Announcing WAAFLE 1.5! Now compatible with SGB-level taxonomy and the ChocoPhlAn 4 gene family database. Includes a new BLAST database, updated SGB pangenome taxonomy, and speed/reliability improvements. WAAFLE now integrates smoothly with other bioBakery 4 tools.
forum.biobakery.org/t/announcing...
IMP ANNOUNCEMENT 🚨 Harvard Chan Microbiome in Public Health Center (co-directed by Wendy Garrett & Curtis) will host its annual symposium on May 18 @ Harvard T.H. Chan School @hsph.harvard.edu. The theme is 'Translating the Microbiome'. Poster abstracts are due April 1. Register : hsph.me/hcmph2026
A big thanks to the University of British Columbia Department of Microbiology and Immunology @ubcmicroimmuno.bsky.social for hosting Curtis for a talk on some of the latest developments in the lab!
mbim.ubc.ca/events/semin...
🎉 Excited to share that Hutlab, collaborating with Laurel Gabard-Durnam @ NEU has been awarded a Wellcome Leap FORM grant! We will explores how early-life gut microbiome dynamics shape infant neurodevelopment and long-term brain health.
Learn more wellcomeleap.org/form/ #Microbiome #Neurodevelopment
Congrats to Yujia for passing her qualifying exam!!
We are excited to be joining the Informatics Technology for Cancer Research (ITCR) program @ NCI. Our work will develop methods to detect cancer-associated viruses and microbial variation from metagenomes, revealing previously hidden contributors to colorectal carcinogenesis. R21 kicking off! 🎉🎉
A big thanks to The Center for Microbiome Informatics and Therapeutics at @mitpress.bsky.social for hosting Curtis for a talk on the endogenous human virome!
Eric @efranzosa.bsky.social and Kelsey from the lab started teaching BST 281 - Genomic Data Manipulation, a couple weeks ago! It covers genomic sequence analysis, high throughput data analysis and cool topics that are currently of importance in the field 🧑🎓
Fun time at Time Out market!
Huge thanks to everyone who took BST272 (Computing Environments for Biology) this year! It’s an intense few weeks as intro to working at the terminal, and we hope folks build on it in courses like BST281. This was our first year integrating AI into the curriculum—thanks for all the great feedback!
Aaaaand this one is from Curtis!
Boston recently had its biggest snow of the season so far. Here are some snow pictures from Hutlab members! ❄️🌨️🐶
🥁 NEW
Our study on infant gut microbiome and #straintransmission is now published in @nature.com:
doi.org/10.1038/s415...
1/10
MaAsLin 3: a comprehensive, flexible framework for microbiome association studies. @hutlab.bsky.social
www.nature.com/articles/s41...
Congratulations to Yehoon Jo @yehoon.bsky.social who finished his PhD lab rotation in the Hutlab last semester and is joining the lab as a PhD student! 🎉
Congratulations to Sagun Maharjan @sagunmaharjann.bsky.social for graduating with a Masters in Computer Science from Georgia Tech while working at the Hutlab!
Congratulations to Curtis and Eric Franzosa from the lab for being featured in the Clarivate Highly Cited Researchers of 2025 (in both Biology/Biochemistry and Microbiology categories)! clarivate.com/highly-cited... 🎉
Happy holidays from the Hutlab!! 🎉☃️
A huge thanks to Cancer Grand Challenges @cancergrand.bsky.social , @cam.ac.uk and Dr. Nic Walton for organizing a two-day Data Workshop to address data and computing challenges across the group. Chahat gave a presentation of his work, and Curtis led a session on best practices for use of AI/ML!
Huge thanks to Curtis for spending some time with us here in Happy Valley - if you missed his talk, you can check it out here on our YouTube channel: youtu.be/andhyvSyt6c?...
10/ Special thanks to our collaborators @hillspet.bsky.social for their contributions and feedback throughout the development of Parathaa.
9/ Any feedback or issues can be directed to our forum at: forum.biobakery.org.
8/ Parathaa is openly available for use by the community and can be used to assign amplicons to both SILVA and GTDB taxonomy. github.com/biobakery/pa...
7/ Moreover, application of Parathaa to real-world data identified cases where taxonomic labels found within databases were likely incorrect or incompatible with sequence phylogeny.
6/ We found that Parathaa performed in F1, precision, and recall just as well or better than commonly used amplicon assignment methods while also allowing for finer species resolution.
5/ We validated Parathaa on seven synthetic Silva datasets and historic holdout data from GTDB using both full‑length 16S rRNA amplicons and amplicons of the V1V2 and V4V5 regions.
4/ Parathaa works in two main steps:
- Build an optimized, primer‑specific map linking phylogenetic placement to taxonomy.
- Apply this map to assign zero or more taxonomic labels to each sequence.
3/ Parathaa aims to address these issues by directly modelling taxonomic sequence ambiguity within sequenced amplicon regions: i.e. allowing for assignments to multiple taxonomic labels when phylogenetically warranted.
2/ Amplicon data often contains unique biases due to primer incompatibilities and the inability to differentiate between certain microbes due to low sequence variability, especially at the species level.
