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Illinois IGB

Research Areas

Microbiome Metabolic Engineering: Publications

Liu, J. J., Zhang, G. C., Kwak, S., Oh, E. J., Yun, E. J., Chomvong, K., ... Jin, Y-S. (2019). Overcoming the thermodynamic equilibrium of an isomerization reaction through oxidoreductive reactions for biotransformation. Nature communications, 10(1), [1356].

Kern, S., & Laurent, H. K. (2019). Childhood abuse predicts affective symptoms via HPA reactivity during mother-infant stress. Psychoneuroendocrinology, 107, 19-25.

Feng, Y., Ibarra-Sánchez, L. A., Luu, L., Miller, M. J., & Lee, Y. (2019). Co-assembly of nisin and zein in microfluidics for enhanced antilisterial activity in Queso Fresco. LWT, 111, 355-362.

Shin, M., Kim, J. W., Ye, S., Kim, S., Jeong, D., Lee, D. Y., ... Kim, S. R. (2019). Comparative global metabolite profiling of xylose-fermenting Saccharomyces cerevisiae SR8 and Scheffersomyces stipitis. Applied Microbiology and Biotechnology, 103(13), 5435-5446.

Zhang, Y., & Liu, W-T. (2019). The application of molecular tools to study the drinking water microbiome–Current understanding and future needs. Critical Reviews in Environmental Science and Technology, 49(13), 1188-1235.

Zhang, L., Holle, M. J., Kim, J. S., Daum, M. A., & Miller, M. J. (2019). Nisin incorporation enhances the inactivation of lactic acid bacteria during the acid wash step of bioethanol production from sugarcane juice. Letters in Applied Microbiology, 69(1), 50-56.

Tang, L., Zhong, L., Xue, K., Wang, S., Xu, Z., Lin, Q., ... Wang, Y. (2019). Warming counteracts grazing effects on the functional structure of the soil microbial community in a Tibetan grassland. Soil Biology and Biochemistry, 134, 113-121.

Gao, H., Mao, Y., Zhao, X., Liu, W-T., Zhang, T., & Wells, G. (2019). Genome-centric metagenomics resolves microbial diversity and prevalent truncated denitrification pathways in a denitrifying PAO-enriched bioprocess. Water Research, 275-287.

Robinson, K. N., Rowitz, B. M., Oliphant, U. J., Donovan, S. M., & Teran-Garcia, M. D. L. (2019). Larger omental adipocytes correlate with greater Fetuin-A reduction following sleeve gastrectomy. BMC Obesity, 6(1), [15].

Schilling, B., Basisty, N., Christensen, D. G., Sorensen, D., Orr, J. S., Wolfe, A. J., & Rao, C. V. (2019). Global lysine acetylation in Escherichia coli results from growth conditions that favor acetate fermentation. Journal of bacteriology, 201(9), [e00768-18].

Barakat, R., Seymore, T., Lin, P. C. P., Park, C. J., & Ko, C. (2019). Prenatal exposure to an environmentally relevant phthalate mixture disrupts testicular steroidogenesis in adult male mice. Environmental Research, 194-201.

Narisetty, N., Mukherjee, B., Chen, Y. H., Gonzalez, R., & Meeker, J. D. (2019). Selection of nonlinear interactions by a forward stepwise algorithm: Application to identifying environmental chemical mixtures affecting health outcomes. Statistics in Medicine, 38(9), 1582-1600.

Petronikolou, N., Ortega, M. A., Borisova, S. A., Nair, S. K., & Metcalf, W. W. (2019). Molecular Basis of Bacillus subtilis ATCC 6633 Self-Resistance to the Phosphono-oligopeptide Antibiotic Rhizocticin. ACS chemical biology, 14(4), 742-750.

Mei, R., Kim, J., Wilson, F. P., Bocher, B. T. W., & Liu, W-T. (2019). Coupling growth kinetics modeling with machine learning reveals microbial immigration impacts and identifies key environmental parameters in a biological wastewater treatment process. Microbiome, 7(1), [65].

Laurent, H. K. (2019). Challenges in Characterizing the “Mommy Brain”. Parenting, 19(1-2), 94-96.

Lin, C. Y., Alexander, C., Steelman, A. J., Warzecha, C. M., Cattai de Godoy, M. R., & Swanson, K. S. (2019). Effects of a Saccharomyces cerevisiae fermentation product on fecal characteristics, nutrient digestibility, fecal fermentative end-products, fecal microbial populations, immune function, and diet palatability in adult dogs. Journal of animal science, 97(4), 1586-1599.

Cannavale, C. N., Hassevoort, K. M., Edwards, C. G., Thompson, S. V., Burd, N. A., Holscher, H. D., ... Khan, N. A. (2019). Serum lutein is related to relational memory performance. Nutrients, 11(4), [768].

Devendran, S., Shrestha, R., Alves, J. M. P., Wolf, P. G., Ly, L., Hernandez, A. G., ... Ridlon, J. M. (2019). Clostridium scindens ATCC 35704: Integration of nutritional requirements, the complete genome sequence, and global transcriptional responses to bile acids. Applied and environmental microbiology, 85(7), [e00052-19].

Kim, D. H., Park, H. J., Park, H. S., Lee, J. U., Ko, C., Gye, M. C., & Choi, J. M. (2019). Estrogen receptor α in T cells suppresses follicular helper T cell responses and prevents autoimmunity. Experimental and Molecular Medicine, 51(4), [41].

Liu, J. J., Lee, J. W., Yun, E. J., Jung, S. M., Seo, J. H., & Jin, Y-S. (2019). L-Fucose production by engineered Escherichia coli. Biotechnology and bioengineering, 116(4), 904-911.

Juneja, A., Zhang, G., Jin, Y-S., & Singh, V. (2019). Bioprocessing and technoeconomic feasibility analysis of simultaneous production of D-psicose and ethanol using engineered yeast strain KAM-2GD. Bioresource Technology, 275, 27-34.

Oba, P. M., Utterback, P. L., Parsons, C. M., Cattai de Godoy, M. R., & Swanson, K. S. (2019). Chemical composition, true nutrient digestibility, and true metabolizable energy of chicken-based ingredients differing by processing method using the precision-fed cecectomized rooster assay. Journal of animal science, 97(3), 998-1009.

