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Alex K Shalek, Ph.D.

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Research
The research activities and funding listed below are automatically derived from NIH ExPORTER and other sources, which might result in incorrect or missing items. Faculty can login to make corrections and additions.
  1. DP1DA053731 (SHALEK, ALEX K) May 1, 2021 - Apr 30, 2026
    NIH
    Defining the impact of drug use on immune function and fitness against HIV-1
    Role: Principal Investigator
  2. R01AI149670 (BAROUCH, DAN H.) Jun 10, 2020 - May 31, 2025
    NIH
    Single-Cell Analysis of the HIV/SIV Reservoir
    Role: Co-Principal Investigator
  3. DP2GM119419 (SHALEK, ALEX K) Sep 30, 2015 - May 31, 2020
    NIH
    Bottom - Up Profiling of Interacting Cellular Systems
    Role: Principal Investigator
  4. U24AI118672 (SHALEK, ALEX K) Jun 24, 2015 - May 31, 2021
    NIH
    An integrated multiplexed genomic assay for low input clinical samples1
    Role: Principal Investigator

Bibliographic
Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
  1. Delorey TM, Ziegler CGK, Heimberg G, Normand R, Yang Y, Segerstolpe Å, Abbondanza D, Fleming SJ, Subramanian A, Montoro DT, Jagadeesh KA, Dey KK, Sen P, Slyper M, Pita-Juárez YH, Phillips D, Biermann J, Bloom-Ackermann Z, Barkas N, Ganna A, Gomez J, Melms JC, Katsyv I, Normandin E, Naderi P, Popov YV, Raju SS, Niezen S, Tsai LT, Siddle KJ, Sud M, Tran VM, Vellarikkal SK, Wang Y, Amir-Zilberstein L, Atri DS, Beechem J, Brook OR, Chen J, Divakar P, Dorceus P, Engreitz JM, Essene A, Fitzgerald DM, Fropf R, Gazal S, Gould J, Grzyb J, Harvey T, Hecht J, Hether T, Jané-Valbuena J, Leney-Greene M, Ma H, McCabe C, McLoughlin DE, Miller EM, Muus C, Niemi M, Padera R, Pan L, Pant D, Pe'er C, Pfiffner-Borges J, Pinto CJ, Plaisted J, Reeves J, Ross M, Rudy M, Rueckert EH, Siciliano M, Sturm A, Todres E, Waghray A, Warren S, Zhang S, Zollinger DR, Cosimi L, Gupta RM, Hacohen N, Hibshoosh H, Hide W, Price AL, Rajagopal J, Tata PR, Riedel S, Szabo G, Tickle TL, Ellinor PT, Hung D, Sabeti PC, Novak R, Rogers R, Ingber DE, Jiang ZG, Juric D, Babadi M, Farhi SL, Izar B, Stone JR, Vlachos IS, Solomon IH, Ashenberg O, Porter CBM, Li B, Shalek AK, Villani AC, Rozenblatt-Rosen O, Regev A. COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets. Nature. 2021 Apr 29. PMID: 33915569.
    Citations:    Fields:    
  2. Khuzwayo S, Mthembu M, Meermeier EW, Prakadan SM, Kazer SW, Bassett T, Nyamande K, Khan DF, Maharaj P, Mitha M, Suleman M, Mhlane Z, Ramjit D, Karim F, Shalek AK, Lewinsohn DM, Ndung'u T, Wong EB. MR1-Restricted MAIT Cells From The Human Lung Mucosal Surface Have Distinct Phenotypic, Functional, and Transcriptomic Features That Are Preserved in HIV Infection. Front Immunol. 2021; 12:631410. PMID: 33897687.
    Citations:    Fields:    
  3. Pae J, Ersching J, Castro TBR, Schips M, Mesin L, Allon SJ, Ordovas-Montanes J, Mlynarczyk C, Melnick A, Efeyan A, Shalek AK, Meyer-Hermann M, Victora GD. Cyclin D3 drives inertial cell cycling in dark zone germinal center B cells. J Exp Med. 2021 Apr 05; 218(4). PMID: 33332554.
    Citations: 1     Fields:    
  4. Goods BA, Askenase MH, Markarian E, Beatty HE, Drake RS, Fleming I, DeLong JH, Philip NH, Matouk CC, Awad IA, Zuccarello M, Hanley DF, Love JC, Shalek AK, Sansing LH. Leukocyte dynamics after intracerebral hemorrhage in a living patient reveal rapid adaptations to tissue milieu. JCI Insight. 2021 Mar 22; 6(6). PMID: 33749664.
    Citations:    Fields:    
  5. Dwyer DF, Ordovas-Montanes J, Allon SJ, Buchheit KM, Vukovic M, Derakhshan T, Feng C, Lai J, Hughes TK, Nyquist SK, Giannetti MP, Berger B, Bhattacharyya N, Roditi RE, Katz HR, Nawijn MC, Berg M, van den Berge M, Laidlaw TM, Shalek AK, Barrett NA, Boyce JA. Human airway mast cells proliferate and acquire distinct inflammation-driven phenotypes during type 2 inflammation. Sci Immunol. 2021 Feb 26; 6(56). PMID: 33637594.
    Citations:    Fields:    
  6. Delorey TM, Ziegler CGK, Heimberg G, Normand R, Yang Y, Segerstolpe A, Abbondanza D, Fleming SJ, Subramanian A, Montoro DT, Jagadeesh KA, Dey KK, Sen P, Slyper M, Pita-Juárez YH, Phillips D, Bloom-Ackerman Z, Barkas N, Ganna A, Gomez J, Normandin E, Naderi P, Popov YV, Raju SS, Niezen S, Tsai LT, Siddle KJ, Sud M, Tran VM, Vellarikkal SK, Amir-Zilberstein L, Atri DS, Beechem J, Brook OR, Chen J, Divakar P, Dorceus P, Engreitz JM, Essene A, Fitzgerald DM, Fropf R, Gazal S, Gould J, Grzyb J, Harvey T, Hecht J, Hether T, Jane-Valbuena J, Leney-Greene M, Ma H, McCabe C, McLoughlin DE, Miller EM, Muus C, Niemi M, Padera R, Pan L, Pant D, Pe'er C, Pfiffner-Borges J, Pinto CJ, Plaisted J, Reeves J, Ross M, Rudy M, Rueckert EH, Siciliano M, Sturm A, Todres E, Waghray A, Warren S, Zhang S, Zollinger DR, Cosimi L, Gupta RM, Hacohen N, Hide W, Price AL, Rajagopal J, Tata PR, Riedel S, Szabo G, Tickle TL, Hung D, Sabeti PC, Novak R, Rogers R, Ingber DE, Gordon Jiang Z, Juric D, Babadi M, Farhi SL, Stone JR, Vlachos IS, Solomon IH, Ashenberg O, Porter CBM, Li B, Shalek AK, Villani AC, Rozenblatt-Rosen O, Regev A. A single-cell and spatial atlas of autopsy tissues reveals pathology and cellular targets of SARS-CoV-2. bioRxiv. 2021 Feb 25. PMID: 33655247.
