Publications

2018

Park YJ, Kenney GE, Schachner LF, Kelleher NL, Rosenzweig AC. Repurposed HisC Aminotransferases Complete the Biosynthesis of Some Methanobactins. Biochemistry.2018 Apr 25. doi: 10.1021/acs.biochem.8b00296. [Epub ahead of print] PubMed PMID:29694778.

Miley GP, Rote JC, Silverman RB, Kelleher NL, Thomson RJ. Total Synthesis of Tambromycin Enabled by Indole C-H Functionalization. Org Lett. 2018 Mar 27. doi: 10.1021/acs.orglett.8b00700. [Epub ahead of print] PubMed PMID: 29584440.

Kenney GE, Dassama LMK, Pandelia ME, Gizzi AS, Martinie RJ, Gao P, DeHart CJ, Schachner LF, Skinner OS, Ro SY, Zhu X, Sadek M, Thomas PM, Almo SC, Bollinger JM Jr., Krebs C, Kelleher NL, Rosenzweig AC. The biosynthesis of methanobactin. Science. 2018 Mar 23;359(6382):1411-1416. doi: 10.1126/ science.aap9437. PubMed PMID: 29567715.

Clevenger KD, Ye R, Bok JW, Thomas PM, Islam MN, Miley GP, Robey MT, Chen C, Yang K, Swyers M, Wu E, Gao P, Wu CC, Keller NP, Kelleher NL. Interrogation of Benzomalvin Biosynthesis Using Fungal Artificial Chromosomes with Metabolomic Scoring (FAC-MS): Discovery of a Benzodiazepine Synthase Activity. Biochemistry. 2018 Mar 20. doi: 10.1021/acs.biochem.8b00076. [Epub ahead of print] PubMed PMID:29533658.

Parkinson EI, Tryon JH, Goering AW, Ju KS, McClure RA, Kemball JD, Zhukovsky S, Labeda DP, Thomson RJ, Kelleher NL, Metcalf WW. Discovery of the Tyrobetaine Natural Products and Their Biosynthetic Gene Cluster via Metabologenomics. ACS Chem Biol. 2018 Mar 13. doi:10.1021/acschembio. 7b01089. [Epub ahead of print] PubMed PMID: 29510029.

Morochnik S, Zhu Y, Duan C, Cai M, Reid RR, He TC, Koh J, Szleifer I, Ameer GA. A thermoresponsive, citrate-based macromolecule for bone regenerative engineering. J Biomed Mater Res A. 2018 Feb 2. doi: 10.1002/jbm.a.36358. [Epub ahead of print] PubMed PMID: 29396921

Skakuj K, Wang S, Qin L, Lee A, Zhang B, Mirkin CA. Conjugation Chemistry-Dependent T-Cell Activation with Spherical Nucleic Acids. J Am Chem Soc. 2018 Jan 31;140(4):1227-1230. doi: 10.1021/jacs.7b12579. Epub 2018 Jan 22. PubMed PMID: 29356509; PubMed Central PMCID: PMC5831183.

Gladstein S, Stawarz A, Almassalha LM, Cherkezyan L, Chandler JE, Zhou X, Subramanian H, Backman V. Measuring Nanoscale Chromatin Heterogeneity with Partial Wave Spectroscopic Microscopy. Methods Mol Biol. 2018;1745:337-360. doi:10.1007/978-1-4939-7680-5_19. PubMed PMID: 29476478.

 

2017

Roca H, Jones JD, Purica MC, Weidner S, Koh AJ, Kuo R, Wilkinson JE, Wang Y, Daignault-Newton S, Pienta KJ, Morgan TM, Keller ET, Nör JE, Shea LD, McCauley LK. Apoptosis-induced CXCL5 accelerates inflammation and growth of prostate tumor metastases in bone. J Clin Invest. 2018 Jan 2;128(1):248-266. doi:10.1172/JCI92466. Epub 2017 Nov 27. PMCID:PMC5749545.

Skinner OS, Haverland NA, Fornelli L, Melani RD, Do Vale LHF, Seckler HS, Doubleday PF, Schachner LF, Srzentić K, Kelleher NL, Compton PD. Top-down characterization of endogenous protein complexes with native proteomics. Nat Chem Biol. 2018 Jan;14(1):36-41. doi: 10.1038/nchembio.2515. Epub 2017 Nov 13. PMCID: PMC5726920.

