My Bibliography

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Neumayer C, Ng D, Requena D, Jiang CS, Qureshi A, Vaughan R, Prakash TP, Revenko A, Simon SM. GalNAc-conjugated siRNA targeting the DNAJB1-PRKACA fusion junction in fibrolamellar hepatocellular carcinoma. Mol Ther. 2024 Jan 3;32(1):140-151. doi: 10.1016/j.ymthe.2023.11.012. Epub 2023 Nov 21. PubMed PMID: 37980543; PubMed Central PMCID: PMC10787139.

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Levin SN, Tomasini MD, Knox J, Shirani M, Shebl B, Requena D, Clark J, Heissel S, Alwaseem H, Surjan R, Lahasky R, Molina H, Torbenson MS, Lyons B, Migler RD, Coffino P, Simon SM. Disruption of proteome by an oncogenic fusion kinase alters metabolism in fibrolamellar hepatocellular carcinoma. Sci Adv. 2023 Jun 23;9(25):eadg7038. doi: 10.1126/sciadv.adg7038. Epub 2023 Jun 21. PubMed PMID: 37343102; PubMed Central PMCID: PMC10284549.

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Simon SM. Fighting rare cancers: lessons from fibrolamellar hepatocellular carcinoma. Nat Rev Cancer. 2023 May;23(5):335-346. doi: 10.1038/s41568-023-00554-w. Epub 2023 Mar 17. Review. PubMed PMID: 36932129; PubMed Central PMCID: PMC10022574.

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Neumayer C, Ng D, Jiang CS, Qureshi A, Lalazar G, Vaughan R, Simon SM. Oncogenic Addiction of Fibrolamellar Hepatocellular Carcinoma to the Fusion Kinase DNAJB1-PRKACA. Clin Cancer Res. 2023 Jan 4;29(1):271-278. doi: 10.1158/1078-0432.CCR-22-1851. PubMed PMID: 36302174; PubMed Central PMCID: PMC9811160.

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Yasir S, Thompson S, Chen ZE, Knudson R, Knutson D, Kloft-Nelson S, Graham RP, Jain D, Simon SM, Wu TT, Torbenson M. Alternative lengthening of telomeres in primary hepatic neoplasms. Hum Pathol. 2023 Jan;131:79-86. doi: 10.1016/j.humpath.2022.11.003. Epub 2022 Nov 9. PubMed PMID: 36370823; PubMed Central PMCID: PMC10756352.

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Berkovitz A, Migler RD, Qureshi A, Rosemore C, Torbenson MS, Vaughan R, Marcotte E, Simon SM. Clinical and demographic predictors of survival for fibrolamellar carcinoma patients-A patient community, registry-based study. Hepatol Commun. 2022 Dec;6(12):3539-3549. doi: 10.1002/hep4.2105. Epub 2022 Oct 17. PubMed PMID: 36245434; PubMed Central PMCID: PMC9701473.

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Wang X, Simon SM, Coffino P. Single molecule microscopy reveals diverse actions of substrate sequences that impair ClpX AAA+ ATPase function. J Biol Chem. 2022 Oct;298(10):102457. doi: 10.1016/j.jbc.2022.102457. Epub 2022 Sep 5. PubMed PMID: 36064000; PubMed Central PMCID: PMC9531181.

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Shebl B, Ng D, Lalazar G, Rosemore C, Finkelstein TM, Migler RD, Zheng G, Zhang P, Jiang CS, Qureshi A, Vaughan R, Yarchoan M, de Jong YP, Rice CM, Coffino P, Ortiz MV, Zhou D, Simon SM. Targeting BCL-XL in fibrolamellar hepatocellular carcinoma. JCI Insight. 2022 Sep 8;7(17). doi: 10.1172/jci.insight.161820. PubMed PMID: 36073545; PubMed Central PMCID: PMC9536265.

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Narayan NJC, Requena D, Lalazar G, Ramos-Espiritu L, Ng D, Levin S, Shebl B, Wang R, Hammond WJ, Saltsman JA 3rd, Gehart H, Torbenson MS, Clevers H, LaQuaglia MP, Simon SM. Human liver organoids for disease modeling of fibrolamellar carcinoma. Stem Cell Reports. 2022 Aug 9;17(8):1874-1888. doi: 10.1016/j.stemcr.2022.06.003. Epub 2022 Jul 7. PubMed PMID: 35803261; PubMed Central PMCID: PMC9391427.

