Alex K. Shalek

Last updated
Alex Shalek
Alex K. Shalek, PhD.jpg
Alex Shalek, August 2019
Born(1981-12-18)December 18, 1981
Alma mater Columbia University
Harvard University
Awards Harold E. Edgerton Faculty Achievement Award, MIT (2020)
Pew Charitable Trust Pew-Stewart Scholar (2018)
Alfred P. Sloan Foundation Sloan Research Fellow (2018)
Searle Scholars Program (2015)
Beckman Young Investigators Award (2015)
NIH Director's New Innovator Award (2015)
Scientific career
Institutions Massachusetts Institute of Technology
Broad Institute
Koch Institute for Integrative Cancer Research
Ragon Institute
Mass General Hospital
Harvard Medical School
Doctoral advisor Hongkun Park
Website www.shaleklab.com

Alex K. Shalek is a biomedical engineer, and a core faculty member of the Institute for Medical Engineering and Science (IMES), an Associate Professor of Chemistry, and an Extramural Member of the Koch Institute for Integrative Cancer Research at the Massachusetts Institute of Technology. Additionally, he is a Member of the Ragon Institute and 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. [1]

Contents

Education and previous research

Shalek received his B.A. summa cum laude in 2004 from Columbia University where he studied chemical physics as a John Jay Scholar with Richard Bersohn and Louis Brus. He then performed graduate work in chemical physics developing arrays of nanowires as cellular "syringes" and electrochemical probes under the direction of Hongkun Park at Harvard University. [2] After, as a postdoctoral fellow, under the direction of Park and Aviv Regev at the Broad Institute, Shalek helped pioneer single-cell patterns in cellular responses to study how cells respond differently to the same condition, showing that genome-wide gene expression covariation across cells could be used to define cellular types and states, their internal "circuitry", from the “bottom-up”. [3] [4] [5] [6]

As an independent investigator, Shalek and his lab have helped scale and simplify single cell genomics to study complex, low-input clinical specimens around the world. [7] [5] [8] In parallel, they have used these and other approaches [8] [9] [10] [11] [12] [13] [14] [ excessive citations ] to help examine the causes and consequences of cellular heterogeneity across cancers, [15] [16] [17] [18] [19] infectious diseases, [5] [8] [9] [10] [20] [21] [22] [23] [24] [25] [26] [27] [ excessive citations ] and inflammation. [28] [29] [30]

Ongoing research

Current work in the Shalek Lab includes both the development of broadly enabling technologies as well as their application to characterize, model, and control multicellular systems. With respect to technology development, the lab brings together areas of research in genomics, chemical biology, and nanotechnology to establish accessible approaches to profile and control cells and their interactions.

In addition to these tools with the global research community, [31] the lab is applying them to dissect human diseases, like COVID-19, [32] [33] methodically linking cellular features and clinical observations. Major areas of focus include how: immune cells coordinate balanced responses to environmental stresses; [28] [29] [8] [34] host cell-pathogen interactions evolve during infection; [8] [9] [10] [21] [22] [23] [26] [ excessive citations ] and, tumor cells evade therapeutic treatment and natural immunity. [15] [17] [18] [19] [25] [35]

From these observations and those of others, the lab aims to understand how disease alters tissue function at the cellular level and realize therapeutic and prophylactic interventions to reestablish or support human health.

Select honors and awards

Select publications

Related Research Articles

<span class="mw-page-title-main">Robert G. Roeder</span>

Robert G. Roeder is an American biochemist. He is known as a pioneer scientist in eukaryotic transcription. He discovered three distinct nuclear RNA polymerases in 1969 and characterized many proteins involved in the regulation of transcription, including basic transcription factors and the first mammalian gene-specific activator over five decades of research. He is the recipient of the Gairdner Foundation International Award in 2000, the Albert Lasker Award for Basic Medical Research in 2003, and the Kyoto Prize in 2021. He currently serves as Arnold and Mabel Beckman Professor and Head of the Laboratory of Biochemical and Molecular Biology at The Rockefeller University.

