Alex K Shalek

Alex K Shalek

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Alex K Shalek

Alex K Shalek

Publications by authors named "Alex K Shalek"

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IL-5Rα marks nasal polyp IgG4 and IgE-expressing cells in aspirin-exacerbated respiratory disease.

J Allergy Clin Immunol 2020 Mar 18. Epub 2020 Mar 18.

Department of Medicine; Division of Allergy and Clinical Immunology, Brigham and Women's Hospital, Boston, MA. Electronic address:

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http://dx.doi.org/10.1016/j.jaci.2020.02.035DOI Listing
March 2020

Distribution and storage of inflammatory memory in barrier tissues.

Nat Rev Immunol 2020 Feb 3. Epub 2020 Feb 3.

Institute for Medical Engineering and Science (IMES), MIT, Cambridge, MA, USA.

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http://dx.doi.org/10.1038/s41577-019-0263-zDOI Listing
February 2020

Identification of a Master Regulator of Differentiation in Toxoplasma.

Cell 2020 Jan 16;180(2):359-372.e16. Epub 2020 Jan 16.

Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2019.12.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6978799PMC
January 2020

Immunological Fingerprints of Controllers Developing Neutralizing HIV-1 Antibodies.

Cell Rep 2020 Jan;30(4):984-996.e4

Ragon Institute of MGH, MIT, and Harvard, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA; Infectious Disease Division, Massachusetts General Hospital, Boston, MA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2019.12.087DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6990401PMC
January 2020

TCR sequencing paired with massively parallel 3' RNA-seq reveals clonotypic T cell signatures.

Nat Immunol 2019 12 19;20(12):1692-1699. Epub 2019 Nov 19.

Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA.

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http://dx.doi.org/10.1038/s41590-019-0544-5DOI Listing
December 2019

Revisiting airway epithelial remodeling in type 2 immunity: Beyond goblet cell metaplasia.

J Allergy Clin Immunol 2019 Nov 7;144(5):1158-1160. Epub 2019 Oct 7.

Institute for Medical Engineering and Science (IMES), Department of Chemistry, and Koch Institute for Integrative Cancer Research, MIT, Cambridge; Broad Institute of MIT and Harvard, Cambridge; Ragon Institute of MGH, MIT, and Harvard, Cambridge.

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http://dx.doi.org/10.1016/j.jaci.2019.09.017DOI Listing
November 2019

Induction of metabolic quiescence defines the transitional to follicular B cell switch.

Sci Signal 2019 Oct 22;12(604). Epub 2019 Oct 22.

Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Department of Medicine, Harvard University, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1126/scisignal.aaw5573DOI Listing
October 2019

Single-Cell Analysis of the Liver Epithelium Reveals Dynamic Heterogeneity and an Essential Role for YAP in Homeostasis and Regeneration.

Cell Stem Cell 2019 07 9;25(1):23-38.e8. Epub 2019 May 9.

Stem Cell Program, Boston Children's Hospital, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Harvard Stem Cell Institute, Boston, MA 02115, USA. Electronic address:

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http://dx.doi.org/10.1016/j.stem.2019.04.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6814390PMC
July 2019

Single-Cell RNA-Seq Reveals AML Hierarchies Relevant to Disease Progression and Immunity.

Cell 2019 03 28;176(6):1265-1281.e24. Epub 2019 Feb 28.

Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Ludwig Center at Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00928674193009
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http://dx.doi.org/10.1016/j.cell.2019.01.031DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6515904PMC
March 2019

T Helper Cell Cytokines Modulate Intestinal Stem Cell Renewal and Differentiation.

Cell 2018 11 1;175(5):1307-1320.e22. Epub 2018 Nov 1.

Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, MA 02114, USA; Center for Microbiome informatics and Therapeutics, MIT, Cambridge, MA 02139, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00928674183131
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http://dx.doi.org/10.1016/j.cell.2018.10.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6239889PMC
November 2018

Selective expansion of myeloid and NK cells in humanized mice yields human-like vaccine responses.

Nat Commun 2018 11 28;9(1):5031. Epub 2018 Nov 28.

Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Washington Road, Princeton, NJ, 08544, USA.

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http://dx.doi.org/10.1038/s41467-018-07478-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6262001PMC
November 2018

Initiation of Antiviral B Cell Immunity Relies on Innate Signals from Spatially Positioned NKT Cells.

