Core/facility: West Campus Analytical Core

Publications

An alphabetized list of publications citing WCAC.

Abulizi A, Cardone RL, Stark R, Lewandowski SL, Zhao X, Hillion J, Ma L, Sehgal R, Alves TC, Thomas C, Kung C, Wang B, Siebel S, Andrews ZB, Mason GF, Rinehart J, Merrins MJ, Kibbey RG. Multi-Tissue Acceleration of the Mitochondrial Phosphoenolpyruvate Cycle Improves Whole-Body Metabolic Health. Cell Metab. 2020 Nov 3;32(5):751-766.e11. doi: 10.1016/j.cmet.2020.10.006. PMID: 33147485; PMCID: PMC7679013.

Adaku N, Park HB, Spakowicz DJ, Tiwari MK, Strobel SA, Crawford JM, Rogers FA. A DNA Repair Inhibitor Isolated from an Ecuadorian Fungal Endophyte Exhibits Synthetic Lethality in PTEN-Deficient Glioblastoma. J Nat Prod. 2020 Jun 26;83(6):1899-1908. doi: 10.1021/acs.jnatprod.0c00012. Epub 2020 May 14. PMID: 32407116.

Apostolidi M, Vathiotis IA, Muthusamy V, Gaule P, Gassaway BM, Rimm DL, Rinehart J. Targeting Pyruvate Kinase M2 Phosphorylation Reverses Aggressive Cancer Phenotypes. Cancer Res. 2021 Aug 15;81(16):4346-4359. doi: 10.1158/0008-5472.CAN-20-4190. Epub 2021 Jun 21. PMID: 34185676; PMCID: PMC8373815.

Arranz-Gibert P, Vanderschuren K, Haimovich A, Halder A, Gupta K, Rinehart J, Isaacs FJ. Chemoselective restoration of para-azido-phenylalanine at multiple sites in proteins. Cell Chem Biol. 2022 Jun 16;29(6):1046-1052.e4. doi: 10.1016/j.chembiol.2021.12.002. Epub 2021 Dec 28. PMID: 34965380; PMCID: PMC10173106.

Baskerville MJ, Kovalyova Y, Mejías-Luque R, Gerhard M, Hatzios SK. Isotope tracing reveals bacterial catabolism of host-derived glutathione during Helicobacter pylori infection. PLoS Pathog. 2023 Jul 26;19(7):e1011526. doi: 10.1371/journal.ppat.1011526. PMID: 37494402; PMCID: PMC10406306.

Brown C, Ghosh S, McAllister R, Kumar M, Walker G, Sun E, Aman T, Panda A, Kumar S, Li W, Coleman J, Liu Y, Rothman JE, Bhattacharyya M, Gupta K. A proteome-wide quantitative platform for nanoscale spatially resolved extraction of membrane proteins into native nanodiscs. Nat Methods. 2025 Feb;22(2):412-421. doi: 10.1038/s41592-024-02517-x. Epub 2024 Nov 28. PMID: 39609567; PMCID: PMC11810782.

Cai WL, Chen JF, Chen H, Wingrove E, Kurley SJ, Chan LH, Zhang M, Arnal-Estape A, Zhao M, Balabaki A, Li W, Yu X, Krop ED, Dou Y, Liu Y, Jin J, Westbrook TF, Nguyen DX, Yan Q. Human WDR5 promotes breast cancer growth and metastasis via KMT2-independent translation regulation. Elife. 2022 Aug 31;11:e78163. doi: 10.7554/eLife.78163. PMID: 36043466; PMCID: PMC9584608.

Cao Y, Oh J, Xue M, Huh WJ, Wang J, Gonzalez-Hernandez JA, Rice TA, Martin AL, Song D, Crawford JM, Herzon SB, Palm NW. Commensal microbiota from patients with inflammatory bowel disease produce genotoxic metabolites. Science. 2022 Oct 28;378(6618):eabm3233. doi: 10.1126/science.abm3233. Epub 2022 Oct 28. PMID: 36302024; PMCID: PMC9993714.

Cao X, Khitun A, Na Z, Dumitrescu DG, Kubica M, Olatunji E, Slavoff SA. Comparative Proteomic Profiling of Unannotated Microproteins and Alternative Proteins in Human Cell Lines. J Proteome Res. 2020 Aug 7;19(8):3418-3426. doi: 10.1021/acs.jproteome.0c00254. Epub 2020 Jun 3. PMID: 32449352; PMCID: PMC7429271.

Cao X, Chen Y, Khitun A, Slavoff SA. BONCAT-based Profiling of Nascent Small and Alternative Open Reading Frame-encoded Proteins. Bio Protoc. 2023 Jan 5;13(1):e4585. doi: 10.21769/BioProtoc.4585. PMID: 36789088; PMCID: PMC9901453.

