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{{Orphan|date=February 2021}}

{{Infobox scientist
{{Infobox scientist
|name = Alex Shalek
|name = Alex Shalek
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|doctoral_advisor = [[Hongkun Park]]
|doctoral_advisor = [[Hongkun Park]]
| website ={{URL|https://www.shaleklab.com}}
| website ={{URL|https://www.shaleklab.com}}
}}
}}


== Alex K. Shalek ==
== Alex K. Shalek ==
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== Education and previous research ==
== 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.<ref>{{Cite journal|last=Robinson|first=Jacob T.|last2=Jorgolli|first2=Marsela|last3=Shalek|first3=Alex K.|last4=Yoon|first4=Myung-Han|last5=Gertner|first5=Rona S.|last6=Park|first6=Hongkun|date=2012-03|title=Vertical nanowire electrode arrays as a scalable platform for intracellular interfacing to neuronal circuits|url=https://www.nature.com/articles/nnano.2011.249|journal=Nature Nanotechnology|language=en|volume=7|issue=3|pages=180–184|doi=10.1038/nnano.2011.249|issn=1748-3395}}</ref> 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”.<ref name=":1">{{Cite journal|last=Shalek|first=Alex K.|last2=Satija|first2=Rahul|last3=Adiconis|first3=Xian|last4=Gertner|first4=Rona S.|last5=Gaublomme|first5=Jellert T.|last6=Raychowdhury|first6=Raktima|last7=Schwartz|first7=Schraga|last8=Yosef|first8=Nir|last9=Malboeuf|first9=Christine|last10=Lu|first10=Diana|last11=Trombetta|first11=John J.|date=2013-06|title=Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells|url=https://www.nature.com/articles/nature12172|journal=Nature|language=en|volume=498|issue=7453|pages=236–240|doi=10.1038/nature12172|issn=1476-4687}}</ref><ref name=":2">{{Cite journal|last=Shalek|first=Alex K.|last2=Satija|first2=Rahul|last3=Shuga|first3=Joe|last4=Trombetta|first4=John J.|last5=Gennert|first5=Dave|last6=Lu|first6=Diana|last7=Chen|first7=Peilin|last8=Gertner|first8=Rona S.|last9=Gaublomme|first9=Jellert T.|last10=Yosef|first10=Nir|last11=Schwartz|first11=Schraga|date=2014-06|title=Single-cell RNA-seq reveals dynamic paracrine control of cellular variation|url=https://www.nature.com/articles/nature13437|journal=Nature|language=en|volume=510|issue=7505|pages=363–369|doi=10.1038/nature13437|issn=1476-4687}}</ref><ref name=":0">{{Cite journal|last=Gierahn|first=Todd M.|last2=Wadsworth|first2=Marc H.|last3=Hughes|first3=Travis K.|last4=Bryson|first4=Bryan D.|last5=Butler|first5=Andrew|last6=Satija|first6=Rahul|last7=Fortune|first7=Sarah|last8=Love|first8=J. Christopher|last9=Shalek|first9=Alex K.|date=2017-04|title=Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput|url=https://www.nature.com/articles/nmeth.4179|journal=Nature Methods|language=en|volume=14|issue=4|pages=395–398|doi=10.1038/nmeth.4179|issn=1548-7105}}</ref>
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.<ref>{{Cite journal|last=Robinson|first=Jacob T.|last2=Jorgolli|first2=Marsela|last3=Shalek|first3=Alex K.|last4=Yoon|first4=Myung-Han|last5=Gertner|first5=Rona S.|last6=Park|first6=Hongkun|date=March 2012|title=Vertical nanowire electrode arrays as a scalable platform for intracellular interfacing to neuronal circuits|url=https://www.nature.com/articles/nnano.2011.249|journal=Nature Nanotechnology|language=en|volume=7|issue=3|pages=180–184|doi=10.1038/nnano.2011.249|issn=1748-3395}}</ref> 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”.<ref name=":1">{{Cite journal|last=Shalek|first=Alex K.|last2=Satija|first2=Rahul|last3=Adiconis|first3=Xian|last4=Gertner|first4=Rona S.|last5=Gaublomme|first5=Jellert T.|last6=Raychowdhury|first6=Raktima|last7=Schwartz|first7=Schraga|last8=Yosef|first8=Nir|last9=Malboeuf|first9=Christine|last10=Lu|first10=Diana|last11=Trombetta|first11=John J.|date=June 2013|title=Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells|url=https://www.nature.com/articles/nature12172|journal=Nature|language=en|volume=498|issue=7453|pages=236–240|doi=10.1038/nature12172|issn=1476-4687}}</ref><ref name=":2">{{Cite journal|last=Shalek|first=Alex K.|last2=Satija|first2=Rahul|last3=Shuga|first3=Joe|last4=Trombetta|first4=John J.|last5=Gennert|first5=Dave|last6=Lu|first6=Diana|last7=Chen|first7=Peilin|last8=Gertner|first8=Rona S.|last9=Gaublomme|first9=Jellert T.|last10=Yosef|first10=Nir|last11=Schwartz|first11=Schraga|date=June 2014|title=Single-cell RNA-seq reveals dynamic paracrine control of cellular variation|url=https://www.nature.com/articles/nature13437|journal=Nature|language=en|volume=510|issue=7505|pages=363–369|doi=10.1038/nature13437|issn=1476-4687}}</ref><ref name=":0">{{Cite journal|last=Gierahn|first=Todd M.|last2=Wadsworth|first2=Marc H.|last3=Hughes|first3=Travis K.|last4=Bryson|first4=Bryan D.|last5=Butler|first5=Andrew|last6=Satija|first6=Rahul|last7=Fortune|first7=Sarah|last8=Love|first8=J. Christopher|last9=Shalek|first9=Alex K.|date=April 2017|title=Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput|url=https://www.nature.com/articles/nmeth.4179|journal=Nature Methods|language=en|volume=14|issue=4|pages=395–398|doi=10.1038/nmeth.4179|issn=1548-7105}}</ref>


