Meet John Paul Shen, M.D.
John Paul Y.C. Shen, MD
Department of Gastrointestinal Medical Oncology, Division of Cancer Medicine
About Dr. John Paul Y.C. Shen
I am a physician-scientist with a scientific background in chemical biology and clinical training in Internal Medicine, Hematology, and Oncology. I am currently an Assistant Professor in the Department of Gastrointestinal Medical Oncology at the University of Texas MD Anderson Cancer Center with a clinical practice focused on colon and appendix cancers. My long-term research goal is to better understand the cancer genome, and to leverage that understanding to better the delivery of chemotherapy. My immediate research goals include the discover of new synthetic lethal genetic relationships as a means to both repurpose already FDA approved drugs and also identify new chemotherapeutic drug targets. I am also actively involved in several projects to identify genomic biomarkers to predict what specific patients will response to a given therapy. This research builds on my prior training in chemical biology and high-throughput screening, functional genomics and the creation of genetic interaction networks, as well as clinical oncology. My training in chemistry began as an undergraduate at MIT and continued at the Broad Institute as an HHMI fellow. Under the direction of Drs. James Bradner and Stuart Schreiber and I learned how small molecule probes could be used to study biological systems. At the Broad I also learned how to design, optimize and ultimately analyze the data from high-throughput and high-content chemo-genetic screens. This work led to publications in Chemistry & Biology and PNAS. After completing medical school at Washington University I matched into a combined Internal Medicine residency and Hematology-Oncology fellowship program at UCSD as part of the Physician-Scientist pathway. During the research portion of my fellowship I joined the laboratory of Dr. Trey Ideker, an internationally recognized leader in the field of network and systems biology. The Ideker lab specializes in utilizing knowledge of network relationships to draw biological conclusions from large datasets as well as performing high-throughput genetic interaction experiments in both human and model organism systems.
In the News
Present Title & Affiliation
Primary Appointment
Assistant Professor, Department of Gastrointestinal (GI) Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
Research Interests
(1) Development and use of systems biology techniques to create comprehensive molecular ‘maps’ of the cancer cell;
(2) high-throughput functional genomic screening with CRISPR-Cas9 to map genetic interaction networks and identify novel synthetic lethal interactions in cancer model systems;
(3) translation of advances in cancer biology to bring about improved outcomes in clinical oncology, in particular use of tumor molecular data to guide precision oncology;
(4) analysis of existing tumor molecular data using systems and network techniques;
(5) development of small molecules for use as targeted chemotherapeutics.
Clinical Interests
Colorectal cancer
Appendix cancer
Education & Training
Degree-Granting Education
| 2008 | Washington University School of Medicine, Saint Louis, Missouri, US, Doctor of Medicine |
| 2002 | Massachusetts Institute of Technology, Cambridge, Massachusetts, US, Chemistry, Bachelor of Science |
Postgraduate Training
| 2015-2018 | Postdoctoral Research Fellow, Genetics, University of California, San Diego, CA |
| 2013-2015 | Senior Clinical Fellow, University of California, San Diego, CA |
| 2012-2013 | Chief Fellow, University of California, San Diego, CA |
| 2010-2012 | Clinical Fellow, Hematology-Oncology, University of California, San Diego, California |
| 2009-2010 | Clinical Residency, Internal Medicine, University of California, San Diego, California |
| 2008-2009 | Clinical Internship, Internal Medicine, Univiersity of California, San Diego, California |
| 2005-2006 | Research Fellow, Chemical Biology, Broad Institute of Harvard & MIT, Cambridge, MA |
Licenses & Certifications
| 2023 | Alabama Board of Medical Examiners |
| 2022 | Georgia Composite Medical Board |
| 2022 | Oklahoma State Board of Medical Licensure |
| 2022 | Tennessee Board of Medical Examiners |
| 2022 | Arizona Board of Medical Examiners |
| 2022 | Washington State Department of Health |
| 2022 | Louisiana State Board of Medical Examiners |
| 2022 | Mississippi State Board of Medical Licensure |
| 2021 | Florida Board of Medicine |
| 2018 | Texas Medical Board |
| 2014 | Hematology |
| 2014 | Medical Oncology |
| 2011 | Internal Medicine |
| 2009 | Medical Board of California |
Experience & Service
Administrative Appointments/Responsibilities
Graduate Medical Education Council, University of California, San Diego, California, 2012 - 2013
Other Professional Positions
Clinical Instructor, Attending Physician, Internal Medicine, focus on Gastrointestinal Cancers, University of California, San Diego, CA, 2013 - 2018
Staff Physician, Hospital Medicine, Veterans Administration Hospital, San Diego, CA, 2011 - 2018
Extramural Institutional Committee Activities
Parliamentarian, Faculty Senate, The University of Texas MD Anderson Cancer Center, 2023 - Present
Senator, Executive Committee of Faculty Senate, The University of Texas MD Anderson Cancer Center, 2022 - 2024
Senator, Faculty Senate, The University of Texas MD Anderson Cancer Center, 2021 - Present
Honors & Awards
| 2022 | ASCO Career Development Award |
| 2019 | MD Anderson New Faculty Award |
| 2017 | Tower Cancer Research Foundation Career Development Award |
| 2017 | Invited to NCI Alliance for Nanotechnology in Cancer Strategic Workshop |
| 2016 | Selected as AACR NextGen Star (one of three in 2016) |
| 2016 | Featured in Molecular Cell "Meet the Author" |
| 2016 | Next Generation Star, American Association of Cancer Research |
| 2014 | California Institute of Regenerative Medicine Interdisciplinary Stem Cell Training Program Fellowship |
| 2013 | Oncology Trainee Travel Award for ASCO Annual Meeting |
| 2013 | AACR Scholar -in-Training Award for Special Conference on the Translation Impact of Model Organisms in Cancer |
| 2013 | ASCO Young Investigator Award, American Society of Clinical Oncology |
| 2013 | Abstract Merit Award for ASCO Gastrointestinal Cancer Symposium |
| 2013 | American Society for Clinical Investigation Career Development Award |
| 2007 | Dr. Lee & Virginia Harrison Scholarship |
| 2006 | Most Valuable Player, MIT Rugby Football Club |
| 2005 | Howard Hughes Medical Institute Medical Student Research Fellowship |
| 2004 | Delegate, American Medical Student Association Annual Meeting |
| 2002 | Phi Beta Kappa Honors Society |
| 2001 | Captain, MIT Rugby Football Club |
| 2001 | President, Sigma Tau chapter of Delta Kappa Epsilon |
| 1998 | Rensselaer Medal winner; Missouri State Principal's Assoc, Saint Louis University High School |
Professional Memberships
Selected Presentations & Talks
National Presentations
- 2018. High-throughput combinatorial CRISPR-Cas9 gene knockout reveals most genetic interactions are context dependent. Conference. High-throughput combinatorial CRISPR-Cas9 gene knockout reveals most genetic interactions are context dependent. Chicago, IL, US.
