Faculty Directory

James Koltes

James Koltes

Assistant Professor

Director Experiment Station

(ANSC)-Animal Science

Phone: 479-575-4855

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Our lab is currently pursuing the following research projects.

1)  Identification of genetic factors associated with reduced heat and fescue stress in cattle.

2) Development of gene expression and epigenetics informatic resources for the livestock research community (Livestock EpiDB).

http://epidb.animalgenome.org/

3) Investigation of mechanisms responsible for improved immune system development in pigs under varying nutritional and management conditions.

ANSC3133: Animal Breeding and Genetics

PhD: Iowa State University

major: Genetics, minor: Statistics

BS: University of Wisconsin- Madison

majors: Dairy Science, Genetics

25. Jia C., Kong X., Koltes JE, Gou X., Yang S., Yan D., Lu S., and Z. Wei. 2016. Gene Co-expression network analysis unraveling transcriptional regulation of high-altitude adaptation of Tibetan pig.  Accepted at PLOS One.

24. Cesar ASM, Regitano LCA, Poleti MD, Andrade SCS, Tizioto PC, Oliveira PSN, Felicio AM, Nascimento ML, Chaves AS, Lanna DPD, Tullio RR, Nassu RT, Koltes JE, Fritz-Waters E, Mourao GB, Zeriotini-Neto A, Reecy JM, and LL Coutinho.  2016. Differences in the skeletal muscle transcriptome profile associated with extreme values of fatty acids content.  2016. BMC Genomics.  7:961.  https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-3306-x

23. Kramer, L.M., J.E. Koltes, E.R. Fritz-Waters, M. Mayes, A. Markey, D.J. Garrick, N.T. Weeks and J.M. Reecy. 2016. Identification of epistatic interactions among fatty acid traits in Angus sired cattle. BMC Genomics. 17:891.  https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5100273/

22. Fleming, D.S., J.E. Koltes, E.R. Fritz-Waters, J.M. Reecy, M.F. Rothschild, C.J. Schmidt, C.M. Ashwell, M.E. Persia and S.J. Lamont.  2016.  Single nucleotide variant discovery of highly inbred Leghorn and Fayoumi chicken breeds using pooled whole genome resequencing data reveals insights into phenotypic differences.  BMC Genomics.  17: 812.  https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-3147-7

21. Buchanan, J.W., J.M. Reecy, D.J. Garrick, J.E. Koltes, M. Saatchi, Q. Duan, D.C. Beitz, and R.G. Mateescu.  2016.  Deriving gene networks from SNP associated with triacylglycerol and phospholipid fatty acid fractions from ribeyes of Angus catle.  In press at Frontiers in Genetics.  7:116. doi: 10.3389/fgene.2016.00116. eCollection 2016. http://journal.frontiersin.org/article/10.3389/fgene.2016.00116/abstract

20. Boddicker, R.L.*, J.E. Koltes*, E.R. Fritz-Waters, L. Koesterke, T. Yin, V. Mani, J.M. Reecy, D. Nettleton, L.H. Baumgard, N.K. Gabler, and J.W. Ross.  2016.  Genome-Wide Methylation Profile Following Prenatal and Postnatal Dietary n-3 Fatty Acid Supplementation in Pigs.  Animal Genetics. Aug 25. doi: 10.1111/age.12468.  http://onlinelibrary.wiley.com/doi/10.1111/age.12468/abstract

19. Weeks N.T., G.R. Luecke, B.M. Groth, M. Kraeva, L. Ma, L.M. Kramer, J.E. Koltes and J.M. Reecy.  2016.  High performance epistasis detection in quantitative trait GWAS.   International Journal of High Performance Computing Applications.  1-16.  DOI: 10.1177/1094342016658110  http://hpc.sagepub.com/content/early/2016/07/12/1094342016658110.full.pdf?ijkey=RZHEcHkE7gCzoBV&keytype=finite                                                                                                                                                    An article was recently published about this work:  https://www.nersc.gov/news-publications/nersc-news/science-news/2016/researchers-use-edison-to-improve-performance-energy-efficiency-of-bioinformatics-application/

18. Fleming, D.S., J.E. Koltes, A.D. Markey, C.J. Schmidt, C.M. Ashwell, M.F. Rothschild, J.M. Reecy, M.E. Persia and S.J. Lamont.  2016. Genomic analysis of Ugandan and Rwandan chicken ecotypes using a 600k genotyping array.  BMC Genomics 17: 407. http://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-2711-5