Cao X, Khitun A, Luo Y, Na Z, Phoodokmai T, Sappakhaw K, Olatunji E, Uttamapinant C, Slavoff SA. Alt-RPL36 downregulates the PI3K-AKT-mTOR signaling pathway by interacting with TMEM24. Nat Commun. 2021 Jan 21;12(1):508. doi: 10.1038/s41467-020-20841-6. PMID: 33479206; PMCID: PMC7820019.

Cao X, Khitun A, Harold CM, Bryant CJ, Zheng SJ, Baserga SJ, Slavoff SA. Nascent alt-protein chemoproteomics reveals a pre-60S assembly checkpoint inhibitor. Nat Chem Biol. 2022 Jun;18(6):643-651. doi: 10.1038/s41589-022-01003-9. Epub 2022 Apr 7. PMID: 35393574; PMCID: PMC9423127.

Chen Y, Cao X, Loh KH, Slavoff SA. Chemical labeling and proteomics for characterization of unannotated small and alternative open reading frame-encoded polypeptides. Biochem Soc Trans. 2023 Jun 28;51(3):1071-1082. doi: 10.1042/BST20221074. Erratum in: Biochem Soc Trans. 2023 Aug 31;51(4):1747-1748. doi: 10.1042/BST20221074_COR. PMID: 37171061; PMCID: PMC10317152.

Chen Y, Su H, Zhao J, Na Z, Jiang K, Bacchiocchi A, Loh KH, Halaban R, Wang Z, Cao X, Slavoff SA. Unannotated microprotein EMBOW regulates the interactome and chromatin and mitotic functions of WDR5. Cell Rep. 2023 Sep 26;42(9):113145. doi: 10.1016/j.celrep.2023.113145. Epub 2023 Sep 19. PMID: 37725512; PMCID: PMC10629662.

Cho W, York AG, Wang R, Wyche TP, Piizzi G, Flavell RA, Crawford JM. N-Acyl Amides from Neisseria meningitidis and Their Role in Sphingosine Receptor Signaling. Chembiochem. 2022 Nov 18;23(22):e202200490. doi: 10.1002/cbic.202200490. Epub 2022 Oct 13. PMID: 36112057; PMCID: PMC9762135.

Codina A, Renauer PA, Wang G, Chow RD, Park JJ, Ye H, Zhang K, Dong MB, Gassaway B, Ye L, Errami Y, Shen L, Chang A, Jain D, Herbst RS, Bosenberg M, Rinehart J, Fan R, Chen S. Convergent Identification and Interrogation of Tumor-Intrinsic Factors that Modulate Cancer Immunity In Vivo. Cell Syst. 2019 Feb 27;8(2):136-151.e7. doi: 10.1016/j.cels.2019.01.004. Epub 2019 Feb 20. PMID: 30797773; PMCID: PMC6592847.

Combs J, Wright T, Chen L, Holmes R, Qin B, Oh J, Crawford J, Herzon S. Enantioselective synthesis of anhydrogukulenin A C2-acetate. ChemRxiv [preprint]. 2023 16 Aug; doi:10.26434/chemrxiv-2023-8dj1k

Culp EJ, Nelson NT, Verdegaal AA, Goodman AL. Microbial transformation of dietary xenobiotics shapes gut microbiome composition. Cell. 2024 Oct 31;187(22):6327-6345.e20. doi: 10.1016/j.cell.2024.08.038. Epub 2024 Sep 24. PMID: 39321800; PMCID: PMC11531382.

Dai X, Park JJ, Du Y, Na Z, Lam SZ, Chow RD, Renauer PA, Gu J, Xin S, Chu Z, Liao C, Clark P, Zhao H, Slavoff S, Chen S. Massively parallel knock-in engineering of human T cells. Nat Biotechnol. 2023 Sep;41(9):1239-1255. doi: 10.1038/s41587-022-01639-x. Epub 2023 Jan 26. PMID: 36702900; PMCID: PMC11260498.

Di Y, Li W, Salovska B, Ba Q, Hu Z, Wang S, Liu Y. A basic phosphoproteomic-DIA workflow integrating precise quantification of phosphosites in systems biology. Biophys Rep. 2023 Apr 30;9(2):82-98. doi: 10.52601/bpr.2023.230007. PMID: 37753060; PMCID: PMC10518521.

Dudkina N, Park HB, Song D, Jain A, Khan SA, Flavell RA, Johnson CH, Palm NW, Crawford JM. Human AKR1C3 binds agonists of GPR84 and participates in an expanded polyamine pathway. Cell Chem Biol. 2025 Jan 16;32(1):126-144.e18. doi: 10.1016/j.chembiol.2024.07.011. Epub 2024 Aug 19. PMID: 39163853; PMCID: PMC11748234.

