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Carl R. Woese Institute for Genomic Biology

Where Science Meets Society

Research Areas

Dong, Y., Sanford, R. A., Boyanov, M. I., Kemner, K. M., Flynn, T. M., O'Loughlin, E. J., ... Fouke, B. W. (2016). Orenia metallireducens sp. nov. strain Z6, a novel metal-reducing member of the phylum firmicutes from the deep subsurface. Applied and Environmental Microbiology, 82(21), 6440-6453. DOI: 10.1128/AEM.02382-16
Choi, E. J., Kim, J. W., Kim, S. J., Seo, S. O., Lane, S., Park, Y. C., ... Seo, J. H. (2016). Enhanced production of 2,3-butanediol in pyruvate decarboxylase-deficient Saccharomyces cerevisiae through optimizing ratio of glucose/galactose. Biotechnology Journal. DOI: 10.1002/biot.201600042
Brannon, P. M., Weaver, C. M., Anderson, C. A. M., Donovan, S. M., Murphy, S. P., & Yaktine, A. L. (2016). Scanning for new evidence to prioritize updates to the Dietary Reference Intakes: Case studies for thiamin and phosphorus1,2. American Journal of Clinical Nutrition, 104(5), 1366-1377. DOI: 10.3945/ajcn.115.128256
Zhang, G. C., Kong, I. I., Wei, N., Peng, D., Turner, T. L., Sung, B. H., ... Jin, Y. S. (2016). Optimization of an acetate reduction pathway for producing cellulosic ethanol by engineered yeast. Biotechnology and Bioengineering, 113(12), 2587-2596. DOI: 10.1002/bit.26021
Donovan, S. M., Fiese, B., Liechty, J. M., & Keck, A. (2016). Publication patterns of PhD students in the Illinois Transdisciplinary Obesity Prevention Program versus traditional programs. Journal of Nutrition Education and Behavior, 48, S118. DOI:
Narihiro, T., Nobu, M. K., Tamaki, H., Kamagata, Y., Sekiguchi, Y., & Liu, W. T. (2016). Comparative genomics of syntrophic branched-chain fatty acid degrading bacteria. Microbes and Environments, 31(3), 288-292. DOI: 10.1264/jsme2.ME16057
Mei, R., Narihiro, T., Nobu, M. K., Kuroda, K., & Liu, W. T. (2016). Evaluating digestion efficiency in full-scale anaerobic digesters by identifying active microbial populations through the lens of microbial activity. Scientific Reports, 6, [34090]. DOI: 10.1038/srep34090
Wang, K., Pereira, G. V., Cavalcante, J. J. V., Zhang, M., Mackie, R., & Cann, I. (2016). Bacteroides intestinalis DSM 17393, a member of the human colonic microbiome, upregulates multiple endoxylanases during growth on xylan. Scientific Reports, 6, [34360]. DOI: 10.1038/srep34360
Zhang, S., Ito, M., Skerker, J. M., Arkin, A. P., & Rao, C. V. (2016). Metabolic engineering of the oleaginous yeast Rhodosporidium toruloides IFO0880 for lipid overproduction during high-density fermentation. Applied Microbiology and Biotechnology, 1-13. DOI: 10.1007/s00253-016-7815-y
Xia, P. F., Zhang, G. C., Liu, J. J., Kwak, S., Tsai, C. S., Kong, I. I., ... Jin, Y. S. (2016). GroE chaperonins assisted functional expression of bacterial enzymes in Saccharomyces cerevisiae. Biotechnology and Bioengineering, 113(10), 2149-2155. DOI: 10.1002/bit.25980
Zhou, J., Wu, K., & Rao, C. V. (2016). Evolutionary engineering of Geobacillus thermoglucosidasius for improved ethanol production. Biotechnology and Bioengineering, 113(10), 2156-2167. DOI: 10.1002/bit.25983
Rutter, C. D., & Rao, C. V. (2016). Production of 1-decanol by metabolically engineered Yarrowia lipolytica. Metabolic Engineering, 38, 139-147. DOI: 10.1016/j.ymben.2016.07.011
Liu, J. J., Zhang, G. C., Oh, E. J., Pathanibul, P., Turner, T. L., & Jin, Y. S. (2016). Lactose fermentation by engineered Saccharomyces cerevisiae capable of fermenting cellobiose. Journal of Biotechnology, 234, 99-104. DOI: 10.1016/j.jbiotec.2016.07.018