- 2017. Combinatorial CRISPR-Cas9 gene knockout to enable genetic interaction mapping in human cells. Conference. Combinatorial CRISPR-Cas9 gene knockout to enable genetic interaction mapping in human cells. Washington, DC, US.
- 2017. Combinatorial CRISPR-Cas9 reveals many cancer synthetic lethal interactions are private to cell type. Conference. Combinatorial CRISPR-Cas9 reveals many cancer synthetic lethal interactions are private to cell type. San Diego, CA, US.
- 2016. A platinum-resistant subtype of high-grade Serous ovarian cancer identified by a network of somatic mutations. Conference. A platinum-resistant subtype of high-grade Serous ovarian cancer identified by a network of somatic mutations. Seattle, WA, US.
- 2016. A network of deeply conserved synthetic-lethal interactions for exploration of precision cancer therapy. Conference. A network of deeply conserved synthetic-lethal interactions for exploration of precision cancer therapy. New Orleans, LA, US.
- 2014. Network-based stratification: Combining genome-scale somatic mutation profiles with genetic interation networks to identify clinically relevant subtypes in high grade serous ovarian carcinoma. Conference. Network-based stratification: Combining genome-scale somatic mutation profiles with genetic interation networks to identify clinically relevant subtypes in high grade serous ovarian carcinoma. Seattle, WA, US.
International Presentations
- 2016. Network-based stratification to identify primary platinum resistance in high grade serous ovarian carcinoma. Conference. Network-based stratification to identify primary platinum resistance in high grade serous ovarian carcinoma. Copenhagan, DK.
Formal Peers
- 2021. A Network Genomic Approach. Invited. Houston, TX, US.
- 2020. Precision Oncology for Colon & Appendiceal Cancer: A Network Genomic Approach.” MD Anderson Department of Bioinformatics and Computational Biology Seminar Series. Invited. Houston, TX, US.
- 2018. “Will CRISPR/Cas9 transform the future of cancer treatment?”. Invited. Louisville, KY, US.
- 2017. “Design of pooled CRISPR experiments.”. Invited. San Diego, CA, US.
- 2016. “Popular designs of pooled CRISPR experiments. Invited. San Diego, CA, US.
- 2016. “Rewiring of genetic interactions in cancer cells revealed by combinatorial CRISPR-Cas9.”. Invited. San Diego, CA, US.
- 2016. “Network-based stratification to identify primary platinum resistance in high grade serous ovarian carcinoma. Invited. Copenhagen, DK.
- 2016. "Systems Biology Approaches for Precision Oncology.". Invited. Mobile, AL, US.
- 2016. A network of deeply conserved synthetic-lethal interactions for exploration of precision cancer therapy. Invited. Woods Hole, MA, US.
- 2015. “Network-based Stratification of Ovarian Cancer and the Ovarian Cancer Stem Cell.”. Invited. San Diego, CA, US.
- 2013. “Applying systems biology techniques to address both diagnostic and therapeutic challenges in oncology.”. Invited. San Diego, CA, US.
Grant & Contract Support
| Date: | 2026 - 2030 |
| Title: | Untangling cellular communication networks in colorectal cancer by integrative multi-omics characterization |
| Funding Source: | Binational Science Foundation |
| Role: | PI |
| ID: | FP00028861 |
| Date: | 2026 - 2028 |
| Title: | Towards Precision Oncology for Goblet Cell Adenocarcinoma of the Appendix |
| Funding Source: | US Department of Defense |
| Role: | PI |
| ID: | FP27982 | RA250265 |
| Date: | 2025 - 2029 |
| Title: | Ivonescimab and Intraperitoneal Paclitaxel for Metastatic Appendiceal Adenocarincoma |
| Funding Source: | Cancer Prevention Research Institute of Texas |
| Role: | Co-I |
| ID: | FP25994 / RP260283 |
| Date: | 2025 - 2028 |
| Title: | Quantitative characterization of CRC tumor microenvironment at cell-type resolution |
| Funding Source: | CANCER PREVENTION RESEARCH INST OF TX |
| Role: | PI |
| ID: | FP00022548_Res1 | RP260185 |
| Date: | 2025 - 2027 |
| Title: | Precision Medicine in Rare Malignancies: Identifying Novel Biomarkers for Targeted and Immune-Based Therapies in Appendiceal Cancer |
| Funding Source: | DoD – Department of Defense |
| Role: | Mentor |
| ID: | FP00023671 / HT942524RCRPCA |
| Date: | 2025 - 2027 |
| Title: | Allele Specific Metabolic and Immune Modulation of KRAS mutated Pancreatic Cancer |
| Funding Source: | MDACC - The Andrew Sabin Family Foundation Fellowship Award FY25 |
| Role: | Consult |
| ID: | The Andrew Sabin Family Foundation Fellowship Award FY25 |
| Date: | 2025 - 2029 |
| Title: | Developing A Platform for Prospective Clinical Trials Appendiceal Cancer |
| Funding Source: | CPRIT |
| Role: | PI |
| ID: | FP22739 / R-25.1-IIRACT |
| Date: | 2025 - Present |
| Title: | Quantitative characterization of CRC tumor microenvironment at cell-type resolution |
| Funding Source: | Cancer Prevention Research Inst Of Texas |
| Role: | Co-I |
| ID: | RP250310 |
| Date: | 2025 - 2028 |
| Title: | Allele Specific Immune Modulation of KRAS Targeting in Pancreatic Cancer |
| Funding Source: | American Cancer Society (ACS) |
| Role: | Collaborator |
| ID: | FP20878 |
| Date: | 2024 - 2029 |
| Title: | Allele Specific Immune Modulation of KRAS Targeting in Pancreatic Cancer |
| Funding Source: | NIH/NCI |
| Role: | Consult |
| ID: | FP00021741/PA-20-185 |
| Date: | 2024 - 2029 |
