Curtis P van Tassell

Summary

Affiliation: Agricultural Research Service
Country: USA

Publications

  1. pmc Imputation of microsatellite alleles from dense SNP genotypes for parental verification
    Matthew McClure
    Bovine Functional Genomics Lab, United States Department of Agriculture, Agriculture Research Service Beltsville, MD, USA
    Front Genet 3:140. 2012
  2. pmc Effect of sample stratification on dairy GWAS results
    Li Ma
    Department of Animal Science, University of Minnesota, St Paul, Minnesota, USA
    BMC Genomics 13:536. 2012
  3. pmc Whole genome SNP discovery and analysis of genetic diversity in Turkey (Meleagris gallopavo)
    Muhammad L Aslam
    Animal Breeding and Genomics Centre, Wageningen University, De Elst 1, 6708WD Wageningen, The Netherlands
    BMC Genomics 13:391. 2012
  4. pmc Genome-wide association study for birth weight in Nellore cattle points to previously described orthologous genes affecting human and bovine height
    Yuri T Utsunomiya
    Faculdade de Medicina Veterinaria de Aracatuba, Univ Estadual Paulista, Aracatuba, Sao Paulo, Brazil
    BMC Genet 14:52. 2013
  5. ncbi request reprint SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries
    Curtis P van Tassell
    Bovine Functional Genomics Laboratory, United States Department of Agriculture, Agricultural Research Service, 10300 Baltimore Avenue, Beltsville, Maryland 20705, USA
    Nat Methods 5:247-52. 2008
  6. pmc An atlas of bovine gene expression reveals novel distinctive tissue characteristics and evidence for improving genome annotation
    Gregory P Harhay
    USDA ARS US Meat Animal Research Center, State Spur 18 D, Clay Center, NE 68901, USA
    Genome Biol 11:R102. 2010
  7. pmc A whole-genome assembly of the domestic cow, Bos taurus
    Aleksey V Zimin
    Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742, USA
    Genome Biol 10:R42. 2009
  8. pmc Prevalence of the prion protein gene E211K variant in U.S. cattle
    Michael P Heaton
    USDA, ARS, U, S, Meat Animal Research Center USMARC, State Spur 18D, P O Box 166, Clay Center, NE 68933, USA
    BMC Vet Res 4:25. 2008
  9. pmc Genomic characteristics of cattle copy number variations
    Yali Hou
    Bovine Functional Genomics Laboratory, ANRI, USDA ARS, Beltsville, Maryland 20705, USA
    BMC Genomics 12:127. 2011
  10. pmc Unlocking the bovine genome
    Ross L Tellam
    CSIRO Livestock Industries, St Lucia, QLD, Australia
    BMC Genomics 10:193. 2009

