John Paul Y.C. Shen, MD

Peer-Reviewed Articles

1. Hornstein NJ, Zeineddine MA, Gunes BB, Pellatt AJ, Knafl M, Zhu H, Willett AF, Yousef A, Liu S, Sun R, Futreal A, Woodman SE, Taggart MW, Overman MJ, Halperin DM, Raghav KP, Shen JP. Efficacy and safety of atezolizumab and bevacizumab in appendiceal adenocarcinoma. Cancer Res Commun. e-Pub 2024. PMID: 38709066.
2. Belmont E, Bansal VV, Yousef MMG, Zeineddine MA, Su D, Dhiman A, Liao CY, Polite B, Eng OS, Fournier KF, White MG, Turaga KK, Shen JP, Shergill A. Multi-Institutional Study Evaluating the Role of Circulating Tumor DNA in the Management of Appendiceal Cancers. JCO Precis Oncol 8:e2300531, 2024. PMID: 38723230.
3. Bhutiani N, Yousef MMG, Yousef A, Zeineddine M, Knafl M, Ratliff O, Fernando UP, Turin A, Zeineddine FA, Jin J, Alfaro-Munoz K, Goldstein D, Chang GJ, Kopetz S, Shen JP, Uppal A. Automated, High-Throughput Platform to Generate a High-Reliability, Comprehensive Rectal Cancer Database. JCO Clin Cancer Inform 8:e2300219, 2024. PMID: 38759125.
4. Johnson B, Morris V, Wang X, Dasari A, Raghav K, Shen JP, Lee MS, Huey R, Parseghian C, Willis J, Wolff R, Drusbosky LM, Overman MJ, Kopetz S. Comprehensive Landscape of BRAF Variant Classes, Clonalities, and Co-Mutations in Metastatic Colorectal Cancer Using ctDNA Profiling. Cancers (Basel) 16(4), 2024. e-Pub 2024. PMID: 38398128.
5. Yousef A, Yousef M, Zeineddine MA, More A, Fanaeian M, Chowdhury S, Knafl M, Edelkamp P, Ito I, Gu Y, Pattalachinti V, Naini ZA, Zeineddine FA, Peterson J, Alfaro K, Foo WC, Jin J, Bhutiani N, Higbie V, Scally CP, Kee B, Kopetz S, Goldstein D, Strach M, Williamson A, Aziz O, Barriuso J, Uppal A, White MG, Helmink B, Fournier KF, Raghav KP, Taggart MW, Overman MJ, Shen JP. Serum Tumor Markers and Outcomes in Patients With Appendiceal Adenocarcinoma. JAMA Netw Open 7(2):e240260, 2024. e-Pub 2024. PMID: 38416491.
6. Pattalachinti VK, Ito I, Chowdhury S, Yousef A, Gu Y, Gunes BB, Salle ER, Taggart M, Fournier K, Fowlkes NW, Shen JP. Peritoneal Microenvironment Promotes Appendiceal Adenocarcinoma Growth: A Multi-omics Approach Using Patient-Derived Xenografts. Mol Cancer Res. e-Pub 2024. PMID: 38226984.
7. Simmons K, Thomas JV, Ludford K, Willis JA, Higbie VS, Raghav KPS, Johnson B, Dasari A, Kee BK, Parseghian CM, Lee MS, Le PH, Morelli MP, Shen JP, Bent A, Vilar E, Wolff RA, Kopetz S, Overman MJ, Morris VK. Sustained Disease Control in Immune Checkpoint Blockade Responders with Microsatellite Instability-high Colorectal Cancer after Treatment Termination. Cancer Res Commun 3(12):2510-2517, 2023. PMID: 38085001.
8. Lin K, Chowdhury S, Zeineddine MA, Zeineddine FA, Hornstein NJ, Villarreal OE, Maru DM, Haymaker CL, Vauthey JN, Chang GJ, Bogatenkova E, Menter D, Kopetz S, Shen JP. Identification of colorectal cancer cell stemness from single-cell RNA sequencing. Mol Cancer Res. e-Pub 2023. PMID: 38156967.
9. Guo S, Liu X, Cheng X, Jiang Y, Ji S, Liang Q, Koval A, Li Y, Owen LA, Kim IK, Aparicio A, Shen JP, Kopetz S, Weinstein JN, DeAngelis MM, Chen R, Wang W. The DeMixSC deconvolution framework uses single-cell sequencing plus a small benchmark dataset for improved analysis of cell-type ratios in complex tissue samples. bioRxiv, 2023. e-Pub 2023. PMID: 37873318.
10. Bhutiani N, Helmink BA, Zeineddine M, Uppal A, Shen JP, Spickard E, White MG. Utility of Circulating Tumor DNA in Appendiceal Tumors. J Gastrointest Surg. e-Pub 2023. PMID: 37709990.
11. Yousef A, Yousef M, Zeineddine M, More A, Chowdhury S, Knafl M, Edelkamp P, Ito I, Gu Y, Pattalachinti V, Naini ZA, Zeineddine F, Peterson J, Alfaro K, Foo WC, Jin J, Bhutiani N, Higbie V, Scally C, Kee B, Kopetz S, Goldstein D, Uppal A, White MG, Helmink B, Fournier K, Raghav K, Taggart M, Overman MJ, Shen JP. The Clinical Significance of CEA, CA19-9, and CA125 in Management of Appendiceal Adenocarcinoma. medRxiv, 2023. e-Pub 2023. PMID: 37745596.
12. Hsu WH, LaBella KA, Lin Y, Xu P, Lee R, Hsieh CE, Yang L, Zhou A, Blecher JM, Wu CJ, Lin K, Shang X, Jiang S, Spring DJ, Xia Y, Chen P, Shen JP, Kopetz S, DePinho RA. Oncogenic KRAS drives lipo-fibrogenesis to promote angiogenesis and colon cancer progression. Cancer Discov. e-Pub 2023. PMID: 37768068.
