Summer updates


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Many things are afoot this summer as the lab has been ramping up. Here are a few updates from over the past few months.

Personnel updates:

- Nathan Escandor, a summer research assistant and CIHR Training Program summer fellowship awardee, also had his poster accepted for presentation at CASCH. Nathan will be presenting his work on the relationship between evolutionary fitness and alignment frequencies. Congratulations Nathan!

- Shams Bhuiyan, a summer research assistant, had his abstract accepted for an oral presentation at the Campus Alberta Student Conference on Health (CASCH) meeting in Banff, Alberta.  Shams will be talking about his summer research on experimental design in comparative genomics and on how it relates to variant impact prediction in personal genomics. Congratulations Shams!

- Chenzhe Qian, a recent graduate from the University of Calgary with dual B.Sc. degrees in Biology and Computer Science (and a recent IGEM awards winner), will be joining the lab in the fall to work on many-core algorithms. Also, Ivan Kryukov, a B.Hsc. Bioinformatics student currently in James Wasmuth's lab, will be joining us in the fall to work on infinite mixture models.  Aaron Mathankeri, a recent physics graduate from UBC, has also joined us for the summer to work on several exciting mathematical projects. Welcome to Chenzhe, Ivan, and Aaron!

- Arnab Saha-Mandal visited us from Alexei Fedorov's lab on a CIHR Training Program sponsored recruitment visit. Arnab gave an interesting talk on his Masters work, "Computational Analysis of the Evolution of Non-Coding Genomic Sequences", and has since been awarded a Doctoral Fellowship from the CIHR Training Program. Arnab will be joining the lab in the fall as a Ph.D. student in the Biochemistry and Molecular Biology program. Congratulations Arnab!

- Nathan Escandor, a summer student from the B.Hsc. Bioinformatics program, has been awarded a CIHR Summer Studentship to support his summer research in the lab. Congratulations Nathan!

Paper updates:

- The Western Painted Turtle Genome paper is out in Genome Biology and has been covered widely in the press.  Some links: GenomeWebNew ScientistLos Angeles TimesCTV News.  The paper was also featured in Gilbert and Corfe (2013) "Turtle origins: Picking up Speed." Developmental Cell 25(4).

Some conference highlights:

- This year we 'virtually attended' the CSHL Biology of Genomes meeting (May 2013). This was the first year that online-only attendance was offered, and it was quite a treat to be able to "take" the entire lab.

- I attended the HPCS 2013 meeting in June (High-Performance Computing Symposium), "Big Data + Big Compute = Big Insights" in Ottawa. There were several relevant and interesting talks on biological and biomedical 'big data' problems, including one from Guilluame Bourque at the McGill Genome Centre. Some favourite anecdotes include these comments from a lunch-time talk by Jean-Luc Chatelain @InformationCTO: "The more you torture your data, the more it will tell you what you want to hear," and "1 millisecond lost per operation on a billion operations is 11.5 days lost".

- I also attended SMBE in Chicago this year (Society for Molecular Biology and Evolution). As usual there were plenty of excellent and interesting talks. Dan Graur gave an especially entertaining talk, which included a few mentions of our work on the repeat-content of the human genome (slides link).