Dumitrescu DG, Gordon EM, Kovalyova Y, Seminara AB, Duncan-Lowey B, Forster ER, Zhou W, Booth CJ, Shen A, Kranzusch PJ, Hatzios SK. A microbial transporter of the dietary antioxidant ergothioneine. Cell. 2022 Nov 23;185(24):4526-4540.e18. doi: 10.1016/j.cell.2022.10.008. Epub 2022 Nov 7. PMID: 36347253; PMCID: PMC9691600.

Ebrahim SAM, Dweck HKM, Weiss BL, Carlson JR. A volatile sex attractant of tsetse flies. Science. 2023 Feb 17;379(6633):eade1877. doi: 10.1126/science.ade1877. Epub 2023 Feb 17. PMID: 36795837; PMCID: PMC10204727.

Gao E, Li W, Wu C, Shao W, Di Y, Liu Y. Data-independent acquisition-based proteome and phosphoproteome profiling across six melanoma cell lines reveals determinants of proteotypes. Mol Omics. 2021 Jun 14;17(3):413-425. doi: 10.1039/d0mo00188k. PMID: 33728422; PMCID: PMC8205956.

Gao Y, Zimmer JT, Vasic R, Liu C, Gbyli R, Zheng SJ, Patel A, Liu W, Qi Z, Li Y, Nelakanti R, Song Y, Biancon G, Xiao AZ, Slavoff S, Kibbey RG, Flavell RA, Simon MD, Tebaldi T, Li HB, Halene S. ALKBH5 modulates hematopoietic stem and progenitor cell energy metabolism through m6A modification-mediated RNA stability control. Cell Rep. 2023 Oct 31;42(10):113163. doi: 10.1016/j.celrep.2023.113163. Epub 2023 Sep 23. PMID: 37742191; PMCID: PMC10636609.

Gassaway BM, Cardone RL, Padyana AK, Petersen MC, Judd ET, Hayes S, Tong S, Barber KW, Apostolidi M, Abulizi A, Sheetz JB, Kshitiz, Aerni HR, Gross S, Kung C, Samuel VT, Shulman GI, Kibbey RG, Rinehart J. Distinct Hepatic PKA and CDK Signaling Pathways Control Activity-Independent Pyruvate Kinase Phosphorylation and Hepatic Glucose Production. Cell Rep. 2019 Dec 10;29(11):3394-3404.e9. doi: 10.1016/j.celrep.2019.11.009. PMID: 31825824; PMCID: PMC6951436.

Gatsios A, Kim CS, Crawford JM. Escherichia coli small molecule metabolism at the host-microorganism interface. Nat Chem Biol. 2021 Oct;17(10):1016-1026. doi: 10.1038/s41589-021-00807-5. Epub 2021 Sep 22. PMID: 34552219; PMCID: PMC8675634.

Gatsios A, Kim CS, York AG, Flavell RA, Crawford JM. Cellular Stress-Induced Metabolites in Escherichia coli. J Nat Prod. 2022 Nov 25;85(11):2626-2640. doi: 10.1021/acs.jnatprod.2c00706. Epub 2022 Nov 8. PMID: 36346625; PMCID: PMC9949963.

Gaudet RG, Zhu S, Halder A, Kim BH, Bradfield CJ, Huang S, Xu D, Mamiñska A, Nguyen TN, Lazarou M, Karatekin E, Gupta K, MacMicking JD. A human apolipoprotein L with detergent-like activity kills intracellular pathogens. Science. 2021 Jul 16;373(6552):eabf8113. doi: 10.1126/science.abf8113. PMID: 34437126; PMCID: PMC8422858.

Girish V, Lakhani AA, Thompson SL, Scaduto CM, Brown LM, Hagenson RA, Sausville EL, Mendelson BE, Kandikuppa PK, Lukow DA, Yuan ML, Stevens EC, Lee SN, Schukken KM, Akalu SM, Vasudevan A, Zou C, Salovska B, Li W, Smith JC, Taylor AM, Martienssen RA, Liu Y, Sun R, Sheltzer JM. Oncogene-like addiction to aneuploidy in human cancers. Science. 2023 Aug 25;381(6660):eadg4521. doi: 10.1126/science.adg4521. Epub 2023 Aug 25. PMID: 37410869; PMCID: PMC10753973.

Goddard TN, Patel J, Park HB, Crawford JM. Dimeric Stilbene Antibiotics Target the Bacterial Cell Wall in Drug-Resistant Gram-Positive Pathogens. Biochemistry. 2020 Jun 2;59(21):1966-1971. doi: 10.1021/acs.biochem.0c00213. Epub 2020 May 20. PMID: 32410442; PMCID: PMC10578317.

Grome MW, Nguyen MTA, Moonan DW, Mohler K, Gurara K, Wang S, Hemez C, Stenton BJ, Cao Y, Radford F, Kornaj M, Patel J, Prome M, Rogulina S, Sozanski D, Tordoff J, Rinehart J, Isaacs FJ. Engineering a genomically recoded organism with one stop codon. Nature. 2025 Mar;639(8054):512-521. doi: 10.1038/s41586-024-08501-x. Epub 2025 Feb 5. PMID: 39910296; PMCID: PMC11903333.

