Papers Archives - Shalek Lab

A New Computational Framework Illuminates the Hidden Ecology of Diseased Tissues

Apr 07, 2025

MESA uses ecological theory to map cellular diversity and spatial patterns in tissues, offering new insights into disease progression. To understand what truly drives disease progression in tissues, scientists need more than just a snapshot of cells in isolation—they need to see where the cells are, how they interact, and how that spatial organization shifts […]

TB Granuloma Paper Reviewed in Immunity

May 10, 2022

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

Pancreatic Cancer Study Now Out in Cell

Dec 09, 2021

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

Jul 27, 2021

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

Jun 29, 2021

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

Jun 29, 2021

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

Jun 03, 2021

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

Cell Atlas of COVID-19 Pathology Released in <em>Nature</em>

Apr 29, 2021

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

Mar 18, 2021

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

Feb 28, 2021

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.

Insights into the Immune Response to Stroke in Science Immunology

Feb 22, 2021

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

Oct 13, 2020

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

Apr 21, 2020

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 […]

New Study on Immune Dynamics in Untreated HIV-1 Infection Now Out

Mar 23, 2020

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

Mar 18, 2020

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.

TB Vaccine Efficacy Study Previewed in Cell

Mar 05, 2020

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

Jan 24, 2020

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

Jan 02, 2020

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 […]

Paired Single-cell Transcriptome-TCR Methods in Nature Immunology

Nov 19, 2019

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 […]

New Paper on Neuroimmune Interactions on BioRxiv

Nov 13, 2019

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 […]

Our Paper on Tuberculosis Infection Featured in NIH News

Jun 06, 2019

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 […]

Alex Shalek Featured in Immunity Voices: “The Next Quarter Century”

Apr 17, 2019

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 […]

From Microfluidics to Metastasis: Shalek Lab Research Featured on MIT News

Jan 22, 2019

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 Paper on Allergic Inflammation Featured in JACI

Dec 05, 2018

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

Nov 13, 2018

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

Oct 29, 2018

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 highlighted in Immunity

Oct 16, 2018

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 […]

Seq-Well featured in MIT News

Feb 13, 2017

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

Apr 11, 2016

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

Feb 26, 2016

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

Jan 07, 2016

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 […]