13. Ito I, Yousef AMG, Chowdhury S, Dickson PN, Naini ZA, White MG, Fleten KG, Flatmark K, Fournier KF, Fowlkes NW, Shen JP. Intraperitoneal paclitaxel is a safe and effective therapeutic strategy for treating mucinous appendiceal adenocarcinoma. Cancer Res. e-Pub 2023. PMID: 37433032.
14. Chowdhury S, Gupta R, Millstein J, Lin K, Haridas V, Zeineddine MA, Parseghian C, Lenz HJ, Kopetz S, Shen JP. Transcriptional Profiling and Consensus Molecular Subtype Assignment to Understand Response and Resistance to Anti-Epidermal Growth Factor Receptor Therapy in Colorectal Cancer. JCO Precis Oncol 7:e2200422, 2023. PMID: 37487150.
15. Shen JP, Yousef AM, Zeineddine FA, Zeineddine MA, Tidwell RS, Beaty KA, Scofield LC, Rafeeq S, Hornstein N, Lano E, Eng C, Matamoros A, Foo WC, Uppal A, Scally C, Mansfield P, Taggart M, Raghav KP, Overman MJ, Fournier K. Efficacy of Systemic Chemotherapy in Patients With Low-grade Mucinous Appendiceal Adenocarcinoma: A Randomized Crossover Trial. JAMA Netw Open 6(6):e2316161, 2023. e-Pub 2023. PMID: 37261831.
16. Zeineddine FA, Zeineddine MA, Yousef A, Gu Y, Chowdhury S, Dasari A, Huey RW, Johnson B, Kee B, Lee MS, Morelli MP, Morris VK, Overman MJ, Parseghian C, Raghav K, Willis J, Wolff RA, Kawaguchi Y, Vauthey JN, Sun R, Kopetz S, Shen JP. Survival improvement for patients with metastatic colorectal cancer over twenty years. NPJ Precis Oncol 7(1):16, 2023. e-Pub 2023. PMID: 36781990.
17. Erstad DJ, Robinson KA, Beaty K, Rafeeq S, Chiang YJ, Raghav K, Shen JP, Overman MJ, Foo WC, Taggart MW, Mansfield PF, Royal RE, Fournier KF, Scally CP. Prognostic significance of acellular mucin in patients undergoing cytoreductive surgery and hyperthermic intraperitoneal chemotherapy (CRS/HIPEC) for appendiceal neoplasms. Langenbecks Arch Surg 408(1):110, 2023. e-Pub 2023. PMID: 36853519.
18. Parseghian CM, Sun R, Woods M, Napolitano S, Lee HM, Alshenaifi J, Willis J, Nunez S, Raghav KP, Morris VK, Shen JP, Eluri M, Sorokin A, Kanikarla P, Vilar E, Rehn M, Ang A, Troiani T, Kopetz S. Resistance Mechanisms to Anti-Epidermal Growth Factor Receptor Therapy in RAS/RAF Wild-Type Colorectal Cancer Vary by Regimen and Line of Therapy. J Clin Oncol 41(3):460-471, 2023. e-Pub 2022. PMID: 36351210.
19. Cao S, Wang JR, Ji S, Yang P, Dai Y, Guo S, Montierth MD, Shen JP, Zhao X, Chen J, Lee JJ, Guerrero PA, Spetsieris N, Engedal N, Taavitsainen S, Yu K, Livingstone J, Bhandari V, Hubert SM, Daw NC, Futreal PA, Efstathiou E, Lim B, Viale A, Zhang J, Nykter M, Czerniak BA, Brown PH, Swanton C, Msaouel P, Maitra A, Kopetz S, Campbell P, Speed TP, Boutros PC, Zhu H, Urbanucci A, Demeulemeester J, Van Loo P, Wang W. Estimation of tumor cell total mRNA expression in 15 cancer types predicts disease progression. Nat Biotechnol, 2022. PMID: 35697807.
20. Davis JS, Chavez JC, Kok M, San Miguel Y, Lee HY, Henderson H, Overman MJ, Morris V, Kee B, Fogelman D, Advani SM, Johnson B, Parseghian C, Shen JP, Dasari A, Shaw KR, Vilar E, Raghav KP, Shureiqi I, Wolff RA, Meric-Bernstam F, Maru D, Menter DG, Kopetz S, Chang S. Association of Prediagnosis Obesity and Postdiagnosis Aspirin With Survival From Stage IV Colorectal Cancer. JAMA Netw Open 5(10):e2236357, 2022. e-Pub 2022. PMID: 36239938.
21. Morris VK, Overman MJ, Lam M, Parseghian CM, Johnson B, Dasari A, Raghav K, Kee BK, Huey R, Wolff RA, Shen JP, Li J, Zorrilla I, Tzeng CD, Tran Cao HS, Chun YS, Newhook TE, Vauthey N, Duose D, Luthra R, Haymaker C, Kopetz S. Bintrafusp alfa, an anti-PD-L1:TGF-β trap fusion protein, in patients with ctDNA-positive, liver-limited metastatic colorectal cancer. Cancer Res Commun 2(9):979-986, 2022. e-Pub 2022. PMID: 36382087.
22. More A, Ito I, Haridas V, Chowdhury S, Gu Y, Dickson P, Fowlkes N, Shen JP. Oncogene addiction to GNAS in GNASR201 mutant tumors. Oncogene 41(35):4159-4168, 2022. e-Pub 2022. PMID: 35879396.