Hamchand R, Wang K, Song D, Palm NW, Crawford JM. Mucosal sugars delineate pyrazine vs pyrazinone autoinducer signaling in Klebsiella oxytoca. Nat Commun. 2024 Oct 16;15(1):8902. doi: 10.1038/s41467-024-53185-6. PMID: 39406708; PMCID: PMC11480411.

Healy AR, Wernke KM, Kim CS, Lees NR, Crawford JM, Herzon SB. Synthesis and reactivity of precolibactin 886. Nat Chem. 2019 Oct;11(10):890-898. doi: 10.1038/s41557-019-0338-2. Epub 2019 Sep 23. Erratum in: Nat Chem. 2019 Dec;11(12):1167. doi: 10.1038/s41557-019-0383-x. PMID: 31548676; PMCID: PMC6761996.

Ba Q, Hei Y, Dighe A, Li W, Maziarz J, Pak I, Wang S, Wagner GP, Liu Y. Proteotype coevolution and quantitative diversity across 11 mammalian species. Sci Adv. 2022 Sep 9;8(36):eabn0756. doi: 10.1126/sciadv.abn0756. Epub 2022 Sep 9. PMID: 36083897; PMCID: PMC9462687.

Hemez C, Mohler K, Radford F, Moen J, Rinehart J, Isaacs FJ. Genomically recoded Escherichia coli with optimized functional phenotypes. bioRxiv [Preprint]. 2024 Aug 29:2024.08.29.610322. doi: 10.1101/2024.08.29.610322. PMID: 39257802; PMCID: PMC11383693.

Hu Z, Chen PH, Li W, Douglas T, Hines J, Liu Y, Crews CM. Targeted Dephosphorylation of Tau by Phosphorylation Targeting Chimeras (PhosTACs) as a Therapeutic Modality. J Am Chem Soc. 2023 Feb 8:10.1021/jacs.2c11706. doi: 10.1021/jacs.2c11706. Epub ahead of print. PMID: 36753634; PMCID: PMC11670127.

Hu Z, Chen PH, Li W, Krone M, Zheng S, Saarbach J, Velasco IU, Hines J, Liu Y, Crews CM. EGFR targeting PhosTACs as a dual inhibitory approach reveals differential downstream signaling. Sci Adv. 2024 Mar 29;10(13):eadj7251. doi: 10.1126/sciadv.adj7251. Epub 2024 Mar 27. PMID: 38536914; PMCID: PMC10971414.

Huseman ED, Lo A, Fedorova O, Elia JL, Gueble SE, Lin K, Sundaram RK, Oh J, Liu J, Menges F, Rees MG, Ronan MM, Roth JA, Batista VS, Crawford JM, Pyle AM, Bindra RS, Herzon SB. Mechanism of Action of KL-50, a Candidate Imidazotetrazine for the Treatment of Drug-Resistant Brain Cancers. J Am Chem Soc. 2024 Jul 10;146(27):18241-18252. doi: 10.1021/jacs.3c06483. Epub 2024 May 30. PMID: 38815248; PMCID: PMC11409917.

Jeong J, Shin JH, Li W, Hong JY, Lim J, Hwang JY, Chung JJ, Yan Q, Liu Y, Choi J, Wysolmerski J. MAL2 mediates the formation of stable HER2 signaling complexes within lipid raft-rich membrane protrusions in breast cancer cells. Cell Rep. 2021 Dec 28;37(13):110160. doi: 10.1016/j.celrep.2021.110160. PMID: 34965434; PMCID: PMC8762588.

Kelly CJ, Verdegaal AA, Anderson BW, Shaw WL, Bencivenga-Barry NA, Folta-Stogniew E, Goodman AL. Metformin inhibits digestive proteases and impairs protein digestion in mice. J Biol Chem. 2023 Dec;299(12):105363. doi: 10.1016/j.jbc.2023.105363. Epub 2023 Oct 19. PMID: 37863262; PMCID: PMC10663847.

Kim CS, Turocy T, Moon G, Shine EE, Crawford JM. Escherichia coli-Derived γ-Lactams and Structurally Related Metabolites Are Produced at the Intersection of Colibactin and Fatty Acid Biosynthesis. Org Lett. 2021 Sep 3;23(17):6895-6899. doi: 10.1021/acs.orglett.1c02461. Epub 2021 Aug 18. PMID: 34406772; PMCID: PMC10577019.

Kim CS, Gatsios A, Cuesta S, Lam YC, Wei Z, Chen H, Russell RM, Shine EE, Wang R, Wyche TP, Piizzi G, Flavell RA, Palm NW, Sperandio V, Crawford JM. Characterization of Autoinducer-3 Structure and Biosynthesis in E. coli. ACS Cent Sci. 2020 Feb 26;6(2):197-206. doi: 10.1021/acscentsci.9b01076. Epub 2020 Jan 22. PMID: 32123737; PMCID: PMC7047286.

