Wenli Li
Research Geneticist

608-890-0056

1925 Linden Dr. W
Madison, WI 53706

Dr. Li joined the Cell Wall Biology and Utilization Research : USDA ARS unit in August of 2016. Dr. Li's research specializes in cattle and cattle microbiome genetics, particularly transcriptomics.

• Publications

  • (Clicking on the reprint icon will take you to the publication reprint.)
  • Effects of early lactation milking frequency in an automated milking system on cow performance -(Peer Reviewed Journal)
    Kammann, E.M., French, E.A., Jozik, N.S., Li, W., Pralle, R.S. 2024. Effects of early lactation milking frequency in an automated milking system on cow performance. Animals. 14(16). Article 2293. https://doi.org/10.3390/ani14162293.
    
  • Microbial inoculum effects on the rumen epithelial transcriptome and rumen epimural metatranscriptome in calves-(Peer Reviewed Journal)
    
    
  • Effects of microbial inoculum on the transcriptome and meta-transcriptome of rumen, reticulum, omasum, and abomasum epithelium in calves-(Abstract Only)
    Fregulia, P., Zanton, G.I., Li, W. 2024. Effects of microbial inoculum on the transcriptome and meta-transcriptome of rumen, reticulum, omasum, and abomasum epithelium in calves. American Dairy Science Association Abstracts. 107 (Supplement 1):28.
    
  • Meta-transcriptome analysis reveals temporal dynamics on the active rumen microbiome in transition Holstein cows-(Abstract Only)
    Fregulia, P., Zanton, G., Li, W. 2024. Meta-transcriptome analysis reveals temporal dynamics on the active rumen microbiome in transition Holstein cows [abstract]. Journal of Dairy Science. 107 (Supplement 1):28.
    
  • Metabolic and transcriptomic responses to dietary-induced milk fat depression and balanced amino acid supplementation in lactating dairy cows-(Abstract Only)
    Ruh, K.E., Millerby, M., de Souza, G.M., Benn, A.D., Cohan, E.M., Krueger, A., Coelho Ribeiro, L.A., Larsen, A.M., Hoppmann, A. Sherlock, D.N., Li, W., Arriola Apelo, S.I. 2024. Metabolic and transcriptomic responses to dietaryinduced milk fat depression and balanced amino acid supplementation [abstract]. Journal of Dairy Science. 107 (Supplement 1):115.
    
  • Blood transcriptome and its microbial community in young claves with prolonged ruminal acidosis-(Abstract Only)
    Larsen, A., Li, W. 2024. Blood transcriptome and its microbial changes in young calves with feed-induced ruminal acidosis [abstract]. International Symposium on Ruminant Physiology. Paper No. 74.
    
  • Whole blood transcriptome and meta-transcriptome changes in transition cows-(Abstract Only)
    Fregulia, P., Zanton G., Li, W. 2024. Whole blood transcriptome and microbial abundance changes in transition cows [abstract]. International Symposium on Ruminant Physiology. Paper No. 26.
    
  • Rumen microbial inoculation effects on the liver transcriptome and meta-transcriptome in weaned calves-(Abstract Only)
    Fregulia, P., Zanton, G., Li, W. 2024. Rumen microbial inoculation effects on the liver transcriptome and meta-transcriptome in weaned calves [abstract]. International Symposium on Ruminant Physiology. Paper No. 27.
    
  • Metabolic responses to AA infused along different energy sources-(Abstract Only)
    Killerby, M., de Souza, G.M., Ruh, K., Larsen, A., Cohan, E., Hoppmann, A., Danes, M., Li, W., Ariolla Apelo, S.I. 2024. Metabolic responses to amino acids infused with different energy sources [abstract]. International Symposium on Ruminant Physiology. Paper No. 36.
    
  • Caecum transcriptome changes upon artificial dosing of rumen content obtained from an adult cow-(Peer Reviewed Journal)
    
    
  • The liver microbiome in calves with feed induced acidosis-(Abstract Only)
    
    
  • Liver microbial community and associated host transcriptome in calves with feed induced acidosis-(Peer Reviewed Journal)
    
    
  • Investigating the impact of feed-induced acidosis on the rumen transcriptome and metatranscriptome in young calves at 8- and 17-weeks of age-(Peer Reviewed Journal)
    
    
  • Genome-wide copy number variation and structural variation: A novel tool for improved livestock genomic selection-(Book / Chapter)
    
    
  • Liver and muscle transcriptomes differ in mid-lactation cows divergent in feed efficiency in the presence or absence of supplemental rumen-protected choline -(Peer Reviewed Journal)
    Caputo, M., Li, W., Kendall, S., Larsen, A., Weigel, K., White, H. 2023. Liver and muscle transcriptomes differ in mid-lactation cows divergent in feed efficiency in the presence or absence of supplemental rumen-protected choline. Metabolites. https://doi.org/10.3390/metabo13091023.
    
