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Items: 1 to 50 of 187

1.

Assessing plant performance in the Enviratron.

Bao Y, Zarecor S, Shah D, Tuel T, Campbell DA, Chapman AVE, Imberti D, Kiekhaefer D, Imberti H, Lübberstedt T, Yin Y, Nettleton D, Lawrence-Dill CJ, Whitham SA, Tang L, Howell SH.

Plant Methods. 2019 Oct 23;15:117. doi: 10.1186/s13007-019-0504-y. eCollection 2019.

2.

Predicting rice blast disease: machine learning versus process-based models.

Nettleton DF, Katsantonis D, Kalaitzidis A, Sarafijanovic-Djukic N, Puigdollers P, Confalonieri R.

BMC Bioinformatics. 2019 Oct 22;20(1):514. doi: 10.1186/s12859-019-3065-1.

3.

Correction to: small RNA discovery in the interaction between barley and the powdery mildew pathogen.

Hunt M, Banerjee S, Surana P, Liu M, Fuerst G, Mathioni S, Meyers BC, Nettleton D, Wise RP.

BMC Genomics. 2019 Sep 4;20(1):697. doi: 10.1186/s12864-019-6012-7.

4.

Fully Bayesian analysis of RNA-seq counts for the detection of gene expression heterosis.

Landau W, Niemi J, Nettleton D.

J Am Stat Assoc. 2019;114(526):610-621. doi: 10.1080/01621459.2018.1497496. Epub 2018 Nov 13.

5.

Small RNA discovery in the interaction between barley and the powdery mildew pathogen.

Hunt M, Banerjee S, Surana P, Liu M, Fuerst G, Mathioni S, Meyers BC, Nettleton D, Wise RP.

BMC Genomics. 2019 Jul 25;20(1):610. doi: 10.1186/s12864-019-5947-z. Erratum in: BMC Genomics. 2019 Sep 4;20(1):697.

6.

Stress response to CO2 deprivation by Arabidopsis thaliana in plant cultures.

Banerjee S, Siemianowski O, Liu M, Lind KR, Tian X, Nettleton D, Cademartiri L.

PLoS One. 2019 Mar 13;14(3):e0212462. doi: 10.1371/journal.pone.0212462. eCollection 2019.

7.

Empirical Comparisons of Different Statistical Models To Identify and Validate Kernel Row Number-Associated Variants from Structured Multi-parent Mapping Populations of Maize.

Yang J, Yeh CE, Ramamurthy RK, Qi X, Fernando RL, Dekkers JCM, Garrick DJ, Nettleton D, Schnable PS.

G3 (Bethesda). 2018 Nov 6;8(11):3567-3575. doi: 10.1534/g3.118.200636.

8.

Crowdsourcing image analysis for plant phenomics to generate ground truth data for machine learning.

Zhou N, Siegel ZD, Zarecor S, Lee N, Campbell DA, Andorf CM, Nettleton D, Lawrence-Dill CJ, Ganapathysubramanian B, Kelly JW, Friedberg I.

PLoS Comput Biol. 2018 Jul 30;14(7):e1006337. doi: 10.1371/journal.pcbi.1006337. eCollection 2018 Jul.

9.

QQS orphan gene and its interactor NF-YC4 reduce susceptibility to pathogens and pests.

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.

Plant Biotechnol J. 2019 Jan;17(1):252-263. doi: 10.1111/pbi.12961. Epub 2018 Jul 6.

10.

A hidden Markov tree model for testing multiple hypotheses corresponding to Gene Ontology gene sets.

Liang K, Du C, You H, Nettleton D.

BMC Bioinformatics. 2018 Mar 27;19(1):107. doi: 10.1186/s12859-018-2106-5.

11.

Single-Parent Expression Is a General Mechanism Driving Extensive Complementation of Non-syntenic Genes in Maize Hybrids.

Baldauf JA, Marcon C, Lithio A, Vedder L, Altrogge L, Piepho HP, Schoof H, Nettleton D, Hochholdinger F.

Curr Biol. 2018 Feb 5;28(3):431-437.e4. doi: 10.1016/j.cub.2017.12.027. Epub 2018 Jan 18.

12.

Distinct genetic architectures for phenotype means and plasticities in Zea mays.

Kusmec A, Srinivasan S, Nettleton D, Schnable PS.

Nat Plants. 2017 Sep;3(9):715-723. doi: 10.1038/s41477-017-0007-7. Epub 2017 Sep 4.

13.

