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Items: 35

1.

Interconversion between Tumorigenic and Differentiated States in Acute Myeloid Leukemia.

McKenzie MD, Ghisi M, Oxley EP, Ngo S, Cimmino L, Esnault C, Liu R, Salmon JM, Bell CC, Ahmed N, Erlichster M, Witkowski MT, Liu GJ, Chopin M, Dakic A, Simankowicz E, Pomilio G, Vu T, Krsmanovic P, Su S, Tian L, Baldwin TM, Zalcenstein DA, DiRago L, Wang S, Metcalf D, Johnstone RW, Croker BA, Lancaster GI, Murphy AJ, Naik SH, Nutt SL, Pospisil V, Schroeder T, Wall M, Dawson MA, Wei AH, de Thé H, Ritchie ME, Zuber J, Dickins RA.

Cell Stem Cell. 2019 Aug 1;25(2):258-272.e9. doi: 10.1016/j.stem.2019.07.001.

PMID:
31374198
2.

Targeting enhancer switching overcomes non-genetic drug resistance in acute myeloid leukaemia.

Bell CC, Fennell KA, Chan YC, Rambow F, Yeung MM, Vassiliadis D, Lara L, Yeh P, Martelotto LG, Rogiers A, Kremer BE, Barbash O, Mohammad HP, Johanson TM, Burr ML, Dhar A, Karpinich N, Tian L, Tyler DS, MacPherson L, Shi J, Pinnawala N, Yew Fong C, Papenfuss AT, Grimmond SM, Dawson SJ, Allan RS, Kruger RG, Vakoc CR, Goode DL, Naik SH, Gilan O, Lam EYN, Marine JC, Prinjha RK, Dawson MA.

Nat Commun. 2019 Jun 20;10(1):2723. doi: 10.1038/s41467-019-10652-9.

3.

Benchmarking single cell RNA-sequencing analysis pipelines using mixture control experiments.

Tian L, Dong X, Freytag S, Lê Cao KA, Su S, JalalAbadi A, Amann-Zalcenstein D, Weber TS, Seidi A, Jabbari JS, Naik SH, Ritchie ME.

Nat Methods. 2019 Jun;16(6):479-487. doi: 10.1038/s41592-019-0425-8. Epub 2019 May 27.

PMID:
31133762
4.

Publisher Correction: Barcoding reveals complex clonal behavior in patient-derived xenografts of metastatic triple negative breast cancer.

Merino D, Weber TS, Serrano A, Vaillant F, Liu K, Pal B, Di Stefano L, Schreuder J, Lin D, Chen Y, Asselin-Labat ML, Schumacher TN, Cameron D, Smyth GK, Papenfuss AT, Lindeman GJ, Visvader JE, Naik SH.

Nat Commun. 2019 Apr 24;10(1):1945. doi: 10.1038/s41467-019-09916-1.

5.

Barcoding reveals complex clonal behavior in patient-derived xenografts of metastatic triple negative breast cancer.

Merino D, Weber TS, Serrano A, Vaillant F, Liu K, Pal B, Di Stefano L, Schreuder J, Lin D, Chen Y, Asselin-Labat ML, Schumacher TN, Cameron D, Smyth GK, Papenfuss AT, Lindeman GJ, Visvader JE, Naik SH.

Nat Commun. 2019 Feb 15;10(1):766. doi: 10.1038/s41467-019-08595-2. Erratum in: Nat Commun. 2019 Apr 24;10(1):1945.

6.

Transcription Factor PU.1 Promotes Conventional Dendritic Cell Identity and Function via Induction of Transcriptional Regulator DC-SCRIPT.

Chopin M, Lun AT, Zhan Y, Schreuder J, Coughlan H, D'Amico A, Mielke LA, Almeida FF, Kueh AJ, Dickins RA, Belz GT, Naik SH, Lew AM, Bouillet P, Herold MJ, Smyth GK, Corcoran LM, Nutt SL.

Immunity. 2019 Jan 15;50(1):77-90.e5. doi: 10.1016/j.immuni.2018.11.010. Epub 2019 Jan 2.

PMID:
30611612
7.

scPipe: A flexible R/Bioconductor preprocessing pipeline for single-cell RNA-sequencing data.

Tian L, Su S, Dong X, Amann-Zalcenstein D, Biben C, Seidi A, Hilton DJ, Naik SH, Ritchie ME.

PLoS Comput Biol. 2018 Aug 10;14(8):e1006361. doi: 10.1371/journal.pcbi.1006361. eCollection 2018 Aug.

8.

DiSNE Movie Visualization and Assessment of Clonal Kinetics Reveal Multiple Trajectories of Dendritic Cell Development.

Lin DS, Kan A, Gao J, Crampin EJ, Hodgkin PD, Naik SH.

