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Items: 1 to 50 of 247

1.

DRUG-NEM: Optimizing drug combinations using single-cell perturbation response to account for intratumoral heterogeneity.

Anchang B, Davis KL, Fienberg HG, Williamson BD, Bendall SC, Karacosta LG, Tibshirani R, Nolan GP, Plevritis SK.

Proc Natl Acad Sci U S A. 2018 Apr 13. pii: 201711365. doi: 10.1073/pnas.1711365115. [Epub ahead of print]

2.

Whole-genome sequencing of Atacama skeleton shows novel mutations linked with dysplasia.

Bhattacharya S, Li J, Sockell A, Kan MJ, Bava FA, Chen SC, Ávila-Arcos MC, Ji X, Smith E, Asadi NB, Lachman RS, Lam HYK, Bustamante CD, Butte AJ, Nolan GP.

Genome Res. 2018 Apr;28(4):423-431. doi: 10.1101/gr.223693.117. Epub 2018 Mar 22.

3.

Single-cell mass cytometry reveals distinct populations of brain myeloid cells in mouse neuroinflammation and neurodegeneration models.

Ajami B, Samusik N, Wieghofer P, Ho PP, Crotti A, Bjornson Z, Prinz M, Fantl WJ, Nolan GP, Steinman L.

Nat Neurosci. 2018 Apr;21(4):541-551. doi: 10.1038/s41593-018-0100-x. Epub 2018 Mar 5.

PMID:
29507414
4.

Publisher Correction: High-resolution myogenic lineage mapping by single-cell mass cytometry.

Porpiglia E, Samusik N, Van Ho AT, Cosgrove BD, Mai T, Davis KL, Jager A, Nolan GP, Bendall SC, Fantl WJ, Blau HM.

Nat Cell Biol. 2018 Mar 5. doi: 10.1038/s41556-018-0043-1. [Epub ahead of print]

PMID:
29507406
5.

Single-cell developmental classification of B cell precursor acute lymphoblastic leukemia at diagnosis reveals predictors of relapse.

Good Z, Sarno J, Jager A, Samusik N, Aghaeepour N, Simonds EF, White L, Lacayo NJ, Fantl WJ, Fazio G, Gaipa G, Biondi A, Tibshirani R, Bendall SC, Nolan GP, Davis KL.

Nat Med. 2018 May;24(4):474-483. doi: 10.1038/nm.4505. Epub 2018 Mar 5.

PMID:
29505032
6.

Commonly Occurring Cell Subsets in High-Grade Serous Ovarian Tumors Identified by Single-Cell Mass Cytometry.

Gonzalez VD, Samusik N, Chen TJ, Savig ES, Aghaeepour N, Quigley DA, Huang YW, Giangarrà V, Borowsky AD, Hubbard NE, Chen SY, Han G, Ashworth A, Kipps TJ, Berek JS, Nolan GP, Fantl WJ.

Cell Rep. 2018 Feb 13;22(7):1875-1888. doi: 10.1016/j.celrep.2018.01.053.

7.

Jak1 Integrates Cytokine Sensing to Regulate Hematopoietic Stem Cell Function and Stress Hematopoiesis.

Kleppe M, Spitzer MH, Li S, Hill CE, Dong L, Papalexi E, De Groote S, Bowman RL, Keller M, Koppikar P, Rapaport FT, Teruya-Feldstein J, Gandara J, Mason CE, Nolan GP, Levine RL.

Cell Stem Cell. 2018 Feb 1;22(2):277. doi: 10.1016/j.stem.2017.12.018. No abstract available.

PMID:
29395057
8.

Scalable multi-sample single-cell data analysis by Partition-Assisted Clustering and Multiple Alignments of Networks.

Li YH, Li D, Samusik N, Wang X, Guan L, Nolan GP, Wong WH.

PLoS Comput Biol. 2017 Dec 27;13(12):e1005875. doi: 10.1371/journal.pcbi.1005875. eCollection 2017 Dec.

9.

