Papers
2010
Humphry A, Pednarek P, Kemmerling B, Koh S, Stein M, Gobel U, Stuber K, Pislewska-Bednarek M, Loraine A, Schulze-Lefert P, Somerville S, Panstruga R. A regulon conserved in monocot and dicot plants defines a functional module in antifungal plant immunity. PNAS 2010, in press.
Article
English A, Patel K, Loraine AE. Prevalence of alternative splicing choices in Arabidopsis. BMC Plant Biology. BMC Plant Biology 2010, 10:102.
PubMed ...
Article
ArabiTag - alternative splicing data-mining tool.
Mutwil M, Usadel B, Schutte M, Loraine A, Ebenhoh O, Persson S. Assembly of an interactive network for the Arabidopsis genome using a novel heuristic clustering algorithm.
Plant Physiol. 2010 Jan;152(1):29-43. Epub 2009 Nov 4.
PubMed
2009
Helt GA, Nicol JW, Blossom E, Blanchard S, Chervitz SA, Harmon C, Loraine AE. The Genoviz Software Development Kit: A Java toolkit for building genomics visualization applications. BMC Bioinformatics. 2009, 10:266.
Article
Nicol JW, Helt GA, Blanchard SG, Raja A, Loraine AE. The Integrated Genome Browser: Free software for distribution and exploration of genome-scale data sets. Bioinformatics. 2009 October 15; 25(20):27302.
Article
Loraine, A. Co-expression Analysis of Metabolic Pathways in Plants. Methods Mol Biol. 2009;553:247-64.
PubMed
Cui X, Loraine AE. 2009. Consistency analysis of redundant probe sets on Affymetrix three-prime expression arrays and applications to differential mRNA processing. PLoSOne. 2009;4(1):e4229. Epub 2009 Jan 23.
PubMed
2008
Srinivasasainagendra V, Page G, Mehta T, Coulibaly I, Loraine AE. CressExpress: A tool for large-scale mining of expression data from Arabidopsis thaliana. Plant Physiology. 2008 Jul;147(3):1004-16.
Article
CressExpress Tool
Dybvig K, Zuhua C, Lao P, Jordan DS, French CT, Tu AH, Loraine AE. The Genome of Mycoplasma arthritidis. Infect Immun. 2008 Jun 23.
PubMed
Yao J, Chang C, Salmi ML, Hung YS, Loraine A, Roux SJ. Genome-scale
cluster analysis of replicated microarrays using shrinkage correlation
coefficient. BMC Bioinformatics. 2008 Jun 18;9:288.
PubMed
Article
French CT, Lao P, Loraine AE, Matthews BT, Yu H, Dybvig K. Large-Scale Transposon Mutagenesis of Mycoplasma pulmonis. Mol Microbiol. Mol Microbiol. 2008 Jul;69(1):67-76. Epub 2008 Apr 28.
PubMed
Shriner D, Baye TM, Padilla MA, Zhang S, Vaughan LK, Loraine AE.
Commonality of functional annotation: a method for prioritization of candidate
genes from genome-wide linkage studies.
Nucleic Acids Res. 2008 Mar;36(4):e26.
PubMed
Article
Results Web site
2007
Ye J, Cui X, Loraine A, Bynum K, Kim NC, White G, De Luca M, Garfinkel MD, Lu
X, Ruden DM.
Methods for nutrigenomics and longevity studies in Drosophila: effects of diets
high in sucrose, palmitic acid, soy, or beef.
Methods Mol Biol. 2007;371:111-41. Review.
PubMed
Results Web site
2006
Wei H, Persson S, Mehta T, Srinivasasainagendra V, Chen L, Page GP,
Somerville C, Loraine A.
Transcriptional coordination of the metabolic network in Arabidopsis.
Plant Physiol. 2006 Oct;142(2):762-74. Epub 2006 Aug 18.
PubMed
Results Web Site
Cui X, Loraine A. Global Correlation Analysis Between Redundant Probe Sets Using a Large Collection of
Arabidopsis ATH1 Expression Profiling Data. Proc. LSS Comp. Systems Bioinf. 2006, p. 223-226.
PDF
Results Web Site
2004
Shapero MH, Zhang J, Loraine A, Liu W, Di X, Liu G, Jones KW.
MARA: a novel approach for highly multiplexed locus-specific SNP genotyping
using high-density DNA oligonucleotide arrays.
Nucleic Acids Res. 2004 Dec 15;32(22):e181.
PubMed
Cline MS, Shigeta R, Wheeler RL, Siani-Rose MA, Kulp D, Loraine AE.
The effects of alternative splicing on transmembrane proteins in the mouse
genome.
Pac Symp Biocomput. 2004;:17-28.
PDF
PubMed
Kim K, Zakharkin SO, Loraine A & Allison DB. Picking the most likely candidates for further development: Novel intersection-union tests for addressing multi-component hypotheses in comparative genomics. Proceedings of the American Statistical Association Joint Statistical Meeting, ENAR Section [CD-ROM], Toronto, Ontario, Canada, Aug 8 - 12, 2004.
2003
Loraine AE, Helt GA, Cline MS, Siani-Rose MA.
Exploring alternative transcript structure in the human genome using blocks and
InterPro.
J Bioinform Comput Biol. 2003 Jul;1(2):289-306.
PubMed
Liu G, Loraine AE, Shigeta R, Cline M, Cheng J, Valmeekam V, Sun S, Kulp D,
Siani-Rose MA.
NetAffx: Affymetrix probesets and annotations.
Nucleic Acids Res. 2003 Jan 1;31(1):82-6.
PubMed
2002
Loraine AE, Helt GA.
Visualizing the genome: techniques for presenting human genome data and
annotations.
BMC Bioinformatics. 2002 Jul 30;3:19.
PubMed
Loraine AE, Helt GA.
Visualization techniques for genomic data.
Proc IEEE Comput Soc Bioinform Conf. 2002;1:321-6.
PubMed
Loraine AE, Helt GA, Cline MS, Siani-Rose MA.
Protein-based analysis of alternative splicing in the human genome.
Proc IEEE Comput Soc Bioinform Conf. 2002;1:118-24.
PubMed
PDF.
Cline M, Liu G, Loraine AE, Shigeta R, Cheng J, Mei G, Kulp D, Siani-Rose
MA.
Structure-based comparison of four eukaryotic genomes.
Pac Symp Biocomput. 2002;:127-38.
PDF
PubMed
1998
Helt GA, Lewis S, Loraine AE, Rubin GM.
BioViews: Java-based tools for genomic data visualization.
Genome Res. 1998 Mar;8(3):291-305.
PubMed
1996
Yalovsky S, Loraine AE, Gruissem W.
Specific Prenylation of Tomato Rab Proteins by Geranylgeranyl Type-II
Transferase Requires a Conserved Cysteine-Cysteine Motif.
Plant Physiol. 1996 Apr;110(4):1349-1359.
PubMed
Loraine AE, Yalovsky S, Fabry S, Gruissem W.
Tomato Rab1A homologs as molecular tools for studying Rab geranylgeranyl
transferase in plant cells.
Plant Physiol. 1996 Apr;110(4):1337-47.
PubMed