Dan Nettleton - Publications

Affiliations: 
Iowa State University, Ames, IA, United States 
Area:
Statistics

149 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2018 Yang J, Yeh CE, Kastoori Ramamurthy R, Qi X, Fernando RL, Dekkers JCM, Garrick DJ, Nettleton D, Schnable PS. Empirical Comparisons of Different Statistical Models To Identify and Validate Kernel Row Number-Associated Variants from Structured Multi-parent Mapping Populations of Maize. G3 (Bethesda, Md.). PMID 30213868 DOI: 10.1534/g3.118.200636  0.64
2018 Qi M, Zheng W, Zhao X, Hohenstein JD, Kandel Y, O'Conner S, Wang Y, Du C, Nettleton D, MacIntosh GC, Tylka GL, Wurtele ES, Whitham SA, Li L. QQS orphan gene and its interactor NF-YC4 reduce susceptibility to pathogens and pests. Plant Biotechnology Journal. PMID 29878511 DOI: 10.1111/pbi.12961  0.64
2018 Liang K, Du C, You H, Nettleton D. A hidden Markov tree model for testing multiple hypotheses corresponding to Gene Ontology gene sets. Bmc Bioinformatics. 19: 107. PMID 29587646 DOI: 10.1186/s12859-018-2106-5  0.6
2017 Kusmec A, Srinivasan S, Nettleton D, Schnable PS. Distinct genetic architectures for phenotype means and plasticities in Zea mays. Nature Plants. 3: 715-723. PMID 29150689 DOI: 10.1038/s41477-017-0007-7  0.44
2017 Lin HY, Liu Q, Li X, Yang J, Liu S, Huang Y, Scanlon MJ, Nettleton D, Schnable PS. Substantial contribution of genetic variation in the expression of transcription factors to phenotypic variation revealed by eRD-GWAS. Genome Biology. 18: 192. PMID 29041960 DOI: 10.1186/s13059-017-1328-6  0.44
2017 Guan X, Okazaki Y, Lithio A, Li L, Zhao X, Jin H, Nettleton D, Saito K, Nikolau BJ. The 3-hydroxyacyl-ACP dehydratase component of the plant mitochondrial fatty acid synthase system. Plant Physiology. PMID 28202596 DOI: 10.1104/pp.16.01732  0.44
2016 Jones DC, Zheng W, Huang S, Du C, Zhao X, Yennamalli RM, Sen TZ, Nettleton D, Wurtele ES, Li L. A Clade-Specific Arabidopsis Gene Connects Primary Metabolism and Senescence. Frontiers in Plant Science. 7: 983. PMID 27462324 DOI: 10.3389/fpls.2016.00983  0.88
2016 Yu P, Baldauf J, Lithio A, Marcon C, Nettleton D, Li C, Hochholdinger F. Root type specific reprogramming of maize pericycle transcriptomes by local high nitrate results in disparate lateral root branching patterns. Plant Physiology. PMID 26811190 DOI: 10.1104/pp.15.01885  0.88
2016 Liu H, Nguyen YT, Nettleton D, Dekkers JC, Tuggle CK. Post-weaning blood transcriptomic differences between Yorkshire pigs divergently selected for residual feed intake. Bmc Genomics. 17: 73. PMID 26801403 DOI: 10.1186/s12864-016-2395-x  0.88
2016 Xu R, Nettleton D, Nordman DJ. Case-Specific Random Forests Journal of Computational and Graphical Statistics. 25: 49-65. DOI: 10.1080/10618600.2014.983641  0.88
2015 Niemi J, Mittman E, Landau W, Nettleton D. Empirical Bayes analysis of RNA-seq data for detection of gene expression heterosis. Journal of Agricultural, Biological, and Environmental Statistics. 20: 614-628. PMID 27147815 DOI: 10.1007/s13253-015-0230-5  0.88
2015 Lithio A, Nettleton D. Hierarchical Modeling and Differential Expression Analysis for RNA-seq Experiments with Inbred and Hybrid Genotypes. Journal of Agricultural, Biological, and Environmental Statistics. 20: 598-613. PMID 27110090 DOI: 10.1007/s13253-015-0232-3  0.88
2015 Nguyen Y, Nettleton D, Liu H, Tuggle CK. Detecting Differentially Expressed Genes with RNA-seq Data Using Backward Selection to Account for the Effects of Relevant Covariates. Journal of Agricultural, Biological, and Environmental Statistics. 20: 577-597. PMID 26660449 DOI: 10.1007/s13253-015-0226-1  0.88
2015 Li L, Zheng W, Zhu Y, Ye H, Tang B, Arendsee ZW, Jones D, Li R, Ortiz D, Zhao X, Du C, Nettleton D, Scott MP, Salas-Fernandez MG, Yin Y, et al. QQS orphan gene regulates carbon and nitrogen partitioning across species via NF-YC interactions. Proceedings of the National Academy of Sciences of the United States of America. PMID 26554020 DOI: 10.1073/pnas.1514670112  0.88
2015 Opitz N, Marcon C, Paschold A, Malik WA, Lithio A, Brandt R, Piepho HP, Nettleton D, Hochholdinger F. Extensive tissue-specific transcriptomic plasticity in maize primary roots upon water deficit. Journal of Experimental Botany. PMID 26463995 DOI: 10.1093/jxb/erv453  0.88
2015 Yang J, Jiang H, Yeh CT, Yu J, Jeddeloh JA, Nettleton D, Schnable PS. Extreme Phenotype-Genome-Wide Association Study (XP-GWAS): a method for identifying trait-associated variants by sequencing pools of individuals selected from a diversity panel. The Plant Journal : For Cell and Molecular Biology. PMID 26386250 DOI: 10.1111/tpj.13029  0.44
2015 Jiang F, An C, Bao Y, Zhao X, Jernigan RL, Lithio A, Nettleton D, Li L, Wurtele ES, Nolan LK, Lu C, Li G. ArcA Controls Metabolism, Chemotaxis and Motility Contributing to the Pathogenicity of Avian Pathogenic E. coli. Infection and Immunity. PMID 26099584 DOI: 10.1128/IAI.00312-15  0.88