    Citations:    
  7. Ziegler CGK, Miao VN, Owings AH, Navia AW, Tang Y, Bromley JD, Lotfy P, Sloan M, Laird H, Williams HB, George M, Drake RS, Christian T, Parker A, Sindel CB, Burger MW, Pride Y, Hasan M, Abraham GE, Senitko M, Robinson TO, Shalek AK, Glover SC, Horwitz BH, Ordovas-Montanes J. Impaired local intrinsic immunity to SARS-CoV-2 infection in severe COVID-19. bioRxiv. 2021 Feb 20. PMID: 33619488.
    Citations:    
  8. Askenase MH, Goods BA, Beatty HE, Steinschneider AF, Velazquez SE, Osherov A, Landreneau MJ, Carroll SL, Tran TB, Avram VS, Drake RS, Gatter GJ, Massey JA, Karuppagounder SS, Ratan RR, Matouk CC, Sheth KN, Ziai WC, Parry-Jones AR, Awad IA, Zuccarello M, Thompson RE, Dawson J, Hanley DF, Love JC, Shalek AK, Sansing LH. Longitudinal transcriptomics define the stages of myeloid activation in the living human brain after intracerebral hemorrhage. Sci Immunol. 2021 Feb 19; 6(56). PMID: 33891558.
    Citations: 1     Fields:    
  9. Tkachev V, Kaminski J, Potter EL, Furlan SN, Yu A, Hunt DJ, McGuckin C, Zheng H, Colonna L, Gerdemann U, Carlson J, Hoffman M, Olvera J, English C, Baldessari A, Panoskaltsis-Mortari A, Watkins B, Qayed M, Suessmuth Y, Betz K, Bratrude B, Langston A, Horan JT, Ordovas-Montanes J, Shalek AK, Blazar BR, Roederer M, Kean LS. Spatiotemporal single-cell profiling reveals that invasive and tissue-resident memory donor CD8+ T cells drive gastrointestinal acute graft-versus-host disease. Sci Transl Med. 2021 Jan 13; 13(576). PMID: 33441422.
    Citations:    Fields:    
  10. Huang S, Ziegler CGK, Austin J, Mannoun N, Vukovic M, Ordovas-Montanes J, Shalek AK, von Andrian UH. Lymph nodes are innervated by a unique population of sensory neurons with immunomodulatory potential. Cell. 2021 Jan 21; 184(2):441-459.e25. PMID: 33333021.
    Citations: 3     Fields:    
  11. Walesky CM, Kolb KE, Winston CL, Henderson J, Kruft B, Fleming I, Ko S, Monga SP, Mueller F, Apte U, Shalek AK, Goessling W. Functional compensation precedes recovery of tissue mass following acute liver injury. Nat Commun. 2020 11 19; 11(1):5785. PMID: 33214549.
    Citations: 2     Fields:    Translation:AnimalsCells
  12. Kazer SW, Walker BD, Shalek AK. Evolution and Diversity of Immune Responses during Acute HIV Infection. Immunity. 2020 11 17; 53(5):908-924. PMID: 33207216.
    Citations:    Fields:    Translation:HumansAnimalsCells
  13. Zhivaki D, Borriello F, Chow OA, Doran B, Fleming I, Theisen DJ, Pallis P, Shalek AK, Sokol CL, Zanoni I, Kagan JC. Inflammasomes within Hyperactive Murine Dendritic Cells Stimulate Long-Lived T Cell-Mediated Anti-tumor Immunity. Cell Rep. 2020 11 17; 33(7):108381. PMID: 33207188.
    Citations: 6     Fields:    
  14. Kotliar D, Lin AE, Logue J, Hughes TK, Khoury NM, Raju SS, Wadsworth MH, Chen H, Kurtz JR, Dighero-Kemp B, Bjornson ZB, Mukherjee N, Sellers BA, Tran N, Bauer MR, Adams GC, Adams R, Rinn JL, Melé M, Schaffner SF, Nolan GP, Barnes KG, Hensley LE, McIlwain DR, Shalek AK, Sabeti PC, Bennett RS. Single-Cell Profiling of Ebola Virus Disease In Vivo Reveals Viral and Host Dynamics. Cell. 2020 11 25; 183(5):1383-1401.e19. PMID: 33159858.
    Citations: 4     Fields:    
  15. Hughes TK, Wadsworth MH, Gierahn TM, Do T, Weiss D, Andrade PR, Ma F, de Andrade Silva BJ, Shao S, Tsoi LC, Ordovas-Montanes J, Gudjonsson JE, Modlin RL, Love JC, Shalek AK. Second-Strand Synthesis-Based Massively Parallel scRNA-Seq Reveals Cellular States and Molecular Features of Human Inflammatory Skin Pathologies. Immunity. 2020 10 13; 53(4):878-894.e7. PMID: 33053333.
    Citations: 3     Fields:    Translation:HumansAnimalsCells
  16. Majumder PP, Mhlanga MM, Shalek AK. The Human Cell Atlas and equity: lessons learned. Nat Med. 2020 10; 26(10):1509-1511. PMID: 33029017.
    Citations:    Fields:    Translation:Humans
  17. Berger E, Yorukoglu D, Zhang L, Nyquist SK, Shalek AK, Kellis M, Numanagic I, Berger B. Improved haplotype inference by exploiting long-range linking and allelic imbalance in RNA-seq datasets. Nat Commun. 2020 09 16; 11(1):4662. PMID: 32938926.
    Citations:    Fields:    Translation:HumansCells
  18. Singh A, Kazer SW, Roider J, Krista KC, Millar J, Asowata OE, Ngoepe A, Ramsuran D, Fardoos R, Ardain A, Muenchhoff M, Kuhn W, Karim F, Ndung'u T, Shalek AK, Goulder P, Leslie A, Kløverpris HN. Innate Lymphoid Cell Activation and Sustained Depletion in Blood and Tissue of Children Infected with HIV from Birth Despite Antiretroviral Therapy. Cell Rep. 2020 09 15; 32(11):108153. PMID: 32937142.
    Citations:    Fields:    
  19. Sangesland M, Yousif AS, Ronsard L, Kazer SW, Zhu AL, Gatter GJ, Hayward MR, Barnes RM, Quirindongo-Crespo M, Rohrer D, Lonberg N, Kwon D, Shalek AK, Lingwood D. A Single Human VH-gene Allows for a Broad-Spectrum Antibody Response Targeting Bacterial Lipopolysaccharides in the Blood. Cell Rep. 2020 08 25; 32(8):108065. PMID: 32846123.
    Citations: 1     Fields:    
  20. Ding J, Adiconis X, Simmons SK, Kowalczyk MS, Hession CC, Marjanovic ND, Hughes TK, Wadsworth MH, Burks T, Nguyen LT, Kwon JYH, Barak B, Ge W, Kedaigle AJ, Carroll S, Li S, Hacohen N, Rozenblatt-Rosen O, Shalek AK, Villani AC, Regev A, Levin JZ. Author Correction: Systematic comparison of single-cell and single-nucleus RNA-sequencing methods. Nat Biotechnol. 2020 06; 38(6):756. PMID: 32341567.
    Citations:    Fields:    
  21. Mitsialis V, Wall S, Liu P, Ordovas-Montanes J, Parmet T, Vukovic M, Spencer D, Field M, McCourt C, Toothaker J, Bousvaros A, Shalek AK, Kean L, Horwitz B, Goldsmith J, Tseng G, Snapper SB, Konnikova L. Single-Cell Analyses of Colon and Blood Reveal Distinct Immune Cell Signatures of Ulcerative Colitis and Crohn's Disease. Gastroenterology. 2020 08; 159(2):591-608.e10. PMID: 32428507.
