Our Work

Some Recent Publications using data generated by the Facility:

Dang Do AN, Sleat DE, Campbell K, Johnson NL, Zheng H, Wassif CA, Dale RK, Porter FD. Cerebrospinal Fluid Protein Biomarker Discovery in CLN3. J Proteome Res. 2023 Jul 7;22(7):2493-2508. doi: 10.1021/acs.jproteome.3c00199. Epub 2023 Jun 20. PMID: 37338096
Retzbach EP, Sheehan SA, Krishnan H, Zheng H, Zhao C, Goldberg GS. Independent effects of Src kinase and podoplanin on anchorage independent cell growth and migration. Mol Carcinog. 2022 Jul;61(7):677-689. doi: 10.1002/mc.23410. Epub 2022 Apr 26. PMID: 35472679
Nikonorova IA, Wang J, Cope AL, Tilton PE, Power KM, Walsh JD, Akella JS, Krauchunas AR, Shah P, Barr MM. (2022) Isolation, profiling, and tracking of extracellular vesicle cargo in Caenorhabditis elegans. Curr Biol. 2022 May 9;32(9):1924-1936.e6. doi: 10.1016/j.cub.2022.03.005. Epub 2022 Mar 24. PMID: 35334227
Barth VC, Chauhan U, Zeng J, Su X, Zheng H, Husson RN, Woychik NA. (2021) Mycobacterium tuberculosis VapC4 toxin engages small ORFs to initiate an integrated oxidative and copper stress response. Proc Natl Acad Sci U S A. 2021 Aug 10;118(32):e2022136118. doi: 10.1073/pnas.2022136118. PMID: 34362841
Wei, Y.; Yee, P. P.; Liu, Z.; Zhang, L.; Guo, H.; Zheng, H.; Anderson, B.; Gulley, M.; Li, W. (2020) NEDD4L-mediated Merlin ubiquitination facilitates Hippo pathway activation. EMBO Rep. 2020 Dec 3;21(12): e50642. doi: 10.15252/embr.202050642. PMID: 33058421
Yan, Z.; Shen, Z.; Li, Z.; Chao, Q.; Kong, L.; Gao, Z.; Li, Q.; Zheng, H.; Zhao, C.; Lu, C.; Wang, Y.; Wang, B. (2020) Genome-wide transcriptome and proteome profiles indicate an active role of alternative splicing during de-etiolation of maize seedlings. Planta. 2020 Sep 22;252(4):60. doi: 10.1007/s00425-020-03464-5. PMID: 32964359
Gao, Z.; Shen, Z.; Chao, Q.; Yan, Z.; Ge, X.; Lu, T.; Zheng, H.; Qian, C.; Wang, B. (2020) Large-scale Proteomic and Phosphoproteomic Analyses of Maize Seedling Leaves During De-etiolation. Genomics Proteomics Bioinformatics. 2020 Aug;18(4):397-414. doi: 10.1016/j.gpb.2020.12.004. PMID: 33385613
Hu, Z.; Ban, H.; Zheng, H.; Liu, M.; Chang, J.; Guo, J. (2020) Protein phosphatase 1 catalyzes HBV core protein dephosphorylation and is co-packaged with viral pregenomic RNA into nucleocapsids. PLoS Pathog. 2020 Jul 23;16(7): e1008669. doi: 10.1371/journal.ppat.1008669. PMID: 32702076
Yan, Z.; Shen, Z.; Gao, Z.; Chao, Q.; Qian, C.; Zheng, H.; Wang, B. (2020) A comprehensive analysis of the lysine acetylome reveals diverse functions of acetylated proteins during de-etiolation in Zea mays. J Plant Physiol. 2020 May; 248:153158. doi: 10.1016/j.jplph.2020.153158. PMID: 32240968
Cai, Y.; Xue, Y.; Truong, C. C.; Carmen-Li, J. D.; Ochoa, C.; Vanselow, J. T.; Murphy, K. A.; Li, Y. H.; Liu, X.; Kunimoto, B. L.; Zheng, H.; Zhao, C.; Zhang, Y.; Schlosser, A.; Chiu, J. C. (2020) CK2 Inhibits TIMELESS Nuclear Export and Modulates CLOCK Transcriptional Activity to Regulate Circadian Rhythms. Curr Biol. 2021 Feb 8;31(3):502-514.e7. doi: 10.1016/j.cub.2020.10.061. PMID: 33217322
Liu, J.; Zhang, C.; Wu, H.; Sun, X. X.; Li, Y.; Huang, S.; Xue, X.; Lu, S.; Shen, Z.; Su, X.; White, E.; Haffy, B.G.; HU, W.; Feng, Z. (2020) Parkin ubiquitinates phosphoglycerate dehydrogenase to suppress serine synthesis and tumor progression. J J Clin Invest. 2020 Jun 1;130(6):3253-3269. doi: 10.1172/JCI132876. PMID: 32478681
Tannous, A.; Boonen, M.; Zheng, H.; Zhao, C.; Germain, C. J.; Moore, D. F.; Sleat, D. E.; Jadot, M.; Lobel, P. (2020) Comparative Analysis of Quantitative Mass Spectrometric Methods for Subcellular Proteomics. J Proteome Res. 2020 Apr 3;19(4):1718-1730. doi: 10.1021/acs.jproteome.9b00862 PMID: 32134668
Wang, Y.; Chao, Q.; Li, Z.; Lu, T.; Zheng, H.; Zhao, C.; Shen, Z.; Li, X.; Wang, B. (2019) Large-scale Identification and Time-course Quantification of Ubiquitylation Events During Maize Seedling De-etiolation. Genomics Proteomics Bioinformatics. 2019 Dec;17(6):603-622. PMID: 32179194
Sleat, D. E.; Wiseman, J. A.; El-Banna, M.; Zheng, H.; Zhao, C.; Soherwardy, A.; Moore, D. F.; Lobel, P. (2019) Analysis of Brain and Cerebrospinal Fluid from Mouse Models of the Three Major Forms of Neuronal Ceroid Lipofuscinosis Reveals Changes in the Lysosomal Proteome. Mol Cell Proteomics. 2019 Nov;18(11):2244-2261. doi: 10.1074/mcp.RA119.001587 PMID: 31501224
