@article{mantri_ford_coram_pang_2010, title={Evidence of unique and shared responses to major biotic and abiotic stresses in chickpea}, volume={69}, ISSN={["1873-7307"]}, DOI={10.1016/j.envexpbot.2010.05.003}, abstractNote={Microarrays have been used extensively for transcriptional profiling of plant responses to biotic and abiotic stresses. However, most studies focused on either biotic or abiotic stresses, making it difficult to construe the genes that that may be common to both biotic and abiotic-stress responses. Such information may help molecular breeders to develop cultivars with broad-spectrum resistances to these stresses. A 768-featured boutique microarray was employed to compare the genes expressed by chickpea in response to drought, cold, high salinity and the fungal pathogen Ascochyta rabiei and 46, 54, 266 and 51 differentially expressed transcripts were identified, respectively. The expression of common genes indicated crosstalk in the genetic pathways involved in responses to these stress conditions. The response of ICC 3996 to A. rabiei was more similar to that of high-salinity stress than to drought or cold stress conditions.}, number={3}, journal={ENVIRONMENTAL AND EXPERIMENTAL BOTANY}, author={Mantri, Nitin L. and Ford, Rebecca and Coram, Tristan E. and Pang, Edwin C. K.}, year={2010}, month={Dec}, pages={286–292} }
 @article{jayasinghe_niu_coram_kong_kaganovitch_xue_li_pang_2009, title={Effectiveness of an Innovative Prototype Subtracted Diversity Array (SDA) for Fingerprinting Plant Species of Medicinal Importance}, volume={75}, ISSN={["1439-0221"]}, DOI={10.1055/s-0029-1185484}, abstractNote={geno-Abstract ! The accurate identification of medicinal plants is}, number={10}, journal={PLANTA MEDICA}, author={Jayasinghe, Ruchira and Niu, Lin Hai and Coram, Tristan E. and Kong, Stephan and Kaganovitch, Janna and Xue, Charlie C. L. and Li, Chun G. and Pang, Edwin C. K.}, year={2009}, month={Aug}, pages={1180–1185} }
 @article{coram_settles_chen_2009, title={Large-scale analysis of antisense transcription in wheat using the Affymetrix GeneChip Wheat Genome Array}, volume={10}, ISSN={["1471-2164"]}, DOI={10.1186/1471-2164-10-253}, abstractNote={Natural antisense transcripts (NATs) are transcripts of the opposite DNA strand to the sense-strand either at the same locus (cis-encoded) or a different locus (trans-encoded). They can affect gene expression at multiple stages including transcription, RNA processing and transport, and translation. NATs give rise to sense-antisense transcript pairs and the number of these identified has escalated greatly with the availability of DNA sequencing resources and public databases. Traditionally, NATs were identified by the alignment of full-length cDNAs or expressed sequence tags to genome sequences, but an alternative method for large-scale detection of sense-antisense transcript pairs involves the use of microarrays. In this study we developed a novel protocol to assay sense- and antisense-strand transcription on the 55 K Affymetrix GeneChip Wheat Genome Array, which is a 3' in vitro transcription (3'IVT) expression array. We selected five different tissue types for assay to enable maximum discovery, and used the 'Chinese Spring' wheat genotype because most of the wheat GeneChip probe sequences were based on its genomic sequence. This study is the first report of using a 3'IVT expression array to discover the expression of natural sense-antisense transcript pairs, and may be considered as proof-of-concept.By using alternative target preparation schemes, both the sense- and antisense-strand derived transcripts were labeled and hybridized to the Wheat GeneChip. Quality assurance verified that successful hybridization did occur in the antisense-strand assay. A stringent threshold for positive hybridization was applied, which resulted in the identification of 110 sense-antisense transcript pairs, as well as 80 potentially antisense-specific transcripts. Strand-specific RT-PCR validated the microarray observations, and showed that antisense transcription is likely to be tissue specific. For the annotated sense-antisense transcript pairs, analysis of the gene ontology terms showed a significant over-representation of transcripts involved in energy production. These included several representations of ATP synthase, photosystem proteins and RUBISCO, which indicated that photosynthesis is likely to be regulated by antisense transcripts.This study demonstrated the novel use of an adapted labeling protocol and a 3'IVT GeneChip array for large-scale identification of antisense transcription in wheat. The results show that antisense transcription is relatively abundant in wheat, and may affect the expression of valuable agronomic phenotypes. Future work should select potentially interesting transcript pairs for further functional characterization to determine biological activity.}, journal={BMC GENOMICS}, author={Coram, Tristan E. and Settles, Matthew L. and Chen, Xianming}, year={2009}, month={May} }