  • A meta-analysis of liver microbiome in beef and dairy cattle using metatranscriptome sequencing reads-(Other)
    
    
  • Microbial inoculum alters the rumen epithelial transcriptome and associated meta-transcriptome in calves-(Abstract Only)
    
    
  • Breeding for alfalfa compatibility with corn-(Proceedings)
    Riday, H., Grabber, J.H., Li, W., Enjalbert, N., Wagner, S., Mickelson, D. 2022. Breeding for alfalfa compatibility with corn. Proceedings of the World Alfalfa Congress. 11/14/2022 - 11/17/2022.
    
  • The rumen liquid meta-transcriptome of post-weaned dairy calves differed by pre-weaning ruminal administration of differentially-enriched, rumen-derived inocula -(Peer Reviewed Journal)
    Park, T., Cersosimo, L.M., Radloff, W.J., Zanton, G.I., Li, W. 2022. The rumen liquid meta-transcriptome of post-weaned dairy calves differed by pre-weaning ruminal administration of differentially-enriched, rumen-derived inocula. Animal Microbiome. 4. Article 4. https://doi.org/10.1186/s42523-021-00142-z.
    
  • Novel facets of the liver transcriptome are associated with the susceptibility and resistance to lipid-related metabolic disorders in periparturient Holstein cows -(Peer Reviewed Journal)
    Pralle, R., Li, W., Murphy, B., Holdorf, H.T., White, H. 2021. Novel facets of the liver transcriptome are associated with the susceptibility and resistance to lipid-related metabolic disorders in periparturient Holstein cows. Animals. 11(9). Article 2558. https://doi.org/10.3390/ani11092558.
    
  • Investigating the effect of positional variation on mid-lactation mammary gland transcriptomics in mice fed either a low-fat or high-fat diet -(Peer Reviewed Journal)
    Cheng, A., Li, W., Hernandez, L. 2021. Investigating the effect of positional variation on mid-lactation mammary gland transcriptomics in mice fed either a low-fat or high-fat diet. PLoS ONE. 16(8): e0255770. https://doi.org/10.1371/journal.pone.0255770.
    
  • Effect of natural pre-luteolytic prostaglandin F2a pulses on the bovine luteal transcriptome during spontaneous luteal regression -(Peer Reviewed Journal)
    Mezera, M., Li, W., Liu, L., Meidan, R., Penagaricano, F., Wiltbank, M. 2021. Effect of natural pre-luteolytic prostaglandin F2a pulses on the bovine luteal transcriptome during spontaneous luteal regression. Biology of Reproduction. 104(5):1016-1029. https://doi.org/10.1093/biolre/ioab123.
    
  • Analysis of host jejunum transcriptome and associated microbial community structure variation in young calves with feed-induced acidosis -(Peer Reviewed Journal)
    Naren, G., Li, W., Gelsinger, S., Murphy, B., Li, S. 2021. Analysis of host jejunum transcriptome and associated microbial community structure variation in young calves with feed-induced acidosis. Metabolites. 11(7). Article 414. https://doi.org/10.3390/metabo11070414.
    
  • The effects of artificially dosed adult rumen contents on abomasum transcriptome and associated microbial community structure in calves -(Peer Reviewed Journal)
    Narengaowa, F., Li, W., Murphy, B., Cox, M., Suen, G. 2021. The effects of artificially dosed adult rumen contents on abomasum transcriptome and associated microbial community structure in calves. Genes. 12(3). Article 424. https://doi.org/10.3390/genes12030424.
    
  • Pregnancy-induced changes in the transcriptome of the bovine corpus luteum during and after embryonic interferon-tau secretion -(Peer Reviewed Journal)
    Mezera, M., Li, W., Meidan, R., Wiltbank, M. 2021. Pregnancy-induced changes in the transcriptome of the bovine corpus luteum during and after embryonic interferon-tau secretion. Biology of Reproduction. 105(1):148-163. https://doi.org/10.1093/biolre/ioab034.
    
  • Pre-weaning ruminal administration of differentially-enriched, rumen-derived inocula shaped rumen bacterial communities and co-occurrence networks of post-weaned dairy calves -(Peer Reviewed Journal)
    Park, T., Cersosimo, L.M., Li, W., Radloff, W.J., Zanton, G.I. 2021. Pre-weaning ruminal administration of differentially-enriched, rumen-derived inocula shaped rumen bacterial communities and co-occurrence networks of post-weaned dairy calves. Frontiers in Microbiology. https://doi.org/10.3389/fmicb.2021.625488.
    