Morochnik S, Nap RJ, Ameer GA, Szleifer I. Structural behavior of competitive temperature and pH-responsive tethered polymer layers. Soft Matter. 2017 Sep 27;13(37):6322-6331. doi: 10.1039/c7sm01538k. PMID: 28905971

Toby TK, Abecassis M, Kim K, Thomas PM, Fellers RT, LeDuc RD, Kelleher NL, Demetris J, Levitsky J. Peripheral blood mononuclear cell proteoforms as novel rejection biomarkers in liver transplant recipients. American Journal of Transplantation. 2017 Sep;17(9):2458-2467. doi: 10.1111/ajt.14359. Epub 2017 Jun 27.. doi: 10.1111/ajt.14359. PMID: 28510335.

Kuo R, Saito E, Miller SD, Shea LD.  Peptide-Conjugated Nanoparticles Reduce Positive Co-stimulatory Expression and T Cell Activity to Induce Tolerance. Mol Ther. 2017 Jul 5;25(7):1676-1685. doi: 10.1016/j.ymthe.2017.03.032. Epub 2017 Apr 10. PMCID: PMC5498812.

Clevenger KD, Bok JW, Ye R, Miley GP, Verdan MH, Velk T, Chen C, Yang K, Robey MT, Gao P, Lamprecht M, Thomas PM, Islam MN, Palmer JM, Wu CC, Keller NP, Kelleher NL. A scalable platform to identify fungal secondary metabolites and their gene clusters. Nat Chem Biol. 2017 Aug;13(8):895-901. doi: 10.1038/nchembio.2408. Epub 2017 Jun 12. PMCID: PMC5577364

Wang S, McGuirk CM, Ross MB, Wang S, Chen P, Xing H, Liu Y, Mirkin CA. General and Direct Method for Preparing Oligonucleotide-Functionalized Metal-Organic Framework Nanoparticles. J Am Chem Soc. 2017 Jul 26;139(29):9827-9830. doi: 10.1021/jacs.7b05633. Epub 2017 Jul 18. PMID: 28718644

Clevenger KD, Bok JW, Ye R, Miley GP, Verdan MH, Velk T, Chen C, Yang KH, Robey MT, Gao P, Lamprecht M, Thomas PM, Islam MN, Palmer J, Wu CC, Keller NP, Kelleher NL. Large-Scale Identification of New Secondary Metabolites Using Heterologous Expression and Metabolomic Screening of Fungal Biosynthetic Gene Clusters. Nature Chemical Biology. 2017 Jun 12. doi:10.1038/nchembio.2408. [Epub ahead of print] PMID:28604695

Yue J, Feliciano TJ, Li W1, Lee A, Odom TW. Gold Nanoparticle Size and Shape Effects on Cellular Uptake and Intracellular Distribution of siRNA Nanoconstructs. Bioconjug Chem. 2017 Jun 21;28(6):1791-1800. doi: 10.1021/acs.bioconjchem.7b00252. Epub 2017 Jun 12. PubMed PMID: 28574255

Betori RC, Miller ER, Scheidt KA, “A Biocatalytic Route to Highly Enantioenriched β-Hydroxydioxinones,”  Synth. Cat2017, 359, 1131-1137. 2017 Mar 3. NIHMSID: NIHMS876300

 

Que E.L., Duncan E.F., Bayer A.R., Philips S.J., Roth E.W., Bleher R., Gleber S.C., Vogt S., Woodruff T.K., O’Halloran T.V. 2017, Zinc sparks induce physiochemical changes in the egg zona pellucida that prevent polyspermy. Integr Biol (Camb). 2017 Feb 20;9(2):135-144. doi: 10.1039/c6ib00212a. PMCID: PMC5439353.

Fornelli L, Toby TK, Schachner LF, Doubleday PF, Srzentić K, DeHart CJ, Kelleher NL. Top-down proteomics: Where we are, where we are going? J Proteomics. 2018 Mar 20;175:3-4. doi: 10.1016/j.jprot.2017.02.002. Epub 2017 Feb 7. PMCID: PMC5547015.

