James Umen, Ph.D.

Algae are hidden drivers of global ecosystem productivity with unrealized potential.  We seek to unlock the secrets of algal growth, reproduction and development in an environment where basic discoveries can be transformed into real-world innovations in biofuels, agriculture and medicine.

Werth EG, McConnell EW, Couso Lianez I, Perrine Z, Crespo JL, Umen JG, Hicks LM. (2018) Investigating the effect of target of rapamycin kinase inhibition on the Chlamydomonas reinhardtii phosphoproteome: from known homologs to new targets. New Phytol., doi: 10.1111/nph.15339.

Geng S, Miyagi A, Umen JG. (2018) Evolutionary divergence of the sex-determining gene MID uncoupled from the transition to anisogamy in volvocine algae. Development, doi: 10.1242/dev.162537.

Hamaji, T., Kawai-Toyooka, H., Uchimura, H., Suzuki, M., Noguchi, H., Minakuchi, Y., Toyoda, A., Fujiyama, A., Miyagishima, S.-Y., Umen, J. G., and Nozaki, H. (2018) Anisogamy Evolved with a Reduced Sex-Determining Region in Volvocine Green Algae. Communications Biology, 1(1):247. doi:10.1038/s42003-018-0019-5.

Matt GY, Umen JG. (2018) Cell-Type Transcriptomes of the Multicellular Green Alga Volvox carteri Yield Insights into the Evolutionary Origins of Germ and Somatic Differentiation Programs. G3 (Bethesda), 8(2):531-550. doi: 10.1534/g3.117.300253.

López-Paz C, Liu D, Geng S, Umen JG. (2017) Identification of Chlamydomonas reinhardtii endogenous genic flanking sequences for improved transgene expression. Plant J., 92(6):1232-1244. doi: 10.1111/tpj.13731.

Couso I, Pérez-Pérez ME, Martinez-Force E, Kim H-S, He Y, Umen JG, Crespo JL. (2017) Autophagic flux is required for the synthesis of triacylglycerols and ribosomal protein turnover in Chlamydomonas. J Exp Bot., doi: 10.1093/jxb/erx372

Umen J, Goodenough U, Heitman J. (2017) Eukaryotic Sexual Reproduction Evoked "with a Little Help from My Friends". Cell, 170(6):1059-1061. doi: 10.1016/j.cell.2017.08.038.

Russell, J. J., Theriot, J. A., Sood, P., Marshall, W. F., Landweber, L. F., Fritz-Laylin, L., Polka, J. K., Oliferenko, S., Gerbich, T., Gladfelter, A., Umen, J. G., Bezanilla, M., Lancaster, M. A., He, S., Gibson, M. C., Goldstein, B., Tanaka, E. M., Hu, C.-K., and Brunet, A. (2017) Non-Model Model Organisms. BMC Biology, 15(1):55. doi:10.1186/s12915-017-0391-5

Werth, E. G., McConnell, E. W., Gilbert, T. S. K., Couso Lianez, I., Perez, C. A., Manley, C. K., Graves, L. M., Umen, J. G., and Hicks, L. M. (2017) Probing the Global Kinome and Phosphoproteome in Chlamydomonas reinhardtii via Sequential Enrichment and Quantitative Proteomics. Plant J., 89(2):416-426. doi: 10.1111/tpj.13384.

Matt G, Umen JG. (2016) Volvox: a simple algal model for embryogenesis, morphogenesis and cellular differentiation. Developmental Biology. 419(1):99-113. doi: 10.1016/j.ydbio.2016.07.014.

Couso I, Evans B, Li J, Liu Y, Ma F, Diamond S, Allen DK, Umen JG. (2016) Synergism between inositol polyphosphates and TOR kinase signaling in nutrient sensing, growth control and lipid metabolism in Chlamydomonas. Plant Cell, 28(9), 2026–2042. http://doi.org/10.1105/tpc.16.00351.

Hamaji T, Lopez D, Pellegrini M, Umen J. (2016) Identification and characterization of a cis-regulatory element for zygotic gene expression in Chlamydomonas reinhardtii. G3 (Bethesda), 6(6):1541-1548.

Hamaji T, Mogi Y, Ferris PJ, Mori T, Miyagishima S, Kabeya Y, Nishimura Y, Toyoda A, Noguchi H, Fujiyama A, Olson BJ, Marriage TN, Nishii I, Umen JG, Nozaki H. (2016) Sequence of the Gonium pectorale mating locus reveals a complex and dynamic history of changes in volvocine algal mating haplotypes. G3 (Bethesda), 6(5):1179-1189.

Li Y, Liu D, López-Paz C, Olson BJ, Umen JG. (2016) A new class of cyclin dependent kinase in Chlamydomonas is required for coupling cell size to cell division. Elife, 5: 2104.

Lopez D, Hamaji T, Kropat J, De Hoff P, Morselli M, Rubbi L, Fitz-Gibbon S, Gallaher SD, Merchant SS, Umen J, Pellegrini M. (2015) Dynamic changes in the transcriptome and methylome of Chlamydomonas reinhardtii throughout its life cycle. Plant Physiology, 169(4):2730-2743.

Zones JM, Blaby IK, Merchant SS, Umen JG. (2015) High-resolution profiling of a synchronized diurnal transcriptome from Chlamydomonas reinhardtii reveals continuous cell and metabolic differentiation. Plant Cell, 27(10):2743-2769.

Umen JG. (2015) Lost and found: the secret sex lives of bdelloid rotifers. Genetics, 200(2):409-412.

Cross FR, Umen JG. (2015) The Chlamydomonas cell cycle. Plant Journal, 82(3):370-392.

