My Bibliography

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Li YD, Ma MW, Hassan MM, Hunkeler M, Teng M, Puvar K, Rutter JC, Lumpkin RJ, Sandoval B, Jin CY, Schmoker AM, Ficarro SB, Cheong H, Metivier RJ, Wang MY, Xu S, Byun WS, Groendyke BJ, You I, Sigua LH, Tavares I, Zou C, Tsai JM, Park PMC, Yoon H, Majewski FC, Sperling HT, Marto JA, Qi J, Nowak RP, Donovan KA, Słabicki M, Gray NS, Fischer ES, Ebert BL. Template-assisted covalent modification underlies activity of covalent molecular glues. Nat Chem Biol. 2024 Dec;20(12):1640-1649. doi: 10.1038/s41589-024-01668-4. Epub 2024 Jul 29. PubMed PMID: 39075252; PubMed Central PMCID: PMC11582070.

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Lee JJ, Kearney JF, Trembath HE, Hariharan A, LaBella ME, Kharitonova EV, Chan PS, Morrison AB, Cliff A, Meyers MO, Kim HJ, Rashid NU, Peng XL, Yeh JJ. Tumor-intrinsic and Cancer-associated Fibroblast Subtypes Independently Predict Outcomes in Pancreatic Cancer. Ann Surg. 2024 Oct 1;280(4):659-666. doi: 10.1097/SLA.0000000000006416. Epub 2024 Jun 18. PubMed PMID: 38887930; PubMed Central PMCID: PMC11379537.

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Lee JJ, Yeh JJ. Updates in Molecular Profiling of Pancreatic Ductal Adenocarcinoma. Surg Clin North Am. 2024 Oct;104(5):939-950. doi: 10.1016/j.suc.2024.04.001. Epub 2024 May 16. Review. PubMed PMID: 39237169; PubMed Central PMCID: PMC11377860.

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Somasundaram A, Yeh JJ. Future of Dendritic Cell-Based Approaches in Pancreatic Cancer. J Clin Oncol. 2024 Sep 10;42(26):3067-3070. doi: 10.1200/JCO.24.00846. Epub 2024 Jul 11. PubMed PMID: 38991191; PubMed Central PMCID: PMC11377165.

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Ong HW, Yang X, Smith JL, Taft-Benz S, Howell S, Dickmander RJ, Havener TM, Sanders MK, Brown JW, Couñago RM, Chang E, Krämer A, Moorman NJ, Heise M, Axtman AD, Drewry DH, Willson TM. Strategic Fluorination to Achieve a Potent, Selective, Metabolically Stable, and Orally Bioavailable Inhibitor of CSNK2. Molecules. 2024 Sep 2;29(17). doi: 10.3390/molecules29174158. PubMed PMID: 39275006; PubMed Central PMCID: PMC11397024.

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Asquith CRM, East MP, Laitinen T, Alamillo-Ferrer C, Hartikainen E, Wells CI, Axtman AD, Drewry DH, Tizzard GJ, Poso A, Willson TM, Johnson GL. Discovery and optimization of narrow spectrum inhibitors of Tousled like kinase 2 (TLK2) using quantitative structure activity relationships. Eur J Med Chem. 2024 May 5;271:116357. doi: 10.1016/j.ejmech.2024.116357. Epub 2024 Apr 2. PubMed PMID: 38636130; PubMed Central PMCID: PMC11421834.

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Gomez SM, Axtman AD, Willson TM, Major MB, Townsend RR, Sorger PK, Johnson GL. Illuminating function of the understudied druggable kinome. Drug Discov Today. 2024 Mar;29(3):103881. doi: 10.1016/j.drudis.2024.103881. Epub 2024 Jan 11. Review. PubMed PMID: 38218213; PubMed Central PMCID: PMC11262466.

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Galal KA, Krämer A, Strickland BG, Smith JL, Dickmander RJ, Moorman NJ, Willson TM. Identification of 4-(6-((2-methoxyphenyl)amino)pyrazin-2-yl)benzoic acids as CSNK2A inhibitors with antiviral activity and improved selectivity over PIM3. Bioorg Med Chem Lett. 2024 Feb 1;99:129617. doi: 10.1016/j.bmcl.2024.129617. Epub 2024 Jan 8. PubMed PMID: 38199328; NIHMSID:NIHMS2028013.

