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 Animal Parasitic Diseases Laboratory: Beltsville, MD
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ARS Home Northeast Area Beltsville, Maryland (BARC) Beltsville Agricultural Research Center Animal Parasitic Diseases Laboratory People & Locations







Robert  Li
                        Animal Parasitic Diseases Laboratory

                        




                        
                        Research Molecular Biologist
                        Phone: (301) 504-5185
                        
                        
                        Fax: (301) 504-8414(Employee information on this page comes from the REE Directory. Please contact your front office staff to update the REE Directory.)
                            ProjectsMolecular, Immune and Microbiome Approaches for Mitigating GI Nematode Infections of Livestock
                                                    In-House Appropriated
                                                                    (D)Accession Number: 441382Characterize Genomic Loci and Epigenetic Events that Contribute to Host Resistance to Gastrointestinal Nematodes in Sheep
                                                    Non-Assistance Cooperative Agreement
                                                                    (S)Accession Number: 443761**Publications**
                                                (Clicking on the reprint icon
                                                    Reprint Icon
                                                    will take you to the publication reprint.)Differential correlation of transcriptome data reveals gene-pairs and pathways involved in treatment of Citrobacter rodentium infection with a fruit bioactive
                                                        

- (Peer Reviewed Journal)Fleming, D.S., Liu, F., Li, R.W. 2023. Differential correlation of transcriptome data reveals gene-pairs and pathways involved in treatment of Citrobacter rodentium infection with a fruit bioactive. Molecules. 28(21):7369. https://doi.org/10.3390/molecules28217369.Recent advances in manipulating the rumen microbiota to diminish the effect of climate changes of ruminant farming

- (Book / Chapter)After bone marrow transplantation, cell-intrinsic T Helper-2 (Th2) pathway promotes recipient T lymphocyte survival and regulates the graft-versus-host disease
                                                        

- (Peer Reviewed Journal)Truscott, J., Guan, X., Fury, H., Atagozli, T., Metwali, A., Liu, W., Li, Y., Urban Jr, J.F., Li, R.W., Brombacher, F., Elliott, D., Blazer, B., Ince, M. 2023. After bone marrow transplantation, cell-intrinsic T Helper-2 (Th2) pathway promotes recipient T lymphocyte survival and regulates the graft-versus-host disease. Journal of Immunology. https://doi.org/10.4049/immunohorizons.2300021.Multi-omics analysis detected multiple pathways by which pomegranate punicalagin exerts its biological effects in modulating host–microbiota interactions in murine colitis models
                                                        

- (Peer Reviewed Journal)Liu, F., Smith, A.D., Wang, T.T., Pham, Q., Yang, H., Li, R.W. 2023. Multi-omics analysis detected multiple pathways by which pomegranate punicalagin exerts its biological effects in modulating host–microbiota interactions in murine colitis models. Food & Function. 14:3824. https://doi.org/10.1039/D3FO00286A.Comparative metagenomics reveal the effect of diet on the fecal virome and the associations with production traits of beef cattle

- (Abstract Only)Ellagitannin punicalagin disrupts the pathways related to bacterial growth and affects multiple pattern recognition receptor signaling by acting as a selective histone deacetylase inhibitor
                                                        

- (Peer Reviewed Journal)Liu, F., Smith, A.D., Wang, T.T., Pham, Q., Yang, H., Li, R.W. 2023. Ellagitannin punicalagin disrupts the pathways related to bacterial growth and affects multiple pattern recognition receptor signaling by acting as a selective histone deacetylase inhibitor. Journal of Agricultural and Food Chemistry. 71(12):5016-5026. https://doi.org/10.1021/acs.jafc.2c08738.Biological pathways via which the anthocyanin malvidin alleviated the murine colitis induced by Citrobacter rodentium
                                                        

- (Peer Reviewed Journal)Liu, F., Smith, A.D., Wang, T.T., Pham, Q., Cheung, L., Yang, H., Li, R.W. 2022. Biological pathways via which the anthocyanin malvidin alleviated the murine colitis induced by Citrobacter rodentium. Food & Function. 14(2):1048-1061. https://doi.org/10.1039/D2FO02873E.Recent advances in developing butyrogenic functional foods to promote gut health
                                                        

- (Review Article)Zhang, M., Li, R.W., Yang, H., Tan, Z., Liu, F. 2022. Recent advances in developing butyrogenic functional foods to promote gut health. Critical Reviews in Food Science and Nutrition. 1-22. https://doi.org/10.1080/10408398.2022.2142194.Rumen microbial predictors for short-chain fatty acid levels and the grass-fed regimen in angus cattle
                                                        

- (Peer Reviewed Journal)Liu, J., Bai, Y., Liu, F., Kohn, R.A., Tadesse, D.A., Sarria, S., Li, R.W., Song, J. 2022. Rumen microbial predictors for short-chain fatty acid levels and the grass-fed regimen in angus cattle. Animals. 12(21). Article 2995. https://doi.org/10.3390/ani12212995.Microbial composition and co-occurrence patterns in the gut microbial community of healthy and obese mice in response to astaxanthin in its native and lipid emulsion forms
                                                        

- (Peer Reviewed Journal)Gao, Y., Liu, F., Li, R.W., Xue, C., Tang, Q. 2022. Microbial composition and co-occurrence patterns in the gut microbial community of healthy and obese mice in response to astaxanthin in its native and lipid emulsion forms. Frontiers in Microbiology. https://doi.org/10.3389/fmicb.2021.671271.Large-scale meta-longitudinal microbiome data with a known batch factor
                                                        

- (Peer Reviewed Journal)Oh, S., Li, R.W. 2022. Large-scale meta-longitudinal microbiome data with a known batch factor. Nature Methods. https://doi.org/10.3390/genes13030392.Tools and resources enabling marker gene-based microbiome studies
                                                        

- (Book / Chapter)Liu, J., Li, R.W. 2022. Tools and resources enabling marker gene-based microbiome studies. In: Wu, V.C.H., editor. The Gut Microbiome: Bench to Table. 1st edition. Boca Raton, FL: CRC Press. p. 3-44. https://doi.org/10.1201/b22970.Transcriptome analysis unravels that triacylglycerol bound docosahexaenoic acid regulates appetite via the mediation of leptin and intestinal epithelial function in animal models
                                                        

- (Peer Reviewed Journal)Cao, W., Liu, F., Li, R.W., Wang, Y. 2022. Transcriptome analysis unravels that triacylglycerol bound docosahexaenoic acid regulates appetite via the mediation of leptin and intestinal epithelial function in animal models. Journal of Nutritional Biochemistry. https://doi.org/10.1016/j.jnutbio.2021.108856.Docosahexaenoic acid prevented insulin resistance by modulating gut microbiome and promoting colonic peptide YY expression in diet-induced obesity mice
                                                        

- (Peer Reviewed Journal)Cao, W., Li, R.W., Chin, Y., Wang, Y., Xue, C., Tang, Q. 2021. Docosahexaenoic acid prevented insulin resistance by modulating gut microbiome and promoting colonic peptide YY expression in diet-induced obesity mice. Food Science and Human Wellness.  https://doi.org/10.1016/j.fshw.2021.07.018.Effects of differences in resistant starch content of rice on intestinal microbial composition
                                                        

- (Peer Reviewed Journal)Wan, J., Wu, Y., Pham, Q., Li, R.W., Yu, L., Chen, M., Boue, S.M., Yokoyama, W., Li, B., Wang, T.T.Y. 2021. Effects of differences in resistant starch content of rice on intestinal microbial composition. Journal of Agricultural and Food Chemistry. 69(28):8017-8027. https://doi.org/10.1021/acs.jafc.0c07887.Transcriptome analysis reveals the protective role of fructo-oligosaccharide in colonic mucosal barriers in exercise-induced stressed mice
                                                        

- (Peer Reviewed Journal)Cao, W., Chin, Y., Li, R.W., Xue, C., Wang, Y., Tang, Q. 2021. Transcriptome analysis reveals the protective role of fructo-oligosaccharide in colonic mucosal barriers in exercise-induced stressed mice. Food and Function. https://doi.org/10.1039/D0FO02556A.Transcriptomic analysis of Androgen-dependent Human Prostate Cancer LNCaP Cells and its Tumor Xenograft to elucidate the components and mechanisms contributed by tumor environment
                                                        

- (Peer Reviewed Journal)Yu, L., Li, R.W., Huang, H., Pham, Q., Yu, L., Wang, T.T.Y. 2021. Transcriptomic analysis of LNCaP tumor xenograft to elucidate the components and mechanisms contributed by tumor environment as targets for dietary prostate cancer prevention studies. Nutrients. 13(3):1000. https://doi.org/10.3390/nu13031000.Temporal dynamic methods for bulk RNA-Seq time series data
                                                        

- (Peer Reviewed Journal)Oh, S., Li, R.W. 2021. Temporal dynamic methods for bulk RNA-Seq time series data. Genes. 12(3):352. https://doi.org/10.3390/genes12030352.Genistein reduces the risk of local mammary cancer recurrence and ameliorates alterations in the gut microbiota in the offspring of obese dams
                                                        

- (Peer Reviewed Journal)Oliveira De Andrade, F., Liu, F., Zhang, X., Mariana, R., Dani, C., Cruz, I., Wang, T.T., Helferiche, W., Li, R.W., Hilakivi-Clarke, L. 2021. Genistein reduces the risk of local mammary cancer recurrence and ameliorates alterations in the gut microbiota in the offspring of obese dams. Nutrients. 12(1):201. https://doi.org/10.3390/nu13010201.New paraprobiotic-based treatment for control of the barber pole worm Haemonchus contortus in sheep
                                                        

- (Peer Reviewed Journal)Sanders, J., Xie, Y., Gazzola, D., Li, H., Abraham, A., Flanagan, K., Rus, F., Miller, M., Hu, Y., Zarlenga, D.S., Li, R.W., Urban Jr, J.F., Ostroff, G., Zajac, A., Aroian, R.V. 2020. New paraprobiotic-based treatment for control of the barber pole worm Haemonchus contortus in sheep. International Journal for Parasitology: Drug and Drug Resistance. 14(230-236). https://doi.org/10.1016/j.ijpddr.2020.11.004.Diet-induced changes in bacterial communities in the jejunum and their associations with bile acids in Angus beef cattle
                                                        

