Check out the preview of our recent paper on TB granulomas here....
Pancreatic Cancer Study Now Out in Cell
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....
Study Comparing Upper Airway Responses in Mild and Severe COVID-19 Out in Cell
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....
Neuroimmune Paper Featured in Science
Our recent work on neuroimmune interactions in lymph nodes, led by Carly Ziegler in our lab, was recently featured in Science....
PDAC Pre-print Featured in Nature Reviews Gastroenterology & Hepatology
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....
COVID-19 Cell Atlas Featured in Nature Reviews Immunology
Our cell atlas of tissues from COVID-19 autopsy tissues was recently featured in Nature Reviews Immunology. Read more here....
Cell Atlas of COVID-19 Pathology Released in Nature
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 Featured in Cell Systems
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....
Pre-print on Severity-associated Epithelial Responses to SARS-CoV-2 Now on bioRxiv
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...
Insights into the Immune Response to Stroke in Science Immunology
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....
Seq-Well S^3 Released
Our improvements to the Seq-Well scRNA-seq platform were release today – read the publication in Immunity here and the press release here....
Study Describing ACE2 as an Interferon-Stimulated Gene Out in Cell
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...
New Study on Immune Dynamics in Untreated HIV-1 Infection Now Out
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....
Pre-print Detailing ACE2 as an Interferon-Stimulated Gene Now Available
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...
TB Vaccine Efficacy Study Previewed in Cell
Our recent publication on increased tuberculosis vaccine efficacy via alternative administration routes is previewed here in Cell. Read the paper here....
New Study on a Master Regulator in Toxoplasma Infection Now Out
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....
New Study on Increased TB Vaccine Efficacy Now Out
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...
Paired Single-cell Transcriptome-TCR Methods in Nature Immunology
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...
New Paper on Neuroimmune Interactions on BioRxiv
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...
Our Paper on Tuberculosis Infection Featured in NIH News
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...
Alex Shalek Featured in Immunity Voices: “The Next Quarter Century”
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...
From Microfluidics to Metastasis: Shalek Lab Research Featured on MIT News
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 Paper on Allergic Inflammation Featured in JACI
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 work on inflammatory memory highlighted in Quanta Magazine
Our paper on inflammatory memory in airway epithelial cells is highlighted in quanta magazine. Learn more at the following link. ...
New Paper on Ulcerative Colitis on BioRxiv
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 highlighted in Immunity
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...
Seq-Well featured in MIT News
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....
Tirosh et al. featured in MIT News and Broad Institute News
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. featured in Nature Methods Research Highlights
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!...
Shalek & Manalis Lab Research Featured on MIT News
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...