Alex Featured in Cell Systems

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.

Seq-Well S^3 Released

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.

Constantine Named 2020 Hertz Fellow!

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

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!

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

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 […]

COVID-19 scRNA-seq Resource Datasets Released

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In light of the spread of SARS-CoV-2, we are sharing multiple unpublished and published scRNA-seq datasets across both health and disease that harbor cells expressing ACE2 (the gene encoding the host receptor) and TMPRSS2 (the gene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 […]

New Study on Increased TB Vaccine Efficacy Now Out

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

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

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”

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

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!

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

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”

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 […]

Alex Shalek Promoted to Associate Professor without Tenure!

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 […]

New Paper on Ulcerative Colitis on BioRxiv

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

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 […]

Shalek Lab Featured in Nature!

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!

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 […]

Lab Member Awards & Fellowships 2017, Part 1

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 […]

Newest Members Join the Team!

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

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

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

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.

Shalek & Manalis Lab Research Featured on MIT News

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

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

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

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

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.

Alex joins MIT & Ragon

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.