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College of Engineering and Computing

Biomedical Engineering

Denovo Assembly of Transcriptomes From Next Generation Sequencing Data

Mutations within an organism's DNA can cause differential expression of genes throughout the body. Discovering the differences in, for example, a healthy cell and a tumorous cell could hold great insight to the mechanism of certain diseases. One way of studying these differences is to compare the transcriptomes of these two cells. A transcriptome is a collection of all the messenger RNA molecules expressed from the genes of an organism. In our lab we utilize our expertise in the software package Trinity to reassemble and analyze transcriptomic data. Our current work has been focused around the novel Uca minax sequence but future projects are in the works including a mouse that is highly resistant to cancer and a type of bacteria that regenerates itself.

More information



  • Hanin Omar, Casey A. Cole, Arjang Fahim, Giuliana Gusmaroli, Stephen Borgianini, Homayoun Valafar, De Novo Assembly of Uca minax Transcriptome from Next Generation Sequencing, Proceedings of the International Conference on Bioinformatics & Computational Biology (BIOCOMP), July 2015, Las Vegas, NV
  • Casey A. Cole, Hanin Omar, Arjang Fahim, Guiliana Gusmaroli, Homayoun Valafar, Transcriptome Assembly of the Uca minax, Poster presented at National IDeA Symposium of Biomedical Research Excellence (NISBRE), June 2014, Washington D.C.

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