My Bibliography

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Patterson SC, Pomeroy AE, Palmer AC. Ultrasensitive Response Explains the Benefit of Combination Chemotherapy Despite Drug Antagonism. Mol Cancer Ther. 2024 Jul 2;23(7):995-1009. doi: 10.1158/1535-7163.MCT-23-0642. PubMed PMID: 38530117; PubMed Central PMCID: PMC11219261.

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Choudhury R, Bonacci T, Arceci A, Lahiri D, Mills CA, Kernan JL, Branigan TB, DeCaprio JA, Burke DJ, Emanuele MJ. APC/C and SCF(cyclin F) Constitute a Reciprocal Feedback Circuit Controlling S-Phase Entry. Cell Rep. 2024 Mar 26;43(3):113974. doi: 10.1016/j.celrep.2024.113974. Epub 2024 Mar 7. PubMed PMID: 38457340; PubMed Central PMCID: PMC11097368.

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Lu X, Chandravanshi M, Sabbasani VR, Gaikwad S, Hughitt VK, Gyabaah-Kessie N, Scroggins BT, Das S, Myint W, Clapp ME, Schwieters CD, Dyba MA, Bolhuis DL, Koscielniak JW, Andresson T, Emanuele MJ, Brown NG, Matsuo H, Chari R, Citrin DE, Mock BA, Swenson RE, Walters KJ. A structure-based designed small molecule depletes hRpn13(Pru) and a select group of KEN box proteins. Nat Commun. 2024 Mar 20;15(1):2485. doi: 10.1038/s41467-024-46644-7. PubMed PMID: 38509117; PubMed Central PMCID: PMC10954691.

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Bodrug T, Welsh KA, Bolhuis DL, Paulаkonis E, Martinez-Chacin RC, Liu B, Pinkin N, Bonacci T, Cui L, Xu P, Roscow O, Amann SJ, Grishkovskaya I, Emanuele MJ, Harrison JS, Steimel JP, Hahn KM, Zhang W, Zhong ED, Haselbach D, Brown NG. Time-resolved cryo-EM (TR-EM) analysis of substrate polyubiquitination by the RING E3 anaphase-promoting complex/cyclosome (APC/C). Nat Struct Mol Biol. 2023 Nov;30(11):1663-1674. doi: 10.1038/s41594-023-01105-5. Epub 2023 Sep 21. PubMed PMID: 37735619; PubMed Central PMCID: PMC10643132.

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Mouery RD, Hsu C, Bonacci T, Bolhuis DL, Wang X, Mills CA, Toomer ED, Canterbury OG, Robertson KC, Branigan TB, Brown NG, Herring LE, Emanuele MJ. Proteomic Analysis Reveals a PLK1-Dependent G2/M Degradation Program and Links PKA-AKAP2 to Cell Cycle Control. bioRxiv. 2023 Oct 12;. doi: 10.1101/2023.10.11.561963. PubMed PMID: 37873169; PubMed Central PMCID: PMC10592729.

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Guzman BB, Son A, Litberg TJ, Huang Z, Dominguez D, Horowitz S. Emerging roles for G-quadruplexes in proteostasis. FEBS J. 2023 Oct;290(19):4614-4625. doi: 10.1111/febs.16608. Epub 2022 Sep 25. Review. PubMed PMID: 36017725; PubMed Central PMCID: PMC10071977.

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Bedard ML, Lord JS, Perez PJ, Bravo IM, Teklezghi AT, Tarantino LM, Diering GH, McElligott ZA. Probing different paradigms of morphine withdrawal on sleep behavior in male and female C57BL/6J mice. Behav Brain Res. 2023 Jun 25;448:114441. doi: 10.1016/j.bbr.2023.114441. Epub 2023 Apr 17. PubMed PMID: 37075956; PubMed Central PMCID: PMC10278096.

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Iskandar SE, Pelton JM, Wick ET, Bolhuis DL, Baldwin AS, Emanuele MJ, Brown NG, Bowers AA. Enabling Genetic Code Expansion and Peptide Macrocyclization in mRNA Display via a Promiscuous Orthogonal Aminoacyl-tRNA Synthetase. J Am Chem Soc. 2023 Jan 25;145(3):1512-1517. doi: 10.1021/jacs.2c11294. Epub 2023 Jan 11. PubMed PMID: 36630539; PubMed Central PMCID: PMC10411329.

