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Items: 34

1.

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.

2.

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.

3.

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.

PMID:
29031026
4.

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.

5.

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.

6.

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.

7.

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.

8.

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.

9.

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.

10.

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.

11.

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.

12.

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.

13.

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.

14.

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.

15.

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.

16.

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.

17.

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.

18.

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.

19.

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.

20.
21.

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.

22.

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.

23.

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.

24.

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.

25.

Visualization techniques for genomic data.

Loraine AE, Helt GA.

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

PMID:
15838148
26.

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
27.

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
28.

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.

29.

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.

30.
31.

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.

32.

BioViews: Java-based tools for genomic data visualization.

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

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

33.
34.

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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