    Citations: 2     Fields:    Translation:Humans
  22. Gawel DR, Serra-Musach J, Lilja S, Aagesen J, Arenas A, Asking B, Bengnér M, Björkander J, Biggs S, Ernerudh J, Hjortswang H, Karlsson JE, Köpsen M, Lee EJ, Lentini A, Li X, Magnusson M, Martínez-Enguita D, Matussek A, Nestor CE, Schäfer S, Seifert O, Sonmez C, Stjernman H, Tjärnberg A, Wu S, Åkesson K, Shalek AK, Stenmarker M, Zhang H, Gustafsson M, Benson M. Correction to: A validated single-cell-based strategy to identify diagnostic and therapeutic targets in complex diseases. Genome Med. 2020 04 28; 12(1):37. PMID: 32345376.
    Citations:    Fields:    
  23. Ziegler CGK, Allon SJ, Nyquist SK, Mbano IM, Miao VN, Tzouanas CN, Cao Y, Yousif AS, Bals J, Hauser BM, Feldman J, Muus C, Wadsworth MH, Kazer SW, Hughes TK, Doran B, Gatter GJ, Vukovic M, Taliaferro F, Mead BE, Guo Z, Wang JP, Gras D, Plaisant M, Ansari M, Angelidis I, Adler H, Sucre JMS, Taylor CJ, Lin B, Waghray A, Mitsialis V, Dwyer DF, Buchheit KM, Boyce JA, Barrett NA, Laidlaw TM, Carroll SL, Colonna L, Tkachev V, Peterson CW, Yu A, Zheng HB, Gideon HP, Winchell CG, Lin PL, Bingle CD, Snapper SB, Kropski JA, Theis FJ, Schiller HB, Zaragosi LE, Barbry P, Leslie A, Kiem HP, Flynn JL, Fortune SM, Berger B, Finberg RW, Kean LS, Garber M, Schmidt AG, Lingwood D, Shalek AK, Ordovas-Montanes J. 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. 2020 05 28; 181(5):1016-1035.e19. PMID: 32413319.
    Citations: 532     Fields:    Translation:HumansAnimalsCellsPHPublic Health
  24. Rozenblatt-Rosen O, Regev A, Oberdoerffer P, Nawy T, Hupalowska A, Rood JE, Ashenberg O, Cerami E, Coffey RJ, Demir E, Ding L, Esplin ED, Ford JM, Goecks J, Ghosh S, Gray JW, Guinney J, Hanlon SE, Hughes SK, Hwang ES, Iacobuzio-Donahue CA, Jané-Valbuena J, Johnson BE, Lau KS, Lively T, Mazzilli SA, Pe'er D, Santagata S, Shalek AK, Schapiro D, Snyder MP, Sorger PK, Spira AE, Srivastava S, Tan K, West RB, Williams EH. The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution. Cell. 2020 04 16; 181(2):236-249. PMID: 32302568.
    Citations: 21     Fields:    Translation:Humans
  25. Ding J, Adiconis X, Simmons SK, Kowalczyk MS, Hession CC, Marjanovic ND, Hughes TK, Wadsworth MH, Burks T, Nguyen LT, Kwon JYH, Barak B, Ge W, Kedaigle AJ, Carroll S, Li S, Hacohen N, Rozenblatt-Rosen O, Shalek AK, Villani AC, Regev A, Levin JZ. Systematic comparison of single-cell and single-nucleus RNA-sequencing methods. Nat Biotechnol. 2020 06; 38(6):737-746. PMID: 32341560.
    Citations: 48     Fields:    Translation:HumansAnimalsCells
  26. Kazer SW, Aicher TP, Muema DM, Carroll SL, Ordovas-Montanes J, Miao VN, Tu AA, Ziegler CGK, Nyquist SK, Wong EB, Ismail N, Dong M, Moodley A, Berger B, Love JC, Dong KL, Leslie A, Ndhlovu ZM, Ndung'u T, Walker BD, Shalek AK. Integrated single-cell analysis of multicellular immune dynamics during hyperacute HIV-1 infection. Nat Med. 2020 04; 26(4):511-518. PMID: 32251406.
    Citations: 9     Fields:    Translation:HumansCells
  27. Buchheit KM, Dwyer DF, Ordovas-Montanes J, Katz HR, Lewis E, Vukovic M, Lai J, Bankova LG, Bhattacharyya N, Shalek AK, Barrett NA, Boyce JA, Laidlaw TM. IL-5Ra marks nasal polyp IgG4- and IgE-expressing cells in aspirin-exacerbated respiratory disease. J Allergy Clin Immunol. 2020 06; 145(6):1574-1584. PMID: 32199912.
    Citations: 2     Fields:    Translation:HumansCells
  28. Ordovas-Montanes J, Beyaz S, Rakoff-Nahoum S, Shalek AK. Distribution and storage of inflammatory memory in barrier tissues. Nat Rev Immunol. 2020 05; 20(5):308-320. PMID: 32015472.
    Citations: 8     Fields:    Translation:HumansCells
  29. Martin-Gayo E, Gao C, Chen HR, Ouyang Z, Kim D, Kolb KE, Shalek AK, Walker BD, Lichterfeld M, Yu XG. Immunological Fingerprints of Controllers Developing Neutralizing HIV-1 Antibodies. Cell Rep. 2020 01 28; 30(4):984-996.e4. PMID: 31995767.
    Citations: 2     Fields:    Translation:HumansCells
  30. Waldman BS, Schwarz D, Wadsworth MH, Saeij JP, Shalek AK, Lourido S. Identification of a Master Regulator of Differentiation in Toxoplasma. Cell. 2020 01 23; 180(2):359-372.e16. PMID: 31955846.
    Citations: 23     Fields:    Translation:HumansAnimalsCells
  31. Darrah PA, Zeppa JJ, Maiello P, Hackney JA, Wadsworth MH, Hughes TK, Pokkali S, Swanson PA, Grant NL, Rodgers MA, Kamath M, Causgrove CM, Laddy DJ, Bonavia A, Casimiro D, Lin PL, Klein E, White AG, Scanga CA, Shalek AK, Roederer M, Flynn JL, Seder RA. Prevention of tuberculosis in macaques after intravenous BCG immunization. Nature. 2020 01; 577(7788):95-102. PMID: 31894150.
    Citations: 80     Fields:    Translation:AnimalsCellsPHPublic Health
  32. Tu AA, Gierahn TM, Monian B, Morgan DM, Mehta NK, Ruiter B, Shreffler WG, Shalek AK, Love JC. TCR sequencing paired with massively parallel 3' RNA-seq reveals clonotypic T cell signatures. Nat Immunol. 2019 12; 20(12):1692-1699. PMID: 31745340.
    Citations: 10     Fields:    Translation:HumansAnimalsCellsPHPublic Health
  33. Menon M, Mohammadi S, Davila-Velderrain J, Goods BA, Cadwell TD, Xing Y, Stemmer-Rachamimov A, Shalek AK, Love JC, Kellis M, Hafler BP. Single-cell transcriptomic atlas of the human retina identifies cell types associated with age-related macular degeneration. Nat Commun. 2019 10 25; 10(1):4902. PMID: 31653841.
