cran: TDA | Projects | Ecosyste.ms: Papers

10.12688/f1000research.13541.1

archiDART v3.0: A new data analysis pipeline allowing the topological analysis of plant root systems
Cited by: 20
Author(s): Benjamin Delory, Li Mao, Christopher N. Topp, Guillaume Lobet
Software Mentions: 8
Published: almost 7 years ago

10.1371/journal.pone.0225577

Designing machine learning workflows with an application to topological data analysis
Cited by: 4
Author(s): Eric Cawi, Patricio S. La Rosa, Arye Nehorai
Software Mentions: 7
Published: almost 5 years ago

10.1038/s41598-021-82951-5

Machine intelligence identifies soluble TNFa as a therapeutic target for spinal cord injury
Cited by: 10
Author(s): J. Russell Huie, Adam R. Ferguson, Nikos Kyritsis, Jonathan Z. Pan, Karen Irvine, Jessica L. Nielson, Patrick G. Schupp, Michael C. Oldham, John C. Gensel, Amity Lin, Mark R. Segal, Rajiv R. Ratan, Jacqueline C. Bresnahan, Michael S. Beattie
Software Mentions: 5
Published: almost 4 years ago

10.3389/frai.2021.680564

Topological Data Analysis Highlights Novel Geographical Signatures of the Human Gut Microbiome
Cited by: 3
Author(s): Eva Lymberopoulos, Giorgia Isabella Gentili, Muhannad Alomari, Nikhil Sharma
Software Mentions: 5
Published: over 3 years ago

10.1186/s40168-017-0261-y

Fecal metagenomic profiles in subgroups of patients with myalgic encephalomyelitis/chronic fatigue syndrome
Cited by: 127
Author(s): Dorottya Nagy‐Szakal, Brent L. Williams, Nischay Mishra, Xiaoyu Che, Bohyun Lee, Lucinda Bateman, Nancy G. Klimas, Anthony L. Komaroff, Susan Levine, José G. Montoya, Daniel L. Peterson, Devi Ramanan, Komal Jain, M L Eddy, Mady Hornig, W. Ian Lipkin
Software Mentions: 5
Published: over 7 years ago

10.1140/epjds/s13688-017-0109-5

A roadmap for the computation of persistent homology
Cited by: 416
Author(s): Nina Otter, Mason A. Porter, Ulrike Tillmann, Peter Grindrod, Heather A. Harrington
Software Mentions: 4
Published: over 7 years ago

10.1016/j.artmed.2020.101930

Using topological data analysis and pseudo time series to infer temporal phenotypes from electronic health records
Cited by: 14
Author(s): Arianna Dagliati, Nophar Geifman, Niels Peek, John H. Holmes, Lucia Sacchi, Riccardo Bellazzi, Seyed Erfan Sajjadi, Allan Tucker
Software Mentions: 4
Published: over 4 years ago

10.3390/molecules26164757

The Need for Community Standards to Enable Accurate Comparison of Glycoproteomics Algorithm Performance
Cited by: 10
Author(s): William Edwin Hackett, Joseph Zaia
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pcbi.1009094

Topological data analysis distinguishes parameter regimes in the Anderson-Chaplain model of angiogenesis
Cited by: 12
Author(s): John T. Nardini, Bernadette J. Stolz, Kevin Flores, Heather A. Harrington, Helen M. Byrne
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pgen.1008009

Reverse GWAS: Using genetics to identify and model phenotypic subtypes
Cited by: 31
Author(s): Andy Dahl, Na Cai, Arthur Ko, Markku Laakso, Päivi Pajukanta, Jonathan Flint, Noah Zaitlen
Software Mentions: 3
Published: over 5 years ago

10.3389/frai.2020.00064

One Hundred Years of Migration Discourse in The Times: A Discourse-Historical Word Vector Space Approach to the Construction of Meaning
Cited by: 5
Author(s): Lorella Viola, Jaap Verheul
Software Mentions: 3
Published: about 4 years ago

10.1038/s41598-020-60676-1

Spatio-temporal dynamics of Plasmodium falciparum transmission within a spatial unit on the Colombian Pacific Coast
Cited by: 20
Author(s): Angélica Knudson, Felipe González-Casabianca, Alejandro Feged-Rivadeneira, Maria Fernanda Pedreros, Samanda Aponte, Adriana Olaya, Carlos F. Castillo, Elvira Mancilla, Anderson Piamba-Dorado, Ricardo Sánchez-Pedraza, Myriam Salazar-Terreros, Naomi W. Lucchi, Venkatachalam Udhayakumar, Chris Jacob, Alena Pance, Manuela Carrasquilla, Giovanni Apráez, Jairo Andrés Angel, Julian C. Rayner, Vladimir Corredor
Software Mentions: 3
Published: over 4 years ago

