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Items: 50

1.

Optofluidic real-time cell sorter for longitudinal CTC studies in mouse models of cancer.

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.

Proc Natl Acad Sci U S A. 2019 Feb 5;116(6):2232-2236. doi: 10.1073/pnas.1814102116. Epub 2019 Jan 23.

2.

Selective expansion of myeloid and NK cells in humanized mice yields human-like vaccine responses.

Douam F, Ziegler CGK, Hrebikova G, Fant B, Leach R, Parsons L, Wang W, Gaska JM, Winer BY, Heller B, Shalek AK, Ploss A.

Nat Commun. 2018 Nov 28;9(1):5031. doi: 10.1038/s41467-018-07478-2.

3.

Linking single-cell measurements of mass, growth rate, and gene expression.

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.

Genome Biol. 2018 Nov 27;19(1):207. doi: 10.1186/s13059-018-1576-0.

4.

T Helper Cell Cytokines Modulate Intestinal Stem Cell Renewal and Differentiation.

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.

Cell. 2018 Nov 15;175(5):1307-1320.e22. doi: 10.1016/j.cell.2018.10.008. Epub 2018 Nov 1.

PMID:
30392957
5.

A Cancer Cell Program Promotes T Cell Exclusion and Resistance to Checkpoint Blockade.

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.

Cell. 2018 Nov 1;175(4):984-997.e24. doi: 10.1016/j.cell.2018.09.006.

PMID:
30388455
6.

High-Frequency, Functional HIV-Specific T-Follicular Helper and Regulatory Cells Are Present Within Germinal Centers in Children but Not Adults.

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.

Front Immunol. 2018 Sep 12;9:1975. doi: 10.3389/fimmu.2018.01975. eCollection 2018.

7.

Allergic inflammatory memory in human respiratory epithelial progenitor cells.

Ordovas-Montanes J, Dwyer DF, Nyquist SK, Buchheit KM, Vukovic M, Deb C, Wadsworth MH 2nd, Hughes TK, Kazer SW, Yoshimoto E, Cahill KN, Bhattacharyya N, Katz HR, Berger B, Laidlaw TM, Boyce JA, Barrett NA, Shalek AK.

Nature. 2018 Aug;560(7720):649-654. doi: 10.1038/s41586-018-0449-8. Epub 2018 Aug 22.

PMID:
30135581
8.

Harnessing single-cell genomics to improve the physiological fidelity of organoid-derived cell types.

Mead BE, Ordovas-Montanes J, Braun AP, Levy LE, Bhargava P, Szucs MJ, Ammendolia DA, MacMullan MA, Yin X, Hughes TK, Wadsworth MH 2nd, Ahmad R, Rakoff-Nahoum S, Carr SA, Langer R, Collins JJ, Shalek AK, Karp JM.

BMC Biol. 2018 Jun 5;16(1):62. doi: 10.1186/s12915-018-0527-2.

9.

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

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.

Genome Biol. 2018 Jan 29;19(1):10. doi: 10.1186/s13059-017-1385-x.

10.

Initiation of Antiviral B Cell Immunity Relies on Innate Signals from Spatially Positioned NKT Cells.

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.

Cell. 2018 Jan 25;172(3):517-533.e20. doi: 10.1016/j.cell.2017.11.036. Epub 2017 Dec 14.

11.

Single-cell analyses to tailor treatments.

Shalek AK, Benson M.

Sci Transl Med. 2017 Sep 20;9(408). pii: eaan4730. doi: 10.1126/scitranslmed.aan4730. Review.

12.

Correction: Novel in vitro booster vaccination to rapidly generate antigen-specific human monoclonal antibodies.

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.

J Exp Med. 2017 Sep 4;214(9):2811. doi: 10.1084/jem.2017063307262017c. Epub 2017 Aug 21. No abstract available.

13.

Novel in vitro booster vaccination to rapidly generate antigen-specific human monoclonal antibodies.

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.

J Exp Med. 2017 Jul 24. pii: jem.20170633. doi: 10.1084/jem.20170633. [Epub ahead of print] Erratum in: J Exp Med. 2017 Aug 21;:.

14.

IFNγ-Dependent Tissue-Immune Homeostasis Is Co-opted in the Tumor Microenvironment.

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.

Cell. 2017 Jun 29;170(1):127-141.e15. doi: 10.1016/j.cell.2017.06.016.

15.

Scaling by shrinking: empowering single-cell 'omics' with microfluidic devices.

Prakadan SM, Shalek AK, Weitz DA.

