4.6 Article

Optimisation Models for Pathway Activity Inference in Cancer

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Review Pharmacology & Pharmacy

Understanding the Emerging Link Between Circadian Rhythm, Nrf2 Pathway, and Breast Cancer to Overcome Drug Resistance

Supriya Bevinakoppamath et al.

Summary: The article discusses the interplay between circadian rhythm and the Nrf2 pathway, their impact on breast cancer pathogenesis, and proposes the significance of treatment strategies regulating circadian rhythm for maximizing treatment efficacy with minimal side effects.

FRONTIERS IN PHARMACOLOGY (2022)

Review Genetics & Heredity

Epigenetic signatures in cancer: proper controls, current challenges and the potential for clinical translation

Daniela Mancarella et al.

Summary: Epigenetic alterations are associated with various diseases, including cancer, driven by genetic mutations and changes in global epigenetic signatures. Recent studies suggest that cancer epigenomes are mainly influenced by pre-existing epigenetic patterns in the cell-of-origin, calling for a redefinition of tumor-specific epigenetic changes.

GENOME MEDICINE (2021)

Review Medicine, General & Internal

Technological readiness and implementation of genomic-driven precision medicine for complex diseases

P. W. Franks et al.

Summary: Genomic approaches to diagnosis, prognostication, prevention and treatment may optimize medical practice. Research is underway to determine the polygenic basis of many complex diseases, which will likely necessitate models for prediction and diagnosis that incorporate genetic and non-genetic data.

JOURNAL OF INTERNAL MEDICINE (2021)

Article Genetics & Heredity

Identifying Breast Cancer-Related Genes Based on a Novel Computational Framework Involving KEGG Pathways and PPI Network Modularity

Yan Zhang et al.

Summary: This study introduces a novel computational framework to analyze the network properties of breast cancer-associated genes and predict novel disease genes using a random-walk-with-restart algorithm. By integrating information from protein-protein interaction networks and KEGG pathways, the proposed method demonstrates better performance in predicting breast cancer-associated genes. Literature search further confirms the validity of the top predicted novel genes, suggesting the potential of this framework for experimental validation.

FRONTIERS IN GENETICS (2021)

Review Genetics & Heredity

Origins of human disease: the chrono-epigenetic perspective

Edward Saehong Oh et al.

Summary: Epigenetics enriches human disease studies with new interpretations, but identifying causal mechanisms has been challenging. Recent findings in intra-individual and cyclical epigenetic variation present new opportunities, and the temporality in the epigenome may help integrate diverse disease studies.

NATURE REVIEWS GENETICS (2021)

Article Oncology

Pathway-based classification of glioblastoma uncovers a mitochondrial subtype with therapeutic vulnerabilities

Luciano Garofano et al.

Summary: Garofano et al. classified glioblastomas into subtypes along metabolic and neurodevelopmental axes using single-cell RNA-sequencing data. Mitochondrial GBM showed the most favorable clinical outcome and vulnerability to inhibitors of oxidative phosphorylation, while glycolytic/plurimetabolic GBM relied on aerobic glycolysis and other metabolic pathways for energy production. This pathway-based classification can inform survival and precision targeting of cancer metabolism.

NATURE CANCER (2021)

Article Biochemistry & Molecular Biology

Transfer of regulatory knowledge from human to mouse for functional genomics analysis

Christian H. Holland et al.

BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS (2020)

Article Oncology

Colorectal cancer statistics, 2020

Rebecca L. Siegel et al.

CA-A CANCER JOURNAL FOR CLINICIANS (2020)

Review Biochemistry & Molecular Biology

Molecular Connections Between Circadian Clocks and Aging

Patrick-Simon Welz et al.

JOURNAL OF MOLECULAR BIOLOGY (2020)

Review Multidisciplinary Sciences

Pathway paradigms revealed from the genetics of inflammatory bowel disease

Daniel B. Graham et al.

NATURE (2020)

Article Multidisciplinary Sciences

Trajectory-based differential expression analysis for single-cell sequencing data

Koen Van den Berge et al.

NATURE COMMUNICATIONS (2020)

Article Pharmacology & Pharmacy

Recent advances in folic acid engineered nanocarriers for treatment of breast cancer

Priti Tagde et al.

JOURNAL OF DRUG DELIVERY SCIENCE AND TECHNOLOGY (2020)

Article Computer Science, Interdisciplinary Applications

A practical perspective on the concordance index for the evaluation and selection of prognostic time-to-event models

Enrico Longato et al.

JOURNAL OF BIOMEDICAL INFORMATICS (2020)

Review Cell Biology

Peroxisome Metabolism in Cancer

Jung-Ae Kim

Review Oncology

GSTM3 Function and Polymorphism in Cancer: Emerging but Promising

Shunda Wang et al.

