Publications
- Normalization of mass cytometry data with bead standards. Bendall SC, Nolan GP, et al. Cytometry. Part A : the journal of the International Society for Analytical Cytology. 2013 May; 83 (5) :483-94.
- Hierarchy in somatic mutations arising during genomic evolution and progression of follicular lymphoma. Green MR, Gentles AJ, Alizadeh AA, et al. Blood. 2013.
- Conservation and divergence in the transcriptional programs of the human and mouse immune systems. Jojic, V, Koller, D, et al. Proceedings of the National Academy of Sciences of the United States of America. 2013 Feb 19.
- Identifying master regulators of cancer and their downstream targets by integrating genomic and epigenomic features. Gevaert, O, Plevritis, SK. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. 2013; 123-34.
- Cross-species functional analysis of cancer-associated fibroblasts identifies a critical role for CLCF1 and IL-6 in non-small cell lung cancer in vivo. Vincent, S, Olivier, G, et al. Cancer research. 2012 Nov 15; 72 (22) :5744-56.
- Deciphering the transcriptional network of the dendritic cell lineage. Jojic, V, et al. Nature immunology. 2012 Sep; 13 (9) :888-99.
- Multiplexed mass cytometry profiling of cellular states perturbed by small-molecule regulators. Bendall SC, Nolan GP, et al. Nature biotechnology. 2012 Sep; 30 (9) :858-67.
- Prognostic PET 18F-FDG uptake imaging features are associated with major oncogenomic alterations in patients with resected non-small cell lung cancer. Nair, V, Plevritis, SK, et al. Cancer research. 2012 Aug 1; 72 (15) :3725-34.
- The chemoattractant chemerin suppresses melanoma by recruiting natural killer cell antitumor defenses. Alizadeh AA, Gentles AJ, et al. The Journal of experimental medicine. 2012 Jul 30; 209 (8) :1427-35.
- From single cells to deep phenotypes in cancer. Bendall SC, Nolan GP. Nat Biotechnol. 2012 Jul 10;30(7):639-47.
- A platinum-based covalent viability reagent for single-cell mass cytometry. Fantl, W, Nolan GP, et al. Cytometry. Part A : the journal of the International Society for Analytical Cytology. 2012 Jun; 81 (6) :467-75.
- Decoupling of tumor-initiating activity from stable immunophenotype in HoxA9-Meis1-driven AML. Gibbs Jr, Kenneth D, Nolan, GP, et al. Cell stem cell. 2012 Feb 3; 10 (2) :210-7.
- Treatment of higher risk myelodysplastic syndrome patients unresponsive to hypomethylating agents with ON 01910.Na. Fan, A, Felsher, D, et al. Leukemia research. 2012 Jan; 36 (1) :98-103.
- Cytometry by Time-of-Flight Shows Combinatorial Cytokine Expression and Virus-Specific Cell Niches within a Continuum of CD8(+) T Cell Phenotypes. Newell EW, Sigal N, Bendall SC, Nolan GP, Davis MM (2012). Immunity Jan 27;36(1):142-52.
- Gene Expression Commons: an open platform for absolute gene expression profiling. Sahoo, D, Dill, D, et al. PloS one. 2012; 7 (7) :e40321.
- Survival and death signals can predict tumor response to therapy after oncogene inactivation. Felsher, D, et al. Science translational medicine. 2011 Oct 5; 3 (103) :103ra99.
- B-cell signaling networks reveal a negative prognostic human lymphoma cell subset that emerges during tumor progression. Irish JM, Alizadeh AA, Nolan GP, Levy R, et al. Proc Natl Acad Sci U S A. 2010;107(29):12747-54.
- CytoSPADE: High-Performance Analysis and Visualization of High-Dimensional Cytometry Data. Linderman MD, Bjornson Z, Simonds EF, Qiu P, Bruggner R, Sheode K, Meng TH, Plevritis SK, Nolan GP. Bioinformatics. 2012.
- Extracting a cellular hierarchy from high-dimensional cytometry data with SPADE. Qiu P, Simonds EF, Bendall SC, Gibbs KD, Bruggner RV, Linderman MD, Sachs K, Nolan GP, Plevritis SK. Nat Biotechnol. 2011; 29 (10): 886-91.
- Lymphomas that recur after MYC suppression continue to exhibit oncogene addiction. Choi PS, van Riggelen J, Gentles AJ, Bachireddy P, Rakhra K, Adam SJ, Plevritis SK, Felsher DW. Proc Natl Acad Sci U S A. 2011 Oct 3.
- Prediction of survival in diffuse large B-cell lymphoma based on the expression of 2 genes reflecting tumor and microenvironment. Alizadeh AA, Gentles AJ, et al.Blood. 2011 Aug 4; 118 (5) :1350-8.
- Single-cell mass cytometry of differential immune and drug responses across a human hematopoietic continuum. Bendall SC, Nolan GP, et al. Science (New York, N.Y.). 2011 May 6; 332 (6030) :687-96.
