Computational Scientist
Computational Scientist


Dr. Lee Ann McCue is a computational scientist and the Chief Data and Analytics Officer for PNNL’s Environmental Molecular Sciences Division and the Environmental Molecular Sciences Laboratory (EMSL) user program. McCue joined PNNL in 2005 as a senior research scientist. After joining EMSL in 2015, she now develops and implements computational strategy for multi-scale modeling, data analysis, and FAIR (Findable, Accessible, Interoperable, and Reusable) data management, as well as develops, acquires, and provides software and hardware to enable the division and the user program’s science areas. She is responsible for infrastructure health, development, procurement, investment, and divestment of computational resources. She also collaborates with EMSL users to ensure integration between experimental and computational resources for improved scientific discovery.

Research Interest

Dr. McCue's early research focused on the development and application of comparative genomics methods for studies of transcription regulation in bacteria. Her research pioneered the phylogenetic footprinting approach for predicting transcription factor binding sites de novo using multiple bacterial genomes and contributed to several algorithmic advances to the Gibbs sampling technique for multiple sequence alignment.  


  • PhD in Microbiology, The Ohio State University, 1994 

  • Research Affiliate Postdoc, Bioinformatics, Wadsworth Center, 1997-1999 

  • Research Affiliate Postdoc, Virology, Wadsworth Center, 1994-1997 

  • BS in Microbiology and Biophysics, Iowa State University, 1986 

Affiliations and Professional Service

  • Member, KBase Scientific Advisory Board, U.S. Department of Energy (DOE) (2020 – Present) 

  • Reviewer (ad hoc), Genomics-Enabled Plant Biology for Determination of Gene Function Review Panel, DOE Biological Environmental Research (BER) (2019) 

  • Biological and Environmental Research Advisory Committee, Subcommittee on User Research Facilities, DOE BER (2018) 

  • Reviewer (ad hoc), Leadership Computing Challenge, DOE Advanced Scientific Computing (ASCR) (2016, 2017) 

  • Co-founder and Organizer, Multi-Omics for Microbiomes Conference (2015, 2017) 

  • Computing Requirements Workshop, DOE BER/ASCR programs (2009, 2016, 2017) 

  • Reviewer (ad hoc), Graduate Student Research Program, DOE (June 2016) 

  • Reviewer (ad hoc), Multicampus-National Lab Collaborative Research and Training Awards, University of California (2016) 

  • Study Section Member (ad hoc), Systems Biology of Bioenergy Review Panel, DOE (2014) 

  • Study Section Member (ad hoc), Postdoctoral Fellowship Panel, NIH National Research Service Award (2004 – 2012) 

  • High Performance Computing to DOE Joint Genome Institute's Data Challenges Workshop, DOE BER/ASCR (2010)  

  • Systems Biology Knowledgebase Workshops, DOE BER (2008, 2010) 

  • Advisory Panel Member, Genomic Sequencing Centers for Infectious Diseases, National Institute of Allergy and Infectious Diseases Genomic Sequencing Centers (2009-2012) 

  • ASCR Extreme Scale Computing in Biology Workshop, DOE BER (2009) 

  • Member, International Society for Computational Biology 

  • Study Section Member (ad hoc), Panel for Early Career Proposals, DOE BER/ASCR (2009) 

  • Study Section Member (ad hoc), SciDAC Panel, DOE (2006) 

  • Reviewer (ad hoc), Research Grant Program, Binational Science Foundation (2004) 

  • Reviewer (ad hoc), Los Alamos National Laboratory/University of California, Riverside Cooperative Research Grant Program (2002) 

  • Study Section Member (ad hoc), Human Genome Panel, DOE (2002) 

Awards and Recognitions

  • Supercomputing High-Performance Computing Analytics Challenge (2008) 



