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Biological Sciences Staff information


Lee Ann McCue

Computational Biology
Pacific Northwest National Laboratory
PO Box 999
MSIN: K8-83
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

  • comparative genomics and metagenomics
  • sequence alignment
  • transcription regulation

Education and Credentials

  • B.S. Microbiology and Biophysics, Iowa State University, 1986
  • Ph.D. Microbiology, The Ohio State University, 1994

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


  • Roy Chowdhury T, LM Bramer, DW Hoyt, YM Kim, TO Metz, LA McCue, HL Diefenderfer, JK Jansson, and VL Bailey. 2018. "Temporal dynamics of CO2and CH4 loss potentials in response to rapid hydrological shifts in tidal freshwater wetland soils." Ecological Engineering 114:104-114.  doi:10.1016/j.ecoleng.2017.06.041


  • Brown JM, MA Pirrung, and LA McCue. 2017. "FQC Dashboard: Integrates FastQC Results into a Web-Based, Interactive, and Extensible FASTQ Quality Control Tool." Bioinformatics 33(19):3137-3139.  doi:10.1093/bioinformatics/btx373
  • Herfort L, BC Crump, CS Fortunato, LA McCue, V Campbell, HM Simon, AM Baptista, and PA Zuber. 2017. "Factors Affecting the Bacterial Community Composition and Heterotrophic Production of Columbia River Estuarine Turbidity Maxima." MicrobiologyOpen 6(6):Article No. e00522.  doi:10.1002/mbo3.522


  • Bond-Lamberty B, H Bolton, Jr, SJ Fansler, A Heredia-Langner, C Liu, LA McCue, JL Smith, and VL Bailey. 2016. "Soil respiration and bacterial structure and function after 17 years of a reciprocal soil transplant experiment." PLoS One 11(3):e0150599.  doi:10.1371/journal.pone.0150599
  • McClure RS, CC Overall, JE McDermott, EA Hill, LM Markillie, LA McCue, RC Taylor, M Ludwig, DA Bryant, and AS Beliaev. 2016. "Network Analysis of Transcriptomics Expands Regulatory Landscapes in Synechococcus sp. PCC 7002." Nucleic Acids Research 44(18):8810-8825.  doi:10.1093/nar/gkw737


  • Aryal UK, SJ Callister, BH McMahon, LA McCue, JN Brown, J Stockel, ML Liberton, S Mishra, X Zhang, CD Nicora, TE Angel, DW Koppenaal, RD Smith, HB Pakrasi, and LA Sherman. 2014. "Proteomic profiles of five strains of oxygenic photosynthetic cyanobacteria of the genus Cyanothece." Journal of Proteome Research 13(7):32623276.  doi:10.1021/pr5000889
  • Webb-Robertson BJM, CD Corley, LA McCue, BH Clowers, CP Dowling, KL Wahl, DS Wunschel, and HW Kreuzer. 2014. "Forensic Signature Detection of Yersinia Pestis Culturing Practices Across Institutions Using a Bayesian Network." Journal of Forensic Investigation 2(1):Article No. 7. 


  • Bailey VL, LA McCue, SJ Fansler, MI Boyanov, F DeCarlo, KM Kemner, and A Konopka. 2013. "Micrometer-Scale Physical Structure and Microbial Composition of Soil Macroaggregates." Soil Biology and Biochemistry 65:60-68.  doi:10.1016/j.soilbio.2013.02.005
  • Bailey VL, SJ Fansler, JC Stegen, and LA McCue. 2013. "Linking Microbial Community Structure to ß-Glucosidic Function in Soil Aggregates." The ISME Journal 7(10):2044-2053.  doi:10.1038/ismej.2013.87
  • Curtis DS, AR Phillips, SJ Callister, S Conlan, and LA McCue. 2013. "SPOCS: Software for Predicting and Visualizing Orthology/Paralogy Relationships Among Genomes." Bioinformatics 29(20):2641-2642.  doi:10.1093/bioinformatics/btt454
  • Curtis DS, AR Phillips, and LA McCue. 2013. SPOCS User GuidePNNL-22365, Pacific Northwest National Laboratory, Richland, WA. 
  • Kozubal M, MF Romine, R Jennings, Z Jay, SG Tringe, DB Rusch, J Beam, LA McCue, and WP Inskeep. 2013. "Geoarchaeota: a new candidate phylum in the Archaea from high-temperature acidic iron mats in Yellowstone National Park." The ISME Journal 7(3):622-634.  doi:10.1038/ismej.2012.132
  • Webb-Robertson BJM, CD Corley, LA McCue, KL Wahl, and HW Kreuzer. 2013. "Fusion of Laboratory and Textual Data for Investigative Bioforensics." Forensic Science International 226(1-3):118-24.  doi:10.1016/j.forsciint.2012.12.016
  • Wilkins MJ, KC Wrighton, CD Nicora, KH Williams, LA McCue, KM Handley, CS Miller, L Giloteaux, AP Montgomery, DR Lovley, JF Banfield, PE Long, and MS Lipton. 2013. "Fluctuations in Species-Level Protein Expression Occur during Element and Nutrient Cycling in the Subsurface ." PLoS One 8(3):e57819.  doi:10.1371/journal.pone.0057819


