Biomarker discovery studies for patient stratification using machine learning analysis of omics data: a scoping review

Using machine learning approaches for multi-omics data analysis: A review

(2021) Parminder S. Reel et al.   BIOTECHNOLOGY ADVANCES

Next-Generation Sequencing Concordance Analysis of Comprehensive Solid Tumor Profiling between a Centralized Specialty Laboratory and the Decentralized Personal Genome Diagnostics, Inc., Elio Tissue Complete Kitted Solution

(2021) Kristen Lee Deak et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Molecular Characteristics and Disease Burden Metrics Determined By Next-Generation Sequencing on Circulating Tumor DNA Correlate with Progression Free Survival in Previously Untreated Diffuse Large B-Cell Lymphoma

(2020) Ehsan Tabari et al.   BLOOD

Genome-wide rare variant analysis for thousands of phenotypes in over 70,000 exomes from two cohorts

(2020) Elizabeth T. Cirulli et al.   Nature Communications

How Machine Learning Will Transform Biomedicine

(2020) Jeremy Goecks et al.   CELL

Population genetic screening efficiently identifies carriers of autosomal dominant diseases

(2020) J. J. Grzymski et al.   NATURE MEDICINE

Large-scale benchmark study of survival prediction methods using multi-omics data

(2020) Moritz Herrmann et al.   BRIEFINGS IN BIOINFORMATICS

Machine Learning SNP Based Prediction for Precision Medicine

(2019) Daniel Sik Wai Ho et al.   Frontiers in Genetics

Current trends in biomarker discovery and analysis tools for traumatic brain injury

(2019) Briana I. Martinez et al.   Journal of Biological Engineering

Machine Learning in Amyotrophic Lateral Sclerosis: Achievements, Pitfalls, and Future Directions

(2019) Vincent Grollemund et al.   Frontiers in Neuroscience

Machine learning and its potential applications to the genomic study of head and neck cancer – a systematic review

(2019) Shankargouda Patil et al.   JOURNAL OF ORAL PATHOLOGY & MEDICINE

Panoptic View of Prognostic Models for Personalized Breast Cancer Management

(2019) Geetanjali Saini et al.   Cancers

Lifecycle Regulation of Artificial Intelligence– and Machine Learning–Based Software Devices in Medicine

(2019) Thomas J. Hwang et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Future Direction for Using Artificial Intelligence to Predict and Manage Hypertension

(2018) Chayakrit Krittanawong et al.   CURRENT HYPERTENSION REPORTS

Omics research ethics considerations

(2018) Janet K. Williams et al.   NURSING OUTLOOK

The use of automated Ki67 analysis to predict Oncotype DX risk-of-recurrence categories in early-stage breast cancer

(2018) Satbir Singh Thakur et al.   PLoS One

Big Data and the Precision Medicine Revolution

(2018) Wallace J. Hopp et al.   PRODUCTION AND OPERATIONS MANAGEMENT

PRISMA Extension for Scoping Reviews (PRISMA-ScR): Checklist and Explanation

(2018) Andrea C. Tricco et al.   ANNALS OF INTERNAL MEDICINE

Determination of the minimally important difference (MID) in multi-biomarker disease activity (MBDA) test scores: impact of diurnal and daily biomarker variation patterns on MBDA scores

(2018) David Chernoff et al.   CLINICAL RHEUMATOLOGY

A systematic review on metabolomics-based diagnostic biomarker discovery and validation in pancreatic cancer

(2018) Nguyen Phuoc Long et al.   Metabolomics

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

Oncotype DX® Recurrence Score as a Predictor of Response to Neoadjuvant Chemotherapy

(2018) Alison M. Pease et al.   ANNALS OF SURGICAL ONCOLOGY

Systematic review or scoping review? Guidance for authors when choosing between a systematic or scoping review approach

(2018) Zachary Munn et al.   BMC Medical Research Methodology

Uptake and Clinical Utility of Multibiomarker Disease Activity Testing in the United States

(2018) Jeffrey R. Curtis et al.   JOURNAL OF RHEUMATOLOGY

Evaluation of the Decipher prostate cancer classifier to predict metastasis and disease-specific mortality from genomic analysis of diagnostic prostate needle biopsy specimens.

(2017) Paul L. Nguyen et al.   JOURNAL OF CLINICAL ONCOLOGY

Comprehensive Determination of Prostate Tumor ETS Gene Status in Clinical Samples Using the CLIA Decipher Assay

(2017) Alba Torres et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Utility of a Precision Medicine Test in Elderly Adults with Symptoms Suggestive of Coronary Artery Disease

(2017) Joseph A. Ladapo et al.   JOURNAL OF THE AMERICAN GERIATRICS SOCIETY

OS11.3 Machine learning for better prognostic stratification and driver genes identification in 1p/19q-codeleted grade III gliomas

(2017) S. Rosenberg et al.   NEURO-ONCOLOGY

PMLB: a large benchmark suite for machine learning evaluation and comparison

(2017) Randal S. Olson et al.   BioData Mining

Abstract B16: Validation and clinical feasibility of a Foundation Medicine assay to identify immunotherapy response potential through tumor mutational burden (TMB)

(2017) Daniel S. Lieber et al.   Cancer Immunology Research

More Is Better: Recent Progress in Multi-Omics Data Integration Methods

(2017) Sijia Huang et al.   Frontiers in Genetics

Clinical and technical validation of a genomic classifier (ColoPrint) for predicting outcome of patients with stage II colon cancer.