    Citations: 30     Fields:    Translation:HumansCells
  34. Farmer JR, Allard-Chamard H, Sun N, Ahmad M, Bertocchi A, Mahajan VS, Aicher T, Arnold J, Benson MD, Morningstar J, Barmettler S, Yuen G, Murphy SJH, Walter JE, Ghebremichael M, Shalek AK, Batista F, Gerszten R, Pillai S. Induction of metabolic quiescence defines the transitional to follicular B cell switch. Sci Signal. 2019 10 22; 12(604). PMID: 31641080.
    Citations: 4     Fields:    Translation:HumansAnimalsCells
  35. Barrett NA, Shalek AK. Revisiting airway epithelial remodeling in type 2 immunity: Beyond goblet cell metaplasia. J Allergy Clin Immunol. 2019 11; 144(5):1158-1160. PMID: 31600548.
    Citations:    Fields:    Translation:HumansAnimalsCells
  36. Anikeeva P, Boyden E, Brangwynne C, Cissé II, Fiehn O, Fromme P, Gingras AC, Greene CS, Heard E, Hell SW, Hillman E, Jensen GJ, Karchin R, Kiessling LL, Kleinstiver BP, Knight R, Kukura P, Lancaster MA, Loman N, Looger L, Lundberg E, Luo Q, Miyawaki A, Myers EW, Nolan GP, Picotti P, Reik W, Sauer M, Shalek AK, Shendure J, Slavov N, Tanay A, Troyanskaya O, van Valen D, Wang HW, Yi C, Yin P, Zernicka-Goetz M, Zhuang X. Voices in methods development. Nat Methods. 2019 10; 16(10):945-951. PMID: 31562479.
    Citations: 1     Fields:    
  37. Sangesland M, Ronsard L, Kazer SW, Bals J, Boyoglu-Barnum S, Yousif AS, Barnes R, Feldman J, Quirindongo-Crespo M, McTamney PM, Rohrer D, Lonberg N, Chackerian B, Graham BS, Kanekiyo M, Shalek AK, Lingwood D. Germline-Encoded Affinity for Cognate Antigen Enables Vaccine Amplification of a Human Broadly Neutralizing Response against Influenza Virus. Immunity. 2019 10 15; 51(4):735-749.e8. PMID: 31563464.
    Citations: 13     Fields:    Translation:HumansAnimalsCells
  38. Tsankov AM, Wadsworth MH, Akopian V, Charlton J, Allon SJ, Arczewska A, Mead BE, Drake RS, Smith ZD, Mikkelsen TS, Shalek AK, Meissner A. Loss of DNA methyltransferase activity in primed human ES cells triggers increased cell-cell variability and transcriptional repression. Development. 2019 09 12; 146(19). PMID: 31515224.
    Citations: 1     Fields:    Translation:HumansCells
  39. Reitman ZJ, Paolella BR, Bergthold G, Pelton K, Becker S, Jones R, Sinai CE, Malkin H, Huang Y, Grimmet L, Herbert ZT, Sun Y, Weatherbee JL, Alberta JA, Daley JF, Rozenblatt-Rosen O, Condurat AL, Qian K, Khadka P, Segal RA, Haas-Kogan D, Filbin MG, Suva ML, Regev A, Stiles CD, Kieran MW, Goumnerova L, Ligon KL, Shalek AK, Bandopadhayay P, Beroukhim R. Mitogenic and progenitor gene programmes in single pilocytic astrocytoma cells. Nat Commun. 2019 08 19; 10(1):3731. PMID: 31427603.
    Citations: 4     Fields:    Translation:HumansAnimalsCells
  40. Ardain A, Domingo-Gonzalez R, Das S, Kazer SW, Howard NC, Singh A, Ahmed M, Nhamoyebonde S, Rangel-Moreno J, Ogongo P, Lu L, Ramsuran D, de la Luz Garcia-Hernandez M, Ulland TK, Darby M, Park E, Karim F, Melocchi L, Madansein R, Dullabh KJ, Dunlap M, Marin-Agudelo N, Ebihara T, Ndung'u T, Kaushal D, Pym AS, Kolls JK, Steyn A, Zúñiga J, Horsnell W, Yokoyama WM, Shalek AK, Kløverpris HN, Colonna M, Leslie A, Khader SA. Publisher Correction: Group 3 innate lymphoid cells mediate early protective immunity against tuberculosis. Nature. 2019 Aug; 572(7768):E10. PMID: 31337923.
    Citations:    Fields:    
  41. Gawel DR, Serra-Musach J, Lilja S, Aagesen J, Arenas A, Asking B, Bengnér M, Björkander J, Biggs S, Ernerudh J, Hjortswang H, Karlsson JE, Köpsen M, Lee EJ, Lentini A, Li X, Magnusson M, Martínez-Enguita D, Matussek A, Nestor CE, Schäfer S, Seifert O, Sonmez C, Stjernman H, Tjärnberg A, Wu S, Åkesson K, Shalek AK, Stenmarker M, Zhang H, Gustafsson M, Benson M. A validated single-cell-based strategy to identify diagnostic and therapeutic targets in complex diseases. Genome Med. 2019 07 30; 11(1):47. PMID: 31358043.
    Citations: 15     Fields:    Translation:HumansAnimals
  42. Smillie CS, Biton M, Ordovas-Montanes J, Sullivan KM, Burgin G, Graham DB, Herbst RH, Rogel N, Slyper M, Waldman J, Sud M, Andrews E, Velonias G, Haber AL, Jagadeesh K, Vickovic S, Yao J, Stevens C, Dionne D, Nguyen LT, Villani AC, Hofree M, Creasey EA, Huang H, Rozenblatt-Rosen O, Garber JJ, Khalili H, Desch AN, Daly MJ, Ananthakrishnan AN, Shalek AK, Xavier RJ, Regev A. Intra- and Inter-cellular Rewiring of the Human Colon during Ulcerative Colitis. Cell. 2019 07 25; 178(3):714-730.e22. PMID: 31348891.
    Citations: 89     Fields:    Translation:HumansCells
  43. Ardain A, Domingo-Gonzalez R, Das S, Kazer SW, Howard NC, Singh A, Ahmed M, Nhamoyebonde S, Rangel-Moreno J, Ogongo P, Lu L, Ramsuran D, de la Luz Garcia-Hernandez M, K Ulland T, Darby M, Park E, Karim F, Melocchi L, Madansein R, Dullabh KJ, Dunlap M, Marin-Agudelo N, Ebihara T, Ndung'u T, Kaushal D, Pym AS, Kolls JK, Steyn A, Zúñiga J, Horsnell W, Yokoyama WM, Shalek AK, Kløverpris HN, Colonna M, Leslie A, Khader SA. Group 3 innate lymphoid cells mediate early protective immunity against tuberculosis. Nature. 2019 06; 570(7762):528-532. PMID: 31168092.
    Citations: 43     Fields:    Translation:HumansAnimalsCells
  44. Ndhlovu ZM, Kazer SW, Nkosi T, Ogunshola F, Muema DM, Anmole G, Swann SA, Moodley A, Dong K, Reddy T, Brockman MA, Shalek AK, Ndung'u T, Walker BD. Augmentation of HIV-specific T cell function by immediate treatment of hyperacute HIV-1 infection. Sci Transl Med. 2019 05 22; 11(493). PMID: 31118290.
