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Research Output

2020

Acidification in corn monocultures favor fungi, ammonia oxidizing bacteria, and nirK-denitrifier groups

Behnke, G. D., Zabaloy, M. C., Riggins, C. W., Rodríguez-Zas, S., Huang, L. & Villamil, M. B., Jun 10 2020, In : Science of the Total Environment. 720, 137514.

Research output: Contribution to journalArticle

Open Access
Open Access
Open Access
2019

Jersey steer ruminal papillae histology and nutrigenomics with diet changes

Novak, T. E., Rodriguez-Zas, S. L., Southey, B. R., Starkey, J. D., Stockler, R. M., Alfaro, G. F. & Moisá, S. J., Nov 1 2019, In : Journal of Animal Physiology and Animal Nutrition. 103, 6, p. 1694-1707 14 p.

Research output: Contribution to journalArticle

Open Access

Long-term N fertilization decreased diversity and altered the composition of soil bacterial and archaeal communities

Sun, R., Zhang, P., Riggins, C. W., Zabaloy, M. C., Rodríguez-Zas, S. & Villamil, M. B., Sep 23 2019, In : Agronomy. 9, 10, 574.

Research output: Contribution to journalArticle

Open Access

Long-term N fertilization imbalances potential N acquisition and transformations by soil microbes

Huang, L., Riggins, C. W., Rodríguez-Zas, S., Zabaloy, M. C. & Villamil, M. B., Nov 15 2019, In : Science of the Total Environment. 691, p. 562-571 10 p.

Research output: Contribution to journalArticle

Open Access

Markov chain Monte Carlo simulation of a Bayesian mixture model for gene network inference

Ko, Y., Kim, J. & Rodriguez-Zas, S. L., May 1 2019, In : Genes and Genomics. 41, 5, p. 547-555 9 p.

Research output: Contribution to journalArticle

Opioid-Induced Hyperalgesia Is Associated with Dysregulation of Circadian Rhythm and Adaptive Immune Pathways in the Mouse Trigeminal Ganglia and Nucleus Accumbens

Zhang, P., Moye, L. S., Southey, B. R., Dripps, I., Sweedler, J. V., Pradhan, A. & Rodriguez-Zas, S. L., Dec 1 2019, In : Molecular Neurobiology. 56, 12, p. 7929-7949 21 p.

Research output: Contribution to journalArticle

2018

Bioinformatics for prohormone and neuropeptide discovery

Southey, B. R., Romanova, E. V., Rodriguez-Zas, S. L. & Sweedler, J. V., Jan 1 2018, Methods in Molecular Biology. Humana Press Inc., p. 71-96 26 p. (Methods in Molecular Biology; vol. 1719).

Research output: Chapter in Book/Report/Conference proceedingChapter

Brain region-dependent gene networks associated with selective breeding for increased voluntary wheel-running behavior

Zhang, P., Rhodes, J. S., Garland, T., Perez, S. D., Southey, B. R. & Rodriguez-Zas, S. L., Aug 2018, In : PloS one. 13, 8, e0201773.

Research output: Contribution to journalArticle

Disruption of microglia histone acetylation and protein pathways in mice exhibiting inflammation-associated depression-like symptoms

Rodriguez-Zas, S. L., Wu, C., Southey, B. R., O'Connor, J. C., Nixon, S. E., Garcia, R., Zavala, C., Lawson, M., McCusker, R. H., Romanova, E. V., Sweedler, J. V., Kelley, K. W. & Dantzer, R., Nov 2018, In : Psychoneuroendocrinology. 97, p. 47-58 12 p.

Research output: Contribution to journalArticle

Interplay Between Amphetamine and Activity Level in Gene Networks of the Mouse Striatum

Goncalves, T. M., Southey, B. R. & Rodriguez-Zas, S. L., Dec 1 2018, In : Bioinformatics and Biology Insights. 12

Research output: Contribution to journalArticle

Striatal transcriptome of a mouse model of ADHD reveals a pattern of synaptic remodeling

Sorokina, A. M., Saul, M., Goncalves, T. M., Gogola, J. V., Majdak, P., Rodriguez-Zas, S. L. & Rhodes, J. S., Aug 2018, In : PloS one. 13, 8, e0201553.

