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ARS Home Northeast Area Beltsville, Maryland (BARC) Beltsville Agricultural Research Center Animal Genomics and Improvement Laboratory People & Locations







Steven G Schroeder

(Steve)
                        Animal Genomics and Improvement Laboratory

                        




                        
                        Computational Biologist
                        Phone: (301) 504-9431
                        
                        
                        Fax: (301) 504-8414(Employee information on this page comes from the REE Directory. Please contact your front office staff to update the REE Directory.)
                            ProjectsAccelerating Genetic Improvement of Ruminants Through Enhanced Genome Assembly, Annotation, and Selection
                                                    In-House Appropriated
                                                                    (D)Accession Number: 442481**Publications**
                                                (Clicking on the reprint icon
                                                    Reprint Icon
                                                    will take you to the publication reprint.)Fruit and vegetable supplemented diet modulates the pig transcriptome and microbiome after a two-week feeding intervention
                                                        

- (Peer Reviewed Journal)Solano-Aguilar, G.I., Lakshman, S., Shao, J.Y., Chen, C.T., Beshah, E., Dawson, H.D., Vinyard, B.T., Schroeder, S.G., Jang, S., Molokin, A., Urban Jr., J.F. 2021. Fruit and vegetable supplemented diet modulates the pig transcriptome and microbiome after a two-week feeding intervention. Nutrients. 13:4350. https://doi.org/10.3390/nu13124350.The effects of consuming white button mushroom-Agaricus Bisporus-on the brain and liver metabolome using a targeted metabolomic analysis
                                                        

- (Peer Reviewed Journal)Solano-Aguilar, G.I., Lakshman, S., Jang, S., Gupta, R., Molokin, A., Schroeder, S.G., Gillevet, P.M., Urban Jr., J.F. 2021. The effects of consuming white button mushroom Agaricus bisporus on the brain and liver metabolome using a targeted metabolomic analysis. Metabolites. 11(11):779. https://doi.org/10.3390/metabo11110779.Driving Innovation through Data in Agriculture (DIDAg): Best Practices and Case Study

- (Peer Reviewed Journal)Comparative whole genome DNA methylation profiling of cattle tissues reveals global and tissue-specific methylation patterns
                                                        

- (Peer Reviewed Journal)Zhou, Y., Liu, S., Hu, Y., Fang, L., Gao, Y., Xia, H., Schroeder, S.G., Rosen, B.D., Connor, E.E., Li, C., Baldwin, R.L., Cole, J.B., Van Tassell, C.P., Yang, L., Ma, L., Liu, G. 2020. Comparative whole genome DNA methylation profiling of cattle tissues reveals global and tissue-specific methylation patterns. BMC Biology. 18(1):85. https://doi.org/10.1186/s12915-020-00793-5.Comprehensive analyses of 723 transcriptomes enhance biological interpretation and genomic prediction for complex traits in cattle
                                                        

- (Peer Reviewed Journal)Fang, L., Cai, W., Liu, S., Canela-Xandri, O., Gao, Y., Jiang, J., Rawlik, K., Li, B., Schroeder, S.G., Rosen, B.D., Li, C., Sonstegard, T.S., Alexander, L.J., Van Tassell, C.P., Van Raden, P.M., Cole, J.B., Yu, Y., Zhang, S., Tenesa, A., Ma, L., Liu, G. 2019. Comprehensive analyses of 723 transcriptomes enhance biological interpretation and genomic prediction for complex traits in cattle. Genome Research. 30(5):790-801. https://doi.org/10.1101/gr.250704.119.An improved pig reference genome sequence to enable pig genetics and genomics research
                                                        

- (Peer Reviewed Journal)Warr, A., Affara, N., Aken, B., Beiki, H., Bickhart, D.M., Billis, K., Chow, W., Eory, L., Finlayson, H.A., Flicek, P., Giron, C.G., Griffin, D.K., Hall, R., Hannum, G., Hourlier, T., Howe, K., Hume, D.A., Izuogu, O., Kim, K., Koren, S., Liu, H., Manchanda, N., Martin, F.J., Nonneman, D.J., O'Connor, R.E., Phillippy, A.M., Rohrer, G.A., Rosen, B.D., Rund, L.A., Sargent, C.A., Schook, L.B., Schroeder, S.G., Shwartz, A.S., Skinner, B.M., Talbot, R., Tseng, E., Tuggle, C.K., Watson, M., Smith, T.P., Archibald, A.L. 2020. An improved pig reference genome sequence to enable pig genetics and genomics research. GigaScience. 9(6):giaa051. https://doi.org/10.1093/gigascience/giaa051.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.Genetic diversity and phylogenetic relationships of annual and perennial Glycine species
                                                        

- (Peer Reviewed Journal)Hwang, E., Schroeder, S.G., Fickus, E.W., Quigley, C.V., Cregan, P., Song, Q. 2019. Genetic diversity and phylogenetic relationships of annual and perennial Glycine species. G3, Genes/Genomes/Genetics. https://doi.org/10.1534/g3.119.400220.Integrating signals from sperm methylome analysis and genome-wide association study for a better understanding of male fertility in cattle
                                                        

- (Peer Reviewed Journal)Fang, L., Zhou, Y., Liu, S., Jiang, J., Bickhart, D.M., Null, D.J., Li, B., Schroeder, S.G., Rosen, B.D., Cole, J.B., Van Tassell, C.P., Ma, L., Liu, G. 2019. Integrating signals from sperm methylome analysis and genome-wide association study for a better understanding of male fertility in cattle. Epigenomes. 3(2):10. https://doi.org/10.3390/epigenomes3020010.Comparative analyses of sperm DNA methylomes among human, mouse and cattle provide insights into epigenomic evolution and complex traits
                                                        

- (Peer Reviewed Journal)Fang, L., Zhou, Y., Liu, S., Jiang, J., Bickhart, D.M., Null, D.J., Li, B., Schroeder, S.G., Rosen, B.D., Cole, J.B., Van Tassell, C.P., Ma, L., Liu, G. 2019. Comparative analyses of sperm DNA methylomes among human, mouse and cattle provide insights into epigenomic evolution and complex traits. Epigenetics. 14(3):260-276. https://doi.org/10.1080/15592294.2019.1582217.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.Draft genome sequence of fish pathogen Aeromonas bestiarum GA97-22

