List of works - Lee Ann McCue

A family of acr-coregulated Mycobacterium tuberculosis genes shares a common DNA motif and requires Rv3133c (dosR or devR) for expression.

scientific article published on September 2003

A model of cyclic transcriptomic behavior in the cyanobacterium Cyanothece sp. ATCC 51142.

scientific article published on 23 June 2011

A phylogenetic Gibbs sampler that yields centroid solutions for cis-regulatory site prediction

scientific article

ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data

scientific article published on 22 June 2020

Analytics challenge---High-throughput visual analytics biological sciences

article

Characterization of Mycobacterium tuberculosis Rv3676 (CRPMt), a cyclic AMP receptor protein-like DNA binding protein.

scientific article

Combined statistical analyses of peptide intensities and peptide occurrences improves identification of significant peptides from MS-based proteomics data

scientific article

Comparative bacterial proteomics: analysis of the core genome concept

scientific article

Comparative systems biology across an evolutionary gradient within the Shewanella genus.

scientific article published in September 2009

Correction for Vangay et al., “Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative’s Workshop and Follow-On Activities”

scientific article published in 2021

Factors influencing the identification of transcription factor binding sites by cross-species comparison.

scientific article published on October 2002

Fluctuations in species-level protein expression occur during element and nutrient cycling in the subsurface

scientific article

Fnr (EtrA) acts as a fine-tuning regulator of anaerobic metabolism in Shewanella oneidensis MR-1.

scientific article

Functional Classification of cNMP-binding Proteins and Nucleotide Cyclases with Implications for Novel Regulatory Pathways in Mycobacterium tuberculosis

scientific article published on 01 February 2000

Fusion of laboratory and textual data for investigative bioforensics ⬇️

scientific article published on January 10, 2013

Geoarchaeota: a new candidate phylum in the Archaea from high-temperature acidic iron mats in Yellowstone National Park

scientific article (publication date: March 2013)

Identification and characterization of a developmentally regulated protein, EshA, required for sporogenic hyphal branches in Streptomyces griseus.

scientific article

Identification of a Mycobacterium tuberculosis putative classical nitroreductase gene whose expression is coregulated with that of the acr aene within macrophages, in standing versus shaking cultures, and under low oxygen conditions.

scientific article

Identification of co-regulated genes through Bayesian clustering of predicted regulatory binding sites

scientific article

Identification of mobile elements and pseudogenes in the Shewanella oneidensis MR-1 genome

scientific article published on 31 March 2008

Let the Data Do the Talking: Hypothesis Discovery from Large-Scale Data Sets in Real Time

Linking microbial community structure to β-glucosidic function in soil aggregates.

scientific article

Making connections between novel transcription factors and their DNA motifs.

scientific article

Measuring global credibility with application to local sequence alignment.

scientific article

Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative’s Workshop and Follow-On Activities

scientific article published on 22 February 2021

Molecular analysis of sporulation in Streptomyces griseus ⬇️

scientific article published on June 15, 1992

PhyloScan: identification of transcription factor binding sites using cross-species evidence

scientific article

Proteomic profiles of five strains of oxygenic photosynthetic cyanobacteria of the genus Cyanothece

scientific article published on 4 June 2014

Rhodopseudomonas palustris regulons detected by cross-species analysis of alphaproteobacterial genomes

scientific article published on November 2005

SPOCS: software for predicting and visualizing orthology/paralogy relationships among genomes

scientific article

Software to perform automated comparisons of pair-wise percent identities for microbial species

scientific article published on 01 May 2006

Soil Metabolomics Predict Microbial Taxa as Biomarkers of Moisture Status in Soils from a Tidal Wetland

scientific article published in 2022

Soil Respiration and Bacterial Structure and Function after 17 Years of a Reciprocal Soil Transplant Experiment

scientific article

Soluble expression and complex formation of proteins required for HCMV DNA replication using the SFV expression system.

scientific article published on August 1998

The Gibbs Centroid Sampler

scientific article published on 5 May 2007

The relative inefficiency of sequence weights approaches in determining a nucleotide position weight matrix.

scientific article

The tricarboxylic acid cycle in Shewanella oneidensis is independent of Fur and RyhB control

scientific article

Using the Gibbs Motif Sampler for Phylogenetic Footprinting

article

Using the Gibbs Motif Sampler to Find Conserved Domains in DNA and Protein Sequences

article

VESPA: software to facilitate genomic annotation of prokaryotic organisms through integration of proteomic and transcriptomic data

scientific article

ftmsRanalysis: An R package for exploratory data analysis and interactive visualization of FT-MS data

scientific article published on 16 March 2020

pmartR: Quality Control and Statistics for Mass Spectrometry-Based Biological Data

scientific article published on 28 January 2019

List of works by Lee Ann McCue

A family of acr-coregulated Mycobacterium tuberculosis genes shares a common DNA motif and requires Rv3133c (dosR or devR) for expression.