- (Peer Reviewed Journal)Liu, J., Liu, F., Cai, W., Jia, C., Ying, B., Yanghua, H., Weiyun, Z., Li, R.W., Song, J. 2020. Diet-induced changes in bacterial communities in the jejunum and their associations with bile acids in Angus beef cattle. Microbiome. 2:33. https://doi.org/10.1186/s42523-020-00051-7.Polymannuronic acid prevents dopaminergic neuronal loss via brain-gut-microbiota axis in Parkinson’s disease model
                                                        

- (Peer Reviewed Journal)Dong, X., Wang, X., Liu, F., Li, R.W., Xue, C., Wong, K., Wong, W., Tang, Q. 2020. Polymannuronic acid prevents dopaminergic neuronal loss via brain-gut-microbiota axis in Parkinson’s disease model. International Journal of Biological Macromolecules. 164:994-1005. https://doi.org/10.1016/j.ijbiomac.2020.07.180.Molecular and metabolomic changes in the proximal colon of pigs infected with Trichuris suis
                                                        

- (Peer Reviewed Journal)Dawson, H.D., Chen, C.T., Li, R.W., Bell, N., Shea-Donohue, T., Kringel, H., Beshah, E., Hill, D.E., Urban Jr, J.F. 2020. Molecular and metabolomic changes in the proximal colon of pigs infected with Trichuris suis. Scientific Reports. 10, 12853. https://doi.org/10.1038/s41598-020-69462-5.Molecular and microbial signatures predictive of prebiotic action of neoagarotetraose in a dextran sulfate sodium-induced murine colitis model
                                                        

- (Peer Reviewed Journal)Liu, F., Liu, J., Wang, T.T., Changhu, X., Ziangzhao, M., Qingjuan, T., Li, R.W. 2020. Molecular and microbial signatures predictive of prebiotic action of neoagarotetraose in a dextran sulfate sodium-induced murine colitis model. Microorganisms. 8(7):995. https://doi.org/10.3390/microorganisms8070995.Mechanistic insights into the attenuation of intestinal inflammation and modulation of the gut microbiome by krill oil using in vitro and in vivo models
                                                        

- (Peer Reviewed Journal)Liu, F., Smith, A.D., Solano Aguilar, G., Wang, T.T., Pham, Q., Tang, Q., Urban Jr, J.F., Xue, C., Li, R.W. 2020. Mechanistic insights into the attenuation of intestinal inflammation and modulation of the gut microbiome by krill oil using in vitro and in vivo models. Microbiome. 8:83. https://doi.org/10.1186/s40168-020-00843-8.An inactivated bacterium (paraprobiotic) expressing Bacillus thuringiensis Cry5B as a therapeutic for Ascaris and Parascaris spp. infections in large animals
                                                        

- (Peer Reviewed Journal)Urban Jr, J.F., Nielsen, M., Gazzola, D., Xie, Y., Beshah, E., Hu, Y., Rus, F., Flanagan, K., Draper, A., Vakalapudi, S., Li, R.W., Ostroff, G.R., Aroian, R.V. 2020. An inactivated bacterium (paraprobiotic) expressing Bacillus thuringiensis Cry5B as a therapeutic for Ascaris and Parascaris spp. infections in large animals. Elsevier. 164:994-1005. https://doi.org/10.1016/j.onehlt.2021.100241.Astaxanthin n-octanoic acid diester ameliorated insulin resistance in high-fat and high-sucrose diet-fed mice by modulating the gut microbiome
                                                        

- (Peer Reviewed Journal)Gao, Y., Yang, L., Chin, Y., Liu, F., Li, R.W., Cao, W., Yuan, S., Xue, C., Xu, J., Tang, Q. 2020. Astaxanthin n-octanoic acid diester ameliorated insulin resistance in high-fat and high-sucrose diet-fed mice by modulating the gut microbiome. Scientific Reports. 21:2149. https://doi.org/10.3390/ijms21062149.Gut microbial signatures with predictive power for moxidectin treatment outcomes in
                                                        

- (Peer Reviewed Journal)Liu, F., Xie, Y., Zajaz, A.M., Hu, Y., Aroian, R.V., Urban Jr, J.F., Li, R.W. 2020. Gut microbial signatures with predictive power for moxidectin treatment outcomes in. Journal of Parasitology. 242(2020):108607. https://doi.org/10.1016/j.vetmic.2020.108607.Complete genome sequence of Escherichia coli phage vB_EcoM Sa157lw, isolated from surface water collected in Salinas, California
                                                        

- (Peer Reviewed Journal)Liu, F., Liao, Y., Li, R.W., Wu, V.C. 2019. Complete genome sequence of Escherichia coli phage vB_EcoM Sa157lw, isolated from surface water collected in Salinas, California. Microbiology Resource Announcements. 8:e00718-19. https://doi.org/10.1128/MRA.00718-19.Malvidin 3-glucoside modulated gut microbial dysbiosis and global metabolome disrupted in a murine colitis model induced by dextran sulfate sodium
                                                        

- (Peer Reviewed Journal)Liu, F., Wang, T.T., Tang, Q., Xue, C., Li, R.W., Wu, V.C. 2019. Malvidin 3-glucoside modulated gut microbial dysbiosis and global metabolome disrupted in a murine colitis model induced by dextran sulfate sodium. Molecular Nutrition and Food Research. 1900455:1-14. https://doi.org/10.1002/mnfr.201900455.Characterization of a lytic bacteriophage as an antimicrobial agent for biocontrol of Shiga toxin-producing Escherichia coli O145 strains
                                                        

- (Peer Reviewed Journal)Liao, Y., Salvador, A., Harden, L.A., Liu, F., Lavenburg, V.M., Li, R.W., Wu, V.C. 2019. Characterization of a lytic bacteriophage as an antimicrobial agent for biocontrol of Shiga toxin-producing Escherichia coli O145 strains. Antibiotics. 8(2):74. https://doi.org/10.3390/antibiotics8020074.Network analysis detected microbial co-occurrence patterns and identified keystone species in the gut microbial community of mice in response to stress and chondroitin sulfate disaccharide dietary supplement
                                                        

- (Peer Reviewed Journal)Liu, F., Li, Z., Wang, Z., Xue, C., Tang, Q., Li, R.W. 2019. Network analysis detected microbial co-occurrence patterns and identified keystone species in the gut microbial community of mice in response to stress and chondroitin sulfate disaccharide dietary supplement. International Journal of Molecular Sciences. 20(9):2130.  https://doi.org/10.3390/ijms20092130Characterization of a Lytic Bacteriophage as an Antimicrobial Agent for Biocontrol of Shiga Toxin-Producing Escherichia coli O145 Strains

- (Abstract Only)Inhibition of tumor growth by indole-3-carbinol in a prostate cancer xenograft model may be associated with disrupted gut microbial interactions
                                                        

- (Peer Reviewed Journal)Wu, Y., Li, R.W., Huang, H., Fletcher, A., Yu, L., Pham, Q., Yu, L., He, Q., Wang, T.T. 2019. Inhibition of tumor growth by indole-3-carbinol in a prostate cancer xenograft model may be associated with disrupted gut microbial interactions. Nutrients. 11(2). pii.E467. https://doi.org/10.3390/nu11020467.The caprine abomasal microbiome

- (Abstract Only)Transcriptome analysis unraveled potential mechanisms of resistance to Haemonchus contortus infection in Merino sheep populations bred for parasite resistance
                                                        

- (Peer Reviewed Journal)Zhang, R., Liu, F., Hunt, P., Li, C., Zhang, L., Ingham, A., Li, R.W. 2019. Transcriptome analysis unraveled potential mechanisms of resistance to Haemonchus contortus infection in Merino sheep populations bred for parasite resistance. Veterinary Research. 50:7. https://doi.org/10.1186/s13567-019-0622-6.Temporal dynamics in meta longitudinal RNA-Seq data
                                                        

- (Peer Reviewed Journal)Oh, S., Li, C., Baldwin, R.L., Song, S., Liu, F., Li, R.W. 2019. Temporal dynamics in meta longitudinal RNA-Seq data. Scientific Reports. 9(1):763. https://doi.org/10.1038/s41598-018-37397-7.The valproic acid rat model of autism present with gut bacterial dysbiosis similar to that in human autism
                                                        

- (Peer Reviewed Journal)Liu, F., Horton-Sparks, K., Hull, V., Li, R.W., Martinez-Cerdeno, V. 2018. The valproic acid rat model of autism present with gut bacterial dysbiosis similar to that in human autism. Molecular Autism. 9:61. https://doi.org/10.1186/s13229-018-0251-3.Ascaris suum infection was associated with a worm-independent reduction in microbial diversity and altered metabolic potential in the porcine gut microbiome
                                                        

- (Peer Reviewed Journal)Wang, Y., Liu, F., Urban Jr, J.F., Paerewijck, O., Geldhof, P., Li, R.W. 2019. Ascaris suum infection was associated with a worm-independent reduction in microbial diversity and altered metabolic potential in the porcine gut microbiome. International Journal for Parasitology. 49(3-4):247-256. https://doi.org/10.1016/j.ijpara.2018.10.007.Transcriptomic analysis reveals effects of fucoxanthin on intestinal glucose transport
                                                        

- (Peer Reviewed Journal)Cao, W., Li, J., Chin, Y., Xue, C., Li, R.W., Tang, Q. 2018. Transcriptomic analysis reveals effects of fucoxanthin on intestinal glucose transport. Journal of Functional Foods. 49:205-213. 10.1016/j.jff.2018.08.018.Transcriptomic impacts of rumen epithelium induced by butyrate infusion in dairy cattle in dry period

- (Abstract Only)Complete genome sequence of Escherichia coli Phage vB_EcoS Sa179lw isolated from surface water in a produce-growing area in northern california
                                                        

- (Peer Reviewed Journal)Liao, Y., Liu, F., Sun, X., Li, R.W., Wu, V.C. 2018. Complete genome sequence of Escherichia coli Phage vB_EcoS Sa179lw isolated from surface water in a produce-growing area in northern California. Genome Announcements. 6(27):e00337-18. https://doi.org/10.1128/genomeA.00337-18.Assembly and analysis of changes in transcriptomes of dairy cattle rumen epithelial during lactation and dry periods
                                                        

- (Peer Reviewed Journal)Baldwin, R.L., Li, C., Li, R.W. 2018. Assembly and analysis of changes in transcriptomes of dairy cattle rumen epithelial during lactation and dry periods. Agricultural Sciences. 9:619-638. https://doi.org/10.4236/as.2018.95043.Transcriptomic impacts of rumen epithelium induced by butyrate infusion in dairy cattle in dry period
                                                        