- (Peer Reviewed Journal)Kumru, S., Tekedar, H., Griffin, M.J., Waldbieser, G.C., Lies, M., Sonstegard, T., Schroeder, S.G., Lawrence, M.L., Karsi, A. 2018. Draft genome sequence of fish pathogen Aeromonas bestiarum GA97-22. Genome Announcements. 6:e00524-18.Genome-wide copy number variant analysis reveals variants associated with 10 diverse production traits in Holstein cattle
                                                        

- (Peer Reviewed Journal)Zhou, Y., Connor, E.E., Wiggans, G.R., Lu, Y., Tempelman, R., Schroeder, S.G., Chen, H., Liu, G. 2018. Genome-wide copy number variant analysis reveals variants associated with 10 diverse production traits in Holstein cattle. BMC Genomics. 19(1):314. https://doi.org/10.1186/s12864-018-4699-5.Comparative whole genome DNA methylation profiling of cattle sperm and somatic tissues reveals striking hypomethylated patterns in sperm
                                                        

- (Peer Reviewed Journal)Zhou, Y., Connor, E.E., Bickhart, D.M., Li, C., Baldwin, R.L., Schroeder, S.G., Rosen, B.D., Yang, L., Van Tassell, C.P., Liu, G. 2018. Comparative whole genome DNA methylation profiling of cattle sperm and somatic tissues reveals striking hypomethylated patterns in sperm. Gigascience. 7(5):1-13. https://doi.org/10.1093/gigascience/giy039.Convergent evolution of slick coat in cattle through truncation mutations in the prolactin receptor
                                                        

- (Peer Reviewed Journal)Porto-Neto, L.R., Bickhart, D.M., Landaeta-Hernandez, A.J., Utsunomiya, Y.T., Morales, M.P., Caban-Jimenez, E., Hansen, P.J., Dikmen, S., Schroeder, S.G., Sun, J., Crespo, E., Amati, N., Cole, J.B., Null, D.J., Garcia, J.F., Reverter, A., Barendse, W., Sonstegard, T.S. 2018. Convergent evolution of slick coat in cattle through truncation mutations in the prolactin receptor. Frontiers in Genetics. 9:57. https://doi.org/10.3389/fgene.2018.00057Genome-wide sequencing and comparative profiling of cattle sperm DNA methylome reveals its hypomethylated patterns

- (Abstract Only)Design and validation of a 90K SNP genotyping assay for the water buffalo (Bubalus bubalis)
                                                        

- (Peer Reviewed Journal)Iamartino, D., Nicolazzi, E.L., Van Tassell, C.P., Reecy, J.M., Fritz-Waters, E.R., Koltes, J.E., Biffani, S., Sonstegard, T., Schroeder, S.G., Ajmone-Marsan, P., Negrini, R., Pasquariello, R., Ramelli, P., Coletta, A., Garcia, J.F., Ali, A., Ramunno, L., Cosenza, G., De Oliveira, D.A., Drummond, M.G., Bastianetto, E., Davassi, A., Pirani, A., Brew, F., Williams, J.L. 2017. Design and validation of a 90K SNP genotyping assay for the water buffalo (Bubalus bubalis). PLoS One. 12(10): e0185220. https://doi.org/10.1371/journal.pone.0185220.Design and validation of a 90K SNP genotyping assay for the Water Buffalo (Bubalus bubalis)

- (Peer Reviewed Journal)Genome-wide copy number variant analysis in Holstein cattle reveals variants associated with 10 production traits including residual feed intake and dry matter intake

- (Abstract Only)Connor, E.E., Zhou, Y., Wiggans, G.R., Lu, Y., Tempelman, R., Schroeder, S.G., Chen, H., Liu, G. 2017. Genome-wide copy number variant analysis in Holstein cattle reveals variants associated with 10 production traits including residual feed intake and dry matter intake. Journal of Dairy Science. 100(Suppl. 2):43 (abstr. M103).Single-molecule sequencing and conformational capture enable de novo mammalian reference genomes

- (Peer Reviewed Journal)Bickhart, D.M., Rosen, B.D., Koren, S., Sayre, B.L., Hastie, A.R., Chan, S., Lee, J., Lam, E.T., Liachko, I., Sullivan, S.T., Burton, J., Huson, H.J., Kelley, C.M., Hutchison, J.L., Zhou, Y., Sun, J., Crisa, A., Ponce De Leon, F.A., Schwartz, J.C., Hammond, J.A., Waldbieser, G.C., Schroeder, S.G., Liu, G., Dunham, M., Shendure, J., Sonstegard, T.S., Phillippy, A.M., Van Tassell, C.P., Smith, T.P. 2017. Single-molecule sequencing and conformational capture enable de novo mammalian reference genomes. Nature Genetics. 49(4):643-650.Genetic characterization of the soybean Nested Association Mapping (NAM) population

- (Peer Reviewed Journal)Song, Q., Yan, L., Quigley, C.V., Jordan, B.D., Fickus, E.W., Schroeder, S.G., Song, B., An, Y., Hyten, D., Nelson, R.L., Rainey, K., Beavis, W.D., Specht, J., Diers, B., Cregan, P. 2017. Genetic characterization of the soybean Nested Association Mapping (NAM) population. The Plant Genome. 10(2). doi: 10.3835/plantgenome2016.10.0109.Draft genome sequences of three Aeromonas hybrophila isolates from catfish and tilapia

- (Peer Reviewed Journal)Tekedar, H.C., Kumru, S., Kalindamar, S., Karsi, A., Waldbieser, G.C., Sonstegard, T.S., Schroeder, S.G., Liles, M.R., Griffin, M.J., Lawrence, M.L. 2017. Draft genome sequences of three Aeromonas hybrophila isolates from catfish and tilapia. Genome Announcements. 5:e01509-e01516.Exploiting long read sequencing technologies to establish high quality highly contiguous pig reference genome assemblies

