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Tracey Ruhlman - Publications

Affiliations: 
2009- University of Texas at Austin, Austin, Texas, U.S.A. 
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44 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Zhou W, Armijos CE, Lee C, Lu R, Wang J, Ruhlman TA, Jansen RK, Jones AM, Jones CD. Plastid Genome Assembly Using Long-read Data (ptGAUL). Molecular Ecology Resources. PMID 36939021 DOI: 10.1111/1755-0998.13787  0.566
2023 Lee C, Ruhlman TA, Jansen RK. Rate accelerations in plastid and mitochondrial genomes of Cyperaceae occur in the same clades. Molecular Phylogenetics and Evolution. 182: 107760. PMID 36921696 DOI: 10.1016/j.ympev.2023.107760  0.681
2022 Choi IS, Wojciechowski MF, Steele KP, Hopkins A, Ruhlman TA, Jansen RK. Plastid phylogenomics uncovers multiple species in Medicago truncatula (Fabaceae) germplasm accessions. Scientific Reports. 12: 21172. PMID 36477422 DOI: 10.1038/s41598-022-25381-1  0.548
2022 Nefissi Ouertani R, Arasappan D, Ruhlman TA, Ben Chikha M, Abid G, Mejri S, Ghorbel A, Jansen RK. Effects of Salt Stress on Transcriptional and Physiological Responses in Barley Leaves with Contrasting Salt Tolerance. International Journal of Molecular Sciences. 23. PMID 35563398 DOI: 10.3390/ijms23095006  0.462
2022 Choi IS, Cardoso D, de Queiroz LP, de Lima HC, Lee C, Ruhlman TA, Jansen RK, Wojciechowski MF. Highly Resolved Papilionoid Legume Phylogeny Based on Plastid Phylogenomics. Frontiers in Plant Science. 13: 823190. PMID 35283880 DOI: 10.3389/fpls.2022.823190  0.619
2022 Choi IS, Wojciechowski MF, Steele KP, Hunter SG, Ruhlman TA, Jansen RK. Born in the mitochondrion and raised in the nucleus: evolution of a novel tandem repeat family in Medicago polymorpha (Fabaceae). The Plant Journal : For Cell and Molecular Biology. PMID 35061308 DOI: 10.1111/tpj.15676  0.676
2021 Nefissi Ouertani R, Arasappan D, Abid G, Ben Chikha M, Jardak R, Mahmoudi H, Mejri S, Ghorbel A, Ruhlman TA, Jansen RK. Transcriptomic Analysis of Salt-Stress-Responsive Genes in Barley Roots and Leaves. International Journal of Molecular Sciences. 22. PMID 34360920 DOI: 10.3390/ijms22158155  0.484
2021 Choi IS, Wojciechowski MF, Ruhlman TA, Jansen RK. In and out: Evolution of viral sequences in the mitochondrial genomes of legumes (Fabaceae). Molecular Phylogenetics and Evolution. 107236. PMID 34147655 DOI: 10.1016/j.ympev.2021.107236  0.575
2021 Ruhlman TA, Jansen RK. Plastid Genomes of Flowering Plants: Essential Principles. Methods in Molecular Biology (Clifton, N.J.). 2317: 3-47. PMID 34028761 DOI: 10.1007/978-1-0716-1472-3_1  0.592
2021 Lee C, Choi IS, Cardoso D, de Lima HC, de Queiroz LP, Wojciechowski MF, Jansen RK, Ruhlman TA. The chicken or the egg? Plastome evolution and an independent loss of the inverted repeat in papilionoid legumes. The Plant Journal : For Cell and Molecular Biology. PMID 34021942 DOI: 10.1111/tpj.15351  0.639
2021 Shrestha B, Gilbert LE, Ruhlman TA, Jansen RK. Clade-Specific Plastid Inheritance Patterns Including Frequent Biparental Inheritance in Interspecific Crosses. International Journal of Molecular Sciences. 22. PMID 33668897 DOI: 10.3390/ijms22052278  0.471
2020 Choi IS, Jansen R, Ruhlman T. Caught in the Act: Variation in plastid genome inverted repeat expansion within and between populations of . Ecology and Evolution. 10: 12129-12137. PMID 33209275 DOI: 10.1002/ece3.6839  0.581
2020 Su Choi K, Weng ML, Ruhlman TA, Jansen RK. Extensive variation in nucleotide substitution rate and gene/intron loss in mitochondrial genomes of Pelargonium. Molecular Phylogenetics and Evolution. 106986. PMID 33059063 DOI: 10.1016/j.ympev.2020.106986  0.635
2020 Ren Y, Yu M, Low WY, Ruhlman TA, Hajrah NH, El Omri A, Alghamdi MK, Sabir MJ, Alhebshi AM, Kamli MR, Sabir JSM, Theriot EC, Jansen RK, Rather IA. Nucleotide substitution rates of diatom plastid encoded protein genes are positively correlated with genome architecture. Scientific Reports. 10: 14358. PMID 32873883 DOI: 10.1038/S41598-020-71473-1  0.66
2020 Gonçalves DJP, Jansen RK, Ruhlman TA, Mandel JR. Under the rug: Abandoning persistent misconceptions that obfuscate organelle evolution. Molecular Phylogenetics and Evolution. 151: 106903. PMID 32628998 DOI: 10.1016/J.Ympev.2020.106903  0.674
2020 Shrestha B, Gilbert LE, Ruhlman TA, Jansen RK. Rampant nuclear transfer and substitutions of plastid genes in Passiflora. Genome Biology and Evolution. PMID 32539116 DOI: 10.1093/Gbe/Evaa123  0.591
2020 Lee C, Ruhlman TA, Jansen RK. Unprecedented intraindividual structural heteroplasmy in Eleocharis (Cyperaceae, Poales) plastomes. Genome Biology and Evolution. PMID 32282915 DOI: 10.1093/Gbe/Evaa076  0.659
2020 Choi IS, Ruhlman TA, Jansen RK. Comparative Mitogenome Analysis of the Genus Reveals Independent Gene Fission of and Intracellular Gene Transfers in Fabaceae. International Journal of Molecular Sciences. 21. PMID 32183014 DOI: 10.3390/Ijms21061959  0.702
2019 Choi IS, Schwarz EN, Ruhlman TA, Khiyami MA, Sabir JSM, Hajarah NH, Sabir MJ, Rabah SO, Jansen RK. Fluctuations in Fabaceae mitochondrial genome size and content are both ancient and recent. Bmc Plant Biology. 19: 448. PMID 31653201 DOI: 10.1186/S12870-019-2064-8  0.656
2019 Shrestha B, Weng ML, Theriot EC, Gilbert LE, Ruhlman TA, Krosnick SE, Jansen RK. Highly accelerated rates of genomic rearrangements and nucleotide substitutions in plastid genomes of Passiflora subgenus Decaloba. Molecular Phylogenetics and Evolution. PMID 31129347 DOI: 10.1016/J.Ympev.2019.05.030  0.69
2019 Choi IS, Jansen R, Ruhlman T. Lost and Found: Return of the Inverted Repeat in the Legume Clade Defined by Its Absence. Genome Biology and Evolution. 11: 1321-1333. PMID 31046101 DOI: 10.1093/Gbe/Evz076  0.637
2019 van de Kerke SJ, Shrestha B, Ruhlman TA, Weng ML, Jansen RK, Jones CS, Schlichting CD, Hosseini S, Mohammadin S, Eric Schranz M, Bakker FT. Plastome based phylogenetics and younger crown node age in Pelargonium. Molecular Phylogenetics and Evolution. PMID 30926482 DOI: 10.1016/J.Ympev.2019.03.021  0.524
2018 Rabah SO, Shrestha B, Hajrah NH, Sabir MJ, Alharby HF, Sabir MJ, Alhebshi AM, Sabir JS, Gilbert LE, Ruhlman TA, Jansen RK. Passifloraplastome sequencing reveals widespread genomic rearrangements Journal of Systematics and Evolution. 57: 1-14. DOI: 10.1111/Jse.12425  0.642
2017 Rabah SO, Lee C, Hajrah NH, Makki RM, Alharby HF, Alhebshi AM, Sabir JSM, Jansen RK, Ruhlman TA. Plastome Sequencing of Ten Nonmodel Crop Species Uncovers a Large Insertion of Mitochondrial DNA in Cashew. The Plant Genome. 10. PMID 29293812 DOI: 10.3835/Plantgenome2017.03.0020  0.669
2017 Park S, Ruhlman TA, Weng ML, Hajrah NH, Sabir JSM, Jansen RK. Contrasting Patterns of Nucleotide Substitution Rates Provide Insight into Dynamic Evolution of Plastid and Mitochondrial Genomes of Geranium. Genome Biology and Evolution. 9: 1766-1780. PMID 28854633 DOI: 10.1093/Gbe/Evx124  0.676
2017 Ruhlman TA, Zhang J, Blazier JC, Sabir JS, Jansen RK. Recombination-dependent replication and gene conversion homogenize repeat sequences and diversify plastid genome structure. American Journal of Botany. PMID 28400415 DOI: 10.3732/Ajb.1600453  0.646
2017 Schwarz EN, Ruhlman TA, Weng ML, Khiyami MA, Sabir JS, Hajarah NH, Alharbi NS, Rabah SO, Jansen RK. Plastome-Wide Nucleotide Substitution Rates Reveal Accelerated Rates in Papilionoideae and Correlations with Genome Features Across Legume Subfamilies. Journal of Molecular Evolution. PMID 28397003 DOI: 10.1007/S00239-017-9792-X  0.577
2016 Weng ML, Ruhlman TA, Jansen RK. Expansion of inverted repeat does not decrease substitution rates in Pelargonium plastid genomes. The New Phytologist. PMID 27991660 DOI: 10.1111/Nph.14375  0.638
2016 Sabir JS, Jansen RK, Arasappan D, Calderon V, Noutahi E, Zheng C, Park S, Sabir MJ, Baeshen MN, Hajrah NH, Khiyami MA, Baeshen NA, Obaid AY, Al-Malki AL, Sankoff D, ... ... Ruhlman TA, et al. The nuclear genome of Rhazya stricta and the evolution of alkaloid diversity in a medically relevant clade of Apocynaceae. Scientific Reports. 6: 33782. PMID 27653669 DOI: 10.1038/Srep33782  0.678
2016 Blazier JC, Jansen RK, Mower JP, Govindu M, Zhang J, Weng ML, Ruhlman TA. Variable presence of the inverted repeat and plastome stability in Erodium. Annals of Botany. PMID 27192713 DOI: 10.1093/Aob/Mcw065  0.604
2016 Weng ML, Ruhlman TA, Jansen RK. Plastid-nuclear interaction and accelerated coevolution in plastid ribosomal genes in Geraniaceae. Genome Biology and Evolution. PMID 27190001 DOI: 10.1093/Gbe/Evw115  0.642
2016 Blazier JC, Ruhlman TA, Weng ML, Rehman SK, Sabir JS, Jansen RK. Divergence of RNA polymerase α subunits in angiosperm plastid genomes is mediated by genomic rearrangement. Scientific Reports. 6: 24595. PMID 27087667 DOI: 10.1038/Srep24595  0.687
2016 Zhang J, Ruhlman TA, Sabir J, Blazier JC, Weng ML, Park S, Jansen RK. Coevolution between nuclear encoded DNA replication, recombination and repair genes and plastid genome complexity. Genome Biology and Evolution. PMID 26893456 DOI: 10.1093/Gbe/Evw033  0.599
2015 Park S, Grewe F, Zhu A, Ruhlman TA, Sabir J, Mower JP, Jansen RK. Dynamic evolution of Geranium mitochondrial genomes through multiple horizontal and intracellular gene transfers. The New Phytologist. PMID 25989702 DOI: 10.1111/Nph.13467  0.695
2015 Ruhlman TA, Chang WJ, Chen JJ, Huang YT, Chan MT, Zhang J, Liao DC, Blazier JC, Jin X, Shih MC, Jansen RK, Lin CS. NDH expression marks major transitions in plant evolution and reveals coordinate intracellular gene loss. Bmc Plant Biology. 15: 100. PMID 25886915 DOI: 10.1186/S12870-015-0484-7  0.553
2015 Zhang J, Ruhlman TA, Sabir J, Blazier JC, Jansen RK. Coordinated rates of evolution between interacting plastid and nuclear genes in Geraniaceae. The Plant Cell. 27: 563-73. PMID 25724640 DOI: 10.1105/Tpc.114.134353  0.68
2015 Schwarz EN, Ruhlman TA, Sabir JSM, Hajrah NH, Alharbi NS, Al-Malki AL, Bailey CD, Jansen RK. Plastid genome sequences of legumes reveal parallel inversions and multiple losses of rps16 in papilionoids Journal of Systematics and Evolution. 53: 458-468. DOI: 10.1111/jse.12179  0.627
2014 Park S, Ruhlman TA, Sabir JS, Mutwakil MH, Baeshen MN, Sabir MJ, Baeshen NA, Jansen RK. Complete sequences of organelle genomes from the medicinal plant Rhazya stricta (Apocynaceae) and contrasting patterns of mitochondrial genome evolution across asterids. Bmc Genomics. 15: 405. PMID 24884625 DOI: 10.1186/1471-2164-15-405  0.689
2014 Sabir J, Schwarz E, Ellison N, Zhang J, Baeshen NA, Mutwakil M, Jansen R, Ruhlman T. Evolutionary and biotechnology implications of plastid genome variation in the inverted-repeat-lacking clade of legumes. Plant Biotechnology Journal. 12: 743-54. PMID 24618204 DOI: 10.1111/Pbi.12179  0.707
2014 Ruhlman TA, Jansen RK. The plastid genomes of flowering plants. Methods in Molecular Biology (Clifton, N.J.). 1132: 3-38. PMID 24599844 DOI: 10.1007/978-1-62703-995-6_1  0.592
2013 Zhang J, Ruhlman TA, Mower JP, Jansen RK. Comparative analyses of two Geraniaceae transcriptomes using next-generation sequencing. Bmc Plant Biology. 13: 228. PMID 24373163 DOI: 10.1186/1471-2229-13-228  0.666
2012 Weng ML, Ruhlman TA, Gibby M, Jansen RK. Phylogeny, rate variation, and genome size evolution of Pelargonium (Geraniaceae). Molecular Phylogenetics and Evolution. 64: 654-70. PMID 22677167 DOI: 10.1016/J.Ympev.2012.05.026  0.61
2010 Ruhlman T, Verma D, Samson N, Daniell H. The Role of Heterologous Chloroplast Sequence Elements in Transgene Integration and Expression Plant Physiology. 152: 2088-2104. PMID 20130101 DOI: 10.1104/Pp.109.152017  0.404
2006 Ruhlman T, Lee SB, Jansen RK, Hostetler JB, Tallon LJ, Town CD, Daniell H. Complete plastid genome sequence of Daucus carota: implications for biotechnology and phylogeny of angiosperms. Bmc Genomics. 7: 222. PMID 16945140 DOI: 10.1186/1471-2164-7-222  0.701
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