23. Ding S, Hsu C, Wang Z, Natesh NR, Millen R, Negrete M, Giroux N, Rivera GO, Dohlman A, Bose S, Rotstein T, Spiller K, Yeung A, Sun Z, Jiang C, Xi R, Wilkin B, Randon PM, Williamson I, Nelson DA, Delubac D, Oh S, Rupprecht G, Isaacs J, Jia J, Chen C, Shen JP, Kopetz S, McCall S, Smith A, Gjorevski N, Walz AC, Antonia S, Marrer-Berger E, Clevers H, Hsu D, Shen X. Patient-derived micro-organospheres enable clinical precision oncology. Cell Stem Cell 29(6):905-917.e6, 2022. e-Pub 2022. PMID: 35508177.
24. Uppal A, Helmink B, Grotz TE, Konishi T, Fournier KF, Nguyen S, Taggart MW, Shen JP, Bednarski BK, You YN, Chang GJ. What is the Risk for Peritoneal Metastases and Survival Afterwards in T4 Colon Cancers?. Ann Surg Oncol. e-Pub 2022. PMID: 35307803.
25. Garmezy B, Gheeya J, Lin HY, Huang Y, Kim T, Jiang X, Thein KZ, Pilié PG, Zeineddine F, Wang W, Shaw KR, Rodon J, Shen JP, Yuan Y, Meric-Bernstam F, Chen K, Yap TA. Clinical and Molecular Characterization of POLE Mutations as Predictive Biomarkers of Response to Immune Checkpoint Inhibitors in Advanced Cancers. JCO Precis Oncol 6:e2100267, 2022. PMID: 35108036.
26. Menter DG, Afshar-Kharghan V, Shen JP, Martch SL, Maitra A, Kopetz S, Honn KV, Sood AK. Of vascular defense, hemostasis, cancer, and platelet biology: an evolutionary perspective. Cancer Metastasis Rev 41(1):147-172. e-Pub 2022. PMID: 35022962.
27. Wang L, Wang E, Prado Balcazar J, Wu Z, Xiang K, Wang Y, Huang Q, Negrete M, Chen KY, Li W, Fu Y, Dohlman A, Mines R, Zhang L, Kobayashi Y, Chen T, Shi G, Shen JP, Kopetz S, Tata PR, Moreno V, Gersbach C, Crawford G, Hsu D, Huang E, Bu P, Shen X. Chromatin Remodeling of Colorectal Cancer Liver Metastasis is Mediated by an HGF-PU.1-DPP4 Axis. Adv Sci (Weinh) 8(19):e2004673, 2021. e-Pub 2021. PMID: 34378358.
28. Chowdhury S, Hofree M, Lin K, Maru D, Kopetz S, Shen JP. Implications of Intratumor Heterogeneity on Consensus Molecular Subtype (CMS) in Colorectal Cancer. Cancers (Basel) 13(19), 2021. e-Pub 2021. PMID: 34638407.
29. Mehrvarz Sarshekeh A, Alshenaifi J, Roszik J, Manyam GC, Advani SM, Katkhuda R, Verma A, Lam M, Willis J, Shen JP, Morris J, Davis JS, Loree JM, Lee HM, Ajani JA, Maru DM, Overman MJ, Kopetz S. ARID1A Mutation May Define an Immunologically Active Subgroup in Patients with Microsatellite Stable Colorectal Cancer. Clin Cancer Res 27(6):1663-1670, 2021. e-Pub 2021. PMID: 33414133.
30. Ma J, Fong SH, Luo Y, Bakkenist CJ, Shen JP, Mourragui S, Wessels LFA, Hafner M, Sharan R, Peng J, Ideker T. Few-shot learning creates predictive models of drug response that translate from high-throughput screens to individual patients. Nature Cancer. Nat Cancer 2(2):233-244, 2021. e-Pub 2021. PMID: 34223192.
31. Henry JT, Coker O, Chowdhury S, Shen JP, Morris VK, Dasari A, Raghav K, Nusrat M, Kee B, Parseghian C, Pant S, Jeyakumar N, Zhu L, Nishioka Y, Fogelman D, Wolff RA, Hong D, Overman MJ, Vauthey J, Kopetz S, Johnson B. Comprehensive clinical and molecular characterization of KRASG12C mutant colorectal cancer. JCO Precis Oncol 5, 2021. e-Pub 2021. PMID: 34250391.
32. Raghav K, Shen JP, Jácome AA, Guerra JL, Scally CP, Taggart MW, Foo WC, Matamoros A, Shaw KR, Fournier K, Overman MJ, Eng C. Integrated clinico-molecular profiling of appendiceal adenocarcinoma reveals a unique grade-driven entity distinct from colorectal cancer. Br J Cancer 123(8):1262-1270, 2020. e-Pub 2020. PMID: 32733093.
33. Lee JJ, Kopetz S, Vilar E, Shen JP, Chen K, Maitra A. Relative Abundance of SARS-CoV-2 Entry Genes in the Enterocytes of the Lower Gastrointestinal Tract. Genes (Basel) 11(6), 2020. e-Pub 2020. PMID: 32545271.
34. Zhou JY, Martinez JA, Shen JP. Lamotrigine-induced hemophagocytic lymphohistiocytosis with Takotsubo cardiomyopathy: a case report. J Med Case Rep 13(1):345, 2019. e-Pub 2019. PMID: 31767022.
35. Shabaik A, Hahn M, Shen JP. Enteric Type - Adenocarcinoma of the Prostate Associated with Atypical Intestinal Metaplasia of the Prostate. Clinics in Oncology, 2019.
36. Wang S, Ma J, Zhang W, Shen JP, Huang J, Peng J, Ideker T. Typing tumors using pathways selected by somatic evolution. Nat Commun 9(1):4159, 2018. e-Pub 2018. PMID: 30297789.
37. Bui N, Huang JK, Bojorquez-Gomez A, Licon K, Sanchez KS, Tang SN, Beckett AN, Wang T, Zhang W, Shen JP, Kreisberg JF, Ideker T. Disruption of NSD1 in Head and Neck Cancer Promotes Favorable Chemotherapeutic Responses Linked to Hypomethylation. Mol Cancer Ther 17(7):1585-1594, 2018. e-Pub 2018. PMID: 29636367.