- (Peer Reviewed Journal)Baldwin, R.L., Li, R.W., Jia, Y., Li, C. 2018. Transcriptomic impacts of rumen epithelium induced by butyrate infusion in dairy cattle in dry period. Gene Regulation and Systems Biology. 12:1–11. https://doi.org/10.1177/1177625018774798.Transcriptome analysis revealed anti-obesity effects of the alginate polysaccharide in high-fat diet-induced obese mice

- (Peer Reviewed Journal)Wang, X., Liu, F., Yuan, G., Xue, C., Li, R.W., Tang, Q. 2018. Transcriptome analysis revealed anti-obesity effects of the alginate polysaccharide in high-fat diet-induced obese mice. International Journal of Biological Macromolecules. 115:861-870.Effects of Eimeria maxima and Clostridium perfringens infections on Cecal Microbiome in Broiler Chickens Analyzed by 16S rRNA Sequencing

- (Abstract Only)Interleukin-17 receptor A (IL-17RA) as a central regulator of the protective immune response against Giardia
                                                        

- (Peer Reviewed Journal)Paerewijck, O., Peelaers, I., Maertens, B., Dreesen, L., Van Meulder, F., De Bosscher, K., Li, R.W., Geldhof, P. 2017. Interleukin-17 receptor A (IL-17RA) as a central regulator of the protective immune response against Giardia. Scientific Reports. 7:8520. https://doi.org/10.1038/s41598-017-08590-x.Chondriotin sulfate disaccharides as a bioactive compound modified the murine gut microbiome under healthy and stressed conditions
                                                        

- (Peer Reviewed Journal)Liu, F., Zhang, N., Li, Z., Wang, X., Shi, H., Xue, C., Li, R.W., Tang, Q. 2017. Chondriotin sulfate disaccharides as a bioactive compound modified the murine gut microbiome under healthy and stressed conditions. Scientific Reports. 7:6783. https://doi.org/10.1038/s41598-017-05860-6.Aspergillus flavus aswA, a gene homolog of Aspergillus nidulans oefC, regulates sclerotial development and biosynthesis of sclerotium-associated secondary metabolites

- (Peer Reviewed Journal)Chang, P.-K., Scharfenstein, L.L., Li, R.W., Arroyo-Manzanares, N., De Saeger, S., Diana Di Mavungu, J. 2017. Aspergillus flavus aswA, a gene homolog of Aspergillus nidulans oefC, regulates sclerotial development and biosynthesis of sclerotium-associated secondary metabolites. Fungal Genetics and Biology. 104:29-37.Transcriptome of Aspergillus flavus aswA (AFLA_085170) deletion strain related to sclerotial development and production of secondary metabolites

- (Other)Chang, P.-K., Scharfenstein, L.L., Mack, B.M., Li, R.W. 2017. Transcriptome of Aspergillus flavus aswA (AFLA_085170) deletion strain related to sclerotial development and production of secondary metabolites. National Center for Biotechnology Information (NCBI). Accession: SRP082149.Selection of internal reference genes for normalization of reverse transcription quantitative polymerase chain reaction (RT-qPCR) analysis in the rumen epithelium

- (Peer Reviewed Journal)Die, J.V., Baldwin, R.L., Rowland, L.J., Li, R.W., Oh, S., Li, C., Connor, E.E., Ranilla, M. 2017. Selection of internal reference genes for normalization of reverse transcription quantitative polymerase chain reaction (RT-qPCR) analysis in the rumen epithelium. PLoS One. 12(2):e0172674.Neoagarotetraose protects mice against intense exercise induced stress by modulating gut microbial composition and function
                                                        

- (Peer Reviewed Journal)Zhang, N., Mao, X., Hou, E., Wang, Y., Xue, C., Li, R.W., Tang, Q. 2017. Neoagarotetraose protects mice against intense exercise induced stress by modulating gut microbial composition and function. Molecular Nutrition and Food Research. https://doi.org/10.1002/mnfr.201600585.Potential immunosuppressive effects of E. coli O157:H7 experimental infection on the bovine host
                                                        

- (Peer Reviewed Journal)Kieckens, E., Rybarczyk, Li, R.W., Vanrompay, D., Cox, E. 2016. Potential immunosuppressive effects of E. coli O157:H7 experimental infection on the bovine host. Biomed Central (BMC) Genomics. 17:1049. https://doi.org/10.1186/s12864-016-3374-y.Web-based bioinformatics workflows for end-to-end RNA-seq data computation and analysis in agricultural animal species

- (Peer Reviewed Journal)Li, W., Richter, A.R., Jung, Y., Li, R.W. 2016. Web-based bioinformatics workflows for end-to-end RNA-seq data computation and analysis in agricultural animal species. Biomed Central (BMC) Genomics. 17:761.Transcriptomic analysis of persistent infection with foot-and-mouth disease virus in cattle suggests impairment of cell-mediated immunity in the nasopharynx

- (Peer Reviewed Journal)Eschbaumer, M., Stenfeldt, C., Smoliga, G.R., Pacheco, J., Rodriguez, L.L., Li, R.W., Zhu, J.J., Arzt, J. 2016. Transcriptomic analysis of persistent infection with foot-and-mouth disease virus in cattle suggests impairment of cell-mediated immunity in the nasopharynx. PLoS One. 11:e0162750.Possible mechanisms of host resistance to Haemonchus contortus infection in sheep breeds native to the Canary Islands

- (Peer Reviewed Journal)Guo, Z., Gonzalez, J., Hernandez, J.N., Mcneilly, T.N., Morrison, T., Yu, P., Li, R.W. 2016. Possible mechanisms of host resistance to Haemonchus contortus infection in sheep breeds native to the Canary Islands. Scientific Reports. 6:26200. doi: 10.1038/srep26200.The effect of helminth infection on the microbial composition and structure of the caprine abomasal microbiome

- (Peer Reviewed Journal)Li, R.W., Li, W., Baldwin, R.L., Yu, P., Urban Jr, J.F. 2016. The effect of helminth infection on the microbial composition and structure of the caprine abomasal microbiome. Scientific Reports. 6:20606.Regulation of aflatoxin biosynthesis and branched-chain amino acids metabolism in Aspergillus flavus by 2-phenylethanol reveal biocontrol mechanism of Pichia anomala

- (Abstract Only)Hua, S.T., Chang, P., Beck, J.J., Li, R.W. 2016. Regulation of aflatoxin biosynthesis and branched-chain amino acids metabolism in Aspergillus flavus by 2-phenylethanol reveal biocontrol mechanism of Pichia anomala. Meeting Abstract. https://pag.confex.com/pag/xxiv/meetingapp.cgi/Paper/21990.Transcriptomic sequencing reveals a set of unique genes activated by butyrate-induced histone modification

- (Peer Reviewed Journal)Li, C., Li, R.W., Baldwin, R.L., Blomberg, L., Wu, S., Li, W. 2016. Transcriptomic sequencing reveals a set of unique genes activated by butyrate-induced histone modification. Scientific Reports. 10:1-8.Splice variants and regulatory networks associated with host resistance to the intestinal worm Cooperia oncophora in cattle

- (Peer Reviewed Journal)Li, R.W., Wu, S., Li, C., Li, W., Schroeder, S.G. 2015. Splice variants and regulatory networks associated with host resistance to the intestinal worm Cooperia oncophora in cattle. Veterinary Parasitology. DOI:10.1016/j.vetpar.2015.05.010.The caprine abomasal microbiome

- (Government Publication)Li, R.W. 2015. The caprine abomasal microbiome. Government Publication/Report. Accession Numbers# 4629311.3-4629350.3.Analysis of the protective immune response following intramuscular vaccination of calves against the intestinal parasite Cooperia oncophora

- (Peer Reviewed Journal)Van Meulder, F., Ratman, D., Van Coppernolle, S., Borloo, J., Li, R.W., Chiers, K., Van Den Broeck, W., Claerebout, E., Geldhof, P. 2015. Analysis of the protective immune response following intramuscular vaccination of calves against the intestinal parasite Cooperia oncophora. International Journal for Parasitology. pii:S0020-7519(15)00112-5. DOI: 10.1016/j.ijpara.2015.03.007.The microbial composition and metabolic potential of the ovine rumen

- (Government Publication)Li, R.W. 2015. The microbial composition and metabolic potential of the ovine rumen. Metagenomics Analysis Server, MG-RAST. Accession numbers 4552886.3-4552888.3, 4552952.3-4552965.3, 4552985.3-4552986.3, 4553942.3-4553951.3, 4554052.3-4554061.3.The effect of 2-phenylethanol treatment on Aspergillus flavus transcriptome

- (Other)Chang, P-K., Hua, S.T., Sarreal, S.L., Scharfenstein, L.L., Li, R.W. 2015. The effect of 2-phenylethanol treatment on Aspergillus flavus transcriptome. National Center for Biotechnology Information (NCBI). Accession: SRP056528.Escherichia coli O-antigen gene clusters of serogroups O62, O68, O131, O140, O142, and O163: DNA sequences and similarity between O62 and O68, and PCR-based serogrouping

- (Peer Reviewed Journal)Liu, Y., Fratamico, P.M., Debroy, C., Yan, X., Needleman, D.S., Li, R.W., Wang, W., Losada, L., Brinkac, L., Radune, D., Toro, M., Meng, J. 2015. Escherichia coli O-antigen gene clusters of serogroups O62, O68, O131, O140, O142, and O163: DNA sequences and similarity between O62 and O68, and PCR-based serogrouping. Biosensors. 5:51-68.A previously uncharacterized, nonphotosynthetic member of the chromatiaceae is the primary CO2-fixing constituent in a self-regenerating biocathode

- (Peer Reviewed Journal)Wang, Z., Leary, D.H., Malanoski, A., Li, R.W., Hervey, W.J., Eddie, B., Vora, G.J., Tender, L.M., Lin, B.C., Strycharz-Glaven, S.M. 2014. A previously uncharacterized, nonphotosynthetic member of the chromatiaceae is the primary CO2-fixing constituent in a self-regenerating biocathode. Applied and Environmental Microbiology. 81:699–712. DOI:10.1128/AEM.02947-14.Integrated metagenomic and metaproteomic analyses of marine biofilm communities

