Publications
*indicates co-first authors
In review or revision
Phillips M.A., Briar R.K., Scaffo M., Zhou S., Burke M.K. Strength of selection potentiates distinct adaptive responses in an evolution experiment with outcrossing yeast. In Review (bioRxiv: https://doi.org/10.1101/2022.05.19.492575)
Wanjalla C., Obare L., Bailin S., Zhang X., Nthenge K., Priest S., Liu Q., Stolze L., Sheng Q., Gangula R., Behrens M., Jenkins B., Prasad P., Neikirk K., Prakash P., Hogan M., Zhang L., Beasley H.K., Shao J., Miller-Fleming T.W., Actkins K.V., Phillips M.A., Hubert D.L, Malone J., Labeb C., Gelbard A., Chaillon A., Mashayekhi M., Gabriel C., Temu T.M., Olson L.M., Jones A., Beeri K., Baker P.G., Kawai K., Ghosh S.K.B., Guo L., Virmani R., Finn A.V., Shah P., Yang T., Bick A., Kirabo A., Su Y., Phillips E., Mallal S., Dash C., Koethe J., Gianella S., McReynolds M.R., Absi T., Hinton A. HIV persists in late coronary atheroma and is associated with increased local inflammation and disease progression. In Review (ResearchSquare: https://doi.org/10.21203/rs.3.rs-5125826/v1)
Vue Z., Murphy A., Le H., Neikirk K., Garza-Lopez E., Marshall A.G., Mungai M., Jenkins B., Vang L., Beasley H.K., Ezedimma M., Manus S., Whiteside A., Forni M.F., Harris C., Crabtree A., Albritton C.F., Jamison S., Demirci M., Prasad P., Oliver A., Actkins K.V., Shao J., Zaganjor E., Scudese E., Rodriguez B., Koh A., Rabago I., Moore J.E., Nguyen D., Aftab M., Kirk B., Li Y., Wandira N., Ahmad T., Saleem M., Kadam A., Katti P., Koh H.-J., Evans C., Koo Y.D., Wang E., Smith Q., Tomar D., Williams C.R., Sweetwyne M.T., Quintana A.M., Phillips M.A., Hubert D.L., Kirabo A., Dash C., Jadiya P., Kinder A., Ajijola O.A., Miller-Fleming T.W., McReynolds M.R., Hinton A. MICOS complex loss governs age-associated murine mitochondrial architecture and metabolism in the liver, while SAM50 dictates diet changes. In Review (bioRxiv: https://doi.org/10.1101/2024.06.28.601037)
Vue Z., Prasad P., Le H., Neikirk K., Harris C., Garza-Lopez E., Wang E., Murphy A., Jenkins B., Vang L., Scudese E., Shao B., Kadam A., Shao J., Marshall A.G., Crabtree A., Kirk B., Koh A., Wilson G., Oliver A., Rodman T., Kabugi K., Koh H.-J., Smith Q., Zaganjor E., Wanjalla C.N., Dash C., Evans C., Phillips M.A., Hubert D.L., Ajijola O., Whiteside A., Koo Y.D., Kinder A., Demirci M., Albritton C.F., Wandira N., Jamison S., Ahmed T., Saleem M., Tomar D., Williams C.R., Sweetwyne M.T., Murray S.A., Cooper A., Kirabo A., Jadiya P., Quintana A., Katti P., Dai D.F., McReynolds M.R., Hinton A. The MICOS complex regulates mitochondrial structure and oxidate stress during age-dependent structural deficits in the kidney. In Review (bioRxiv: https://doi.org/10.1101/2024.06.09.598108)
Vue Z., Ajayi P.T., Neikirk K., Murphy A.C., Prasad P., Jenkins B.C., Vang L., Garza-Lopez E., Mungai M., Marshall A.G., Beasley H.K., Killion M., Parker R., Anukodem J., Lavine K., Ajijola O., Mobley B.C., Dai D.-F., Exil V., Kirabo A., Su Y.R., Tomasek K., Zhang X., Wanjalla C., Hubert D.L., Phillips M.A., Shao J., McReynolds M.R., Glancy B., Hinton A. Human heart failure alters mitochondria and fiber 3D structure triggering metabolic shifts. In Review (bioRxiv: https://doi.org/10.1101/2023.11.28.569095)