10.1002/dvdy.175

The shape of things to come: Topological data analysis and biology, from molecules to organisms
Cited by: 35
Author(s): Erik J. Amézquita, Michelle Quigley, Tim Ophelders, Elizabeth Munch, Daniel H. Chitwood
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0217413

Topological data analysis of high resolution diabetic retinopathy images
Cited by: 27
Author(s): Kathryn Garside, Robin Henderson, Irina Makarenko, Cristina Masoller
Software Mentions: 2
Published: over 5 years ago

10.3389/fpls.2017.01669

Improved Quantitative Plant Proteomics via the Combination of Targeted and Untargeted Data Acquisition
Cited by: 15
Author(s): Gene Hart‐Smith, Rodrigo S. Reis, Peter M. Waterhouse, Marc R. Wilkins
Software Mentions: 2
Published: about 7 years ago

10.1016/j.cels.2018.08.004

Assembling the Community-Scale Discoverable Human Proteome
Cited by: 121
Author(s): Mingxun Wang, Wang Jian, Jeremy Carver, Benjamin Pullman, Seong Won, Nuno Bandeira
Software Mentions: 2
Published: about 6 years ago

10.1038/s41598-020-69181-x

Poorly known 2018 floods in Bosra UNESCO site and Sergiopolis in Syria unveiled from space using Sentinel-1/2 and COSMO-SkyMed
Cited by: 15
Author(s): Deodato Tapete, Francesca Cigna
Software Mentions: 2
Published: over 4 years ago

10.1063/1.5125493

Analyzing collective motion with machine learning and topology
Cited by: 22
Author(s): Dhananjay Bhaskar, Angelika Manhart, Jesse Milzman, John T. Nardini, Kathleen M. Storey, Chad M. Topaz, Lori Ziegelmeier
Software Mentions: 2
Published: almost 5 years ago

10.1186/s13321-018-0308-5

Improved understanding of aqueous solubility modeling through topological data analysis
Cited by: 16
Author(s): Mariam Pirashvili, Lee Steinberg, Francisco Belchi Guillamon, Mahesan Niranjan, Jeremy G. Frey, Jacek Brodzki
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pcbi.1005071

Inference of Ancestral Recombination Graphs through Topological Data Analysis
Cited by: 36
Author(s): Pablo G. Cámara, Arnold J. Levine, Raúl Rabadán
Software Mentions: 2
Published: over 8 years ago

10.1016/j.bpj.2020.04.032

Protein-Folding Analysis Using Features Obtained by Persistent Homology
Cited by: 12
Author(s): Takashi Ichinomiya, Ippei Obayashi, Yasuaki Hiraoka
Software Mentions: 2
Published: over 4 years ago

10.1155/2015/587923

Incremental Discriminant Analysis in Tensor Space
Cited by: 0
Author(s): Chang Liu, Weidong Zhang, Tao Yan, Qiang Pu, Xiaoyong Du
Software Mentions: 1
Published: almost 10 years ago

10.1186/s12889-016-3015-z

Particulate matter and atherosclerosis: a bibliometric analysis of original research articles published in 1973–2014
Cited by: 18
Author(s): Feifei Wang, Xin Jia, Xianliang Wang, Yichao Zhao, Weidong Hao
Software Mentions: 1
Published: over 8 years ago

10.3390/e23091211

Understanding Changes in the Topology and Geometry of Financial Market Correlations during a Market Crash
Cited by: 8
Author(s): T. W. Yen, Kelin Xia, Siew Ann Cheong
Software Mentions: 1
Published: about 3 years ago

10.1186/s12859-020-03659-3

A topological data analysis based classification method for multiple measurements
Cited by: 13
Author(s): Henri Riihimäki, Wojciech Chachólski, Jakob Theorell, J. Hillert, Ryan Ramanujam
Software Mentions: 1
Published: over 4 years ago

10.1186/1471-2105-8-45

Identifying allosteric fluctuation transitions between different protein conformational states as applied to Cyclin Dependent Kinase 2
Cited by: 9
Author(s): Jenny Gu, Philip E. Bourne
Software Mentions: 1
Published: almost 18 years ago

10.18383/j.tom.2016.00178

Comparison of Voxel-Wise Tumor Perfusion Changes Measured with Dynamic Contrast-Enhanced (DCE) MRI and Volumetric DCE CT in Patients with Metastatic Brain Cancer Treated with Radiosurgery
Cited by: 12
Author(s): Catherine Coolens, Brandon Driscoll, Warren D. Foltz, Carly Pellow, Cynthia Ménard, Caroline Chung
Software Mentions: 1
Published: almost 8 years ago