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Chen J, Bolhuis DL, Laggner C, Kong D, Yu L, Wang X, Emanuele MJ, Brown NG, Liu P. AtomNet-Aided OTUD7B Inhibitor Discovery and Validation. Cancers (Basel). 2023 Jan 14;15(2). doi: 10.3390/cancers15020517. PubMed PMID: 36672466; PubMed Central PMCID: PMC9856706.

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Sey NYA, Pratt BM, Won H. Annotating genetic variants to target genes using H-MAGMA. Nat Protoc. 2023 Jan;18(1):22-35. doi: 10.1038/s41596-022-00745-z. Epub 2022 Oct 26. Review. PubMed PMID: 36289406; PubMed Central PMCID: PMC10026181.

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Kim R, Testen A, Harder EV, Brown NE, Witt EA, Bellinger TJ, Franklin JP, Reissner KJ. Abstinence-Dependent Effects of Long-Access Cocaine Self-Administration on Nucleus Accumbens Astrocytes Are Observed in Male, But Not Female, Rats. eNeuro. 2022 Sep-Oct;9(5). doi: 10.1523/ENEURO.0310-22.2022. Print 2022 Sep-Oct. PubMed PMID: 35995558; PubMed Central PMCID: PMC9491344.

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Shi Y, Daugird TA, Legant WR. A quantitative analysis of various patterns applied in lattice light sheet microscopy. Nat Commun. 2022 Aug 8;13(1):4607. doi: 10.1038/s41467-022-32341-w. PubMed PMID: 35941165; PubMed Central PMCID: PMC9360440.

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Bolhuis DL, Martinez-Chacin RC, Welsh KA, Bodrug T, Cui L, Emanuele MJ, Brown NG. Examining the mechanistic relationship of APC/C(CDH1) and its interphase inhibitor EMI1. Protein Sci. 2022 Jun;31(6):e4324. doi: 10.1002/pro.4324. PubMed PMID: 35634770; PubMed Central PMCID: PMC9112349.

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Hinkle ER, Wiedner HJ, Torres EV, Jackson M, Black AJ, Blue RE, Harris SE, Guzman BB, Gentile GM, Lee EY, Tsai YH, Parker J, Dominguez D, Giudice J. Alternative splicing regulation of membrane trafficking genes during myogenesis. RNA. 2022 Apr;28(4):523-540. doi: 10.1261/rna.078993.121. Epub 2022 Jan 26. PubMed PMID: 35082143; PubMed Central PMCID: PMC8925968.

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Welsh KA, Bolhuis DL, Nederstigt AE, Boyer J, Temple BRS, Bonacci T, Gu L, Ordureau A, Harper JW, Steimel JP, Zhang Q, Emanuele MJ, Harrison JS, Brown NG. Functional conservation and divergence of the helix-turn-helix motif of E2 ubiquitin-conjugating enzymes. EMBO J. 2022 Feb 1;41(3):e108823. doi: 10.15252/embj.2021108823. Epub 2021 Dec 23. PubMed PMID: 34942047; PubMed Central PMCID: PMC8804933.

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Quadir SG, Arleth GM, Jahad JV, Echeveste Sanchez M, Effinger DP, Herman MA. Sex differences in affective states and association with voluntary ethanol intake in Sprague-Dawley rats. Psychopharmacology (Berl). 2022 Feb;239(2):589-604. doi: 10.1007/s00213-021-06052-x. Epub 2022 Jan 19. PubMed PMID: 35044485; NIHMSID:NIHMS1945156.

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Pratt BM, Won H. Advances in profiling chromatin architecture shed light on the regulatory dynamics underlying brain disorders. Semin Cell Dev Biol. 2022 Jan;121:153-160. doi: 10.1016/j.semcdb.2021.08.013. Epub 2021 Sep 3. Review. PubMed PMID: 34483043; PubMed Central PMCID: PMC8761161.

