Todd J Treangen
@traingene
Computational tools for metagenomics and public health. Associate Professor at @RiceCompSci
After 14 years here time to try something blue: treangen dot 🟦
ID: 72510146
https://www.treangenlab.com 08-09-2009 09:02:49
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Our latest methods paper "Minmers are a generalization of minimizers that enable unbiased local Jaccard estimation" (aka MashMap3) is out with Bryce Kille Erik Garrison Todd J Treangen! There's an interesting backstory here 🧵 \ biorxiv.org/content/10.110…
Excited to share that our paper "Enabling accurate and early detection of recently emerged SARS-CoV-2 variants of concern in wastewater", introducing QuaID: a tool for detection of variants of concern in wastewater samples, was published in Nat. Comms nature.com/articles/s4146… 1/🧵
I look forward to attending #ASMicrobe over the next 3 days! Posters/talks from students in my group: antibiotic resistance + nanopore sequencing (Yilei Fu), QuaID (Nicolae Sapoval), Olivar (Michael Wang), Parsnp (Bryce Kille), SeqScreen Nano(Advait Balaji), & Squeegee (Yunxi Liu)
#ASMicrobe folks if of interest attend my rapid fire talk & poster tomorrow! It focuses on antibiotic resistance detection in wastewater with various approaches! This work is joint first author work with Esther Ge Lou and great collaboration with the Stadler lab Lauren Stadler
Great talk by Dr. Rita Colwell at #ASMMicrobe titled "Cholera in the time of climate change" Dr. Colwell covered over 40 years of research on pathogen🦠surveillance and ended by highlighting recent study on microbiome analysis for wastewater surveillance: journals.asm.org/doi/full/10.11…
Really excited to see fresh Parsnp at #ASMicrobe , Bryce Kille has been working on some exciting (and long overdue) improvements to Parsnp (github.com/marbl/parsnp). More updates soon!
That's a wrap for the first day of CINEMA 2023 (events.rice.edu/event/345710-w…) at Rice University Global Paris Center Dr. Nicola Segata (Nicola Segata) kicked things off with a wonderful keynote on “Large-scale strain-level computational metagenomics of the human microbiome” On to day 2!
Day 2 of #CINEMA2023 is just getting started at the Rice University Paris Center!🦉🇫🇷 Today features a full-day, interactive tutorial on microbiome sampling and sequencing 🦠🧬, led by Dr. Joshua Quick (Josh Quick), with CINEMA co-director Lauren Stadler moderating todays session
Only at #CINEMAParis, live Oxford Nanopore sequencing run of a zymo mock microbiome by Josh Quick next to lighting talk session🔥 We will dive into bioinformatics methods for environmental and clinical microbiome analysis over the next few days ! (Ps. Josh Quick said it was a good run!)
#CINEMAParis day 3- learning and collaboratively working on environmental microbiome analysis led by Jeseth Delgado Vela ! Todd J Treangen Rice University
Day 4 of #CinemaParis2023: my former colleague at Institut Pasteur, since 1887, Dr. Sara Vieira-Silva (now Professor at the Johannes Gutenberg University Medical Center in Germany) presenting on gut microbiome, clinical metagenomics and population level studies 🦠🧬@saramavs Lauren Stadler
Day 5 of #Cinema2023 was superb! Alexander Dilthey and Kristen Curry described techniques for microbiome profiling, then Zamin Iqbal was our invited speaker and gave a great talk on "Using revived 100-year old bacteria and new algorithms to study plasmid evolution" Lauren Stadler
Day 6 of #CinemaParis2023 is just underway! Great group discussion on relevant research questions for microbiome data led by Kristen Curry. This afternoon will focus on analyzing datasets the participants brought with them & prep for final presentations tomorrow Lauren Stadler
Our final speaker of #CINEMAParis2023 is Dr. Laurent Moulin from Eau de Paris 🚰, talk: “SARS CoV 2 genome monitoring in wastewater by the French OBEPINE network, deciphering the viral dynamics and VOC evolution” Great work on wastewater pathogen monitoring in Paris Lauren Stadler
Just over a week to go for JXTX Scholarships for Cold Spring Harbor Laboratory Genome Informatics! The application process is lightweight and just needs a short statement of goals in addition to your conf abstract. Please help spread the word! jxtxfoundation.org/news/2023-04-0…
Great day in my life!! Finally defended my Ph.D.! I can’t do this without the guidance of my Ph.D. advisor Todd J Treangen and my co-advisor Fritz Sedlazeck! I’ll soon join Fritz Sedlazeck’s group at as an postdoc focusing on cancer genetics and cancer epigenetics.
