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Items: 47

1.

Many rice genes are differentially spliced between roots and shoots but cytokinin has minimal effect on splicing.

Freese NH, Estrada AR, Blakley IC, Duan J, Loraine AE.

Plant Direct. 2019 May 17;3(5):e00136. doi: 10.1002/pld3.136. eCollection 2019 May.

2.

Coordination of Chloroplast Development through the Action of the GNC and GLK Transcription Factor Families.

Zubo YO, Blakley IC, Franco-Zorrilla JM, Yamburenko MV, Solano R, Kieber JJ, Loraine AE, Schaller GE.

Plant Physiol. 2018 Sep;178(1):130-147. doi: 10.1104/pp.18.00414. Epub 2018 Jul 12.

3.

Cell-specific cis-natural antisense transcripts (cis-NATs) in the sperm and the pollen vegetative cells of Arabidopsis thaliana.

Qin P, Loraine AE, McCormick S.

F1000Res. 2018 Jan 22;7:93. doi: 10.12688/f1000research.13311.1. eCollection 2018.

4.

Genome-wide characterization of differential transcript usage in Arabidopsis thaliana.

Vaneechoutte D, Estrada AR, Lin YC, Loraine AE, Vandepoele K.

Plant J. 2017 Dec;92(6):1218-1231. doi: 10.1111/tpj.13746. Epub 2017 Nov 20.

5.

Salt tolerance response revealed by RNA-Seq in a diploid halophytic wild relative of sweet potato.

Luo Y, Reid R, Freese D, Li C, Watkins J, Shi H, Zhang H, Loraine A, Song BH.

Sci Rep. 2017 Aug 29;7(1):9624. doi: 10.1038/s41598-017-09241-x.

6.

Cytokinin induces genome-wide binding of the type-B response regulator ARR10 to regulate growth and development in Arabidopsis.

Zubo YO, Blakley IC, Yamburenko MV, Worthen JM, Street IH, Franco-Zorrilla JM, Zhang W, Hill K, Raines T, Solano R, Kieber JJ, Loraine AE, Schaller GE.

Proc Natl Acad Sci U S A. 2017 Jul 18;114(29):E5995-E6004. doi: 10.1073/pnas.1620749114. Epub 2017 Jul 3.

7.

Characterization of the cytokinin-responsive transcriptome in rice.

Raines T, Blakley IC, Tsai YC, Worthen JM, Franco-Zorrilla JM, Solano R, Schaller GE, Loraine AE, Kieber JJ.

BMC Plant Biol. 2016 Dec 8;16(1):260.

8.

RNA-Seq Links the Transcription Factors AINTEGUMENTA and AINTEGUMENTA-LIKE6 to Cell Wall Remodeling and Plant Defense Pathways.

Krizek BA, Bequette CJ, Xu K, Blakley IC, Fu ZQ, Stratmann JW, Loraine AE.

Plant Physiol. 2016 Jul;171(3):2069-84. doi: 10.1104/pp.15.01625. Epub 2016 May 20.

9.

Integrated genome browser: visual analytics platform for genomics.

Freese NH, Norris DC, Loraine AE.

Bioinformatics. 2016 Jul 15;32(14):2089-95. doi: 10.1093/bioinformatics/btw069. Epub 2016 Mar 16.

10.

ProtAnnot: an App for Integrated Genome Browser to display how alternative splicing and transcription affect proteins.

Mall T, Eckstein J, Norris D, Vora H, Freese NH, Loraine AE.

Bioinformatics. 2016 Aug 15;32(16):2499-501. doi: 10.1093/bioinformatics/btw068. Epub 2016 Apr 7.

11.

A Comparison of transgenic and wild type soybean seeds: analysis of transcriptome profiles using RNA-Seq.

Lambirth KC, Whaley AM, Blakley IC, Schlueter JA, Bost KL, Loraine AE, Piller KJ.

BMC Biotechnol. 2015 Oct 1;15:89. doi: 10.1186/s12896-015-0207-z.

12.

Analysis of pollen-specific alternative splicing in Arabidopsis thaliana via semi-quantitative PCR.

Estrada AD, Freese NH, Blakley IC, Loraine AE.

PeerJ. 2015 Apr 28;3:e919. doi: 10.7717/peerj.919. eCollection 2015.

13.

RNA-Seq analysis and annotation of a draft blueberry genome assembly identifies candidate genes involved in fruit ripening, biosynthesis of bioactive compounds, and stage-specific alternative splicing.

Gupta V, Estrada AD, Blakley I, Reid R, Patel K, Meyer MD, Andersen SU, Brown AF, Lila MA, Loraine AE.

Gigascience. 2015 Feb 13;4:5. doi: 10.1186/s13742-015-0046-9. eCollection 2015.