| Title: | Towards Precision Treatment: Harnessing Molecular Signatures and Computational Models of Colorectal Cancer |
| Funding Source: | NIH |
| Role: | Consult |
| ID: | FP00019595_Res1 |
| Date: | 2024 - 2029 |
| Title: | Integrated Clinical and Preclinical Approach for the Development of Effective Therapy in the Drug Resistant GNAS/KRAS Subtype of Appendiceal Adenocarcinoma |
| Funding Source: | NIH/NCI |
| Role: | PI |
| ID: | FP00021749 |
| Date: | 2024 - 2026 |
| Title: | Developing Effective Therapy for Appendiceal Adenocarcinoma, An Orphan Disease |
| Funding Source: | MDACC - The Andrew Sabin Family Foundation Fellowship Award FY24 |
| Role: | PI |
| ID: | 2024-00063813-Y1 |
| Date: | 2024 - 2029 |
| Title: | Identifying biomolecular underpinnings of cancer and patient stratification |
| Funding Source: | University of Tx Health Science Center - Houston |
| Role: | PI |
| ID: | PA-20-185 / FP19664 |
| Date: | 2024 - 2029 |
| Title: | Harnessing Molecular Signatures and Computational Modeling for Precision Treatment of Colorectal Cancer: A Paradigm Shift in Patient Stratification |
| Funding Source: | NATIONAL INSTITUTES OF HEALTH |
| Role: | Mentor |
| ID: | PA-20-188 |
| Date: | 2024 - 2026 |
| Title: | Defining the clinical and molecular landscape of Goblet Cell Adenocarcinoma of the Appendix |
| Funding Source: | Appendix Cancer Pseudomyxoma Peritonei Research Foundation |
| Role: | PI |
| ID: | FP00021449 |
| Date: | 2024 - 2027 |
| Title: | Identifying Tumor Specific Vulnerabilities in Appendiceal Adenocarcinoma: A Systems Approach |
| Funding Source: | Cancer Prevention & Research Institute of Texas (CPRIT) |
| Role: | PI |
| ID: | RFA R-24.1-IIRA |
| Date: | 2024 - 2027 |
| Title: | Understanding the Allele Specific Mechanisms of Response and Resistance to KRAS Inhibitors in Pancreatic Cancer |
| Funding Source: | Cancer Prevention & Research Institute of Texas (CPRIT) |
| Role: | Collaborator |
| ID: | RFA R-24.1-IIRA / FP00019598 |
| Date: | 2023 - 2028 |
| Title: | Quantitative characterization of clonal expansion and microenvironment in metastatic CRC at single cell resolution |
| Funding Source: | NIH/NCI |
| Role: | MPI |
| ID: | 1R01CA283083-01 |
| Date: | 2023 - 2025 |
| Title: | Understanding KRAS Allele Specific Outcomes in Pancreatic Cancer |
| Funding Source: | Pancreatic Cancer Action |
| Role: | Mentor |
| ID: | FP00018997 |
| Date: | 2023 - 2024 |
| Title: | Defining the Tumor Microenvironment of Small Bowel Adenocarcinoma and Identifying Prognostic Biomarkers |
| Funding Source: | Conquer Cancer Foundation |
| Role: | Mentor |
| ID: | FP17586 / 2023YIA-8905766605 |
| Date: | 2023 - 2024 |
| Title: | NO TITLE PROVIDED |
| Funding Source: | IRG |
| Role: | PI |
| ID: | N/A |
| Date: | 2023 - 2025 |
| Title: | Racial genetic mutations disparities effect on colorectal cancer outcomes |
| Funding Source: | American Association for Cancer Research (AACR) |
| Role: | Mentor |
| ID: | FP00019038 |
| Date: | 2023 - 2025 |
| Title: | A Comprehensive Approach for the Development of Novel Chemotherapy Treatments for Appendiceal Adenocarcinoma |
| Funding Source: | ACPMP |
| Role: | PI |
| ID: | FP18762 |
| Date: | 2023 - 2026 |
| Title: | Identifying Tumor Specific Vulnerabilities in Appendiceal Adenocarcinoma: A Systems Approach |
| Funding Source: | Cancer Prevention & Research Institute of Texas (CPRIT) |
| Role: | PI |
| ID: | RFA-R-23.1-IIRA |
| Date: | 2022 - 2025 |
| Title: | Developing Appendix Cancer Specific Chemotherapy: A Molecular & Clinical Approach |
| Funding Source: | Conquer Cancer Foundation |
| Role: | PI |
| ID: | FP14937 |
| Date: | 2022 - 2024 |
| Title: | Credentialing novel syngeneic glioma models for immunotherapy development and testing |
| Funding Source: | Methodist Hospital Research Institute |
| Role: | PI |
| ID: | FP15128 |
| Date: | 2022 - 2024 |
| Title: | Small Molecule Targeting of GNAS for the Treatment of Mucinous Adenocarcinoma of the Appendix |
| Funding Source: | University of California - San Diego |
| Role: | PI |
| ID: | FP15131 |
| Date: | 2022 - 2025 |
| Title: | A Precision Oncology Micro-Organosphere-Based Platform to Guide Colorectal Cancer |
| Funding Source: | Subcontract with Xilis |
| Role: | Co-I |
| ID: | FP13331_Res1 |
| Date: | 2022 - 2027 |
| Title: | Integrated Approach for the Development of Effective Therapy for GNAS Mutant Appendiceal Adenocarcinoma |
| Funding Source: | NIH/NCI |
| Role: | PI |
| ID: | GRANT13378754 |
| Date: | 2022 - 2024 |
| Title: | Next Generation consensus molecular subtypes (CMS) in Colorectal Cancer (CRC) |
| Funding Source: | Andrew Sabin Family Foundation Fellowship Award |
| Role: | PI |
| Date: | 2022 - 2024 |
| Title: | Development of Gαs inhibitors for GNAS mutant appendiceal adenocarcinoma |
| Funding Source: | The Harrington Project |
| Role: | PI |
| ID: | n/a |
| Date: | 2021 - 2023 |
| Title: | Building a Foundation for Precision Medicine in the Treatment of Appendiceal Adenocarcinoma: A Network Genomic Approach |
| Funding Source: | MD Anderson Cancer Center Institutional Research Grant Program |
| Role: | PI |
| Date: | 2019 - 2020 |
| Title: | Subtype Specific Vulnerabilities in Colorectal Cancer: A Functional Genomic Approach |
| Funding Source: | SPORE |
| Role: | PI |
| Date: | 2019 - 2022 |
| Title: | UT System Rising Stars |
| Funding Source: | The University of Texas System |