Levitan O, Chen M, Kuang X, Cheong KY, Jiang J, Banal M, Nambiar N, Gorbunov MY, Ludtke SJ, Falkowski PG, Dai W. (2019) Structural and functional analyses of photosystem II in the marine diatom Phaeodactylum tricornutum. Proc Natl Acad Sci U S A 2019 Aug 27;116(35) 17316-17322. PMID: 31409711
Ithier MC, Parobchak N, Yadava S, Cheng J, Wang B, Rosen T. (2019) Fetal lung C4BPA induces p100 processing in human placenta. Sci Rep. 2019 Apr 2;9(1): 5519. PMID: 30940885
Li YH, Liu X, Vanselow JT, Zheng H, Schlosser A, Chiu JC. (2019) O-GlcNAcylation of PERIOD regulates its interaction with CLOCK and timing of circadian transcriptional repression. PLoS Genet. 2019 Jan 31;15(1): e1007953. PMID: 30703153
Zhou J, Yang L, Ozohanics O, Zhang X, Wang J, Ambrus A, Arjunan P, Brukh R, Nemeria NS, Furey W, Jordan F. (2018) A multipronged approach unravels unprecedented protein-protein interactions in the human 2-oxoglutarate dehydrogenase multienzyme complex. J Biol Chem. 2018 Dec 14; 293(50): 19213-19227 PMID: 30323066
Lam VH, Li YH, Liu X, Murphy KA, Diehl JS, Kwok RS, Chiu JC. (2018) CK1a Collaborates with DOUBLETIME to Regulate PERIOD Function in the Drosophila Circadian Clock. J Neurosci. 2018 Dec 12; 38(50): 10631-10643. PMID: 30373768
Poillet-Perez L, Xie X, Zhan L, Yang Y, Sharp DW, Hu ZS, Su X, Maganti A, Jiang C, Lu W, Zheng H, Bosenberg MW, Mehnert JM, Guo JY, Lattime E, Rabinowitz JD, White E. (2018) Autophagy maintains tumour growth through circulating arginine. Nature 2018 Nov; 563(7732): 569-573. PMID: 30429607
Woody MS, Greenberg MJ, Barua B, Winkelmann DA, Goldman YE, Ostap EM. (2018) Positive cardiac inotrope omecamtiv mecarbil activates muscle despite suppressing the myosin working stroke. Nat Commun. 2018 Sep 21; 9(1): 3838. PMID: 30242219
Cheng LC, Li Z, Graeber TG, Graham NA, Drake JM. (2018) Phosphopeptide Enrichment Coupled with Label-free Quantitative Mass Spectrometry to Investigate the Phosphoproteome in Prostate Cancer. J Vis Exp. 2018 Aug 2;(138):57996. doi: 10.3791/57996. PMID: 30124664
James JK, Pike DH, Khan IJ, Nanda V. (2018) Structural and Dynamic Properties of Allergen and Non-Allergen Forms of Tropomyosin. Structure 2018 Jul 3;26(7):997-1006.e5. doi: 10.1016/j.str.2018.05.002. PMID: 29887498
Jelen, B., Giovannelli, D., Falkowski, P. G., and Vetriani, C. (2018) Elemental sulfur reduction in the deep-sea vent thermophile, Thermovibrio ammonificans. Environ Microbiol. 2018 Jun;20(6):2301-2316. doi: 10.1111/1462-2920.14280. PMID: 29799164
Her J, Ray C, Altshuler J, Zheng H, Bunting SF. (2018) 53BP1 Mediates ATR-Chk1 signaling and protects replication forks under conditions of replication stress. Mol Cell Biol. 2018 Mar 29;38(8): e00472-17. doi: 10.1128/MCB.00472-17. PMID: 29378830
Sole-Domenech, S., Rojas, A. V., Maisuradze, G. G., Scheraga, H. A., Lobel, P. and Maxfield, F. R. (2018) Lysosomal enzyme tripeptidyl peptidase 1 destabilizes fibrillar Abeta by multiple endoproteolytic cleavages within the beta-sheet domain. Proc Natl Acad Sci U S A. 2018 Feb 13;115(7):1493-1498. doi: 10.1073/pnas.1719808115. PMID: 29378960
Bu, T. T., Shen, J., Chao, Q., Shen, Z., Yan, Z., Zheng, H. Y., Wang, B. C. (2017) Dynamic N-glycoproteome analysis of maize seedling leaves during de-etiolation using Concanavalin A lectin affinity chromatography and a nano-LC-MS/MS-based iTRAQ approach. Plant Cell Rep. 2017 Dec;36(12):1943-1958. doi: 10.1007/s00299-017-2209-x. PMID: 28942497
Liu, J., Zhang, C., Zhao, Y., Yue, X., Wu, H., Huang, S., Chen, J., Tomsky, K., Xie, H., Khella, C. A., Gatza, M. L., Xia, D., Gao, J., White, E., Haffty, B. G., Hu, W., and Feng, Z. (2017) Parkin targets HIF-1alpha for ubiquitination and degradation to inhibit breast tumor progression. Nat Commun. 2017 Nov 28;8(1):1823. doi: 10.1038/s41467-017-01947-w. PMID: 29180628
Giovannelli, D., Sievert, S. M., Hugler, M., Markert, S., Becher, D., Schweder, T., and Vetriani, C. (2017) Insight into the evolution of microbial metabolism from the deep-branching bacterium, Thermovibrio ammonificans. Elife. 2017 Apr 24;6: e18990. doi: 10.7554/eLife.18990. PMID: 28436819