Fornelli L, Toby TK, Schachner LF, Doubleday PF, Srzentić K, DeHart CJ,Kelleher NL. Top-down proteomics: Where we are, where we are going? J Proteomics. 2018 Mar 20;175:3-4. doi: 10.1016/j.jprot.2017.02.002. Epub 2017 Feb 7. P PMCID: PMC5547015.

2016

Skinner OS, Schachner LF, Kelleher NL. The Search Engine for Multi-Proteoform Complexes: An Online Tool for the Identification and Stoichiometry Determination of Protein Complexes. Curr Protoc Bioinformatics. 2016 Dec 8;56:13.30.1-13.30.11. doi: 10.1002/cpbi.16. PubMed PMID: 27930806; PubMed Central PMCID: PMC5152683

McClure RA, Goering AW, Ju KS, Baccile JA, Schroeder FC, Metcalf WW, Thomson RJ, Kelleher NL. 2016, Elucidating the rimosamide-detoxin natural product families and their biosynthesis using metabolite/gene cluster correlations. ACS Chem Biol. 11:3452-3460.

Chinen AB, Ferrer JR, Merkel TJ, Mirkin CA. Relationships between Poly(ethylene glycol) Modifications on RNA-Spherical Nucleic Acid Conjugates and Cellular Uptake and Circulation Time. Bioconjug Chem. 2016 Oct 20. [Epub ahead of print] PMID: 27762539

Savaryn JP, Toby TK, Kelleher NL. A researcher’s guide to mass spectrometry-based proteomics. Proteomics. 2016 Sep;16(18):2435-43. doi: 10.1002/pmic.201600113. PMID: 27553853

Goering AW, Li J, McClure RA, Thomson RJ, Jewett MC, Kelleher NL. In Vitro Reconstruction of Nonribosomal Peptide Biosynthesis Directly from DNA Using Cell-Free Protein Synthesis. ACS Synth Biol. 2016 Aug 9. [Epub ahead of print] PMID: 27478992

Henke MT, Soukup AA, Goering AW, McClure RA, Thomson RJ, Keller NP, Kelleher NL. New Aspercryptins, Lipopeptide Natural Products, Revealed by HDAC Inhibition in Aspergillus nidulans. ACS Chem Biol. 2016 Aug 19;11(8):2117-23. doi: 10.1021/acschembio.6b00398. PMID: 27310134

Kathman SG, Statsyuk AV. Covalent Tethering of Fragments For Covalent Probe Discovery. Medchemcomm. 2016 Apr 1;7(4):576-585. PMID: 27398190

Toby TK, Fornelli L, Kelleher NL. Progress in Top-Down Proteomics and the Analysis of Proteoforms. Annu Rev Anal Chem (Palo Alto Calif). 2016 Jun 12;9(1):499-519. doi: 10.1146/annurev-anchem-071015-041550. PMID: 27306313

Savaryn JP, Toby TK, Catherman AD, Fellers RT, LeDuc RD, Thomas PM, Friedewald JJ, Salomon DR, Abecassis MM, Kelleher NL. Comparative top down proteomics of peripheral blood mononuclear cells from kidney transplant recipients with normal kidney biopsies or acute rejection. Proteomics. 2016 Jul;16(14):2048-58. doi: 10.1002/pmic.201600008. PMID:27120713

Goering AW, McClure RA, Doroghazi JR, Albright JC, Haverland NA, Zhang Y, Ju KS, Thomson RJ, Metcalf WW, Kelleher NL. Metabologenomics: Correlation of Microbial Gene Clusters with Metabolites Drives Discovery of a Nonribosomal Peptide with an Unusual Amino Acid Monomer. ACS Cent Sci. 2016 Feb 24;2(2):99-108. doi: 10.1021/acscentsci.5b00331. PMID: 27163034

Ntai I, Toby TK, LeDuc RD, Kelleher NL. A Method for Label-Free, Differential Top-Down Proteomics. Methods Mol Biol. 2016;1410:121-33. doi: 10.1007/978-1-4939-3524-6_8. PMID: 26867742

Chen Y, McClure RA, Kelleher NL. Screening for Expressed Nonribosomal Peptide Synthetases and Polyketide Synthases Using LC-MS/MS-Based Proteomics. Methods Mol Biol. 2016;1401:135-47. doi: 10.1007/978-1-4939-3375-4_9. PMID: 26831706

 