| Role: | PI |
| Date: | 2019 - 2022 |
| Title: | High-Throughput Functional Genomics to Guide Precision Oncology in Gastrointestinal Tumors |
| Funding Source: | NIH/NCI |
| Role: | PI |
| ID: | K22CA234406-01 |
| Date: | 2018 - 2023 |
| Title: | Recruitment of First Time Tenure-Track Faculty Members |
| Funding Source: | Cancer Prevention & Research Institute of Texas (CPRIT) |
| Role: | PI |
| ID: | RR180035 |
| Date: | 2017 - 2018 |
| Title: | A Systems Approach to Mapping the DNA Damage Response |
| Funding Source: | NIH |
| Role: | Postdoctoral Fellow |
| Date: | 2017 - 2018 |
| Title: | Synthetic Lethal Networks to Guide Precision Oncology in GI Tumors |
| Funding Source: | Tower Cancer Research Foundation, Career Development Grant |
| Role: | PI |
| Date: | 2017 - 2018 |
| Title: | The Cancer Cell Map Initiative: A National Research Center For Cancer Systems Biology |
| Funding Source: | NIH |
| Role: | Postdoctoral Fellow |
| Date: | 2015 - 2018 |
| Title: | San Diego Center for Systems Biology: From Maps to Models |
| Funding Source: | NIH |
| Role: | Postdoctoral Fellow |
| Date: | 2014 - 2015 |
| Title: | Genomic and Epigenomic Characterization of the Ovarian Cancer Stem Cell: A Network Approach |
| Funding Source: | California Institute of Regenerative Medicine, Intedisciplinary Stem Cell Training Program |
| Role: | PI |
| Date: | 2013 - 2014 |
| Title: | Improving Outcomes in Ovarian Cancer: A Network Genomics Approach |
| Funding Source: | American Society of Clinical Oncology, Young Investigator Award |
| Role: | PI |
| Date: | 2013 - 2014 |
| Title: | Translational Cancer Genomics: Application of the novel Network-based Stratification technique to identify clinically relevant prognostic information from tumor somatic mutation profiles |
| Funding Source: | UC San Diego Moores Cancer Center, Pilot Project |
| Role: | Postdoctoral Fellow |
| Date: | 2013 - 2014 |
| Title: | NO TITLE PROVIDED |
| Funding Source: | Marsha Rivkin Center for Ovarian Cancer Research, Scientific Scholar |
| Role: | PI |
| Date: | 2011 - 2013 |
| Title: | Howard Hughes Midical Institute, ResearchTraining Fellowships for Medical Students |
| Funding Source: | NIH |
| Role: | Trainee |
| Date: | 2005 - 2006 |
| Title: | Howard Hughes Medical Institute, Research Training Fellowship for Medical Students |
| Funding Source: | NIH |
| Role: | PI |
Selected Publications
Peer-Reviewed Articles
- Godfrey EL, Mahoney F, Bansal VV, Su DG, Hanna DN, Lopez-Ramirez F, Baron E, Turaga KK, Benson AB 3rd, Setia N, Winer JH, Gunderson CG, Shah R, Magge DR, Solsky I, Eng C, Eng OS, Shergill A, Shen JP, Misdraji J, Foote MB, Luo W. Consensus guideline for the management of patients with appendiceal tumors, part 2: Appendiceal tumors with peritoneal involvement. Cancer 131(13):e35874, 2025. e-Pub 2025. PMID: 40558065.
- Schultz KS, Bansal VV, Wach MM, Bhutiani N, Godley FA 4th, Wang JJ, Waheed MT, Buchheit JT, Papai E, Campbell S, Schleimer LE, Su DG, Turaga KK, Gunderson CG, White MG, Uppal A, Raghav KPS, Labow DM, Sarpel U, Shergill AP, Shen JP, Eng C, Foote MB, Baumgartner JM. Consensus guideline for the management of colorectal cancer with peritoneal metastases. Cancer 131(13):e35869, 2025. e-Pub 2025. PMID: 40558054.
- Godfrey EL, Mahoney F, Bansal VV, Su DG, Hanna DN, Lopez-Ramirez F, Baron E, Turaga KK, Benson AB, Cusack J, Winer JH, Gunderson CG, Misdraji J, Shah R, Magge DR, Solsky I, Eng C, Eng OS, Shergill A, Shen JP, Foote MB. Consensus guideline for the management of patients with appendiceal tumors, part 1: Appendiceal tumors without peritoneal involvement. Cancer 131(13):e35867, 2025. e-Pub 2025. PMID: 40558045.
- Pellatt AJ, Bent A, Hornstein N, Parseghian C, Huey R, Raghav K, Morris V, Overman M, Morelli P, Willis J, Le P, Shen JP, Kee B, Eluri M, Higbie V, Alfaro-Munoz K, Aziz K, Kell R, Sun R, Kopetz S, Dasari A. Phase II Trial of TAS-102 in Colorectal Cancer Patients With Circulating Tumor DNA-Defined Minimal Residual Disease After Adjuvant Therapy: INTERCEPT-TT. JCO Precis Oncol 9:e2500142, 2025. e-Pub 2025. PMID: 40669021.
- Godfrey EL, Mahoney F, Bansal VV, Su DG, Hanna DN, Lopez-Ramirez F, Baron E, Turaga KK, Benson AB 3rd, Setia N, Winer JH, Gunderson CG, Shah R, Magge DR, Solsky I, Eng C, Eng OS, Shergill A, Shen JP, Misdraji J, Foote MB, Luo W. Consensus Guideline for the Management of Patients with Appendiceal Tumors, Part 2: Appendiceal Tumors with Peritoneal Involvement. Ann Surg Oncol, 2025. e-Pub 2025. PMID: 40560501.
- Schultz KS, Bansal VV, Wach MM, Bhutiani N, Godley FA 4th, Wang JJ, Waheed MT, Buchheit JT, Papai E, Campbell S, Schleimer LE, Su DG, Turaga KK, Gunderson CG, White MG, Uppal A, Raghav KPS, Labow DM, Sarpel U, Shergill AP, Shen JP, Eng C, Foote MB, Baumgartner JM. Consensus Guideline for the Management of Colorectal Cancer with Peritoneal Metastases. Ann Surg Oncol, 2025. e-Pub 2025. PMID: 40560497.
- Godfrey EL, Mahoney F, Bansal VV, Su DG, Hanna DN, Lopez-Ramirez F, Baron E, Turaga KK, Benson AB 3rd, Cusack J, Winer JH, Gunderson CG, Misdraji J, Shah R, Magge DR, Solsky I, Eng C, Eng OS, Shergill A, Shen JP, Foote MB. Consensus Guideline for the Management of Patients with Appendiceal Tumors, Part 1: Appendiceal Tumors Without Peritoneal Involvement. Ann Surg Oncol, 2025. e-Pub 2025. PMID: 40560498.
