CABBI Research Publications

(CABBI researchers in bold)

Shen. F., Sun, R., Yao, J., Li, J., Liu, Q., Price, N.D., Liu, C., Wang Z. March 8, 2019. “OptRAM: In-silico strain design via integrative regulatory-metabolic network modeling.” PLOS Computational Biology. e1006835. DOI:10.1371/journal.pcbi.1006835.

Tye, B.W., Commins, N., Ryazanova, L.V., Wühr, M., Springer, M., Pincus, D., Churchman, L.S. March 7, 2019. “Proteotoxicity from Aberrant Ribosome Biogenesis Compromises Cell Fitness.” eLife. 8:e43002. DOI:10.7554/eLife.43002.

Wang, Z., Dien, B.S., Rausch, K.D., Tumbleson, M.E., Singh, V. March 1, 2019. “Improving Ethanol Yields with Deacetylated and Two-Stage Pretreated Corn Stover and Sugarcane Bagasse by Blending Commercial Xylose-Fermenting and Wild Type Saccharomyces Yeast.” Bioresource Technology. 282:103-109. DOI: 10.1016/j.biortech.2019.02.123.

Kwak S., Jo J.H., Yun E.U., Jin Y.S., Seo J.H., March 2019. “Production of Biofuels and Chemicals from Xylose Using Native and Engineered Yeast Strains.” Biotechnology Advances 37:271-283. doi: 10.1016/j.biotechadv.2018.12.003.

Bradley, P.H., Gibney, P.A., Botstein, D., Troyanskaya, O.G., Rabinowitz, J.D., Feb. 26, 2019. “Minor Isozymes Tailor Yeast Metabolism to Carbon Availability.” mSystems 4:1-19. DOI: 10.1016/j.bcab.2019.101056.
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Wang, J., Li, Y., Zhu, F., Ming, R., Chen, L., Feb. 21, 2019. “Genome-Wide Analysis of Nitrate Transporter (NRT/NPF) Family in Sugarcane Saccharum spontaneum L.” Tropical Plant Biology. DOI: 10.1007/s12042-019-09220-8.
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Oh E.J., Wei N., Kwak S., Kim H., Jin Y.S., Feb. 20, 2019. “Overexpression of RCK1 Improves Acetic Acid Tolerance in Saccharomyces cerevisiae.” Journal of Biotechnology 292:1-4. doi: 10.1016/j.jbiotec.2018.12.013.
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Cheng M.H., Huang H., Dien B.S.Singh V., Feb. 16, 2019. “The Costs of Sugar Production from Different Feedstocks and Processing Technologies.” Biofuels, Bioproducts, and Biorefining. doi:10.1002/bbb.1976.

Dunivin, T.K., Choi, J., Howe, A., Shade A., January/February 2019. “RefSoil+: A Reference Database for Genes and Traits of Soil Plasmids.” mSystems 4:e00349-18. DOI:10.1128/mSystems.00349-18.
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Zhang, S., Jagtap, S.S.,Deewan, A., Rao, C.V., Jan. 20, 2019. “pH Selectively Regulates Citric Acid and Lipid Production in Yarrowia lipolytica W29 During Nitrogen-limited Growth on Glucose.” Journal of Biotechnology 290: 10-15. doi: 10.1016/j.jbiotec.2018.10.012.
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Yu, L., Fan, J., Xu, C., Jan. 8, 2019. “Peroxisomal fatty acid β-oxidation negatively impacts plant survival under salt stress.” Plant Signaling & Behavior 14. doi: 10.1080/15592324.2018.1561121
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Older Publications from CABBI Researchers

