Genotyping of Transcriptomes links somatic mutations and cell identity
暂无分享,去创建一个
Joseph M. Scandura | Alessandro Pastore | Raul Rabadan | Omar Abdel-Wahab | Juan R. Cubillos-Ruiz | Wayne Tam | Peter Smibert | Nathaniel D. Omans | Dan A. Landau | Kyu-Tae Kim | Ryan Brand | R. Rabadán | D. Landau | O. Abdel-Wahab | W. Tam | Peter Smibert | E. Harrington | R. Hoffman | A. Pastore | J. Scandura | R. Chaligné | Xiaoguang Dai | C. Sheridan | J. Cubillos-Ruiz | Justin Taylor | Franco Izzo | Justin Taylor | Alicia Alonso | Ronald Hoffman | F. Izzo | Anna S. Nam | Ronan Chaligne | Chelston Ang | Robert M. Myers | Ghaith Abu-Zeinah | Caroline Sheridan | Marisa Mariani | Xiaoguang Dai | Eoghan Harrington | Chelston R Ang | Kyu-Tae Kim | G. Abu-Zeinah | A. Alonso | Marisa Mariani | W. Tam | Ryan M. Brand | Caroline Sheridan | Franco Izzo | Ryan Brand
[1] L. Glimcher,et al. XBP-1 Regulates a Subset of Endoplasmic Reticulum Resident Chaperone Genes in the Unfolded Protein Response , 2003, Molecular and Cellular Biology.
[2] Hedi Peterson,et al. g:Profiler—a web server for functional interpretation of gene lists (2016 update) , 2016, Nucleic Acids Res..
[3] Adam Bagg,et al. Oligomonocytic chronic myelomonocytic leukemia (chronic myelomonocytic leukemia without absolute monocytosis) displays a similar clinicopathologic and mutational profile to classical chronic myelomonocytic leukemia , 2017, Modern Pathology.
[4] Charles H. Yoon,et al. Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq , 2016, Science.
[5] H. Saito,et al. The production of transforming growth factor-beta in acute megakaryoblastic leukemia and its possible implications in myelofibrosis. , 1990, Blood.
[6] C. Hetz,et al. The Unfolded Protein Response and Cell Fate Control. , 2017, Molecular cell.
[7] Michael Karin,et al. IKK/NF-κB signaling: balancing life and death – a new approach to cancer therapy , 2005 .
[8] B. Bernstein,et al. Dual Targeting of Oncogenic Activation and Inflammatory Signaling Increases Therapeutic Efficacy in Myeloproliferative Neoplasms. , 2018, Cancer cell.
[9] E. Dermitzakis,et al. Distinct clinical phenotypes associated with JAK2V617F reflect differential STAT1 signaling. , 2010, Cancer cell.
[10] Paul Hoffman,et al. Integrating single-cell transcriptomic data across different conditions, technologies, and species , 2018, Nature Biotechnology.
[11] Michael I. Jordan,et al. Deep Generative Modeling for Single-cell Transcriptomics , 2018, Nature Methods.
[12] R. Sandberg,et al. Single-cell transcriptomics uncovers distinct molecular signatures of stem cells in chronic myeloid leukemia , 2017, Nature Medicine.
[13] Heng Li,et al. Minimap2: pairwise alignment for nucleotide sequences , 2017, Bioinform..
[14] Paul J. Hoffman,et al. Comprehensive Integration of Single-Cell Data , 2018, Cell.
[15] Andy Liaw,et al. Classification and Regression by randomForest , 2007 .
[16] C. Pecquet,et al. Calreticulin mutants in mice induce an MPL-dependent thrombocytosis with frequent progression to myelofibrosis. , 2016, Blood.
[17] Cole Trapnell,et al. On the design of CRISPR-based single cell molecular screens , 2018, Nature Methods.
[18] J. D. Fitzpatrick,et al. Somatic CALR mutations in myeloproliferative neoplasms with nonmutated JAK2. , 2013, The New England journal of medicine.
[19] Michelle C. Chen,et al. Physiologic Expression of Sf3b1(K700E) Causes Impaired Erythropoiesis, Aberrant Splicing, and Sensitivity to Therapeutic Spliceosome Modulation. , 2016, Cancer cell.
[20] T. Golub,et al. Integrated genomic analysis illustrates the central role of JAK-STAT pathway activation in myeloproliferative neoplasm pathogenesis. , 2014, Blood.
[21] Li Ding,et al. Comprehensive Characterization of Cancer Driver Genes and Mutations (vol 173, 371.e1, 2018) , 2018 .
[22] K. Kinzler,et al. Cancer Genome Landscapes , 2013, Science.
[23] E. Birney,et al. Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt , 2009, Nature Protocols.
[24] A. Green,et al. The JAK-STAT signaling pathway is differentially activated in CALR-positive compared with JAK2V617F-positive ET patients. , 2015, Blood.
[25] Allon M. Klein,et al. Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells , 2015, Cell.
[26] Juan R. Cubillos-Ruiz,et al. ER Stress Sensor XBP1 Controls Anti-tumor Immunity by Disrupting Dendritic Cell Homeostasis , 2015, Cell.
[27] D. Neuberg,et al. The evolutionary landscape of chronic lymphocytic leukemia treated with ibrutinib targeted therapy , 2017, Nature Communications.
[28] Stephen R Quake,et al. Single-cell multimodal profiling reveals cellular epigenetic heterogeneity , 2016, Nature Methods.
[29] U. McDermott,et al. A novel signalling screen demonstrates that CALR mutations activate essential MAPK signalling and facilitate megakaryocyte differentiation , 2016, Leukemia.