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.<ref name=":6" /><ref name=":0" /><ref name=":13" /> In parallel, they have used these and other approaches <ref name=":13" /><ref name=":9">{{Cite journal|last=Kazer|first=Samuel W.|last2=Aicher|first2=Toby P.|last3=Muema|first3=Daniel M.|last4=Carroll|first4=Shaina L.|last5=Ordovas-Montanes|first5=Jose|last6=Miao|first6=Vincent N.|last7=Tu|first7=Ang A.|last8=Ziegler|first8=Carly G. K.|last9=Nyquist|first9=Sarah K.|last10=Wong|first10=Emily B.|last11=Ismail|first11=Nasreen|date=2020-04|title=Integrated single-cell analysis of multicellular immune dynamics during hyperacute HIV-1 infection|url=https://www.nature.com/articles/s41591-020-0799-2|journal=Nature Medicine|language=en|volume=26|issue=4|pages=511–518|doi=10.1038/s41591-020-0799-2|issn=1546-170X}}</ref><ref name=":10" /><ref name=":11">{{Cite journal|last=Genshaft|first=Alex S.|last2=Li|first2=Shuqiang|last3=Gallant|first3=Caroline J.|last4=Darmanis|first4=Spyros|last5=Prakadan|first5=Sanjay M.|last6=Ziegler|first6=Carly G. K.|last7=Lundberg|first7=Martin|last8=Fredriksson|first8=Simon|last9=Hong|first9=Joyce|last10=Regev|first10=Aviv|last11=Livak|first11=Kenneth J.|date=2016-09-19|title=Multiplexed, targeted profiling of single-cell proteomes and transcriptomes in a single reaction|url=https://doi.org/10.1186/s13059-016-1045-6|journal=Genome Biology|volume=17|issue=1|pages=188|doi=10.1186/s13059-016-1045-6|issn=1474-760X|pmc=PMC5027636|pmid=27640647}}</ref><ref name=":12">{{Cite journal|last=Kimmerling|first=Robert J.|last2=Lee Szeto|first2=Gregory|last3=Li|first3=Jennifer W.|last4=Genshaft|first4=Alex S.|last5=Kazer|first5=Samuel W.|last6=Payer|first6=Kristofor R.|last7=de Riba Borrajo|first7=Jacob|last8=Blainey|first8=Paul C.|last9=Irvine|first9=Darrell J.|last10=Shalek|first10=Alex K.|last11=Manalis|first11=Scott R.|date=2016-01-06|title=A microfluidic platform enabling single-cell RNA-seq of multigenerational lineages|url=https://www.nature.com/articles/ncomms10220|journal=Nature Communications|language=en|volume=7|issue=1|pages=10220|doi=10.1038/ncomms10220|issn=2041-1723}}</ref><ref>{{Cite journal|last=Tu|first=Ang A.|last2=Gierahn|first2=Todd M.|last3=Monian|first3=Brinda|last4=Morgan|first4=Duncan M.|last5=Mehta|first5=Naveen K.|last6=Ruiter|first6=Bert|last7=Shreffler|first7=Wayne G.|last8=Shalek|first8=Alex K.|last9=Love|first9=J. Christopher|date=2019-12|title=TCR sequencing paired with massively parallel 3′ RNA-seq reveals clonotypic T cell signatures|url=https://www.nature.com/articles/s41590-019-0544-5|journal=Nature Immunology|language=en|volume=20|issue=12|pages=1692–1699|doi=10.1038/s41590-019-0544-5|issn=1529-2916}}</ref><ref>{{Cite journal|last=Galen|first=Peter van|last2=Hovestadt|first2=Volker|last3=Ii|first3=Marc H. Wadsworth|last4=Hughes|first4=Travis K.|last5=Griffin|first5=Gabriel K.|last6=Battaglia|first6=Sofia|last7=Verga|first7=Julia A.|last8=Stephansky|first8=Jason|last9=Pastika|first9=Timothy J.|last10=Story|first10=Jennifer Lombardi|last11=Pinkus|first11=Geraldine S.|date=2019-03-07|title=Single-Cell RNA-Seq Reveals AML Hierarchies Relevant to Disease Progression and Immunity|url=https://www.cell.com/cell/abstract/S0092-8674(19)30094-7|journal=Cell|language=English|volume=176|issue=6|pages=1265–1281.e24|doi=10.1016/j.cell.2019.01.031|issn=0092-8674|pmid=30827681}}</ref> to help examine the causes and consequences of cellular heterogeneity across cancers<ref name=":3">{{Cite journal|last=Tirosh|first=Itay|last2=Izar|first2=Benjamin|last3=Prakadan|first3=Sanjay M.|last4=Wadsworth|first4=Marc H.|last5=Treacy|first5=Daniel|last6=Trombetta|first6=John J.|last7=Rotem|first7=Asaf|last8=Rodman|first8=Christopher|last9=Lian|first9=Christine|last10=Murphy|first10=George|last11=Fallahi-Sichani|first11=Mohammad|date=2016-04-08|title=Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq|url=https://science.sciencemag.org/content/352/6282/189|journal=Science|language=en|volume=352|issue=6282|pages=189–196|doi=10.1126/science.aad0501|issn=0036-8075|pmid=27124452}}</ref><ref>{{Cite journal|last=Lohr|first=Jens G.|last2=Adalsteinsson|first2=Viktor A.|last3=Cibulskis|first3=Kristian|last4=Choudhury|first4=Atish D.|last5=Rosenberg|first5=Mara|last6=Cruz-Gordillo|first6=Peter|last7=Francis|first7=Joshua M.|last8=Zhang|first8=Cheng-Zhong|last9=Shalek|first9=Alex K.|last10=Satija|first10=Rahul|last11=Trombetta|first11=John J.|date=2014-05|title=Whole-exome sequencing of circulating tumor cells provides a window into metastatic prostate cancer|url=https://www.nature.com/articles/nbt.2892|journal=Nature Biotechnology|language=en|volume=32|issue=5|pages=479–484|doi=10.1038/nbt.2892|issn=1546-1696}}</ref><ref name=":19">{{Cite journal|last=Patel|first=Anoop P.|last2=Tirosh|first2=Itay|last3=Trombetta|first3=John J.|last4=Shalek|first4=Alex K.|last5=Gillespie|first5=Shawn M.|last6=Wakimoto|first6=Hiroaki|last7=Cahill|first7=Daniel P.|last8=Nahed|first8=Brian V.|last9=Curry|first9=William T.|last10=Martuza|first10=Robert L.|last11=Louis|first11=David N.