Wanjalla C., Obare L., Bailin S., Zhang X., Nthenge K., Priest S., Liu Q., Stolze L., Sheng Q., Gangula R., Behrens M., Jenkins B., Prasad P., Neikirk K., Prakash P., Hogan M., Zhang L., Beasley H.K., Shao J., Miller-Fleming T.W., Actkins K.V., Phillips M.A., Hubert D.L, Malone J., Labeb C., Gelbard A., Chaillon A., Mashayekhi M., Gabriel C., Temu T.M., Olson L.M., Jones A., Beeri K., Baker P.G., Kawai K., Ghosh S.K.B., Guo L., Virmani R., Finn A.V., Shah P., Yang T., Bick A., Kirabo A., Su Y., Phillips E., Mallal S., Dash C., Koethe J., Gianella S., McReynolds M.R., Absi T., Hinton A. HIV persists in late coronary atheroma and is associated with increased local inflammation and disease progression. In Review (ResearchSquare: https://doi.org/10.21203/rs.3.rs-5125826/v1)
Vue Z., Murphy A., Le H., Neikirk K., Garza-Lopez E., Marshall A.G., Mungai M., Jenkins B., Vang L., Beasley H.K., Ezedimma M., Manus S., Whiteside A., Forni M.F., Harris C., Crabtree A., Albritton C.F., Jamison S., Demirci M., Prasad P., Oliver A., Actkins K.V., Shao J., Zaganjor E., Scudese E., Rodriguez B., Koh A., Rabago I., Moore J.E., Nguyen D., Aftab M., Kirk B., Li Y., Wandira N., Ahmad T., Saleem M., Kadam A., Katti P., Koh H.-J., Evans C., Koo Y.D., Wang E., Smith Q., Tomar D., Williams C.R., Sweetwyne M.T., Quintana A.M., Phillips M.A., Hubert D.L., Kirabo A., Dash C., Jadiya P., Kinder A., Ajijola O.A., Miller-Fleming T.W., McReynolds M.R., Hinton A. MICOS complex loss governs age-associated murine mitochondrial architecture and metabolism in the liver, while SAM50 dictates diet changes. In Review (bioRxiv: https://doi.org/10.1101/2024.06.28.601037)
Vue Z., Prasad P., Le H., Neikirk K., Harris C., Garza-Lopez E., Wang E., Murphy A., Jenkins B., Vang L., Scudese E., Shao B., Kadam A., Shao J., Marshall A.G., Crabtree A., Kirk B., Koh A., Wilson G., Oliver A., Rodman T., Kabugi K., Koh H.-J., Smith Q., Zaganjor E., Wanjalla C.N., Dash C., Evans C., Phillips M.A., Hubert D.L., Ajijola O., Whiteside A., Koo Y.D., Kinder A., Demirci M., Albritton C.F., Wandira N., Jamison S., Ahmed T., Saleem M., Tomar D., Williams C.R., Sweetwyne M.T., Murray S.A., Cooper A., Kirabo A., Jadiya P., Quintana A., Katti P., Dai D.F., McReynolds M.R., Hinton A. The MICOS complex regulates mitochondrial structure and oxidate stress during age-dependent structural deficits in the kidney. In Review (bioRxiv: https://doi.org/10.1101/2024.06.09.598108)
Vue Z., Ajayi P.T., Neikirk K., Murphy A.C., Prasad P., Jenkins B.C., Vang L., Garza-Lopez E., Mungai M., Marshall A.G., Beasley H.K., Killion M., Parker R., Anukodem J., Lavine K., Ajijola O., Mobley B.C., Dai D.-F., Exil V., Kirabo A., Su Y.R., Tomasek K., Zhang X., Wanjalla C., Hubert D.L., Phillips M.A., Shao J., McReynolds M.R., Glancy B., Hinton A. Human heart failure alters mitochondria and fiber 3D structure triggering metabolic shifts. In Review (bioRxiv: https://doi.org/10.1101/2023.11.28.569095)
2025
Hubert D.L., Arnold K.R., Greenspan Z.G., Pupo A., Robinson R.D., Chavarin V.V., Barter T.T., Djukovic D., Raftery D., Vue Z, Hinton A., McReynolds M.R., Harrison B.R., Phillips M.A. Selection for early reproduction leads to accelerated aging and extensive metabolic remodeling in Drosophila melanogaster populations. Accepted Genome Biology and Evolution evaf082 https://doi.org/10.1093/gbe/evaf082
