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 collaborative cell atlases of multiple organs at autopsy from COVID-19 donors – a joint work with many at the Broad Institute and the broader research community – is now available in Nature here, and its accompanying press release here.
Alex was recently features in Cell Systems’ “Voices” piece on the future of understanding cell behavior and cellular communities. Read his opinion, and that of other leading voices in the field, 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 the Shalek lab. Read more here.
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 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 study are described here and can be downloaded from our single-cell portal here. We hope […]
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 the data themselves.
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 immune protection and outcome compared to traditional intradermal injection of the TB vaccine BCG, which […]
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 from pre-existing scRNA-seq libraries, increasing the amount of orthogonal information recoverable from archived samples. Read […]
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 with Uli von Andrian, we find that lymph nodes are not only innervated by sensory […]
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 of defense against tuberculosis (TB). This understanding of the initial immune response to TB may […]
Immunity celebrates its 25th anniversary at an exciting time in immunology, marked by the advent of new, door-opening approaches and a deeper understanding of the centrality of the immune system to both health and disease. Alex is among 25 investigators asked to look forward and share a vision of the next quarter century of immunology […]
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 between the Shalek and Manalis labs, headed by Jay Prakadan.
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 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 their cell type and pathway specificities are often unknown. Here, we generate an atlas of […]
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 cellular ecosystem in allergic chronic rhinosinusitis. They showed that basal epithelial cells “remember” type […]
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 the technology has several potential applications, Kimmerling explains one focus of interest: “In the future, this […]
