Hutlab
@hutlab.bsky.social
The Huttenhower Lab at the Harvard T.H. Chan School of Public Health: microbial community function and human microbiome population health;
Moderators: @jtnearing.bsky.social, @chahat.bsky.social
Moderators: @jtnearing.bsky.social, @chahat.bsky.social
Fun time at Time Out market!
January 29, 2026 at 8:08 PM
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!
January 29, 2026 at 4:21 PM
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!
Boston recently had its biggest snow of the season so far. Here are some snow pictures from Hutlab members! ❄️🌨️🐶
January 27, 2026 at 8:25 PM
Boston recently had its biggest snow of the season so far. Here are some snow pictures from Hutlab members! ❄️🌨️🐶
Reposted by Hutlab
🥁 NEW
Our study on infant gut microbiome and #straintransmission is now published in @nature.com:
doi.org/10.1038/s415...
1/10
Our study on infant gut microbiome and #straintransmission is now published in @nature.com:
doi.org/10.1038/s415...
1/10
Baby-to-baby strain transmission shapes the developing gut microbiome - Nature
A metagenomic survey of babies attending the first year of nursery detected extensive baby-to-baby microbial strain transmission, pointing to social interactions in infancy as crucial drivers of infan...
doi.org
January 21, 2026 at 6:24 PM
🥁 NEW
Our study on infant gut microbiome and #straintransmission is now published in @nature.com:
doi.org/10.1038/s415...
1/10
Our study on infant gut microbiome and #straintransmission is now published in @nature.com:
doi.org/10.1038/s415...
1/10
MSPCA-Angell with FMT for cats!!
www.facebook.com/mspcaangell/...
www.facebook.com/mspcaangell/...
MSPCA-Angell
This holiday season, Baby Duff received the gift of… poop!
Baby Duff recently underwent his third fecal transplant to help manage his chronic intermittent diarrhea, which he has suffered from since....
www.facebook.com
January 23, 2026 at 4:35 PM
MSPCA-Angell with FMT for cats!!
www.facebook.com/mspcaangell/...
www.facebook.com/mspcaangell/...
Reposted by Hutlab
MaAsLin 3: a comprehensive, flexible framework for microbiome association studies. @hutlab.bsky.social
www.nature.com/articles/s41...
www.nature.com/articles/s41...
MaAsLin 3: refining and extending generalized multivariable linear models for meta-omic association discovery - Nature Methods
MaAsLin 3 is a comprehensive and flexible framework for microbiome association studies with expanded toolsets of statistical models, tests and types of inference.
www.nature.com
January 22, 2026 at 2:05 PM
MaAsLin 3: a comprehensive, flexible framework for microbiome association studies. @hutlab.bsky.social
www.nature.com/articles/s41...
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! 🎉
January 16, 2026 at 3:24 AM
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!
January 16, 2026 at 3:18 AM
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... 🎉
Clarivate Highly Cited Researchers 2025
The Highly Cited Researchers 2025 list identifies and celebrates individuals who have demonstrated significant and broad influence in their fields of research. Through rigorous selection criteria and ...
clarivate.com
January 9, 2026 at 4:23 PM
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!! 🎉☃️
December 25, 2025 at 10:11 PM
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!
December 19, 2025 at 3:45 PM
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!
Reposted by Hutlab
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?...
December 16, 2025 at 3:31 PM
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?...
1/ We are excited to announce Parathaa: a new method for improving taxonomic classification of amplicon sequencing data. Parathaa aims to directly model sequence ambiguity to identify amplicons to the finest taxonomic level possible. academic.oup.com/nar/article/...
Capturing sequence ambiguity among taxa in a primer-specific manner to improve taxonomic classification of amplicon sequencing
Abstract. Amplicon sequencing, a common strategy to taxonomically profile microbial communities, is relatively low cost and high throughput. However, it is
academic.oup.com
December 18, 2025 at 8:08 PM
1/ We are excited to announce Parathaa: a new method for improving taxonomic classification of amplicon sequencing data. Parathaa aims to directly model sequence ambiguity to identify amplicons to the finest taxonomic level possible. academic.oup.com/nar/article/...
Meet @efranzosa.bsky.social!
Eric was recently reappointed as a Senior Research Scientist at @hsph.harvard.edu (congrats!🎉). Eric’s research focuses on computational methods development for microbiome analysis, with an emphasis on functional characterization.
Eric was recently reappointed as a Senior Research Scientist at @hsph.harvard.edu (congrats!🎉). Eric’s research focuses on computational methods development for microbiome analysis, with an emphasis on functional characterization.