2015

Lee E. and Scheidt K., 2015, Studies toward the total synthesis of chrolactomycin and the development of novel small molecule telomerase inhibitors.  249th ACS National Meeting, Denver, 2015, Poster presentation 41 BIOL: Current Topics in Biological Chemistry ABSTRACT

Damon PL, Liss CJ, Lewis RA, Morochnik S, Szpunar DE, Telser J, Hayton TW. Quantifying the Electron Donor and Acceptor Abilities of the Ketimide Ligands in M(N═C(t)Bu2)4 (M = V, Nb, Ta). Inorg Chem. 2015 Oct 19;54(20):10081-95. doi: 10.1021/acs.inorgchem.5b02017. PMID: 26419513

McShan D, Kathman S, Lowe B, Xu Z, Zhan J, Statsyuk A, Ogungbe IV. Identification of non-peptidic cysteine reactive fragments as inhibitors of cysteine protease rhodesain. Bioorg Med Chem Lett. 2015 Oct 15;25(20):4509-12. doi: 10.1016/j.bmcl.2015.08.074. PMID: 26342866

Chinen AB, Guan CM, Ferrer JR, Barnaby SN, Merkel TJ, Mirkin CA. Nanoparticle Probes for the Detection of Cancer Biomarkers, Cells, and Tissues by Fluorescence. Chem Rev. 2015 Oct 14;115(19):10530-74. doi: 10.1021/acs.chemrev.5b00321. Review. PMID:26313138

Stawarz A, Kalman R, Subramanian H, Zhang D, Roy H, Backman V. P-Rf-454 Detectable Nanoscale Alterations for Prediction of Future Risk of Hepatocellular Carcinoma. 2015 Biomedical Engineering Society, Oct. 7-10, Tampa FL; ABSTRACT

Kathman SG, Span I, Smith AT, Xu Z, Zhan J, Rosenzweig AC, Statsyuk AV. A Small Molecule That Switches a Ubiquitin Ligase From a Processive to a Distributive Enzymatic Mechanism. J Am Chem Soc. 2015 Oct 7;137(39):12442-5. doi: 10.1021/jacs.5b06839. PMID: 26371805

Kim K, Compton PD, Toby TK, Thomas PM, Wilkins JT, Mutharasan RK, Kelleher NL. Reducing protein oxidation in low-flow electrospray enables deeper investigation of proteoforms by top down proteomics. EuPA Open Proteom. 2015 Sep;8:40-47. PMID: 26753126

Dennis KL, Saadalla A, Blatner NR, Wang S, Venkateswaran V, Gounari F, Cheroutre H, Weaver CT, Roers A, Egilmez NK, Khazaie K. T-cell Expression of IL10 Is Essential for Tumor Immune Surveillance in the Small Intestine. Cancer Immunol Res. 2015 Jul;3(7):806-14. doi: 10.1158/2326-6066.CIR-14-0169. PMID: 25855122

Bayer A., Que E., Duncan F., Woodruff T.K., O’Halloran T.V. Zinc fluxes in control of gamete maturation, cell cycle and fertilization.2015 Cell Biology of Metals Gordon Conference, West Dover, Vermont, July 2015. ABSTRACT

Wu HC, Yamankurt G, Luo J, Subramaniam J, Hashmi SS, Hu H, Cunha SR. Identification and characterization of two ankyrin-B isoforms in mammalian heart. Cardiovasc Res. 2015 Sep 1;107(4):466-77. doi: 10.1093/cvr/cvv184. Epub 2015 Jun 24.

Albright JC, Henke MT, Soukup AA, McClure RA, Thomson RJ, Keller NP, Kelleher NL. Large-scale metabolomics reveals a complex response of Aspergillus nidulans to epigenetic perturbation. ACS Chem Biol. 2015 Jun 19;10(6):1535-41. doi: 10.1021/acschembio.5b00025. PMID: 25815712

Ferrer JR, Chokechanachaisakul A, Wertheim JA. New Tools in Experimental Cellular Therapy for the Treatment of Liver Diseases. Curr Transplant Rep. 2015 Jun 1;2(2):202-210. PMID: 26317066

Toby, T.K., Fornelli, L., Kim, K., Salomon, D.R., Abecassis, M.M., Kelleher, N.L. MP 557: Proteoform reaction monitoring by top-down proteomics: Moving from discovery to targeted64 validation of intact protein biomarkers. 2015 ASMS National Conference. May 31 – June 4, St. Louis, MO. ABSTRACT

Yamankurt G, Wu HC, McCarthy M, Cunha SR. Exon organization and novel alternative splicing of Ank3 in mouse heart. PLoS One. 2015 May 29;10(5):e0128177. doi: 10.1371/journal.pone.0128177. eCollection 2015.