Kim CS, Li JH, Barco B, Park HB, Gatsios A, Damania A, Wang R, Wyche TP, Piizzi G, Clay NK, Crawford JM. Cellular Stress Upregulates Indole Signaling Metabolites in Escherichia coli. Cell Chem Biol. 2020 Jun 18;27(6):698-707.e7. doi: 10.1016/j.chembiol.2020.03.003. Epub 2020 Apr 2. PMID: 32243812; PMCID: PMC7306003.

Kim NY, Goddard TN, Sohn S, Spiegel DA, Crawford JM. Biocatalytic Reversal of Advanced Glycation End Product Modification. Chembiochem. 2019 Sep 16;20(18):2402-2410. doi: 10.1002/cbic.201900158. Epub 2019 Aug 9. PMID: 31013547; PMCID: PMC6768434.

Khitun A, Slavoff SA. Proteomic Detection and Validation of Translated Small Open Reading Frames. Curr Protoc Chem Biol. 2019 Dec;11(4):e77. doi: 10.1002/cpch.77. PMID: 31750990; PMCID: PMC6878975.

Lam YC, Hamchand R, Mucci NC, Kauffman SJ, Dudkina N, Reagle EV, Casanova-Torres ÁM, DeCuyper J, Chen H, Song D, Thomas MG, Palm NW, Goodrich-Blair H, Crawford JM. The Xenorhabdus nematophila LrhA transcriptional regulator modulates production of γ-keto-N-acyl amides with inhibitory activity against mutualistic host nematode egg hatching. Appl Environ Microbiol. 2024 Jul 24;90(7):e0052824. doi: 10.1128/aem.00528-24. Epub 2024 Jun 25. PMID: 38916293; PMCID: PMC11267870.

Li JH, Cho W, Hamchand R, Oh J, Crawford JM. A Conserved Nonribosomal Peptide Synthetase in Xenorhabdus bovienii Produces Citrulline-Functionalized Lipopeptides. J Nat Prod. 2021 Oct 22;84(10):2692-2699. doi: 10.1021/acs.jnatprod.1c00573. Epub 2021 Sep 28. PMID: 34581573; PMCID: PMC9970011.

Li JH, Oh J, Kienesberger S, Kim NY, Clarke DJ, Zechner EL, Crawford JM. Making and Breaking Leupeptin Protease Inhibitors in Pathogenic Gammaproteobacteria. Angew Chem Int Ed Engl. 2020 Oct 5;59(41):17872-17880. doi: 10.1002/anie.202005506. Epub 2020 Aug 13. PMID: 32609431.

Li W, Chi H, Salovska B, Wu C, Sun L, Rosenberger G, Liu Y. Assessing the Relationship Between Mass Window Width and Retention Time Scheduling on Protein Coverage for Data-Independent Acquisition. J Am Soc Mass Spectrom. 2019 Aug;30(8):1396-1405. doi: 10.1007/s13361-019-02243-1. Epub 2019 May 30. PMID: 31147889.

Li W, Salovska B, Fornasiero EF, Liu Y. Toward a hypothesis-free understanding of how phosphorylation dynamically impacts protein turnover. Proteomics. 2023 Feb;23(3-4):e2100387. doi: 10.1002/pmic.202100387. Epub 2022 Dec 7. PMID: 36422574; PMCID: PMC10964180.

Liao X, Li W, Zhou H, Rajendran BK, Li A, Ren J, Luan Y, Calderwood DA, Turk B, Tang W, Liu Y, Wu D. The CUL5 E3 ligase complex negatively regulates central signaling pathways in CD8+ T cells. Nat Commun. 2024 Jan 19;15(1):603. doi: 10.1038/s41467-024-44885-0. PMID: 38242867; PMCID: PMC10798966.

Lozano GL, Bravo JI, Garavito Diago MF, Park HB, Hurley A, Peterson SB, Stabb EV, Crawford JM, Broderick NA, Handelsman J. Introducing THOR, a Model Microbiome for Genetic Dissection of Community Behavior. mBio. 2019 Mar 5;10(2):e02846-18. doi: 10.1128/mBio.02846-18. PMID: 30837345; PMCID: PMC6401489.

Lozano GL, Park HB, Bravo JI, Armstrong EA, Denu JM, Stabb EV, Broderick NA, Crawford JM, Handelsman J. Bacterial Analogs of Plant Tetrahydropyridine Alkaloids Mediate Microbial Interactions in a Rhizosphere Model System. Appl Environ Microbiol. 2019 May 2;85(10):e03058-18. doi: 10.1128/AEM.03058-18. PMID: 30877115; PMCID: PMC6498172.