December 12, 2025 at 2:31 PM
Meet @efranzosa.bsky.social!
Eric was recently reappointed as a Senior Research Scientist at @hsph.harvard.edu (congrats!🎉). Eric’s research focuses on computational methods development for microbiome analysis, with an emphasis on functional characterization.
Eric was recently reappointed as a Senior Research Scientist at @hsph.harvard.edu (congrats!🎉). Eric’s research focuses on computational methods development for microbiome analysis, with an emphasis on functional characterization.
Thank you to @psumbiome.bsky.social for inviting Curtis recently for a talk at their microbiome seminar series (www.huck.psu.edu/institutes-a...) & for a great visit. Its amazing to see such an institutionally well supported microbiome community, and the seminar series hosts really diverse topics!
Seminar Series - The Huck Institutes (en-US)
www.huck.psu.edu
December 10, 2025 at 7:42 PM
Thank you to @psumbiome.bsky.social for inviting Curtis recently for a talk at their microbiome seminar series (www.huck.psu.edu/institutes-a...) & for a great visit. Its amazing to see such an institutionally well supported microbiome community, and the seminar series hosts really diverse topics!
Meet Sagun!
Sagun completed his Master's in Computer Science at Georgia Tech, specializing in Machine Learning and Interactive Intelligence. He now works as a Software Developer at the Harvard Chan School and the Hutlab, building and maintaining large-scale data infrastructure and tools.
Sagun completed his Master's in Computer Science at Georgia Tech, specializing in Machine Learning and Interactive Intelligence. He now works as a Software Developer at the Harvard Chan School and the Hutlab, building and maintaining large-scale data infrastructure and tools.
December 5, 2025 at 4:39 PM
Meet Sagun!
Sagun completed his Master's in Computer Science at Georgia Tech, specializing in Machine Learning and Interactive Intelligence. He now works as a Software Developer at the Harvard Chan School and the Hutlab, building and maintaining large-scale data infrastructure and tools.
Sagun completed his Master's in Computer Science at Georgia Tech, specializing in Machine Learning and Interactive Intelligence. He now works as a Software Developer at the Harvard Chan School and the Hutlab, building and maintaining large-scale data infrastructure and tools.
New preprint out now!
Comparative Assessment of Large Language Models for Microbial Phenotype Annotation
www.biorxiv.org/content/10.1...
Comparative Assessment of Large Language Models for Microbial Phenotype Annotation
www.biorxiv.org/content/10.1...
Comparative Assessment of Large Language Models for Microbial Phenotype Annotation
Large language models (LLMs) are increasingly used to extract knowledge from text, yet their coverage and reliability in biology remain unclear. Microbial phenotypes are especially important to assess...
www.biorxiv.org
December 2, 2025 at 7:48 PM
New preprint out now!
Comparative Assessment of Large Language Models for Microbial Phenotype Annotation
www.biorxiv.org/content/10.1...
Comparative Assessment of Large Language Models for Microbial Phenotype Annotation
www.biorxiv.org/content/10.1...
Happy Thanksgiving to you from the Hutlab!!
November 26, 2025 at 10:31 PM
Happy Thanksgiving to you from the Hutlab!!
Meet @jtnearing.bsky.social!
Jacob earned their PhD at Dalhousie U. with @betascience.bsky.social. Their microbiome–cancer work there led them to study how bioinformatic tools shape results. They’re now in the Hutlab as a postdoc working on dog microbiomes, creating association methods and tools!
Jacob earned their PhD at Dalhousie U. with @betascience.bsky.social. Their microbiome–cancer work there led them to study how bioinformatic tools shape results. They’re now in the Hutlab as a postdoc working on dog microbiomes, creating association methods and tools!
November 21, 2025 at 4:19 PM
Meet @jtnearing.bsky.social!
Jacob earned their PhD at Dalhousie U. with @betascience.bsky.social. Their microbiome–cancer work there led them to study how bioinformatic tools shape results. They’re now in the Hutlab as a postdoc working on dog microbiomes, creating association methods and tools!
Jacob earned their PhD at Dalhousie U. with @betascience.bsky.social. Their microbiome–cancer work there led them to study how bioinformatic tools shape results. They’re now in the Hutlab as a postdoc working on dog microbiomes, creating association methods and tools!
Reposted by Hutlab
Also, congrats to @medschool.umaryland.edu's @genomescience.bsky.social on its 5-year $14.5M Human Virome Program grant to establish its Consortium Organization and Data Collaboration Center.
Run by Owen White, Michelle Giglio, & @hutlab.bsky.social.
www.medschool.umaryland.edu/news/2025/ni...
