Gene-network analysis predicts clinical response to immunotherapy in patients affected by NSCLC.

[1]  F. Gao,et al.  Natural killer cells: a promising immunotherapy for cancer , 2022, Journal of Translational Medicine.

[2]  F. de Marinis,et al.  Gene network Analysis Defines a Subgroup of Small Cell Lung Cancer patients With Short Survival. , 2022, Clinical lung cancer.

[3]  Joe Y. Chang,et al.  Non-Small Cell Lung Cancer, Version 3.2022, NCCN Clinical Practice Guidelines in Oncology. , 2022, Journal of the National Comprehensive Cancer Network : JNCCN.

[4]  Z. Qiu,et al.  Chromatin remodeling induced by ARID1A loss in lung cancer promotes glycolysis and confers JQ1 vulnerability. , 2022, Cancer research.

[5]  J. Wolf,et al.  Comprehensive Analysis of TP53 and KEAP1 Mutations and their Impact on Survival in Localized and Advanced Stage Non-Small Cell Lung Cancer. , 2021, Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer.

[6]  Chunmei Wang,et al.  Chromatin remodeler ARID1A binds IRF3 to selectively induce antiviral interferon production in macrophages , 2021, Cell Death & Disease.

[7]  A. Addeo,et al.  TMB or not TMB as a biomarker: That is the question. , 2021, Critical reviews in oncology/hematology.

[8]  K. Rock,et al.  Cancer Immune Evasion Through Loss of MHC Class I Antigen Presentation , 2021, Frontiers in Immunology.

[9]  C. Porta,et al.  A multiparametric approach to improve the prediction of response to immunotherapy in patients with metastatic NSCLC , 2020, Cancer Immunology, Immunotherapy.

[10]  J. Carretero,et al.  Comprehensive Analysis of SWI/SNF Inactivation in Lung Adenocarcinoma Cell Models , 2020, Cancers.

[11]  G. Giaccone,et al.  Atezolizumab for First-Line Treatment of PD-L1-Selected Patients with NSCLC. , 2020, The New England journal of medicine.

[12]  T. Chan,et al.  The FDA approval of pembrolizumab for adult and pediatric patients with tumor mutational burden (TMB) ≥10: a decision centered on empowering patients and their physicians. , 2020, Annals of oncology : official journal of the European Society for Medical Oncology.

[13]  Lauren L. Hsu,et al.  Impact of Data Preprocessing on Integrative Matrix Factorization of Single Cell Data , 2020, Frontiers in Oncology.

[14]  M. Galsky,et al.  ARID1A mutation plus CXCL13 expression act as combinatorial biomarkers to predict responses to immune checkpoint therapy in mUCC , 2020, Science Translational Medicine.

[15]  Guangming Wu,et al.  Histone demethylase KDM6A promotes somatic cell reprogramming by epigenetically regulating the PTEN and IL‐6 signal pathways , 2020, Stem cells.

[16]  S. Postel-Vinay,et al.  Exploiting epigenetic vulnerabilities in solid tumors: novel therapeutic opportunities in the treatment of SWI/SNF-defective cancers. , 2020, Seminars in cancer biology.

[17]  Jeffrey S. Morris,et al.  ARID1A mutation to define an immunologically active subgroup in patients with microsatellite-stable colorectal cancer. , 2020 .

[18]  J. Sicklick,et al.  ARID1A alterations function as a biomarker for longer progression-free survival after anti-PD-1/PD-L1 immunotherapy , 2020, Journal for ImmunoTherapy of Cancer.

[19]  G. Peng,et al.  ARID1A deficiency and immune checkpoint blockade therapy: from mechanisms to clinical application. , 2020, Cancer letters.

[20]  Runan Yao,et al.  ShinyGO: a graphical gene-set enrichment tool for animals and plants , 2019, Bioinform..

[21]  K. Syrigos,et al.  Nivolumab plus Ipilimumab in Advanced Non-Small-Cell Lung Cancer. , 2019, The New England journal of medicine.

[22]  J. Heymach,et al.  Co-occurring genomic alterations in non-small-cell lung cancer biology and therapy , 2019, Nature Reviews Cancer.

[23]  S. Fröhling,et al.  Spatial and temporal heterogeneity of panel-based tumor mutational burden (TMB) in pulmonary adenocarcinoma: separating biology from technical artifacts. , 2019, Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer.

[24]  J. Kaifi,et al.  PD-L1 Expression with Epithelial Mesenchymal Transition of Circulating Tumor Cells Is Associated with Poor Survival in Curatively Resected Non-Small Cell Lung Cancer , 2019, Cancers.

[25]  T. Ideker,et al.  Identifying Epistasis in Cancer Genomes: A Delicate Affair , 2019, Cell.