2015 Whigham E, Qi S, Mistry D, Surana P, Xu R, Fuerst GS, Pliego C, Bindschedler LV, Spanu P, Dickerson JA, Innes R, Nettleton D, Bogdanove AJ, Wise RP. Broadly conserved fungal effector BEC1019 suppresses host cell death and enhances pathogen virulence in powdery mildew of barley (Hordeum vulgare L.). Molecular Plant-Microbe Interactions : Mpmi. PMID 25938194 DOI: 10.1094/MPMI-02-15-0027-FI  0.88
2015 Benidt S, Nettleton D. SimSeq: a nonparametric approach to simulation of RNA-sequence datasets. Bioinformatics (Oxford, England). 31: 2131-40. PMID 25725090 DOI: 10.1093/bioinformatics/btv124  0.88
2015 Li L, Hur M, Lee JY, Zhou W, Song Z, Ransom N, Demirkale CY, Nettleton D, Westgate M, Arendsee Z, Iyer V, Shanks J, Nikolau B, Wurtele ES. A systems biology approach toward understanding seed composition in soybean. Bmc Genomics. 16: S9. PMID 25708381 DOI: 10.1186/1471-2164-16-S3-S9  0.88
2015 Li L, Hill-Skinner S, Liu S, Beuchle D, Tang HM, Yeh CT, Nettleton D, Schnable PS. The maize brown midrib4 (bm4) gene encodes a functional folylpolyglutamate synthase. The Plant Journal : For Cell and Molecular Biology. 81: 493-504. PMID 25495051 DOI: 10.1111/tpj.12745  0.44
2015 Knetter SM, Bearson SM, Huang TH, Kurkiewicz D, Schroyen M, Nettleton D, Berman D, Cohen V, Lunney JK, Ramer-Tait AE, Wannemuehler MJ, Tuggle CK. Salmonella enterica serovar Typhimurium-infected pigs with different shedding levels exhibit distinct clinical, peripheral cytokine and transcriptomic immune response phenotypes. Innate Immunity. 21: 227-41. PMID 24632525 DOI: 10.1177/1753425914525812  0.88
2015 Nettleton D, Tempelman RJ. Guest Editors’ Introduction to the Special Issue on “Statistical Genomics and Transcriptomics in Agriculture” Journal of Agricultural, Biological, and Environmental Statistics. 20: 439-441. DOI: 10.1007/s13253-015-0235-0  0.88
2014 Ji T, Liu P, Nettleton D. Estimation and Testing of Gene Expression Heterosis. Journal of Agricultural, Biological, and Environmental Statistics. 19: 319-337. PMID 25435758 DOI: 10.1007/s13253-014-0173-2  0.88
2014 Paschold A, Larson NB, Marcon C, Schnable JC, Yeh CT, Lanz C, Nettleton D, Piepho HP, Schnable PS, Hochholdinger F. Nonsyntenic genes drive highly dynamic complementation of gene expression in maize hybrids. The Plant Cell. 26: 3939-48. PMID 25315323 DOI: 10.1105/tpc.114.130948  0.88
2014 Yu X, Lund SP, Greenwald JW, Records AH, Scott RA, Nettleton D, Lindow SE, Gross DC, Beattie GA. Transcriptional analysis of the global regulatory networks active in Pseudomonas syringae during leaf colonization. Mbio. 5: e01683-14. PMID 25182327 DOI: 10.1128/mBio.01683-14  0.88
2014 Orr M, Liu P, Nettleton D. An improved method for computing q-values when the distribution of effect sizes is asymmetric. Bioinformatics (Oxford, England). 30: 3044-53. PMID 25024290 DOI: 10.1093/bioinformatics/btu432  0.88
2014 Wang H, Nettleton D, Ying K. Copy number variation detection using next generation sequencing read counts Bmc Bioinformatics. 15. PMID 24731174 DOI: 10.1186/1471-2105-15-109  0.88
2014 Cernadas RA, Doyle EL, Niño-Liu DO, Wilkins KE, Bancroft T, Wang L, Schmidt CL, Caldo R, Yang B, White FF, Nettleton D, Wise RP, Bogdanove AJ. Code-assisted discovery of TAL effector targets in bacterial leaf streak of rice reveals contrast with bacterial blight and a novel susceptibility gene. Plos Pathogens. 10: e1003972. PMID 24586171 DOI: 10.1371/journal.ppat.1003972  0.88
2014 Gu T, Zhu MJ, Schroyen M, Qu L, Nettleton D, Kuhar D, Lunney JK, Ross JW, Zhao SH, Tuggle CK. Endometrial gene expression profiling in pregnant Meishan and Yorkshire pigs on day 12 of gestation. Bmc Genomics. 15: 156. PMID 24564230 DOI: 10.1186/1471-2164-15-156  0.88
2014 Tang HM, Liu S, Hill-Skinner S, Wu W, Reed D, Yeh CT, Nettleton D, Schnable PS. The maize brown midrib2 (bm2) gene encodes a methylenetetrahydrofolate reductase that contributes to lignin accumulation. The Plant Journal : For Cell and Molecular Biology. 77: 380-92. PMID 24286468 DOI: 10.1111/tpj.12394  0.44
2014 Xu R, Nettleton D, Nordman DJ. Predictor augmentation in random forests Statistics and Its Interface. 7: 177-186. DOI: 10.4310/SII.2014.v7.n2.a3  0.88
2014 Lock D, Nettleton D. Using random forests to estimate win probability before each play of an NFL game Journal of Quantitative Analysis in Sports. 10: 197-205. DOI: 10.1515/jqas-2013-0100  0.88
2014 O'Brien JJ, Spry PG, Nettleton D, Xu R, Teale GS. Using Random Forests to distinguish gahnite compositions as an exploration guide to Broken Hill-type Pb-Zn-Ag deposits in the Broken Hill domain, Australia Journal of Geochemical Exploration. 149: 74-86. DOI: 10.1016/j.gexplo.2014.11.010  0.88
2013 Pliego C, Nowara D, Bonciani G, Gheorghe DM, Xu R, Surana P, Whigham E, Nettleton D, Bogdanove AJ, Wise RP, Schweizer P, Bindschedler LV, Spanu PD. Host-induced gene silencing in barley powdery mildew reveals a class of ribonuclease-like effectors. Molecular Plant-Microbe Interactions : Mpmi. 26: 633-42. PMID 23441578 DOI: 10.1094/MPMI-01-13-0005-R  0.88
2013 Bancroft T, Du C, Nettleton D. Estimation of false discovery rate using sequential permutation p-values. Biometrics. 69: 1-7. PMID 23379645 DOI: 10.1111/j.1541-0420.2012.01825.x  0.88
