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
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
NEW publication from our lab: One of the first methodologies (FUGAsseM) for gene function prediction from microbial community multi-omics data!
www.nature.com/articles/s41...
🧵⬇️
1/8
www.nature.com/articles/s41...
🧵⬇️
1/8
Predicting functions of uncharacterized gene products from microbial communities - Nature Biotechnology
FUGAsseM predicts protein function in microbiomes using coexpression patterns from metatranscriptomes and diverse community-wide data.
www.nature.com
October 23, 2025 at 6:53 PM
NEW publication from our lab: One of the first methodologies (FUGAsseM) for gene function prediction from microbial community multi-omics data!
www.nature.com/articles/s41...
🧵⬇️
1/8
www.nature.com/articles/s41...
🧵⬇️
1/8
We had a fun visit to the lab by @zymoresearch.bsky.social discussing their solutions and products with the folks in the lab! And thank you for the cool sweatshirts! 😎
October 21, 2025 at 11:11 PM
We had a fun visit to the lab by @zymoresearch.bsky.social discussing their solutions and products with the folks in the lab! And thank you for the cool sweatshirts! 😎
Congrats to Yancong, Amrisha, Xochitl, Eric and all co-authors!!!
Predicting functions of uncharacterized gene products from microbial communities - @hutlab.bsky.social @hsph.harvard.edu @broadinstitute.org go.nature.com/435C4lp
Predicting functions of uncharacterized gene products from microbial communities - Nature Biotechnology
FUGAsseM predicts protein function in microbiomes using coexpression patterns from metatranscriptomes and diverse community-wide data.
go.nature.com
October 17, 2025 at 3:36 PM
Congrats to Yancong, Amrisha, Xochitl, Eric and all co-authors!!!
Curtis and Kelsey attended the PROSPECT Team Retreat last week in Paris and Curtis gave a wonderful talk! A big thanks to Institut Pasteur @institutpasteur.bsky.social for hosting the event.
October 8, 2025 at 9:10 PM
Curtis and Kelsey attended the PROSPECT Team Retreat last week in Paris and Curtis gave a wonderful talk! A big thanks to Institut Pasteur @institutpasteur.bsky.social for hosting the event.
Meet @orakov.bsky.social!
Askarbek is an academic nomad with research stints in US and Japan. He holds a B.S. from Nazarbayev University, M.S. from Paris-Saclay, and PhD from EMBL. As a postdoc, he studies the female genital tract virome & is developing a viral quantification method using spike-ins.
Askarbek is an academic nomad with research stints in US and Japan. He holds a B.S. from Nazarbayev University, M.S. from Paris-Saclay, and PhD from EMBL. As a postdoc, he studies the female genital tract virome & is developing a viral quantification method using spike-ins.
October 2, 2025 at 10:11 PM
Meet @orakov.bsky.social!
Askarbek is an academic nomad with research stints in US and Japan. He holds a B.S. from Nazarbayev University, M.S. from Paris-Saclay, and PhD from EMBL. As a postdoc, he studies the female genital tract virome & is developing a viral quantification method using spike-ins.
Askarbek is an academic nomad with research stints in US and Japan. He holds a B.S. from Nazarbayev University, M.S. from Paris-Saclay, and PhD from EMBL. As a postdoc, he studies the female genital tract virome & is developing a viral quantification method using spike-ins.
A huge thanks to the ASM Young Ambassadors program in northern Africa for inviting Curtis to give a keynote talk to kickoff the 4th African Microbiome Day series!
September 25, 2025 at 9:11 PM
A huge thanks to the ASM Young Ambassadors program in northern Africa for inviting Curtis to give a keynote talk to kickoff the 4th African Microbiome Day series!
Meet @dongyuwang.bsky.social!
Dongyu earned her Ph.D. in Microbiology and M.Sc. in Data Science. She studied microbial structure–function via multiomics and modeling, and virus–host interactions with Nanopore. As a postdoc, she explores microbial dynamics, coevolution, and human–animal convergence.
Dongyu earned her Ph.D. in Microbiology and M.Sc. in Data Science. She studied microbial structure–function via multiomics and modeling, and virus–host interactions with Nanopore. As a postdoc, she explores microbial dynamics, coevolution, and human–animal convergence.
September 23, 2025 at 8:48 PM
Meet @dongyuwang.bsky.social!
Dongyu earned her Ph.D. in Microbiology and M.Sc. in Data Science. She studied microbial structure–function via multiomics and modeling, and virus–host interactions with Nanopore. As a postdoc, she explores microbial dynamics, coevolution, and human–animal convergence.
Dongyu earned her Ph.D. in Microbiology and M.Sc. in Data Science. She studied microbial structure–function via multiomics and modeling, and virus–host interactions with Nanopore. As a postdoc, she explores microbial dynamics, coevolution, and human–animal convergence.
Long and Kelsey just won the 2025 Microbiome SMRT Grant for HiFi shotgun metagenomics!! They will collaborate to optimize PacBio-compatible protocols for gut metagenomics, specifically generating high quality long-read data from IBD patients. Congrats to both! 🎉 🎉 www.pacb.com/blog/2025-mi...
September 17, 2025 at 6:58 PM
Long and Kelsey just won the 2025 Microbiome SMRT Grant for HiFi shotgun metagenomics!! They will collaborate to optimize PacBio-compatible protocols for gut metagenomics, specifically generating high quality long-read data from IBD patients. Congrats to both! 🎉 🎉 www.pacb.com/blog/2025-mi...
Curtis will be presenting at GloMiNe tomorrow! Register to tune in.
Tomorrow begins #GloMiNe2025 organized by @microbiotavault.bsky.social & #MVIF
Atlantic session will be open by Gloria Dominguez-Bello & @cpavloud.bsky.social
Pacific session by Safarina Malik & Célio Dias Santos Júnior
Both sessions will be LIVE!
Check the details: cassyni.com/s/mvif-glomi...
Atlantic session will be open by Gloria Dominguez-Bello & @cpavloud.bsky.social
Pacific session by Safarina Malik & Célio Dias Santos Júnior
Both sessions will be LIVE!
Check the details: cassyni.com/s/mvif-glomi...
September 8, 2025 at 6:52 PM
Curtis will be presenting at GloMiNe tomorrow! Register to tune in.