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Bioinformatics for Prohormone and Neuropeptide Discovery.

Southey BR, Romanova EV, Rodriguez-Zas SL, Sweedler JV.

Methods Mol Biol. 2018;1719:71-96. doi: 10.1007/978-1-4939-7537-2_5.


Transcriptional changes in mesenteric and subcutaneous adipose tissue from Holstein cows in response to plane of dietary energy.

Moisá SJ, Ji P, Drackley JK, Rodriguez-Zas SL, Loor JJ.

J Anim Sci Biotechnol. 2017 Dec 4;8:85. doi: 10.1186/s40104-017-0215-z. eCollection 2017.


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

Agrawal A, Khan MJ, Graugnard DE, Vailati-Riboni M, Rodriguez-Zas SL, Osorio JS, Loor JJ.

Bioinform Biol Insights. 2017 Apr 28;11:1177932217704667. doi: 10.1177/1177932217704667. eCollection 2017.


Cerebellum Transcriptome of Mice Bred for High Voluntary Activity Offers Insights into Locomotor Control and Reward-Dependent Behaviors.

Caetano-Anollés K, Rhodes JS, Garland T Jr, Perez SD, Hernandez AG, Southey BR, Rodriguez-Zas SL.

PLoS One. 2016 Nov 28;11(11):e0167095. doi: 10.1371/journal.pone.0167095. eCollection 2016.


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 CR, Kay JK, Mitchell MD, Walker CG, Crookenden MA, Heiser A, Rodriguez-Zas SL, Roche JR, Loor JJ.

BMC Genomics. 2016 Nov 2;17(1):854.


Differential Transcriptome Networks between IDO1-Knockout and Wild-Type Mice in Brain Microglia and Macrophages.

Gonzalez-Pena D, Nixon SE, Southey BR, Lawson MA, McCusker RH, Hernandez AG, Dantzer R, Kelley KW, Rodriguez-Zas SL.

PLoS One. 2016 Jun 17;11(6):e0157727. doi: 10.1371/journal.pone.0157727. eCollection 2016.


Microglia Transcriptome Changes in a Model of Depressive Behavior after Immune Challenge.

Gonzalez-Pena D, Nixon SE, O'Connor JC, Southey BR, Lawson MA, McCusker RH, Borras T, Machuca D, Hernandez AG, Dantzer R, Kelley KW, Rodriguez-Zas SL.

PLoS One. 2016 Mar 9;11(3):e0150858. doi: 10.1371/journal.pone.0150858. eCollection 2016.


Characterization of Genomic Variants Associated with Scout and Recruit Behavioral Castes in Honey Bees Using Whole-Genome Sequencing.

Southey BR, Zhu P, Carr-Markell MK, Liang ZS, Zayed A, Li R, Robinson GE, Rodriguez-Zas SL.

PLoS One. 2016 Jan 19;11(1):e0146430. doi: 10.1371/journal.pone.0146430. eCollection 2016.


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

Wheeler MM, Ament SA, Rodriguez-Zas SL, Southey B, Robinson GE.

J Exp Biol. 2015 Dec;218(Pt 24):4005-14. doi: 10.1242/jeb.119420. Epub 2015 Nov 13.


Contribution of semen trait selection, artificial insemination technique, and semen dose to the profitability of pig production systems: A simulation study.

Gonzalez-Pena D, Knox RV, Rodriguez-Zas SL.

Theriogenology. 2016 Jan 15;85(2):335-44. doi: 10.1016/j.theriogenology.2015.09.014. Epub 2015 Sep 12.


Maternal Plane of Nutrition during Late Gestation and Weaning Age Alter Angus × Simmental Offspring Longissimus Muscle Transcriptome and Intramuscular Fat.

Moisá SJ, Shike DW, Shoup L, Rodriguez-Zas SL, Loor JJ.

PLoS One. 2015 Jul 8;10(7):e0131478. doi: 10.1371/journal.pone.0131478. eCollection 2015.


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 SL, Nardone A, Bernabucci U, Loor JJ.

J Dairy Sci. 2015 Aug;98(8):5401-13. doi: 10.3168/jds.2015-9409.


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 RV, MacNeil MD, Rodriguez-Zas SL.

