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List of works by Levi Waldron

A gene signature in histologically normal surgical margins is predictive of oral carcinoma recurrence

scientific article

A guide to enterotypes across the human body: meta-analysis of microbial community structures in human microbiome datasets

scientific article

A reproducible approach to high-throughput biological data acquisition and integration

scientific article

Abstract 2353: A comparative meta-analysis of prognostic gene signatures for late-stage ovarian cancer

article

Abstract 3161: Identification of HPV/p16-associated microRNAs in primary oropharyngeal carcinoma

Abstract 5073: Proteomic profiling of head and neck squamous cell carcinoma cell lines

Accessible, curated metagenomic data through ExperimentHub.

scientific article

Assessment of colorectal cancer molecular features along bowel subsites challenges the conception of distinct dichotomy of proximal versus distal colorectum

scientific article

Associations between host gene expression, the mucosal microbiome, and clinical outcome in the pelvic pouch of patients with inflammatory bowel disease

scientific article published on 8 April 2015

Author Correction: Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation

scientific article published on 01 December 2019

Bayesian nonparametric cross-study validation of prediction methods ⬇️

CNVRanger: association analysis of CNVs with gene expression and quantitative phenotypes

scientific article published on 01 February 2020

CellMapper: rapid and accurate inference of gene expression in difficult-to-isolate cell types

scientific article published on 29 September 2016

Collisional broadening and shifting of Raman lines, and the potential energy surface for H2–Ar

article

Comparing Platforms for Messenger RNA Expression Profiling of Archival Formalin-Fixed, Paraffin-Embedded Tissues

scientific article published on 30 April 2015

Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples

scientific article

Comprehensive MicroRNA profiling for head and neck squamous cell carcinomas

scientific article

Creation of a Human Secretome: A Novel Composite Library of Human Secreted Proteins: Validation Using Ovarian Cancer Gene Expression Data and a Virtual Secretome Array

scientific article

Cross-study validation for the assessment of prediction algorithms

scientific article

Data and Statistical Methods To Analyze the Human Microbiome.

scientific article

Engagement of introductory biostatistics students in a novel hybrid course format

scholarly article by Marcel Ramos et al published 2 November 2016 in F1000Research

Evaluation of Oral Cavity DNA Extraction Methods on Bacterial and Fungal Microbiota

scientific article published in Scientific Reports

Expression profiling of archival tumors for long-term health studies

scientific article

Genotype and time of day shape the Populus drought response

scientific article published on 8 August 2009

HMP16SData: Efficient Access to the Human Microbiome Project Through Bioconductor

scientific article published on 01 June 2019

HMP16SData: Efficient Access to the Human Microbiome Project through Bioconductor

Integrative approaches for microarray data analysis

scientific article

Lineage-specific interface proteins match up the cell cycle and differentiation in embryo stem cells

scientific article published on 4 August 2014

Machine Learning Meta-analysis of Large Metagenomic Datasets: Tools and Biological Insights

scientific article

Meta-Analysis in Gene Expression Studies

scientific article published on January 2016

Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer

scientific article published on 01 April 2019

MetaGxData: Breast and Ovarian Clinically Annotated Transcriptomics Datasets

MetaGxData: Clinically Annotated Breast, Ovarian and Pancreatic Cancer Datasets and their Use in Generating a Multi-Cancer Gene Signature.

scientific article

Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation

scientific article published on 01 April 2019

Metagenomic biomarker discovery and explanation

scientific article published on 24 June 2011

Metagenomic microbial community profiling using unique clade-specific marker genes

scientific article

MicroRNA-301 mediates proliferation and invasion in human breast cancer.

scientific article

Microbial community function and biomarker discovery in the human microbiome

scientific article published on 19 September 2011

Microbial community function and biomarker discovery in the human microbiome

Microbiome connections with host metabolism and habitual diet from 1,098 deeply phenotyped individuals

Mo1306 Rapid and Accurate Inference of Gene Expression in Difficult-to-Isolate Cell Types

article

Modeling of simultaneous three-dimensional leaching and chemical reaction of CCA components in unfixed wood exposed to water

Modeling of simultaneous unidirectional leaching and reduction of Cr6+ in unfixed CCA treated wood

article published in 2007

Modeling the Leaching of Inorganic Components of Wood Preservatives in Service

Molecular Subtypes of High-Grade Serous Ovarian Cancer: The Holy Grail?