- (Peer Reviewed Journal)Leski, T.A., Li, R.W., Hervey, J.W., Lebedev, N., Hamdan, L.J., Wang, Z., Deschamps, J.R., Kusterbeck, A.W., Vora, G.J. 2014. Integrated metagenomic and metaproteomic analyses of marine biofilm communities. BIOFOULING. 30:10, 1211-1223. DOI:10.1080/08927014.2014.977267.Metagenomic insights into RDX-degrading potential of the ovine rumen microbiome

- (Peer Reviewed Journal)Li, R.W., Giarrizzo, G., Wu, S., Li, W., Duringer, J.M., Craig, M.A. 2014. Metagenomic insights into RDX-degrading potential of the ovine rumen microbiome. PLoS One. 9(11):e110505. DOI:10.1371/journal.pone.0110505.Biomolecular and metagenomic analyses of biofouling communities

- (Proceedings)Leavy, D.H., hervey, W.J., Hamdan, L.J., Lebedev, N., Wang, Z., Deschamps, J.R., 1 Kusterbeck, A., Li, R.W., Vora, G.J. 2014. Biomolecular and metagenomic analyses of skip hull biofouling communities. In: Annual Naval Research Laboratory Review 2014, pp. 130-133.Rumen Metagenomics

- (Book / Chapter)Li, R.W. 2015. Rumen Metagenomics. Book Chapter. New Delhi, India: Springer India. 379 p. doi: 10.1007/978-81-322-2401-3.Transcriptional regulators transforming growth factor-beta 1 and estrogen-related receptor-alpha identified as putative mediators of calf rumen epithelial tissue development and function during weaning
                                                        

- (Peer Reviewed Journal)Connor, E.E., Baldwin, R.L., Walker, M.P., Ellis, S., Li, C., Kahl, S., Chung, H., Li, R.W. 2014. Transcriptional regulators transforming growth factor-beta 1 and estrogen-related receptor-alpha identified as putative mediators of calf rumen epithelial tissue development and function during weaning. Journal of Dairy Science. 97:4193-4207.A high-resolution whole-genome map of the distinctive epigenomic landscape induced by butyrate in bovine cells

- (Peer Reviewed Journal)Shin, J., Xu, L., Li, R.W., Gao, Y., Bickhart, D.M., Liu, G., Baldwin, R.L., Li, C. 2014. A high-resolution whole-genome map of the distinctive epigenomic landscape induced by butyrate in bovine cells. Animal Genetics. 45:40–50. DOI:10.1111.age.12147.Butyrate: A dietary inhibitor of histone deacetylases and an epigenetic regulator

- (Book / Chapter)Li, C., Li, R.W., Baldwin, R.L., Elsasser, T.H. 2014. Butyrate: A dietary inhibitor of histone deacetylases and an epigenetic regulator. Butyrate: Food Sources, Functions and Health Benefits. New York, NY:Nova Science Publishers. p.233-258.DNA sequence and analysis of the O-antigen gene clusters of Escherichia coli serogroups O62, O68, O131, O140, O142, and O163 and serogroup-specific PCR assays

- (Abstract Only)Liu, Y., Fratamico, P.M., Debroy, C., Yan, X., Needleman, D.S., Li, R.W., Wang, W., Losada, L., Brinkac, L., Rodune, D., Toro, M., Meng, J. 2014. DNA sequence and analysis of the O-antigen gene clusters of Escherichia coli serogroups O62, O68, O131, O140, O142, and O163 and serogroup-specific PCR assays. Meeting Abstract. March 22-25, 2014.Bioinformatic dissecting of TP53 regulation pathway underlying butyrate-induced histone modification in epigenetic regulation

- (Peer Reviewed Journal)Li, C., Li, R.W. 2014. Bioinformatic dissecting of TP53 regulation pathway underlying butyrate-induced histone modification in epigenetic regulation. Genetics and Epigenetics. Doi: 10.4137/GEG.S14176.Collection, handling and analysis of specimens for studies of mucosal immunity in animals of veterinary importance - Appendix III

- (Book / Chapter)Urban Jr, J.F., Dawson, H.D., Solano Aguilar, G., Li, R.W., Shea-Donohue, T. 2015. Appendix III - Collection, handling and analysis of specimens for studies of mucosal immunity in animals of veterinary importance. In: Mucosal Immunity,4th edition. Mestecky, Strober, Russell, Cheroutre, Lambrecht, and Kelsall (eds). Elsevier. p. 2369–2391. DOI:10.1016/B978-0-12-415847-4.15003-7.Epigenomic landscape modified by histone modification correlated with activation of IGF2 gene

- (Abstract Only)Carter, O.L., Li, R.W., Li, C. 2013. Epigenomic landscape modified by histone modification correlated with activation of IGF2 gene. BARC Poster Day. 1:10.ChIp-seq of bovine cells (MDBK) to study butyrate-induced histone modification with 10 datasets

- (Other)Li, C., Li, R.W. 2014. ChIp-seq of bovine cells (MDBK) to study butyrate-induced histone modification with 10 datasets. NIH Gene Expression Omnibus Respository: (GEO Accession GSE38973).Molecular networks associated with host resistance to gastrointestional nematodes in cattle

- (Abstract Only)Lowbush wild blueberries have the potentail to modify gut microbiota and xenobiotic metabolism in the rat colon

- (Peer Reviewed Journal)Lacombe, A., Li, R.W., Klimia-Zacasa, D., Tadepallia, S., Kraussa, E., Young, R., Wu, V.C. 2013. Lowbush wild blueberries have the potentail to modify gut microbiota and xenobiotic metabolism in the rat colon. PLoS One. 10.1371.Identification of blaOXA-51, blaOXA-58, blaDIM-1 and blaVIM carbapenemase genes in hospital enterobacteriaceae isolates from Sierra Leone

- (Peer Reviewed Journal)Leski, T., Bangura, U., Jimmy, D.H., Ansumana, R., Lizewski, S.E., Li, R.W., Stenger, D.A., Taitt, C.R., Vora, G. 2013. Identification of blaOXA-51, blaOXA-58, blaDIM-1 and blaVIM carbapenemase genes in hospital enterobacteriaceae isolates from Sierra Leone. Journal of Clinical Microbiology. 51:2435-2438.Granule-exocytosis of granulysin and granzyme B as a potential key mechanism in vaccine-induced immunity in cattle against the nematode ostertagia ostertagi

- (Peer Reviewed Journal)Van, M., Van, C., Borloo, J., Rinaldi, M., Li, R.W., Chiers, K., Van Den Broeck, W., Vercruysse, J., Claerebout, E., Geldhof, P. 2013. Granule-exocytosis of granulysin and granzyme B as a potential key mechanism in vaccine-induced immunity in cattle against the nematode ostertagia ostertagi. Infection and Immunity. 81(15):1798-1809.Recent progresses in metagenomics

- (Abstract Only)Comparison of the transcriptpmes of long-tern label retaining-cells and C cells microdissected from mammary epithelium: an initial study to character potential stem/progenitor cells

- (Peer Reviewed Journal)Choudhary, R.K., Li, R.W., Clover, C.M., Capuco, A.V. 2013. Comparison of the transcriptpmes of long-tern label retaining-cells and C cells microdissected from mammary epithelium: an initial study to character potential stem/progenitor cells. Frontiers in Oncology. 3:21.Gene expression in bovine rumen epithelium during weaning indentifies molecular regulators of rumen development and growth

- (Peer Reviewed Journal)Connor, E.E., Baldwin, R.L. 6th , Li, C., Li, R.W., Chung, H. 2013. Gene expression in bovine rumen epithelium during weaning indentifies molecular regulators of rumen development and growth. Functional and Integrative Genomics. 13:133-142.In vitro and in vivo study of transcriptome alternation induced by butyrate in cattle using deep RNA-seq

- (Abstract Only)Li, C., Li, R.W. 2013. In vitro and in vivo study of transcriptome alternation induced by butyrate in cattle using deep RNA-seq. Meeting Abstract. PAG XX Meeting.Searching for Synbiotics to increase Colonic Butyrate Concentration

- (Proceedings)Li, R.W., Li, C. 2012. Searching for Synbiotics to increase Colonic Butyrate Concentrations. In: Functional Foods and chronicle Inflammation; Science and practicaal application, Vol II (ed. D.M. Mastirosyan). pp. 69-71.Metagenomic sequences of host associated gut microbiome in response to helminth infections.

- (Other)Li, R.W. 2012.  Metagenomic sequences of host associated gut microbiome in response to helminth infections.. Metagenomics Analysis Server, MG-RAST. 4474250.3.Assembled sequence contigs by SOAPdenova and Volvet algorithms from metagenomic short reads of a new bacterial isolate of gut origin

- (Other)Li, R.W. 2012. Assembled sequence contigs by SOAPdenova and Volvet algorithms from metagenomic short reads of a new bacterial isolate of gut origin. Metagenomics Analysis Server, MG-RAST. 4471171.3.Epigenetics and environmental impacts in cattle

- (Book / Chapter)Li, C., Li, R.W. 2013. Epigenetics and environmental impacts in cattle. Hauppauge, NY: Nova Science Publisher, Inc. 59-82 p.RNA sequences of the bovine epithelial transcriptome

- (Other)Li, R.W., Li, C. 2012. RNA sequences of the bovine epithelial transcriptome. National Center for Biotechnology Information (NCBI). SRX130570.Whole genome shotgun metagenomic sequences from the proximal colon microbiota in response to helminth parasites

- (Other)Li, R.W., Wu, S., Li, W., Hill, D.C., Urban Jr, J.F. 2012. Whole genome shotgun metagenomic sequences from the proximal colon microbiota in response to helminth parasites . National Center for Biotechnology Information (NCBI). SRX065855.Whole genome shotgun sequences for a novel Salmonella strain

- (Other)Li, R.W. 2012. Whole genome shotgun sequences for a novel Salmonella strain. Metagenomics Analysis Server, MG-RAST. 4469966.3.The transcriptomic profiles of Giardia duodenalis infected calves

- (Other)Li, R.W., Dreesen, L., Rinaldi, M., Claerbout, E., Geldhof, P. 2012. The transcriptomic profiles of Giardia duodenalis infected calves. NIH Gene Expression Omnibus (GEO) Database. GSE35920.Micro array analysis of the intestinal host response in Giardia duodenalis assemblage E infected cattle