Glycoconjugates are the classification family for carbohydrates – referred to as glycans – which are covalently linked with chemical species such as proteins, peptides, lipids, and other compounds. Glycoconjugates are formed in processes termed glycosylation.

<span class="mw-page-title-main">Catherine Dulac</span> French–American biologist

Catherine Dulac is a French–American biologist. She is the Higgins Professor in Molecular and Cellular Biology at Harvard University, where she served as department chair from 2007 to 2013. She is also an investigator at the Howard Hughes Medical Institute. She was born in 1963 in France. She came to the United States for her postdoctoral study in 1991.

<span class="mw-page-title-main">Cellular senescence</span> Phenomenon characterized by the cessation of cell division

Cellular senescence is a phenomenon characterized by the cessation of cell division. In their experiments during the early 1960s, Leonard Hayflick and Paul Moorhead found that normal human fetal fibroblasts in culture reach a maximum of approximately 50 cell population doublings before becoming senescent. This process is known as "replicative senescence", or the Hayflick limit. Hayflick's discovery of mortal cells paved the path for the discovery and understanding of cellular aging molecular pathways. Cellular senescence can be initiated by a wide variety of stress inducing factors. These stress factors include both environmental and internal damaging events, abnormal cellular growth, oxidative stress, autophagy factors, among many other things.

<span class="mw-page-title-main">RNA-Seq</span> Lab technique in cellular biology

RNA-Seq is a technique that uses next-generation sequencing (NGS) to reveal the presence and quantity of RNA molecules in a biological sample, providing a snapshot of gene expression in the sample, also known as transcriptome.

Maternal to zygotic transition (MZT), also known as embryonic genome activation, is the stage in embryonic development during which development comes under the exclusive control of the zygotic genome rather than the maternal (egg) genome. The egg contains stored maternal genetic material mRNA which controls embryo development until the onset of MZT. After MZT the diploid embryo takes over genetic control. This requires both zygotic genome activation (ZGA), and degradation of maternal products. This process is important because it is the first time that the new embryonic genome is utilized and the paternal and maternal genomes are used in combination. The zygotic genome now drives embryo development.

MicroRNA sequencing (miRNA-seq), a type of RNA-Seq, is the use of next-generation sequencing or massively parallel high-throughput DNA sequencing to sequence microRNAs, also called miRNAs. miRNA-seq differs from other forms of RNA-seq in that input material is often enriched for small RNAs. miRNA-seq allows researchers to examine tissue-specific expression patterns, disease associations, and isoforms of miRNAs, and to discover previously uncharacterized miRNAs. Evidence that dysregulated miRNAs play a role in diseases such as cancer has positioned miRNA-seq to potentially become an important tool in the future for diagnostics and prognostics as costs continue to decrease. Like other miRNA profiling technologies, miRNA-Seq has both advantages and disadvantages.

Jeannie T. Lee is a Professor of Genetics at Harvard Medical School and the Massachusetts General Hospital, and a Howard Hughes Medical Institute Investigator. She is known for her work on X-chromosome inactivation and for discovering the functions of a new class of epigenetic regulators known as long noncoding RNAs (lncRNAs), including Xist and Tsix.

<span class="mw-page-title-main">Bradley Bernstein</span> Biologist

Bradley E. Bernstein is a biologist and Professor of Cell Biology at Harvard Medical School. He is Chair of the Department of Cancer Biology at the Dana–Farber Cancer Institute and the Director of the Broad Institute's Gene Regulation Observatory. He is known for contributions to the fields of epigenetics and cancer biology.

<span class="mw-page-title-main">Nina Papavasiliou</span> Immunologist

Nina Papavasiliou is an immunologist and Helmholtz Professor in the Division of Immune Diversity at the German Cancer Research Center in Heidelberg, Germany. She is also an adjunct professor at the Rockefeller University, where she was previously associate professor and head of the Laboratory of Lymphocyte Biology. She is best known for her work in the fields of DNA and RNA editing.