Detweiler, K. B., He, F., Mangian, H. F., Davenport, G. M., & Cattai de Godoy, M. R. (2019). Effects of high inclusion of soybean hulls on apparent total tract macronutrient digestibility, fecal quality, and fecal fermentative end-product concentrations in extruded diets of adult dogs. Journal of animal science, 97(3), 1027-1035.

Detweiler, K. B., He, F., Mangian, H. F., Davenport, G. M., & Cattai de Godoy, M. R. (2019). Extruded feline diets formulated with high inclusion of soybean hulls: Effects on apparent total tract macronutrient digestibility, and fecal quality and metabolites. Journal of animal science, 97(3), 1042-1051.

Kim, K., Golubeva, Y. A., Vanderpool, C., & Slauch, J. M. (2019). Oxygen-dependent regulation of SPI1 type three secretion system by small RNAs in Salmonella enterica serovar Typhimurium. Molecular Microbiology, 111(3), 570-587.

Kwak, S., Jo, J. H., Yun, E. J., Jin, Y-S., & Seo, J. H. (2019). Production of biofuels and chemicals from xylose using native and engineered yeast strains. Biotechnology Advances, 37(2), 271-283.

Zukher, I., Pavlov, M., Tsibulskaya, D., Kulikovsky, A., Zyubko, T., Bikmetov, D., ... Severinova, K. (2019). Reiterative synthesis by the ribosome and recognition of the N-terminal formyl group by biosynthetic machinery contribute to evolutionary conservation of the length of antibiotic microcin c peptide precursor. mBio, 10(2), [e00768-19].

Park, C. J., Barakat, R., Ulanov, A., Li, Z. L., Lin, P. C., Chiu, K., ... Ko, C. (2019). Sanitary pads and diapers contain higher phthalate contents than those in common commercial plastic products. Reproductive Toxicology, 84, 114-121.

Oh, E. J., Wei, N., Kwak, S., Kim, H., & Jin, Y-S. (2019). Overexpression of RCK1 improves acetic acid tolerance in Saccharomyces cerevisiae. Journal of Biotechnology, 292, 1-4.

Yun, E. J., Liu, J. J., Lee, J. W., Kwak, S., Yu, S., Kim, K. H., & Jin, Y-S. (2019). Biosynthetic Routes for Producing Various Fucosyl-Oligosaccharides. ACS synthetic biology, 8(2), 415-424.

Hannon, B. A., Thompson, S. V., Edwards, C. G., Skinner, S. K., Niemiro, G. M., Burd, N. A., ... Khan, N. A. (2019). Dietary fiber is independently related to blood triglycerides among adults with overweight and obesity. Current Developments in Nutrition, 3(2), [nzy094].

Kim, J. H., Shin, J. C., & Donovan, S. M. (2019). Effectiveness of Workplace Lactation Interventions on Breastfeeding Outcomes in the United States: An Updated Systematic Review. Journal of Human Lactation, 35(1), 100-113.

Siegel, M. H., Gurung, R. B., & Donovan, S. M. (2019). Safety evaluation of 3′-siallylactose sodium salt supplementation on growth and clinical parameters in neonatal piglets. Regulatory Toxicology and Pharmacology, 101, 57-64.

Zhang, S., Jagtap, S. S., Deewan, A., & Rao, C. V. (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.

Bobeica, S. C., Dong, S. H., Huo, L., Mazo, N., McLaughlin, M. I., Jiménez-Osés, G., ... van der Donk, W. A. (2019). Insights into AMS/PCAT transporters from biochemical and structural characterization of a double Glycine motif protease. eLife, 8.

Khan, F., & Laurent, H. K. (2019). Assessing the Impact of Mindfulness and Life Stress on Maternal Well-Being. Mindfulness, 10(1), 26-35.

Taylor, A. M., Thompson, S. V., Edwards, C. G., Musaad, S. M. A., Khan, N. A., & Holscher, H. D. (2019). Associations among diet, the gastrointestinal microbiota, and negative emotional states in adults. Nutritional Neuroscience.

Dong, S. H., Kulikovsky, A., Zukher, I., Estrada, P., Dubiley, S., Severinov, K., & Nair, S. K. (2019). Biosynthesis of the RiPP trojan horse nucleotide antibiotic microcin C is directed by the N-formyl of the peptide precursor. Chemical Science, 10(8), 2391-2395.

Kaczmarek, J. L., Liu, X., Charron, C. S., Novotny, J. A., Jeffery, E. H., Seifried, H. E., ... Holscher, H. D. (2019). Broccoli consumption affects the human gastrointestinal microbiota. Journal of Nutritional Biochemistry, 63, 27-34.

Nguyen, K., DeSieno, M. A., Bae, B., Johannes, T. W., Cobb, R. E., Zhao, H., & Nair, S. K. (2019). Characterization of the flavin monooxygenase involved in biosynthesis of the antimalarial FR-900098. Organic and Biomolecular Chemistry, 17(6), 1506-1518.

Li, Y., Li, Y., Jin, W., Sharpton, T. J., Mackie, R. I., Cann, I., ... Zhu, W. (2019). Combined genomic, transcriptomic, proteomic, and physiological characterization of the growth of Pecoramyces sp. F1 in Monoculture and Co-culture with a Syntrophic Methanogen. Frontiers in Microbiology, 10(MAR), [435].

Hull, N. M., Ling, F., Pinto, A. J., Albertsen, M., Jang, H. G., Hong, P. Y., ... Liu, W-T. (2019). Drinking Water Microbiome Project: Is it Time? Trends in Microbiology.

Orr, J. S., Christensen, D. G., Wolfe, A. J., & Rao, C. V. (2019). Extracellular acidic pH inhibits acetate consumption by decreasing gene transcription of the tricarboxylic acid cycle and the glyoxylate shunt. Journal of bacteriology, 201(2), [e00410-18].

