Check out the preview of our recent paper on TB granulomas here....

Our study on pancreatic cancer with collaborators at MIT, the Broad Institute, and Dana-Farmer Cancer Institute is now out in Cell – read the publication here and about the study here....

Our study on upper respiratory tract epithelial responses to SARS-CoV-2 infection receding mild and severe COVID-19 is now out in Cell. Read more about the study here, here, or here....

Our recent work on neuroimmune interactions in lymph nodes, led by Carly Ziegler in our lab, was recently featured in Science....

Our pre-print led by Peter Winter and Andrew Navia in our lab was recently featured in a piece on single-cell RNA sequencing in pancreatic cancer....

Our cell atlas of tissues from COVID-19 autopsy tissues was recently featured in Nature Reviews Immunology. Read more here....

Our pre-print detailing how different nasal epithelial and immune populations respond to SARS-CoV-2 infection across the spectrum of COVID-19 severity is now out on bioRxiv. This work was led by Carly Ziegler, Vincent Miao, Andrew Navia, and Josh Bromley in...

Our findings detailing the longitudinal response of myeloid cells to stroke are now out in Science Immunology. Read more about the study, co-led by post-doc Britt Goods, here....

Our improvements to the Seq-Well scRNA-seq platform were release today – read the publication in Immunity here and the press release here....

Our study showing ACE2, the entry receptor for SARS-CoV-2, as an interferon-stimulated gene is now out in Cell here. Read about the study in The Boston Globe and MIT News, C&EN, NIH Director’s blog, among others. Datasets analyzed in this...

Our study of untreated HIV-1 infection is now out in Nature Medicine! We profile longitudinal peripheral blood samples from pre-infection through chronic infection to characterize gene programs that are temporally-correlated in and between cell types. Read the press release here....

Our pre-print work detailing ACE2 upregulation in response to interferons, and type I interferons in particular, is now available here. Descriptions of the datasets analyzed in the study are found here on our COVID-19 Resource page, along with links to...

Our recent publication on increased tuberculosis vaccine efficacy via alternative administration routes is previewed here in Cell. Read the paper here....

With collaborators in the Lourido lab, our paper on a master regulator for the differentiation of Toxoplasma gondii from its acute- to chronic-stage form is now out in Cell. Read press releases about the study here and here....

Our paper on increased tuberculosis (TB) vaccine efficacy with intravenous injection in nonhuman primates is now out in Nature. With collaborators at the National Institutes of Health’s National Institute of Allergy and Infectious Diseases and others, we show greatly enhanced...

Our recent paper details a strategy, co-developed with the Love Lab at MIT, for pairing TCR sequencing with whole-transcriptome profiling in single-cells via 3′-barcoded techniques. Using a targeted pulldown and amplification method, we are able to sequence TCR CDR3 regions...

We’re stoked to have this paper up! We present our work finding new roles for sensory neurons within inflammatory responses and previously unappreciated axes of neuro-immune crosstalk. Led by Shalek lab MD-PhD student Carly Ziegler and post doc Tracy Huang...

A recent paper published in Nature from the Shalek lab and collaborators was featured in NIH News. Ardain et. al. demonstrate that group 3 innate lymphoid cells localize to the lungs soon after M. tuberculosis infection, providing an early line...

Our work combining microfluidic identification of circulating tumor cells (CTCs) and single-cell profiling is currently highlighted on MIT News, while the forthcoming paper is set to appear in the Jan. 21 issue of PNAS. This work represents an ongoing collaboration...

Our recent Nature paper on inflammatory memory within the nasal epithelium is featured in the News Beyond our Pages Section of the Journal of Allergy and Clinical Immunology (JACI). Download Link...

Our paper on inflammatory memory in airway epithelial cells is highlighted in quanta magazine.  Learn more at the following link.      ...

Our collaborative work with the Regev and Xavier labs is now available as a pre-print. Read the abstract below or read the complete version on the BioRxiv. Abstract Genome-wide association studies (GWAS) have revealed risk alleles for ulcerative colitis (UC), but...

Our paper on basal cell memory in type 2 inflammation published in a recent issue of Nature is the subject of a preview article in Immunity: “In a recent issue of Nature, Ordovas-Montanes et al. (2018) used cutting-edge genomic, epigenetic, and interventional techniques to characterize...

The Shalek Lab’s latest publication in Nature Methods describes Seq-Well, a portable, low-cost platform for single-cell RNA-sequencing that was developed in collaboration with the Love lab....

The Shalek Lab’s latest publication exploring metastatic melanoma using single cell RNA-sequencing (scRNA-seq) in collaboration with the Regev and Garraway labs was previewed in an answer and question session with its lead authors Itay Tirosh nd Benjamin Izar. ...

Kimmerling et al., a joint paper between the Manalis and Shalek labs, has now been featured in Nature Methods Research Highlights. Check out the coverage of our microfluidic generation tracking device below!...

A recent Nature Communications publication between the Shalek and Manalis labs has been featured in MIT news. Kimmerling et al., demonstrate a micro-fluidic device capable of tracking of gene expression in single cells as cells divide and generate progeny. While...