Susan P. Holmes

Orcid: 0000-0002-2208-8168

Affiliations:
  • Stanford University, Department of Statistics, USA
  • Montpellier 2 University, France (PhD 1985)


According to our database1, Susan P. Holmes authored at least 38 papers between 1997 and 2022.

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Bibliography

2022
Labeling Self-Tracked Menstrual Health Records With Hidden Semi-Markov Models.
IEEE J. Biomed. Health Informatics, 2022

2021
Arcsine laws for random walks generated from random permutations with applications to genomics.
J. Appl. Probab., 2021

CytoGLMM: conditional differential analysis for flow and mass cytometry experiments.
BMC Bioinform., 2021

Integrating trees and networks into reproducible data analytic workflows.
Proceedings of the Extraction et Gestion des Connaissances, 2021

2020
Geomstats: A Python Package for Riemannian Geometry in Machine Learning.
CoRR, 2020

Introduction to Geometric Learning in Python with Geomstats.
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.
Proceedings of the 2020 IEEE/CVF Conference on Computer Vision and Pattern Recognition, 2020

Learning Weighted Submanifolds With Variational Autoencoders and Riemannian Variational Autoencoders.
Proceedings of the 2020 IEEE/CVF Conference on Computer Vision and Pattern Recognition, 2020

2019
Ten quick tips for effective dimensionality reduction.
PLoS Comput. Biol., 2019

Convex Hierarchical Clustering for Graph-Structured Data.
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.
SIAM J. Appl. Algebra Geom., 2018

Multi-Table Differential Correlation Analysis of Neuroanatomical and Cognitive Interactions in Turner Syndrome.
Neuroinformatics, 2018

Tracking Network Dynamics: a review of distances and similarity metrics.
CoRR, 2018

2017
Template Shape Estimation: Correcting an Asymptotic Bias.
SIAM J. Imaging Sci., 2017

Multidomain analyses of a longitudinal human microbiome intestinal cleanout perturbation experiment.
PLoS Comput. Biol., 2017

Bayesian Unidimensional Scaling for visualizing uncertainty in high dimensional datasets with latent ordering of observations.
BMC Bioinform., 2017

2016
Reproducible Research Workflow in R for the Analysis of Personalized Human Microbiome Data.
Proceedings of the Biocomputing 2016: Proceedings of the Pacific Symposium, 2016

2015
de Finetti Priors using Markov chain Monte Carlo computations.
Stat. Comput., 2015

Shiny-phyloseq: Web application for interactive microbiome analysis with provenance tracking.
Bioinform., 2015

2014
Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible.
PLoS Comput. Biol., 2014

Positive Curvature and Hamiltonian Monte Carlo.
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.
Proceedings of the Geometric Science of Information - First International Conference, 2013

2012
Denoising PCR-amplified metagenome data.
BMC Bioinform., 2012

phyloseq: A Bioconductor Package for Handling and Analysis of High-Throughput Phylogenetic Sequence Data.
Proceedings of the Biocomputing 2012: Proceedings of the Pacific Symposium, 2012

Comparisons of Distance Methods for Combining Covariates and Abundances in Microbiome Studies.
Proceedings of the Biocomputing 2012: Proceedings of the Pacific Symposium, 2012

2011
A multifaceted analysis of HIV-1 protease multidrug resistance phenotypes.
BMC Bioinform., 2011

Adaptive importance sampling for network growth models.
Ann. Oper. Res., 2011

Visualization and Statistical Comparisons of Microbial Communities Using R Packages on Phylochip Data.
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.
Bioinform., 2010

2008
Threshold Graph Limits and Random Threshold Graphs.
Internet Math., 2008

2007
Dynamical Bias in the Coin Toss.
SIAM Rev., 2007

HIV-1 Subtype B Protease and Reverse Transcriptase Amino Acid Covariation.
PLoS Comput. Biol., 2007

Gene expression network analysis and applications to immunology.
Bioinform., 2007

Statistical approaches to test involving phylogenetics.
Proceedings of the Mathematics of Evolution and Phylogeny., 2007

2004
Bioinformatics and Management Science: Some Common Tools and Techniques.
Oper. Res., 2004

2002
Erratum to: "Geometry of the Space of Phylogenetic Trees": [Adv. in Appl. Math. 27 (2001) 733-767].
Adv. Appl. Math., 2002

2001
Geometry of the Space of Phylogenetic Trees.
Adv. Appl. Math., 2001

1997
Addressing Geographical Data Errors in a Classification Tree for Soil Unit Prediction.
Int. J. Geogr. Inf. Sci., 1997


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