Publications
Google Scholar citations *here*
Weaver, W. N., B. R. Ruhfel, K. J. Lough, and S. A. Smith. 2023. Herbarium specimen label transcription reimagined with large language models: capabilities, productivity, and risks. American Journal of Botany n/a: doi: https://doi.org/10.1002/ajb2.16256
McFadden, T., N. Koenig, and B. R. Ruhfel. 2023. A Preliminary Vascular Flora of the Taylor Fork Ecological Area, Madison County, Kentucky. Journal of the Kentucky Academy of Science 84: doi: 10.3101/1098-7096-84.1.1
Chen, C., B. R. Ruhfel, J. Li, Z. Wang, L. Zhang, L. Zhang, X. Mao, et al. 2023. Phylotranscriptomics of Swertiinae (Gentianaceae) reveals that key floral traits are not phylogenetically correlated. Journal of Integrated Plant Biology.
Koenig, N., M. Scholer, T. Littlefield, AND B. R. Ruhfel. 2021. Phylogenetic placement of Trifolium kentuckiense (Fabaceae), a new member of the native eastern North American clover clade. Castanea 86: 283–295.
Monfils, A. K., E. R. Krimmel, D. L. Linton, T. D. Marsico, A. B. Morris, AND B. R. Ruhfel. 2021. Collections Education: The Extended Specimen and Data Acumen. BioScience.
Powell, C., A. Krakowiak, R. Fuller, E. Rylander, E. Gillespie, S. Krosnik, B. Ruhfel, A. B. Morris, and J. Shaw. 2021. Estimating herbarium specimen digitization rates: Accounting for human experience. Applications in Plant Sciences 9.
Bedoya, A. M., B. R. Ruhfel, C. T. Philbrick, S. Madriñán, C. P. Bove, A. Mesterházy, and R. G. Olmstead. 2020. Corrigendum: Plastid Genomes of Five Species of Riverweeds (Podostemaceae): Structural Organization and Comparative Analysis in Malpighiales. Frontiers in Plant Science 11.
Andries, C., and B. Ruhfel. 2020. Vascular flora of two wetlands in the Red River Gorge Geological Area and Clifty Wilderness in Menifee and Powell Counties of Kentucky. Journal of the Kentucky Academy of Science 81: 1-12.
Bedoya, A. M., B. R. Ruhfel, C. T. Philbrick, S. Madriñán, C. P. Bove, A. Mesterházy, AND R. G. Olmstead. 2019. Plastid genomes of five species of riverweeds (Podostemaceae): structural organization and comparative analysis in Malpighiales. Frontiers in Plant Science 10.
Marinho L.C., L. Cai, X. Duan, B.R. Ruhfel, P. Fiaschi, A.M. Amorim, C. van den Berg, C.C. Davis. 2019. Plastomes resolve generic limits within tribe Clusieae (Clusiaceae) and reveal the new genus Arawakia. Molecular Phylogenetics and Evolution 134: 142-151.
Philbrick, C.T., B.R. Ruhfel, and C.P. Bove. 2018. Contributions to the taxonomy of Rhyncholacis (Podostemaceae): Evidence of monophyly, description of a new species, and transfer of the monotypic Macarenia. Phytotaxa 357: 107-116.
Gitzendanner, M.A., P.S. Soltis, G. K.-S. Wong, B.R. Ruhfel, D.E. Soltis. 2018. Plastid phylogenomic analysis of green plants: a billion years of evolutionary history. American Journal of Botany 105: 291-301.
Meseguer, A.S., J.M. Lobo, J. Cornuault, D. Beerling, B.R. Ruhfel, C.C. Davis, E. Jousselin, and I. Sanmartin. 2018. Reconstructing deep-time paleoclimate legacies unveil the demise and turnover of the ancient (boreo)tropical flora. Global Ecology and Biogeography 27: 616-628.
Ruhfel, B. R., C. P. Bove, C. T. Philbrick, and C. C.Davis. 2016. Dispersal largely explains the Gondwanan distribution of the ancient tropical clusioid plant clade. American Journal of Botany. 103: 1117-1128.
Nelson G., P. Sweeney, L.E. Wallace, R.K. Rabeler, D. Allard, H. Brown, J.R. Carter, M.W. Denslow, E.R. Ellwood, C.C. Germain-Aubrey, E. Gilbert, E. Gillespie, L.R. Goertzen, B. Legler, D.B. Marchant, T.D. Marsico, A.B. Morris, Z. Murrell, M. Nazaire, C. Neefus, S. Oberreiter, D. Paul, B.R. Ruhfel, T. Sasek, J. Shaw, P.S. Soltis, K. Watson, A. Weeks, A.R. Mast. 2015. Digitization Workflows for Flat Sheets and Packets of Plants, Algae, and Fungi. Applications in Plant Sciences 3: 1-9.