Research output: Contribution to journalArticle

2017

Nutrition, reproduction, and young stock performance on dairy farms throughout Illinois: A Dairy Focus Team approach

Rivelli, M. I., Morrison, S. Y., Haerr, K. J., Zas, S. R. & Cardoso, F. C., Aug 2017, In : Professional Animal Scientist. 33, 4, p. 409-419 11 p.

Research output: Contribution to journalArticle

Prepartal Energy Intake Alters Blood Polymorphonuclear Leukocyte Transcriptome During the Peripartal Period in Holstein Cows

Agrawal, A., Khan, M. J., Graugnard, D. E., Vailati-Riboni, M., Rodriguez-Zas, S. L., Osorio, J. S. & Loor, J. J., Apr 27 2017, In : Bioinformatics and Biology Insights. 11

Research output: Contribution to journalArticle

2016

Cerebellum transcriptome of mice bred for high voluntary activity offers insights into locomotor control and reward-dependent behaviors

Caetano-Anollés, K., Rhodes, J. S., Garland, T., Perez, S. D., Hernandez, A. G., Southey, B. R. & Rodriguez-Zas, S. L., Nov 2016, In : PloS one. 11, 11, e0167095.

Research output: Contribution to journalArticle

Characterization of genomic variants associated with scout and recruit behavioral castes in honey bees using whole-genome sequencing

Southey, B. R., Zhu, P., Carr-Markell, M. K., Liang, Z. S., Zayed, A., Li, R., Robinson, G. E. & Rodriguez-Zas, S. L., Jan 1 2016, In : PloS one. 11, 1, e0146430.

Research output: Contribution to journalArticle

Comprehensive identification of sexually dimorphic genes in diverse cattle tissues using RNA-seq

Seo, M., Caetano-Anolles, K., Rodriguez-Zas, S., Ka, S., Jeong, J. Y., Park, S., Kim, M. J., Nho, W. G., Cho, S., Kim, H. & Lee, H. J., Jan 27 2016, In : BMC genomics. 17, 1, 81.

Research output: Contribution to journalArticle

Differential transcriptome networks between IDO1-Knockout and wild-type mice in brain microglia and macrophages

Gonzalez-Pena, D., Nixon, S. E., Southey, B. R., Lawson, M. A., McCusker, R. H., Hernandez, A. G., Dantzer, R., Kelley, K. W. & Rodriguez-Zas, S. L., Jun 2016, In : PloS one. 11, 6, e0157727.

Research output: Contribution to journalArticle

Microglia transcriptome changes in a model of depressive behavior after immune challenge

Gonzalez-Pena, D., Nixon, S. E., O'Connor, J. C., Southey, B. R., Lawson, M. A., McCusker, R. H., Borras, T., Machuca, D., Hernandez, A. G., Dantzer, R., Kelley, K. W. & Rodriguez-Zas, S. L., Mar 2016, In : PloS one. 11, 3, e0150858.

Research output: Contribution to journalArticle

Prepartum body condition score and plane of nutrition affect the hepatic transcriptome during the transition period in grazing dairy cows

Vailati-Riboni, M., Meier, S., Burke, C. R., Kay, J. K., Mitchell, M. D., Walker, C. G., Crookenden, M. A., Heiser, A., Rodriguez-Zas, S. L., Roche, J. R. & Loor, J. J., Nov 2 2016, In : BMC genomics. 17, 1, 854.

Research output: Contribution to journalArticle

Transcriptomic profiling of central nervous system regions in three species of honey bee during dance communication behavior

Sarma, M. S., Rodriguez-Zas, S. L., Hong, F., Zhong, S. & Robinson, G. E., Apr 19 2016, Animal Behavior: An Evolutionary Approach. Apple Academic Press, p. 210-230 21 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

2015

Acute mammary and liver transcriptome responses after an intramammary escherichia coli lipopolysaccharide challenge in postpartal dairy cows

Minuti, A., Zhou, Z., Graugnard, D. E., Rodriguezzas, S. L., Palladino, A. R., Cardoso, F. C., Trevisi, E. & Loor, J. J., Jan 1 2015, In : Physiological Reports. 3, 4, e12388.