J Anim Sci. 2015 Mar;93(3):879-91. doi: 10.2527/jas.2014-8035.


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

Minuti A, Zhou Z, Graugnard DE, Rodriguez-Zas SL, Palladino AR, Cardoso FC, Trevisi E, Loor JJ.

Physiol Rep. 2015 Apr;3(4). pii: e12388. doi: 10.14814/phy2.12388.


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

Daigneault BW, McNamara KA, Purdy PH, Krisher RL, Knox RV, Rodriguez-Zas SL, Miller DJ.

Andrology. 2015 May;3(3):558-68. doi: 10.1111/andr.12035. Epub 2015 Apr 24.


Synergistic and antagonistic interplay between myostatin gene expression and physical activity levels on gene expression patterns in triceps Brachii muscles of C57/BL6 mice.

Caetano-Anollés K, Mishra S, Rodriguez-Zas SL.

PLoS One. 2015 Feb 24;10(2):e0116828. doi: 10.1371/journal.pone.0116828. eCollection 2015.


Analytical workflow profiling gene expression in murine macrophages.

Nixon SE, González-Peña D, Lawson MA, McCusker RH, Hernandez AG, O'Connor JC, Dantzer R, Kelley KW, Rodriguez-Zas SL.

J Bioinform Comput Biol. 2015 Apr;13(2):1550010. doi: 10.1142/S0219720015500109. Epub 2015 Jan 14.


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

Akhtar MN, Southey BR, Andrén PE, Sweedler JV, Rodriguez-Zas SL.

J Bioinform Comput Biol. 2014 Oct;12(5):1440001. doi: 10.1142/S0219720014400010.


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

Liang ZS, Mattila HR, Rodriguez-Zas SL, Southey BR, Seeley TD, Robinson GE.

Proc Biol Sci. 2014 Dec 22;281(1797). pii: 20141868. doi: 10.1098/rspb.2014.1868.


Accurate assignment of significance to neuropeptide identifications using Monte Carlo k-permuted decoy databases.

Akhtar MN, Southey BR, Andrén PE, Sweedler JV, Rodriguez-Zas SL.

PLoS One. 2014 Oct 17;9(10):e111112. doi: 10.1371/journal.pone.0111112. eCollection 2014.


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

Rodriguez-Zas SL, Nixon SE, Lawson MA, Mccusker RH, Southey BR, O'Connor JC, Dantzer R, Kelley KW.

Brain Behav Immun. 2015 Feb;44:176-86. doi: 10.1016/j.bbi.2014.09.018. Epub 2014 Oct 7.


Integrative analyses of hepatic differentially expressed genes and blood biomarkers during the peripartal period between dairy cows overfed or restricted-fed energy prepartum.

Shahzad K, Bionaz M, Trevisi E, Bertoni G, Rodriguez-Zas SL, Loor JJ.

PLoS One. 2014 Jun 10;9(6):e99757. doi: 10.1371/journal.pone.0099757. eCollection 2014.


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

Akbar H, Cardoso FC, Meier S, Burke C, McDougall S, Mitchell M, Walker C, Rodriguez-Zas SL, Everts RE, Lewin HA, Roche JR, Loor JJ.

Bioinform Biol Insights. 2014 Feb 19;8:45-63. doi: 10.4137/BBI.S13735. eCollection 2014.


Impact of pig insemination technique and semen preparation on profitability.

Gonzalez-Peña D, Knox RV, Pettigrew J, Rodriguez-Zas SL.

J Anim Sci. 2014 Jan;92(1):72-84. doi: 10.2527/jas.2013-6836. Epub 2013 Dec 18.


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

Naeem A, Drackley JK, Lanier JS, Everts RE, Rodriguez-Zas SL, Loor JJ.

Funct Integr Genomics. 2014 Mar;14(1):261-73. doi: 10.1007/s10142-013-0351-2. Epub 2013 Dec 7.


Relationship among performance, carcass, and feed efficiency characteristics, and their ability to predict economic value in the feedlot.

Retallick KM, Faulkner DB, Rodriguez-Zas SL, Nkrumah JD, Shike DW.

J Anim Sci. 2013 Dec;91(12):5954-61. doi: 10.2527/jas.2013-6156.