Madak-Erdogan, Z., Band, S., Zhao, Y. C., Smith, B. P., Kulkoyluoglu-Cotul, E., Zuo, Q., ... Flaws, J. A. (2019). Free fatty acids rewire cancer metabolism in obesity-associated breast cancer via estrogen receptor and mTOR signaling. Cancer Research, 79(10), 2494-2510.

the STRONG Kids Research Team, Donovan, S. M., & Teran-Garcia, M. D. L. (2019). Genetic risk scores demonstrate the cumulative association of single nucleotide polymorphisms in gut microbiome-related genes with obesity phenotypes in preschool age children. Pediatric Obesity, [e12530].

Donovan, S. M. (2019). Human Milk Proteins: Composition and Physiological Significance. Nestle Nutrition Institute Workshop Series, 90, 93-101.

Nelson, B. W., Wright, D. B., Allen, N. B., & Laurent, H. K. (2019). Maternal stress and social support prospectively predict infant inflammation. Brain, Behavior, and Immunity.

Dong, S. H., Liu, A., Mahanta, N., Mitchell, D. A., & Nair, S. K. (2019). Mechanistic Basis for Ribosomal Peptide Backbone Modifications. ACS Central Science.

Duffy, D. M., Ko, C., Jo, M., Brannstrom, M., & Curry, T. E. (2019). Ovulation: Parallels with inflammatory processes. Endocrine reviews, 40(2), 369-416.

Donovan, S. M., German, J. B., Lönnerdal, B., & Lucas, A. (2019). Preface. Nestle Nutrition Institute Workshop Series, 90, VII-IX.

King, A. M., Vanderpool, C., & Degnan, P. H. (2019). sRNA target prediction organizing tool (SPOT) integrates computational and experimental data to facilitate functional characterization of bacterial small RNAs. mSphere, 4(1), [e00561-18].

Donovan, S. M. (2019). Summary on Clinical Aspects of Human Milk on Infant Health Outcomes. Nestle Nutrition Institute Workshop Series, 90, 175-178.

Dawson, D. N., Volpe, V. V., & Laurent, H. K. (2019). Synergistic Effects of Psychological Intimate Partner Violence Exposure and Gender Discrimination on Postnatal Mental Health Trajectories. Journal of Interpersonal Violence.

Jones, A. R., Robbs, C. M., Edwards, C. G., Walk, A. M., Thompson, S. V., Reeser, G. E., ... Khan, N. A. (2018). Retinal morphometric markers of crystallized and fluid intelligence among adults with overweight and obesity. Frontiers in Psychology, 9(DEC), [2650].

Mei, R., Nobu, M. K., Narihiro, T., Yu, J., Sathyagal, A., Willman, E., & Liu, W-T. (2018). Novel Geobacter species and diverse methanogens contribute to enhanced methane production in media-added methanogenic reactors. Water Research, 147, 403-412.

Surya, A., Liu, X., & Miller, M. J. (2018). Glutathione Utilization in Lactobacillus fermentum CECT 5716. Journal of Agricultural and Food Chemistry, 66(48), 12651-12656.

Klurfeld, D. M., Davis, C. D., Karp, R. W., Allen-Vercoe, E., Chang, E. B., Chassaing, B., ... Lynch, C. J. (2018). Considerations for best practices in studies of fiber or other dietary components and the intestinal microbiome. American Journal of Physiology - Endocrinology and Metabolism, 315(6), E1087-E1097.

Narihiro, T., Nobu, M. K., Bocher, B. T. W., Mei, R., & Liu, W-T. (2018). Co-occurrence network analysis reveals thermodynamics-driven microbial interactions in methanogenic bioreactors. Environmental Microbiology Reports, 10(6), 673-685.

Edwards, C. G., Walk, A. M., Thompson, S. V., Mullen, S. P., Holscher, H. D., & Khan, N. A. (2018). Disordered eating attitudes and behavioral and neuroelectric indices of cognitive flexibility in individuals with overweight and obesity. Nutrients, 10(12), [1902].

Albanna, A., Sim, M., Hoskisson, P. A., Gillespie, C., Rao, C. V., & Aldridge, P. D. (2018). Driving the expression of the Salmonella enterica sv Typhimurium flagellum using flhDC from Escherichia coli results in key regulatory and cellular differences. Scientific Reports, 8(1), [16705].

Shen, Y., Huang, P. C., Huang, C., Sun, P., Monroy, G. L., Wu, W., ... Nguyen, T. H. (2018). Effect of divalent ions and a polyphosphate on composition, structure, and stiffness of simulated drinking water biofilms. npj Biofilms and Microbiomes, 4(1), [15].

Hernandez, J., Volland, A., Leyshon, B. J., Juda, M., Ridlon, J. M., Johnson, R. W., & Steelman, A. J. (2018). Effect of imidacloprid ingestion on immune responses to porcine reproductive and respiratory syndrome virus. Scientific Reports, 8(1), [11615].

Lane, S., Xu, H., Oh, E. J., Kim, H., Lesmana, A., Jeong, D., ... Kim, S. R. (2018). Glucose repression can be alleviated by reducing glucose phosphorylation rate in Saccharomyces cerevisiae. Scientific Reports, 8(1), [2613].

Donovan, S. M., & Hutkins, R. (2018). Introduction to the Fifth Global Summit on the Health Effects of Yogurt. Nutrition Reviews, 76(1), 1-3.

Hidalgo-Ahumada, C. A. P., Nobu, M. K., Narihiro, T., Tamaki, H., Liu, W-T., Kamagata, Y., ... Sousa, D. Z. (2018). Novel energy conservation strategies and behaviour of Pelotomaculum schinkii driving syntrophic propionate catabolism. Environmental Microbiology, 20(12), 4503-4511.

Ammar, E. M., Wang, X., & Rao, C. V. (2018). Regulation of metabolism in Escherichia coli during growth on mixtures of the non-glucose sugars: Arabinose, lactose, and xylose. Scientific Reports, 8(1), [609].

Xia, P. F., Li, Q., Tan, L. R., Liu, M. M., Jin, Y-S., & Wang, S. G. (2018). Synthetic Whole-Cell Biodevices for Targeted Degradation of Antibiotics. Scientific Reports, 8(1), [2906].

Shiraishi, M., Ishino, S., Heffernan, M., Cann, I., & Ishino, Y. (2018). The mesophilic archaeon Methanosarcina acetivorans counteracts uracil in DNA with multiple enzymes: EndoQ, ExoIII, and UDG. Scientific Reports, 8(1), [15791].