2013 Yu X, Lund SP, Scott RA, Greenwald JW, Records AH, Nettleton D, Lindow SE, Gross DC, Beattie GA. Transcriptional responses of Pseudomonas syringae to growth in epiphytic versus apoplastic leaf sites. Proceedings of the National Academy of Sciences of the United States of America. 110: E425-34. PMID 23319638 DOI: 10.1073/pnas.1221892110  0.88
2013 Aluru M, Zola J, Nettleton D, Aluru S. Reverse engineering and analysis of large genome-scale gene networks. Nucleic Acids Research. 41: e24. PMID 23042249 DOI: 10.1093/nar/gks904  0.88
2013 Froelich AG, Nettleton D. Does my baby really look like me? Using tests for resemblance between parent and child to teach topics in categorical data analysis Journal of Statistics Education. 21.  0.88
2012 Lund SP, Nettleton D, McCarthy DJ, Smyth GK. Detecting differential expression in RNA-sequence data using quasi-likelihood with shrunken dispersion estimates. Statistical Applications in Genetics and Molecular Biology. 11. PMID 23104842 DOI: 10.1515/1544-6115.1826  0.88
2012 Paschold A, Jia Y, Marcon C, Lund S, Larson NB, Yeh CT, Ossowski S, Lanz C, Nettleton D, Schnable PS, Hochholdinger F. Complementation contributes to transcriptome complexity in maize (Zea mays L.) hybrids relative to their inbred parents. Genome Research. 22: 2445-54. PMID 23086286 DOI: 10.1101/gr.138461.112  0.88
2012 Qu L, Nettleton D, Dekkers JC. A hierarchical semiparametric model for incorporating intergene information for analysis of genomic data. Biometrics. 68: 1168-77. PMID 22994883 DOI: 10.1111/j.1541-0420.2012.01778.x  0.88
2012 Takacs EM, Li J, Du C, Ponnala L, Janick-Buckner D, Yu J, Muehlbauer GJ, Schnable PS, Timmermans MC, Sun Q, Nettleton D, Scanlon MJ. Ontogeny of the maize shoot apical meristem. The Plant Cell. 24: 3219-34. PMID 22911570 DOI: 10.1105/tpc.112.099614  0.88
2012 Wilke VL, Nettleton D, Wymore MJ, Gallup JM, Demirkale CY, Ackermann MR, Tuggle CK, Ramer-Tait AE, Wannemuehler MJ, Jergens AE. Gene expression in intestinal mucosal biopsy specimens obtained from dogs with chronic enteropathy. American Journal of Veterinary Research. 73: 1219-29. PMID 22849683 DOI: 10.2460/ajvr.73.8.1219  0.88
2012 Swanson RK, Xu R, Nettleton D, Glatz CE. Proteomics-based, multivariate random forest method for prediction of protein separation behavior during cation-exchange chromatography. Journal of Chromatography. A. 1249: 103-14. PMID 22748375 DOI: 10.1016/j.chroma.2012.06.009  0.88
2012 Liu S, Ying K, Yeh CT, Yang J, Swanson-Wagner R, Wu W, Richmond T, Gerhardt DJ, Lai J, Springer N, Nettleton D, Jeddeloh JA, Schnable PS. Changes in genome content generated via segregation of non-allelic homologs. The Plant Journal : For Cell and Molecular Biology. 72: 390-9. PMID 22731681 DOI: 10.1111/j.1365-313X.2012.05087.x  0.88
2012 Ji T, Liu P, Nettleton D. Borrowing information across genes and experiments for improved error variance estimation in microarray data analysis. Statistical Applications in Genetics and Molecular Biology. 11: Article 12. PMID 22611597  0.88
2012 Liu S, Yeh CT, Tang HM, Nettleton D, Schnable PS. Gene mapping via bulked segregant RNA-Seq (BSR-Seq). Plos One. 7: e36406. PMID 22586469 DOI: 10.1371/journal.pone.0036406  0.88
2012 Qu L, Nettleton D, Dekkers JC. Improved estimation of the noncentrality parameter distribution from a large number of t-statistics, with applications to false discovery rate estimation in microarray data analysis. Biometrics. 68: 1178-87. PMID 22551000 DOI: 10.1111/j.1541-0420.2012.01764.x  0.88
2012 Hewezi T, Maier TR, Nettleton D, Baum TJ. The Arabidopsis microRNA396-GRF1/GRF3 regulatory module acts as a developmental regulator in the reprogramming of root cells during cyst nematode infection. Plant Physiology. 159: 321-35. PMID 22419826 DOI: 10.1104/pp.112.193649  0.88
2012 Lund SP, Nettleton D. The importance of distinct modeling strategies for gene and gene-specific treatment effects in hierarchical models for microarray data Annals of Applied Statistics. 6: 1118-1133. DOI: 10.1214/12-AOAS535  0.88
2012 Liang K, Nettleton D. Adaptive and dynamic adaptive procedures for false discovery rate control and estimation Journal of the Royal Statistical Society. Series B: Statistical Methodology. 74: 163-182. DOI: 10.1111/j.1467-9868.2011.01001.x  0.88
2012 Liebman M, Graef RL, Nettleton D, Cambardella CA. Use of legume green manures as nitrogen sources for corn production Renewable Agriculture and Food Systems. 27: 180-191. DOI: 10.1017/S1742170511000299  0.88
2012 Orr M, Liu P, Nettleton D. Estimating the Number of Genes That Are Differentially Expressed in Both of Two Independent Experiments Journal of Agricultural, Biological, and Environmental Statistics. 17: 583-600. DOI: 10.1007/s13253-012-0108-8  0.88
2012 Nettleton D. Design of Gene Expression Microarray Experiments Design and Analysis of Experiments. 3: 73-108. DOI: 10.1002/9781118147634.ch2  0.88