Luo Y, Schofield JA, Na Z, Hann T, Simon MD, Slavoff SA. Discovery of cellular substrates of human RNA-decapping enzyme DCP2 using a stapled bicyclic peptide inhibitor. Cell Chem Biol. 2021 Apr 15;28(4):463-474.e7. doi: 10.1016/j.chembiol.2020.12.003. Epub 2020 Dec 22. PMID: 33357462; PMCID: PMC8052284.

Lyu K, Zhang Y, Zhang D, Kahn M, Ter Horst KW, Rodrigues MRS, Gaspar RC, Hirabara SM, Luukkonen PK, Lee S, Bhanot S, Rinehart J, Blume N, Rasch MG, Serlie MJ, Bogan JS, Cline GW, Samuel VT, Shulman GI. A Membrane-Bound Diacylglycerol Species Induces PKCϵ-Mediated Hepatic Insulin Resistance. Cell Metab. 2020 Oct 6;32(4):654-664.e5. doi: 10.1016/j.cmet.2020.08.001. Epub 2020 Sep 2. PMID: 32882164; PMCID: PMC7544641.

Martins FH, Rosay T, Rajan A, Carter HE, Turocy T, Mejia A, Crawford JM, Maresso AW, Sperandio V. Enterococcus faecalis-derived adenine enhances enterohaemorrhagic Escherichia coli Type 3 Secretion System-dependent virulence. Nat Microbiol. 2024 Sep;9(9):2448-2461. doi: 10.1038/s41564-024-01747-1. Epub 2024 Jul 4. PMID: 38965331; PMCID: PMC11585081.

Mehnert M, Li W, Wu C, Salovska B, Liu Y. Combining Rapid Data Independent Acquisition and CRISPR Gene Deletion for Studying Potential Protein Functions: A Case of HMGN1. Proteomics. 2019 Jul;19(13):e1800438. doi: 10.1002/pmic.201800438. Epub 2019 Jun 14. PMID: 30901150.

Miller CJ, Lou HJ, Simpson C, van de Kooij B, Ha BH, Fisher OS, Pirman NL, Boggon TJ, Rinehart J, Yaffe MB, Linding R, Turk BE. Comprehensive profiling of the STE20 kinase family defines features essential for selective substrate targeting and signaling output. PLoS Biol. 2019 Mar 21;17(3):e2006540. doi: 10.1371/journal.pbio.2006540. PMID: 30897078; PMCID: PMC6445471.

Mohler K, Rinehart J. Expression of authentic post-translationally modified proteins in organisms with expanded genetic codes. Methods Enzymol. 2019;626:539-559. doi: 10.1016/bs.mie.2019.07.017. Epub 2019 Aug 1. PMID: 31606090.

Mohler K, Moen JM, Rogulina S, Rinehart J. System-wide optimization of an orthogonal translation system with enhanced biological tolerance. Mol Syst Biol. 2023 Aug 8;19(8):e10591. doi: 10.15252/msb.202110591. Epub 2023 Jul 21. PMID: 37477096; PMCID: PMC10407733.

Mohsen JJ, Mohsen MG, Jiang K, Landajuela A, Quinto L, Isaacs FJ, Karatekin E, Slavoff SA. Cellular function of the GndA small open reading frame-encoded polypeptide during heat shock. bioRxiv [Preprint]. 2024 Jun 29:2024.06.29.601336. doi: 10.1101/2024.06.29.601336. PMID: 38979229; PMCID: PMC11230408.

Na Z, Luo Y, Cui DS, Khitun A, Smelyansky S, Loria JP, Slavoff SA. Phosphorylation of a Human Microprotein Promotes Dissociation of Biomolecular Condensates. J Am Chem Soc. 2021 Aug 18;143(32):12675-12687. doi: 10.1021/jacs.1c05386. Epub 2021 Aug 4. Erratum in: J Am Chem Soc. 2021 Oct 27;143(42):17871. doi: 10.1021/jacs.1c10483. PMID: 34346674; PMCID: PMC8564862.

Na Z, Dai X, Zheng SJ, Bryant CJ, Loh KH, Su H, Luo Y, Buhagiar AF, Cao X, Baserga SJ, Chen S, Slavoff SA. Mapping subcellular localizations of unannotated microproteins and alternative proteins with MicroID. Mol Cell. 2022 Aug 4;82(15):2900-2911.e7. doi: 10.1016/j.molcel.2022.06.035. Epub 2022 Jul 28. PMID: 35905735; PMCID: PMC9662605.

Nassar AF, Wu T, Nassar SF, Wisnewski AV. UPLC-MS for metabolomics: a giant step forward in support of pharmaceutical research. Drug Discov Today. 2017 Feb;22(2):463-470. doi: 10.1016/j.drudis.2016.11.020. Epub 2016 Dec 2. PMID: 27919805; PMCID: PMC5721520.

Oh J, Kim NY, Chen H, Palm NW, Crawford JM. An Ugi-like Biosynthetic Pathway Encodes Bombesin Receptor Subtype-3 Agonists. J Am Chem Soc. 2019 Oct 16;141(41):16271-16278. doi: 10.1021/jacs.9b04183. Epub 2019 Oct 2. PMID: 31537063.