SEPTEMBER-DECEMBER 2018 PUBLICATIONS

Wang L., Xing X., Chen L., Yang L., Su X., Rabitz H., Lu W., Rabinowitz J.D., Dec. 26, 2018. “Peak Annotation and Verification Engine for Untargeted LC-MS Metabolomics.” Analytical Chemistry. 91:1838-1846. DOI: 10.1021/acs.analchem.8b03132.
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Dien, B.S., Mitchell, R.B., Bowman, M.J., Jin, V.L., Quarterman, J., Schmer, M.R., Singh, V., Slininger, P.J., Dec. 4, 2018. “Bioconversion of Pelletized Big Bluestem, Switchgrass, and Low-Diversity Grass Mixtures into Sugars and Bioethanol.” Frontiers in Energy Research 6: 1-15. doi: 10.3389/fenrg.2018.00129.
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Kim, S.M., Lee, D.K., Thapa, S., Dien, B.S., Tumbleson, M.E., Rausch, K.D., Singh V., December 2018. “Cellulosic ethanol potential of feedstocks grown on marginal land.” Transactions of the ASABE 61(6): 1775-1782. doi: 10.13031/trans.12945.
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Kurambhatti, C.V., Kumar, D., Rausch, K.D., Tumbleson, M.E., Singh, V., October 2018. “Ethanol Production from Corn Fiber Separated after Liquefaction in the Dry Grind Process.” Energies 201811 (11), 2921; doi: 10.3390/en11112921.
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Kurambhatti, C.V., Kumar, D., Rausch, K.D., Tumbleson, M.E., Singh, V., October 2018. “Increasing Ethanol Yield through Fiber Conversion in Corn Dry Grind Process.” Bioresource Technology, Volume 270, Pages 742-745,  DOI: 10.1016/j.biortech.2018.09.120.
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Zhang, J., Zhang, X., Tang, H., Zhang, Q., Hudson, M., Chen, L., Chifumi, N., Ming, R., Oct. 8, 2018. “Allele-defined Genome of the Autopolyploid Sugarcane Saccharum spontaneum L.” Nature Genetics Vol. 50, Issue 11, pp.1565-1573, DOI: 10.1038/s41588-018-0237-2.
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Teter, J., Yeh, S., Khanna, M., Berndes, G., Sept. 28, 2018. “Water Impacts of U.S. biofuels: Insights from an Assessment Combining Economic and Biophysical Models.” PLOS (Public Library of Science) ONE 13(9): e0204298, DOI: 10.1371/journal.pone.0204298.
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Xu Y.F., Lu W., Chen J.C., Johnson S.A., Gibney P.A., Thomas D.G., Grown G., May A.L., Campagna S.R., Yakunin A.F., Botstein D., Rabinowitz J.D. Sept. 21, 2018. “Discovery and Functional Characterization of a Yeast Sugar Alcohol Phosphatase.” ACS Chemical Biology, 13:3011-3020. DOI: 10.1021/acschembio.8b00804.
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Clifton‐Brown, J., Harfouche, A., Smart, L.B., Awty‐Carroll, D., Clark, L.V., Huang, L., McCalmont, J.P., Robson, P., Sacks, E.J., Swaminathan, K., Taylor, G., Sept. 19, 2018. “Breeding Progress and Preparedness for Mass‐scale Deployment of Perennial Lignocellulosic Biomass Crops Switchgrass, Miscanthus, Willow, and Poplar.” GCB Bioenergy, DOI: 10.1111/gcbb.12566.

Mirts, E.N., Petrik, I.D., Hosseinzadeh, P., Nilges, M.J., Lu, Y., Sept. 14, 2018. “A Designed Heme-[4Fe-4S] Metalloenzyme Catalyzes Sulfite Reduction Like the Native Enzyme.” Science Vol. 361, Issue 6407, pp. 1098-1101, DOI: 10.1126/science.aat8474.
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Si, T., Tian, Q., Min, Y., Zhang, L., Sweedler, J.V., van der Donk, W.A., Zhao, H., Sept. 5, 2018. “Rapid Screening of Lanthipeptide Analogs via In-Colony Removal of Leader Peptides in Escherichia coli.” Journal of the American Chemical Society 2018, 140, 11884-11888, DOI: 10.1021/jacs.8b05544.
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SUMMER 2018 PUBLICATIONS

Jagtap S.S., Rao C.V. Aug. 24, 2018. “Microbial Conversion of Xylose into Useful Bioproducts.” Applied Microbiology and Biotechnology, 102:9015-9036. DOI: 10.1007/s00253-018-9294-9.

