Publications


Hindorff, L.A., Psaty, B.M., Carlson, C.S., Heckbert, S.R., Lumley, T., Smith, N.L., Lemaitre, R.N., Rieder, M.J., Nickerson, D.A., Reiner, A.P. 2006. Common Genetic Variation in the Prothrombin Gene, Hormone Therapy, and Incident Nonfatal Myocardial Infarction in Postmenopausal Women. Am J Epidemiol. Epub 2006 Feb 8.
PubMed ID: 16467413

Mackelprang, R., Livingston, R.J., Eberle, M.A., Carlson, C.S., Yi, Q., Akey, J.M., Nickerson, D.A. 2006. Sequence diversity, natural selection and linkage disequilibrium in the human T cell receptor alpha/delta locus. Hum. Genet. Epub 2006 Jan 20.
PubMed ID: 16425038

Carlson, C.S., Thomas, D.J., Eberle, M.E., Swanson, J.E., Livingston, R.J., Rieder, M.J., Nickerson, D.A. 2005. Genomic regions exhibiting positive selection identified from dense genotype data. Genome Res. 15: 1553-1565
PubMed ID: 16251465

Crawford, D.C., Akey, D.T., Nickerson, D.A. 2005. The patterns of natural variation in human genes. Annu. Rev. Genomics Hum. Genet. 6: 287-312
PubMed ID: 16124863

Rieder, M.J., Reiner, A.P., Gage, B.F., Nickerson, D.A., Eby, C.S., McLeod, H.L., Blough, D.K., Thummel, K.E., Veenstra, D.L., Rettie A.E. 2005. Effect of VKORC1 haplotypes on transcriptional regulation and warfarin dose. NEJM 352:2285-2293
PubMed ID: 15930419

Carlson, C.S., Aldred, S.F., Lee, P.K., Tracy, R.P., Schwartz, S.M., Rieder, M., Liu, K., Williams, O.D., Iribarren, C., Lewis, E.C., Fornage, M., Boerwinkle, E., Gross, M., Jaquish, C., Nickerson, D.A., Myers, R.M., Siscovick, D.S., Reiner, A.P. 2005. Polymorphisms within the C-reactive protein (CRP) promoter region are associated with plasma CRP levels. Am J Hum Genet. 77(1):64-77. Epub 2005 May 16
PubMed ID: 15897982

Crawford D.C., Nickerson D.A. 2005. Definition and clinical importance of haplotypes. Annu. Rev. Med. 56: 303-20.
PubMed ID: 15660514

Bhangale, T.R., Rieder, M.J., Livingston, R., Nickerson, D.A. 2005. Comprehensive identification and characterization of diallelic insertion-deletion polymorphisms in 330 human candidate genes. Hum. Mol. Genet. 14: 59-69
PubMed ID: 15525656

Livingston, R.J., von Niederhausern, A., Jegga, A.G., Crawford, D.C., Carlson, C.S., Rieder, M.J., Gowrisankar, S., Aronow, B.J., Weiss, R.B., Nickerson, D.A. 2004. Pattern of sequence variation across 213 environmental response genes. Genome. Res. 14: 1821-31
PubMed ID: 15364900

Akey, J.M., Eberle, M.A., Rieder, M.J., Carlson, C.S., Shriver, M.D., Nickerson D.A., Kruglyak, L. 2004. Population history and natural selection shape patterns of genetic variation in 132 genes. PloS Biol 2: 1591-1599
PubMed ID: 15361935

Carlson, C.S., Reider, M.J., Nickerson, D.A., Eberle, M.A., Kruglyak, L. 2005. Comment on 'Discrepancies in dbSNP confirmations rates and allele frequency distributions from varying genotyping error rates and patterns'. Bioinformatics 21 (2): 141-3
PubMed ID: 15333455

Furman, I., Rieder, M.J., Da Ponte, S., Carrington, D.P., Nickerson, D.A., Kruglyak, L., Markianos, K. 2004. Sequence-based linkage analysis. Am. J. Hum. Genet. 75: 647-53
PubMed ID: 15329798