Bramer L.M., A.M. White, K.G. Stratton, A.M. Thompson, D.M. Claborne, K.S. Hofmockel, and L. McCue. 2020. "ftmsRanalysis: An R package for exploratory data analysis and interactive visualization of FT-MS data." PLoS Computational Biology 16, no. 3:Article No. e1007654. PNNL-SA-152118. doi:10.1371/journal.pcbi.1007654 

Wood-Charlson E.M., Anubhav, D.L. Auberry, H. Blanco, M.I. Borkum, Y. Eberlim de Corilo, and K.W. Davenport, et al. 2020. "The National Microbiome Data Collaborative: Enabling Microbiome Science." Nature Reviews Microbiology 18, no. 6:313-314. PNNL-SA-152551. doi:10.1038/s41579-020-0377-0 

Kieser S., J. Brown J., E.M. Zdobnov, M. Trajkovski M., L.A. McCue. 2020. “ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data.” BMC bioinformatics  21, 257. 


Challacombe J., J. Challacombe, C.N. Hesse, L.M. Bramer, L. McCue, M.S. Lipton, and S.O. Purvine, et al. 2019. "Genomes and Secretomes of Ascomycota Fungi Reveal Diverse Functions in Plant Biomass Decomposition and Pathogenesis." BMC Genomics 20, no. 1:Article No. 976. PNNL-SA-140986. doi:10.1186/s12864-019-6358-x 

Stratton K.G., B.M. Webb-Robertson, L. McCue, B.A. Stanfill, D.M. Claborne, I.G. Godinez, and T. Johansen, et al. 2019. "pmartR: Quality Control and Statistics for Mass Spectrometry-Based Biological Data." Journal of Proteome Research 18, no. 3:1418-1425. PNNL-SA-123105. doi:10.1021/acs.jproteome.8b00760 

Roy Chowdhury, T., Lee, J-Y., Bottos, E.M., Brislawn, C.J., White, R.A., Bramer, L.M., Brown, J., Zucker, J.D., Kim, Y-M., Jumpponen, A., Rice, C.W., Fansler, S.J., Metz, T.O., McCue, L.A., Callister, S.J., Song, H-S., and J.K. Jansson. 2019. “Metaphenomic responses of a native prairie soil microbiome to moisture perturbations.” mSystems, 4(4): e00061-19. 


Callister S.J., L. McCue, A.A. Boaro, B.L. Lamarche, R.A. White, J.M. Brown, and B.K. Ahring. 2018. "Identification of metabolite and protein explanatory variables governing microbiome establishment and re-establishment within a cellulose-degrading anaerobic bioreactor." PLoS One 13, no. 10:Article number e0204831. PNNL-SA-133574. doi:10.1371/journal.pone.0204831 

Roy Chowdhury T., L.M. Bramer, D.W. Hoyt, Y. Kim, T.O. Metz, L. McCue, and H.L. Diefenderfer, et al. 2018. "Temporal dynamics of CO2 and CH4 loss potentials in response to rapid hydrological shifts in tidal freshwater wetland soils." Ecological Engineering 114. PNNL-SA-123359. doi:10.1016/j.ecoleng.2017.06.041 


Brown J.M., M.A. Pirrung, and L. McCue. 2017. "FQC Dashboard: Integrates FastQC Results into a Web-Based, Interactive, and Extensible FASTQ Quality Control Tool." Bioinformatics 33, no. 19:3137-3139. PNNL-SA-124428. doi:10.1093/bioinformatics/btx373 

Herfort L., B.C. Crump, C.S. Fortunato, L.A. McCue, V. Campbell, H.M. Simon, and A.M. Baptista, et al. 2017. "Factors Affecting the Bacterial Community Composition and Heterotrophic Production of Columbia River Estuarine Turbidity Maxima." MicrobiologyOpen 6, no. 6:Article No. e00522. PNWD-SA-10529. doi:10.1002/mbo3.522 


