Staff information

PNNL Publications

2024

• Clair G., H. Soloyan, P. Cravedi, A. Angeletti, F. Salem, L. Al-Rabadi, and R.E. De Filippo, et al. 2024. "The spatially resolved transcriptome signatures of glomeruli in chronic kidney disease." JCI Insight 9, no. 6:Art. No. e165515. PNNL-SA-192997. doi:10.1172/jci.insight.165515
• Gaddis N., J. Fortriede, M. Guo, E.E. Bardes, M. Kouril, S. Tabar, and K. Burns, et al. 2024. "LungMAP Portal Ecosystem: Systems-Level Exploration of the Lung." American Journal of Respiratory Cell and Molecular Biology 70, no. 2:129-139. PNNL-SA-193628. doi:10.1165/rcmb.2022-0165OC
• Vang S., E.S. Helton, Y. Guo, B. Burpee, E. Rose, M. Easter, and S. Bollenbecker, et al. 2024. "O-GlcNAc transferase regulates collagen deposition and fibrosis resolution in idiopathic pulmonary fibrosis." Frontiers in Immunology 15, no. _:Art. No. 1387197. PNNL-SA-202240. doi:10.3389/fimmu.2024.1387197
• Zhang Y., V. Bharathi, T. Dokoshi, J. de Anda, L. Tumey Ursery, N.N. Kulkarni, and Y. Nakamura, et al. 2024. "Viral afterlife: SARS-CoV-2 as a reservoir of immunomimetic peptides that reassemble into proinflammatory supramolecular complexes." Proceedings of the National Academy of Sciences (PNAS) 121, no. 6:Art. No. e2300644120. PNNL-SA-192774. doi:10.1073/pnas.2300644120

2023

• Day N.J., J. Wang, C.J. Johnston, S. Kim, H.M. Olson, E. House, and I.K. Attah, et al. 2023. "Rat Bronchoalveolar Lavage Proteome Changes Following E-cigarette Aerosol Exposures." American Journal of Physiology-Lung Cellular and Molecular Physiology 324, no. 5:L571 - L583. PNNL-SA-182179. doi:10.1152/ajplung.00016.2023
• Devine A.J., N.J. Smith, R. Joshi, Q. Fan, M.T. Borchers, G. Clair, and J.N. Adkins, et al. 2023. "Chymotrypsin-like Elastase-1 Mediates Progressive Emphysema in Alpha-1 Antitrypsin Deficiency." Chronic Obstructive Pulmonary Diseases 10, no. 4:380-391. PNNL-SA-183995. doi:10.15326/jcopdf.2023.0416
• Dylag A.M., R. Misra, G. Bandyopadhyay, C. Poole, H.L. Huyck, M.G. Jehrio, and J. Haak, et al. 2023. "New Insights into the Natural History of Bronchopulmonary Dysplasia from Proteomics and Multiplexed Immunohistochemistry." American Journal of Physiology-Lung Cellular and Molecular Physiology 325, no. 4:L419-L433. PNNL-SA-187074. doi:10.1152/ajplung.00130.2023
• Gabbert A.D., J.L. Mydosh, P.K. Talukdar, L.M. Gloss, J.E. McDermott, K.K. Cooper, and G. Clair, et al. 2023. "The missing pieces: the role of secretion systems in Campylobacter jejuni virulence." Biomolecules 13, no. 1:Art. No. 135. PNNL-SA-181015. doi:10.3390/biom13010135
• Groves A.M., R. Misra, G. Clair, E. Hernady, H.M. Olson, D.J. Orton, and J.N. Finkelstein, et al. 2023. "Influence of the irradiated pulmonary microenvironment on macrophage and T cell dynamics." Radiotherapy and Oncology 183. PNNL-SA-178170. doi:10.1016/j.radonc.2023.109543
• Guo M., M.P. Morley, C. Jiang, Y. Wu, G. Li, Y. Du, and S. Zhao, et al. 2023. "Guided construction of single cell reference for human and mouse lung." Nature Communications 14. PNNL-SA-181480. doi:10.1038/s41467-023-40173-5
• Park J., F. Yu, J.M. Fulcher, S.M. Williams, K.M. Engbrecht, R.J. Moore, and G. Clair, et al. 2023. "Evaluating linear ion trap for MS3-based multiplexed single-cell proteomics." Analytical Chemistry 95, no. 3:1888-1898. PNNL-SA-176981. doi:10.1021/acs.analchem.2c03739
• You Y., C. Tsai, R. Patel, S. Sarkar, G. Clair, M. Zhou, and T. Liu, et al. 2023. "Analysis of a macrophage carbamylated proteome reveals a function in post-translational modification crosstalk." Cell Communication and Signaling 21, no. 1:241. PNNL-SA-186292. doi:10.1186/s12964-023-01257-3

