Select publications
The human and mouse enteric nervous system at single-cell resolution
Drokhlyansky E*, Smillie CS*, Van Wittenberghe N*, …, RJ Xavier, A Regev
Cell, 2020
Intra- and inter-cellular rewiring of the human colon during ulcerative colitis
Smillie CS*, Biton M*, Ordovas-Montanes J*, …, Ananthakrishnan AN, Shalek AK, Xavier RJ, Regev A
Cell, 2019
Strain tracking reveals the determinants of bacterial engraftment in the human gut following fecal microbiota transplantation
Smillie CS, …, Alm EJ
Cell Host Microbe, 2018
Ecology drives a global network of gene exchange connecting the human microbiome
Smillie CS*, Smith MB*, …, Alm EJ
Nature, 2011
All publications
In preparation
An integrated taxonomy for monogenic inflammatory bowel disease.
Bolton C*, Smillie CS*, Elementaite R, Wei G, Argmann C, Aschenbrenner D, …, Regev A., & Uhlig H.
* Co-first authors
Preprints
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.
bioRxiv (2020)
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.
bioRxiv (2020)
* Co-first authors
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.
medRxiv (2020)
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.
medRxiv (2020)
* Co-second authors
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)