Staff information

PNNL Publications

2025

• Bramer L.M., E.S. Nakayasu, J.E. Flores, J. Van Eyk, M. MacCoss, H.M. Parikh, and T.O. Metz, et al. 2025. "Data from a Multi-Year Targeted Proteomics Study of a Longitudinal Birth Cohort of Type 1 Diabetes." Scientific Data 12:Art No. 112. PNNL-SA-201884. doi:10.1038/s41597-024-04249-1
• Degnan D.J., D.M. Claborne, A.M. White, S.M. Akers, N.M. Winans, Y. Eberlim de Corilo, and C.W. Strauch, et al. 2025. "FREDA: A web application for the processing, analysis, and visualization of Fourier-transform mass spectrometry data." Rapid Communications in Mass Spectrometry 39, no. 7:Art No. e9980. PNNL-SA-204933. doi:10.1002/rcm.9980
• Flores J.E., A.V. Prymolenna, L.A. Lewis, N.M. Winans, E.K. Eder, W.R. Kew, and R.P. Young, et al. 2025. "nmRanalysis: An Open-Source Web Application for Semi-Automated NMR Metabolite Profiling." Analytical Chemistry 97, no. 13:7037-7046. PNNL-SA-195593. doi:10.1021/acs.analchem.4c05104
• Velickovic M., L. Kadam, J. Kim, K. Zemaitis, D. Velickovic, Y. Gao, and R. Wu, et al. 2025. "Advanced multi-modal mass spectrometry imaging reveals functional differences of placental villous compartments at microscale resolution." Nature Communications 16:Art. No. 2061. PNNL-SA-201502. doi:10.1038/s41467-025-57107-y
• Webb-Robertson B.M., W. Wu, J.E. Flores, L.M. Bramer, F. Syed, S.A. Tersey, and S. May, et al. 2025. "RNA Splicing Events in Circulation Distinguish Individuals With and Without New-Onset Type 1 Diabetes." Journal of Clinical Endocrinology and Metabolism 110, no. 4:1148-1157. PNNL-SA-208201. doi:10.1210/clinem/dgae622
• Yang C., L. Shorey-Kendrick, C. Puy, A. Benson, P. Wilmarth, A. Reddy, and K. Zientek, et al. 2025. "Characterization of the Procoagulant Phenotype of Amniotic Fluid Across Gestation in Rhesus Macaques and Humans." Research and Practice in Thrombosis and Haemostasis 9, no. 1:Art No. 102676. PNNL-SA-205454. doi:10.1016/j.rpth.2024.102676
• Zemaitis K., J.M. Fulcher, R. Kumar, D.J. Degnan, L.A. Lewis, Y. Liao, and M. Velickovic, et al. 2025. "Spatial top-down proteomics for the functional characterization of human kidney." Clinical Proteomics 22:Art. No. 9. PNNL-SA-193767. doi:10.1186/s12014-025-09531-x

