Dahlia Nielsen

Knight, M. S., Doherty, C. J., & Nielsen, D. M. (2022, December 2). Assessing the Nucleotide-Level Impact of Spaceflight Stress using RNA-Sequencing Data. https://doi.org/10.1101/2022.12.01.518235

Ferguson, S. H., Foster, D. M., Sherry, B., Magness, S. T., Nielsen, D. M., & Gookin, J. L. (2019). Interferon-λ3 Promotes Epithelial Defense and Barrier Function Against Cryptosporidium parvum Infection. Cellular and Molecular Gastroenterology and Hepatology, 8(1), 1–20. https://doi.org/10.1016/j.jcmgh.2019.02.007

Urkasemsin, G., Nielsen, D. M., Singleton, A., Arepalli, S., Hernandez, D., Agler, C., & Olby, N. J. (2017). Genetics of Hereditary Ataxia in Scottish Terriers. Journal of Veterinary Internal Medicine, 31(4), 1132–1139. https://doi.org/10.1111/jvim.14738

Guo, Y., Fudali, S., Gimeno, J., DiGennaro, P., Chang, S., Williamson, V. M., … Nielsen, D. M. (2017). Networks Underpinning Symbiosis Revealed Through Cross-Species eQTL Mapping. Genetics, 206(4), 2175–2184. https://doi.org/10.1534/genetics.117.202531

Jackson, S., Nielsen, D. M., & Singh, N. D. (2015). Increased exposure to acute thermal stress is associated with a non-linear increase in recombination frequency and an independent linear decrease in fitness in Drosophila. BMC EVOLUTIONARY BIOLOGY, 15. https://doi.org/10.1186/s12862-015-0452-8

Wang, G. F., He, Y., Strauch, R., Olukolu, B. A., Nielsen, D., Li, X., & Balint-Kurti, P. J. (2015). Maize Homologs of Hydroxycinnamoyltransferase, a Key Enzyme in Lignin Biosynthesis, Bind the Nucleotide Binding Leucine-Rich Repeat Rp1 Proteins to Modulate the Defense Response. Plant Physiol, 169(3), 2230–2243.

Olukolu, B. A., Wang, G.-F., Vontimitta, V., Venkata, B. P., Marla, S., Ji, J., … Johal, G. (2014). A Genome-Wide Association Study of the Maize Hypersensitive Defense Response Identifies Genes That Cluster in Related Pathways. PLoS Genetics, 10(8), e1004562. https://doi.org/10.1371/journal.pgen.1004562

Dolezal, A. L., Shu, X., OBrian, G. R., Nielsen, D. M., Woloshuk, C. P., Boston, R. S., & Payne, G. A. (2014). Aspergillus flavus infection induces transcriptional and physical changes in developing maize kernels. Frontiers in Microbiology, 5. https://doi.org/10.3389/fmicb.2014.00384

Agler, C., Nielsen, D. M., Urkasemsin, G., Singleton, A., Tonomura, N., Sigurdsson, S., … Olby, N. J. (2014). Canine hereditary ataxia in old english sheepdogs and gordon setters is associated with a defect in the autophagy gene encoding RAB24. PLoS Genet, 10(2), e1003991.

Guo, Y., Bird, D. M. K., & Nielsen, D. M. (2014). Improved structural annotation of protein-coding genes in the Meloidogyne hapla genome using RNA-Seq. Worm, 3(1), e29158. https://doi.org/10.4161/worm.29158

Franck, C. T., Nielsen, D. M., & Osborne, J. A. (2013). A method for detecting hidden additivity in two-factor unreplicated experiments. Computational Statistics & Data Analysis, 67, 95–104. https://doi.org/10.1016/j.csda.2013.05.002

Richards, K. L., Motsinger-Reif, A. A., Chen, H.-W., Fedoriw, Y., Fan, C., Nielsen, D. M., … Suter, S. E. (2013). Gene Profiling of Canine B-Cell Lymphoma Reveals Germinal Center and Postgerminal Center Subtypes with Different Survival Times, Modeling Human DLBCL. Cancer Research, 73(16), 5029–5039. https://doi.org/10.1158/0008-5472.can-12-3546

Su, Y., Nielsen, D., Zhu, L., Richards, K., Suter, S., Breen, M., … Osborne, J. (2013). Gene selection and cancer type classification of diffuse large-B-cell lymphoma using a bivariate mixture model for two-species data. Hum Genomics, 7, 2.