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Sheehy RN, Quintanilla LJ, Song J. Epigenetic regulation in the neurogenic niche of the adult dentate gyrus. Neurosci Lett. 2022 Jan 1;766:136343. doi: 10.1016/j.neulet.2021.136343. Epub 2021 Nov 11. Review. PubMed PMID: 34774980; PubMed Central PMCID: PMC8691367.

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Simpson JB, Sekela JJ, Graboski AL, Borlandelli VB, Bivins MM, Barker NK, Sorgen AA, Mordant AL, Johnson RL, Bhatt AP, Fodor AA, Herring LE, Overkleeft H, Lee JR, Redinbo MR. Metagenomics combined with activity-based proteomics point to gut bacterial enzymes that reactivate mycophenolate. Gut Microbes. 2022 Jan-Dec;14(1):2107289. doi: 10.1080/19490976.2022.2107289. PubMed PMID: 35953888; PubMed Central PMCID: PMC9377255.

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DeLiberty JM, Robb R, Gates CE, Bryant KL. Unraveling and targeting RAS-driven metabolic signaling for therapeutic gain. Adv Cancer Res. 2022;153:267-304. doi: 10.1016/bs.acr.2021.07.010. Epub 2021 Aug 26. Review. PubMed PMID: 35101233.

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Enrico TP, Stallaert W, Wick ET, Ngoi P, Wang X, Rubin SM, Brown NG, Purvis JE, Emanuele MJ. Cyclin F drives proliferation through SCF-dependent degradation of the retinoblastoma-like tumor suppressor p130/RBL2. Elife. 2021 Dec 1;10. doi: 10.7554/eLife.70691. PubMed PMID: 34851822; PubMed Central PMCID: PMC8670743.

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Klomp JE, Lee YS, Goodwin CM, Papke B, Klomp JA, Waters AM, Stalnecker CA, DeLiberty JM, Drizyte-Miller K, Yang R, Diehl JN, Yin HH, Pierobon M, Baldelli E, Ryan MB, Li S, Peterson J, Smith AR, Neal JT, McCormick AK, Kuo CJ, Counter CM, Petricoin EF 3rd, Cox AD, Bryant KL, Der CJ. CHK1 protects oncogenic KRAS-expressing cells from DNA damage and is a target for pancreatic cancer treatment. Cell Rep. 2021 Nov 30;37(9):110060. doi: 10.1016/j.celrep.2021.110060. PubMed PMID: 34852220; PubMed Central PMCID: PMC8665414.

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Altinok S, Sanchez-Hodge R, Stewart M, Smith K, Schisler JC. With or without You: Co-Chaperones Mediate Health and Disease by Modifying Chaperone Function and Protein Triage. Cells. 2021 Nov 11;10(11). doi: 10.3390/cells10113121. Review. PubMed PMID: 34831344; PubMed Central PMCID: PMC8619055.

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Bodrug T, Welsh KA, Hinkle M, Emanuele MJ, Brown NG. Intricate Regulatory Mechanisms of the Anaphase-Promoting Complex/Cyclosome and Its Role in Chromatin Regulation. Front Cell Dev Biol. 2021;9:687515. doi: 10.3389/fcell.2021.687515. eCollection 2021. Review. PubMed PMID: 34109183; PubMed Central PMCID: PMC8182066.

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Mills CA, Wang X, Bhatt DP, Grimsrud PA, Matson JP, Lahiri D, Burke DJ, Cook JG, Hirschey MD, Emanuele MJ. Sirtuin 5 Is Regulated by the SCF(Cyclin F) Ubiquitin Ligase and Is Involved in Cell Cycle Control. Mol Cell Biol. 2021 Jan 25;41(2). doi: 10.1128/MCB.00269-20. Print 2021 Jan 25. PubMed PMID: 33168699; PubMed Central PMCID: PMC8093487.

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Wasserman D, Nachum S, Noach-Hirsh M, Auerbach N, Sheinberger-Chorni E, Enrico TP, Lahmi R, Emanuele MJ, Tzur A. Elucidating Human Mitosis Using an Anaphase-Like Cell-Free System. Methods Mol Biol. 2021;2329:143-164. doi: 10.1007/978-1-0716-1538-6_11. PubMed PMID: 34085221; PubMed Central PMCID: PMC8628539.