Wickett, N.J., S. Mirarab, N. Nguyen, T. Warnow, E. Carpenter, N. Matasci, S. Ayyampalayam, M.S. barker, J.G. Burleigh, M.A. Gitzendanner, B.R. Ruhfel, E. Wafula, J.P. Der, S.W. Graham, S. Mathews, M. Melkonian, D.E. Soltis, P.S. Soltis, N.W. Miles, C.J. Rothfels, L. Pokorny, A.J. Shaw, L. Degironimo, D.W. Stevenson, B. Surek, J.C. Villarreal, B. Roure, H. Philippe, C.W. dePamphilis, T. Chen, M.K. Deyholos, R.S. Baucom, T.M. Kutchan, M.M. Augustin, J. Wang, Y. Zhang, Z. Tian, Z. Yan, X. Wu, X. Sun, G. K.-S. Wong, and J. Leebens-Mack. 2014. Phylotranscriptomic analysis of the origin and early diversification of land plants. Proceedings of the National Academy of Sciences 111: E4859-E4868.
Matasci, N., L.-H. Hung, Z. Yan, E. Carpenter, N. Wickett, S. Mirarab, N. Nguyen, T. Warnow, S. Ayyampalayam, M. Barker, J. Burleigh, M. Gitzendanner, E. Wafula, J. Der, C. Depamphilis, B. Roure, H. Philippe, B. Ruhfel, N. Miles, S. Graham, S. Mathews, B. Surek, M. Melkonian, D. Soltis, P. Soltis, C. Rothfels, L. Pokorny, J. Shaw, L. Degironimo, and D. Stevenson. 2014. Data access for the 1,000 Plants (1KP) project. GigaScience 3: 17.
Ruhfel, B.R., M.A. Gitzendanner, P.S. Soltis, D.E. Soltis, and J.G. Burleigh. 2014. From algae to angiosperms-inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes. BMC Evolutionary Biology 14: 23.
***A BMC Editors Pick and a BMC Highly Accessed article. See also commentary by Davis et al. 2014
*** A top 10 article in BMC Evolutionary Biology for 2014
Drew, B.T., B.R. Ruhfel, S.A. Smith, M.J. Moore, B.G. Briggs, M.A. Gitzendanner, P.S. Soltis, and D.E. Soltis. 2014. Another Look at the Root of the Angiosperms Reveals a Familiar Tale. Systematic Biology 63: 368-382.
Davis, C.C., H. Schaefer, B.R. Ruhfel, M.J. Donoghue, and E.J. Edwards. 2014. Climates and clades: biased methods, biased results. arXiv preprint arXiv:14065211.
Ruhfel, B. R., P.F. Stevens, and C. C.Davis. 2013. Combined morphological and molecular phylogeny of the clusioid clade (Malpighiales) and the placement of the ancient rosid macrofossil Paleoclusia. International Journal of Plant Sciences 174:910-936.
Xi, Z., B.R. Ruhfel, H. Schaefer, A.M. Amorim, M. Sugumaran, K.J. Wurdack, P.K. Endress, M.L. Matthews, P.F. Stevens, S. Mathews, and C.C. Davis. 2012. Phylogenomics and a posteriori data partitioning resolve the Cretaceous angiosperm radiation Malpighiales. Proceedings of the National Academy of Sciences 109:17519-17524.
Ruhfel, B. R., V. Bittrich, C. P. Bove, M. H. G. Gustafsson, C. T. Philbrick, R. Rutishauser, Z. Xi, and C. C.Davis. 2011. Phylogeny of the clusioid clade (Malpighiales): Evidence from the plastid and mitochondrial genomes. American Journal of Botany 98:306-325.
Willis, C. G., B. Ruhfel, R. B. Primack, A. J. Miller-Rushing, J. B. Losos, and C. C. Davis. 2010. Favorable climate change response explains non-native species success in Thoreaus woods. PLoS ONE 5:e8878.
Willis, C. G., B. Ruhfel, R. B. Primack, A. J. Miller-Rushing, and C. C. Davis. 2009. Reply to McDonald et al.: Climate change, not deer herbivory, has shaped species decline in Concord, Massachusetts. Proceedings of the National Academy of Sciences 106:E29-E29.
Willis, C.G., B. Ruhfel, R.B. Primack, A.J. Miller-Rushing, and C.C. Davis. 2008. Phylogenetic patterns of species loss in Thoreaus woods are driven by climate change. Proceedings of the National Academy of Sciences 105:17029-17033.
Ruhfel, B., S. Lindsay, and C.C. Davis. 2008. Phylogenetic placement of Rheopteris and the polyphyly of Monogramma (Pteridaceae s.l.): Evidence from rbcL sequence data. Systematic Botany 33:37-43.
