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2020

Identification of Plasmodium falciparum proteoforms from liver stage models

Winer, B., Edgel, K. A., Zou, X., Sellau, J., Hadiwidjojo, S., Garver, L. S., McDonough, C. E., Kelleher, N. L., Thomas, P. M., Villasante, E., Ploss, A. & Gerbasi, V. R., Jan 7 2020, In : Malaria journal. 19, 1, 10.

Research output: Contribution to journalArticle

Open Access

NMT1 and NMT2 are lysine myristoyltransferases regulating the ARF6 GTPase cycle

Kosciuk, T., Price, I. R., Zhang, X., Zhu, C., Johnson, K. N., Zhang, S., Halaby, S. L., Komaniecki, G. P., Yang, M., DeHart, C. J., Thomas, P. M., Kelleher, N. L., Christopher Fromme, J. & Lin, H., Dec 1 2020, In : Nature communications. 11, 1, 1067.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Thorough performance evaluation of 213 nm ultraviolet photodissociation for top-down proteomics

Fornelli, L., Srzentić, K., Toby, T. K., Doubleday, P. F., Huguet, R., Mullen, C., Melani, R. D., Seckler, H. D. S., DeHart, C. J., Weisbrod, C. R., Durbin, K. R., Greer, J. B., Early, B. P., Fellers, R. T., Zabrouskov, V., Thomas, P. M., Compton, P. D. & Kelleher, N. L., Jan 1 2020, In : Molecular and Cellular Proteomics. 19, 2, p. 405-420 16 p.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations
2019

Accurate estimation of context-dependent false discovery rates in top-down proteomics

LeDuc, R. D., Fellers, R. T., Early, B. P., Greer, J. B., Shams, D. P., Thomas, P. M. & Kelleher, N. L., Jan 1 2019, In : Molecular and Cellular Proteomics. 18, 4, p. 796-805 10 p.

Research output: Contribution to journalArticle

10 Scopus citations
10 Scopus citations

A comprehensive pipeline for translational top-down proteomics from a single blood draw

Toby, T. K., Fornelli, L., Srzentić, K., DeHart, C. J., Levitsky, J., Friedewald, J. & Kelleher, N. L., Jan 1 2019, In : Nature Protocols. 14, 1, p. 119-152 34 p.

Research output: Contribution to journalArticle

8 Scopus citations

A Highly Productive, One-Pot Cell-Free Protein Synthesis Platform Based on Genomically Recoded Escherichia coli

Des Soye, B. J., Gerbasi, V. R., Thomas, P. M., Kelleher, N. L. & Jewett, M. C., Dec 19 2019, In : Cell Chemical Biology. 26, 12, p. 1743-1754.e9

Research output: Contribution to journalArticle

4 Scopus citations

Chromatin occupancy and epigenetic analysis reveal new insights into the function of the GATA1 N terminus in erythropoiesis

Ling, T., Birger, Y., Stankiewicz, M. J., Ben-Haim, N., Kalisky, T., Rein, A., Kugler, E., Chen, W., Fu, C., Zhang, K., Patel, H., Sikora, J. W., Goo, Y. A., Kelleher, N., Zou, L., Izraeli, S. & Crispino, J. D., Jan 1 2019, In : Blood. 134, 19, p. 1619-1631 13 p.

Research output: Contribution to journalArticle

6 Scopus citations

Comprehensive analysis of aspergillus nidulans PKA phosphorylome identifies a novel mode of CreA regulation

Ribeiro, L. F. C., Chelius, C., Boppidi, K. R., Naik, N. S., Hossain, S., Ramsey, J. J. J., Kumar, J., Ribeiro, L. F., Ostermeier, M., Tran, B., Goo, Y. A., Assis, L. J., Ulas, M., Bayram, O., Goldman, G. H., Lincoln, S., Srivastava, R., Harris, S. D. & Martena, M. R., Mar 1 2019, In : mBio. 10, 2, e02825-18.

Research output: Contribution to journalArticle

Open Access
6 Scopus citations

Coupling Fluorescence-Activated Cell Sorting and Targeted Analysis of Histone Modification Profiles in Primary Human Leukocytes

Camarillo, J. M., Swaminathan, S., Abshiru, N. A., Sikora, J. W., Thomas, P. M. & Kelleher, N. L., Dec 1 2019, In : Journal of the American Society for Mass Spectrometry. 30, 12, p. 2526-2534 9 p.

