Publications

Refereed Journal Articles:

1. Fox SE, Geniza, M, Preece J, Sage A, Jaiswal P. De novo Transcriptome assembly and co-expression network analysis of genes regulating photomorphogenesis in diploid wheat Triticum monococcm. Accepted, Plos One.

2. Fox SE, Christie M, Marine M, Mockler TC, Blouin M. De novo assembly and characterization of steelhead
trout (Oncorhyncus mykiss) transcriptome and analysis of gene expression in hatchery and wild fish. Accepted. Marine Genomics.

3. Priest HD, Fox SE, Murray JR, Mockler TC. Analysis of global gene expression in Brachypodium distachyon reveals extensive potential network plasticity in response to abiotic stress. Accepted, Plos One.

4. Castoe TA,…Fox SE,…[39 total authors],…Pollock DD. The Burmese python genome reveals the molecular basis for extreme adaptation in snakes. PNAS. December 2, 2013.

5. Jeong D-H, Schmidt SA, Rymarquis LA, Park S, Ganssmann M, German MA, Accerbi M, Zhai J, De Paoli E, Fahlgren N, Fox SE, Garvin DF, Mockler TC, Carrington JC, Meyers BC, Green PJ. Parallel Analysis of RNA ends enhances global investigation of microRNAs and target RNAs of Brachypodium distachyon. In press, Genome Biology.

6. Fox SE, Preece J, Kimbrel J, Sage A, Marchini G, Cruzan M, Jaiswal P. Sequencing, assembly and characterization of a transcriptome resource for Brachypodium sylvaticum. Applications in Plant Sciences. March, 2013.

7. Rowley ER, Fox SE, Bryant DW, Priest HD, Mehlenbacher SK, Mockler TC. Transcriptome analysis of European
hazelnut (Corylus avellana). Crop Science. November, 2012.

8. Li C, Rudi H, Stockinger EJ, Cheng H, Cao M, Fox SE, Mockler TC, Westereng B, Fjellheim S, Rognli OA, Sandve SR. Comparative analyses reveal potential uses of Brachypodium distachyon as a model for cold stress responses in temperate grasses. BMC Plant Biology. May, 2012.

9. Castoe TA, Fox SE, de Konig APJ, Poole AW, Daza JM, Smith EN, Mockler TC, Secor S, Pollock DD. A multi-organ transcriptome resource for the Burmese Python (Python molurus bivittatus). BMC Research Notes. August, 2011.

10. Cumbie JS, Kimbrel JA, Di Y, Schafer DW, Wilhelm LJ, Fox SE, Sullivan CM, Curzon AD, Carrington JC, Mockler TC, Chang JH. GENE-counter: a computational and statistical pipeline for assessing RNA-Seq data for genome- wide expression differences. PLoS One. October, 2011.

11. Castoe TA, Hall KT, Guibotsy Mboulas ML, Gu W, de Koning APJ, Fox SE, Poole AW, Daza JM, Vemulapalli V, Mockler TC, Smith EN, Feschotte C, Pollock DD. Discovery of highly divergent repeat landscapes in snake genomes using high throughput sequencing. Genome Biology and Evolution. May, 2011.

12. Filichkin SA, Priest HD, Dharmawardhana P, Jaiswal P, Breton G, Fox SE, Chory J, Michael TP, Kay S, Mockler TC. Comparative diurnal and circadian transcript profiling in rice, poplar and Arabidopsis. Plos One. June, 2011.

13. Peremyslov VV, Mockler TC, Filichkin SA, Fox SE, Jaiswal P, Makarova KS, Koonin EV, Dolja V. Expression, splicing, and evolution of the myosin gene family in plants. Plant Physiology. January 13, 2011.

14. Shulaev V,…Fox SE,…[71 total authors],…Folta KM. The genome of woodland strawberry (Fragaria vesca). Nature Genetics. December 26, 2010.

15. Vogel JP,…Fox SE…[134 total authors],….Baxter I. Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature. February 11, 2010.

16. Bryant DW, Fox SE, Rowley ER, Priest HD, Wong W-K, Mockler TC. Discovery of SNP markers in expressed genes of hazelnut. Acta Horticulturae. International Symposium on Molecular Markers in Horticulture. April 30, 2010.

17. Priest HD, Fox SE, Filichkin SA, Mockler TC. Utility of next-generation sequencing for analysis of horticultural crop transcriptomes. Acta Horticulturae. International Symposium on Molecular Markers in Horticulture. April 30, 2010.

18. Filichkin SA, Priest HD, Givan SA, Shen R, Bryant DW, Fox SE, Wong WK, Mockler TC. Genome-wide mapping of alternative splicing in Arabidopsis thaliana. Genome Research. 20(1):45-58. January, 2010.

19. Bethea CL, Pau FK, Fox SE, Hess DL, Berga SL, Cameron JL. Sensitivity to stress-induced reproductive dysfunction linked to activity of the serotonin system. Fertility and Sterility. 60(7):448-450, July, 2005.

20. Lu W, Maheshwari A, Misiuta I, Fox SE, Chen N, Zigova T, Christensen RD, Calhoun DA. Neutrophil-specific chemokines are produced by astrocytic cells but not by neuronal cells. Brain Research. Developmental Brain Research. 155(2):127-34. March 31, 2010.

21. Fox SE, Lu W, Maheshwari A, Christensen RD, Calhoun DA. The effects and comparative differences of neutrophil specific chemokines on neutrophil chemotaxis of the neonate. Cytokine. 29:135-40. February, 2005.

22. Maheshwari A, Lacson A, Lu W, Fox SE, Barleycorn AA, Christensen RD, Calhoun DA. Interleukin-8/CXCL8 forms an autocrine loop in fetal intestinal mucosa. Pediatric Research. 56(2):240-9. August, 2004.

23. Kotto-Kome AC, Fox SE, Yang BB, Christensen RD, Calhoun DA. Evidence that the granulocytecolony-stimulating (G-CSF) receptor plays a role in the pharmacokinetics of G-CSF and PEG-G-CSF using a CSF-R KO model. Pharmacological Research. 50:55-8. July, 2004.

Book Chapter:

Fox SE, Filichkin, S, Mockler TC. Applications of ultra-high throughput sequencing. Book Chapter; Methods in Molecular Biology: Plant Systems Biology. 553:79-108. 2009.