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Joisa CU, Chen KA, Beville S, Stuhlmiller T, Berginski ME, Okumu D, Golitz BT, East MP, Johnson GL, Gomez SM. Combined kinome inhibition states are predictive of cancer cell line sensitivity to kinase inhibitor combination therapies. Pac Symp Biocomput. 2024;29:276-290. PubMed PMID: 38160286; PubMed Central PMCID: PMC11413988.

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Chen H, Lye MF, Gorgulla C, Ficarro SB, Cuny GD, Scott DA, Wu F, Rothlauf PW, Wang X, Fernandez R, Pesola JM, Draga S, Marto JA, Hogle JM, Arthanari H, Coen DM. A small molecule exerts selective antiviral activity by targeting the human cytomegalovirus nuclear egress complex. PLoS Pathog. 2023 Nov;19(11):e1011781. doi: 10.1371/journal.ppat.1011781. eCollection 2023 Nov. PubMed PMID: 37976321; PubMed Central PMCID: PMC10691697.

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Cruite JT, Nowak RP, Donovan KA, Ficarro SB, Huang H, Liu H, Liu Y, Marto JA, Metivier RJ, Fischer ES, Jones LH. Covalent Stapling of the Cereblon Sensor Loop Histidine Using Sulfur-Heterocycle Exchange. ACS Med Chem Lett. 2023 Nov 9;14(11):1576-1581. doi: 10.1021/acsmedchemlett.3c00371. eCollection 2023 Nov 9. PubMed PMID: 37974938; PubMed Central PMCID: PMC10641907.

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Wamsley NT, Wilkerson EM, Guan L, LaPak KM, Schrank TP, Holmes BJ, Sprung RW, Gilmore PE, Gerndt SP, Jackson RS, Paniello RC, Pipkorn P, Puram SV, Rich JT, Townsend RR, Zevallos JP, Zolkind P, Le QT, Goldfarb D, Major MB. Targeted Proteomic Quantitation of NRF2 Signaling and Predictive Biomarkers in HNSCC. Mol Cell Proteomics. 2023 Nov;22(11):100647. doi: 10.1016/j.mcpro.2023.100647. Epub 2023 Sep 15. PubMed PMID: 37716475; PubMed Central PMCID: PMC10587640.

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Flint AC, Mitchell DK, Angus SP, Smith AE, Bessler W, Jiang L, Mang H, Li X, Lu Q, Rodriguez B, Sandusky GE, Masters AR, Zhang C, Dang P, Koenig J, Johnson GL, Shen W, Liu J, Aggarwal A, Donoho GP, Willard MD, Bhagwat SV, Clapp DW, Rhodes SD. Combined CDK4/6 and ERK1/2 Inhibition Enhances Antitumor Activity in NF1-Associated Plexiform Neurofibroma. Clin Cancer Res. 2023 Sep 1;29(17):3438-3456. doi: 10.1158/1078-0432.CCR-22-2854. PubMed PMID: 37406085; PubMed Central PMCID: PMC11060649.

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Sahu I, Zhu H, Buhrlage SJ, Marto JA. Proteomic approaches to study ubiquitinomics. Biochim Biophys Acta Gene Regul Mech. 2023 Jun;1866(2):194940. doi: 10.1016/j.bbagrm.2023.194940. Epub 2023 Apr 29. Review. PubMed PMID: 37121501; PubMed Central PMCID: PMC10612121.

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Durcan TM, Axtman AD. Editorial: The next generation of tools and technologies for studying human neurons in a dish. Front Cell Neurosci. 2023;17:1196543. doi: 10.3389/fncel.2023.1196543. eCollection 2023. PubMed PMID: 37124399; PubMed Central PMCID: PMC10140577.

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Davis-Gilbert ZW, Krämer A, Dunford JE, Howell S, Senbabaoglu F, Wells CI, Bashore FM, Havener TM, Smith JL, Hossain MA, Oppermann U, Drewry DH, Axtman AD. Discovery of a Potent and Selective Naphthyridine-Based Chemical Probe for Casein Kinase 2. ACS Med Chem Lett. 2023 Apr 13;14(4):432-441. doi: 10.1021/acsmedchemlett.2c00530. eCollection 2023 Apr 13. PubMed PMID: 37077385; PubMed Central PMCID: PMC10108397.