Cell Rep. 2018 Mar 6;22(10):2557-2566. doi: 10.1016/j.celrep.2018.02.046.

9.

Deciphering the Innate Lymphoid Cell Transcriptional Program.

Seillet C, Mielke LA, Amann-Zalcenstein DB, Su S, Gao J, Almeida FF, Shi W, Ritchie ME, Naik SH, Huntington ND, Carotta S, Belz GT.

Cell Rep. 2016 Oct 4;17(2):436-447. doi: 10.1016/j.celrep.2016.09.025.

10.

Site-specific recombinatorics: in situ cellular barcoding with the Cre Lox system.

Weber TS, Dukes M, Miles DC, Glaser SP, Naik SH, Duffy KR.

BMC Syst Biol. 2016 Jun 30;10(1):43. doi: 10.1186/s12918-016-0290-3.

11.

Editorial: Dendritic Cell and Macrophage Nomenclature and Classification.

Ginhoux F, Guilliams M, Naik SH.

Front Immunol. 2016 May 2;7:168. doi: 10.3389/fimmu.2016.00168. eCollection 2016. No abstract available.

12.

Reproducibility of Illumina platform deep sequencing errors allows accurate determination of DNA barcodes in cells.

Beltman JB, Urbanus J, Velds A, van Rooij N, Rohr JC, Naik SH, Schumacher TN.

BMC Bioinformatics. 2016 Apr 2;17:151. doi: 10.1186/s12859-016-0999-4.

13.

Toward defining a 'lineage'--The case for dendritic cells.

Perié L, Naik SH.

Semin Cell Dev Biol. 2015 May;41:3-8. doi: 10.1016/j.semcdb.2015.02.004. Epub 2015 Feb 17. Review.

PMID:
25701440
14.

Segmentation of occluded hematopoietic stem cells from tracking.

Mankowski WC, Winter MR, Wait E, Lodder M, Schumacher T, Naik SH, Cohen AR.

Conf Proc IEEE Eng Med Biol Soc. 2014;2014:5510-3. doi: 10.1109/EMBC.2014.6944874.

15.

RB family tumor suppressor activity may not relate to active silencing of E2F target genes.

Vormer TL, Wojciechowicz K, Dekker M, de Vries S, van der Wal A, Delzenne-Goette E, Naik SH, Song JY, Dannenberg JH, Hansen JB, Te Riele H.

Cancer Res. 2014 Sep 15;74(18):5266-76. doi: 10.1158/0008-5472.CAN-13-3706. Epub 2014 Jul 23.

16.

Lymphoid tissue and plasmacytoid dendritic cells and macrophages do not share a common macrophage-dendritic cell-restricted progenitor.

Sathe P, Metcalf D, Vremec D, Naik SH, Langdon WY, Huntington ND, Wu L, Shortman K.

Immunity. 2014 Jul 17;41(1):104-15. doi: 10.1016/j.immuni.2014.05.020.

17.

Dendritic cells, monocytes and macrophages: a unified nomenclature based on ontogeny.

Guilliams M, Ginhoux F, Jakubzick C, Naik SH, Onai N, Schraml BU, Segura E, Tussiwand R, Yona S.

Nat Rev Immunol. 2014 Aug;14(8):571-8. doi: 10.1038/nri3712. Epub 2014 Jul 18. Review.

18.

Cellular barcoding: a technical appraisal.

Naik SH, Schumacher TN, Perié L.

Exp Hematol. 2014 Aug;42(8):598-608. doi: 10.1016/j.exphem.2014.05.003. Epub 2014 Jul 1. Review.

PMID:
24996012
19.

Determining lineage pathways from cellular barcoding experiments.

Perié L, Hodgkin PD, Naik SH, Schumacher TN, de Boer RJ, Duffy KR.

Cell Rep. 2014 Feb 27;6(4):617-24. doi: 10.1016/j.celrep.2014.01.016. Epub 2014 Feb 6.

20.

Diverse and heritable lineage imprinting of early haematopoietic progenitors.

Naik SH, Perié L, Swart E, Gerlach C, van Rooij N, de Boer RJ, Schumacher TN.

Nature. 2013 Apr 11;496(7444):229-32. doi: 10.1038/nature12013. Epub 2013 Apr 3.

PMID:
23552896
21.

Heterogeneous differentiation patterns of individual CD8+ T cells.

Gerlach C, Rohr JC, Perié L, van Rooij N, van Heijst JW, Velds A, Urbanus J, Naik SH, Jacobs H, Beltman JB, de Boer RJ, Schumacher TN.

Science. 2013 May 3;340(6132):635-9. doi: 10.1126/science.1235487. Epub 2013 Mar 14.

22.

The invariant chain transports TNF family member CD70 to MHC class II compartments in dendritic cells.

