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Staff information


Lee Ann McCue

Computational Biology
Computational Scientist
Pacific Northwest National Laboratory
PO Box 999
MSIN: K8-91
Richland, WA 99352


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 a number of algorithmic advances to the Gibbs sampling technique for multiple sequence alignment. Her research at PNNL has expanded to include the analysis of microbial populations and metagenomes for microbial ecology studies, and the application of high performance computing techniques to handle the quantity of data being generated by current sequencing technologies.

Research Interests

  • ad hoc reviewer, DOE ASCR Leadership Computing Challenge, April 2016, March 2017
  • ad hoc reviewer, DOE Graduate Student Research Program, June 2016
  • ad hoc reviewer, UC Multicampus-National Lab Collaborative Research and Training Awards, Sept 2016
  • ad hoc study section member, DOE Systems Biology of Bioenergy Review Panel, May 2014
  • ad hoc study section member, DOE ASCR/BER Panel for Early Career Proposals, October 2009
  • ad hoc study section member, DOE SciDAC Panel, April 2006
  • ad hoc study section member, NIH NRSA postdoctoral fellowship panel, July 2004 - 2012
  • ad hoc reviewer, Binational Science Foundation research grant program, March 2004
  • ad hoc reviewer, LANL/UC-Riverside cooperative research grant program, August 2002
  • ad hoc study section member, DOE Human Genome Panel, June 2002

Education and Credentials

  • B.S. Microbiology and Biophysics, Iowa State University, 1986
  • Ph.D. Microbiology, The Ohio State University, 1994
  • 2018-present Deputy for Computing
  • 2018 BER Biological and Environmental Research Advisory Committee (BERAC) Subcommittee on User Research Facilities
  • 2017, 2016, 2009 DOE BER/ASCR Computing Requirements Workshop
  • 2017, 2015 Conference co-founder and current organizer of the Multi-omics for Microbiomes Conference
  • 2013-2015 Senior Research Scientist V, Computational Biology, Biological Sciences Division, PNNL, Richland, WA
  • 2010 BER/ASCR High Performance Computing to DOE Joint Genome Institute's Data Challenges Workshop
  • 2009 DOE BER/ASCR Extreme Scale Computing in Biology Workshop
  • 2005-2013 Senior Research Scientist IV, Computational Biology & Bioinformatics, Computational Sciences & Mathematics Division, PNNL, Richland, WA
  • 2000-2005 Research Scientist, Bioinformatics, Wadsworth Center, Albany, NY
  • 1997-1999 Research Affiliate (Post-doc), Bioinformatics, Wadsworth Center, Albany, NY
  • 1994-1997 Research Affiliate (Post-doc), Virology, Wadsworth Center, Albany, NY
  • 1986-1987 Research Assistant, Microbiology, Iowa State University, Ames, IA
  • 1989-1994 Graduate Research Associate, Microbiology, The Ohio State University, Columbus, OH
  • 1987-1989 Graduate Teaching Associate, Microbiology, The Ohio State University, Columbus, OH

Affiliations and Professional Service

  • Member of the American Society for Microbiology
  • Member of the International Society for Computational Biology

Awards and Recognitions

  • 2008 Winner, Supercomputing High Performance Computing Analytics Challenge

PNNL Publications


  • 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., F. 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


  • 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


  • 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


  • 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.

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