Weaver, W. N., B. R. Ruhfel, K. J. Lough, and S. A. Smith. 2023. Herbarium specimen label transcription reimagined with large language models: capabilities, productivity, and risks. American Journal of Botany n/a: doi: https://doi.org/10.1002/ajb2.16256
McFadden, T., N. Koenig, and B. R. Ruhfel. 2023. A Preliminary Vascular Flora of the Taylor Fork Ecological Area, Madison County, Kentucky. Journal of the Kentucky Academy of Science 84: doi: 10.3101/1098-7096-84.1.1
Chen, C., B. R. Ruhfel, J. Li, Z. Wang, L. Zhang, L. Zhang, X. Mao, et al. 2023. Phylotranscriptomics of Swertiinae (Gentianaceae) reveals that key floral traits are not phylogenetically correlated. Journal of Integrated Plant Biology.
Koenig, N., M. Scholer, T. Littlefield, AND B. R. Ruhfel. 2021. Phylogenetic placement of Trifolium kentuckiense (Fabaceae), a new member of the native eastern North American clover clade. Castanea 86: 283–295.
Monfils, A. K., E. R. Krimmel, D. L. Linton, T. D. Marsico, A. B. Morris, AND B. R. Ruhfel. 2021. Collections Education: The Extended Specimen and Data Acumen. BioScience.
Powell, C., A. Krakowiak, R. Fuller, E. Rylander, E. Gillespie, S. Krosnik, B. Ruhfel, A. B. Morris, and J. Shaw. 2021. Estimating herbarium specimen digitization rates: Accounting for human experience. Applications in Plant Sciences 9.
Bedoya, A. M., B. R. Ruhfel, C. T. Philbrick, S. Madriñán, C. P. Bove, A. Mesterházy, and R. G. Olmstead. 2020. Corrigendum: Plastid Genomes of Five Species of Riverweeds (Podostemaceae): Structural Organization and Comparative Analysis in Malpighiales. Frontiers in Plant Science 11.
Andries, C., and B. Ruhfel. 2020. Vascular flora of two wetlands in the Red River Gorge Geological Area and Clifty Wilderness in Menifee and Powell Counties of Kentucky. Journal of the Kentucky Academy of Science 81: 1-12.
Bedoya, A. M., B. R. Ruhfel, C. T. Philbrick, S. Madriñán, C. P. Bove, A. Mesterházy, AND R. G. Olmstead. 2019. Plastid genomes of five species of riverweeds (Podostemaceae): structural organization and comparative analysis in Malpighiales. Frontiers in Plant Science 10.
Marinho L.C., L. Cai, X. Duan, B.R. Ruhfel, P. Fiaschi, A.M. Amorim, C. van den Berg, C.C. Davis. 2019. Plastomes resolve generic limits within tribe Clusieae (Clusiaceae) and reveal the new genus Arawakia. Molecular Phylogenetics and Evolution 134: 142-151.
Philbrick, C.T., B.R. Ruhfel, and C.P. Bove. 2018. Contributions to the taxonomy of Rhyncholacis (Podostemaceae): Evidence of monophyly, description of a new species, and transfer of the monotypic Macarenia. Phytotaxa 357: 107-116.
Gitzendanner, M.A., P.S. Soltis, G. K.-S. Wong, B.R. Ruhfel, D.E. Soltis. 2018. Plastid phylogenomic analysis of green plants: a billion years of evolutionary history. American Journal of Botany 105: 291-301.
Meseguer, A.S., J.M. Lobo, J. Cornuault, D. Beerling, B.R. Ruhfel, C.C. Davis, E. Jousselin, and I. Sanmartin. 2018. Reconstructing deep-time paleoclimate legacies unveil the demise and turnover of the ancient (boreo)tropical flora. Global Ecology and Biogeography 27: 616-628.
Ruhfel, B. R., C. P. Bove, C. T. Philbrick, and C. C.Davis. 2016. Dispersal largely explains the Gondwanan distribution of the ancient tropical clusioid plant clade. American Journal of Botany. 103: 1117-1128.
Nelson G., P. Sweeney, L.E. Wallace, R.K. Rabeler, D. Allard, H. Brown, J.R. Carter, M.W. Denslow, E.R. Ellwood, C.C. Germain-Aubrey, E. Gilbert, E. Gillespie, L.R. Goertzen, B. Legler, D.B. Marchant, T.D. Marsico, A.B. Morris, Z. Murrell, M. Nazaire, C. Neefus, S. Oberreiter, D. Paul, B.R. Ruhfel, T. Sasek, J. Shaw, P.S. Soltis, K. Watson, A. Weeks, A.R. Mast. 2015. Digitization Workflows for Flat Sheets and Packets of Plants, Algae, and Fungi. Applications in Plant Sciences 3: 1-9.
