Susan P. Holmes

45 papers A* 1Misc 5Journal 33Unranked 5
YearRankTypeTitle / Venue / Authors
2025 J jnl
Estimating the size of a set using cascading exclusion.
CoRR
Sourav Chatterjee, Persi Diaconis, Susan P. Holmes
2025 J jnl
Learning and teaching biological data science in the Bioconductor community.
PLoS Comput. Biol.
Jenny Drnevich, Frederick J. Tan, Fabricio Almeida-Silva, Robert Castelo, Aedín C. Culhane, Sean R. Davis, Maria A. Doyle, Ludwig Geistlinger, Andrew R. Ghazi, Susan P. Holmes, Leo Lahti, Alexandru Mahmoud, Kozo Nishida, Marcel Ramos, Kevin C. Rue-Albrecht, David J. H. Shih, Laurent Gatto, Charlotte Soneson
2024 J jnl
Learning and teaching biological data science in the Bioconductor community.
CoRR
Jenny Drnevich, Frederick J. Tan, Fabricio Almeida-Silva, Robert Castelo, Aedín C. Culhane, Sean Davis, Maria A. Doyle, Susan P. Holmes, Leo Lahti, Alexandru Mahmoud, Kozo Nishida, Marcel Ramos, Kevin C. Rue-Albrecht, David J. H. Shih, Laurent Gatto, Charlotte Soneson
2022 J jnl
Labeling Self-Tracked Menstrual Health Records With Hidden Semi-Markov Models.
IEEE J. Biomed. Health Informatics
Laura Symul, Susan P. Holmes
2021 J jnl
Arcsine laws for random walks generated from random permutations with applications to genomics.
J. Appl. Probab.
Xiao Fang, Han L. Gan, Susan P. Holmes, Haiyan Huang, Erol Peköz, Adrian Röllin, Wenpin Tang
2021 J jnl
CytoGLMM: conditional differential analysis for flow and mass cytometry experiments.
BMC Bioinform.
Christof Seiler, Anne-Maud Ferreira, Lisa M. Kronstad, Laura J. Simpson, Mathieu Le Gars, Elena Vendrame, Catherine A. Blish, Susan P. Holmes
2021 — conf
Integrating trees and networks into reproducible data analytic workflows.
EGC
Susan P. Holmes
2020 — conf
Estimation of Orientation and Camera Parameters from Cryo-Electron Microscopy Images with Variational Autoencoders and Generative Adversarial Networks.
CVPR Workshops
Nina Miolane, Frédéric Poitevin, Yee-Ting Li, Susan P. Holmes
2020 J jnl
Geomstats: A Python Package for Riemannian Geometry in Machine Learning.
CoRR
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
2020 — conf
Introduction to Geometric Learning in Python with Geomstats.
SciPy
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
2020 A* conf
Learning Weighted Submanifolds With Variational Autoencoders and Riemannian Variational Autoencoders.
CVPR
Nina Miolane, Susan P. Holmes
2019 Misc conf
Convex Hierarchical Clustering for Graph-Structured Data.
ACSSC
Claire Donnat, Susan P. Holmes
2019 J jnl
Convex Hierarchical Clustering for Graph-Structured Data.
CoRR
Claire Donnat, Susan P. Holmes
2019 J jnl
Estimation of Orientation and Camera Parameters from Cryo-Electron Microscopy Images with Variational Autoencoders and Generative Adversarial Networks.
CoRR
Nina Miolane, Frédéric Poitevin, Yee-Ting Li, Susan P. Holmes
2019 J jnl
Learning Weighted Submanifolds with Variational Autoencoders and Riemannian Variational Autoencoders.
CoRR
Nina Miolane, Susan P. Holmes
2019 J jnl
Ten quick tips for effective dimensionality reduction.
PLoS Comput. Biol.
Lan H. Nguyen, Susan P. Holmes
2018 J jnl
Multi-Table Differential Correlation Analysis of Neuroanatomical and Cognitive Interactions in Turner Syndrome.
Neuroinformatics
Christof Seiler, Tamar Green, David Hong, Lindsay Chromik, Lynne Huffman, Susan P. Holmes, Allan L. Reiss
2018 J jnl
Topologically Constrained Template Estimation via Morse-Smale Complexes Controls Its Statistical Consistency.
SIAM J. Appl. Algebra Geom.
Nina Miolane, Susan P. Holmes, Xavier Pennec
2018 J jnl
Tracking Network Dynamics: a review of distances and similarity metrics.
CoRR
Claire Donnat, Susan P. Holmes
2017 J jnl
Bayesian Unidimensional Scaling for visualizing uncertainty in high dimensional datasets with latent ordering of observations.
BMC Bioinform.
Lan H. Nguyen, Susan P. Holmes
2017 J jnl
Multidomain analyses of a longitudinal human microbiome intestinal cleanout perturbation experiment.
PLoS Comput. Biol.