  • Investigating the complex interplay between genotype and high-fat-diet feeding in the lactating mammary gland using the Tph1 and Ldlr knockout models -(Peer Reviewed Journal)
    Cheng, A., Li, W., Walker, T., Silver, C., Ardendt, L., Hernandez, L. 2021. Investigating the complex interplay between genotype and high-fat-diet feeding in the lactating mammary gland using the Tph1 and Ldlr knockout models. American Journal of Physiology. 320(3):E438-E452. https://doi.org/10.1152/ajpendo.00456.2020.
    
  • Changes in the host transcriptome and microbial metatranscriptome of the ileum of dairy calves subjected to artificial dosing of exogenous rumen contents -(Peer Reviewed Journal)
    Li, W., Edwards, A., Murphy, B., Cox, M., Raabis, S., Skarlupka, J., Steinberger, A. 2020. Changes in the host transcriptome and microbial metatranscriptome of the ileum of dairy calves subjected to artificial dosing of exogenous rumen contents. Physiological Genomics. 52:333-346. https://doi.org/10.1152/physiolgenomics.00005.2020.
    
  • De novo assembly of the cattle reference genome with single-molecule sequencing -(Peer Reviewed Journal)
    Rosen, B.D., Bickhart, D.M., Schnabel, R.D., Koren, S., Elsik, C.G., Tseng, E., Rowan, T.N., Low, W.Y., Zimin, A., Couldrey, C., Hall, R., Li, W., Rhie, A., Ghurye, J., McKay, S.D., Thibaud-Nissen, F., Hoffman, J., Murdoch, B.M., Snelling, W.M., McDaneld, T.G., Hammond, J.A., Schwartz, J.C., Nandolo, W., Hagen, D.E., Dreischer, C., Schultheiss, S.J., Schroeder, S.G., Phillippy, A.M.,Cole, J.B., Van Tassell, C.P., Liu, G., Smith, T.P.L., Medrano, J.F. 2020. De novo assembly of the cattle reference genome with single-molecule sequencing. GigaScience. 9(3):1-9. https://doi.org/10.1093/gigascience/giaa021.
    
  • Identification of stable genes in the corpus luteum of lactating Holstein cows in pregnancy and luteolysis: implications for selection of RT-qPCR reference genes -(Peer Reviewed Journal)
    Mezera, M., Li, W., Edwards, A., Koch, D., Beard, A., Wiltbank, M. 2020. Identification of stable genes in the corpus luteum of lactating Holstein cows in pregnancy and luteolysis: implications for selection of RT-qPCR reference genes. Journal of Dairy Science. 103(5):4846-4857. https://doi.org/10.3168/jds.2019-17526.
    
  • The bovine epimural microbiota displays compositional and structural heterogeneity across different ruminal locations -(Peer Reviewed Journal)
    Sbardellati, D., Fischer, A., Cox, M.S., Li, W., Kalscheur, K., Suen, G. 2020. The bovine epimural microbiota displays compositional and structural heterogeneity across different ruminal locations. Journal of Dairy Science. 103(4):3636–3647. https://doi.org/10.3168/jds.2019-17649.
    
  • Changes in meta-transcriptome of rumen epimural microbial community and liver transcriptome in young calves with feed induced acidosis. -(Peer Reviewed Journal)
    Li, W., Gelsinger, S., Edwards, A., Riehle, C., Koch, D. 2019. Changes in meta-transcriptome of rumen epimural microbial community and liver transcriptome in young calves with feed induced acidosis.. Scientific Reports. 9. Article 18967. https://doi.org/10.1038/s41598-019-54055-8.
    
  • Identification of single nucleotide polymorphism in Red Clover (Trifolium Pratense L.) using targeted genomic ampliconsequencing and RNA-seq -(Peer Reviewed Journal)
    Li, W., Riday, H., Riehle, C., Edwards, A., Dinkins, R.D. 2019. Identification of single nucleotide polymorphism in Red Clover (Trifolium Pratense L.) using targeted genomic ampliconsequencing and RNA-seq. Frontiers in Plant Science. 10. Article 1257. https://doi.org/10.3389/fpls.2019.01257.
    
  • Transcriptome analysis of rumen epithelium and metatranscriptome analysis of rumen epimural microbial community in young calves with feed induced acidosis -(Peer Reviewed Journal)
    Li, W., Arnold, S., Edwards, A., Riehle, C. 2019. Transcriptome analysis of rumen epithelium and metatranscriptome analysis of rumen epimural microbial community in young calves with feed induced acidosis. Scientific Reports. 9. Article 4744. https://doi.org/10.1038/s41598-019-40375-2.
    