Bond-Lamberty B., H. Bolton, S.J. Fansler, A. Heredia-Langner, C. Liu, L.A. McCue, and J.L. Smith, et al. 2016. "Soil respiration and bacterial structure and function after 17 years of a reciprocal soil transplant experiment." PLoS One 11, no. 3:e0150599. PNNL-SA-94916. doi:10.1371/journal.pone.0150599 

McClure R.S., C.C. Overall, J.E. McDermott, E.A. Hill, L.M. Markillie, L.A. McCue, and R.C. Taylor, et al. 2016. "Network Analysis of Transcriptomics Expands Regulatory Landscapes in Synechococcus sp. PCC 7002." Nucleic Acids Research 44, no. 18:8810-8825. PNNL-SA-113421. doi:10.1093/nar/gkw737 


Aryal U.K., S.J. Callister, B.H. McMahon, L.A. McCue, J.N. Brown, J. Stockel, and M.L. Liberton, et al. 2014. "Proteomic profiles of five strains of oxygenic photosynthetic cyanobacteria of the genus Cyanothece." Journal of Proteome Research 13, no. 7:3262-3276. PNNL-SA-102687. doi:10.1021/pr5000889 

Webb-Robertson B.M., C.D. Corley, L.A. McCue, B.H. Clowers, C.P. Dowling, K.L. Wahl, and D.S. Wunschel, et al. 2014. "Forensic Signature Detection of Yersinia Pestis Culturing Practices Across Institutions Using a Bayesian Network." Journal of Forensic Investigation 2, no. 1: Article No. 7. PNNL-SA-96751. 


Bailey V.L., L.A. McCue, S.J. Fansler, M.I. Boyanov, F. DeCarlo, K.M. Kemner, and A. Konopka. 2013. "Micrometer-Scale Physical Structure and Microbial Composition of Soil Macroaggregates." Soil Biology and Biochemistry 65. PNNL-SA-84756. doi:10.1016/j.soilbio.2013.02.005 

Bailey V.L., S.J. Fansler, J.C. Stegen, and L.A. McCue. 2013. "Linking Microbial Community Structure to ß-Glucosidic Function in Soil Aggregates." The ISME Journal 7, no. 10:2044-2053. PNNL-SA-90744. doi:10.1038/ismej.2013.87 

Curtis D.S., A.R. Phillips, and L.A. McCue. 2013. SPOCS User Guide. PNNL-22365. Richland, WA: Pacific Northwest National Laboratory. SPOCS User Guide 

Curtis D.S., A.R. Phillips, S.J. Callister, S. Conlan, and L.A. McCue. 2013. "SPOCS: Software for Predicting and Visualizing Orthology/Paralogy Relationships Among Genomes." Bioinformatics 29, no. 20:2641-2642. PNNL-SA-94621. doi:10.1093/bioinformatics/btt454 

Kozubal M., M.F. Romine, R. Jennings, Z. Jay, S.G. Tringe, D.B. Rusch, and J. Beam, et al. 2013. "Geoarchaeota: a new candidate phylum in the Archaea from high-temperature acidic iron mats in Yellowstone National Park." The ISME Journal 7, no. 3:622-634. PNNL-SA-85899. doi:10.1038/ismej.2012.132 

Webb-Robertson B.M., C.D. Corley, L.A. McCue, K.L. Wahl, and H.W. Kreuzer. 2013. "Fusion of Laboratory and Textual Data for Investigative Bioforensics." Forensic Science International 226, no. 1-3:118-24. PNNL-SA-88567. doi:10.1016/j.forsciint.2012.12.016 

Wilkins M.J., K.C. Wrighton, C.D. Nicora, K.H. Williams, L.A. McCue, K.M. Handley, and C.S. Miller, et al. 2013. "Fluctuations in Species-Level Protein Expression Occur during Element and Nutrient Cycling in the Subsurface." PLoS One 8, no. 3:e57819. PNNL-SA-91270. doi:10.1371/journal.pone.0057819 