38. Bulbl A, Shen JP, Xui J, Tamayo P, Husain, H. Genomic and Proteomic Alterations in Desmoplastic Small Round Blue Cell Tumors. JCO Precision Oncology(2):1-9, 2018.
39. Zhang W, Bojorquez-Gomez A, Velez DO, Xu G, Sanchez KS, Shen JP, Chen K, Licon K, Melton C, Olson KM, Yu MK, Huang JK, Carter H, Farley EK, Snyder M, Fraley SI, Kreisberg JF, Ideker T. A global transcriptional network connecting noncoding mutations to changes in tumor gene expression. Nat Genet 50(4):613-620, 2018. e-Pub 2018. PMID: 29610481.
40. Ang CS, Shen JP, Hardy-Abeloos CJ, Huang JK, Ross JS, Miller VA, Jacobs MT, Chen IL, Xu D, Ali SM, Baumgartner J, Lowy A, Fanta P, Ideker T, Millis SZ, Harismendy O. Genomic Landscape of Appendiceal Neoplasms. JCO Precis Oncol 2, 2018. e-Pub 2018. PMID: 32913983.
41. Shen JP, Zhao D, Sasik R, Luebeck J, Birmingham A, Bojorquez-Gomez A, Licon K, Klepper K, Pekin D, Beckett AN, Sanchez KS, Thomas A, Kuo CC, Du D, Roguev A, Lewis NE, Chang AN, Kreisberg JF, Krogan N, Qi L, Ideker T, Mali P. Combinatorial CRISPR-Cas9 screens for de novo mapping of genetic interactions. Nat Methods 14(6):573-576, 2017. e-Pub 2017. PMID: 28319113.
42. Du D, Roguev A, Gordon DE, Chen M, Chen SH, Shales M, Shen JP, Ideker T, Mali P, Qi LS, Krogan NJ. Genetic interaction mapping in mammalian cells using CRISPR interference. Nat Methods 14(6):577-580, 2017. e-Pub 2017. PMID: 28481362.
43. Srivas R, Shen JP, Yang CC, Sun SM, Li J, Gross AM, Jensen J, Licon K, Bojorquez-Gomez A, Klepper K, Huang J, Pekin D, Xu JL, Yeerna H, Sivaganesh V, Kollenstart L, van Attikum H, Aza-Blanc P, Sobol RW, Ideker T. A Network of Conserved Synthetic Lethal Interactions for Exploration of Precision Cancer Therapy. Mol Cell 63(3):514-25, 2016. e-Pub 2016. PMID: 27453043.
44. Johnson TC, Chin MR, Han T, Shen JP, Rana T, Siegel D. Synthesis of Eupalinilide E, a Promoter of Human Hematopoietic Stem and Progenitor Cell Expansion. J Am Chem Soc 138(18):6068-73, 2016. e-Pub 2016. PMID: 27096704.
45. Shen JP, Srivas R, Gross A, Li J, Jaehnig EJ, Sun SM, Bojorquez-Gomez A, Licon K, Sivaganesh V, Xu JL, Klepper K, Yeerna H, Pekin D, Qiu CP, van Attikum H, Sobol RW, Ideker T. Chemogenetic profiling identifies RAD17 as synthetically lethal with checkpoint kinase inhibition. Oncotarget 6(34):35755-69, 2015. PMID: 26437225.
46. Choueiri MB, Shen JP, Gross AM, Huang JK, Ideker T, Fanta P. ERCC1 and TS Expression as Prognostic and Predictive Biomarkers in Metastatic Colon Cancer. PLoS One 10(6):e0126898, 2015. e-Pub 2015. PMID: 26083491.
47. Agrawal N, Akbani R, Aksoy BA, Ally A,Arachchi H,Asa SL, Auman JT, Balasundaram M, Balu S, Baylin SB, Behera M, Bernard B, Beroukhim R, Bishop JA, Black AD,Bodenheimer T, Boice L, Bootwalla MS, Bowen J, Bowlby R, Bristow CA, Brookens R, Brooks D, Bryant R, Buda E, Butterfield YS, Carling T, Carlsen R, Carter SL, Carty SE, Chan TA, Chen AY, Cherniack AD, Cheung D, Chin L, Cho J, Chu A, Chuah E, Cibulskis K, Ciriello G, Clarke A, Clayman GL, Cope L, Copland JA, Covington K, Danilova L, Davidsen T, Demchok JA, DiCara D, Dhalla N, Dhir R, Dookran SS, Dresdner G, Eldridge J, Eley G, El-Naggar AK, Eng S, Fagin JA, Fennell T, Ferris RL, Fisher S, Frazer S, Frick J, Gabriel SB, Ganly I, Gao J, Garraway LA, Gastier-Foster JM, Getz G, Gehlenborg N, Ghossein R, Gibbs RA, Giordano TJ, Gomez-Hernandez K, Grimsby J, Gross B, Guin R, Hadjipanayis A, Harper HA, Hayes DN, Heiman DI, Herman JG, Hoadley KA, Hofree M, Holt RA, Hoyle AP, Huang FW, Huang M, Hutter CM, Ideker T, Iype L, Jacobsen A, Jefferys SR, Jones CD, Jones SJ, Kasaian K, Kebebew E, Khuri FR, Kim J, Kramer R, Kreisberg R, Kucherlapati R, Kwiatkowski DJ, Ladanyi M, Lai PH, Laird PW, Lander E, Lawrence MS, Lee D, Lee E, Lee S, Lee W, Leraas KM, Lichtenberg TM, Lichtenstein L, Lin P, Ling S, Liu J, Liu W, Liu Y, LiVolsi VA, Lu Y, Ma Y, Mahadeshwar HS, Marra MA, Mayo M, McFadden DG, Meng S, Meyerson M, Mieczkowski PA, Miller M, Mills G, Moore RA, Mose LE, Mungall AJ, Murray BA, Nikiforov YE, Noble MS, Ojesina AI, Owonikoko TK, Ozenberger BA, Pantazi A, Parfenov M, Park PJ, Parker JS, Paull EO, Pedamallu CS, Perou CM, Prins JF, Protopopov A, Ramalingam SS, Ramirez NC, Ramirez R, Raphael BJ, Rathmell WK, Ren X, Reynolds SM, Rheinbay E, Ringel MD, Rivera M, Roach J, Robertson AG, Rosenberg MW, Rosenthal M, Sadeghi S, Saksena G, Sander C, Santoso N, Schein JE, Schultz N, Schumacher SE, Seethala RR, Seidman J, Senbabaoglu Y, Seth S, Sharpe S, Shaw KR, Shen JP, Shen R,Sherman S, Sheth M,Shi Y, Shmulevich I, Sica GL, Simons. Integrated genomic characterization of papillary thyroid carcinoma. Cell 159(3):676-90, 2014. PMID: 25417114.