|date=2014-06-20|title=Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma|url=https://science.sciencemag.org/content/344/6190/1396|journal=Science|language=en|volume=344|issue=6190|pages=1396–1401|doi=10.1126/science.1254257|issn=0036-8075|pmid=24925914}}</ref><ref name=":20">{{Cite journal|last=Hamza|first=Bashar|last2=Ng|first2=Sheng Rong|last3=Prakadan|first3=Sanjay M.|last4=Delgado|first4=Francisco Feijó|last5=Chin|first5=Christopher R.|last6=King|first6=Emily M.|last7=Yang|first7=Lucy F.|last8=Davidson|first8=Shawn M.|last9=DeGouveia|first9=Kelsey L.|last10=Cermak|first10=Nathan|last11=Navia|first11=Andrew W.|date=2019-02-05|title=Optofluidic real-time cell sorter for longitudinal CTC studies in mouse models of cancer|url=https://www.pnas.org/content/116/6/2232|journal=Proceedings of the National Academy of Sciences|language=en|volume=116|issue=6|pages=2232–2236|doi=10.1073/pnas.1814102116|issn=0027-8424|pmid=30674677}}</ref><ref name=":21">{{Cite journal|last=Kimmerling|first=Robert J.|last2=Prakadan|first2=Sanjay M.|last3=Gupta|first3=Alejandro J.|last4=Calistri|first4=Nicholas L.|last5=Stevens|first5=Mark M.|last6=Olcum|first6=Selim|last7=Cermak|first7=Nathan|last8=Drake|first8=Riley S.|last9=Pelton|first9=Kristine|last10=De Smet|first10=Frederik|last11=Ligon|first11=Keith L.|date=2018-11-27|title=Linking single-cell measurements of mass, growth rate, and gene expression|url=https://doi.org/10.1186/s13059-018-1576-0|journal=Genome Biology|volume=19|issue=1|pages=207|doi=10.1186/s13059-018-1576-0|issn=1474-760X|pmc=PMC6260722|pmid=30482222}}</ref>, infectious diseases <ref name=":0" /><ref name=":13" /><ref name=":9" /><ref name=":10" /><ref name=":4">{{Cite journal|last=Ziegler|first=Carly G. K.|last2=Allon|first2=Samuel J.|last3=Nyquist|first3=Sarah K.|last4=Mbano|first4=Ian M.|last5=Miao|first5=Vincent N.|last6=Tzouanas|first6=Constantine N.|last7=Cao|first7=Yuming|last8=Yousif|first8=Ashraf S.|last9=Bals|first9=Julia|last10=Hauser|first10=Blake M.|last11=Feldman|first11=Jared|date=2020-05-28|title=SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues|url=https://www.cell.com/cell/abstract/S0092-8674(20)30500-6|journal=Cell|language=English|volume=181|issue=5|pages=1016–1035.e19|doi=10.1016/j.cell.2020.04.035|issn=0092-8674|pmid=32413319}}</ref><ref name=":5">{{Cite journal|last=Gideon|first=Hannah P.|last2=Hughes|first2=Travis K.|last3=Wadsworth|first3=Marc H.|last4=Tu|first4=Ang Andy|last5=Gierahn|first5=Todd M.|last6=Hopkins|first6=Forrest F.|last7=Wei|first7=Jun-Rong|last8=Kummerlowe|first8=Conner|last9=Grant|first9=Nicole L.|last10=Nargan|first10=Kievershen|last11=Phuah|first11=JiaYao|date=2020-10-26|title=Single-cell profiling of tuberculosis lung granulomas reveals functional lymphocyte signatures of bacterial control|url=https://www.biorxiv.org/content/10.1101/2020.10.24.352492v1|journal=bioRxiv|language=en|pages=2020.10.24.352492|doi=10.1101/2020.10.24.352492}}</ref><ref name=":15">{{Cite journal|last=Waldman|first=Benjamin S.|last2=Schwarz|first2=Dominic|last3=Wadsworth|first3=Marc H.|last4=Saeij|first4=Jeroen P.|last5=Shalek|first5=Alex K.|last6=Lourido|first6=Sebastian|date=2020-01-23|title=Identification of a Master Regulator of Differentiation in Toxoplasma|url=https://www.cell.com/cell/abstract/S0092-8674(19)31375-3|journal=Cell|language=English|volume=180|issue=2|pages=359–372.e16|doi=10.1016/j.cell.2019.12.013|issn=0092-8674|pmid=31955846}}</ref><ref name=":16">{{Cite journal|last=Darrah|first=Patricia A.|last2=Zeppa|first2=Joseph J.|last3=Maiello|first3=Pauline|last4=Hackney|first4=Joshua A.|last5=Wadsworth|first5=Marc H.|last6=Hughes|first6=Travis K.|last7=Pokkali|first7=Supriya|last8=Swanson|first8=Phillip A.|last9=Grant|first9=Nicole L.|last10=Rodgers|first10=Mark A.|last11=Kamath|first11=Megha|date=2020-01|title=Prevention of tuberculosis in macaques after intravenous BCG immunization|url=https://www.nature.com/articles/s41586-019-1817-8|journal=Nature|language=en|volume=577|issue=7788|pages=95–102|doi=10.1038/s41586-019-1817-8|issn=1476-4687}}</ref><ref>{{Cite journal|last=Ranasinghe|first=Srinika|last2=Lamothe|first2=Pedro A.|last3=Soghoian|first3=Damien Z.|last4=Kazer|first4=Samuel W.|last5=Cole|first5=Michael B.|last6=Shalek|first6=Alex K.|last7=Yosef|first7=Nir|last8=Jones|first8=R. Brad|last9=Donaghey|first9=Faith|last10=Nwonu|first10=Chioma|last11=Jani|first11=Priya|date=2016-10-18|title=Antiviral CD8+ T Cells Restricted by Human Leukocyte Antigen Class II Exist during Natural HIV Infection and Exhibit Clonal Expansion|url=https://www.cell.com/immunity/abstract/S1074-7613(16)30384-3|journal=Immunity|language=English|volume=45|issue=4|pages=917–930|doi=10.1016/j.immuni.2016.09.015|issn=1074-7613|pmid=27760342}}</ref><ref name=":22">{{Cite journal|last=Raghavan|first=Srivatsan|last2=Winter|first2=Peter S.|last3=Navia|first3=Andrew W.|last4=Williams|first4=Hannah L.|last5=DenAdel|first5=Alan|last6=Kalekar|first6=Radha L.|last7=Galvez-Reyes|first7=Jennyfer|last8=Lowder|first8=Kristen E.|last9=Mulugeta|first9=Nolawit|last10=Raghavan|first10=Manisha S.|last11=Borah|first11=Ashir A.