17. Schroyen, M., Eisley C.J., J.E. Koltes, E. Fritz-Waters, Choi I., Plastow G.S., Guan L.L., Stothard P., Bao H., Kommadath A., Reecy J.M., Lunney J.K., Rowland R.R.R., Dekkers J.C.M., and Tuggle C.K.  2016.  Bioinformatic analyses in early host response to Porcine Reproductive and Respiratory Syndrome virus (PRRS) reveals pathway differences between pigs with alternate genotypes for a major host response QTL. BMC Genomics 17: 196. http://www.biomedcentral.com/1471-2164/17/196

16. Luecke, G.R., N.T. Weeks, B.M. Groth, M. Kraeva, L. Ma, L.M. Kramer, J.E. Koltes and J.M. Reecy.  2015.  Fast epistasis detection in large-scale GWAS for Intel Xeon Phi Clusters.  Trustcom/BigDataSE/ISPA IEEE, 3: 228-235. doi:10.1109/Trustcom.2015.637. http://ieeexplore.ieee.org/xpl/login.jsp?tp=&arnumber=7345653&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Farnumber%3D7345653

 15.  Schroyen, M., J.P. Steibel, J.E. Koltes, I. Choi, N.E. Raney, C. Eisley, E. Fritz-Waters, J.M. Reecy, J.C.M. Dekkers, R.R.R. Rowland, J.K. Lunney, C.W. Ernst, and C.K. Tuggle.  2015. Whole blood microarray analysis of pigs showing extreme phenotypes after a porcine reproductive and respiratory syndrome virus infection.  BMC Genomics 16: 516 http://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-015-1741-8

14.  Cesar, A.S.M., Regitano L.C.A., Koltes J.E., Fritz-Waters E., Gasparin G., Mourao G.B., Oliveira P.S.N., Reecy J.M., and LL Coutinho.  2015.  Putative regulatory factors associated with intramuscular fat content.  PLOS ONE. 10(6):e0128350. doi: 10.1371/journal.pone.0128350. eCollection 2015.  http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4456163/

 13.  Koltes J.E. *, Fritz-Waters E.*, Eisley C.J., Choi I., Bao, H., Kommadath A., Serão N.V.L., Boddicker N., Abrams S.M., Schroyen M., Loyd H., Tuggle C.K., Plastow G.S., Guan L.L.,  Stothard P., Lunney J.K., Liu P., Carpenter S., Rowland R.R.R., J.C.M. Dekkers, and J.M. Reecy.  2015.  Identification of a putative quantitative trait nucleotide in Guanylate Binding Protein 5 for host response to PRRS virus infection. BMC Genomics. 16:412.  http://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-015-1635-9

 12.  Koltes, J.E., D. Kumar, R.S. Kataria, V.L. Cooper, and J.M. Reecy. Transcriptional profiling of PRKG2-null growth plate identifies down-stream targets of PRKG2. 2015. BMC Research Notes. 8:177.  http://bmcresnotes.biomedcentral.com/articles/10.1186/s13104-015-1136-6

 11.  Pilcher, C., Jones C.,Schroyen M., Severin A., Tuggle C.K., Patience J.F., and J.E. Koltes. 2015.  Gene expression profiling of longissimus dorsi and adipose tissue in pigs with differing post-weaning growth rates.  Journal of Animal Science. 93(5): 2134-43.  http://www.ncbi.nlm.nih.gov/pubmed/26020309

 10. Yang, X.*, Koltes, J.E*., Park, C.A., Chen, D., and JM Reecy. Gene co-expression network analysis provides novel insights into important factors involved in myostatin regulation across developmental timepoints in mouse skeletal muscle.  2015. PLoS One. Feb 19: 10(2):e0117607. doi: 10.1371/journal.pone.0117607  http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0117607

 9. Baes C.F., Dolezal M.A., Bapst B., Fritz-Waters E., Koltes J.E., Jansen S., Flury C., Signer-Hasler H., Stricker C., Fernando R., Fries R., Moll J., Garrick D.J., Reecy J.M., and Gredler B. Evaluation of variant identification methods for whole genome sequencing data in dairy cattle. 2014. BMC Genomics. Nov 1; 15:948.  http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-15-948

 8.   Koesterke,L., J.E. Koltes, N.T. Weeks, K. Milfeld, M. Vaughn,J.M. Reecy and D. Stanzione. Discovery of biological networks using an optimized PCIT algorithm on Stampede’s Intel Xeon and Xeon Phi processors. 2014.Concurrency and Computation Practice and Experience.  26: 2178-2190.  http://onlinelibrary.wiley.com/doi/10.1002/cpe.3252/abstract  This paper does not show up on pubmed as it is in a computing journal.  The paper has been cited 4 times. 

