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CAHNRS Department of Horticulture Genomics Lab

CisSERS: Customizable In Silico Sequence Evaluation for Restriction Sites, now available

CisSERS, open source software for analyzing sequence data, developed at WSU.

High-throughput sequencing continues to produce an immense volume of information that is processed and assembled into mature sequence data. Data analysis tools are urgently needed that leverage the embedded DNA sequence polymorphisms and consequent changes to restriction sites or sequence motifs in a high-throughput manner to enable biological experimentation. CisSERS was developed as a standalone open source tool to analyze sequence datasets and provide biologists with individual or comparative genome organization information in terms of presence and frequency of patterns or motifs such as restriction enzymes. Predicted agarose gel visualization of the custom analyses results was also integrated to enhance the usefulness of the software. Read the rest of this PLOS article.

 

Citation: Sharpe RM, Koepke T, Harper A, Grimes J, Galli M, Satoh-Cruz M, et al. (2016) CisSERS: Customizable In Silico Sequence Evaluation for Restriction Sites. PLoS ONE 11(4): e0152404. doi:10.1371/journal.pone.0152404

Congratulations Seanna!

Congratulations to PhD student Seanna Hewitt! She received an Honorable Mention for her application for the 2016 National Science Foundation (NSF) Graduate Research Fellowship Program. An Honorable Mention is considered a significant academic achievement by NSF and provides recipients with enhanced access to resources, such as supercomputing time, in support of their graduate program.

Faculty mentors will improve WSU commercialization, impact

PULLMAN, Wash. – A peer-mentoring program to help Washington State University faculty commercialize their research will launch on Jan. 19 with a reception 4-6 p.m. in the CUB junior ballroom.

The goal of the Entrepreneurial Faculty Ambassadors (EFA) is to build a stronger entrepreneurial infrastructure at WSU by creating a resource of faculty mentors who are both outstanding academic scholars and have successfully commercialized university research.

Read more at WSU NEWS

Sliced pears show potential

Sliced apples account for ten percent of the U.S. apple market. A Washington State University scientist believes sliced pears could give the pear industry a similar boost if technical challenges can be resolved.

If the pear market could be expanded by 10 percent, by delivering high-quality sliced pears, that would translate to a $40 million positive impact on the pear industry, says Dr. Amit Dhingra, WSU geneticist. Importantly, it would increase the demand for small fruit, in the less-preferred 120 to 135 size range.

Read the full article by Geraldine Warner here

Better Plantlets for Better Plants

Using a proprietary growing method developed at Washington State University (WSU), startup company Phytelligenceis producing plants and trees faster than ever, offering a fresh alternative to tree farmers in an industry overripe for innovation.

“We can produce in one year what is typically produced in three years: a 10-foot tall tree,” says Amit Dhingra, Ph.D., associate professor of horticultural genomics and biotechnology in the molecular plant sciences graduate program at WSU.

 

Read the full article here

Plant biotech startup speeds propagation

Washington State University researchers-turned-entrepreneurs have developed a method for growing trees three times faster while conserving water and reducing the need for pesticides – and they just made their first sale. Read the full article by Kate Wilhite at WSU News.

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Phytelligence founders Amit Dhingra, left, Kathie Nicholson, Tyson Koepke and Scott Schaeffer.

Not pictured are Nathan Tarlyn and Derick Jiwan.