|date=2020-08-25|title=Transcriptional subtype-specific microenvironmental crosstalk and tumor cell plasticity in metastatic pancreatic cancer|url=https://www.biorxiv.org/content/10.1101/2020.08.25.256214v1|journal=bioRxiv|language=en|pages=2020.08.25.256214|doi=10.1101/2020.08.25.256214}}</ref><ref name=":17" /><ref name=":14">{{Cite journal|last=Kløverpris|first=Henrik N.|last2=Kazer|first2=Samuel W.|last3=Mjösberg|first3=Jenny|last4=Mabuka|first4=Jenniffer M.|last5=Wellmann|first5=Amanda|last6=Ndhlovu|first6=Zaza|last7=Yadon|first7=Marisa C.|last8=Nhamoyebonde|first8=Shepherd|last9=Muenchhoff|first9=Maximilian|last10=Simoni|first10=Yannick|last11=Andersson|first11=Frank|date=2016-02-16|title=Innate Lymphoid Cells Are Depleted Irreversibly during Acute HIV-1 Infection in the Absence of Viral Suppression|url=https://www.cell.com/immunity/abstract/S1074-7613(16)00030-3|journal=Immunity|language=English|volume=44|issue=2|pages=391–405|doi=10.1016/j.immuni.2016.01.006|issn=1074-7613|pmid=26850658}}</ref>, and inflammation.<ref name=":7">{{Cite journal|last=Ordovas-Montanes|first=Jose|last2=Dwyer|first2=Daniel F.|last3=Nyquist|first3=Sarah K.|last4=Buchheit|first4=Kathleen M.|last5=Vukovic|first5=Marko|last6=Deb|first6=Chaarushena|last7=Wadsworth|first7=Marc H.|last8=Hughes|first8=Travis K.|last9=Kazer|first9=Samuel W.|last10=Yoshimoto|first10=Eri|last11=Cahill|first11=Katherine N.|date=2018-08|title=Allergic inflammatory memory in human respiratory epithelial progenitor cells|url=https://www.nature.com/articles/s41586-018-0449-8|journal=Nature|language=en|volume=560|issue=7720|pages=649–654|doi=10.1038/s41586-018-0449-8|issn=1476-4687}}</ref><ref name=":8" />
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.<ref name=":6" /><ref name=":0" /><ref name=":13" /> In parallel, they have used these and other approaches <ref name=":13" /><ref name=":9">{{Cite journal|last=Kazer|first=Samuel W.|last2=Aicher|first2=Toby P.|last3=Muema|first3=Daniel M.|last4=Carroll|first4=Shaina L.|last5=Ordovas-Montanes|first5=Jose|last6=Miao|first6=Vincent N.|last7=Tu|first7=Ang A.|last8=Ziegler|first8=Carly G. K.|last9=Nyquist|first9=Sarah K.|last10=Wong|first10=Emily B.|last11=Ismail|first11=Nasreen|date=April 2020|title=Integrated single-cell analysis of multicellular immune dynamics during hyperacute HIV-1 infection|url=https://www.nature.com/articles/s41591-020-0799-2|journal=Nature Medicine|language=en|volume=26|issue=4|pages=511–518|doi=10.1038/s41591-020-0799-2|issn=1546-170X}}</ref><ref name=":10" /><ref name=":11">{{Cite journal|last=Genshaft|first=Alex S.|last2=Li|first2=Shuqiang|last3=Gallant|first3=Caroline J.|last4=Darmanis|first4=Spyros|last5=Prakadan|first5=Sanjay M.|last6=Ziegler|first6=Carly G. K.|last7=Lundberg|first7=Martin|last8=Fredriksson|first8=Simon|last9=Hong|first9=Joyce|last10=Regev|first10=Aviv|last11=Livak|first11=Kenneth J.|date=2016-09-19|title=Multiplexed, targeted profiling of single-cell proteomes and transcriptomes in a single reaction|url=https://doi.org/10.1186/s13059-016-1045-6|journal=Genome Biology|volume=17|issue=1|pages=188|doi=10.1186/s13059-016-1045-6|issn=1474-760X|pmc=5027636|pmid=27640647}}</ref><ref name=":12">{{Cite journal|last=Kimmerling|first=Robert J.|last2=Lee Szeto|first2=Gregory|last3=Li|first3=Jennifer W.|last4=Genshaft|first4=Alex S.|last5=Kazer|first5=Samuel W.|last6=Payer|first6=Kristofor R.|last7=de Riba Borrajo|first7=Jacob|last8=Blainey|first8=Paul C.|last9=Irvine|first9=Darrell J.|last10=Shalek|first10=Alex K.|last11=Manalis|first11=Scott R.|date=2016-01-06|title=A microfluidic platform enabling single-cell RNA-seq of multigenerational lineages|url=https://www.nature.com/articles/ncomms10220|journal=Nature Communications|language=en|volume=7|issue=1|pages=10220|doi=10.1038/ncomms10220|issn=2041-1723}}</ref><ref>{{Cite journal|last=Tu|first=Ang A.|last2=Gierahn|first2=Todd M.|last3=Monian|first3=Brinda|last4=Morgan|first4=Duncan M.|last5=Mehta|first5=Naveen K.|last6=Ruiter|first6=Bert|last7=Shreffler|first7=Wayne G.|last8=Shalek|first8=Alex K.|last9=Love|first9=J. 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K.|last2=Allon|first2=Samuel J.|last3=Nyquist|first3=Sarah K.|last4=Mbano|first4=Ian M.|last5=Miao|first5=Vincent N.|last6=Tzouanas|first6=Constantine N.|last7=Cao|first7=Yuming|last8=Yousif|first8=Ashraf S.|last9=Bals|first9=Julia|last10=Hauser|first10=Blake M.|last11=Feldman|first11=Jared|date=2020-05-28|title=SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues|url=https://www.cell.com/cell/abstract/S0092-8674(20)30500-6|journal=Cell|language=English|volume=181|issue=5|pages=1016–1035.e19|doi=10.1016/j.cell.2020.04.035|issn=0092-8674|pmid=32413319}}</ref><ref name=":5">{{Cite journal|last=Gideon|first=Hannah P.|last2=Hughes|first2=Travis K.|last3=Wadsworth|first3=Marc H.|last4=Tu|first4=Ang Andy|last5=Gierahn|first5=Todd M.|last6=Hopkins|first6=Forrest F.|last7=Wei|first7=Jun-Rong|last8=Kummerlowe|first8=Conner|last9=Grant|first9=Nicole L.