Bansal, S., Kim, H.J., Na, G., Hamilton, M.E., Cahoon, E.B., Lu, C., Durrett, T.P., Aug. 14, 2018. “Towards the Synthetic Design of Camelina Oil Enriched in Tailored Acetyl-triacylglycerols with Medium-chain Fatty Acids.” Journal of Experimental Botany 69,: 4395-4402, DOI:10.1093/jxb/ery225.
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Asao, S., Parton, W.J., Chen, M., and Gao. W., Aug. 13, 2018. “Photodegradation Accelerates Ecosystem N Cycling in a Simulated California Grassland.” Ecosphere 9(8):e02370. DOI: 10.1002/ecs2.2370.
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Litman Z.C., Wang Y., Zhao H., Hartwig J.F., Aug. 13, 2018. “Cooperative Asymmetric Reactions Combining Photocatalysis and Enzymatic Catalysis.” Nature 560, 335-359 (2018).
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View the article by Emily Scott >>>

Lane S., Dong J., Jin Y.S., July 2018. “Value-added Biotransformation of Cellulosic Sugars by Engineered Saccharomyces cerevisiae.” Bioresource Technology, 260: 380-394, DOI: 10.1016/j.biortech.2018.04.013.

Li, A., Jia, S., Yobi, A., Ge, Z., Sato, S.J., Zhang, C., Angelovici, R., Clemente, T.E., Holding, D.R. June 20, 2018. “Editing of an Alpha-kafirin Gene Family Increases Digestibility and Protein Quality in Sorghum.” Plant Physiology00200.2018, DOI: 10.1104/pp.18.00200.
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EARLY 2018 PUBLICATIONS

Jang, C., Chen, L., Rabinowitz, J.D. May 3, 2018. “Metabolomics and Isotope Tracing.” Cell,173:822-837. DOI: 10.1016/j.cell.2018.03.055

Lian, J., Mishra, S., Zhao, H. April 25, 2018. “Recent Advances in Metabolic Engineering of Saccharomyces cerevisiae: New Tools and Their Applications.” Metabolic Engineering, DOI: 10.1016/j.ymben.2018.04.011.

Zhu, X., Liang, C., Masters, M.D., Kantola, I.B., DeLucia, E.H. April 23, 2018. “The Impacts of Four Potential Bioenergy Crops on Soil Carbon Dynamics as Shown by Biomarker Analyses and DRIFT Spectroscopy.” Global Change Biology Bioenergy, 10, 489-500, DOI: 10.1111.gcbb.12520.
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Lian, J., HamediRad, M., Zhao, H. April 18, 2018. “Advancing Metabolic Engineering of Saccharomyces cerevisiae Using the CRISPR/Cas System.” Biotechnology Journal, DOI: 10.1002/biot.201700601.

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Sonnett M., Young, E., Wühr, M. March 9, 2018. “Accurate, Sensitive, and Precise Multiplexed Proteomics Using the Complement Reporter Ion Cluster.” Analytical Chemistry, DOI: 10.1021/acs.analchem.7b04713.
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Lian, J., Bao, Z., Hu, S., Zhao, H. Feb. 20, 2018. “Engineered CRISPR/Cas9 System for Multiplex Genome Engineering of Polyploid Industrial Yeast Strains.” Biotechnology and Bioengineering, DOI: 10.1002/bit.26569.
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HamediRad, M., Lian, J., Li, H., Zhao, H. Feb. 20, 2018. “RNAi-assisted Genome Evolution Unveils Yeast Mutants with Improved Xylose Utilization.” Biotechnology and Bioengineering,115:1552-1560. DOI: 10.1002/bit.26570.
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