10.3389/fcimb.2014.00122

Topological data analysis of Escherichia coli O157:H7 and non-O157 survival in soils
Cited by: 19
Author(s): A. Mark Ibekwe, Jincai Ma, David E. Crowley, Ching‐Hong Yang, Alexis M. Johnson, Tanya C. Petrossian, Pek Yee Lum
Software Mentions: 1
Published: about 10 years ago

10.3389/fpls.2018.01714

Long-Distance and Trans-Generational Stomatal Patterning by CO2 Across Arabidopsis Organs
Cited by: 12
Author(s): Miranda J. Haus, Mao Li, Daniel H. Chitwood, Thomas Jacobs
Software Mentions: 1
Published: almost 6 years ago

10.1186/s13059-014-0486-z

Topographical transcriptome mapping of the mouse medial ganglionic eminence by spatially resolved RNA-seq
Cited by: 26
Author(s): Sabrina Zechel, Paweł Zając, Peter Lönnerberg, Carlos F. Ibáñez, Sten Linnarsson
Software Mentions: 1
Published: about 10 years ago

10.1073/pnas.1917763117

Topological data analysis of zebrafish patterns
Cited by: 45
Author(s): Melissa R. McGuirl, Alexandria Volkening, Björn Sandstede
Software Mentions: 1
Published: over 4 years ago

10.1038/srep43845

Identification of Topological Network Modules in Perturbed Protein Interaction Networks
Cited by: 29
Author(s): Mihaela E. Sardiu, Joshua M. Gilmore, Brad D. Groppe, Laurence Florens, Michael P. Washburn
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-018-28477-9

Insights into myalgic encephalomyelitis/chronic fatigue syndrome phenotypes through comprehensive metabolomics
Cited by: 65
Author(s): Dorottya Nagy-Szakál, Dinesh Kumar Barupal, Bohyun Lee, Xiaoyu Che, Brent L. Williams, Ellie J. R. Kahn, Joy Ukaigwe, Lucinda Bateman, Nancy G. Klimas, Anthony L. Komaroff, Susan Levine, José G. Montoya, Daniel L. Peterson, Bruce Levin, Mady Hornig, Oliver Fiehn, W. Ian Lipkin
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-019-42873-9

Efficient message passing for cascade size distributions
Cited by: 3
Author(s): Rebekka Burkholz
Software Mentions: 1
Published: over 5 years ago

10.1155/2014/262194

Solubility Enhancement of Budesonide and Statistical Optimization of Coating Variables for Targeted Drug Delivery
Cited by: 17
Author(s): Himanshu Bhatt, Naik Bhargavi, Abhay Dharamsi
Software Mentions: 1
Published: over 10 years ago

10.1038/s41598-020-79391-y

Topological data analysis (TDA) enhances bispectral EEG (BSEEG) algorithm for detection of delirium
Cited by: 13
Author(s): Takehiko Yamanashi, Mari Kajitani, Masaaki Iwata, Kaitlyn J. Crutchley, Pedro S. Marra, Johnny R. Malicoat, Jessica C Williams, Lydia R Leyden, Hailey Long, Duachee Lo, Cassidy J Schacher, Kazuaki Hiraoka, Tomoyuki Tsunoda, Kurima Kobayashi, Yoshiaki Ikai, Koichi Kaneko, Yohtaro Umeda, Yoshimasa Kadooka, Gen Shinozaki
Software Mentions: 1
Published: almost 4 years ago

10.1038/s41598-021-81369-3

Complex networks of marine heatwaves reveal abrupt transitions in the global ocean
Cited by: 13
Author(s): Lisandro Benedetti‐Cecchi
Software Mentions: 1
Published: almost 4 years ago

10.1186/1471-2105-13-S16-S2

False discovery rates in spectral identification
Cited by: 119
Author(s): Kyowon Jeong, Sangtae Kim, Nuno Bandeira
Software Mentions: 1
Published: about 12 years ago

10.1038/s41598-021-86739-5

Using persistent homology as preprocessing of early warning signals for critical transition in flood
Cited by: 5
Author(s): Syed Mohamad Sadiq Syed Musa, Mohd Salmi Md Noorani, Fatimah Abdul Razak, Munira Ismail, Mohd Almie Alias, Saiful Izzuan Hussain
Software Mentions: 1
Published: over 3 years ago

10.1038/s41598-021-90070-4

Classification of apatite structures via topological data analysis: a framework for a ‘Materials Barcode’ representation of structure maps
Cited by: 3
Author(s): Scott Broderick, Ruhil Dongol, Tianmu Zhang, Krishna Rajan
Software Mentions: 1
Published: over 3 years ago

10.1038/s41598-021-94847-5

Topological analysis of interaction patterns in cancer-specific gene regulatory network: persistent homology approach
Cited by: 10
Author(s): Hosein Masoomy, B. Askari, Samin Tajik, Abbas K. Rizi, G. R. Jafari
Software Mentions: 1
Published: over 3 years ago