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Coffino P, Cheng Y. Allostery Modulates Interactions between Proteasome Core Particles and Regulatory Particles. Biomolecules. 2022 May 30;12(6). doi: 10.3390/biom12060764. Review. PubMed PMID: 35740889; PubMed Central PMCID: PMC9221237.

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Rheinemann L, Downhour DM, Bredbenner K, Mercenne G, Davenport KA, Schmitt PT, Necessary CR, McCullough J, Schmitt AP, Simon SM, Sundquist WI, Elde NC. RetroCHMP3 blocks budding of enveloped viruses without blocking cytokinesis. Cell. 2021 Oct 14;184(21):5419-5431.e16. doi: 10.1016/j.cell.2021.09.008. Epub 2021 Sep 30. PubMed PMID: 34597582; PubMed Central PMCID: PMC8929533.

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Lalazar G, Requena D, Ramos-Espiritu L, Ng D, Bhola PD, de Jong YP, Wang R, Narayan NJC, Shebl B, Levin S, Michailidis E, Kabbani M, Vercauteren KOA, Hurley AM, Farber BA, Hammond WJ, Saltsman JA 3rd, Weinberg EM, Glickman JF, Lyons BA, Ellison J, Schadde E, Hertl M, Leiting JL, Truty MJ, Smoot RL, Tierney F, Kato T, Wendel HG, LaQuaglia MP, Rice CM, Letai A, Coffino P, Torbenson MS, Ortiz MV, Simon SM. Identification of Novel Therapeutic Targets for Fibrolamellar Carcinoma Using Patient-Derived Xenografts and Direct-from-Patient Screening. Cancer Discov. 2021 Oct;11(10):2544-2563. doi: 10.1158/2159-8290.CD-20-0872. Epub 2021 Jun 14. PubMed PMID: 34127480; PubMed Central PMCID: PMC8734228.

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Rowan DJ, Yasir S, Chen ZE, Mounajjed T, Erdogan Damgard S, Cummins L, Zhang L, Whitcomb E, Falck V, Simon SM, Singhi AD, Torbenson MS. Morphologic and Molecular Findings in Myxoid Hepatic Adenomas. Am J Surg Pathol. 2021 Aug 1;45(8):1098-1107. doi: 10.1097/PAS.0000000000001711. PubMed PMID: 34232602; PubMed Central PMCID: PMC8608350.

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Johnson DS, Deneau T, Toledo-Crow R, Simon SM. Microscope Enclosure for Temperature Regulation and Light Isolation. Applied Sciences. 2021 July; 11(15):6812. doi: 10.3390/app11156812.

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Olivieri C, Walker C, Karamafrooz A, Wang Y, Manu VS, Porcelli F, Blumenthal DK, Thomas DD, Bernlohr DA, Simon SM, Taylor SS, Veglia G. Defective internal allosteric network imparts dysfunctional ATP/substrate-binding cooperativity in oncogenic chimera of protein kinase A. Commun Biol. 2021 Mar 10;4(1):321. doi: 10.1038/s42003-021-01819-6. PubMed PMID: 33692454; PubMed Central PMCID: PMC7946884.

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Lu TW, Aoto PC, Weng JH, Nielsen C, Cash JN, Hall J, Zhang P, Simon SM, Cianfrocco MA, Taylor SS. Structural analyses of the PKA RIIβ holoenzyme containing the oncogenic DnaJB1-PKAc fusion protein reveal protomer asymmetry and fusion-induced allosteric perturbations in fibrolamellar hepatocellular carcinoma. PLoS Biol. 2020 Dec;18(12):e3001018. doi: 10.1371/journal.pbio.3001018. eCollection 2020 Dec. PubMed PMID: 33370777; PubMed Central PMCID: PMC7793292.

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Pulupa J, Prior H, Johnson DS, Simon SM. Conformation of the nuclear pore in living cells is modulated by transport state. Elife. 2020 Dec 21;9. doi: 10.7554/eLife.60654. PubMed PMID: 33346731; PubMed Central PMCID: PMC7752133.

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Saltsman JA, Hammond WJ, Narayan NJC, Requena D, Gehart H, Lalazar G, LaQuaglia MP, Clevers H, Simon S. A Human Organoid Model of Aggressive Hepatoblastoma for Disease Modeling and Drug Testing. Cancers (Basel). 2020 Sep 18;12(9). doi: 10.3390/cancers12092668. PubMed PMID: 32962010; PubMed Central PMCID: PMC7563272.