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Franks JL, Martinez-Chacin RC, Wang X, Tiedemann RL, Bonacci T, Choudhury R, Bolhuis DL, Enrico TP, Mouery RD, Damrauer JS, Yan F, Harrison JS, Major MB, Hoadley KA, Suzuki A, Rothbart SB, Brown NG, Emanuele MJ. In silico APC/C substrate discovery reveals cell cycle-dependent degradation of UHRF1 and other chromatin regulators. PLoS Biol. 2020 Dec;18(12):e3000975. doi: 10.1371/journal.pbio.3000975. eCollection 2020 Dec. PubMed PMID: 33306668; PubMed Central PMCID: PMC7758050.

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Bonacci T, Emanuele MJ. Dissenting degradation: Deubiquitinases in cell cycle and cancer. Semin Cancer Biol. 2020 Dec;67(Pt 2):145-158. doi: 10.1016/j.semcancer.2020.03.008. Epub 2020 Mar 20. Review. PubMed PMID: 32201366; PubMed Central PMCID: PMC7502435.

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Bird KE, Xander C, Murcia S, Schmalstig AA, Wang X, Emanuele MJ, Braunstein M, Bowers AA. Thiopeptides Induce Proteasome-Independent Activation of Cellular Mitophagy. ACS Chem Biol. 2020 Aug 21;15(8):2164-2174. doi: 10.1021/acschembio.0c00364. Epub 2020 Jul 14. PubMed PMID: 32589399; PubMed Central PMCID: PMC7442609.

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Emanuele MJ, Enrico TP, Mouery RD, Wasserman D, Nachum S, Tzur A. Complex Cartography: Regulation of E2F Transcription Factors by Cyclin F and Ubiquitin. Trends Cell Biol. 2020 Aug;30(8):640-652. doi: 10.1016/j.tcb.2020.05.002. Epub 2020 Jun 5. Review. PubMed PMID: 32513610; PubMed Central PMCID: PMC7859860.

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Goering R, Hudish LI, Guzman BB, Raj N, Bassell GJ, Russ HA, Dominguez D, Taliaferro JM. FMRP promotes RNA localization to neuronal projections through interactions between its RGG domain and G-quadruplex RNA sequences. Elife. 2020 Jun 8;9. doi: 10.7554/eLife.52621. PubMed PMID: 32510328; PubMed Central PMCID: PMC7279889.

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Martinez-Chacin RC, Bodrug T, Bolhuis DL, Kedziora KM, Bonacci T, Ordureau A, Gibbs ME, Weissmann F, Qiao R, Grant GD, Cook JG, Peters JM, Wade Harper J, Emanuele MJ, Brown NG. Ubiquitin chain-elongating enzyme UBE2S activates the RING E3 ligase APC/C for substrate priming. Nat Struct Mol Biol. 2020 Jun;27(6):550-560. doi: 10.1038/s41594-020-0424-6. Epub 2020 May 11. PubMed PMID: 32393902; PubMed Central PMCID: PMC7293561.

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Wasserman D, Nachum S, Cohen M, Enrico TP, Noach-Hirsh M, Parasol J, Zomer-Polak S, Auerbach N, Sheinberger-Chorni E, Nevenzal H, Levi-Dadon N, Wang X, Lahmi R, Michaely E, Gerber D, Emanuele MJ, Tzur A. Cell cycle oscillators underlying orderly proteolysis of E2F8. Mol Biol Cell. 2020 Apr 1;31(8):725-740. doi: 10.1091/mbc.E19-12-0725. Epub 2020 Jan 29. PubMed PMID: 31995441; PubMed Central PMCID: PMC7185961.

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McDonald IM, Grant GD, East MP, Gilbert TSK, Wilkerson EM, Goldfarb D, Beri J, Herring LE, Vaziri C, Cook JG, Emanuele MJ, Graves LM. Mass spectrometry-based selectivity profiling identifies a highly selective inhibitor of the kinase MELK that delays mitotic entry in cancer cells. J Biol Chem. 2020 Feb 21;295(8):2359-2374. doi: 10.1074/jbc.RA119.011083. Epub 2020 Jan 2. PubMed PMID: 31896573; PubMed Central PMCID: PMC7039562.

