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List of works by Susan P. Holmes

1,2-Dichloroethane Exposure Alters the Population Structure, Metabolism, and Kinetics of a Trichloroethene-Dechlorinating Dehalococcoides mccartyi Consortium

scientific article published on 3 November 2016

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

scientific article published on October 11, 2010

A multifaceted analysis of HIV-1 protease multidrug resistance phenotypes

scientific article

A spatial gradient of bacterial diversity in the human oral cavity shaped by salivary flow

scientific article published on 14 February 2018

Adaptive importance sampling for network growth models.

scientific article published on September 2011

Addressing geographical data errors in a classification tree for soil unit prediction

article published in 1997

Advancing our understanding of the human microbiome using QIIME

scientific article

Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology

Review of the book

An Interactive Java Statistical Image Segmentation System: GemIdent ⬇️

scientific article (publication date: June 2009)

An Interactive Statistical Image Segmentation and Visualization System

scientific article (publication date: July 2007)

An in vitro human cell-based assay to rank the relative immunogenicity of proteins

scientific article

Analysis of casino shelf shuffling machines

Are there Still Things to Do in Bayesian Statistics?

Author Correction: Gut microbiota plasticity is correlated with sustained weight loss on a low-carb or low-fat dietary intervention

scientific article published on 01 July 2020

Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

scientific article published on 01 September 2019

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

scholarly article published 18 July 2017

Bioconductor Workflow for Microbiome Data Analysis: from raw reads to community analyses.

scientific article

Bioinformatics and Data Analysis

Bootstrap confidence levels for phylogenetic trees

scientific article

Colonic contribution to uremic solutes.

scientific article

Colony variation in the collective regulation of foraging by harvester ants ⬇️

scientific article published on February 25, 2011

Comment on "A Model for Studying Display Methods of Statistical Graphics"

Community-wide hackathons to identify central themes in single-cell multi-omics

publication published in 2021

Computational Tools for Evaluating Phylogenetic and Hierarchical Clustering Trees

scientific article published on 16 August 2012

DADA2: High-resolution sample inference from Illumina amplicon data

scientific article

Denoising PCR-amplified metagenome data

scientific article

Detection of cytomegalovirus drug resistance mutations by next-generation sequencing

scientific article

Differential Induction of IFN-α and Modulation of CD112 and CD54 Expression Govern the Magnitude of NK Cell IFN-γ Response to Influenza A Viruses

scientific article published on 24 August 2018

Diversity and recognition efficiency of T cell responses to cancer

scientific article

Doom01: biological mathematics in evolutionary processes

scientific article published in 2001

Down-regulation of the interferon signaling pathway in T lymphocytes from patients with metastatic melanoma.

scientific article

Dynamical Bias in the Coin Toss

article by Persi Diaconis et al published January 2007 in SIAM Review

Elements of Large-Sample Theory

article

Elements of Large-Sample Theory

Enhanced natural killer-cell and T-cell responses to influenza A virus during pregnancy.

scientific article

Erratum to: “Geometry of the Space of Phylogenetic Trees”

scholarly article by Louis J. Billera et al published July 2002 in Advances in Applied Mathematics

Error distribution for gene expression data.

scientific article

Evolutionary Games and Population Dynamics

review of book

Forager activation and food availability in harvester ants

article

Gene expression diversity among Mycobacterium tuberculosis clinical isolates

scientific article published in January 2005

Gene expression network analysis and applications to immunology.

scientific article published on 31 January 2007

Genetically dictated change in host mucus carbohydrate landscape exerts a diet-dependent effect on the gut microbiota

scientific article

Genomic interrogation of ancestral Mycobacterium tuberculosis from south India

scientific article published on 29 September 2007

Geometry of the Space of Phylogenetic Trees

scholarly article by Louis J. Billera et al published November 2001 in Advances in Applied Mathematics

Gut microbiome transition across a lifestyle gradient in Himalaya

Gut microbiota plasticity is correlated with sustained weight loss on a low-carb or low-fat dietary intervention

scientific article published on 29 January 2020

HIV-1 Protease, Reverse Transcriptase, and Integrase Variation

scientific article

HIV-1 subtype B protease and reverse transcriptase amino acid covariation

scientific article

HIV-1 transmission networks in a small world

scientific article published on 22 October 2013

Horseshoes in multidimensional scaling and local kernel methods

Human NK cell repertoire diversity reflects immune experience and correlates with viral susceptibility

scientific article

Human population-based identification of CD4+ T-cell peptide epitope determinants

scientific article published on 01 October 2003

Interval Graph Limits

scientific article

Localized plasticity in the streamlined genomes of vinyl chloride respiring Dehalococcoides

scientific article

Low-level persistence of drug resistance mutations in hepatitis B virus-infected subjects with a past history of Lamivudine treatment.

scientific article published on 31 October 2012

Mass Cytometry Analysis of the NK Cell Receptor-Ligand Repertoire Reveals Unique Differences between Dengue-Infected Children and Adults

scientific article published on 16 October 2020

Mass Cytometry Analytical Approaches Reveal Cytokine-Induced Changes in Natural Killer Cells.

scientific article published on 09 December 2016

Measuring multivariate association and beyond

scientific article published on 17 November 2016

Metagenomic analysis with strain-level resolution reveals fine-scale variation in the human pregnancy microbiome

scientific article published in October 2018

Metrics on Compositions and Coincidences among Renewal Sequences

article

Microarray analysis reveals differences in gene expression of circulating CD8(+) T cells in melanoma patients and healthy donors.