Denzin, L. K., Khan, A. A., Virdis, F., Wilks, J., Kane, M., Beilinson, H. A., Dikiy, S., Case, L. K., Roopenian, D., Witkowski, M., Chervonsky, A. V., and Golovkina, T. V. (2017) Neutralizing Antibody Responses to Viral Infections Are Linked to the Non-classical MHC Class II Gene H2-Ob. Immunity. 2017 Aug 15;47(2):310-322.e7. doi: 10.1016/j.immuni.2017.07.013. PMID: 28813660
Wang JJ, Liu G Huang YB, Zeng QH, Hou Y, Li L1, Ou S, Zhang M, Hu SQ (2017) Dissecting the disulfide linkage of the N-terminal Domain of HMW 1Dx5 and its contributions to dough functionality. J Agric Food Chem. 2017 Aug 2;65(30):6264-6273. doi: 10.1021/acs.jafc.7b02449. PMID: 28692254
Kobayashi, Y., Gelinas, C., and Dougherty, J. P. (2017) Histone deacetylase inhibitors containing a benzamide functional group and a pyridyl cap are preferentially effective human immunodeficiency virus-1 latency-reversing agents in primary resting CD4+ T cells. J Gen Virol. 2017 Apr;98(4):799-809. doi: 10.1099/jgv.0.000716. PMID: 28113052
Sleat, D. E., Tannous, A., Sohar, I., Wiseman, J. A., Zheng, H., Qian, M., Zhao, C., Xin, W., Barone, R., Sims, K. B., Moore, D. F., and Lobel, P. (2017) Proteomic Analysis of Brain and Cerebrospinal Fluid from the Three Major Forms of Neuronal Ceroid Lipofuscinosis Reveals Potential Biomarkers. J Proteome Res. 2017 Oct 6;16(10):3787-3804. doi: 10.1021/acs.jproteome.7b00460. PMID: 28792770
Cai, N., Bai, Z., Nanda, V., and Runnels, L. W. (2017) Mass Spectrometric Analysis of TRPM6 and TRPM7 Phosphorylation Reveals Regulatory Mechanisms of the Channel-Kinases. Sci Rep. 2017 Feb 21; 7:42739. doi: 10.1038/srep42739. PMID: 28220887
Norton, P., Comunale, M. A., Herrera, H., Wang, M., Houser, J., Wimmerova, M., Romano, P. R., and Mehta, A. (2016) Development and application of a novel recombinant Aleuria aurantia lectin with enhanced core fucose binding for identification of glycoprotein biomarker of hepatocellular carcinoma. Proteomics. 2016 Dec;16(24):3126-3136. doi: 10.1002/pmic.201600064. PMID: 27650323
Yue, X., Zhao, Y., Huang, G., Li, J., Zhu, J., Feng, Z., and Hu, W. (2016) A novel mutant p53 binding partner BAG5 stabilizes mutant p53 and promotes mutant p53 GOFs in tumorigenesis. Cell Discov. 2016 Nov 1; 2: 16039. doi: 10.1038/celldisc.2016.39. eCollection 2016. PMID: 27807478
Li, M., Cole, F., Patel, D. S., Misenko, S. M., Her, J., Malhowski, A., Alhamza, A., Zheng, H., Baer, R., Ludwig, T., Jasin, M., Nussenzweig, A., Serrano, L., Bunting, S. F. (2016) 53BP1 ablation rescues genomic instability in mice expressing RING-less BRCA1. EMBO Rep. 2016 Nov;17(11):1532-1541. doi: 10.15252/embr.201642497. PMID: 27670884
Misra, J. R., and Irvine, K. D. (2016) Vamana Couples Fat Signaling to the Hippo Pathway. Dev Cell. 2016 Oct 24;39(2):254-266. doi: 10.1016/j.devcel.2016.09.017. PMID: 27746048
Hong, X., Liu, W., Song, R., Shah, J. J., Feng, X., Tsang, C. K., Morgan, K. M., Bunting, S. F., Inuzuka, H., Zheng, X. F., Shen, Z., Sabaawy, H. E., Liu, L., and Pine, S. R. (2016) SOX9 is targeted for proteasomal degradation by the E3 ligase FBW7 in response to DNA damage. Nucleic Acids Res. 2016 Oct 14;44(18):8855-8869. doi: 10.1093/nar/gkw748. PMID: 27566146
Ma X, Xu Q, Meyer WA, Huang B. (2016) Hormone regulation of rhizome development in tall fescue (Festuca arundinacea) associated with proteomic changes controlling respiratory and amino acid metabolism. Ann Bot. 2016 Sep;118(3):481-94. doi: 10.1093/aob/mcw120. PMID: 27443301
Zhang, C., Liu, J., Huang, G., Zhao, Y., Yue, X., Wu, H., Li, J., Zhu, J., Shen, Z., Haffty, B. G., Hu, W., and Feng, Z. (2016) Cullin3-KLHL25 ubiquitin ligase targets ACLY for degradation to inhibit lipid synthesis and tumor progression. Genes Dev. 2016 Sep 1;30(17):1956-70. doi: 10.1101/gad.283283.116. PMID: 27664236
Wang, M., Comunale, M. A., Herrera, H., Betesh, L., Kono, Y., and Mehta, A. (2016) Identification of IgM as a contaminant in lectin-FLISA assays for HCC detection. Biochem Biophys Res Commun. 2016 Jul 29;476(3):140-5. doi: 10.1016/j.bbrc.2016.05.027. PMID: 27181357
Mehta, A., Comunale, M. A., Rawat, S., Casciano, J. C., Lamontagne, J., Herrera, H., Ramanathan, A., Betesh, L., Wang, M., Norton, P., Steel, L. F., and Bouchard, M. J. (2016) Intrinsic hepatocyte dedifferentiation is accompanied by upregulation of mesenchymal markers, protein sialylation and core alpha 1,6 linked fucosylation. Sci Rep. 2016 Jun 22; 6: 27965. doi: 10.1038/srep27965. PMID: 27328854
