Integration of machine learning and genome-scale metabolic modeling identifies multi-omics biomarkers for radiation resistance

Personalized Genome-Scale Metabolic Models Identify Targets of Redox Metabolism in Radiation-Resistant Tumors

(2021) Joshua E. Lewis et al.   Cell Systems

Genomics models in radiotherapy: From mechanistic to machine learning

(2020) John Kang et al.   MEDICAL PHYSICS

A biochemically-interpretable machine learning classifier for microbial GWAS

(2020) Erol S. Kavvas et al.   Nature Communications

Stacked Generalization with Applicability Domain Outperforms Simple QSAR on in Vitro Toxicological Data

(2019) Ingrid Grenet et al.   Journal of Chemical Information and Modeling

A White-Box Machine Learning Approach for Revealing Antibiotic Mechanisms of Action

(2019) Jason H. Yang et al.   CELL

The landscape of cancer cell line metabolism

(2019) Haoxin Li et al.   NATURE MEDICINE

Identification of a Radiosensitivity Molecular Signature Induced by Enzalutamide in Hormone-sensitive and Hormone-resistant Prostate Cancer Cells

(2019) Maryam Ghashghaei et al.   Scientific Reports

Machine and deep learning meet genome-scale metabolic modeling

(2019) Guido Zampieri et al.   PLoS Computational Biology

RadiationGeneSigDB: a database of oxic and hypoxic radiation response gene signatures and their utility in pre-clinical research

(2019) Venkata SK Manem et al.   BRITISH JOURNAL OF RADIOLOGY

Key challenges for delivering clinical impact with artificial intelligence

(2019) Christopher J. Kelly et al.   BMC Medicine

Mouse Phenome Database: a data repository and analysis suite for curated primary mouse phenotype data

(2019) Molly A Bogue et al.   NUCLEIC ACIDS RESEARCH

Ionizing Radiation induction of cholesterol biosynthesis in Lung tissue

(2019) Erica Werner et al.   Scientific Reports

Historical Biobanks in Breast Cancer Metabolomics— Challenges and Opportunities

(2019) Torfinn S. Madssen et al.   Metabolites

PanCancer insights from The Cancer Genome Atlas: the pathologist's perspective

(2018) Lee AD Cooper et al.   JOURNAL OF PATHOLOGY

Machine learning algorithms for outcome prediction in (chemo)radiotherapy: An empirical comparison of classifiers

(2018) Timo M. Deist et al.   MEDICAL PHYSICS

Recon3D enables a three-dimensional view of gene variation in human metabolism

(2018) Elizabeth Brunk et al.   NATURE BIOTECHNOLOGY

Predicting cancer outcomes from histology and genomics using convolutional networks

(2018) Pooya Mobadersany et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Adaptive radiation therapy

(2018) Di Yan et al.   Zeitschrift fur Medizinische Physik

Simvastatin Sensitizes Radioresistant Prostate Cancer Cells by Compromising DNA Double-Strand Break Repair

(2018) Yu-An Chen et al.   Frontiers in Pharmacology

Ensemble of machine learning algorithms using the stacked generalization approach to estimate the warfarin dose

(2018) Zhiyuan Ma et al.   PLoS One

Effects of ionizing radiation on DNA methylation: from experimental biology to clinical applications

(2017) Isabelle R. Miousse et al.   INTERNATIONAL JOURNAL OF RADIATION BIOLOGY

Improved prediction accuracy for disease risk mapping using Gaussian process stacked generalization

(2017) Samir Bhatt et al.   Journal of the Royal Society Interface

Genome scale metabolic modeling of cancer

(2017) Avlant Nilsson et al.   METABOLIC ENGINEERING

HMG-CoA Reductase Inhibition Delays DNA Repair and Promotes Senescence After Tumor Irradiation

(2017) Elena V. Efimova et al.   MOLECULAR CANCER THERAPEUTICS

Differential radiation response between normal astrocytes and glioma cells revealed by comparative transcriptome analysis

(2017) Liang Gong et al.   OncoTargets and Therapy

Function of capric acid in cyclophosphamide-induced intestinal inflammation, oxidative stress, and barrier function in pigs

(2017) Sang In Lee et al.   Scientific Reports

mRNA and methylation profiling of radioresistant esophageal cancer cells: the involvement of Sall2 in acquired aggressive phenotypes

(2017) Judong Luo et al.   Journal of Cancer

Genome-Scale Modeling of NADPH-Driven β-Lapachone Sensitization in Head and Neck Squamous Cell Carcinoma

(2017) Joshua E. Lewis et al.   ANTIOXIDANTS & REDOX SIGNALING

Radiation-induced changes in the glycome of endothelial cells with functional consequences