<span class="mw-page-title-main">Trajectory inference</span>

Trajectory inference or pseudotemporal ordering is a computational technique used in single-cell transcriptomics to determine the pattern of a dynamic process experienced by cells and then arrange cells based on their progression through the process. Single-cell protocols have much higher levels of noise than bulk RNA-seq, so a common step in a single-cell transcriptomics workflow is the clustering of cells into subgroups. Clustering can contend with this inherent variation by combining the signal from many cells, while allowing for the identification of cell types. However, some differences in gene expression between cells are the result of dynamic processes such as the cell cycle, cell differentiation, or response to an external stimuli. Trajectory inference seeks to characterize such differences by placing cells along a continuous path that represents the evolution of the process rather than dividing cells into discrete clusters. In some methods this is done by projecting cells onto an axis called pseudotime which represents the progression through the process.

CITE-Seq is a method for performing RNA sequencing along with gaining quantitative and qualitative information on surface proteins with available antibodies on a single cell level. So far, the method has been demonstrated to work with only a few proteins per cell. As such, it provides an additional layer of information for the same cell by combining both proteomics and transcriptomics data. For phenotyping, this method has been shown to be as accurate as flow cytometry by the groups that developed it. It is currently one of the main methods, along with REAP-Seq, to evaluate both gene expression and protein levels simultaneously in different species.

Richard William Carthew is a developmental biologist and quantitative biologist at Northwestern University. He is a professor of molecular biosciences and is the director of the NSF-Simons Center for Quantitative Biology.

<span class="mw-page-title-main">Proximity labeling</span>

Enzyme-catalyzed proximity labeling (PL), also known as proximity-based labeling, is a laboratory technique that labels biomolecules, usually proteins or RNA, proximal to a protein of interest. By creating a gene fusion in a living cell between the protein of interest and an engineered labeling enzyme, biomolecules spatially proximal to the protein of interest can then be selectively marked with biotin for pulldown and analysis. Proximity labeling has been used for identifying the components of novel cellular structures and for determining protein-protein interaction partners, among other applications.

Bryan Richard Cullen is a James B. Duke Professor of Molecular Genetics and Microbiology at Duke University Medical Center in Durham, North Carolina. Cullen was the Founding Director of the Duke University Center for Virology.

Aging is characterized by a progressive loss of physiological integrity, leading to impaired function and increased vulnerability to death. The hallmarks of aging are the types of biochemical changes that occur in all organisms that experience biological aging and lead to a progressive loss of physiological integrity, impaired function and, eventually, death. They were first listed in a landmark paper in 2013 to conceptualize the essence of biological aging and its underlying mechanisms.

Deterministic Barcoding in Tissue for Spatial Omics Sequencing (DBiT-seq) was developed at Yale University by Rong Fan and colleagues in 2020 to create a multi-omics approach for studying spatial gene expression heterogenicity within a tissue sample. This method can be used for the co-mapping mRNA and protein levels at a near single-cell resolution in fresh or frozen formaldehyde-fixed tissue samples. DBiT-seq utilizes next generation sequencing (NGS) and microfluidics. This method allows for simultaneous spatial transcriptomic and proteomic analysis of a tissue sample. DBiT-seq improves upon previous spatial transcriptomics applications such as High-Definition Spatial Transcriptomics (HDST) and Slide-seq by increasing the number of detectable genes per pixel, increased cellular resolution, and ease of implementation.

Single-cell genome and epigenome by transposases sequencing (scGET-seq) is a DNA sequencing method for profiling open and closed chromatin. In contrast to single-cell assay for transposase-accessible chromatin with sequencing (scATAC-seq), which only targets active euchromatin. scGET-seq is also capable of probing inactive heterochromatin.

<span class="mw-page-title-main">Hunchback (gene)</span> Maternal effect gene and gap gene

Hunchback is a maternal effect and zygotic gene expressed in the embryos of the fruit fly Drosophila melanogaster. In maternal effect genes, the RNA or protein from the mother’s gene is deposited into the oocyte or embryo before the embryo can express its own zygotic genes.