|last10=Nargan|first10=Kievershen|last11=Phuah|first11=JiaYao|date=2020-10-26|title=Single-cell profiling of tuberculosis lung granulomas reveals functional lymphocyte signatures of bacterial control|url=https://www.biorxiv.org/content/10.1101/2020.10.24.352492v1|journal=bioRxiv|language=en|pages=2020.10.24.352492|doi=10.1101/2020.10.24.352492}}</ref><ref name=":15">{{Cite journal|last=Waldman|first=Benjamin S.|last2=Schwarz|first2=Dominic|last3=Wadsworth|first3=Marc H.|last4=Saeij|first4=Jeroen P.|last5=Shalek|first5=Alex K.|last6=Lourido|first6=Sebastian|date=2020-01-23|title=Identification of a Master Regulator of Differentiation in Toxoplasma|url=https://www.cell.com/cell/abstract/S0092-8674(19)31375-3|journal=Cell|language=English|volume=180|issue=2|pages=359–372.e16|doi=10.1016/j.cell.2019.12.013|issn=0092-8674|pmid=31955846}}</ref><ref name=":16">{{Cite journal|last=Darrah|first=Patricia A.|last2=Zeppa|first2=Joseph J.|last3=Maiello|first3=Pauline|last4=Hackney|first4=Joshua A.|last5=Wadsworth|first5=Marc H.|last6=Hughes|first6=Travis K.|last7=Pokkali|first7=Supriya|last8=Swanson|first8=Phillip A.|last9=Grant|first9=Nicole L.|last10=Rodgers|first10=Mark A.|last11=Kamath|first11=Megha|date=January 2020|title=Prevention of tuberculosis in macaques after intravenous BCG immunization|url=https://www.nature.com/articles/s41586-019-1817-8|journal=Nature|language=en|volume=577|issue=7788|pages=95–102|doi=10.1038/s41586-019-1817-8|issn=1476-4687}}</ref><ref>{{Cite journal|last=Ranasinghe|first=Srinika|last2=Lamothe|first2=Pedro A.|last3=Soghoian|first3=Damien Z.|last4=Kazer|first4=Samuel W.|last5=Cole|first5=Michael B.|last6=Shalek|first6=Alex K.|last7=Yosef|first7=Nir|last8=Jones|first8=R. 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== Ongoing research ==
== 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.
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<ref>{{Cite journal|last=Majumder|first=Partha P.|last2=Mhlanga|first2=Musa M.|last3=Shalek|first3=Alex K.|date=2020-10|title=The Human Cell Atlas and equity: lessons learned|url=https://www.nature.com/articles/s41591-020-1100-4|journal=Nature Medicine|language=en|volume=26|issue=10|pages=1509–1511|doi=10.1038/s41591-020-1100-4|issn=1546-170X}}</ref>, the lab is applying them to dissect human disease methodically linking cellular features and clinical observations. Major areas of focus include how: immune cells coordinate balanced responses to environmental stresses<ref name=":7" /><ref name=":8" /><ref name=":13" /><ref name=":18" />; host cell-pathogen interactions evolve during infection<ref name=":13" /><ref name=":9" /><ref name=":10" /><ref name=":5" /><ref name=":15" /><ref name=":16" /><ref name=":17" />; and, tumor cells evade therapeutic treatment and natural immunity.<ref name=":3" /><ref name=":19" /><ref name=":20" /><ref name=":21" /><ref name=":22" /><ref>{{Cite journal|last=Nirschl|first=Christopher J.|last2=Suárez-Fariñas|first2=Mayte|last3=Izar|first3=Benjamin|last4=Prakadan|first4=Sanjay|last5=Dannenfelser|first5=Ruth|last6=Tirosh|first6=Itay|last7=Liu|first7=Yong|last8=Zhu|first8=Qian|last9=Devi|first9=K. Sanjana P.|last10=Carroll|first10=Shaina L.|last11=Chau|first11=David|date=2017-06-29|title=IFNγ-Dependent Tissue-Immune Homeostasis Is Co-opted in the Tumor Microenvironment|url=https://www.cell.com/cell/abstract/S0092-8674(17)30699-2|journal=Cell|language=English|volume=170|issue=1|pages=127–141.e15|doi=10.1016/j.cell.2017.06.016|issn=0092-8674|pmid=28666115}}</ref>
In addition to these tools with the global research community,<ref>{{Cite journal|last=Majumder|first=Partha P.|last2=Mhlanga|first2=Musa M.|last3=Shalek|first3=Alex K.|date=October 2020|title=The Human Cell Atlas and equity: lessons learned|url=https://www.nature.com/articles/s41591-020-1100-4|journal=Nature Medicine|language=en|volume=26|issue=10|pages=1509–1511|doi=10.1038/s41591-020-1100-4|issn=1546-170X}}</ref> the lab is applying them to dissect human disease methodically linking cellular features and clinical observations. Major areas of focus include how: immune cells coordinate balanced responses to environmental stresses;<ref name=":7" /><ref name=":8" /><ref name=":13" /><ref name=":18" /> host cell-pathogen interactions evolve during infection;<ref name=":13" /><ref name=":9" /><ref name=":10" /><ref name=":5" /><ref name=":15" /><ref name=":16" /><ref name=":17" /> and, tumor cells evade therapeutic treatment and natural immunity.<ref name=":3" /><ref name=":19" /><ref name=":20" /><ref name=":21" /><ref name=":22" /><ref>{{Cite journal|last=Nirschl|first=Christopher J.|last2=Suárez-Fariñas|first2=Mayte|last3=Izar|first3=Benjamin|last4=Prakadan|first4=Sanjay|last5=Dannenfelser|first5=Ruth|last6=Tirosh|first6=Itay|last7=Liu|first7=Yong|last8=Zhu|first8=Qian|last9=Devi|first9=K. Sanjana P.|last10=Carroll|first10=Shaina L.|last11=Chau|first11=David|date=2017-06-29|title=IFNγ-Dependent Tissue-Immune Homeostasis Is Co-opted in the Tumor Microenvironment|url=https://www.cell.com/cell/abstract/S0092-8674(17)30699-2|journal=Cell|language=English|volume=170|issue=1|pages=127–141.e15|doi=10.1016/j.cell.2017.06.016|issn=0092-8674|pmid=28666115}}</ref>