Research output: Contribution to journalArticle

Identification and targeting of novel CDK9 complexes in acute myeloid leukemia

Beauchamp, E. M., Abedin, S. M., Radecki, S. G., Fischietti, M., Arslan, A. DI., Blyth, G. T., Yang, A., Lantz, C., Nelson, A., Goo, Y. A., Akpan, I., Eklund, E. A., Frankfurt, O., Fish, E. N., Thomas, P. M., Altman, J. K. & Platanias, L. C., Jan 1 2019, In : Blood. 133, 11, p. 1171-1185 15 p.

Research output: Contribution to journalArticle

7 Scopus citations

Microbial and metabolic succession on common building materials under high humidity conditions

Lax, S., Cardona, C., Zhao, D., Winton, V. J., Goodney, G., Gao, P., Gottel, N., Hartmann, E. M., Henry, C., Thomas, P. M., Kelley, S. T., Stephens, B. & Gilbert, J. A., Dec 1 2019, In : Nature communications. 10, 1, 1767.

Research output: Contribution to journalArticle

Open Access
4 Scopus citations

Multidimensional Top-Down Proteomics of Brain-Region-Specific Mouse Brain Proteoforms Responsive to Cocaine and Estradiol

Park, H. M., Satta, R., Davis, R. G., Goo, Y. A., Leduc, R. D., Fellers, R. T., Greer, J. B., Romanova, E. V., Rubakhin, S. S., Tai, R., Thomas, P. M., Sweedler, J. V., Kelleher, N. L., Patrie, S. M. & Lasek, A. W., Nov 1 2019, In : Journal of Proteome Research. 18, 11, p. 3999-4012 14 p.

Research output: Contribution to journalArticle

1 Scopus citations

Native top-down mass spectrometry provides insights into the copper centers of membrane-bound methane monooxygenase

Ro, S. Y., Schachner, L. F., Koo, C. W., Purohit, R., Remis, J. P., Kenney, G. E., Liauw, B. W., Thomas, P. M., Patrie, S. M., Kelleher, N. L. & Rosenzweig, A. C., Dec 1 2019, In : Nature communications. 10, 1, 2675.

Research output: Contribution to journalArticle

Open Access
10 Scopus citations

Phosphoproteomic and transcriptomic analyses reveal multiple functions for Aspergillus nidulans MpkA independent of cell wall stress

Chelius, C. L., Ribeiro, L. F. C., Huso, W., Kumar, J., Lincoln, S., Tran, B., Goo, Y. A., Srivastava, R., Harris, S. D. & Marten, M. R., Apr 2019, In : Fungal Genetics and Biology. 125, p. 1-12 12 p.

Research output: Contribution to journalArticle

1 Scopus citations

USP7 cooperates with NOTch1 to drive the oncogenic transcriptional program in T-cell leukemia

Jin, Q., Martinez, C. A., Arcipowski, K. M., Zhu, Y., Gutierrez-Diaz, B. T., Wang, K. K., Johnson, M. R., Volk, A. G., Wang, F., Wu, J., Grove, C., Wang, H., Sokirniy, I., Thomas, P. M., Goo, Y. A., Abshiru, N. A., Hijiya, N., Peirs, S., Vandamme, N., Berx, G. & 27 others, Goosens, S., Marshall, S. A., Rendleman, E. J., Takahashi, Y. H., Wang, L., Rawat, R., Bartom, E. T., Collings, C. K., Van Vlierberghe, P., Strikoudis, A., Kelly, S., Ueberheide, B., Mantis, C., Kandela, I., Bourquin, J. P., Bornhauser, B., Serafin, V., Bresolin, S., Paganin, M., Accordi, B., Basso, G., Kelleher, N. L., Weinstock, J., Kumar, S., Crispino, J. D., Shilatifard, A. & Ntziachristos, P., Jan 1 2019, In : Clinical Cancer Research. 25, 1, p. 222-239 18 p.