    Citations: 9     Fields:    Translation:HumansCellsCTClinical Trials
  45. Pepe-Mooney BJ, Dill MT, Alemany A, Ordovas-Montanes J, Matsushita Y, Rao A, Sen A, Miyazaki M, Anakk S, Dawson PA, Ono N, Shalek AK, van Oudenaarden A, Camargo FD. Single-Cell Analysis of the Liver Epithelium Reveals Dynamic Heterogeneity and an Essential Role for YAP in Homeostasis and Regeneration. Cell Stem Cell. 2019 07 03; 25(1):23-38.e8. PMID: 31080134.
    Citations: 28     Fields:    Translation:HumansAnimalsCells
  46. Lossos C, Liu Y, Kolb KE, Christie AL, Van Scoyk A, Prakadan SM, Shigemori K, Stevenson KE, Morrow S, Plana OD, Fraser C, Jones KL, Liu H, Pallasch CP, Modiste R, Nguyen QD, Craig JW, Morgan EA, Vega F, Aster JC, Sarosiek KA, Shalek AK, Hemann MT, Weinstock DM. Mechanisms of Lymphoma Clearance Induced by High-Dose Alkylating Agents. Cancer Discov. 2019 07; 9(7):944-961. PMID: 31040105.
    Citations: 7     Fields:    Translation:HumansAnimalsCells
  47. van Galen P, Hovestadt V, Wadsworth Ii MH, Hughes TK, Griffin GK, Battaglia S, Verga JA, Stephansky J, Pastika TJ, Lombardi Story J, Pinkus GS, Pozdnyakova O, Galinsky I, Stone RM, Graubert TA, Shalek AK, Aster JC, Lane AA, Bernstein BE. Single-Cell RNA-Seq Reveals AML Hierarchies Relevant to Disease Progression and Immunity. Cell. 2019 03 07; 176(6):1265-1281.e24. PMID: 30827681.
    Citations: 96     Fields:    Translation:HumansCells
  48. Hamza B, Ng SR, Prakadan SM, Delgado FF, Chin CR, King EM, Yang LF, Davidson SM, DeGouveia KL, Cermak N, Navia AW, Winter PS, Drake RS, Tammela T, Li CM, Papagiannakopoulos T, Gupta AJ, Shaw Bagnall J, Knudsen SM, Vander Heiden MG, Wasserman SC, Jacks T, Shalek AK, Manalis SR. Optofluidic real-time cell sorter for longitudinal CTC studies in mouse models of cancer. Proc Natl Acad Sci U S A. 2019 02 05; 116(6):2232-2236. PMID: 30674677.
    Citations: 7     Fields:    Translation:AnimalsCells
  49. Aicher TP, Carroll S, Raddi G, Gierahn T, Wadsworth MH, Hughes TK, Love C, Shalek AK. Seq-Well: A Sample-Efficient, Portable Picowell Platform for Massively Parallel Single-Cell RNA Sequencing. Methods Mol Biol. 2019; 1979:111-132. PMID: 31028635.
    Citations: 4     Fields:    Translation:HumansAnimalsCells
  50. Douam F, Ziegler CGK, Hrebikova G, Fant B, Leach R, Parsons L, Wang W, Gaska JM, Winer BY, Heller B, Shalek AK, Ploss A. Selective expansion of myeloid and NK cells in humanized mice yields human-like vaccine responses. Nat Commun. 2018 11 28; 9(1):5031. PMID: 30487575.
    Citations: 10     Fields:    Translation:HumansAnimalsCells
  51. Kimmerling RJ, Prakadan SM, Gupta AJ, Calistri NL, Stevens MM, Olcum S, Cermak N, Drake RS, Pelton K, De Smet F, Ligon KL, Shalek AK, Manalis SR. Linking single-cell measurements of mass, growth rate, and gene expression. Genome Biol. 2018 11 27; 19(1):207. PMID: 30482222.
    Citations: 5     Fields:    Translation:HumansAnimalsCells
  52. Jerby-Arnon L, Shah P, Cuoco MS, Rodman C, Su MJ, Melms JC, Leeson R, Kanodia A, Mei S, Lin JR, Wang S, Rabasha B, Liu D, Zhang G, Margolais C, Ashenberg O, Ott PA, Buchbinder EI, Haq R, Hodi FS, Boland GM, Sullivan RJ, Frederick DT, Miao B, Moll T, Flaherty KT, Herlyn M, Jenkins RW, Thummalapalli R, Kowalczyk MS, Cañadas I, Schilling B, Cartwright ANR, Luoma AM, Malu S, Hwu P, Bernatchez C, Forget MA, Barbie DA, Shalek AK, Tirosh I, Sorger PK, Wucherpfennig K, Van Allen EM, Schadendorf D, Johnson BE, Rotem A, Rozenblatt-Rosen O, Garraway LA, Yoon CH, Izar B, Regev A. A Cancer Cell Program Promotes T Cell Exclusion and Resistance to Checkpoint Blockade. Cell. 2018 11 01; 175(4):984-997.e24. PMID: 30388455.
    Citations: 164     Fields:    Translation:HumansAnimalsCells
  53. Biton M, Haber AL, Rogel N, Burgin G, Beyaz S, Schnell A, Ashenberg O, Su CW, Smillie C, Shekhar K, Chen Z, Wu C, Ordovas-Montanes J, Alvarez D, Herbst RH, Zhang M, Tirosh I, Dionne D, Nguyen LT, Xifaras ME, Shalek AK, von Andrian UH, Graham DB, Rozenblatt-Rosen O, Shi HN, Kuchroo V, Yilmaz OH, Regev A, Xavier RJ. T Helper Cell Cytokines Modulate Intestinal Stem Cell Renewal and Differentiation. Cell. 2018 11 15; 175(5):1307-1320.e22. PMID: 30392957.
    Citations: 76     Fields:    Translation:AnimalsCells
  54. Roider J, Maehara T, Ngoepe A, Ramsuran D, Muenchhoff M, Adland E, Aicher T, Kazer SW, Jooste P, Karim F, Kuhn W, Shalek AK, Ndung'u T, Morris L, Moore PL, Pillai S, Kløverpris H, Goulder P, Leslie A. High-Frequency, Functional HIV-Specific T-Follicular Helper and Regulatory Cells Are Present Within Germinal Centers in Children but Not Adults. Front Immunol. 2018; 9:1975. PMID: 30258437.
    Citations: 7     Fields:    Translation:HumansCellsCTClinical Trials
  55. Ordovas-Montanes J, Dwyer DF, Nyquist SK, Buchheit KM, Vukovic M, Deb C, Wadsworth MH, Hughes TK, Kazer SW, Yoshimoto E, Cahill KN, Bhattacharyya N, Katz HR, Berger B, Laidlaw TM, Boyce JA, Barrett NA, Shalek AK. Allergic inflammatory memory in human respiratory epithelial progenitor cells. Nature. 2018 08; 560(7720):649-654. PMID: 30135581.