Substantial contribution of genetic variation in the expression of transcription factors to phenotypic variation revealed by eRD-GWAS.

Lin HY, Liu Q, Li X, Yang J, Liu S, Huang Y, Scanlon MJ, Nettleton D, Schnable PS.

Genome Biol. 2017 Oct 17;18(1):192. doi: 10.1186/s13059-017-1328-6.

14.

Interchromosomal Transfer of Immune Regulation During Infection of Barley with the Powdery Mildew Pathogen.

Surana P, Xu R, Fuerst G, Chapman AVE, Nettleton D, Wise RP.

G3 (Bethesda). 2017 Oct 5;7(10):3317-3329. doi: 10.1534/g3.117.300125.

15.

Microbial community sequencing analysis of the calf eye microbiota and relationship to infectious bovine keratoconjunctivitis.

Cullen JN, Lithio A, Seetharam AS, Zheng Y, Li G, Nettleton D, O'Connor AM.

Vet Microbiol. 2017 Aug;207:267-279. doi: 10.1016/j.vetmic.2017.07.003. Epub 2017 Jul 5.

PMID:
28757034
16.

Complexity and specificity of the maize (Zea mays L.) root hair transcriptome.

Hey S, Baldauf J, Opitz N, Lithio A, Pasha A, Provart N, Nettleton D, Hochholdinger F.

J Exp Bot. 2017 Apr 1;68(9):2175-2185. doi: 10.1093/jxb/erx104.

17.

Non-syntenic genes drive RTCS-dependent regulation of the embryo transcriptome during formation of seminal root primordia in maize (Zea mays L.).

Tai H, Opitz N, Lithio A, Lu X, Nettleton D, Hochholdinger F.

J Exp Bot. 2017 Jan 1;68(3):403-414. doi: 10.1093/jxb/erw422.

18.

Discovery and Characterization of the 3-Hydroxyacyl-ACP Dehydratase Component of the Plant Mitochondrial Fatty Acid Synthase System.

Guan X, Okazaki Y, Lithio A, Li L, Zhao X, Jin H, Nettleton D, Saito K, Nikolau BJ.

Plant Physiol. 2017 Apr;173(4):2010-2028. doi: 10.1104/pp.16.01732. Epub 2017 Feb 15.

19.

Medicinal Chemistry Profiling of Monocyclic 1,2-Azaborines.

Zhao P, Nettleton DO, Karki RG, Zécri FJ, Liu SY.

ChemMedChem. 2017 Mar 7;12(5):358-361. doi: 10.1002/cmdc.201700047. Epub 2017 Feb 21.

20.

Stability of Single-Parent Gene Expression Complementation in Maize Hybrids upon Water Deficit Stress.

Marcon C, Paschold A, Malik WA, Lithio A, Baldauf JA, Altrogge L, Opitz N, Lanz C, Schoof H, Nettleton D, Piepho HP, Hochholdinger F.

Plant Physiol. 2017 Feb;173(2):1247-1257. doi: 10.1104/pp.16.01045. Epub 2016 Dec 20.

21.

Genome-wide methylation profile following prenatal and postnatal dietary omega-3 fatty acid supplementation in pigs.

Boddicker RL, Koltes JE, Fritz-Waters ER, Koesterke L, Weeks N, Yin T, Mani V, Nettleton D, Reecy JM, Baumgard LH, Spencer JD, Gabler NK, Ross JW.

Anim Genet. 2016 Dec;47(6):658-671. doi: 10.1111/age.12468. Epub 2016 Aug 25.

PMID:
27558209
22.

Accounting for host cell protein behavior in anion-exchange chromatography.

Swanson RK, Xu R, Nettleton DS, Glatz CE.

Biotechnol Prog. 2016 Nov;32(6):1453-1463. doi: 10.1002/btpr.2342. Epub 2016 Oct 21.

PMID:
27556579
23.

A Clade-Specific Arabidopsis Gene Connects Primary Metabolism and Senescence.

Jones DC, Zheng W, Huang S, Du C, Zhao X, Yennamalli RM, Sen TZ, Nettleton D, Wurtele ES, Li L.

Front Plant Sci. 2016 Jul 12;7:983. doi: 10.3389/fpls.2016.00983. eCollection 2016.

24.

Empirical Bayes analysis of RNA-seq data for detection of gene expression heterosis.

Niemi J, Mittman E, Landau W, Nettleton D.

J Agric Biol Environ Stat. 2015 Dec;20(4):614-628.

25.