(2017) Josep Tabernero et al.   JOURNAL OF CLINICAL ONCOLOGY

Prospective, multicenter French study evaluating the clinical impact of the Breast Cancer Intrinsic Subtype-Prosigna® Test in the management of early-stage breast cancers

(2017) Delphine Hequet et al.   PLoS One

Integrated genomic DNA/RNA profiling of hematologic malignancies in the clinical setting

(2016) J. He et al.   BLOOD

Methods for the integration of multi-omics data: mathematical aspects

(2016) Matteo Bersanelli et al.   BMC BIOINFORMATICS

Validation of the Decipher prostate cancer classifier for predicting 10-year postoperative metastasis from analysis of diagnostic needle biopsy specimens.

(2016) Cristina Magi-Galluzzi et al.   JOURNAL OF CLINICAL ONCOLOGY

Comparing Breast Cancer Multiparameter Tests in the OPTIMA Prelim Trial: No Test Is More Equal Than the Others

(2016) John M. S. Bartlett et al.   JNCI-Journal of the National Cancer Institute

70-Gene Signature as an Aid to Treatment Decisions in Early-Stage Breast Cancer

(2016) Fatima Cardoso et al.   NEW ENGLAND JOURNAL OF MEDICINE

Decipher Genomic Classifier Measured on Prostate Biopsy Predicts Metastasis Risk

(2016) Eric A. Klein et al.   UROLOGY

Comparing Breast Cancer Multiparameter Tests in the OPTIMA Prelim Trial: No Test Is More Equal Than the Others

(2016) John M. S. Bartlett et al.   JNCI-Journal of the National Cancer Institute

A Prospective Comparison of the 21-Gene Recurrence Score and the PAM50-Based Prosigna in Estrogen Receptor-Positive Early-Stage Breast Cancer

(2015) Michael D. Alvarado et al.   ADVANCES IN THERAPY

Transparent Reporting of a multivariable prediction model for Individual Prognosis Or Diagnosis (TRIPOD): Explanation and Elaboration

(2015) Karel G.M. Moons et al.   ANNALS OF INTERNAL MEDICINE

Development and verification of the PAM50-based Prosigna breast cancer gene signature assay

(2015) Brett Wallden et al.   BMC Medical Genomics

Using prior knowledge from cellular pathways and molecular networks for diagnostic specimen classification

(2015) Enrico Glaab   BRIEFINGS IN BIOINFORMATICS

Randomized Pilot Trial of Gene Expression Profiling Versus Heart Biopsy in the First Year After Heart Transplant: Early Invasive Monitoring Attenuation Through Gene Expression Trial

(2015) J. Kobashigawa et al.   Circulation-Heart Failure

Genomic Classifier ColoPrint Predicts Recurrence in Stage II Colorectal Cancer Patients More Accurately Than Clinical Factors

(2015) S. Kopetz et al.   ONCOLOGIST

Analytical validation of the PAM50-based Prosigna Breast Cancer Prognostic Gene Signature Assay and nCounter Analysis System using formalin-fixed paraffin-embedded breast tumor specimens

(2014) Torsten Nielsen et al.   BMC CANCER

Implications of a suspicious afirma test result in thyroid fine-needle aspiration cytology: An institutional experience

(2014) Ricardo R. Lastra et al.   CANCER CYTOPATHOLOGY

An Independent Study of a Gene Expression Classifier (Afirma) in the Evaluation of Cytologically Indeterminate Thyroid Nodules

(2014) Bryan McIver et al.   JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM

MammaPrint Molecular Diagnostics on Formalin-Fixed, Paraffin-Embedded Tissue

(2014) Anna Sapino et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

A scoping review of scoping reviews: advancing the approach and enhancing the consistency

(2014) Mai T. Pham et al.   Research Synthesis Methods

Multicenter Validation of the Diagnostic Accuracy of a Blood-Based Gene Expression Test for Assessing Obstructive Coronary Artery Disease in Nondiabetic Patients

(2013) Steven Rosenberg   ANNALS OF INTERNAL MEDICINE

Independent Validation of a Prognostic Genomic Signature (ColoPrint) for Patients With Stage II Colon Cancer

(2013) Matthias Maak et al.   ANNALS OF SURGERY

Analytical validation of the Oncotype DX prostate cancer assay – a clinical RT-PCR assay optimized for prostate needle biopsies

