My primary research interests involve the determination of phylogenetic relationships among plants and genome evolution.

Research in my lab is concentrated in four areas: (1) organization and evolution of plastid genomes; (2) computational methods for comparative  genomics, (3) coordinated evolution between mitochondrial. nuclear and plastid genomes, and (4) systematics and the evolution of the Geraniaceae and Fabaceae.

Google Scholar Link:

https://scholar.google.com/citations?hl=en&user=utnDy7MAAAAJ

Google Scholar Link: https://scholar.google.com/citations?hl=en&user=utnDy7MAAAAJ 

Ruhlman T.A. and Jansen R.K. 2018. Aberration or analogy? The atypical plastomes of Geraniaceae. In: Chaw, S.-M., Jansen R.K. (Eds.), Advances in Botanical Research 85: Plastid Genome Evolution. Elsevier, Amsterdam, The Netherlands, Chapter 8, pp 223-262. https://doi.org/10.1016/bs.abr.2017.11.017.

Yu, M., Ashworth, M.P., Hajrah, N.H., Khiyami, M.A., Sabir, M.J., Alhebshi, A.M., Al-Malki, A.L., Sabir, J.S.M., Theriot, E.C., Jansen, R.K. 2018. Evolution of the plastid genomes in diatoms. In: Chaw, S.-M., Jansen R.K. (Eds.), Advances in Botanical Research 85: Plastid Genome Evolution. Elsevier, Amsterdam, The Netherlands, Chapter 5, 33 pp. https://doi.org/10.1016/bs.abr.2017.11.009.

Sabir J.M.S., Theriot E.C., Lobban C.S., Alhebshi A., Al-Malki A.L., Hajrah N.H., Khiyami M.A., Jansen, R.K., Ashworth M.P. 2018. Systematics of araphid diatoms with asymmetric rimoportulae or densely packed fascicles, with a redefinition of Hyalosynedra Round and Williams, and a description of two new genera and twelve new species, including five from the Red Sea. Phytotaxa 347 (1): 001–049.

Weng M.-L., Ruhlman T.A. and Jansen R.K. 2017. Expansion of inverted repeat does not decrease substitution rates in Pelargonium plastid genomes. New Phytologist 214: 842–851.

Mutwakil M.Z., Hajrah N.H., Atef A., Edris S., Sabir M.J., Nelson C.A., Makki R.M., Hani M., El-Domyati F.M., Al-Hajar A.S.M., Sabir J.S.M., Jansen R.K., Bahieldin A, Hall N. 2017. Transcriptomic and metabolic responses of Calotropis procera to salt and drought stress. BMC Plant Biology 17: 231.

Gruenstaeudl M., Carstens B.C., Santos-Guerra A., and Jansen R.K. 2017. The impact of hybrid taxa on ancestral area reconstructions of Tolpis (Asteraceae). Biological Journal of the Linnaean Society 121 (1): 133-149.

Ruhlman T.A., Zhang J., Blazier J.C., Sabir J.S.M., Jansen R.K. 2017. Recombination-dependent replication and gene conversion homogenize repeat sequences and diversify plastid genome structure. American Journal of Botany 104: 1–14.

Schwarz E.N., Ruhlman T.A., Weng M.-L., Khiyami M.A., Sabir J.M.S., Hajarah N.H., Alharbi N.S., Rabah S.O., and Jansen R.K. 2017. Plastome-wide nucleotide substitution rates reveal accelerated rates in Papilionoideae and correlations with genome features across legume subfamilies. Journal of Molecular Evolution 84: 187-203.

Park S., Ruhlman T.A., Weng M.-L., Hajrah N.H., Sabir J.M.S., and Jansen R.K. 2017. Contrasting patterns of nucleotide substitution rates provide insights into dynamic evolution of plastid and mitochondrial genomes of Geranium. Genome Biology and Evolution 9: 1766-1780. DOI: https://doi.org/10.1093/gbe/evx124.

Rabah S.O., Lee C, Hajrah N.H., Makki R.M., Alharby H.F., Alhebshi A.M., Sabir J.M.S., Jansen, R.K., and Ruhlman T.A. 2017. Plastome sequencing of 10 non-model crop species uncovers a recent, large insertion of mitochondrial DNA in cashew (Anacardium, Anacardiaceae). The Plant Genome, doi: 10.3835/plantgenome2017.03.0020.

Hajrah N.H., Obaid A.Y., Atef A., Ramadan A.M., Arasappan D., Nelson C.A., Edris S., Mutwakil M.Z., Alhebshi, A., Gadalla N.O., Makki R.M., Al-Kordy M.A., El-Domyati F.M., Sabir J.S.M., Khiyami M.A., Hall N., Bahieldin A, and Jansen R.K. 2017. Transcriptomic analysis of salt stress responsive genes in Rhazya stricta. PLoS ONE 12: e0177589. https://doi.org/10.1371/journal.pone.0177589. pone.0177589.

Sabir J.S.M.*, Jansen R.K.*, Arasappan D., Calderon V., Noutahi E., Zheng C., Park S., Sabir M.J., Baeshen M.N., Hajrah N.H., Khiyami M.A., Baeshen N.A., Obaid A.Y., Al-Malki A.L., Sankoff D., El-Mabrouk N. and Ruhlman T.A.  2016. The nuclear genome of Rhazya stricta and the evolution of alkaloid diversity in a medically relevant clade of Apocynaceae. Scientific Reports 6:33782, DOI: 10.1038/srep33782.  *co-first authors.

Weng M.-L., Ruhlman T.A. and Jansen R.K.  2016. Nonsynonymous substitutions in nuclear-encoded plastid targeted genes drive evolution of plastid-encoded genes in Geraniaceae.  Genome Biology and Evolution 8:1824-1838, doi: 10.1093/gbe/evw115. 

Blazier J.C., Jansen R.K., Mower J.P., Govindu M., Zhang J., Weng M.-L., and Ruhlman T.A.  2016. Variable presence of the inverted repeat and plastome stability in Erodium.  Annals of Botany 117:1209-1220, doi:10.1093/aob/mcw065.

Blazier J.C., Ruhlman T.A., Weng M.-L., Rehman S.K., Sabir J.S.M., and Jansen R.K.  2016. Divergence of RNA polymerase α subunits in angiosperm plastid genomes is mediated by genomic rearrangement.  Scientific Reports 6:24595, DOI: 10.1038/srep24595.

Zhang J., Ruhlman T.A., Sabir J.S.M., Blazier J.C., Weng M.-L., Park S., and Jansen R.K.  2016. Coevolution between nuclear encoded DNA replication, recombination and repair genes and plastid genome complexity.  Genome Biology and Evolution 8: 622-634, doi:10.1093/gbe/evw033.

Dugas D.V., Hernandez D., Koenen E., Schwarz E., Straub S., Hughes C.E., Jansen R.K., Nageswara-Rao M., Staats M., Trujillo J., Hajrah N.H., Alharbi N.S., Al-Malki A.L., Sabir J.S.M., and Bailey C.D.  2015. Mimosoid legume plastome evolution: IR expansion, tandem repeat expansions, and accelerated rate of evolution in clpP. Scientific Reports 5: 16958.

Schwarz E., Ruhlman T.A., Sabir J.S.M., Hajrah N.H., Alharbi N.S., Al-Malki A.L., Bailey C.D. and Jansen R.K.  2015. 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.

Park S., Grewe F., Zhu A., Ruhlman T.A., Sabir H., Mower J.P., and Jansen R.K.  2015. Dynamic evolution of Geranium mitochondrial genomes through multiple horizontal and intracellular gene transfers.  New Phytologist 208: 570-583.  DOI: 10.1111/nph.13467.

Li C.L., Ashworth M.P., Witkowski A., Dabek P., Medlin L.K., Kooistra W.H.C.F., Sato S., Zglobicka I., Kurzydlowski K.J., Theriot E.C., Sabir J.S.M., Khiyami M.A., Mutwakil M.H.Z., Sabir M.J., Alharbi N.S., Hajarah N.H., Qing S. and Jansen R.K. 2015.  New insights into Plagiogrammaceae (Bacillariophyta) based on multigene phylogenies and morphological characteristics with the description of a new genus and three new species. PLoS ONE 10(10): e0139300. doi:10.1371/journal.pone.0139300.

Ruhlman T.A., Chang W.J., Chen J.J.W., Huang Y.-T., Chan M.-T., Zhang J., Liao D.-C., Blazier J.C., Jin X., Shih M.-C., Jansen R.K., and Lin C.-S.  2015. NDH expression marks major transitions in plant evolution and reveals coordinate intracellular gene loss.  BMC Plant Biology 15: 100.