Genes and Small RNA Transcripts Exhibit Dosage-Dependent Expression Pattern in Maize Copy-Number Alterations.

Zuo T, Zhang J, Lithio A, Dash S, Weber DF, Wise R, Nettleton D, Peterson T.

Genetics. 2016 Jul;203(3):1133-47. doi: 10.1534/genetics.116.188235. Epub 2016 Apr 29.

26.

Hierarchical Modeling and Differential Expression Analysis for RNA-seq Experiments with Inbred and Hybrid Genotypes.

Lithio A, Nettleton D.

J Agric Biol Environ Stat. 2015 Dec;20(4):598-613. Epub 2015 Oct 5.

27.

Root Type-Specific Reprogramming of Maize Pericycle Transcriptomes by Local High Nitrate Results in Disparate Lateral Root Branching Patterns.

Yu P, Baldauf JA, Lithio A, Marcon C, Nettleton D, Li C, Hochholdinger F.

Plant Physiol. 2016 Mar;170(3):1783-98. doi: 10.1104/pp.15.01885. Epub 2016 Jan 25.

28.

Post-weaning blood transcriptomic differences between Yorkshire pigs divergently selected for residual feed intake.

Liu H, Nguyen YT, Nettleton D, Dekkers JC, Tuggle CK.

BMC Genomics. 2016 Jan 22;17:73. doi: 10.1186/s12864-016-2395-x.

29.

Detecting Differentially Expressed Genes with RNA-seq Data Using Backward Selection to Account for the Effects of Relevant Covariates.

Nguyen Y, Nettleton D, Liu H, Tuggle CK.

J Agric Biol Environ Stat. 2015;20(4):577-597. Epub 2015 Oct 1.

30.

Transcriptomic and anatomical complexity of primary, seminal, and crown roots highlight root type-specific functional diversity in maize (Zea mays L.).

Tai H, Lu X, Opitz N, Marcon C, Paschold A, Lithio A, Nettleton D, Hochholdinger F.

J Exp Bot. 2016 Feb;67(4):1123-35. doi: 10.1093/jxb/erv513. Epub 2015 Nov 30.

31.

QQS orphan gene regulates carbon and nitrogen partitioning across species via NF-YC interactions.

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, Wurtele ES.

Proc Natl Acad Sci U S A. 2015 Nov 24;112(47):14734-9. doi: 10.1073/pnas.1514670112. Epub 2015 Nov 9.

32.

Extensive tissue-specific transcriptomic plasticity in maize primary roots upon water deficit.

Opitz N, Marcon C, Paschold A, Malik WA, Lithio A, Brandt R, Piepho HP, Nettleton D, Hochholdinger F.

J Exp Bot. 2016 Feb;67(4):1095-107. doi: 10.1093/jxb/erv453. Epub 2015 Oct 13.

33.

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.

Yang J, Jiang H, Yeh CT, Yu J, Jeddeloh JA, Nettleton D, Schnable PS.

Plant J. 2015 Nov;84(3):587-96. doi: 10.1111/tpj.13029.

34.

ArcA Controls Metabolism, Chemotaxis, and Motility Contributing to the Pathogenicity of Avian Pathogenic Escherichia coli.

Jiang F, An C, Bao Y, Zhao X, Jernigan RL, Lithio A, Nettleton D, Li L, Wurtele ES, Nolan LK, Lu C, Li G.

Infect Immun. 2015 Sep;83(9):3545-54. doi: 10.1128/IAI.00312-15. Epub 2015 Jun 22.

35.

The knottin-like Blufensin family regulates genes involved in nuclear import and the secretory pathway in barley-powdery mildew interactions.

Xu W, Meng Y, Surana P, Fuerst G, Nettleton D, Wise RP.

Front Plant Sci. 2015 Jun 4;6:409. doi: 10.3389/fpls.2015.00409. eCollection 2015.

36.

Investigation of the efficacy of albumin removal procedures on porcine serum proteome profile.

Grubbs JK, Tuggle CK, Dekkers JC, Boddicker NJ, Nguyen YT, Huff-Lonergan E, Nettleton D, Lonergan SM.

J Anim Sci. 2015 Apr;93(4):1592-8. doi: 10.2527/jas.2014-8559.

PMID:
26020181
37.

Broadly Conserved Fungal Effector BEC1019 Suppresses Host Cell Death and Enhances Pathogen Virulence in Powdery Mildew of Barley (Hordeum vulgare L.).

