Emily M. Catania, Nicole M. Dubs, Shejal Soumen and Todd J. Barkman 2024.  The mutational road not taken: using Ancestral Sequence Resurrection to evaluate the evolution of plant enzyme substrate preferences.  Genome Biology and Evolution. 16(2): evae016. https://doi.org/10.1093/gbe/evae016

​

Roshan Javanshad, Christopher J. Taylor, Niusha Delavari, Todd J. Barkman, Frederick Stull and Andre R. Venter.  2023.  Analysis of histidine-tagged recombinant proteins from nickel and copper coated surfaces by direct electrospray ionization and desorption electrospray ionization mass spectrometry.  Rapid Commun Mass Spectrom. 2023:e9516. https://pubs.acs.org/doi/10.1021/acs.analchem.0c02162

​

Choudhary, Vishakha, Kevin Wu, Zhiyao Zhang, Mark Dulchavsky, Todd J. Barkman, James C. A. Bardwell and Frederick Stull.  2022.  The enzyme pseudooxynicotine amine oxidase from Pseudomonas putida S16 is not an oxidase, but a dehydrogenase.  Journal of Biological Chemistry.  298(8): 102251.  https://www.jbc.org/article/S0021-9258(22)00693-7/fulltext

​

Dubs, Nicole M., Breck R. Davis, Victor de Brito, Kate C. Colebrook, Ian J. Tiefel, Madison B. Nakayama, Ruiqi Huang, Audrey E. Ledvina, Samantha J. Hack, Brent Inkelaar, Talline R. Martins, Sarah M. Aartila, Kelli S. Albritton, Sarah Almuhanna, Ryan J. Arnoldi, Clara K. Austin, Amber C. Battle, Gregory R. Begeman, Caitlin M. Bickings, Jonathon T. Bradfield, Eric C. Branch, Eric P. Conti, Breana Cooley, Nicole M. Dotson, Cheyone J. Evans, Amber S. Fries, Ivan G. Gilbert, Weston D. Hillier, Pornkamol Huang, Kaitlin W. Hyde, Filip Jevtovic, Mark C. Johnson, Julie L. Keeler, Albert Lam, Kyle M. Leach, Jeremy D. Livsey, Jonathan T. Lo, Kevin R. Loney, Nich W. Martin, Amber S. Mazahem, Aurora N. Mokris, Destiny M. Nichols, Ruchi Ojha, Nnanna N. Okorafor,  Joshua R. Paris, Thais Fuscaldi Reboucas, Pedro Beretta Sant'Anna, Mathew R. Seitz, Nathan R. Seymour, Lila K. Slaski, Stephen O. Stemaly, Benjamin R. Ulrich, Emile N. Van Meter, Meghan L. Young & Todd J. Barkman. 2022.  A collaborative classroom investigation of the evolution of SABATH methyltransferase substrate preference shifts over 120 million years of flowering plant history.  2022.  Molecular Biology and Evolution. 39(3): msac007.  https://doi.org/10.1093/molbev/msac007

​

O’Donnell, A. J., R. Huang, J. Barboline and T. J. Barkman.  2021.  Convergent biochemical pathways for xanthine alkaloid production in plants evolved from ancestral enzymes with different catalytic properties.  Molecular Biology and Evolution.  38(7):2704-2714.  https://doi.org/10.1093/molbev/msab059

​

Straight, B. Fisher G. Needham, B. L., Naugle, A., Olungah, C.,  Wanitjirattikal, P., Root, C., Farman, J., Barkman, T. J., Lalancette, C.., 2020.  Lifetime Stress and War Exposure Timing May Predict Methylation Changes at NR3C1 based on a Pilot Study in a Warrior Cohort in a Small-Scale Society in Kenya.  American Journal of Human Biology.  https://doi.org/10.1002/ajhb.23515

​

One Thousand Plant Transcriptomes Initiative (100+ authors).  2019.  A Phylogenomic view of evolutionary complexity in green plants.  Nature 574:  679-684.  https://www.nature.com/articles/s41586-019-1693-2

​

Pedersen, H. Æ., G. Petersen, B. Gravendeel, T. J. Barkman, H. de Boer, B. P. Sulistyo and O. Seberg.  2019.  Phylogenetics of Dendrochilum (Orchidaceae): evidence of pronounced morphological homoplasy and predominantly centric endemism. Taxon 68(6): 1173-1188. https://doi.org/10.1002/tax.12184

​

Straight, B., B. L. Needham, G. Onicescu, P. Wanitjirattika, T. J. Barkman, C. Root, J. Farman, A. Naugle, C. Lalancette, C. Olungah, and S. Lekalgitele 2019.  Prosocial Emotion, Adolescence, and Warfare: DNA Methylation Associates with Culturally Salient Combat Variables.  Human Nature https://doi.org/10.1007/s12110-019-09344-6