Research output: Contribution to journalArticle

Open Access
14 Scopus citations
2018

Bifunctional Immunity Proteins Protect Bacteria against FtsZ-Targeting ADP-Ribosylating Toxins

Ting, S. Y., Bosch, D. E., Mangiameli, S. M., Radey, M. C., Huang, S., Park, Y. J., Kelly, K. A., Filip, S. K., Goo, Y. A., Eng, J. K., Allaire, M., Veesler, D., Wiggins, P. A., Peterson, S. B. & Mougous, J. D., Nov 15 2018, In : Cell. 175, 5, p. 1380-1392.e14

Research output: Contribution to journalArticle

22 Scopus citations

Cell-free protein synthesis from genomically recoded bacteria enables multisite incorporation of noncanonical amino acids

Martin, R. W., Des Soye, B. J., Kwon, Y. C., Kay, J., Davis, R. G., Thomas, P. M., Majewska, N. I., Chen, C. X., Marcum, R. D., Weiss, M. G., Stoddart, A. E., Amiram, M., Ranji Charna, A. K., Patel, J. R., Isaacs, F. J., Kelleher, N. L., Hong, S. H. & Jewett, M. C., Dec 1 2018, In : Nature communications. 9, 1, 1203.

Research output: Contribution to journalArticle

50 Scopus citations

Characterization of a long overlooked copper protein from methane- and ammonia-oxidizing bacteria

Fisher, O. S., Kenney, G. E., Ross, M. O., Ro, S. Y., Lemma, B. E., Batelu, S., Thomas, P. M., Sosnowski, V. C., DeHart, C. J., Kelleher, N. L., Stemmler, T. L., Hoffman, B. M. & Rosenzweig, A. C., Dec 1 2018, In : Nature communications. 9, 1, 4276.

Research output: Contribution to journalArticle

13 Scopus citations

Identification of the First Diketomorpholine Biosynthetic Pathway Using FAC-MS Technology

Robey, M. T., Ye, R., Bok, J. W., Clevenger, K. D., Islam, M. N., Chen, C., Gupta, R., Swyers, M., Wu, E., Gao, P., Thomas, P. M., Wu, C. C., Keller, N. P. & Kelleher, N. L., May 18 2018, In : ACS chemical biology. 13, 5, p. 1142-1147 6 p.

Research output: Contribution to journalArticle

10 Scopus citations

Interrogation of Benzomalvin Biosynthesis Using Fungal Artificial Chromosomes with Metabolomic Scoring (FAC-MS): Discovery of a Benzodiazepine Synthase Activity

Clevenger, K. D., Ye, R., Bok, J. W., Thomas, P. M., Islam, M. N., Miley, G. P., Robey, M. T., Chen, C., Yang, K., Swyers, M., Wu, E., Gao, P., Wu, C. C., Keller, N. P. & Kelleher, N. L., Jun 12 2018, In : Biochemistry. 57, 23, p. 3237-3243 7 p.

Research output: Contribution to journalArticle

9 Scopus citations

Precise characterization of KRAS4b proteoforms in human colorectal cells and tumors reveals mutation/modification cross-talk

Ntai, I., Fornelli, L., DeHart, C. J., Hutton, J. E., Doubleday, P. F., LeDuc, R. D., van Nispen, A. J., Fellers, R. T., Whiteley, G., Boja, E. S., Rodriguez, H. & Kelleher, N. L., Apr 17 2018, In : Proceedings of the National Academy of Sciences of the United States of America. 115, 16, p. 4140-4145 6 p.

Research output: Contribution to journalArticle

19 Scopus citations

Stability of histone post-translational modifications in samples derived from liver tissue and primary hepatic cells

Gruppuso, P. A., Boylan, J. M., Zabala, V., Neretti, N., Abshiru, N. A., Sikora, J. W., Doud, E. H., Camarillo, J. M., Thomas, P. M., Kelleher, N. L. & Sanders, J. A., Sep 2018, In : PloS one. 13, 9, e0203351.

Research output: Contribution to journalArticle

1 Scopus citations

The biosynthesis of methanobactin

Kenney, G. E., Dassama, L. M. K., Pandelia, M. E., Gizzi, A. S., Martinie, R. J., Gao, P., DeHart, C. J., Schachner, L. F., Skinner, O. S., Ro, S. Y., Zhu, X., Sadek, M., Thomas, P. M., Almo, S. C., Bollinger, J. M., Krebs, C., Kelleher, N. L. & Rosenzweig, A. C., Mar 23 2018, In : Science. 359, 6382, p. 1411-1416 6 p.