High-Dimensional Phenotypic Mapping of Human Dendritic Cells Reveals Interindividual Variation and Tissue Specialization.

Alcántara-Hernández M, Leylek R, Wagar LE, Engleman EG, Keler T, Marinkovich MP, Davis MM, Nolan GP, Idoyaga J.

Immunity. 2017 Dec 19;47(6):1037-1050.e6. doi: 10.1016/j.immuni.2017.11.001. Epub 2017 Dec 5.

PMID:
29221729
10.

Atomic mass tag of bismuth-209 for increasing the immunoassay multiplexing capacity of mass cytometry.

Han G, Chen SY, Gonzalez VD, Zunder ER, Fantl WJ, Nolan GP.

Cytometry A. 2017 Dec;91(12):1150-1163. doi: 10.1002/cyto.a.23283. Epub 2017 Dec 4.

11.

A gut bacterial pathway metabolizes aromatic amino acids into nine circulating metabolites.

Dodd D, Spitzer MH, Van Treuren W, Merrill BD, Hryckowian AJ, Higginbottom SK, Le A, Cowan TM, Nolan GP, Fischbach MA, Sonnenburg JL.

Nature. 2017 Nov 30;551(7682):648-652. doi: 10.1038/nature24661. Epub 2017 Nov 22.

PMID:
29168502
12.

Jak1 Integrates Cytokine Sensing to Regulate Hematopoietic Stem Cell Function and Stress Hematopoiesis.

Kleppe M, Spitzer MH, Li S, Hill CE, Dong L, Papalexi E, De Groote S, Bowman RL, Keller M, Koppikar P, Rapaport FT, Teruya-Feldstein J, Gandara J, Mason CE, Nolan GP, Levine RL.

Cell Stem Cell. 2017 Oct 5;21(4):489-501.e7. doi: 10.1016/j.stem.2017.08.011. Epub 2017 Sep 28. Erratum in: Cell Stem Cell. 2018 Feb 1;22(2):277.

13.

Upregulation of Human Endogenous Retrovirus-K Is Linked to Immunity and Inflammation in Pulmonary Arterial Hypertension.

Saito T, Miyagawa K, Chen SY, Tamosiuniene R, Wang L, Sharpe O, Samayoa E, Harada D, Moonen JAJ, Cao A, Chen PI, Hennigs JK, Gu M, Li CG, Leib RD, Li D, Adams CM, Del Rosario PA, Bill M, Haddad F, Montoya JG, Robinson WH, Fantl WJ, Nolan GP, Zamanian RT, Nicolls MR, Chiu CY, Ariza ME, Rabinovitch M.

Circulation. 2017 Nov 14;136(20):1920-1935. doi: 10.1161/CIRCULATIONAHA.117.027589. Epub 2017 Sep 21.

PMID:
28935667
14.

An immune clock of human pregnancy.

Aghaeepour N, Ganio EA, Mcilwain D, Tsai AS, Tingle M, Van Gassen S, Gaudilliere DK, Baca Q, McNeil L, Okada R, Ghaemi MS, Furman D, Wong RJ, Winn VD, Druzin ML, El-Sayed YY, Quaintance C, Gibbs R, Darmstadt GL, Shaw GM, Stevenson DK, Tibshirani R, Nolan GP, Lewis DB, Angst MS, Gaudilliere B.

Sci Immunol. 2017 Sep 1;2(15). pii: eaan2946. doi: 10.1126/sciimmunol.aan2946.

15.

Deep Immune Profiling of an Arginine-Enriched Nutritional Intervention in Patients Undergoing Surgery.

Aghaeepour N, Kin C, Ganio EA, Jensen KP, Gaudilliere DK, Tingle M, Tsai A, Lancero HL, Choisy B, McNeil LS, Okada R, Shelton AA, Nolan GP, Angst MS, Gaudilliere BL.

J Immunol. 2017 Aug 9. pii: ji1700421. doi: 10.4049/jimmunol.1700421. [Epub ahead of print]

PMID:
28794234
16.

