Alex K. Shalek

Alex Shalek, August 2019 Alex K. Shalek, a biomedical engineer, is the Director of the Institute for Medical Engineering and Science (IMES) and the J. W. Kieckhefer Professor in IMES and the Department of Chemistry at the Massachusetts Institute of Technology. He is an Extramural Member of the Koch Institute for Integrative Cancer Research at MIT. Additionally, he is a Member of the Ragon Institute, an Institute Member of the Broad Institute, an Assistant in Immunology at Massachusetts General Hospital, and an Instructor in Health Sciences and Technology at Harvard Medical School. The multi-disciplinary research of the Shalek Lab aims to create and implement broadly-applicable methods to study and engineer cellular responses in tissues, to drive biological discovery and improve prognostics, diagnostics, and therapeutics for autoimmune, infectious, and cancerous diseases. Shalek and his lab are best known for their work in single-cell genomics and for studying a number of devastating, but difficult to study, human diseases with partners around the world. Provided by Wikipedia
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  1. 1
    Identification and Tracking of Alloreactive T Cell Clones in Rhesus Macaques Through the RM-scTCR-Seq Platform

    Identification and Tracking of Alloreactive T Cell Clones in Rhesus Macaques Through the RM-scTCR-Seq Platform by Ulrike Gerdemann, Ryan A. Fleming, James Kaminski, James Kaminski, James Kaminski, James Kaminski, Connor McGuckin, Xianliang Rui, Jennifer F. Lane, Paula Keskula, Lorenzo Cagnin, Alex K. Shalek, Alex K. Shalek, Alex K. Shalek, Victor Tkachev, Leslie S. Kean

    Published 2022-01-01
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  2. 2
    scRNA-seq reveals elevated interferon responses and TNF-α signaling via NFkB in monocytes in children with uncomplicated malaria

    scRNA-seq reveals elevated interferon responses and TNF-α signaling via NFkB in monocytes in children with uncomplicated malaria by Collins M. Morang’a, Riley S. Drake, Riley S. Drake, Riley S. Drake, Riley S. Drake, Vincent N. Miao, Vincent N. Miao, Vincent N. Miao, Vincent N. Miao, Nancy K. Nyakoe, Dominic S. Y. Amuzu, Vincent Appiah, Yaw Aniweh, Yaw Bediako, Saikou Y. Bah, Alex K. Shalek, Alex K. Shalek, Alex K. Shalek, Alex K. Shalek, Gordon A. Awandare, Thomas D. Otto, Lucas Amenga-Etego

    Published 2025-01-01
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  3. 3
    Improved haplotype inference by exploiting long-range linking and allelic imbalance in RNA-seq datasets

    Improved haplotype inference by exploiting long-range linking and allelic imbalance in RNA-seq datasets by Emily Berger, Deniz Yorukoglu, Lillian Zhang, Sarah K. Nyquist, Alex K. Shalek, Manolis Kellis, Ibrahim Numanagić, Bonnie Berger

    Published 2020-09-01
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  4. 4
    Enteric Coronavirus Infection and Treatment Modeled With an Immunocompetent Human Intestine-On-A-Chip

    Enteric Coronavirus Infection and Treatment Modeled With an Immunocompetent Human Intestine-On-A-Chip by Amir Bein, Seongmin Kim, Girija Goyal, Wuji Cao, Cicely Fadel, Arash Naziripour, Sanjay Sharma, Ben Swenor, Nina LoGrande, Atiq Nurani, Vincent N. Miao, Vincent N. Miao, Vincent N. Miao, Vincent N. Miao, Andrew W. Navia, Andrew W. Navia, Andrew W. Navia, Carly G. K. Ziegler, Carly G. K. Ziegler, Carly G. K. Ziegler, Carly G. K. Ziegler, Carly G. K. Ziegler, José Ordovas Montañes, José Ordovas Montañes, José Ordovas Montañes, Pranav Prabhala, Min Sun Kim, Rachelle Prantil-Baun, Melissa Rodas, Amanda Jiang, Lucy O’Sullivan, Gladness Tillya, Alex K. Shalek, Alex K. Shalek, Alex K. Shalek, Alex K. Shalek, Donald E. Ingber, Donald E. Ingber, Donald E. Ingber

    Published 2021-10-01
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  5. 5
    Pro-inflammatory feedback loops define immune responses to pathogenic Lentivirus infection

    Pro-inflammatory feedback loops define immune responses to pathogenic Lentivirus infection by Aaron J. Wilk, Joshua O. Marceau, Samuel W. Kazer, Ira Fleming, Vincent N. Miao, Jennyfer Galvez-Reyes, Jason T. Kimata, Alex K. Shalek, Susan Holmes, Julie Overbaugh, Catherine A. Blish

    Published 2024-02-01
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  6. 6
    Functional compensation precedes recovery of tissue mass following acute liver injury

    Functional compensation precedes recovery of tissue mass following acute liver injury by Chad M. Walesky, Kellie E. Kolb, Carolyn L. Winston, Jake Henderson, Benjamin Kruft, Ira Fleming, Sungjin Ko, Satdarshan P. Monga, Florian Mueller, Udayan Apte, Alex K. Shalek, Wolfram Goessling

    Published 2020-11-01
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  7. 7
    Single-cell transcriptomic atlas of the human retina identifies cell types associated with age-related macular degeneration

    Single-cell transcriptomic atlas of the human retina identifies cell types associated with age-related macular degeneration by Madhvi Menon, Shahin Mohammadi, Jose Davila-Velderrain, Brittany A. Goods, Tanina D. Cadwell, Yu Xing, Anat Stemmer-Rachamimov, Alex K. Shalek, John Christopher Love, Manolis Kellis, Brian P. Hafler

    Published 2019-10-01
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  8. 8
    Selective expansion of myeloid and NK cells in humanized mice yields human-like vaccine responses

    Selective expansion of myeloid and NK cells in humanized mice yields human-like vaccine responses by Florian Douam, Carly G. K. Ziegler, Gabriela Hrebikova, Bruno Fant, Robert Leach, Lance Parsons, Wei Wang, Jenna M. Gaska, Benjamin Y. Winer, Brigitte Heller, Alex K. Shalek, Alexander Ploss

    Published 2018-11-01
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  9. 9
    HIV specific CD8+ TRM-like cells in tonsils express exhaustive signatures in the absence of natural HIV control

    HIV specific CD8+ TRM-like cells in tonsils express exhaustive signatures in the absence of natural HIV control by Rabiah Fardoos, Rabiah Fardoos, Sarah K. Nyquist, Sarah K. Nyquist, Osaretin E. Asowata, Samuel W. Kazer, Alveera Singh, Abigail Ngoepe, Jennifer Giandhari, Ntombifuthi Mthabela, Dirhona Ramjit, Samita Singh, Farina Karim, Søren Buus, Frank Anderson, J. Zachary Porterfield, J. Zachary Porterfield, J. Zachary Porterfield, J. Zachary Porterfield, Andile L. Sibiya, Rishan Bipath, Kumeshan Moodley, Warren Kuhn, Warren Kuhn, Bonnie Berger, Son Nguyen, Tulio de Oliveira, Thumbi Ndung’u, Thumbi Ndung’u, Thumbi Ndung’u, Philip Goulder, Philip Goulder, Philip Goulder, Alex K. Shalek, Alex K. Shalek, Alex K. Shalek, Alasdair Leslie, Alasdair Leslie, Henrik N. Kløverpris, Henrik N. Kløverpris, Henrik N. Kløverpris

    Published 2022-10-01
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  10. 10
    MR1-Restricted MAIT Cells From The Human Lung Mucosal Surface Have Distinct Phenotypic, Functional, and Transcriptomic Features That Are Preserved in HIV Infection

    MR1-Restricted MAIT Cells From The Human Lung Mucosal Surface Have Distinct Phenotypic, Functional, and Transcriptomic Features That Are Preserved in HIV Infection by Sharon Khuzwayo, Sharon Khuzwayo, Maphe Mthembu, Maphe Mthembu, Erin W. Meermeier, Sanjay M. Prakadan, Sanjay M. Prakadan, Sanjay M. Prakadan, Samuel W. Kazer, Samuel W. Kazer, Samuel W. Kazer, Thierry Bassett, Kennedy Nyamande, Dilshaad Fakey Khan, Priya Maharaj, Mohammed Mitha, Moosa Suleman, Moosa Suleman, Zoey Mhlane, Dirhona Ramjit, Farina Karim, Alex K. Shalek, Alex K. Shalek, Alex K. Shalek, David M. Lewinsohn, David M. Lewinsohn, David M. Lewinsohn, Thumbi Ndung’u, Thumbi Ndung’u, Thumbi Ndung’u, Thumbi Ndung’u, Thumbi Ndung’u, Thumbi Ndung’u, Emily B. Wong, Emily B. Wong, Emily B. Wong, Emily B. Wong

    Published 2021-04-01
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  11. 11
    Follicle-intrinsic and spatially distinct molecular programs drive follicle rupture and luteinization during ex vivo mammalian ovulation

    Follicle-intrinsic and spatially distinct molecular programs drive follicle rupture and luteinization during ex vivo mammalian ovulation by Emily J. Zaniker, Jiyang Zhang, Daniela Russo, Ruixu Huang, Kristine Suritis, Riley S. Drake, Esther Barlow-Smith, Alex K. Shalek, Teresa K. Woodruff, Shuo Xiao, Brittany A. Goods, Francesca E. Duncan

    Published 2024-10-01
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  12. 12
    A Reproducibility-Based Computational Framework Identifies an Inducible, Enhanced Antiviral State in Dendritic Cells from HIV-1 Elite Controllers

    A Reproducibility-Based Computational Framework Identifies an Inducible, Enhanced Antiviral State in Dendritic Cells from HIV-1 Elite Controllers by Enrique Martin-Gayo, Michael B. Cole, Kellie E. Kolb, Zhengyu Ouyang, Jacqueline Cronin, Samuel W. Kazer, Jose Ordovas-Montanes, Mathias Lichterfeld, Bruce D. Walker, Nir Yosef, Alex K. Shalek, Xu G. Yu