References

  1. ↑ "Shalek Lab". shaleklab.com. Retrieved 2020-10-30.
  2. ↑ Robinson, Jacob T.; Jorgolli, Marsela; Shalek, Alex K.; Yoon, Myung-Han; Gertner, Rona S.; Park, Hongkun (March 2012). "Vertical nanowire electrode arrays as a scalable platform for intracellular interfacing to neuronal circuits". Nature Nanotechnology. 7 (3): 180–184. Bibcode:2012NatNa...7..180R. doi:10.1038/nnano.2011.249. ISSN   1748-3395. PMC   4209482 . PMID   22231664.
  3. 1 2 Shalek, Alex K.; Satija, Rahul; Adiconis, Xian; Gertner, Rona S.; Gaublomme, Jellert T.; Raychowdhury, Raktima; Schwartz, Schraga; Yosef, Nir; Malboeuf, Christine; Lu, Diana; Trombetta, John J. (June 2013). "Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells". Nature. 498 (7453): 236–240. Bibcode:2013Natur.498..236S. doi:10.1038/nature12172. ISSN   1476-4687. PMC   3683364 . PMID   23685454.
  4. 1 2 Shalek, Alex K.; Satija, Rahul; Shuga, Joe; Trombetta, John J.; Gennert, Dave; Lu, Diana; Chen, Peilin; Gertner, Rona S.; Gaublomme, Jellert T.; Yosef, Nir; Schwartz, Schraga (June 2014). "Single-cell RNA-seq reveals dynamic paracrine control of cellular variation". Nature. 510 (7505): 363–369. Bibcode:2014Natur.510..363S. doi:10.1038/nature13437. ISSN   1476-4687. PMC   4193940 . PMID   24919153.
  5. 1 2 3 4 Gierahn, Todd M.; Wadsworth, Marc H.; Hughes, Travis K.; Bryson, Bryan D.; Butler, Andrew; Satija, Rahul; Fortune, Sarah; Love, J. Christopher; Shalek, Alex K. (April 2017). "Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput". Nature Methods. 14 (4): 395–398. doi:10.1038/nmeth.4179. hdl: 1721.1/113430 . ISSN   1548-7105. PMC   5376227 . PMID   28192419.
  6. ↑ "Making single-cell RNA sequencing widely available". MIT News | Massachusetts Institute of Technology. 13 February 2017. Retrieved 2021-02-17.
  7. 1 2 Macosko, Evan Z.; Basu, Anindita; Satija, Rahul; Nemesh, James; Shekhar, Karthik; Goldman, Melissa; Tirosh, Itay; Bialas, Allison R.; Kamitaki, Nolan; Martersteck, Emily M.; Trombetta, John J. (2015-05-21). "Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets". Cell. 161 (5): 1202–1214. doi:10.1016/j.cell.2015.05.002. ISSN   0092-8674. PMC   4481139 . PMID   26000488.
  8. 1 2 3 4 5 6 Hughes, Travis K.; Wadsworth, Marc H.; Gierahn, Todd M.; Do, Tran; Weiss, David; Andrade, Priscila R.; Ma, Feiyang; Silva, Bruno J. de Andrade; Shao, Shuai; Tsoi, Lam C.; Ordovas-Montanes, Jose (2020-10-13). "Second-Strand Synthesis-Based Massively Parallel scRNA-Seq Reveals Cellular States and Molecular Features of Human Inflammatory Skin Pathologies". Immunity. 53 (4): 878–894.e7. doi: 10.1016/j.immuni.2020.09.015 . ISSN   1074-7613. PMC   7562821 . PMID   33053333.
  9. 1 2 3 4 Kazer, Samuel W.; Aicher, Toby P.; Muema, Daniel M.; Carroll, Shaina L.; Ordovas-Montanes, Jose; Miao, Vincent N.; Tu, Ang A.; Ziegler, Carly G. K.; Nyquist, Sarah K.; Wong, Emily B.; Ismail, Nasreen (April 2020). "Integrated single-cell analysis of multicellular immune dynamics during hyperacute HIV-1 infection". Nature Medicine. 26 (4): 511–518. doi: 10.1038/s41591-020-0799-2 . ISSN   1546-170X. PMC   7237067 . PMID   32251406.