2024

• Bramer L.M., H.M. Dixon, D. Rohlman, R.P. Scott, R.L. Miller, L. Kincl, and J.B. Herbstman, et al. 2024. "PM2.5 is insufficient to explain personal PAH exposure." Geohealth 8, no. 2:Art. No. e2023GH000937. PNNL-SA-184349. doi:10.1029/2023GH000937
• Bramer L.M., H.M. Dixon, D.J. Degnan, D. Rohlman, J.B. Herbstman, K.A. Anderson, and K.M. Waters. 2024. "Expanding the access of wearable silicone wristbands in community-engaged research through best practices in data analysis and integration." In Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing (Biocomputing 2024), January 3-7, 2024, Kohala Coast, HI, edited by R.B. Altman, L. Hunter, M.D. Ritchie, and T. Murray, 170-186. PNNL-SA-188524. doi:10.1142/9789811286421_0014
• Colvin V., L.M. Bramer, B.N. Rivera, J. Pennington, K.M. Waters, and S.C. Tilton. 2024. "Modeling PAH mixture interactions in a human in vitro organotypic respiratory model." International Journal of Molecular Sciences 25, no. 8:Art. No. 4326. PNNL-SA-195907. doi:10.3390/ijms25084326
• Couvillion S.P., E.S. Nakayasu, B.M. Webb-Robertson, I.H. Yang, J.G. Eder, C.D. Nicora, and L.M. Bramer, et al. 2024. "Associations between SARS-CoV-2 Infection or COVID-19 Vaccination and Human Milk Composition: A Multi-Omics Approach." The Journal of Nutrition 154, no. 12:3566-3574. PNNL-SA-197322. doi:10.1016/j.tjnut.2024.09.032
• Degnan D.J., C.W. Strauch, M.Y. Obiri, E.D. VonKaenel, G. Kim, J. Kershaw, and D.L. Novelli, et al. 2024. "Protein-Protein Interaction Networks Derived from Classical and Machine Learning-Based Natural Language Processing Tools." Journal of Proteome Research 23, no. 12:5395-5404. PNNL-SA-199871. doi:10.1021/acs.jproteome.4c00535
• Degnan D.J., L.A. Lewis, L.M. Bramer, L. McCue, J. Pesavento, M. Zhou, and A. Bilbao. 2024. "IsoForma: An R Package for Quantifying and Visualizing Positional Isomers in Top-Down LC-MS/MS Data." Journal of Proteome Research 23, no. 8:3318-3321. PNNL-SA-191449. doi:10.1021/acs.jproteome.3c00681
• Diaz Ludovico I., S.M. Powell, G.M. Many, L.M. Bramer, S. Sarkar, K.G. Stratton, and T. Liu, et al. 2024. "A fast and sensitive size-exclusion chromatography method for plasma extracellular vesicle proteomic analysis." Proteomics 24, no. 16:2400025. PNNL-SA-194254. doi:10.1002/pmic.202400025
• Estevao Da Silva I.L., J. Kazman, L.M. Bramer, C.D. Nicora, M. Qiang Ren, N. Sambuughin, and N. Munoz Munoz, et al. 2024. "The human plasma lipidome response to exertional heat tolerance testing." Lipids in Health and Disease 23, no. 1:Art No. 380. PNNL-SA-199090. doi:10.1186/s12944-024-02322-7
• Fulcher J.M., L. Markillie, H.D. Mitchell, S.M. Williams, K.M. Engbrecht, D.J. Degnan, and L.M. Bramer, et al. 2024. "Parallel measurement of transcriptomes and proteomes from same single cells using nanodroplet splitting." Nature Communications 15, no. _:Art. No. 10614. PNNL-SA-205430. doi:10.1038/s41467-024-54099-z
• Liu J., S. Cao, K.J. Imbach, M.A. Gritsenko, T.M. Lih, J.E. Kyle, and T.M. Yaron, et al. 2024. "Multi-scale signaling and tumor evolution in high-grade gliomas." Cancer Cell 42, no. 7:P1217-1238.E19. PNNL-SA-189873. doi:10.1016/j.ccell.2024.06.004
• Oostrom M.T., M. Muniak, R.M. Eichler West, S.M. Akers, P. Pande, M.Y. Obiri, and W. Wang, et al. 2024. "Fine-tuning TrailMap: The utility of transfer learning to improve the performance of deep learning in axon segmentation of light-sheet microscopy images." PLoS One 19, no. 3:Art. No. e0293856. PNNL-SA-190650. doi:10.1371/journal.pone.0293856
• Richardson R.E., D.T. Leach, N.M. Winans, D.J. Degnan, A.V. Prymolenna, and L.M. Bramer. 2024. "Race-Specific Risk Factors for Homeownership Disparity in the United States." Journal of Data Science 22, no. 4:591-604. PNNL-SA-180676. doi:10.6339/23-JDS1116
• Webb-Robertson B.M., E.S. Nakayasu, F. Dong, K.C. Waugh, J.E. Flores, L.M. Bramer, and A.A. Schepmoes, et al. 2024. "Decrease in multiple complement protein levels associated with development of islet autoimmunity and type 1 diabetes." iScience 27, no. 2:Art. No. 108769. PNNL-SA-177389. doi:10.1016/j.isci.2023.108769

