smith, Ya Yang, S. Brockington, 2017, bioRxiv.

Dissecting Molecular Evolution in the Highly Diverse Plant Clade Caryophyllales Using Transcriptome Sequencing

Yinlong Xie, Gane Ka-Shu Wong, Douglas E. Soltis, 2015, Molecular biology and evolution.

On the hybrid origin of the C2 Salsola divaricata agg. (Amaranthaceae) from C3 and C4 parental lineages

Diego F. Morales-Briones, G. Edwards, Ya Yang, 2021, bioRxiv.

FAD2 Gene Radiation and Positive Selection Contributed to Polyacetylene Metabolism Evolution in Campanulids1[OPEN]

E. Cahoon, Tao Feng, Shiyou Lü, 2019, Plant Physiology.

Lineage-specific gene radiations underlie the evolution of novel betalain pigmentation in Caryophyllales

G. Wong, Stephen A. Smith, R. Sage, 2015, The New phytologist.

Evaluating the Effects of Propiconazole on Hard Fescue (Festuca brevipila) via RNA sequencing and Liquid Chromatography–Mass Spectrometry

Y. Qiu, Ya Yang, E. Watkins, 2020, bioRxiv.

Performance of gene expression analyses using de novo assembled transcripts in polyploid species

Diego F. Morales-Briones, C. Passow, Ya Yang, 2018, bioRxiv.

Building a Reference Transcriptome for the Hexaploid Hard Fescue Turfgrass (Festuca brevipila) Using a Combination of PacBio Iso-Seq and Illumina Sequencing

Y. Qiu, Ya Yang, E. Watkins, 2020, bioRxiv.

Towards Improved Molecular Identification Tools in Fine Fescue (Festuca L., Poaceae) Turfgrasses: Nuclear Genome Size, Ploidy, and Chloroplast Genome Sequencing

Y. Qiu, Ya Yang, E. Watkins, 2019, Frontiers in genetics.

Disparity, diversity, and duplications in the Caryophyllales.

Stephen A. Smith, Ya Yang, Joseph W. Brown, 2018, The New phytologist.

Disparity, Diversity, and Duplications in the Caryophyllales

Stephen A. Smith, Ya Yang, Joseph W. Brown, 2017, bioRxiv.

Evaluating phylogenetic positions of four liverworts from New Zealand, Neogrollea notabilis, Jackiella curvata, Goebelobryum unguiculatum and Herzogianthus vaginatus, using three chloroplast genes

Y. Qiu, Ya Yang, T. Hendry, 2007 .

An efficient field and laboratory workflow for plant phylotranscriptomic projects1

Stephen A. Smith, Tao Feng, Hannah E. Marx, 2017, Applications in Plant Sciences.

An efficient field and laboratory workflow for plant phylotranscriptomic projects

Stephen A. Smith, Tao Feng, Hannah E. Marx, 2016, bioRxiv.

Phylogenomic analyses in Phrymaceae reveal extensive gene tree discordance in relationships among major clades

Diego F. Morales-Briones, David C. Tank, Ya Yang, 2022, American journal of botany.

Evolutionary blocks to anthocyanin accumulation and the loss of an anthocyanin carrier protein in betalain-pigmented Caryophyllales

Boas Pucker, John Cushman, Ya Yang, 2022, bioRxiv.

Widespread paleopolyploidy, gene tree conflict, and recalcitrant relationships among the carnivorous Caryophyllales.

Stephen A. Smith, Ya Yang, Joseph F. Walker, 2017, American journal of botany.

Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants

Stephen A. Smith, Ya Yang, Joseph W. Brown, 2015, BMC Evolutionary Biology.

Phylogenetics of the Chamaesyce clade (Euphorbia, Euphorbiaceae): reticulate evolution and long-distance dispersal in a prominent C4 lineage.

Ya Yang, P. Berry, 2011, American journal of botany.

