Ryan Senger

Courses Taught Last Five Years

• BSE 3144 - Engineering Analysis for Biological Systems (Numerical Methods)
• BSE 3154 - Thermodynamics of Biological Systems
• BSE 3534 - Bioprocess Engineering
• BSE 4224 - Biological Processing Plant Design
• BSE 4654 - Metabolic Engineering
• BSE/BMES/CHE 5044 - Engineering Mathematics
• BSE 5564G - Advanced Metabolic Engineering

Other Teaching and Advising

I advise graduate students, postdoctoral researchers, undergraduate researchers, and senior design teams in BSE.  I also advise and guide medical resident research projects at multiple hospitals and research institutions.

Program Focus

My research program develops novel experimental and computational approaches related to (i) metabolic engineering of microbes (ii) biocatalysis and cell-free enzymatic conversions, (iii) real-time physiological and environmental monitoring, and (iv) bodily fluid and tissue analysis by Raman spectroscopy.

We have developed novel techniques in genome-scale metabolic flux modeling to derive metabolic engineering strategies for production of valuable chemicals, therapeutics, and biofuels by microbes, plants, and cell-free biological extracts.

We are also innovators in using Raman spectroscopy and surface-enhanced Raman scattering to (i) monitor physiological changes of cells, tissues, and organs in real-time and (ii) detect the presence of disease.

Current Projects

• Design of small RNA molecules as synthetic regulatory circuits in microbes
• Thermodynamics of DNA assembly and design of protein expression systems
• Regeneration of NAD(P)H reducing power through in vitro biocatalysis
• Detection and staging of chronic kidney disease (CKD) and bladder cancer with Raman spectroscopy
• Real-time monitoring of dialysis therapies with Raman spectroscopy
• Whole cell biosensors to detect environmental contaminants

Selected Recent Publications

(* Denotes a student in my laboratory)

Senger, R.S., Scherr*, D. (2020) Resolving complex phenotypes with Raman spectroscopy and chemometrics. Current Opinion in Biotechnology. In press.

Wang, Z., Lee, Y-Y., Scherr*, D., Senger, R.S., Li, Y., He, Z. (2020) Mitigating nutrient accumulation with microalgal growth towards enhanced nutrient removal and biomass production in an osmotic photobioreactor. Water Research. 182:116038. http://doi.org/10.1016/j.waters.2020.116038.

Huttanus*, H.M., Senger, R.S. (2020) A synthetic biosensor to detect peroxisomal acetyl-CoA concentration for compartmentalized metabolic engineering. PeerJ. 8:e9805. https://doi.org/10.7717/peerj.9805.

Huttanus*, H.M., Vu*, T., Guruli, G., Tracey, A., Carswell*, W., Said, N., Du, P., Parkinson, B.G., Orlando, G., Robertson, J.L., Senger, R.S. (2020) Ramen chemometric urinalysis (Rametrix) as a screen for bladder cancer. PLOS One. 15(8): e0237070. https://doi.org/10.1371/journal.pone.0237070.

Wilson*, N., Sheng, J., McMaster, N., Feng, X., Senger, R.S., Schmale, D.G. (2020) Modification of the trichothecene mycotoxin deoxynivalenol using a cell free protein synthesis system.  Bioengineering. In Press.

Tanniche*, I., Colla’kova’, E., Denbow, C., Senger, R.S. (2020) Characterizing metabolic stress-induced phenotypes of Synechocystis with Raman spectroscopy. PeerJ. 8:e8535. https://doi.org/10.7717/peerj.8535.

Tanniche*, I., Colla’kova’, E., Denbow, C., Senger, R.S. (2020) Characterizing glucose, illumination, and nitrogen-deprivation phenotypes of Synechocystis PCC6803 with Raman spectroscopy. PeerJ. 8:e8585 https://doi.org/10.7717/peerj.8585.

Senger, R.S., Robertson, J.L. (2020) The Rametrix™ PRO Toolbox v1.0 for MATLAB®. PeerJ. 8:e8179. https://doi:10.7717/peerj.8179.