NKG2D ligand expression in Crohn's disease and NKG2D-dependent stimulation of CD8+ T cell migration.

Vadstrup K, Galsgaard ED, Jensen H, Lanier LL, Ryan JC, Chen SY, Nolan GP, Vester-Andersen MK, Pedersen JS, Gerwien J, Jensen T, Bendtsen F.

Exp Mol Pathol. 2017 Aug;103(1):56-70. doi: 10.1016/j.yexmp.2017.06.010. Epub 2017 Jul 3.

17.

In silico modeling identifies CD45 as a regulator of IL-2 synergy in the NKG2D-mediated activation of immature human NK cells.

Mukherjee S, Jensen H, Stewart W, Stewart D, Ray WC, Chen SY, Nolan GP, Lanier LL, Das J.

Sci Signal. 2017 Jun 27;10(485). pii: eaai9062. doi: 10.1126/scisignal.aai9062.

18.

High-resolution myogenic lineage mapping by single-cell mass cytometry.

Porpiglia E, Samusik N, Ho ATV, Cosgrove BD, Mai T, Davis KL, Jager A, Nolan GP, Bendall SC, Fantl WJ, Blau HM.

Nat Cell Biol. 2017 May;19(5):558-567. doi: 10.1038/ncb3507. Epub 2017 Apr 17. Erratum in: Nat Cell Biol. 2018 Mar 5;:.

19.

Mass cytometry identifies a distinct monocyte cytokine signature shared by clinically heterogeneous pediatric SLE patients.

O'Gorman WE, Kong DS, Balboni IM, Rudra P, Bolen CR, Ghosh D, Davis MM, Nolan GP, Hsieh EW.

J Autoimmun. 2017 Apr 4. pii: S0896-8411(16)30412-7. doi: 10.1016/j.jaut.2017.03.010. [Epub ahead of print]

PMID:
28389038
20.

The histone deacetylase inhibitor givinostat (ITF2357) exhibits potent anti-tumor activity against CRLF2-rearranged BCP-ALL.

Savino AM, Sarno J, Trentin L, Vieri M, Fazio G, Bardini M, Bugarin C, Fossati G, Davis KL, Gaipa G, Izraeli S, Meyer LH, Nolan GP, Biondi A, Te Kronnie G, Palmi C, Cazzaniga G.

Leukemia. 2017 Nov;31(11):2365-2375. doi: 10.1038/leu.2017.93. Epub 2017 Mar 23.

PMID:
28331226
21.

EBI3 regulates the NK cell response to mouse cytomegalovirus infection.

Jensen H, Chen SY, Folkersen L, Nolan GP, Lanier LL.

Proc Natl Acad Sci U S A. 2017 Feb 14;114(7):1625-1630. doi: 10.1073/pnas.1700231114. Epub 2017 Jan 31.

22.

Systemic Immunity Is Required for Effective Cancer Immunotherapy.

Spitzer MH, Carmi Y, Reticker-Flynn NE, Kwek SS, Madhireddy D, Martins MM, Gherardini PF, Prestwood TR, Chabon J, Bendall SC, Fong L, Nolan GP, Engleman EG.

Cell. 2017 Jan 26;168(3):487-502.e15. doi: 10.1016/j.cell.2016.12.022. Epub 2017 Jan 19.

23.

Microsphere cytometry to interrogate microenvironment-dependent cell signaling.

Ertsås HC, Nolan GP, LaBarge MA, Lorens JB.

Integr Biol (Camb). 2017 Feb 20;9(2):123-134. doi: 10.1039/c6ib00207b.

PMID:
28102399
24.

High-throughput precision measurement of subcellular localization in single cells.

Burns TJ, Frei AP, Gherardini PF, Bava FA, Batchelder JE, Yoshiyasu Y, Yu JM, Groziak AR, Kimmey SC, Gonzalez VD, Fantl WJ, Nolan GP.

Cytometry A. 2017 Feb;91(2):180-189. doi: 10.1002/cyto.a.23054. Epub 2017 Jan 17.