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Dao Thi VL, Wu X, Belote RL, Andreo U, Takacs CN, Fernandez JP, Vale-Silva LA, Prallet S, Decker CC, Fu RM, Qu B, Uryu K, Molina H, Saeed M, Steinmann E, Urban S, Singaraja RR, Schneider WM, Simon SM, Rice CM. Stem cell-derived polarized hepatocytes. Nat Commun. 2020 Apr 3;11(1):1677. doi: 10.1038/s41467-020-15337-2. PubMed PMID: 32245952; PubMed Central PMCID: PMC7125181.

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Belote RL, Simon SM. Ca2+ transients in melanocyte dendrites and dendritic spine-like structures evoked by cell-to-cell signaling. J Cell Biol. 2020 Jan 6;219(1). doi: 10.1083/jcb.201902014. PubMed PMID: 31821412; PubMed Central PMCID: PMC7039208.

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Bredbenner K, Simon SM. Video abstracts and plain language summaries are more effective than graphical abstracts and published abstracts. PLoS One. 2019;14(11):e0224697. doi: 10.1371/journal.pone.0224697. eCollection 2019. PubMed PMID: 31743342; PubMed Central PMCID: PMC6863540.

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Cao B, Lu TW, Martinez Fiesco JA, Tomasini M, Fan L, Simon SM, Taylor SS, Zhang P. Structures of the PKA RIα Holoenzyme with the FLHCC Driver J-PKAcα or Wild-Type PKAcα. Structure. 2019 May 7;27(5):816-828.e4. doi: 10.1016/j.str.2019.03.001. Epub 2019 Mar 21. PubMed PMID: 30905674; PubMed Central PMCID: PMC6506387.

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Simon JS, Botero S, Simon SM. Sequencing the peripheral blood B and T cell repertoire - Quantifying robustness and limitations. J Immunol Methods. 2018 Dec;463:137-147. doi: 10.1016/j.jim.2018.10.003. Epub 2018 Oct 10. PubMed PMID: 30312601; PubMed Central PMCID: PMC6355145.

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Graham RP, Lackner C, Terracciano L, González-Cantú Y, Maleszewski JJ, Greipp PT, Simon SM, Torbenson MS. Fibrolamellar carcinoma in the Carney complex: PRKAR1A loss instead of the classic DNAJB1-PRKACA fusion. Hepatology. 2018 Oct;68(4):1441-1447. doi: 10.1002/hep.29719. Epub 2018 May 11. PubMed PMID: 29222914; PubMed Central PMCID: PMC6151295.

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Johnson DS, Bleck M, Simon SM. Timing of ESCRT-III protein recruitment and membrane scission during HIV-1 assembly. Elife. 2018 Jul 4;7. doi: 10.7554/eLife.36221. PubMed PMID: 29972351; PubMed Central PMCID: PMC6080951.

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Tomasini MD, Johnson DS, Mincer JS, Simon SM. Modeling the dynamics and kinetics of HIV-1 Gag during viral assembly. PLoS One. 2018;13(4):e0196133. doi: 10.1371/journal.pone.0196133. eCollection 2018. PubMed PMID: 29677208; PubMed Central PMCID: PMC5909904.

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Simon SM. Günter Blobel (1936–2018). Cell. 2018 Apr 5;173(2):278-280. doi: 10.1016/j.cell.2018.03.047. PubMed PMID: 29975496; PubMed Central PMCID: PMC6018020.

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Simon S. Günter Blobel (1936-2018). Nature. 2018 Apr 5;556(7699):32. doi: 10.1038/d41586-018-03849-3. PubMed PMID: 29620764; PubMed Central PMCID: PMC6033325.

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Günter Blobel: Pioneer of molecular cell biology (1936-2018). J Cell Biol. 2018 Apr 2;217(4):1163-1167. doi: 10.1083/jcb.201803048. Epub 2018 Mar 21. PubMed PMID: 29563215; PubMed Central PMCID: PMC5881517.

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Hammond WJ, Lalazar G, Saltsman JA, Farber BA, Danzer E, Sherpa TC, Banda CD, Andolina JR, Karimi S, Brennan CW, Torbenson MS, La Quaglia MP, Simon SM. Intracranial metastasis in fibrolamellar hepatocellular carcinoma. Pediatr Blood Cancer. 2018 Apr;65(4). doi: 10.1002/pbc.26919. Epub 2017 Dec 29. PubMed PMID: 29286561; PubMed Central PMCID: PMC6028006.