    Published 2018-01-01
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  13. 13
    Single-cell immunophenotyping of the skin lesion erythema migrans identifies IgM memory B cells

    Single-cell immunophenotyping of the skin lesion erythema migrans identifies IgM memory B cells by Ruoyi Jiang, Hailong Meng, Khadir Raddassi, Ira Fleming, Kenneth B. Hoehn, Kenneth R. Dardick, Alexia A. Belperron, Ruth R. Montgomery, Alex K. Shalek, David A. Hafler, Steven H. Kleinstein, Linda K. Bockenstedt

    Published 2021-06-01
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  14. 14
    A Single Human VH-gene Allows for a Broad-Spectrum Antibody Response Targeting Bacterial Lipopolysaccharides in the Blood

    A Single Human VH-gene Allows for a Broad-Spectrum Antibody Response Targeting Bacterial Lipopolysaccharides in the Blood by Maya Sangesland, Ashraf S. Yousif, Larance Ronsard, Samuel W. Kazer, Alex Lee Zhu, G. James Gatter, Matthew R. Hayward, Ralston M. Barnes, Maricel Quirindongo-Crespo, Daniel Rohrer, Nils Lonberg, Douglas Kwon, Alex K. Shalek, Daniel Lingwood

    Published 2020-08-01
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  15. 15
    Regulation of X-linked gene expression during early mouse development by Rlim

    Regulation of X-linked gene expression during early mouse development by Rlim by Feng Wang, JongDae Shin, Jeremy M Shea, Jun Yu, Ana Bošković, Meg Byron, Xiaochun Zhu, Alex K Shalek, Aviv Regev, Jeanne B Lawrence, Eduardo M Torres, Lihua J Zhu, Oliver J Rando, Ingolf Bach

    Published 2016-09-01
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  16. 16
    Linking single-cell measurements of mass, growth rate, and gene expression

    Linking single-cell measurements of mass, growth rate, and gene expression by Robert J. Kimmerling, Sanjay M. Prakadan, Alejandro J. Gupta, Nicholas L. Calistri, Mark M. Stevens, Selim Olcum, Nathan Cermak, Riley S. Drake, Kristine Pelton, Frederik De Smet, Keith L. Ligon, Alex K. Shalek, Scott R. Manalis

    Published 2018-11-01
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  17. 17
    A multi-omics spatial framework for host-microbiome dissection within the intestinal tissue microenvironment

    A multi-omics spatial framework for host-microbiome dissection within the intestinal tissue microenvironment by Bokai Zhu, Yunhao Bai, Yao Yu Yeo, Xiaowei Lu, Xavier Rovira-Clavé, Han Chen, Jason Yeung, Dingani Nkosi, Jonathan Glickman, Antonio Delgado-Gonzalez, Georg K. Gerber, Mike Angelo, Alex K. Shalek, Garry P. Nolan, Sizun Jiang

    Published 2025-01-01
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  18. 18
    B cell heterogeneity in human tuberculosis highlights compartment-specific phenotype and functional roles

    B cell heterogeneity in human tuberculosis highlights compartment-specific phenotype and functional roles by Robert Krause, Paul Ogongo, Liku Tezera, Mohammed Ahmed, Ian Mbano, Mark Chambers, Abigail Ngoepe, Magalli Magnoumba, Daniel Muema, Farina Karim, Khadija Khan, Kapongo Lumamba, Kievershen Nargan, Rajhmun Madansein, Adrie Steyn, Alex K. Shalek, Paul Elkington, Al Leslie

    Published 2024-05-01
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  19. 19
    Identification and characterization of the T cell receptor (TCR) repertoire of the cynomolgus macaque (Macaca Fascicularis)

    Identification and characterization of the T cell receptor (TCR) repertoire of the cynomolgus macaque (Macaca Fascicularis) by Swati Jaiswal, Sarah K. Nyquist, Shayla Boyce, Tasneem Jivanjee, Samira Ibrahim, Joshua D. Bromley, G. James Gatter, Hannah Gideon, Kush Patel, Sharie Keanne Ganchua, Bonnie Berger, Sarah M. Fortune, JoAnne L. Flynn, Alex K. Shalek, Samuel M. Behar

    Published 2022-09-01
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  20. 20
    Publisher Correction: Live cell tagging tracking and isolation for spatial transcriptomics using photoactivatable cell dyes

    Publisher Correction: Live cell tagging tracking and isolation for spatial transcriptomics using photoactivatable cell dyes by Alex S. Genshaft, Carly G. K. Ziegler, Constantine N. Tzouanas, Benjamin E. Mead, Alex M. Jaeger, Andrew W. Navia, Ryan P. King, Miyeko D. Mana, Siyi Huang, Vanessa Mitsialis, Scott B. Snapper, Ömer H. Yilmaz, Tyler Jacks, Jeffrey F. Van Humbeck, Alex K. Shalek

    Published 2021-09-01
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