48. Gross AM, Orosco RK, Shen JP, Egloff AM, Carter H, Hofree M, Choueiri M, Coffey CS, Lippman SM, Hayes DN, Cohen EE, Grandis JR, Nguyen QT, Ideker T. Multi-tiered genomic analysis of head and neck cancer ties TP53 mutation to 3p loss. Nat Genet 46(9):939-43, 2014. e-Pub 2014. PMID: 25086664.
49. Ghashghaei R, Popa R, Shen JP. Evans syndrome. Am J Med 126(11):e7-8, 2013. PMID: 24157305.
50. Hofree M, Shen JP, Carter H, Gross A, Ideker T. Network-based stratification of tumor mutations. Nat Methods 10(11):1108-15, 2013. e-Pub 2013. PMID: 24037242.
51. Bradner JE, Mak R, Tanguturi SK, Mazitschek R, Haggarty SJ, Ross K, Chang CY, Bosco J, West N, Morse E, Lin K, Shen JP, Kwiatkowski NP, Gheldof N, Dekker J, DeAngelo DJ, Carr SA, Schreiber SL, Golub TR, Ebert BL. Chemical genetic strategy identifies histone deacetylase 1 (HDAC1) and HDAC2 as therapeutic targets in sickle cell disease. Proc Natl Acad Sci U S A 107(28):12617-22, 2010. e-Pub 2010. PMID: 20616024.
52. Bradner JE, McPherson OM, Mazitschek R, Barnes-Seeman D, Shen JP, Dhaliwal J, Stevenson KE, Duffner JL, Park SB, Neuberg DS, Nghiem P, Schreiber SL, Koehler AN. A robust small-molecule microarray platform for screening cell lysates. Chem Biol 13(5):493-504, 2006. PMID: 16720270.

Other Articles

1. Abdelrahman Yousef1, Mahmoud Yousef1, Saikat Chowdhury1, Kawther Abdilleh2, Mark Knafl3, Paul Edelkamp4, Kristin Alfaro-Munoz1, Ray Chacko1, Jennifer Peterson1, Brandon G. Smaglo1, Robert A. Wolff1, Shubham Pant1, Michael S. Lee1, Jason Willis1, Michael Overman1, Sudheer Doss2, Lynn Matrisian2, Mark W. Hurd5, Rebecca Snyder6, Matthew H.G. Katz6, Huamin Wang7, Anirban Maitra5,7, John Paul Shen1, Dan Zhao1* Impact of KRAS Mutations and Co-mutations on Clinical Outcomes in Pancreatic Ductal Adenocarcinoma. npj| precision oncology, 2023.
2. Zhao D, Yousef A, Yousef M, Chowdhury S, Abdilleh K, Knafl M, Edelkamp P, Alfaro-Munoz K, Chacko R, Peterson J, Smaglo B, Wolff RAW, Pant S, Lee M, Willis J, Overman M, Doss S, Matrisian L, Hurd M, Snyder R, Katz M, Wang H, Maitra A, Shen JP Impact of KRAS Mutations and Co-mutations on Clinical Outcome in Pancreatic Ductal Adenocarcinoma. Res Sq, 2023. PMID: 37609177.
3. Ito I, Yousef AM, Dickson PN, Naini ZA, White MG, Fleten KG, Flatmark K, Fournier KF, Fowlkes NW, Shen JP Antitumor activity of intraperitoneal paclitaxel in orthotopic patient-derived xenograft models of mucinous appendiceal adenocarcinoma. bioRxiv, 2023. PMID: 36993681.
4. Julia Dansby, Aditya More, Mohammad Zeineddine, Abdelrahman Yousef, Alisha Bent, Farshid Dayyani, Robert Wolff, Michael Overman, View ORCID ProfileJohn Paul Shen Taxane-based Chemotherapy is Effective in Metastatic Appendiceal Adenocarcinoma. medRxiv.

Editorials

1. Shen JP. Artificial Intelligence, Molecular Subtyping, Biomarkers, and Precision Oncology. Emerg Top Life Sci 5(6):747-756, 2021. PMID: 34881776.
2. Kanikarla Marie P, Fowlkes NW, Afshar-Kharghan V, Martch SL, Sorokin A, Shen JP, Morris VK, Dasari A, You N, Sood AK, Overman MJ, Kopetz S, Menter DG. The Provocative Roles of Platelets in Liver Disease and Cancer. Frontiers in Oncology. Front Oncol 11:643815, 2021. PMID: 34367949.
3. Murtuza A, Shen JP, Keshavarzian P, Woodward B, Diaz FL, Lippman SM, Husain H.. Third Generation EGFR Tyrosine Kinase Inhibitors and Strategies to Overcome Therapeutic Resistance in Lung Cancer:689-698, 2019. PMID: 30718357.
