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L. McCue · SciRah

Researcher profile · Semantic Scholar

L. McCue

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L. McCue — researcher profile on SciRah

h-index: 39
Works: 114
Citations: 5,270

Most-cited papers

FQC Dashboard: integrates FastQC results into a web-based, interactive, and extensible FASTQ quality control tool
Joseph Brown, M. Pirrung, L. McCue
2017Bioinform.963 citations Open access
Semantic Scholar
Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes.
L. McCue, William A. Thompson, C. S. Carmack, Michael P. Ryan +3 more
2001Nucleic Acids Research285 citations Open access
Semantic Scholar
Genomes and secretomes of Ascomycota fungi reveal diverse functions in plant biomass decomposition and pathogenesis
J. Challacombe, C. Hesse, Lisa M. Bramer, L. McCue +6 more
2019BMC Genomics228 citations Open access
Semantic Scholar
ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data
Silas Kieser, Joseph N. Brown, E. Zdobnov, M. Trajkovski +1 more
2019BMC Bioinformatics196 citations Open access
Semantic Scholar
Transcriptomic and Proteomic Characterization of the Fur Modulon in the Metal-Reducing Bacterium Shewanella oneidensis
Xiu-Feng Wan, N. Verberkmoes, L. McCue, Dawn M Stanek +9 more
2004Journal of Bacteriology146 citations Open access
Semantic Scholar
Soil texture and environmental conditions influence the biogeochemical responses of soils to drought and flooding
Kaizad F. Patel, S. Fansler, Tayte P. Campbell, B. Bond-Lamberty +5 more
2021Communications Earth & Environment143 citations Open access
Semantic Scholar
Global profiling of Shewanella oneidensis MR-1: expression of hypothetical genes and improved functional annotations.
E. Kolker, Alex F Picone, Michael Y. Galperin, M. Romine +36 more
2005Proceedings of the National Academy of Sciences of the United States of America128 citations Open access
Semantic Scholar
Factors influencing the identification of transcription factor binding sites by cross-species comparison.
L. McCue, William A. Thompson, C. S. Carmack, C. Lawrence
2002Genome Research126 citations Open access
Semantic Scholar
Linking microbial community structure to β-glucosidic function in soil aggregates
V. Bailey, S. Fansler, J. Stegen, L. McCue
2013The ISME Journal124 citations Open access
Semantic Scholar
Characterization of Mycobacterium tuberculosis Rv3676 (CRPMt), a Cyclic AMP Receptor Protein-Like DNA Binding Protein
G. Bai, L. McCue, K. McDonough
2005Journal of Bacteriology124 citations Open access
Semantic Scholar
Comparative systems biology across an evolutionary gradient within the Shewanella genus
K. Konstantinidis, M. Serres, M. Romine, Jorge L. M. Rodrigues +8 more
2009Proceedings of the National Academy of Sciences of the United States of America111 citations Open access
Semantic Scholar
Geoarchaeota: a new candidate phylum in the Archaea from high-temperature acidic iron mats in Yellowstone National Park
M. Kozubal, M. Romine, R. Jennings, Z. Jay +5 more
2012The ISME Journal107 citations Open access
Semantic Scholar
A Family of acr-Coregulated Mycobacterium tuberculosis Genes Shares a Common DNA Motif and Requires Rv3133c (dosR or devR) for Expression
M. Florczyk, L. McCue, A. Purkayastha, E. Currenti +2 more
2003Infection and Immunity106 citations Open access
Semantic Scholar
Identification of co-regulated genes through Bayesian clustering of predicted regulatory binding sites
Z. Qin, L. McCue, William A. Thompson, Linda E. Mayerhofer +2 more
2003Nature Biotechnology105 citations
Semantic Scholar
Combined Statistical Analyses of Peptide Intensities and Peptide Occurrences Improves Identification of Significant Peptides from MS-Based Proteomics Data
B. Webb-Robertson, L. McCue, K. Waters, M. Matzke +4 more
2010Journal of Proteome Research97 citations Open access
Semantic Scholar
Identification of a novel class in the α/β hydrolase fold superfamily: The N‐myc differentiation‐related proteins