 7.  Koesterke,L., J.E. Koltes, N.T. Weeks, K. Milfeld, M. Vaughn,J.M. Reecy and D. Stanzione. Optimizing the PCIT algorithm on Stampede’s Xeon and Xeon Phi processors for faster discovery of biological networks. 2013.  Proceedings of the XSEDE2013 Conference.  ACM. New York, NY, USA. doi>10.1145/2484762.2484794.  This paper does not show up on pubmed as it is in a computing journal.  This paper won an award as best lightning talk at the XSEDE 2013 conference, has been downloaded more than 120 times and cited twice. http://dl.acm.org/citation.cfm?id=2484794

 6. Hu, Z-L*, Koltes, J.E.*, Park, C.A., Fritz, E.R., and J.M. Reecy.  Invited Review: Bioinformatics approaches to livestock animal genomics research. CABI Reviews. 2011, 6: 1-15.  http://www.cabi.org/cabreviews/search/?q=Bioinformatics+approaches+to+livestock+animal+genomics+research

 5.  Lavine, J.A., Raess, P.W., Stapleton, D.S., Rabaglia, M.E., Suhonen, J.I., Schueler, K.L., Koltes, J.E., Dawson, J.A., Yandell, B.S., Samuelson, L.C., Beinfeld, M.C., Belt Davis, D., Hellerstein, M.K., Keller, M.P. and A.D. Attie.  Cholecystokinin is upregulated in obese islets and expands b-cell mass by increasing b-cell survival. Endocrinology. 2010. 151(8): 3577-88.  http://press.endocrine.org/doi/full/10.1210/en.2010-0233

 4.  Koltes, J.E., B.P. Mishra, D. Kumar, R.S. Kataria, L.R. Totir, R.L. Fernando, R. Cobbold, D. Steffen, W. Coppieters, M. Georges, and J.M. Reecy.  A Nonsense mutation in the Kinase domain of cGMP-dependant, type II protein kinase (PRKG2) is the causative mutation for Angus dwarfism. Proceedings of the National Academy of Science. 2009, 106 (46): 19250-5.  http://www.pnas.org/content/106/46/19250.long

 3.  Koltes, J.E., Z-L. Hu, E. Fritz, and J.M. Reecy.  BEAP: BLAST extension and alignment program- a tool for contig construction and analysis of preliminary genome sequence. BMC Research Notes.  2009, 2:11.  http://bmcresnotes.biomedcentral.com/articles/10.1186/1756-0500-2-11

 2.  Alexander, L.J., L.A. Kuehn, T.L.P. Smith, L. Matukumalli, B. Mote, J.E. Koltes, J. Reecy, T.W. Geary, and M.D. MacNeil.  A Limousin specific myostatin allele affects longissimus muscle area and fatty acid profiles in a Wagyu-Limousin F2 population.  J. Animal Science.  2009, 87(5):1576-81.  http://www.ncbi.nlm.nih.gov/pubmed/?term=19213716

 1.  Tshipuliso, N.O.M, L.J. Alexander, T.W. Geary, W.M. Snelling, D.C. Rule, J.E. Koltes, B.E. Mote, and M.D. MacNeil.  Mapping QTL for fatty acid composition that segregate between Japaneese Black and Limousin breeds.  South African Journal of Animal Science.  2008. 38 (2): 126-130.  http://www.sasas.co.za/mapping-qtl-fatty-acid-composition-segregates-between-japanese-black-and-limousin-cattle-breeds

 

SELECTED ABSTRACTS

12. Fritz-Waters E.R., Reecy J.M., and J.E. Koltes. 2017.  Facilitating comparative functional genomics through data reuse with livestock EpiDB.  Proc. of Plant and Animal Genome XXV.  San Diego, CA, USA.

11. Bao H., Kommadath A., Choi I., Reecy J.M., Koltes J.E., Fritz-Waters E., Eisley C, Rowland R.R.R., Tuggle C.K., Dekkers J.C.M., Guan L., Stothard P., Plastow. G.S., and J.K. Lunney.  2016.  Associations between cis-expression quantitative trait loci (cis-eQTL) markers and host response to porcine reproductive and respiratory syndrome virus (PRRS) infection.  Proceedings of the International Veterinary Immunology Symposium.  Gold Coast, Australia.  