Scudese E., Vue Z., Katti P., Marshall A.G., Demirci M., Vang L., Garza López E., Neikirk K., Shao B., Le H., Stephens D., Hall D.D., Rostami R., Rodman T., Kabugi K., Harris C., Shao J., Mungai M., AshShareef S.T., Hicsasmaz I., Manus S., Wanjalla C., Whiteside A., Dasari R., Williams C., Damo S.M., Gaddy J.A., Glancy B., Dantas E.H.M., Kinder A., Kadam A., Tomar D., Scartoni F., Baffi M., McReynolds M.R., Phillips M.A., Cooper A., Murray S.A., Quintana A.M., Exil V., Kirabo A., Mobley B.C., Hinton A. 3D mitochondrial structure in aging human skeletal muscles: Insights into MFN-2 mediated changes. Aging Cell e70054. https://doi.org/10.1111/acel.70054
Scudese E., Vue Z., Katti P., Marshall A.G., Demirci M., Vang L., Garza López E., Neikirk K., Shao B., Le H., Stephens D., Hall D.D., Rostami R., Rodman T., Kabugi K., Harris C., Shao J., Mungai M., AshShareef S.T., Hicsasmaz I., Manus S., Wanjalla C., Whiteside A., Dasari R., Williams C., Damo S.M., Gaddy J.A., Glancy B., Dantas E.H.M., Kinder A., Kadam A., Tomar D., Scartoni F., Baffi M., McReynolds M.R., Phillips M.A., Cooper A., Murray S.A., Quintana A.M., Exil V., Kirabo A., Mobley B.C., Hinton A. 3D mitochondrial structure in aging human skeletal muscles: Insights into MFN-2 mediated changes. Aging Cell e70054. https://doi.org/10.1111/acel.70054
2024
Greenspan Z.S., Barter T.T., Phillips M.A., Ranz J.M., Rose M.R., Mueller L.D. Genomewide architecture of adaptation in experimentally evolved Drosophila characterized by widespread pleiotropy. Journal of Genetics 103:8.
2023
Vue Z., Garza-Lopez E., Neikirk K., Katti P., Vang L., Beasley H.K., Jianqiang S., Marshall A.G., Crabtree A., Murphy A.C., Jenkin B.C., Prasad P., Evans C., Taylor B., Mungai M., Killion M., Stephens D., Christensen T.A., Lam J., Rodriguez B., Phillips M.A., Daneshgar N., Koh H-J., Koh A., Davis J., Devine N., Muhammod S., Scudese E., Arnold K.R., Chavarin V.V., Robinson R.D., Chakraborty M., Gaddy J.A., Sweetwyne M.T., Wilson G., Zaganjor E., Kezos J.N., Dondi C., Reddy A.K., Glancy B., Kirabo A., Quintana A.M., Dai D-F., Ocorr K., Murray S.A., Damo S.M., Exil V., Riggs B., Mobley B.C., Gomez J.A., McReynolds M.R., Hinton A. 3D reconstruction of murine mitochondria reveals changes in structure during aging linked to the MICOS complex. Aging Cell e14009. https://doi.org/10.1111/acel.14009
Vue Z., Neikirk K., Vang L., Garza-Lopez E., Christensen T.A., Shao J., Lam J., Beasley H.K., Marshall A.G., Crabtree A., Anudokem Jr J., Rodriguez B., Kirk B., Bacevac S., Barongan T., Shao B., Stephens D.C., Kabugi K., Koh H.J., Koh A., Evans C.S., Taylor B., Reddy A.K., Miller-Fleming T., Actkins K.V., Zaganjor E., Daneshgar N., Murray S.A., Mobley B.C., Damo S., Gaddy J.A., Riggs B., Wanjalla C., Kirabo A., McReynolds M., Gomez J.A., Phillips M.A., Exil V., Dai D-F., Hinton A. Three-dimensional mitochondria reconstructions of murine cardiac muscle changes in size across aging. American Journal of Physiology: Heart and Circulatory Physiology DOI: 10.1152/ajpheart.00202.2023.