Eudean Shaw, L. McCue, C. Lawrence, J. Dordick
200292 citations
Semantic Scholar
Identification of a Mycobacterium tuberculosis Putative Classical Nitroreductase Gene Whose Expression Is Coregulated with That of the acr Gene within Macrophages, in Standing versus Shaking Cultures, and under Low Oxygen Conditions
A. Purkayastha, L. McCue, K. McDonough
2002Infection and Immunity82 citations Open access
Semantic Scholar
Comparative Bacterial Proteomics: Analysis of the Core Genome Concept
Stephen J. Callister, L. McCue, Joshua E. Turse, Matthew E. Monroe +4 more
2008PLoS ONE79 citations Open access
Semantic Scholar
Metaphenomic Responses of a Native Prairie Soil Microbiome to Moisture Perturbations
Taniya Roy Chowdhury, Joon-Yong Lee, E. Bottos, C. Brislawn +13 more
2019mSystems76 citations Open access
Semantic Scholar
Micrometer-scale physical structure and microbial composition of soil macroaggregates
V. Bailey, L. McCue, S. Fansler, M. Boyanov +3 more
201371 citations
Semantic Scholar
Identification of Mobile Elements and Pseudogenes in the Shewanella oneidensis MR-1 Genome
M. Romine, Tim Carlson, A. Norbeck, L. McCue +1 more
2008Applied and Environmental Microbiology70 citations Open access
Semantic Scholar
Modeling Microbial Dynamics in Heterogeneous Environments: Growth on Soil Carbon Sources
H. Resat, V. Bailey, L. McCue, A. Konopka
2011Microbial Ecology67 citations
Semantic Scholar
pmartR: Quality Control and Statistics for Mass Spectrometry-Based Biological Data
K. Stratton, B. Webb-Robertson, L. McCue, B. Stanfill +7 more
2019Journal of Proteome Research66 citations Open access
Semantic Scholar
Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative’s Workshop and Follow-On Activities
P. Vangay, J. Burgin, Anjanette Johnston, Kristen L. Beck +38 more
2021mSystems60 citations Open access
Semantic Scholar
Soil Respiration and Bacterial Structure and Function after 17 Years of a Reciprocal Soil Transplant Experiment
B. Bond-Lamberty, H. Bolton, S. Fansler, A. Heredia-Langner +4 more
2016PLoS ONE59 citations Open access
Semantic Scholar
Niche differentiation of bacteria and fungi in carbon and nitrogen cycling of different habitats in a temperate coniferous forest: A metaproteomic approach
R. Starke, Rubén López Mondéjar, Z. Human, Diana Navrátilová +11 more
202156 citations Open access
Semantic Scholar
Making connections between novel transcription factors and their DNA motifs.
Kai Tan, L. McCue, G. Stormo
2005Genome Research54 citations Open access
Semantic Scholar
ftmsRanalysis: An R package for exploratory data analysis and interactive visualization of FT-MS data
L. Bramer, Amanda M. White, K. Stratton, Allison M. Thompson +3 more
2020PLoS Comput. Biol.53 citations Open access
Semantic Scholar
Measurements of microbial community activities in individual soil macroaggregates
V. Bailey, Christina L. Bilskis, S. Fansler, L. McCue +2 more
201252 citations
Semantic Scholar
Identification of a novel class in the alpha/beta hydrolase fold superfamily: the N-myc differentiation-related proteins.
Eudean Shaw, L. McCue, C. Lawrence, J. Dordick
2002Proteins: Structure, Function, and Bioinformatics51 citations
Semantic Scholar
Myrionecta rubra population genetic diversity and its cryptophyte chloroplast specificity in recurrent red tides in the Columbia River estuary
L. Herfort, T. Peterson, L. McCue, B. Crump +7 more
201149 citations Open access
Semantic Scholar
A phylogenetic Gibbs sampler that yields centroid solutions for cis-regulatory site prediction
L. Newberg, William A. Thompson, S. Conlan, Thomas M. Smith +2 more
2007Bioinform.48 citations Open access
Semantic Scholar
The National Microbiome Data Collaborative: enabling microbiome science
E. Wood-Charlson, Anubhav, D. Auberry, H. Blanco +33 more
2020Nature Reviews Microbiology46 citations Open access
Semantic Scholar