- Lee HM, Zheng Z, Sorokin A, Wong CW, Napolitano S, Chowdhury S, Kanikarla PM, Singh AK, Kochat V, Bristow CA, Srinivasan S, Peoples M, Arslan E, Alshenaifi JY, Villarreal OE, Morris VK, Shen JP, Meric-Bernstam F, Jain AK, Fowlkes NW, Anderson A, Menter DG, Saw AK, Rai K, Kopetz S. Reprogramming of Cellular Plasticity via ETS and MYC Core-regulatory Circuits During Response to MAPK Inhibition in BRAF-mutant Colorectal Cancer. bioRxiv, 2025. e-Pub 2025. PMID: 40611889.
- Jiang Y, Montierth MD, Yu K, Ji S, Tran Q, Liu X, Lal JC, Guo S, Wu A, Dai Y, Shin SJ, Li R, Cao S, Tang Y, Lesluyes T, Kopetz S, Msaouel P, Sood AK, Devonshire G, Jones CM, Ajani J, Subudhi SK, Aparicio A, Sharma P, Shen JP, Kimmel M, Wang JR, Tarabichi M, Fitzgerald RC, Zhu H, Loo PV, Wang W. Subclonal mutation load predicts survival and response to immunotherapy in cancers with low to moderate tumor mutation burden. bioRxiv, 2025. e-Pub 2025. PMID: 39005348.
- Bhutiani N, Yousef MM, Yousef AM, Haque EU, Chang GJ, Konishi T, Bednarski BK, You YN, Shen JP, Uppal A. Does Extramural Vascular Invasion Predict Response to Neoadjuvant Therapy in Locally Advanced Rectal Cancer?. Clin Colorectal Cancer 24(2):272-279.e2, 2025. e-Pub 2025. PMID: 40038019.
- White MG, Ayabe RI, Zeineddine MA, Zeineddine FA, Yousef AMG, Yousef M, Galbraith NJ, Iorgulescu JB, Scally C, Fournier K, Newhook TE, You NY, Willis J, Kopetz S, Chang GJ, Shen JP, Uppal A. Tumoral and circulating genomic landscape inform survival differences in colorectal carcinomatosis. Transl Oncol 55:102379, 2025. e-Pub 2025. PMID: 40184716.
- Ciombor KK, Bae SW, Whisenant JG, Ayers GD, Sheng Q, Peterson TE, Smith GT, Lin K, Chowdhury S, Kanikarla Marie P, Sorokin A, Cohen AS, Goff LW, Cardin DB, Shen JP, Kopetz S, Eng C, Shyr Y, Berlin J, Manning HC. Results of the Phase I/II Study and Preliminary B-cell Gene Signature of Combined Inhibition of Glutamine Metabolism and EGFR in Colorectal Cancer. Clin Cancer Res 31(8):1437-1448, 2025. e-Pub 2025. PMID: 39927885.
- Pattalachinti VK, Haque E, Yousef M, Yousef A, Chowdhury S, Overman M, Parseghian CM, Morris VK, Kee B, Huey RW, Raghav K, Court CM, Shen JP. BRAF mutant appendiceal adenocarcinoma differs from colorectal cancer but responds to BRAF-targeted therapy. NPJ Precis Oncol 9(1):38, 2025. e-Pub 2025. PMID: 39910160.
- White MG, Zeineddine MA, Fallon EA, Zeineddine FA, Dansby J, Chowdhury S, Hornstein N, Yousef A, Yousef M, Bhutiani N, Gu Y, Kee B, Dasari A, Overman MJ, Raghav K, Kopetz S, Uppal A, Taggart M, Newhook T, Fournier K, Helmink B, Drusbosky LM, Shen JP. The Landscape of ctDNA in Appendiceal Adenocarcinoma. Clin Cancer Res 31(3):551-560, 2025. e-Pub 2025. PMID: 39679931.
- Alshenaifi JY, Vetere G, Maddalena G, Yousef M, White MG, Shen JP, Vilar E, Parseghian C, Dasari A, Morris VK, Huey R, Overman MJ, Wolff R, Raghav KP, Willis J, Alfaro K, Futreal A, You YN, Kopetz S. Mutational and co-mutational landscape of early onset colorectal cancer. Biomarkers 30(1):64-76, 2025. e-Pub 2025. PMID: 39761813.
- Villarreal OE, Xu Y, Tran H, Machado A, Prescod D, Anderson A, Minelli R, Peoples M, Martinez AH, Lee HM, Wong CW, Fowlkes N, Kanikarla P, Sorokin A, Alshenaifi J, Coker O, Lin K, Bristow C, Viale A, Shen JP, Parseghian C, Marszalek JR, Corcoran R, Kopetz S. Adaptive Plasticity Tumor Cells Modulate MAPK-Targeting Therapy Response in Colorectal Cancer. bioRxiv, 2025. e-Pub 2025. PMID: 39896605.
- Guo S, Liu X, Cheng X, Jiang Y, Ji S, Liang Q, Koval A, Li Y, Owen LA, Kim IK, Aparicio A, Lee S, Sood AK, Kopetz S, Shen JP, Weinstein JN, DeAngelis MM, Chen R, Wang W. A deconvolution framework that uses single-cell sequencing plus a small benchmark data set for accurate analysis of cell type ratios in complex tissue samples. Genome Res 35(1):147-161, 2025. e-Pub 2025. PMID: 39586714.
- Yousef M, Hurd MW, Yousef A, Ludmir EB, Pillai AB, Peterson J, Koay EJ, Albarouki S, Tzeng CW, Snyder R, Katz MHG, Wang H, Overman MJ, Maitra A, Pant S, Smaglo BG, Wolff RA, Yao J, Shen JP, Zhao D. Clinical and molecular characteristics of patients with brain metastasis secondary to pancreatic ductal adenocarcinoma. Oncologist 30(1), 2025. e-Pub 2025. PMID: 39014543.
- Yazdani A, Lenz HJ, Pillonetto G, Mendez-Giraldez R, Yazdani A, Sanoff H, Hadi R, Samiei E, Venook AP, Ratain MJ, Rashid N, Vincent BG, Qu X, Wen Y, Kosorok M, Symmans WF, Shen JPYC, Lee MS, Kopetz S, Nixon AB, Bertagnolli MM, Perou CM, Innocenti F. Gene signatures derived from transcriptomic-causal networks stratify colorectal cancer patients for effective targeted therapy. Commun Med (Lond) 5(1):9, 2025. e-Pub 2025. PMID: 39779996.
- Fong SH, Kuenzi BM, Mattson NM, Lee J, Sanchez K, Bojorquez-Gomez A, Ford K, Munson BP, Licon K, Bergendahl S, Shen JP, Kreisberg JF, Mali P, Hager JH, White MA, Ideker T. A multilineage screen identifies actionable synthetic lethal interactions in human cancers. Nat Genet 57(1):154-164, 2025. e-Pub 2025. PMID: 39558023.