- (Abstract Only)Warr, A., Hall, R., Kim, K., Tseng, E., Koren, S., Phillippy, A.M., Bickhart, D.M., Rosen, B.D., Schroeder, S.G., Hume, D.A., Talbot, R., Rund, L., Schook, L.B., Chow, W., Howe, K., Nonneman, D.J., Rohrer, G.A., Putnam, N., Green, E., Watson, M., Smith, T.P., Archibald, A.L. 2017. Exploiting long read sequencing technologies to establish high quality highly contiguous pig reference genome assemblies [abstract]. Plant and Animal Genome Conference XX, January 14-18, 2017, San Diego, California. Paper No. 25025.Reduced representation bisulphite sequencing of the cattle genome reveals DNA methylation patterns

- (Peer Reviewed Journal)Zhou, Y., Xu, L., Bickhart, D.M., Hay, E., Schroeder, S.G., Connor, E.E., Leeson, A.J., Sonstegard, T., Van Tassell, C.P., Hong, C., Liu, G. 2016. Reduced representation bisulphite sequencing of the cattle genome reveals DNA methylation patterns. BMC Genomics. 17(1):779.Draft genome sequences of four virulent aeromonas hydrophila strains from catfish aquaculture

- (Peer Reviewed Journal)Tekedar, H., Kumru, S., Karsi, A., Waldbieser, G.C., Sonstegard, T.S., Schroeder, S.G., Liles, M., Griffin, M., Lawrence, M. 2016. Draft genome sequences of four virulent aeromonas hydrophila strains from catfish aquaculture. Genome Announcements. 4:e00860-16.The channel catfish genome sequence provides insights into the evolution of scale formation in teleosts

- (Peer Reviewed Journal)Liu, Z., Liu, S., Yao, J., Bao, L., Jiang, C., Want, R., Sun, L., Li, Y., Zhang, Y., Zhang, J., Zhou, T., Zeng, Q., Fu, Q., Gao, S., Li, N., Koren, S., Jiang, Y., Zimim, A., Xu, P., Phillippy, A., Geng, X., Song, L., Sun, F., Li, C., Want, X., Chen, A., Jin, Y., Yuan, Z., Yang, Y., Tan, S., Peatman, E., Lu, J., Qin, Z., Dunham, R., Li, Z., Sonstegard, T.S., Feng, J., Danzmann, R.G., Schroeder, S.G., Scheffler, B.E., Duke, M.V., Ballard, L.L., Kucuktas, H., Kaltenboeck, L., Liu, H., Armbruster, J., Xie, Y., Kirby, M.A., Tian, Y., Moore Flanagan, M.E., Mu, W., Waldbieser, G.C. 2016. The channel catfish genome sequence provides insights into the evolution of scale formation in teleosts. Nature Communications. 7:11757.Exploring the feasibility of using copy number variants as genetic markers through large-scale whole genome sequencing experiments

- (Abstract Only)Bickhart, D.M., Xu, L., Hutchison, J.L., Cole, J.B., Null, D.J., Schroeder, S.G., Song, J., Garcia, J.F., Sonstegardq, T.S., Van Tassell, C.P., Schnabel, R.D., Taylor, J.F., Lewin, H.A., Liu, G. 2016. Exploring the feasibility of using copy number variants as genetic markers through large-scale whole genome sequencing experiments. Journal of Dairy Science. 99(E-Suppl. 1)/Journal of Animal Science. 94(E-Suppl. 5):142(abstr. 0306).Draft genome sequence of Aeromonas hydrophila TN97-08

- (Peer Reviewed Journal)Tekedar, H., Kumru, S., Karsi, A., Waldbieser, G.C., Sonstegard, T., Schroeder, S.G., Liles, M., Griffin, M., Lawrence, M. 2016. Draft genome sequence of Aeromonas hydrophila TN97-08. Genome Announcements. 4:e00436-16.Whole-genome sequencing reveals the diversity of cattle copy number variations and multicopy genes

- (Peer Reviewed Journal)Bickhart, D.M., Xu, L., Hutchison, J.L., Cole, J.B., Schroeder, S.G., Song, J., Garcia, J., Van Tassell, C.P., Sonstegard, T.S., Schnabel, R.D., Taylor, J.F., Lewin, H.A., Liu, G. 2016. Whole-genome sequencing reveals the diversity of cattle copy number variations and multicopy genes. DNA Research. 23(3):253-62.Improving the goat long-read assembly with optical mapping

- (Abstract Only)Bickhart, D.M., Smith, T.P., Rosen, B.D., Koren	, S., Phillippy, A., Hastie, A.R., Sullivan, S.T., Liachko, I., Burton, J.N., Sayre, B.L., Liu, G., Schroeder, S.G., Sonstegard, T.S., Van Tassell, C.P. 2016. Improving the goat long-read assembly with optical mapping. Plant and Animal Genome Conference Proceedings. San Diego, CA, Jan. 9–13.Do you really know where this SNP goes?

- (Abstract Only)Rohrer, G.A., Nonneman, D., Schroeder, S.G., Chin, J., Koren, S., Phillippy, A., Green, R., Putnam, N., Smith, T.P.L. 2016. Do you really know where this SNP goes? [abstract] Plant and Animal Genome XXIV Conference Proceedings. Abstract #W909.Diversity and population-genetic properties of copy number variations and multicopy genes in cattle

- (Abstract Only)Bickhart, D.M., Xu, L., Hutchison, J.L., Cole, J.B., Null, D.J., Schroeder, S.G., Song, J., Garcia, J., Van Tassell, C.P., Sonstegard, T.S., Schnabel, R.D., Taylor, J.F., Lewin, H.A., Liu, G. 2016. Diversity and population-genetic properties of copy number variations and multicopy genes in cattle [abstract]. USDA NIFA Animal Genome Program PD Meeting, January 8, 2016, San Diego, California.Comparative ruminant genomics highlights segmental duplication and mobile element insertion diversity