Red Waters of Myrionecta rubra are Biogeochemical Hotspots for the Columbia River Estuary with Impacts on Primary/Secondary Productions and Nutrient Cycles
L. Herfort, T. Peterson, F. Prahl, L. McCue +5 more
2012Estuaries and Coasts46 citations
Semantic Scholar
VESPA: software to facilitate genomic annotation of prokaryotic organisms through integration of proteomic and transcriptomic data
Elena S. Peterson, L. McCue, Alexandra C Schrimpe-Rutledge, Jeffrey L. Jensen +8 more
2012BMC Genomics36 citations Open access
Semantic Scholar
PhyloScan: identification of transcription factor binding sites using cross-species evidence
C. S. Carmack, L. McCue, L. Newberg, C. Lawrence
2007Algorithms for Molecular Biology36 citations Open access
Semantic Scholar
Fnr (EtrA) acts as a fine-tuning regulator of anaerobic metabolism in Shewanella oneidensis MR-1
C. Cruz-García, A. Murray, Jorge L. M. Rodrigues, J. Gralnick +4 more
2011BMC Microbiology35 citations Open access
Semantic Scholar
Challenges in Bioinformatics Workflows for Processing Microbiome Omics Data at Scale
Bin Hu, S. Canon, E. Eloe-Fadrosh, Anubhav +24 more
2022Frontiers in Bioinformatics28 citations Open access
Semantic Scholar
Quantum Mechanical Methods Predict Accurate Thermodynamics of Biochemical Reactions
R. P. Joshi, Andrew D. McNaughton, Dennis G. Thomas, C. Henry +3 more
2021ACS Omega27 citations Open access
Semantic Scholar
Temporal dynamics of CO2 and CH4 loss potentials in response to rapid hydrological shifts in tidal freshwater wetland soils
Taniya RoyChowdhury, L. Bramer, D. Hoyt, Young-Mo Kim +5 more
201727 citations Open access
Semantic Scholar
Using the Gibbs Motif Sampler to Find Conserved Domains in DNA and Protein Sequences
William A. Thompson, L. McCue, C. Lawrence
2005Current Protocols in Bioinformatics27 citations
Semantic Scholar
Network analysis of transcriptomics expands regulatory landscapes in Synechococcus sp. PCC 7002
Ryan S. McClure, Christopher C. Overall, J. Mcdermott, E. Hill +6 more
2016Nucleic Acids Research26 citations Open access
Semantic Scholar
Rhodopseudomonas palustris Regulons Detected by Cross-Species Analysis of Alphaproteobacterial Genomes
S. Conlan, C. Lawrence, L. McCue
2005Applied and Environmental Microbiology24 citations Open access
Semantic Scholar
Identification and Characterization of a Developmentally Regulated Protein, EshA, Required for Sporogenic Hyphal Branches in Streptomyces griseus
Jangyul Kwak, L. McCue, Kristen Trczianka, K. E. Kendrick
2001Journal of Bacteriology24 citations Open access
Semantic Scholar
Factors affecting the bacterial community composition and heterotrophic production of Columbia River estuarine turbidity maxima
L. Herfort, B. Crump, Caroline S. Fortunato, L. McCue +4 more
2017MicrobiologyOpen23 citations Open access
Semantic Scholar
A model of cyclic transcriptomic behavior in the cyanobacterium Cyanothece sp. ATCC 51142.
J. Mcdermott, Christopher S. Oehmen, L. McCue, E. Hill +5 more
2011Molecular Biosystems21 citations
Semantic Scholar
STREAMS guidelines: Standards for technical reporting in environmental and host-associated microbiome studies
Julia M. Kelliher, C. Mirzayi, S. Bordenstein, Aaron Oliver +244 more
2025Nature Microbiology20 citations Open access
Semantic Scholar
SPOCS: software for predicting and visualizing orthology/paralogy relationships among genomes
Darren S. Curtis, Aaron R. Phillips, Stephen J. Callister, Sean P. Conlan +1 more
2013Bioinform.20 citations Open access
Semantic Scholar
Measuring Global Credibility with Application to Local Sequence Alignment
B. Webb-Robertson, L. McCue, C. Lawrence
2008PLoS Comput. Biol.19 citations Open access
Semantic Scholar
Protist 18S rRNA gene Sequence Analysis Reveals Multiple Sources of Organic Matter Contributing to Turbidity Maxima of the Columbia River Estuary
L. Herfort, T. Peterson, L. McCue, P. Zuber
201118 citations Open access
Semantic Scholar

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