Run by Owen White, Michelle Giglio, & @hutlab.bsky.social.
www.medschool.umaryland.edu/news/2025/ni...
November 17, 2025 at 3:59 AM
Also, congrats to @medschool.umaryland.edu's @genomescience.bsky.social on its 5-year $14.5M Human Virome Program grant to establish its Consortium Organization and Data Collaboration Center.
Run by Owen White, Michelle Giglio, & @hutlab.bsky.social.
www.medschool.umaryland.edu/news/2025/ni...
Run by Owen White, Michelle Giglio, & @hutlab.bsky.social.
www.medschool.umaryland.edu/news/2025/ni...
Grad student Jordan Jensen recently provided testimonial to the MA Legislature backing bills (S.747 / H.1336) to extend unemployment & Paid Family & Medical Leave to grad workers. These protections exist for other campus employees but not grad students. Proposed by HGSU & other Mass. grad unions 🫶🎉
November 13, 2025 at 10:29 PM
Grad student Jordan Jensen recently provided testimonial to the MA Legislature backing bills (S.747 / H.1336) to extend unemployment & Paid Family & Medical Leave to grad workers. These protections exist for other campus employees but not grad students. Proposed by HGSU & other Mass. grad unions 🫶🎉
Kudos to the organizers for successfully organizing the 10th International Conference on Clinical Metagenomics (clinicalmetagenomics.org?page_id=286) and thank you for inviting Curtis and Nicola! #IccMg 🎉
Programme – ICCMG 2025
clinicalmetagenomics.org
November 12, 2025 at 9:35 PM
Kudos to the organizers for successfully organizing the 10th International Conference on Clinical Metagenomics (clinicalmetagenomics.org?page_id=286) and thank you for inviting Curtis and Nicola! #IccMg 🎉
Meet Marina from the Hutlab!
Marina recently earned her Ph.D. in Molecular Epidemiology and is currently continuing her work as a postdoctoral researcher in the lab. Her work focuses on human–environment microbial interactions and transmission, particularly within built environments.
Marina recently earned her Ph.D. in Molecular Epidemiology and is currently continuing her work as a postdoctoral researcher in the lab. Her work focuses on human–environment microbial interactions and transmission, particularly within built environments.
November 7, 2025 at 4:25 PM
Meet Marina from the Hutlab!
Marina recently earned her Ph.D. in Molecular Epidemiology and is currently continuing her work as a postdoctoral researcher in the lab. Her work focuses on human–environment microbial interactions and transmission, particularly within built environments.
Marina recently earned her Ph.D. in Molecular Epidemiology and is currently continuing her work as a postdoctoral researcher in the lab. Her work focuses on human–environment microbial interactions and transmission, particularly within built environments.
Great coverage for @ycongzhang.bsky.social and our recent FUGAsseM paper -
news.sciencenet.cn/htmlnews/202...
Also, Yancong will be giving a seminar on this work tomorrow for anyone who would like to know more about it!
mp.weixin.qq.com/s/vvwPjfmFSk...
news.sciencenet.cn/htmlnews/202...
Also, Yancong will be giving a seminar on this work tomorrow for anyone who would like to know more about it!
mp.weixin.qq.com/s/vvwPjfmFSk...
创新方法让AI“见微知著”—新闻—科学网
news.sciencenet.cn
October 29, 2025 at 10:07 PM
Great coverage for @ycongzhang.bsky.social and our recent FUGAsseM paper -
news.sciencenet.cn/htmlnews/202...
Also, Yancong will be giving a seminar on this work tomorrow for anyone who would like to know more about it!
mp.weixin.qq.com/s/vvwPjfmFSk...
news.sciencenet.cn/htmlnews/202...
Also, Yancong will be giving a seminar on this work tomorrow for anyone who would like to know more about it!
mp.weixin.qq.com/s/vvwPjfmFSk...
Huge congratulations to Wendy for getting elected to Natural Academy of Medicine! 🎉
hsph.harvard.edu/news/wendy-g... @hsph.harvard.edu
hsph.harvard.edu/news/wendy-g... @hsph.harvard.edu
Wendy Garrett elected to National Academy of Medicine | Harvard T.H. Chan School of Public Health
Wendy Garrett, Irene Heinz Given Professor of Immunology and Infectious Diseases at Harvard T.H. Chan School of Public Health, has been elected to the
hsph.harvard.edu
October 28, 2025 at 1:04 AM
Huge congratulations to Wendy for getting elected to Natural Academy of Medicine! 🎉
hsph.harvard.edu/news/wendy-g... @hsph.harvard.edu
hsph.harvard.edu/news/wendy-g... @hsph.harvard.edu