- (Abstract Only)Bickhart, D.M., Rosen, B.D., Schroeder, S.G., Van Tassell, C.P. 2016. Comparative ruminant genomics highlights segmental duplication and mobile element insertion diversity. Plant and Animal Genome Conference Proceedings. San Diego, CA, Jan. 9–13, W109.Progress toward a low budget reference grade genome assembly
                                                        

- (Abstract Only)Rosen, B.D., Bickhart, D.M., Koren, S., Hastie, A.R., Schroeder, S.G., Smith, T.P., Sullivan, S.T., Liachko, I., Burton, J.N., Dunham, M.J., Sendure, J., Sayre, B.L., Huson, H.J., Liu, G., Connor, E.E., Sonstegard, T.S., Phillippy, A., Van Tassell, C.P. 2016. Progress toward a low budget reference grade genome assembly. Plant and Animal Genome Conference Proceedings. San Diego, CA, Jan. 9–13, P0612.What's in your next-generation sequence data? An exploration of unmapped DNA and RNA sequence reads from the bovine reference individual

- (Peer Reviewed Journal)Whitacre, L.K., Tizioto, P.C., Kim, J., Sonstegard, T., Schroeder, S.G., Alexander, L.J., Medrano, J.F., Schnabel, R.D., Taylor, J.F., Decker, J.E. 2015.  What's in your next-generation sequence data? An exploration of unmapped DNA and RNA sequence reads from the bovine reference individual. BMC Genomics. 16:1114.Genome sequencing of the extinct Eurasian wild aurochs illuminates the phylogeography and evolution of cattle

- (Peer Reviewed Journal)Park, S.D., Magee, D.A., Mcgettigan, P.A., Teasdale, M.D., Edwards, C.J., Lohan, A.J., Murphy, A., Braud, M., Donoghue, M.T., Liu, Y., Chamberlain, A.T., Rue-Albrecht, K., Schroeder, S.G., Spillane, C., Tai, S., Bradley, D.G., Sonstegard, T.S., Loftus, B.J., Machugh, D.E. 2015. Genome sequencing of the extinct Eurasian wild aurochs illuminates the phylogeography and evolution of cattle. Genome Biology. 16(1):1-15.MicroRNA expression profiles of bovine milk exosomes in response to Staphylococcus aureus infection

- (Peer Reviewed Journal)Sun, J., Aswath, K., Schroeder, S.G., Lippolis, J.D., Reinhardt, T.A., Sonstegard, T.S. 2015. MicroRNA expression profiles of bovine milk exosomes in response to Staphylococcus aureus infection. Biomed Central (BMC) Genomics. 16:806.SNP marker development for linkage map construction, anchoring of the common bean whole genome sequence and genetic research

- (Peer Reviewed Journal)Song, Q., Jia, G., Hyten, D.L., Jenkins, J., Hwang, E., Schroeder, S.G., Schmutz, J., Jackson, S.A., Mcclean, P., Cregan, P. 2015. SNP marker development for linkage map construction, anchoring of the common bean whole genome sequence and genetic research. G3, Genes/Genomes/Genetics. doi: 10.1534/g3.115.020594.Splice variants and regulatory networks associated with host resistance to the intestinal worm Cooperia oncophora in cattle

- (Peer Reviewed Journal)Li, R.W., Wu, S., Li, C., Li, W., Schroeder, S.G. 2015. Splice variants and regulatory networks associated with host resistance to the intestinal worm Cooperia oncophora in cattle. Veterinary Parasitology. DOI:10.1016/j.vetpar.2015.05.010.Complete genome sequence of Aeromonas hydrophila AL06-06

- (Peer Reviewed Journal)Tekedar, H., Karsi, A., Akgul, A., Kalindamar, S., Waldbieser, G.C., Sonstegard, T.S., Schroeder, S.G., Lawrence, M. 2015. Complete genome sequence of Aeromonas hydrophila AL06-06. Genome Announcements. 3(2):e00368-15.RAPTR-SV: a hybrid method for the detection of structural variants
                                                        

- (Peer Reviewed Journal)Bickhart, D.M., Hutchison, J.L., Xu, L., Schnabel, R.D., Taylor, J.F., Reecy, J.M., Schroeder, S.G., Van Tassell, C.P., Sonstegard, T.S., Liu, G. 2015. RAPTR-SV: a hybrid method for the detection of structural variants. Bioinformatics. 31(13):2084-2090.The use of PacBio and Hi-C data in denovo assembly of the goat genome

- (Abstract Only)Bickhart, D.M., Koren, S., Phillippy, A.M., Smith, T.P., Burton, J.N., Llachko, I., Sayre, B.L., Huson, H.J., Schroeder, S.G., Van Tassell, C.P., Sonstegard, T.S. 2015. The use of PacBio and Hi-C data in denovo assembly of the goat genome. Plant and Animal Genome Conference Proceedings. San Diego, CA, January 10–14, W144.Genomic signatures reveal geographic adaption and human selection in cattle

- (Peer Reviewed Journal)Xu, L., Bickhart, D.M., Cole, J.B., Schroeder, S.G., Song, J., Van Tassell, C.P., Sonstegard, T.S., Liu, G. 2014. Genomic signatures reveal geographic adaption and human selection in cattle. Molecular Biology and Evolution. 32(3):711-25.Genome-wide signatures of selection revealed through massive parallel sequencing of DNA across ten turkey populations

- (Peer Reviewed Journal)Aslam, M.L., Bastiaansen, J.W., Elferink, M., Megens, H., Crooijmans, R., Blomberg, L., Van Tassell, C.P., Sonstegard, T.S., Schroeder, S.G., Groenen, M., Long, J.A. 2014. Genome-wide signatures of selection revealed through massive parallel sequencing of DNA across ten turkey populations. Biomed Central (BMC) Genomics. 15:117.The hunt for a functional mutation affecting conformation and calving traits on chromosome 18 in Holstein cattle