Collaborators

Detail Information

Publications37

  1. pmc Imputation of microsatellite alleles from dense SNP genotypes for parental verification
    Matthew McClure
    Bovine Functional Genomics Lab, United States Department of Agriculture, Agriculture Research Service Beltsville, MD, USA
    Front Genet 3:140. 2012
    ..This approach may be applicable to additional cattle breeds and other species that wish to migrate from MS- to SNP-based parental verification...
  2. pmc Effect of sample stratification on dairy GWAS results
    Li Ma
    Department of Animal Science, University of Minnesota, St Paul, Minnesota, USA
    BMC Genomics 13:536. 2012
    ....
  3. pmc Whole genome SNP discovery and analysis of genetic diversity in Turkey (Meleagris gallopavo)
    Muhammad L Aslam
    Animal Breeding and Genomics Centre, Wageningen University, De Elst 1, 6708WD Wageningen, The Netherlands
    BMC Genomics 13:391. 2012
    ..Genomic selection requires a large number of genetic markers such as e.g. single nucleotide polymorphisms (SNPs) the most abundant source of genetic variation within the genome...
  4. pmc Genome-wide association study for birth weight in Nellore cattle points to previously described orthologous genes affecting human and bovine height
    Yuri T Utsunomiya
    Faculdade de Medicina Veterinaria de Aracatuba, Univ Estadual Paulista, Aracatuba, Sao Paulo, Brazil
    BMC Genet 14:52. 2013
    ....
  5. ncbi request reprint SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries
    Curtis P van Tassell
    Bovine Functional Genomics Laboratory, United States Department of Agriculture, Agricultural Research Service, 10300 Baltimore Avenue, Beltsville, Maryland 20705, USA
    Nat Methods 5:247-52. 2008
    ..67. This approach for simultaneous de novo discovery of high-quality SNPs and population characterization of allele frequencies may be applied to any species with at least a partially sequenced genome...
  6. pmc An atlas of bovine gene expression reveals novel distinctive tissue characteristics and evidence for improving genome annotation
    Gregory P Harhay
    USDA ARS US Meat Animal Research Center, State Spur 18 D, Clay Center, NE 68901, USA
    Genome Biol 11:R102. 2010
    ..We present an atlas of RNA abundance for 92 adult, juvenile and fetal cattle tissues and three cattle cell lines...
  7. pmc A whole-genome assembly of the domestic cow, Bos taurus
    Aleksey V Zimin
    Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742, USA
    Genome Biol 10:R42. 2009
    ..The genome of the domestic cow, Bos taurus, was sequenced using a mixture of hierarchical and whole-genome shotgun sequencing methods...
  8. pmc Prevalence of the prion protein gene E211K variant in U.S. cattle
    Michael P Heaton
    USDA, ARS, U, S, Meat Animal Research Center USMARC, State Spur 18D, P O Box 166, Clay Center, NE 68933, USA
    BMC Vet Res 4:25. 2008
    ..S. cattle...
  9. pmc Genomic characteristics of cattle copy number variations
    Yali Hou
    Bovine Functional Genomics Laboratory, ANRI, USDA ARS, Beltsville, Maryland 20705, USA
    BMC Genomics 12:127. 2011
    ..In the dairy industry, a large quantity of SNP genotyping results are becoming available and can be used for CNV discovery to understand and accelerate genetic improvement for complex traits...
  10. pmc Unlocking the bovine genome
    Ross L Tellam
    CSIRO Livestock Industries, St Lucia, QLD, Australia
    BMC Genomics 10:193. 2009
    ....
  11. pmc High-resolution haplotype block structure in the cattle genome
    Rafael Villa-Angulo
    Department of Bioinformatics and Computational Biology, George Mason University, VA, USA
    BMC Genet 10:19. 2009
    ..6 Mb with an average density of approximately one SNP per 4 kb, and characterized the linkage disequilibrium (LD) and haplotype block structure within individual breeds and groups of breeds in relation to their geographic origin and use...
  12. ncbi request reprint Discovery and profiling of bovine microRNAs from immune-related and embryonic tissues
    Luiz L Coutinho
    United States Department of Agriculture, Agricultural Research Center, Beltsville Area Research Center, Beltsville, Maryland 20705, USA
    Physiol Genomics 29:35-43. 2007
    ..These results support the premise that species differences in regulation of gene expression by miR occur primarily at the level of expression and processing...
  13. pmc Effects of increased milking frequency on gene expression in the bovine mammary gland
    Erin E Connor
    Bovine Functional Genomics Laboratory, USDA ARS, Beltsville Agricultural Research Center, 10300 Baltimore Avenue, Beltsville, MD 20705, USA
    BMC Genomics 9:362. 2008
    ....
  14. doi request reprint Comparative transcriptome analysis of in vivo- and in vitro-produced porcine blastocysts by small amplified RNA-serial analysis of gene expression (SAR-SAGE)
    Jeremy R Miles
    USDA ARS, Biotechnology and Germplasm Laboratory, Beltsville, Maryland 20705, USA
    Mol Reprod Dev 75:976-88. 2008
    ....
  15. pmc SNP-PHAGE--High throughput SNP discovery pipeline
    Lakshmi K Matukumalli
    US Department of Agriculture, ARS, Beltsville Agricultural Research Center, Bovine Functional Genomics Laboratory, Beltsville, MD 20705, USA