Neu, L., Bänziger, C., Proctor, C. R., Zhang, Y., Liu, W-T., & Hammes, F. (2018). Ugly ducklings - The dark side of plastic materials in contact with potable water. npj Biofilms and Microbiomes, 4(1), [7].

Ozgen, V. C., Kong, W., Blanchard, A. E., Liu, F., & Lu, T. (2018). Spatial interference scale as a determinant of microbial range expansion. Science Advances, 4(11), [eaau0695].

Liu, J. J., Kwak, S., Pathanibul, P., Lee, J. W., Yu, S., Yun, E. J., ... Jin, Y-S. (2018). Biosynthesis of a Functional Human Milk Oligosaccharide, 2′-Fucosyllactose, and l -Fucose Using Engineered Saccharomyces cerevisiae. ACS synthetic biology, 7(11), 2529-2536.

Sutter, C., Fiese, B., Lundquist, A., Davis, E. C., McBride, B. A., & Donovan, S. M. (2018). Sources of information and support for breastfeeding: Alignment with centers for disease control and prevention strategies. Breastfeeding Medicine, 13(9), 598-606.

An, R., Guan, C., Ji, M., & Donovan, S. M. (2018). State laws governing competitive foods and beverages sold in schools and childhood obesity among children with special healthcare needs, 2007-2016. American Journal of Health Behavior, 42(6), 124-133.

Hale, V. L., Jeraldo, P., Chen, J., Mundy, M., Yao, J., Priya, S., ... Chia, N. (2018). Distinct microbes, metabolites, and ecologies define the microbiome in deficient and proficient mismatch repair colorectal cancers. Genome medicine, 10(1).

Donovan, S. M. (2018). 90th Anniversary Commentary: Prebiotics in Infancy for Allergy Prevention: Promising Findings, but No Consensus. Journal of Nutrition, 148(10), 1691-1692.

Raina, M., King, A., Bianco, C., & Vanderpool, C. (2018). Dual-function RNAs. Microbiology spectrum, 6(5), [RWR-0032-2018].

Park, J. H., Yoon, J. J., Kumar, G., Jin, Y-S., & Kim, S. H. (2018). Effects of acclimation and pH on ammonia inhibition for mesophilic methanogenic microflora. Waste Management, 80, 218-223.

Madden, G., Arnold, E. R., Karsten, J., & Ambrose, S. H. (2018). Evaluating competition and conflict among western Ukraine Neolithic farmers with stable isotope analyses of human teeth. Journal of Archaeological Science: Reports, 21, 897-903.

Zealand, A. M., Mei, R., Papachristodoulou, P., Roskilly, A. P., Liu, W-T., & Graham, D. W. (2018). Microbial community composition and diversity in rice straw digestion bioreactors with and without dairy manure. Applied Microbiology and Biotechnology, 102(19), 8599-8612.

Niemiro, G. M., Skinner, S. K., Walk, A. M., Edwards, C. G., De Lisio, M., Holscher, H. D., ... Khan, N. A. (2018). Oral Glucose Tolerance is Associated with Neuroelectric Indices of Attention Among Adults with Overweight and Obesity. Obesity, 26(10), 1550-1557.

An, L., Cogan, D. P., Navo, C. D., Jiménez-Osés, G., Nair, S. K., & van der Donk, W. A. (2018). Substrate-assisted enzymatic formation of lysinoalanine in duramycin. Nature chemical biology, 14(10), 928-933.

Marshall, F., Reid, R. E. B., Goldstein, S., Storozum, M., Wreschnig, A., Hu, L., ... Ambrose, S. H. (2018). Ancient herders enriched and restructured African grasslands. Nature, 561(7723), 387-390.

O'Reilly, M. C., Dong, S. H., Rossi, F. M., Karlen, K. M., Kumar, R. S., Nair, S. K., & Blackwell, H. E. (2018). Structural and Biochemical Studies of Non-native Agonists of the LasR Quorum-Sensing Receptor Reveal an L3 Loop “Out” Conformation for LasR. Cell chemical biology, 25(9), 1128-1139.e3.

Kapoor, I., & Nair, S. K. (2018). Structure-Guided Analyses of a Key Enzyme Involved in the Biosynthesis of an Antivitamin. Biochemistry, 57(36), 5282-5288.

Algya, K. M., Cross, T. W. L., Leuck, K. N., Kastner, M. E., Baba, T., Lye, L., ... Swanson, K. S. (2018). Apparent total-tract macronutrient digestibility, serum chemistry, urinalysis, and fecal characteristics, metabolites and microbiota of adult dogs fed extruded, mildly cooked, and raw diets. Journal of animal science, 96(9), 3670-3683.

Zhao, X. L., Chen, J. J., SI, S. Y., Chen, L-F., & Wang, Z. (2018). T63 inhibits osteoclast differentiation through regulating MAPKs and Akt signaling pathways. European Journal of Pharmacology, 834, 30-35.

Khatun, M. A., Hoque, M. A., Zhang, Y., Lu, T., Cui, L., Zhou, N. Y., & Feng, Y. (2018). Bacterial Consortium-Based Sensing System for Detecting Organophosphorus Pesticides. Analytical chemistry, 90(17), 10577-10584.

Perry, E., Cross, T. W. L., Francis, J. M., Holscher, H. D., Clark, S. D., & Swanson, K. S. (2018). Effect of Road Transport on the Equine Cecal Microbiota. Journal of Equine Veterinary Science, 68, 12-20.

Alexander, C., Cross, T. W. L., Devendran, S., Neumer, F., Theis, S., Ridlon, J. M., ... Swanson, K. S. (2018). Effects of prebiotic inulin-Type fructans on blood metabolite and hormone concentrations and faecal microbiota and metabolites in overweight dogs. Clay Minerals, 120(6), 711-720.

Holle, M. J., Ibarra-Sánchez, L. A., Liu, X., Stasiewicz, M. J., & Miller, M. J. (2018). Microbial analysis of commercially available US Queso Fresco. Journal of Dairy Science, 101(9), 7736-7745.

D'Alessandro-Gabazza, C. N., Méndez-García, C., Hataji, O., Westergaard, S., Watanabe, F., Yasuma, T., ... Gabazza, E. C. (2018). Identification of halophilic microbes in lung fibrotic tissue by oligotyping. Frontiers in Microbiology, 9(AUG), [1892].