  10. 1 2 3 4 Kotliar, Dylan; Lin, Aaron E.; Logue, James; Hughes, Travis K.; Khoury, Nadine M.; Raju, Siddharth S.; Wadsworth, Marc H.; Chen, Han; Kurtz, Jonathan R.; Dighero-Kemp, Bonnie; Bjornson, Zach B. (2020-11-25). "Single-Cell Profiling of Ebola Virus Disease In Vivo Reveals Viral and Host Dynamics". Cell. 183 (5): 1383–1401.e19. doi: 10.1016/j.cell.2020.10.002 . ISSN   0092-8674. PMC   7707107 . PMID   33159858.
  11. ↑ Genshaft, Alex S.; Li, Shuqiang; Gallant, Caroline J.; Darmanis, Spyros; Prakadan, Sanjay M.; Ziegler, Carly G. K.; Lundberg, Martin; Fredriksson, Simon; Hong, Joyce; Regev, Aviv; Livak, Kenneth J. (2016-09-19). "Multiplexed, targeted profiling of single-cell proteomes and transcriptomes in a single reaction". Genome Biology. 17 (1): 188. doi: 10.1186/s13059-016-1045-6 . ISSN   1474-760X. PMC   5027636 . PMID   27640647.
  12. ↑ Kimmerling, Robert J.; Lee Szeto, Gregory; Li, Jennifer W.; Genshaft, Alex S.; Kazer, Samuel W.; Payer, Kristofor R.; de Riba Borrajo, Jacob; Blainey, Paul C.; Irvine, Darrell J.; Shalek, Alex K.; Manalis, Scott R. (2016-01-06). "A microfluidic platform enabling single-cell RNA-seq of multigenerational lineages". Nature Communications. 7 (1): 10220. Bibcode:2016NatCo...710220K. doi: 10.1038/ncomms10220 . ISSN   2041-1723. PMC   4729820 . PMID   26732280.
  13. ↑ Tu, Ang A.; Gierahn, Todd M.; Monian, Brinda; Morgan, Duncan M.; Mehta, Naveen K.; Ruiter, Bert; Shreffler, Wayne G.; Shalek, Alex K.; Love, J. Christopher (December 2019). "TCR sequencing paired with massively parallel 3′ RNA-seq reveals clonotypic T cell signatures". Nature Immunology. 20 (12): 1692–1699. doi: 10.1038/s41590-019-0544-5 . ISSN   1529-2916. PMC   7528220 . PMID   31745340.
  14. ↑ Galen, Peter van; Hovestadt, Volker; Ii, Marc H. Wadsworth; Hughes, Travis K.; Griffin, Gabriel K.; Battaglia, Sofia; Verga, Julia A.; Stephansky, Jason; Pastika, Timothy J.; Story, Jennifer Lombardi; Pinkus, Geraldine S. (2019-03-07). "Single-Cell RNA-Seq Reveals AML Hierarchies Relevant to Disease Progression and Immunity". Cell. 176 (6): 1265–1281.e24. doi: 10.1016/j.cell.2019.01.031 . ISSN   0092-8674. PMC   6515904 . PMID   30827681.
  15. 1 2 3 Tirosh, Itay; Izar, Benjamin; Prakadan, Sanjay M.; Wadsworth, Marc H.; Treacy, Daniel; Trombetta, John J.; Rotem, Asaf; Rodman, Christopher; Lian, Christine; Murphy, George; Fallahi-Sichani, Mohammad (2016-04-08). "Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq". Science. 352 (6282): 189–196. Bibcode:2016Sci...352..189T. doi: 10.1126/science.aad0501 . ISSN   0036-8075. PMC   4944528 . PMID   27124452.
  16. ↑ Lohr, Jens G.; Adalsteinsson, Viktor A.; Cibulskis, Kristian; Choudhury, Atish D.; Rosenberg, Mara; Cruz-Gordillo, Peter; Francis, Joshua M.; Zhang, Cheng-Zhong; Shalek, Alex K.; Satija, Rahul; Trombetta, John J. (May 2014). "Whole-exome sequencing of circulating tumor cells provides a window into metastatic prostate cancer". Nature Biotechnology. 32 (5): 479–484. doi:10.1038/nbt.2892. ISSN   1546-1696. PMC   4034575 . PMID   24752078.