14.

Analysis and visualization of RNA-Seq expression data using RStudio, Bioconductor, and Integrated Genome Browser.

Loraine AE, Blakley IC, Jagadeesan S, Harper J, Miller G, Firon N.

Methods Mol Biol. 2015;1284:481-501. doi: 10.1007/978-1-4939-2444-8_24.

15.

COBRA-LIKE2, a member of the glycosylphosphatidylinositol-anchored COBRA-LIKE family, plays a role in cellulose deposition in arabidopsis seed coat mucilage secretory cells.

Ben-Tov D, Abraham Y, Stav S, Thompson K, Loraine A, Elbaum R, de Souza A, Pauly M, Kieber JJ, Harpaz-Saad S.

Plant Physiol. 2015 Mar;167(3):711-24. doi: 10.1104/pp.114.240671. Epub 2015 Jan 12.

16.

Comparisons of computational methods for differential alternative splicing detection using RNA-seq in plant systems.

Liu R, Loraine AE, Dickerson JA.

BMC Bioinformatics. 2014 Dec 16;15:364. doi: 10.1186/s12859-014-0364-4.

17.

A protocol for visual analysis of alternative splicing in RNA-Seq data using integrated genome browser.

Gulledge AA, Vora H, Patel K, Loraine AE.

Methods Mol Biol. 2014;1158:123-37. doi: 10.1007/978-1-4939-0700-7_8.

18.

Efficient quantification of the health-relevant anthocyanin and phenolic acid profiles in commercial cultivars and breeding selections of blueberries ( Vaccinium spp.).

Yousef GG, Brown AF, Funakoshi Y, Mbeunkui F, Grace MH, Ballington JR, Loraine A, Lila MA.

J Agric Food Chem. 2013 May 22;61(20):4806-15. doi: 10.1021/jf400823s. Epub 2013 May 13.

PMID:
23635035
19.

RNA-seq of Arabidopsis pollen uncovers novel transcription and alternative splicing.

Loraine AE, McCormick S, Estrada A, Patel K, Qin P.

Plant Physiol. 2013 Jun;162(2):1092-109. doi: 10.1104/pp.112.211441. Epub 2013 Apr 16.

20.

Identification of cytokinin-responsive genes using microarray meta-analysis and RNA-Seq in Arabidopsis.

Bhargava A, Clabaugh I, To JP, Maxwell BB, Chiang YH, Schaller GE, Loraine A, Kieber JJ.

Plant Physiol. 2013 May;162(1):272-94. doi: 10.1104/pp.113.217026. Epub 2013 Mar 22.

21.

Mining Arabidopsis thaliana RNA-seq data with Integrated Genome Browser reveals stress-induced alternative splicing of the putative splicing regulator SR45a.

Gulledge AA, Roberts AD, Vora H, Patel K, Loraine AE.

Am J Bot. 2012 Feb;99(2):219-31. doi: 10.3732/ajb.1100355. Epub 2012 Jan 30.

22.

A regulon conserved in monocot and dicot plants defines a functional module in antifungal plant immunity.

Humphry M, Bednarek P, Kemmerling B, Koh S, Stein M, Göbel U, Stüber K, Pislewska-Bednarek M, Loraine A, Schulze-Lefert P, Somerville S, Panstruga R.

Proc Natl Acad Sci U S A. 2010 Dec 14;107(50):21896-901. doi: 10.1073/pnas.1003619107. Epub 2010 Nov 22.

23.

Prevalence of alternative splicing choices in Arabidopsis thaliana.

English AC, Patel KS, Loraine AE.

BMC Plant Biol. 2010 Jun 4;10:102. doi: 10.1186/1471-2229-10-102.

24.

Assembly of an interactive correlation network for the Arabidopsis genome using a novel heuristic clustering algorithm.

Mutwil M, Usadel B, Schütte M, Loraine A, Ebenhöh O, Persson S.

Plant Physiol. 2010 Jan;152(1):29-43. doi: 10.1104/pp.109.145318. Epub 2009 Nov 4.

25.

Genoviz Software Development Kit: Java tool kit for building genomics visualization applications.

Helt GA, Nicol JW, Erwin E, Blossom E, Blanchard SG Jr, Chervitz SA, Harmon C, Loraine AE.

BMC Bioinformatics. 2009 Aug 25;10:266. doi: 10.1186/1471-2105-10-266.

26.

The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets.

Nicol JW, Helt GA, Blanchard SG Jr, Raja A, Loraine AE.

Bioinformatics. 2009 Oct 15;25(20):2730-1. doi: 10.1093/bioinformatics/btp472. Epub 2009 Aug 4.

27.