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Blake DR, Vaseva AV, Hodge RG, Kline MP, Gilbert TSK, Tyagi V, Huang D, Whiten GC, Larson JE, Wang X, Pearce KH, Herring LE, Graves LM, Frye SV, Emanuele MJ, Cox AD, Der CJ. Application of a MYC degradation screen identifies sensitivity to CDK9 inhibitors in KRAS-mutant pancreatic cancer. Sci Signal. 2019 Jul 16;12(590). doi: 10.1126/scisignal.aav7259. PubMed PMID: 31311847; PubMed Central PMCID: PMC6728149.

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Bonacci T, Emanuele MJ. Impressionist portraits of mitotic exit: APC/C, K11-linked ubiquitin chains and Cezanne. Cell Cycle. 2019 Mar-Apr;18(6-7):652-660. doi: 10.1080/15384101.2019.1593646. Epub 2019 Mar 28. Review. PubMed PMID: 30874463; PubMed Central PMCID: PMC6464587.

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Arceci A, Bonacci T, Wang X, Stewart K, Damrauer JS, Hoadley KA, Emanuele MJ. FOXM1 Deubiquitination by USP21 Regulates Cell Cycle Progression and Paclitaxel Sensitivity in Basal-like Breast Cancer. Cell Rep. 2019 Mar 12;26(11):3076-3086.e6. doi: 10.1016/j.celrep.2019.02.054. PubMed PMID: 30865895; PubMed Central PMCID: PMC6425951.

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Kernan J, Bonacci T, Emanuele MJ. Who guards the guardian? Mechanisms that restrain APC/C during the cell cycle. Biochim Biophys Acta Mol Cell Res. 2018 Dec;1865(12):1924-1933. doi: 10.1016/j.bbamcr.2018.09.011. Epub 2018 Oct 2. Review. PubMed PMID: 30290241; PubMed Central PMCID: PMC6198803.

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Bonacci T, Suzuki A, Grant GD, Stanley N, Cook JG, Brown NG, Emanuele MJ. Cezanne/OTUD7B is a cell cycle-regulated deubiquitinase that antagonizes the degradation of APC/C substrates. EMBO J. 2018 Aug 15;37(16). doi: 10.15252/embj.201798701. Epub 2018 Jul 4. PubMed PMID: 29973362; PubMed Central PMCID: PMC6092620.

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Dronamraju R, Jha DK, Eser U, Adams AT, Dominguez D, Choudhury R, Chiang YC, Rathmell WK, Emanuele MJ, Churchman LS, Strahl BD. Set2 methyltransferase facilitates cell cycle progression by maintaining transcriptional fidelity. Nucleic Acids Res. 2018 Feb 16;46(3):1331-1344. doi: 10.1093/nar/gkx1276. PubMed PMID: 29294086; PubMed Central PMCID: PMC5814799.

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Gray KM, Kaifer KA, Baillat D, Wen Y, Bonacci TR, Ebert AD, Raimer AC, Spring AM, Have ST, Glascock JJ, Gupta K, Van Duyne GD, Emanuele MJ, Lamond AI, Wagner EJ, Lorson CL, Matera AG. Self-oligomerization regulates stability of survival motor neuron protein isoforms by sequestering an SCF(Slmb) degron. Mol Biol Cell. 2018 Jan 15;29(2):96-110. doi: 10.1091/mbc.E17-11-0627. Epub 2017 Nov 22. PubMed PMID: 29167380; PubMed Central PMCID: PMC5909936.

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Mills CA, Suzuki A, Arceci A, Mo JY, Duncan A, Salmon ED, Emanuele MJ. Nucleolar and spindle-associated protein 1 (NUSAP1) interacts with a SUMO E3 ligase complex during chromosome segregation. J Biol Chem. 2017 Oct 20;292(42):17178-17189. doi: 10.1074/jbc.M117.796045. Epub 2017 Sep 12. PubMed PMID: 28900032; PubMed Central PMCID: PMC5655498.