[30] E. Pronier,et al. Targeting the CALR interactome in myeloproliferative neoplasms. , 2018, JCI insight.
[31] L. Steinmetz,et al. Human haematopoietic stem cell lineage commitment is a continuous process , 2017, Nature Cell Biology.
[32] Mingming Jia,et al. COSMIC: somatic cancer genetics at high-resolution , 2016, Nucleic Acids Res..
[33] B. Ebert,et al. The genetics of myelodysplastic syndrome: from clonal haematopoiesis to secondary leukaemia , 2016, Nature Reviews Cancer.
[34] R. Kaufman,et al. ATF6alpha optimizes long-term endoplasmic reticulum function to protect cells from chronic stress. , 2007, Developmental cell.
[35] R. Tiu,et al. Mutated calreticulin retains structurally disordered C terminus that cannot bind Ca2+: some mechanistic and therapeutic implications , 2014, Blood Cancer Journal.
[36] L. Pachter,et al. A discriminative learning approach to differential expression analysis for single-cell RNA-seq , 2019, Nature Methods.
[37] W. Park,et al. Allelic imbalance of somatic mutations in cancer genomes and transcriptomes , 2017, Scientific Reports.
[38] Mollie E. Brooks,et al. Generalized linear mixed models: a practical guide for ecology and evolution. , 2009, Trends in ecology & evolution.
[39] G. Superti-Furga,et al. Somatic mutations of calreticulin in myeloproliferative neoplasms. , 2013, The New England journal of medicine.
[40] Martin A. Nowak,et al. Mutations driving CLL and their evolution in progression and relapse , 2015, Nature.
[41] M. Rubin,et al. SOX2 promotes lineage plasticity and antiandrogen resistance in TP53- and RB1-deficient prostate cancer , 2017, Science.
[42] C. Pecquet,et al. Thrombopoietin receptor is required for the oncogenic function of CALR mutants , 2016, Leukemia.
[43] Grace X. Y. Zheng,et al. Massively parallel digital transcriptional profiling of single cells , 2016, Nature Communications.
[44] E. Laurenti,et al. The unfolded protein response governs integrity of the haematopoietic stem-cell pool during stress , 2014, Nature.
[45] Y. Niitsu,et al. The production of transforming growth factor-beta in acute megakaryoblastic leukemia and its possible implications in myelofibrosis , 1990 .
[46] A. Baldwin,et al. Deletion of the NF-κB subunit p65/RelA in the hematopoietic compartment leads to defects in hematopoietic stem cell function. , 2013, Blood.
[47] Simon Kasif,et al. Reconstructing and Reprogramming the Tumor-Propagating Potential of Glioblastoma Stem-like Cells , 2014, Cell.
[48] A. Regev,et al. Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis , 2018, Science.
[49] A. Yen,et al. Human megakaryocyte stimulation of proliferation of bone marrow fibroblasts. , 1981, Blood.
[50] M. Cazzola,et al. CALR mutational status identifies different disease subtypes of essential thrombocythemia showing distinct expression profiles , 2017, Blood Cancer Journal.
[51] Gonçalo R. Abecasis,et al. The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..
[52] C. Pecquet,et al. Oncogenic activation of MPL/thrombopoietin receptor by 17 mutations at W515: implications for myeloproliferative neoplasms , 2016, Leukemia.
[53] B. Bernstein,et al. Dual Targeting of Oncogenic Activation and Inflammatory Signaling Increases Therapeutic Efficacy in Myeloproliferative Neoplasms. , 2018, Cancer cell.
[54] Steven J. M. Jones,et al. Comprehensive Characterization of Cancer Driver Genes and Mutations , 2018, Cell.
[55] A. McKenna,et al. Evolution and Impact of Subclonal Mutations in Chronic Lymphocytic Leukemia , 2012, Cell.
[56] F. Al-Shahrour,et al. Mutant Calreticulin Requires Both Its Mutant C-terminus and the Thrombopoietin Receptor for Oncogenic Transformation. , 2016, Cancer discovery.
[57] N. Mahmud,et al. Pivotal contributions of megakaryocytes to the biology of idiopathic myelofibrosis. , 2007, Blood.
[58] Evan Z. Macosko,et al. Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets , 2015, Cell.
[59] Jeanne Kowalski,et al. Microarray and Serial Analysis of Gene Expression Analyses Identify Known and Novel Transcripts Overexpressed in Hematopoietic Stem Cells , 2004, Cancer Research.
[60] R. Silver,et al. Myeloproliferative Neoplasm (MPN) Driver Mutations Are Enriched during Hematopoietic Stem Cell Differentiation in Patterns That Correlate with Clinical Phenotype and Treatment Response , 2018, Blood.
[61] Charles G. Danko,et al. Simultaneous multiplexed amplicon sequencing and transcriptome profiling in single cells , 2018, bioRxiv.
[62] Shuqiang Li,et al. Clonal evolution in patients with chronic lymphocytic leukaemia developing resistance to BTK inhibition , 2016, Nature Communications.
[63] Cole Trapnell,et al. The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells , 2014, Nature Biotechnology.
[64] A. Regev,et al. Spatial reconstruction of single-cell gene expression , 2015, Nature Biotechnology.
[65] K. Mori,et al. XBP1 mRNA Is Induced by ATF6 and Spliced by IRE1 in Response to ER Stress to Produce a Highly Active Transcription Factor , 2001, Cell.
[66] R. Sandberg,et al. Random monoallelic expression of autosomal genes: stochastic transcription and allele-level regulation , 2015, Nature Reviews Genetics.