CANCER MANAGEMENT AND RESEARCH (2020)

Article Computer Science, Artificial Intelligence

From local explanations to global understanding with explainable AI for trees

Scott M. Lundberg et al.

NATURE MACHINE INTELLIGENCE (2020)

Article Biochemical Research Methods

Predictive modelling using pathway scores: robustness and significance of pathway collections

Marcelo P. Segura-Lepe et al.

BMC BIOINFORMATICS (2019)

Article Computer Science, Information Systems

Topology potential based seed-growth method to identify protein complexes on dynamic PPI data

Xiujuan Lei et al.

INFORMATION SCIENCES (2018)

Article Computer Science, Artificial Intelligence

SMOTE for Learning from Imbalanced Data: Progress and Challenges, Marking the 15-year Anniversary

Alberto Fernandez et al.

JOURNAL OF ARTIFICIAL INTELLIGENCE RESEARCH (2018)

Article Biotechnology & Applied Microbiology

Inferring metabolic pathway activity levels from RNA-Seq data

Yvette Temate-Tiagueu et al.

BMC GENOMICS (2016)

Article Oncology

Cancer Statistics, 2016

Rebecca L. Siegel et al.

CA-A CANCER JOURNAL FOR CLINICIANS (2016)

Article Biochemistry & Molecular Biology

The consensus molecular subtypes of colorectal cancer

Justin Guinney et al.

NATURE MEDICINE (2015)

Article

Review The Cancer Genome Atlas (TCGA): an immeasurable source of knowledge

Katarzyna Tomczak et al.

Wspolczesna Onkologia-Contemporary Oncology (2015)

Article Oncology

Biological subtypes of breast cancer: Prognostic and therapeutic implications

Ozlem Yersal et al.

WORLD JOURNAL OF CLINICAL ONCOLOGY (2014)

Article Biochemical Research Methods

GSVA: gene set variation analysis for microarray and RNA-Seq data

Sonja Haenzelmann et al.

BMC BIOINFORMATICS (2013)

Article Multidisciplinary Sciences

Pathway-based personalized analysis of cancer

Yotam Drier et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)

Article Biochemical Research Methods

Core module biomarker identification with network exploration for breast cancer metastasis

Ruoting Yang et al.

BMC BIOINFORMATICS (2012)

Article Biochemical Research Methods

Identifying dysregulated pathways in cancers from pathway interaction networks

Ke-Qin Liu et al.

BMC BIOINFORMATICS (2012)

Article Oncology

Supervised Risk Predictor of Breast Cancer Based on Intrinsic Subtypes

Joel S. Parker et al.

JOURNAL OF CLINICAL ONCOLOGY (2009)

Article Biochemical Research Methods

Integrating Biological Knowledge with Gene Expression Profiles for Survival Prediction of Cancer

Xi Chen et al.

JOURNAL OF COMPUTATIONAL BIOLOGY (2009)

Article Statistics & Probability

RANDOM SURVIVAL FORESTS

Hemant Ishwaran et al.

ANNALS OF APPLIED STATISTICS (2008)

Review Medical Laboratory Technology

Alcohol dehydrogenase (ADH) and aldehyde dehydrogenase (ALDH) in the cancer diseases

Wojciech Jelski et al.

CLINICA CHIMICA ACTA (2008)

Article Biochemical Research Methods

Inferring Pathway Activity toward Precise Disease Classification

Eunjung Lee et al.

PLOS COMPUTATIONAL BIOLOGY (2008)

Article Biochemical Research Methods

Integration of biological networks and gene expression data using Cytoscape

Melissa S. Cline et al.

NATURE PROTOCOLS (2007)

Article Robotics

Iterative MILP methods for vehicle-control problems

MG Earl et al.

IEEE TRANSACTIONS ON ROBOTICS (2005)

Article Multidisciplinary Sciences

Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles

A Subramanian et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)

Article Biochemical Research Methods

Towards precise classification of cancers based on robust gene functional expression profiles

Z Guo et al.

BMC BIOINFORMATICS (2005)

Article Biochemistry & Molecular Biology

The KEGG resource for deciphering the genome

M Kanehisa et al.

NUCLEIC ACIDS RESEARCH (2004)

Article Oncology

Low penetrance genes associated with increased risk for breast cancer

BL Weber et al.

EUROPEAN JOURNAL OF CANCER (2000)

Article Biochemistry & Molecular Biology

KEGG: Kyoto Encyclopedia of Genes and Genomes

M Kanehisa et al.

NUCLEIC ACIDS RESEARCH (2000)