  17. 1 2 Patel, Anoop P.; Tirosh, Itay; Trombetta, John J.; Shalek, Alex K.; Gillespie, Shawn M.; Wakimoto, Hiroaki; Cahill, Daniel P.; Nahed, Brian V.; Curry, William T.; Martuza, Robert L.; Louis, David N. (2014-06-20). "Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma". Science. 344 (6190): 1396–1401. Bibcode:2014Sci...344.1396P. doi:10.1126/science.1254257. ISSN   0036-8075. PMC   4123637 . PMID   24925914.
  18. 1 2 Hamza, Bashar; Ng, Sheng Rong; Prakadan, Sanjay M.; Delgado, Francisco Feijó; Chin, Christopher R.; King, Emily M.; Yang, Lucy F.; Davidson, Shawn M.; DeGouveia, Kelsey L.; Cermak, Nathan; Navia, Andrew W. (2019-02-05). "Optofluidic real-time cell sorter for longitudinal CTC studies in mouse models of cancer". Proceedings of the National Academy of Sciences. 116 (6): 2232–2236. Bibcode:2019PNAS..116.2232H. doi: 10.1073/pnas.1814102116 . ISSN   0027-8424. PMC   6369805 . PMID   30674677.
  19. 1 2 Kimmerling, Robert J.; Prakadan, Sanjay M.; Gupta, Alejandro J.; Calistri, Nicholas L.; Stevens, Mark M.; Olcum, Selim; Cermak, Nathan; Drake, Riley S.; Pelton, Kristine; De Smet, Frederik; Ligon, Keith L. (2018-11-27). "Linking single-cell measurements of mass, growth rate, and gene expression". Genome Biology. 19 (1): 207. doi: 10.1186/s13059-018-1576-0 . ISSN   1474-760X. PMC   6260722 . PMID   30482222.
  20. 1 2 Ziegler, Carly G. K.; Allon, Samuel J.; Nyquist, Sarah K.; Mbano, Ian M.; Miao, Vincent N.; Tzouanas, Constantine N.; Cao, Yuming; Yousif, Ashraf S.; Bals, Julia; Hauser, Blake M.; Feldman, Jared (2020-05-28). "SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues". Cell. 181 (5): 1016–1035.e19. doi: 10.1016/j.cell.2020.04.035 . ISSN   0092-8674. PMC   7252096 . PMID   32413319.
  21. 1 2 Gideon, Hannah P.; Hughes, Travis K.; Wadsworth, Marc H.; Tu, Ang Andy; Gierahn, Todd M.; Hopkins, Forrest F.; Wei, Jun-Rong; Kummerlowe, Conner; Grant, Nicole L.; Nargan, Kievershen; Phuah, JiaYao (2020-10-26). "Single-cell profiling of tuberculosis lung granulomas reveals functional lymphocyte signatures of bacterial control". bioRxiv: 2020.10.24.352492. doi:10.1101/2020.10.24.352492. S2CID   226229228.
  22. 1 2 Waldman, Benjamin S.; Schwarz, Dominic; Wadsworth, Marc H.; Saeij, Jeroen P.; Shalek, Alex K.; Lourido, Sebastian (2020-01-23). "Identification of a Master Regulator of Differentiation in Toxoplasma". Cell. 180 (2): 359–372.e16. doi: 10.1016/j.cell.2019.12.013 . ISSN   0092-8674. PMC   6978799 . PMID   31955846.
  23. 1 2 Darrah, Patricia A.; Zeppa, Joseph J.; Maiello, Pauline; Hackney, Joshua A.; Wadsworth, Marc H.; Hughes, Travis K.; Pokkali, Supriya; Swanson, Phillip A.; Grant, Nicole L.; Rodgers, Mark A.; Kamath, Megha (January 2020). "Prevention of tuberculosis in macaques after intravenous BCG immunization". Nature. 577 (7788): 95–102. Bibcode:2020Natur.577...95D. doi: 10.1038/s41586-019-1817-8 . ISSN   1476-4687. PMC   7015856 . PMID   31894150.