  • Computational detection and experimental validation of segmental duplications and associated copy number variations in water buffalo (Bubalus bubalis) -(Peer Reviewed Journal)
    Liu, S., Kang, X., Catacchio, C.R., Liu, M., Fang, L., Schroeder, S.G., Li, W., Rosen, B.D., Iamartino, D., Iannuzzi, L., Sonstegard, T.S., Van Tassell, C.P., Ventura, M., Low, W., Williams, J.L., Bickhart, D.M., Liu, G. 2019. Computational detection and experimental validation of segmental duplications and associated copy number variations in water buffalo (Bubalus bubalis). Functional and Integrative Genomics. 19(3):409–419. https://doi.org/10.1007/s10142-019-00657-4.
    
  • Effects and immune responses of probiotic treatment in ruminants-(Literature Review)
    
    
  • Transcriptomics analysis of host liver and meta-transcriptome analysis of rumen epimural microbial community in young calves treated with artificial dosing of rumen content from adult donor cow -(Peer Reviewed Journal)
    Li, W., Edwards, A., Riehle, C., Cox, M., Raabis, S., Steinberger, A., Skarlupka, J., Walling, J.G., Bickhart, D.M., Suen, G. 2019. Transcriptomics analysis of host liver and meta-transcriptome analysis of rumen epimural microbial community in young calves treated with artificial dosing of rumen content from adult donor cow. Scientific Reports. 9. Article 790. https://doi.org/10.1038/s41598-018-37033-4.
    
  • Effect of high-fat diet feeding and associated transcriptome changes in the peak lactation mammary gland in C57BL/6 dams -(Peer Reviewed Journal)
    Cheng, A., Hernandez, L., Li, W. 2018. Effect of high-fat diet feeding and associated transcriptome changes in the peak lactation mammary gland in C57BL/6 dams. Physiological Genomics. 50(12):1059-1070. https://doi.org/10.1152/physiolgenomics.00052.2018.
    
  • Examination of the xanthosine response on gene expression of mammary epithelial cells using RNA-seq technology -(Peer Reviewed Journal)
    Choudhary, S., Li, W., Bickhart, D.M., Ramneek, V., Sethi, R.S., Mukhopadhyay, C.S., Choudhary, R.K. 2018. Examination of the xanthosine response on gene expression of mammary epithelial cells using RNA-seq technology. Journal of Animal Science and Technology. 60. Article 18. https://doi.org/10.1186/s40781-018-0177-5.
    
  • Genomic structural differences between cattle and river buffalo identified through a combination and genomic and transcriptomic analysis-(Peer Reviewed Journal)
    Li, W., Bickhart, D.M., Ramunno, L., Lamartino, D., Williams, J., Liu, G. 2018. Genomic structural differences between cattle and river buffalo identified through a combination and genomic and transcriptomic analysis. Data in Brief. 19:236-239.
    
  • Comparative sequence alignment reveals River Buffalo genomic structural differences compared with cattle-(Peer Reviewed Journal)
    Li, W., Bickhart, D.M., Ramunno, L., Iamartino, D., Williams, J., Liu, G. 2018. Comparative sequence alignment reveals River Buffalo genomic structural differences compared with cattle. Genomics. https://doi.org/10.1016/j.ygeno.2018.02.018.
    
  • Adverse Maternal Environment Increases Fetal Liver Hydroxymethylation and Alters the Transcriptome-(Abstract Only)
    
    
  • Comparative sequence alignment reveals River Buffalo genomic structural differences compared with cattle-(Abstract Only)
    
    
  • Transcriptome changes in artificial dosing of rumen content in neonatal calves-(Abstract Only)
    
    
  • Effects of xanthosine in isoform switch and splice variants of expressed genes in mammary epithelial cells-(Abstract Only)
    
    
  • Effects of xanthosine on gene expression of mammary epithelial cells using RNA sequencing of goat milk fat globules-(Abstract Only)
    
    

• Projects

  Targeted Depletion of Cattle Host Transcripts for High-resolution, Metatranscriptomics Analysis of Tissue-embedded Microbial Communities Cooperative Agreement (A)   Accession Number:444511

  Developing Strategies to Improve Dairy Cow Performance and Nutrient Use Efficiency with Nutrition, Genetics, and Microbiology In-House Appropriated (D)   Accession Number:442971

  Using Metatranscriptomics to Investigate the Liver and Blood Microbiome in the Young Calf and Mid-lactation Cows with Feed-induced Acidosis Interagency Reimbursable Agreement (I)   Accession Number:444183

  Utilizing the University of Wisconsin Institutional Animal Care and Use Committee Non-Funded Cooperative Agreement (N)   Accession Number:440145

  Institutional Biological Safety Committee (IBC) Agreement - University of Wisconsin Madison Non-Funded Cooperative Agreement (N)   Accession Number:441643

• ARS News Articles

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