Welcome to my website! I’m a postdoctoral researcher and biostatistician at the University of Massachusetts Medical School. My research is in statistical methods for systems genetics. My colleagues and I use mice to study biology of complex traits, like body weight, that are affected by many genes and other factors. We design and perform experiments to map quantitative trait loci (QTL). In other words, we identify where in the genome are genes that affect a given complex trait.
Blog
qtl2pleio on CRAN
10 January 2020
CRAN now hosts the packages qtl2pleio and gemma2. qtl2pleio performs a d-variate, d-QTL scan over a select genomic region. gemma2 is used by qtl2pleio for the inference of multivariate variance components.
They can be installed with:
install.packages("qtl2pleio") The statistical model that qtl2pleio fits for each d-tuple of markers (or pseudomarkers) is
\[ vec(Y) = Xvec(B) + vec(G) + vec(E) \] where \(Y\) is a n by d matrix of d traits (for each of n subjects), X is a dn by df block-diagonal matrix of founder allele probabilities, B is a f by d matrix of allele effects for each of d traits, G is a n by d matrix of polygenic random effects, and E is a n by d matrix of random errors.
ImprovBoston Student Showcase video
5 January 2020
I have now completed ImprovBoston’s Improv Comedy 101 class. I’m happy to share the video of my class’s show from December 2019. You can view it here.
(Last modified: 2020-02-08 12:40:41)
World-wide Web and Social Media
22 December 2018
I’ve followed a series of blog posts from Cal Newport at http://calnewport.com/blog/ (with posts like this) in which Newport criticizes social media platforms for, among other things, limiting the scope of internet browsing. Newport, a computer science professor and writer, proudly has never had a social media account.
Until March 2018, I regularly consumed information from Facebook, Twitter, and even Instagram and Linkedin. Termination of these accounts aligned with my larger professional and scholarly goals of wanting to focus more on my studies and other, engaging, activities.
R package site incorporation into my personal website
24 November 2018
Overview I’ve been developing the R package qtl2pleio. It’s now at a stage where others can use it. I recently found the R package pkgdown, which allows developers to build, in an automated fashion, websites for their packages. I posted an entry on pkgdown earlier this year. I now wish to communicate my strategy for incorporating the package site into my personal website, https://fboehm.us. I write this primarily as a reminder to myself.
reticulate R package & Travis
1 April 2018
I like to use Travis CI with my R packages. I recently wrote a R package, limmbo2, that is a wrapper for the python module limmbo. I used the R package reticulate, from Rstudio. I struggled for about 3 hours to write a .travis.yml file for limmbo2. Finally, I found a viable solution. I’m writing this blog post in hopes that it might be useful to myself and others in the future.
Recent Works
- Genetic Background Modifies Phenotypic Severity and Longevity in a Mouse Model of Niemann-Pick Disease Type C1. Jorge L. Rodriguez-Gil, Dawn E. Watkins-Chow, Laura L. Baxter, Gene Elliot, Ursula L. Harper, Stephen M. Wincovitch, Julia C. Wedel, Arturo A. Incao, Mylene Huebecker, Frederick J. Boehm, William S. Garver, Forbes D. Porter, Karl W. Broman, Frances M. Platt and William J. Pavan (2020 ) doi:10.1242/dmm.042614
- qtl2pleio: Testing pleiotropy vs. separate QTL after Jiang & Zeng (1995). (2019)
qtl2pleioperforms a d-variate, d-QTL scan over a genomic region of interest before calculating a likelihood ratio test statistic for the competing hypotheses of pleiotropy and separate QTL. - Testing pleiotropy in multiparental populations, Early career scientist seminar, Genetics Society of America, online, Oct 17, 2019
- gemma2: Multivariate random effects for systems genetics studies. (2019)
gemma2uses restricted maximum likelihood methods to infer variance components in a multivariate linear mixed effects model for QTL mapping. - Genetic determinants of gut microbiota composition and bile acid profiles in mice. Julia H. Kemis, Vanessa Linke, Kelsey L. Barrett, Frederick J. Boehm, Lindsay L. Traeger, Mark P. Keller, Mary E. Rabaglia, Kathryn L. Schueler, Donald S. Stapleton, Daniel M. Gatti, Gary A. Churchill, Daniel Amador-Noguez, Jason D. Russell, Brian S. Yandell, Karl W. Broman, Joshua J. Coon, Alan D. Attie and Federico E. Rey (2019 ) doi:10.1371/journal.pgen.1008073
- qtl2pleio: Testing pleiotropy vs. separate QTL in multiparental populations. Frederick Boehm, Brian Yandell and Karl Broman (2019 ) doi:10.21105/joss.01435
- Testing Pleiotropy vs. Separate QTL in Multiparental Populations. Frederick J. Boehm, Elissa J. Chesler, Brian S. Yandell and Karl W. Broman (2019 ) doi:10.1534/g3.119.400098
- Testing pleiotropy in multiparental populations, Thesis defense, University of Wisconsin-Madison, Madison, Wisconsin, USA, Apr 21, 2019
Slides for my thesis defense
- Testing pleiotropy in multiparental populations, International Mammalian Genomics Conference, Rio Mar, Puerto Rico, USA, Nov 6, 2018
Awarded best poster honor.
- Testing pleiotropy in multiparental populations, Joint Statistical Meetings, Vancouver, British Columbia, Canada, Aug 1, 2018
Slide presentation on testing pleiotropy vs. separate QTL in multiparental populations.