2023

• Bramer L.M., R. Hontz, A.J. Eisfeld, A.C. Sims, Y. Kim, K.G. Stratton, and C.D. Nicora, et al. 2023. "Multi-omics of NET Formation and Correlations with CNDP1, PSPB, and L-Cystine Levels in Severe and Mild COVID-19 Infections." Heliyon 9, no. 3:13795. PNNL-SA-169411. doi:10.1016/j.heliyon.2023.e13795
• Clendinen C.S., J.E. Flores, L.M. Bramer, D.J. Degnan, V.L. Paurus, and Y. Eberlim de Corilo. 2023. Enter Gaussian Mixture Modeling Extensions for Improved False Discovery Rate Estimation in GC-MS Metabolomics. PNNL-33865. Richland, WA: Pacific Northwest National Laboratory. Enter Gaussian Mixture Modeling Extensions for Improved False Discovery Rate Estimation in GC-MS Metabolomics
• Couvillion S.P., R.E. Danczak, D.T. Naylor, M.L. Smith, K.G. Stratton, V.L. Paurus, and K.J. Bloodsworth, et al. 2023. "Rapid remodeling of the soil lipidome in response to a drying-rewetting event." Microbiome 11, no. 2023:34. PNNL-SA-172149. doi:10.1186/s40168-022-01427-4
• Degnan D.J., J.E. Flores, E. Brayfindley, V.L. Paurus, B.M. Webb-Robertson, C.S. Clendinen, and L.M. Bramer. 2023. "Characterizing Families of Spectral Similarity Scores and their Use Cases for Gas Chromatography-Mass Spectrometry Small Molecule Identification." Metabolites 13, no. 10:Art. No. 1101. PNNL-SA-189894. doi:10.3390/metabo13101101
• Degnan D.J., K. Zemaitis, L.A. Lewis, L. McCue, L.M. Bramer, J.M. Fulcher, and D. Velickovic, et al. 2023. "IsoMatchMS: Open-Source Software for Automated Annotation and Visualization of High Resolution MALDI-MS Spectra." Journal of the American Society for Mass Spectrometry 34, no. 9:2061-2064. PNNL-SA-184623. doi:10.1021/jasms.3c00180
• Degnan D.J., K.G. Stratton, R.E. Richardson, D.M. Claborne, E.A. Martin, N.A. Johnson, and D.T. Leach, et al. 2023. "pmartR 2.0: A Quality Control, Visualization, and Statistics Pipeline for Multiple Omics Datatypes." Journal of Proteome Research 22, no. 2:570-576. PNNL-SA-177968. doi:10.1021/acs.jproteome.2c00610
• Degnan D.J., L.M. Bramer, J.E. Flores, V.L. Paurus, Y. Eberlim de Corilo, and C.S. Clendinen. 2023. "Evaluating Retention Index Score Assumptions to Refine GC-MS Metabolite Identification." Analytical Chemistry 95, no. 19:7536-7544. PNNL-SA-181303. doi:10.1021/acs.analchem.2c05783
• Flores J.E., D.M. Claborne, Z.D. Weller, B.M. Webb-Robertson, K.M. Waters, and L.M. Bramer. 2023. "Missing Data in Multi-Omics Integration: Recent Advances Through Artificial Intelligence." Frontiers in Artificial Intelligence 6. PNNL-SA-179732. doi:10.3389/frai.2023.1098308
• Hess B.M., L.M. Bramer, and T.D. Alfaro. 2023. Threat Agnostic Virulence Assessment of Pathogens. PNNL-34828. Richland, WA: Pacific Northwest National Laboratory. Threat Agnostic Virulence Assessment of Pathogens
• Leach D.T., K.G. Stratton, J. Irvahn, R.E. Richardson, B.M. Webb-Robertson, and L.M. Bramer. 2023. "malbacR: A package for standardized implementation of batch correction methods for omics data." Analytical Chemistry 95, no. 35:12195-12199. PNNL-SA-183164. doi:10.1021/acs.analchem.3c01289
• Liao Y., J.M. Fulcher, D.J. Degnan, S.M. Williams, L.M. Bramer, D. Velickovic, and K. Zemaitis, et al. 2023. "Spatially resolved top-down proteomics of tissue sections based on a microfluidic nanodroplet sample preparation platform." Molecular & Cellular Proteomics 22, no. 2:Art. No. 100491. PNNL-SA-174522. doi:10.1016/j.mcpro.2022.100491
• Nakayasu E.S., L.M. Bramer, C.K. Ansong, A.A. Schepmoes, T.L. Fillmore, M.A. Gritsenko, and T.R. Clauss, et al. 2023. "Plasma protein biomarkers predict the development of persistent autoantibodies and type 1 diabetes 6 months prior to the onset of autoimmunity." Cell Reports Medicine 4, no. 7:Art. No. 101093. PNNL-SA-137771. doi:10.1016/j.xcrm.2023.101093
• Nakayasu E.S., M.A. Gritsenko, Y. Kim, J.E. Kyle, K.G. Stratton, C.D. Nicora, and N. Munoz Munoz, et al. 2023. "Elucidating regulatory processes of intense physical activity by multi-omics analysis." Military Medical Research 10, no. 1:48. PNNL-SA-158793. doi:10.1186/s40779-023-00477-5
• Riley K.W., K. Burke, A. Cole, M. Ureno, H.M. Dixon, L.P. Calero, and L.M. Bramer, et al. 2023. "Factors that Influence Environmental Health Literacy from Returning Polycyclic Aromatic Hydrocarbon Exposure Results." International Public Health Journal 15, no. 3:317-331. PNNL-SA-178413.