4. John P Shen, Trey Ideker. Synthetic Lethal Networks for Precision Oncology: Promises and Pitfalls. Journal of Molecular Biology 430(18), 2018.
5. Shen JP, Ideker T. Correcting CRISPR for copy number. Nat Genet 49(12):1674-1675, 2017. PMID: 29186130.

Abstracts

1. John Paul Shen, MD1; Abdelrahman M. Yousef, MD1; Fadl A. Zeineddine, MD2; Mohammad A. Zeineddine, MD1; Rebecca S. Tidwell, MS3; Karen A. Beaty, PA-C4; Lisa C. Scofield, PA1; Safia Rafeeq, MD4; Nicholas Hornstein, MD1; Elizabeth Lano, MD5; Cathy Eng, MD7; Aurelio Matamoros, MD5; Wai Chin Foo, MD6; Abhineet Uppal, MD4; Christopher Scally, MD4; Paul Mansfield, MD4; Melissa Taggart, MD6; Kanwal P. Raghav, MD1; Michael J. Overman, MD1; Keith Fournier, MD4. Efficacy of Systemic Chemotherapy in Patients With Low-grade Mucinous Appendiceal Adenocarcinoma. JAMA Netw Open, 2023.
2. Saikat Chowdhury; Vinay K. Pattalachinti; Valsala Haridas; Scott Kopetz; John Paul Shen. Abstract B004: Multi-omics profiling to identify mechanisms of resistance to KRAS inhibition: A comparative study on colorectal and lung cancer. Molecular Cancer Research 21(5), 2023.
3. Benny Johnson; Cara Haymaker; Van K. Morris; Arvind Dasari; Victoria Serpas Higbie; John Paul Shen; Christine Parseghian; Maria Pia Morelli; Ryan Huey; Michael S. Lee; Jason Willis; Kanwal P. Raghav; Ying Yuan; John Zebala; Ronald A. DePinho; Scott Kopetz; Michael Overman. Abstract CT118: A phase I/II trial of a CXCR1/2 inhibitor in combination with anti-PD-1 for circulating tumor DNA (ctDNA) positive & refractoryRAS-mutated microsatellite stable (MSS) colorectal cancer. AACR Cancer Research 83(8), 2023.
4. Shuai Guo; Xuesen Cheng; Andrew Koval; Shuangxi Ji; Qingnan Liang; Yumei Li; Leah A. Owen; Ivana K. Kim; John Weinstein; Scott Kopetz; John Paul Shen; Margaret M. DeAngelis; Rui Chen; Wenyi Wang. Abstract 4273: Integration with benchmark data of paired bulk and single-cell RNA sequencing data substantially improves the accuracy of bulk tissue deconvolution. Cancer Research 83(7), 2023.
5. Saikat Chowdhury; Ichiaki Ito; Vinay K. Pattalachinti; John Paul Shen. Abstract 880: Activation of the Wnt pathway is associated with GNASR201 mutant appendiceal cancer in the peritoneum. Cancer Research 83(7), 2023.
6. Kangyu Lin; Mohammad Zeineddine; Saikat Chowdhury; Nicholas Hornstein; Sendurai Mani; Scott Kopetz; John Paul Shen. Abstract 2454: Identification of colorectal cancer stem cells from single cell RNA sequencing. Cancer Research 83(7), 2023.
7. Oscar E. Villarreal; Fadl Zeineddine; Ray Chacko; Christine Parseghian; Benny Johnson; Jason Willis; Michael Lee; Van Karlyle Morris; Arvind Dasari; Kanwal Raghav; Michael Overman; Y. Nancy You; Yinghong Wang; Dipen Maru; John Paul Shen; Scott Kopetz. Abstract PR005: Outcomes in colitis-associated metastatic colorectal cancer and intersection with early-onset and signet ring cell carcinoma. Cancer Research 82(23), 2022.
8. Jennifer S. Davis; Janelle C. Chavez; Melissa Kok; Yazmin San Miguel; Hwa Young Lee; Henry Henderson; Michael J. Overman; Van Karlyle Morris; Bryan Kee; David Fogelman; Shailesh M. Advani; Benny Johnson; Christine Parseghian; John Paul Shen; Arvind Dasari; Kenna R. Shaw; Eduardo Vilar; Kanwal P. Raghav; Imad Shureiqi; Robert A. Wolff; Funda Meric-Bernstam; Dipen Maru; David G. Menter; Scott Kopetz; Shine Chang. Abstract A023: Influence of pre-diagnosis obesity and post-diagnosis aspirin use on survival from stage IV colorectal cancer. Cancer Research 82(23), 2022.
9. Saikat Chowdhury; Ria Gupta; Valsala Haridas; Mohammad A. Zeineddine; Scott Kopetz; John Paul Shen. Abstract 1246: Consensus molecular subtypes (CMS) of colorectal cancer predict anti-EGFR response irrespective of tumor sidedness. Cancer Research 82(12), 2022.
10. Yue Gu; Abdelrahman M. Yousef; Saikat Chowdhury; John Paul Shen. Abstract 5794: Gene expression analysis of appendiceal adenocarcinomas highlights tumor heterogeneity between high and low-grade. Cancer Research 82(12), 2022.
11. Hey Min Lee; Stefania Napolitano; Alexy Sorokin; Melanie N. Woods; Saikat Chowdhury; Jumanah Y. Alshenaifi; Anand K. Singh; John Paul Shen; Funda Meric-Bernstam; Kunal Rai; Scott Kopetz. Abstract 3275: Bromodomain and extraterminal (BET) protein inhibition sensitize BRAFV600E colorectal cancer to standard targeted therapies. Cancer Research 82(12), 2022.
12. Kangyu Lin; John Paul Shen. Abstract 6066: Elucidating cancer stem cells heterogeneity in colorectal cancer by single-cell RNA sequencing. Cancer Research 82(12), 2022.
