Susan P. Holmes

According to our database, Susan P. Holmes authored at least 38 papers between 1997 and 2022.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2022

Labeling Self-Tracked Menstrual Health Records With Hidden Semi-Markov Models.

Laura Symul, Susan P. Holmes

IEEE J. Biomed. Health Informatics, 2022

2021

Arcsine laws for random walks generated from random permutations with applications to genomics.

Xiao Fang, Han L. Gan, Susan P. Holmes, Haiyan Huang, Erol Peköz, Adrian Röllin, Wenpin Tang

J. Appl. Probab., 2021

CytoGLMM: conditional differential analysis for flow and mass cytometry experiments.

Christof Seiler, Anne-Maud Ferreira, Lisa M. Kronstad, Laura J. Simpson, Mathieu Le Gars, Elena Vendrame, Catherine A. Blish, Susan P. Holmes

BMC Bioinform., 2021

Integrating trees and networks into reproducible data analytic workflows.

Susan P. Holmes

Proceedings of the Extraction et Gestion des Connaissances, 2021

2020

Geomstats: A Python Package for Riemannian Geometry in Machine Learning.

Nina Miolane, Alice Le Brigant, Johan Mathe, Benjamin Hou, Nicolas Guigui, Yann Thanwerdas, Stefan Heyder, Olivier Peltre, Niklas Koep, Hadi Zaatiti, Hatem Hajri, Yann Cabanes, Thomas Gerald, Paul Chauchat, Christian Shewmake, Bernhard Kainz, Claire Donnat, Susan P. Holmes, Xavier Pennec

CoRR, 2020

Introduction to Geometric Learning in Python with Geomstats.

Nina Miolane, Nicolas Guigui, Hadi Zaatiti, Christian Shewmake, Hatem Hajri, Daniel Brooks, Alice Le Brigant, Johan Mathe, Benjamin Hou, Yann Thanwerdas, Stefan Heyder, Olivier Peltre, Niklas Koep, Yann Cabanes, Thomas Gerald, Paul Chauchat, Bernhard Kainz, Claire Donnat, Susan P. Holmes, Xavier Pennec

Proceedings of the 19th Python in Science Conference 2020 (SciPy 2020), Virtual Conference, July 6, 2020

Estimation of Orientation and Camera Parameters from Cryo-Electron Microscopy Images with Variational Autoencoders and Generative Adversarial Networks.

Nina Miolane, Frédéric Poitevin, Yee-Ting Li, Susan P. Holmes

Proceedings of the 2020 IEEE/CVF Conference on Computer Vision and Pattern Recognition, 2020

Learning Weighted Submanifolds With Variational Autoencoders and Riemannian Variational Autoencoders.

Nina Miolane, Susan P. Holmes

Proceedings of the 2020 IEEE/CVF Conference on Computer Vision and Pattern Recognition, 2020

2019

Ten quick tips for effective dimensionality reduction.

Lan H. Nguyen, Susan P. Holmes

PLoS Comput. Biol., 2019

Convex Hierarchical Clustering for Graph-Structured Data.

Claire Donnat, Susan P. Holmes

Proceedings of the 53rd Asilomar Conference on Signals, Systems, and Computers, 2019

2018

Topologically Constrained Template Estimation via Morse-Smale Complexes Controls Its Statistical Consistency.

Nina Miolane, Susan P. Holmes, Xavier Pennec

SIAM J. Appl. Algebra Geom., 2018

Multi-Table Differential Correlation Analysis of Neuroanatomical and Cognitive Interactions in Turner Syndrome.

Christof Seiler, Tamar Green, David Hong, Lindsay Chromik, Lynne Huffman, Susan P. Holmes, Allan L. Reiss

Neuroinformatics, 2018

Tracking Network Dynamics: a review of distances and similarity metrics.

Claire Donnat, Susan P. Holmes

CoRR, 2018

2017

Template Shape Estimation: Correcting an Asymptotic Bias.

Nina Miolane, Susan P. Holmes, Xavier Pennec

SIAM J. Imaging Sci., 2017

Multidomain analyses of a longitudinal human microbiome intestinal cleanout perturbation experiment.

Julia Fukuyama, Laurie Rumker, Kris Sankaran, Pratheepa Jeganathan, Les Dethlefsen, David A. Relman, Susan P. Holmes

PLoS Comput. Biol., 2017

Bayesian Unidimensional Scaling for visualizing uncertainty in high dimensional datasets with latent ordering of observations.

Lan H. Nguyen, Susan P. Holmes

BMC Bioinform., 2017

2016

Reproducible Research Workflow in R for the Analysis of Personalized Human Microbiome Data.