Kezos J.N., Barter T.T., Phillips M.A., Cabral L.G., Greenspan Z.S., Arnold K.R., Azatian G., Buenprostro J.E., Bhangoo P.S., Khong A., Reyes G.T., Rahman A., Humphrey L.A., Bradley T.J., Mueller L.D., Rose M.R. Building bridges from genome to physiology using machine learning and Drosophila experimental evolution. Physiological and Biochemical Zoology https://doi.org/10.1086/724827
Ahmed I., Armstrong A., Clemons T.A., Clune-Taylor C., Love-Rutledge S.T., Phillips M.A., Rogers C.D., Williams M.J. How do DEI initiative impact STEMM, and do we still need them? Cell 186:2506-2509
Vue Z., Vang C., Vue N., Kamalumpundi V., Barongan T., Shao B., Huang S., Vang, L, Vue M., Vang N., Shao J., Coombes C., Katti P., Liu K, Yoshimura K., Biete M., Dai D-F., Phillips M.A., Behringer R.R. Asian Americans in STEM are not a monolith. Cell 186:3138-3142
Vue Z., Neikirk K., Vang L., Garza-Lopez E., Christensen T.A., Shao J., Lam J., Beasley H.K., Marshall A.G., Crabtree A., Anudokem Jr J., Rodriguez B., Kirk B., Bacevac S., Barongan T., Shao B., Stephens D.C., Kabugi K., Koh H.J., Koh A., Evans C.S., Taylor B., Reddy A.K., Miller-Fleming T., Actkins K.V., Zaganjor E., Daneshgar N., Murray S.A., Mobley B.C., Damo S., Gaddy J.A., Riggs B., Wanjalla C., Kirabo A., McReynolds M., Gomez J.A., Phillips M.A., Exil V., Dai D-F., Hinton A. Three-dimensional mitochondria reconstructions of murine cardiac muscle changes in size across aging. American Journal of Physiology: Heart and Circulatory Physiology DOI: 10.1152/ajpheart.00202.2023.
Kezos J.N., Barter T.T., Phillips M.A., Cabral L.G., Greenspan Z.S., Arnold K.R., Azatian G., Buenprostro J.E., Bhangoo P.S., Khong A., Reyes G.T., Rahman A., Humphrey L.A., Bradley T.J., Mueller L.D., Rose M.R. Building bridges from genome to physiology using machine learning and Drosophila experimental evolution. Physiological and Biochemical Zoology https://doi.org/10.1086/724827
Ahmed I., Armstrong A., Clemons T.A., Clune-Taylor C., Love-Rutledge S.T., Phillips M.A., Rogers C.D., Williams M.J. How do DEI initiative impact STEMM, and do we still need them? Cell 186:2506-2509
Vue Z., Vang C., Vue N., Kamalumpundi V., Barongan T., Shao B., Huang S., Vang, L, Vue M., Vang N., Shao J., Coombes C., Katti P., Liu K, Yoshimura K., Biete M., Dai D-F., Phillips M.A., Behringer R.R. Asian Americans in STEM are not a monolith. Cell 186:3138-3142
2022
Phillips M.A., Arnold K.R., Vue Z., Beasley H., Garza Lopez E., Marshall A., Morton D., McReynolds M.R., Barter T.T., Hinton A. (2022) Combining metabolomics and experimental evolution reveals key mechanisms underlying longevity differences in laboratory evolved Drosophila melanogaster populations. Int. J. Mol. Sci. doi:https://doi.org/10.3390/ijms23031082
2021
Phillips M.A., McHugh K.M., Taggard S.K., Kutch I.C., Burke M.K. (2021) Crossing design shapes patterns of genetic variation in synthetic recombinant populations of Saccharomyces cerevisiae. Scientific Reports 11:19551 doi:10.1038/s41598-021-99026-0
Shahrestani P., King E., Ramezan R., Phillips M.A., Riddle M., Thornburg M., Greenspan Z.S., Estrella Y., Garcia K., Chowdhury P., Malarat G., Zhu M., Rottshaefer S.M., Wraight S., Griggs M., Vandenberg J., Long A.D., Clark A.G., Lazzaro B.P. (2021) The molecular architecture of Drosophila melanogaster defense against Beauveria bassiana explored through evolve and resequence and quantitative trait locus mapping. G3: Genes, Genomes, Genetics 11:324.