  24. ↑ Ranasinghe, Srinika; Lamothe, Pedro A.; Soghoian, Damien Z.; Kazer, Samuel W.; Cole, Michael B.; Shalek, Alex K.; Yosef, Nir; Jones, R. Brad; Donaghey, Faith; Nwonu, Chioma; Jani, Priya (2016-10-18). "Antiviral CD8+ T Cells Restricted by Human Leukocyte Antigen Class II Exist during Natural HIV Infection and Exhibit Clonal Expansion". Immunity. 45 (4): 917–930. doi: 10.1016/j.immuni.2016.09.015 . ISSN   1074-7613. PMC   5077698 . PMID   27760342.
  25. 1 2 Raghavan, Srivatsan; Winter, Peter S.; Navia, Andrew W.; Williams, Hannah L.; DenAdel, Alan; Kalekar, Radha L.; Galvez-Reyes, Jennyfer; Lowder, Kristen E.; Mulugeta, Nolawit; Raghavan, Manisha S.; Borah, Ashir A. (2020-08-25). "Transcriptional subtype-specific microenvironmental crosstalk and tumor cell plasticity in metastatic pancreatic cancer". bioRxiv: 2020.08.25.256214. doi:10.1101/2020.08.25.256214. S2CID   221355597.
  26. 1 2 3 Martin-Gayo, Enrique; Cole, Michael B.; Kolb, Kellie E.; Ouyang, Zhengyu; Cronin, Jacqueline; Kazer, Samuel W.; Ordovas-Montanes, Jose; Lichterfeld, Mathias; Walker, Bruce D.; Yosef, Nir; Shalek, Alex K. (2018-01-29). "A Reproducibility-Based Computational Framework Identifies an Inducible, Enhanced Antiviral State in Dendritic Cells from HIV-1 Elite Controllers". Genome Biology. 19 (1): 10. doi: 10.1186/s13059-017-1385-x . ISSN   1474-760X. PMC   5789701 . PMID   29378643.
  27. ↑ Kløverpris, Henrik N.; Kazer, Samuel W.; Mjösberg, Jenny; Mabuka, Jenniffer M.; Wellmann, Amanda; Ndhlovu, Zaza; Yadon, Marisa C.; Nhamoyebonde, Shepherd; Muenchhoff, Maximilian; Simoni, Yannick; Andersson, Frank (2016-02-16). "Innate Lymphoid Cells Are Depleted Irreversibly during Acute HIV-1 Infection in the Absence of Viral Suppression". Immunity. 44 (2): 391–405. doi: 10.1016/j.immuni.2016.01.006 . ISSN   1074-7613. PMC   6836297 . PMID   26850658.
  28. 1 2 3 Ordovas-Montanes, Jose; Dwyer, Daniel F.; Nyquist, Sarah K.; Buchheit, Kathleen M.; Vukovic, Marko; Deb, Chaarushena; Wadsworth, Marc H.; Hughes, Travis K.; Kazer, Samuel W.; Yoshimoto, Eri; Cahill, Katherine N. (August 2018). "Allergic inflammatory memory in human respiratory epithelial progenitor cells". Nature. 560 (7720): 649–654. Bibcode:2018Natur.560..649O. doi:10.1038/s41586-018-0449-8. hdl: 1721.1/122932 . ISSN   1476-4687. PMC   6133715 . PMID   30135581.
  29. 1 2 3 Smillie, Christopher S.; Biton, Moshe; Ordovas-Montanes, Jose; Sullivan, Keri M.; Burgin, Grace; Graham, Daniel B.; Herbst, Rebecca H.; Rogel, Noga; Slyper, Michal; Waldman, Julia; Sud, Malika (2019-07-25). "Intra- and Inter-cellular Rewiring of the Human Colon during Ulcerative Colitis". Cell. 178 (3): 714–730.e22. doi: 10.1016/j.cell.2019.06.029 . ISSN   0092-8674. PMC   6662628 . PMID   31348891.
  30. ↑ "Technique identifies T cells primed for certain allergies or infections: Researchers develop a method to isolate and sequence the RNA of T cells that react to a specific target". ScienceDaily. Retrieved 2021-02-17.