25.

Expression of specific inflammasome gene modules stratifies older individuals into two extreme clinical and immunological states.

Furman D, Chang J, Lartigue L, Bolen CR, Haddad F, Gaudilliere B, Ganio EA, Fragiadakis GK, Spitzer MH, Douchet I, Daburon S, Moreau JF, Nolan GP, Blanco P, Déchanet-Merville J, Dekker CL, Jojic V, Kuo CJ, Davis MM, Faustin B.

Nat Med. 2017 Feb;23(2):174-184. doi: 10.1038/nm.4267. Epub 2017 Jan 16.

26.

Mass cytometry analysis reveals hyperactive NF Kappa B signaling in myelofibrosis and secondary acute myeloid leukemia.

Fisher DAC, Malkova O, Engle EK, Miner CA, Fulbright MC, Behbehani GK, Collins TB, Bandyopadhyay S, Zhou A, Nolan GP, Oh ST.

Leukemia. 2017 Sep;31(9):1962-1974. doi: 10.1038/leu.2016.377. Epub 2016 Dec 23.

27.

AN UPDATED DEBARCODING TOOL FOR MASS CYTOMETRY WITH CELL TYPE-SPECIFIC AND CELL SAMPLE-SPECIFIC STRINGENCY ADJUSTMENT.

Fread KI, Strickland WD, Nolan GP, Zunder ER.

Pac Symp Biocomput. 2017;22:588-598. doi: 10.1142/9789813207813_0054.

28.

Distinct signaling programs control human hematopoietic stem cell survival and proliferation.

Knapp DJ, Hammond CA, Aghaeepour N, Miller PH, Pellacani D, Beer PA, Sachs K, Qiao W, Wang W, Humphries RK, Sauvageau G, Zandstra PW, Bendall SC, Nolan GP, Hansen C, Eaves CJ.

Blood. 2017 Jan 19;129(3):307-318. doi: 10.1182/blood-2016-09-740654. Epub 2016 Nov 8.

29.

Mapping the Fetomaternal Peripheral Immune System at Term Pregnancy.

Fragiadakis GK, Baca QJ, Gherardini PF, Ganio EA, Gaudilliere DK, Tingle M, Lancero HL, McNeil LS, Spitzer MH, Wong RJ, Shaw GM, Darmstadt GL, Sylvester KG, Winn VD, Carvalho B, Lewis DB, Stevenson DK, Nolan GP, Aghaeepour N, Angst MS, Gaudilliere BL.

J Immunol. 2016 Dec 1;197(11):4482-4492. Epub 2016 Oct 28.

30.

Mutant IDH1 Downregulates ATM and Alters DNA Repair and Sensitivity to DNA Damage Independent of TET2.

Inoue S, Li WY, Tseng A, Beerman I, Elia AJ, Bendall SC, Lemonnier F, Kron KJ, Cescon DW, Hao Z, Lind EF, Takayama N, Planello AC, Shen SY, Shih AH, Larsen DM, Li Q, Snow BE, Wakeham A, Haight J, Gorrini C, Bassi C, Thu KL, Murakami K, Elford AR, Ueda T, Straley K, Yen KE, Melino G, Cimmino L, Aifantis I, Levine RL, De Carvalho DD, Lupien M, Rossi DJ, Nolan GP, Cairns RA, Mak TW.

Cancer Cell. 2016 Aug 8;30(2):337-348. doi: 10.1016/j.ccell.2016.05.018. Epub 2016 Jul 14.

31.

Visualization and cellular hierarchy inference of single-cell data using SPADE.

Anchang B, Hart TD, Bendall SC, Qiu P, Bjornson Z, Linderman M, Nolan GP, Plevritis SK.

Nat Protoc. 2016 Jul;11(7):1264-79. doi: 10.1038/nprot.2016.066. Epub 2016 Jun 16.

PMID:
27310265
32.

In Reply.

Angst MS, Fragiadakis GK, Gaudillière B, Aghaeepour N, Nolan GP.