Barakat, R., Lin, P. C., Park, C. J., Best, C., Bakry, H. H., Abosalem, M. E., ... Ko, C. (2018). Corrigendum to "Prenatal Exposure to DEHP Induces Neuronal Degeneration and Neurobehavioral Abnormalities in Adult Male Mice". Toxicological sciences : an official journal of the Society of Toxicology, 164(2).

Kong, W., Meldgin, D. R., Collins, J. J., & Lu, T. (2018). Designing microbial consortia with defined social interactions. Nature chemical biology, 14(8), 821-829.

the STRONG Kids Team (2018). Home feeding environment and picky eating behavior in preschool-aged children: A prospective analysis. Eating Behaviors, 30, 76-82.

Cattai de Godoy, M. R. (2018). Pancosma Comparative Gut Physiology Symposium: All About Appetite Regulation: Effects of diet and gonadal steroids on appetite regulation and food intake of companion animals. Journal of animal science, 96(8), 3526-3536.

Tang, Q., Lu, T., & Liu, S. J. (2018). Developing a Synthetic Biology Toolkit for Comamonas testosteroni, an Emerging Cellular Chassis for Bioremediation. ACS synthetic biology, 7(7), 1753-1762.

Niemiro, G. M., Allen, J. M., Mailing, L. J., Khan, N. A., Holscher, H. D., Woods, J. A., & De Lisio, M. (2018). Effects of endurance exercise training on inflammatory circulating progenitor cell content in lean and obese adults. Journal of Physiology, 596(14), 2811-2822.

Petronikolou, N., & Nair, S. K. (2018). Structural and Biochemical Studies of a Biocatalyst for the Enzymatic Production of Wax Esters. ACS Catalysis, 8(7), 6334-6344.

Estrada, P., Morita, M., Hao, Y., Schmidt, E. W., & Nair, S. K. (2018). A Single Amino Acid Switch Alters the Isoprene Donor Specificity in Ribosomally Synthesized and Post-Translationally Modified Peptide Prenyltransferases. Journal of the American Chemical Society, 140(26), 8124-8127.

He, F., Posselt, D. J., Narisetty, N., Zarzycki, C. M., & Nair, V. N. (2018). Application of multivariate sensitivity analysis techniques to AGCM-simulated tropical cyclones. Monthly Weather Review, 146(7), 2065-2088.

Liu, G., Zhang, Y., van der Mark, E., Magic-Knezev, A., Pinto, A., van den Bogert, B., ... Medema, G. (2018). Assessing the origin of bacteria in tap water and distribution system in an unchlorinated drinking water system by SourceTracker using microbial community fingerprints. Water Research, 138, 86-96.

Lipscomb, S. T., Becker, D. R., Laurent, H. K., Neiderhiser, J. M., Shaw, D. S., Natsuaki, M. N., ... Leve, L. D. (2018). Examining morning HPA axis activity as a moderator of hostile, over-reactive parenting on children's skills for success in school. Infant and Child Development, 27(4), [e2083].

Wei, L. J., Kwak, S., Liu, J. J., Lane, S., Hua, Q., Kweon, D. H., & Jin, Y-S. (2018). Improved squalene production through increasing lipid contents in Saccharomyces cerevisiae. Biotechnology and bioengineering, 115(7), 1793-1800.

Yu, S., Liu, J. J., Yun, E. J., Kwak, S., Kim, K. H., & Jin, Y-S. (2018). Production of a human milk oligosaccharide 2'-fucosyllactose by metabolically engineered Saccharomyces cerevisiae. Microbial cell factories, 17(1), [101].

Karig, D., Michael Martini, K., Lu, T., DeLateur, N. A., Goldenfeld, N. D., & Weiss, R. (2018). Stochastic Turing patterns in a synthetic bacterial population. Proceedings of the National Academy of Sciences of the United States of America, 115(26), 6572-6577.

Ongpipattanakul, C., & Nair, S. K. (2018). Biosynthetic Proteases That Catalyze the Macrocyclization of Ribosomally Synthesized Linear Peptides. Biochemistry, 57(23), 3201-3209.

Kim, H., Oh, E. J., Lane, S. T., Lee, W. H., Cate, J. H. D., & Jin, Y-S. (2018). Enhanced cellobiose fermentation by engineered Saccharomyces cerevisiae expressing a mutant cellodextrin facilitator and cellobiose phosphorylase. Journal of Biotechnology, 275, 53-59.

Wang, Y., Jeffery, E. H., Miller, M. J., Wallig, M. A., & Wu, Y. (2018). Lightly cooked broccoli is as effective as raw broccoli in mitigating dextran sulfate sodium-induced colitis in mice. Nutrients, 10(6), [748].

Ibarra-Sánchez, L. A., Van Tassell, M. L., & Miller, M. J. (2018). Antimicrobial behavior of phage endolysin PlyP100 and its synergy with nisin to control Listeria monocytogenes in Queso Fresco. Food Microbiology, 72, 128-134.

Ling, F., Whitaker, R., LeChevallier, M. W., & Liu, W-T. (2018). Drinking water microbiome assembly induced by water stagnation. ISME Journal, 12(6), 1520-1531.

Berding, K., Holscher, H. D., Parker, A. A., & Donovan, S. M. (2018). Fecal microbiome composition and stability in 4- to 8-year old children is associated with dietary patterns and nutrient intake. Journal of Nutritional Biochemistry, 56, 165-174.

Hylemon, P. B., Harris, S. C., & Ridlon, J. M. (2018). Metabolism of hydrogen gases and bile acids in the gut microbiome. FEBS Letters, 592(12), 2070-2082.

Holscher, H. D., Guetterman, H. M., Swanson, K. S., An, R., Matthan, N. R., Lichtenstein, A. H., ... Baer, D. J. (2018). Walnut consumption alters the gastrointestinal microbiota, microbially derived secondary bile acids, and health markers in healthy adults: A randomized controlled trial. Journal of Nutrition, 148(6), 861-867.

