Updates are underway

We haven't posted any news in quite a while! Updates are coming soon.

Congratulations to students for recent achievements

2014-til-May 212


Ivan Kryukov graduated from the B.H.Sc. Bioinformatics program and joined the lab as a Ph.D. student with a prestigious four year doctoral fellowship in 'Omics from Alberta Innovates (AITF; May 2014). Ivan was also just accepted into the outstanding Workshop on Molecular Evolution at the Marine Biological Laboratories at Wood's Hole this summer. Update: Upon graduating from the B.H.Sc. programme, Ivan was awarded the Silver Medallion in Bioinformatics (2014), the top award for a graduating student.

Aaron Mathankeri (B.Sc. Physics) left his post as lab mathematician and joined the lab as an M.Sc. student in the Biochemistry and Molecular Biology graduate program (May 2014). Update: Aaron has been awarded a CIHR Training Program Graduate Fellowship for his Masters work on mutational heterogeneity in cancer genomes.

Ph.D. student Arnab Saha Mandal gave one of only a few invited trainee talks at the CIHR Human and Statistical Genetics meeting in Victoria B.C. (May 2014).  Arnab was also just accepted into the prestigious Cold Spring Harbor Laboratory summer course in the Genetics of Complex Diseases. Update: Arnab was awarded a prestigious Eyes High International Doctoral Scholarship in recognition of his academic success.

Ivan Kryukov, Arnab Saha Mandal, Aaron Mathankeri, Nathan Escandor, and Shams Bhuiyan all presented posters at the CIHR Human and Statistical Genetics meeting in Victoria B.C. (May 2014) and at our Biochemistry and Molecular Biology (BMB) Advance in Banff (April 2014).

Undergraduate research assistant extraordinare Nathan Escandor (B.H.Sc. Bioinformatics program) was awarded both a CIHR-ACHRI summer studentship and an OCSS summer studentship (May 2014).

Shams Bhuiyan successfully defended his Honours thesis in the B.H.Sc. Bioinformatics program (April 2014).

Hyperion arrives


Thanks to a generous grant from the Canada Foundation for Innovation, a gift from Dell Canada, and matching funds from ACHRI, our lab's new 30+ TeraFLOP computing cluster, Hyperion, recently arrived and has been installed in the Faculty of Medicine's server facility.

Hyperion (and his little brother Ozymandias) together have 11 Intel Xeon Phi accelerators with a combined 660 CPU cores with 4X hyper threading (capable of running 2,640 simultaneous threads), 240 Intel Xeon CPUs (with 2X hyper threading, capable of running 480 simultaneous threads), Infiniband, about 50 TB of combined storage, and other advanced technologies. This new facility is being used for the development and analysis of algorithms for large-scale inference and data analysis of large genomic datasets.

For more information, see the University of Calgary's feature on Hyperion.


Snake genome papers published

Science Magazine, Dec 6 2013

Our pair of snake genome papers has been published online in PNAS Early Edition and is being featured in lots of press articles and blogs (e.g., see Science NOW (AAAS) news, the Huffington Post, and an 8 page News Feature in the Dec. 6 issue of Science).

For the Burmese python genome, see Castoe, de Koning et al. (2013). The King Cobra genome paper is Vonk et al. (2013).


Congratulations to Todd Castoe, David Pollock, Freek Vonk, Michael Richardson and the rest of the snake genome teams!

Summer updates


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).

Finally, a website (almost!)

As you can see, I've finally gotten around to updating the lab website. Welcome!

New additions will be coming soon.

We have arrived...

in beautiful Alberta!

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