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.
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 honors and awards ==
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*Hughes, Travis K. et al (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.<ref name=":13">{{Cite journal|last=Hughes|first=Travis K.|last2=Wadsworth|first2=Marc H.|last3=Gierahn|first3=Todd M.|last4=Do|first4=Tran|last5=Weiss|first5=David|last6=Andrade|first6=Priscila R.|last7=Ma|first7=Feiyang|last8=Silva|first8=Bruno J. de Andrade|last9=Shao|first9=Shuai|last10=Tsoi|first10=Lam C.|last11=Ordovas-Montanes|first11=Jose|date=2020-10-13|title=Second-Strand Synthesis-Based Massively Parallel scRNA-Seq Reveals Cellular States and Molecular Features of Human Inflammatory Skin Pathologies|url=https://www.cell.com/immunity/abstract/S1074-7613(20)30409-X|journal=Immunity|language=English|volume=53|issue=4|pages=878–894.e7|doi=10.1016/j.immuni.2020.09.015|issn=1074-7613|pmid=33053333}}</ref>
*Hughes, Travis K. et al (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.<ref name=":13">{{Cite journal|last=Hughes|first=Travis K.|last2=Wadsworth|first2=Marc H.|last3=Gierahn|first3=Todd M.|last4=Do|first4=Tran|last5=Weiss|first5=David|last6=Andrade|first6=Priscila R.|last7=Ma|first7=Feiyang|last8=Silva|first8=Bruno J. de Andrade|last9=Shao|first9=Shuai|last10=Tsoi|first10=Lam C.|last11=Ordovas-Montanes|first11=Jose|date=2020-10-13|title=Second-Strand Synthesis-Based Massively Parallel scRNA-Seq Reveals Cellular States and Molecular Features of Human Inflammatory Skin Pathologies|url=https://www.cell.com/immunity/abstract/S1074-7613(20)30409-X|journal=Immunity|language=English|volume=53|issue=4|pages=878–894.e7|doi=10.1016/j.immuni.2020.09.015|issn=1074-7613|pmid=33053333}}</ref>
*Kotliar, Dylan et al (2020-11-25). "Single-Cell Profiling of Ebola Virus Disease In Vivo Reveals Viral and Host Dynamics". ''Cell''. '''183''' (5): 1383–1401.e19.<ref name=":10">{{Cite journal|last=Kotliar|first=Dylan|last2=Lin|first2=Aaron E.|last3=Logue|first3=James|last4=Hughes|first4=Travis K.|last5=Khoury|first5=Nadine M.|last6=Raju|first6=Siddharth S.|last7=Wadsworth|first7=Marc H.|last8=Chen|first8=Han|last9=Kurtz|first9=Jonathan R.|last10=Dighero-Kemp|first10=Bonnie|last11=Bjornson|first11=Zach B.|date=2020-11-25|title=Single-Cell Profiling of Ebola Virus Disease In Vivo Reveals Viral and Host Dynamics|url=https://www.cell.com/cell/abstract/S0092-8674(20)31308-8|journal=Cell|language=English|volume=183|issue=5|pages=1383–1401.e19|doi=10.1016/j.cell.2020.10.002|issn=0092-8674|pmid=33159858}}</ref>
*Kotliar, Dylan et al (2020-11-25). "Single-Cell Profiling of Ebola Virus Disease In Vivo Reveals Viral and Host Dynamics". ''Cell''. '''183''' (5): 1383–1401.e19.<ref name=":10">{{Cite journal|last=Kotliar|first=Dylan|last2=Lin|first2=Aaron E.|last3=Logue|first3=James|last4=Hughes|first4=Travis K.|last5=Khoury|first5=Nadine M.|last6=Raju|first6=Siddharth S.|last7=Wadsworth|first7=Marc H.|last8=Chen|first8=Han|last9=Kurtz|first9=Jonathan R.|last10=Dighero-Kemp|first10=Bonnie|last11=Bjornson|first11=Zach B.|date=2020-11-25|title=Single-Cell Profiling of Ebola Virus Disease In Vivo Reveals Viral and Host Dynamics|url=https://www.cell.com/cell/abstract/S0092-8674(20)31308-8|journal=Cell|language=English|volume=183|issue=5|pages=1383–1401.e19|doi=10.1016/j.cell.2020.10.002|issn=0092-8674|pmid=33159858}}</ref>
*Kazer, Samuel W. et al (2020-04). "Integrated single-cell analysis of multicellular immune dynamics during hyperacute HIV-1 infection". ''Nature Medicine''. '''26''' (4): 511–518.<ref>{{Cite journal|last=Kazer|first=Samuel W.|last2=Aicher|first2=Toby P.|last3=Muema|first3=Daniel M.|last4=Carroll|first4=Shaina L.|last5=Ordovas-Montanes|first5=Jose|last6=Miao|first6=Vincent N.|last7=Tu|first7=Ang A.|last8=Ziegler|first8=Carly G. K.|last9=Nyquist|first9=Sarah K.|last10=Wong|first10=Emily B.|last11=Ismail|first11=Nasreen|date=2020-04|title=Integrated single-cell analysis of multicellular immune dynamics during hyperacute HIV-1 infection|url=https://www.nature.com/articles/s41591-020-0799-2|journal=Nature Medicine|language=en|volume=26|issue=4|pages=511–518|doi=10.1038/s41591-020-0799-2|issn=1546-170X}}</ref>
*Kazer, Samuel W. et al (2020-04). "Integrated single-cell analysis of multicellular immune dynamics during hyperacute HIV-1 infection". ''Nature Medicine''. '''26''' (4): 511–518.<ref name=":9"/>
* Smillie, C.# et al (2019). “Intra- and inter-cellular rewiring of the human colon during ulcerative colitis” ''Cell'', '''178''', 714 (2019).<ref name=":8">{{Cite journal|last=Smillie|first=Christopher S.|last2=Biton|first2=Moshe|last3=Ordovas-Montanes|first3=Jose|last4=Sullivan|first4=Keri M.|last5=Burgin|first5=Grace|last6=Graham|first6=Daniel B.|last7=Herbst|first7=Rebecca H.|last8=Rogel|first8=Noga|last9=Slyper|first9=Michal|last10=Waldman|first10=Julia|last11=Sud|first11=Malika|date=2019-07-25|title=Intra- and Inter-cellular Rewiring of the Human Colon during Ulcerative Colitis|url=https://www.cell.com/cell/abstract/S0092-8674(19)30732-9|journal=Cell|language=English|volume=178|issue=3|pages=714–730.e22|doi=10.1016/j.cell.2019.06.029|issn=0092-8674|pmid=31348891}}</ref>
* Smillie, C.# et al (2019). “Intra- and inter-cellular rewiring of the human colon during ulcerative colitis” ''Cell'', '''178''', 714 (2019).<ref name=":8">{{Cite journal|last=Smillie|first=Christopher S.|last2=Biton|first2=Moshe|last3=Ordovas-Montanes|first3=Jose|last4=Sullivan|first4=Keri M.|last5=Burgin|first5=Grace|last6=Graham|first6=Daniel B.|last7=Herbst|first7=Rebecca H.|last8=Rogel|first8=Noga|last9=Slyper|first9=Michal|last10=Waldman|first10=Julia|last11=Sud|first11=Malika|date=2019-07-25|title=Intra- and Inter-cellular Rewiring of the Human Colon during Ulcerative Colitis|url=https://www.cell.com/cell/abstract/S0092-8674(19)30732-9|journal=Cell|language=English|volume=178|issue=3|pages=714–730.e22|doi=10.1016/j.cell.2019.06.029|issn=0092-8674|pmid=31348891}}</ref>