2022

• Lukowski J.K., H.M. Olson, M. Velickovic, J. Wang, J.E. Kyle, Y. Kim, and S.M. Williams, et al. 2022. "An optimized approach and inflation media for obtaining complimentary mass spectrometry-based omics data from human lung tissue." Frontiers in Molecular Biosciences 9. PNNL-SA-170826. doi:10.3389/fmolb.2022.1022775
• Nicolas Frank C., X. Hou, A. Petrosyan, V. Villani, R. Zhao, J.R. Hansen, and G. Clair, et al. 2022. "Effect of disease progression on the podocyte cell cycle in Alport Syndrome." Kidney International 101, no. 1:106-118. PNNL-SA-159893. doi:10.1016/j.kint.2021.08.026
• Park J., S. Mani, G. Clair, H.M. Olson, V.L. Paurus, C.K. Ansong, and C. Blundell, et al. 2022. "A microphysiological model of human trophoblast invasion during implantation." Nature Communications 13, no. 1:1252. PNNL-SA-169569. doi:10.1038/s41467-022-28663-4
• Woo J., G. Clair, S.M. Williams, S. Feng, C. Tsai, R.J. Moore, and W.B. Chrisler, et al. 2022. "Three-dimensional feature matching improves coverage for single-cell proteomics based on ion mobility filtering." Cell Systems 13, no. 5:426-434.e4. PNNL-SA-156470. doi:10.1016/j.cels.2022.02.003

2021

• Campbell C., C. Fingleton, M.S. Zeden, E. Bueno, L. Gallagher, D. Shinde, and J. Ahm, et al. 2021. "Accumulation of Succinyl Coenzyme A Perturbs the Methicillin-Resistant Staphylococcus aureus (MRSA) Succinylome and Is Associated with Increased Susceptibility to Beta-Lactam Antibiotics." mBio 12, no. 3:Art. No. e00530-21. PNNL-SA-166791. doi:10.1128/mBio.00530-21
• Kyle J.E., L. Aimo, A.J. Bridge, G. Clair, M. Fedorova, J.B. Helms, and M.R. Molenaar, et al. 2021. "Interpreting the Lipidome: Bioinformatic Approaches to Embrace the Complexity." Metabolomics 17, no. 8:55. PNNL-SA-162774. doi:10.1007/s11306-021-01802-6
• Negretti N.M., C.R. Gourley, P.K. Talukdar, G. Clair, C.M. Klappenbach, C.J. Lauritsen, and J.N. Adkins, et al. 2021. "The Campylobacter jejuni CiaD effector co-opts the host cell protein IQGAP1 to promote cell entry." Nature Communications 12, no. 1:1339. PNNL-SA-152634. doi:10.1038/s41467-021-21579-5
• Petyuk V.A., L. Yu, H.M. Olson, F. Yu, G. Clair, W. Qian, and J.M. Shulman, et al. 2021. "Proteomic Profiling of the Substantia Nigra to Identify Determinants of Lewy Body Pathology and Dopaminergic Neuronal Loss." Journal of Proteome Research 20, no. 5:2266-2282. PNNL-SA-153429. doi:10.1021/acs.jproteome.0c00747
• Wang J., S. Kim, E. House, H.M. Olson, C.J. Johnston, D. Chalupa, and E. Hernady, et al. 2021. "Repetitive diacetyl vapor exposure promotes ubiquitin proteasome stress and precedes bronchiolitis obliterans pathology." Archives of Toxicology 95, no. 7:2469-2483. PNNL-SA-159891. doi:10.1007/s00204-021-03076-2
• Woo J., S.M. Williams, L. Markillie, S. Feng, C. Tsai, V. Aguilera-Vazquez, and R.L. Sontag, et al. 2021. "High-throughput and high-efficiency sample preparation for single-cell proteomics using a nested nanowell chip." Nature Communications 12, no. 1:Art. No. 6246. PNNL-SA-159977. doi:10.1038/s41467-021-26514-2
• Zamith-Miranda D., H.M. Heyman, M.C. Burnet, S.P. Couvillion, X. Zheng, N. Munoz Munoz, and W.C. Nelson, et al. 2021. "A Histoplasma capsulatum lipid metabolic map identifies antifungal targets." mBio 12, no. 6:e02972-21. PNNL-SA-152496. doi:10.1128/mBio.02972-21