2022

• Bhattacharjee A., O. Qafoku, J. Richardson, L.N. Anderson, K.C. Schwarz, L.M. Bramer, and G.X. Lomas, et al. 2022. "A Mineral-Doped Micromodel Platform Demonstrates Fungal Bridging of Carbon Hot Spots and Hyphal Transport of Mineral-Derived Nutrients." mSystems 7, no. 6:Art. No. e00913-22. PNNL-SA-167557. doi:10.1128/msystems.00913-22
• Dixon H.M., L.M. Bramer, R.P. Scott, L.P. Calero, D. Holmes, E.A. Gibson, and H.M. Cavalier, et al. 2022. "Evaluating predictive relationships between wristbands and urine for assessment of personal PAH exposure." Environment International 163. PNNL-SA-163167. doi:10.1016/j.envint.2022.107226
• Eloe-Fadrosh E., F. Ahmed, F. Anubhav, M. Babinski, J. Baumes, M.I. Borkum, and L.M. Bramer, et al. 2022. "The National Microbiome Data Collaborative Data Portal: an integrated multi-omics microbiome data resource." Nucleic Acids Research 50, no. D1:D828-D836. PNNL-SA-165796. doi:10.1093/nar/gkab990
• Evoy R., L. Kincl, D. Rohlman, L.M. Bramer, H.M. Dixon, P. Hystad, and H. Bae, et al. 2022. "Impact of acute temperature and air pollution exposures on adult lung function: a study of asthmatics." PLoS One 17, no. 6:Art. No. e0270412. PNNL-SA-156426. doi:10.1371/journal.pone.0270412
• Farley S.E., J.E. Kyle, H.C. Leier, L.M. Bramer, J.B. Weinstein, T.A. Bates, and J. Lee, et al. 2022. "A global lipid map reveals host dependency factors conserved across SARS-CoV-2 variants." Nature Communications 13. PNNL-SA-165174. doi:10.1038/s41467-022-31097-7
• Plubell D., L. Kall, B.M. Webb-Robertson, L.M. Bramer, A. Ives, N. Kelleher, and L.M. Smith, et al. 2022. "Putting Humpty Dumpty Back Together Again: What Does Protein Quantification Mean in Bottom-Up Proteomics?." Journal of Proteome Research 2022 21, no. 4:891-898. PNNL-SA-159627. doi:10.1021/acs.jproteome.1c00894
• Roychowdhury T., L.M. Bramer, J.M. Brown, Y. Kim, E.M. Zink, T.O. Metz, and L. McCue, et al. 2022. "Soil metabolomics predict microbial taxa as biomarkers of moisture status in soils from a tidal wetland." Microorganisms 10, no. 8:Art. No. 1653. PNNL-SA-172681. doi:10.3390/microorganisms10081653