- (Peer Reviewed Journal)Dreesen, L., Rinaldi, M., Chiers, K., Li, R.W., Geurden, T., Van Den Broeck, W., Goddeeris, B., Vercruysse, J., Claerebout, E., Geldhof, P. 2012. Micro array analysis of the intestinal host response in Giardia duodenalis assemblage E infected cattle. PLoS One. 7(7):e40985.Sequences from the hypervariable V3-V5 regions of the 16S rRNA gene amplified from the porcine proximal colon

- (Other)Li, R.W., Wu, S., Li, W., Hill, D.C., Urban Jr, J.F. 2012. Sequences from the hypervariable V3-V5 regions of the 16S rRNA gene amplified from the porcine proximal colon . National Center for Biotechnology Information (NCBI). SRX065852.Exploring the host transcriptome for mechanisms underlying protective immunity and resistance to helminth infection in ruminants

- (Review Article)Li, R.W., Choudhary, R.K., Capuco, A.V., Urban, Jr., J.F. 2012. Exploring the host transcriptome for mechanisms underlying protective immunity and resistance to helminth infection in ruminants. Veterinary Parasitology. 190(1-2):1-11.Lowbush blueberries, vaccinium angustifolium, modulate the functional potential of nutrient utilization and DNA maintenance mechanisms in the rat proximal colon microbiota

- (Peer Reviewed Journal)Lacombe, A., Li, R.W., Klimis-Zacasa, D., Kristoa, A.S., Tadepallia, S., Kraussa, E., Young, R., Wu, V.C. 2012. Lowbush blueberries, vaccinium angustifolium, modulate the functional potential of nutrient utilization and DNA maintenance mechanisms in the rat proximal colon microbiota. Functional Foods in Health and Disease. 2(6):228-241.Comparative analyses of transcriptomic profiles of the bovine small intestine in response to both a primary infection and a drug-attenuated reinfection

- (Other)Li, R.W., Li, C., Gasbarre, L.C. 2012. Comparative analyses of transcriptomic profiles of the bovine small intestine in response to both a primary infection and a drug-attenuated reinfection . NIH Gene Expression Omnibus (GEO) Database. GSE24402.Regulatory networks and pathways in the bovine small intestine during Cooperia oncophora infection

- (Other)Li, R.W., Gasbarre, L.C. 2012. Regulatory networks and pathways in the bovine small intestine during Cooperia oncophora infection. NIH Gene Expression Omnibus (GEO) Database. 39:813-824.Metagenomic sequences of the bovine abomasal microbiota of immune cattle in response to parasitic nematode Ostertagia ostertagi

- (Other)Li, R.W. 2012. Metagenomic sequences of the bovine abomasal microbiota of immune cattle in response to parasitic nematode Ostertagia ostertagi. National Center for Biotechnology Information (NCBI). 6(9):e24417. doi:10.1371/journal.pone.0024417.Complement activation in the development of protective immunity against Ostertagia ostertagi infections in cattle

- (Other)Li, R.W., Hou, Y.L., Li, C., Gasbarree, L.C. 2012. Complement activation in the development of protective immunity against Ostertagia ostertagi infections in cattle. NIH Gene Expression Omnibus (GEO) Database. 190:1-11.2012.Gene expression profiling of a temperature-sensitive strain of Neospora caninum

- (Other)Li, R.W. 2012. Gene expression profiling of a temperature-sensitive strain of Neospora caninum. National Center for Biotechnology Information (NCBI). 129:346-354.Alternate splicing regulated by butyrate in the bovine epithelial cell

- (Peer Reviewed Journal)Wu, S., Li, C., Huang, W., Li, W., Li, R.W. 2012. Alternate splicing regulated by butyrate in the bovine epithelial cell. PLoS One. 7(6):e39182.Worm burden-dependent disruption of the porcine colon microbiota by Trichuris suis infection

- (Peer Reviewed Journal)Wu, S., Li, R.W., Li, W., Beshah, E., Dawson, H., Uban, J.P. 2012. Worm burden-dependent disruption of the porcine colon microbiota by Trichuris suis infection. PLoS One. 10.1371/journal.pone.0035470.Quantification of transcriptome responses of the rumen epithelium to butyrate infusion

- (Peer Reviewed Journal)Baldwin, R.L., Wu, S., Li, W., Li, C., Bequette, B.J., Li, R.W. 2012. Quantification of transcriptome responses of the rumen epithelium to butyrate infusion. Gene Regulation and Systems Biology. 6:67–80.The bacterial community composition of the bovine rumen detected using pyrosequencing of 16S rRNA genes

- (Peer Reviewed Journal)Wu, S., Baldwin, R.L., Li, W., Li, C., Connor, E.E., Li, R.W. 2012. The bacterial community composition of the bovine rumen detected using pyrosequencing of 16S rRNA genes. Metagenomics. 1:11. DOI:10.4303/mg/235571.Butyrate induced IGF2 activation correlated with distinct chromatin landscapes due to histone modification

- (Peer Reviewed Journal)Shin, J., Li, R.W., Goa, Y., Bickhart, D.M., Liu, G., Li, W., Wu, S., Li, C. 2013. Butyrate induced IGF2 activation correlated with distinct chromatin landscapes due to histone modification. PLoS Genetics. DOI:10.4137/GRSB.S11243.Alterations in the Porcine Colon Microbiota Induced by the Gastrointestinal Nematode Trichuris suis

- (Peer Reviewed Journal)Li, R.W., Wu, S., Li, W., Hill, D.E., Urban, Jr., J.F., Navarro, K., Couch, R.D. 2012. Alterations in the Porcine Colon Microbiota Induced by the Gastrointestinal Nematode Trichuris suis. Infection and Immunity. 80(6):2150-2157.Transcriptome characterization by deep-RNA-sequencing underlies the mechanisms of butyrate-induced epigenomic regulation in bovine cells

- (Peer Reviewed Journal)Sitao, W., Li, R.W., Li, W., Li, C. 2012. Transcriptome characterization by deep-RNA-sequencing underlies the mechanisms of butyrate-induced epigenomic regulation in bovine cells. PLoS One. DOI:10.1371/journal.pone.0036940.Method Development for Metaproteomic Analyses of Marine Biofilms

- (Peer Reviewed Journal)Hajkova, D., Hervey, W., Li, R.W., Deschamps, J., Kusterbeck, A., Vora, G. 2012. Method Development for Metaproteomic Analyses of Marine Biofilms. Analytical Chemistry. 84(9):4006–4013.Method Development for Metaproteomic Analyses of Marine Biofilms

- (Peer Reviewed Journal)Hajkova, D., Hervey, W., Li, R.W., Deschamps, J., Kusterbeck, A., Vora, G. 2012. Method Development for Metaproteomic Analyses of Marine Biofilms. Analytical Chemistry. 84: 4006-4013. 2012.Characterization of the longissimus lumborum transcriptome response to adding propionate to the diet of growing Angus beef steers

- (Peer Reviewed Journal)Baldwin, R.L., Li, R.W., Li, C., Song, J., Bequette, B.J. 2012. Characterization of the longissimus lumborum transcriptome response to adding propionate to the diet of growing Angus beef steers. Physiological Genomics. 44:543-550. DOI:10.1152/physiolgenomics.The Microbiome (Chapter 378)

- (Book / Chapter)Li, R.W. 2014. The Microbiome (Chapter 378). In: Encyclopedia of Food Microbiology, Vol 2. Eds. C.A. Batt and M.L. Tortorello. Elsevier,  pp. 788-792.Worm burden-dependent disruption of the porcine colon microbiota by Trichuris suis infection

- (Peer Reviewed Journal)Wu, S., Li, R.W., Li, W., Urban Jr, J.F., Dawson, H.D., Beshah, E. 2012. Worm burden-dependent disruption of the porcine colon microbiota by Trichuris suis infection. PLoS One. 7(4):e35470.Analysis of copy number variations among cattle breeds

- (Abstract Only)Liu, G., Hou, Y., Zhu, B., Cardone, M.F., Jiang, L., Cellamare, A., Mitra, A., Alexander, L.J., Coutinho, L.L., Gasbarre, L.C., Li, R.W., Matukumalli, L.K., Nonneman, D.J., Regitano, L.C., Smith, T.P., Song, J., Sonstegard, T.S., Van Tassell, C.P., Ventura, M., Eichler, E.E., Mcdaneld, T.G., Keele, J.W. 2012. Analysis of copy number variations among cattle breeds. [abstract] CONFERENCE ON THE BIOLOGY OF GENOMES. P. 182.Chimeric classical swine fever (CSF)-Japanese encephalitis (JE) viral particles as a non-transmissible bivalent marker vaccine candidate against CSF and JE infections

- (Peer Reviewed Journal)Yang, Z., Wu, R., Li, L., Xiong, Z., Zhao, H., Li, R.W., Guo, D., Pan, Z. 2012. Chimeric classical swine fever (CSF)-Japanese encephalitis (JE) viral particles as a non-transmissible bivalent marker vaccine candidate against CSF and JE infections. Virus Research. 165(1):61-70.The IGF2 Locus

- (Peer Reviewed Journal)Li, R.W., Sperling, A.K. 2013. The IGF2 Locus. Journal of Clinical Microbiology. 51(7):2435-2438.Repetitive Sequences

- (Book / Chapter)Sperling, A.K., Li, R.W. 2013. Repetitive Sequences.In: Brenner's Encyclopedia of Genetics (Eds. S. Maloy and V. Houghes), Academic press, San Diego, pp.150-154.Transcriptomic alterations in human prostate cancer cell LNCaP tumor xenograft modulated by dietary phenethyl isothiocyanate

- (Peer Reviewed Journal)Li, R.W., Li, C., Wang, T.T. 2012. Transcriptomic alterations in human prostate cancer cell LNCaP tumor xenograft modulated by dietary phenethyl isothiocyanate. Molecular Carcinogenesis. DOI: 10.1002/mc.21873.Genome-wide ChIP-seq mapping and analysis of butyrate-induced H3K9 and H3K27 acetylation and epigenomic landscape alteration in bovine cells

- (Peer Reviewed Journal)Heon Shin, J., Li, R.W., Gao, Y., Baldwin, R.L., Li, C. 2012. Genome-wide ChIP-seq mapping and analysis of butyrate-induced H3K9 and H3K27 acetylation and epigenomic landscape alteration in bovine cells. Functional and Integrative Genomics. 12(1):119-130.Cytoskeleton remodling and alterations in smooth muscle contractility in the bovine jejunum during the early stage of Cooperia oncophora infection