​

Su, H.-J., T. J. Barkman, W. Hao, S. S. Jones, J. Naumann, E. Skippington, E. K. Wafula, J.-M. Hu, J. D. Palmer and C. W. dePamphilis.  2018.  A novel genetic code and record-setting AT-richness in the highly reduced plastid genome of the holoparasitic plant Balanophora. Proceedings of the National Academy of Sciences, USA.  116 (3): 934-943.  https://doi.org/10.1073/pnas.1816822116

​

Barkman, T. J. M. Klooster, K. Gaddis, B. Franzone, S. Calhoun, S. Manickam, S. Vessabutr, S. Pak, C. C. Davis. 2017.  Reading between the vines: hosts as islands for extreme holoparasitic plants.  American Journal of Botany.  104: 1382-11389.   https://bsapubs.onlinelibrary.wiley.com/doi/pdf/10.3732/ajb.1700117

​

Skippington, E. Barkman, T. J., Rice, D. W. and J. D. Palmer  2017.  Comparative mitogenomics indicates respiratory competence in parasitic Viscum despite loss of complex I and extreme sequence divergence, and reveals horizontal gene transfer and remarkable variation in genome size.  BMC Plant Biology. 17(1): 49. 10.1186/s12870-017-0992-8

​

Huang, R., A. J. O’Donnell, J. J. Barboline, and T. J. Barkman  2016.  Convergent evolution of caffeine in plants by co-option of exapted ancestral enzymes. Proceedings of the National Academy of Sciences, USA.  113 (38) 10613-10618.  https://doi.org/10.1073/pnas.1602575113

​

Barkman, T. J., R. Repin, and J. Sugau 2016.  The parasitic plant families Loranthaeae and Viscaceae in Sabah, Malaysia.  Sandakania 21: 131-169.  

​

Skippington, E., Danny J. Rice, T. J. Barkman, J. D. Palmer 2015. The miniaturized mitogenome of the parasitic plant Viscum scurruloideum is extremely divergent and dynamic and has lost all nad genes.  Proceedings of the National Academy of Sciences, USA.  112: E3515-E3524.  https://doi.org/10.1073/pnas.1504491112.

​

Huang, R. Frank Hippauf, Diana Rohrbeck, Maria Haustein, Katrin Wenke, Janie Feike, Noah Sorrelle, Birgit Piechulla and Todd J. Barkman.  2012.  Enzyme functional evolution through improved catalysis of ancestrally non-preferred substrates. Proceedings of the National Academy of Sciences, USA.  109: 2966-2971.  10.1073/pnas.1019605109

​

Laureto, P. and T. J. Barkman.  2011.  Nuclear and chloroplast DNA suggest a complex single origin for the threatened allopolyploid Solidago houghtonii (Asteraceae) involving reticulate evolution and introgression. Systematic Botany. 36: 209-226.  https://doi.org/10.1600/036364411X553289

​

Bendiksby, M.,  Galina Gussarova, Jamili Nais, Kamarudin Mat-Salleh, Nery Sofiyanti, Domingo Madulid, Trond Schumacher, and Todd Barkman. 2010.  Elucidating the evolutionary history of the Southeast Asian holoparasitic giant-flowered Rafflesiaceae: Pliocene vicariance, morphological convergence and character displacement.  Molecular Phylogenetics and Evolution. 57: 620-633.  https://doi.org/10.1016/j.ympev.2010.08.005

​

Hippauf, F., E. Michalsky, R. Huang, R. Preissner, T. J. Barkman, and B. Piechulla.  2010.  Enzymatic, Expression and Structural Divergences among Carboxyl O-methyltransferases after gene duplication and speciation in Nicotiana.  Plant Molecular Biology 72: 311-330.  10.1007/s11103-009-9572-0

​

Barkman. T. J. and J. Zhang. 2009.  Evidence for escape from adaptive conflict?  Nature (Brief Communications Arising).  462: E1-2.  https://www.nature.com/articles/nature08663

​

Barkman, T. J.,  M. Bendiksby, S.-H. Lim, K. Mat Salleh, J. Nais, D. Madulid and T. Schumacher. 2008.  Accelerated rates of floral evolution at the upper size limit for flowers.  Current Biology 18:1508-1513.  https://doi.org/10.1016/j.cub.2008.08.046

​

Barkman. T. J., McNeal, J. R., Lim, S.-H., Coat, G. Croom, H. B., Young, N. and dePamphilis, C. W.  2007.  Mitochondrial DNA suggests 12 origins of parasitism in angiosperms and reveals genomic chimerism in parasitic plants.  BMC Evolutionary Biology 7: 248.   https://bmcecolevol.biomedcentral.com/articles/10.1186/1471-2148-7-248

​

Barkman, T. J., Martins, T. R., Sutton, E., and Stout, J. T.  2007.  Positive selection for single amino acid change promotes substrate discrimination of a plant volatile-producing enzyme.  Molecular Biology and Evolution 24: 1320-1329.  10.1093/molbev/msm053