Theriot E.C., Ashworth M., Nakov T., Ruck E., and Jansen R.K.  2015.  Dissecting signal and noise in Diatom chloroplast protein encoding genes with phylogenetic information profiling.  Molecular Phylogenetics and Evolution 89: 28-36.

Zhang J., Ruhlman T.A., Sabir J.S.M., Blazier J.C. and Jansen R.K.  2015. Coordinated rates of evolution between interacting plastid and nuclear genes in Geraniaceae.  Plant Cell 27: 563-573.

Park S., Jansen R.K., Park S-J.  2015. Complete plastome sequence of Thalictrum coreanum (Ranunculaceae) and the transfer of ribosomal protein L32 to the nucleus in the ancestor of the subfamily Thalictroideae. BMC Plant Biology 15:40.

Downie SR and Jansen RK.  2015. A comparative analysis of whole plastid genomes from the Apiales: expansion and contraction of the inverted repeat, mitochondrial to plastid transfer of DNA, and identification of highly divergent noncoding regions. Systematic Botany 40: 336–351.

Park S, Ruhlman TA, Sabir JSM, Mutwakil MHZ, Baeshen MN, Sabir MJ, Baeshen NA, Jansen RK. 2014. 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.

Ruck EC, Nakov T, Jansen RK, Theriot EC, Alverson AJ.  2014. Serial gene losses and foreign DNA underlie size and sequence variation in the plastid genomes of diatoms.  Genome Biology and Evolution 6: 644-654, doi:10.1093/gbe/evu039. 

Weng, M.-L., Blazier, J.C., Govindu, M., Jansen, R.K. 2014. Reconstruction of the ancestral plastid genome in Geraniaceae reveals a correlation between genome rearrangements, repeats and nucleotide substitution rates. Molecular Biology and Evolution, doi: 10.1093/molbev/mst257.

Gruenstaeudl M., Santos-Guerra A, Jansen RK.  2013.  Phylogenetic analyses of Tolpis Adans. (Asteraceae) reveal patterns of adaptive radiation, multiple colonization, and interspecific hybridization. Cladistics 29: 416-434.

Zhang J, Ruhlman TA, Mower JP, Jansen RK. 2013.  Comparative analyses of two Geraniaceae transcriptomes using next-generation sequencing. BMC Plant Biology 13:228.

Sabir JS, Baeshen NA, Shokry AM, Gadalla NO, Edris S, Mutwakil MH, Ramadan AM, Atef A, Al-Kordy MA, Abuzinadah OA, El-Domyati FM, Jansen RK, Bahieldin A. 2013.  Detection of phytochrome-like genes from Rhazya stricta (Apocynaceae) using de novo genome assembly. C R Biologies 336: 521-529

Alzohairy A.M., Gyulai G., Jansen R.K., Bahieldin A.  2013.  Transposable elements domesticated and neofunctionalized by eukaryotic genomes. Plasmid 69: 1-15.

Weng M.-L., Ruhlman T.A., Gibby M., and R. K. Jansen.  2012.  Phylogeny, rate variation, and genome size evolution of Pelargonium (Geraniaceae). Molecular Phylogenetics and Evolution 64: 654-670.

Jansen, R.K. and T.A. Ruhlman.   2012.  Plastid genomes of seed plants. In: Advances in Photosynthesis and Respiration 35, Genomics of chloroplasts and mitochondria.  Bock, R. and Knoop, V. (eds), Springer, Dordrecht Advances, pp. 103–126.

Blazier J.C., Guisinger M.M., Jansen R.K. 2011.  Recent loss of plastid-encoded ndh genes within Erodium (Geraniaceae).  Plant Molecular Biology 76: 263-272.

Jansen, RK, C Saski, S-B Lee, A K Hansen, and H Daniell.  2011.  Complete plastid genome sequences of three rosids (Castanea, Prunus, Theobroma): evidence for at least two independent transfers of rpl22 to the nucleus.  Molecular Biology and Evolution 28: 835-847 

Guisinger MM, Kuehl JV, Boore JL, and RK Jansen.  2011.  Extreme Reconfiguration of Plastid Genomes in the Angiosperm Family Geraniaceae: Rearrangements, Repeats, and Codon Usage.  Molecular Biology and Evolution 28: 583-600.