10.1186/1475-925X-11-26

Sleep/wake estimation using only anterior tibialis electromyography data
Cited by: 13
Author(s): Su-Hwan Hwang, GihSung Chung, Jeongsu Lee, Jaehyuk Shin, So-Jin Lee, Do-Un Jeong, Kwangsuk Park
Software Mentions: 1
Published: almost 13 years ago

10.1007/s11192-017-2325-y

Patent information retrieval: approaching a method and analysing nanotechnology patent collaborations
Cited by: 17
Author(s): Sercan Ozcan, Nazrul Islam
Software Mentions: 1
Published: over 7 years ago

10.1002/brb3.1277

Spectral and topological analyses of the cortical representation of the head position: Does hypnotizability matter?
Cited by: 14
Author(s): Esther Ibáñez‐Marcelo, Lisa Campioni, Diego Manzoni, ‪Enrica Laura Santarcangelo, Giovanni Petri
Software Mentions: 1
Published: over 5 years ago

10.3390/ma13102335

Nonlinear Regression Operating on Microstructures Described from Topological Data Analysis for the Real-Time Prediction of Effective Properties
Cited by: 12
Author(s): Minyoung Yun, Clara Argerich, Elías Cueto, Jean‐Louis Duval, Francisco Chinesta
Software Mentions: 1
Published: over 4 years ago

10.3390/ma13102319

A Data-Driven Learning Method for Constitutive Modeling: Application to Vascular Hyperelastic Soft Tissues
Cited by: 11
Author(s): David González, A. García, Francisco Chinesta, Elías Cueto
Software Mentions: 1
Published: over 4 years ago

10.1038/s41598-021-97218-2

Risk prediction of clinical adverse outcomes with machine learning in a cohort of critically ill patients with atrial fibrillation
Cited by: 8
Author(s): Lorenzo Falsetti, Matteo Rucco, Marco Proietti, Giovanna Viticchi, Vincenzo Zaccone, Mattia Scarponi, Laura Giovenali, Gianluca Moroncini, Cinzia Nitti, Aldo Salvi
Software Mentions: 1
Published: about 3 years ago

10.7717/peerj-cs.145

MCLEAN: Multilevel Clustering Exploration As Network
Cited by: 4
Author(s): Daniel Alcaide, Jan Aerts
Software Mentions: 1
Published: almost 7 years ago

10.3390/s110808085

Common Criteria Related Security Design Patterns for Intelligent Sensors—Knowledge Engineering-Based Implementation
Cited by: 18
Author(s): Andrzej Białas
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pcbi.1008407

Tracking collective cell motion by topological data analysis
Cited by: 14
Author(s): L. L. Bonilla, Ana Carpio, Carolina Trenado
Software Mentions: 1
Published: almost 4 years ago

10.3390/s20072006

Gait Rhythm Dynamics for Neuro-Degenerative Disease Classification via Persistence Landscape- Based Topological Representation
Cited by: 8
Author(s): Yan Yan, Kamen Ivanov, Olatunji Mumini Omisore, Tobore Igbe, Qiuhua Liu, Zedong Nie, Lei Wang
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pone.0169490

Uncovering precision phenotype-biomarker associations in traumatic brain injury using topological data analysis
Cited by: 72
Author(s): Jessica L. Nielson, Shelly R. Cooper, John K. Yue, Marco D. Sorani, Tomoo Inoue, Esther L. Yuh, Pratik Mukherjee, Tanya C. Petrossian, Jesse Paquette, Pek Yee Lum, Gunnar Carlsson, Mary J. Vassar, Hester F. Lingsma, Wayne A. Gordon, Alex B. Valadka, David O. Okonkwo, Geoffrey T. Manley, Adam R. Ferguson, Track-Tbi Investigators
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0255859

From mathematics to medicine: A practical primer on topological data analysis (TDA) and the development of related analytic tools for the functional discovery of latent structure in fMRI data
Cited by: 7
Author(s): Andrew Salch, Adam Regalski, Hassan H. Abdallah, Raviteja Suryadevara, Michael J. Catanzaro, Vaibhav A. Diwadkar
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pone.0192120

Modeling the spread of the Zika virus using topological data analysis
Cited by: 20
Author(s): Derek Lo, Briton Park
Software Mentions: 1
Published: almost 7 years ago

10.3390/biology3010022

Contemporary Network Proteomics and Its Requirements
Cited by: 8
Author(s): Wilson Wen Bin Goh, Limsoon Wong, Judy Sng
Software Mentions: 1
Published: almost 11 years ago

Projects: cran: TDA

Papers Mentioning TDA 55