Supple, M. A., Hines, H. M., Dasmahapatra, K. K., Lewis, J. J., Nielsen, D. M., Lavoie, C., … Counterman, B. A. (2013). Genomic architecture of adaptive color pattern divergence and convergence in Heliconius butterflies. GENOME RESEARCH, 23(8), 1248–1257. https://doi.org/10.1101/gr.150615.112

Dolezal, A. L., Obrian, G. R., Nielsen, D. M., Woloshuk, C. P., Boston, R. S., & Payne, G. A. (2013). Localization, morphology and transcriptional profile of Aspergillus flavus during seed colonization. MOLECULAR PLANT PATHOLOGY, 14(9), 898–909. https://doi.org/10.1111/mpp.12056

Angstadt, A. Y., Motsinger-Reif, A., Thomas, R., Kisseberth, W. C., Couto, C. G., Duval, D. L., … Breen, M. (2011). Characterization of Canine Osteosarcoma by Array Comparative Genomic Hybridization and RT-qPCR: Signatures of Genomic Imbalance in Canine Osteosarcoma Parallel the Human Counterpart. GENES CHROMOSOMES & CANCER, 50(11), 859–874. https://doi.org/10.1002/gcc.20908

Reese, B. N., Payne, G. A., Nielsen, D. M., & Woloshuk, C. P. (2011). Gene Expression profile and response to maize kernels by Aspergillus flavus. Phytopathology, 101(7), 797–804. https://doi.org/10.1094/PHYTO-09-10-0261

Salzmann, C. A., Olivry, T. J. M., Nielsen, D. M., Paps, J. S., Harris, T. L., & Olby, N. J. (2011). Genome-wide linkage study of atopic dermatitis in West Highland White Terriers. BMC Genetics, 12(1), 37. https://doi.org/10.1186/1471-2156-12-37

Counterman, B. A., Araujo-Perez, F., Hines, H. M., Baxter, S. W., Morrison, C. M., Lindstrom, D. P., … McMillan, W. O. (2010). Genomic Hotspots for Adaptation: The Population Genetics of Müllerian Mimicry in Heliconius erato. PLoS Genetics, 6(2), e1000796. https://doi.org/10.1371/journal.pgen.1000796

Reininga, J. M., Nielsen, D., & Purugganan, M. D. (2009). Functional and geographical differentiation of candidate balanced polymorphisms in Arabidopsis thaliana. MOLECULAR ECOLOGY, 18(13), 2844–2855. https://doi.org/10.1111/j.1365-294X.2009.04206.x

Bushel, P. R., Nielsen, D., & Tong, W. (2009). Proceedings of the First International Conference on Toxicogenomics Integrated with Environmental Sciences (TIES-2007). BMC Proceedings, 3(S2). https://doi.org/10.1186/1753-6561-3-s2-s1

Nielsen, D. M., Suchindran, S., & Smith, C. P. (2008). Does strong linkage disequilibrium guarantee redundant association results? Genetic Epidemiology, 32(6), 546–552. https://doi.org/10.1002/gepi.20328

Olby, N. J., Harris, T., Mehta, P. M., Breen, M., Thomas, R., Myers, R., & Nielsen, D. (2008). Linkage Analysis in American Staffordshire Terriers with Hereditary Cerebellar Cortical Degeneration. Journal of Veterinary Internal Medicine, 22(3), 723–724.