- (Proceedings)Cole, J.B., Hutchison, J.L., Null, D.J., Van Raden, P.M., Liu, G., Schroeder, S.G., Smith, T.P., Sonstegard, T.S., Van Tassell, C.P., Bickhart, D.M. 2014. The hunt for a functional mutation affecting conformation and calving traits on chromosome 18 in Holstein cattle. World Congress of Genetics Applied in Livestock Production. Vancouver, Canada, Aug. 17–22. 3 pp.MicroRNA content in milk exosomes as a phenotypic indicator of Staphylococcus aureus infection in the bovine mammary gland

- (Abstract Only)Jiajie, S., Kshama, A., Schroeder, S.G., Reinhardt, T.A., Lippolis, J.D., Sonstegard, T.S. 2014. MicroRNA content in milk exosomes as a phenotypic indicator of Staphylococcus aureus infection in the bovine mammary gland. BARC Poster Day, Poster 61, pp. 73.Computational analysis of bovine milk exosomal miRNAs profiles derived from uninfected and Streptococcus uberis infected mammary gland

- (Abstract Only)Aswath, K., Jiajie, S., Schroeder, S.G., Reinhardt, T.A., Lippolis, J.D., Sonstegard, T.S. 2014. Computational analysis of bovine milk exosomal miRNAs profiles derived from uninfected and Streptococcus uberis infected mammary gland. BARC Poster Day, Poster 62, pp. 74.Population sequencing reveals breed and sub-species specific CNVs in cattle

- (Abstract Only)Bickhart, D.M., Xu, L., Hutchison, J.L., Sonstegard, T.S., Van Tassell, C.P., Schroeder, S.G., Fernando Garcia, J., Taylor, J.F., Schnabel, R.D., Lewin, H.A., Liu, G. 2014. Population sequencing reveals breed and sub-species specific CNVs in cattle. CONFERENCE ON THE BIOLOGY OF GENOMES. Conference on the Biology of Genomes, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY. p199.Bovine exome sequence analysis and targeted SNP genotyping of recessive fertility defects HH2, HH3, and BH1 reveals causative mutation in SMC2 for HH3
                                                        

- (Peer Reviewed Journal)Mc Clure, M., Bickhart, D.M., Null, D.J., Van Raden, P.M., Xu, L., Wiggans, G.R., Liu, G., Schroeder, S.G., Glasscock, J., Armstrong, J., Cole, J.B., Sonstegard, T.S., Van Tassell, C.P. 2014. Bovine exome sequence analysis and targeted SNP genotyping of recessive fertility defects HH2, HH3, and BH1 reveals causative mutation in SMC2 for HH3. PLoS One. 9(3):e92769.Candidate causative mutation on BTA18 associated with calving and conformation traits in Holstein bulls

- (Abstract Only)Cole, J.B., Hutchison, J.L., Null, D.J., Van Raden, P.M., Liu, G., Schroeder, S.G., Sonstegard, T.S., Van Tassell, C.P., Bickhart, D.M. 2014. Candidate causative mutation on BTA18 associated with calving and conformation traits in Holstein bulls. Plant and Animal Genome Conference Proceedings. Plant Animal Genome XXII, San Diego, CA, Jan. 11–15, P1097.The use of population-scale sequencing to identify CNVs impacting productive traits in different cattle breeds

- (Abstract Only)Bickhart, D.M., Xu, L., Hutchison, J.L., Sonstegard, T.S., Van Tassell, C.P., Schroeder, S.G., Garcia, J.F., Taylor, J.F., Schnabel, R.D., Lewin, H., Liu, G. 2014. The use of population-scale sequencing to identify CNVs impacting productive traits in different cattle breeds. Plant and Animal Genome Conference Proceedings. Plant Animal Genome XXII, San Diego, CA, Jan. 11–15, P078.Population sequencing reveals breed and sub-species specific CNVs in cattle

- (Abstract Only)Liu, G., Bickhart, D.M., Xu, L., Hutchison, J.L., Sonstegard, T.S., Van Tassell, C.P., Schroeder, S.G., Garcia, J., Taylor, J.F., Schnabel, R.D., Lewin, H.A. 2014. Population sequencing reveals breed and sub-species specific CNVs in cattle. Meeting Abstract. Advances in Genome Biology & Technology Conference Meeting Abstract. p.58.Implication of lateral genetic transfer in the emergence of Aeromonas hydrophila isolates of epidemic outbreaks in channel catfish

- (Peer Reviewed Journal)Hossain, M., Waldbieser, G.C., Sun, D., Capps, N., Hemstreet, W., Griffin, M.J., Khoo, L., Goodwin, A., Sonstegard, T.S., Schroeder, S.G., Hayden, K., Terhune, J.S., Lies, M.R. 2013. Implication of lateral genetic transfer in the emergence of Aeromonas hydrophila isolates of epidemic outbreaks in channel catfish. PLoS One. 8:e80943.Complete genome sequence of channel catfish epidemic isolate Aeromonas hydrophila ML09-119

- (Peer Reviewed Journal)Tekedar, H., Waldbieser, G.C., Karsi, A., Liles, M., Griffin, M., Vamenta, S., Sonstegard, T.S., Hossain, M., Schroeder, S.G., Khoo, L., Lawrence, M. 2013. Complete genome sequence of channel catfish epidemic isolate Aeromonas hydrophila ML09-119. Genome Announcements. 1(5):e00755-13.Laser capture microdissection coupled with RNA-seq reveals that short cuboidal trophoblast cells of the porcine placenta possess a transcriptome consistent with a migratory cell type

- (Abstract Only)McNeel, A.K., Chen, C.T., Schroeder, S.G., Sonstegard, T.S., Dawson, H.D., Vallet, J.L. 2013. Laser capture microdissection coupled with RNA-seq reveals that short cuboidal trophoblast cells of the porcine placenta possess a transcriptome consistent with a migratory cell type [abstract]. Biology of Reproduction Supplement (46th Annual Meeting of the Society for the Study of Reproduction). pp. 239-240 (Abstract #516).Application of RNA-seq transcriptomic analysis to reproductive physiology of the pig: Insights into differential trophoblast function within the late gestation porcine placenta

