A new framework to efficiently screen drugs

Oct 22, 2024

Novel method to scale phenotypic drug screening drastically reduces the number of input samples, costs, and labor required to execute a screen. Read the full article on MIT News.

Collaborative work featured in MIT News

Sep 16, 2024

Learn more about this collaborative work featuring Alex Shalek and a discovery that yields a potent immune response, which could be used to develop a potential tumor vaccine.

Listen to Alex Shalek on the Lab Coats and Life Podcast

May 24, 2024

Hear Alex talk about “Reducing Barriers Through Open Data” on the Lab Coats and Life Podcast.

Alex Profiled in MIT News

Jul 22, 2022

Read Alex’s new profile in MIT News here.

TB Granuloma Paper Reviewed in Immunity

May 10, 2022

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

Listen to Alex Shalek on the Bioinformatics CRO Podcast

Mar 18, 2022

Listen to Alex Shalek on the Bioinformatics CRO Podcast Hear Alex talk about the Shalek Lab’s multi-disciplinary approach to answering some of science’s toughest and complex questions.

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.

Profile of Omer Yilmaz and Alex in MIT Spectrum

Nov 08, 2021

Learn about how Omer Yilmaz, Associate Professor of Biology at MIT, and Alex combine their expertise to tackle the largest problems in colon cancer 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.

Alex and Lab Awarded NIDA Pioneer Award for HIV/AIDS and Substance Use Disorder Research

Apr 30, 2021

We’re incredibly grateful to receive an NIH Pioneer Award to define, at unprecedented resolution, how substance use disorders influence immune function and the response to HIV-1 and other pathogens by developing and applying innovative single-cell and bulk profiling and perturbation tools to inform the design of novel cure and prevention strategies. Read more here.

Cell Atlas of COVID-19 Pathology Released in Nature

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.

HCA Equity Working Group Leaders Share Lessons Learned

Oct 07, 2020

Alex, along with HCA Equity Working Group co-leaders Partha Majumder and Musa Mhlanga, details some of the lessons they’ve learned in their timing leading the initiative and their thoughts moving forward in this piece for Nature Medicine.

Alex Recipient of HMS Young Mentor Award!

Sep 30, 2020

Congratulations to Alex for being awarded a Young Mentor Award from Harvard Medical School! Read more here.

Alex Outlines Recommendation Letter Process

Jul 23, 2020

Alex was recently featured in Nature on how he approaches writing recommendation letters for his trainees and students. Read it here!

Constantine Named 2020 Hertz Fellow!

May 20, 2020

Our very own Constantine Tzouanas has been named a 2020 Hertz Fellow! We’re very excited for this achievement, and looking forward to what’s in store. Read more about the Hertz Fellowship and Constantine here.

Partnership with Chan Zuckerberg Initiative to Profile Pediatric COVID-19 Announced

May 06, 2020

With Boston Children’s Hospital PI (and former post-doc!) Jose Ordovas-Montanes, we will expand our COVID-19-related research to include understanding disease pathogenesis in a pediatric cohort – the data and findings of which will be readily accessible to the scientific community. Learn more about our and others’ efforts from CZI here and about single-cell genomics in […]

Alex Wins Edgerton Faculty Award!

Apr 23, 2020

Congratulations to Alex for winning the 2019-2020 Harold E. Edgerton Faculty Achievement Award, given for “his leadership and pioneering spirit; his vision, inventiveness, and enthusiasm for mentorship and collaboration; and his tremendous contributions to a critical area at the intersection of science and medicine.” Read about the award and Alex 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.

COVID-19 scRNA-seq Resource Datasets Released

Mar 14, 2020

In light of the spread of SARS-CoV-2, we are sharing multiple unpublished and published scRNA-seq datasets across both health and disease that harbor cells expressing ACE2 (the gene encoding the host receptor) and TMPRSS2 (the gene involved in processing the viral spike protein). We are sharing these resources for SARS-CoV-2 on the Alexandria Project. This […]

Marc Wadsworth Graduates from the Shalek Lab!

Mar 13, 2020

A belated congratulations to Marc Wadsworth for successfully defending his thesis! We wish Marc the best of luck in his future endeavors, and we’re excited for all the upcoming defenses this semester!

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.

Jay Prakadan Graduates from the Shalek Lab!

