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Alex K. Shalek

massachusetts institute of technology

81H-index
490Paper Count
4.8WCitation Count
Published Papers 153
Publication Date
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Ketogenic diet mediates intestinal tumorigenesis through lipids not ketones
errNature
IF48.5
err2026-07-15
err0
PREAI
errJessica E. S. Shay; Fangtao Chi; Constantine N. Tzouanas; Shixun Han; Xiao Zhang; Johanna Ten Hoeve; Kevin J. Williams; Seda Neptun; Tolga Sever; Isabela Fuentes; Sangeeta N. Bhatia; Gizem Calibasi-Kocal; Matthew G. Vander Heiden; Alex K. Shalek; Ömer H. Yilmaz
errShare
errSave
Aging disrupts spatiotemporal coordination in the cycling murine ovary
errNature Aging
IF19.4
err2026-06-17
err0
errOAAI
errTammy C. T. Lan; Alison Kochersberger; Ruth Raichur; Sophia Szady; Hien Tran; Radiana Simeonova; Ashley Helmuth; Andrew Minagar; Maria José Orozco Fuentes; Vipin Kumar; Giovanni Marrero; Irving Barrera; Sarah Mangiameli; Alex K. Shalek; Pardis C. Sabeti; Fei Chen; David S. Fischer; Jennifer L. Garrison; Hattie Chung
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errSave
The Single Cell Notebooks for inclusive and accessible training in single-cell and spatial omics
errNature Genetics
IF29
err2026-05-05
err0
PREAI
errAdolfo Rojas-Hidalgo; Raúl Arias-Carrasco; Joyce Karoline Silva; Erick Armingol; Sebastián Urquiza-Zurich; Bruno Vinagre; Cesar A. Prada-Medina; Sergio Triana; Daniela D. Russo; Diego Pérez-Stuardo; Emiliano Vicencio; Gerardo Muñoz; Cristóvão Antunes de Lanna; Leandro Santos; Gabriela Rapozo; Natalia Tavares; Andrés Moreno-Estrada; John Randell; Patricia Severino; Ricardo Khouri; Orr Ashenberg; Alex K. Shalek; Mariana Boroni; Yesid Cuesta-Astroz; Benilton S. Carvalho; Vinicius Maracaja-Coutinho
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errSave
Disordered protein LAT encodes relative levels of signaling pathways in T cell activation
errScience
IF45.8
err2026-04-30
err0
PREAI
errAdam J. Rubin; Tyler T. Dao; Amelia V. Schueppert; Saehyun Choi; Jay T. Groves; Aviv Regev; Alex K. Shalek
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errSave
Understanding tumor-immune-stromal dynamics driving response and resistance to immune checkpoint blockade in melanoma
errJOURNAL OF IMMUNOLOGY
IF3.4
err2025-11-01
err0
PREAI
errTarantino, Giuseppe; He, Yiwen; Solanky, Priyanka; Cui, Xinyu; Pfaff, Kathleen; Thorner, Aaron R.; Blosser, Timothy; Boblitt, Elliot; Frangieh, Allison; Aprati, Tyler; Zhang, Boyang; Chen, Jiajia; Faulkner, Hannah Mae; Lawless, Aleigha; Manos, Michael; Helvie, Karla; Sharova, Tatyana; Frederick, Dennie; Krishna, Sachi; Mangum, Chanell; Abbondanza, Domenic; Mccann, Cai; Johnson, Bruce; Shalek, Alex K.; Van Allen, Eliezer; Zhuang, Xiaowei; Sullivan, Ryan; Engelhardt, Barbara; Farhi, Sami; Rodig, Scott; Hodi, F. Stephen; Boland, Genevieve M.; Liu, David
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errSave
Single-cell profiling reveals a role for tuberculosis-induced myofibroblasts in the immunopathology of infected lungs
errJOURNAL OF IMMUNOLOGY
IF3.4
err2025-11-01
err0
PREAI
errLiu, Nuo; Mbano, Ian Maheti; Wardsworth, Marc; Chambers, Mark; Mpotje, Thabo; Asowata, Osaretin; Nyquist, Sarah; Nargan, Kievershen; Ramsuran, Duran; Karim, Farina; Hughes, Travis; Bromley, Joshua; Krause, Robert; Tezera, Liku; Reichmann, Michaela; Keanne, Sharie; Ganchua, C.; Kloverpris, Henrik; Dullabh, Kaylesh; Madansein, Rajhmun; Triana, Sergio; Steyn, Adrie; Berger, Bonnie; Marakalala, Mohlopheni; Fortune, Sarah; Flynn, Joanne L.; Elkington, Paul T.; Shalek, Alex K.; Leslie, Alasdair
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errSave
Synergistic CD8+T and CD4+T cell concomitant immunity controls M. tuberculosis bacterial burden following M. tuberculosis reinfection in non-human primates
errJOURNAL OF IMMUNOLOGY
IF3.4
err2025-11-01
err0
PREAI
errShan, Feng; Simonson, Andrew W.; Bromley, Joshua D.; Chao, Michael; Megahed, Doaa; Flynn, JoAnne L.; Fortune, Sarah M.; Shalek, Alex K.