Research output: Contribution to journalArticle

21 Scopus citations

The unique biomineralization transcriptome and proteome of Lytechinus variegatus teeth

Alvares, K., DeHart, C. J., Thomas, P. M., Kelleher, N. L. & Veis, A., Nov 8 2018, In : Connective tissue research. 59, p. 20-29 10 p.

Research output: Contribution to journalArticle

The Value of Activated Ion Electron Transfer Dissociation for High-Throughput Top-Down Characterization of Intact Proteins

Riley, N. M., Sikora, J. W., Seckler, H. S., Greer, J. B., Fellers, R. T., Leduc, R. D., Westphall, M. S., Thomas, P. M., Kelleher, N. L. & Coon, J. J., Jul 17 2018, In : Analytical Chemistry. 90, 14, p. 8553-8560 8 p.

Research output: Contribution to journalArticle

12 Scopus citations

The vermiform appendix impacts the risk of developing Parkinson’s disease

Killinger, B. A., Madaj, Z., Sikora, J. W., Rey, N., Haas, A. J., Vepa, Y., Lindqvist, D., Chen, H., Thomas, P. M., Brundin, P., Brundin, L. & Labrie, V., Oct 31 2018, In : Science translational medicine. 10, 465, aar5280.

Research output: Contribution to journalArticle

55 Scopus citations

Top-Down Proteomics Enables Comparative Analysis of Brain Proteoforms between Mouse Strains

Davis, R. G., Park, H. M., Kim, K., Greer, J. B., Fellers, R. T., Leduc, R. D., Romanova, E. V., Rubakhin, S. S., Zombeck, J. A., Wu, C., Yau, P. M., Gao, P., Van Nispen, A. J., Patrie, S. M., Thomas, P. M., Sweedler, J. V., Rhodes, J. S. & Kelleher, N. L., Mar 20 2018, In : Analytical Chemistry. 90, 6, p. 3802-3810 9 p.

Research output: Contribution to journalArticle

8 Scopus citations
2017

A broadly distributed toxin family mediates contact-dependent antagonism between gram-positive bacteria

Whitney, J. C., Peterson, S. B., Kim, J., Pazos, M., Verster, A. J., Radey, M. C., Kulasekara, H. D., Ching, M. Q., Bullen, N. P., Bryant, D., Goo, Y. A., Surette, M. G., Borenstein, E., Vollmer, W. & Mougous, J. D., Jul 11 2017, In : eLife. 6, e26938.

Research output: Contribution to journalArticle

39 Scopus citations

A Deep Proteome Analysis Identifies the Complete Secretome as the Functional Unit of Human Cardiac Progenitor Cells

Sharma, S., Mishra, R., Bigham, G. E., Wehman, B., Khan, M. M., Xu, H., Saha, P., Goo, Y. A., Datla, S. R., Chen, L., Tulapurkar, M. E., Taylor, B. S., Yang, P., Karathanasis, S., Goodlett, D. R. & Kaushal, S., Mar 3 2017, In : Circulation research. 120, 5, p. 816-834 19 p.

Research output: Contribution to journalArticle

61 Scopus citations

A scalable platform to identify fungal secondary metabolites and their gene clusters

Clevenger, K. D., Bok, J. W., Ye, R., Miley, G. P., Verdan, M. H., Velk, T., Chen, C., Yang, K. H., Robey, M. T., Gao, P., Lamprecht, M., Thomas, P. M., Islam, M. N., Palmer, J. M., Wu, C. C., Keller, N. P. & Kelleher, N. L., Aug 1 2017, In : Nature Chemical Biology. 13, 8, p. 895-901 7 p.

Research output: Contribution to journalArticle

54 Scopus citations

Assessment of the therapeutic potential of persimmon leaf extract on prediabetic subjects

Khan, M. M., Tran, B. Q., Jang, Y. J., Park, S. H., Fondrie, W. E., Chowdhury, K., Yoon, S. H., Goodlett, D. R., Chae, S. W., Chae, H. J., Seo, S. Y. & Goo, Y. A., Jan 1 2017, In : Molecules and Cells. 40, 7, p. 466-475 10 p.