[26]  C. Leonetti,et al.  Cell communication and signaling: how to turn bad language into positive one , 2019, Journal of Experimental & Clinical Cancer Research.

[27]  K. Kerr,et al.  Comparing and contrasting predictive biomarkers for immunotherapy and targeted therapy of NSCLC , 2019, Nature Reviews Clinical Oncology.

[28]  C. Brennan,et al.  Tumor mutational load predicts survival after immunotherapy across multiple cancer types , 2019, Nature Genetics.

[29]  A. Tafreshi,et al.  Updated Analysis of KEYNOTE-024: Pembrolizumab Versus Platinum-Based Chemotherapy for Advanced Non-Small-Cell Lung Cancer With PD-L1 Tumor Proportion Score of 50% or Greater. , 2019, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[30]  T A Chan,et al.  Development of tumor mutation burden as an immunotherapy biomarker: utility for the oncology clinic , 2018, Annals of oncology : official journal of the European Society for Medical Oncology.

[31]  Sandra Healy,et al.  The role of the unfolded protein response in cancer progression: From oncogenesis to chemoresistance , 2018, Biology of the cell.

[32]  Yassen Assenov,et al.  Maftools: efficient and comprehensive analysis of somatic variants in cancer , 2018, Genome research.

[33]  P. V. Van Schil,et al.  Metastatic non-small cell lung cancer: ESMO Clinical Practice Guidelines for diagnosis, treatment and follow-up. , 2018, Annals of oncology : official journal of the European Society for Medical Oncology.

[34]  L. Kma,et al.  Dysregulation of Glucose Metabolism by Oncogenes and Tumor Suppressors in Cancer Cells , 2018, Asian Pacific journal of cancer prevention : APJCP.

[35]  T. Fukumoto,et al.  SWI/SNF Complexes in Ovarian Cancer: Mechanistic Insights and Therapeutic Implications , 2018, Molecular Cancer Research.

[36]  G. Getz,et al.  Genomic correlates of response to immune checkpoint blockade in microsatellite-stable solid tumors , 2018, Nature Genetics.

[37]  Arun Ahuja,et al.  Genomic Features of Response to Combination Immunotherapy in Patients with Advanced Non-Small-Cell Lung Cancer , 2018, Cancer cell.

[38]  B D Satoto,et al.  Integration K-Means Clustering Method and Elbow Method For Identification of The Best Customer Profile Cluster , 2018, IOP Conference Series: Materials Science and Engineering.

[39]  S. Gettinger,et al.  Nivolumab versus docetaxel in previously treated advanced non-small-cell lung cancer (CheckMate 017 and CheckMate 057): 3-year update and outcomes in patients with liver metastases , 2018, Annals of oncology : official journal of the European Society for Medical Oncology.

[40]  Ahmet Zehir,et al.  Molecular Determinants of Response to Anti-Programmed Cell Death (PD)-1 and Anti-Programmed Death-Ligand 1 (PD-L1) Blockade in Patients With Non-Small-Cell Lung Cancer Profiled With Targeted Next-Generation Sequencing. , 2018, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[41]  E. Felip,et al.  Nivolumab Versus Docetaxel in Previously Treated Patients With Advanced Non-Small-Cell Lung Cancer: Two-Year Outcomes From Two Randomized, Open-Label, Phase III Trials (CheckMate 017 and CheckMate 057). , 2017, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[42]  Devin K Porter,et al.  Chromatin accessibility underlies synthetic lethality of SWI/SNF subunits in ARID1A-mutant cancers , 2017, eLife.

[43]  Tarek Mekhail,et al.  Durvalumab after Chemoradiotherapy in Stage III Non–Small‐Cell Lung Cancer , 2017, The New England journal of medicine.

[44]  M. Wiese,et al.  Predicting response and toxicity to immune checkpoint inhibitors using routinely available blood and clinical markers , 2017, British Journal of Cancer.

[45]  P. Stephens,et al.  Tumor Mutational Burden as an Independent Predictor of Response to Immunotherapy in Diverse Cancers , 2017, Molecular Cancer Therapeutics.

[46]  N. Schultz,et al.  Conditional Selection of Genomic Alterations Dictates Cancer Evolution and Oncogenic Dependencies. , 2017, Cancer cell.

[47]  Dan Han,et al.  Methyltransferase SETD2-Mediated Methylation of STAT1 Is Critical for Interferon Antiviral Activity , 2017, Cell.

[48]  M. Socinski,et al.  First‐Line Nivolumab in Stage IV or Recurrent Non–Small‐Cell Lung Cancer , 2017, The New England journal of medicine.