- (Review Article)McNeel, A.K., Chen, C.T., Schroeder, S.G., Sonstegard, T.S., Dawson, H.D., Vallet, J.L. 2013. Application of RNA-seq transcriptomic analysis to reproductive physiology of the pig: Insights into differential trophoblast function within the late gestation porcine placenta. In: Rodriquez-Martinez, H., Soede, N.M., Flowers, W.L., editors. Control of Pig Reproduction IX. Leicestershire, UK: Context Products Ltd. pp. 175-183.Fine mapping for Weaver Syndrome in the Brown Swiss breed with the identification of possible casual mutations across NRCAM, PNPLA8, and CTTNBP2 and Developement of a diagnostic SNP haplotype

- (Peer Reviewed Journal)Mcclure, M.C., Kim, E., Bickhart, D.M., Null, D.J., Cooper, T.A., Cole, J.B., Wiggans, G.R., Marsan, P.A., Colli, L., Santus, E., Liu, G., Schroeder, S.G., Matukumalli, L., Van Tassell, C.P., Sonstegard, T.S. 2013. Fine mapping for Weaver Syndrome in the Brown Swiss breed with the identification of possible casual mutations across NRCAM, PNPLA8, and CTTNBP2 and Developement of a diagnostic SNP haplotype. PLoS One. 8(3):e59251.Multi-platform next generation sequencing of a high quality genome assembly for the goat

- (Abstract Only)Sonstegard, T.S., Smith, T.P., Schroeder, S.G., Huson, H.J., Zimin, A., Woodward Greene, M.J., Mujibi, D.F., Mcclure, M.C., Silverstein, J., Van Tassell, C.P., Sayre, B.L. 2013. Multi-platform next generation sequencing of a high quality genome assembly for the goat. Plant Animal Genome XXI, paper W417,  pp. 171.Bos taurus indicus (Nelore) hybrid assembly improvement using PacBio reads

- (Abstract Only)Schroeder, S.G., Zimin, A., Bickhart, D.M., Sonstegard, T.S., Van Tassell, C.P., Garcia, F.J. 2013. Bos taurus indicus (Nelore) hybrid assembly improvement using PacBio reads. Poster  P0523, pp.237.Gene expression analysis of copper tolerance and wood decay in the brown rot fungus Fibroporia radiculosa

- (Peer Reviewed Journal)Tang, J.D., Perkins, A.D., Sonstegard, T.S., Schroeder, S.G., Nicholas, D.D., Diehl, S.V. 2012. Gene expression analysis of copper tolerance and wood decay in the brown rot fungus Fibroporia radiculosa. Applied and Environmental Microbiology. 79(5):1523-33.Identification of a nonsense mutation in CWC15 associated with decreased reproductive efficiency in Jersey cattle

- (Peer Reviewed Journal)Sonstegard, T.S., Cole, J.B., Van Raden, P.M., Van Tassell, C.P., Null, D.J., Schroeder, S.G., Bickhart, D.M., Mcclure, M.C. 2013. Identification of a nonsense mutation in CWC15 associated with decreased reproductive efficiency in Jersey cattle. PLoS One. 8(1):e54872.Bos taurus indicus (Nelore) hybrid assembly improvement using PacBio reads

- (Abstract Only)Copy number variation detection in cattle reveals potential breed specific differences

- (Abstract Only)Bickhart, D.M., Hou, Y., Schroeder, S.G., Alkan, C., Cardone, M., Matukumalli, L.K., Song, J., Schnabel, R.D., Ventura, M., Taylor, J., Garcia, J., Van Tassell, C.P., Sonstegard, T.S., Eichler, E.E., Liu, G. 2012. Copy number variation detection in cattle reveals potential breed specific differences. BARC Poster Day. p. 13Copy number variation of individual cattle genomes using next-generation sequencing

- (Peer Reviewed Journal)Bickhart, D.M., Hou, Y., Schroeder, S.G., Alkan, C., Cardone, M., Matukumalli, L.K., Song, J., Schnabel, R.D., Ventura, M., Taylor, J., Garcia, J., Van Tassell, C.P., Sonstegard, T.S., Eichler, E.E., Liu, G. 2012. Copy number variation of individual cattle genomes using next-generation sequencing. Genome Research. 22(4):778-90.Short read sequencing for Genomic Analysis of the brown rot fungus Fibroporia radiculosa

- (Peer Reviewed Journal)Tang, J.D., Perkins, A.D., Sonstegard, T.S., Schroeder, S.G., Burgess, S.C., Diehl, S.V. 2012. Short read sequencing for Genomic Analysis of the brown rot fungus Fibroporia radiculosa. Applied and Environmental Microbiology. 78(7):2272-81.Cytoskeleton remodling and alterations in smooth muscle contractility in the bovine jejunum during the early stage of Cooperia oncophora infection

- (Peer Reviewed Journal)Li, R.W., Schroeder, S.G. 2011. Cytoskeleton remodling and alterations in smooth muscle contractility in the bovine jejunum during the early stage of Cooperia oncophora infection. Functional and Integrative Genomics. 12(1):35-44.Copy number variation of individual cattle genomes using next-generation sequencing

- (Abstract Only)Bickhart, D.M., Hou, Y., Schroeder, S.G., Alkan, C., Cardone, M., Matukumalli, L.K., Song, J., Schnabel, R.D., Ventura, M., Taylor, J.F., Garcia, J., Van Tassell, C.P., Sonstegard, T.S., Eichler, E.E., Liu, G. 2012. Copy number variation of individual cattle genomes using next-generation sequencing. Plant and Animal Genome Conference. p. 549.Individualized cattle copy number and segmental duplication maps using next generation sequencing

- (Abstract Only)Bickhart, D.M., Hou, Y., Schroeder, S.G., Alkan, C., Cardone, M., Matukumalli, L., Song, J., Schnabel, R.D., Ventura, M., Taylor, J.F., Garcia, J., Eichler, E.E., Sonstegard, T.S., Van Tassell, C.P., Liu, G. 2011. Individualized cattle copy number and segmental duplication maps using next generation sequencing. Meeting Abstract. No. 8.A high-resolution cattle CNV map by population-scale genome sequencing