Benjamin J. Callahan, Diana Proctor, David A. Relman, Julia Fukuyama, Susan P. Holmes

Proceedings of the Biocomputing 2016: Proceedings of the Pacific Symposium, 2016

2015

de Finetti Priors using Markov chain Monte Carlo computations.

Sergio Bacallado, Persi Diaconis, Susan P. Holmes

Stat. Comput., 2015

Shiny-phyloseq: Web application for interactive microbiome analysis with provenance tracking.

Paul J. McMurdie, Susan P. Holmes

Bioinform., 2015

2014

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible.

Paul J. McMurdie, Susan P. Holmes

PLoS Comput. Biol., 2014

Positive Curvature and Hamiltonian Monte Carlo.

Christof Seiler, Simon Rubinstein-Salzedo, Susan P. Holmes

Proceedings of the Advances in Neural Information Processing Systems 27: Annual Conference on Neural Information Processing Systems 2014, 2014

2013

Random Spatial Structure of Geometric Deformations and Bayesian Nonparametrics.

Christof Seiler, Xavier Pennec, Susan P. Holmes

Proceedings of the Geometric Science of Information - First International Conference, 2013

2012

Denoising PCR-amplified metagenome data.

Michael J. Rosen, Benjamin J. Callahan, Daniel S. Fisher, Susan P. Holmes

BMC Bioinform., 2012

phyloseq: A Bioconductor Package for Handling and Analysis of High-Throughput Phylogenetic Sequence Data.

Paul J. McMurdie, Susan P. Holmes

Proceedings of the Biocomputing 2012: Proceedings of the Pacific Symposium, 2012

Comparisons of Distance Methods for Combining Covariates and Abundances in Microbiome Studies.

Julia Fukuyama, Paul J. McMurdie, Les Dethlefsen, David A. Relman, Susan P. Holmes

Proceedings of the Biocomputing 2012: Proceedings of the Pacific Symposium, 2012

2011

A multifaceted analysis of HIV-1 protease multidrug resistance phenotypes.

Kathleen M. Doherty, Priyanka Nakka, Bracken M. King, Soo-Yon Rhee, Susan P. Holmes, Robert W. Shafer, Mala L. Radhakrishnan

BMC Bioinform., 2011

Adaptive importance sampling for network growth models.

Adam Guetz, Susan P. Holmes

Ann. Oper. Res., 2011

Visualization and Statistical Comparisons of Microbial Communities Using R Packages on Phylochip Data.

Susan P. Holmes, Alexander V. Alekseyenko, Alden Timme, Tyrrell Nelson, Pankaj Jay Pasricha, Alfred Spormann

Proceedings of the Biocomputing 2011: Proceedings of the Pacific Symposium, 2011

2010

A classification model for G-to-A hypermutation in hepatitis B virus ultra-deep pyrosequencing reads.

Elizabeth C. Reuman, Severine Margeridon-Thermet, Harrison B. Caudill, Tommy F. Liu, Katyna Borroto-Esoda, Evguenia S. Svarovskaia, Susan P. Holmes, Robert W. Shafer

Bioinform., 2010

2008

Threshold Graph Limits and Random Threshold Graphs.

Persi Diaconis, Susan P. Holmes, Svante Janson

Internet Math., 2008

2007

Dynamical Bias in the Coin Toss.

Persi Diaconis, Susan P. Holmes, Richard Montgomery

SIAM Rev., 2007

HIV-1 Subtype B Protease and Reverse Transcriptase Amino Acid Covariation.

Soo-Yon Rhee, Tommy F. Liu, Susan P. Holmes, Robert W. Shafer

PLoS Comput. Biol., 2007

Gene expression network analysis and applications to immunology.

Serban Nacu, Rebecca Critchley-Thorne, Peter P. Lee, Susan P. Holmes

Bioinform., 2007

Statistical approaches to test involving phylogenetics.

Susan P. Holmes

Proceedings of the Mathematics of Evolution and Phylogeny., 2007

2004

Bioinformatics and Management Science: Some Common Tools and Techniques.

Ali E. Abbas, Susan P. Holmes

Oper. Res., 2004

2002

Erratum to: "Geometry of the Space of Phylogenetic Trees": [Adv. in Appl. Math. 27 (2001) 733-767].

Louis J. Billera, Susan P. Holmes, Karen Vogtmann

Adv. Appl. Math., 2002

2001

Geometry of the Space of Phylogenetic Trees.

Louis J. Billera, Susan P. Holmes, Karen Vogtmann

Adv. Appl. Math., 2001

1997

Addressing Geographical Data Errors in a Classification Tree for Soil Unit Prediction.

Philippe Lagacherie, Susan P. Holmes

Int. J. Geogr. Inf. Sci., 1997