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United States Department of Agriculture

Agricultural Research Service

Robert Li
Bovine Functional Genomics
Research Molecular Biologist

Phone: (301) 504-5185
Fax: (301) 504-8414
Room 110
10300 BALTIMORE AVENUE
BLDG 306 BARC-EAST
BOVINE FUNCTIONAL GENOMICS LAB
BELTSVILLE, MD, 20705-2350

Projects
DEVELOPMENT OF GENOMIC TOOLS TO STUDY RUMINANT RESISTANCE TO GASTROINTESTINAL NEMATODES
Appropriated (D)
  Accession Number: 422162
UNDERSTANDING GENETIC AND PHYSIOLOGICAL FACTORS AFFECTING NUTRIENT USE EFFICIENCY OF DAIRY CATTLE
Appropriated (D)
  Accession Number: 423564

Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)
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.
Gastrointestinal Metagenomics - (Book / Chapter) - (25-Jan-13)
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 Reprint Icon - (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 Reprint Icon - (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 Synbiotics to increase Colonic Butyrate Concentration. Meeting Proceedings. 2:69-71.
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.
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.
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.
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.
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.
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 Reprint Icon - (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: 4006-4013. 2012.
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. 2012, 84 (9), pp 4006–4013.
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) - (17-Mar-12)
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) - (07-Jan-12)
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) - (27-Oct-11)
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 Reprint Icon - (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.
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.
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.
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.
Analysis of copy number variations reveals differences among cattle breeds Reprint Icon - (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) - (30-Oct-09)
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 Reprint Icon - (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) - (30-Aug-09)
Enhanced mitochondrial complex gene function and reduced liver size may mediate improved feed efficiency of beef cattle during compensatory growth Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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.
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.
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.
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 Reprint Icon - (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.
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.
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.
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.
Last Modified: 4/20/2014
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