Research output: Contribution to journalArticle

Advancing the understanding of behaviors associated with Bacille Calmette Guérin infection using multivariate analysis

Rodriguez-Zas, S. L., Nixon, S. E., Lawson, M. A., Mccusker, R. H., Southey, B. R., O'Connor, J. C., Dantzer, R. & Kelley, K. W., Feb 1 2015, In : Brain, Behavior, and Immunity. 44, p. 176-186 11 p.

Research output: Contribution to journalArticle

Analytical workflow profiling gene expression in murine macrophages

Nixon, S. E., Gonzalez-Peña, D., Lawson, M. A., McCusker, R. H., Hernandez, A. G., O'Connor, J. C., Dantzer, R., Kelley, K. W. & Rodriguez-Zas, S. L., Apr 25 2015, In : Journal of Bioinformatics and Computational Biology. 13, 2, 1550010.

Research output: Contribution to journalArticle

Beef cow prepartum supplement level and age at weaning: II. Effects of developmental programming on performance and carcass composition of steer progeny

Shoup, L. M., Wilson, T. B., González-Peña, D., Ireland, F. A., Rodriguez-Zas, S., Felix, T. L. & Shike, D. W., Oct 2015, In : Journal of animal science. 93, 10, p. 4936-4947 12 p.

Research output: Contribution to journalArticle

Comprehensive identification of sexual dimorphism-associated differentially expressed genes in two-way factorial designed RNA-seq data on Japanese quail (Coturnix coturnix japonica)

Caetano-Anolles, K., Seo, M., Rodriguez-Zas, S., Oh, J. D., Han, J. Y., Lee, K., Park, T. S., Shin, S., Jiao, Z. J., Ghosh, M., Jeong, D. K., Cho, S., Kim, H., Song, K. D. & Lee, H. K., Sep 29 2015, In : PloS one. 10, 9, e0139324.

Research output: Contribution to journalArticle

Diet and endocrine effects on behavioral maturation-related gene expression in the pars intercerebralis of the honey bee brain

Wheeler, M. M., Ament, S. A., Rodriguez-Zas, S. L., Southey, B. & Robinson, G. E., Dec 1 2015, In : Journal of Experimental Biology. 218, 24, p. 4005-4014 10 p.

Research output: Contribution to journalArticle

Enhanced fertility prediction of cryopreserved boar spermatozoa using novel sperm function assessment

Daigneault, B. W., Mcnamara, K. A., Purdy, P. H., Krisher, R. L., Knox, R. V., Rodriguez-Zas, S. L. & Miller, D. J., May 1 2015, In : Andrology. 3, 3, p. 558-568 11 p.

Research output: Contribution to journalArticle

Genetic gain and economic values of selection strategies including semen traits in three- and four-way crossbreeding systems for swine production

González-Peña, D., Knox, R. V., Macneil, M. D. & Rodriguez-Zas, S. L., Mar 31 2015, In : Journal of animal science. 93, 3, p. 879-891 13 p.

Research output: Contribution to journalArticle

Prepartum supplement level and age at weaning: I. Effects on pre- and postpartum beef cow performance and calf performance through weaning

Shoup, L. M., Kloth, A. C., Wilson, T. B., González-Peña, D., Ireland, F. A., Rodriguez-Zas, S., Felix, T. L. & Shike, D. W., Oct 2015, In : Journal of animal science. 93, 10, p. 4926-4935 10 p.

Research output: Contribution to journalArticle

The effect of calving in the summer on the hepatic transcriptome of Holstein cows during the peripartal period

Shahzad, K., Akbar, H., Vailati-Riboni, M., Basiricò, L., Morera, P., Rodriguez-Zas, S. L., Nardone, A., Bernabucci, U. & Loor, J. J., Aug 1 2015, In : Journal of Dairy Science. 98, 8, p. 5401-5413 13 p.

Research output: Contribution to journalArticle

2014

Accurate assignment of significance to neuropeptide identifications using monte carlo K-permuted decoy databases

Akhtar, M. N., Southey, B. R., Andrén, P. E., Sweedler, J. V. & Rodriguez-Zas, S. L., Oct 17 2014, In : PloS one. 9, 10, e111112.