Crawford, D.C., Bhangale, T., Li, N., Hellenthal, G., Rieder, M.J., Nickerson, D.A., Stephens, M. 2004. Evidence for substantial fine-scale variation in recombination rates across the human genome. Nature Genetics 36: 700-6
PubMed ID: 15184900

Carlson, C.S., Eberle, M.A., Kruglyak, L., Nickerson, D.A. 2004. Mapping complex disease loci in whole-genome association sutdies. Nature 429: 446-52
PubMed ID: 15164069

Fullerton, S.M., Buchanan, A.V., Sonpar, V., Taylor, S.L., Smith, J., Carlson, C.S., Salomaa, V., Stengard, J., Boerwinkle, E., Clark, A.G., Nickerson, D.A., Weiss, K.M. 2004. The effects of scale: variation in the APOA1/C3/A4/A5 gene cluster. Hum Genet. 115: 36-56
PubMed ID: 15108119

Crawford, D.C., Carlson, C.S., Rieder, M.J., Carrington, D.P., Yi, Q., Smith, J.D., Eberle, M., Kruglyak, L., and Nickerson, D.A. 2004. Haplotype diversity across 100 candidate genes for inflammation, lipid metabolism, and blood pressure regulation in two populations. Am. J. Hum. Genet. 74: 610-622
PubMed ID: 15015130

Austin, M.A., Talmud, P., Farin, F.M., Nickerson, D.A., Edwards, K., Leonetti, D., McNeely, M.J., Viernes, H.M., Humphries, S.E., Fujimoto, W.Y. 2004. Association of Apolipoprotein A5 Variants with LDL Particle Size and Triglyceride in Japanese Americans. Biochim Biophys Acta. 1688:1-9
PubMed ID: 14732475

Carlson, C.S., Eberle, M., Rieder, M.J., Yi, Q., Kruglyak, L., Nickerson, D.A. 2004. Selecting a maximally informative set of SNPs for association analyses using linkage disequilibrium. Am. J. Hum. Genet. 74: 106-20
PubMed ID: 14681826

Wu, X., Luke, A., Rieder, M., Lee, K., Toth, E.J., Nickerson, D., Zhu, X., Kan, D., Cooper, R.S. 2003. An association study of angiotensinogen polymorphisms with serum level and hypertension in an African-American population. J. Hypertens. 21: 1847-52
PubMed ID: 14508190

Jarvik, G.P., Hatsukami, T.S., Carlson, C.S., Richter, R.J., Jampsa, R., Brophy, V.H., Margolin, S., Rieder, M.J., Nickerson, D.A., Schellenberg, G.D., Heagerty, P.J., Furlong, C.E. 2003. Paraoxonase activity, but not haplotype utilizing the linkage disequilibrium structure, predicts vascular disease. Arterioscler Thromb Vasc Biol 23: 1465-1471
PubMed ID: 12805074

Jarvik, G.P., Carlson, C.S., Richter, R.J., Jampsa, R., Rieder, M.J., Nickerson, D.A., and Furlong, C.E. 2003. Novel Paraoxonase (PON1) nonsense and missense mutations predicted by functional genomic assay of PON1 status. Pharmacogenetics 13: 291-295
PubMed ID: 12724622

Carlson, C., Eberle, M.A., Rieder, M.J., Smith, J.D., Kruglyak, L., and Nickerson, D.A. 2003. Additional SNPs and linkage-disequilibrium analyses are necessary for whole-genome association studies in humans. Nature Genetics 33: 518-521
PubMed ID: 12652300

Mackelprang, R., Carlson, C.S., Subrahmanyan, L., Livingston, R.J., Eberle, M.A., Nickerson, D.A. 2002. Sequence variation in the human T-cell receptor loci. Immunol. Rev.
PubMed ID: 12493004

