@cssmillie

Assistant Professor @HarvardMed @MGHMedicine @broadinstitute | human microbiome, evolution, mucosal immunology, computational biology

Joined October 2020
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Excited to share the Smillie Lab's first paper! We discovered distinct lineages of the gut microbiota that are exquisitely adapted to inflammatory disease. This was a monumental effort led by Adarsh Kumbhari @mgh_ri @harvardmed @broadinstitute More: doi.org/10.1016/j.chom.2024.…
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Excited to see our recent paper profiled by @Nature! Thanks to @heidiledford for the fantastic article. Congratulations to the Lee and Doffinger labs on their recent discoveries. Exciting times for IBD research! nature.com/articles/d41586-0…

The mysteries of inflammatory bowel disease are being cracked — offering hope for new therapies

Nature - Advances in understanding the causes of the autoimmune disorder could aid in matching people with the right treatment.

nature.com
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Our recent work: Discovery of disease-adapted bacterial lineages in inflammatory bowel diseases cell.com/cell-host-microbe/f…
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Replying to @cssmillie @Nature @heidiledford
The two other publications covered in the article: A disease-associated gene desert directs macrophage inflammation through ETS2 nature.com/articles/s41586-0… Autoantibodies against Interleukin-10 in Inflammatory Bowel Disease nejm.org/doi/10.1056/NEJMoa2…
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Many thanks to @adarsh_k1, @thomasnhcheng, @AshwinMDIBD, @bkocharmd, and @TheXavierLab on this team effort!
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Mathieu Groussin@mgroussi25 Apr 2023
PhD opportunities to join our lab! IMPRS is a great graduate school. Check it out! Deadline for applications: May 15th - contact us if interested 😉
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Congrats Itzhak Khait, @Ohad_LE, and @HadanyL for their brilliant use of #ML to study plant communication by sound! Ohad is a new postdoc in our lab who is studying how the #microbiome controls its human host - excited to see what he comes up with next! cell.com/cell/fulltext/S0092…

Sounds emitted by plants under stress are airborne and informative

Plants emit species- and stress-specific airborne sounds that can be detected in acoustic chambers and greenhouses.

cell.com
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Congrats to our collaborators Peijun Ma and Deb Hung on publication of BacDrop, a new method for bacterial #singlecell RNA-seq. Highly scalable methods will be essential for studying the transcriptional heterogeneity of pathogens and the #microbiome. cell.com/cell/fulltext/S0092…

Bacterial droplet-based single-cell RNA-seq reveals antibiotic-associated heterogeneous cellular...

BacDrop is a droplet-based technology for single-cell RNA-seq in bacteria that can be scaled to millions of bacterial cells or hundreds of samples and was used to elucidate transcriptionally distinct...

cell.com
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Also congrats to Shivam Gandhi on his stellar contributions to this paper! He will make an amazing graduate student this fall.
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Lynne Chantranupong@Lchantran12 Sep 2022
Very excited to share our work that defines how dopamine and acetylcholine interact in the brain during decision making! biorxiv.org/content/10.1101/…

Local and long-distance inputs dynamically regulate striatal acetylcholine during decision making

Within the basal ganglia, striatal dopamine (DA) and acetylcholine (Ach) are essential for the selection and reinforcement of motor actions and decision making. In vitro studies have revealed a...

biorxiv.org
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Great lab @HarvardChanSPH for genomics, lung biology, and asthma!
Adam Haber@haber_lab_hsph17 Mar 2022
We are looking for awesome computational postdocs to work on a range of projects, please share!
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Christopher Smillie retweeted
Martin Polz@MartinPolz22 Oct 2021
Congratulations to Fatima Hussain @fatiays and @JavierDubert on their new paper in Science describing surprising ways how bacteria in the wild defend themselves against phage. See also perspective by Perspective by Meaden and Fineran. science.org/doi/10.1126/scie…

Rapid evolutionary turnover of mobile genetic elements drives bacterial resistance to phages

For wild microbes, horizontal gene transfer of phage-defense elements decouples phage resistance from host core function.

science.org
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The Smillie Lab is hiring for an exciting collaboration @broadinstitute to identify microbiome products that control gut disease. We are a new computational lab @harvardmed @mghmedicine studying #microbiome #immunology #metabolomics #ML. Please share! smillielab.org
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Christopher Smillie retweeted
Matan@matanhofree14 Sep 2021
We are excited to share our study on spatially organized multicellular immune hubs in human colorectal cancer cell.com/cell/fulltext/S0092… @CellCellPress. Joint effort with @karin_pelka, @chenchirps, @AnaAndersonlab, Orit Rozenblatt-Rosen, Aviv Regev, Nir Hacohen, many others!
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Alex Cagan@ATJCagan20 Aug 2021
I am incredibly excited to share our preprint ‘Somatic mutation rates scale with lifespan across mammals’In this paper we provide an unprecedented description of somatic mutation across mammals. biorxiv.org/content/10.1101/… An illustrated tweetorial…[1/17]
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Fabian Theis
@fabian_theis2 Mar 2021
Happy that our single-cell meta-analysis of SARS-CoV-2 entry genes is out @NatureMedicine. Headed by Chris Muus & @MDLuecken in a big effort of the whole @humancellatlas Lung Network, we find age&sex-dependent cell-type specific effects across 31 studies. nature.com/articles/s41591-0…
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The Smillie Lab opens March at @MGHMedicine! We develop methods (wet/dry) to understand microbial life on the human body #microbiome #singlecell #evolution #deeplearning. Hiring grad students, postdocs, and RAs @harvardmed @broadinstitute. Please share! smillielab.org

SMILLIE LAB

smillielab.org
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David R. Liu
@davidrliu6 Jan 2021
Today we report the use of base editing in patient-derived cells and in mice to correct the most common cause of progeria, the devastating rapid aging disease. Progeria is typically caused by a dominant negative C•G-to-T•A point mutation in LMNA. 1/11 drive.google.com/file/d/1oH4…
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David Fawkner-Corbett@davefc88B5 Jan 2021
Really excited to see our work out mapping the development of the human intestine at single cell resolution. An amazing amount of work from a fantastic team. cell.com/cell/fulltext/S0092…
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Christopher Smillie retweeted
Otto X. Cordero@oxcordero5 Jan 2021
Proud to share our latest work showing that interactions between strains govern the eco-evo dynamics of microbial communities, led by Akshit Goyal @eltanin4, Leonora Bittleston @leonorabit and Gabriel Leventhal @gaberoo ... biorxiv.org/content/10.1101/…

Interactions between strains govern the eco-evolutionary dynamics of microbial communities

Genomic data has revealed that genotypic variants of the same species, i.e., strains, coexist and are abundant in natural microbial communities. However, it is not clear if strains are ecologically...

biorxiv.org
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