    Citations: 54     Fields:    Translation:HumansCells
  56. Mead BE, Ordovas-Montanes J, Braun AP, Levy LE, Bhargava P, Szucs MJ, Ammendolia DA, MacMullan MA, Yin X, Hughes TK, Wadsworth MH, Ahmad R, Rakoff-Nahoum S, Carr SA, Langer R, Collins JJ, Shalek AK, Karp JM. Harnessing single-cell genomics to improve the physiological fidelity of organoid-derived cell types. BMC Biol. 2018 06 05; 16(1):62. PMID: 29871632.
    Citations: 11     Fields:    Translation:HumansCells
  57. Martin-Gayo E, Cole MB, Kolb KE, Ouyang Z, Cronin J, Kazer SW, Ordovas-Montanes J, Lichterfeld M, Walker BD, Yosef N, Shalek AK, Yu XG. A Reproducibility-Based Computational Framework Identifies an Inducible, Enhanced Antiviral State in Dendritic Cells from HIV-1 Elite Controllers. Genome Biol. 2018 01 29; 19(1):10. PMID: 29378643.
    Citations: 9     Fields:    Translation:HumansCells
  58. Gaya M, Barral P, Burbage M, Aggarwal S, Montaner B, Warren Navia A, Aid M, Tsui C, Maldonado P, Nair U, Ghneim K, Fallon PG, Sekaly RP, Barouch DH, Shalek AK, Bruckbauer A, Strid J, Batista FD. Initiation of Antiviral B Cell Immunity Relies on Innate Signals from Spatially Positioned NKT Cells. Cell. 2018 01 25; 172(3):517-533.e20. PMID: 29249358.
    Citations: 48     Fields:    Translation:HumansAnimalsCells
  59. Regev A, Teichmann SA, Lander ES, Amit I, Benoist C, Birney E, Bodenmiller B, Campbell P, Carninci P, Clatworthy M, Clevers H, Deplancke B, Dunham I, Eberwine J, Eils R, Enard W, Farmer A, Fugger L, Göttgens B, Hacohen N, Haniffa M, Hemberg M, Kim S, Klenerman P, Kriegstein A, Lein E, Linnarsson S, Lundberg E, Lundeberg J, Majumder P, Marioni JC, Merad M, Mhlanga M, Nawijn M, Netea M, Nolan G, Pe'er D, Phillipakis A, Ponting CP, Quake S, Reik W, Rozenblatt-Rosen O, Sanes J, Satija R, Schumacher TN, Shalek A, Shapiro E, Sharma P, Shin JW, Stegle O, Stratton M, Stubbington MJT, Theis FJ, Uhlen M, van Oudenaarden A, Wagner A, Watt F, Weissman J, Wold B, Xavier R, Yosef N. The Human Cell Atlas. Elife. 2017 12 05; 6. PMID: 29206104.
    Citations: 283     Fields:    Translation:HumansCells
  60. Shalek AK, Benson M. Single-cell analyses to tailor treatments. Sci Transl Med. 2017 Sep 20; 9(408). PMID: 28931656.
    Citations: 33     Fields:    Translation:Humans
  61. Nandin IS, Fong C, Deantonio C, Torreno-Pina JA, Pecetta S, Maldonado P, Gasparrini F, Ordovas-Montanes J, Kazer SW, Kjaer S, Borley DW, Nair U, Coleman JA, Lingwood D, Shalek AK, Meffre E, Poignard P, Burton DR, Batista FD. Correction: Novel in vitro booster vaccination to rapidly generate antigen-specific human monoclonal antibodies. J Exp Med. 2017 09 04; 214(9):2811. PMID: 28827449.
    Citations: 2     Fields:    
  62. Sanjuan Nandin I, Fong C, Deantonio C, Torreno-Pina JA, Pecetta S, Maldonado P, Gasparrini F, Ordovas-Montanes J, Kazer SW, Kjaer S, Borley DW, Nair U, Coleman JA, Lingwood D, Shalek AK, Meffre E, Poignard P, Burton DR, Batista FD. Novel in vitro booster vaccination to rapidly generate antigen-specific human monoclonal antibodies. J Exp Med. 2017 Aug 07; 214(8):2471-2490. PMID: 28739603.
    Citations: 5     Fields:    
  63. Nirschl CJ, Suárez-Fariñas M, Izar B, Prakadan S, Dannenfelser R, Tirosh I, Liu Y, Zhu Q, Devi KSP, Carroll SL, Chau D, Rezaee M, Kim TG, Huang R, Fuentes-Duculan J, Song-Zhao GX, Gulati N, Lowes MA, King SL, Quintana FJ, Lee YS, Krueger JG, Sarin KY, Yoon CH, Garraway L, Regev A, Shalek AK, Troyanskaya O, Anandasabapathy N. IFN?-Dependent Tissue-Immune Homeostasis Is Co-opted in the Tumor Microenvironment. Cell. 2017 Jun 29; 170(1):127-141.e15. PMID: 28666115.
    Citations: 49     Fields:    Translation:HumansAnimalsCells
  64. Prakadan SM, Shalek AK, Weitz DA. Scaling by shrinking: empowering single-cell 'omics' with microfluidic devices. Nat Rev Genet. 2017 06; 18(6):345-361. PMID: 28392571.
    Citations: 59     Fields:    Translation:HumansAnimals
  65. Shalek AK. Baring cellular souls. Sci Transl Med. 2017 02 15; 9(377). PMID: 28202776.
    Citations:    Fields:    Translation:Cells
  66. Gierahn TM, Wadsworth MH, Hughes TK, Bryson BD, Butler A, Satija R, Fortune S, Love JC, Shalek AK. Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput. Nat Methods. 2017 Apr; 14(4):395-398. PMID: 28192419.
    Citations: 172     Fields:    Translation:HumansAnimalsCells
  67. Martin-Gayo E, Cronin J, Hickman T, Ouyang Z, Lindqvist M, Kolb KE, Schulze Zur Wiesch J, Cubas R, Porichis F, Shalek AK, van Lunzen J, Haddad EK, Walker BD, Kaufmann DE, Lichterfeld M, Yu XG. Circulating CXCR5+CXCR3+PD-1lo Tfh-like cells in HIV-1 controllers with neutralizing antibody breadth. JCI Insight. 2017 01 26; 2(2):e89574. PMID: 28138558.
    Citations: 14     Fields:    Translation:HumansCells
  68. Shalek AK. A case of mistaken identity. Sci Transl Med. 2017 01 04; 9(371). PMID: 28053155.
    Citations:    Fields:    
  69. Shalek AK. Size no longer matters. Sci Transl Med. 2016 11 16; 8(365):365ec185. PMID: 27856794.
    Citations:    Fields:    
  70. Ranasinghe S, Lamothe PA, Soghoian DZ, Kazer SW, Cole MB, Shalek AK, Yosef N, Jones RB, Donaghey F, Nwonu C, Jani P, Clayton GM, Crawford F, White J, Montoya A, Power K, Allen TM, Streeck H, Kaufmann DE, Picker LJ, Kappler JW, Walker BD. Antiviral CD8+ T Cells Restricted by Human Leukocyte Antigen Class II Exist during Natural HIV Infection and Exhibit Clonal Expansion. Immunity. 2016 10 18; 45(4):917-930. PMID: 27760342.