Research output: Contribution to journalArticle

3 Scopus citations

A synthetic biology approach to probing nucleosome symmetry

Ichikawa, Y., Connelly, C. F., Appleboim, A., Miller, T. C. R., Jacobi, H., Abshiru, N. A., Chou, H. J., Chen, Y., Sharma, U., Zheng, Y., Thomas, P. M., Chen, H. V., Bajaj, V., Müller, C. W., Kelleher, N. L., Friedman, N., Bolon, D. N. A., Rando, O. J. & Kaufman, P. D., Sep 12 2017, In : eLife. 6, e28836.

Research output: Contribution to journalArticle

4 Scopus citations

Autopiquer - a Robust and Reliable Peak Detection Algorithm for Mass Spectrometry

Kilgour, D. P. A., Hughes, S., Kilgour, S. L., Mackay, C. L., Palmblad, M., Tran, B. Q., Goo, Y. A., Ernst, R. K., Clarke, D. J. & Goodlett, D. R., Feb 1 2017, In : Journal of the American Society for Mass Spectrometry. 28, 2, p. 253-262 10 p.

Research output: Contribution to journalArticle

10 Scopus citations

Diversity of Amyloid-beta Proteoforms in the Alzheimer's Disease Brain

Wildburger, N. C., Esparza, T. J., Leduc, R. D., Fellers, R. T., Thomas, P. M., Cairns, N. J., Kelleher, N. L., Bateman, R. J. & Brody, D. L., Dec 1 2017, In : Scientific reports. 7, 1, 9520.

Research output: Contribution to journalArticle

38 Scopus citations

EphA2 proteomics in human keratinocytes reveals a novel association with afadin and epidermal tight junctions

Perez White, B. E., Ventrella, R., Kaplan, N., Cable, C. J., Thomas, P. M. & Getsios, S., 2017, In : Journal of cell science. 130, 1, p. 111-118 8 p.

Research output: Contribution to journalArticle

11 Scopus citations

Expansion for the Brachylophosaurus canadensis Collagen i Sequence and Additional Evidence of the Preservation of Cretaceous Protein

Schroeter, E. R., DeHart, C. J., Cleland, T. P., Zheng, W., Thomas, P. M., Kelleher, N. L., Bern, M. & Schweitzer, M. H., Feb 3 2017, In : Journal of Proteome Research. 16, 2, p. 920-932 13 p.

Research output: Contribution to journalArticle

28 Scopus citations

High-Throughput Analysis of Intact Human Proteins Using UVPD and HCD on an Orbitrap Mass Spectrometer

Cleland, T. P., Dehart, C. J., Fellers, R. T., Vannispen, A. J., Greer, J. B., LeDuc, R. D., Parker, W. R., Thomas, P. M., Kelleher, N. L. & Brodbelt, J. S., May 5 2017, In : Journal of Proteome Research. 16, 5, p. 2072-2079 8 p.

Research output: Contribution to journalArticle

42 Scopus citations

Hyper-phosphorylation of sequestosome-1 distinguishes resistance to cisplatin in patient derived high grade serous ovarian cancer cells

Nguyen, E. V., Huhtinen, K., Goo, Y. A., Kaipio, K., Andersson, N., Rantanen, V., Hynninen, J., Lahesmaa, R., Carpen, O. & Goodlett, D. R., Jul 2017, In : Molecular and Cellular Proteomics. 16, 7, p. 1377-1392 16 p.

Research output: Contribution to journalArticle

5 Scopus citations

Identification and Characterization of Human Proteoforms by Top-Down LC-21 Tesla FT-ICR Mass Spectrometry

Anderson, L. C., DeHart, C. J., Kaiser, N. K., Fellers, R. T., Smith, D. F., Greer, J. B., Leduc, R. D., Blakney, G. T., Thomas, P. M., Kelleher, N. L. & Hendrickson, C. L., Feb 3 2017, In : Journal of Proteome Research. 16, 2, p. 1087-1096 10 p.

Research output: Contribution to journalArticle

42 Scopus citations

PAI-1 is a critical regulator of FGF23 homeostasis

Eren, M., Place, A. T., Thomas, P. M., Flevaris, P., Miyata, T. & Vaughan, D. E., Jan 1 2017, In : Science Advances. 3, 9, 1603259.