Smith, C. A., Robertson, D., Yates, B., Nielsen, D. M., Brown, D., Dean, R. A., & Payne, G. A. (2008). The effect of temperature on Natural Antisense Transcript (NAT) expression in Aspergillus flavus. Current Genetics, 54(5), 241–269. https://doi.org/10.1007/s00294-008-0215-9

Schaff, J. E., Nielsen, D. M., Smith, C. P., Scholl, E. H., & Bird, D. M. K. (2007). Comprehensive Transcriptome Profiling in Tomato Reveals a Role for Glycosyltransferase in Mi-Mediated Nematode Resistance. Plant Physiology, 144(2), 1079–1092. https://doi.org/10.1104/pp.106.090241

Cary, J. W., OBrian, G. R., Nielsen, D. M., Nierman, W., Harris-Coward, P., Yu, J., … Calvo, A. M. (2007). Elucidation of veA-dependent genes associated with aflatoxin and sclerotial production in Aspergillus flavus by functional genomics. Applied Microbiology and Biotechnology, 76(5), 1107–1118. https://doi.org/10.1007/s00253-007-1081-y

Yu, J., Pressoir, G., Briggs, W. H., Vroh Bi, I., Yamasaki, M., Doebley, J. F., … Buckler, E. S. (2006). A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nature Genetics, 38(2), 203–208. https://doi.org/10.1038/ng1702

Stafford-Smith, M., Podgoreanu, M., Swaminathan, M., Phillips-Bute, B., Mathew, J. P., Hauser, E. H., … Schwinn, D. A. (2005). Association of genetic polymorphisms with risk of renal injury after coronary bypass graft surgery. American Journal of Kidney Diseases, 45(3), 519–530. https://doi.org/10.1053/j.ajkd.2004.11.021

Grocott, H. P., White, W. D., Morris, R. W., Podgoreanu, M. V., Mathew, J. P., Nielsen, D. M., … Newman, M. F. (2005). Genetic Polymorphisms and the Risk of Stroke After Cardiac Surgery. Stroke, 36(9), 1854–1858. https://doi.org/10.1161/01.str.0000177482.23478.dc

Weir, B. S., Cardon, L. R., Anderson, A. D., Nelson, D. M., & Hill, W. G. (2005). Measures of human population structure show heterogeneity among genomic regions. Genome Research, 15(11), 1468–1476. https://doi.org/10.1101/gr.4398405

Weir, B. S., Cardon, L. R., Anderson, A. D., Nielsen, D. M., & Hill, W. G. (2005). Measures of human population structure show heterogeneity among genomic regions. Genome Res, 15(11), 1468–1476.

Nielsen, D. M., Ehm, M. G., Zaykin, D. V., & Weir, B. S. (2004). Effect of Two- and Three-Locus Linkage Disequilibrium on the Power to Detect Marker/Phenotype Associations. Genetics, 168(2), 1029–1040. https://doi.org/10.1534/genetics.103.022335

Nielsen, D. (2004). Multi-locus Linkage Disequilibrium and Haplotype-Based Tests of Association. Computational Methods for SNPs and Haplotype Inference, 139–139. https://doi.org/10.1007/978-3-540-24719-7_19

Leipzig, J., Nielsen, D. M., & Heber, S. (2004). The Splicing Graph – A Tool for Visualising Gene Structure and Alternative Splicing. Future Drug Discovery, 62–65.

Czika, W. A., Weir, B. S., Edwards, S. R., Thompson, R. W., Nielsen, D. M., Brocklebank, J. C., … Nobler, K. E. (2001). Applying Data Mining Techniques to the Mapping of Complex Disease Genes. Genetic Epidemiology, 21(S1), S435–S440. https://doi.org/10.1002/gepi.2001.21.s1.s435

Nielsen, D. M., & Weir, B. S. (2001). Association Studies under General Disease Models. Theoretical Population Biology, 60(3), 253–263. https://doi.org/10.1006/tpbi.2001.1539