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Mills CE, Subramanian K, Hafner M, Niepel M, Gerosa L, Chung M, Victor C, Gaudio B, Yapp C, Nirmal AJ, Clark N, Sorger PK. Multiplexed and reproducible high content screening of live and fixed cells using Dye Drop. Nat Commun. 2022 Nov 14;13(1):6918. doi: 10.1038/s41467-022-34536-7. PubMed PMID: 36376301; PubMed Central PMCID: PMC9663587.

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Yang X, Dickmander RJ, Bayati A, Taft-Benz SA, Smith JL, Wells CI, Madden EA, Brown JW, Lenarcic EM, Yount BL Jr, Chang E, Axtman AD, Baric RS, Heise MT, McPherson PS, Moorman NJ, Willson TM. Host Kinase CSNK2 is a Target for Inhibition of Pathogenic SARS-like β-Coronaviruses. ACS Chem Biol. 2022 Jul 15;17(7):1937-1950. doi: 10.1021/acschembio.2c00378. Epub 2022 Jun 19. PubMed PMID: 35723434; PubMed Central PMCID: PMC9236220.

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Zhu H, Mellors JS, Chan WC, Thompson JW, Ficarro SB, Tavares I, Bratt AS, Decker J, Krause M, Kruppa G, Buhrlage SJ, Marto JA. On-Chip Preconcentration Microchip Capillary Electrophoresis Based CE-PRM-LIVE for High-Throughput Selectivity Profiling of Deubiquitinase Inhibitors. Anal Chem. 2022 Jul 12;94(27):9508-9513. doi: 10.1021/acs.analchem.2c01337. Epub 2022 Jun 21. PubMed PMID: 35729701; PubMed Central PMCID: PMC10654755.

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Asquith CRM, Temme L, East MP, Laitinen T, Pickett J, Kwarcinski FE, Sinha P, Wells CI, Johnson GL, Zutshi R, Drewry DH. Identification of 4-Anilinoquin(az)oline as a Cell-Active Protein Kinase Novel 3 (PKN3) Inhibitor Chemotype. ChemMedChem. 2022 Jun 20;17(12):e202200161. doi: 10.1002/cmdc.202200161. Epub 2022 May 9. PubMed PMID: 35403825; PubMed Central PMCID: PMC9233141.

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Mishra S, Kinoshita C, Axtman AD, Young JE. Evaluation of a Selective Chemical Probe Validates That CK2 Mediates Neuroinflammation in a Human Induced Pluripotent Stem Cell-Derived Microglial Model. Front Mol Neurosci. 2022;15:824956. doi: 10.3389/fnmol.2022.824956. eCollection 2022. PubMed PMID: 35774866; PubMed Central PMCID: PMC9239073.

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Kirchoff KE, Gomez SM. EMBER: multi-label prediction of kinase-substrate phosphorylation events through deep learning. Bioinformatics. 2022 Apr 12;38(8):2119-2126. doi: 10.1093/bioinformatics/btac083. PubMed PMID: 35157015; PubMed Central PMCID: PMC9004653.

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East MP, Johnson GL. Adaptive chromatin remodeling and transcriptional changes of the functional kinome in tumor cells in response to targeted kinase inhibition. J Biol Chem. 2022 Feb;298(2):101525. doi: 10.1016/j.jbc.2021.101525. Epub 2021 Dec 24. Review. PubMed PMID: 34958800; PubMed Central PMCID: PMC8888345.

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Drewry DH, Annor-Gyamfi JK, Wells CI, Pickett JE, Dederer V, Preuss F, Mathea S, Axtman AD. Identification of Pyrimidine-Based Lead Compounds for Understudied Kinases Implicated in Driving Neurodegeneration. J Med Chem. 2022 Jan 27;65(2):1313-1328. doi: 10.1021/acs.jmedchem.1c00440. Epub 2021 Aug 1. PubMed PMID: 34333981; PubMed Central PMCID: PMC8802302.

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Axtman AD. Characterizing the role of the dark kinome in neurodegenerative disease - A mini review. Biochim Biophys Acta Gen Subj. 2021 Dec;1865(12):130014. doi: 10.1016/j.bbagen.2021.130014. Epub 2021 Sep 20. Review. PubMed PMID: 34547390.