2020

• Clair G., J. Esbelin, S. Mallea, I. Bornard, and F. Carlin. 2020. "The spore coat is essential for Bacillus subtilis spore resistance to pulsed light, and pulsed light treatment eliminates some spore coat proteins." International Journal of Food Microbiology 323. PNNL-SA-152796. doi:10.1016/j.ijfoodmicro.2020.108592
• Negretti N.M., Y. Ye, L.M. Malavasi, S.M. Pokharel, S. Huynh, S. Noh, and C. Klima, et al. 2020. "A porcine ligated loop model reveals new insight into the host immune response against Campylobacter jejuni." Gut Microbes 12, no. 1:1-25. PNNL-SA-152772. doi:10.1080/19490976.2020.1814121
• Negretti N.M., Y. Ye, L.M. Malavasi, S.M. Pokharel, S. Huynh, S. Noh, and C. Klima, et al. 2020. "A porcine ligated loop model reveals new insight into the host immune response against Campylobacter jejuni." Gut Microbes 12, no. 1:25. PNNL-SA-166370. doi:10.1080/19490976.2020.1814121
• Nunn K.L., G. Clair, J.N. Adkins, K.M. Engbrecht, T.L. Fillmore, and L.J. Forney. 2020. "Amylases in the human vagina." mSphere 5, no. 6:Article No. e00943-20. PNNL-SA-155005. doi:10.1128/mSphere.00943-20

2019

• Clair G. 2019. "A Multiomics Focusing Towards the Molecular Networks of Lung Development." American Journal of Physiology-Lung Cellular and Molecular Physiology 317, no. 5:L554-L555. PNNL-SA-147553. doi:10.1152/ajplung.00364.2019
• Clair G., S.M. Reehl, K.G. Stratton, M.E. Monroe, M. Tfaily, C.K. Ansong, and J.E. Kyle. 2019. "Lipid Mini-On: Mining and ontology tool for enrichment analysis of lipidomic data." Bioinformatics 35, no. 21:4507-4508. PNNL-SA-142630. doi:10.1093/bioinformatics/btz250
• Dou M., G. Clair, C. Tsai, K. Xu, W.B. Chrisler, R.L. Sontag, and R. Zhao, et al. 2019. "High-Throughput Single Cell Proteomics Enabled by Multiplex Isobaric Labelling in a Nanodroplet Sample Preparation Platform." Analytical Chemistry 91, no. 20:13119-13127. PNNL-SA-146297. doi:10.1021/acs.analchem.9b03349
• Du Y., G. Clair, D.A. Alam, S. Danopoulos, D. Schnell, J. Kitzmiller, and R. Misra, et al. 2019. "Integration of transcriptomic and proteomic data identifies biological functions in cell populations from human infant lung." American Journal of Physiology-Lung Cellular and Molecular Physiology 317, no. 3:L347-L360. PNNL-SA-142451. doi:10.1152/ajplung.00475.2018
• Negretti N.M., G. Clair, P.K. Talukdar, C.R. Gourley, S. Huynh, J.N. Adkins, and C.T. Parker, et al. 2019. "Campylobacter jejuni demonstrates conserved proteomic and transcriptomic responses when co-cultured with human INT 407 and Caco-2 epithelial cells." Frontiers in Microbiology 10. PNNL-SA-144950. doi:10.3389/fmicb.2019.00755
• Zalis E.A., A.S. Nuxoll, S. Manuse, G. Clair, L.C. Radlinski, B.P. Conlon, and J.N. Adkins, et al. 2019. "Stochastic Variation in Expression of the Tricarboxylic Acid Cycle Produces Persister Cells." mBio 10, no. 5:Article No. e01930-19. PNNL-SA-147078. doi:10.1128/mBio.01930-19
• Zamith-Miranda D., H.M. Heyman, L.G. Cleare, S.P. Couvillion, G. Clair, E.L. Bredeweg, and A. Gacser, et al. 2019. "Multi-omics signature of Candida Auris, an emerging and multidrug-resistant pathogen." mSystems 4, no. 4:e00257-19. PNNL-SA-140174. doi:10.1128/mSystems.00257-19