Anesthesiology. 2016 Jun;124(6):1414-5. doi: 10.1097/ALN.0000000000001091. No abstract available.

33.

Automated mapping of phenotype space with single-cell data.

Samusik N, Good Z, Spitzer MH, Davis KL, Nolan GP.

Nat Methods. 2016 Jun;13(6):493-6. doi: 10.1038/nmeth.3863. Epub 2016 May 16.

34.

Mass Cytometry: Single Cells, Many Features.

Spitzer MH, Nolan GP.

Cell. 2016 May 5;165(4):780-91. doi: 10.1016/j.cell.2016.04.019. Review.

35.

Highly multiplexed simultaneous detection of RNAs and proteins in single cells.

Frei AP, Bava FA, Zunder ER, Hsieh EW, Chen SY, Nolan GP, Gherardini PF.

Nat Methods. 2016 Mar;13(3):269-75. doi: 10.1038/nmeth.3742. Epub 2016 Jan 25.

36.

Coordinate actions of innate immune responses oppose those of the adaptive immune system during Salmonella infection of mice.

Hotson AN, Gopinath S, Nicolau M, Khasanova A, Finck R, Monack D, Nolan GP.

Sci Signal. 2016 Jan 12;9(410):ra4. doi: 10.1126/scisignal.aaa9303.

PMID:
26758212
37.

Patient-specific Immune States before Surgery Are Strong Correlates of Surgical Recovery.

Fragiadakis GK, Gaudillière B, Ganio EA, Aghaeepour N, Tingle M, Nolan GP, Angst MS.

Anesthesiology. 2015 Dec;123(6):1241-55. doi: 10.1097/ALN.0000000000000887.

38.

Deletions in the cytoplasmic domain of iRhom1 and iRhom2 promote shedding of the TNF receptor by the protease ADAM17.

Maney SK, McIlwain DR, Polz R, Pandyra AA, Sundaram B, Wolff D, Ohishi K, Maretzky T, Brooke MA, Evers A, Vasudevan AA, Aghaeepour N, Scheller J, Münk C, Häussinger D, Mak TW, Nolan GP, Kelsell DP, Blobel CP, Lang KS, Lang PA.

Sci Signal. 2015 Nov 3;8(401):ra109. doi: 10.1126/scisignal.aac5356.

PMID:
26535007
39.

A benchmark for evaluation of algorithms for identification of cellular correlates of clinical outcomes.

Aghaeepour N, Chattopadhyay P, Chikina M, Dhaene T, Van Gassen S, Kursa M, Lambrecht BN, Malek M, McLachlan GJ, Qian Y, Qiu P, Saeys Y, Stanton R, Tong D, Vens C, Walkowiak S, Wang K, Finak G, Gottardo R, Mosmann T, Nolan GP, Scheuermann RH, Brinkman RR.

Cytometry A. 2016 Jan;89(1):16-21. doi: 10.1002/cyto.a.22732. Epub 2015 Oct 8.

40.

Implementing Mass Cytometry at the Bedside to Study the Immunological Basis of Human Diseases: Distinctive Immune Features in Patients with a History of Term or Preterm Birth.

Gaudillière B, Ganio EA, Tingle M, Lancero HL, Fragiadakis GK, Baca QJ, Aghaeepour N, Wong RJ, Quaintance C, El-Sayed YY, Shaw GM, Lewis DB, Stevenson DK, Nolan GP, Angst MS.

Cytometry A. 2015 Sep;87(9):817-29. doi: 10.1002/cyto.a.22720. Epub 2015 Jul 17.

41.

IMMUNOLOGY. An interactive reference framework for modeling a dynamic immune system.

Spitzer MH, Gherardini PF, Fragiadakis GK, Bhattacharya N, Yuan RT, Hotson AN, Finck R, Carmi Y, Zunder ER, Fantl WJ, Bendall SC, Engleman EG, Nolan GP.

Science. 2015 Jul 10;349(6244):1259425. doi: 10.1126/science.1259425.