Cell 2018 01 14;172(3):517-533.e20. Epub 2017 Dec 14.

Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; The Francis Crick Institute, London NW1A 1AT, UK; Department of Microbiology and Immunobiology & HMS Center for Immune Imaging, Harvard Medical School, Boston, MA 02115, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2017.11.036DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5786505PMC
January 2018

Single-cell analyses to tailor treatments.

Sci Transl Med 2017 Sep;9(408)

The Centre for Personalised Medicine and Division of Pediatrics, Department of Clinical and Experimental Medicine, Linköping University, 58183 Linköping, Sweden.

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http://dx.doi.org/10.1126/scitranslmed.aan4730DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5645080PMC
September 2017

Scaling by shrinking: empowering single-cell 'omics' with microfluidic devices.

Nat Rev Genet 2017 06 10;18(6):345-361. Epub 2017 Apr 10.

School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA.

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http://dx.doi.org/10.1038/nrg.2017.15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5495114PMC
June 2017

Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput.

Nat Methods 2017 Apr 13;14(4):395-398. Epub 2017 Feb 13.

Institute for Medical Engineering &Science (IMES) and Department of Chemistry, MIT, Cambridge, Massachusetts, USA.

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http://dx.doi.org/10.1038/nmeth.4179DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5376227PMC
April 2017

Baring cellular souls.

Authors:
Alex K Shalek

Sci Transl Med 2017 02;9(377)

Institute for Medical Engineering & Science (IMES) and Department of Chemistry, MIT, Cambridge, MA 02139, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Email:

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http://dx.doi.org/10.1126/scitranslmed.aam6064DOI Listing
February 2017

A case of mistaken identity.

Authors:
Alex K Shalek

Sci Transl Med 2017 01;9(371)

Institute for Medical Engineering & Science (IMES) and Department of Chemistry, MIT, Cambridge, MA 02139, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Email:

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http://dx.doi.org/10.1126/scitranslmed.aal4988DOI Listing
January 2017

Size no longer matters.

Authors:
Alex K Shalek

Sci Transl Med 2016 11;8(365):365ec185

Institute for Medical Engineering & Science (IMES) and Department of Chemistry, MIT, Cambridge, MA 02139, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Email:

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http://dx.doi.org/10.1126/scitranslmed.aal0073DOI Listing
November 2016

Antiviral CD8 T Cells Restricted by Human Leukocyte Antigen Class II Exist during Natural HIV Infection and Exhibit Clonal Expansion.

Immunity 2016 10;45(4):917-930

Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 01239, USA; Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 01239, USA; Broad Institute, Cambridge, MA 01239, USA. Electronic address:

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http://dx.doi.org/10.1016/j.immuni.2016.09.015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5077698PMC
October 2016

Regulation of X-linked gene expression during early mouse development by .

Elife 2016 09 19;5. Epub 2016 Sep 19.

Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, United States.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5059138PMC
http://dx.doi.org/10.7554/eLife.19127DOI Listing
September 2016

Multiplexed barcoded CRISPR-Cas9 screening enabled by CombiGEM.

Proc Natl Acad Sci U S A 2016 Mar 10;113(9):2544-9. Epub 2016 Feb 10.

Synthetic Biology Group, Massachusetts Institute of Technology (MIT) Synthetic Biology Center, MIT, Cambridge, MA 02139; Research Laboratory of Electronics, MIT, Cambridge, MA 02139; Department of Biological Engineering, MIT, Cambridge, MA 02139; Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA 02139;

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http://dx.doi.org/10.1073/pnas.1517883113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4780610PMC
March 2016

Innate Lymphoid Cells Are Depleted Irreversibly during Acute HIV-1 Infection in the Absence of Viral Suppression.

Immunity 2016 Feb 2;44(2):391-405. Epub 2016 Feb 2.

KwaZulu-Natal Research Institute for Tuberculosis & HIV (K-RITH), University of KwaZulu-Natal (UKZN), 4001 Durban, South Africa; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139-4307, USA.

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http://dx.doi.org/10.1016/j.immuni.2016.01.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6836297PMC
February 2016

A microfluidic platform enabling single-cell RNA-seq of multigenerational lineages.

Nat Commun 2016 Jan 6;7:10220. Epub 2016 Jan 6.

Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachussets 02139, USA.