Jan 12, 2020

Congratulations to Jay Prakadan for successfully defending his thesis! We wish Jay the best of luck in his future endeavors, and we’re excited for all the upcoming defenses this year!

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 […]

Carly’s Visualizations Selected as One of 2019’s Best Science Images by the Nature News Team

Dec 17, 2019

Carly’s data visualization of SHIV infection in rhesus macaques (previously lauded here and here) has been selected as one of the best science images of 2019 by the Nature news team. Read about it here.

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 […]

Alex Shalek Featured in Nature Methods: “Voices in Methods Development”

Oct 04, 2019

Alex was recently featured in Nature Methods to discuss challenges and future opportunities in high-throughput genomics techniques. He joins researchers spanning across the spectrum of biology disciplines in laying out technological challenges of their respective fields and the great potential next-generation techniques hold in better understanding complex biological systems. Read Alex’s vision and those of […]

Human Cell Atlas Launches in Latin America

Sep 11, 2019

Alex was recently in Sao Paulo to kick off work with the the Human Cell Atlas in Latin America. Alongside both Brazilian and international researchers, Alex introduced the scope and potential impact of the initiative, which seeks to create comprehensive reference maps of all human cells—the fundamental units of life—as a basis for both understanding human […]

Kellie Kolb Graduates from the Shalek Lab!

Jun 06, 2019

Congratulations to Kellie Kolb, the first student from the Shalek Lab to receive her PhD! We wish Kellie the best of luck in her future endeavors, and we’re excited for many more graduations in the coming years!

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 […]

Carly’s Visualizations are in the Final Round of the 2019 Wellcome Photography Prize

Jun 03, 2019

Carly’s data visualization from a non-human primate atlas is one of 28 entries from 12 countries shortlisted for the Wellcome Photography Prize 2019. The overall winner will be announced on 3 July 2019. Learn more at the following link.

Alex Shalek named Institute Member at the Broad!

May 16, 2019

Alex was recently made an Institute Member at the Broad. Visit the link to see the full list of Institute Members.

Thank you Immunity for Highlight the Shalek Lab in Immunology Unplugged at AAI 2019!

May 16, 2019

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 […]

Carly Ziegler’s Image Selected in 2019 Koch Institute Image Awards

Mar 24, 2019

Carly’s visualization of single-cell mRNA sequencing data of 45,782 cells from 14 organs was selected in the 2019 Koch Institute Image Awards. Carly’s image and the other 9 awardees are featured in Stat News. Congratulations Carly!

Shalek Lab Celebrates 25 Years of Immunity.

Feb 14, 2019

The Shalek Lab is featured in the Immunity 25th Anniversary Photo Gallery.    

Alex Shalek Promoted to Associate Professor without Tenure!

Feb 06, 2019

Alex K. Shalek has been approved for promotion to Associate Professor without Tenure! The official promotion will be effective July 1. Congratulations Alex! Alex’s research is directed towards the creation and implementation of new technologies to understand how cells collectively perform systems-level functions in healthy and diseased states. His lab’s technology development efforts leverage recent […]

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.

Shalek 2018 Year-End Review

Dec 31, 2018

2018 Highlights from the Shalek Lab. 2018 was a great year, and we are looking forward to a fun and productive 2019! Happy New Year!  

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 […]

Alex Shalek Named Pew-Stewart Scholar for Cancer Research

Jun 20, 2018

Alex Shalek is one of five early career investigators selected as a Pew-Scholar for Cancer Research. To learn more about the Pew-Stewart Scholars visit the following link: http://www.pewtrusts.org/en/projects/pew-stewart-scholars-for-cancer-research

Shalek Lab Featured in Nature!

May 24, 2018

The Shalek Lab features prominently in a Technology Feature that appears in this week’s issue of Nature.  Seq-Well, a technology platform developed by members of the Shalek and Love labs, is highlighted with particular emphasis on the lab’s ongoing efforts using Seq-Well to understand infectious disease around the world. Download the full version.

Welcome Conner and Michelle!

May 21, 2018

We are excited that two new graduate students have decided to join the lab. Conner Kummerlowe is a first-year graduate student in the Computational and Systems Biology program at MIT. Before joining the Shalek lab, Conner studied Chemistry and Mathematics at Pomona College and Computational Biology the University of Cambridge. Michelle Ramseier is a first-year […]

Sarah Receives NSF Graduate Research Fellowship

May 17, 2018

Sarah Nyquist received a Graduate Research Fellowship from the National Science Foundation. Congratulations Sarah!

