Comparative analysis of transcriptomic profile, histology, and IDH mutation for classification of gliomas

[1]  A. Kassambara,et al.  Drawing Survival Curves using 'ggplot2' [R package survminer version 0.4.8] , 2020 .

[2]  Klaus-Robert Müller,et al.  Machine learning analysis of DNA methylation profiles distinguishes primary lung squamous cell carcinomas from head and neck metastases , 2019, Science Translational Medicine.

[3]  Eric Topol,et al.  Deep Medicine: How Artificial Intelligence Can Make Healthcare Human Again , 2019 .

[4]  A. Bentivegna,et al.  Role of Notch Signaling Pathway in Glioblastoma Pathogenesis , 2019, Cancers.

[5]  G. Reifenberger,et al.  cIMPACT-NOW update 3: recommended diagnostic criteria for “Diffuse astrocytic glioma, IDH-wildtype, with molecular features of glioblastoma, WHO grade IV” , 2018, Acta Neuropathologica.

[6]  N. Razavian,et al.  Classification and mutation prediction from non–small cell lung cancer histopathology images using deep learning , 2018, Nature Medicine.

[7]  Leland McInnes,et al.  UMAP: Uniform Manifold Approximation and Projection , 2018, J. Open Source Softw..

[8]  Z. Tezak,et al.  Right data for right patient—a precisionFDA NCI–CPTAC Multi-omics Mislabeling Challenge , 2018, Nature Medicine.

[9]  S. Madhavan,et al.  The REMBRANDT study, a large collection of genomic data from brain cancer patients , 2018, Scientific Data.

[10]  N. Butowski,et al.  Primary brain tumours in adults , 2018, The Lancet.

[11]  M. Weller,et al.  Suppression of antitumor T cell immunity by the oncometabolite (R)-2-hydroxyglutarate , 2018, Nature Medicine.

[12]  Mary Goldman,et al.  The UCSC Xena platform for public and private cancer genomics data visualization and interpretation , 2018, bioRxiv.

[13]  Till Acker,et al.  DNA methylation-based classification of central nervous system tumours , 2018, Nature.

[14]  Leland McInnes,et al.  UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction , 2018, ArXiv.

[15]  Thawfeek M. Varusai,et al.  The Reactome Pathway Knowledgebase , 2017, Nucleic acids research.

[16]  Andrew H. Beck,et al.  Diagnostic Assessment of Deep Learning Algorithms for Detection of Lymph Node Metastases in Women With Breast Cancer , 2017, JAMA.

[17]  Jacob M. Keaton,et al.  Population Stratification in Genetic Association Studies , 2017, Current protocols in human genetics.

[18]  Edward F. Chang,et al.  Tumor Evolution of Glioma-Intrinsic Gene Expression Subtypes Associates with Immunological Changes in the Microenvironment. , 2017, Cancer cell.

[19]  Christopher. Simons,et al.  Machine learning with Python , 2017 .

[20]  Basten L. Snoek,et al.  reGenotyper: Detecting mislabeled samples in genetic data , 2017, PloS one.

[21]  Alexey Sergushichev,et al.  An algorithm for fast preranked gene set enrichment analysis using cumulative statistic calculation , 2016 .

[22]  Subha Madhavan,et al.  G-DOC Plus – an integrative bioinformatics platform for precision medicine , 2016, BMC Bioinformatics.

[23]  Steven J. M. Jones,et al.  Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma , 2016, Cell.

[24]  Henning Hermjakob,et al.  The Reactome pathway Knowledgebase , 2015, Nucleic acids research.

[25]  Joel H. Saltz,et al.  Patch-Based Convolutional Neural Network for Whole Slide Tissue Image Classification , 2015, 2016 IEEE Conference on Computer Vision and Pattern Recognition (CVPR).

[26]  Steven J. M. Jones,et al.  Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas. , 2015, The New England journal of medicine.

[27]  Alexander R. Pico,et al.  Glioma Groups Based on 1p/19q, IDH, and TERT Promoter Mutations in Tumors. , 2015, The New England journal of medicine.

[28]  D. Ellison.  Multiple Molecular Data Sets and the Classification of Adult Diffuse Gliomas. , 2015, The New England journal of medicine.

[29]  Matthew E. Ritchie,et al.  limma powers differential expression analyses for RNA-sequencing and microarray studies , 2015, Nucleic acids research.

[30]  G. Reifenberger,et al.  Glioma , 2015, Nature Reviews Disease Primers.