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

Serão NV, González-Peña D, Beever JE, Bollero GA, Southey BR, Faulkner DB, Rodriguez-Zas SL.

PLoS One. 2013 Oct 29;8(10):e78530. doi: 10.1371/journal.pone.0078530. eCollection 2013.


Single nucleotide polymorphisms and haplotypes associated with feed efficiency in beef cattle.

Serão NV, González-Peña D, Beever JE, Faulkner DB, Southey BR, Rodriguez-Zas SL.

BMC Genet. 2013 Sep 25;14:94. doi: 10.1186/1471-2156-14-94.


The effect of breed and individual heterosis on the feed efficiency, performance, and carcass characteristics of feedlot steers.

Retallick KM, Faulkner DB, Rodriguez-Zas SL, Nkrumah JD, Shike DW.

J Anim Sci. 2013 Nov;91(11):5161-6. doi: 10.2527/jas.2012-6155. Epub 2013 Sep 17.


Multifactorial Understanding of Ion Abundance in Tandem Mass Spectrometry Experiments.

Fazal Z, Southey BR, Sweedler JV, Rodriguez-Zas SL.

J Proteomics Bioinform. 2013 Jan 29;6(2):23-29.


Bioinformatics analysis of transcriptome dynamics during growth in angus cattle longissimus muscle.

Moisá SJ, Shike DW, Graugnard DE, Rodriguez-Zas SL, Everts RE, Lewin HA, Faulkner DB, Berger LL, Loor JJ.

Bioinform Biol Insights. 2013 Aug 4;7:253-70. doi: 10.4137/BBI.S12328. eCollection 2013.


Bioinformatics and Gene Network Analyses of the Swine Mammary Gland Transcriptome during Late Gestation.

Zhao W, Shahzad K, Jiang M, Graugnard DE, Rodriguez-Zas SL, Luo J, Loor JJ, Hurley WL.

Bioinform Biol Insights. 2013 Jul 14;7:193-216. doi: 10.4137/BBI.S12205. Print 2013.


Brain gene expression changes elicited by peripheral vitellogenin knockdown in the honey bee.

Wheeler MM, Ament SA, Rodriguez-Zas SL, Robinson GE.

Insect Mol Biol. 2013 Oct;22(5):562-73. doi: 10.1111/imb.12043. Epub 2013 Jul 24.


Trans-10, cis 12-Conjugated Linoleic Acid-Induced Milk Fat Depression Is Associated with Inhibition of PPARγ Signaling and Inflammation in Murine Mammary Tissue.

Kadegowda AK, Khan MJ, Piperova LS, Teter BB, Rodriguez-Zas SL, Erdman RA, Loor JJ.

J Lipids. 2013;2013:890343. doi: 10.1155/2013/890343. Epub 2013 May 14.


Transcription factor-microRNA-target gene networks associated with ovarian cancer survival and recurrence.

Delfino KR, Rodriguez-Zas SL.

PLoS One. 2013;8(3):e58608. doi: 10.1371/journal.pone.0058608. Epub 2013 Mar 12.


Feed restriction, but not l-carnitine infusion, alters the liver transcriptome by inhibiting sterol synthesis and mitochondrial oxidative phosphorylation and increasing gluconeogenesis in mid-lactation dairy cows.

Akbar H, Bionaz M, Carlson DB, Rodriguez-Zas SL, Everts RE, Lewin HA, Drackley JK, Loor JJ.

J Dairy Sci. 2013 Apr;96(4):2201-2213. doi: 10.3168/jds.2012-6036. Epub 2013 Feb 22.


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

Kelley KW, O'Connor JC, Lawson MA, Dantzer R, Rodriguez-Zas SL, McCusker RH.

Brain Behav Immun. 2013 Aug;32:63-9. doi: 10.1016/j.bbi.2013.02.003. Epub 2013 Feb 26.


Identification and characterization of alternative exon usage linked glioblastoma multiforme survival.

Sadeque A, Serão NV, Southey BR, Delfino KR, Rodriguez-Zas SL.

BMC Med Genomics. 2012 Dec 4;5:59. doi: 10.1186/1755-8794-5-59.


First survey and functional annotation of prohormone and convertase genes in the pig.

Porter KI, Southey BR, Sweedler JV, Rodriguez-Zas SL.