scientific article published in May 2004

Minority human immunodeficiency virus type 1 variants in antiretroviral-naive persons with reverse transcriptase codon 215 revertant mutations.

scientific article published on 20 August 2008

More effective drugs lead to harder selective sweeps in the evolution of drug resistance in HIV-1

scientific article published on 15 February 2016

Multi-omic profiling reveals widespread dysregulation of innate immunity and hematopoiesis in COVID-19

scientific article

Multidomain analyses of a longitudinal human microbiome intestinal cleanout perturbation experiment

scientific article

Multivariate Heteroscedasticity Models for Functional Brain Connectivity

Multivariate data analysis: The French way

article

Nasal microenvironments and interspecific interactions influence nasal microbiota complexity and S. aureus carriage

scientific article

Natural Killer Cell Receptors and Ligands Are Associated With Markers of HIV-1 Persistence in Chronically Infected ART Suppressed Patients

scientific article published on 10 February 2022

Natural variation of HIV-1 group M integrase: implications for a new class of antiretroviral inhibitors

scientific article

Nest site and weather affect the personality of harvester ant colonies ⬇️

scientific article published on May 5, 2012

Nonpolymorphic human immunodeficiency virus type 1 protease and reverse transcriptase treatment-selected mutations.

scientific article published on 31 August 2009

Nucleoside reverse transcriptase inhibitor resistance mutations associated with first-line stavudine-containing antiretroviral therapy: programmatic implications for countries phasing out stavudine

scientific article published on June 2013

PHYLOSEQ: A BIOCONDUCTOR PACKAGE FOR HANDLING AND ANALYSIS OF HIGH-THROUGHPUT PHYLOGENETIC SEQUENCE DATA

article

PRC2/EED-EZH2 complex is up-regulated in breast cancer lymph node metastasis compared to primary tumor and correlates with tumor proliferation in situ

scientific article

Parallel imaging of Drosophila embryos for quantitative analysis of genetic perturbations of the Ras pathway

scientific article published on 11 May 2017

PhyloChip microarray analysis reveals altered gastrointestinal microbial communities in a rat model of colonic hypersensitivity

scientific article

Phylogenies: An Overview

scholarly article published 1999

Phyloseq: a bioconductor package for handling and analysis of high-throughput phylogenetic sequence data ⬇️

scientific article published on January 1, 2012

Positive Curvature and Hamiltonian Monte Carlo ⬇️

scientific article published in January 2014

Profile of immune cells in axillary lymph nodes predicts disease-free survival in breast cancer.

scientific article published on 6 September 2005

Prototypical Recombinant Multi-Protease-Inhibitor-Resistant Infectious Molecular Clones of Human Immunodeficiency Virus Type 1

scientific article published on 24 June 2013

Quantitative, architectural analysis of immune cell subsets in tumor-draining lymph nodes from breast cancer patients and healthy lymph nodes

scientific article

Random Spatial Structure of Geometric Deformations and Bayesian Nonparametrics

Replication and refinement of a vaginal microbial signature of preterm birth in two racially distinct cohorts of US women

scientific article published on 28 August 2017

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

scientific article published on 01 August 2019

Sequential Monte Carlo Methods for Statistical Analysis of Tables

article

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

scientific article

Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data

article

Site-specific mobilization of vinyl chloride respiration islands by a mechanism common in Dehalococcoides

scientific article

Specific gut microbiome members are associated with distinct immune markers in allogeneic hematopoietic stem cell transplantation

Statistical Graphics for Visualizing Multivariate Data

scholarly article by Susan Holmes et al published September 1999 in Journal of the American Statistical Association

Statistical problems involving permutations with restricted positions

scientific article published in 2001

Statistics for phylogenetic trees.

scientific article

Stein’s method for the bootstrap

THE DUALITY DIAGRAM IN DATA ANALYSIS: EXAMPLES OF MODERN APPLICATIONS

scientific article

Template Shape Estimation: Correcting an Asymptotic Bias

article

Temporal and spatial variation of the human microbiota during pregnancy

scientific article published on 17 August 2015

Ten quick tips for effective dimensionality reduction.

scientific article published on 20 June 2019

The effect of individual variation on the structure and function of interaction networks in harvester ants ⬇️

scientific article (publication date: 7 November 2011)

The molecular architecture of the eukaryotic chaperonin TRiC/CCT

scientific article

The short-term regulation of foraging in harvester ants

scientific article published in 2007

Three Examples of Monte-Carlo Markov Chains: At the Interface Between Statistical Computing, Computer Science, and Statistical Mechanics

scholarly article published 1995

Threshold Graph Limits and Random Threshold Graphs

scientific article published on January 2008

Ultra-deep pyrosequencing of hepatitis B virus quasispecies from nucleoside and nucleotide reverse-transcriptase inhibitor (NRTI)-treated patients and NRTI-naive patients.

scientific article

Unusual codon bias in vinyl chloride reductase genes of Dehalococcoides species.

scientific article published on 16 February 2007

Use of exchangeable pairs in the analysis of simulations

VISUALISING DATA

VISUALIZATION AND STATISTICAL COMPARISONS OF MICROBIAL COMMUNITIES USING PACKAGES ON PHYLOCHIP DATA

scholarly article published November 2010

Variability in the analysis of a single neuroimaging dataset by many teams

scientific article published on 20 May 2020

Waste not, want not: why rarefying microbiome data is inadmissible

scientific article

de Finetti Priors using Markov chain Monte Carlo computations.

scientific article

phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data

scientific article

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