* Ordovas-Montanes, J. et al (2018). “Reduced cellular diversity and an altered basal progenitor cell state inform epithelial barrier dysfunction in human type 2 immunity,” ''Nature'', '''560''', 649 (2018).<ref>{{Cite journal|last=Ordovas-Montanes|first=Jose|last2=Dwyer|first2=Daniel F.|last3=Nyquist|first3=Sarah K.|last4=Buchheit|first4=Kathleen M.|last5=Vukovic|first5=Marko|last6=Deb|first6=Chaarushena|last7=Wadsworth|first7=Marc H.|last8=Hughes|first8=Travis K.|last9=Kazer|first9=Samuel W.|last10=Yoshimoto|first10=Eri|last11=Cahill|first11=Katherine N.|date=2018-08|title=Allergic inflammatory memory in human respiratory epithelial progenitor cells|url=https://www.nature.com/articles/s41586-018-0449-8|journal=Nature|language=en|volume=560|issue=7720|pages=649–654|doi=10.1038/s41586-018-0449-8|issn=1476-4687}}</ref>
* Ordovas-Montanes, J. et al (2018). “Reduced cellular diversity and an altered basal progenitor cell state inform epithelial barrier dysfunction in human type 2 immunity,” ''Nature'', '''560''', 649 (2018).<ref name=":7"/>
*Martin-Gayo, E. et al (2018). “A Rational Framework for Modulating Ensemble Immune Behaviors Inspired by HIV-1 Elite Control”, ''Genome Biol.''''', 19''', 10 (2018).<ref name=":17">{{Cite journal|last=Martin-Gayo|first=Enrique|last2=Cole|first2=Michael B.|last3=Kolb|first3=Kellie E.|last4=Ouyang|first4=Zhengyu|last5=Cronin|first5=Jacqueline|last6=Kazer|first6=Samuel W.|last7=Ordovas-Montanes|first7=Jose|last8=Lichterfeld|first8=Mathias|last9=Walker|first9=Bruce D.|last10=Yosef|first10=Nir|last11=Shalek|first11=Alex K.|date=2018-01-29|title=A Reproducibility-Based Computational Framework Identifies an Inducible, Enhanced Antiviral State in Dendritic Cells from HIV-1 Elite Controllers|url=https://doi.org/10.1186/s13059-017-1385-x|journal=Genome Biology|volume=19|issue=1|pages=10|doi=10.1186/s13059-017-1385-x|issn=1474-760X|pmc=PMC5789701|pmid=29378643}}</ref>
*Martin-Gayo, E. et al (2018). “A Rational Framework for Modulating Ensemble Immune Behaviors Inspired by HIV-1 Elite Control”, ''Genome Biol.''''', 19''', 10 (2018).<ref name=":17">{{Cite journal|last=Martin-Gayo|first=Enrique|last2=Cole|first2=Michael B.|last3=Kolb|first3=Kellie E.|last4=Ouyang|first4=Zhengyu|last5=Cronin|first5=Jacqueline|last6=Kazer|first6=Samuel W.|last7=Ordovas-Montanes|first7=Jose|last8=Lichterfeld|first8=Mathias|last9=Walker|first9=Bruce D.|last10=Yosef|first10=Nir|last11=Shalek|first11=Alex K.|date=2018-01-29|title=A Reproducibility-Based Computational Framework Identifies an Inducible, Enhanced Antiviral State in Dendritic Cells from HIV-1 Elite Controllers|url=https://doi.org/10.1186/s13059-017-1385-x|journal=Genome Biology|volume=19|issue=1|pages=10|doi=10.1186/s13059-017-1385-x|issn=1474-760X|pmc=5789701|pmid=29378643}}</ref>
* T. M. Gierahn et al (2017) “Seq-Well: A Portable, Low-cost Platform for Single-Cell RNA-Seq of Low-Input Samples.” ''Nature Meth''. 14 (2017): 395.<ref name=":0" />
* T. M. Gierahn et al (2017) “Seq-Well: A Portable, Low-cost Platform for Single-Cell RNA-Seq of Low-Input Samples.” ''Nature Meth''. 14 (2017): 395.<ref name=":0" />
* I. Tirosh et al (2017) “Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq.” ''Science'' 352.6282 (2016): 189-96.<ref name=":3" />
* I. Tirosh et al (2017) “Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq.” ''Science'' 352.6282 (2016): 189-96.<ref name=":3" />
Line 77: Line 79:
* A. K. Shalek et al (2014). “Large-Scale Single-Cell RNA-Seq Reveals Strategies for Regulating Cell-to-Cell Dynamic Variability through Paracrine Signaling.” ''Nature'' 510 (2014): 363.<ref name=":2" />
* A. K. Shalek et al (2014). “Large-Scale Single-Cell RNA-Seq Reveals Strategies for Regulating Cell-to-Cell Dynamic Variability through Paracrine Signaling.” ''Nature'' 510 (2014): 363.<ref name=":2" />
* A. K. Shalek et al (2013). “Single-Cell Transcriptomics Reveals Bimodality in Expression and Splicing in Immune Cells.” ''Nature'' 498 (2013): 236-40.<ref name=":1" />
* A. K. Shalek et al (2013). “Single-Cell Transcriptomics Reveals Bimodality in Expression and Splicing in Immune Cells.” ''Nature'' 498 (2013): 236-40.<ref name=":1" />
* N. Yosef et al (2013). “Dynamic Regulatory Network Controlling Th17 Cell Differentiation.” ''Nature'' 496 (2013): 461-68.<ref>{{Cite journal|last=Yosef|first=Nir|last2=Shalek|first2=Alex K.|last3=Gaublomme|first3=Jellert T.|last4=Jin|first4=Hulin|last5=Lee|first5=Youjin|last6=Awasthi|first6=Amit|last7=Wu|first7=Chuan|last8=Karwacz|first8=Katarzyna|last9=Xiao|first9=Sheng|last10=Jorgolli|first10=Marsela|last11=Gennert|first11=David|date=2013-04|title=Dynamic regulatory network controlling T H 17 cell differentiation|url=https://www.nature.com/articles/nature11981|journal=Nature|language=en|volume=496|issue=7446|pages=461–468|doi=10.1038/nature11981|issn=1476-4687}}</ref>
* N. Yosef et al (2013). “Dynamic Regulatory Network Controlling Th17 Cell Differentiation.” ''Nature'' 496 (2013): 461-68.<ref>{{Cite journal|last=Yosef|first=Nir|last2=Shalek|first2=Alex K.|last3=Gaublomme|first3=Jellert T.|last4=Jin|first4=Hulin|last5=Lee|first5=Youjin|last6=Awasthi|first6=Amit|last7=Wu|first7=Chuan|last8=Karwacz|first8=Katarzyna|last9=Xiao|first9=Sheng|last10=Jorgolli|first10=Marsela|last11=Gennert|first11=David|date=April 2013|title=Dynamic regulatory network controlling T H 17 cell differentiation|url=https://www.nature.com/articles/nature11981|journal=Nature|language=en|volume=496|issue=7446|pages=461–468|doi=10.1038/nature11981|issn=1476-4687}}</ref>