Stengard, J.H., Clark, A.G., Weiss, K.M., Kardia, S., Nickerson, D.A., Salomaa, V., Ehnholm, C., Boerwinkle, E., and Sing, C.F. 2002. Contributions of 18 additional DNA sequence variations in the gene encoding Apolipoprotein E to explaining variation in quantitative measures of lipid metabolism. Am. J. Hum. Genet. 71:501-517
PubMed ID: 12165926

Fullerton, S.M., Clark, A.G., Weiss, K.M., Taylor, S.L., Stengard, J.H., Salomaa, V., Boerwinkle, E. and Nickerson, D.A. 2002. Sequence Polymorphism at the Human Apolipoprotein AII Gene (APOA2): Unexpected Deficit of Variation in an African-American Sample. Hum. Genetics 111: 75-87
PubMed ID: 12136239

Edland S.D., Tobe, V.O., Rieder, M.J., Bowen, J.D., McCormick, W., Teri, L., Schellenberg, G.D., Larson, E.B., Nickerson, D.A., and Kukull, W.A. 2002. Mitochondrial genetic variants and Alzheimer disease: a case-control study of the T4336C and G5460A variants. Alzheimer Dis. Assoc. Disord. 16:1-7
PubMed ID: 11882743

Nickerson, D.A., Kolker, N., Taylor, S.L., Rieder, M.J. 2001. Sequence-based detection of single nucleotide polymorphisms. Methods Mol. Biol. 175: 29-35
PubMed ID: 11462842

Subrahmanyan, L., Eberle, M. A., Kruglyak, L., and Nickerson, D.A. 2001. Sequence variation and linkage disequilibrium in the human T-cell receptor beta (TCRB) locus. Am. J. Hum. Genet. 69:381-395
PubMed ID: 11438886

Kruglyak, L. and Nickerson, D.A. 2001. Variation is the spice of life. Nature Genetics 27:234-236
PubMed ID: 11242096

Carlson, C.S., Newman, T.L., Nickerson, D.A. 2001. SNPing in the Human Genome. Current Opinion in Chemical Biology 5: 78-85
PubMed ID: 11166653

Templeton, A.R., Weiss , K.M., Nickerson, D.A., Boerwinkle, E., and Sing, C.F. 2000. Cladistic structure within the human lipoprotein lipase gene. Genetics 156: 1259-1275
PubMed ID: 11063700

Nickerson, D.A., Taylor, S.L., Fullerton, S.M., Weiss, K.M., Clark, A.G., Stengard, J.H., Salomaa, V., Boerwinkle, E., and Sing, C. F. 2000. Sequence diversity and large-scale typing of SNPs in the human apolipoprotein E gene. Genome Res. 10: 1546-1560
PubMed ID: 11042151

Zhu, X., McKenzie, C.A., Forrester, T., Nickerson, D.A., Broeckel, U., Schunkert, H., Doering, A. Jacob, H.J., Cooper, R.S., and Rieder, M.J. 2000. Localization of a small genomic region associated with elevated ACE. Am. J. Hum. Genet. 67: 1144-1153
PubMed ID: 11001581

Fullerton, S.M., Clark, A.G., Weiss, K.M., Nickerson, D.A., Taylor ,S.L., Stengard , J.H., Salomaa, V., Vartiainen, E., Perola, M., Boerwinkle, E., and Sing, C.F. 2000. Apolipoprotein E variation at the sequence haplotype level: Implications for the origin and maintenance of a major human polymorphism. Am. J. Hum. Genet. 67: 881-900
PubMed ID: 10986041

Rieder, M.J., Nickerson, D.A. 2000. Hypertension and Single Nucleotide Polymorphisms. Curr. Hypertens. Rep. 2: 44-49.
PubMed ID: 10981126

Templeton, A.R., Clark, A.G., Weiss, K.M., Nickerson, D.A., Boerwinkle, E, and Sing, C.F. 2000. Recombinational and mutational hotspots within the human lipoprotein lipase gene. Am. J. Hum. Genet. 66: 69-83
PubMed ID: 10631137