BMC Genomics. 2012 Nov 15;13:582. doi: 10.1186/1471-2164-13-582.


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

Knox RV, Rodriguez Zas SL, Sloter NL, McNamara KA, Gall TJ, Levis DG, Safranski TJ, Singleton WL.

J Anim Sci. 2013 Jan;91(1):433-45. doi: 10.2527/jas.2012-5189. Epub 2012 Oct 24.


Evaluation of database search programs for accurate detection of neuropeptides in tandem mass spectrometry experiments.

Akhtar MN, Southey BR, Andrén PE, Sweedler JV, Rodriguez-Zas SL.

J Proteome Res. 2012 Dec 7;11(12):6044-55. doi: 10.1021/pr3007123. Epub 2012 Nov 6.


Space allowance for gestating sows in pens: behavior and immunity.

Salak-Johnson JL, DeDecker AE, Horsman MJ, Rodriguez-Zas SL.

J Anim Sci. 2012 Sep;90(9):3232-42. doi: 10.2527/jas.2011-4531. Epub 2012 Aug 7.


New meta-analysis tools reveal common transcriptional regulatory basis for multiple determinants of behavior.

Ament SA, Blatti CA, Alaux C, Wheeler MM, Toth AL, Le Conte Y, Hunt GJ, Guzmán-Novoa E, Degrandi-Hoffman G, Uribe-Rubio JL, Amdam GV, Page RE Jr, Rodriguez-Zas SL, Robinson GE, Sinha S.

Proc Natl Acad Sci U S A. 2012 Jun 26;109(26):E1801-10. doi: 10.1073/pnas.1205283109. Epub 2012 Jun 12.


Level of nutrient intake affects mammary gland gene expression profiles in preweaned Holstein heifers.

Piantoni P, Daniels KM, Everts RE, Rodriguez-Zas SL, Lewin HA, Hurley WL, Akers RM, Loor JJ.

J Dairy Sci. 2012 May;95(5):2550-61. doi: 10.3168/jds.2011-4539.


The transcription factor ultraspiracle influences honey bee social behavior and behavior-related gene expression.

Ament SA, Wang Y, Chen CC, Blatti CA, Hong F, Liang ZS, Negre N, White KP, Rodriguez-Zas SL, Mizzen CA, Sinha S, Zhong S, Robinson GE.

PLoS Genet. 2012;8(3):e1002596. doi: 10.1371/journal.pgen.1002596. Epub 2012 Mar 29.


A novel dynamic impact approach (DIA) for functional analysis of time-course omics studies: validation using the bovine mammary transcriptome.

Bionaz M, Periasamy K, Rodriguez-Zas SL, Hurley WL, Loor JJ.

PLoS One. 2012;7(3):e32455. doi: 10.1371/journal.pone.0032455. Epub 2012 Mar 16.


Old and new stories: revelations from functional analysis of the bovine mammary transcriptome during the lactation cycle.

Bionaz M, Periasamy K, Rodriguez-Zas SL, Everts RE, Lewin HA, Hurley WL, Loor JJ.

PLoS One. 2012;7(3):e33268. doi: 10.1371/journal.pone.0033268. Epub 2012 Mar 12.


Molecular determinants of scouting behavior in honey bees.

Liang ZS, Nguyen T, Mattila HR, Rodriguez-Zas SL, Seeley TD, Robinson GE.

Science. 2012 Mar 9;335(6073):1225-8. doi: 10.1126/science.1213962.


Microarray analysis of natural socially regulated plasticity in circadian rhythms of honey bees.

Rodriguez-Zas SL, Southey BR, Shemesh Y, Rubin EB, Cohen M, Robinson GE, Bloch G.

J Biol Rhythms. 2012 Feb;27(1):12-24. doi: 10.1177/0748730411431404.


Association of the porcine transforming growth factor beta type I receptor (TGFBR1) gene with growth and carcass traits.

Chen K, Hawken R, Flickinger GH, Rodriguez-Zas SL, Rund LA, Wheeler MB, Abrahamsen M, Rutherford MS, Beever JE, Schook LB.

Anim Biotechnol. 2012;23(1):43-63. doi: 10.1080/10495398.2011.630897.


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