2011 Huang TH, Uthe JJ, Bearson SM, Demirkale CY, Nettleton D, Knetter S, Christian C, Ramer-Tait AE, Wannemuehler MJ, Tuggle CK. Distinct peripheral blood RNA responses to Salmonella in pigs differing in Salmonella shedding levels: intersection of IFNG, TLR and miRNA pathways. Plos One. 6: e28768. PMID 22174891 DOI: 10.1371/journal.pone.0028768  0.88
2011 Uthe JJ, Qu L, Couture O, Bearson SM, O'Connor AM, McKean JD, Torres YR, Dekkers JC, Nettleton D, Tuggle CK. Use of bioinformatic SNP predictions in differentially expressed genes to find SNPs associated with Salmonella colonization in swine. Journal of Animal Breeding and Genetics = Zeitschrift FüR TierzüChtung Und ZüChtungsbiologie. 128: 354-65. PMID 21906181 DOI: 10.1111/j.1439-0388.2011.00935.x  0.88
2011 Uthe JJ, Bearson SM, Qu L, Dekkers JC, Nettleton D, Rodriguez Torres Y, O'Connor AM, McKean JD, Tuggle CK. Integrating comparative expression profiling data and association of SNPs with Salmonella shedding for improved food safety and porcine disease resistance. Animal Genetics. 42: 521-34. PMID 21906103 DOI: 10.1111/j.1365-2052.2010.02171.x  0.88
2011 Liu JZ, Horstman HD, Braun E, Graham MA, Zhang C, Navarre D, Qiu WL, Lee Y, Nettleton D, Hill JH, Whitham SA. Soybean homologs of MPK4 negatively regulate defense responses and positively regulate growth and development. Plant Physiology. 157: 1363-78. PMID 21878550 DOI: 10.1104/pp.111.185686  0.88
2011 Schneider KT, van de Mortel M, Bancroft TJ, Braun E, Nettleton D, Nelson RT, Frederick RD, Baum TJ, Graham MA, Whitham SA. Biphasic gene expression changes elicited by Phakopsora pachyrhizi in soybean correlate with fungal penetration and haustoria formation. Plant Physiology. 157: 355-71. PMID 21791600 DOI: 10.1104/pp.111.181149  0.88
2011 Liu Z, Ramer-Tait AE, Henderson AL, Demirkale CY, Nettleton D, Wang C, Hostetter JM, Jergens AE, Wannemuehler MJ. Helicobacter bilis colonization enhances susceptibility to Typhlocolitis following an inflammatory trigger. Digestive Diseases and Sciences. 56: 2838-48. PMID 21503679 DOI: 10.1007/s10620-011-1701-3  0.88
2011 Kandoth PK, Ithal N, Recknor J, Maier T, Nettleton D, Baum TJ, Mitchum MG. The Soybean Rhg1 locus for resistance to the soybean cyst nematode Heterodera glycines regulates the expression of a large number of stress- and defense-related genes in degenerating feeding cells. Plant Physiology. 155: 1960-75. PMID 21335526 DOI: 10.1104/pp.110.167536  0.88
2011 Moscou MJ, Lauter N, Caldo RA, Nettleton D, Wise RP. Quantitative and temporal definition of the Mla transcriptional regulon during barley-powdery mildew interactions. Molecular Plant-Microbe Interactions : Mpmi. 24: 694-705. PMID 21323465 DOI: 10.1094/MPMI-09-10-0211  0.88
2011 Boddicker N, Gabler NK, Spurlock ME, Nettleton D, Dekkers JCM. Effects of ad libitum and restricted feed intake on growth performance and body composition of Yorkshire pigs selected for reduced residual feed intake Journal of Animal Science. 89: 40-51. PMID 20833771 DOI: 10.2527/jas.2010-3106  0.88
2011 Sadler LJ, Johnson AK, Lonergan SM, Nettleton D, Dekkers JC. The effect of selection for residual feed intake on general behavioral activity and the occurrence of lesions in Yorkshire gilts. Journal of Animal Science. 89: 258-66. PMID 20833769 DOI: 10.2527/jas.2009-2595  0.88
2011 Boddicker N, Gabler NK, Spurlock ME, Nettleton D, Dekkers JCM. Effects of ad libitum and restricted feeding on early production performance and body composition of Yorkshire pigs selected for reduced residual feed intake Animal. 5: 1344-1353. DOI: 10.1017/S175173111100036X  0.88
2011 Melnykov V, Maitra R, Nettleton D. Accounting for spot matching uncertainty in the analysis of proteomics data from two-dimensional gel electrophoresis Sankhya: the Indian Journal of Statistics. 73: 123-143. DOI: 10.1007/s13571-011-0016-x  0.88
2011 Swanson RK, Xu R, Nettleton DS, Glatz CE. Proteomics approach for predicting separation behavior of a mixture of proteins during downstream purification Aiche Annual Meeting, Conference Proceedings 0.88
2010 Fu Y, Springer NM, Ying K, Yeh CT, Iniguez AL, Richmond T, Wu W, Barbazuk B, Nettleton D, Jeddeloh J, Schnable PS. High-resolution genotyping via whole genome hybridizations to microarrays containing long oligonucleotide probes. Plos One. 5: e14178. PMID 21152036 DOI: 10.1371/journal.pone.0014178  0.88
2010 Ciraci C, Tuggle CK, Wannemuehler MJ, Nettleton D, Lamont SJ. Unique genome-wide transcriptome profiles of chicken macrophages exposed to Salmonella-derived endotoxin. Bmc Genomics. 11: 545. PMID 20929591 DOI: 10.1186/1471-2164-11-545  0.88
2010 Lkhagvadorj S, Qu L, Cai W, Couture OP, Barb CR, Hausman GJ, Nettleton D, Anderson LL, Dekkers JC, Tuggle CK. Gene expression profiling of the short-term adaptive response to acute caloric restriction in liver and adipose tissues of pigs differing in feed efficiency. American Journal of Physiology. Regulatory, Integrative and Comparative Physiology. 298: R494-507. PMID 19939971 DOI: 10.1152/ajpregu.00632.2009  0.88
2010 Demirkale CY, Nettleton D, Maiti T. Linear mixed model selection for false discovery rate control in microarray data analysis. Biometrics. 66: 621-9. PMID 19522873 DOI: 10.1111/j.1541-0420.2009.01286.x  0.88