Whigham E, Qi S, Mistry D, Surana P, Xu R, Fuerst G, Pliego C, Bindschedler LV, Spanu PD, Dickerson JA, Innes RW, Nettleton D, Bogdanove AJ, Wise RP.

Mol Plant Microbe Interact. 2015 Sep;28(9):968-83. doi: 10.1094/MPMI-02-15-0027-FI. Epub 2015 Aug 26.

38.

SimSeq: a nonparametric approach to simulation of RNA-sequence datasets.

Benidt S, Nettleton D.

Bioinformatics. 2015 Jul 1;31(13):2131-40. doi: 10.1093/bioinformatics/btv124. Epub 2015 Feb 26.

39.

A systems biology approach toward understanding seed composition in soybean.

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.

BMC Genomics. 2015;16 Suppl 3:S9. doi: 10.1186/1471-2164-16-S3-S9. Epub 2015 Jan 29.

40.

The maize brown midrib4 (bm4) gene encodes a functional folylpolyglutamate synthase.

Li L, Hill-Skinner S, Liu S, Beuchle D, Tang HM, Yeh CT, Nettleton D, Schnable PS.

Plant J. 2015 Feb;81(3):493-504. doi: 10.1111/tpj.12745. Epub 2015 Jan 9. Erratum in: Plant J. 2017 Mar;89(5):1076.

41.

Estimation and Testing of Gene Expression Heterosis.

Ji T, Liu P, Nettleton D.

J Agric Biol Environ Stat. 2014 Sep;19(3):319-337.

42.

Nonsyntenic genes drive highly dynamic complementation of gene expression in maize hybrids.

Paschold A, Larson NB, Marcon C, Schnable JC, Yeh CT, Lanz C, Nettleton D, Piepho HP, Schnable PS, Hochholdinger F.

Plant Cell. 2014 Oct;26(10):3939-48. doi: 10.1105/tpc.114.130948. Epub 2014 Oct 14.

43.

Transcriptional analysis of the global regulatory networks active in Pseudomonas syringae during leaf colonization.

Yu X, Lund SP, Greenwald JW, Records AH, Scott RA, Nettleton D, Lindow SE, Gross DC, Beattie GA.

MBio. 2014 Sep 2;5(5):e01683-14. doi: 10.1128/mBio.01683-14.

44.

An improved method for computing q-values when the distribution of effect sizes is asymmetric.

Orr M, Liu P, Nettleton D.

Bioinformatics. 2014 Nov 1;30(21):3044-53. doi: 10.1093/bioinformatics/btu432. Epub 2014 Jul 14.

45.

Copy number variation detection using next generation sequencing read counts.

Wang H, Nettleton D, Ying K.

BMC Bioinformatics. 2014 Apr 14;15:109. doi: 10.1186/1471-2105-15-109.

46.

Salmonella enterica serovar Typhimurium-infected pigs with different shedding levels exhibit distinct clinical, peripheral cytokine and transcriptomic immune response phenotypes.

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.

Innate Immun. 2015 Apr;21(3):227-41. doi: 10.1177/1753425914525812. Epub 2014 Mar 14.

PMID:
24632525
47.

Code-assisted discovery of TAL effector targets in bacterial leaf streak of rice reveals contrast with bacterial blight and a novel susceptibility gene.

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.

PLoS Pathog. 2014 Feb 27;10(2):e1003972. doi: 10.1371/journal.ppat.1003972. eCollection 2014 Feb. Erratum in: PLoS Pathog. 2014 Apr;10(4):e1004126.

48.

Endometrial gene expression profiling in pregnant Meishan and Yorkshire pigs on day 12 of gestation.

Gu T, Zhu MJ, Schroyen M, Qu L, Nettleton D, Kuhar D, Lunney JK, Ross JW, Zhao SH, Tuggle CK.

BMC Genomics. 2014 Feb 24;15:156. doi: 10.1186/1471-2164-15-156.

49.

The maize brown midrib2 (bm2) gene encodes a methylenetetrahydrofolate reductase that contributes to lignin accumulation.

Tang HM, Liu S, Hill-Skinner S, Wu W, Reed D, Yeh CT, Nettleton D, Schnable PS.

Plant J. 2014 Feb;77(3):380-92. doi: 10.1111/tpj.12394. Epub 2014 Jan 10.

50.

Host-induced gene silencing in barley powdery mildew reveals a class of ribonuclease-like effectors.

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.

Mol Plant Microbe Interact. 2013 Jun;26(6):633-42. doi: 10.1094/MPMI-01-13-0005-R.

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