2021

• Barklis E.W., A. Alfadhli, J.E. Kyle, L.M. Bramer, K.J. Bloodsworth, R. Lid Barklis, and H.C. Leier, et al. 2021. "Ceramide Synthase 2 Deletion Decreases the Infectivity of HIV-1." Journal of Biological Chemistry 296. PNNL-SA-156982. doi:10.1016/j.jbc.2021.100340
• Bramer L.M., J. Irvahn, P.D. Piehowski, K.D. Rodland, and B.M. Webb-Robertson. 2021. "A review of imputation strategies for isobaric labeling-based shotgun proteomics." Journal of Proteome Research 20, no. 1:1-13. PNNL-SA-149520. doi:10.1021/acs.jproteome.0c00123
• Cao X., X. Pan, S.P. Couvillion, T. Zhang, C. Tamez, L.M. Bramer, and J. White, et al. 2021. "Fate, cytotoxicity and cellular metabolomic impact of ingested nanoscale carbon dots using simulated digestion and a triculture small intestinal epithelial model." NanoImpact 23. PNNL-SA-166081. doi:10.1016/j.impact.2021.100349
• Feng S., E. Heath, B.A. Jefferson, C.A. Joslyn, H.J. Kvinge, H.D. Mitchell, and B.L. Praggastis, et al. 2021. "Hypergraph Models of Biological Networks to Identify Genes Critical to Pathogenic Viral Response." BMC Bioinformatics 22, no. 1:287. PNNL-SA-155930. doi:10.1186/s12859-021-04197-2
• Thompson A.M., K.G. Stratton, L.M. Bramer, N.S. Zavoshy, and L. McCue. 2021. "Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) Peak Intensity Normalization for Complex Mixture Analyses." Rapid Communications in Mass Spectrometry 35, no. 9:e9068. PNNL-SA-158398. doi:10.1002/rcm.9068
• Velickovic D., R.K. Chu, C. Henkel, A. Nyhuis, N. Tao, J.E. Kyle, and J.N. Adkins, et al. 2021. "Preserved and variable spatial-chemical changes of lipids across tomato leaves in response to central vein wounding reveals potential origin of linolenic acid in signal transduction cascade." Plant-Environment Interactions 2, no. 1:28-35. PNNL-SA-158820. doi:10.1002/pei3.10038
• Wang L., A. Karpova, M.A. Gritsenko, J.E. Kyle, S. Cao, Y. Li, and D. Rykunov, et al. 2021. "Proteogenomic and Metabolomic Characterization of Human Glioblastoma." Cancer Cell 39, no. 4:509-528.e20. PNNL-SA-151124. doi:10.1016/j.ccell.2021.01.006
• Webb-Robertson B.M., L.M. Bramer, B.A. Stanfill, S.M. Reehl, E.S. Nakayasu, T.O. Metz, and B. Frohnert, et al. 2021. "Prediction of the Development of Islet Autoantibodies through Integration of Environmental, Genetic, and Metabolic Markers." Journal of Diabetes 13, no. 2:143-153. PNNL-SA-146734. doi:10.1111/1753-0407.13093

2020

• 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
• Khare S., G.M. Deloid, R.M. Molina, K. Gokulan, S.P. Couvillion, K.J. Bloodsworth, and E.K. Eder, et al. 2020. "Effects of ingested nanocellulose on intestinal microbiota and homeostasis in Wistar Han rats." NanoImpact 18. PNNL-SA-149247. doi:10.1016/j.impact.2020.100216
• Leier H.C., J.B. Weinstein, J.E. Kyle, J. Lee, L.M. Bramer, K.G. Stratton, and D. Kempthorne, et al. 2020. "A global lipid map defines a network essential for Zika virus replication." Nature Communications 11, no. 3652. PNNL-SA-139745. doi:10.1038/s41467-020-17433-9
• Leier H.C., J.B. Weinstein, J.E. Kyle, J. Lee, L.M. Bramer, K.G. Stratton, and D. Kempthorne, et al. 2020. "A global lipid map defines a network essential for Zika virus replication." Nature Communications 11. PNNL-SA-148085. doi:10.1038/s41467-020-17433-9
• Metz T.O., A.C. Sims, L.M. Bramer, and H.D. Mitchell. 2020. Multi-omics Characterization of the Host Response to COVID-19. PNNL-30763. Richland, WA: Pacific Northwest National Laboratory. Multi-omics Characterization of the Host Response to COVID-19
• Odenkirk M.T., K.G. Stratton, L.M. Bramer, B.M. Webb-Robertson, K.J. Bloodsworth, M.E. Monroe, and K.E. Burnum-Johnson, et al. 2020. "From prevention to disease perturbations: A multi-omic assessment of exercise and myocardial infarctions." Biomolecules 11, no. 1:Article No. 40. PNNL-SA-158202. doi:10.3390/biom11010040
• Odenkirk M.T., K.G. Stratton, M.A. Gritsenko, L.M. Bramer, B.M. Webb-Robertson, K.J. Bloodsworth, and K.K. Weitz, et al. 2020. "Unveiling molecular signatures of preeclampsia and gestational diabetes mellitus with multi-omics and innovative cheminformatics visualization tools." Molecular Omics 16, no. 6:521-532. PNNL-SA-152804. doi:10.1039/d0mo00074d
• Piehowski P.D., Y. Zhu, L.M. Bramer, K.G. Stratton, R. Zhao, D.J. Orton, and R.J. Moore, et al. 2020. "Automated mass spectrometry imaging of over 2000 proteins from tissue sections at 100-µm spatial resolution." Nature Communications 11, no. 1:Article No. 8. PNNL-SA-138884. doi:10.1038/s41467-019-13858-z
• Raman A., S.M. Burrows, E. King, and L.M. Bramer. 2020. EBSD seed LDRD project: Does Corona Virus - 2019 (COVID-19) and Seasonal Flu have similar meteorology and air quality controls driving their spread?. PNNL-30778. Richland, WA: Pacific Northwest National Laboratory. EBSD seed LDRD project: Does Corona Virus - 2019 (COVID-19) and Seasonal Flu have similar meteorology and air quality controls driving their spread?
• Webb-Robertson B.M., K.G. Stratton, J.E. Kyle, Y. Kim, L.M. Bramer, K.M. Waters, and D. Koeller, et al. 2020. "Statistically Driven Metabolite and Lipid Profiling of Patients from the Undiagnosed Diseases Network." Analytical Chemistry 92, no. 2:1796-1803. PNNL-SA-145014. doi:10.1021/acs.analchem.9b03522
• Zhao Q., S.J. Callister, A.M. Thompson, R.K. Kukkadapu, M. Tfaily, L.M. Bramer, and N. Qafoku, et al. 2020. "Strong mineralogic control of soil organic matter composition in response to nutrient addition across diverse grassland sites." Science of the Total Environment 736. PNNL-SA-144529. doi:10.1016/j.scitotenv.2020.137839