2010 Liang K, Nettleton D. A hidden Markov model approach to testing multiple hypotheses on a tree-transformed Gene Ontology graph Journal of the American Statistical Association. 105: 1444-1454. DOI: 10.1198/jasa.2010.tm10195  0.88
2009 Swanson-Wagner RA, DeCook R, Jia Y, Bancroft T, Ji T, Zhao X, Nettleton D, Schnable PS. Paternal dominance of trans-eQTL influences gene expression patterns in maize hybrids. Science (New York, N.Y.). 326: 1118-20. PMID 19965432 DOI: 10.1126/science.1178294  0.88
2009 Springer NM, Ying K, Fu Y, Ji T, Yeh CT, Jia Y, Wu W, Richmond T, Kitzman J, Rosenbaum H, Iniguez AL, Barbazuk WB, Jeddeloh JA, Nettleton D, Schnable PS. Maize inbreds exhibit high levels of copy number variation (CNV) and presence/absence variation (PAV) in genome content. Plos Genetics. 5: e1000734. PMID 19956538 DOI: 10.1371/journal.pgen.1000734  0.88
2009 Liu S, Yeh CT, Ji T, Ying K, Wu H, Tang HM, Fu Y, Nettleton D, Schnable PS. Mu transposon insertion sites and meiotic recombination events co-localize with epigenetic marks for open chromatin across the maize genome. Plos Genetics. 5: e1000733. PMID 19936291 DOI: 10.1371/journal.pgen.1000733  0.76
2009 Xi L, Moscou MJ, Meng Y, Xu W, Caldo RA, Shaver M, Nettleton D, Wise RP. Transcript-based cloning of RRP46, a regulator of rRNA processing and R gene-independent cell death in barley-powdery mildew interactions. The Plant Cell. 21: 3280-95. PMID 19861556 DOI: 10.1105/tpc.109.066167  0.88
2009 Li X, Wei Y, Nettleton D, Brummer EC. Comparative gene expression profiles between heterotic and non-heterotic hybrids of tetraploid Medicago sativa. Bmc Plant Biology. 9: 107. PMID 19678936 DOI: 10.1186/1471-2229-9-107  0.32
2009 Schwab CR, Baas TJ, Stalder KJ, Nettleton D. Results from six generations of selection for intramuscular fat in Duroc swine using real-time ultrasound. I. Direct and correlated phenotypic responses to selection Journal of Animal Science. 87: 2774-2780. PMID 19502499 DOI: 10.2527/jas.2008-1335  0.88
2009 Brooks L, Strable J, Zhang X, Ohtsu K, Zhou R, Sarkar A, Hargreaves S, Elshire RJ, Eudy D, Pawlowska T, Ware D, Janick-Buckner D, Buckner B, Timmermans MCP, Schnable PS, ... Nettleton D, et al. Microdissection of shoot meristem functional domains Plos Genetics. 5. PMID 19424435 DOI: 10.1371/journal.pgen.1000476  0.88
2009 Liu Z, Henderson AL, Nettleton D, Wilson-Welder JH, Hostetter JM, Ramer-Tait A, Jergens AE, Wannemuehler MJ. Mucosal gene expression profiles following the colonization of immunocompetent defined-flora C3H mice with Helicobacter bilis: a prelude to typhlocolitis. Microbes and Infection / Institut Pasteur. 11: 374-83. PMID 19397886 DOI: 10.1016/j.micinf.2008.12.013  0.88
2009 Lkhagvadorj S, Qu L, Cai W, Couture OP, Barb CR, Hausman GJ, Nettleton D, Anderson LL, Dekkers JC, Tuggle CK. Microarray gene expression profiles of fasting induced changes in liver and adipose tissues of pigs expressing the melanocortin-4 receptor D298N variant. Physiological Genomics. 38: 98-111. PMID 19366786 DOI: 10.1152/physiolgenomics.90372.2008  0.88
2009 Elling AA, Mitreva M, Gai X, Martin J, Recknor J, Davis EL, Hussey RS, Nettleton D, McCarter JP, Baum TJ. Sequence mining and transcript profiling to explore cyst nematode parasitism. Bmc Genomics. 10: 58. PMID 19183474 DOI: 10.1186/1471-2164-10-58  0.88
2009 Li L, Foster CM, Gan Q, Nettleton D, James MG, Myers AM, Wurtele ES. Identification of the novel protein QQS as a component of the starch metabolic network in Arabidopsis leaves. The Plant Journal : For Cell and Molecular Biology. 58: 485-98. PMID 19154206 DOI: 10.1111/j.1365-313X.2009.03793.x  0.88
2009 Uthe JJ, Wang Y, Qu L, Nettleton D, Tuggle CK, Bearson SM. Correlating blood immune parameters and a CCT7 genetic variant with the shedding of Salmonella enterica serovar Typhimurium in swine. Veterinary Microbiology. 135: 384-8. PMID 18996651 DOI: 10.1016/j.vetmic.2008.09.074  0.88
2009 Nettleton D. Testing for the supremacy of a multinomial cell probability Journal of the American Statistical Association. 104: 1052-1059. DOI: 10.1198/jasa.2009.tm08213  0.88
2008 Skibbe DS, Wang X, Borsuk LA, Ashlock DA, Nettleton D, Schnable PS. Floret-specific differences in gene expression and support for the hypothesis that tapetal degeneration of Zea mays L. occurs via programmed cell death. Journal of Genetics and Genomics = Yi Chuan Xue Bao. 35: 603-16. PMID 18937917 DOI: 10.1016/S1673-8527(08)60081-8  0.88
2008 Tuggle CK, Wang YF, Couture OP, Qu L, Uthe JJ, Kuhar D, Lunney JK, Nettleton D, Dekkers JC, Bearson SM. Computational integration of structural and functional genomics data across species to develop information on the porcine inflammatory gene regulatory pathway. Developments in Biologicals. 132: 105-13. PMID 18817292  0.88
2008 Wang Y, Couture OP, Qu L, Uthe JJ, Bearson SM, Kuhar D, Lunney JK, Nettleton D, Dekkers JC, Tuggle CK. Analysis of porcine transcriptional response to Salmonella enterica serovar Choleraesuis suggests novel targets of NFkappaB are activated in the mesenteric lymph node. Bmc Genomics. 9: 437. PMID 18811943 DOI: 10.1186/1471-2164-9-437  0.88