Phillips M.A. and Burke M.K. (2021) Can laboratory evolution experiments teach us about natural populations? Molecular Ecology 30:877-87
Shahrestani P., King E., Ramezan R., Phillips M.A., Riddle M., Thornburg M., Greenspan Z.S., Estrella Y., Garcia K., Chowdhury P., Malarat G., Zhu M., Rottshaefer S.M., Wraight S., Griggs M., Vandenberg J., Long A.D., Clark A.G., Lazzaro B.P. (2021) The molecular architecture of Drosophila melanogaster defense against Beauveria bassiana explored through evolve and resequence and quantitative trait locus mapping. G3: Genes, Genomes, Genetics 11:324.
Phillips M.A. and Burke M.K. (2021) Can laboratory evolution experiments teach us about natural populations? Molecular Ecology 30:877-87
2020
Phillips M.A., Kutch I.C., Long A.D., Burke M.K. (2020) Increasing time-sampling in an evolve and resequence experiment with outcrossing Saccharomyces cerevisiae reveals multiple paths of adaptive change. Molecular Ecology 29:4898-4912
Wing K.M., Phillips M.A, Baker A.R., Burke M.K. (2020) Consequences of cryopreservation in diverse natural isolates of Saccharomyces cerevisiae. Genome Biology and Evolution 12:1302-131
Wing K.M., Phillips M.A, Baker A.R., Burke M.K. (2020) Consequences of cryopreservation in diverse natural isolates of Saccharomyces cerevisiae. Genome Biology and Evolution 12:1302-131
2019
Kezos J.N., Phillips M.A., Thomas M.D., Ewunkem A.J., Rutledge G.A., Barter T.T., Santos M.A., Wong B.D., Arnold K.R., Humphrey L.A., Yan A., Nouzille C., Sanchez I., Cabral L.G., Bradley T.J., Mueller L.D., Graves J.L., Rose M.R. (2019) Genomic and phenotypic effects of selection for starvation resistance in Drosophila. Physiological and Biochemical Zoology 92:591-611
Barter T.T., Greenspan Z.S., Phillips M.A., Mueller L.D., Rose M.R., Ranz J.M. (2019) Drosophila transcriptomics with and without ageing. Biogerontology 20:699-710
Barter T.T., Greenspan Z.S., Phillips M.A., Mueller L.D., Rose M.R., Ranz J.M. (2019) Drosophila transcriptomics with and without ageing. Biogerontology 20:699-710
2018
Phillips M.A.*, Rutledge G.A.*, Kezos J.N., Talbott A., Matty S., Arian H., Mueller L.D., Rose M.R, Shahrestani P. (2018) Effects of evolutionary history on genome wide and phenotypic convergence in Drosophila populations. BMC Genomics 19:743
Mueller L.D., Phillips M.A., Barter T.T., Greenspan Z.S., Rose M.R. (2018). Genome-wide mapping of gene-phenotype relationship in experimentally evolved populations. Molecular Biology and Evolution 35:2085-2095
Phillips M.A. and Rose M.R. Experimental evolution. (2018) Oxford Bibliographies in Evolutionary Biology. New York: Oxford University Press. DOI: 10.1093/OBO/9780199941728-0107
Mueller L.D., Phillips M.A., Barter T.T., Greenspan Z.S., Rose M.R. (2018). Genome-wide mapping of gene-phenotype relationship in experimentally evolved populations. Molecular Biology and Evolution 35:2085-2095