    Citations: 20     Fields:    Translation:HumansCells
  71. Wang F, Shin J, Shea JM, Yu J, Boškovic A, Byron M, Zhu X, Shalek AK, Regev A, Lawrence JB, Torres EM, Zhu LJ, Rando OJ, Bach I. Regulation of X-linked gene expression during early mouse development by Rlim. Elife. 2016 09 19; 5. PMID: 27642011.
    Citations: 9     Fields:    Translation:Animals
  72. Genshaft AS, Li S, Gallant CJ, Darmanis S, Prakadan SM, Ziegler CG, Lundberg M, Fredriksson S, Hong J, Regev A, Livak KJ, Landegren U, Shalek AK. Multiplexed, targeted profiling of single-cell proteomes and transcriptomes in a single reaction. Genome Biol. 2016 09 19; 17(1):188. PMID: 27640647.
    Citations: 42     Fields:    Translation:HumansCells
  73. Tirosh I, Izar B, Prakadan SM, Wadsworth MH, Treacy D, Trombetta JJ, Rotem A, Rodman C, Lian C, Murphy G, Fallahi-Sichani M, Dutton-Regester K, Lin JR, Cohen O, Shah P, Lu D, Genshaft AS, Hughes TK, Ziegler CG, Kazer SW, Gaillard A, Kolb KE, Villani AC, Johannessen CM, Andreev AY, Van Allen EM, Bertagnolli M, Sorger PK, Sullivan RJ, Flaherty KT, Frederick DT, Jané-Valbuena J, Yoon CH, Rozenblatt-Rosen O, Shalek AK, Regev A, Garraway LA. Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq. Science. 2016 Apr 08; 352(6282):189-96. PMID: 27124452.
    Citations: 757     Fields:    Translation:HumansCells
  74. Wong AS, Choi GC, Cui CH, Pregernig G, Milani P, Adam M, Perli SD, Kazer SW, Gaillard A, Hermann M, Shalek AK, Fraenkel E, Lu TK. Multiplexed barcoded CRISPR-Cas9 screening enabled by CombiGEM. Proc Natl Acad Sci U S A. 2016 Mar 01; 113(9):2544-9. PMID: 26864203.
    Citations: 52     Fields:    Translation:HumansCells
  75. Kløverpris HN, Kazer SW, Mjösberg J, Mabuka JM, Wellmann A, Ndhlovu Z, Yadon MC, Nhamoyebonde S, Muenchhoff M, Simoni Y, Andersson F, Kuhn W, Garrett N, Burgers WA, Kamya P, Pretorius K, Dong K, Moodley A, Newell EW, Kasprowicz V, Abdool Karim SS, Goulder P, Shalek AK, Walker BD, Ndung'u T, Leslie A. Innate Lymphoid Cells Are Depleted Irreversibly during Acute HIV-1 Infection in the Absence of Viral Suppression. Immunity. 2016 Feb 16; 44(2):391-405. PMID: 26850658.
    Citations: 55     Fields:    Translation:HumansCells
  76. Kimmerling RJ, Lee Szeto G, Li JW, Genshaft AS, Kazer SW, Payer KR, de Riba Borrajo J, Blainey PC, Irvine DJ, Shalek AK, Manalis SR. A microfluidic platform enabling single-cell RNA-seq of multigenerational lineages. Nat Commun. 2016 Jan 06; 7:10220. PMID: 26732280.
    Citations: 33     Fields:    Translation:AnimalsCells
  77. Finak G, McDavid A, Yajima M, Deng J, Gersuk V, Shalek AK, Slichter CK, Miller HW, McElrath MJ, Prlic M, Linsley PS, Gottardo R. MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data. Genome Biol. 2015 Dec 10; 16:278. PMID: 26653891.
    Citations: 361     Fields:    Translation:HumansAnimalsCells
  78. Gaublomme JT, Yosef N, Lee Y, Gertner RS, Yang LV, Wu C, Pandolfi PP, Mak T, Satija R, Shalek AK, Kuchroo VK, Park H, Regev A. Single-Cell Genomics Unveils Critical Regulators of Th17 Cell Pathogenicity. Cell. 2015 Dec 03; 163(6):1400-12. PMID: 26607794.
    Citations: 174     Fields:    Translation:HumansAnimalsCells
  79. Avraham R, Haseley N, Brown D, Penaranda C, Jijon HB, Trombetta JJ, Satija R, Shalek AK, Xavier RJ, Regev A, Hung DT. Pathogen Cell-to-Cell Variability Drives Heterogeneity in Host Immune Responses. Cell. 2015 Sep 10; 162(6):1309-21. PMID: 26343579.
    Citations: 84     Fields:    Translation:AnimalsCells
  80. Wadsworth MH, Hughes TK, Shalek AK. Marrying microfluidics and microwells for parallel, high-throughput single-cell genomics. Genome Biol. 2015 Jun 20; 16:129. PMID: 26087845.
    Citations: 2     Fields:    Translation:Humans
  81. Shalek AK, Satija R. MERFISHing for spatial context. Trends Immunol. 2015 Jul; 36(7):390-1. PMID: 26013647.
    Citations: 1     Fields:    Translation:HumansCells
  82. Macosko EZ, Basu A, Satija R, Nemesh J, Shekhar K, Goldman M, Tirosh I, Bialas AR, Kamitaki N, Martersteck EM, Trombetta JJ, Weitz DA, Sanes JR, Shalek AK, Regev A, McCarroll SA. Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. Cell. 2015 May 21; 161(5):1202-1214. PMID: 26000488.
    Citations: 1507     Fields:    Translation:Animals
  83. Kumar RM, Cahan P, Shalek AK, Satija R, DaleyKeyser A, Li H, Zhang J, Pardee K, Gennert D, Trombetta JJ, Ferrante TC, Regev A, Daley GQ, Collins JJ. Deconstructing transcriptional heterogeneity in pluripotent stem cells. Nature. 2014 Dec 04; 516(7529):56-61. PMID: 25471879.
    Citations: 147     Fields:    Translation:AnimalsCells
  84. Trombetta JJ, Gennert D, Lu D, Satija R, Shalek AK, Regev A. Preparation of Single-Cell RNA-Seq Libraries for Next Generation Sequencing. Curr Protoc Mol Biol. 2014 Jul 01; 107:4.22.1-17. PMID: 24984854.
    Citations: 76     Fields:    Translation:HumansAnimals
  85. Patel AP, Tirosh I, Trombetta JJ, Shalek AK, Gillespie SM, Wakimoto H, Cahill DP, Nahed BV, Curry WT, Martuza RL, Louis DN, Rozenblatt-Rosen O, Suvà ML, Regev A, Bernstein BE. Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma. Science. 2014 Jun 20; 344(6190):1396-401. PMID: 24925914.
    Citations: 1165     Fields:    Translation:Humans
  86. Shalek AK, Satija R, Shuga J, Trombetta JJ, Gennert D, Lu D, Chen P, Gertner RS, Gaublomme JT, Yosef N, Schwartz S, Fowler B, Weaver S, Wang J, Wang X, Ding R, Raychowdhury R, Friedman N, Hacohen N, Park H, May AP, Regev A. Single-cell RNA-seq reveals dynamic paracrine control of cellular variation. Nature. 2014 Jun 19; 510(7505):363-9. PMID: 24919153.