- Yousef M, Yousef A, Chowdhury S, Fanaeian MM, Knafl M, Peterson J, Zeineddine M, Alfaro K, Zeineddine F, Goldstein D, Hornstein N, Dasari A, Huey R, Johnson B, Higbie V, Bent A, Kee B, Lee M, Morelli MP, Morris VK, Halperin D, Overman MJ, Parseghian C, Vilar E, Wolff R, Raghav KP, White MG, Uppal A, Sun R, Wang W, Kopetz S, Willis J, Shen JP. Molecular, Socioeconomic, and Clinical Factors Affecting Racial and Ethnic Disparities in Colorectal Cancer Survival. JAMA Oncol 10(11):1519-1529, 2024. e-Pub 2024. PMID: 39264607.
- Chowdhury S, Xiu J, Ribeiro JR, Nicolaides T, Zhang J, Korn WM, Poorman KA, Lenz HJ, Marshall JL, Oberley MJ, Sledge GW Jr, Spetzler D, Kopetz S, Shen JP. Consensus molecular subtyping of metastatic colorectal cancer expands biomarker-directed therapeutic benefit for patients with CMS1 and CMS2 tumors. Br J Cancer 131(8):1328-1339, 2024. e-Pub 2024. PMID: 39227409.
- Balachandran Pillai A, Yousef M, Yousef A, Alfaro-Munoz KD, Smaglo BG, Willis J, Wolff RA, Pant S, Hurd MW, Maitra A, Wang H, Katz MHG, Prakash LR, Tzeng CD, Snyder R, Castelnovo LF, Chen A, Kravets A, Kudriavtseva K, Tarasov A, Kryukov K, Ying H, Shen JP, Zhao D. Molecular and Clinical Features of Pancreatic Acinar Cell Carcinoma: A Single-Institution Case Series. Cancers (Basel) 16(19), 2024. e-Pub 2024. PMID: 39410042.
- Klomp JA, Klomp JE, Stalnecker CA, Bryant KL, Edwards AC, Drizyte-Miller K, Hibshman PS, Diehl JN, Lee YS, Morales AJ, Taylor KE, Peng S, Tran NL, Herring LE, Prevatte AW, Barker NK, Hover LD, Hallin J, Sorokin A, Kanikarla PM, Chowdhury S, Coker O, Lee HM, Goodwin CM, Gautam P, Olson P, Christensen JG, Shen JP, Kopetz S, Graves LM, Lim KH, Wang-Gillam A, Wennerberg K, Cox AD, Der CJ. Defining the KRAS- and ERK-dependent transcriptome in KRAS-mutant cancers. Science 384(6700):eadk0775, 2024. e-Pub 2024. PMID: 38843331.
- 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. e-Pub 2024. PMID: 38759125.
- 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.
- 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. e-Pub 2024. PMID: 38723230.
- Deng N, Gubry-Rangin C, Song XT, Ju XT, Liu SY, Shen JP, Di HJ, Han LL, Zhang LM. AOB Nitrosospira cluster 3a.2 (D11) dominates N(2)O emissions in fertilised agricultural soils. J Environ Manage 355:120504, 2024. e-Pub 2024. PMID: 38447513.
- Yousef A, Yousef M, Chowdhury S, Abdilleh K, Knafl M, Edelkamp P, Alfaro-Munoz K, Chacko R, Peterson J, Smaglo BG, Wolff RA, Pant S, Lee MS, Willis J, Overman M, Doss S, Matrisian L, Hurd MW, Snyder R, Katz MHG, Wang H, Maitra A, Shen JP, Zhao D. Impact of KRAS mutations and co-mutations on clinical outcomes in pancreatic ductal adenocarcinoma. NPJ Precis Oncol 8(1):27, 2024. e-Pub 2024. PMID: 38310130.
- 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.
- 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.
- 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.
- Dansby J, More A, Zeineddine M, Yousef A, Bent A, Dayyani F, Wolff R, Overman M, Shen JP. Taxane-Based Chemotherapy Is Effective in Metastatic Appendiceal Adenocarcinoma. Oncologist 28(12):e1303-e1305, 2023. e-Pub 2023. PMID: 37738316.
- 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.
- 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. e-Pub 2023. PMID: 38085001.
- 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.
- 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.
- 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.
- 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.
- 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. e-Pub 2023. PMID: 37487150.
- 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.
- 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.
- 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.
- 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.
- 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 2023. PMID: 36351210.
- 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. e-Pub 2022. PMID: 35697807.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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. e-Pub 2022. PMID: 35108036.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- Shabaik A, Hahn M, Shen JP. Enteric Type - Adenocarcinoma of the Prostate Associated with Atypical Intestinal Metaplasia of the Prostate. Clinics in Oncology, 2019. e-Pub 2019.
- 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.
- 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.
- 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. e-Pub 2018.
- 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.
- Bulbul A, Shen JP, Xiu J, Tamayo P, Husain H. Genomic and Proteomic Alterations in Desmoplastic Small Round Blue-Cell Tumors. JCO Precis Oncol 2, 2018. e-Pub 2018. PMID: 32913982.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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. e-Pub 2015. PMID: 26437225.
- 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.
- 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. e-Pub 2014. PMID: 25417114.
- 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.
- 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.
- Ghashghaei R, Popa R, Shen JP. Evans syndrome. Am J Med 126(11):e7-8, 2013. e-Pub 2013. PMID: 24157305.
- 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.
- 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. e-Pub 2006. PMID: 16720270.
Review Articles
- 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.
- 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. e-Pub 2019. PMID: 30718357.
- Shen JP, Ideker T. Synthetic Lethal Networks for Precision Oncology: Promises and Pitfalls. J Mol Biol 430(18 Pt A):2900-2912, 2018. e-Pub 2018. PMID: 29932943.
- Shen JP, Ideker T. Synthetic Lethal Networks for Precision Oncology: Promises and Pitfalls. Journal of Molecular Biology 430(18), 2018. e-Pub 2018.
Other Articles
- Yousef M, Yousef A, Hurd MW, Pillai A, Chowdhury S, Snyder R, Knafl M, Lewis RL, Roy PM, Fanaeian M, Albarouki S, Castelnovo LF, Peterson J, Smaglo BG, Wolff RA, Pant S, Willis J, Huey R, Overman M, Tzeng CW, Kim MP, Ikoma N, Maxwell JE, Katz MHG, Wang H, Maitra A, Koay E, Ludmir EB, Chen A, Lopez C, Ying H, Shen JP, Zhao D KRAS mutation detection by liquid biopsy for pancreatic ductal adenocarcinoma. J Hematol Oncol 18(1):44, 2025. PMID: 40247392.