Zwart W, Peperzak V, de Vries E, Keller AM, van der Horst G, Veraar EA, Geumann U, Janssen H, Janssen L, Naik SH, Neefjes J, Borst J.

J Cell Sci. 2010 Nov 1;123(Pt 21):3817-27. doi: 10.1242/jcs.068510.

23.

Deficient CD40-TRAF6 signaling in leukocytes prevents atherosclerosis by skewing the immune response toward an antiinflammatory profile.

Lutgens E, Lievens D, Beckers L, Wijnands E, Soehnlein O, Zernecke A, Seijkens T, Engel D, Cleutjens J, Keller AM, Naik SH, Boon L, Oufella HA, Mallat Z, Ahonen CL, Noelle RJ, de Winther MP, Daemen MJ, Biessen EA, Weber C.

J Exp Med. 2010 Feb 15;207(2):391-404. doi: 10.1084/jem.20091293. Epub 2010 Jan 25.

24.

Generation of large numbers of pro-DCs and pre-DCs in vitro.

Naik SH.

Methods Mol Biol. 2010;595:177-86. doi: 10.1007/978-1-60761-421-0_11.

PMID:
19941112
25.

CD8+, CD8-, and plasmacytoid dendritic cell generation in vitro using flt3 ligand.

Naik SH, O'Keeffe M, Proietto A, Shortman HH, Wu L.

Methods Mol Biol. 2010;595:167-76. doi: 10.1007/978-1-60761-421-0_10.

PMID:
19941111
26.

Costimulatory ligand CD70 allows induction of CD8+ T-cell immunity by immature dendritic cells in a vaccination setting.

Keller AM, Xiao Y, Peperzak V, Naik SH, Borst J.

Blood. 2009 May 21;113(21):5167-75. doi: 10.1182/blood-2008-03-148007. Epub 2009 Mar 11.

27.

Dendritic cells in the thymus contribute to T-regulatory cell induction.

Proietto AI, van Dommelen S, Zhou P, Rizzitelli A, D'Amico A, Steptoe RJ, Naik SH, Lahoud MH, Liu Y, Zheng P, Shortman K, Wu L.

Proc Natl Acad Sci U S A. 2008 Dec 16;105(50):19869-74. doi: 10.1073/pnas.0810268105. Epub 2008 Dec 10. Erratum in: Proc Natl Acad Sci U S A. 2009 Feb 3;106(5):1679.

28.

Demystifying the development of dendritic cell subtypes, a little.

Naik SH.

Immunol Cell Biol. 2008 Jul;86(5):439-52. doi: 10.1038/icb.2008.28. Epub 2008 Apr 15. Review.

PMID:
18414430
29.

Normal proportion and expression of maturation markers in migratory dendritic cells in the absence of germs or Toll-like receptor signaling.

Wilson NS, Young LJ, Kupresanin F, Naik SH, Vremec D, Heath WR, Akira S, Shortman K, Boyle J, Maraskovsky E, Belz GT, Villadangos JA.

Immunol Cell Biol. 2008 Feb;86(2):200-5. Epub 2007 Nov 20.

PMID:
18026177
30.
31.

Development of plasmacytoid and conventional dendritic cell subtypes from single precursor cells derived in vitro and in vivo.

Naik SH, Sathe P, Park HY, Metcalf D, Proietto AI, Dakic A, Carotta S, O'Keeffe M, Bahlo M, Papenfuss A, Kwak JY, Wu L, Shortman K.

Nat Immunol. 2007 Nov;8(11):1217-26. Epub 2007 Oct 7.

PMID:
17922015
32.

Steady-state and inflammatory dendritic-cell development.

Shortman K, Naik SH.

Nat Rev Immunol. 2007 Jan;7(1):19-30. Epub 2006 Dec 15. Review.

PMID:
17170756
33.

Intrasplenic steady-state dendritic cell precursors that are distinct from monocytes.

Naik SH, Metcalf D, van Nieuwenhuijze A, Wicks I, Wu L, O'Keeffe M, Shortman K.

Nat Immunol. 2006 Jun;7(6):663-71. Epub 2006 May 7.

PMID:
16680143
34.

Development of murine plasmacytoid dendritic cell subsets.

Naik SH, Corcoran LM, Wu L.

Immunol Cell Biol. 2005 Oct;83(5):563-70. Review.

PMID:
16174108
35.

Cutting edge: generation of splenic CD8+ and CD8- dendritic cell equivalents in Fms-like tyrosine kinase 3 ligand bone marrow cultures.

Naik SH, Proietto AI, Wilson NS, Dakic A, Schnorrer P, Fuchsberger M, Lahoud MH, O'Keeffe M, Shao QX, Chen WF, Villadangos JA, Shortman K, Wu L.

J Immunol. 2005 Jun 1;174(11):6592-7.

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