Kim, J. S., Daum, M. A., Jin, Y-S., & Miller, M. J. (2018). Yeast derived lysA2 can control bacterial contamination in ethanol fermentation. Viruses, 10(6), [281].

Morita, M., Hao, Y., Jokela, J. K., Sardar, D., Lin, Z., Sivonen, K., ... Schmidt, E. W. (2018). Post-Translational Tyrosine Geranylation in Cyanobactin Biosynthesis. Journal of the American Chemical Society, 140(19), 6044-6048.

Harris, S. C., Devendran, S., Méndez- García, C., Mythen, S. M., Wright, C. L., Fields, C. J., ... Ridlon, J. M. (Accepted/In press). Bile acid oxidation by Eggerthella lenta strains C592 and DSM 2243TGut Microbes, 1-17.

Tang, Q., Lu, T., & Liu, S. J. (2018). Engineering the bacterium Comamonas testosteroni CNB-1: Plasmid curing and genetic manipulation. Biochemical Engineering Journal, 133, 74-82.

Yun, E. J., Oh, E. J., Liu, J. J., Yu, S., Kim, D. H., Kwak, S., ... Jin, Y-S. (2018). Promiscuous activities of heterologous enzymes lead to unintended metabolic rerouting in Saccharomyces cerevisiae engineered to assimilate various sugars from renewable biomass. Biotechnology for Biofuels, 11(1), [140].

Liu, J. J., Zhang, G. C., Kong, I. I., Yun, E. J., Zheng, J. Q., Kweon, D. H., & Jin, Y-S. (2018). A mutation in PGM2 causing inefficient galactose metabolism in the probiotic yeast Saccharomyces boulardii. Applied and Environmental Microbiology, 84(10), [e02858-17].

Nishihama, K., Yasuma, T., Yano, Y., D' Alessandro-Gabazza, C. N., Toda, M., Hinneh, J. A., ... Gabazza, E. C. (2018). Anti-apoptotic activity of human matrix metalloproteinase-2 attenuates diabetes mellitus. Metabolism: Clinical and Experimental, 82, 88-99.

Li, Q., Lawrence, C. R., Nowak, R. A., Flaws, J. A., Bagchi, M. K., & Bagchi, I. C. (2018). Bisphenol A and phthalates modulate peritoneal macrophage function in female mice involving SYMD2-H3K36 dimethylation. Endocrinology, 159(5), 2216-2228.

Luo, J., Han, L., Liu, L., Gao, L., Xue, B., Wang, Y., ... Peng, X. (2018). Catechin supplemented in a FOS diet induces weight loss by altering cecal microbiota and gene expression of colonic epithelial cells. Food and Function, 9(5), 2962-2969.

Lee-Thacker, S., Choi, Y., Taniuchi, I., Takarada, T., Yoneda, Y., Ko, C., & Jo, M. (2018). Core binding factor b expression in ovarian granulosa cells is essential for female fertility. Endocrinology, 159(5), 2094-2109.

Laurent, H. K., Goodman, S. H., Stowe, Z. N., Halperin, M., Khan, F., Wright, D., ... Knight, B. (2018). Course of ante-and postnatal depressive symptoms related to mothers' HPA axis regulation. Journal of Abnormal Psychology, 127(4), 404-416.

Doden, H., Sallam, L. A., Devendran, S., Ly, L., Doden, G., Daniel, S. L., ... Ridlon, J. M. (2018). Metabolism of oxo-bile acids and characterization of recombinant 12α- hydroxysteroid dehydrogenases from bile acid 7α-dehydroxylating human gut bacteria. Applied and environmental microbiology, 84(10), [e00235-18].

Bailey, M. A., & Holscher, H. D. (2018). Microbiome-mediated effects of the Mediterranean diet on inflammation. Advances in Nutrition, 9(3), 93-206.

Yun, E. J., Lee, J., Kim, D. H., Kim, J., Kim, S., Jin, Y-S., & Kim, K. H. (2018). Metabolomic elucidation of the effects of media and carbon sources on fatty acid production by Yarrowia lipolytica. Journal of Biotechnology, 272-273, 7-13.

Petronikolou, N., Hollatz, A. J., Schuler, M. A., & Nair, S. K. (2018). Loganic Acid Methyltransferase: Insights into the Specificity of Methylation on an Iridoid Glycoside. ChemBioChem, 19(8), 784-788.

Yang, X., Narisetty, N., & He, X. (2018). A New Approach to Censored Quantile Regression Estimation. Journal of Computational and Graphical Statistics, 27(2), 417-425.

Beloshapka, A. N., Cattai de Godoy, M. R., Carter, R. A., Fascetti, A. J., Yu, Z., McIntosh, B. J., ... Buff, P. R. (2018). Longitudinal changes in blood metabolites, amino acid profile, and oxidative stress markers in american foxhounds fed a nutrient-fortified diet. Journal of animal science, 96(3), 930-940.

the STRONG Kids Team (2018). Child body mass index, genotype and parenting in the prediction of restrictive feeding. Pediatric Obesity, 13(4), 239-246.

Richardson, K. A., Hannon, P. R., Johnson-Walker, Y. J., Myint, M. S., Flaws, J. A., & Nowak, R. A. (2018). Di (2-ethylhexyl) phthalate (DEHP) alters proliferation and uterine gland numbers in the uteri of adult exposed mice. Reproductive Toxicology, 77, 70-79.

Reznikov, E. A., Comstock, S. S., Hoeflinger, J. L., Wang, M., Miller, M. J., & Donovan, S. M. (2018). Dietary bovine Lactoferrin reduces Staphylococcus aureus in the tissues and modulates the immune response in piglets systemically infected with S. aureus. Current Developments in Nutrition, 2(4), [nzy001].

Fleming, S. A., Chichlowski, M., Berg, B. M., Donovan, S. M., & Dilger, R. N. (2018). Dietary sialyllactose does not influence measures of recognition memory or diurnal activity in the young pig. Nutrients, 10(4), [395].

Allen, J. M., Mailing, L. J., Niemiro, G. M., Moore, R., Cook, M. D., White, B. A., ... Woods, J. A. (2018). Exercise Alters Gut Microbiota Composition and Function in Lean and Obese Humans. Medicine and Science in Sports and Exercise, 50(4), 747-757.

