Lista de obras - Susan P. Holmes - Dominio Público Uruguay

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

artículo científico publicado en 2016

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

artículo científico publicado el 11 de octubre de 2010

A multifaceted analysis of HIV-1 protease multidrug resistance phenotypes

artículo científico publicado en 2011

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

artículo científico publicado en 2018

Adaptive importance sampling for network growth models.

artículo científico publicado en 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

artículo científico publicado en 2013

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

Review of the book

An Interactive Java Statistical Image Segmentation System: GemIdent ⬇️

artículo científico publicado el 1 de junio de 2009

An Interactive Statistical Image Segmentation and Visualization System

artículo científico publicado en 2007

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

artículo científico publicado en 2003

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

artículo científico publicado en 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.

artículo científico publicado en 2016

Bioinformatics and Data Analysis

Bootstrap confidence levels for phylogenetic trees

artículo científico publicado en 1996

Colonic contribution to uremic solutes.

artículo científico publicado en 2011

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

artículo científico publicado el 25 de febrero de 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

artículo científico publicado en 2016

Denoising PCR-amplified metagenome data

artículo científico publicado en 2012

Detection of cytomegalovirus drug resistance mutations by next-generation sequencing

artículo científico publicado en 2013

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

artículo científico publicado en 2018

Diversity and recognition efficiency of T cell responses to cancer

artículo científico publicado en 2004

Doom01: biological mathematics in evolutionary processes

artículo científico publicado en 2001

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

artículo científico publicado en 2007

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.

artículo científico publicado en 2014

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.

artículo científico publicado en 2005

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

artículo científico publicado en 2005

Gene expression network analysis and applications to immunology.

artículo científico publicado en 2007

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

artículo científico publicado en 2013

Genomic interrogation of ancestral Mycobacterium tuberculosis from south India

artículo científico publicado en 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

artículo científico publicado en 2016

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

artículo científico publicado en 2007

HIV-1 transmission networks in a small world

artículo científico publicado en 2013

Horseshoes in multidimensional scaling and local kernel methods

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

artículo científico publicado en 2015

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

artículo científico publicado en 2003

Interval Graph Limits

artículo científico publicado en 2013

Localized plasticity in the streamlined genomes of vinyl chloride respiring Dehalococcoides

artículo científico publicado en 2009

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

artículo científico publicado en 2012

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

artículo científico publicado en 2020

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

artículo científico publicado en 2016

Measuring multivariate association and beyond

artículo científico publicado en 2016

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

artículo científico publicado en 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.

artículo científico publicado en 2004

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

artículo científico publicado en 2008

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

artículo científico publicado en 2016

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

artículo científico publicado en 2021

Multidomain analyses of a longitudinal human microbiome intestinal cleanout perturbation experiment

artículo científico publicado en 2017

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

artículo científico publicado en 2013

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

artículo científico publicado en 2022

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

artículo científico publicado en 2008

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

artículo científico publicado el 5 de mayo de 2012

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

artículo científico publicado en 2009

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

artículo científico publicado en 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

artículo científico publicado en 2012

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

artículo científico publicado en 2017

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

artículo científico publicado en 2010

Phylogenies: An Overview

scholarly article published 1999

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

artículo científico publicado el 1 de enero de 2012

Positive Curvature and Hamiltonian Monte Carlo ⬇️

artículo científico publicado en 2014

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

artículo científico publicado en 2005

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

artículo científico publicado en 2013

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

artículo científico publicado en 2010

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

artículo científico

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

artículo científico publicado en 2019

Sequential Monte Carlo Methods for Statistical Analysis of Tables

article

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

artículo científico publicado en 2014

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

artículo científico publicado en 2011

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

artículo científico publicado en 2001

Statistics for phylogenetic trees.

artículo científico publicado en 2003

Stein’s method for the bootstrap

THE DUALITY DIAGRAM IN DATA ANALYSIS: EXAMPLES OF MODERN APPLICATIONS

artículo científico publicado en 2011

Template Shape Estimation: Correcting an Asymptotic Bias

article

Temporal and spatial variation of the human microbiota during pregnancy

artículo científico publicado en 2015

Ten quick tips for effective dimensionality reduction.

artículo científico publicado en 2019

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

artículo científico publicado el 13 de abril de 2011

The molecular architecture of the eukaryotic chaperonin TRiC/CCT

artículo científico publicado en 2012

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

artículo científico publicado en 2008

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

artículo científico publicado en 2009

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

artículo científico publicado en 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

artículo científico publicado en 2020

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

artículo científico publicado en 2014

de Finetti Priors using Markov chain Monte Carlo computations.

artículo científico publicado en 2015

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data ⬇️

artículo científico publicado el 22 de abril de 2013

Lista de obras de Susan P. Holmes

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

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

A multifaceted analysis of HIV-1 protease multidrug resistance phenotypes

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

Adaptive importance sampling for network growth models.

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

Advancing our understanding of the human microbiome using QIIME

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

An Interactive Java Statistical Image Segmentation System: GemIdent ⬇️

An Interactive Statistical Image Segmentation and Visualization System

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

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

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

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

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

Bioinformatics and Data Analysis

Bootstrap confidence levels for phylogenetic trees

Colonic contribution to uremic solutes.

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

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

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

Computational Tools for Evaluating Phylogenetic and Hierarchical Clustering Trees

DADA2: High-resolution sample inference from Illumina amplicon data

Denoising PCR-amplified metagenome data

Detection of cytomegalovirus drug resistance mutations by next-generation sequencing

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

Diversity and recognition efficiency of T cell responses to cancer

Doom01: biological mathematics in evolutionary processes

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

Dynamical Bias in the Coin Toss

Elements of Large-Sample Theory

Elements of Large-Sample Theory

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

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

Error distribution for gene expression data.

Evolutionary Games and Population Dynamics

Forager activation and food availability in harvester ants

Gene expression diversity among Mycobacterium tuberculosis clinical isolates

Gene expression network analysis and applications to immunology.

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

Genomic interrogation of ancestral Mycobacterium tuberculosis from south India

Geometry of the Space of Phylogenetic Trees

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

HIV-1 Protease, Reverse Transcriptase, and Integrase Variation

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

HIV-1 transmission networks in a small world

Horseshoes in multidimensional scaling and local kernel methods

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

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

Interval Graph Limits

Localized plasticity in the streamlined genomes of vinyl chloride respiring Dehalococcoides

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

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

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

Measuring multivariate association and beyond

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

Metrics on Compositions and Coincidences among Renewal Sequences

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

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

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

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

Multidomain analyses of a longitudinal human microbiome intestinal cleanout perturbation experiment

Multivariate Heteroscedasticity Models for Functional Brain Connectivity

Multivariate data analysis: The French way

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

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

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

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

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

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

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

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

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

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

Phylogenies: An Overview

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