2018

• Kushner I.K., G. Clair, S.O. Purvine, J. Lee, J.N. Adkins, and S.H. Payne. 2018. "Individual variability of protein expression in human tissues." Journal of Proteome Research 17, no. 11:3914-3922. PNNL-SA-136429. doi:10.1021/acs.jproteome.8b00580
• Kyle J.E., G. Clair, G. Bandyopadhyay, R. Misra, E.M. Zink, K.J. Bloodsworth, and A.K. Shukla, et al. 2018. "Cell type-resolved human lung lipidome reveals cellular cooperation in lung function." Scientific Reports 8, no. 1:Article No. 13455. PNNL-SA-132404. doi:10.1038/s41598-018-31640-x
• Moghieb A.M., G. Clair, H.D. Mitchell, J. Kitzmiller, E.M. Zink, Y. Kim, and V.A. Petyuk, et al. 2018. "Time-resolved Proteome Profiling of Normal Lung Development." American Journal of Physiology-Lung Cellular and Molecular Physiology 315, no. 1:L11-L24. PNNL-SA-127218. doi:10.1152/ajplung.00316.2017
• Piehowski P.D., R. Zhao, R.J. Moore, G. Clair, and C.K. Ansong. 2018. "Quantitative Proteomic Analysis of Mass Limited Tissue Samples for Spatially Resolved Tissue Profiling." In Tissue Proteomics: Methods and Protocols, 2nd Edition. Methods in Molecular Biology, edited by MM Sarwal and TK Sigdel. 269-277. New York, New York:Humana Press. PNNL-SA-133218. doi:10.1007/7651_2017_78
• Zhu Y., G. Clair, W.B. Chrisler, Y. Shen, R. Zhao, A.K. Shukla, and R.J. Moore, et al. 2018. "Proteomic Analysis of Single Mammalian Cells Enabled by Microfluidic Nanodroplet Sample Preparation and Ultrasensitive NanoLC-MS." Angewandte Chemie International Edition 57, no. 38:12370-12374. PNNL-SA-132946. doi:10.1002/anie.201802843

2017

• Ardini-Poleske M.E., R.F. Clark, C.K. Ansong, J.P. Carson, R.A. Corley, G. Deutsch, and J.S. Hagood, et al. 2017. "LungMAP: The Molecular Atlas of Lung Development Program." American Journal of Physiology-Lung Cellular and Molecular Physiology 313, no. 5:L733-L740. PNNL-SA-136379. doi:10.1152/ajplung.00139.2017
• Dautel S.E., J.E. Kyle, G. Clair, R.L. Sontag, K.K. Weitz, A.K. Shukla, and S.N. Nguyen, et al. 2017. "Lipidomics reveals dramatic lipid compositional changes in the maturing postnatal lung." Scientific Reports 7. PNNL-SA-121148. doi:10.1038/srep40555
• Negretti N.M., C.R. Gourley, G. Clair, J.N. Adkins, and M. Konkel. 2017. "The food-borne pathogen Campylobacter jejuni responds to the bile salt deoxycholate with countermeasures to reactive oxygen species." Scientific Reports 7. PNNL-SA-122926. doi:10.1038/s41598-017-15379-5
• Rindler T.N., C.A. Stockman, A.L. Filuta, K.M. Brown, J.M. Snowball, W. Zhou, and R. Veldhuizen, et al. 2017. "Alveolar injury and regeneration following deletion of ABCA3." JCI Insight 2, no. 24:Article No. e97381. PNNL-SA-142637. doi:10.1172/jci.insight.97381
• Tang X., J.M. Snowball, Y. Xu, C. Na, T.E. Weaver, G. Clair, and J.E. Kyle, et al. 2017. "EMC3 coordinates surfactant protein and lipid homeostasis required for respiration." Journal of Clinical Investigation 127, no. 12:4314-4325. PNNL-SA-127808. doi:10.1172/JCI94152
• Waters E.M., J.K. Rudkin, S. Coughlan, G. Clair, J.N. Adkins, S. Gore, and G. Xia, et al. 2017. "Redeploying ß-Lactam Antibiotics as a Novel Antivirulence Strategy for the Treatment of Methicillin-Resistant Staphylococcus aureus Infections." The Journal of Infectious Diseases 215, no. 1:80-87. PNNL-SA-120576. doi:10.1093/infdis/jiw461

2016

• Clair G., P.D. Piehowski, T. Nicola, J. Kitzmiller, E.L. Huang, E.M. Zink, and R.L. Sontag, et al. 2016. "Spatially-Resolved Proteomics: Rapid Quantitative Analysis of Laser Capture Microdissected Alveolar Tissue Samples." Scientific Reports 6. PNNL-SA-119185. doi:10.1038/srep39223
• Conlon B.P., S.E. Rowe, A.V. Brown-Gandt, A.S. Nuxoll, N.P. Donegan, E.A. Zalis, and G. Clair, et al. 2016. "Persister formation in Staphylococcus aureus is associated with ATP depletion." Nature Microbiology 1. PNNL-SA-116412. doi:10.1038/nmicrobiol.2016.51