Publications

2024

2023

  • Daradur, J., Kesserwan, M., Freese, N.H., Loraine, A.E. and Riggs, C.D., 2023. Genomic targets of HOP2 are enriched for features found at recombination hotspots. PubMed.

2022

  • Nambeesan, S.U., Wang, Y.W., Jing, S., Loraine, A. and NeSmith, D.S., 2022, September. Transcriptome Regulation of Postharvest Fruit Quality in Blueberry. In HORTSCIENCE (Vol. 57, No. 9S, pp. S260-S260). 113 S WEST ST, STE 200, ALEXANDRIA, VA 22314-2851 USA: AMER SOC HORTICULTURAL SCIENCE. https://doi.org/10.21273/HORTSCI.57.9S.S1
  • Karthik Raveendran, Nowlan H. Freese, Chaitanya Kintali, Srishti Tiwari, Pawan Bole, Chester Dias, Ann E. Loraine. BioViz Connect: Web Application Linking CyVerse Cloud Resources to Genomic Visualization in the Integrated Genome Browser Front. Bioinform., 23 May 2022, Sec. Data Visualization.
  • Shanbhag S, Patil R, Zahara N, Shetty C, Weidenhammer R, Watharkar S, Tambvekar P, Badzuh PP, Dias C, Vankayala N, Kulkarni P, Vallapureddy C, Kulkarni S, Nikhare P, Freese NH, Loraine AE. Integrated Genome Browser App Store. Bioinformatics. 2022 Feb 18;. doi: 10.1093/bioinformatics/btac109. [Epub ahead of print] PubMed PMID: 35179566; PubMed Central PMCID: PMC9004644.

2021

  • Krizek BA, Bantle AT, Heflin JM, Han H, Freese NH, Loraine AE. AINTEGUMENTA and AINTEGUMENTA-LIKE6 directly regulate floral homeotic, growth, and vascular development genes in young Arabidopsis flowers. J Exp Bot. 2021 Jul 28;72(15):5478-5493. doi: 10.1093/jxb/erab223. PMID: 34013313; PMCID: PMC8318262.
  • Provart NJ, Brady SM, Parry G, Schmitz RJ, Queitsch C, Bonetta D, Waese J, Schneeberger K, Loraine AE. Anno genominis XX: 20 years of Arabidopsis genomics. Plant Cell. 2021 May 31;33(4):832-845. doi: 10.1093/plcell/koaa038. PMID: 33793861; PMCID: PMC8226293.

2020

  • Krizek B, Blakley IC, Ho Y-Y, Freese NH, Loraine AE. The Arabidopsis Transcription Factor AINTEGUMENTA Orchestrates Patterning Genes and Auxin Signaling in the Establishment of Floral Growth and Form. Plant J. 2020 Apr 12. PubMed
  • Raveendran K, Freese NH, Kintali C, Tiwari S, Bole P, Dias C, Loraine AE. BioViz Connect: Web application linking CyVerse cloud resources to genomic visualization in the Integrated Genome Browser. Preprint on BioRxiv.

2019

  • Freese NH, Estrada AR, Blakley IC, Duan J, Loraine AE. Many rice genes are
    differentially spliced between roots and shoots but cytokinin has minimal effect
    on splicing. Plant Direct. 2019 May 17;3(5):e00136. doi: 10.1002/pld3.136.
    eCollection 2019 May. Source Code and Pubmed.
  • Sullivan A, Purohit PK, Freese NH, Pasha A, Esteban E, Waese J, Wu A, Chen M, Chin CY, Song R, Watharkar SR, Chan AP, Krishnakumar V, Vaughn MW, Town C,
    Loraine AE, Provart NJ. An eFP-Seq Browser for visualizing and exploring RNA
    sequencing data. Plant J. 2019 Nov;100(3):641-654. doi: 10.1111/tpj.14468. Epub
    2019 Aug 23. PubMed.
  • International Arabidopsis Informatics Consortium. Arabidopsis Bioinformatics resources: The current state, challenges, and priorities for the future. Plant Direct. 2019 Jan. Link to Article

2018

  • Zubo YO, Blakley IC, Franco-Zorrilla JM, Yamburenko MV, Solano R, Kieber JJ,
    Loraine AE, Schaller GE. Coordination of Chloroplast Development through the
    Action of the GNC and GLK Transcription Factor Families. Plant Physiol. 2018
    Sep;178(1):130-147. Pubmed

2017

  • 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.
  • Luo Y, Reid R, Freese D, Li C, Watkins J, Shi H, Zhang H, Loraine A, Song BH. Salt tolerance response revealed by RNA-Seq in a diploid halophytic wild relative of sweet potato. Sci Rep. 2017 Aug 29;7(1):9624. PubMed.
  • Vaneechoutte D, Estrada AR, Lin YC, Loraine AE, Vandepoele K. Genome-wide characterization of differential transcript usage in Arabidopsis thaliana. Plant J. 2017. 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 Article |  Code 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