42.

Reversibility of Defective Hematopoiesis Caused by Telomere Shortening in Telomerase Knockout Mice.

Raval A, Behbehani GK, Nguyen le XT, Thomas D, Kusler B, Garbuzov A, Ramunas J, Holbrook C, Park CY, Blau H, Nolan GP, Artandi SE, Mitchell BS.

PLoS One. 2015 Jul 2;10(7):e0131722. doi: 10.1371/journal.pone.0131722. eCollection 2015.

43.

Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis.

Levine JH, Simonds EF, Bendall SC, Davis KL, Amir el-AD, Tadmor MD, Litvin O, Fienberg HG, Jager A, Zunder ER, Finck R, Gedman AL, Radtke I, Downing JR, Pe'er D, Nolan GP.

Cell. 2015 Jul 2;162(1):184-97. doi: 10.1016/j.cell.2015.05.047. Epub 2015 Jun 18.

44.

Mass Cytometric Functional Profiling of Acute Myeloid Leukemia Defines Cell-Cycle and Immunophenotypic Properties That Correlate with Known Responses to Therapy.

Behbehani GK, Samusik N, Bjornson ZB, Fantl WJ, Medeiros BC, Nolan GP.

Cancer Discov. 2015 Sep;5(9):988-1003. doi: 10.1158/2159-8290.CD-15-0298. Epub 2015 Jun 19.

45.

Synthetically Modified Viral Capsids as Versatile Carriers for Use in Antibody-Based Cell Targeting.

ElSohly AM, Netirojjanakul C, Aanei IL, Jager A, Bendall SC, Farkas ME, Nolan GP, Francis MB.

Bioconjug Chem. 2015 Aug 19;26(8):1590-6. doi: 10.1021/acs.bioconjchem.5b00226. Epub 2015 Jul 6.

46.

Single-cell systems-level analysis of human Toll-like receptor activation defines a chemokine signature in patients with systemic lupus erythematosus.

O'Gorman WE, Hsieh EW, Savig ES, Gherardini PF, Hernandez JD, Hansmann L, Balboni IM, Utz PJ, Bendall SC, Fantl WJ, Lewis DB, Nolan GP, Davis MM.

J Allergy Clin Immunol. 2015 Nov;136(5):1326-36. doi: 10.1016/j.jaci.2015.04.008. Epub 2015 May 30.

47.

Mass cytometry as a platform for the discovery of cellular biomarkers to guide effective rheumatic disease therapy.

Nair N, Mei HE, Chen SY, Hale M, Nolan GP, Maecker HT, Genovese M, Fathman CG, Whiting CC.

Arthritis Res Ther. 2015 May 18;17:127. doi: 10.1186/s13075-015-0644-z. Review.

48.

Nomenclature of Toso, Fas apoptosis inhibitory molecule 3, and IgM FcR.

Kubagawa H, Carroll MC, Jacob CO, Lang KS, Lee KH, Mak T, McAndrews M, Morse HC 3rd, Nolan GP, Ohno H, Richter GH, Seal R, Wang JY, Wiestner A, Coligan JE.

J Immunol. 2015 May 1;194(9):4055-7. doi: 10.4049/jimmunol.1500222.

49.

Early reprogramming regulators identified by prospective isolation and mass cytometry.

Lujan E, Zunder ER, Ng YH, Goronzy IN, Nolan GP, Wernig M.

Nature. 2015 May 21;521(7552):352-6. doi: 10.1038/nature14274. Epub 2015 Apr 1.

50.

Unipotent Megakaryopoietic Pathway Bridging Hematopoietic Stem Cells and Mature Megakaryocytes.

Nishikii H, Kanazawa Y, Umemoto T, Goltsev Y, Matsuzaki Y, Matsushita K, Yamato M, Nolan GP, Negrin R, Chiba S.

Stem Cells. 2015 Jul;33(7):2196-207. doi: 10.1002/stem.1985. Epub 2015 Apr 27.

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