Topological data analysis in biomedicine: A review

A Persistent Homology Approach to Heart Rate Variability Analysis With an Application to Sleep-Wake Classification

(2021) Yu-Min Chung et al.   Frontiers in Physiology

Clustering datasets with demographics and diagnosis codes

(2020) Haodi Zhong et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Weighted persistent homology for biomolecular data analysis

(2020) Zhenyu Meng et al.   Scientific Reports

Protein-Folding Analysis Using Features Obtained by Persistent Homology

(2020) Takashi Ichinomiya et al.   BIOPHYSICAL JOURNAL

Using topological data analysis and pseudo time series to infer temporal phenotypes from electronic health records

(2020) Arianna Dagliati et al.   ARTIFICIAL INTELLIGENCE IN MEDICINE

Topological data analysis to model the shape of immune responses during co-infections

(2020) Karin Sasaki et al.   Communications in Nonlinear Science and Numerical Simulation

Weighted-persistent-homology-based machine learning for RNA flexibility analysis

(2020) Chi Seng Pun et al.   PLoS One

Persistent Homology for the Quantitative Evaluation of Architectural Features in Prostate Cancer Histology

(2019) Peter Lawson et al.   Scientific Reports

Network Tomography for Understanding Phenotypic Presentations in Aortic Stenosis

(2019) Grace Casaclang-Verzosa et al.   JACC-Cardiovascular Imaging

Two-Tier Mapper, an unbiased topology-based clustering method for enhanced global gene expression analysis

(2019) Rachel Jeitziner et al.   BIOINFORMATICS

A Primer on Persistent Homology of Finite Metric Spaces

(2019) Facundo Mémoli et al.   BULLETIN OF MATHEMATICAL BIOLOGY

Signal Processing and Machine Learning for Biomedical Big Data

(2019) Paul H. King   IEEE Pulse

Fast and accurate tumor segmentation of histology images using persistent homology and deep convolutional features

(2019) Talha Qaiser et al.   MEDICAL IMAGE ANALYSIS

Sputum microbiomic clustering in asthma and COPD reveals a Haemophilus ‐predominant subgroup

(2019) Sarah Diver et al.   ALLERGY

Exploring hyperspectral imaging data sets with topological data analysis

(2018) Ludovic Duponchel   ANALYTICA CHIMICA ACTA

Airway pathological heterogeneity in asthma: Visualization of disease microclusters using topological data analysis

(2018) Salman Siddiqui et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

Patient similarity for precision medicine: A systematic review

(2018) E. Parimbelli et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Using multidimensional topological data analysis to identify traits of hip osteoarthritis

(2018) Jasmine Rossi-deVries et al.   JOURNAL OF MAGNETIC RESONANCE IMAGING

Modeling the spread of the Zika virus using topological data analysis

(2018) Derek Lo et al.   PLoS One

Disrupted Resting State Network of Fibromyalgia in Theta frequency

(2018) Mi Kyung Choe et al.   Scientific Reports

Lung Topology Characteristics in patients with Chronic Obstructive Pulmonary Disease

(2018) Francisco Belchi et al.   Scientific Reports

Topological Data Analysis

(2018) Larry Wasserman   Annual Review of Statistics and Its Application

Topological data analysis of single-trial electroencephalographic signals

(2018) Yuan Wang et al.   Annals of Applied Statistics

Using Persistent Homology as a New Approach for Super-Resolution Localization Microscopy Data Analysis and Classification of γH2AX Foci/Clusters

(2018) Andreas Hofmann et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Decoding of Neural Data Using Cohomological Feature Extraction

(2018) Erik Rybakken et al.   NEURAL COMPUTATION

MRI and biomechanics multidimensional data analysis reveals R2 -R1ρ as an early predictor of cartilage lesion progression in knee osteoarthritis

(2017) Valentina Pedoia et al.   JOURNAL OF MAGNETIC RESONANCE IMAGING

A Novel Approach to Identifying a Neuroimaging Biomarker for Patients With Serious Mental Illness

(2017) Alok Madan et al.   JOURNAL OF NEUROPSYCHIATRY AND CLINICAL NEUROSCIENCES

Robust detection and segmentation of cell nuclei in biomedical images based on a computational topology framework

(2017) Rodrigo Rojas-Moraleda et al.   MEDICAL IMAGE ANALYSIS

Single-cell topological RNA-seq analysis reveals insights into cellular differentiation and development

(2017) Abbas H Rizvi et al.   NATURE BIOTECHNOLOGY

Semantics derived automatically from language corpora contain human-like biases

(2017) Aylin Caliskan et al.   SCIENCE

Persistent homology index as a robust quantitative measure of immunohistochemical scoring

