Publications

2017

  • Yan Luo, Robert Reid, Daniella Freese, Changbao Li, Jonathan Watkins, Huazhong Shi, Hengyou Zhang, Ann Loraine, and Bao-Hua Song. Salt tolerance response revealed by RNA-Seq in a diploid halophytic wild relative of sweet potato.  Accepted for publication in Nature Scientific Reports.
  • 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** . Cytokinin induces genome-wide binding of the type-B response regulator ARR10 to regulate growth and development in Arabidopsis. Proc Natl Acad Sci U S A. 2017 Jul 18;114(29):E5995-E6004. doi: 10.1073/pnas.1620749114. Epub 2017 Jul 3. PubMed PMID: 28673986. *Co-first authors, **Co-contributing authors. PubMed.

2016

  • Raines T*, Blakley I*, Tsai Y-C, Worthen JM, Franco-Zorilla JM, Solano R, Schaller GE, Loraine AE**, Kieber JJ**. Characterization of the cytokinin-responsive transcriptome in rice. BMC Plant Biol. 2016 Dec 8;16(1):260. PubMed PMID: 27931185; PubMed Central PMCID: PMC5146874. *Co-first authors, **Co-contributing authors. Open Access Article | Source Code
  • Freese NH, Norris DC, Loraine AE. Integrated Genome Browser: visual analytics
    platform for genomics. Bioinformatics. 2016 Mar 16. pii: btw069. [Epub ahead of
    print] PubMed PMID: 27153568. Open Access Article | Source Code
  • Mall T, Eckstein J, Norris D, Vora H, Freese NH, Loraine AE. ProtAnnot: an App
    for Integrated Genome Browser to display how alternative splicing and
    transcription affect proteins. Bioinformatics. 2016 Apr 7. pii: btw068. [Epub
    ahead of print] PubMed PMID: 27153567. Open Access Article | Source Code (in IGB repository)
  • Krizek BA, Bequette CJ, Xu K, Blakley IC, Fu ZQ, Stratmann J, Loraine AE.
    RNA-Seq links AINTEGUMENTA and AINTEGUMENTA-LIKE6 to cell wall remodeling and plant defense pathways in Arabidopsis. Plant Physiol. 2016 May 20. pii:
    pp.01625.2015. [Epub ahead of print] PubMed PMID: 27208279. Open Access Article | Code repository

2015

  • Lambirth KC, Whaley AM, Blakley IC, Schlueter JA, Bost KL, Loraine AE, Piller KJ. (2015) A comparison of transgenic and wild type soybean seeds: Analysis of transcriptome profiles using RNA-Seq. BMC Biotechnology 2015, 15:89  Open Access ArticleCode Repository
  • Loraine AE, Blakley IC, Jagadeesan S, Harper J, Miller G, Firon N (2015) Analysis and visualization of RNA-Seq expression data using RStudio, Bioconductor, and Integrated Genome Browser. Methods Mol Biol. 1284:481-501. PMID: 25757788 | Free Full Text | Code Repository | Dropbox
  • Estrada AD, Freese NH, Blakley IC, Loraine AE (2015) Analysis of pollen-specific alternative splicing in Arabidopsis thaliana via semi-quantitative PCR. PeerJ. PMID: 25945312 | Free Full Text | Code Repository
  • Gupta V, Estrada A, Blakley I, Reid R, Patel K, Meyer M, Andersen S, Brown A, Lila M, Loraine A (2015) 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. GigaScience 4: 5 PMID: 25830017 | Free Full Text | Code Repository | IGBQuickload Site
  • Ben-Tov D, Abraham Y, Stav S, Thompson K, Loraine A, Elbaum R, de Souza A, Pauly M, Kieber JJ, Harpaz-Saad S (2015) COBRA-LIKE2, a Member of the Glycosylphosphatidylinositol-Anchored COBRA-LIKE Family, Plays a Role in Cellulose Deposition in Arabidopsis Seed Coat Mucilage Secretory Cells. Plant Physiol 167: 711-724. Free PMC Article PMID:25583925

2014

  • Liu R, Loraine AE, Dickerson JA (2014) Comparisons of computational methods for differential alternative splicing detection using RNA-seq in plant systems. BMC Bioinformatics 15: 364. Free PMC Article PMID:25511303
  • Gulledge AA, Vora H, Patel K, Loraine AE (2014) A protocol for visual analysis of alternative splicing in RNA-Seq data using integrated genome browser. Methods Mol Biol 1158: 123-137. Free PMC Article PMID:24792048

2013

  • Yousef GG, Brown AF, Funakoshi Y, Mbeunkui F, Grace MH, Ballington JR, Loraine A, Lila MA (2013) Efficient quantification of the health-relevant anthocyanin and phenolic acid profiles in commercial cultivars and breeding selections of blueberries (Vaccinium spp.). J Agric Food Chem 61: 4806-4815. PMID:23635035
  • Loraine A, McCormick S, Estrada A, Patel K, Qin P (2013) RNA-seq of Arabidopsis pollen uncovers novel transcription and alternative splicing. Plant Physiol 162: 1092-1109. Free PMC Article PMID:23590974 | IGBQuickload Site | Code Repository
  • Bhargava A, Clabaugh I, To JP, Maxwell BB, Chiang YH, Schaller GE, Loraine A, Kieber JJ (2013) Identification of cytokinin-responsive genes using microarray meta-analysis and RNA-Seq in Arabidopsis. Plant Physiol 162: 272-294. Free PMC Article PMID:23524861

2012

  • Gulledge AA, Roberts AD, Vora H, Patel K, Loraine AE (2012) Mining Arabidopsis thaliana RNA-seq data with Integrated Genome Browser reveals stress-induced alternative splicing of the putative splicing regulator SR45a. Am J Bot 99: 219-231. Free Full Text PMID:22291167

2010

  • Mutwil M, Usadel B, Schutte M, Loraine A, Ebenhoh O, Persson S (2010) Assembly of an interactive correlation network for the Arabidopsis genome using a novel heuristic clustering algorithm. Plant Physiol 152: 29-43. Free PMC Article PMID:19889879
  • Humphry M, Bednarek P, Kemmerling B, Koh S, Stein M, Gobel U, Stuber K, Pislewska-Bednarek M, Loraine A, Schulze-Lefert P, Somerville S, Panstruga R (2010) A regulon conserved in monocot and dicot plants defines a functional module in antifungal plant immunity. Proc Natl Acad Sci U S A 107: 21896-21901. Free PMC Article PMID:21098265
  • English AC, Patel KS, Loraine AE (2010) Prevalence of alternative splicing choices in Arabidopsis thaliana. BMC Plant Biol 10: 102. Free PMC Article PMID:20525311

2009

  • Nicol JW, Helt GA, Blanchard SG, Jr., Raja A, Loraine AE (2009) The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets. Bioinformatics 25: 2730-2731. Free PMC Article PMID:19654113
  • Loraine A (2009) Co-expression analysis of metabolic pathways in plants. Methods Mol Biol 553: 247-264. PMID:19588109
  • Helt GA, Nicol JW, Erwin E, Blossom E, Blanchard SG, Jr., Chervitz SA, Harmon C, Loraine AE (2009) Genoviz Software Development Kit: Java tool kit for building genomics visualization applications. BMC Bioinformatics 10: 266. Free PMC Article PMID:19706180
  • Cui X, Loraine AE (2009) Consistency analysis of redundant probe sets on affymetrix three-prime expression arrays and applications to differential mRNA processing. PLoS One 4: e4229. Free PMC Article PMID:19165320

2008

  • Yao J, Chang C, Salmi ML, Hung YS, Loraine A, Roux SJ (2008) Genome-scale cluster analysis of replicated microarrays using shrinkage correlation coefficient. BMC Bioinformatics 9: 288. Free PMC Article PMID:18564431
  • Srinivasasainagendra V, Page GP, Mehta T, Coulibaly I, Loraine AE (2008) CressExpress: a tool for large-scale mining of expression data from Arabidopsis. Plant Physiol 147: 1004-1016. Free PMC Article PMID:18467456
  • Shriner D, Baye TM, Padilla MA, Zhang S, Vaughan LK, Loraine AE (2008) Commonality of functional annotation: a method for prioritization of candidate genes from genome-wide linkage studies. Nucleic Acids Res 36: e26. Free PMC Article PMID:18263617
  • French CT, Lao P, Loraine AE, Matthews BT, Yu H, Dybvig K (2008) Large-scale transposon mutagenesis of Mycoplasma pulmonis. Mol Microbiol 69: 67-76. Free PMC Article PMID:18452587
  • Dybvig K, Zuhua C, Lao P, Jordan DS, French CT, Tu AH, Loraine AE (2008) Genome of Mycoplasma arthritidis. Infect Immun 76: 4000-4008. Free PMC Article PMID:18573899