Research output: Contribution to journalArticle

Advanced statistical analysis of RNA-Seq differential gene expression profiles of animal gene-environment interactions

Caetano-Anollés, K., Nixon, S., Mishra, S. & Rodriguez-Zas, S. L., Jan 1 2014, Proceedings of the 6th International Conference on Bioinformatics and Computational Biology, BICOB 2014. International Society for Computers and Their Applications, p. 43-47 5 p. (Proceedings of the 6th International Conference on Bioinformatics and Computational Biology, BICOB 2014).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Comparative brain transcriptomic analyses of scouting across distinct behavioural and ecological contexts in honeybees

Liang, Z. S., Mattila, H. R., Rodriguez-Zas, S. L., Southey, B. R., Seeley, T. D. & Robinson, G. E., Oct 29 2014, In : Proceedings of the Royal Society B: Biological Sciences. 281, 1797, 20141868.

Research output: Contribution to journalArticle

Evaluation of significance level assignment of database search programs using monte carlo permutation approach

Akhtar, M. N., Southey, B. R., Andrén, P. E., Sweedler, J. V. & Rodriguez-Zas, S. L., Jan 1 2014, Proceedings of the 6th International Conference on Bioinformatics and Computational Biology, BICOB 2014. International Society for Computers and Their Applications, p. 103-107 5 p. (Proceedings of the 6th International Conference on Bioinformatics and Computational Biology, BICOB 2014).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Identification of best indicators of peptide-spectrum match using a permutation resampling approach

Akhtar, M. N., Southey, B. R., Andrén, P. E., Sweedler, J. V. & Rodriguez-Zas, S. L., Oct 30 2014, In : Journal of Bioinformatics and Computational Biology. 12, 5, 1440001.

Research output: Contribution to journalArticle

Impact of bias correction methods and increasing the biological samples in transcriptomic analysis

González-Peña, D., Nixon, S. E., Southey, B. R., Lawson, M. A., McCusker, R. H., Dantzer, R., Kelley, K. W. & Rodriguez-Zas, S. L., Jan 1 2014, Proceedings of the 6th International Conference on Bioinformatics and Computational Biology, BICOB 2014. International Society for Computers and Their Applications, p. 115-118 4 p. (Proceedings of the 6th International Conference on Bioinformatics and Computational Biology, BICOB 2014).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Impact of pig insemination technique and semen preparation on profitability

Gonzalez-Peña, D., Knox, R. V., Pettigrew, J. & Rodriguez-Zas, S. L., Jan 2014, In : Journal of animal science. 92, 1, p. 72-84 13 p.

Research output: Contribution to journalArticle

Postpartal subclinical endometritis alters transcriptome profiles in liver and adipose tissue of dairy cows

Akbar, H., Cardoso, F. C., Meier, S., Burke, C., McDougall, S., Mitchell, M., Walker, C., Rodriguez-Zas, S. L., Everts, R. E., Lewin, H. A., Roche, J. R. & Loor, J. J., Feb 19 2014, In : Bioinformatics and Biology Insights. 8, p. 45-63 19 p.

Research output: Contribution to journalArticle

Ruminal epithelium transcriptome dynamics in response to plane of nutrition and age in young Holstein calves

Naeem, A., Drackley, J. K., Lanier, J. S., Everts, R. E., Rodriguez-Zas, S. L. & Loor, J. J., Mar 2014, In : Functional and Integrative Genomics. 14, 1, p. 261-273 13 p.

Research output: Contribution to journalArticle

Transcriptomic analysis by RNA-Seq and gene enrichment analysis

Nixon, S. E., González-Peña, D., Lawson, M. A., McCusker, R. H., O'Connor, J. C., Dantzer, R., Kelley, K. W. & Rodriguez-Zas, S. L., Jan 1 2014, Proceedings of the 6th International Conference on Bioinformatics and Computational Biology, BICOB 2014. International Society for Computers and Their Applications, p. 27-31 5 p. (Proceedings of the 6th International Conference on Bioinformatics and Computational Biology, BICOB 2014).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Understanding the impact of fractionation and dynamic exclusion on proteomics

Zavala, C., Nixon, S., Southey, B. R., Wu, C., Romanova, E. V., Sweedler, J. V. & Rodriguez-Zas, S. L., Jan 1 2014, Proceedings of the 6th International Conference on Bioinformatics and Computational Biology, BICOB 2014. International Society for Computers and Their Applications, p. 93-96 4 p. (Proceedings of the 6th International Conference on Bioinformatics and Computational Biology, BICOB 2014).

Research output: Chapter in Book/Report/Conference proceedingConference contribution