Wickett, N.J., S. Mirarab, N. Nguyen, T. Warnow, E. Carpenter, N. Matasci, S. Ayyampalayam, M.S. barker, J.G. Burleigh, M.A. Gitzendanner, B.R. Ruhfel, E. Wafula, J.P. Der, S.W. Graham, S. Mathews, M. Melkonian, D.E. Soltis, P.S. Soltis, N.W. Miles, C.J. Rothfels, L. Pokorny, A.J. Shaw, L. Degironimo, D.W. Stevenson, B. Surek, J.C. Villarreal, B. Roure, H. Philippe, C.W. dePamphilis, T. Chen, M.K. Deyholos, R.S. Baucom, T.M. Kutchan, M.M. Augustin, J. Wang, Y. Zhang, Z. Tian, Z. Yan, X. Wu, X. Sun, G. K.-S. Wong, and J. Leebens-Mack. 2014. Phylotranscriptomic analysis of the origin and early diversification of land plants. Proceedings of the National Academy of Sciences 111: E4859-E4868.
Matasci, N., L.-H. Hung, Z. Yan, E. Carpenter, N. Wickett, S. Mirarab, N. Nguyen, T. Warnow, S. Ayyampalayam, M. Barker, J. Burleigh, M. Gitzendanner, E. Wafula, J. Der, C. Depamphilis, B. Roure, H. Philippe, B. Ruhfel, N. Miles, S. Graham, S. Mathews, B. Surek, M. Melkonian, D. Soltis, P. Soltis, C. Rothfels, L. Pokorny, J. Shaw, L. Degironimo, and D. Stevenson. 2014. Data access for the 1,000 Plants (1KP) project. GigaScience 3: 17.
Ruhfel, B.R., M.A. Gitzendanner, P.S. Soltis, D.E. Soltis, and J.G. Burleigh. 2014. From algae to angiosperms-inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes. BMC Evolutionary Biology 14: 23.
***A BMC Editors Pick and a BMC Highly Accessed article. See also commentary by Davis et al. 2014
*** A top 10 article in BMC Evolutionary Biology for 2014
Drew, B.T., B.R. Ruhfel, S.A. Smith, M.J. Moore, B.G. Briggs, M.A. Gitzendanner, P.S. Soltis, and D.E. Soltis. 2014. Another Look at the Root of the Angiosperms Reveals a Familiar Tale. Systematic Biology 63: 368-382.
Davis, C.C., H. Schaefer, B.R. Ruhfel, M.J. Donoghue, and E.J. Edwards. 2014. Climates and clades: biased methods, biased results. arXiv preprint arXiv:14065211.
Ruhfel, B. R., P.F. Stevens, and C. C.Davis. 2013. Combined morphological and molecular phylogeny of the clusioid clade (Malpighiales) and the placement of the ancient rosid macrofossil Paleoclusia. International Journal of Plant Sciences 174:910-936.
Xi, Z., B.R. Ruhfel, H. Schaefer, A.M. Amorim, M. Sugumaran, K.J. Wurdack, P.K. Endress, M.L. Matthews, P.F. Stevens, S. Mathews, and C.C. Davis. 2012. Phylogenomics and a posteriori data partitioning resolve the Cretaceous angiosperm radiation Malpighiales. Proceedings of the National Academy of Sciences 109:17519-17524.
Ruhfel, B. R., V. Bittrich, C. P. Bove, M. H. G. Gustafsson, C. T. Philbrick, R. Rutishauser, Z. Xi, and C. C.Davis. 2011. Phylogeny of the clusioid clade (Malpighiales): Evidence from the plastid and mitochondrial genomes. American Journal of Botany 98:306-325.
Willis, C. G., B. Ruhfel, R. B. Primack, A. J. Miller-Rushing, J. B. Losos, and C. C. Davis. 2010. Favorable climate change response explains non-native species success in Thoreaus woods. PLoS ONE 5:e8878.
Willis, C. G., B. Ruhfel, R. B. Primack, A. J. Miller-Rushing, and C. C. Davis. 2009. Reply to McDonald et al.: Climate change, not deer herbivory, has shaped species decline in Concord, Massachusetts. Proceedings of the National Academy of Sciences 106:E29-E29.
Willis, C.G., B. Ruhfel, R.B. Primack, A.J. Miller-Rushing, and C.C. Davis. 2008. Phylogenetic patterns of species loss in Thoreaus woods are driven by climate change. Proceedings of the National Academy of Sciences 105:17029-17033.
Ruhfel, B., S. Lindsay, and C.C. Davis. 2008. Phylogenetic placement of Rheopteris and the polyphyly of Monogramma (Pteridaceae s.l.): Evidence from rbcL sequence data. Systematic Botany 33:37-43.