Garg, K., Green, P. and Nickerson, D.A. 1999. Identification of candidate coding region single nucleotide polymorphisms in 165 human genes using assembled expressed sequence tags. Genome Res. 9: 1087-1092
PubMed ID: 10568748

Rieder, M.J., Taylor, S.L., Clark, A.G., and Nickerson, D.A. 1999. Sequence variation in the human angiotensin converting enzyme. Nature Genetics 22(1): 59-62
PubMed ID: 10319862

Picoult-Newberg, L., Ideker, R., Pohl, M., Taylor, S., Addelston, M.B., Nickerson, D.A. and Boyce-Jacino, M. 1999. Mining Single Nucleotide Polymorphisms (SNPs) from Expressed Sequence Tag (EST) Databases. Genome Res. 9:167-174
PubMed ID: 10022981

Yokota, H., Nickerson, D.A., Trask, B., Engh, G., and Aebersold, R. 1998. Mapping DNA and Protein Interactions with Atomic Force Microscopy. Anal. Biochem 264: 158-164
PubMed ID: 9866677

Clark, A.G., Weiss, K.M., Nickerson, D.A., Taylor, S.L., Buchanan, A., Stengard, J., Salomaa, V., Vartianinen, E., Perola, M., Boerwinkle, E. and Sing, C.F. 1998. Haplotype structure and population genetic inferences from nucleotide sequence variation in human lipoprotein lipase. Am. J. Hum. Genet. 63: 595-612
PubMed ID: 9683608

Nickerson, D.A., Taylor, S.L., Weiss, K.M., Clark, A.G., Hutchinson, R.G., Stengard, J., Salomaa, V., Vartianinen, E., Boerwinkle, E. and Sing, C.F. 1998. DNA sequence diversity in a 9.7 kb Region of the human lipoprotein lipase gene. Nature Genetics 19: 233-240
PubMed ID: 9662394

Rieder, M.J., Taylor, S.L., Tobe, V.O., and Nickerson, D.A., 1998. Automating the identification of DNA variations using quality-based fluorescence re-sequencing: analysis of the human mitochondrial genome. Nucleic Acids Research 26: 967-973
PubMed ID: 9461455

Edelstein, R.E., Nickerson, D.A., Tobe, V.O., Manns-Arcuino, L.A., and Frenkel, L.M. 1998. Oligonucleotide ligation assay for detecting mutations in the human immunodeficiency virus type 1 pol gene that are associated with resistance to zidovudine, didanosine, and lamivudine. J. Clin. Microbiol. 36: 569-572
PubMed ID: 9466779

Nickerson, D.A., Tobe, V.O., and Taylor, S.L. 1997, PolyPhred: automating the detection and genotyping of single nucleotide substitutions using fluorescence-based resequencing. Nucleic Acids Research 25: 2745 - 2751
PubMed ID: 9207020

Parker, L.T., Zakeri, Z, Deng, Q., Spurgeon, S. Kwok, P.Y. and Nickerson, D.A. 1996. Amplitaq DNA Polymerase, FS Dye-Terminator Sequencing: Analysis of Peak Height Patterns. Biotechniques 21: 694-699
PubMed ID: 8891223

Tobe, V. O., Taylor, S. L., and Nickerson, D. A., 1996, Single-well genotyping of diallelic sequence variations by a two-color ELISA-based oligonucleotide ligation assay. Nucleic Acids Research 24: 3728-3732
PubMed ID: 8871551

Delahunty, C., Ankener, W., Deng, Q., Eng, J. and Nickerson, D.A. 1996. Testing the Feasibility of DNA Typing for Human Identification by PCR and an Oligonucleotide Ligation Assay. Am. J. Hum. Genet. 58:1239-1246
PubMed ID: 8651301

Kwok, P.-Y., Deng, Q., Zakeri, H., and Nickerson, D.A. 1996. Increasing the Information Content of STS-based Genome Maps: Identifying Polymorphisms in Mapped STSs. Genomics 31: 123-126
PubMed ID: 8808290