Fang SC, Chung CL, Chen CH, Lopez-Paz C, Umen JG
(2014).Defects in a new class of sulfate/anion transporter link sulfur acclimation responses to intracellular glutathione levels and cell cycle control.Plant Physiol. pii: pp.114.251009.

Li X, Umen JG, Jonikas MC.(2014).Waking sleeping algal cells.Proc Natl Acad Sci U S A.  pii: 201418295.

Umen JG.(2014). Green Algae and the Origins of Multicellularity in the Plant Kingdom. Cold Spring Harb Perspect Biol.  doi: 10.1101/cshperspect.a016170

Goodenough U, Blaby I, Casero D, Gallaher SD, Goodson C, Johnson S, Lee JH, Merchant SS, Pellegrini M, Roth R, Rusch J, Singh M, Umen JG, Weiss TL, Wulan T.(2014). The path to triacylglyceride obesity in the sta6 strain of Chlamydomonas reinhardtii. Eukaryot Cell. 13(5):591-613.

Geng S, De Hoff PL, Umen JG. (2014). Evolution of Sexes from an Ancestral Mating-Type Specification Pathway. PLoS Biol. (7): e1001904. doi:10.1371/journal.pbio.1001904

De Hoff PL, Ferris P, Olson BJ, Miyagi A, Geng S, Umen JG. (2013). Species and Population Level Molecular Profiling Reveals Cryptic Recombination and Emergent Asymmetry in the Dimorphic Mating Locus of C. reinhardtii. PLoS Genet. 9(8):e1003724.

Umen JG.(2013). Genetics: swinging ciliates' seven sexes. Curr Biol. 3;23(11):R475-7.

Hiraide, R., Kawai-Toyooka, H., Hamaji, T., Matsuzaki, R., Kawafune, K., Abe, J., Sekimoto, H., Umen, J. and Nozaki, H. 
(2013). The evolution of male-female sexual dimorphism predates the gender-based divergence of the mating locus gene MAT3/RB. Mol Biol Evol. 30, 1038-1040.

Umen, J.G. and Olson, B.J.S.C. (2012). Chapter Six: Genomics of volvocine algae. Adv Bot Res. 64, 185-243.

Wood, C.R., Wang, Z., Diener, D., Zones, J.M., Rosenbaum, J., Umen, J. (2012). IFT proteins accumulate during cell division and localize to the cleavage furrow in Chlamydomonas. PLoSONE 7(2): e30729. doi:10.1371/journal.pone.0030729

Umen, J.G. (2011). Evolution of sex and mating loci: An expanded view from Volvocine algae. Curr Opin Microbiol.14, 634-641.

Balsemão-Pires E, Jaillais Y, Olson BJ, Andrade LR, Umen JG, Chory J, Sachetto-Martins G. (2011). The Arabidopsis translocator protein (AtTSPO) is regulated at multiple levels in response to salt stress and perturbations in tetrapyrrole metabolism. BMC Plant Biol.11,108.

Olson, B.J.S.C., Oberholzer, M., Li, Y., Zones, J.M., Kohli, H., Bisova, K., Fang, S.-C., Meisenhelder, J., Hunter, T., and Umen, J.G. (2010). Regulation of the Chlamydomonascell cycle by a stable chromatin-associated retinoblastoma tumor suppressor complex. Plant Cell.22, 3331-3347.

Umen, J.G. (2010). Controlled chaos: New insights into genetically controlled asynchrony. Cell Cycle.9, 3843-3844.

Prochnik, S.*, Umen, J.*‡, Nedelcu, A., Hallmann, A., Miller, S., Nishii, I., Ferris, P., Kuo, A., Mitros, T., Hellsten, U., Chapman, J., Simakov, O., Rensing, S., Terry, A., Pangilinan, J., Salamov, A., Shapiro, H., Lindquist, E., Lucas, S., Kapitonov, V., Grigoriev, I., Schmitt, R., Kirk, D., and Rokhsar, D.‡. (2010). Genomic analysis of organismal complexity in the multicellular green alga Volvox carteri. Science. 329, 223-226. *Equal author contribution. ‡ Co-corresponding authors.

Ferris, P., Olson, B.J.S.C., De Hoff, P.L., Douglass, S., Diaz-Cano, D.C., Prochnik, S., Geng, S., Rai, R., Grimwood, J., Schmutz, J., Nishii, I., Hamaji, T., Nozaki, H., Pellegrini, M., and Umen, J.G. (2010). Evolution of an expanded sex determining locus in Volvox. Science. 328, 351-354.

Cízková, M., Pichová, A., Vítová, M., Hlavová, M., Hendrychová, J., Umysová, D., Gálová, E., Sevcovicová, A., Zachleder, V., Umen, James G., and Bisová, K. (2008). CDKA and CDKB kinases from Chlamydomonas reinhardtii are able to complement cdc28 temperature-sensitive mutants of Saccharomyces cerevisiae. Protoplasma.232, 183-191.

Vítová, M., Hendrychová, J., Cízková, M., Cepák, V., Umen, James G., Zachleder V., and Bisová K. (2008). Accumulation, activity and localization of cell cycle regulatory proteins and the chloroplast division protein FtsZ in the alga scenedesmus quadricauda under inhibition of nuclear DNA replication. Plant Cell Physiol.49, 1805-1817.

Fang, S.-C. and Umen, J.G. (2008). A suppressor screen in Chlamydomonas identifies novel components of the retinoblastoma tumor suppressor pathway. Genetics.178, 1295-1310.

Merchant, S., Umen, J. (of 117 total authors), Grossman A. (2007). The Chlamydomonasgenome reveals the evolution of key animal and plant functions. Science. 318, 245-250.

Fang, S.-C., del los Reyes, C. and Umen, J. G. (2006). Cell size checkpoint control by the retinoblastoma tumor suppressor pathway. PLoSGenet6, 1565-1679.