2007

  • Ye J, Cui X, Loraine A, Bynum K, Kim NC, White G, De Luca M, Garfinkel MD, Lu X, Ruden DM (2007) Methods for nutrigenomics and longevity studies in Drosophila: effects of diets high in sucrose, palmitic acid, soy, or beef. Methods Mol Biol 371: 111-141. PMID:17634578

2006

  • Wei H, Persson S, Mehta T, Srinivasasainagendra V, Chen L, Page GP, Somerville C, Loraine A (2006) Transcriptional coordination of the metabolic network in Arabidopsis. Plant Physiol 142: 762-774. Free PMC Article PMID:16920875
  • Cui X, Loraine A (2006) Global correlation analysis between redundant probe sets using a large collection of Arabidopsis ath1 expression profiling data. Comput Syst Bioinformatics Conf: 223-226.  PMID:17369640

2004

  • Shapero MH, Zhang J, Loraine A, Liu W, Di X, Liu G, Jones KW (2004) MARA: a novel approach for highly multiplexed locus-specific SNP genotyping using high-density DNA oligonucleotide arrays. Nucleic Acids Res 32: e181. Free PMC Article PMID:15601992
  • Cline MS, Shigeta R, Wheeler RL, Siani-Rose MA, Kulp D, Loraine AE (2004) The effects of alternative splicing on transmembrane proteins in the mouse genome. Pac Symp Biocomput: 17-28. PMID:14992489

2003

  • Loraine AE, Helt GA, Cline MS, Siani-Rose MA (2003) Exploring alternative transcript structure in the human genome using blocks and InterPro. J Bioinform Comput Biol 1: 289-306. PMID:15290774 PDF: Loraine.03.JBCB.AltSpliceProteinEffects
  • Liu G, Loraine AE, Shigeta R, Cline M, Cheng J, Valmeekam V, Sun S, Kulp D, Siani-Rose MA (2003) NetAffx: Affymetrix probesets and annotations. Nucleic Acids Res 31: 82-86. Free PMC Article PMID:12519953

2002

  • Loraine AE, Helt GA, Cline MS, Siani-Rose MA (2002) Protein-based analysis of alternative splicing in the human genome. Proc IEEE Comput Soc Bioinform Conf 1: 118-124. PMID:15838129
  • Loraine AE, Helt GA (2002) Visualizing the genome: techniques for presenting human genome data and annotations. BMC Bioinformatics 3: 19. Free PMC Article PMID:12149135
  • Loraine AE, Helt GA (2002) Visualization techniques for genomic data. Proc IEEE Comput Soc Bioinform Conf 1: 321-326. PMID:15838148
  • Cline M, Liu G, Loraine AE, Shigeta R, Cheng J, Mei G, Kulp D, Siani-Rose MA (2002) Structure-based comparison of four eukaryotic genomes. Pac Symp Biocomput: 127-138. PMID:11928469

1999

  • FlyBase Consortium (1999) The FlyBase database of the Drosophila Genome Projects and community literature. Nucleic Acids Res 27: 85-88. Free PMC Article PMID:9847148

1998

  • Helt GA, Lewis S, Loraine AE, Rubin GM (1998) BioViews: Java-based tools for genomic data visualization. Genome Res 8: 291-305. Free PMC Article PMID:9521932

1996

  • Yalovsky S, Loraine AE, Gruissem W (1996) Specific Prenylation of Tomato Rab Proteins by Geranylgeranyl Type-II Transferase Requires a Conserved Cysteine-Cysteine Motif. Plant Physiol 110: 1349-1359. Free PMC Article PMID:12226265
  • Loraine AE, Yalovsky S, Fabry S, Gruissem W (1996) Tomato Rab1A homologs as molecular tools for studying Rab geranylgeranyl transferase in plant cells. Plant Physiol 110: 1337-1347. Free PMC Article PMID:8934628