[31]  Martin J. van den Bent,et al.  Practice changing mature results of RTOG study 9802: another positive PCV trial makes adjuvant chemotherapy part of standard of care in low-grade glioma , 2014 .

[32]  George Michailidis,et al.  Critical limitations of consensus clustering in class discovery , 2014, Scientific Reports.

[33]  H. Olsson.  Heuristics and Biases , 2013 .

[34]  G. Getz,et al.  Inferring tumour purity and stromal and immune cell admixture from expression data , 2013, Nature Communications.

[35]  Winand N M Dinjens,et al.  Adjuvant procarbazine, lomustine, and vincristine chemotherapy in newly diagnosed anaplastic oligodendroglioma: long-term follow-up of EORTC brain tumor group study 26951. , 2013, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[36]  A. McKenna,et al.  Absolute quantification of somatic DNA alterations in human cancer , 2012, Nature Biotechnology.

[37]  Yuchen Jiao,et al.  Mutations in CIC and FUBP1 Contribute to Human Oligodendroglioma , 2011, Science.

[38]  Gaël Varoquaux,et al.  Scikit-learn: Machine Learning in Python , 2011, J. Mach. Learn. Res..

[39]  Rafael A. Irizarry,et al.  A framework for oligonucleotide microarray preprocessing , 2010, Bioinform..

[40]  Martin J. Bent,et al.  Interobserver variation of the histopathological diagnosis in clinical trials on glioma: a clinician’s perspective , 2010, Acta Neuropathologica.

[41]  S. Gabriel,et al.  Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1. , 2010, Cancer cell.

[42]  R. McLendon,et al.  IDH1 and IDH2 mutations in gliomas. , 2009, The New England journal of medicine.

[43]  D. Busam,et al.  An Integrated Genomic Analysis of Human Glioblastoma Multiforme , 2008, Science.

[44]  Elizabeth Eisenhauer,et al.  Nomograms for predicting survival of patients with newly diagnosed glioblastoma: prognostic factor analysis of EORTC and NCIC trial 26981-22981/CE.3. , 2008, The Lancet. Oncology.

[45]  B. Scheithauer,et al.  The 2007 WHO classification of tumours of the central nervous system , 2007, Acta Neuropathologica.

[46]  D. Louis.  WHO classification of tumours of the central nervous system , 2007 .

[47]  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.

[48]  Jill P. Mesirov,et al.  Consensus Clustering: A Resampling-Based Method for Class Discovery and Visualization of Gene Expression Microarray Data , 2003, Machine Learning.

[49]  Jill P. Mesirov,et al.  A resampling-based method for class discovery and visualization of gene expression microarray data , 2003 .

[50]  J. Edmeads,et al.  The Clinician's Perspective , 2001, Headache.

[51]  Scar,et al.  Inactivation of the DNA-repair gene MGMT and the clinical response of gliomas to alkylating agents. , 2000, The New England journal of medicine.

[52]  Eric M. Morrow,et al.  rax, Hes1, and notch1 Promote the Formation of Müller Glia by Postnatal Retinal Progenitor Cells , 2000, Neuron.

[53]  Hans-Peter Kriegel,et al.  A Density-Based Algorithm for Discovering Clusters in Large Spatial Databases with Noise , 1996, KDD.

[54]  D. Louis,et al.  Shared Allelic Losses on Chromosomes 1p and 19q Suggest a Common Origin of Oligodendroglioma and Oligoastrocytoma , 1995, Journal of neuropathology and experimental neurology.

[55]  Y. Benjamini,et al.  Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .

[56]  G. Reifenberger,et al.  Molecular genetic analysis of oligodendroglial tumors shows preferential allelic deletions on 19q and 1p. , 1994, The American journal of pathology.

[57]  P. Grambsch,et al.  A Package for Survival Analysis in S , 1994 .

[58]  I. Petersen,et al.  Evidence for a tumor suppressor gene on chromosome 19q associated with human astrocytomas, oligodendrogliomas, and mixed gliomas. , 1992, Cancer research.

[59]  J. Cairncross,et al.  Successful chemotherapy for newly diagnosed aggressive oligodendroglioma , 1990, Annals of neurology.

[60]  R. Barnard,et al.  The classification of tumours of the central nervous system. , 1982, Neuropathology and applied neurobiology.

[61]  A. Tversky,et al.  Judgment under Uncertainty: Heuristics and Biases , 1974, Science.

[62]  E. B. Jackson,et al.  Effects of Colchicine and Radiation on Growth of Normal Tissues and Tumors , 1940 .