Just in time for Thanksgiving, COV-IRT, an international COVID-19 research team that I'm fortunate to co-lead (cov-irt.org) along w/ Afshin Beheshti , just launched a COVID-19 Exposure Assessment Tool. Download the interactive PDF here --> cov-irt.org/exposure-asses….

Just in time for Thanksgiving, COV-IRT, an international COVID-19 research team that I co-lead along w/Todd J Treangen, just launched a COVID-19 Exposure Assessment Tool --> cov-irt.org/exposure-asses…. Maybe The Late Show & The Daily Show will help bring awareness to the public?

Thrilled to share a new software tool from my PhD student Kristen Curry. Emu is designed for microbial community profiling and leverages an expectation-maximization (EM) algorithm to generate taxonomic abundance profiles from full-length 16S rRNA reads. biorxiv.org/content/10.110…

Two key questions we focused on for Emu were: 1) Can we improve on relative abundance estimation compared to previous approaches on Oxford Nanopore data? 2) Does full-length 16S rRNA analysis w/ Emu offer benefits over Illumina 16S rRNA analyses that are not full length, e.g. V3-V4?

Turns out, the answer was yes for both (1) and (2)! Table 1 from the preprint captures the improvement in relative abundance estimation with Emu, and also improvements in genus-level and species-level 16S based assignments with Oxford Nanopore vs Illumina.

We also demonstrate the benefits of the EM algorithm in Emu by highlighting the decrease in relative abundance estimation error throughout EM iterations:

Emu is open-source and readily available for download and use at gitlab.com/treangenlab/emu and also available via ‘conda install emu’: anaconda.org/bioconda/emu.

Last but not least, huge thanks to all the co-authors! Tor Savidge lab (Tor & Qinglong), Villapol lab (Sonia Villapol, Ph.D. 🔬🧠 & Sirena), Mendling lab (Werner, Partick, & Enid), Dilthey lab (Alexander Dilthey & Alona), & my group Rice Computer Science: Michael Nute, Qi (Maria) Wang, Libby, and Kristen Curry

Excited to share work from my first year as a PhD student! Huge thank you to the many collaborators on this project :)

Delighted to share this microbiome + machine learning review article from my group titled: "It takes guts to learn: machine learning techniques for disease detection from the gut microbiome" Superb job by Kristen Curry & Michael Nute Rice Computer Science #ETLS portlandpress.com/emergtoplifesc…

Please join us for a virtual symposium organized by The Ken Kennedy Institute Rice Computer Science, featuring a stellar speaker lineup & taking place on Friday, March 11th (2-year anniversary of WHO declaration of #COVID19 pandemic). Register today! (free but limited spots) eventbrite.com/e/covid-19-sym…

Excellent to see Emu, led by my Rice University Rice Computer Science PhD student Kristen Curry (Kristen Curry) & closely developed alongside Alexander Dilthey (Heinrich-Heine-Universität Düsseldorf), among many other collaborators, now out in Nature Methods ! paper: nature.com/articles/s4159… code: gitlab.com/treangenlab/emu

Out now in Nature Methods: Emu, a new method for 16S rRNA Oxford Nanopore-based profiling of microbial communities! Great transatlantic collaboration with Kristen Curry, Todd J Treangen, et al.. Brief thread follows. nature.com/articles/s4159…

Emu, a new microbial community profiling software, identifies bacterial species by leveraging long DNA sequences that span the entire length of a gene. This research, led by Rice CS' Kristen Curry & her advisor Todd J Treangen, is out now in Nature Methods. bit.ly/3bFYhhK

The Rice Computer Science team of Todd J Treangen and graduate student Kristen Curry have develop Emu, a program that could simplify sorting harmful from helpful bacteria in microbiomes like those in the gut or in agriculture and the environment. bit.ly/3AsKK7y

Thrilled to announce a microbial genomics and metagenomics workshop (CINEMA) that I've organized with Lauren Stadler taking place this summer (July 3rd-10th) at the Rice University Global Paris Center. Registration page now live (April 15th deadline): events.rice.edu/event/345710-w… 1/n