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Lalazar G, Simon SM. Fibrolamellar Carcinoma: Recent Advances and Unresolved Questions on the Molecular Mechanisms. Semin Liver Dis. 2018 Feb;38(1):51-59. doi: 10.1055/s-0037-1621710. Epub 2018 Feb 22. Review. PubMed PMID: 29471565; PubMed Central PMCID: PMC6020845.

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Farber BA, Lalazar G, Simon EP, Hammond WJ, Requena D, Bhanot UK, La Quaglia MP, Simon SM. Non coding RNA analysis in fibrolamellar hepatocellular carcinoma. Oncotarget. 2018 Feb 13;9(12):10211-10227. doi: 10.18632/oncotarget.23325. eCollection 2018 Feb 13. PubMed PMID: 29535801; PubMed Central PMCID: PMC5828204.

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Tomasini MD, Wang Y, Karamafrooz A, Li G, Beuming T, Gao J, Taylor SS, Veglia G, Simon SM. Conformational Landscape of the PRKACA-DNAJB1 Chimeric Kinase, the Driver for Fibrolamellar Hepatocellular Carcinoma. Sci Rep. 2018 Jan 15;8(1):720. doi: 10.1038/s41598-017-18956-w. PubMed PMID: 29335433; PubMed Central PMCID: PMC5768683.

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Itano MS, Arnion H, Wolin SL, Simon SM. Recruitment of 7SL RNA to assembling HIV-1 virus-like particles. Traffic. 2018 Jan;19(1):36-43. doi: 10.1111/tra.12536. Epub 2017 Dec 1. PubMed PMID: 29044909; PubMed Central PMCID: PMC6781622.

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Kastenhuber ER, Lalazar G, Houlihan SL, Tschaharganeh DF, Baslan T, Chen CC, Requena D, Tian S, Bosbach B, Wilkinson JE, Simon SM, Lowe SW. DNAJB1-PRKACA fusion kinase interacts with β-catenin and the liver regenerative response to drive fibrolamellar hepatocellular carcinoma. Proc Natl Acad Sci U S A. 2017 Dec 12;114(50):13076-13084. doi: 10.1073/pnas.1716483114. Epub 2017 Nov 21. PubMed PMID: 29162699; PubMed Central PMCID: PMC5740683.

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Takacs CN, Andreo U, Dao Thi VL, Wu X, Gleason CE, Itano MS, Spitz-Becker GS, Belote RL, Hedin BR, Scull MA, Rice CM, Simon SM. Differential Regulation of Lipoprotein and Hepatitis C Virus Secretion by Rab1b. Cell Rep. 2017 Oct 10;21(2):431-441. doi: 10.1016/j.celrep.2017.09.053. PubMed PMID: 29020629; PubMed Central PMCID: PMC5685655.

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Pulupa J, Rachh M, Tomasini MD, Mincer JS, Simon SM. A coarse-grained computational model of the nuclear pore complex predicts Phe-Gly nucleoporin dynamics. J Gen Physiol. 2017 Oct 2;149(10):951-966. doi: 10.1085/jgp.201711769. Epub 2017 Sep 8. PubMed PMID: 28887410; PubMed Central PMCID: PMC5694938.

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Takacs CN, Andreo U, Belote RL, Pulupa J, Scull MA, Gleason CE, Rice CM, Simon SM. Green fluorescent protein-tagged apolipoprotein E: A useful marker for the study of hepatic lipoprotein egress. Traffic. 2017 Mar;18(3):192-204. doi: 10.1111/tra.12467. Epub 2017 Jan 31. PubMed PMID: 28035714; PubMed Central PMCID: PMC5334657.

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Sreetama SC, Takano T, Nedergaard M, Simon SM, Jaiswal JK. Injured astrocytes are repaired by Synaptotagmin XI-regulated lysosome exocytosis. Cell Death Differ. 2016 Apr;23(4):596-607. doi: 10.1038/cdd.2015.124. Epub 2015 Oct 9. PubMed PMID: 26450452; PubMed Central PMCID: PMC4986631.

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Itano MS, Bleck M, Johnson DS, Simon SM. Readily Accessible Multiplane Microscopy: 3D Tracking the HIV-1 Genome in Living Cells. Traffic. 2016 Feb;17(2):179-86. doi: 10.1111/tra.12347. Epub 2015 Dec 14. PubMed PMID: 26567131; PubMed Central PMCID: PMC4729623.