- Fong SH, Kuenzi BM, Mattson NM, Lee J, Sanchez K, Bojorquez-Gomez A, Ford K, Munson BP, Licon K, Bergendahl S, Shen JP, Kreisberg JF, Mali P, Hager JH, White MA, Ideker T Author Correction: A multilineage screen identifies actionable synthetic lethal interactions in human cancers. Nat Genet 57(2):480, 2025. PMID: 39833330.
- Maddalena G, Zeineddine FA, Rivero-Hinojosa S, Aushev VN, Chowdhury S, Zeineddine MA, Yousef AM, Yap TA, EINaggar AC, Liu MC, White M, Overman MJ, Kopetz S, Shen JP Defining the subset of mutations in polymerase epsilon (POLE) associated with loss-of-proofreading (LOP) functionality. Ann Oncol 35(7):678-680, 2024. PMID: 38734075.
- 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.
- Yousef A, Yousef M, Chowdhury S, Abdilleh K, Knafl M, Edelkamp P, Alfaro-Munoz K, Chacko R, Peterson J, Smaglo BG, Wolff RA, Pant S, Lee MS, Willis J, Overman M, Doss S, Matrisian L, Hurd MW, Snyder R, Katz MH, Wang H, Maitra A, Shen JP, Zhao D Impact of KRAS Mutations and Co-mutations on Clinical Outcomes in Pancreatic Ductal Adenocarcinoma. npj| precision oncology, 2023.
- 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.
Editorials
- Shen JP. Artificial Intelligence, Molecular Subtyping, Biomarkers, and Precision Oncology. Emerg Top Life Sci 5(6):747-756, 2021. PMID: 34881776.
- 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.
- Shen JP, Ideker T. Correcting CRISPR for copy number. Nat Genet 49(12):1674-1675, 2017. PMID: 29186130.
Abstracts
- Vinocha A, Dasari A, Li JJ, Thomas JV, Kopetz S, Hu ZI, YC Shen JP, Singh Raghav KP, Overman MJ. Brain metastasis in patients with primary gastrointestinal malignancy on anti-HER2 therapy. 2025 ASCO Annual Meeting 43(16):e16067-e16067, 2025.
- Vetere G, Sun R, Morris VK, Dasari A, Kee BK, YC Shen JP, Willis J, Morelli MP, Sorokin A, Marie PK, Wolff RA, Overman MJ, Singh Raghav KP, Sanchez EV, Huey RW, Higbie V, Le P, Baig Y, Kopetz S, Parseghian C. Open-label phase Ib/II study of cetuximab (CET) plus LY3214996 with or without abemaciclib in patients (pts) with anti-EGFR-refractory metastatic colorectal cancer (mCRC). 2025 ASCO Annual Meeting 43(16):3534-3534, 2025.
- Osterlund E, Maddalena G, Pellatt AJ, Eluri M, Parseghian C, Aziz K, Alfaro K, Kell RJ, Manyam GC, Konishi T, Overman MJ, Morelli MP, Willis J, YC Shen JP, Singh Raghav KP, Newhook TE, Dasari A, Maitra A, Morris VK, Kopetz S. Biologic correlates of circulating tumor DNA (ctDNA) shedding in the INTERCEPT colorectal cancer (CRC) study. 2025 ASCO Annual Meeting, 2025.
- Shah P, Singh Raghav KP, Serpas V, Pedersen KS, Kalyan A, Salem ME, Huey RW, YC Shen JP, Wang H, Wang H, Vinocha A, Thomas JV, Wolff RA, Overman MJ. A retrospective analysis of taxane-based chemotherapy in small bowel adenocarcinoma (SBA). 2025 ASCO Annual Meeting 43(16):e16479-e16479, 2025.
- Lim M, Lin K, Abdelfattah N, Parseghian C, Morelli MP, Willis J, Huey RW, Higbie V, Bent AH, Eluri M, Kee BK, Wolff RA, Singh Raghav KP, Dasari A, Overman MJ, YC Shen JP, Kopetz S, Morris VK. Clinicopathologic features of complement activation signatures in colorectal cancer. 2025 ASCO Annual Meeting 43(16):3573-3573, 2025.
- Bent AH, Parseghian C, Morris VK, Kee BK, Huey RW, Morelli MP, YC Shen JP, Jernigan K, Fernandez A, Harrison C, Horodecky K, Dasari A, Alfaro K, Aziz K, Kell RJ, Kopetz S. DAILY: A prospective single arm study evaluating the impact of vitamin D, aspirin, exercise, and diet in colorectal cancer patients with ctDNA-defined minimal residual disease 43(16):e15534-e15534, 2025.
- YC Shen JP, Reiter J, Babiarz J, Srinivasan P, Lu F, Haghshenas E, Chen T, Liang N, Joshi J, Huang H, Cerna L, Alexander S, Gutman B, Kushwaha G, Aushev VN, Cruz-Correa MR, Rabinowitz M, Kawli T, Aleshin A, Cohen SA. Development of a methylation-based, tissue-free test for the detection of molecular residual disease by circulating tumor DNA. 2025 ASCO Annual Meeting 43(16):3048-3048, 2025.
- Yousef MM, Albarouki S, Elhariri A, Vetere G, Fanaeian MM, Hurd MW, Roy P, Alfaro K, Yousef AM, Smaglo BG, Wolff RA, Katz MH, Snyder RA, Pant S, Willis J, Huey RW, Overman MJ, Ludmir EB, YC Shen JP, Zhao D. Clinical outcomes and molecular characteristics of patients with metastatic pancreatic ductal adenocarcinoma according to involved metastatic sites. 2025 ASCO Annual Meeting 43(16):4179-4179, 2025.
- Shen JP, MD, Yousef AM, MD, Zeineddine FA, MD, Zeineddine MA, MD, Tidwell RS, MS, Beaty KA, PA-C, Scofield LC, PA, Rafeeq S, MD, Hornstein N, MD, Lano E, MD, Eng C, MD, Matamoros A, MD, Foo WC, MD, Uppal A, MD, Scally C, MD, Mansfield P, MD, Taggart M, MD, Raghav KP, MD, Overman MJ, MD, Fournier K, MD. Efficacy of Systemic Chemotherapy in Patients With Low-grade Mucinous Appendiceal Adenocarcinoma, 2023. e-Pub 2023.
- Chowdhury S, Pattalachinti VK, Haridas V, Kopetz S, Shen JP. Abstract B004: Multi-omics profiling to identify mechanisms of resistance to KRAS inhibition: A comparative study on colorectal and lung cancer 21(5), 2023. e-Pub 2023.