10. Koltes, J.E., Reecy J.M., Lyons E., McCarthy, F., Vaughn M., Carson J.P., Fritz-Waters E., and Williams J. 2016.  Bioinformatics resources for animal genomics using CyVerse cyberinfrastructure.  Proceedings of the 35th International Society of Animal Genetics.  Salt Lake City, USA.    http://www.isag.us/docs/Proceedings/ISAG_Proceedings_2016.pdf

9. Fritz-Waters E., Reecy J.M., Vaughn M., Carson J.P., and Koltes, J.E., 2016.  Mining functional genomics and epigenetics data with livestock EpiDB.  Proceedings of the 35th International Society of Animal Genetics.  Salt Lake City, USA.   http://www.isag.us/docs/Proceedings/ISAG_Proceedings_2016.pdf

8. Seibert J.T., Boddicker R.L., Koltes J.E., Nettleton D., Reecy J.M., Baumgard L.H., Ross J.W.  2016. Alterations in CpG Methylation as a result of prenatal heat stress exposure in pigs.   Proceedings of the Society for the Study of Reproduction meeting.  San Diego, CA, USA.

7. Koltes, J.E., Fritz-Waters E., and Reecy J.M.  2016.  Differential expression of small RNAs and mRNAs in bovine skeletal muscle with extreme saturated fatty acid levels.  Proc of Plant and Animal Genome XXIV.  San Diego, CA, USA.  https://pag.confex.com/pag/xxiv/webprogram/Paper21440.html

6. Koltes, J.E., Fritz-Waters E., and Reecy J.M.  2016.  EpiDB: an omics data resource for cattle.  Proc of Plant and Animal Genome XXIV.  San Diego, CA, USA.      https://pag.confex.com/pag/xxiv/webprogram/Paper21766.html

5. Cesar A. S. M., Regitano L. C. A., Lanna D.P.D., Poleti M.D., Koltes, J.E, Reecy J. M., Fritz-Waters, E. R., Kramer L., Garrick D., Mudadu M.A., Tullio R.R., and Coutinho, L. L.  2016.  Expression quantitative trait loci (eQTL) hotspot regions from whole genome analysis of Nellore steers.  Proc of Plant and Animal Genome XXIV.  San Diego, CA, USA.     https://pag.confex.com/pag/xxiv/webprogram/Paper18847.html

4. The FAANG Bioinformatics & Data Analysis Consortium. 2015. Towards common standardized procedures for the Functional Annotation of Animal Genomes (FAANG).  Proceedings of the Gathering on Functional Annotation of Animal Genomes (GO-FAANG) workshop.  Washington D.C., USA.     

3. Koltes, J.E., Fritz-Waters E., and Reecy J.M.  2015.  Livestock EpiDB: A resource for mining functional NGS data.  Proceedings of the Gathering on Functional Annotation of Animal Genomes (GO-FAANG) workshop.  Washington D.C., USA.

2. Schroyen, M., Eisley C.J., Koltes J.E. , Fritz-Waters E., Choi I., Plastow G.S., Guan L.L., Stothard P., Reecy J.M., Lunney J.K., Rowland R.R.R., Dekkers J.C.M., and Tuggle C.K.  2015.  Bioinformatic analyses of early host response to Porcine Reproductive and Respiratory Syndrome (PRRS) virus reveals pathway differences between pigs with alternate genotypes for a major host response QTL. Proc of the 2015 North American PRRS Symposium.  

1. Cesar A. S. M., Regitano L. C. A., Lanna D.P.D., Poleti M.D., Andrade S.C.S., do Nascimento M.L., Chaves A.S., Koltes, J.E, Reecy J. M., Fritz-Waters, E. R., Tullio R.R., and Coutinho, L. L.  2015.  Functional annotation of Logissimus dorsi transcriptome muscle with extreme values of oleic acid content.  Proceedings of the Next Generation Sequencing USA Congress and co-located Single Cell Genomics & Transcriptomics USA Congress. Boston, MA, USA.

 

 

SELECTED INDUSTRY REPORTS 

2. Su H., J.E. Koltes, and D. Garrick. 2016. Evaluating sequence-based customized SNP in addition to GeneSeek LD chip for predicting birth weight in beef cattle.  Iowa State University Animal Industry Report.

1. Flemming, D.S., J.E. Koltes, A.D. Markey, C.J. Schmidt, C.M. Ashwell, M.F. Rothschild, M.E. Persia, J.M. Reecy and S.J. Lamont.  2015.  Genomes of African chickens show evolutionary response to environmental stress.  Iowa State University Animal Industry Report.

 

*Indicates co-first authorship

  • NSF travel fellowship to the Gathering on Functional Annotation of ANimal Genomes (GO-FAANG) workshop (Arkansas 2015)
  • USDA-NIFA Post-Doctoral Fellow (Iowa State 2011 – 2013)
  • NIH-NLM CIBM Traineeship/ Fellow: grant number T15 LM007359 (Wisconsin 2009-2010)
  • Fulbright Fellowship (Belgium 2008)
  • Belgian-American Educational Foundation Research Fellowship (2008)