2018 Sloan Research Fellowships Announcement is Live!

Feb 15, 2018

Alex Shalek is one of 126 early-career scholars to receive a 2018 Sloan Fellowship in Chemistry. Sloan fellows receive $65,000 over a 2-year period in support of their research programs.

Lab Member Awards & Fellowships 2017, Part 1

Sep 05, 2017

Several Shalek Lab members have been recognized for their fantastic achievements! To note: Sam Allon was awarded a Graduate Research Fellowship through the National Science Foundation. Travis Hughes was awarded the Martha Gray Prize in Bioinformatics and Integrative Genomics at the 2017 HST forum. Travis Hughes was selected as a Tip-Top Junior Investigator by the […]

Alex Shalek named Pfizer-Laubach Career Development Professor

Jul 02, 2017

Alex Shalek has been appointed to the Pfizer-Laubach Career Development Professorship at MIT. The Pfizer-Laubach Chair was established by Pfizer to honor Dr. Gerald D. Laubach, MIT alumnus and former president of Pfizer Inc. Congratulations, Alex!

Newest Members Join the Team!

Jul 01, 2017

We welcomed several brand new members to the Shalek Lab this Spring! Brittany Goods joins the lab as a postdoctoral scholar following her PhD from Chris Love’s lab here at MIT. Sarah Nyquist joins as a co-advised PhD student at MIT in Computational & Systems Biology with Bonnie Berger. Alejandro Gupta and Toby Aicher join as new technicians, and Jenna Melanson joins as a new MIT-sponsored UROP. Welcome everyone!

Shalek Lab Bids Our First Alumnus Adieu

Jun 06, 2017

Sophia Liu, a Shalek Lab UROP from 2015-2017, graduated from MIT in June, completing her bachelor’s degree in chemical engineering. Thankfully, Sophia won’t be traveling too far; she will be pursuing a PhD in Medical Engineering and Medical Physics at Harvard University’s Health Sciences and Technology program. Congratulations, Sophia!

Shalek Lab Welcomes Newest Generation of Future Scientists

Mar 31, 2017

Kellie & her husband Pyae and Alex & his wife Heidi became first-time parents to their respective newborns, Tina and Orion! Tina was born March 12, 2017 and is already a steadfast Green Bay Packers fan like her mom. Orion was born just twelve days later on March 24th and was born with the same love of […]

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 […]

Alex Shalek Named 2015 NIH Director’s New Innovator Awardee

Oct 06, 2015

On October 6th, in a press release by issued the NIH, Alex Shalek was named as one of the recipients of the prestigious NIH Director’s New Innovator Award. Part of the Common Fund’s High-Risk, High-Reward Research program, the New Innovator Award supports exceptionally creative, early-career investigators who propose innovative, high-impact projects.  Alex and the lab are honored to receive this […]

Alex Shalek Named 2015 Beckman Young Investigator

Aug 07, 2015

Alex Shalek has been chosen as one of the eight young faculty members around the US to be awarded a Beckman Young Investigators Prize. The Beckman Young Investigators Program is intended to provide research support to the most promising young faculty members in the early stages of academic careers in the chemical and life sciences particularly to […]

Shalek Lab visits Durban

Jul 07, 2015

With the generous support of a MISTI grant from MIT, the Shalek Lab had the opportunity to visit collaborators at the Kwazulu-Natal Research Institute for Tuberculosis and HIV (K-RITH) in Durban, South Africa during the last week of June. The group met with professors Al Leslie and Thumbi Ndung’u and their labs to discuss current and […]

Alex Shalek Named 2015 Searle Scholar

Apr 15, 2015

Alex Shalek has been named as a 2015 Searle Scholar! Searle Scholar funding will generously support the Shalek Lab for the next three years. Alex would like to thank the Searle Scholars Program for their support. Find out more about Searle Scholars Program and see the other winners here.

Shalek Lab Welcomes its First Set of Students

Nov 18, 2014

Alex is joined by eight students this fall. Six embark on their Ph.D. in Chemistry while two are M.D. students at HST! Check out the full roster here.

Alex joins MIT & Ragon

Jul 01, 2014

Alex joins MIT as an assistant professor in Chemistry and a core member of IMES, with a joint appointment at the Ragon Institute and MGH.