Phillips M.A. and Rose M.R. Experimental evolution. (2018) Oxford Bibliographies in Evolutionary Biology. New York: Oxford University Press. DOI: 10.1093/OBO/9780199941728-0107
2017
Graves J.L.*, Hertweck K.L*, Phillips M.A.*, Han M.V.*, Cabral L.G., Barter T.T., Greer L.F., Burke M.K., Mueller L.D., and Rose M.R. (2017) Genomics of parallel experimental evolution in Drosophila. Molecular Biology and Evolution 34:831-842
Rose M.R., Greer L.F., Phung K.H., Rutledge G.A., Phillips M.A., Anderson C.N.K., and Mueller L.D. (2017). A Hamiltonian Demography of Life History. In R. Shefferson, O. Jones, & R. Salguero-Gómez (Eds.), The Evolution of Senescence in the Tree of Life (pp. 40-55). Cambridge: Cambridge University Press
Rose M.R., Greer L.F., Phung K.H., Rutledge G.A., Phillips M.A., Anderson C.N.K., and Mueller L.D. (2017). A Hamiltonian Demography of Life History. In R. Shefferson, O. Jones, & R. Salguero-Gómez (Eds.), The Evolution of Senescence in the Tree of Life (pp. 40-55). Cambridge: Cambridge University Press
2016
Phillips M.A., Long A.D., Greenspan Z.S., Greer L.F., Burke M.K., Bryant V., Matsagas K.C., Rizza C.L., Mueller L.D., and Rose M.R. (2016) Genome-wide analysis of long-term evolutionary domestication in Drosophila melanogaster. Scientific Reports 6:39281; doi:10.1038/srep39281
Burke M.K., Barter T.B., Cabral L.G., Kezos J.N., Phillips M.A., Rutledge G.A., Phung K.H., Chen R.H., Nguyen H.D., Mueller L.D., and Rose M.R. (2016) Rapid convergence and divergence of life-history in experimentally evolved Drosophila melanogaster. Evolution 70:2085-2098
Burke M.K., Barter T.B., Cabral L.G., Kezos J.N., Phillips M.A., Rutledge G.A., Phung K.H., Chen R.H., Nguyen H.D., Mueller L.D., and Rose M.R. (2016) Rapid convergence and divergence of life-history in experimentally evolved Drosophila melanogaster. Evolution 70:2085-2098
2015
Rose M.R., Cabral L.G., Kezos J.N, Phillips M.A., Smith B.L., and Burnham T.C. (2015). Four steps towards the control of aging: Following the example of infectious disease. Biogerontology 17:21-31
2014
Rose M.R., Rutledge, G.A., Phung K.H., Phillips M.A., Greer L.F., and Mueller L.D. (2014) An evolutionary and genomic approach to the challenges and opportunities for eliminating aging. Current Aging Science 7:54-49
Rose M. R, Cabral L.G., Phillips M.A., Rutledge G.A., Phung K.H., Mueller L.D., and Greer L.F. (2014). The Great Evolutionary Divide: Two Genomic Systems Biologies of Aging. Interdisciplinary Topics in Gerontology and Geriatrics 40:63-73
Rose M. R, Cabral L.G., Phillips M.A., Rutledge G.A., Phung K.H., Mueller L.D., and Greer L.F. (2014). The Great Evolutionary Divide: Two Genomic Systems Biologies of Aging. Interdisciplinary Topics in Gerontology and Geriatrics 40:63-73