Ontai-Brenning A, Hamchand R, Crawford JM, Goodman AL. Gut microbes modulate (p)ppGpp during a time-restricted feeding regimen. mBio. 2023 Dec 19;14(6):e0190723. doi: 10.1128/mbio.01907-23. Epub 2023 Nov 16. PMID: 37971266; PMCID: PMC10746209.

Padovano V, Kuo IY, Stavola LK, Aerni HR, Flaherty BJ, Chapin HC, Ma M, Somlo S, Boletta A, Ehrlich BE, Rinehart J, Caplan MJ. The polycystins are modulated by cellular oxygen-sensing pathways and regulate mitochondrial function. Mol Biol Cell. 2017 Jan 15;28(2):261-269. doi: 10.1091/mbc.E16-08-0597. Epub 2016 Nov 23. PMID: 27881662; PMCID: PMC5231895.

Panda A, Giska F, Duncan AL, Welch AJ, Brown C, McAllister R, Hariharan P, Goder JND, Coleman J, Ramakrishnan S, Pincet F, Guan L, Krishnakumar S, Rothman JE, Gupta K. Direct determination of oligomeric organization of integral membrane proteins and lipids from intact customizable bilayer. Nat Methods. 2023 Jun;20(6):891-897. doi: 10.1038/s41592-023-01864-5. Epub 2023 Apr 27. PMID: 37106230; PMCID: PMC10932606.

Papini C, Ullah I, Ranjan AP, Zhang S, Wu Q, Spasov KA, Zhang C, Mothes W, Crawford JM, Lindenbach BD, Uchil PD, Kumar P, Jorgensen WL, Anderson KS. Proof-of-concept studies with a computationally designed Mpro inhibitor as a synergistic combination regimen alternative to Paxlovid. Proc Natl Acad Sci U S A. 2024 Apr 23;121(17):e2320713121. doi: 10.1073/pnas.2320713121. Epub 2024 Apr 15. PMID: 38621119; PMCID: PMC11046628.

Park HB, Wei Z, Oh J, Xu H, Kim CS, Wang R, Wyche TP, Piizzi G, Flavell RA, Crawford JM. Sulfamethoxazole drug stress upregulates antioxidant immunomodulatory metabolites in Escherichia coli. Nat Microbiol. 2020 Nov;5(11):1319-1329. doi: 10.1038/s41564-020-0763-4. Epub 2020 Jul 27. PMID: 32719505; PMCID: PMC7581551.

Park HB, Goddard TN, Oh J, Patel J, Wei Z, Perez CE, Mercado BQ, Wang R, Wyche TP, Piizzi G, Flavell RA, Crawford JM. Bacterial Autoimmune Drug Metabolism Transforms an Immunomodulator into Structurally and Functionally Divergent Antibiotics. Angew Chem Int Ed Engl. 2020 May 11;59(20):7871-7880. doi: 10.1002/anie.201916204. Epub 2020 Mar 17. PMID: 32097515; PMCID: PMC7200298.

Park HB, Lam YC, Gaffney JP, Weaver JC, Krivoshik SR, Hamchand R, Pieribone V, Gruber DF, Crawford JM. Bright Green Biofluorescence in Sharks Derives from Bromo-Kynurenine Metabolism. iScience. 2019 Sep 27;19:1291-1336. doi: 10.1016/j.isci.2019.07.019. Epub 2019 Aug 8. PMID: 31402257; PMCID: PMC6831821.

Patel JR, Oh J, Wang S, Crawford JM, Isaacs FJ. Cross-kingdom expression of synthetic genetic elements promotes discovery of metabolites in the human microbiome. Cell. 2022 Apr 28;185(9):1487-1505.e14. doi: 10.1016/j.cell.2022.03.008. Epub 2022 Apr 1. PMID: 35366417; PMCID: PMC10619838.

Perez CE, Crawford JM. Characterization of a Hybrid Nonribosomal Peptide-Carbohydrate Biosynthetic Pathway in Photorhabdus luminescens. Biochemistry. 2019 Feb 26;58(8):1131-1140. doi: 10.1021/acs.biochem.8b01120. Epub 2019 Feb 13. PMID: 30694662.

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Rosenberger G, Li W, Turunen M, He J, Subramaniam PS, Pampou S, Griffin AT, Karan C, Kerwin P, Murray D, Honig B, Liu Y, Califano A. Network-based elucidation of colon cancer drug resistance mechanisms by phosphoproteomic time-series analysis. Nat Commun. 2024 May 9;15(1):3909. doi: 10.1038/s41467-024-47957-3. PMID: 38724493; PMCID: PMC11082183.