  • Resat H, VL Bailey, LA McCue, and A Konopka. 2012. "Modeling microbial dynamics in heterogeneous environments: Growth on soil carbon sources." Microbial Ecology 63(4):883-897.  doi:10.1007/s00248-011-9965-x
  • Bailey VL, CL Bilskis, SJ Fansler, LA McCue, JL Smith, and A Konopka. 2012. "Measurements of Microbial Community Activities in Individual Soil Macroaggregates." Soil Biology and Biochemistry 48:192-195.  doi:10.1016/j.soilbio.2012.01.004
  • Herfort L, TD Peterson, FG Prahl, LA McCue, JA Needoba, BC Crump, GC Roegner, V Campbell, and PA Zuber. 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(3):878-891.  doi:10.1007/s12237-012-9485-z
  • Peterson ES, LA McCue, AC Rutledge, JL Jensen, J Walker, MA Kobold, SR Webb, SH Payne, C Ansong, JN Adkins, WR Cannon, and BJM Webb-Robertson. 2012. "VESPA: Software to Facilitate Genomic Annotation of Prokaryotic Organisms Through Integration of Proteomic and Transcriptomic Data." BMC Genomics 13(1):Article No. 131.  doi:10.1186/1471-2164-13-131


  • McDermott JE, CS Oehmen, LA McCue, EA Hill, DM Choi, J Stockel, ML Liberton, HB Pakrasi, and LA Sherman. 2011. "A Model of Cyclic Transcriptomic Behavior in Cyanobacterium Cyanothece sp. ATCC 51142." Molecular Biosystems 7(8):2407-2418.  doi:10.1039/C1MB05006K
  • Cruz-Garza C, AE Murray, JLM Rodrigues, JA Gralnick, LA McCue, MF Romine, FE Loffler, and JM Tiedje. 2011. "Fnr (EtrA) acts as a fine-tuning regulator of anaerobic metabolism in Shewanella oneidensis MR-1." BMC Microbiology 11:Article No. 64.  doi:10.1186/1471-2180-11-64
  • Herfort L, TD Peterson, LA McCue, and PA 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 438:19-31.  doi:10.3354/meps09303
  • Herfort L, TD Peterson, LA McCue, BC Crump, FG Prahl, AM Baptista, V Campbell, R Warnick, M Selby, GC Roegner, and PA Zuber. 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(1):85-87.  doi:10.3354/ame01460


  • Webb-Robertson BJM, LA McCue, KM Waters, MM Matzke, JM Jacobs, TO Metz, SM Varnum, and JG Pounds. 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(11):5748-5756. 
  • Yang Y, LA McCue, AB Parsons, S Feng, and J Zhou. 2010. "The tricarboxylic acid cycle in Shewanella oneidensis is independent of Fur and RyhB control." BMC Microbiology 10:264.  doi:10.1186/1471-2180-10-264


  • Cannon WR, BJM Webb-Robertson, AR Willse, M Singhal, LA McCue, JE McDermott, RC Taylor, KM Waters, and CS Oehmen. 2009. "An Integrative Computational Framework for Hypotheses-Driven Systems Biology Research in Proteomics and Genomics." Chapter 4 in Computational and Systems Biology: Methods and Applications, pp. 63-85.  Research Signpost, Trivandrum, India. 
  • Konstantinidis K, MH Serres, MF Romine, JLM Rodrigues, JM Auchutung, LA McCue, MS Lipton, A Obraztsova, CS Giometti, KH Nealson, JK Fredrickson, and JM Tiedje. 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(37):15909-15914.  doi:10.1073/pnas.0902000106
  • Webb-Robertson BJM, LA McCue, N Beagley, JE McDermott, DS Wunschel, SM Varnum, JZ Hu, NG Isern, GW Buchko, K Mcateer, JG Pounds, SJ Skerret, D Liggitt, and CW Frevert. 2009. "A Bayesian Integration Model of High-Throughput Proteomics and Metabolomics Data for Improved Early Detection of Microbial Infections." In Pacific Symposium on Biocomputing, vol. 14, pp. 451-463.  World Scientific Publishing Co., Singapore, Singapore. 


  • Webb-Robertson BJM, LA McCue, and CE Lawrence. 2008. "Measuring Global Credibility with Application to Local Sequence Alignment." PLoS Computational Biology 4(5):Art. No e1000077.  doi:10.1371/journal.pcbi.1000077
  • Callister SJ, LA McCue, JE Turse, ME Monroe, KJ Auberry, RD Smith, JN Adkins, and MS Lipton. 2008. "Comparative Bacterial Proteomics: Analysis of the Core Genome Concept." PLoS One 3(2):e1542.  doi:10.1371/journal.pone.0001542
  • Romine MF, T Carlson, AD Norbeck, LA McCue, and MS Lipton. 2008. "Identification of Mobile Elements and Pseudogenes in the Shewanella oneidensis MR-1 Genome." Applied and Environmental Microbiology 74(10):3257-3265. 


  • Driscoll ME, MF Romine, FS Juhn, MH Serres, LA McCue, AS Beliaev, JK Fredrickson, and TS Gardner. 2007. "Identification of diverse carbon utilization pathways in Shewanella oneidensis MR-1 via expression profiling." Genome Informatics 18:287-298. 
  • Newberg LA, WA Thompson, S Conlan, TM Smith, LA McCue, and CE Lawrence. 2007. "A phylogenetic Gibbs sampler that yields centroid solutions of cis-regulatory sites." Bioinformatics 23(14):1718-1727. 
  • Thompson W, S Conlan, LA McCue, and C Lawrence. 2007. "Using the Gibbs Motif Sampler for Phylogenetic Footprinting." Chapter 25 in Methods in Molecular Biology: Comparative Genomics, vol. 1, ed. Nicholas H. Bergman.  Humana Press, Totowa, NJ. 
  • Thompson WA, LA Newberg, S Conlan, LA McCue, and CE Lawrence. 2007. "The Gibbs Centroid Sampler." Nucleic Acids Research 35(Suppl. 2):W232-W237.  doi:10.1093/nar/gkm265


  • Conlan S, and LA McCue. 2006. "Software to perform automated comparisons of pairwise percent identities for microbial species." BioTechniques 40(5):578-582. 

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