(2017) Cyprien Jaillet et al.   Scientific Reports

A genetic basis for the variation in the vulnerability of cancer to DNA damage

(2016) Brian D. Yard et al.   Nature Communications

Alternative preprocessing of RNA-Sequencing data in The Cancer Genome Atlas leads to improved analysis results

(2015) Mumtahena Rahman et al.   BIOINFORMATICS

Transient elevation of glycolysis confers radio-resistance by facilitating DNA repair in cells

(2015) Anant Narayan Bhatt et al.   BMC CANCER

Therapeutic Implications for Overcoming Radiation Resistance in Cancer Therapy

(2015) Byeong Kim et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Machine Learning Approaches for Predicting Radiation Therapy Outcomes: A Clinician's Perspective

(2015) John Kang et al.   INTERNATIONAL JOURNAL OF RADIATION ONCOLOGY BIOLOGY PHYSICS

Energy Metabolism in a Matched Model of Radiation Resistance for Head and Neck Squamous Cell Cancer

(2015) Jade Mims et al.   RADIATION RESEARCH

Tumor Cells Switch to Mitochondrial Oxidative Phosphorylation under Radiation via mTOR-Mediated Hexokinase II Inhibition - A Warburg-Reversing Effect

(2015) Chung-Ling Lu et al.   PLoS One

Aspirin improves outcome in high risk prostate cancer patients treated with radiation therapy

(2014) Corbin D Jacobs et al.   CANCER BIOLOGY & THERAPY

Radiation-induced autophagy potentiates immunotherapy of cancer via up-regulation of mannose 6-phosphate receptor on tumor cells in mice

(2014) Sungjune Kim et al.   CANCER IMMUNOLOGY IMMUNOTHERAPY

Screening tests: a review with examples

(2014) L. Daniel Maxim et al.   INHALATION TOXICOLOGY

Metabolic Phenotyping Reveals a Lipid Mediator Response to Ionizing Radiation

(2014) Evagelia C. Laiakis et al.   JOURNAL OF PROTEOME RESEARCH

Ionizing radiations sustain glioblastoma cell dedifferentiation to a stem-like phenotype through survivin: possible involvement in radioresistance

(2014) P Dahan et al.   Cell Death & Disease

Phenotype-based cell-specific metabolic modeling reveals metabolic liabilities of cancer

(2014) Keren Yizhak et al.   eLife

microRNAs in Cancer Cell Response to Ionizing Radiation

(2013) Jennifer R. Czochor et al.   ANTIOXIDANTS & REDOX SIGNALING

Chemotherapy and Radiotherapy Downregulate the Activity and Expression of DNA Methyltransferase and Enhance Bcl-2/E1B-19-kDa Interacting Protein-3-Induced Apoptosis in Human Colorectal Cancer Cells

(2013) Qian Deng et al.   CHEMOTHERAPY

Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

The Cancer Genome Atlas Pan-Cancer analysis project

(2013) John N Weinstein et al.   NATURE GENETICS

Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments

(2013) J. M. Monk et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The law of Bergonié and Tribondeau: A nice formula for a first approximation

(2012) Guillaume Vogin et al.   INTERNATIONAL JOURNAL OF RADIATION BIOLOGY

The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity

(2012) Jordi Barretina et al.   NATURE

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

Emerging molecular biomarkers—blood-based strategies to detect and monitor cancer

(2011) Samir M. Hanash et al.   Nature Reviews Clinical Oncology

Hypoxia inducible factors in cancer stem cells

(2010) J M Heddleston et al.   BRITISH JOURNAL OF CANCER

A genetic screen identifies the Triple T complex required for DNA damage signaling and ATM and ATR stability

(2010) K. E. Hurov et al.   GENES & DEVELOPMENT

Radiation pharmacogenomics: A genome-wide association approach to identify radiation response biomarkers using human lymphoblastoid cell lines

(2010) N. Niu et al.   GENOME RESEARCH

EFFECT OF BUTYRIC ACID SUPPLEMENTATION ON SERUM AND RENAL ANTIOXIDANT ENZYME ACTIVITIES IN STREPTOZOTOCIN-INDUCED DIABETIC RATS

(2010) A. PUNEETH KUMAR et al.   JOURNAL OF FOOD BIOCHEMISTRY

Cancer-associated IDH1 mutations produce 2-hydroxyglutarate

(2009) Lenny Dang et al.   NATURE

Integrating Global Gene Expression and Radiation Survival Parameters across the 60 Cell Lines of the National Cancer Institute Anticancer Drug Screen

(2008) S. A. Amundson et al.   CANCER RESEARCH