Senger, R.S., Sullivan*, M. Gouldin*, A., Lundgren*, S., Merrifield*, K., Steen*, C., Baker*, E., Vu*, T., Agnor*, B., Martinez*, G., Coogan*, H., Carswell*, W., Kavuru, V., Karageorge, L., Dev, D., Du, P., Sklar, A., Pirkle, J., Guelich, S., Orlando, G., Robertson, J.L. (2020) Spectral characteristics of urine from patients with end-stage kidney disease analyzed by Raman Chemometric Urinalysis (Rametrix) PLoS One. 15(1):e0227281. https://doi:10.1371/journal.pone.0227281.

Jimenez-Sanchez, C., Wilson*, N., McMaster, N., Gantulga, D., Freedman*, B.G., Senger, R.S., Schmale, D.G. (2020) A mycotoxin transporter (4D) from a library of deoxynivalenol-tolerant microorganisms. Toxicon:X. 5. https://doi:10.1016/j.toxcx.2020.100023.

Kavuru, V., Vu, T., Karageorge, L., Choudhury, D., Senger, R.S., Robertson, J.L. (2019) Dipstick analysis of urine chemistry: Benefits and limitations of dry chemistry-based assays. Postgraduate Medicine. https://doi:10.1080/00325481.2019.1679540.

Senger, R.S., Kavuru, V., Sullivan*, M., Gouldin*, A., Lundgren*, S., Merrifield*, K., Steen*, C., Baker*, E., Vu*, T., Agnor*, B., Martinez*, G., Coogan*, H., Carswell*, W., Karageorge, L., Dev, D., Du, P., Sklar, A., Orlando, G., Pirkle, J., Robertson, J.L. (2019) Spectral characteristics of urine specimens from healthy human volunteers analyzed using Raman chemometric urinalysis (Rametrix). PLoS One. 14(9):e0222115. https://doi:10.1371/journal.pone.0222115. 

Packard, H., Taylor, Z.W., Williams, S.L., Guimaraes*, P.I., Toth*, J. Jensen, R.V., Senger, R.S., Kuhn, D.D., Stevens, A.M. (2019) Identification of soil bacteria capable of utilizing a corn ethanol fermentation byproduct. PLoS One. 14(3):e0212685. https://doi:10.1371/journal.pone.0212685.

Fisher*, A.K., Carswell*, W.F., Athamneh*, A.I.M., Sullivan*, M.C., Robertson, J.L., Bevan, D.R., Senger, R.S. (2018) The RametrixTM LITE Toolbox v1.0 for MATLAB®. Journal of Raman Spectroscopy. 2018:1-12. https://doi:10.1002/jrs.5348. 

Nazem-Bokaee*, H., Yen*, J.Y., Athamneh*, A.I.M., McAnulty*, M.J., Senger, R.S. (2017) SyM-GEM: A pathway builder for genome-scale models. Advances in Biochemistry and Biotechnology. ABIO-141:18.

Nazem-Bokaee*, H., Yen*, J.Y., Athamneh*, A.I.M., McAnulty*, M.J., Senger, R.S. (2017) SyM-GEM: A biosynthetic metabolic pathway builder and genome-scale model database. Advances in Biochemistry and Biotechnology.  ABIO-141:18. 

Singh, M., Tong, Y., Webster, K., Cesewski, K., Haring, A.P., Laheri, S., Carswell*, W.F., O’Brien, T.J., Aardema, C.H., Senger, R.S., Robertson, J.L., Johnson, B.N. (2017) 3D printed conformal microfluidics for isolation and profiling of biomarkers for whole organs. Lab on a Chip. 17:2561-2571. https://doi:10.1039/C7LC00468K. 

Wilson*, N.M., McMaster, N., Gantulga, D., Soyars, C., McCormick, S., Knott, K., Senger, R.S., Schmale, D. (2017) Modification of the mycotoxin deoxynivalenol using microorganisms isolated from environmental samples. Toxins. 9(4):141.  https://doi:10.3390/toxins9040141.

