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-====== Proposed Projects for Fall 2014 ======
+====== Proposed Projects for Fall 2015 ======
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+===Genome-wide identification of plant micro RNAs===
+**Supervisor: Katalin Hudak**
+The Hudak Lab in the Biology Department has an opening for a fourth-year Honours student to assist with a bioinformatics project. We study the pokeweed plant, Phytolacca americana, which displays broad-spectrum virus resistance. To evaluate pokeweed gene expression, we recently sequenced the plant’s mRNA and small RNA transcriptomes under jasmonic acid (JA) treatment. JA is a plant hormone that mediates defence against pathogens and insect herbivores. We are interested in learning how pokeweed gene expression is regulated by miRNAs during biotic stress.  Please note: no previous knowledge of biology is required.
+Working with the support of a PhD student, your project will involve:
+) Prediction of micro RNA (miRNA) targets on the basis of complementary sequence matches
+) Correlation of miRNA and mRNA expression changes to identify genes that are regulated by miRNAs
+) Conducting pathway analysis to determine which biological processes are controlled by miRNAs
+) Construction of a miRNA/target interaction network to visualize predictions
+This work will contribute to a scientific manuscript on miRNA-mediated gene regulation in pokeweed during response to JA.
+Requirements:
+) Pre-requisites as per EECS Calendar
+) Facility with script-writing/modification (in Perl or Python)
+) Preference for students with knowledge of statistics and familiarity with R programming
+) Able to begin in September 2015
+Learning outcomes:
+) Manipulate and analyze quantitative biological data
+) Develop and test hypotheses by modifying existing software and writing new script
+) Manage a CentOS computer server to store and facilitate ongoing research
+No knowledge of biology is required.
+For more information, please see:
+ Hudak Lab website- http://hudak.lab.yorku.ca/
+RNA sequencing- http://www.illumina.com/applications/sequencing/rna.html
+miRNAs- http://en.wikipedia.org/wiki/MicroRNA
+\\
 ===Dynamic Interface Detection and Control Project===