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United States Department of Agriculture

Agricultural Research Service

Related Topics

Steven G Schroeder (Steve)
Animal Genomics and Improvement Laboratory
General Biological Science

Phone: (301) 504-9431
Fax: (301) 504-8414
Room 117

10300 BALTIMORE AVENUE
ANIMAL GENOMICS AND IMPROVEMENT LAB
BLDG 306 BARC-EAST
BELTSVILLE , MD 207052350

Projects
ENHANCING GENETIC MERIT OF RUMINANTS THROUGH GENOME SELECTION AND ANALYSIS
Appropriated (D)
  Accession Number: 423740
Systems Biology Analyses Comparison of Gene and Protein Expression from Slick and Normal Haired Cattle
Specific Cooperative Agreement (S)
  Accession Number: 427589

Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)
Draft genome sequences of four virulent aeromonas hydrophila strains from catfish aquaculture -
The channel catfish genome sequenc provides insights into the evolution of scale formation in teleosts -
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 sequenc provides insights into the evolution of scale formation in teleosts. Nature Communications. doi:10.1038/ncomms11757.
Exploring the feasibility of using copy number variants as genetic markers through large-scale whole genome sequencing experiments -
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 -
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 -
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 -
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? -
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 -
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 -
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 Reprint Icon -
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 -
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 -
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 -
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 -
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 -
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 -
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 Reprint Icon -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 Reprint Icon -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 Reprint Icon -
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 -
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 -
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 -
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 Reprint Icon -
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 -
Copy number variation detection in cattle reveals potential breed specific differences -
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. 13
Copy number variation of individual cattle genomes using next-generation sequencing Reprint Icon -
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 -
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 -
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 -
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 -
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 -
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 -
A Statistical Approach for Ambiguous Sequence Mappings -
A high-resolution cattle CNV map by population-scale genome sequencing -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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. -
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 -
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 -
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 -
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.
Profiling miRNA Expression in Bovine Tissues by Deep Sequencing -
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.
GENOME-WIDE ASSOCIATION ANALYSIS IDENTIFIES LOCI FOR PRODUCTIVE TRAITS IN JERSEY BREED -
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.
Prediction of total genetic value using genome-wide dense marker in Holstein breed by Bayesian method -
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 -
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 -
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. -
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 -
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.
Last Modified: 5/2/2016
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