Zhang, M., Yu, X. W., Swapna, G. V., Xiao, R., Zheng, H., Sha, C., Xu, Y., and Montelione, G. T. (2016) Efficient production of (2)H, (13)C, (15)N-enriched industrial enzyme Rhizopus chinensis lipase with native disulfide bonds. Microb Cell Fact. 2016 Jul 13;15(1):123. doi: 10.1186/s12934-016-0522-7. PMID: 27411547
Tu, S., Narendra, V., Yamaji, M., Vidal, S. E., Rojas, L. A., Wang, X., Kim, S. Y., Garcia, B. A., Tuschl, T., Stadtfeld, M., and Reinberg, D. (2016) Co-repressor CBFA2T2 regulates pluripotency and germline development. Nature. 2016 Jun 16;534(7607):387-90. doi: 10.1038/nature18004. PMID: 27281218
Zhang, W., Xu, J., Bennetzen, J. L., and Messing, J. (2016) Teff, an Orphan Cereal in the Chloridoideae, Provides Insightsinto the Evolution of Storage Proteins in Grasses. Genome Biol Evol. 2016 Jun 13;8(6):1712-21. doi: 10.1093/gbe/evw117. PMID: 27190000
Parmar, A. S., James, J. K., Grisham, D. R., Pike, D. H., and Nanda, V. (2016) Dissecting Electrostatic Contributions to Folding and Self-Assembly Using Designed Multicomponent Peptide Systems. J Am Chem Soc. 2016 Apr 6;138(13):4362-7. doi: 10.1021/jacs.5b10304. PMID: 26966815
Tan, W., Schauder, C., Naryshkina, T., Minakhina, S., Steward, R. (2016) Zfrp8 forms a complex with Fragile-X Mental Retardation Protein and regulates its localization and function. Dev Biol. 2016 Feb 15;410(2):202-212. doi: 10.1016/j.ydbio.2015.12.008. PMID: 26772998
Jadot, M., Boonen, M., Thirion, J., Wang, N., Xing, J., Zhao, C., Tannous, A., Qian, M., Zheng, H., Everett, J. K., Moore, D. F., Sleat, D. E. and Lobel, P. (2017) Accounting for Protein Subcellular Localization: A Compartmental Map of the Rat Liver Proteome. Mol Cell Proteomics. 2017 Feb;16(2):194-212. doi: 10.1074/mcp.M116.064527. PMID: 27923875
Zhang, C., Liu, J., Zhao, Y. H., Yue, X. T., Zhu, Y., Wang, X. L., Wu, H., Blanco, F., Li, S. H., Bhanot, G., Haffty, B. G., Hu, W. W., and Feng, Z. H. (2016) Glutaminase 2 is a novel negative regulator of small GTPase Rac1 and mediates p53 function in suppressing metastasis. Elife. 2016 Jan 11; 5: e10727. doi: 10.7554/eLife.10727. PMID: 26751560
Yildirim, E., Chiu, J. C., and Edery, I. (2015) Identification of light-sensitive phosphorylation sites on PERIOD that regulate the pace of circadian rhythms in Drosophila. Mol Cell Biol. 2015 Dec 28;36(6):855-70. doi: 10.1128/MCB.00682-15. PMID: 26711257
Campos, E. I., Smits, A. H., Kang, Y. H., Landry, S., Escobar, T. M., Nayak, S., Ueberheide, B. M., Durocher, D., Vermeulen, M., Hurwitz, J., and Reinberg, D. (2015) Analysis of the Histone H3.1 Interactome: A Suitable Chaperone for the Right Event. Mol Cell. 2015 Nov 19;60(4):697-709. doi: 10.1016/j.molcel.2015.08.005. PMID: 26527279
Zhao, Y., Zhang, C., Yue, X., Li, X., Liu, J., Yu, H., Belyi, V. A., Yang, Q., Feng, Z., and Hu, W. (2015) Pontin, a new mutant p53-binding protein, promotes gain-of-function of mutant p53. Cell Death Differ. 2015 Nov;22(11):1824-36. doi: 10.1038/cdd.2015.33. PMID: 25857266
Hornsby, M., Paduch, M., Miersch, S., Saaf, A., Matsuguchi, T., Lee, B., Wypisniak, K., Doak, A., King, D., Usatyuk, S., Perry, K., Lu, V., Thomas, W., Luke, J., Goodman, J., Hoey, R. J., Lai, D., Griffin, C., Li, Z., Vizeacoumar, F. J., Dong, D., Campbell, E., Anderson, S., Zhong, N., Graslund, S., Koide, S., Moffat, J., Sidhu, S., Kossiakoff, A., and Wells, J. (2015) A High Through-put Platform for Recombinant Antibodies to Folded Proteins. Mol Cell Proteomics. 2015 Oct;14(10):2833-47. doi: 10.1074/mcp.O115.052209. PMID: 26290498
Kwok, R. S., Lam, V. H., and Chiu, J. C. (2015) Understanding the role of chromatin remodeling in the regulation of circadian transcription in Drosophila. Fly (Austin). 2015;9(4):145-54. doi: 10.1080/19336934.2016.1143993. PMID: 26926115
Yue, X. T., Zhao, Y. H., Liu, J., Zhang, C., Yu, H. Y., Wang, J. B., Zheng, T. S., Liu, L. X., Li, J., Feng, Z. H., and Hu, W. W. (2015) BAG2 promotes tumorigenesis through enhancing mutant p53 protein levels and function. Elife. 2015 Aug 13; 4: e08401. doi: 10.7554/eLife.08401. PMID: 26271008