Boysen, C., Carlson, C., Hood, E., Hood, L., and Nickerson, D.A. 1996. DNA Identifying DNA polymorphisms in human TCRA/D variable genes by direct sequencing of PCR products. Immunogenetics 44: 121-127
PubMed ID: 8662074

Parker, L.T., Deng, Q., Zakeri, H., Carlson, C., Nickerson, D.A., Kwok, P.-Y. 1995. Peak height variations in automated sequencing of PCR products using Taq dye-terminator chemistry. Biotechniques 19: 116-121
PubMed ID: 7669285

Delahunty, C.M., Ankener, W., Brainerd, S., Nickerson, D.A., and Mononen, I.T. 1995. Finnish-type aspartylglucosaminuria detected by oligonucleotide ligation assay. Clin. Chem. 41: 59-61
PubMed ID: 7813081

Charmley, P., Nickerson, D.A. and Hood, L.E. 1994. Polymorphism detection and sequence analysis of human T-cell receptor V alpha-chain-encoding gene segments.Immunogenetics 39: 138-145
PubMed ID: 8276457

Kwok, P.-Y., Carlson, C., Yager, T.D., Ankener, W. and Nickerson, D.A. 1994. Comparative analysis of human DNA variations by fluorescence-based sequencing of PCR products. Genomics 23: 138-144
PubMed ID: 7829062

Nickerson, D.A. 1993. Gene probe assays and their detection. Curr. Opin. Biotech. 4: 48-51
PubMed ID: 7763393

Charmley, P., Wang, K., Hood, L.E. and Nickerson, D.A. 1993. Identification and physical mapping of a polymorphic human T cell receptor Vb gene with a frequent null allele. J. Exp. Med. 177: 135-143
PubMed ID: 7678110

Kwok, P., Gremaud, M.F., Nickerson, D.A., Hood, L.E. and Olson, M.V. 1992. Automatable screening of yeast artifical chromosome libraries based on the oligonucleotide ligation assay. Genomics 13: 935-941
PubMed ID: 1505984

Donis-Keller, H., Weaver, R., Ramachandra, S., Warlick, C. Burgress, A.K., Weber, J.L., Litt, M., Nickerson, D.A., Boysen, C.A., Hood, L., and Mishra, S.K. 1992. A comprehensive genetic linkage map of the human genome: Chromosome 14. Science 258: 72-73
PubMed ID: 1439770

Nickerson, D.A., Whitehurst, C., Boysen, C., Charmley, P., Kaiser, R. and Hood, L.E. 1992. Identification of clusters of biallelic polymorphic sequence-tagged sites (pSTSs) that generate highly-informative and automatable markers for genetic linkage mapping. Genomics 12: 377-387
PubMed ID: 1531472

Yager, T., Nickerson, D.A. and Hood, L.E. 1991. The human genome project: Creating an infrastructure for biology and medicine. Trends in Biochemical Sciences 16: 454-458
PubMed ID: 1781022

Cheroutre, H., Kronenberg, M., Brorson, K., Hunt, S.W., Eghtesady, P., Hood, L.E. and Nickerson, D.A. 1991. Analysis of class I gene expression in adult bone marrow and fetal liver of Balb/c mice. J. Immunol. 146: 3263-3272
PubMed ID: 2026867

Nickerson, D. A., Kaiser, R., Lappin, S., Stewart, J., Hood, L., Landegren, U., 1990, Automated DNA diagnostics using and ELISA-based oligonucleotide ligation assay. PNAS 87: 8923-8927.
PubMed ID: 2247466

Brorson, K.A., Hunt, S.W., Hunkapiller, T., Sun, Y.H., Cheroutre, H., Nickerson, D.A. and Hood, L. 1989. Comparison of exon 5 sequences from 35 class I genes of the Balb/c mouse. J. Exp. Med. 170: 1837-1858
PubMed ID: 2584927