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Choudhury R, Bonacci T, Wang X, Truong A, Arceci A, Zhang Y, Mills CA, Kernan JL, Liu P, Emanuele MJ. The E3 Ubiquitin Ligase SCF(Cyclin F) Transmits AKT Signaling to the Cell-Cycle Machinery. Cell Rep. 2017 Sep 26;20(13):3212-3222. doi: 10.1016/j.celrep.2017.08.099. PubMed PMID: 28954236; PubMed Central PMCID: PMC5662023.

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Yi JJ, Paranjape SR, Walker MP, Choudhury R, Wolter JM, Fragola G, Emanuele MJ, Major MB, Zylka MJ. The autism-linked UBE3A T485A mutant E3 ubiquitin ligase activates the Wnt/β-catenin pathway by inhibiting the proteasome. J Biol Chem. 2017 Jul 28;292(30):12503-12515. doi: 10.1074/jbc.M117.788448. Epub 2017 May 30. PubMed PMID: 28559284; PubMed Central PMCID: PMC5535025.

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Wang X, Arceci A, Bird K, Mills CA, Choudhury R, Kernan JL, Zhou C, Bae-Jump V, Bowers A, Emanuele MJ. VprBP/DCAF1 Regulates the Degradation and Nonproteolytic Activation of the Cell Cycle Transcription Factor FoxM1. Mol Cell Biol. 2017 Jul 1;37(13). doi: 10.1128/MCB.00609-16. Print 2017 Jul 1. PubMed PMID: 28416635; PubMed Central PMCID: PMC5472828.

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Choudhury R, Bonacci T, Arceci A, Lahiri D, Mills CA, Kernan JL, Branigan TB, DeCaprio JA, Burke DJ, Emanuele MJ. APC/C and SCF(cyclin F) Constitute a Reciprocal Feedback Circuit Controlling S-Phase Entry. Cell Rep. 2016 Sep 20;16(12):3359-3372. doi: 10.1016/j.celrep.2016.08.058. PubMed PMID: 27653696; PubMed Central PMCID: PMC5111906.

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Wei D, Goldfarb D, Song S, Cannon C, Yan F, Sakellariou-Thompson D, Emanuele M, Major MB, Weissman BE, Kuwahara Y. SNF5/INI1 deficiency redefines chromatin remodeling complex composition during tumor development. Mol Cancer Res. 2014 Nov;12(11):1574-85. doi: 10.1158/1541-7786.MCR-14-0005. Epub 2014 Jul 9. PubMed PMID: 25009291; PubMed Central PMCID: PMC4233162.

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Olive AJ, Haff MG, Emanuele MJ, Sack LM, Barker JR, Elledge SJ, Starnbach MN. Chlamydia trachomatis-induced alterations in the host cell proteome are required for intracellular growth. Cell Host Microbe. 2014 Jan 15;15(1):113-24. doi: 10.1016/j.chom.2013.12.009. PubMed PMID: 24439903; PubMed Central PMCID: PMC3932326.

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Ly T, Ahmad Y, Shlien A, Soroka D, Mills A, Emanuele MJ, Stratton MR, Lamond AI. A proteomic chronology of gene expression through the cell cycle in human myeloid leukemia cells. Elife. 2014 Jan 1;3:e01630. doi: 10.7554/eLife.01630. PubMed PMID: 24596151; PubMed Central PMCID: PMC3936288.

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Weng MT, Lee JH, Wei SC, Li Q, Shahamatdar S, Hsu D, Schetter AJ, Swatkoski S, Mannan P, Garfield S, Gucek M, Kim MK, Annunziata CM, Creighton CJ, Emanuele MJ, Harris CC, Sheu JC, Giaccone G, Luo J. Evolutionarily conserved protein ERH controls CENP-E mRNA splicing and is required for the survival of KRAS mutant cancer cells. Proc Natl Acad Sci U S A. 2012 Dec 26;109(52):E3659-67. doi: 10.1073/pnas.1207673110. Epub 2012 Dec 10. PubMed PMID: 23236152; PubMed Central PMCID: PMC3535619.