19972019
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Research Output 1997 2019

2019
Betaine-Homocysteine S-Methyltransferase
betaine-homocysteine S-methyltransferase
5-Methyltetrahydrofolate-Homocysteine S-Methyltransferase
methionine synthase
choline

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., Jan 1 2019, (Accepted/In press) In : Journal of Animal Physiology and Animal Nutrition.

Research output: Contribution to journalArticle

Open Access
Nutrigenomics
nutrigenomics
Jersey
histology
Histology

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

Huang, L., Riggins, C. W., Rodriguez-Zas, S. L., 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
Nitrification
maize
Soils
Genes
Denitrification

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

Markov Chains
Gene Regulatory Networks
Markov processes
Genes
Biological Phenomena
Trigeminal Nuclei
Trigeminal Ganglion
Hyperalgesia
Nucleus Accumbens
Circadian Rhythm
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

Computational Biology
Neuropeptides
Peptide Hormones
Post Translational Protein Processing
Proteomics

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 1 2018, In : PLoS One. 13, 8, e0201773.

Research output: Contribution to journalArticle

Gene Regulatory Networks
selection methods
wheels
Running
Brain

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 1 2018, In : Psychoneuroendocrinology. 97, p. 47-58 12 p.

Research output: Contribution to journalArticle

Microglia
Acetylation
Histones
Depression
Inflammation
Trigeminal Nuclei
Trigeminal Ganglion
Gene Regulatory Networks
Hyperalgesia
Nucleus Accumbens

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

Gene Networks
Gene Regulatory Networks
Amphetamine
Mouse
Genes

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 1 2018, In : PloS one. 13, 8, e0201553.

Research output: Contribution to journalArticle

Corpus Striatum
Attention Deficit Disorder with Hyperactivity
Transcriptome
transcriptome
Genes
2017

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

Leukocytes
Nutrition
Energy Intake
Transcriptome
Blood
Subcutaneous Fat
adipose tissue
Adipose Tissue
Holstein
Tissue
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 1 2016, In : PloS one. 11, 11, e0167095.

Research output: Contribution to journalArticle

cerebellum
Reward
Transcriptome
transcriptome
Cerebellum

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

Honey
Bees
Social Class
honey bees
Genes

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

Seo, M., Caetano-Anolles, K., Rodriguez-Zas, S. L., 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

RNA
Genes
Gene Expression
Sex Characteristics
Biological Phenomena
Artificial Insemination
Semen
artificial insemination
profitability
semen

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 1 2016, In : PloS one. 11, 6, e0157727.

Research output: Contribution to journalArticle

Indoleamine-Pyrrole 2,3,-Dioxygenase
Macrophages
neuroglia
Microglia
Transcriptome

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 1 2016, In : PloS one. 11, 3, e0150858.

Research output: Contribution to journalArticle

neuroglia
Microglia
Transcriptome
transcriptome
Genes

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

Transcriptome
Liver
Lactation
Amino Acids
Carbohydrates

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

bee dances
Honey
Bees
Neurology
transcriptomics
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., Rodriguez-Zas, S. L., Palladino, A. R., Cardoso, F., Trevisi, E. & Loor, J. J., Jan 1 2015, In : Physiological Reports. 3, 4, e12388.

Research output: Contribution to journalArticle

Transcriptome
Lipopolysaccharides
Breast
Escherichia coli
Liver

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

Multivariate Analysis
Depression
Infection
Therapeutics
Sucrose

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

Workflow
Macrophages
Gene Expression Profiling
Gene expression
RNA

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. L., Felix, T. L. & Shike, D. W., Oct 1 2015, In : Journal of animal science. 93, 10, p. 4936-4947 12 p.

Research output: Contribution to journalArticle

beef cows
carcass composition
Weaning
weaning
Insulin

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. L., 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

Coturnix
Sex Characteristics
sexual dimorphism
Genes
RNA

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

Honey
Bees
juvenile hormones
honey
bee

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

Fertility
Spermatozoa
Artificial Insemination
Acrosome
Herpes Zoster

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

Genetic Hybridization
Semen
economic valuation
genetic improvement
semen
Simmental
intramuscular fat
feeding level
Angus
Nutrition

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. L., Felix, T. L. & Shike, D. W., Oct 1 2015, In : Journal of animal science. 93, 10, p. 4926-4935 10 p.