- (Peer Reviewed Journal)Li, R.W., Schroeder, S.G. 2011. Cytoskeleton remodling and alterations in smooth muscle contractility in the bovine jejunum during the early stage of Cooperia oncophora infection. Functional and Integrative Genomics. 12(1):35-44.Characterization of the abomasal transcriptome for mechanisms of resistance to gastrointestinal nematodes in cattle

- (Peer Reviewed Journal)Li, R.W., Rinaldi, M., Capuco, A.V. 2011. Characterization of the abomasal transcriptome for mechanisms of resistance to gastrointestinal nematodes in cattle. Veterinary Research. 42(1):114.Perturbation dynamics of the rumen microbiota in response to exogenous butyrate

- (Peer Reviewed Journal)Li, R.W., Wu, S., Li, W., Baldwin, R.L., Li, C. 2012. Perturbation dynamics of the rumen microbiota in response to exogenous butyrate. Public Library of Science Biology. 7(1):e29392. DOI:10.1371/journal.pone.0029392.Genome-wide ChIP-seq mapping and analysis of butyrate-induced H3K9 and H3K27 acetylation and epigenomic landscapes alteration in bovine cells

- (Abstract Only)Li, C., Li, R.W., Gao, Y., Shin, J., Baldwin, R.L. 2012. Genome-wide ChIP-seq mapping and analysis of butyrate-induced H3K9 and H3K27 acetylation and epigenomic landscapes alteration in bovine cells [abstract]. Annual International Plant & Animal Genome Conference. W. 020.Drug Resistance

- (Book / Chapter)Li, R.W., Sperling, A.K. 2013. Drug Resistance. In: Brenner's Encyclopedia of Genetics. Ed. S. Maloy and K. Hughes. Academic press, San Diego, pp. 418-420.Alpha-Tocopherol alters transcription activities that modulate tumor necrosis factor alpha (TNF-¿)-induced inflammatory response in bovine cells

- (Peer Reviewed Journal)Li, C., Li, R.W., Elsasser, T.H., Kahl, S. 2011. Alpha-Tocopherol alters transcription activities that modulate tumor necrosis factor alpha (TNF-a)-induced inflammatory response in bovine cells. Gene Regulation and Systems Biology. 6:1-14.Galectin-11 induction in the gastrointestinal tract of cattle following nematode and protozoan infections

- (Peer Reviewed Journal)Hoorens, P., Rinaldi, M., Mihi, B., Dreseen, L., Grit, G., Meeusen, E., Li, R.W., Geldhof, P. 2011. Galectin-11 induction in the gastrointestinal tract of cattle following nematode and protozoan infections. Parasite Immunology. 33:669–678.Metagenome plasticity of the bovine abomasal microbiota in immune animals in response to Ostertagia ostertagi infection

- (Peer Reviewed Journal)Li, R.W., Huang, Y., Gasbarre, L. 2011. Metagenome plasticity of the bovine abomasal microbiota in immune animals in response to Ostertagia ostertagi infection. PLoS One. 6:e24417.Characterization of the rumen microbiota in pre-ruminant calves using metagenomic tools

- (Peer Reviewed Journal)Li, R.W., Connor, E.E., Li, C., Baldwin, R.L., Sparks, M. 2011. Characterization of the rumen microbiota in pre-ruminant calves using metagenomic tools. Environmental Microbiology. 14(1):129-139.Infection with the gastrointestinal nematode Ostertagia ostertagi affects mucus biosynthesis in the abomasum of cattle

- (Peer Reviewed Journal)Rinaldi, M., Dreesen, L., Hoorens, P., Li, R.W., Claerebout, E., Goddeeris, B., Vercruysse, J., Vandenbroeck, W., Geldhof, P. 2011. Infection with the gastrointestinal nematode Ostertagia ostertagi affects mucus biosynthesis in the abomasum of cattle. Veterinary Research. 42(1):61.The vitamin D receptor and inducible nitric oxide synthase associated pathways in the development of acquired resistance to Cooperia oncophora infection in cattle

- (Peer Reviewed Journal)Li, R.W., Li, C., Gasbarre, L.C. 2011. The vitamin D receptor and inducible nitric oxide synthase associated pathways in the development of acquired resistance to Cooperia oncophora infection in cattle. Veterinary Research. 42(1):48.Genome wide analysis of the bovine mucin genes and their gastrointestinal transcription profile

- (Peer Reviewed Journal)Hoorens, P.R., Rinaldi, M., Li, R.W., Goddeeris, B., Claerebout, E., Vercruysse, J., Geldhof, P. 2011. Genome wide analysis of the bovine mucin genes and their gastrointestinal transcription profile. Biomed Central (BMC) Genomics. 12:140.NUTRIENTS AND EPIGENETICS IN BOVINE CELLS

- (Book / Chapter)Li, C., Li, R.W., Elsasser, T.H. 2012. Nutrients and Epigenetics in Bovine Cells. In:  Hasan Khatib, Editors. Nutrients and Epigenetics in Bovine Cells. In:  Hasan Khatib, Editor. Livestock Epigenetics. New York, NY.  Nova Science Publishers. p. 161-177.MicroRNA (miRNA) expression is regulated by butyrate-induced epigenetic modulation of gene expression in bovine cells

- (Abstract Only)Li, C., Li, R.W., Elsasser, T.H. 2011. MicroRNA (miRNA) expression is regulated by butyrate-induced epigenetic modulation of gene expression in bovine cells. Plant and Animal Genome Conference Proceedings. W021.Bovine mammary stem cells: Cell biology meets production agriculture

- (Peer Reviewed Journal)Capuco, A.V., Choudhary, R.K., Daniels, K.M., Li, R.W., Clover, C.M. 2012. Bovine mammary stem cells: Cell biology meets production agriculture. Animal. 6:382-393.Alpha-Tocopherol modulates transcriptional activities that affect essential biological processes in Bovine Cells

- (Peer Reviewed Journal)Li, C., Li, R.W., Elsasser, T.H. 2010. Alpha-Tocopherol modulates transcriptional activities that affect essential biological processes in Bovine Cells. Gene Regulation and Systems Biology. 4:109-124.Localized complement activation in the development of protective immunity against Ostertagia ostertagi infections in cattle

- (Peer Reviewed Journal)Li, R.W., Hou, Y., Li, C., Gasbarre, L.C. 2010. Localized complement activation in the development of protective immunity against Ostertagia ostertagi infections in cattle. Veterinary Parasitology. 174(3-4):247-256.Mastitis associated transcriptomic disruptions in cattle

- (Review Article)Rinaldi, M., Li, R.W., Capuco, A.V. 2010. Mastitis associated transcriptomic disruptions in cattle. Veterinary Immunology and Immunopathology. 138(4):267-279.MicroRNA (miRNA) expression is regulated by butyrate induced epigenetic modulation of gene expression in bovine cells

- (Peer Reviewed Journal)Li, C., Li, R.W., Elsasser, T.H. 2010. MicroRNA (miRNA) expression is regulated by butyrate induced epigenetic modulation of gene expression in bovine cells. Genetics and Epigenetics. 3:23-32.Characteristics of peri-implantation porcine concepti population and maternal milieu influence the transcriptome profile

- (Peer Reviewed Journal)Blomberg, L., Schreier, L.L., Li, R.W. 2010. Characteristics of peri-implantation porcine concepti population and maternal milieu influence the transcriptome profile. Journal of Molecular Reproduction and Development. 77:978-989.Cytochrome P450 Induction and Gene Expression in Channel Catfish (Ictalurus punctatus) Following Wastewater Treatment Plant Effluent Exposure in Field and Laboratory Settings

- (Peer Reviewed Journal)Whatley, A., Cho, I.K., Magrath, C., Stewart, P.M., Li, R.W. 2010. Cytochrome P450 Induction and Gene Expression in Channel Catfish (Ictalurus punctatus) Following Wastewater Treatment Plant Effluent Exposure in Field and Laboratory Settings. Journal of Environmental Protection. 1:362-373.Bovine mammary stem cells: Transcriptome profiling and the stem cell niche

- (Abstract Only)Choudhary, R.K., Li, R.W., Clover, C.M., Capuco, A.V. 2010. Bovine mammary stem cells: Transcriptome profiling and the stem cell niche [abstract]. Journal of Dairy Science. 93 (E-Suppl. 1):ii-iii.Hepatic transcriptome of beef steers is differentially modulated by composition of energy-substrate supply in growing beef

- (Proceedings)Baldwin, R.L., Sumner-Thomson, J., Connor, E.E., Li, R.W., Mcleod, K.R., Bequette, B.J. 2010. Hepatic transcriptome of beef steers is differentially modulated by composition of energy-substrate supply in growing beef. In: G.M. Crovetto (Ed.), Energy and Protein Metabolism and Nutrition; Parma, Italy. pp. 313-314. Wageningen Academic Publishers, The Netherlands.Metagenomics detects functional shifts in the bovine rumen microbiota in response to propionate intake

- (Book / Chapter)Sparks, M., Huang, Y., Baldwin, R.L., Connor, E.E., Li, C., Sonstegard, T.S., Schroeder, S.G., Li, R.W. 2011. Metagenomics detects functional shifts in the bovine rumen microbiota in response to propionate intake. In: Li, R.W. editor. Metagenomics and its Applications in Agriculture. New York, NY: Nova Science Publishers. p. 165-183.Dynamics of the rumen microbiota

- (Book / Chapter)Li, R.W., Sparks, M., Connor, E.E. 2011. Dynamics of the rumen microbiota. In: Li, R.W., editor. Metagenomics and its Applications in Agriculture. New York, NY: Nova Science Publishers. p. 135-164.Towards a more complete metagenomics toolkit

- (Book / Chapter)Sparks, M., Li, R.W. 2011. Towards a more complete metagenomics toolkit. In: Li, R.W. editor. Metagenomics and its Applications in Agriculture. New York, NY: Nova Science Publishers. p. 33-45.Comparison of de novo short read assemblers on metagenomic data

- (Book / Chapter)Huang, Y., Li, W., Perkins, D., Li, R.W. 2011. Comparison of de novo short read assemblers on metagenomic data. In: Li, R.W. editor. Metagenomics and its Applications in Agriculture. New York, NY: Nova Science Publishers. p. 107-120.Analysis of copy number variations reveals differences among cattle breeds