Guisinger, M.M., T.W. Chumley, J.V. Kuehl, J.L. Boore, and R.K. Jansen.  2010.  Implications of the plastid genome sequence of Typha latifolia (Typhaceae, Poales) for understanding genome evolution in Poaceae. Journal of Molecular Evolution 70: 149-166 

Haberle, R.S., A. Dang, T. Lee, C. Penaflor, H. Cortes-Burns, A. Oestreich, L. Raubeson, E. Edwards, S.-T. Tang, N. Cellinese, W.M.M. Eddie, and R.K. Jansen.  2009.  Molecular systematics of Campanulaceae sensu stricto using chloroplast DNA sequences of atpB, matK, and rbcL. Taxon 58: 715–734 

Guisinger MM, Kuehl JV, Boore JL, Jansen RK.  2008.  Genome-wide analyses of Geraniaceae plastid DNA reveal unprecedented patterns of increased nucleotide substitutions. Proc Natl Acad Sci U S A 105(47): 18424-9. 

Cai Z, Guisinger M, Kim HG, Ruck E, Blazier JC, McMurtry V, Kuehl JV, Boore J, Jansen RK.  2008.  Extensive reorganization of the plastid genome of Trifolium subterraneum (Fabaceae) is associated with numerous repeated sequences and novel DNA insertions, J Mol Evol 67(6): 696-704.

Raubeson, L.A., Peery, R., Chumley, T., Dziubek, C,, Fourcade, H.M., Boore, J.L., Jansen, R.K.  2007.  Comparative chloroplast genomics: analyses including new sequences from the angiosperms Nuphar advena and Ranunculus macranthus, BMC Genomics 8: 174.

Jansen, R. K., Cai, Z., Raubeson, L.A., Daniell, H., dePamphilis, C.W., Leebens-Mack, J., Müller, K.F., Guisinger-Bellian, M., Haberle, R.C., Hansen, A.K., Chumley, T.W., Lee, S.-B., Peery, R., McNeal, J., Kuehl, J.V., and Boore, J.L. 2007. Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns. Proceedings of the National Academy of Sciences USA 104: 19369-19374.

Hansen, D.R., Dastidar, S.G., Cai, Z., Penaflor, C., Kuehl, J.V., Boore, J.L., Jansen, R.K.  2007.  Phylogenetic and evolutionary implications of complete chloroplast genome sequences of four early-diverging angiosperms: Buxus (Buxaceae), Chloranthus (Chloranthaceae), Dioscorea (Dioscoreaceae), and Illicium (Schisandraceae), Mol Phylogenet Evol 45: 547-563 

Jansen, R.K., C. Kaittanis, C. Saski, S-B. Lee, J. Tompkins, A. J. Alverson, and, H. Daniell.  2006.  Phylogenetic analyses of Vitis (Vitaceae) based on complete chloroplast genome sequences: Effects of taxon sampling and phylogenetic methods on resolving relationships among Rosids, BMC Evolutionary Biology 6: 32 

Cui, L., N. Veeraraghavan, K. Wall, R.K. Jansen, J. Leebens-Mack, I. Makalowska, C. W. dePamphilis. 2006. ChloroplastDB: the chloroplast genome database, Nucleic Acids Research 34: D692-D696

Chumley, T.W., J.D. Palmer, J.P. Mower, J.L. Boore, H.M. Fourcade, P.J. Caile, and R.K. Jansen.  2006.  The completed chloroplast genome sequence of Pelargonium x hortorum: Organization and evolution of the largest and most highly rearranged chloroplast genome of land plants, Molecular Biology and Evolution 23: 1-16 

Leebens-Mack, J., L.A. Raubeson, L. Cui, J. Kuehl, M. Fourcade, T. Chumley, J.L. Boore, R.K. Jansen, and C.W. dePamphilis.  2005.  Identifying the basal angiosperms in chloroplast genome phylogenies: Sampling one's way out of the Felsenstein zone. Molecular Biology and Evolution 22: 1948-1963 

Wyman, S.K., J.L. Boore, and R.K. Jansen.  2004.   Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20: 3252-325 

ISI Highly cited 2002 - present

Honorary Distinguished Professor, King Abdulaziz University, Faculty of Science, Genomics and Biotechnology Section, Department of Biological Sciences 2011 - present