Saltzman, J. A., Pineros-Leano, M., Liechty, J. M., Bost, K. K., Fiese, B. H., Harrison, K., ... the STRONG Kids Team (2016). Eating, feeding, and feeling: Emotional responsiveness mediates longitudinal associations between maternal binge eating, feeding practices, and child weight. International Journal of Behavioral Nutrition and Physical Activity, 13(1), [89]. DOI: 10.1186/s12966-016-0415-5
Iakiviak, M., Devendran, S., Skorupski, A., Moon, Y. H., Mackie, R. I., & Cann, I. (2016). Functional and modular analyses of diverse endoglucanases from Ruminococcus albus 8, a specialist plant cell wall degrading bacterium. Scientific Reports, 6, [29979]. DOI: 10.1038/srep29979
Shim, J. E., Kim, J., Lee, Y., Harrison, K., Bost, K., McBride, B., ... Fies, B. (2016). Fruit and Vegetable Intakes of Preschool Children Are Associated With Feeding Practices Facilitating Internalization of Extrinsic Motivation. Journal of Nutrition Education and Behavior, 48(5), 311-317.e1. DOI: 10.1016/j.jneb.2016.01.003
Wang, Y., Zhang, Z. T., Seo, S. O., Lynn, P., Lu, T., Jin, Y. S., & Blaschek, H. P. (2016). Bacterial Genome Editing with CRISPR-Cas9: Deletion, Integration, Single Nucleotide Modification, and Desirable "clean" Mutant Selection in Clostridium beijerinckii as an Example. ACS Synthetic Biology, 5(7), 721-732. DOI: 10.1021/acssynbio.6b00060
Wang, Y., Zhang, Z. T., Seo, S. O., Lynn, P., Lu, T., Jin, Y. S., & Blaschek, H. P. (2016). Gene transcription repression in Clostridium beijerinckii using CRISPR-dCas9. Biotechnology and Bioengineering, 113(12), 2739-2743. DOI: 10.1002/bit.26020
Whitaker, R. J., & Vanderpool, C. K. (2016). CRISPR-Cas Gatekeeper: Slow on the Uptake but Gets the Job Done. Cell Host and Microbe, 19(2), 135-137. DOI: 10.1016/j.chom.2016.01.015
Oh, S., Yoo, D., & Liu, W. T. (2016). Metagenomics reveals a novel virophage population in a Tibetan mountain lake. Microbes and Environments, 31(2), 173-177. DOI: 10.1264/jsme2.ME16003
Yasuma, T., Yano, Y., D'Alessandro-Gabazza, C. N., Toda, M., Gil-Bernabe, P., Kobayashi, T., ... Gabazza, E. C. (2016). Amelioration of diabetes by protein S. Diabetes, 65(7), 1940-1951. DOI: 10.2337/db15-1404
Musaad, S. M. A., Donovan, S. M., & Fiese, B. H. (2016). The Independent and Cumulative Effect of Early Life Risk Factors on Child Growth: A Preliminary Report. Childhood Obesity, 12(3), 193-201. DOI: 10.1089/chi.2016.0018
Oh, E. J., Skerker, J. M., Kim, S. R., Wei, N., Turner, T. L., Maurer, M. J., ... Jin, Y. S. (2016). Gene amplification on demand accelerates cellobiose utilization in engineered Saccharomyces cerevisiae. Applied and Environmental Microbiology, 82(12), 3631-3639. DOI: 10.1128/AEM.00410-16
Donovan, S. M. (2016). The Role of Lactoferrin in Gastrointestinal and Immune Development and Function: A Preclinical Perspective. Journal of Pediatrics, 173, S16-S28. DOI: 10.1016/j.jpeds.2016.02.072
Donovan, S. M., & Lönnerdal, B. (2016). Introduction: Emerging Roles of Bioactive Components in Pediatric Nutrition. Journal of Pediatrics, 173, S1-S3. DOI: 10.1016/j.jpeds.2016.02.069
Li, Q., Davila, J., Kannan, A., Flaws, J. A., Bagchi, M. K., & Bagchi, I. C. (2016). Chronic exposure to bisphenol a affects uterine function during early pregnancy in mice. Endocrinology, 157(5), 1764-1774. DOI: 10.1210/en.2015-2031
Shiraishi, M., Ishino, S., Yoshida, K., Yamagami, T., Cann, I., & Ishino, Y. (2016). PCNA is involved in the EndoQ-mediated DNA repair process in Thermococcales. Scientific Reports, 6, [25532]. DOI: 10.1038/srep25532
Quarterman, J., Skerker, J. M., Feng, X., Liu, I. Y., Zhao, H., Arkin, A. P., & Jin, Y. S. (2016). Rapid and efficient galactose fermentation by engineered Saccharomyces cerevisiae. Journal of Biotechnology, 229, 13-21. DOI: 10.1016/j.jbiotec.2016.04.041