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Simon EP, Freije CA, Farber BA, Lalazar G, Darcy DG, Honeyman JN, Chiaroni-Clarke R, Dill BD, Molina H, Bhanot UK, La Quaglia MP, Rosenberg BR, Simon SM. Transcriptomic characterization of fibrolamellar hepatocellular carcinoma. Proc Natl Acad Sci U S A. 2015 Nov 3;112(44):E5916-25. doi: 10.1073/pnas.1424894112. Epub 2015 Oct 21. PubMed PMID: 26489647; PubMed Central PMCID: PMC4640752.

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Stabley DR, Oh T, Simon SM, Mattheyses AL, Salaita K. Real-time fluorescence imaging with 20 nm axial resolution. Nat Commun. 2015 Sep 22;6:8307. doi: 10.1038/ncomms9307. PubMed PMID: 26392382; PubMed Central PMCID: PMC4595625.

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Ceglia I, Reitz C, Gresack J, Ahn JH, Bustos V, Bleck M, Zhang X, Martin G, Simon SM, Nairn AC, Greengard P, Kim Y. APP intracellular domain-WAVE1 pathway reduces amyloid-β production. Nat Med. 2015 Sep;21(9):1054-9. doi: 10.1038/nm.3924. Epub 2015 Aug 17. PubMed PMID: 26280122; PubMed Central PMCID: PMC4560977.

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Jaiswal JK, Simon SM. Imaging Live Cells Using Quantum Dots. Cold Spring Harb Protoc. 2015 Jul 1;2015(7):619-25. doi: 10.1101/pdb.top086322. PubMed PMID: 26134913.

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Darcy DG, Chiaroni-Clarke R, Murphy JM, Honeyman JN, Bhanot U, LaQuaglia MP, Simon SM. The genomic landscape of fibrolamellar hepatocellular carcinoma: whole genome sequencing of ten patients. Oncotarget. 2015 Jan 20;6(2):755-70. doi: 10.18632/oncotarget.2712. PubMed PMID: 25605237; PubMed Central PMCID: PMC4359253.

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Bleck M, Itano MS, Johnson DS, Thomas VK, North AJ, Bieniasz PD, Simon SM. Temporal and spatial organization of ESCRT protein recruitment during HIV-1 budding. Proc Natl Acad Sci U S A. 2014 Aug 19;111(33):12211-6. doi: 10.1073/pnas.1321655111. Epub 2014 Aug 6. PubMed PMID: 25099357; PubMed Central PMCID: PMC4142993.

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Rich BS, Honeyman JN, Darcy DG, Smith PT, Williams AR, Lim II, Johnson LK, Gönen M, Simon JS, LaQuaglia MP, Simon SM. Endogenous antibodies for tumor detection. Sci Rep. 2014 May 30;4:5088. doi: 10.1038/srep05088. PubMed PMID: 24875800; PubMed Central PMCID: PMC4038850.

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Jaiswal JK, Lauritzen SP, Scheffer L, Sakaguchi M, Bunkenborg J, Simon SM, Kallunki T, Jäättelä M, Nylandsted J. S100A11 is required for efficient plasma membrane repair and survival of invasive cancer cells. Nat Commun. 2014 May 8;5:3795. doi: 10.1038/ncomms4795. PubMed PMID: 24806074; PubMed Central PMCID: PMC4026250.

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Johnson DS, Toledo-Crow R, Mattheyses AL, Simon SM. Polarization-controlled TIRFM with focal drift and spatial field intensity correction. Biophys J. 2014 Mar 4;106(5):1008-19. doi: 10.1016/j.bpj.2013.12.043. PubMed PMID: 24606926; PubMed Central PMCID: PMC4026788.

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Honeyman JN, Simon EP, Robine N, Chiaroni-Clarke R, Darcy DG, Lim II, Gleason CE, Murphy JM, Rosenberg BR, Teegan L, Takacs CN, Botero S, Belote R, Germer S, Emde AK, Vacic V, Bhanot U, LaQuaglia MP, Simon SM. Detection of a recurrent DNAJB1-PRKACA chimeric transcript in fibrolamellar hepatocellular carcinoma. Science. 2014 Feb 28;343(6174):1010-4. doi: 10.1126/science.1249484. PubMed PMID: 24578576; PubMed Central PMCID: PMC4286414.