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Salovska B, Li W, Di Y, Liu Y. BoxCarmax: A High-Selectivity Data-Independent Acquisition Mass Spectrometry Method for the Analysis of Protein Turnover and Complex Samples. Anal Chem. 2021 Feb 16;93(6):3103-3111. doi: 10.1021/acs.analchem.0c04293. Epub 2021 Feb 3. PMID: 33533601; PMCID: PMC8959401.

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Shine EE, Xue M, Patel JR, Healy AR, Surovtseva YV, Herzon SB, Crawford JM. Model Colibactins Exhibit Human Cell Genotoxicity in the Absence of Host Bacteria. ACS Chem Biol. 2018 Dec 21;13(12):3286-3293. doi: 10.1021/acschembio.8b00714. Epub 2018 Nov 20. PMID: 30403848; PMCID: PMC7001666.

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Turocy T, Crawford JM. Bacterial small molecule metabolites implicated in gastrointestinal cancer development. Nat Rev Microbiol. 2025 Feb;23(2):106-121. doi: 10.1038/s41579-024-01103-4. Epub 2024 Oct 7. PMID: 39375475.

Urdaneta-Páez V, Hamchand R, Anthony K, Crawford J, Sutherland AG, Kazmierczak BI. Identification of Efflux Substrates Using a Riboswitch-Based Reporter in Pseudomonas aeruginosa. mSphere. 2023 Apr 20;8(2):e0006923. doi: 10.1128/msphere.00069-23. Epub 2023 Mar 22. PMID: 36946743; PMCID: PMC10117056.

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Wang S, Li W, Hu L, Cheng J, Yang H, Liu Y. NAguideR: performing and prioritizing missing value imputations for consistent bottom-up proteomic analyses. Nucleic Acids Res. 2020 Aug 20;48(14):e83. doi: 10.1093/nar/gkaa498. PMID: 32526036; PMCID: PMC7641313.

Wang S, Di Y, Yang Y, Salovska B, Li W, Hu L, Yin J, Shao W, Zhou D, Cheng J, Liu D, Yang H, Liu Y. PTMoreR-enabled cross-species PTM mapping and comparative phosphoproteomics across mammals. Cell Rep Methods. 2024 Sep 16;4(9):100859. doi: 10.1016/j.crmeth.2024.100859. Epub 2024 Sep 9. PMID: 39255793; PMCID: PMC11440062.

Wei Z, Oh J, Flavell RA, Crawford JM. LACC1 bridges NOS2 and polyamine metabolism in inflammatory macrophages. Nature. 2022 Sep;609(7926):348-353. doi: 10.1038/s41586-022-05111-3. Epub 2022 Aug 17. Erratum in: Nature. 2023 Jun;618(7965):E21. doi: 10.1038/s41586-023-06244-9. PMID: 35978195; PMCID: PMC9813773.

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Wu Q, Song D, Zhao Y, Verdegaal AA, Turocy T, Duncan-Lowey B, Goodman AL, Palm NW, Crawford JM. Activity of GPCR-targeted drugs influenced by human gut microbiota metabolism. Nat Chem. 2025 Apr 3. doi: 10.1038/s41557-025-01789-w. Epub ahead of print. PMID: 40181149.

Xue M, Kim CS, Healy AR, Wernke KM, Wang Z, Frischling MC, Shine EE, Wang W, Herzon SB, Crawford JM. Structure elucidation of colibactin and its DNA cross-links. Science. 2019 Sep 6;365(6457):eaax2685. doi: 10.1126/science.aax2685. Epub 2019 Aug 8. PMID: 31395743; PMCID: PMC6820679.

York AG, Skadow MH, Oh J, Qu R, Zhou QD, Hsieh WY, Mowel WK, Brewer JR, Kaffe E, Williams KJ, Kluger Y, Smale ST, Crawford JM, Bensinger SJ, Flavell RA. IL-10 constrains sphingolipid metabolism to limit inflammation. Nature. 2024 Mar;627(8004):628-635. doi: 10.1038/s41586-024-07098-5. Epub 2024 Feb 21. PMID: 38383790; PMCID: PMC10954550.

Yu C, Wang X, Li W, Liu Y, Huang L. Developing a Bimolecular Affinity Purification Strategy to Isolate 26S Proteasome Holocomplexes for Complex-Centric Proteomic Analysis. Anal Chem. 2021 Oct 5;93(39):13407-13413. doi: 10.1021/acs.analchem.1c03551. Epub 2021 Sep 22. PMID: 34550675; PMCID: PMC8999942.

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Zhang H, Lyu Z, Fan Y, Evans CR, Barber KW, Banerjee K, Igoshin OA, Rinehart J, Ling J. Metabolic stress promotes stop-codon readthrough and phenotypic heterogeneity. Proc Natl Acad Sci U S A. 2020 Sep 8;117(36):22167-22172. doi: 10.1073/pnas.2013543117. Epub 2020 Aug 24. PMID: 32839318; PMCID: PMC7486758.

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