Nielsen, D. M., & Zaykin, D. (2001). Association mapping: where we’ve been, where we’re going. Expert Review of Molecular Diagnostics, 1(3), 334–342. https://doi.org/10.1586/14737159.1.3.334

Thornsberry, J. M., Goodman, M. M., Doebley, J., Kresovich, S., Nielsen, D., & Buckler, E. S. (2001). Dwarf8 polymorphisms associate with variation in flowering time. Nature Genetics, 28(3), 286–289. https://doi.org/10.1038/90135

Thomas, D. C., Borecki, I. B., Thomson, G., Weiss, K., Almasy, L., Blangero, J., … MacCluer, J. (2001). Evolution of the Simulated Data Problem. Genetic Epidemiology, 21(S1), S325–S331. https://doi.org/10.1002/gepi.2001.21.s1.s325

Almasy, L., Terwilliger, J. D., Nielsen, D., Dyer, T. D., Zaykin, D., & Blangero, J. (2001). GAW12: Simulated Genome Scan, Sequence, and Family Data for a Common Disease. Genetic Epidemiology, 21(S1), S332–S338. https://doi.org/10.1002/gepi.2001.21.s1.s332

Nielsen, D. M., & Weir, B. S. (1999). A classical setting for associations between markers and loci 
affecting quantitative traits. Genetical Research, 74(3), 271–277. https://doi.org/10.1017/s0016672399004231

Cockett, N. E., Shay, T. L., Beever, J. E., Nielsen, D., Albretsen, J., Georges, M., … Bunch, T. D. (1999). Localization of the locus causing Spider Lamb Syndrome to the distal end of ovine Chromosome 6. Mammalian Genome, 10(1), 35–38. https://doi.org/10.1007/s003359900938

Nielsen, D., & Zaykin, D. (1999). Novel tests for marker-disease association using the collaborative study on the genetics of alcoholism data. Genetic Epidemiology, 17(S1), S265–S270. https://doi.org/10.1002/gepi.1370170745

Nielsen, D. M., Ehm, M. G., & Weir, B. S. (1998). Detecting Marker-Disease Association by Testing for Hardy-Weinberg Disequilibrium at a Marker Locus. The American Journal of Human Genetics, 63(5), 1531–1540. https://doi.org/10.1086/302114

Cockett, N. E., Jackson, S. P., Shay, T. L., Farnir, F., Berghmans, S., Snowder, G. D., … Georges, M. (1996). Polar Overdominance at the Ovine callipyge Locus. Science, 273(5272), 236–238. https://doi.org/10.1126/science.273.5272.236

Georges, M., Nielsen, D., Mackinnon, M., Mishra, A., Okimoto, R., Pasquino, A. T., … Hoeschele, I. (1995). Mapping Quantitative Trait Loci Controlling Milk Production in Dairy Cattle by Exploiting Progeny Testing. Genetics, 139(2), 907–920. https://doi.org/10.1093/genetics/139.2.907

Cockett, N. E., Jackson, S. P., Shay, T. L., Nielsen, D., Moore, S. S., Steele, M. R., … Georges, M. (1994). Chromosomal localization of the callipyge gene in sheep (Ovis aries) using bovine DNA markers. Proceedings of the National Academy of Sciences, 91(8), 3019–3023. https://doi.org/10.1073/pnas.91.8.3019

Georges, M., Drinkwater, R., King, T., Mishra, A., Moore, S. S., Nielsen, D., … Hetzel, J. (1993). Microsatellite mapping of a gene affecting horn development in Bos taurus. Nature Genetics, 4(2), 206–210. https://doi.org/10.1038/ng0693-206

Georges, M., Dietz, A. B., Mishra, A., Nielsen, D., Sargeant, L. S., Sorensen, A., … Womack, J. E. (1993). Microsatellite mapping of the gene causing weaver disease in cattle will allow the study of an associated quantitative trait locus. Proceedings of the National Academy of Sciences, 90(3), 1058–1062. https://doi.org/10.1073/pnas.90.3.1058