2008 Strable J, Borsuk L, Nettleton D, Schnable PS, Irish EE. Microarray analysis of vegetative phase change in maize. The Plant Journal : For Cell and Molecular Biology. 56: 1045-57. PMID 18764925 DOI: 10.1111/j.1365-313X.2008.03661.x  0.88
2008 Flagel L, Udall J, Nettleton D, Wendel J. Duplicate gene expression in allopolyploid Gossypium reveals two temporally distinct phases of expression evolution. Bmc Biology. 6: 16. PMID 18416842 DOI: 10.1186/1741-7007-6-16  0.88
2008 Wang D, Nettleton D. Combining classical trait and microarray data to dissect transcriptional regulation: a case study. Tag. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik. 116: 683-90. PMID 18189124 DOI: 10.1007/s00122-007-0701-3  0.88
2008 Guo B, Wang Y, Shi F, Barton YW, Plummer P, Reynolds DL, Nettleton D, Grinnage-Pulley T, Lin J, Zhang Q. CmeR functions as a pleiotropic regulator and is required for optimal colonization of Campylobacter jejuni in vivo. Journal of Bacteriology. 190: 1879-90. PMID 18178742 DOI: 10.1128/JB.01796-07  0.88
2008 Nettleton D, Recknor J, Reecy JM. Identification of differentially expressed gene categories in microarray studies using nonparametric multivariate analysis. Bioinformatics (Oxford, England). 24: 192-201. PMID 18042553 DOI: 10.1093/bioinformatics/btm583  0.88
2007 Elling AA, Mitreva M, Recknor J, Gai X, Martin J, Maier TR, McDermott JP, Hewezi T, McK Bird D, Davis EL, Hussey RS, Nettleton D, McCarter JP, Baum TJ. Divergent evolution of arrested development in the dauer stage of Caenorhabditis elegans and the infective stage of Heterodera glycines. Genome Biology. 8: R211. PMID 17919324 DOI: 10.1186/gb-2007-8-10-r211  0.88
2007 Madsen ML, Oneal MJ, Gardner SW, Strait EL, Nettleton D, Thacker EL, Minion FC. Array-based genomic comparative hybridization analysis of field strains of Mycoplasma hyopneumoniae. Journal of Bacteriology. 189: 7977-82. PMID 17873054 DOI: 10.1128/JB.01068-07  0.88
2007 Dembinsky D, Woll K, Saleem M, Liu Y, Fu Y, Borsuk LA, Lamkemeyer T, Fladerer C, Madlung J, Barbazuk B, Nordheim A, Nettleton D, Schnable PS, Hochholdinger F. Transcriptomic and proteomic analyses of pericycle cells of the maize primary root. Plant Physiology. 145: 575-88. PMID 17766395 DOI: 10.1104/pp.107.106203  0.44
2007 Ohtsu K, Smith MB, Emrich SJ, Borsuk LA, Zhou R, Chen T, Zhang X, Timmermans MC, Beck J, Buckner B, Janick-Buckner D, Nettleton D, Scanlon MJ, Schnable PS. Global gene expression analysis of the shoot apical meristem of maize (Zea mays L.). The Plant Journal : For Cell and Molecular Biology. 52: 391-404. PMID 17764504 DOI: 10.1111/j.1365-313X.2007.03244.x  0.88
2007 van de Mortel M, Recknor JC, Graham MA, Nettleton D, Dittman JD, Nelson RT, Godoy CV, Abdelnoor RV, Almeida AM, Baum TJ, Whitham SA. Distinct biphasic mRNA changes in response to Asian soybean rust infection. Molecular Plant-Microbe Interactions : Mpmi. 20: 887-99. PMID 17722693 DOI: 10.1094/MPMI-20-8-0887  0.88
2007 Ruppert D, Nettleton D, Hwang JT. Exploring the information in p-values for the analysis and planning of multiple-test experiments. Biometrics. 63: 483-95. PMID 17715492 DOI: 10.1111/j.1541-0420.2006.00704.x  0.88
2007 Zhang X, Madi S, Borsuk L, Nettleton D, Elshire RJ, Buckner B, Janick-Buckner D, Beck J, Timmermans M, Schnable PS, Scanlon MJ. Laser microdissection of narrow sheath mutant maize uncovers novel gene expression in the shoot apical meristem. Plos Genetics. 3: e101. PMID 17571927 DOI: 10.1371/journal.pgen.0030101  0.88
2007 Zhao H, Nettleton D, Dekkers JCM. Evaluation of linkage disequilibrium measures between multi-allelic markers as predictors of linkage disequilibrium between single nucleotide polymorphisms Genetical Research. 89: 1-6. PMID 17517154 DOI: 10.1017/S0016672307008634  0.88
2007 Ithal N, Recknor J, Nettleton D, Maier T, Baum TJ, Mitchum MG. Developmental transcript profiling of cyst nematode feeding cells in soybean roots. Molecular Plant-Microbe Interactions : Mpmi. 20: 510-25. PMID 17506329 DOI: 10.1094/MPMI-20-5-0510  0.88
2007 Wang Y, Qu L, Uthe JJ, Bearson SM, Kuhar D, Lunney JK, Couture OP, Nettleton D, Dekkers JC, Tuggle CK. Global transcriptional response of porcine mesenteric lymph nodes to Salmonella enterica serovar Typhimurium. Genomics. 90: 72-84. PMID 17499962 DOI: 10.1016/j.ygeno.2007.03.018  0.88
2007 Yang C, Guo R, Jie F, Nettleton D, Peng J, Carr T, Yeakley JM, Fan JB, Whitham SA. Spatial analysis of arabidopsis thaliana gene expression in response to Turnip mosaic virus infection. Molecular Plant-Microbe Interactions : Mpmi. 20: 358-70. PMID 17427806 DOI: 10.1094/MPMI-20-4-0358  0.88
2007 Udall JA, Flagel LE, Cheung F, Woodward AW, Hovav R, Rapp RA, Swanson JM, Lee JJ, Gingle AR, Nettleton D, Town CD, Chen ZJ, Wendel JF. Spotted cotton oligonucleotide microarrays for gene expression analysis. Bmc Genomics. 8: 81. PMID 17389046 DOI: 10.1186/1471-2164-8-81  0.88