Khan, N. A., Walk, A. M., Edwards, C. G., Jones, A. R., Cannavale, C. N., Thompson, S. V., ... Holscher, H. D. (2018). Macular xanthophylls are related to intellectual ability among adults with overweight and obesity. Nutrients, 10(4), [396].

Laurent, H. K., Wright, D., & Finnegan, M. (2018). Mindfulness-related differences in neural response to own infant negative versus positive emotion contexts. Developmental Cognitive Neuroscience, 30, 70-76.

Mythen, S. M., Devendran, S., Méndez-García, C., Cann, I., & Ridlon, J. M. (2018). Targeted synthesis and characterization of a gene cluster encoding NAD(P)H-dependent 3α-, 3β-, and 12α-hydroxysteroid dehydrogenases from Eggerthella CAG:298, a gut metagenomic sequence. Applied and environmental microbiology, 84(7), [e02475-17].

Mahanta, N., Liu, A., Dong, S., Nair, S. K., & Mitchell, D. A. (2018). Enzymatic reconstitution of ribosomal peptide backbone thioamidation. Proceedings of the National Academy of Sciences of the United States of America, 115(12), 3030-3035.

Li, Y., Liu, M., Chen, L-F., & Chen, R. (2018). P-TEFb: Finding its ways to release promoter-proximally paused RNA polymerase II. Transcription, 9(2), 88-94.

Harris, S. C., Devendran, S., Alves, J. M. P., Mythen, S. M., Hylemon, P. B., & Ridlon, J. M. (2018). Identification of a gene encoding a flavoprotein involved in bile acid metabolism by the human gut bacterium Clostridium scindens ATCC 35704. Biochimica et Biophysica Acta - Molecular and Cell Biology of Lipids, 1863(3), 276-283.

STRONG Kids Team (2018). Predictors and Outcomes of Mealtime Emotional Climate in Families with Preschoolers. Journal of Pediatric Psychology, 43(2), 195-206.

Baumgartner, N. W., Walk, A. M., Edwards, C. G., Covello, A. R., Chojnacki, M. R., Reeser, G. E., ... Khan, N. A. (2018). Relationship Between Physical Activity, Adiposity, and Attentional Inhibition. Journal of physical activity & health, 15(3), 191-196.

Blanchard, A. E., Liao, C., & Lu, T. (2018). Circuit-Host Coupling Induces Multifaceted Behavioral Modulations of a Gene Switch. Biophysical journal, 114(3), 737-746.

Holscher, H. D., Taylor, A. M., Swanson, K. S., Novotny, J. A., & Baer, D. J. (2018). Almond consumption and processing affects the composition of the gastrointestinal microbiota of healthy adult men and women: A randomized controlled trial. Nutrients, 10(2), [126].

Dong, X., Hu, X., Chen, J., Hu, D., & Chen, L-F. (2018). BRD4 regulates cellular senescence in gastric cancer cells via E2F/miR-106b/p21 axis. Cell Death and Disease, 9(2), [203].

Fang, T., Cui, Q., Huang, Y., Dong, P., Wang, H., Liu, W-T., & Ye, Q. (2018). Distribution comparison and risk assessment of free-floating and particle-attached bacterial pathogens in urban recreational water: Implications for water quality management. Science of the Total Environment, 613-614, 428-438.

Pallotto, M. R., Cattai de Godoy, M. R., Holscher, H. D., Buff, P. R., & Swanson, K. S. (2018). Effects of weight loss with a moderate-protein, high-fiber diet on body composition, voluntary physical activity, and fecal microbiota of obese cats. American journal of veterinary research, 79(2), 181-190.

Nelson, B. W., Allen, N. B., & Laurent, H. K. (2018). Infant HPA axis as a potential mechanism linking maternal mental health and infant telomere length. Psychoneuroendocrinology, 88, 38-46.

Mackie, R. I., & Cann, I. (2018). Let them eat fruit. Nature Microbiology, 3(2), 127-129.

Delker, B. C., Bernstein, R. E., & Laurent, H. K. (2018). Out of harm's way: Secure versus insecure-disorganized attachment predicts less adolescent risk taking related to childhood poverty. Development and Psychopathology, 30(1), 283-296.

Rao, C. V. (2018). Sparsity of Linear Discrete-Time Optimal Control Problems with $l-1$ Objectives. IEEE Transactions on Automatic Control, 63(2), 513-517. [7993042].

Bae, J. H., Kim, H. J., Kim, M. J., Sung, B. H., Jeon, J. H., Kim, H. S., ... Sohn, J. H. (2018). Direct fermentation of Jerusalem artichoke tuber powder for production of L-lactic acid and D-lactic acid by metabolically engineered Kluyveromyces marxianus. Journal of Biotechnology, 266, 27-33.

Seo, S. O., Lu, T., Jin, Y-S., & Blaschek, H-P. M. (2018). Development of an oxygen-independent flavin mononucleotide-based fluorescent reporter system in Clostridium beijerinckii and its potential applications. Journal of Biotechnology, 265, 119-126.

Zhang, Z. T., Jiménez-Bonilla, P., Seo, S. O., Lu, T., Jin, Y-S., Blaschek, H-P. M., & Wang, Y. (2018). Bacterial genome editing with CRISPR-Cas9: Taking clostridium beijerinckii as an example. In Methods in Molecular Biology (pp. 297-325). (Methods in Molecular Biology; Vol. 1772). Humana Press Inc..

Gan, L., Narisetty, N., & Liang, F. (Accepted/In press). Bayesian Regularization for Graphical Models With Unequal Shrinkage. Journal of the American Statistical Association.

Naas, A. E., Solden, L. M., Norbeck, A. D., Brewer, H., Hagen, L. H., Heggenes, I. M., ... Pope, P. B. (2018). "Candidatus Paraporphyromonas polyenzymogenes" encodes multi-modular cellulases linked to the type IX secretion system. Microbiome, 6(1), [44].

Jayakody, L. N., Liu, J. J., Yun, E. J., Turner, T. L., Oh, E. J., & Jin, Y-S. (Accepted/In press). Direct conversion of cellulose into ethanol and ethyl-β-d-glucoside via engineered Saccharomyces cerevisiae. Biotechnology and Bioengineering.