Olson, M.L., Johnson, J., Carswell*, W.F., Reyes, L.H., Senger, R.S., Kao, K.C. (2016) Characterization of an evolved carotenoids hyper-producer of Saccharomyces cerevisiae through bioreactor parameter optimization and Raman spectroscopy. Journal of Industrial Microbiology & Biotechnology. 43(10):1355-1363. https://doi:10.1007/s10295-016-1808-9.

Freedman*, B.G., Zu*, T.N.K., Athamneh*, A.I.M., Wallace*, R.S., Senger, R.S. (2016) Raman spectroscopy detects phenotypic differences among E. coli enriched for 1-butanol tolerance using a metagenomic DNA library. Biotechnology Journal. 11(7):877-889. https://doi:10.1002/biot.201500144.

Zu*, T.N.K., Athamneh*, A.I.M., Senger, R.S. (2016) Characterizing the phenotypic responses of Escherichia coli to multiple 4-carbon alcohols with Raman spectroscopy. Fermentation. 2(1):3. https://doi:10.3390/fermentation2010003.

Nazem-Bokaee*, H., Senger, R.S. (2015) ToMI-FBA: A genome-scale metabolic flux based algorithm to select optimum hosts and media formulations for expressing pathways of interest. AIMS Bioengineering. 2(4):355-73. https://doi:10.3934/bioeng.2015.4.335. 

Ebrahim, A., Almass, E., Bauer, E., Bordbar, A., Burgard, A.P., Chang, R.L., Drager, A., Famili, I., Feist, A.M., Fleming, R.M.T., Fong, S.S., Hatzimanikatis, V., Herrgard, M.J., Holder, A., Hucka, M., Hyduke, D., Jamshidi, N., Lee, S.Y., Le Novere, N., Lerman, J.A., Lewis, N.E., Ma, D., Mahadevan, R., Maranas, C. Nagarajan, H., Navid, A., Nielsen, J., Nielsen, L.K., Nogales, J., Noronha, A., Pal, C., Palsson, B.O., Papin, J.A., Patil, K.R., Price, N.D., Reed, J.L., Saunders, M., Senger, R.S., Sonnenschein, N., Sun, Y., Thiele, I. (2015) Do genome-scale models need exact solvers or clearer standards? Molecular Systems Biology. 11(10):831. https://doi:10.15252/msb.20156157. 

Rollin, J.A., Martin del Campo, J., Myung, S., Sun, F., Bakovic, A.E., Castro, R.L., Candrayan, S., Adams, M.W.W., Senger, R.S., Zhang, Y.H.P. (2015) High-yield enzymatic hydrogen production from biomass by in vitro metabolic engineering. Proceedings of the National Academy of Sciences USA. 112(16):4964-9. https://doi:10.1073/pnas.1417719112.Zu*, T.N.K., Athamneh*, A.I.M., Collakova, E., Robertson, J., Hawken, T., Aardema, C., Senger, R.S. (2015) Assessment of ex vivo perfused liver health by Raman spectroscopy. Journal of Raman Spectroscopy. 46:551-8. https://doi:10.1002/jrs.4688.

Selected Recent Funding

• “Screening veterans for chronic kidney disease,” Project in collaboration with the Veterans Administration Medical Center in Salem, VA.
• “Redefining the management of renal disease through Chemometric Fingerprinting of urine and dialysate,” Commercial project.
• “Multi-scale metabolic modeling and engineering workshop,” NSF CBET
• “Microbial protein substitutions in aquaculture diets: Phase II+: Bacterial strain characterization, application, and validation,” Commercial project.
• “Microbial protein substitutions in aquaculture diets: Phase I bacteria strain selection,” Commercial project.
• “Dialysensing: Improving the efficacy and patient outcomes of hemodialysis and peritoneal dialysis through the use of Raman spectroscopy and multivariate statistical analysis” Commercial project.
• “Production of the building block 2-pyrrolidone using a model-guided platform for de novo biosynthetic pathway integration,” NSF CBET BBBE Program, Award NSF1254242, $398,394, 2013-2016.
• “Enabling phenotype predictions of cyanobacteria,” NSF MCB Networks and Regulation Program, Award: NSF1243988, $621,182, 2013-2016.