2019

• Bramer L.M., K.G. Stratton, A.M. White, A.A. Bleeker, M.A. Kobold, K.M. Waters, and T.O. Metz, et al. 2019. "P-Mart: Interactive Analysis of Ion Abundance Global Proteomics Data." Journal of Proteome Research 18, no. 3:1426-1432. PNNL-SA-140572. doi:10.1021/acs.jproteome.8b00840
• 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
• Mehdi B.L., A. Stevens, L. Kovarik, N. Jiang, H.S. Mehta, A.V. Liyu, and S.M. Reehl, et al. 2019. "Controlling the Spatio-Temporal Dose Distribution During STEM Imaging by Subsampled Acquisition: In-Situ Observations of Kinetic Processes in Liquids." Applied Physics Letters 115, no. 6:Article Number 063102. PNNL-SA-145156. doi:10.1063/1.5096595
• Messier K.P., L.G. Tidwell, C. Ghetu, D. Rohlman, R.P. Scott, L.M. Bramer, and H.M. Dixon, et al. 2019. "Indoor versus Outdoor Air Quality During Wildfires." Environmental Science & Technology Letters 6, no. 12:696-701. PNNL-SA-147722. doi:10.1021/acs.estlett.9b00599
• Mitchell H.D., A.J. Eisfeld, K.G. Stratton, N.C. Heller, L.M. Bramer, J. Wen, and J.E. McDermott, et al. 2019. "The Role of EGFR in Influenza Pathogenicity: Multiple Network-based Approaches To Identify a Key Regulator of Non-Lethal Infections." Frontiers in Cell and Developmental Biology 7. PNNL-SA-142083. doi:10.3389/fcell.2019.00200
• Reehl S.M., B.A. Stanfill, M. Johnson, D. Ries, N.D. Browning, B.L. Mehdi, and L.M. Bramer. 2019. "Event Detection for Undersampled Electron Microscopy Experiments: A Control Chart Case Study." Quality Engineering 32, no. 2:244-254. PNNL-SA-132442. doi:10.1080/08982112.2019.1638515
• Sharon G., N.J. Cruz, D. Kang, M. Gandal, B. Wang, Y. Kim, and E.M. Zink, et al. 2019. "Human Gut Microbiota from Autism Spectrum Disorder Promote Behavioral Symptoms in Mice." Cell 177, no. 6:1600-1618. PNNL-SA-131563. doi:10.1016/j.cell.2019.05.004
• Stanfill B.A., L.M. Bramer, T. Liu, and S.M. Akers. 2019. Machine Learning for Rapid Biomarker Discovery via Image-Omic Fusion. PNNL-29450. Richland, WA: Pacific Northwest National Laboratory. Machine Learning for Rapid Biomarker Discovery via Image-Omic Fusion
• Stanfill B.A., S.M. Reehl, L.M. Bramer, E.S. Nakayasu, S.S. Rich, T.O. Metz, and M. Rewers, et al. 2019. "Extending Classification Algorithms to Case-Control Studies." Biomedical Engineering and Computational Biology 10. PNNL-SA-135302. doi:10.1177/1179597219858954
• 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
• Whidbey C., N.C. Sadler, R.N. Nair, R.F. Volk, A.J. DeLeon, L.M. Bramer, and S.J. Fansler, et al. 2019. "A Probe-Enabled Approach for the Selective Isolation and Characterization of Functionally Active Subpopulations in the Gut Microbiome." Journal of the American Chemical Society 141, no. 1:42-47. PNNL-SA-127532. doi:10.1021/jacs.8b09668