    Citations: 318     Fields:    Translation:AnimalsCells
  87. Wang L, Shalek AK, Lawrence M, Ding R, Gaublomme JT, Pochet N, Stojanov P, Sougnez C, Shukla SA, Stevenson KE, Zhang W, Wong J, Sievers QL, MacDonald BT, Vartanov AR, Goldstein NR, Neuberg D, He X, Lander E, Hacohen N, Regev A, Getz G, Brown JR, Park H, Wu CJ. Somatic mutation as a mechanism of Wnt/ß-catenin pathway activation in CLL. Blood. 2014 Aug 14; 124(7):1089-98. PMID: 24778153.
    Citations: 31     Fields:    Translation:HumansCells
  88. Lohr JG, Adalsteinsson VA, Cibulskis K, Choudhury AD, Rosenberg M, Cruz-Gordillo P, Francis JM, Zhang CZ, Shalek AK, Satija R, Trombetta JJ, Lu D, Tallapragada N, Tahirova N, Kim S, Blumenstiel B, Sougnez C, Lowe A, Wong B, Auclair D, Van Allen EM, Nakabayashi M, Lis RT, Lee GS, Li T, Chabot MS, Ly A, Taplin ME, Clancy TE, Loda M, Regev A, Meyerson M, Hahn WC, Kantoff PW, Golub TR, Getz G, Boehm JS, Love JC. Whole-exome sequencing of circulating tumor cells provides a window into metastatic prostate cancer. Nat Biotechnol. 2014 May; 32(5):479-84. PMID: 24752078.
    Citations: 222     Fields:    Translation:HumansCells
  89. Satija R, Shalek AK. Heterogeneity in immune responses: from populations to single cells. Trends Immunol. 2014 May; 35(5):219-29. PMID: 24746883.
    Citations: 42     Fields:    Translation:HumansAnimalsCells
  90. Suvà ML, Rheinbay E, Gillespie SM, Patel AP, Wakimoto H, Rabkin SD, Riggi N, Chi AS, Cahill DP, Nahed BV, Curry WT, Martuza RL, Rivera MN, Rossetti N, Kasif S, Beik S, Kadri S, Tirosh I, Wortman I, Shalek AK, Rozenblatt-Rosen O, Regev A, Louis DN, Bernstein BE. Reconstructing and reprogramming the tumor-propagating potential of glioblastoma stem-like cells. Cell. 2014 Apr 24; 157(3):580-94. PMID: 24726434.
    Citations: 306     Fields:    Translation:HumansCells
  91. Shalek AK, Satija R, Adiconis X, Gertner RS, Gaublomme JT, Raychowdhury R, Schwartz S, Yosef N, Malboeuf C, Lu D, Trombetta JJ, Gennert D, Gnirke A, Goren A, Hacohen N, Levin JZ, Park H, Regev A. Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells. Nature. 2013 Jun 13; 498(7453):236-40. PMID: 23685454.
    Citations: 437     Fields:    Translation:AnimalsCells
  92. Gifford CA, Ziller MJ, Gu H, Trapnell C, Donaghey J, Tsankov A, Shalek AK, Kelley DR, Shishkin AA, Issner R, Zhang X, Coyne M, Fostel JL, Holmes L, Meldrim J, Guttman M, Epstein C, Park H, Kohlbacher O, Rinn J, Gnirke A, Lander ES, Bernstein BE, Meissner A. Transcriptional and epigenetic dynamics during specification of human embryonic stem cells. Cell. 2013 May 23; 153(5):1149-63. PMID: 23664763.
    Citations: 191     Fields:    Translation:HumansCells
  93. Gat-Viks I, Chevrier N, Wilentzik R, Eisenhaure T, Raychowdhury R, Steuerman Y, Shalek AK, Hacohen N, Amit I, Regev A. Deciphering molecular circuits from genetic variation underlying transcriptional responsiveness to stimuli. Nat Biotechnol. 2013 Apr; 31(4):342-9. PMID: 23503680.
    Citations: 24     Fields:    Translation:AnimalsCells
  94. Yosef N, Shalek AK, Gaublomme JT, Jin H, Lee Y, Awasthi A, Wu C, Karwacz K, Xiao S, Jorgolli M, Gennert D, Satija R, Shakya A, Lu DY, Trombetta JJ, Pillai MR, Ratcliffe PJ, Coleman ML, Bix M, Tantin D, Park H, Kuchroo VK, Regev A. Dynamic regulatory network controlling TH17 cell differentiation. Nature. 2013 Apr 25; 496(7446):461-8. PMID: 23467089.
    Citations: 255     Fields:    Translation:AnimalsCells
  95. Na YR, Kim SY, Gaublomme JT, Shalek AK, Jorgolli M, Park H, Yang EG. Probing enzymatic activity inside living cells using a nanowire-cell "sandwich" assay. . 2013 Jan 09; 13(1):153-8. PMID: 23244056.
    Citations: 15     Translation:HumansCells
  96. Shalek AK, Gaublomme JT, Wang L, Yosef N, Chevrier N, Andersen MS, Robinson JT, Pochet N, Neuberg D, Gertner RS, Amit I, Brown JR, Hacohen N, Regev A, Wu CJ, Park H. Nanowire-mediated delivery enables functional interrogation of primary immune cells: application to the analysis of chronic lymphocytic leukemia. . 2012 Dec 12; 12(12):6498-504. PMID: 23190424.
    Citations: 23     Translation:HumansAnimalsCells
  97. Robinson JT, Jorgolli M, Shalek AK, Yoon MH, Gertner RS, Park H. Vertical nanowire electrode arrays as a scalable platform for intracellular interfacing to neuronal circuits. Nat Nanotechnol. 2012 Jan 10; 7(3):180-4. PMID: 22231664.
    Citations: 98     Fields:    Translation:HumansAnimalsCells
  98. Chevrier N, Mertins P, Artyomov MN, Shalek AK, Iannacone M, Ciaccio MF, Gat-Viks I, Tonti E, DeGrace MM, Clauser KR, Garber M, Eisenhaure TM, Yosef N, Robinson J, Sutton A, Andersen MS, Root DE, von Andrian U, Jones RB, Park H, Carr SA, Regev A, Amit I, Hacohen N. Systematic discovery of TLR signaling components delineates viral-sensing circuits. Cell. 2011 Nov 11; 147(4):853-67. PMID: 22078882.
    Citations: 85     Fields:    Translation:HumansAnimalsCells
  99. Shalek AK, Robinson JT, Karp ES, Lee JS, Ahn DR, Yoon MH, Sutton A, Jorgolli M, Gertner RS, Gujral TS, MacBeath G, Yang EG, Park H. Vertical silicon nanowires as a universal platform for delivering biomolecules into living cells. Proc Natl Acad Sci U S A. 2010 Feb 02; 107(5):1870-5. PMID: 20080678.
    Citations: 108     Fields:    Translation:HumansAnimalsCells
  100. Chen L, Cherniavskaya O, Shalek A, Brus LE. Photoinduced interfacial charging and "explosion" of monolayer pentacene islands. . 2005 Nov; 5(11):2241-5. PMID: 16277461.
    Citations: 1     
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Funded by the NIH National Center for Advancing Translational Sciences through its Clinical and Translational Science Awards Program, grant number UL1TR002541.