2018 Year In Review
Updated: Feb 7
It has been another fun-filled year and kudos to the group for making it one! A lot has happened this year that would like to recognize here.
I cannot tell you how proud I am about who we are and what we have going as a team – the unquantifiable that makes me leap out of bed and bound to work everyday! This year:
Kayla Johnson (Central Michigan University) and Alex McKim (Clemson University) joined us as graduate students.
Remy Liu joined us as an undergrad student and is continuing as a research assistant.
Jainil Shah (Okemos High School) joined our group as our first resident high school student researcher.
For about 10 weeks in Summer, Jesus Vasquez (University of New Mexico), Chinaza Nnawulezi (Hampton University), and Essenam Bruce (Santa Clara) hung out with us thanks to programs like the REU and HSPSP.
It’s hard to believe that – together with our first-graduate-student Anna Yannakopoulos, founding-postdoc Christopher Mancuso, and three awesome undergrads Marc Maldaver, Nate Davis, & Jake Canfield who all joined last year – there are now 10 of us! (Esp. thinking back to when the "group" started with empty chairs at empty tables two years back!)
Posters, Presentations, & Papers
Many group members bravely took on presenting early stages of their work at various avenues this year. In addition to being an important responsibility, communicating our science is a hard-yet-critical component of your professional development, which I’m glad to see them do, and do it with elan! This year:
Anna presented a poster at the MSU Engineering Graduate Research Symposium.
Kayla and Anna presented posters at the Intelligent Systems for Molecular Biology 2018, Chicago, a premiere international conference in computational biology.
Jake, Nate, Chinaza, and Jesus presented posters describing their summer research projects at the Mid-SURE Symposium.
Essenam presented his work at the HSPSP Symposium.
Arjun gave a talk at the Dept. of Genetics, Rutgers University.
Some papers we contributed to this year:
Lee Y et al., A computational framework for genome-wide characterization of the human disease landscape. Cell Systems, Accepted • Iyer J et al., Pervasive epistasis in cell proliferation pathways modulates neurodevelopmental defects of autism-associated 16p11.2 deletion. Nature Communications, 9:2548 • Wong AK et al., GIANT 2.0: Genome-scale Integrated Analysis of gene Networks in Tissues. Nucleic Acids Research, 46:W65 • Pizzo L et al., Rare variants in the genetic background modulate the expressivity of neurodevelopmental disorders. Genetics in Medicine, doi:10.1038/s41436-018-0266-3 • Rangan AV et al., A loop-counting method for covariate-corrected low-rank biclustering of gene-expression and genome-wide association study data. PLoS Computational Biology, 14: e1006105.
Services & Outreach
Democratizing science-training-and-education, leveling playing fields, and improving access to (& entry into) our work are all intertwined core values of our group. Here are some notable steps we took in that direction this year:
R-Ladies: We have consistently supported the recently-started local chapter of this global effort to provide a welcoming and supportive environment for women and gender minorities to learn and discuss R and data science. Our group (financially) sponsored one meeting. Nate & I have shown-up to many meetings. Anna gave a lighting-talk. And, Kayla has been a pivotal member of the core group working at all levels to help pull off all the events.
Skype-a-Scientist: Through this wonderful international program, I got a chance to talk to 7th and 8th grade students at Quitman High School in Quitman, AR about genetics and computing.
Professional development for grad students and postdocs: Towards my goal to formalize hidden curricula and make professional development a required part of graduate and postdoc training, for the past two years, I have been giving regular workshops and talks on these topics to the MSU Postdoc Association and MSU NIH-BEST Program (for grad students). With my visit to Rutgers recently, I have begun taking this to other universities when I travel for scientific talks/meetings.
Open courseware: Following the example of so many generous instructors out there, I have been making all my course materials open (both “Bioinformatics & computational biology” & “Gaps, missteps, & errors in statistical data analysis”), and will continue to do so in the future.
Awards & Grants
Some success is sweet. And, we got some!
Anna secured 1st place among CMSE posters in the Engineering Graduate Research Symposium. Judges also nominated her poster for the EGRS Best Poster award!
Alex won the Engineering Distinguished Fellowship (Anna won this last year, so, good track record!)
Marc, Nate, and Jake received summer research support from the EnSURE program.
Funding: We got the: 1) BEACON Pilot Grant to study the evolutionary changes in rapidly evolving killifish; funds two undergrads for a year; 2) BMB Collaborative Research Award to study gene regulation at the single-cell level; funds a postdoc for 2 years; and 3) NIH NIGMS Maximizing Investigators' Research Award (MIRA) to do everything we are doing; funds a bunch of us for five years.