A model of cyclic transcriptomic behavior in the cyanobacterium Cyanothece sp. ATCC 51142.

A phylogenetic Gibbs sampler that yields centroid solutions for cis-regulatory site prediction

ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data

Analytics challenge---High-throughput visual analytics biological sciences

Characterization of Mycobacterium tuberculosis Rv3676 (CRPMt), a cyclic AMP receptor protein-like DNA binding protein.

Combined statistical analyses of peptide intensities and peptide occurrences improves identification of significant peptides from MS-based proteomics data

Comparative bacterial proteomics: analysis of the core genome concept

Comparative systems biology across an evolutionary gradient within the Shewanella genus.

Correction for Vangay et al., “Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative’s Workshop and Follow-On Activities”

Factors influencing the identification of transcription factor binding sites by cross-species comparison.

Fluctuations in species-level protein expression occur during element and nutrient cycling in the subsurface

Fnr (EtrA) acts as a fine-tuning regulator of anaerobic metabolism in Shewanella oneidensis MR-1.

Functional Classification of cNMP-binding Proteins and Nucleotide Cyclases with Implications for Novel Regulatory Pathways in Mycobacterium tuberculosis

Fusion of laboratory and textual data for investigative bioforensics ⬇️

Geoarchaeota: a new candidate phylum in the Archaea from high-temperature acidic iron mats in Yellowstone National Park

Identification and characterization of a developmentally regulated protein, EshA, required for sporogenic hyphal branches in Streptomyces griseus.

Identification of a Mycobacterium tuberculosis putative classical nitroreductase gene whose expression is coregulated with that of the acr aene within macrophages, in standing versus shaking cultures, and under low oxygen conditions.

Identification of co-regulated genes through Bayesian clustering of predicted regulatory binding sites

Identification of mobile elements and pseudogenes in the Shewanella oneidensis MR-1 genome

Let the Data Do the Talking: Hypothesis Discovery from Large-Scale Data Sets in Real Time

Linking microbial community structure to β-glucosidic function in soil aggregates.

Making connections between novel transcription factors and their DNA motifs.

Measuring global credibility with application to local sequence alignment.

Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative’s Workshop and Follow-On Activities

Molecular analysis of sporulation in Streptomyces griseus ⬇️

PhyloScan: identification of transcription factor binding sites using cross-species evidence

Proteomic profiles of five strains of oxygenic photosynthetic cyanobacteria of the genus Cyanothece

Rhodopseudomonas palustris regulons detected by cross-species analysis of alphaproteobacterial genomes

SPOCS: software for predicting and visualizing orthology/paralogy relationships among genomes

Software to perform automated comparisons of pair-wise percent identities for microbial species

Soil Metabolomics Predict Microbial Taxa as Biomarkers of Moisture Status in Soils from a Tidal Wetland

Soil Respiration and Bacterial Structure and Function after 17 Years of a Reciprocal Soil Transplant Experiment

Soluble expression and complex formation of proteins required for HCMV DNA replication using the SFV expression system.

The Gibbs Centroid Sampler

The relative inefficiency of sequence weights approaches in determining a nucleotide position weight matrix.

The tricarboxylic acid cycle in Shewanella oneidensis is independent of Fur and RyhB control

Using the Gibbs Motif Sampler for Phylogenetic Footprinting

Using the Gibbs Motif Sampler to Find Conserved Domains in DNA and Protein Sequences

VESPA: software to facilitate genomic annotation of prokaryotic organisms through integration of proteomic and transcriptomic data

ftmsRanalysis: An R package for exploratory data analysis and interactive visualization of FT-MS data

pmartR: Quality Control and Statistics for Mass Spectrometry-Based Biological Data