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http://dx.doi.org/10.1038/ncomms10220DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4729820PMC
January 2016

Single-Cell Genomics Unveils Critical Regulators of Th17 Cell Pathogenicity.

Cell 2015 Dec 19;163(6):1400-12. Epub 2015 Nov 19.

Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA; Howard Hughes Medical Institute and David H. Koch Institute of Integrative Cancer Biology, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2015.11.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4671824PMC
December 2015

Pathogen Cell-to-Cell Variability Drives Heterogeneity in Host Immune Responses.

Cell 2015 Sep 3;162(6):1309-21. Epub 2015 Sep 3.

Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA. Electronic address:

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http://www.cell.com/cms/attachment/2035742002/2051265527/mmc
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http://linkinghub.elsevier.com/retrieve/pii/S009286741501041
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http://dx.doi.org/10.1016/j.cell.2015.08.027DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4578813PMC
September 2015

MERFISHing for spatial context.

Trends Immunol 2015 Jul 23;36(7):390-1. Epub 2015 May 23.

New York Genome Center, New York, NY, USA; New York University, Center for Genomics and Systems Biology, New York, NY, USA. Electronic address:

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http://dx.doi.org/10.1016/j.it.2015.05.002DOI Listing
July 2015

Marrying microfluidics and microwells for parallel, high-throughput single-cell genomics.

Genome Biol 2015 Jun 20;16:129. Epub 2015 Jun 20.

Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.

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http://dx.doi.org/10.1186/s13059-015-0695-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4474330PMC
June 2015

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets.

Cell 2015 May;161(5):1202-1214

Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2015.05.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4481139PMC
May 2015

Preparation of Single-Cell RNA-Seq Libraries for Next Generation Sequencing.

Curr Protoc Mol Biol 2014 Jul 1;107:4.22.1-17. Epub 2014 Jul 1.

Broad Institute of MIT and Harvard, Cambridge, Massachusetts.

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http://doi.wiley.com/10.1002/0471142727.mb0422s107
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http://dx.doi.org/10.1002/0471142727.mb0422s107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4338574PMC
July 2014

Single-cell RNA-seq reveals dynamic paracrine control of cellular variation.

Nature 2014 Jun 11;510(7505):363-9. Epub 2014 Jun 11.

1] Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA [2] Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02140, USA.

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http://dx.doi.org/10.1038/nature13437DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4193940PMC
June 2014

Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma.

Science 2014 Jun 12;344(6190):1396-401. Epub 2014 Jun 12.

Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA. Broad Institute of Harvard and Massachusetts Institute of Techonology (MIT), Cambridge, MA 02142, USA. Howard Hughes Medical Institute Chevy Chase, MD 20815, USA.

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http://www.sciencemag.org/cgi/doi/10.1126/science.1254257
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http://dx.doi.org/10.1126/science.1254257DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4123637PMC
June 2014

Heterogeneity in immune responses: from populations to single cells.

Trends Immunol 2014 May 16;35(5):219-29. Epub 2014 Apr 16.

Department of Chemistry and Chemical Biology and Department of Physics, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA. Electronic address:

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http://dx.doi.org/10.1016/j.it.2014.03.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4035247PMC
May 2014

Reconstructing and reprogramming the tumor-propagating potential of glioblastoma stem-like cells.

Cell 2014 Apr 10;157(3):580-94. Epub 2014 Apr 10.

Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2014.02.030DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4004670PMC
April 2014

Probing enzymatic activity inside living cells using a nanowire-cell "sandwich" assay.

Nano Lett 2013 Jan 20;13(1):153-8. Epub 2012 Dec 20.

Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 136-791, South Korea.

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http://pubs.acs.org/doi/10.1021/nl3037068
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http://dx.doi.org/10.1021/nl3037068DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3541459PMC
January 2013

Vertical nanowire electrode arrays as a scalable platform for intracellular interfacing to neuronal circuits.

Nat Nanotechnol 2012 Jan 10;7(3):180-4. Epub 2012 Jan 10.

Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA.

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http://www.nature.com/articles/nnano.2011.249
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http://dx.doi.org/10.1038/nnano.2011.249DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4209482PMC
January 2012

Vertical silicon nanowires as a universal platform for delivering biomolecules into living cells.

Proc Natl Acad Sci U S A 2010 Feb 11;107(5):1870-5. Epub 2010 Jan 11.

Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA.

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http://dx.doi.org/10.1073/pnas.0909350107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2836617PMC
February 2010