The properties of high-dimensional data spaces: implications for exploring gene and protein expression data

R Clarke, HW Ressom, A Wang, J Xuan, MC Liu… - Nature reviews …, 2008 - nature.com
High-throughput genomic and proteomic technologies are widely used in cancer research to
build better predictive models of diagnosis, prognosis and therapy, to identify and …

The advantages of the Matthews correlation coefficient (MCC) over F1 score and accuracy in binary classification evaluation

D Chicco, G Jurman - BMC genomics, 2020 - Springer
Background To evaluate binary classifications and their confusion matrices, scientific
researchers can employ several statistical rates, accordingly to the goal of the experiment …

Data integration and predictive modeling methods for multi-omics datasets

M Kim, I Tagkopoulos - Molecular omics, 2018 - pubs.rsc.org
Translating data to knowledge and actionable insights is the Holy Grail for many scientific
fields, including biology. The unprecedented massive and heterogeneous data have created …

Intratumoral and peritumoral radiomics for the pretreatment prediction of pathological complete response to neoadjuvant chemotherapy based on breast DCE-MRI

NM Braman, M Etesami, P Prasanna, C Dubchuk… - Breast Cancer …, 2017 - Springer
Background In this study, we evaluated the ability of radiomic textural analysis of
intratumoral and peritumoral regions on pretreatment breast cancer dynamic contrast …

Machine learning-based analysis of MR multiparametric radiomics for the subtype classification of breast cancer

T Xie, Z Wang, Q Zhao, Q Bai, X Zhou, Y Gu… - Frontiers in …, 2019 - frontiersin.org
Objective: To investigate whether machine learning analysis of multiparametric MR
radiomics can help classify immunohistochemical (IHC) subtypes of breast cancer. Study …

[HTML][HTML] Strategies to design clinical studies to identify predictive biomarkers in cancer research

JL Perez-Gracia, MF Sanmamed, A Bosch… - Cancer Treatment …, 2017 - Elsevier
The discovery of reliable biomarkers to predict efficacy and toxicity of anticancer drugs
remains one of the key challenges in cancer research. Despite its relevance, no efficient …

Predictive value of quantitative 18F-FDG-PET radiomics analysis in patients with head and neck squamous cell carcinoma

RM Martens, T Koopman, DP Noij, E Pfaehler… - EJNMMI research, 2020 - Springer
Background Radiomics is aimed at image-based tumor phenotyping, enabling application
within clinical-decision-support-systems to improve diagnostic accuracy and allow for …

Use of natural language processing in electronic medical records to identify pregnant women with suicidal behavior: towards a solution to the complex classification …

QY Zhong, LP Mittal, MD Nathan, KM Brown… - European journal of …, 2019 - Springer
We developed algorithms to identify pregnant women with suicidal behavior using
information extracted from clinical notes by natural language processing (NLP) in electronic …

Predicting the hepatocarcinogenic potential of alkenylbenzene flavoring agents using toxicogenomics and machine learning

SS Auerbach, RR Shah, D Mav, CS Smith… - Toxicology and applied …, 2010 - Elsevier
Identification of carcinogenic activity is the primary goal of the 2-year bioassay. The expense
of these studies limits the number of chemicals that can be studied and therefore chemicals …

Proteomics and phosphoproteomics in precision medicine: applications and challenges

G Giudice, E Petsalaki - Briefings in bioinformatics, 2019 - academic.oup.com
Recent advances in proteomics allow the accurate measurement of abundances for
thousands of proteins and phosphoproteins from multiple samples in parallel. Therefore, for …