Julia Fukuyama, Laurie Rumker, Kris Sankaran, Pratheepa Jeganathan, Les Dethlefsen, David A. Relman, Susan P. Holmes
2017 J jnl
Template Shape Estimation: Correcting an Asymptotic Bias.
SIAM J. Imaging Sci.
Nina Miolane, Susan P. Holmes, Xavier Pennec
2016 Misc conf
Reproducible Research Workflow in R for the Analysis of Personalized Human Microbiome Data.
PSB
Benjamin J. Callahan, Diana Proctor, David A. Relman, Julia Fukuyama, Susan P. Holmes
2016 J jnl
Template shape estimation: correcting an asymptotic bias.
CoRR
Nina Miolane, Susan P. Holmes, Xavier Pennec
2015 J jnl
Shiny-phyloseq: Web application for interactive microbiome analysis with provenance tracking.
Bioinform.
Paul J. McMurdie, Susan P. Holmes
2015 J jnl
de Finetti Priors using Markov chain Monte Carlo computations.
Stat. Comput.
Sergio Bacallado, Persi Diaconis, Susan P. Holmes
2014 — conf
Positive Curvature and Hamiltonian Monte Carlo.
NIPS
Christof Seiler, Simon Rubinstein-Salzedo, Susan P. Holmes
2014 J jnl
Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible.
PLoS Comput. Biol.
Paul J. McMurdie, Susan P. Holmes
2013 — conf
Random Spatial Structure of Geometric Deformations and Bayesian Nonparametrics.
GSI
Christof Seiler, Xavier Pennec, Susan P. Holmes
2012 Misc conf
Comparisons of Distance Methods for Combining Covariates and Abundances in Microbiome Studies.
Pacific Symposium on Biocomputing
Julia Fukuyama, Paul J. McMurdie, Les Dethlefsen, David A. Relman, Susan P. Holmes
2012 J jnl
Denoising PCR-amplified metagenome data.
BMC Bioinform.
Michael J. Rosen, Benjamin J. Callahan, Daniel S. Fisher, Susan P. Holmes
2012 Misc conf
phyloseq: A Bioconductor Package for Handling and Analysis of High-Throughput Phylogenetic Sequence Data.
Pacific Symposium on Biocomputing
Paul J. McMurdie, Susan P. Holmes
2011 J jnl
A multifaceted analysis of HIV-1 protease multidrug resistance phenotypes.
BMC Bioinform.
Kathleen M. Doherty, Priyanka Nakka, Bracken M. King, Soo-Yon Rhee, Susan P. Holmes, Robert W. Shafer, Mala L. Radhakrishnan
2011 J jnl
Adaptive importance sampling for network growth models.
Ann. Oper. Res.
Adam Guetz, Susan P. Holmes
2011 Misc conf
Visualization and Statistical Comparisons of Microbial Communities Using R Packages on Phylochip Data.
Pacific Symposium on Biocomputing
Susan P. Holmes, Alexander V. Alekseyenko, Alden Timme, Tyrrell Nelson, Pankaj Jay Pasricha, Alfred Spormann
2010 J jnl
A classification model for G-to-A hypermutation in hepatitis B virus ultra-deep pyrosequencing reads.
Bioinform.
Elizabeth C. Reuman, Severine Margeridon-Thermet, Harrison B. Caudill, Tommy F. Liu, Katyna Borroto-Esoda, Evguenia S. Svarovskaia, Susan P. Holmes, Robert W. Shafer
2008 J jnl
Threshold Graph Limits and Random Threshold Graphs.
Internet Math.
Persi Diaconis, Susan P. Holmes, Svante Janson
2007 J jnl
Dynamical Bias in the Coin Toss.
SIAM Rev.
Persi Diaconis, Susan P. Holmes, Richard Montgomery
2007 J jnl
Gene expression network analysis and applications to immunology.
Bioinform.
Serban Nacu, Rebecca Critchley-Thorne, Peter P. Lee, Susan P. Holmes
2007 J jnl
HIV-1 Subtype B Protease and Reverse Transcriptase Amino Acid Covariation.
PLoS Comput. Biol.
Soo-Yon Rhee, Tommy F. Liu, Susan P. Holmes, Robert W. Shafer
2007 — ch.
Statistical approaches to test involving phylogenetics.
Mathematics of Evolution and Phylogeny
Susan P. Holmes
2004 J jnl
Bioinformatics and Management Science: Some Common Tools and Techniques.
Oper. Res.
Ali E. Abbas, Susan P. Holmes
2002 J jnl
Erratum to: "Geometry of the Space of Phylogenetic Trees": [Adv. in Appl. Math. 27 (2001) 733-767].
Adv. Appl. Math.
Louis J. Billera, Susan P. Holmes, Karen Vogtmann
2001 J jnl
Geometry of the Space of Phylogenetic Trees.
Adv. Appl. Math.
Louis J. Billera, Susan P. Holmes, Karen Vogtmann
1997 J jnl
Addressing Geographical Data Errors in a Classification Tree for Soil Unit Prediction.
Int. J. Geogr. Inf. Sci.
Philippe Lagacherie, Susan P. Holmes