Publications

2021

Ma Jianzhu, Fong S, Luo Y, Bakkenish 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, Jan 2021, in press. https://doi.org/10.1038/s43018-020-00169-2

Henry JT, Coker Oluwadara, Chowdhury S, Shen JP, Morris VK, Raghav KPS, Nusrat M, Kee B, Parseghian C, Pant S, Jeyakumar N, Xhu L, Nishioka Y, Fogelman D, Wolff R, Hong D, Overman M, Vauthey JN, Kopetz S, Johnson B. Comprehensive clinical and molecular characterization of KRAS G12C mutant colorectal cancer. JCO Precision Oncology, in review

2020

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 may define an immunologically active subgroup in patients with microsatellite-stable colorectal cancer. Journal of Clinical Oncology, February 2020: 38 (4) 215-215. DOI: 10.1200/JCO.2020.38.4_suppl.215

Lee JL, 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, June 2020: 11 (6) 645.

Raghav K, Shen JP, Jacome AA, Guerra JL, Scally CP, Taggart MW, Foo WC, Matamoros A, Shaw KR, Fournier K, Overman MJ, Eng C. Integrated clinicomolecular profiling of appendiceal adenocarcinoma reveals a unique grade-driven entity distinct from colorectal cancer. British Journal of Cancer, July 2020: 254 (7) doi.org/10.1038/s41416-020-1015-3

Shen JP. Regarding Blood‐Based Next‐Generation Sequencing Analysis of Appendiceal Cancers. The Oncologist, Oct 2020 in press. doi.org/10.1002/onco.13559

2019

Licon K, Shen JP, Munson P, Michaca M, Fassino C, Fassino L, Kreisberg JF, Ideker T. Ultrahigh-Density Screens for Genome-Wide Yeast EMAPs in a Single Plate. Yeast Systems Biology; Methods in Molecular Biology, 2019; vol 2049. Humana, New York, NY. https://10.0.4.134/0008-5472.CAN-18-1281

Murtuza A, Bulbul A, Shen JP, Keshavarzian P, Woodward B, Diaz FL, Lippman SM, Husain H. Novel Third Generation EGFR Tyrosine Kinase Inhibitors and Strategies to Overcome Therapeutic Resistance in Lung Cancer. Cancer Res. 2019: 79: 689-698. PMID: 30718357. https://10.0.4.134/0008-5472.CAN-18-1281

Shabaik A, Hahn M, Shen JP. Enteric Type - Adenocarcinoma of the prostate associated with atypical intestinal metaplasia of the prostate. Clin Oncol, 2019: 4: 1650.

2018

Ang CSP*, 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. The genomic landscape of appendiceal neoplasms. JCO Precis. Oncol. 2018: 2: 1-18. https://doi.org/10.1200/PO.17.00302

Shen JP, Ideker T. Synthetic Lethal Networks for Precision Oncology: Promises and Pitfalls. J Mol. Biol. 2018; 430: 2900-2912. PMID: 29932943. doi.org/10.1016/j.jmb.2018.06.026

Wang S, Ma J, Zhang W, Shen JP, Huang JK, Peng J, Ideker T. Typing tumors using pathways selected by somatic evolution. Nat Commun. 2018; 9 (1): 4159. PMID: 30297789. 10.1038/s41467-018-06464-y

Zhang W, Bojorquez-Gomez A, Velez DO, Xu G, Sanchez K, Shen JP, Chen K, Licon K, Melton C, Olson K, Yu MK, Huang JK, Carter H, Farley E, Synder M, Fraley S, Kreisberg JF, Ideker T. A global transcriptional network connecting noncoding mutations to changes in tumor gene expression. Nat Genetics. 2018; 50 (4): 613–620. PMID: 29610481. 10.1038/s41588-018-0091-2

Bulbul A, Shen JP, Xiu J, Tamayo P, Husain H. Genomic and proteomic alterations in desmoplastic small round blue cell tumors. JCO Precis Oncol. June 2018; 2, 1-9. doi.org/10.1200/PO.17.00170

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. 2018; 17(7), 1585-1594. PMID: 29636367. 10.1158/1535-7163.MCT-17-0937

2017

Shen JP & Ideker T. Correcting CRISPR for copy number. Nat Genet. 2017; 49: 1674-1675. PMID: 29186130. https://www.nature.com/articles/ng.3994

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. 2017; 14 (6): 577-580. PMID: 28481362. 10.1038/nmeth.4286

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 C, Du D, Roguev A, Lewis NE, Chang AN, Kreisberg JF, Krogan NJ, Qi LS, Ideker T, Mali P. Combinatorial CRISPR-Cas9 screens for de novo mapping of genetic interactions. Nat Methods. 2017; 14 (6): 573-576. PMID: 28319113. 10.1038/nmeth.4225

2016

Srivas R*, Shen JP*, Yang CC, Sun SM, Li J, Gross AM, Jensen J, Licon K, Bojorquez-Gomez A, Klepper K, Huang JK, 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. 2016; 63 (3): 514-525. PMID: 27453043. 10.1016/j.molcel.2016.06.022

Johnson TC, Chin MR, Han T, Shen JP, Rana TM, Siegel DR. Synthesis of Eupalinilide E a Promoter of Human Hematopoietic Stem and Progenitor Cell Expansion. J Am Chem Soc. 2016; 138 (18): 6068-6073. PMID: 27096704. 10.1021/jacs.6b03055

2015

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. 2015; 6 (34): 35755-35769. PMID: 26437225. 10.18632/oncotarget.5928

2014

Gross A, Orosco R, Shen JP, Egloff AM, Carter H, Hofree M, Choueiri M, Coffey C, Lippman S, Hayes DN, Cohen E, Grandis J, Nguyen Q, Ideker T. Multi-tiered genomic analysis of head and neck cancer ties TP53 mutation to 3p loss. Nat Genetics. 2014; 46 (9): 939-943. PMID: 25086664. 10.1038/ng.3051

2013

Hofree M, Shen JP, Carter H, Gross A, Ideker T. Network-based stratification of tumor mutations. Nat Methods. 2013; 10(11): 1108-1115. PMID: 24037242. 10.1038/nmeth.2651

2010

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 HDAC1 and HDAC2 as therapeutic targets in sickle cell disease. Proc Natl Acad Sci. 2010; 107 (28): 12617-12622. PMID: 20616024. 10.1073/pnas.1006774107

2006

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. 2006; 5 (5): 493-504. PMID: 16720270. 10.1016/j.chembiol.2006.03.004

* Indicates co-first authorship, †Indicates corresponding authorship