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Zhu H, Ficarro SB, Alexander WM, Fleming LE, Adelmant G, Zhang T, Willetts M, Decker J, Brehmer S, Krause M, East MP, Gray NS, Johnson GL, Kruppa G, Marto JA. PRM-LIVE with Trapped Ion Mobility Spectrometry and Its Application in Selectivity Profiling of Kinase Inhibitors. Anal Chem. 2021 Oct 19;93(41):13791-13799. doi: 10.1021/acs.analchem.1c02349. Epub 2021 Oct 4. PubMed PMID: 34606255; PubMed Central PMCID: PMC9297317.

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Perez VM, Kearney JF, Yeh JJ. The PDAC Extracellular Matrix: A Review of the ECM Protein Composition, Tumor Cell Interaction, and Therapeutic Strategies. Front Oncol. 2021;11:751311. doi: 10.3389/fonc.2021.751311. eCollection 2021. Review. PubMed PMID: 34692532; PubMed Central PMCID: PMC8526858.

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Cichońska A, Ravikumar B, Allaway RJ, Wan F, Park S, Isayev O, Li S, Mason M, Lamb A, Tanoli Z, Jeon M, Kim S, Popova M, Capuzzi S, Zeng J, Dang K, Koytiger G, Kang J, Wells CI, Willson TM, Oprea TI, Schlessinger A, Drewry DH, Stolovitzky G, Wennerberg K, Guinney J, Aittokallio T. Crowdsourced mapping of unexplored target space of kinase inhibitors. Nat Commun. 2021 Jun 3;12(1):3307. doi: 10.1038/s41467-021-23165-1. PubMed PMID: 34083538; PubMed Central PMCID: PMC8175708.

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Jiang B, Gao Y, Che J, Lu W, Kaltheuner IH, Dries R, Kalocsay M, Berberich MJ, Jiang J, You I, Kwiatkowski N, Riching KM, Daniels DL, Sorger PK, Geyer M, Zhang T, Gray NS. Discovery and resistance mechanism of a selective CDK12 degrader. Nat Chem Biol. 2021 Jun;17(6):675-683. doi: 10.1038/s41589-021-00765-y. Epub 2021 Mar 22. PubMed PMID: 33753926; PubMed Central PMCID: PMC8590456.

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Weighill D, Ben Guebila M, Glass K, Platig J, Yeh JJ, Quackenbush J. Gene Targeting in Disease Networks. Front Genet. 2021;12:649942. doi: 10.3389/fgene.2021.649942. eCollection 2021. PubMed PMID: 33968133; PubMed Central PMCID: PMC8103030.

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Wells CI, Drewry DH, Pickett JE, Tjaden A, Krämer A, Müller S, Gyenis L, Menyhart D, Litchfield DW, Knapp S, Axtman AD. Development of a potent and selective chemical probe for the pleiotropic kinase CK2. Cell Chem Biol. 2021 Apr 15;28(4):546-558.e10. doi: 10.1016/j.chembiol.2020.12.013. Epub 2021 Jan 22. PubMed PMID: 33484635; PubMed Central PMCID: PMC8864761.

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Rodriguez S, Hug C, Todorov P, Moret N, Boswell SA, Evans K, Zhou G, Johnson NT, Hyman BT, Sorger PK, Albers MW, Sokolov A. Machine learning identifies candidates for drug repurposing in Alzheimer's disease. Nat Commun. 2021 Feb 15;12(1):1033. doi: 10.1038/s41467-021-21330-0. PubMed PMID: 33589615; PubMed Central PMCID: PMC7884393.

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Berginski ME, Moret N, Liu C, Goldfarb D, Sorger PK, Gomez SM. The Dark Kinase Knowledgebase: an online compendium of knowledge and experimental results of understudied kinases. Nucleic Acids Res. 2021 Jan 8;49(D1):D529-D535. doi: 10.1093/nar/gkaa853. PubMed PMID: 33079988; PubMed Central PMCID: PMC7778917.

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Rashid NU, Luckett DJ, Chen J, Lawson MT, Wang L, Zhang Y, Laber EB, Liu Y, Yeh JJ, Zeng D, Kosorok MR. High-Dimensional Precision Medicine From Patient-Derived Xenografts. J Am Stat Assoc. 2021;116(535):1140-1154. doi: 10.1080/01621459.2020.1828091. Epub 2020 Nov 12. PubMed PMID: 34548714; PubMed Central PMCID: PMC8451968.