Kraushar, M.L., B. Viljetic, H.R. Wijeratne, K. Thompson, X. Jiao, J.W. Pike, V. Medvedeva, M. Groszer, M. Kiledjian, R.P. Hart, and M.R. Rasin (2015) Thalamic wnt3 secretion spatiotemporally regulates the neocortical ribosome signature and mRNA translation to specify neocortical cell subtypes. J Neurosci. 2015 Aug 5;35(31):10911-26. doi: 10.1523/JNEUROSCI.0601-15.2015. PMID: 26245956
Xie, X. J., Hsu, F. N., Gao, X., Xu, W., Ni, J. Q., Xing, Y., Huang, L., Hsiao, H. C., Zheng, H., Wang, C., Zheng, Y., Xiaoli, A. M., Yang, F., Bondos, S. E., Ji, J. Y. (2015) CDK8-Cyclin C Mediates Nutritional Regulation of Developmental Transitions through the Ecdysone Receptor in Drosophila. PLoS Biol. 2015 Jul 29;13(7): e1002207. doi: 10.1371/journal.pbio.1002207. PMID: 26222308
Kwok, R. S., Li, Y. H., Lei, A. J., Edery, I., and Chiu, J. C. (2015) The catalytic and non-catalytic functions of the brahma chromatin-remodeling protein collaborate to fine-tune circadian transcription in Drosophila. PLoS Genet. 2015 Jul 1;11(7): e1005307. doi: 10.1371/journal.pgen.1005307. PMID: 26132408
Lecona, E., Narendra, V., and Reinberg, D. (2015) USP7 cooperates with SCML2 to regulate the activity of PRC1. Mol Cell Biol. 2015 Apr;35(7):1157-68. doi: 10.1128/MCB.01197-14. PMID: 25605328
Yang, M., Yu, X. W., Zheng, H., Sha, C., Zhao, C., Qian, M., and Xu, Y. (2015) Role of N-linked glycosylation in the secretion and enzymatic properties of Rhizopus chinensis lipase expressed in Pichia pastoris. Microb Cell Fact. 2015 Mar 21; 14:40. doi: 10.1186/s12934-015-0225-5. PMID: 25880561
Kustka, A. B., Milligan, A. J., Zheng, H., New, A. M., Gates, C., Bidle, K. D., and Reinfelder, J. R. (2014) Low CO2 results in a rearrangement of carbon metabolism to support C4 photosynthetic carbon assimilation in Thalassiosira pseudonana. New Phytol. 2014 Nov;204(3):507-520. doi: 10.1111/nph.12926. PMID: 25046577
Kraushar, M.L., K. Thompson, H.R. Wijeratne, B. Viljetic, K. Sakers, J.W. Marson, D.L. Kontoyiannis, S. Buyske, R.P. Hart, and M.R. Rasin (2014) Temporally defined neocortical translation and polysome assembly are determined by the rna-binding protein Hu antigen R. Proc Natl Acad Sci U S A. 2014 Sep 9; 111(36): E3815-24. doi: 10.1073/pnas.1408305111. PMID: 25157170
Khan, A. G., Whidby, J., Miller, M. T., Scarborough, H., Zatorski, A. V., Cygan, A., Price, A. A., Yost, S. A., Bohannon, C. D., Jacob, J., Grakoui, A., and Marcotrigiano, J. (2014) Structure of the core ectodomain of the hepatitis C virus envelope glycoprotein 2. Nature. 2014 May 15;509(7500):381-4. doi: 10.1038/nature13117. PMID: 24553139
Rose, S. L., Fulton, J. M., Brown, C. M., Natale, F., Van Mooy, B. A., and Bidle, K. D. (2014) Isolation and characterization of lipid rafts in Emiliania huxleyi: a role for membrane microdomains in host-virus Interactions. Environ Microbiol. 2014 Apr;16(4):1150-66. doi: 10.1111/1462-2920.12357. PMID: 24330022
Jan, Y. H., Heck, D. E., Malaviya, R., Casillas, R. P., Laskin, D. L., and Laskin, J. D. (2014) Cross-Linking of Thioredoxin Reductase by the Sulfur Mustard Analogue Mechlorethamine (Methylbis(2-chloroethyl)amine) in Human Lung Epithelial Cells and Rat Lung: Selective Inhibition of Disulfide Reduction but Not Redox Cycling. Chem Res Toxicol. 2014 Jan 21;27(1):61-75. doi: 10.1021/tx400329a. PMID: 24274902
MacDonald, L. C., and Berger, B. W. (2014) A polysaccharide lyase from Stenotrophomonas maltophilia with a unique, pH-regulated substrate specificity. J Biol Chem. 2014 Jan 3;289(1):312-25. doi: 10.1074/jbc.M113.489195. PMID: 24257754
Lecona, E., Rojas, L. A., Bonasio, R., Johnston, A., Fernandez-Capetillo, O., and Reinberg, D. (2013) Polycomb Protein SCML2 Regulates the Cell Cycle by Binding and Modulating CDK/CYCLIN/p21 Complexes. PLoS Biol. 2013 Dec;11(12): e1001737. doi: 10.1371/journal.pbio.1001737. PMID: 24358021
Sun, G., and Irvine K.D. (2013) Ajuba Family Proteins Link JNK to Hippo Signaling. Sci Signal. 2013 Sep 10;6(292): ra81. doi: 10.1126/scisignal.2004324. PMID: 24023255
Khan, I. J., Di, R., Patel, P., and Nanda, V. (2013) Evaluating pH-induced Gastrointestinal Aggregation of Arachis Hypogea 1 Fragments as Potential Components of Peanut Allergy. J Agric Food Chem. 2013 Sep 4;61(35):8430-5. doi: 10.1021/jf401701t. PMID: 23926999