- Johnson B, Haymaker C, Morris VK, Dasari A, Higbie VS, Shen JP, Parseghian C, Morelli MP, Huey R, Lee MS, Willis J, Raghav KP, Yuan Y, Zebala J, DePinho RA, Kopetz S, Overman M. 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 83(8), 2023. e-Pub 2023.
- Guo S, Cheng X, Koval A, Ji S, Liang Q, Li Y, Owen LA, Kim IK, Weinstein J, Kopetz S, Shen JP, DeAngelis MM, Chen R, Wang W. Abstract 4273: Integration with benchmark data of paired bulk and single-cell RNA sequencing data substantially improves the accuracy of bulk tissue deconvolution 83(7), 2023. e-Pub 2023.
- Chowdhury S, Ito I, Pattalachinti VK, Shen JP. Abstract 880: Activation of the Wnt pathway is associated with GNASR201 mutant appendiceal cancer in the peritoneum 83(7), 2023. e-Pub 2023.
- Lin K, Zeineddine M, Chowdhury S, Hornstein N, Mani S, Kopetz S, Shen JP. Abstract 2454: Identification of colorectal cancer stem cells from single cell RNA sequencing 83(7), 2023. e-Pub 2023.
- Villarreal OE, Zeineddine F, Chacko R, Parseghian C, Johnson B, Willis J, Lee M, Morris VK, Dasari A, Raghav K, Overman M, You Y, Wang Y, Maru D, Shen JP, Kopetz S. Abstract PR005: Outcomes in colitis-associated metastatic colorectal cancer and intersection with early-onset and signet ring cell carcinoma 82(23), 2022. e-Pub 2022.
- Davis JS, Chavez JC, Kok M, Miguel YS, Lee HY, Henderson H, Overman MJ, Morris VK, 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. Abstract A023: Influence of pre-diagnosis obesity and post-diagnosis aspirin use on survival from stage IV colorectal cancer 82(23), 2022. e-Pub 2022.
- Lin K, Shen JP. Abstract 6066: Elucidating cancer stem cells heterogeneity in colorectal cancer by single-cell RNA sequencing 82(12), 2022. e-Pub 2022.
- Lee HM, Napolitano S, Sorokin A, Woods MN, Chowdhury S, Alshenaifi JY, Singh AK, Shen JP, Meric-Bernstam F, Rai K, Kopetz S. Abstract 3275: Bromodomain and extraterminal (BET) protein inhibition sensitize BRAFV600E colorectal cancer to standard targeted therapies 82(12), 2022. e-Pub 2022.
- Gu Y, Yousef AM, Chowdhury S, Shen JP. Abstract 5794: Gene expression analysis of appendiceal adenocarcinomas highlights tumor heterogeneity between high and low-grade 82(12), 2022. e-Pub 2022.
- Chowdhury S, Gupta R, Haridas V, Zeineddine MA, Kopetz S, Shen JP. Abstract 1246: Consensus molecular subtypes (CMS) of colorectal cancer predict anti-EGFR response irrespective of tumor sidedness 82(12), 2022. e-Pub 2022.
- 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, 2021. e-Pub 2021.
- 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, 2021. e-Pub 2021.
- 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, 2020. e-Pub 2020.
- 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, 2020. e-Pub 2020.
- 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), 2020. e-Pub 2020.
- 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), 2020. e-Pub 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 to define an immunologically active subgroup in patients with microsatellite-stable colorectal cancer, 2020. e-Pub 2020.
- 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, 2018. e-Pub 2018.
- 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, 2018. e-Pub 2018.
- Shen JP, Zhao D, Munson B, Birmingham A, Sasik R, Bojorquez-Gomez A, Licon K, Klepper K, Beckett A, Sanchez KS, Mali P, Ideker T. High-throughput combinatorial CRISPR-Cas9 gene knockout reveals most genetic interactions are context dependent 78, 2018. e-Pub 2018.
- 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, 2018. e-Pub 2018.
- Shen JP, Jacobs MT, Fuh IL, Baumgartner JM, Fanta PT, Lowy AM, Harismendy O. Somatic mutation landscape of appendiceal cancer, 2018. e-Pub 2018.
- 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 77, 2017. e-Pub 2017.
- 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 16(10), 2017. e-Pub 2017.
- 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, 2016. e-Pub 2016.
- 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. e-Pub 2016.
- 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. e-Pub 2015.
- 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. e-Pub 2014.
- 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. e-Pub 2014.
- 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 15562, 2013. e-Pub 2013.
- 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 11105, 2013. e-Pub 2013.
- JP S, McGee DM, Lowy AM, Fanta PT. Molecular profiles of appendiceal adenocarcinoma: The UCSD experience:397, 2013. e-Pub 2013.
- cGee DM, Shen JP, Fanta PT. Molecular profiles of gastric cancer: The UCSD experience:29, 2013. e-Pub 2013.
- 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, 2013. e-Pub 2013.
- 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 11, 2013. e-Pub 2013.
- 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, 2013. e-Pub 2013.
- Hofree M, Shen JP, Carter H, Gross A, Ideker T. Network-based stratification of tumor mutations, 2012. e-Pub 2012.
- Hofree M, Shen JP, Ideker T. Network-based stratification of tumor mutations, 2012. e-Pub 2012.
- 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(14069), 2012. e-Pub 2012.
- Greenberg EF, Silver S, Shen JP, Le H, Bradner JE. Autophagy and Aging: A Novel High-Content, Image-based RNAi screen, 2011. e-Pub 2011.
- Ponduro S, Moellering R, Greenberg EF, Shen JP, Stanton B, nm BJ. Discovery and Characterization of Macrocyclic Thiopeptide Proteasome Inhibitors for Hematologic Malignancies(112):2755, 2008. e-Pub 2008.
- 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. e-Pub 2008.
- 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. e-Pub 2007.
- 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 108(11):2606, 2006. e-Pub 2006.
- 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. e-Pub 2005.
- Shen JP, Yousef AM, Zeineddine FA, Zeineddine MA, Tidwell RS, Beaty KA, Scofield, Hornstein N, Lano E, Eng C, Matamoros A, Chin FW, Abhinheet U, Christoopher S, 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.
Book Chapters
- 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.
- 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
- Shen JP. Regarding Blood-Based Next-Generation Sequencing Analysis of Appendiceal Cancers. Oncologist 25: e2019-e2020, 2020.
Patents
- Shen JP, Siegel D. SMALL MOLECULE FOR TREATMENT OF CANCER OF THE APPENDIX. Patent Number: PCT/US2023/027939.
Patient Reviews
CV information above last modified February 18, 2026