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Wang CB, Lorente-Macías Á, Wells C, Pickett JE, Picado A, Zuercher WJ, Axtman AD. Towards a RIOK2 chemical probe: cellular potency improvement of a selective 2-(acylamino)pyridine series. RSC Med Chem. 2021 Jan 1;12(1):129-136. doi: 10.1039/d0md00292e. eCollection 2021 Jan 1. PubMed PMID: 34046605; PubMed Central PMCID: PMC8130602.

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Picado A, Chaikuad A, Wells CI, Shrestha S, Zuercher WJ, Pickett JE, Kwarcinski FE, Sinha P, de Silva CS, Zutshi R, Liu S, Kannan N, Knapp S, Drewry DH, Willson TM. A Chemical Probe for Dark Kinase STK17B Derives Its Potency and High Selectivity through a Unique P-Loop Conformation. J Med Chem. 2020 Dec 10;63(23):14626-14646. doi: 10.1021/acs.jmedchem.0c01174. Epub 2020 Nov 20. PubMed PMID: 33215924; PubMed Central PMCID: PMC7816213.

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Goulet DR, Foster JP 2nd, Zawistowski JS, Bevill SM, Noël MP, Olivares-Quintero JF, Sciaky N, Singh D, Santos C, Pattenden SG, Davis IJ, Johnson GL. Discrete Adaptive Responses to MEK Inhibitor in Subpopulations of Triple-Negative Breast Cancer. Mol Cancer Res. 2020 Nov;18(11):1685-1698. doi: 10.1158/1541-7786.MCR-19-1011. Epub 2020 Aug 4. PubMed PMID: 32753473; PubMed Central PMCID: PMC7642176.

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Liu Y, Ferguson FM, Li L, Kuljanin M, Mills CE, Subramanian K, Harshbarger W, Gondi S, Wang J, Sorger PK, Mancias JD, Gray NS, Westover KD. Chemical Biology Toolkit for DCLK1 Reveals Connection to RNA Processing. Cell Chem Biol. 2020 Oct 15;27(10):1229-1240.e4. doi: 10.1016/j.chembiol.2020.07.011. Epub 2020 Aug 4. PubMed PMID: 32755567; PubMed Central PMCID: PMC8053042.

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Tamir TY, Drewry DH, Wells C, Major MB, Axtman AD. PKIS deep dive yields a chemical starting point for dark kinases and a cell active BRSK2 inhibitor. Sci Rep. 2020 Sep 28;10(1):15826. doi: 10.1038/s41598-020-72869-9. PubMed PMID: 32985588; PubMed Central PMCID: PMC7522982.

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Jiang H, Torphy RJ, Steiger K, Hongo H, Ritchie AJ, Kriegsmann M, Horst D, Umetsu SE, Joseph NM, McGregor K, Pishvaian MJ, Blais EM, Lu B, Li M, Hollingsworth M, Stashko C, Volmar K, Yeh JJ, Weaver VM, Wang ZJ, Tempero MA, Weichert W, Collisson EA. Pancreatic ductal adenocarcinoma progression is restrained by stromal matrix. J Clin Invest. 2020 Sep 1;130(9):4704-4709. doi: 10.1172/JCI136760. PubMed PMID: 32749238; PubMed Central PMCID: PMC7456216.

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Tamir TY, Bowman BM, Agajanian MJ, Goldfarb D, Schrank TP, Stohrer T, Hale AE, Siesser PF, Weir SJ, Murphy RM, LaPak KM, Weissman BE, Moorman NJ, Major MB. Gain-of-function genetic screen of the kinome reveals BRSK2 as an inhibitor of the NRF2 transcription factor. J Cell Sci. 2020 Jul 15;133(14). doi: 10.1242/jcs.241356. PubMed PMID: 32546533; PubMed Central PMCID: PMC7375482.

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Wells CI, Vasta JD, Corona CR, Wilkinson J, Zimprich CA, Ingold MR, Pickett JE, Drewry DH, Pugh KM, Schwinn MK, Hwang BB, Zegzouti H, Huber KVM, Cong M, Meisenheimer PL, Willson TM, Robers MB. Quantifying CDK inhibitor selectivity in live cells. Nat Commun. 2020 Jun 2;11(1):2743. doi: 10.1038/s41467-020-16559-0. PubMed PMID: 32488087; PubMed Central PMCID: PMC7265341.