Kalman, R., Subramanian, H., Nunes, D., DeLaCruz, M., Wali, R.K., Jepeal, L.I., Stawarz, A., Zhang, D., Backman, V., and Hemant, H.K. 951 Biophonotic Detection of High Order Chromatin Alterations in Field Carcinogenesis Predicts Risk of Future Hepatocellular Carcinoma: A Pilot Study. Gastroenterology 148.4 (2015): S-184. April 2015Volume 148, Issue 4, Supplement 1, Pages S-184–S-185

Bayer A., Que E., Duncan F., Woodruff T.K., O’Halloran T.V. 2015,107-Zinc fluxes in control of gamete maturation, cell cycle and fertilization. 249th American Chemical Society National Meeting, Denver, Colorado, March 2015. BIOL: Current Topics in Biological Chemistry.  ABSTRACT.

Ferrer J., Chernyak N., Wertheim J., Mirkin C.  MEDI 106: Design and synthesis of a dual-targeting liposomal spherical nucleic acid.  American Chemical Society (ACS) National Meeting, Boulder, CO Spring 2015 ABSTRACT

Que EL, Bleher R, Duncan FE, Kong BY, Gleber SC, Vogt S, Chen S, Garwin SA, Bayer AR, Dravid VP, Woodruff TK, O’Halloran TV. Quantitative mapping of zinc fluxes in the mammalian egg reveals the origin of fertilization-induced zinc sparks. Nat Chem. 2015 Feb;7(2):130-9. doi: 10.1038/nchem.2133. PMID: 25615666

 

2014

Boehler RM, Kuo R, Shin S, Goodman AG, Pilecki MA, Gower RM, Leonard JN, Shea LD. Lentivirus delivery of IL-10 to promote and sustain macrophage polarization towards an anti-inflammatory phenotype. Biotechnol Bioeng. 2014 Jun;111(6):1210-21. doi: 10.1002/bit.25175. Erratum in: Biotechnol Bioeng. 2014 Jul;111(7):1469. Gower, R M [added]. PMID: 24375008

Kathman SG, Xu Z, Statsyuk AV. A fragment-based method to discover irreversible covalent inhibitors of cysteine proteases. J Med Chem. 2014 Jun 12;57(11):4969-74. doi: 10.1021/jm500345q. PMID: 24870364

 

2013

Ye H, Toby TK, Sommers CD, Ghasriani H, Trehy ML, Ye W, Kolinski RE, Buhse LF, Al-Hakim A, Keire DA. Characterization of currently marketed heparin products: key tests for LMWH quality assurance. J Pharm Biomed Anal. 2013 Nov;85:99-107. doi: 10.1016/j.jpba.2013.06.033. PMID: 23917037

Dennis KL, Wang Y, Blatner NR, Wang S, Saadalla A, Trudeau E, Roers A, Weaver CT, Lee JJ, Gilbert JA, Chang EB, Khazaie K. Adenomatous polyps are driven by microbe-instigated focal inflammation and are controlled by IL-10-producing T cells. Cancer Res. 2013 Oct 1;73(19):5905-13. doi: 10.1158/0008-5472.CAN-13-1511. PMID: 23955389

Chen Y, McClure RA, Zheng Y, Thomson RJ, Kelleher NL. Proteomics guided discovery of flavopeptins: anti-proliferative aldehydes synthesized by a reductase domain-containing non-ribosomal peptide synthetase. J Am Chem Soc. 2013 Jul 17;135(28):10449-56. doi: 10.1021/ja4031193. PMID:23763305

Chen Y, Unger M, Ntai I, McClure RA, Albright JC, Thomson RJ, Kelleher NL. Gobichelin A and B: Mixed-Ligand Siderophores Discovered Using Proteomics. Medchemcomm. 2013 Jan 1;4(1):233-238. PMID:23336063