​

Martins, T., J. T. Stout, S. E. Todd, K. Kuipers, and T. J. Barkman. 2007.  Molecular phylogenetic tests of floral scent evolution in the Solanaceae.  Acta Hort. 745:  183-200.  10.17660/ActaHortic.2007.745.7

​

Barkman, T. J. 2006. A role for evolutionary predictions in gene isolation and characterization studies. Journal of Plant Biology 49(4): 331-335. https://doi.org/10.1007/BF03031165

​

Martins, T. and Barkman, T. J.  2005.  Reconstruction of Solanaceae phylogeny using the nuclear gene SAMT.  Systematic Botany 30(2): 433-445. https://doi.org/10.1600/0363644054223675

​

Tan, W. G. H., T. J. Barkman, V. G. Chinchar, and K. Essani.  2004.  Comparative genomic analyses of frog virus 3, type species of the genus Ranavirus (Family Iridoviridae).  Virology  323: 70-84.  10.1016/j.virol.2004.02.019

​

Barkman, T. J., S.-H. Lim, K. Mat Salleh, and J. Nais.  2004.  Mitochondrial DNA sequences reveal the photosynthetic relatives of Rafflesia, the world’s largest flower. Proceedings of the National Academy of Sciences, USA. 787-792. https://doi.org/10.1073/pnas.0305562101

​

Barkman, T. J., B. E. Emoi, R. Repin.  2003.  The genus Balanophora (Balanophoraceae) in Sabah, Malaysia  Blumea. 48: 465-474. https://doi.org/10.3767/000651903X489410

​

Barkman, T. J.  2003.  Evidence for positive selection on the floral scent gene Isoeugenol-O-methyltransferase. Molecular Biology and Evolution 20: 168-172. https://doi.org/10.1093/molbev/msg030

​

Barkman, T. J. & Simpson, B. B.  2002. Hybridization and parentage of Dendrochilum acuiferum (Orchidaceae) inferred in a phylogenetic context using nuclear and chloroplast DNA sequence data.  Systematic Botany 27(2): 209-220. https://www.jstor.org/stable/3093866?seq=1#metadata_info_tab_contents

​

Stahlhut, J. K., Cowan, D. P., Essani, K., Shoemaker, D.D., and Barkman, T. J.  2002.  Microsatellite markers for the wasp Euodynerus foraminatus (Vespidae: Eumeninae).  Molecular Ecology Notes 2(4): 467-468.

​

Barkman, T J.  2001. Character coding of secondary chemical variation for use in phylogenetic analyses.  Biochemical Systematics and Ecology 29: 1-20. 10.1016/s0305-1978(00)00031-4

​

Barkman T. J. & Simpson, B. B. 2001. Origin of High-Elevation Dendrochilum Species (Orchidaceae) Endemic to Mount Kinabalu, Sabah, Malaysia.  Systematic Botany  26(3): 658-669.  https://www.jstor.org/stable/3093987?seq=1#metadata_info_tab_contents

​

Barkman, T. J. 2001. Evolution of vegetative morphology in Mount Kinabalu high-elevation endemics: insights from the orchid genus Dendrochilum.  Sabah Parks Nature Journal 4: 9-24.

​

Barkman, T. J., G. Chenery, J. R. McNeal, J. Lyons-Weiler, W. J. Ellisens, G. Moore, A. D. Wolfe, and C. W. dePamphilis 2000.  Independent and combined analyses of sequences from all three genomic compartments converge on the root of flowering plant phylogeny. Proceedings of the National Academy of Sciences, USA. 13166-13171. 10.1073/pnas.220427497

​

Argent, G. and Barkman, T. J.  2000.  Two exciting new species of Rhododendron section Vireya (Ericaceae) from Mount Kinabalu, Sabah, Malaysia.  The New Plantsman 7:  209-219.

​

Wood, J. J. & Barkman, T. J.  1998.  Notes on the orchid flora of Mount Kinabalu, Borneo.  Sandakania 12:  7–24.

​

Barkman, T. J., Beaman, J. H. and Gage, D. A.  1997.  Floral fragrance variation in Cypripedium (Orchidaceae):  implications for evolutionary and ecological studies.  Phytochemistry 44(5):  875–882. https://doi.org/10.1016/S0031-9422(96)00614-0

​

Barkman, T. J. & Wood, J. J.  1997.  Re-recognition of Pholidota sigmatochilus:  an enigmatic species from Mt. Kinabalu, Sabah, Malaysia.  Lindleyana 12(3):  153–157.

​

Chan, C. L. & Barkman, T. J.  1997.  A new species of Calanthe (Orchidaceae:  Epidendroideae:  Arethuseae) from Mt.  Kinabalu, Sabah.  Sandakania 9:  27–34.

​

Barkman, T. J. & Wood, J. J.  1996.  A new species of Dendrochilum from Mt. Kinabalu.  Orchid Review 104:  178–182.

​

Kamden, P. D., Gruber, K., Barkman, T. J., and Gage, D. A.  1994.  Characterization of Black Locust Floral Fragrance.  Journal of Essential Oil Research 6:  199–200.