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Lipner MB, Peng XL, Jin C, Xu Y, Gao Y, East MP, Rashid NU, Moffitt RA, Herrera Loeza SG, Morrison AB, Golitz BT, Vaziri C, Graves LM, Johnson GL, Yeh JJ. Irreversible JNK1-JUN inhibition by JNK-IN-8 sensitizes pancreatic cancer to 5-FU/FOLFOX chemotherapy. JCI Insight. 2020 Apr 23;5(8). doi: 10.1172/jci.insight.129905. PubMed PMID: 32213714; PubMed Central PMCID: PMC7205424.

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Mirlekar B, Michaud D, Lee SJ, Kren NP, Harris C, Greene K, Goldman EC, Gupta GP, Fields RC, Hawkins WG, DeNardo DG, Rashid NU, Yeh JJ, McRee AJ, Vincent BG, Vignali DAA, Pylayeva-Gupta Y. B cell-Derived IL35 Drives STAT3-Dependent CD8(+) T-cell Exclusion in Pancreatic Cancer. Cancer Immunol Res. 2020 Mar;8(3):292-308. doi: 10.1158/2326-6066.CIR-19-0349. Epub 2020 Feb 5. PubMed PMID: 32024640; PubMed Central PMCID: PMC7056532.

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Rashid NU, Li Q, Yeh JJ, Ibrahim JG. Modeling Between-Study Heterogeneity for Improved Replicability in Gene Signature Selection and Clinical Prediction. J Am Stat Assoc. 2020;115(531):1125-1138. doi: 10.1080/01621459.2019.1671197. Epub 2019 Oct 29. PubMed PMID: 33012902; PubMed Central PMCID: PMC7528965.

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Rashid NU, Peng XL, Jin C, Moffitt RA, Volmar KE, Belt BA, Panni RZ, Nywening TM, Herrera SG, Moore KJ, Hennessey SG, Morrison AB, Kawalerski R, Nayyar A, Chang AE, Schmidt B, Kim HJ, Linehan DC, Yeh JJ. Purity Independent Subtyping of Tumors (PurIST), A Clinically Robust, Single-sample Classifier for Tumor Subtyping in Pancreatic Cancer. Clin Cancer Res. 2020 Jan 1;26(1):82-92. doi: 10.1158/1078-0432.CCR-19-1467. Epub 2019 Nov 21. PubMed PMID: 31754050; PubMed Central PMCID: PMC6942634.

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Peng XL, Moffitt RA, Torphy RJ, Volmar KE, Yeh JJ. De novo compartment deconvolution and weight estimation of tumor samples using DECODER. Nat Commun. 2019 Oct 18;10(1):4729. doi: 10.1038/s41467-019-12517-7. PubMed PMID: 31628300; PubMed Central PMCID: PMC6802116.

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Asquith CRM, Murray NH, Pagliarini DJ. ADCK3/COQ8A: the choice target of the UbiB protein kinase-like family. Nat Rev Drug Discov. 2019 Oct;18(11):815. doi: 10.1038/d41573-019-00158-w. PubMed PMID: 31673128; PubMed Central PMCID: PMC7062282.

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Bevill SM, Olivares-Quintero JF, Sciaky N, Golitz BT, Singh D, Beltran AS, Rashid NU, Stuhlmiller TJ, Hale A, Moorman NJ, Santos CM, Angus SP, Zawistowski JS, Johnson GL. GSK2801, a BAZ2/BRD9 Bromodomain Inhibitor, Synergizes with BET Inhibitors to Induce Apoptosis in Triple-Negative Breast Cancer. Mol Cancer Res. 2019 Jul;17(7):1503-1518. doi: 10.1158/1541-7786.MCR-18-1121. Epub 2019 Apr 18. PubMed PMID: 31000582; PubMed Central PMCID: PMC6610760.

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Axtman A, Drewry D, Wells C. CDK16: the pick of the understudied PCTAIRE kinases. Nat Rev Drug Discov. 2019 Jul;18(7):489. doi: 10.1038/d41573-019-00076-x. PubMed PMID: 31267068.