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2024

Unraveling the diversity and functions of tissue-resident plasma cells
Tellier J, Tarasova I, Nie J, Smillie CS, Fedele PL, Cao WHJ, Groom JR, Belz GT, Bhattacharya D, Smyth GK, Nutt SL
Nature Immunology (2024)

2023

Bacterial droplet-based single-cell RNA-seq reveals antibiotic-associated heterogeneous cellular states
Ma P, Amemiya HM, He LL, Gandhi SJ, Nicol R, Bhattacharyya RP, Smillie CS, Hung DT
Cell (2023)

Leveraging polygenic enrichments of gene features to predict genes underlying complex traits and diseases.
Weeks EM, Ulirsch JC, Cheng NY, Trippe BL, Fine RS, Miao J, …, Finucaine HK.
Nature Genetics (2023)

2022

An integrated taxonomy for monogenic inflammatory bowel disease.
Bolton C*, Smillie CS*, Elementaite R, Wei G, Argmann C, Aschenbrenner D, …, Regev A., & Uhlig H.
Gastroenterology (2022)
* Co-first authors

2021

Integrated analyses of single-cell atlases reveal age, gender, and smoking status associations with cell type-specific expression of mediators of SARS-CoV-2 viral entry and highlights inflammatory programs in putative target cells.
Muus C*, Luecken MD*, Eraslan G*, Waghray A*, Heimberg G*, Sikkema L*, Kobayashi Y*, Vaishnav ED*, Subramanian A*, Smillie CS*, Jagadeesh K*, Duong ET*, Fiskin E*, Triglia ET*, Ansari M*, Cai P*, Lin B*, Buchanan J*, Chen S*, Shu J*, Haber AL*, Chung H*, Montoro DT*, …, The Human Cell Atlas Lung Biological Network.
Nature Medicine (2021)
* Co-first authors

GWAS of stool frequency reveals genes, pathways, and cell types relevant to human gastrointestinal motility and irritable bowel syndrome.
Bonfiglio F, Liu X*, Smillie CS*, Pandit A*, Kurilshikov A*, Bacigalupe R*, …, D’Amato M.
Cell Genomics (2021)
* Co-second authors

Plasma proteomics reveals tissue-specific cell death and mediators of cell-cell interactions in severe COVID-19 patients.
Filbin MR, Mehta A, Schneider AM, Kays KR, Guess JR, Gentili M, …, Hacohen N, & Goldberg M.
Cell Reports Medicine (2021)

2020

The Human and Mouse Enteric Nervous System at Single-Cell Resolution.
Drokhlyansky E*, Smillie CS*, Van Wittenberghe* N, Ericsson M, Griffin GK, Eraslan G, …, Rozenblatt-Rosen O, Xavier RJ, & Regev A.
Cell (2020)
* Co-first authors

Genome and sequence determinants governing the expression of horizontally acquired DNA in bacteria.
Gomes ALC, Johns NI, Yang A, Velez-Cortes F, Smillie CS, Smith MB, Alm EJ, & Wang HH.
ISME J (2020)

A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors.
Slyper M, Porter CBM, Ashenberg O, Waldman J, Drokhlyansky E, Wakiro I, …, Rozenblatt-Rosen O, & Regev A.
Nature medicine (2020)

2019

Intra- and Inter-cellular Rewiring of the Human Colon during Ulcerative Colitis.
Smillie CS*, Biton M*, Ordovas-Montanes J*, Sullivan KM, Burgin G, Graham DB, …, Ananthakrishnan AN, Shalek AK, Xavier RJ, & Regev A.
Cell (2019)
* Co-first authors

2018

T Helper Cell Cytokines Modulate Intestinal Stem Cell Renewal and Differentiation.
Biton M, Haber AL, Rogel N, Burgin G, Beyaz S, Schnell A, …, Regev A, & Xavier RJ.
Cell (2018)

Metagenomic mining of regulatory elements enables programmable species-selective gene expression.
Johns NI, Gomes ALC, Yim SS, Yang A, Blazejewski T, Smillie CS, Smith MB, Alm EJ, Kosuri S & Wang HH.
Nature methods (2018)

Strain Tracking Reveals the Determinants of Bacterial Engraftment in the Human Gut Following Fecal Microbiota Transplantation.
Smillie CS, Sauk J, Gevers D, Friedman J, Sung J, Youngster I, …, Alm EJ.
Cell host & microbe (2018)

2017

A single-cell survey of the small intestinal epithelium.
Haber AL, Biton M, Rogel N, Herbst RH, Shekhar K, Smillie CS, …, Xavier RJ, & Regev A.
Nature (2017)

Unraveling the processes shaping mammalian gut microbiomes over evolutionary time.
Groussin M, Mazel F, Sanders JG, Smillie CS, Lavergne S, Thuiller W & Alm EJ.
Nature communications (2017)

Two dynamic regimes in the human gut microbiome.
Gibbons SM, Kearney SM, Smillie CS & Alm EJ.
PLoS computational biology (2017)

2016

The Microbial Olympics 2016.
Nelson MB, Chase AB, Martiny JBH, Stocker R, Nguyen J, Lloyd K, et al.
Nature microbiology (2016)

Mobile genes in the human microbiome are structured from global to individual scales.
Brito IL, Yilmaz S, Huang K, Xu L, Jupiter SD, Jenkins AP, …, Alm EJ.
Nature (2016)

2015

Natural bacterial communities serve as quantitative geochemical biosensors.
Smith MB, Rocha AM, Smillie CS, Olesen SW, Paradis C, Wu L, …, Hazen, TC.
mBio (2015)

2013

Microbial reprogramming inhibits Western diet-associated obesity.
Poutahidis T, Kleinewietfeld M, Smillie CS, Levkovich T, Perrotta A, Bhela S, …, Hafler DA, Alm EJ, & Erdman SE.
PLoS ONE (2013)

Probiotic Bacteria Induce a ‘Glow of Health’.
Levkovich T, Poutahidis T, Smillie CS, Varian BJ, Ibrahim YM, Lakritz JR, Alm EJ & Erdman SE.
PLoS ONE (2013)

2012

Non-invasive mapping of the gastrointestinal microbiota identifies children with inflammatory bowel disease.
Papa E, Docktor M, Smillie CS, Weber S, Preheim SP, Gevers D, …, Bousvaros A, & Alm EJ.
PLoS ONE (2012)

2011

Ecology drives a global network of gene exchange connecting the human microbiome.
Smillie CS*, Smith MB*, Friedman J, Cordero OX, David LA & Alm EJ.
Nature (2011)
* Co-first authors

pre-2011

Mobility of plasmids.
Smillie CS, Garcillán-Barcia MP, Francia MV, Rocha EPC & de la Cruz F.
Microbiology and molecular biology reviews (2010)

Short-term signatures of evolutionary change in the Salmonella enterica serovar typhimurium 14028 genome.
Jarvik T, Smillie CS, Groisman EA & Ochman H.
Journal of bacteriology (2010)

Gene decay in archaea.
van Passel MWJ, Smillie CS & Ochman H.
Archaea (2007)