    BMC Bioinformatics 7:468. 2006
    ..Although these tasks are routinely performed by several groups, an integrated open source SNP discovery pipeline that can be easily adapted by new groups interested in SNP marker development is currently unavailable...
  16. pmc Copy number variation of individual cattle genomes using next-generation sequencing
    Derek M Bickhart
    USDA ARS, ANRI, Bovine Functional Genomics Laboratory, Beltsville, Maryland 20705, USA
    Genome Res 22:778-90. 2012
    ..By providing the first individualized cattle CNV and segmental duplication maps and genome-wide gene copy number estimates, we enable future CNV studies into highly duplicated regions in the cattle genome...
  17. doi request reprint Identification of conserved regulatory elements in mammalian promoter regions: a case study using the PCK1 promoter
    George E Liu
    Bovine Functional Genomics Laboratory, Beltsville Agricultural Research Center, Beltsville, MD 20705, USA
    Genomics Proteomics Bioinformatics 6:129-43. 2008
    ..Our full set of TFBS predictions is freely available at http://bfgl.anri.barc.usda.gov/tfbsConsSites...
  18. pmc A soybean transcript map: gene distribution, haplotype and single-nucleotide polymorphism analysis
    Ik Young Choi
    Soybean Genomics and Improvement Laboratory, USDA, ARS, Beltsville, Maryland 20705, USA
    Genetics 176:685-96. 2007
    ....
  19. pmc Fine mapping of copy number variations on two cattle genome assemblies using high density SNP array
    Yali Hou
    Bovine Functional Genomics Laboratory, ANRI, USDA ARS, BARC East, Beltsville, MD 20705, USA
    BMC Genomics 13:376. 2012
    ..In our previous study using the low density BovineSNP50 array, we reported a copy number variation (CNV) analysis on Btau_4.0 with 521 animals of 21 cattle breeds, yielding 682 CNV regions with a total length of 139.8 megabases...
  20. doi request reprint Genomic regions showing copy number variations associate with resistance or susceptibility to gastrointestinal nematodes in Angus cattle
    Yali Hou
    Bovine Functional Genomics Laboratory, ANRI, USDA ARS, Building 200, Room 124B, BARC East, Beltsville, MD 20705, USA
    Funct Integr Genomics 12:81-92. 2012
    ..Network analyses indicated that the PS-specific genes were particularly enriched for inflammatory response, immune cell trafficking, metabolic disease, cell cycle, and cellular organization and movement...
  21. ncbi request reprint Identification of estrogen-responsive genes in the parenchyma and fat pad of the bovine mammary gland by microarray analysis
    Robert W Li
    Bovine Functional Genomics Laboratory, United States Department of Agriculture Agricultural Research Service, Beltsville, Maryland 20705, USA
    Physiol Genomics 27:42-53. 2006
    ..The distinctive expression patterns regulated by estrogen in parenchyma and fat pad shed light on the need for both tissues to obtain normal mammary development...
  22. pmc Effect of artificial selection on runs of homozygosity in u.s. Holstein cattle
    Eui Soo Kim
    Bovine Functional Genomics Laboratory, USDA ARS, Beltsville, Maryland, United States of America
    PLoS ONE 8:e80813. 2013
    ..Many of these selection signatures corresponded to quantitative trait loci for milk, fat, and protein yield previously found in contemporary Holsteins. ..
  23. pmc Identification of a nonsense mutation in CWC15 associated with decreased reproductive efficiency in Jersey cattle
    Tad S Sonstegard
    Bovine Functional Genomics, United States Department of Agriculture, Agricultural Research Service, Beltsville, Maryland, USA
    PLoS ONE 8:e54872. 2013
    ..Whole-genome resequencing proved to be a powerful strategy to rapidly identify a previously mapped deleterious mutation in a known carrier of a recessive lethal allele...
  24. ncbi request reprint Serial analysis of gene expression during elongation of the peri-implantation porcine trophectoderm (conceptus)
    Le Ann Blomberg
    Biotechnology and Germplasm Laboratory, United States Department of Agriculture Agricultural Research Service, Beltsville, Maryland 20705, USA
    Physiol Genomics 20:188-94. 2005
    ..These results validate the utility of SAGE in the pig and establish an initial model linking gene expression profiles at the pathway level with phenotypic progression from ovoid to filamentous stages of conceptus development...
  25. pmc Genome-wide association analysis of thirty one production, health, reproduction and body conformation traits in contemporary U.S. Holstein cows
    John B Cole
    Animal Improvement Programs Laboratory, Agricultural Research Service, USDA, Beltsville, Maryland, USA
    BMC Genomics 12:408. 2011
    ..Here, we report results of a genome-wide analysis of predicted transmitting ability (PTA) of 31 production, health, reproduction and body conformation traits in contemporary Holstein cows...
  26. ncbi request reprint Transcriptome profiling of the tubular porcine conceptus identifies the differential regulation of growth and developmentally associated genes
    Le Ann Blomberg
    Biotechnology and Germplasm Laboratory, USDA Agricultural Research Service, Beltsville, MD 20705, USA
    Mol Reprod Dev 73:1491-502. 2006