2007 Ithal N, Recknor J, Nettleton D, Hearne L, Maier T, Baum TJ, Mitchum MG. Parallel genome-wide expression profiling of host and pathogen during soybean cyst nematode infection of soybean. Molecular Plant-Microbe Interactions : Mpmi. 20: 293-305. PMID 17378432 DOI: 10.1094/MPMI-20-3-0293  0.88
2007 Zhang W, Carriquiry A, Nettleton D, Dekkers JC. Pooling mRNA in microarray experiments and its effect on power. Bioinformatics (Oxford, England). 23: 1217-24. PMID 17344238 DOI: 10.1093/bioinformatics/btm081  0.88
2006 Nettleton D. A discussion of statistical methods for design and analysis of microarray experiments for plant scientists. The Plant Cell. 18: 2112-21. PMID 16968907 DOI: 10.1105/tpc.106.041616  0.88
2006 Caldo RA, Nettleton D, Peng J, Wise RP. Stage-specific suppression of basal defense discriminates barley plants containing fast- and delayed-acting Mla powdery mildew resistance alleles. Molecular Plant-Microbe Interactions : Mpmi. 19: 939-47. PMID 16941898 DOI: 10.1094/MPMI-19-0939  0.88
2006 Wang D, Nettleton D. Identifying genes associated with a quantitative trait or quantitative trait locus via selective transcriptional profiling. Biometrics. 62: 504-14. PMID 16918915 DOI: 10.1111/j.1541-0420.2005.00491.x  0.88
2006 Nettleton D, Wang D. Selective transcriptional profiling for trait-based eQTL mapping Animal Genetics. 37: 13-17. PMID 16886997 DOI: 10.1111/j.1365-2052.2006.01478.x  0.88
2006 Zhao SH, Kuhar D, Lunney JK, Dawson H, Guidry C, Uthe JJ, Bearson SM, Recknor J, Nettleton D, Tuggle CK. Gene expression profiling in Salmonella Choleraesuis-infected porcine lung using a long oligonucleotide microarray. Mammalian Genome : Official Journal of the International Mammalian Genome Society. 17: 777-89. PMID 16845603 DOI: 10.1007/s00335-005-0155-3  0.88
2006 Skibbe DS, Wang X, Zhao X, Borsuk LA, Nettleton D, Schnable PS. Scanning microarrays at multiple intensities enhances discovery of differentially expressed genes. Bioinformatics (Oxford, England). 22: 1863-70. PMID 16731695 DOI: 10.1093/bioinformatics/btl270  0.44
2006 Udall JA, Swanson JM, Nettleton D, Percifield RJ, Wendel JF. A novel approach for characterizing expression levels of genes duplicated by polyploidy. Genetics. 173: 1823-7. PMID 16702424 DOI: 10.1534/genetics.106.058271  0.88
2006 Che P, Lall S, Nettleton D, Howell SH. Gene expression programs during shoot, root, and callus development in Arabidopsis tissue culture. Plant Physiology. 141: 620-37. PMID 16648215 DOI: 10.1104/pp.106.081240  0.32
2006 Swanson-Wagner RA, Jia Y, DeCook R, Borsuk LA, Nettleton D, Schnable PS. All possible modes of gene action are observed in a global comparison of gene expression in a maize F1 hybrid and its inbred parents. Proceedings of the National Academy of Sciences of the United States of America. 103: 6805-10. PMID 16641103 DOI: 10.1073/pnas.0510430103  0.88
2006 Madsen ML, Nettleton D, Thacker EL, Minion FC. Transcriptional profiling of Mycoplasma hyopneumoniae during iron depletion using microarrays. Microbiology (Reading, England). 152: 937-44. PMID 16549658 DOI: 10.1099/mic.0.28674-0  0.88
2006 Steelman CA, Recknor JC, Nettleton D, Reecy JM. Transcriptional profiling of myostatin-knockout mice implicates Wnt signaling in postnatal skeletal muscle growth and hypertrophy. Faseb Journal : Official Publication of the Federation of American Societies For Experimental Biology. 20: 580-2. PMID 16423875 DOI: 10.1096/fj.05-5125fje  0.88
2006 Madsen ML, Nettleton D, Thacker EL, Edwards R, Minion FC. Transcriptional profiling of Mycoplasma hyopneumoniae during heat shock using microarrays. Infection and Immunity. 74: 160-6. PMID 16368969 DOI: 10.1128/IAI.74.1.160-166.2006  0.88
2006 DeCook R, Lall S, Nettleton D, Howell SH. Genetic regulation of gene expression during shoot development in Arabidopsis. Genetics. 172: 1155-64. PMID 15956669 DOI: 10.1534/genetics.105.042275  0.52
2006 Nettleton D, Hwang JTG, Caldo RA, Wise RP. Estimating the number of true null hypotheses from a histogram of p values Journal of Agricultural, Biological, and Environmental Statistics. 11: 337-356. DOI: 10.1198/108571106X129135  0.88
2006 DeCook R, Nettleton D, Foster C, Wurtele ES. Identifying differentially expressed genes in unreplicated multiple-treatment microarray timecourse experiments Computational Statistics and Data Analysis. 50: 518-532. DOI: 10.1016/j.csda.2004.09.004  0.88
2005 Cocciolone SM, Nettleton D, Snook ME, Peterson T. Transformation of maize with the p1 transcription factor directs production of silk maysin, a corn earworm resistance factor, in concordance with a hierarchy of floral organ pigmentation. Plant Biotechnology Journal. 3: 225-35. PMID 17173622 DOI: 10.1111/j.1467-7652.2005.00120.x  0.88
2005 Zhao SH, Recknor J, Lunney JK, Nettleton D, Kuhar D, Orley S, Tuggle CK. Validation of a first-generation long-oligonucleotide microarray for transcriptional profiling in the pig. Genomics. 86: 618-25. PMID 16216716 DOI: 10.1016/j.ygeno.2005.08.001  0.88
2005 Woll K, Borsuk LA, Stransky H, Nettleton D, Schnable PS, Hochholdinger F. Isolation, characterization, and pericycle-specific transcriptome analyses of the novel maize lateral and seminal root initiation mutant rum1. Plant Physiology. 139: 1255-67. PMID 16215225 DOI: 10.1104/pp.105.067330  0.44