(2017) Akihiro Takiyama et al.   Scientific Reports

Ten quick tips for machine learning in computational biology

(2017) Davide Chicco   BioData Mining

A roadmap for the computation of persistent homology

(2017) Nina Otter et al.   EPJ Data Science

Machine Learning With Big Data: Challenges and Approaches

(2017) Alexandra L'Heureux et al.   IEEE Access

Uncovering precision phenotype-biomarker associations in traumatic brain injury using topological data analysis

(2017) Jessica L. Nielson et al.   PLoS One

Novel subgroups of attention-deficit/hyperactivity disorder identified by topological data analysis and their functional network modular organizations

(2017) Sunghyon Kyeong et al.   PLoS One

Persistent homology analysis of brain artery trees

(2016) Paul Bendich et al.   Annals of Applied Statistics

What can topology tell us about the neural code?

(2016) Carina Curto   BULLETIN OF THE AMERICAN MATHEMATICAL SOCIETY

Evaluating the impact of a computerized surveillance algorithm and decision support system on sepsis mortality

(2016) Sharad Manaktala et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Wishbone identifies bifurcating developmental trajectories from single-cell data

(2016) Manu Setty et al.   NATURE BIOTECHNOLOGY

The classification of endoscopy images with persistent homology

(2016) Olga Dunaeva et al.   PATTERN RECOGNITION LETTERS

WDR76 Co-Localizes with Heterochromatin Related Proteins and Rapidly Responds to DNA Damage

(2016) Joshua M. Gilmore et al.   PLoS One

Using persistent homology and dynamical distances to analyze protein binding

(2016) Violeta Kovacev-Nikolic et al.   Statistical Applications in Genetics and Molecular Biology

Using persistent homology and dynamical distances to analyze protein binding

(2016) Violeta Kovacev-Nikolic et al.   Statistical Applications in Genetics and Molecular Biology

Persistent homology for time series and spatial data clustering

(2015) Cássio M.M. Pereira et al.   EXPERT SYSTEMS WITH APPLICATIONS

Innate and adaptive T cells in asthmatic patients: Relationship to severity and disease mechanisms

(2015) Timothy S.C. Hinks et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

Identification of type 2 diabetes subgroups through topological analysis of patient similarity

(2015) Li Li et al.   Science Translational Medicine

Topological data analysis for discovery in preclinical spinal cord injury and traumatic brain injury

(2015) Jessica L. Nielson et al.   Nature Communications

Topological data analysis of contagion maps for examining spreading processes on networks

(2015) Dane Taylor et al.   Nature Communications

Biochemical Association of Metabolic Profile and Microbiome in Chronic Pressure Ulcer Wounds

(2015) Mary Cloud B. Ammons et al.   PLoS One

Conserved abundance and topological features in chromatin-remodeling protein interaction networks

(2014) M. E. Sardiu et al.   EMBO REPORTS

Topological methods reveal high and low functioning neuro-phenotypes within fragile X syndrome

(2014) David Romano et al.   HUMAN BRAIN MAPPING

Persistent homology analysis of protein structure, flexibility, and folding

(2014) Kelin Xia et al.   International Journal for Numerical Methods in Biomedical Engineering

A topological measurement of protein compressibility

(2014) Marcio Gameiro et al.   JAPAN JOURNAL OF INDUSTRIAL AND APPLIED MATHEMATICS

Topographical transcriptome mapping of the mouse medial ganglionic eminence by spatially-resolved RNA-seq

(2014) Sabrina Zechel et al.   GENOME BIOLOGY

Morse Theory for Filtrations and Efficient Computation of Persistent Homology

(2013) Konstantin Mischaikow et al.   DISCRETE & COMPUTATIONAL GEOMETRY

Topology of viral evolution

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

Extracting insights from the shape of complex data using topology

(2013) P. Y. Lum et al.   Scientific Reports

Persistent Brain Network Homology From the Perspective of Dendrogram

(2012) Hyekyoung Lee et al.   IEEE TRANSACTIONS ON MEDICAL IMAGING

Topology-Based Kernels With Application to Inference Problems in Alzheimer's Disease

(2011) Deepti Pachauri et al.   IEEE TRANSACTIONS ON MEDICAL IMAGING

Topology based data analysis identifies a subgroup of breast cancers with a unique mutational profile and excellent survival

(2011) M. Nicolau et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An empirical evaluation of the comprehensibility of decision table, tree and rule based predictive models

(2010) Johan Huysmans et al.   DECISION SUPPORT SYSTEMS

Uniform definition of asthma severity, control, and exacerbations: Document presented for the World Health Organization Consultation on Severe Asthma

(2010) Jean Bousquet et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

Topology and data

(2009) Gunnar Carlsson   BULLETIN OF THE AMERICAN MATHEMATICAL SOCIETY

Structural Insight into RNA Hairpin Folding Intermediates

(2008) Gregory R. Bowman et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY