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
The Wheeler lab has been awarded the CBSD COBRE Junior Investigator project grant to develop “methods for fast bio-sequence comparison with profile hidden Markov models”. The grant will provide $450K in funding over three years, starting … now!
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.
Since its inception in 2012, Dfam has demonstrated the promise of using profile hidden Markov Models (HMMs) to improve the detection sensitivity and annotation quality of Transposable Element (TEs) families in human and subsequently for four additional reference organisms. Despite these advances, the tools used to discover new families ( de-novo repeat finders ), improve families ( extend, defragment, subfamily clustering ), and classify TE families continue to depend on consensus sequence models. This discordance between methodologies is a direct impediment to Dfam’s expansion.
Read more: Introducing Dfam_consensus – Dfam’s consensus sequence twin
Daniel Olson has been named as a 2017 CBSD Summer Graduate Fellow. Each year, the University of Montana’s Center for Biomolecular and Structural Dynamics supports a small number of graduate students for a summer of research. Daniel, will enter the grad program here in the fall but has already begun research on models for repetitive biological sequences. That he was granted a fellowship for the summer prior to his first year in a grad program is a testimony to the excellent contributions he has already made to research on this campus, beginning with Art Woods and continuing in the Wheeler lab. Congratulations, Daniel!
Congratulations to Joyce Liu, a Sentinel High student who has been working with the Wheeler lab for the past couple years. She was recently awarded 2nd place in the Montana Tech Regional Science and Engineering Fair (link), for her project Investigating the Role of Pseudogenes as the Source of Conserved Non-Coding Elements in the Human Genome.