  31. ↑ Majumder, Partha P.; Mhlanga, Musa M.; Shalek, Alex K. (October 2020). "The Human Cell Atlas and equity: lessons learned". Nature Medicine. 26 (10): 1509–1511. arXiv: 2010.16154 . doi: 10.1038/s41591-020-1100-4 . ISSN   1546-170X. PMID   33029017.
  32. ↑ "Researchers identify cells likely targeted by Covid-19 virus". MIT News | Massachusetts Institute of Technology. 22 April 2020. Retrieved 2021-02-17.
  33. ↑ "Into the Lungs and Beyond". hms.harvard.edu. 29 April 2020. Retrieved 2021-02-17.
  34. 1 2 Huang, Siyi; Ziegler, Carly G. K.; Austin, John; Mannoun, Najat; Vukovic, Marko; Ordovas-Montanes, Jose; Shalek, Alex K.; Andrian, Ulrich H. von (2021-01-21). "Lymph nodes are innervated by a unique population of sensory neurons with immunomodulatory potential". Cell. 184 (2): 441–459.e25. doi: 10.1016/j.cell.2020.11.028 . ISSN   0092-8674. PMC   9612289 . PMID   33333021.
  35. ↑ Nirschl, Christopher J.; Suárez-Fariñas, Mayte; Izar, Benjamin; Prakadan, Sanjay; Dannenfelser, Ruth; Tirosh, Itay; Liu, Yong; Zhu, Qian; Devi, K. Sanjana P.; Carroll, Shaina L.; Chau, David (2017-06-29). "IFNγ-Dependent Tissue-Immune Homeostasis Is Co-opted in the Tumor Microenvironment". Cell. 170 (1): 127–141.e15. doi: 10.1016/j.cell.2017.06.016 . ISSN   0092-8674. PMC   5569303 . PMID   28666115.
  36. ↑ "Alex Shalek wins Edgerton Faculty Award". MIT News | Massachusetts Institute of Technology. 23 April 2020. Retrieved 2020-12-11.
  37. ↑ "Excellence in Mentoring Awards". The Office for Diversity Inclusion and Community Partnership at Harvard Medical School. Retrieved 2020-12-11.
  38. ↑ "Shalek named 2018 Pew-Stewart Scholar for Cancer Research – MIT Department of Chemistry". 14 June 2018. Retrieved 2020-12-11.
  39. ↑ "IMES Professor Alex Shalek wins 2018 Sloan Research Fellowship". Institute for Medical Engineering & Science. 2018-02-15. Retrieved 2021-02-09.
  40. ↑ "Alex Shalek named Pfizer-Laubach Career Development Professor – Shalek Lab". shaleklab.com. Retrieved 2020-12-11.
  41. ↑ "Previous ASAs | Science Translational Medicine". stm.sciencemag.org. Retrieved 2021-02-17.
  42. ↑ "Shalek Awarded NIH New Innovator Award". Ragon Institute of MGH, MIT and Harvard. 2015-10-06. Retrieved 2020-12-11.
  43. ↑ "Alex Shalek". Arnold and Mabel Beckman Foundation. Retrieved 2020-12-11.
  44. ↑ "Searle Scholars Program". Scholar Profile Alex Shalek. Archived from the original on September 5, 2015. Retrieved 2 June 2023.
  45. 1 2 3 4 5 6 7 8 "Alex K. Shalek". Institute for Medical Engineering & Science. Retrieved 2021-02-09.
  46. ↑ Yosef, Nir; Shalek, Alex K.; Gaublomme, Jellert T.; Jin, Hulin; Lee, Youjin; Awasthi, Amit; Wu, Chuan; Karwacz, Katarzyna; Xiao, Sheng; Jorgolli, Marsela; Gennert, David (April 2013). "Dynamic regulatory network controlling T H 17 cell differentiation". Nature. 496 (7446): 461–468. Bibcode:2013Natur.496..461Y. doi:10.1038/nature11981. ISSN   1476-4687. PMC   3637864 . PMID   23467089.
This page is based on this Wikipedia article
Text is available under the CC BY-SA 4.0 license; additional terms may apply.
Images, videos and audio are available under their respective licenses.