- (Abstract Only)Bickhart, D.M., Hou, Y., Schroeder, S.G., Alkan, C., Cardone, M.F., Matukumalli, L.K., Schnabel, R.D., Ventura, M., Taylor, J.F., Eichler, E.E., Sonstegard, T.S., Van Tassell, C.P., Liu, G. 2011. A high-resolution cattle CNV map by population-scale genome sequencing [abstract]. Gordon Research Conference. No. 48.Discovery of Genetic Variation that Enhances Improvement of Dairy Production and Health in Cattle and Buffalos

- (Abstract Only)A Statistical Approach for Ambiguous Sequence Mappings

- (Abstract Only)A high-resolution cattle CNV map by population-scale genome sequencing

- (Abstract Only)Bickhart, D.M., Hou, Y., Liu, G., Schroeder, S.G., Can, A., Maria, C., Matukumalli, L., Song, J., Schnabel, R., Ventura, M., Taylor, J., Eichler, E., Sonstegard, T.S., Van Tassell, C.P., Illumina Bovine Hd, C. 2011. A high-resolution cattle CNV map by population-scale genome sequencing. BARC Poster Day [abstract].  No. 5.A high-resolution cattle CNV map by population-scale genome sequencing

- (Abstract Only)Bickhart, D.M., Hou, Y., Schroeder, S.G., Alkan, C., Cardone, M.F., Matukumalli, L.K., Schnabel, R.D., Ventura, M., Taylor, J.F., Eichler, E.E., Sonstegard, T.S., Van Tassell, C.P., Liu, G. 2011. A high-resolution cattle CNV map by population-scale genome sequencing. CONFERENCE ON THE BIOLOGY OF GENOMES [abstract]. p. 32.An atlas of bovine gene expression reveals novel distinctive tissue characteristics and evidence for improving genome annotation

- (Peer Reviewed Journal)Harhay, G.P., Smith, T.P.L., Alexander, L.J., Haudenschild, C.D., Keele, J.W., Matukumalli, L.K., Schroeder, S.G., Van Tassell, C.P., Gresham, C.R., Bridges, S.M., Burgess, S.C., Sonstegard, T.S. 2010. An atlas of bovine gene expression reveals novel distinctive tissue characteristics and evidence for improving genome annotation. Genome Biology [online serial]. 11:R102.Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo) genome assembly and analysis

- (Peer Reviewed Journal)Dalloul, R.A., Long, J.A., Zimin, A.V., Reed, K.M., Blomberg, L., Van Tassell, C.P., Schroeder, S.G., Sonstegard, T.S., Aslam, L., Beal, K., Biedler, J., Burt, D.W., Crasta, O., Crooijmans, R.P., Cooper, K., Coulombe, R.A., De, S., Delany, M.E., Dodgson, J.B., Dong, J.J., Evans, C., Flicek, P., Florea, L., Folkerts, O., Groenen, M.A., Harkins, T.T., Herrero, J., Hoffmann, S., Megens, H., Jiang, A., Jong, P., Kaiser, P., Kim, H., Kim, K., Kim, S., Langenberger, D., Lee, M., Lee, T., Mane, S., Marcais, G., Marz, M., Mcelroy, A.P., Modise, T., Nefedov, M., Notredame, C., Paton, I.R., Payne, W.S., Pertea, G., Prickett, D., Puiu, D., Qioa, D., Raineri, E., Salzberg, S.L., Schatz, M.C., Scheuring, C., Schmidt, C.J., Schroeder, S.G., Smith, E.J., Smith, J., Sonstegard, T.S., Stadler, P.F., Tafer, H., Tu, Z., Van Tassell, C.P., Vilella, A.J., Williams, K., Yorke, J.A., Zhang, L., Zhang, H., Zhang, Z., Zhang, Y. 2010. Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo) genome assembly and analysis. PLoS Biology. 8(9):e1000475.Sequence analysis for a de novo genome assembly of Bos indicus (Nelore) cattle

- (Abstract Only)Sonstegard, T.S., Schroeder, S.G., Smith, T.P., Zimin, A., Matukumalli, L.K., Ajmone-Marsan, P., Wiedmann, R.T., Negrini, R., Yorke, J., Van Tassell, C.P., Garcia, J.F. 2010. Sequence analysis for a de novo genome assembly of Bos indicus (Nelore) cattle. Animal Genetics International Conference Proceedings.Metagenomics detects functional shifts in the bovine rumen microbiota in response to propionate intake

- (Book / Chapter)Sparks, M., Huang, Y., Baldwin, R.L., Connor, E.E., Li, C., Sonstegard, T.S., Schroeder, S.G., Li, R.W. 2011. Metagenomics detects functional shifts in the bovine rumen microbiota in response to propionate intake. In: Li, R.W. editor. Metagenomics and its Applications in Agriculture. New York, NY: Nova Science Publishers. p. 165-183.WHOLE GENOME ASSOCIATION ANALYSIS IDENTIFIES SUSCEPTIBILITY ALLELES FOR PARASITIC INFECTION IN BOS TAURUS CATTLE

- (Abstract Only)Sonstegard, T.S., Silva, M.V., Kim, E., Matukumalli, L.K., Schroeder, S.G., Gasbarre, L.C., Van Tassell, C.P. 2010. Whole genome association analysis identifies susceptibility alleles for parasitic infection in Bos taurus cattle. International Symposium on Animal Genomics for Animal Health.High Throughput Sequence Analysis for Disease Resistance in Maize

- (Abstract Only)Gautam, D., Johnston, I., Bhowmik, T., Ankala, A., Sonstegard, T.S., Schroeder, S.G., Wilkinson, J., Perkins, A.D. 2010. High Throughput Sequence Analysis for Disease Resistance in Maize. International Conference on Bioinformatics and Computational Biology.A Digital Gene Expression-Based Bovine Gene Atlas Evaluating 92 Adult, Juvenile and Fetal Cattle Tissues

- (Abstract Only)Harhay, G.P., Alexander, L.J., Smith, T.P.L., Matukumalli, L.K., Schroeder, S.G., Sonstegard, T.S. 2010. A Digital Gene Expression-Based Bovine Gene Atlas Evaluating 92 Adult, Juvenile and Fetal Cattle Tissues [abstract]. In: Proceedings of the Advances in Genome Biology & Technology Conference, February 24-27, 2010, Marco Island, Florida. p. 67.Information Theoretical Analysis of a Bovine Gene Atlas Reveals Chromosomal Regions with Tissue Specific Gene Expression.