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errSave
Epithelial cells regulate immune and microbial populations in oral mucosal inflammatory diseases - periodontitis and peri-implantitis
errJOURNAL OF IMMUNOLOGY
IF3.4
err2025-11-01
err0
PREAI
errBasak, Ankit; Cho, Ye Won Stacy; Shiba, Takahiro; Chen, Chia-Yu; Kim, David Minjoon; Shalek, Alex K.
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errSave
Assessing single-cell transcriptomic changes of human lung myeloid cells after in vivo exposure to S. pneumoniae and live attenuated influenza virus
errJOURNAL OF IMMUNOLOGY
IF3.4
err2025-11-01
err0
PREAI
errTong, Evelyn Yuzhou; Triana, Sergio; Russo, Daniela; Shalek, Alex K.; Ferreira, Daniela; Mitsi, Elena
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errSave
Active learning framework leveraging transcriptomics identifies modulators of disease phenotypes
errScience
IF45.8
err2025-10-23
err0
PREAI
errBenjamin DeMeo; Charlotte Nesbitt; Samuel A. Miller; Daniel B. Burkhardt; Inna Lipchina; Doris Fu; Peter Holderrieth; David Kim; Sergey Kolchenko; Artur Szalata; Ishan Gupta; Christine Kerr; Thomas Pfefer; Raziel Rojas-Rodriguez; Sunil Kuppassani; Laurens Kruidenier; Parul B. Doshi; Mahdi Zamanighomi; James J. Collins; Alex K. Shalek; Fabian J. Theis; Mauricio Cortes
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errSave
Immunometabolic defects of CD8+ T cells disrupt gut barrier integrity in people with HIV
errCell
IF42.5
err2025-09-11
err0
errOAAI
errUpasana Das Adhikari; Leah M. Froehle; Alexandra N. Pipkin; Heeva Baharlou; Alice H. Linder; Palak Shah; Amanda Hussey; Qiming Zhang; Sarah Nyquist; Saleh Khwaled; Fangtao Chi; Swagata Goswami; Sabhyata Sedhain; Salina Hussain; Thomas J. Diefenbach; Benjamin J. Read; Byungji Kim; Darrell Irvine; Osaretin Asowata; Mark Ladinsky; Pamela Bjorkman; Fusi Madela; Shakeel Kader; Alex K. Shalek; Musie Ghebremichael; Henrik Kloverpris; Alison E. Ringel; Ömer H. Yilmaz; Douglas S. Kwon
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errSave
Autoimmune disease risk gene ANKRD55 promotes TH17 effector function through metabolic modulation
errJOURNAL OF EXPERIMENTAL MEDICINE
IF10.6
err2025-09-11
err0
PREAI
errXu, Jinjin; Kong, Lingjia; Creasey, Elizabeth A.; Rath, Sneha; Deng, Lei; Avila-Pacheco, Julian; Li, Chenhao; Oliver, Blayne A.; Dao, Tyler T.; Shih, Angela R.; Daly, Mark J.; Shalek, Alex K.; Clish, Clary B.; Graham, Daniel B.; Deguine, Jacques; Xavier, Ramnik J.
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errSave
Host-intrinsic and host-extrinsic factors modulate immunity to Mtb infection, reinfection, and noncanonical vaccination routes
errCell Reports Medicine
IF10.6
err2025-08-07
err0
errOAAI
errJoshua D. Bromley; Andrew W. Simonson; Alex K. Shalek; JoAnne L. Flynn
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errSave
Artificial variables help to avoid over-clustering in single-cell RNA sequencing
errAMERICAN JOURNAL OF HUMAN GENETICS
IF8.1
err2025-04-01
err0
PREAI
errDenAdel, Alan; Ramseier, Michelle L.; Navia, Andrew W.; Shalek, Alex K.; Raghavan, Srivatsan; Winter, Peter S.; Amini, Ava P.; Crawford, Lorin
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errSave
Quantitative characterization of tissue states using multiomics and ecological spatial analysis
errNATURE GENETICS
IF0
err2025-04-01
err0
errOAAI
errDing, Daisy Yi; Tang, Zeyu; Zhu, Bokai; Ren, Hongyu; Shalek, Alex K.; Tibshirani, Robert; Nolan, Garry P.