Mateyak, M. K., and Kinzy, T. G. (2013) ADP-ribosylation of translation Elongation Factor 2 by diphtheria toxin in yeast inhibits translation and cell separation. J Biol Chem. 2013 Aug 23;288(34):24647-55. doi: 10.1074/jbc.M113.488783. PMID: 23853096
Henriquez, D. R., Zhao, C., Zheng, H., Arbildua, J. J., Acevedo, M. L., Roth, M. J., and Leon, O. (2013) Crosslinking and mass spectrometry suggest that the isolated NTD domain dimer of Moloney murine leukemia virus integrase adopts a parallel arrangement in solution. BMC Struct Biol. 2013 Jul 11; 13:14. doi: 10.1186/1472-6807-13-14. PMID: 23844665
Sleat, D. E., Sun, P., Wiseman, J. A., Huang, L., El-Banna, M., Zheng, H., Moore, D. F., and Lobel, P. (2013) Extending the mannose-6 phosphate glycoproteome by high resolutionaccuracy mass spectrometry analysis of control and acid phosphatase 5-deficient mice. Mol Cell Proteomics. 2013 Jul;12(7):1806-17. doi: 10.1074/mcp.M112.026179. PMID: 23478313
Drake, J. L., Mass, T., Haramaty, L., Zelzion, E., Bhattacharya, D., and Falkowski, P. G. (2013) Proteomic analysis of skeletal organic matrix from the stony coral Stylophora pistillata. Proc Natl Acad Sci U S A. 2013 Mar 5;110(10):3788-93. doi: 10.1073/pnas.1301419110. PMID: 23431140
Kim, D. M., Zheng, H., Huang, Y. J., Montelione, G. T., and Hunt, J. F. (2013) ATPase Active-Site Electrostatic Interactions Control the Global Conformation of the 100 kDa SecA Translocase. J Am Chem Soc. 2013 Feb 27;135(8):2999-3010. doi: 10.1021/ja306361q. PMID: 23167435
Oh, H., Slattery, M., Ma, L., Crofts, A., White, K. P., Mann, R. S., and Irvine, K. D. (2013) Genome-wide Association of Yorkie with Chromatin and Chromatin-Remodeling Complexes. Cell Rep. 2013 Feb 21;3(2):309-18. doi: 10.1016/j.celrep.2013.01.008. PMID: 23395637
Woronowicz, K., Harrold, J. W., Kay, J. M., and Niederman, R. A. (2013) Structural and functional proteomics of intracytoplasmic membrane assembly in Rhodobacter sphaeroides. J Mol Microbiol Biotechnol. 2013;23(1-2):48-62. doi: 10.1159/000346520. PMID: 23615195
Zhang, J., Bonasio, R., Strino, F., Kluger, Y., Holloway, J. K., Modzelewski, A. J., Cohen, P. E., and Reinberg, D. (2013) SFMBT1 functions with LSD1 to regulate expression of canonical histone genes and chromatin-related factors. Genes Dev. 2013 Apr 1;27(7):749-66. doi: 10.1101/gad.210963.112. PMID: 23592795
Sleat, D. E., Wiseman, J. A., Sohar, I., El-Banna, M., Zheng, H., Moore, D. F., and Lobel, P. (2012) Proteomic analysis of mouse models of Niemann-Pick C disease reveals alterations in the steady-state levels of lysosomal proteins within the brain. Proteomics. 2012 Dec;12(23-24):3499-509. doi: 10.1002/pmic.201200205. PMID: 23070805
Kilfoyle, B. E., Sheihet, L., Zhang, Z., Laohoo, M., Kohn, J., and Michniak-Kohn, B. B. (2012) Development of paclitaxel-TyroSpheres for topical skin treatment. J Control Release. 2012 Oct 10;163(1):18-24. doi: 10.1016/j.jconrel.2012.06.021. PMID: 22732474
Kusch, T. (2012) Histone H3 lysine 4 methylation revisited. Transcription. Nov-Dec 2012;3(6):310-4. doi: 10.4161/trns.21911. PMID: 23117820
Bao, X., Nickels, B. E., and Fan, H. (2012) Chlamydia trachomatis protein GrgA activates transcription by contacting the nonconserved region of delta66. Proc Natl Acad Sci U S A. 2012 Oct 16;109(42):16870-5. doi: 10.1073/pnas.1207300109. PMID: 23027952
Ertekin, A., Aramini, J. M., Rossi, P., Leonard, P. G., Janjua, H., Xiao, R., Maglaqui, M., Lee, H. W., Prestegard, J. H., and Montelione, G. T. (2012) Human cyclin-dependent kinase 2-associated protein 1 (CDK2AP1) is dimeric in its disulfide-reduced state, with natively disordered N-terminal region. J Biol Chem. 2012 May 11;287(20):16541-9. doi: 10.1074/jbc.M112.343863. PMID: 22427660
Ma, J., Cai, H., Wu, T., Sobhian, B., Huo, Y., Alcivar, A., Mehta, M., Cheung, K. L., Ganesan, S., Kong, A. N., Zhang, D. D., and Xia, B. (2012) PALB2 interacts with KEAP1 to promote NRF2 nuclear accumulation and function. Mol Cell Biol. 2012 Apr;32(8):1506-17. doi: 10.1128/MCB.06271-11. PMID: 22331464
Choi, J., Ababon, M. R., Matteson, P. G., and Millonig, J. H. (2012) Cut-like homeobox 1 and nuclear factor I/B mediate ENGRAILED2 autism spectrum disorder-associated haplotype function. Hum Mol Genet. 2012 Apr 1;21(7):1566-80. doi: 10.1093/hmg/ddr594. PMID: 22180456