- (Abstract Only)Sonstegard, T.S., Harhay, G.P., Alexander, L.J., Schroeder, S.G., Keele, J.W., Matukumalli, L., Bridges, S., Burgess, S., Van Tassell, C.P., Smith, T.P. 2010. Information Theoretical Analysis of a Bovine Gene Atlas Reveals Chromosomal Regions with Tissue Specific Gene Expression. Plant and Animal Genome VX Conference Abstracts.Análise de Associação por Todo o Genoma para Identificar Locos Relacionados ao Lucro Líquido, à Vida Produtiva e ao Escore de Células Somáticas na raça Jersey1

- (Peer Reviewed Journal)Silva, M., Van Raden, P.M., Van Tassell, C.P., Sonstegard, T.S., Matukumalli, L.K., Schroeder, S.G., Kim, E., Wiggans, G.R. 2009. Análise de Associação por Todo o Genoma para Identificar Locos Relacionados ao Lucro Líquido, à Vida Produtiva e ao Escore de Células Somáticas na raça Jersey1. Brazilian Animal Science Society.WHOLE GENOME-WIDE SNP ASSOCIATION: IDENTIFICATION OF SUSCEPTIBILITY ALLELES FOR PARASITIC INFECTION

- (Abstract Only)Silva, M.V., Van Tassell, C.P., Sonstegard, T.S., Matukumalli, L.K., Schroeder, S.G., Kim, E., Gasbarre, L.C. 2009. WHOLE GENOME-WIDE SNP ASSOCIATION: IDENTIFICATION OF SUSCEPTIBILITY ALLELES FOR PARASITIC INFECTION. BARC Poster Day.Accelerating genetic improvement with SNP chips and DNA sequencing

- (Abstract Only)Van Tassell, C.P., Van Raden, P.M., Wiggans, G.R., Matukumalli, L.K., Schroeder, S.G., O'Connell, J., Schnabel, R.D., Taylor, J.F., Pollak, E.J., Munson, M., Bailey, D., Sonstegard, T.S. 2009. Accelerating genetic improvement with SNP chips and DNA sequencing. Joint Abstracts of the American Dairy Science and Society of Animal Science.GENOME-WIDE ASSOCIATION ANALYSIS IDENTIFIES LOCI FOR PRODUCTIVE TRAITS IN JERSEY BREED

- (Abstract Only)Silva, M.V., Van Raden, P.M., Van Tassell, C.P., Sonstegard, T.S., Matukumalli, L.K., Schroeder, S.G., Wiggans, G.R. 2009. GENOME-WIDE ASSOCIATION ANALYSIS IDENTIFIES LOCI FOR PRODUCTIVE TRAITS IN JERSEY BREED. Plant and Animal Genome Conference.Profiling miRNA Expression in Bovine Tissues by Deep Sequencing

- (Abstract Only)Matukumalli, L.K., Alexander, L.J., Mcdaneld, T.G., Smith, T.P., Schroeder, S.G., Sonstegard, T.S., Van Tassell, C.P. 2009. Profiling miRNA Expression in Bovine Tissues by Deep Sequencing. Plant and Animal Genome Conference.Prediction of total genetic value using genome-wide dense marker in Holstein breed by Bayesian method

- (Abstract Only)Silva, M.V., Van Tassell, C.P., Sonstegard, T.S., Matkumalli, L., Schroeder, S.G., Van Raden, P.M., Wiggans, G.R. 2008. Prediction of total genetic value using genome-wide dense marker in Holstein breed by Bayesian method. Congress of the Brazilian Animal Breeding Society.A WHOLE-GENOME ASSOCIATION STUDY OF MAJOR DETERMINANTS FOR PARASITIC INFECTION IN ANGUS BREED

- (Abstract Only)Da Silva, M., Sonstegard, T.S., Van Tassell, C.P., Matukumalli, L.K., Schroeder, S.G., Gasbarre, L.C. 2008. A WHOLE-GENOME ASSOCIATION STUDY OF MAJOR DETERMINANTS FOR PARASITIC INFECTION IN ANGUS BREED. Animal Genetics International Conference Proceedings.MAPPING QUANTITATIVE TRAIT LOCI ASSOCIATED WITH PARASITIC INFECTION USING 50K SNP CHIP IN ANGUS BREED

- (Abstract Only)Silva, M.V., Van Tassell, C.P., Sonstegard, T.S., Matukumalli, L.K., Schroeder, S.G., Gasbarre, L.C. 2008. MAPPING QUANTITATIVE TRAIT LOCI ASSOCIATED WITH PARASITIC INFECTION USING 50K SNP CHIP IN ANGUS BREED. BARC Poster Day.Applied Bovine Genomics: Chipping away at the genetics underlying disease traits.

- (Abstract Only)Sonstegard, T.S., Vanraden, P., Wiggans, G., Schnabel, S., Liu, G., Matukumalli, L.K., Silva, M.V., Mckay, S., Schroeder, S.G., Gasbarre, L.C., Taylor, J.F., Van Tassell, C.P. 2008. Applied Bovine Genomics: Chipping away at the genetics underlying disease traits.. International Symposium of Animal Functional Genomics.Description and analysis of the Bovine Gene Atlas - An extensive compendium of bovine transcript profiles

- (Abstract Only)Harhay, G.P., Keele, J.W., Smith, T.P., Alexander, L.J., Matukumalli, L.K., Schroeder, S.G., Liu, G., Van Tassell, C.P., Sonstegard, T.S. 2008. Description and analysis of the Bovine Gene Atlas - An extensive compendium of bovine transcript profiles (abstract).  Plant and Animal Genome XVI Conference.  Poster No. P516.


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