Nat Rev Genet. 2017 Jun;18(6):345-361. doi: 10.1038/nrg.2017.15. Epub 2017 Apr 10. Review.

16.

Baring cellular souls.

Shalek AK.

Sci Transl Med. 2017 Feb 15;9(377). pii: eaam6064. doi: 10.1126/scitranslmed.aam6064.

PMID:
28202776
17.

Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput.

Gierahn TM, Wadsworth MH 2nd, Hughes TK, Bryson BD, Butler A, Satija R, Fortune S, Love JC, Shalek AK.

Nat Methods. 2017 Apr;14(4):395-398. doi: 10.1038/nmeth.4179. Epub 2017 Feb 13.

18.

Circulating CXCR5+CXCR3+PD-1lo Tfh-like cells in HIV-1 controllers with neutralizing antibody breadth.

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.

JCI Insight. 2017 Jan 26;2(2):e89574. doi: 10.1172/jci.insight.89574.

19.

A case of mistaken identity.

Shalek AK.

Sci Transl Med. 2017 Jan 4;9(371). pii: eaal4988. doi: 10.1126/scitranslmed.aal4988. No abstract available.

PMID:
28053155
20.

Size no longer matters.

Shalek AK.

Sci Transl Med. 2016 Nov 16;8(365):365ec185. No abstract available.

PMID:
27856794
21.

Antiviral CD8+ T Cells Restricted by Human Leukocyte Antigen Class II Exist during Natural HIV Infection and Exhibit Clonal Expansion.

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.

Immunity. 2016 Oct 18;45(4):917-930. doi: 10.1016/j.immuni.2016.09.015.

22.

Regulation of X-linked gene expression during early mouse development by Rlim.

Wang F, Shin J, Shea JM, Yu J, Bošković A, Byron M, Zhu X, Shalek AK, Regev A, Lawrence JB, Torres EM, Zhu LJ, Rando OJ, Bach I.

Elife. 2016 Sep 19;5. pii: e19127. doi: 10.7554/eLife.19127.

23.

Multiplexed, targeted profiling of single-cell proteomes and transcriptomes in a single reaction.

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.

Genome Biol. 2016 Sep 19;17(1):188. doi: 10.1186/s13059-016-1045-6.

24.

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq.

Tirosh I, Izar B, Prakadan SM, Wadsworth MH 2nd, 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.

Science. 2016 Apr 8;352(6282):189-96. doi: 10.1126/science.aad0501.

25.

Multiplexed barcoded CRISPR-Cas9 screening enabled by CombiGEM.

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.

Proc Natl Acad Sci U S A. 2016 Mar 1;113(9):2544-9. doi: 10.1073/pnas.1517883113. Epub 2016 Feb 10.

26.

Innate Lymphoid Cells Are Depleted Irreversibly during Acute HIV-1 Infection in the Absence of Viral Suppression.

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.

Immunity. 2016 Feb 16;44(2):391-405. doi: 10.1016/j.immuni.2016.01.006. Epub 2016 Feb 2.

27.

A microfluidic platform enabling single-cell RNA-seq of multigenerational lineages.

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.

Nat Commun. 2016 Jan 6;7:10220. doi: 10.1038/ncomms10220.

28.

MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data.

Finak G, McDavid A, Yajima M, Deng J, Gersuk V, Shalek AK, Slichter CK, Miller HW, McElrath MJ, Prlic M, Linsley PS, Gottardo R.

Genome Biol. 2015 Dec 10;16:278. doi: 10.1186/s13059-015-0844-5.

29.

Single-Cell Genomics Unveils Critical Regulators of Th17 Cell Pathogenicity.

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.

Cell. 2015 Dec 3;163(6):1400-12. doi: 10.1016/j.cell.2015.11.009. Epub 2015 Nov 19.

30.

Pathogen Cell-to-Cell Variability Drives Heterogeneity in Host Immune Responses.

Avraham R, Haseley N, Brown D, Penaranda C, Jijon HB, Trombetta JJ, Satija R, Shalek AK, Xavier RJ, Regev A, Hung DT.

Cell. 2015 Sep 10;162(6):1309-21. doi: 10.1016/j.cell.2015.08.027. Epub 2015 Sep 3. Erratum in: Cell. 2015 Oct 8;163(2):523.

31.

Marrying microfluidics and microwells for parallel, high-throughput single-cell genomics.

Wadsworth MH 2nd, Hughes TK, Shalek AK.

Genome Biol. 2015 Jun 20;16:129. doi: 10.1186/s13059-015-0695-0.

32.

MERFISHing for spatial context.

Shalek AK, Satija R.