[49]  Janet Iwasa,et al.  Mechanisms of action and regulation of ATP-dependent chromatin-remodelling complexes , 2017, Nature Reviews Molecular Cell Biology.

[50]  S. Wiemann,et al.  Co-Inflammatory Roles of TGFβ1 in the Presence of TNFα Drive a Pro-inflammatory Fate in Mesenchymal Stem Cells , 2017, Front. Immunol..

[51]  Nicolai J. Birkbak,et al.  Tracking the Evolution of Non‐Small‐Cell Lung Cancer , 2017, The New England journal of medicine.

[52]  R. Weinberg,et al.  Epithelial-to-Mesenchymal Transition Contributes to Immunosuppression in Breast Carcinomas. , 2017, Cancer research.

[53]  T. Rynearson,et al.  Evidence for environmental and ecological selection in a microbe with no geographic limits to gene flow , 2017, Proceedings of the National Academy of Sciences.

[54]  Carlos Barrios,et al.  Atezolizumab versus docetaxel in patients with previously treated non-small-cell lung cancer (OAK): a phase 3, open-label, multicentre randomised controlled trial , 2017, The Lancet.

[55]  Y. Shentu,et al.  Pembrolizumab versus Chemotherapy for PD-L1-Positive Non-Small-Cell Lung Cancer. , 2016, The New England journal of medicine.

[56]  Jorge Cadima,et al.  Principal component analysis: a review and recent developments , 2016, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences.

[57]  Y. Shentu,et al.  Pembrolizumab versus docetaxel for previously treated, PD-L1-positive, advanced non-small-cell lung cancer (KEYNOTE-010): a randomised controlled trial , 2016, The Lancet.

[58]  Gianluca Bontempi,et al.  TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data , 2015, Nucleic acids research.

[59]  J. Mesirov,et al.  The Molecular Signatures Database Hallmark Gene Set Collection , 2015 .

[60]  Olfat Al-Harazi,et al.  Bidirectional crosstalk between PD-L1 expression and epithelial to mesenchymal transition: Significance in claudin-low breast cancer cells , 2015, Molecular Cancer.

[61]  Martin L. Miller,et al.  Mutational landscape determines sensitivity to PD-1 blockade in non–small cell lung cancer , 2015, Science.

[62]  K. Tomczak,et al.  The Cancer Genome Atlas (TCGA): an immeasurable source of knowledge , 2015, Contemporary oncology.

[63]  Steven J. M. Jones,et al.  Comprehensive molecular profiling of lung adenocarcinoma , 2014, Nature.

[64]  J. Wolf,et al.  Widespread evidence for incipient ecological speciation: a meta-analysis of isolation-by-ecology. , 2013, Ecology letters.

[65]  Benjamin E. Gross,et al.  Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal , 2013, Science Signaling.

[66]  Patricio A. Vela,et al.  A Comparative Study of Efficient Initialization Methods for the K-Means Clustering Algorithm , 2012, Expert Syst. Appl..

[67]  Benjamin E. Gross,et al.  The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. , 2012, Cancer discovery.

[68]  Amit Awasthi,et al.  IL-6 controls Th17 immunity in vivo by inhibiting the conversion of conventional T cells into Foxp3+ regulatory T cells , 2008, Proceedings of the National Academy of Sciences.

[69]  M. Neurath,et al.  Cutting Edge: Trans-Signaling via the Soluble IL-6R Abrogates the Induction of FoxP3 in Naive CD4+CD25− T Cells1 , 2007, The Journal of Immunology.

[70]  Jenine K. Harris,et al.  Network Analysis in Public Health: History, Methods, and Applications , 2022 .

[71]  H. Weiner,et al.  Reciprocal developmental pathways for the generation of pathogenic effector TH17 and regulatory T cells , 2006, Nature.

[72]  Douglas Steinley,et al.  K-means clustering: a half-century synthesis. , 2006, The British journal of mathematical and statistical psychology.

[73]  Pablo Tamayo,et al.  Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[74]  P. Bonacich.  Power and Centrality: A Family of Measures , 1987, American Journal of Sociology.

[75]  S. P. Lloyd,et al.  Least squares quantization in PCM , 1982, IEEE Trans. Inf. Theory.

[76]  Sofia C. Nunes.  Tumor Microenvironment - Selective Pressures Boosting Cancer Progression. , 2020, Advances in experimental medicine and biology.

[77]  MA Katharina Schwarze BSc,et al.  Are whole-exome and whole-genome sequencing approaches cost-effective? A systematic review of the literature , 2018, Genetics in Medicine.

[78]  Jian Ye,et al.  The role and regulation of human Th17 cells in tumor immunity. , 2013, The American journal of pathology.

[79]  Gábor Csárdi,et al.  The igraph software package for complex network research , 2006 .