Gao, Z., Zhang, J., Bonasio, R., Strino, F., Sawai, A., Parisi, F., Kluger, Y., and Reinberg, D. (2012) PCGF Homologs, CBX Proteins, and RYBP Define Functionally Distinct PRC1 Family Complexes. Mol Cell. 2012 Feb 10;45(3):344-56. doi: 10.1016/j.molcel.2012.01.002. PMID: 22325352
Jiang, F., Ramanathan, A., Miller, M. T., Tang, G. Q., Gale, M., Jr., Patel, S. S., and Marcotrigiano, J. (2011) Structural basis of RNA recognition and activation by innate immune receptor RIG-I. Nature. 2011 Sep 25;479(7373):423-7. doi: 10.1038/nature10537. PMID: 21947008
Woronowicz, K., Olubanjo, O. B., Sung, H. C., Lamptey, J. L., and Niederman, R. A. (2011) Differential assembly of polypeptides of the light-harvesting 2 complex encoded by distinct operons during acclimation of Rhodobacter sphaeroides to low light intensity. Photosynth Res. 2011 Sep; 108(2-3):201-14. doi: 10.1007/s11120-011-9681-x. PMID: 21863386
Ardehali, M. B., Mei, A., Zobeck, K. L., Caron, M., Lis, J. T., and Kusch, T. (2011) Drosophila Set1 is the major histone H3 lysine 4 trimethyltransferase with role in transcription. MBO J. 2011 Jun 21;30(14):2817-28. doi: 10.1038/emboj.2011.194. PMID: 21694722
Woronowicz, K., Sha, D., Frese, R. N., and Niederman, R. A. (2011) The accumulation of the light-harvesting 2 complex during remodeling of the Rhodobacter sphaeroides intracytoplasmic membrane results in a slowing of the electron transfer turnover rate of photochemical reaction centers. Biochemistry. 2011 Jun 7;50(22):4819-29. doi: 10.1021/bi101667e. PMID: 21366273
Sims, R. J., 3rd, Rojas, L. A., Beck, D., Bonasio, R., Schuller, R., Drury, W. J., 3rd, Eick, D., and Reinberg, D. (2011) The C-terminal domain of RNA polymerase II is modified by site-specific methylation. Science. 2011 Apr 1;332(6025):99-103. doi: 10.1126/science.1202663. PMID: 21454787
Della Valle, M. C., Sleat, D. E., Zheng, H., Moore, D. F., Jadot, M., and Lobel, P. (2011) Classification of Subcellular Location by Comparative Proteomic Analysis of Native and Density-shifted Lysosomes. Mol Cell Proteomics. 2011 Apr;10(4):M110.006403. doi: 10.1074/mcp.M110.006403. PMID: 21252268
Riddle, N. C., Minoda, A., Kharchenko, P. V., Alekseyenko, A. A., Schwartz, Y. B., Tolstorukov, M. Y., Gorchakov, A. A., Jaffe, J. D., Kennedy, C., Linder-Basso, D., Peach, S. E., Shanower, G., Zheng, H., Kuroda, M. I., Pirrotta, V., Park, P. J., Elgin, S. C., and Karpen, G. H. (2011) Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin. Genome Res. 2011 Feb;21(2):147-63. doi: 10.1101/gr.110098.110. PMID: 21177972
Esposito, A. M., and Kinzy, T. G. (2010) The eukaryotic translation elongation factor 1B{gamma} has a non-guanine nucleotide exchange factor role in protein metabolism. J Biol Chem. 2010 Dec 3;285(49):37995-8004. doi: 10.1074/jbc.M110.160887. PMID: 20926387
Campos, E. I., Fillingham, J., Li, G., Zheng, H., Voigt, P., Kuo, W. H., Seepany, H., Gao, Z., Day, L. A., Greenblatt, J. F., and Reinberg, D. (2010) The program for processing newly synthesized histones H3.1 and H4. Nat Struct Mol Biol. 2010 Nov;17(11):1343-51. doi: 10.1038/nsmb.1911. PMID: 20953179
Jan, Y. H., Heck, D. E., Gray, J. P., Zheng, H., Casillas, R. P., Laskin, D. L., and Laskin, J. D. (2010) Selective targeting of selenocysteine in thioredoxin reductase by the half mustard 2-chloroethyl ethyl sulfide in lung epithelial cells. Chem Res Toxicol. 2010 Jun 21;23(6):1045-53. doi: 10.1021/tx100040k. PMID: 20345183
Schneider, W. M., Tang, Y., Vaiphei, S. T., Mao, L., Maglaqui, M., Inouye, M., Roth, M. J., and Montelione, G. T. (2010) Efficient condensed-phase production of perdeuterated soluble and membrane proteins. J Struct Funct Genomics. 2010 Jun;11(2):143-154. doi: 10.1007/s10969-010-9083-x. PMID: 20333498
Schwartz, Y. B., Kahn, T. G., Stenberg, P., Ohno, K., Bourgon, R., and Pirrotta, V. (2010) Alternative Epigenetic Chromatin States of Polycomb Target Genes. PLoS Genet. 2010 Jan;6(1): e1000805. doi: 10.1371/journal.pgen.1000805. PMID: 20062800
Woronowicz, K., and Niederman, R. A. (2010) Proteomic analysis of the developing intracytoplasmic membrane in Rhodobacter sphaeroides during adaptation to low light intensity. Adv Exp Med Biol. 2010; 675:161-78. doi: 10.1007/978-1-4419-1528-3_10. PMID: 20532741