Trends Immunol. 2015 Jul;36(7):390-1. doi: 10.1016/j.it.2015.05.002. Epub 2015 May 23.

PMID:
26013647
33.

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets.

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.

Cell. 2015 May 21;161(5):1202-1214. doi: 10.1016/j.cell.2015.05.002.

34.

Deconstructing transcriptional heterogeneity in pluripotent stem cells.

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.

Nature. 2014 Dec 4;516(7529):56-61. doi: 10.1038/nature13920.

35.

Preparation of Single-Cell RNA-Seq Libraries for Next Generation Sequencing.

Trombetta JJ, Gennert D, Lu D, Satija R, Shalek AK, Regev A.

Curr Protoc Mol Biol. 2014 Jul 1;107:4.22.1-17. doi: 10.1002/0471142727.mb0422s107. Review.

36.

Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma.

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.

Science. 2014 Jun 20;344(6190):1396-401. doi: 10.1126/science.1254257. Epub 2014 Jun 12.

37.

Single-cell RNA-seq reveals dynamic paracrine control of cellular variation.

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.

Nature. 2014 Jun 19;510(7505):363-9. doi: 10.1038/nature13437. Epub 2014 Jun 11.

38.

Somatic mutation as a mechanism of Wnt/β-catenin pathway activation in CLL.

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.

Blood. 2014 Aug 14;124(7):1089-98. doi: 10.1182/blood-2014-01-552067. Epub 2014 Apr 28.

39.

Whole-exome sequencing of circulating tumor cells provides a window into metastatic prostate cancer.

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.

Nat Biotechnol. 2014 May;32(5):479-84. doi: 10.1038/nbt.2892. Epub 2014 Apr 20.

40.

Heterogeneity in immune responses: from populations to single cells.

Satija R, Shalek AK.

Trends Immunol. 2014 May;35(5):219-29. doi: 10.1016/j.it.2014.03.004. Epub 2014 Apr 16. Review.

41.

Reconstructing and reprogramming the tumor-propagating potential of glioblastoma stem-like cells.

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.

Cell. 2014 Apr 24;157(3):580-94. doi: 10.1016/j.cell.2014.02.030. Epub 2014 Apr 10.

42.

Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells.

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.

Nature. 2013 Jun 13;498(7453):236-40. doi: 10.1038/nature12172. Epub 2013 May 19.

43.

Transcriptional and epigenetic dynamics during specification of human embryonic stem cells.

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.

Cell. 2013 May 23;153(5):1149-63. doi: 10.1016/j.cell.2013.04.037. Epub 2013 May 9.

44.

Deciphering molecular circuits from genetic variation underlying transcriptional responsiveness to stimuli.

Gat-Viks I, Chevrier N, Wilentzik R, Eisenhaure T, Raychowdhury R, Steuerman Y, Shalek AK, Hacohen N, Amit I, Regev A.

Nat Biotechnol. 2013 Apr;31(4):342-9. doi: 10.1038/nbt.2519. Epub 2013 Mar 17.

45.

Dynamic regulatory network controlling TH17 cell differentiation.

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.

Nature. 2013 Apr 25;496(7446):461-8. doi: 10.1038/nature11981. Epub 2013 Mar 6.

46.

Probing enzymatic activity inside living cells using a nanowire-cell "sandwich" assay.

Na YR, Kim SY, Gaublomme JT, Shalek AK, Jorgolli M, Park H, Yang EG.

Nano Lett. 2013 Jan 9;13(1):153-8. doi: 10.1021/nl3037068. Epub 2012 Dec 20.

47.

Nanowire-mediated delivery enables functional interrogation of primary immune cells: application to the analysis of chronic lymphocytic leukemia.

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.

Nano Lett. 2012 Dec 12;12(12):6498-504. doi: 10.1021/nl3042917. Epub 2012 Dec 3.

48.

Vertical nanowire electrode arrays as a scalable platform for intracellular interfacing to neuronal circuits.

Robinson JT, Jorgolli M, Shalek AK, Yoon MH, Gertner RS, Park H.

Nat Nanotechnol. 2012 Jan 10;7(3):180-4. doi: 10.1038/nnano.2011.249.

49.

Systematic discovery of TLR signaling components delineates viral-sensing circuits.

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.

Cell. 2011 Nov 11;147(4):853-67. doi: 10.1016/j.cell.2011.10.022.

50.

Vertical silicon nanowires as a universal platform for delivering biomolecules into living cells.

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.

Proc Natl Acad Sci U S A. 2010 Feb 2;107(5):1870-5. doi: 10.1073/pnas.0909350107. Epub 2010 Jan 11.

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