Co-expression analysis of metabolic pathways in plants.

Loraine A.

Methods Mol Biol. 2009;553:247-64. doi: 10.1007/978-1-60327-563-7_12. Review.

PMID:
19588109
28.
29.

Genome of Mycoplasma arthritidis.

Dybvig K, Zuhua C, Lao P, Jordan DS, French CT, Tu AH, Loraine AE.

Infect Immun. 2008 Sep;76(9):4000-8. doi: 10.1128/IAI.00516-08. Epub 2008 Jun 23.

30.

Genome-scale cluster analysis of replicated microarrays using shrinkage correlation coefficient.

Yao J, Chang C, Salmi ML, Hung YS, Loraine A, Roux SJ.

BMC Bioinformatics. 2008 Jun 18;9:288. doi: 10.1186/1471-2105-9-288.

31.

CressExpress: a tool for large-scale mining of expression data from Arabidopsis.

Srinivasasainagendra V, Page GP, Mehta T, Coulibaly I, Loraine AE.

Plant Physiol. 2008 Jul;147(3):1004-16. doi: 10.1104/pp.107.115535. Epub 2008 May 8.

32.

Large-scale transposon mutagenesis of Mycoplasma pulmonis.

French CT, Lao P, Loraine AE, Matthews BT, Yu H, Dybvig K.

Mol Microbiol. 2008 Jul;69(1):67-76. doi: 10.1111/j.1365-2958.2008.06262.x. Epub 2008 Apr 28.

33.

Commonality of functional annotation: a method for prioritization of candidate genes from genome-wide linkage studies.

Shriner D, Baye TM, Padilla MA, Zhang S, Vaughan LK, Loraine AE.

Nucleic Acids Res. 2008 Mar;36(4):e26. doi: 10.1093/nar/gkn007. Epub 2008 Feb 7.

34.

Methods for nutrigenomics and longevity studies in Drosophila: effects of diets high in sucrose, palmitic acid, soy, or beef.

Ye J, Cui X, Loraine A, Bynum K, Kim NC, White G, De Luca M, Garfinkel MD, Lu X, Ruden DM.

Methods Mol Biol. 2007;371:111-41. Review.

PMID:
17634578
36.

Transcriptional coordination of the metabolic network in Arabidopsis.

Wei H, Persson S, Mehta T, Srinivasasainagendra V, Chen L, Page GP, Somerville C, Loraine A.

Plant Physiol. 2006 Oct;142(2):762-74. Epub 2006 Aug 18.

37.

Visualization techniques for genomic data.

Loraine AE, Helt GA.

Proc IEEE Comput Soc Bioinform Conf. 2002;1:321-6. Review.

PMID:
15838148
38.

Protein-based analysis of alternative splicing in the human genome.

Loraine AE, Helt GA, Cline MS, Siani-Rose MA.

Proc IEEE Comput Soc Bioinform Conf. 2002;1:118-24.

PMID:
15838129
39.

MARA: a novel approach for highly multiplexed locus-specific SNP genotyping using high-density DNA oligonucleotide arrays.

Shapero MH, Zhang J, Loraine A, Liu W, Di X, Liu G, Jones KW.

Nucleic Acids Res. 2004 Dec 15;32(22):e181.

40.

Exploring alternative transcript structure in the human genome using blocks and InterPro.

Loraine AE, Helt GA, Cline MS, Siani-Rose MA.

J Bioinform Comput Biol. 2003 Jul;1(2):289-306.

PMID:
15290774
41.

The effects of alternative splicing on transmembrane proteins in the mouse genome.

Cline MS, Shigeta R, Wheeler RL, Siani-Rose MA, Kulp D, Loraine AE.

Pac Symp Biocomput. 2004:17-28.

42.

NetAffx: Affymetrix probesets and annotations.

Liu G, Loraine AE, Shigeta R, Cline M, Cheng J, Valmeekam V, Sun S, Kulp D, Siani-Rose MA.

Nucleic Acids Res. 2003 Jan 1;31(1):82-6.

43.
44.

Structure-based comparison of four eukaryotic genomes.

Cline M, Liu G, Loraine AE, Shigeta R, Cheng J, Mei G, Kulp D, Siani-Rose MA.

Pac Symp Biocomput. 2002:127-38.

45.

BioViews: Java-based tools for genomic data visualization.

Helt GA, Lewis S, Loraine AE, Rubin GM.

Genome Res. 1998 Mar;8(3):291-305.

46.
47.

Tomato Rab1A homologs as molecular tools for studying Rab geranylgeranyl transferase in plant cells.

Loraine AE, Yalovsky S, Fabry S, Gruissem W.

Plant Physiol. 1996 Apr;110(4):1337-47.

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