2018

• Bottos E.M., D.W. Kennedy, E.B. Romero, S.J. Fansler, J.M. Brown, L.M. Bramer, and R.K. Chu, et al. 2018. "Dispersal Limitation and Thermodynamic Constraints Govern Spatial Structure of Permafrost Microbial Communities." FEMS Microbiology Ecology 94, no. 8:fiy110. PNNL-SA-130968. doi:10.1093/femsec/fiy110
• Burrows S.M., A. Dasgupta, S.M. Reehl, L.M. Bramer, P. Ma, P.J. Rasch, and Y. Qian. 2018. "Characterizing the relative importance assigned to physical variables by climate scientists when assessing atmospheric climate model fidelity." Advances in Atmospheric Sciences 35, no. 9:1101-1113. PNNL-SA-129346. doi:10.1007/s00376-018-7300-x
• Liu C., L.M. Bramer, B.M. Webb-Robertson, K. Waugh, M. Rewers, and Q. Zhang. 2018. "Temporal Expression Profiling of Plasma Proteins Reveals Oxidative Stress in Early Stages of Type 1 Diabetes Progression." Journal of Proteomics 172. PNNL-SA-125485. doi:10.1016/j.jprot.2017.10.004
• 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
• Stanfill B.A., E.S. Nakayasu, L.M. Bramer, A.M. Thompson, C.K. Ansong, T. Clauss, and M.A. Gritsenko, et al. 2018. "Quality Control Analysis in Real-time (QC-ART): A Tool for Real-time Quality Control Assessment of Mass Spectrometry-based Proteomics Data." Molecular & Cellular Proteomics 17, no. 9:1824-1836. PNNL-SA-129934. doi:10.1074/mcp.RA118.000648
• Stanfill B.A., S.M. Reehl, M. Johnson, N.D. Browning, B.L. Mehdi, P. Caragea, and L.M. Bramer. 2018. "Quantitative Mapping of Nanoscale Chemical Dynamics in Sub-sampled Operando (S)TEM Images Using Spatio-Temporal Analytics." ChemCatChem 10, no. 14:3115-3120. PNNL-SA-127193. doi:10.1002/cctc.201800333

2017

• Bramer L.M., J. Rounds, C.D. Burleyson, D.C. Fortin, J.E. Hathaway, J.S. Rice, and I.P. Kraucunas. 2017. "Evaluating Penalized Logistic Regression Models to Predict Heat-Related Electric Grid Stress Days." Applied Energy 205. PNNL-SA-126567. doi:10.1016/j.apenergy.2017.09.087
• Graham E.B., M.M. Tfaily, A.R. Crump, A.E. Goldman, L.M. Bramer, E.V. Arntzen, and E.B. Romero, et al. 2017. "Carbon inputs from riparian vegetation limit oxidation of physically bound organic carbon via biochemical and thermodynamic processes." Journal of Geophysical Research: Biogeosciences 122, no. 12:3188-3205. PNNL-SA-125144. doi:10.1002/2017JG003967
• Halfvarson J., C.J. Brislawn, R. Lamendella, Y. Vazquez-Baeza, W.A. Walters, L.M. Bramer, and M. D'Amato, et al. 2017. "Dynamics of the Human Gut Microbiome in Inflammatory Bowel Disease." Nature Microbiology 2, no. 5:Article No. 17004. PNNL-SA-122629. doi:10.1038/nmicrobiol.2017.4
• Liu C., L.M. Bramer, B.M. Webb-Robertson, K. Waugh, M. Rewers, and Q. Zhang. 2017. "Temporal profiles of plasma proteome during childhood development." Journal of Proteomics 152. PNNL-SA-122850. doi:10.1016/j.jprot.2016.11.016
• Madeen E.P., C.V. Lohr, H. You, L.E. Siddens, S.K. Krueger, R.H. Dashwood, and F.J. Gonzalez, et al. 2017. "Dibenzo[def,p]chrysene transplacental carcinogenesis in wild-type, Cyp1b1 knockout, and CYP1B1 humanized mice." Molecular Carcinogenesis 56, no. 1:163-171. PNWD-SA-10523. doi:10.1002/mc.22480
• Webb-Robertson B.M., L.M. Bramer, J.L. Jensen, M.A. Kobold, K.G. Stratton, A.M. White, and K.D. Rodland. 2017. "P-MartCancer-Interactive Online Software to Enable Analysis of Shotgun Cancer Proteomic Datasets." Cancer Research 77, no. 21:e47-e50. PNNL-SA-123730. doi:10.1158/0008-5472.CAN-17-0335