- (Peer Reviewed Journal)Liu, G., Hou, Y., Zhu, B., Cardone, M.F., Jiang, L., Cellamare, A., Mitra, A., Alexander, L.J., Coutinho, L.L., Gasbarre, L.C., Heaton, M.P., Li, R.W., Matukumalli, L.K., Nonneman, D.J., De A Regitano, L.C., Smith, T.P., Song, J., Sonstegard, T.S., Van Tassell, C.P., Eichler, E.E., Mcdaneld, T.G., Keele, J.W. 2010. Analysis of copy number variations among cattle breeds. Genome Research. 20:693-703.Nutrient-induced modulation of gene expression and cellular functions: modeling epigenetic regulation in bovine cells

- (Abstract Only)Comparative gene expression profiling of Neospora caninum strains

- (Peer Reviewed Journal)Li, R.W., Tuo, W. 2010. Comparative gene expression profiling of Neospora caninum strains. Experimental Parasitology. 129:346-354.Epigenetic regulation of gene expression and cellular functions induced by butyrate, an example of interactions between gene and nutrients

- (Abstract Only)Li, C., Li, R.W., Elsasser, T.H., Connor, E.E. 2009. Epigenetic regulation of gene expression and cellular functions induced by butyrate, an example of interactions between gene and nutrients. American Dairy Science Association Discover Conference.Global Genetic Profiles of Gene Network Disruption in Bovine Peripheral Blood Mononuclear Cells Induced Bovine Leukemia Virus (BLV) Infection

- (Peer Reviewed Journal)Li, C., Li, R.W., Elsasser, T.H., Kahl, S. 2009. Global genetic profiles of gene network disruption in bovine peripheral blood mononuclear cells induced bovine leukemia virus (BLV) infection. Genetics and Epigenetics.2:17-27.Gene expression profiling in bovine rumen during development and weaning

- (Other)Connor, E.E., Baldwin, R.L., Li, R.W. 2009. Gene expression profiling in bovine rumen during development and weaning. Accession Number GSE18382.Gene expression in the digestive tissues of ruminants and their relationships with feeding and digestive processes

- (Review Article)Connor, E.E., Li, R.W., Baldwin, R.L., Li, C. 2009. Gene expression in the digestive tissues of ruminants and their relationships with feeding and digestive processes. Animal. 4(7):993-1007.Transcriptome profiling and network analysis of tissues from regions of the bovine teat and mammary gland during E. coli mastitis.

- (Abstract Only)Enhanced mitochondrial complex gene function and reduced liver size may mediate improved feed efficiency of beef cattle during compensatory growth

- (Peer Reviewed Journal)Connor, E.E., Kahl, S., Elsasser, T.H., Parker, J., Li, R.W., Van Tassell, C.P., Baldwin, R.L., Barao, S.M. 2009. Enhanced mitochondrial complex gene function and reduced liver size may mediate improved feed efficiency of beef cattle during compensatory growth. Functional and Integrative Genomics. 10(1):39-51.Transcriptome Profiling of Tissues from the Teat and Other Regions of the Bovine Mammary Gland during E. coli Mastitis.

- (Peer Reviewed Journal)Rinaldi, M., Li, R.W., Bannerman, D.D., Daniels, K.M., Clover, C.M., Silva, M.V., Paape, M.J., Van Ryssen, B., Burvenich, C., Capuco, A.V. 2010. A sentinel function for teat tissues in dairy cows: Dominant innate immune response elements define early response to E. coli mastitis. Functional and Integrative Genomics. 10(1):21-38.Epigenetic mechanisms of  nutrient-induced modulation of gene expression and cellular functions

- (Abstract Only)Li, C., Li, R.W., Elsasser, T.H. 2009. Epigenetic mechanisms of  nutrient-induced modulation of gene expression and cellular functions. Gordon Research Conference Proceedings. Epigenetics. August 9-14, Holderness, NH.Mucin biosynthesis in the bovine goblet cell induced by Cooperia oncophora infection

- (Peer Reviewed Journal)Li, R.W., Li, C., Elsasser, T.H., Liu, G., Garrett, W.M., Gasbarre, L.C. 2009. Mucin biosynthesis in the bovine goblet cell induced by Cooperia oncophora infection. Veterinary Parasitology. PMID 19647371.Gene expression in the digestive tissues of ruminants and their relationships with feeding and digestive processes

- (Abstract Only)Connor, E.E., Li, R.W., Baldwin, R.L., Li, C. 2009. Gene expression in the digestive tissues of ruminants and their relationships with feeding and digestive processes.ISRP XIth International Symposium on Ruminant Physiology, Clermont-Ferrand, France, September 6-9.Characteristics of Peri-Implantation Porcine Concepti Population Influence Transcriptome Profile.

- (Abstract Only)Blomberg, L., Schreier, L.L., Li, R. 2009. Characteristics of Peri-Implantation Porcine Concepti Population Influence Transcriptome Profile. Biological Reproduction 81 (Suppl 1) p. 57, #41.EPIGENETIC REGULATION IN BOVINE CELLS: NUTRIENT-INDUCED MODULATION OF GENE EXPRESSION AND CELLULAR FUNCTIONS

- (Book / Chapter)Li, C., Elsasser, T.H., Li, R.W. 2009. Epigenetic regulation in bovine cells: Nutrient-induced modulation of gene expression and cellular functions. In: Rech, Leopold J., editor. Animal Genetics. Nova Science Pubilshers, Inc. (ISBN:978-60741-844-3).Lipopolysaccharide-induced early response genes in bovine peripheral blood mononuclear cells implicate GLG1/E-selectin as a key ligand–receptor interaction

- (Peer Reviewed Journal)Li, C., Li, R.W., Elsasser, T.H., Kahl, S. 2009. Lipopolysaccharide-induced early response genes in bovine peripheral blood mononuclear cells implicate GLG1/E-selectin as a key ligand–receptor interaction. Functional and Integrative Genomics. 9(3):335-349.Comparative Proteomic and Regulatory Network Analyses of the Elongating Pig Conceptus

- (Peer Reviewed Journal)Degrelle, S.A., Blomberg, L., Garrett, W.M., Li, R.W., Talbot, N.C. 2009. Comparative Proteomic and Regulatory Network Analyses of the Elongating Pig Conceptus. Proteomics. 9(10):2678-94.Canonical Pathways and Networks Regulated by Estrogen in the Bovine Mammary Glands

- (Peer Reviewed Journal)Li, R.W., Capuco, A.V. 2008. Canonical Pathways and Networks Regulated by Estrogen in the Bovine Mammary Glands. Biomed Central (BMC) Genomics. 8:55-68.A temporal shift in regulatory networks and pathways in the bovine small intestine during Cooperia oncophora infection

- (Peer Reviewed Journal)Li, R.W., Gasbarre, L.C. 2009. A temporal shift in regulatory networks and pathways in the bovine small intestine during Cooperia oncophora infection. International Journal for Parasitology. 39:813-824.Epigenetic regulation in bovine cells: nutrient-induced modulation of gene expression and cellular functions

- (Abstract Only)Li, C., Li, R.W., Elsasser, T.H. 2008. Epigenetic regulation in bovine cells: nutrient-induced modulation of gene expression and cellular functions. International Plant and Animal Genome IX Conference.Serial hepatic gene expression profiling in Angus steers during feed restriction and realimentation

- (Other)Connor, E.E., Kahl, S., Elsasser, T.H., Li, R.W., Barao, S.M. 2008. Serial hepatic gene expression profiling in Angus steers during feed restriction and realimentation. NIH Gene Expression Omnibus (GEO) Database. GSE12853.Transcriptome Characterization of Bovine Peripheral Blood Mononuclear Cells Stimulated by LPS

- (Abstract Only)Li, C., Li, R.W. 2008. Transcriptome Characterization of Bovine Peripheral Blood Mononuclear Cells Stimulated by LPS. [abstract].  . NIH Gene Expression Omnibus (GEO) Database.Characterization of a novel microdeletion polymorphism on BTA5 in cattle

- (Peer Reviewed Journal)Liu, G., Li, R.W., Sonstegard, T.S., Matukumalli, L.K., Silva, M.V., Van Tassell, C.P. 2008. Characterization of a novel microdeletion polymorphism on BTA5 in cattle. Animal Genetics. 39(6):655-658.ANALYSIS OF CATTLE COPY NUMBER VARIATION REVEALS INSIGHTS INTO THE EVOLUTION OF RUMINANTS

- (Abstract Only)Liu, G., Keele, J.W., Van Tassell, C.P., Sonstegard, T.S., Li, R.W., Alexander, L.J., Matukumalli, L.K., Smith, T.P., Gasbarre, L.C. 2008.  Analysis of cattle copy number variation reveals insights into the evolution of ruminants. [abstract]. 2008 meeting on the Biology of Genomes, May 6-10, 2007, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY. p197.Butyrate Induced Cell Cycle Arrest in Bovine Cells through Targeting Gene Expression relevance to DNA Replication Apparatus

- (Peer Reviewed Journal)Li, C., Li, R.W. 2008. Butyrate Induced Cell Cycle Arrest in Bovine Cells through Targeting Gene Expression relevance to DNA Replication Apparatus.  Gene Regulation and Systems Biology. 2:113-123.Effects of butyrate on the expression of insulin-like growth factor binding proteins in bovine kidney epithelial cells

- (Peer Reviewed Journal)Li, R.W., Li, C. 2008. Effects of butyrate on the expression of insulin-like growth factor binding proteins in bovine kidney epithelial cells. The Open Veterinary Science Journal. 2:1-6.EPIGENETIC REGULATION OF GENOMES: NUTRIENT-SPECIFIC MODULATION OF GENETIC NETWORKS IN BOVINE CELLS

- (Proceedings)Li, C., Elsasser, T.H., Li, R.W. 2008. Epigenetic regulation of genomes: nutrient-specific modulation of genetic networks in bovine cells. Animal Genetics International Conference Proceedings. 132:391-398.Analysis of copy number variation in the bovine genome

- (Abstract Only)Liu, G., Van Tassell, C.P., Sonstegard, T.S., Li, R.W., Alexander, L.J., Keele, J.W., Matukumalli, L.K., Brown, T., Smith, T.P., Gasbarre, L.C. 2008. Analysis of copy number variation in the bovine genome. Plant and Animal Genome (PAG) XVI Conference. San Diego, CA. p517.A high-resolution map of copy number variation in the cattle genome