    ..The function(s) of these factors and potential modulation by estrogen clearly needs to be elucidated to understand their physiological role in normal conceptus development...
  27. ncbi request reprint A genome-wide survey reveals a deletion polymorphism associated with resistance to gastrointestinal nematodes in Angus cattle
    Lingyang Xu
    GEL Bovine Functional Genomics Laboratory, BARC, USDA ARS, Building 306, Room 111, BARC East, Beltsville, MD, 20705, USA
    Funct Integr Genomics 14:333-9. 2014
    ..As this CNV co-segregates with linked SNPs and associated genes, we suspect that it could contribute to the detected variations in gene expression and thus differences in host parasite resistance. ..
  28. pmc Genomic divergences among cattle, dog and human estimated from large-scale alignments of genomic sequences
    George E Liu
    USDA, ARS, ANRI, Bovine Functional Genomics Laboratory, Beltsville Agricultural Research Center BARC East, 10300 Baltimore Avenue, Beltsville, MD 20705, USA
    BMC Genomics 7:140. 2006
    ..Approximately 11 Mb of finished high quality genomic sequences were sampled from cattle, dog and human to estimate genomic divergences and their regional variation among these lineages...
  29. pmc Application of machine learning in SNP discovery
    Lakshmi K Matukumalli
    Beltsville Agricultural Research Center, Bovine Functional Genomics Laboratory, US Department of Agriculture, ARS, Beltsville, MD 20705, USA
    BMC Bioinformatics 7:4. 2006
    ..ML methods have also been successfully applied to other bioinformatics problems in predicting genes, promoters, transcription factor binding sites and protein structures...
  30. ncbi request reprint EST-PAGE--managing and analyzing EST data
    Lakshmi K Matukumalli
    US Department of Agriculture, ARS, Beltsville Agricultural Research Center, Bovine Functional Genomics Laboratory, Beltsville, MD 20705, USA
    Bioinformatics 20:286-8. 2004
    ....
  31. ncbi request reprint Local inflammation as a possible mechanism of resistance to gastrointestinal nematodes in Angus heifers
    Robert W Li
    Bovine Functional Genomics Laboratory, USDA ARS, Beltsville, MD 20705, USA
    Vet Parasitol 145:100-7. 2007
    ..These data indicate that resistant animals can better maintain inflammatory responses at the site of infection, suggesting a possible novel mechanism of resistance...
  32. pmc Bovine exome sequence analysis and targeted SNP genotyping of recessive fertility defects BH1, HH2, and HH3 reveal a putative causative mutation in SMC2 for HH3
    Matthew C McClure
    United States Department of Agriculture, Agriculture Research Service, Bovine Functional Genomics Laboratory, Beltsville, Maryland, United States of America
    PLoS ONE 9:e92769. 2014
    ..The absence of concordant variations for HH2 or BH1 suggests either the underlying causative mutations lie within a non-exomic region or in exome regions not covered by the capture array. ..
  33. ncbi request reprint Bovine genomics update: making a cow jump over the moon
    Tad S Sonstegard
    USDA, ARS, Bovine Functional Genomics Laboratory, Beltsville Agricultural Research Center BARC East, Beltsville, MD 20705, USA
    Genet Res 84:3-9. 2004
    ....
  34. ncbi request reprint Expressed sequence tag analysis of Eimeria-stimulated intestinal intraepithelial lymphocytes in chickens
    Wongi Min
    Animal Parasitic Diseases Laboratory, Animal and Natural Resources Institute, US Dept of Agriculture, Beltsville, MD 20705, USA
    Mol Biotechnol 30:143-50. 2005
    ..This EST library will provide a valuable resource for profiling global gene expression in normal and pathogen-infected chickens and identifying additional unique immune-related genes...
  35. ncbi request reprint Serial analysis of gene expression in turkey sperm storage tubules in the presence and absence of resident sperm
    Ezhou L Long
    Biotechnology and Germplasm Laboratory, Animal and Natural Resources Institute, USDA ARS, Beltsville, Maryland 20705, USA
    Biol Reprod 69:469-74. 2003
    ..The bioinformatics and experimental procedures employed to clone turkey avidin and confirm its differential expression represent a useful paradigm for analyzing SAGE tag data from relatively uncharacterized model systems...
  36. ncbi request reprint Analysis of bovine mammary gland EST and functional annotation of the Bos taurus gene index
    Tad S Sonstegard
    USDA, ARS, Beltsville Agricultural Research Center, Beltsville, Maryland 20705, USA
    Mamm Genome 13:373-9. 2002
    ..These results demonstrate that bovine sequence expression data serve as a resource for characterizing mammalian transcriptomes and identifying those genes potentially unique to ruminants...
  37. ncbi request reprint Predicting perchlorate exposure in milk from concentrations in dairy feed
    Clifford P Rice
    Environmental Management and Byproduct Utilization Laboratory, USDA, Agricultural Research Service, Beltsville, Maryland 20715, USA
    J Agric Food Chem 55:8806-13. 2007
    ..The study suggests that reducing perchlorate concentration in dairy feed may reduce perchlorate concentrations in milk as well as the potential to reduce human exposure to perchlorate in milk...