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errSave
A single-nucleus and spatial transcriptomic atlas of the COVID-19 liver reveals topological, functional, and regenerative organ disruption in patients
errGENOME BIOLOGY
IF9.4
err2025-03-14
err2
errOAAI
errPita-Juarez, Yered; Karagkouni, Dimitra; Kalavros, Nikolaos; Melms, Johannes C.; Niezen, Sebastian; Delorey, Toni M.; Essene, Adam L.; Brook, Olga R.; Pant, Deepti; Skelton-Badlani, Disha; Naderi, Pourya; Huang, Pinzhu; Pan, Liuliu; Hether, Tyler; Andrews, Tallulah S.; Ziegler, Carly G. K.; Reeves, Jason; Myloserdnyy, Andriy; Chen, Rachel; Nam, Andy; Phelan, Stefan; Liang, Yan; Gregory, Mark; He, Shanshan; Patrick, Michael; Rane, Tushar; Wardhani, Aster; Amin, Amit Dipak; Biermann, Jana; Hibshoosh, Hanina; Veregge, Molly; Kramer, Zachary; Jacobs, Christopher; Yalcin, Yusuf; Phillips, Devan; Slyper, Michal; Subramanian, Ayshwarya; Ashenberg, Orr; Bloom-Ackermann, Zohar; Tran, Victoria M.; Gomez, James; Sturm, Alexander; Zhang, Shuting; Fleming, Stephen J.; Warren, Sarah; Beechem, Joseph; Hung, Deborah; Babadi, Mehrtash; Padera Jr, Robert F.; Macparland, Sonya A.; Bader, Gary D.; Imad, Nasser; Solomon, Isaac H.; Miller, Eric; Riedel, Stefan; Porter, Caroline B. M.; Villani, Alexandra-Chloe; Tsai, Linus T. -Y.; Hide, Winston; Szabo, Gyongyi; Hecht, Jonathan; Rozenblatt-Rosen, Orit; Shalek, Alex K.; Izar, Benjamin; Popov, Yury V.; Jiang, Z. Gordon; Vlachos, Ioannis S.
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errSave
Adapting systems biology to address the complexity of human disease in the single-cell era
errNATURE REVIEWS GENETICS
IF52
err2025-03-10
err0
PREAI
errFischer, David S.; Villanueva, Martin A.; Winter, Peter S.; Shalek, Alex K.
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errSave
scRNA-seq reveals elevated interferon responses and TNF-α signaling via NFkB in monocytes in children with uncomplicated malaria
errEXPERIMENTAL BIOLOGY AND MEDICINE
IF2.7
err2025-01-03
err0
errOAAI
errMorang'a, Collins M.; Drake, Riley S.; Miao, Vincent N.; Nyakoe, Nancy K.; Amuzu, Dominic S. Y.; Appiah, Vincent; Aniweh, Yaw; Bediako, Yaw; Bah, Saikou Y.; Shalek, Alex K.; Awandare, Gordon A.; Amenga-Etego, Lucas
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errSave
Follicle-intrinsic and spatially distinct molecular programs drive follicle rupture and luteinization during ex vivo mammalian ovulation
errCOMMUNICATIONS BIOLOGY
IF5.1
err2024-10-23
err0
errOAAI
errZaniker, Emily J.; Zhang, Jiyang; Russo, Daniela; Huang, Ruixu; Suritis, Kristine; Drake, Riley S.; Barlow-Smith, Esther; Shalek, Alex K.; Woodruff, Teresa K.; Xiao, Shuo; Goods, Brittany A.; Duncan, Francesca E.
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errSave
Scalable, compressed phenotypic screening using pooled perturbations
errNATURE BIOTECHNOLOGY
IF41.7
err2024-10-07
err0
errOAAI
errLiu, Nuo; Kattan, Walaa E.; Mead, Benjamin E.; Kummerlowe, Conner; Cheng, Thomas; Ingabire, Sarah; Cheah, Jaime H.; Soule, Christian K.; Vrcic, Anita; Mcininch, Jane K.; Triana, Sergio; Guzman, Manuel; Dao, Tyler T.; Peters, Joshua M.; Lowder, Kristen E.; Crawford, Lorin; Amini, Ava P.; Blainey, Paul C.; Hahn, William C.; Cleary, Brian; Bryson, Bryan; Winter, Peter S.; Raghavan, Srivatsan; Shalek, Alex K.
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Research Directions

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Co-authors
Cooperation Journals
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Róbert Langer
H-index: 262 · Papers: 2.0K
R
Rob Knight
H-index: 255 · Papers: 1.8K
G
Gad Getz
H-index: 248 · Papers: 1.8K
M
Mark J. Daly
H-index: 224 · Papers: 1.2K
M
Matthew Meyerson
H-index: 223 · Papers: 1.9K
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