- (Abstract Only)Liu, G., Keele, J.W., Van Tassell, C.P., Sonstegard, T.S., Alexander, L.J., Li, R.W., Matukumalli, L.K., Smith, T.P., Gasbarre, L.C. 2008. A high-resolution map of copy number variation in the cattle genome. Plant and Animal Genome VX Conference Abstracts. The NRI Animal Genome PD Meeting, San Diego, CA. p84.Detection of germline and somatic copy number variations in cattle

- (Proceedings)Liu, G., Van Tassell, C.P., Sonstegard, T.S., Li, R.W., Alexander, L.J., Keele, J.W., Matukumalli, L.K., Smith, T.P., Gasbarre, L.C. 2008. Detection of germline and somatic copy number variations in cattle. Developments in Biologicals. 132:231-237.Utilization of microarray technology for functional genomics in ictalurid catfish

- (Peer Reviewed Journal)Liu, Z., Li, R.W., Waldbieser, G.C. 2008. Utilization of microarray technology for functional genomics in ictalurid catfish. Journal of Fish Biology. 72:2377-2390.Initial analysis of copy number variation in the cow genome

- (Abstract Only)Liu, G., Van Tassell, C.P., Sonstegard, T.S., Li, R.W., Alexander, L.J., Keele, J.W., Matukumalli, L.K., Smith, T.P., Gasbarre, L.C. 2007. Initial analysis of copy number variation in the cow genome. [abstract}. Gordon Research Conference Proceedings.Identification of conserved regulatory elements in upstream promoter regions of mammals at relaxed thresholds by comparative genomics - a case study using PEPCK

- (Peer Reviewed Journal)Liu, G., Weirauch, M., Van Tassell, C.P., Li, R.W., Sonstegard, T.S., Matukumalli, L.K., Connor, E.E., Hanson, R.W., Yang, J. 2008. Identification of conserved regulatory elements in mammalian promoter regions: a case study using the PCK1 promoter. Genomics, Proteomics and Bioinformatics. 6(3-4):129-143.Epigenetic regulation of genomes: Nutrient-specific modulation of genetic networks in bovine cells

- (Abstract Only)Li, C.-L, Elsasser, T.H., Li, R.W. 2008. Epigenetic regulation of genomes: nutrient-specific modulation of genetic networks in bovine cells [abstract]. International Symposium on Anima Genomics for Animal Health, Paris, France, October 23-25, 2007. Developments in Biologicals. 132:391-398.Epigenetic mechanisms at work: Exploiting nutrient-specific modulation of genetic networks

- (Abstract Only)Li, C.-J, Elsasser, T.H., Li, R.W. 2007. Epigenetic mechanisms at work: Exploiting nutrient-specific modulation of genetic networks [abstract]. 29th General Assembly of the International Union of Biological Sciences and Scientific Symposium. Proceedings p7, Washington, DC.Identification of Weakly Conserved Regulatory Elements in Upstream Promoter Regions of Mammals

- (Book / Chapter)Liu, G., Weirauch, M., Van Tassell, C.P., Li, R.W., Sonstegard, T.S., Matukumalli, L.K., Connor, E.E., Hanson, R.W., Yang, J. 2007. Identification of Weakly Conserved Regulatory Elements in Upstream Promoter Regions of Mammals. Conference on the Biology og Genomes, pp. 218.POLY I:C INHIBITS THE EXPRESSION OF CHANNEL CATFISH VIRUS IMMEDIATE-EARLY GENE ORF 1 AT EARLY TIMES AFTER INFECTION

- (Peer Reviewed Journal)Silverstein, P.S., Li, R.W., Murdock, C.A., Waldbieser, G.C. 2007. Poly i:c inhibits the expression of channel catfish virus immediate-early gene orf 1 at early times after infection. Fish and Shellfish Immunology 23:479-484.Local Inflammation as a Possible Mechanism of Resistance to Gastrointestinal Nematodes in Angus Heifers

- (Peer Reviewed Journal)Li, R.W., Sonstegard, T.S., Van Tassell, C.P., Gasbarre, L.C. 2007. Local Inflammation as a Possible Mechanism of Resistance to Gastrointestinal Nematodes in Angus Heifers. Veterinary Parasitology. 145:100-107.Pathways analysis identifies perturbation of genetic networks induced by butyrate in a bovine kidney epithelial cell line

- (Peer Reviewed Journal)Li, C.J., Li, R.W., Wang, Y.H. Elsasser, T.H. 2007. Pathway analysis identifies perturbation of genetic networks induced by butyrate in a bovine kidney epithelial cell line. Functional and Integrative Genomics. 7:193-205.REGULATION OF GENE EXPRESSION IN THE BOVINE MAMMARY GLAND BY OVARIAN STEROIDS

- (Peer Reviewed Journal)Connor, E.E., Meyer, M.J., Li, R.W., Van Amburgh, M.E., Boisclair, Y.R., Capuco, A.V. 2007. Regulation of gene expression in the bovine mammary gland by ovarian steroids. Journal of Dairy Science. 90 (E. Suppl):E55-E65.IDENTIFICATION OF ESTROGEN-RESPONSIVE GENES IN THE PARENCHYMA AND FAT PAD OF THE BOVINE MAMMARY GLAND BY MICROARRAY ANALYSIS

- (Peer Reviewed Journal)Li, R.W., Meyer, M.J., Van Tassell, C.P., Sonstegard, T.S., Connor, E.E., Van Amburgh, M.E., Boisclair, Y.R., Capuco, A.V. 2006. Identification of estrogen responsive genes in the parenchyma and fat pad of the bovine mammary gland by microarray analysis. Physiological Genomics 27(1):42-53.Production and Utilization of a High-Density Oligonucleotide Microarray in Channel Catfish, Ictalurus punctatus

- (Peer Reviewed Journal)Li, R.W., Waldbieser, G.C. 2006. Production and Utilization of a High-Density Oligonucleotide Microarray in Channel Catfish, Ictalurus punctatus. Biomed Central (BMC) Genomics 2006, vol. 7:134.Resistance to Gastrointestinal nematodse of cattle: Identification of genomic regions affecting resistance and potential mechanisms

- (Abstract Only)Gasbarre, L.C., Sonstegard, T.S., Li, R.W., Araujo, R., Van Tassell, C.P. 2006. Resistance to Gastrointestinal nematodse of cattle: Identification of genomic regions affecting resistance and potential mechanisms [abstract]. American Association of Veterinary Parasitologists Proceedings.A MAMMARY GLAND BIOLOGIST'S PERSEPECTIVE ON FUNCTIONAL GENOMICS

- (Proceedings)Capuco, A.V., Meyer, M.J., Li, R.W., Connor, E.E., Van Tassell, C.P., Boisclair, Y.R., Van Amburgh, M.E., Sonstegard, T.S., Urban Jr, J.F. 2006. A mammary gland biologist's persepective on functional genomics. World Congress on Genetics Applied to Livestock Production. Belo Horizonte, Brazil, August 13-18, pp 01-6.BOS TAURUS 60MER OLIGONUCLEOTIDE MICROARRAY

- (Other)Li, R.W., Capuco, A.V., Van Tassell, C.P., Sonstegard, T.S., Connor, E.E., Gasbarre, L.C. 2006. Bos taurus 60mer oligonucleotide microarray. NIH Gene Expression Omnibus (GEO) Database.ADVANCEMENTS AND FUTURE CHALLENGES IN UNDERSTANDING MAMMARY GLAND FUNCTION

- (Abstract Only)Capuco, A.V., Connor, E.E., Meyer, M.J., Li, R.W., Van Tassell, C.P., Sonstegard, T.S., Van Amburgh, M.E., Boisclair, Y.R. 2006. Advancements and future challenges in understanding mammary gland function [abstract]. J. Dairy Sci. 89(Suppl. 1):409.REGULATION OF GENE EXPRESSION IN THE BOVINE MAMMARY GLAND BY OVARIAN STEROIDS

- (Abstract Only)Connor, E.E., Meyer, M.J., Li, R.W., Van Amburgh, M.E., Boisclair, Y.R., Capuco, A.V. 2006. Regulation of gene expression in the bovine mammary gland by ovarian steroids [abstract]. J. Dairy Sci. 89(Suppl. 1):426.SODIUM BUTYRATE INDUCED GENE EXPRESSION CHANGES IN THE MADIN-DARBY BOVINE KIDNEY EPITHELIAL CELLS

- (Other)Li, R.W., Li, C. 2006. Sodium butyrate induced gene expression changes in the madin-darby bovine kidney epithelial cells [abstract]. Gene expression Omnibus. GSE 3970.GENOMIC CHARACTERIZATION AND EXPRESSION ANALYSIS OF THE BACULOVIRAL IAP REPEAT CONTAINING 2 (BIRC2) GENE IN CHANNEL CATFISH, ICTALURUS PUNCTATUS

- (Peer Reviewed Journal)Li, R.W., Silverstein, P.S., Waldbieser, G.C. 2005. Genomic characterization and expression analysis of the baculoviral iap repeat containing 2 (birc2) gene in channel catfish, ictalurus punctatus. Animal Genetics 36:537-539.DEVELOPING HIGH-DENSITY BOVINE OLIGO MICROARRAYS TO INVESTIGATE GENES INVOLVED IN MAMMARY GLAND DEVELOPMENT

- (Abstract Only)Li, R.W., Capuco, A.V., Meyer, M., Boisclair, Y., Van Amburgh, M. 2005. Developing high-density bovine oligo microarrays to investigate genes involved in mammary gland development [abstract]. BARC Poster Day. Paper No. 40.CHARACTERIZATION OF FEZL EFFECTS ON SCS IN A SAMPLE OF NORTH AMERICAN HOLSTEINS

- (Abstract Only)Sonstegard, T.S., Van Tassell, C.P. 2005. Characterization of fezl effects on scs in a sample of north american Holsteins [abstract]. ADSA/ASAS Joint Meeting. p. 248.GENOMIC ORGANIZATION AND EXPRESSION OF THE NATURAL KILLER CELL ENHANCING FACTOR (NKEF) GENE IN CHANNEL CATFISH, ICTALURUS PUNCTATUS (RAFINESQUE)

- (Peer Reviewed Journal)Li, R.W., Waldbieser, G.C. 2006. Genomic organization and expression of the natural killer cell enhancing factor (nkef) gene in channel catfish, ictalurus punctatus (rafinesque). Fish and Shellfish Immunology 20:72-82.


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