2016

• Webb-Robertson B.M., L.M. Bramer, S.M. Reehl, T.O. Metz, Q. Zhang, M. Rewers, and B. Frohnert. 2016. "ROFI - The use of Repeated Optimization for Feature Interpretation." In International Conference on Computational Science and Computational Intelligence (CSCI 2016), December 15-17, 206, Las Vegas, Nevada, edited by HR Arabnia, L Deligiannidis and M Yang. Piscataway, New Jersey:IEEE. PNWD-SA-10276. doi:10.1109/CSCI.2016.0013

2015

• Bramer L.M., S. Chatterjee, A.E. Holmes, S.M. Robinson, S.F. Bradley, and B.M. Webb-Robertson. 2015. "A Machine Learning Approach for Business Intelligence Analysis using Commercial Shipping Transaction Data." In The 11th International Conference on Data Mining (DMIN 2015), July 27-30, 2015, Las Vegas, Nevada, 162-167. Athens, Georgia:CSREA Press. PNNL-SA-110014.
• Hejazi M.I., N. Voisin, L. Liu, L.M. Bramer, D.C. Fortin, J.E. Hathaway, and M. Huang, et al. 2015. "21st Century United States Emissions Mitigation Could Increase Water Stress more than the Climate Change it is Mitigating." Proceedings of the National Academy of Sciences (PNAS) 112, no. 34:10635-10640. PNNL-SA-105956. doi:10.1073/pnas.1421675112
• Lafontaine S., J. Schrlau, J. Butler, Y. Jia, B.L. Harper, S.G. Harris, and L.M. Bramer, et al. 2015. "RELATIVE INFLUENCE OF TRANS-PACIFIC AND REGIONAL ATMOSPHERIC TRANSPORT OF PAHS IN THE PACIFIC NORTHWEST, U.S." Environmental Science & Technology 49, no. 23:13807-13816. PNWD-SA-10478. doi:10.1021/acs.est.5b00800
• Siddens L.K., K.L. Bunde, T.A. Harper Jr., T.J. McQuistan, C.V. Lohr, L.M. Bramer, and K.M. Waters, et al. 2015. "Cytochrome P450 1b1 in Polycyclic Aromatic Hydrocarbon (PAH)-Induced Skin Carcinogenesis: Tumorigenicity of Individual PAHs and Coal-Tar Extract, DNA Adduction and Expression of Select Genes in the Cyp1b1 Knockout Mouse Toxicology and Applied Pharmacology." Toxicology and Applied Pharmacology 287, no. 2:149-160. PNWD-SA-10455. doi:10.1016/j.taap.2015.05.019
• Townsend P., Q. Zhang, J. Shapiro, B.M. Webb-Robertson, L.M. Bramer, A.A. Schepmoes, and K.K. Weitz, et al. 2015. "Serum Proteome Profiles in Stricturing Crohn’s Disease: A pilot study." Inflammatory Bowel Diseases 21, no. 8:1935-41. PNNL-SA-108499. doi:10.1097/MIB.0000000000000445

2014

• Webb-Robertson B.M., M.M. Matzke, S. Datta, S.H. Payne, J. Kang, L.M. Bramer, and C.D. Nicora, et al. 2014. "Bayesian Proteoform Modeling Improves Protein Quantification of Global Proteomic Measurements." Molecular and Cellular Proteomics 13, no. 12:3639-3646. PNNL-SA-95335. doi:10.1074/mcp.M113.030932