Oh, S., Zhang, R., Wu, Q. L., & Liu, W. T. (2016). Evolution and adaptation of SAR11 and Cyanobium in a saline Tibetan lake. Environmental Microbiology Reports. DOI: 10.1111/1758-2229.12408
Wang, M., Monaco, M. H., & Donovan, S. M. (2016). Impact of early gut microbiota on immune and metabolic development and function. Seminars in Fetal and Neonatal Medicine, 21(6), 380-387. DOI: 10.1016/j.siny.2016.04.004
Liu, G., Ling, F. Q., Van Der Mark, E. J., Zhang, X. D., Knezev, A., Verberk, J. Q. J. C., ... Van Dijk, J. C. (2016). Comparison of Particle-Associated Bacteria from a Drinking Water Treatment Plant and Distribution Reservoirs with Different Water Sources. Scientific Reports, 6, [20367]. DOI: 10.1038/srep20367
Shenoy, A., Rao, C. V., & Schroeder, C. M. (2016). Stokes trap for multiplexed particle manipulation and assembly using fluidics. Proceedings of the National Academy of Sciences of the United States of America, 113(15), 3976-3981. DOI: 10.1073/pnas.1525162113
Liu, J. J., Kong, I. I., Zhang, G. C., Jayakody, L. N., Kim, H., Xia, P. F., ... Jin, Y. S. (2016). Metabolic engineering of probiotic Saccharomyces boulardii. Applied and Environmental Microbiology, 82(8), 2280-2287. DOI: 10.1128/AEM.00057-16
Cao, Y., Ryser, M. D., Payne, S., Li, B., Rao, C. V., & You, L. (2016). Collective Space-Sensing Coordinates Pattern Scaling in Engineered Bacteria. Cell, 165(3), 620-630. DOI: 10.1016/j.cell.2016.03.006
Kim, J. S., Cho, D. H., Heo, P., Jung, S. C., Park, M., Oh, E. J., ... Kweon, D. H. (2016). Fumarate-mediated persistence of Escherichia coli against antibiotics. Antimicrobial Agents and Chemotherapy, 60(4), 2232-2240. DOI: 10.1128/AAC.01794-15
Bian, G., Ma, S., Zhu, Z., Su, Y., Zoetendal, E. G., Mackie, R., ... Zhu, W. (2016). Age, introduction of solid feed and weaning are more important determinants of gut bacterial succession in piglets than breed and nursing mother as revealed by a reciprocal cross-fostering model. Environmental Microbiology, 18(5), 1566-1577. DOI: 10.1111/1462-2920.13272
Saltzman, J. A., Liechty, J. M., Bost, K. K., Fiese, B. H., Harrison, K., Bost, K., ... the STRONG Kids Program (2016). Parent binge eating and restrictive feeding practices: Indirect effects of parent's responses to child's negative emotion. Eating Behaviors, 21, 150-154. DOI: 10.1016/j.eatbeh.2016.02.001
Cann, I., Bernardi, R. C., & Mackie, R. I. (2016). Cellulose degradation in the human gut: Ruminococcus champanellensis expands the cellulosome paradigm. Environmental Microbiology, 18(2), 307-310. DOI: 10.1111/1462-2920.13152
Li, Y., Lin, Q., Wang, S., Li, X., Liu, W., Luo, C., ... Li, X. (2016). Soil bacterial community responses to warming and grazing in a Tibetan alpine meadow. FEMS Microbiology Ecology, 92(1), [fiv152]. DOI: 10.1093/femsec/fiv152
Nobu, M. K., Narihiro, T., Kuroda, K., Mei, R., & Liu, W. T. (2016). Chasing the elusive Euryarchaeota class WSA2: Genomes reveal a uniquely fastidious methyl-reducing methanogen. ISME Journal, 10(10), 2478-2487. DOI: 10.1038/ismej.2016.33
Lu, H., Ulanov, A. V., Nobu, M., & Liu, W. T. (2016). Global metabolomic responses of Nitrosomonas europaea 19718 to cold stress and altered ammonia feeding patterns. Applied Microbiology and Biotechnology, 100(4), 1843-1852. DOI: 10.1007/s00253-015-7095-y
Shen, Y., Huang, C., Monroy, G. L., Janjaroen, D., Derlon, N., Lin, J., ... Nguyen, T. H. (2016). Response of Simulated Drinking Water Biofilm Mechanical and Structural Properties to Long-Term Disinfectant Exposure. Environmental Science and Technology, 50(4), 1779-1787. DOI: 10.1021/acs.est.5b04653