- Topology based data analysis identifies a subgroup of breast cancers with a unique mutational profile and excellent survival. Nicolau M, Levine AJ, Carlsson G. Proc Natl Acad Sci U S A. 2011 Apr 11.
- Discovering Biological Progression Underlying Microarray Samples. Qiu P, Gentles AJ, Plevritis SK (2011) Discovering Biological Progression Underlying Microarray Samples. PLoS Comput Biol 7(4).
- Prospective separation of normal and leukemic stem cells based on differential expression of TIM3, a human acute myeloid leukemia stem cell marker. Jan M, Chao MP, Cha AC, et al. Proc Natl Acad Sci U S A. 2011 Mar 22;108(12):5009-14.
- Novel IL-21 signaling pathway up-regulates c-Myc and induces apoptosis of diffuse large B-cell lymphomas. Sarosiek KA, Malumbres R, Nechushtan H, et al. Blood. 2010 Jan 21;115(3):570-80.
- Calreticulin is the dominant pro-phagocytic signal on multiple human cancers and is counterbalanced by CD47. Chao MP, Jaiswal S, Weissman-Tsukamoto R, et al. Sci Transl Med. Dec 22 2010;2(63):63ra94
- Association of a leukemic stem cell gene expression signature with clinical outcomes in acute myeloid leukemia. JAMA. Gentles AJ, Plevritis SK, Majeti R, Alizadeh AA. Dec 22 2010;304(24):2706-2715
- Efficacy of bortezomib in a direct xenograft model of primary effusion lymphoma. Sarosiek KA, Cavallin LE, Bhatt S, et al. Proc Natl Acad Sci U S A. Jul 20 2010;107(29):13069-13074
- Computational solutions to large-scale data management and analysis. Schadt EE, Linderman MD, Sorenson J, Lee L, Nolan GP. Nat Rev Genet. 2010; Sep 11(9):647-57.
- MiDReG: a method of mining developmentally regulated genes using Boolean implications. Sahoo D, Seita J, Bhattacharya D, Inlay MA, Weissman IL, Plevritis SK, Dill DL. Proc Natl Acad Sci U S A. 2010; 107 (13): 5732-7
- Reducing the computational complexity of information theoretic approaches for reconstructing gene regulatory networks. Qiu P, Gentles AJ, Plevritis SK. J Comput Biol. 2010; 17 (2): 169-76
- Tyramide signal amplification for analysis of kinase activity by intracellular flow cytometry. Clutter MR, Heffner GC, Krutzik PO, Sachen KL, Nolan GP. Cytometry A. (2010)
- B-cell signaling networks reveal a negative prognostic human lymphoma cell subset that emerges during tumor progression. Irish JM, Myklebust JH, Alizadeh AA, Houot R, Sharman JP, Czerwinski DK, Nolan GP, Levy R. Proc Natl Acad Sci U S A. 2010; Jul 20;107(29):12747-54
- Novel mutations in the inhibitory adaptor protein LNK drive JAK-STAT signaling in patients with myeloproliferative neoplasms. Oh ST, Simonds EF, Jones C, Hale MB, Goltsev Y, Gibbs KD Jr, Merker JD, Zehnder JL, Nolan GP, Gotlib J. (2010)
- Characterization of patient specific signaling via augmentation of bayesian networks with disease and patient state nodes. Sachs K, Gentles AJ, Youland R, Itani S, Irish J, Nolan GP, Plevritis SK. (2009) Conf Proc IEEE Eng Med Biol Soc. 1:6624-7
- Web-based analysis and publication of flow cytometry experiments. Kotecha N, Krutzik PO, Irish JM. Curr Protoc Cytom. 2010;Chapter 10:Unit10 7.
- The interaction between Myc and Miz1 is required to antagonize TGFbeta-dependent autocrine signaling during lymphoma formation and maintenance. van Riggelen J, Müller J, Otto T, Beuger V, Yetil A, Choi PS, Kosan C, Möröy T, Felsher DW, Eilers M. Genes Dev. 2010 Jun 15;24 (12):1281-94.
- TGFbeta-dependent gene expression shows that senescence correlates with abortive differentiation along several lineages in Myc-induced lymphomas. Müller J, Samans B, Riggelen JV, Fagà G, Kn RP, Wei CL, Muller H, Amati B, Felsher DW, Eilers M. Cell Cycle. 2010 Dec 1;9 (23):4622-4626.
- CD4(+) T cells contribute to the remodeling of the microenvironment required for sustained tumor regression upon oncogene inactivation. Rakhra K, Bachireddy P, Zabuawala T, Zeiser R, Xu L, Kopelman A, Fan AC, Yang Q, Braunstein L, Crosby E, Ryeom S, Felsher DW. Cancer Cell. 2010 18(5):485-98.
Book Chapters:
- Kotecha N, Krutzik P, Irish J M, Web-based analysis and publication of flow cytometry experiments. Current Protocols in Cytometry 10.17.1-10.17.24, July (2010).
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