== References ==
== References ==
<references />
<references />

{{Uncategorized|date=February 2021}}

Revision as of 23:28, 12 February 2021

Alex Shalek
Alex Shalek, August 2019
Born(1981-12-18)December 18, 1981
AwardsHarold 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
InstitutionsMassachusetts Institute of Technology
Broad Institute
Koch Institute
Ragon Institute
Mass General Hospital
Koch Institute
Harvard Medical School
Doctoral advisorHongkun Park
Websitewww.shaleklab.com

Alex K. Shalek

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]

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]

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.[6][5][7] In parallel, they have used these and other approaches [7][8][9][10][11][12][13] to help examine the causes and consequences of cellular heterogeneity across cancers,[14][15][16][17][18] infectious diseases,[5][7][8][9][19][20][21][22][23][24][25][26] and inflammation.[27][28]

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,[29] the lab is applying them to dissect human disease methodically linking cellular features and clinical observations. Major areas of focus include how: immune cells coordinate balanced responses to environmental stresses;[27][28][7][30] host cell-pathogen interactions evolve during infection;[7][8][9][20][21][22][25] and, tumor cells evade therapeutic treatment and natural immunity.[14][16][17][18][24][31]

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

2019-20 Harold E. Edgerton Faculty Achievement Award 2020[32]

Young Mentor Award, Harvard Medical School, 2020[33]

Pew-Stewart Scholar, Pew Charitable Trust Charitable Trust, 2018 – 2022[34]

Sloan Research Fellow in Chemistry, Alfred P. Sloan Foundation, 2018 – 2020[35]

Pfizer-Laubach Career Development Professorship, MIT, 2017 – 2020[36]

Associate Scientific Advisor, Science Translational Medicine, 2016[37]

NIH Director's New Innovator Award, 2015 – 2020[38]

Beckman Young Investigators Award Arnold and Mabel Beckman Foundation, 2015 – 2019[39]

Searle Scholars Program, Kinship Foundation, 2015 – 2018[40]

"Follow That Cell” Competition First Place (team member), NIH, 2015[37]

Hermann L.F. von Helmholtz Career Development Professorship, MIT, 2014 – 2016[37]

Excellence Award, Broad Institute of Harvard and MIT, 2013[37]

Dudley R. Herschbach Teaching Award, Harvard University, 2006[37]

Graduate Research Fellowship, NSF, 2005 – 2008[37]

Certificate of Distinction in Teaching, Harvard University, 2005[37]

Phi Beta Kappa, Columbia University, 2004[37]

John Jay Scholar, Columbia University, 2000 – 2004[37]

Dean’s List, Columbia University, 2000 – 2004[37]

Select publications

  • Huang, Siyi et al (2021-01-21). "Lymph nodes are innervated by a unique population of sensory neurons with immunomodulatory potential". Cell. 184 (2): 441–459.e25[30]
  • Ziegler, C.G.K. et al (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, 1016 (2020).[19]
  • Hughes, Travis K. et al (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.[7]
  • Kotliar, Dylan et al (2020-11-25). "Single-Cell Profiling of Ebola Virus Disease In Vivo Reveals Viral and Host Dynamics". Cell. 183 (5): 1383–1401.e19.[9]
  • Kazer, Samuel W. et al (2020-04). "Integrated single-cell analysis of multicellular immune dynamics during hyperacute HIV-1 infection". Nature Medicine. 26 (4): 511–518.[8]
  • Smillie, C.# et al (2019). “Intra- and inter-cellular rewiring of the human colon during ulcerative colitis” Cell, 178, 714 (2019).[28]
  • Ordovas-Montanes, J. et al (2018). “Reduced cellular diversity and an altered basal progenitor cell state inform epithelial barrier dysfunction in human type 2 immunity,” Nature, 560, 649 (2018).[27]
  • Martin-Gayo, E. et al (2018). “A Rational Framework for Modulating Ensemble Immune Behaviors Inspired by HIV-1 Elite Control”, Genome Biol., 19, 10 (2018).[25]
  • T. M. Gierahn et al (2017) “Seq-Well: A Portable, Low-cost Platform for Single-Cell RNA-Seq of Low-Input Samples.” Nature Meth. 14 (2017): 395.[5]
  • I. Tirosh et al (2017) “Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq.” Science 352.6282 (2016): 189-96.[14]
  • E. Z. Macosko et al (2015). “Genome-wide expression profiling of thousands of individual cells using nanoliter droplets.” Cell 161 (2015): 1202-14.[6]
  • A. K. Shalek et al (2014). “Large-Scale Single-Cell RNA-Seq Reveals Strategies for Regulating Cell-to-Cell Dynamic Variability through Paracrine Signaling.” Nature 510 (2014): 363.[4]
  • A. K. Shalek et al (2013). “Single-Cell Transcriptomics Reveals Bimodality in Expression and Splicing in Immune Cells.” Nature 498 (2013): 236-40.[3]
  • N. Yosef et al (2013). “Dynamic Regulatory Network Controlling Th17 Cell Differentiation.” Nature 496 (2013): 461-68.[41]

References

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  3. ^ a b 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. doi:10.1038/nature12172. ISSN 1476-4687.
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  12. ^ 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.
  13. ^ 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. PMID 30827681.
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  15. ^ 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.
  16. ^ a b 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. doi:10.1126/science.1254257. ISSN 0036-8075. PMID 24925914.
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