Bailey V.L., C.L. Bilskis, S.J. Fansler, L.A. McCue, J.L. Smith, and A. Konopka. 2012. "Measurements of Microbial Community Activities in Individual Soil Macroaggregates." Soil Biology and Biochemistry 48. PNNL-SA-82792. doi:10.1016/j.soilbio.2012.01.004 

Herfort L., T.D. Peterson, F.G. Prahl, L.A. McCue, J.A. Needoba, B.C. Crump, and G.C. Roegner, et al. 2012. "Red waters of Myrionecta rubra are biogeochemical hotspots for the Columbia River estuary with impacts on primary/secondary productions and nutrient cycles." Estuaries and Coasts 35, no. 3:878-891. PNNL-SA-82992. doi:10.1007/s12237-012-9485-z 

Peterson E.S., L.A. McCue, A.C. Rutledge, J.L. Jensen, J. Walker, M.A. Kobold, and S.R. Webb, et al. 2012. "VESPA: Software to Facilitate Genomic Annotation of Prokaryotic Organisms Through Integration of Proteomic and Transcriptomic Data." BMC Genomics 13, no. 1:Article No. 131. PNNL-SA-82717. doi:10.1186/1471-2164-13-131 

Resat H., V.L. Bailey, L.A. McCue, and A. Konopka. 2012. "Modeling microbial dynamics in heterogeneous environments: Growth on soil carbon sources." Microbial Ecology 63, no. 4:883-897. PNNL-SA-80353. doi:10.1007/s00248-011-9965-x 


Cruz-Garza C., A.E. Murray, J. Rodrigues, J.A. Gralnick, L.A. McCue, M.F. Romine, and F.E. Loffler, et al. 2011. "Fnr (EtrA) acts as a fine-tuning regulator of anaerobic metabolism in Shewanella oneidensis MR-1." BMC Microbiology 11. PNNL-SA-74924. doi:10.1186/1471-2180-11-64 

Herfort L., T.D. Peterson, L.A. McCue, and P.A. Zuber. 2011. "Protist 18S rRNA gene Sequence Analysis Reveals Multiple Sources of Organic Matter Contributing to Turbidity Maxima of the Columbia River Estuary." Marine Ecology Progress Series 438. PNNL-SA-78218. doi:10.3354/meps09303 

Herfort L., T.D. Peterson, L.A. McCue, B.C. Crump, F.G. Prahl, A.M. Baptista, and V. Campbell, et al. 2011. "Myrionecta Rubra Population Genetic Diversity and Its Cryptophyte Chloroplast Specificity in Recurrent Red Tides in the Columbia River Estuary." Aquatic Microbial Ecology. International Journal 62, no. 1:85-87. PNNL-SA-68686. doi:10.3354/ame01460 

McDermott J.E., C.S. Oehmen, L.A. McCue, E.A. Hill, D.M. Choi, J. Stockel, and M.L. Liberton, et al. 2011. "A Model of Cyclic Transcriptomic Behavior in Cyanobacterium Cyanothece sp. ATCC 51142." Molecular Biosystems 7, no. 8:2407-2418. PNNL-SA-74409. doi:10.1039/C1MB05006K 


Webb-Robertson B.M., L.A. McCue, K.M. Waters, M.M. Matzke, J.M. Jacobs, T.O. Metz, and S.M. Varnum, et al. 2010. "Combined Statistical Analyses of Peptide Intensities and Peptide Occurrences Improves Identification of Significant Peptides from MS-based Proteomics Data." Journal of Proteome Research 9, no. 11:5748-5756. PNNL-SA-72886. 

Yang Y., L.A. McCue, A.B. Parsons, S. Feng, and J. Zhou. 2010. "The tricarboxylic acid cycle in Shewanella oneidensis is independent of Fur and RyhB control." BMC Microbiology 10. PNNL-SA-66348. doi:10.1186/1471-2180-10-264 


Cannon W.R., B.M. Webb-Robertson, A.R. Willse, M. Singhal, L.A. McCue, J.E. McDermott, and R.C. Taylor, et al. 2009. "An Integrative Computational Framework for Hypotheses-Driven Systems Biology Research in Proteomics and Genomics." In Computational and Systems Biology: Methods and Applications. 63-85. Trivandrum:Research Signpost. PNNL-SA-57999. 