(2013) Dejan Knezevic et al.   BMC GENOMICS

Criteria for the use of omics-based predictors in clinical trials: explanation and elaboration

(2013) Lisa M McShane et al.   BMC Medicine

The impact of the Oncotype Dx breast cancer assay in clinical practice: a systematic review and meta-analysis

(2013) Josh J. Carlson et al.   BREAST CANCER RESEARCH AND TREATMENT

Research ethics in the post-genomic era

(2013) Kirsi Vähäkangas   ENVIRONMENTAL AND MOLECULAR MUTAGENESIS

Comparison of PAM50 Risk of Recurrence Score With Oncotype DX and IHC4 for Predicting Risk of Distant Recurrence After Endocrine Therapy

(2013) Mitch Dowsett et al.   JOURNAL OF CLINICAL ONCOLOGY

Blinded Comparator Study of Immunohistochemical Analysis versus a 92-Gene Cancer Classifier in the Diagnosis of the Primary Site in Metastatic Tumors

(2013) Lawrence M. Weiss et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing

(2013) Garrett M Frampton et al.   NATURE BIOTECHNOLOGY

Pitfalls and limitations in translation from biomarker discovery to clinical utility in predictive and personalised medicine

(2013) Elisabeth Drucker et al.   EPMA Journal

Diagnostic Use of Molecular Markers in the Evaluation of Thyroid Nodules

(2012) Matthew Kim et al.   Endocrine Practice

Retraction

(2012)   JOURNAL OF CLINICAL ONCOLOGY

Molecular Gene Expression Profiling to Predict the Tissue of Origin and Direct Site-Specific Therapy in Patients With Carcinoma of Unknown Primary Site: A Prospective Trial of the Sarah Cannon Research Institute

(2012) John D. Hainsworth et al.   JOURNAL OF CLINICAL ONCOLOGY

Novel Antibacterial Activity of β2-Microglobulin in Human Amniotic Fluid

(2012) Jin-Young Kim et al.   PLoS One

Validation of a novel multibiomarker test to assess rheumatoid arthritis disease activity

(2012) Jeffrey R. Curtis et al.   ARTHRITIS CARE & RESEARCH

High-dimensional bolstered error estimation

(2011) C. Sima et al.   BIOINFORMATICS

Development of a blood-based gene expression algorithm for assessment of obstructive coronary artery disease in non-diabetic patients

(2011) Michael R Elashoff et al.   BMC Medical Genomics

Neoadjuvant Concurrent Chemoradiation for Advanced Esthesioneuroblastoma: A Case Series and Review of the Literature

(2011) Sohrab Sohrabi et al.   JOURNAL OF CLINICAL ONCOLOGY

Translating biomarkers to clinical practice

(2011) R H Perlis   MOLECULAR PSYCHIATRY

An 18-gene signature (ColoPrint®) for colon cancer prognosis

(2011) Iain B. Tan et al.   Nature Reviews Clinical Oncology

Metastatic Potential of T1 Breast Cancer can be Predicted by the 70-gene MammaPrint Signature

(2010) Stella Mook et al.   ANNALS OF SURGICAL ONCOLOGY

Personalized medicine in oncology: tailoring the right drug to the right patient

(2010) Yuqiu Jiang et al.   Biomarkers in Medicine

Utility of oncotype DX risk estimates in clinically intermediate risk hormone receptor-positive, HER2-normal, grade II, lymph node-negative breast cancers

(2010) Catherine M. Kelly et al.   CANCER

Molecular Classification of Thyroid Nodules Using High-Dimensionality Genomic Data

(2010) Darya Chudova et al.   JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM

Prospective Multicenter Study of the Impact of the 21-Gene Recurrence Score Assay on Medical Oncologist and Patient Adjuvant Breast Cancer Treatment Selection

(2010) Shelly S. Lo et al.   JOURNAL OF CLINICAL ONCOLOGY

Molecular Profiling in Unknown Primary Cancer: Accuracy of Tissue of Origin Prediction

(2010) F. A. Greco et al.   ONCOLOGIST

MammaPrint™ 70-gene signature: another milestone in personalized medical care for breast cancer patients

(2009) Elzbieta A Slodkowska et al.   EXPERT REVIEW OF MOLECULAR DIAGNOSTICS

Supervised Risk Predictor of Breast Cancer Based on Intrinsic Subtypes

(2009) Joel S. Parker et al.   JOURNAL OF CLINICAL ONCOLOGY

Correlation of Peripheral-Blood Gene Expression With the Extent of Coronary Artery Stenosis

(2008) James A. Wingrove et al.   Circulation-Cardiovascular Genetics

Analysis of the MammaPrint Breast Cancer Assay in a Predominantly Postmenopausal Cohort

(2008) B. S. Wittner et al.   CLINICAL CANCER RESEARCH