13. Coker O, Sorokin A, Gale K, Gao F, Shen JP, Kwong L, Wu J, Lee HM, Woods M, Villareal O, Kopetz S.. Oncogenic KRASG12C dependency in colorectal cancer. Cancer Research (AACR Annual Meeting), 2021.
14. Fong SH, Kuenzi BM, Lee J, Sanchez K, Bojorquez-Gomez A, Ford K, Munson BP, Licon K, Hager J, Shen JP, Kreisberg JF, Mali P, Ideker T. Systematic mapping of genetic interactions in human cancer cells reveals context dependent cancer signaling pathways. Cancer Research (AACR Annual Meeting), 2021.
15. Shen JP, Chowdhury S, Wu J, Fournier K, Kopetz S, Raghav K. Transcriptional profiling confirms appendiceal adenocarcinoma is distinct from colorectal cancer, in vivo models needed. Cancer Research (AACR: The Evolving Landscape of Cancer Modeling), 2020.
16. Sarshekeh AM, Lam M, Zorrilla IR, Holliday EB, Das P, Kee BK, Overman MJ, Parseghian CM, Shen JP, Tam A, Cuentas ERP, Zhang L, Wang X, Duose DY, Luthra R, Reddy N, Maru DM, Kopetz S, Morris VK. Consensus molecular subtype (CMS) as a novel integral biomarker in colorectal cancer: A phase II trial of bintrafusp alfa in CMS4 metastatic CRC. J Clin Oncol (ASCO Meeting Abstracts), 2020.
17. Raghav K, Wang XS, Xiao L, Dasari A, Morris VK, Johnson B, Shen JP, Parseghian C, Kee B, Shureiqi I, Fogelman D, Wolff R, Raymond V, Odegaard J, Lanman R, Overman M, Kopetz S. A randomized study evaluating tailoring of advanced/metastatic colorectal cancer (mCRC) therapy using circulating cell-free tumor DNA (TACT-D). J Clin Oncol (ASCO-GI Meeting Abstracts), 2020.
18. Sarshekeh AM, Roszik J, Manyam GC, Advani SM, Willis J, Shen JP, Morris J, Davis JS, Ajani JA, Maru DM, Overman MJ, Kopetz S.. ARID1A mutation to define an immunologically active subgroup in patients with microsatellite-stable colorectal cancer. J Clin Oncol (ASCO-GI Meeting Abstracts), 2020.
19. Shen JP, Munson B, Mali P, Ideker T. High-throughput combinatorial CRISPR-Cas9 gene knockout and novel analysis platform to identify therapeutically-relevant synthetic lethal interactions. 30th EORTC-NCI-AACR Symposium on Molecular Targets and Cancer Therapeutics, 2018.
20. Shen JP, Huang JK, Ideker T, Millis SZ, Harismendy O. Analysis of the genomic landscape of appendiceal neoplasms identifies GNAS and TP53 mutation as prognostic biomarkers. 30th Anniversary AACR Special Conference Convergence: Artificial Intelligence, Big Data, and Prediction in Cancer, 2018.
21. Shen JP, Dongxin Zhao, Brenton Munson, Amanda Birmingham, Roman Sasik, Ana Bojorquez-Gomez, Katherine Licon, Kristin Klepper, Alex Beckett, Kyle Salinas Sanchez, Prashant Mali, Trey Ideker. High-throughput combinatorial CRISPR-Cas9 gene knockout reveals most genetic interactions are context dependent. Cancer Research 78, 2018.
22. Shen JP, Munson B, Fong S, Birmingham A, Sasik R, Zhao D, Kreisberg JF, Mali P, Ideker T. Compositional and Time-course Aware Genetic Analysis (CTG): A novel analysis platform for high-throughput functional genetic interaction screens. Winter Quantitative Biology Meeting,, 2018.
23. Shen JP, Jacobs MT, Fuh IL, Baumgartner JM, Fanta PT, Lowy AM, Harismendy O. Somatic mutation landscape of appendiceal cancer. . J Clin Oncol (ASCO-GI Meeting Abstracts), 2018.
24. Shen JP, Zhao D, Sasik R, Luebeck J, Bojoquez-Gomez A, Licon K, Ideker T, Mali P. Combinatorial CRISPR-Cas9 gene knockout to enable genetic interaction mapping in human cells. American Association for Cancer Research 77, 2017.
25. Shen JP, Zhao D, Sasik R, Luebeck J, Birmingham A, Bojoquez-Gomez A, Klepper K, Kreisberg J, Ideker T.. Combinatorial CRISPR-Cas9 reveals many cancer synthetic lethal interactions are private to cell type. AACR Precision Medicine Series Special Conference: Opportunities and Challenges of Exploiting Synthetic Lethality in Cancer 16(10), 2017.
26. Shen JP, Bojoquez-Gomez A, Huang J, Mantan H, Kurnit K, Klepper K, Beckett A, Kreisberg JF, Saenz CC, Ideker T. A platinum-resistant subtype of high-grade Serous ovarian cancer identified by a network of somatic mutations. Marsha Rivkin 11th Biennial Ovarian Cancer Research Symposium, 2016.
27. Shen JP, Srivas R, Yang CC, Sun SM, Li JF, Gross A, Jensen J, Licon K, Bojoquez-Gomez A, Klepper K, van Attikum H, Aza-Blanc P, Sobol S, Ideker T. A network of deeply conserved synthetic-lethal interactions for exploration of precision cancer therapy. Proceedings of the 107th Annual Meeting of the American Association for Cancer Research, 2016.
28. Shen JP, Srivas R, Bojorquez-Gomez A, Licon K, Sivaganesh V, Xu JL, Yeerna H, Gross A, Li JF, Sobol RW, Ideker T. RAD17 loss of function is synthetically lethal with the checkpoint kinase inhibitors AZD7762 or MK-1775. Proceedings of the 106th Annual Meeting of the American Association for Cancer Research, 2015.