Research output: Contribution to journalArticle

9 Scopus citations

Programmed Ribosomal Frameshifting Generates a Copper Transporter and a Copper Chaperone from the Same Gene

Meydan, S., Klepacki, D., Karthikeyan, S., Margus, T., Thomas, P., Jones, J. E., Khan, Y., Briggs, J., Dinman, J. D., Vázquez-Laslop, N. & Mankin, A. S., Jan 19 2017, In : Molecular cell. 65, 2, p. 207-219 13 p.

Research output: Contribution to journalArticle

25 Scopus citations

Proteoforms in Peripheral Blood Mononuclear Cells as Novel Rejection Biomarkers in Liver Transplant Recipients

Toby, T. K., Abecassis, M., Kim, K., Thomas, P. M., Fellers, R. T., LeDuc, R. D., Kelleher, N. L., Demetris, J. & Levitsky, J., Sep 2017, In : American Journal of Transplantation. 17, 9, p. 2458-2467 10 p.

Research output: Contribution to journalArticle

13 Scopus citations

Sensing of Bacterial Cyclic Dinucleotides by the Oxidoreductase RECON Promotes NF-κB Activation and Shapes a Proinflammatory Antibacterial State

McFarland, A. P., Luo, S., Ahmed-Qadri, F., Zuck, M., Thayer, E. F., Goo, Y. A., Hybiske, K., Tong, L. & Woodward, J. J., Mar 21 2017, In : Immunity. 46, 3, p. 433-445 13 p.

Research output: Contribution to journalArticle

32 Scopus citations
2016

Bone protein "extractomics": Comparing the efficiency of bone protein extractions of Gallus gallus in tandem mass spectrometry, with an eye towards paleoproteomics

Schroeter, E. R., DeHart, C. J., Schweitzer, M. H., Thomas, P. M. & Kelleher, N. L., 2016, In : PeerJ. 2016, 10, e2603.

Research output: Contribution to journalArticle

21 Scopus citations

Characterization of Methanobactin from Methylosinus sp. LW4

Kenney, G. E., Goering, A. W., Ross, M. O., DeHart, C. J., Thomas, P. M., Hoffman, B. M., Kelleher, N. L. & Rosenzweig, A. C., Sep 7 2016, In : Journal of the American Chemical Society. 138, 35, p. 11124-11127 4 p.

Research output: Contribution to journalArticle

13 Scopus citations

Comparative top down proteomics of peripheral blood mononuclear cells from kidney transplant recipients with normal kidney biopsies or acute rejection

Savaryn, J. P., Toby, T. K., Catherman, A. D., Fellers, R. T., LeDuc, R. D., Thomas, P. M., Friedewald, J. J., Salomon, D. R., Abecassis, M. M. & Kelleher, N. L., Jul 1 2016, In : Proteomics. 16, 14, p. 2048-2058 11 p.

Research output: Contribution to journalArticle

12 Scopus citations

Comprehensive glycosylation profiling of IgG and IgG-fusion proteins by top-down MS with multiple fragmentation techniques

Tran, B. Q., Barton, C., Feng, J., Sandjong, A., Yoon, S. H., Awasthi, S., Liang, T., Khan, M. M., Kilgour, D. P. A., Goodlett, D. R. & Goo, Y. A., Feb 16 2016, In : Journal of Proteomics. 134, p. 93-101 9 p.

Research output: Contribution to journalArticle

29 Scopus citations

Detection of Carbofuran-Protein Adducts in Serum of Occupationally Exposed Pesticide Factory Workers in Pakistan

Rehman, T., Khan, M. M., Shad, M. A., Hussain, M., Oyler, B. L., Goo, Y. A. & Goodlett, D. R., Oct 17 2016, In : Chemical Research in Toxicology. 29, 10, p. 1720-1728 9 p.

Research output: Contribution to journalArticle

4 Scopus citations

Global analysis and comparison of the transcriptomes and proteomes of group a Streptococcus biofilms

Freiberg, J. A., Le Breton, Y., Tran, B. Q., Scott, A. J., Harro, J. M., Ernst, R. K., Goo, Y. A., Mongodin, E. F., Goodlett, D. R., McIver, K. S. & Shirtliff, M. E., Nov 1 2016, In : mSystems. 1, 6, e00149.

Research output: Contribution to journalArticle

7 Scopus citations