Li, X., Park, A., Estrela, R., Kim, S. R., Jin, Y. S., & Cate, J. H. D. (2016). Comparison of xylose fermentation by two high-performance engineered strains of Saccharomyces cerevisiae. Biotechnology Reports, 9, 53-56. DOI: 10.1016/j.btre.2016.01.003
Seo, J. H., & Jin, Y. S. (2016). Editorial overview: Food biotechnology: Critical gap filler in the nexus of food, energy, and waste for a prosperous future. Current Opinion in Biotechnology, 37, 4-7. DOI: 10.1016/j.copbio.2016.01.001
Nobu, M. K., Dodsworth, J. A., Murugapiran, S. K., Rinke, C., Gies, E. A., Webster, G., ... Hedlund, B. P. (2016). Phylogeny and physiology of candidate phylum 'Atribacteria' (OP9/JS1) inferred from cultivation-independent genomics. ISME Journal, 10(2), 273-286. DOI: 10.1038/ismej.2015.97
Liu, Y. Q., Zhang, X., Zhang, R., Liu, W. T., & Tay, J. H. (2016). Effects of hydraulic retention time on aerobic granulation and granule growth kinetics at steady state with a fast start-up strategy. Applied Microbiology and Biotechnology, 100(1), 469-477. DOI: 10.1007/s00253-015-6993-3
Park, Y. C., Oh, E. J., Jo, J. H., Jin, Y. S., & Seo, J. H. (2016). Recent advances in biological production of sugar alcohols. Current Opinion in Biotechnology, 37, 105-113. DOI: 10.1016/j.copbio.2015.11.006
Kim, N. K., Oh, S., & Liu, W. T. (2016). Enrichment and characterization of microbial consortia degrading soluble microbial products discharged from anaerobic methanogenic bioreactors. Water Research, 90, 395-404. DOI: 10.1016/j.watres.2015.12.021
Zhang, M., Sun, Y., Liu, Y., Qiao, F., Chen, L., Liu, W. T., ... Li, E. (2016). Response of gut microbiota to salinity change in two euryhaline aquatic animals with reverse salinity preference. Aquaculture, 454, 72-80. DOI: 10.1016/j.aquaculture.2015.12.014
Jayakody, L. N., Lane, S., Kim, H., & Jin, Y. S. (2016). Mitigating health risks associated with alcoholic beverages through metabolic engineering. Current Opinion in Biotechnology, 37, 173-181. DOI: 10.1016/j.copbio.2015.12.001
Xu, H., Kim, S., Sorek, H., Lee, Y., Jeong, D., Kim, J., ... Jin, Y. S. (2016). PHO13 deletion-induced transcriptional activation prevents sedoheptulose accumulation during xylose metabolism in engineered Saccharomyces cerevisiae. Metabolic Engineering, 34, 88-96. DOI: 10.1016/j.ymben.2015.12.007
Zhang, S., Skerker, J. M., Rutter, C. D., Maurer, M. J., Arkin, A. P., & Rao, C. V. (2016). Engineering Rhodosporidium toruloides for increased lipid production. Biotechnology and Bioengineering, 113(5), 1056-1066. DOI: 10.1002/bit.25864
Turner, T. L., Zhang, G. C., Oh, E. J., Subramaniam, V., Adiputra, A., Subramaniam, V., ... Jin, Y. S. (2016). Lactic acid production from cellobiose and xylose by engineered Saccharomyces cerevisiae. Biotechnology and Bioengineering, 113(5), 1075-1083. DOI: 10.1002/bit.25875
Lu, H., Xue, Z., Saikaly, P., Nunes, S. P., Bluver, T. R., & Liu, W. T. (2016). Membrane biofouling in a wastewater nitrification reactor: Microbial succession from autotrophic colonization to heterotrophic domination. Water Research, 88, 337-345. DOI: 10.1016/j.watres.2015.10.013
Lonnerdal, B., Kvistgaard, A. S., Peerson, J. M., Donovan, S. M., & Peng, Y. M. (2016). Growth, nutrition, and cytokine response of breast-fed infants and infants fed formula with added bovine osteopontin. Journal of Pediatric Gastroenterology and Nutrition, 62(4), 650-657. DOI: 10.1097/MPG.0000000000001005
Ling, F., Hwang, C., LeChevallier, M. W., Andersen, G. L., & Liu, W. T. (2016). Core-satellite populations and seasonality of water meter biofilms in a metropolitan drinking water distribution system. ISME Journal, 10(3), 582-595. DOI: 10.1038/ismej.2015.136