Evolutionary bursts in Euphorbia (Euphorbiaceae) are linked with photosynthetic pathway

C. Davis, K. Wurdack, Ya Yang, 2014, Evolution; international journal of organic evolution.

Molecular phylogenetics and classification of Euphorbia subgenus Chamaesyce (Euphorbiaceae)

J. Morawetz, X. Aubriot, Ya Yang, 2012 .

Relaxation of tyrosine pathway regulation underlies the evolution of betalain pigmentation in Caryophyllales.

Stephen A. Smith, Tao Feng, Ya Yang, 2018, The New phytologist.

Disentangling Sources of Gene Tree Discordance in Phylotranscriptomic Datasets: A Case Study from Amaranthaceae s.l.

Diego F. Morales-Briones, Stephen A. Smith, J. Cushman, 2019 .

Practical considerations for plant phylogenomics

Michael R McKain, Matthew G. Johnson, Deren A. R. Eaton, 2018, Applications in plant sciences.

Disparity , Diversity , and Duplications in the Caryophyllales 1

Stephen A. Smith, Ya Yang, Joseph W. Brown, 2017 .

Phylogenomic analyses using genomes and transcriptomes do not “resolve” relationships among major clades in Phrymaceae

Diego F. Morales-Briones, David C. Tank, Ya Yang, 2021, bioRxiv.

Widespread paleopolyploidy, gene tree conflict, and recalcitrant relationships among the carnivorous Caryophyllales

Stephen A. Smith, Ya Yang, Joseph F. Walker, 2017, bioRxiv.

Large-scale patterns of stomatal traits in Tibetan and Mongolian grassland species

Tao Feng, Yue Shi, Ya Yang, 2014 .

Towards Improved Molecular Identification Tools in Fine Fescue (Festuca L., Poaceae) Turfgrasses: Nuclear Genome Size, Ploidy, and Chloroplast Genome Sequencing

Y. Qiu, Ya Yang, E. Watkins, 2019, bioRxiv.

Towards Improved Molecular Identification Tools in Fine Fescue (Festuca L., Poaceae) Turfgrasses: Nuclear Genome Size, Ploidy, and Chloroplast Genome Sequencing

Y. Qiu, Ya Yang, E. Watkins, 2019, Front. Genet..

Chloroplast Genome Sequencing and Comparative Analysis for Five Species of the Turfgrass Fine Fescues (Festuca L., Poaceae)

Y. Qiu, Ya Yang, E. Watkins, 2019 .

From cacti to carnivores: Improved phylotranscriptomic sampling and hierarchical homology inference provide further insight into the evolution of Caryophyllales.

Ning Wang, Tao Feng, Helga Ochoterena, 2018, American journal of botany.

Methods for exploring the plant tree of life

M. McKain, Ya Yang, N. Wickett, 2018, Applications in Plant Sciences.

Optimizing de novo assembly of short-read RNA-seq data for phylogenomics

Stephen A. Smith, Ya Yang, 2013, BMC Genomics.

The genome of the glasshouse plant noble rhubarb (Rheum nobile) provides a window into alpine adaptation

Tao Feng, Ya Yang, Michael J. Moore, 2023, Communications biology.

Repeated range expansion and niche shift in a volcanic hotspot archipelago: radiation of Hawaiian Euphorbia (Euphorbiaceae)

L. Sack, C. Morden, Ya Yang, 2016, bioRxiv.

Repeated range expansion and niche shift in a volcanic hotspot archipelago: Radiation of C4 Hawaiian Euphorbia subgenus Chamaesyce (Euphorbiaceae)

L. Sack, C. Morden, Ya Yang, 2018, Ecology and evolution.

Phylogenetics of the Chamaesyce clade (Euphorbia, Euphorbiaceae): reticulate evolution and long-distance dispersal in a prominent C4 lineage.

Ya Yang, P. Berry, 2011, American journal of botany.

Chloroplast Genome Sequencing and Comparative Analysis for 1 Five Species of the Turfgrass Fine Fescues (Festuca L . , Poaceae ) 2

Y. Qiu, Ya Yang, E. Watkins, 2019 .