Whidby, J., Mateu, G., Scarborough, H., Demeler, B., Grakoui, A., and Marcotrigiano, J. (2009) Blocking hepatitis C virus infection with recombinant form of envelope protein 2 ectodomain. Virol. 2009 Nov;83(21):11078-89. doi: 10.1128/JVI.00800-09. PMID: 19710151
Schneider, W. M., Inouye, M., Montelione, G. T., and Roth, M. J. (2009) Independently inducible system of gene expression for condensed single protein production (cSPP) suitable for high efficiency isotope enrichment. J Struct Funct Genomics. 2009 Sep;10(3):219-25. doi: 10.1007/s10969-009-9067-x. PMID: 19642019
Sharma, S., Zheng, H., Huang, Y. J., Ertekin, A., Hamuro, Y., Rossi, P., Tejero, R., Acton, T. B., Xiao, R., Jiang, M., Zhao, L., Ma, L. C., Swapna, G. V., Aramini, J. M., and Montelione, G. T. (2009) Construct optimization for protein NMR structure analysis using amide hydrogen/deuterium exchange mass spectrometry. Proteins. 2009 Sep;76(4):882-94. doi: 10.1002/prot.22394. PMID: 19306341
Trojer, P., Zhang, J., Yonezawa, M., Schmidt, A., Zheng, H., Jenuwein, T., and Reinberg, D. (2009) Dynamic Histone H1 Isotype 4 Methylation and Demethylation by Histone Lysine Methyltransferase G9a/KMT1C and the Jumonji Domain-containing JMJD2/KDM4 Proteins. J Biol Chem. 2009 Mar 27;284(13):8395-405. doi: 10.1074/jbc.M807818200. PMID: 19144645
Sleat, D. E., Ding, L., Wang, S., Zhao, C., Wang, Y., Xin, W., Zheng, H., Moore, D. F., Sims, K. B., and Lobel, P. (2009) Mass Spectrometry-based Protein Profilng to Determine the Cause of Lysosomal Storage Diseases of Unknown Etiology. Mol Cell Proteomics. 2009 Jul;8(7):1708-18. doi: 10.1074/mcp.M900122-MCP200. PMID: 19383612
Sleat, D. E., Della Valle, M. C., Zheng, H., Moore, D. F., and Lobel, P. (2008) The mannose 6-phosphate glycoprotein proteome. J Proteome Res. 2008 Jul;7(7):3010-21. doi: 10.1021/pr800135v. PMID: 18507433
Schneider, W. M., Zheng, H., Cote, M. L., and Roth, M. J. (2008) The MuLV 4070A G541R Env mutation decreases the stability and alters the conformation of the TM ectodomain. Virology. 2008 Feb 5;371(1):165-74. doi: 10.1016/j.virol.2007.09.033. PMID: 17961622
Qian, M., Sleat, D. E., Zheng, H., Moore, D., and Lobel, P. (2008) Proteomic analysis of serum from mutant mice reveals lysosomal proteins selectively transported by each of the two mannose 6-phosphate receptors. Mol Cell Proteomics. 2008 Jan;7(1):58-70. doi: 10.1074/mcp.M700217-MCP200. PMID: 17848585
Pungaliya, P., Kulkarni, D., Park, H. J., Marshall, H., Zheng, H., Lackland, H., Saleem, A., and Rubin, E. H. (2007) TOPORS functions as A SUMO-1 E3 ligase forcChromatin-modifying proteins. J Proteome Res. 2007 Oct;6(10):3918-23. doi: 10.1021/pr0703674. PMID: 17803295
Sleat, D. E., Zheng, H., and Lobel, P. (2007) The human urine mannose 6-phosphate glycoproteome. Biochim Biophys Acta. 2007 Mar;1774(3):368-72. doi: 10.1016/j.bbapap.2006.12.004. PMID: 17258946
Suzuki, M., Roy, R., Zheng, H., Woychik, N., and Inouye, M. (2006) Bacteria bioreactors for high yield production of recombinant protein. J Biol Chem. 2006 Dec 8;281(49):37559-65. doi: 10.1074/jbc.M608806200.PMID: 17020876
Ortiz, P. A., Ulloque, R., Kihara, G. K., Zheng, H., and Kinzy, T. G. (2006) Translation elongation factor 2 anticodon mimicry domain mutants affect fidelity and diphtheria toxin resistance. J Biol Chem. 2006 Oct 27;281(43):32639-48. doi: 10.1074/jbc.M607076200. PMID: 16950777
Sleat, D. E., Wang, Y., Sohar, I., Lackland, H., Li, Y., Li, H., Zheng, H., and Lobel, P. (2006) Identification and validation of mannose 6-phosphate glycoproteins in human plasma reveal a wide range of lysosomal and non-lysosomal proteins. Mol Cell Proteomics. 2006 Oct;5(10):1942-56. doi: 10.1074/mcp.M600030-MCP200. PMID: 16709564
Perez, E., Zheng, H., and Stock, A. M. (2006) Identification of methylation sites in Thermotoga maritima chemotaxis receptors. J Bacteriol. 2006 Jun;188(11):4093-100. doi: 10.1128/JB.00181-06. PMID: 16707700
Sleat, D. E., Zheng, H., Qian, M., and Lobel, P. (2006) Identification of sites of mannose 6-phosphorylation on lysosomal proteins. Mol Cell Proteomics. 2006 Apr;5(4):686-701. doi: 10.1074/mcp.M500343-MCP200. PMID: 16399764