2005 Zhao H, Nettleton D, Soller M, Dekkers JCM. Evaluation of linkage disequilibrium measures between multi-allelic markers as predictors of linkage disequilibrium between markers and QTL Genetical Research. 86: 77-87. PMID 16181525 DOI: 10.1017/S001667230500769X  0.88
2005 Lee SH, Zhao SH, Recknor JC, Nettleton D, Orley S, Kang SK, Lee BC, Hwang WS, Tuggle CK. Transcriptional profiling using a novel cDNA array identifies differential gene expression during porcine embryo elongation. Molecular Reproduction and Development. 71: 129-39. PMID 15791594 DOI: 10.1002/mrd.20291  0.88
2005 Cook RN, Xin H, Nettleton D. Effects of cage stocking density on feeding behaviors of group-housed laying hens 2005 Asae Annual International Meeting 0.88
2004 Peterson-Burch BD, Nettleton D, Voytas DF. Genomic neighborhoods for Arabidopsis retrotransposons: a role for targeted integration in the distribution of the Metaviridae. Genome Biology. 5: R78. PMID 15461796 DOI: 10.1186/gb-2004-5-10-r78  0.88
2004 Lall S, Nettleton D, DeCook R, Che P, Howell SH. Quantitative trait loci associated with adventitious shoot formation in tissue culture and the program of shoot development in Arabidopsis. Genetics. 167: 1883-92. PMID 15342526 DOI: 10.1534/genetics.103.025213  0.52
2004 Caldo RA, Nettleton D, Wise RP. Interaction-dependent gene expression in Mla-specified response to barley powdery mildew. The Plant Cell. 16: 2514-28. PMID 15319481 DOI: 10.1105/tpc.104.023382  0.88
2004 Manly KF, Nettleton D, Hwang JT. Genomics, prior probability, and statistical tests of multiple hypotheses. Genome Research. 14: 997-1001. PMID 15173107 DOI: 10.1101/gr.2156804  0.88
2004 Steward BL, Tian LF, Nettleton D, Tang L. Reduced-dimension clustering for vegetation segmentation Transactions of the American Society of Agricultural Engineers. 47: 609-616.  0.88
2004 Persyn KE, Xin H, Nettleton D, Ikeguchi A, Gates RS. Feeding behaviors of laying hens with or without beak trimming Transactions of the American Society of Agricultural Engineers. 47: 591-596.  0.88
2003 Puthoff DP, Nettleton D, Rodermel SR, Baum TJ. Arabidopsis gene expression changes during cyst nematode parasitism revealed by statistical analyses of microarray expression profiles. The Plant Journal : For Cell and Molecular Biology. 33: 911-21. PMID 12609032 DOI: 10.1046/j.1365-313X.2003.01677.x  0.88
2003 Hwang JTG, Nettleton D. Principal components regression with data-chosen components and related methods Technometrics. 45: 70-79.  0.88
2002 Frame BR, Shou H, Chikwamba RK, Zhang Z, Xiang C, Fonger TM, Pegg SE, Li B, Nettleton DS, Pei D, Wang K. Agrobacterium tumefaciens-mediated transformation of maize embryos using a standard binary vector system. Plant Physiology. 129: 13-22. PMID 12011333 DOI: 10.1104/pp.000653  0.44
2002 Hwang JT, Nettleton D. Investigating the probability of sign inconsistency in the regression coefficients of markers flanking quantitative trait loci. Genetics. 160: 1697-705. PMID 11973322  0.88
2002 Ding J, Berleant D, Nettleton D, Wurtele E. Mining MEDLINE: abstracts, sentences, or phrases? Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 326-37. PMID 11928487  0.88
2002 Carson JA, Nettleton D, Reecy JM. Differential gene expression in the rat soleus muscle during early work overload-induced hypertrophy. Faseb Journal : Official Publication of the Federation of American Societies For Experimental Biology. 16: 207-9. PMID 11744623 DOI: 10.1096/fj.01-0544fje  0.88
2002 Nettleton D. Testing for ordered means in a variation of the normal mixture model Journal of Statistical Planning and Inference. 107: 143-153. DOI: 10.1016/S0378-3758(02)00249-5  0.88
2002 Huang W, Nettleton D, Gu X. Expression pattern of yeast sporulation: A case study for regulatory changes after yeast genome duplication Information Sciences. 145: 261-269. DOI: 10.1016/S0020-0255(02)00236-0  0.88
2001 Nettleton D, Banerjee T. Testing the equality of distributions of random vectors with categorial components Computational Statistics and Data Analysis. 37: 195-208. DOI: 10.1016/S0167-9473(01)00015-9  0.88
2000 Nettleton D, Doerge RW. Accounting for variability in the use of permutation testing to detect quantitative trait loci Biometrics. 56: 52-58. PMID 10783776  0.88
2000 Bilder CR, Loughin TM, Nettleton D. Multiple marginal independence testing for pick any/c variables Communications in Statistics - Theory and Methods. 29: 1285-1316.  0.88
1999 Nettleton D. Convergence properties of the EM algorithm in constrained parameter spaces Canadian Journal of Statistics. 27: 639-648.  0.88
1999 Nettleton D. Order-restricted hypothesis testing in a variation of the normal mixture model Canadian Journal of Statistics. 27: 383-394.  0.88
1998 Nettleton D, Praestgaard J. Interval mapping of quantitative trait loci through order-restricted inference Biometrics. 54: 74-87. DOI: 10.2307/2533997  0.88
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