Multiomic Integration of Public Oncology Databases in Bioconductor

scientific article published on 01 October 2020

Multivariable association discovery in population-scale meta-omics studies

scientific article published on 16 November 2021

Más-o-menos: a simple sign averaging method for discrimination in genomic data analysis

scientific article

Optimization and analysis of a quantitative real-time PCR-based technique to determine microRNA expression in formalin-fixed paraffin-embedded samples

scientific article published on 23 June 2010

Optimized application of penalized regression methods to diverse genomic data

scientific article

Orchestrating a community-developed computational workshop and accompanying training materials

scientific article published on 17 October 2018

Orchestrating high-throughput genomic analysis with Bioconductor

scientific article

Orchestrating single-cell analysis with Bioconductor

scientific article published on 02 December 2019

Patterns of SARS-CoV-2 testing preferences in a national cohort in the United States

scientific article published on 24 December 2020

Potentially prognostic miRNAs in HPV-associated oropharyngeal carcinoma

scientific article published on 4 March 2013

Prediction of long-term leaching potential of preservative-treated wood by diffusion modeling

article published in 2005

Public data and open source tools for multi-assay genomic investigation of disease

scientific article

Publisher Correction: Orchestrating single-cell analysis with Bioconductor

scientific article published on 01 February 2020

Racial/Ethnic Disparities in Genomic Sequencing

scientific article published on 30 June 2016

Relating the metatranscriptome and metagenome of the human gut.

scientific article

Report on emerging technologies for translational bioinformatics: a symposium on gene expression profiling for archival tissues

scientific article published on 29 March 2012

Risk prediction for late-stage ovarian cancer by meta-analysis of 1525 patient samples.

scientific article

SIMON: Open-Source Knowledge Discovery Platform

scientific article published in 2021

Shear Wave Elastography of the Spleen for Monitoring Transjugular Intrahepatic Portosystemic Shunt Function

Sociodemographic variation in the oral microbiome

Sociodemographic variation in the oral microbiome

scientific article published on 08 May 2019

Stem cell gene expression programs influence clinical outcome in human leukemia.

scientific article published on 28 August 2011

Sustainable urban community development from the grassroots: Challenges and opportunities in a pedestrian street initiative

article

Testing, Testing: What SARS-CoV-2 testing services do adults in the United States actually want?

scientific article published on 18 September 2020

The Doppelgänger Effect: Hidden Duplicates in Databases of Transcriptome Profiles

scientific article published on 5 July 2016

The impact of stroma on the discovery of molecular subtypes and prognostic gene signatures in serous ovarian cancer:

article

The murine caecal microRNA signature depends on the presence of the endogenous microbiota

scientific article published on 19 December 2011

The relationship between anxiety, health, and potential stressors among adults in the United States during the COVID-19 pandemic

scientific article published on 04 November 2020

Tobacco exposure associated with oral microbiota oxygen utilization in the New York City Health and Nutrition Examination Study

scientific article published on 28 March 2019

Tobacco exposure associated with oral microbiota oxygen utilization in the New York City Health and Nutrition Examination Study

Two-stage microbial community experimental design

scientific article published on 15 August 2013

Using Registry Data to Construct a Comparison Group for Programmatic Effectiveness Evaluation - the New York City HIV Care Coordination Program.

scientific article

Waldron et al. Reply to “Commentary on the HMP16SData Bioconductor Package”

scientific article published on 01 June 2019

Widespread modulation of gene expression by copy number variation in skeletal muscle

scientific article

bioBakery: A meta'omic analysis environment

scientific article published in April 2018

curatedOvarianData: clinically annotated data for the ovarian cancer transcriptome

scientific article

mRNA transcript quantification in archival samples using multiplexed, color-coded probes ⬇️

scientific article published on 9 May 2011

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