Sirk, S. (2018). Directed evolution of targeted recombinases for genome engineering. In Methods in Molecular Biology (pp. 89-102). (Methods in Molecular Biology; Vol. 1867). Humana Press Inc..

Eckstrum, K. S., Edwards, W., Banerjee, A., Wang, W., Flaws, J. A., Katzenellenbogen, J. A., ... Raetzman, L. T. (2018). Effects of exposure to the endocrine-Disrupting chemical bisphenol a during critical windows of murine pituitary development. Endocrinology, 159(1), 119-131.

Turner, T. L., Kim, H., Kong, I. I., Liu, J. J., Zhang, G. C., & Jin, Y-S. (2018). Engineering and evolution of saccharomyces cerevisiae to produce biofuels and chemicals. In Advances in Biochemical Engineering/Biotechnology (pp. 175-215). (Advances in Biochemical Engineering/Biotechnology; Vol. 162). Springer Science and Business Media Deutschland GmbH.

Siegel, M. H., Wang, M., Pan, X., Li, Q., Richards, J. D., Chichlowski, M., ... Donovan, S. M. (2018). Evaluation of sialyllactose supplementation of a prebiotic-containing formula on growth, intestinal development, and bacterial colonization in the neonatal piglet. Current Developments in Nutrition, 2(11), [nzy067].

Jayakody, L. N., Turner, T. L., Yun, E. J., Kong, I. I., Liu, J. J., & Jin, Y-S. (Accepted/In press). Expression of Gre2p improves tolerance of engineered xylose-fermenting Saccharomyces cerevisiae to glycolaldehyde under xylose metabolism. Applied Microbiology and Biotechnology.

Walukiewicz, H. E., Ordal, G. W., & Rao, C. V. (2018). In vitro assay for measuring receptor-kinase activity in the bacillus subtilis chemotaxis pathway. In Methods in Molecular Biology (pp. 95-105). (Methods in Molecular Biology; Vol. 1729). Humana Press Inc..

Brooks, A. S., Yellen, J. E., Potts, R., Behrensmeyer, A. K., Deino, A. L., Leslie, D. E., ... Clark, J. B. (2018). Long-distance stone transport and pigment use in the earliest Middle Stone Age. Science, 360(6384), 90-94.

Kim, D. H., Kim, I. J., Yun, E. J., Kwak, S., Jin, Y-S., & Kim, K. H. (Accepted/In press). Metabolic engineering of Saccharomyces cerevisiae by using the CRISPR-Cas9 system for enhanced fatty acid production. Process Biochemistry.

Oh, S., Hammes, F., & Liu, W-T. (2018). Metagenomic characterization of biofilter microbial communities in a full-scale drinking water treatment plant. Water Research, 128, 278-285.

Jagtap, S. S., & Rao, C. V. (Accepted/In press). Microbial conversion of xylose into useful bioproducts. Applied Microbiology and Biotechnology.

Ongpipattanakul, C., & Nair, S. K. (Accepted/In press). Molecular Basis for Autocatalytic Backbone N-Methylation in RiPP Natural Product Biosynthesis. ACS Chemical Biology.

Kong, I. I., Turner, T. L., Kim, H., Kim, S. R., & Jin, Y-S. (2018). Phenotypic evaluation and characterization of 21 industrial Saccharomyces cerevisiae yeast strains. FEMS yeast research, 18(1).

Park, C. J., Kim, H., Jin, J., Barakat, R., Lin, P. C., Choi, J. M., & Ko, C. (2018). Porcine intestinal lymphoid tissues synthesize estradiol. Journal of Veterinary Science, 19(4), 477-482.

Barakat, R., Lin, P. C., Park, C. J., Best, C., Bakry, H. H., Abosalem, M. E., ... Ko, C. (2018). Prenatal exposure to DEHP induces neuronal degeneration and neurobehavioral abnormalities in adult male mice. Toxicological Sciences, 164(2), 439-452.

Jagtap, S. S., & Rao, C. V. (2018). Production of d-arabitol from d-xylose by the oleaginous yeast Rhodosporidium toruloides IFO0880. Applied Microbiology and Biotechnology, 102(1), 143-151.

Narisetty, N., Shen, J., & He, X. (Accepted/In press). Skinny Gibbs: A Consistent and Scalable Gibbs Sampler for Model Selection. Journal of the American Statistical Association.

Cogan, D. P., Baraquet, C., Harwood, C. S., & Nair, S. K. (2018). Structural basis of transcriptional regulation by cour, a repressor of coumarate catabolism, in rhodopseudomonas palustris. Journal of Biological Chemistry, 293(30), 11727-11735.

Gu, W., Dong, S. H., Sarkar, S., Nair, S. K., & Schmidt, E. W. (2018). The Biochemistry and Structural Biology of Cyanobactin Pathways: Enabling Combinatorial Biosynthesis. In B. S. Moore (Ed.), Methods in Enzymology (pp. 113-163). (Methods in Enzymology; Vol. 604). Academic Press Inc..

Devendran, S., Mythen, S. M., & Ridlon, J. M. (2018). The desA and desB genes from Clostridium scindens ATCC 35704 encode steroid-17,20-desmolase. Journal of Lipid Research, 59(6), 1005-1014.

Lee, D. G., Jeon, J. M., Yang, Y. H., Jin, Y-S., & Yoon, J. J. (Accepted/In press). The pH-stat Butyric Acid Feeding Strategy Coupled with Gas-Stripping for n-Butanol Production by Clostridium beijerinckii. Waste and Biomass Valorization.

Azam, M. S., & Vanderpool, C. (2018). Translational regulation by bacterial small RNAs via an unusual Hfq-dependent mechanism. Nucleic acids research, 46(5), 2585-2599.

Lane, S., Dong, J., & Jin, Y-S. (Accepted/In press). Value-added biotransformation of cellulosic sugars by engineered Saccharomyces cerevisiae. Bioresource Technology.

Dent, S. C., Hutchinson, D. L., Hedman, K. M., Fort, M. A., & Ambrose, S. H. (2018). Purification of dental calculus organic and carbonate biofractions improves correlations with bone stable isotope ratios. 65. Abstract from 2018 Annual Meeting of the American Association of Physical Anthropologists, Austin, United States.