29. Gross A, Orosco RK, Shen JP, Egloff AM, Carter H, Hofree M, Choueiri M, Coffey CS, Lippman SM, Hayes DN, Cohen EE, Grandis JR, Nguyen QT, Ideker T. A prognostic model of head and neck cancer ties TP53 mutation to 3p loss. Proceedings of the 105th Annual Meeting of the American Association for Cancer Research, 2014.
30. Hofree M, Shen JP, Ideker T. Network-based stratification of thyroid cancer. Proceedings of the 105th Annual Meeting of the American Association for Cancer Research, 2014.
31. Gross A, Choueiri M, Shen JP, Randall JM, Ideker T, Hofree M. Association of methylation of genes in the taurine/hypotaurine pathway with worse prognosis in renal cell carcinoma. J Clin Oncol (ASCO Meeting Abstracts) 15562, 2013.
32. Shen JP, Srivas R, Bojorquez-Gomez A, Licon K, Li JF, Sobol RW, Ideker T. Cross-species synthetic lethal interaction screening as a strategy for the identification of novel therapeutic targets in cancer. J Clin Oncol (ASCO Meeting Abstracts) 11105, 2013.
33. Shen JP , McGee DM, Lowy AM, Fanta PT. Molecular profiles of appendiceal adenocarcinoma: The UCSD experience. J Clin Oncol (ASCO-GI Meeting Abstracts):397, 2013.
34. cGee DM, Shen JP, Fanta PT. Molecular profiles of gastric cancer: The UCSD experience. J Clin Oncol (ASCO-GI Meeting Abstracts):29, 2013.
35. Srivas R*, Shen JP*, Bojorquez-Gomez A, Licon K, Xu J, Wang ZZ, Li JF, Gross A, Bean G, Sobol RW, Ideker T. High-Throughput Synthetic Lethal Interaction Screening in Model Organisms as a Strategy for the Identification of Novel Therapeutic Targets in Cancer. Proceedings of the AACR Special Conference. The Translational Impact of Model Organisms in Cancer 11, 2013.
36. Hofree M, Shen JP, Carter H, Gross A, Ideker T. Network-based stratification: Combining genome-scale somatic mutation profiles with genetic interaction networks to identify clinically relevant subtypes in high grade serous ovarian carcinoma. Clin Cancer Res, 2013.
37. Hofree M, Shen JP, Carter H, Gross A, Ideker T. Network-based stratification of tumor mutations. The Cancer Genome Atlas 2nd Annual Scientific Symposium, 2012.
38. Hofree M, Shen JP, Ideker T. Network-based stratification of tumor mutations. The 13th International Conference on Systems Biology, 2012.
39. Shen JP, Roeland E, Hwang M, Shimabukuro KA, Sicklick JK, Ramamoorthy S, McLemore EC, Reid TR, Lowy A, Fanta P. Molecular predictors of treatment response in colon and gastric cancer. J Clin Oncol (ASCO Meeting Abstracts)(14069), 2012.
40. Greenberg EF, Silver S, Shen JP, Le H, Bradner JE. Autophagy and Aging: A Novel High-Content, Image-based RNAi screen, 2011.
41. Shen JP, Divakaran S, Ponduro S, Vogl DT, Amaravadi RK, Bradner JE. The rational for combined proteasome and autophagy inhibition in multiple myeloma established using novel translational platforms(112):2755, 2008.
42. Ponduro S, Moellering R, Greenberg EF, Shen JP, Stanton B, Bradner JE nm. Discovery and Characterization of Macrocyclic Thiopeptide Proteasome Inhibitors for Hematologic Malignancies(112):2755, 2008.
43. Shen JP, Divakaran S, Kuai LT, Wang X, Ong SE, Amaravadi R, Wood J, Carr S, Haggarty S, Bradner JE. Autophagy as a Target Pathway in Multiple Myeloma: a Forward Chemical Genetic Approach 110(11):2510, 2007.
44. Bradner JE, Shen JP, Perlstein EO, Divakaran S, Greenberg EF, Amaravadi R, Schreiber SL. Discovery and Characterization of Small Molecule Inhibitors of Autophagy for Cancer Therapy. ASH Annual Meeting Abstracts 108(11):2606, 2006.
45. Shen JP, Greenberg EF, Hideshima T, Anderson KC, Schreiber SL, Bradner JE. Targeting the Protein Degradation Pathway in Multiple Myeloma with Synergistic, Selective Small Molecules 106(11):2606, 2005.
46. Shen JP, Yousef AM, Zeineddine FA, Zeineddine MA, Tidwell RS, Beaty KA, Scofield, Hornstein N, Lano E, Eng C, Matamoros A, Foo Wai Chin, Uppal Abhinheet, Scaly Christoopher, Mansfield P, Taggert M, Raghav KP, Overmann M, Fournier K.. A Prospective Randomized Crossover Trial of Systemic Chemotherapy in Patients with Low-Grade Mucinous Appendiceal Adenocarcinoma. JAMA Network Open.

Book Chapters

1. Licon K, Shen JP, Munson BP, Michaca M, Fassino C, Fassino L, Kreisberg JF, Ideker T. Ultrahigh-Density Screens for Genome-Wide Yeast EMAPs in a Single Plate. In: Methods Mol Biol, 73-85, 2019.
2. Shen JP, Gulhati, P, Raghav K, Overman MJ. Small Bowel Cancer and Appendiceal Tumors. In: The MD Anderson Manual of Medical Oncology. 4th.

Letters to the Editor

1. Shen JP. Regarding Blood-Based Next-Generation Sequencing Analysis of Appendiceal Cancers. Oncologist 25: e2019-e2020, 2020.