Research output: Contribution to journalArticle

beef cows
Weaning
Postpartum Period
weaning
calves
Myostatin
myostatin
Gene expression
physical activity
Muscle

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

Transcriptome
transcriptome
calving
Holstein
cows
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

neuropeptides
Neuropeptides
Databases
testing
peptides

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

Gene-Environment Interaction
RNA
Transcriptome
Gene expression
Statistical methods

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

honeybee
transcriptomics
honey bees
brain
Brain

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

Databases
Peptides
Neuropeptides
Tandem Mass Spectrometry
Mass spectrometry

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

Peptides
Databases
Software

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

RNA
Sample Size
Indoleamine-Pyrrole 2,3,-Dioxygenase
RNA Sequence Analysis
Macrophages

Impact of pig insemination technique and semen preparation on profitability

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

Research output: Contribution to journalArticle

Insemination
Semen
insemination
profitability
Semen Preservation
Dairies
Biomarkers
Liver
biomarkers
Blood

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

Akbar, H., Cardoso, F., 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

Endometritis
Dairies
Transcriptome
Liver
Adipose Tissue

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., Jan 1 2014, In : Functional and Integrative Genomics. 14, 1, p. 261-273 13 p.

Research output: Contribution to journalArticle

Transcriptome
Epithelium
Proteins
Fats
Basal Metabolism

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

RNA
Genes
Gene Expression Profiling
Binomial Distribution
Biological Phenomena

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

Fractionation
Proteomics
Proteins
Peptides
Databases
2013

Aging leads to prolonged duration of inflammation-induced depression-like behavior caused by Bacillus Calmette-Guérin

Kelley, K. W., O'Connor, J. C., Lawson, M. A., Dantzer, R., Rodriguez-Zas, S. L. & McCusker, R. H., Jan 1 2013, In : Brain, Behavior, and Immunity. 32, p. 63-69 7 p.

Research output: Contribution to journalArticle

Bacillus
Depression
Inflammation
Tryptophan
Infection

An analysis of survey data by size of the breeding herd for the reproductive management practices of North American sow farms

Knox, R. V., Rodriguez-Zas, S. L., Sloter, N. L., McNamara, K. A., Gall, T. J., Levis, D. G., Safranski, T. J. & Singleton, W. L., Jan 1 2013, In : Journal of animal science. 91, 1, p. 433-445 13 p.

Research output: Contribution to journalArticle

Practice Management
Breeding
sows
herds
farms

Bioinformatics analysis of transcriptome dynamics during growth in Angus cattle longissimus muscle

Moisá, S. J., Shike, D. W., Graugnard, D. E., Rodriguez-Zas, S. L., Everts, R. E., Lewin, H. A., Faulkner, D. B., Berger, L. L. & Loor, J. J., Jan 1 2013, In : Bioinformatics and Biology Insights. 7, p. 253-270 18 p.

Research output: Contribution to journalArticle

Gene Expression Profiling
Bioinformatics
Computational Biology
Muscle
Genes

Bioinformatics and gene network analyses of the swine mammary gland transcriptome during late gestation

Zhao, W., Shahzad, K., Jiang, M., Graugnard, D. E., Rodriguez-Zas, S. L., Luo, J., Loor, J. J. & Hurley, W. L., Jul 19 2013, In : Bioinformatics and Biology Insights. 7, p. 193-216 24 p.

Research output: Contribution to journalArticle

Interleukin-4 Receptors
Gene Networks
Gene Regulatory Networks
Human Mammary Glands
Bioinformatics

Bivariate genome-wide association analysis of the growth and intake components of feed efficiency

Serão, N. V. L., González-Peña, D., Beever, J. E., Bollero, G. A., Southey, B. R., Faulkner, D. B. & Rodriguez-Zas, S. L., Jan 1 2013, In : PloS one. 8, 10, p. e78530

Research output: Contribution to journalArticle

Genome-Wide Association Study
Polymorphism
single nucleotide polymorphism
Single Nucleotide Polymorphism
feed conversion