Konstantinidis K., M.H. Serres, M.F. Romine, J. Rodrigues, J.M. Auchutung, L.A. McCue, and M.S. Lipton, et al. 2009. "Comparative systems biology across an evolutionary gradient within the Shewanella genus." Proceedings of the National Academy of Sciences of the United States of America 106, no. 37:15909-15914. PNNL-SA-63930. doi:10.1073/pnas.0902000106 

Webb-Robertson B.M., L.A. McCue, N. Beagley, J.E. McDermott, D.S. Wunschel, S.M. Varnum, and J.Z. Hu, et al. 2009. "A Bayesian Integration Model of High-Throughput Proteomics and Metabolomics Data for Improved Early Detection of Microbial Infections." In Pacific Symposium on Biocomputing, 14, 451-463. Singapore: World Scientific Publishing Co. PNNL-SA-61531. 


Callister S.J., L.A. McCue, J.E. Turse, M.E. Monroe, K.J. Auberry, R.D. Smith, and J.N. Adkins, et al. 2008. "Comparative Bacterial Proteomics: Analysis of the Core Genome Concept." PLoS One 3, no. 2:e1542. PNNL-SA-58389. doi:10.1371/journal.pone.0001542 

Romine M.F., T. Carlson, A.D. Norbeck, L.A. McCue, and M.S. Lipton. 2008. "Identification of Mobile Elements and Pseudogenes in the Shewanella oneidensis MR-1 Genome." Applied and Environmental Microbiology 74, no. 10:3257-3265. PNNL-SA-60499. 

Webb-Robertson B.M., L.A. McCue, and C.E. Lawrence. 2008. "Measuring Global Credibility with Application to Local Sequence Alignment." PLoS Computational Biology 4, no. 5:Art. No e1000077. PNWD-SA-8141. doi:10.1371/journal.pcbi.1000077 


Driscoll M.E., M.F. Romine, F.S. Juhn, M.H. Serres, L.A. McCue, A.S. Beliaev, and J.K. Fredrickson, et al. 2007. "Identification of diverse carbon utilization pathways in Shewanella oneidensis MR-1 via expression profiling." Genome Informatics 18. PNNL-SA-52139. 

Newberg L.A., W.A. Thompson, S. Conlan, T.M. Smith, L.A. McCue, and C.E. Lawrence. 2007. "A phylogenetic Gibbs sampler that yields centroid solutions of cis-regulatory sites." Bioinformatics 23, no. 14:1718-1727. PNWD-SA-7675. 

Thompson W., S. Conlan, L.A. McCue, and C. Lawrence. 2007. "Using the Gibbs Motif Sampler for Phylogenetic Footprinting." In Methods in Molecular Biology: Comparative Genomics, edited by Nicholas H. Bergman. Totowa, New Jersey:Humana Press. PNWD-SA-7289. 

Thompson W.A., L.A. Newberg, S. Conlan, L.A. McCue, and C.E. Lawrence. 2007. "The Gibbs Centroid Sampler." Nucleic Acids Research 35, no. Suppl. 2:W232-W237. PNWD-SA-7783. doi:10.1093/nar/gkm265 

Carmack, C.S., McCue, L.A., Newberg, L.A., and C.E. Lawrence. 2007. “PhyloScan: identification of transcription factor binding sites using cross-species evidence.” Algorithms Mol Biol. 2:1. 


Conlan S., and L.A. McCue. 2006. "Software to perform automated comparisons of pairwise percent identities for microbial species." BioTechniques 40, no. 5:578-582. PNWD-SA-7338.