Rory Johnson

Research interests

Publications

• Long non-coding RNAs: definitions, functions, challenges and recommendations

  Nature Reviews Molecular Cell Biology · 2023 · https://doi.org/10.1038/s41580-022-00566-8

• GENCODE: reference annotation for the human and mouse genomes in 2023

  Nucleic Acids Research · 2022 · https://doi.org/10.1093/nar/gkac1071

• GENCODE 2021

  Nucleic Acids Research · 2020 · https://doi.org/10.1093/nar/gkaa1087

• GENCODE reference annotation for the human and mouse genomes

  Nucleic Acids Research · 2018 · https://doi.org/10.1093/nar/gky955

• An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

  Cell · 2018 · https://doi.org/10.1016/j.cell.2018.02.052

• Somatic Mutational Landscape of Splicing Factor Genes and Their Functional Consequences across 33 Cancer Types

  Cell Reports · 2018 · 10.1016/j.celrep.2018.01.088

• A Comprehensive Pan-Cancer Molecular Study of Gynecologic and Breast Cancers

  Cancer Cell · 2018 · https://doi.org/10.1016/j.ccell.2018.03.014

• The Immune Landscape of Cancer

  Immunity · 2018 · https://doi.org/10.1016/j.immuni.2018.03.023

• Towards a complete map of the human long non-coding RNA transcriptome

  Nature Reviews Genetics · 2018 · 10.1038/s41576-018-0017-y

• Comprehensive Molecular Characterization of the Hippo Signaling Pathway in Cancer

  Cell Reports · 2018 · 10.1016/j.celrep.2018.10.001

• lncRNA Epigenetic Landscape Analysis Identifies EPIC1 as an Oncogenic lncRNA that Interacts with MYC and Promotes Cell-Cycle Progression in Cancer

  Cancer Cell · 2018 · 10.1016/j.ccell.2018.03.006

• Oncogenic Signaling Pathways in The Cancer Genome Atlas

  Cell · 2018 · 10.1016/j.cell.2018.03.035

• Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer

  Cell · 2018 · 10.1016/j.cell.2018.03.022

• Comprehensive Characterization of Cancer Driver Genes and Mutations

  Cell · 2018 · 10.1016/j.cell.2018.02.060

• Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation

  Cell · 2018 · 10.1016/j.cell.2018.03.034

• Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas

  Cell Reports · 2018 · 10.1016/j.celrep.2018.03.076

• Genomic and Functional Approaches to Understanding Cancer Aneuploidy

  Cancer Cell · 2018 · 10.1016/j.ccell.2018.03.007

• Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

  Cell Reports · 2018 · 10.1016/j.celrep.2018.03.086

• Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients

  Cancer Cell · 2018 · 10.1016/j.ccell.2018.07.001

• Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines

  Cell Systems · 2018 · 10.1016/j.cels.2018.03.002

• Pathogenic Germline Variants in 10,389 Adult Cancers

  Cell · 2018 · 10.1016/j.cell.2018.03.039

• The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma

  Cell Reports · 2018 · 10.1016/j.celrep.2018.03.075

• Driver Fusions and Their Implications in the Development and Treatment of Human Cancers

  Cell Reports · 2018 · 10.1016/j.celrep.2018.03.050

• Comparative Molecular Analysis of Gastrointestinal Adenocarcinomas

  Cancer Cell · 2018 · 10.1016/j.ccell.2018.03.010

• The human transcriptome across tissues and individuals

  Science · 2015 · 10.1126/science.aaa0355

• The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression

  Genome Research · 2012 · https://doi.org/10.1101/gr.132159.111

• Landscape of transcription in human cells

  Nature · 2012 · https://doi.org/10.1038/nature11233

Current projects

No projects listed.