Several of us recently attended AlCoB 2019 in Berkeley. All six attending students presented both talks and posters (sampled in pictures below). Alex Nord discussed his work on splice aware profile HMMs, Jack Roddy presented work on reducing the nasty problem of overextension of sequence alignments, Kaitlin Carey described her cool results on using sequence annotation confidence to improve annotation (including of homologous recombination), Tim Anderson described his new FPGA accelerator for profile HMM search, Sarah Walling described progress in understanding surprising alternative splicing outcomes, and Daniel Olson presented advances in annotating tandemly-repetitive sequence regions with ULTRA.
We also got a chance to visit the Computer Research Division at LBNL (where Genevieve Krause will be spending a summer). Part of that visit included an introduction to a test FPGA system (thanks Andrew and Farzad!)
Several of us recently returned from attending ISMB 2018 in Chicago.
Alex Nord presented his work on Mirage, a tool for aligning protein isoforms in a talk, and later a poster. The work will appear in the Proceedings of the ACM-BCB 2018 conference.
Daniel Olson presented his work on ULTRA, a model-based method for labeling repetitive regions of biological sequences. His work will also appear in the ACM-BCB 2018 Proceedings. Genevieve Krause presented rapidly-progressing work on an implementation of a profile HMM for annotating protein-coding DNA containing frameshift-inducing indels. Kaitlin Carey‘s poster described a method for assessing confidence in annotation when multiple related families compete for labeling a sequence. Tim Anderson described steps toward a new FPGA-acceleration approach to profile HMM search. Jack Roddy presented exciting early results for methods to reduce the overextension of sequence alignments into nonhomologous sequence regions.
(After review of the photos of everyone presenting their posters, you can see that they’re mostly doing a great job of following my instructions to talk to people while position your hands as if you’re holding a watermelon! 😄 )
Over the past year, several undergrads have participated in research with the group. Three of them shared the results of their work at the “UM Conference on Undergraduate Research” on April 27. Kudos to Jack Roddy, Conner Copeland, and Sarah Walling. A special congratulations to Sarah, who was awarded a “best poster” award!
Also, a belated congratulations to Joyce Liu, a high school student working in our lab, who was awarded the 1st place poster award in the 63rd Annual Montana Science Fair, hosted at UM.
Jack Roddy – Machine Learning strategies for improving sequence alignment boundaries
Conner Copeland – Southeast Asian plant phylogeny
Sarah Walling – Characterizing proteins containing Alternative Reading Frames
Sarah Walling – “Best poster” award
A good chunk of the lab had the pleasure of attending the ISMB 2017 in Prague, ending just a couple days ago. Before and during the conference, we had a chance to meet up with several lab collaborators, and to attend an endless stream of informative talks. We also managed to get a little touring in, with trips to the castle, the Charles bridge, a unique marionette performance of Don Giovanni, and exposure to the singularly Czech style of table service.
Congratulations to lab member Gilia Patterson, who today was recognized as the University of Montana Outstanding Senior in Genetics and Evolution. Gilia has done great work with me on understanding sources of transposable element mis-classification (manuscript coming soon to a theatre near you), and we’re happy as can be for her!
I’m wrapping up a lengthy trip to England and Ireland, in which I had the chance to catch up with a member of the lab, Rutger Evans, who has been working on a summer project at the EBI, under the guidance of one of my favorite collaborators, Rob Finn.
Alex Nord has just been awarded a Center for Biomolecular Structure and Dynamics Graduate Student Fellowship for the summer of 2016. The fellowship will support Alex while he continues research on using spaced seeds to boost both speed and sensitivity in the context of database search with profile hidden Markov models (in HMMER, of course).
Read more at: http://news.umt.edu/2015/06/060915cbsd.php