John Carpten Lab
With expertise in fields including molecular biology, cancer genomics and bioinformatics, our team takes a multi-faceted approach to our mission. We utilize multi-omic techniques to interrogate the genomes, transcriptomes and proteomes of tumors and their microenvironment at single-cell resolution. This gives us a comprehensive view into cancer biology, including characteristics that may indicate how well the patient may respond to treatment or how aggressively the disease may progress.
Our Lab’s Focus Areas
Led by John D. Carpten, Ph.D., our team uses leading-edge research techniques to support the lab’s unique focus areas, which include:
Cancer genomics, the study of genetic changes taking place in tumor cells and driving tumor initiation and progression
Multi-omics, technologies that allow us to study several types of molecules (such as DNA, RNA, and protein) simultaneously to better understand cancer biology
Cancer health disparities, in particular the genomic and cellular factors that may explain why patients of Black or African American ancestry tend to be more frequently diagnosed with and have poorer outcomes for diseases such as endometrial and breast cancer
Tumor microenvironment studies that investigate how non-malignant cells surrounding the tumor contribute to tumor growth or progression
Bioinformatics approaches to collecting and analyzing large and complex biological datasets, such as those obtained from sequencing cancer DNA specimens
Past and Current Projects at the Carpten Lab
The Carpten Lab is dedicated to conducting research that helps relieve the cancer burden and improve patient outcomes for patients everywhere, with a particular focus on understanding the biological factors that cause cancers to be more aggressive in certain patient groups. Below are a few of the past and current projects underway at the Carpten Lab.
Triple Negative Breast Cancer
Breast cancer is the most commonly diagnosed cancer in women. Triple negative breast cancer is a subtype that is aggressive and difficult to treat. It also disproportionately affects Black and African American women. By leveraging a combination of genomic and molecular techniques, we aim to understand the biological factors that drive aggressive disease in these patients. To do this, we examine the genome, transcriptome and proteome of clinical samples, which helps us build a comprehensive understanding of the molecular and genomic drivers of these types of tumors. This in turn allows us to identify gene and protein candidates that may be useful in cancer screening or as drug targets.
Ovarian Cancer
Most ovarian cancers are diagnosed at an advanced stage, when the disease is most difficult to treat. Using single-cell and spatial genomics, we are investigating the composition and complexity of ovarian tumors. Because ovarian cancers typically develop treatment resistance, we are particularly interested in understanding genomic events associated with ovarian tumor development and evolution, both before and after chemotherapy, and in inherited and sporadic forms of ovarian cancer. We are also examining the features of a tumor and its environment to better understand how these factors dictate the tumor’s response to immunotherapy. This can help provide information that may be incorporated into personalized treatment strategies.
Endometrial Cancer
Endometrial (uterine) cancer is a highly heterogeneous disease with very different outcomes across patient populations. Black and African American women with endometrial cancer often experience poorer outcomes. We are using a multi-omic approach, including bulk, single-cell and spatial analyses, to help characterize ovarian cancer tumors and their microenvironments on a molecular and genomic level. The goal is to better understand tumor biology and identify better therapeutic options for ovarian cancer.
John D. Carpten, Ph.D. is the Director of City of Hope’s National Cancer Institute-designated Comprehensive Cancer Center, Director of Beckman Research Institute of City of Hope and chief scientific officer.
Lab Members
The Carpten Lab team includes experts in molecular biology, bioinformatics, genomics and translational research, working together to better understand the mechanisms that control how aggressive certain types of cancer can be.
Rania Bassiouni, Ph.D., is a molecular biologist and genomic
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Rania Bassiouni, Ph.D., is a molecular biologist and genomic scientist with research expertise in breast cancer and ovarian cancer. Dr. Bassiouni earned her doctorate at the University of Central Florida, where she investigated the use of novel peptide therapeutics and nanoparticle delivery systems in treating breast cancer. She completed a postdoctoral fellowship at the University of Southern California under the mentorship of Dr. Carpten, gaining expertise in leading-edge omics technologies and bioinformatics. Dr. Bassiouni continues to work with Dr. Carpten at City of Hope, where she investigates the molecular and genomic factors that contribute to aggressive disease and treatment failure in both breast and ovarian cancer.
Danyelle Hill, Ph.D., is a clinical translational and genomic
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Danyelle Hill, Ph.D., is a clinical translational and genomic scientist with a research focus on Type I uterine endometrial cancer. Dr. Paine earned her doctorate from the University of Arizona College of Medicine in Phoenix, and completed her dissertation at the Translational Genomics Research Institute, where she investigated the therapeutic potential of the epigenetic drug Quisinostat in targeting H3K27M diffuse midline glioma of the pons. She is currently a T32 postdoctoral fellow in DNA damage response research at City of Hope under Dr. Carpten’s mentorship. Her postdoctoral work integrates multi-omics and bioinformatics approaches, aimed at characterizing the molecular and genetic alterations shaping the tumor microenvironment of uterine endometrial cancer. In this work, she has a particular emphasis on understanding disease disparities affecting African American women.
Jing Qian, M.S., has a passion for unraveling the complexities of
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Jing Qian, M.S., has a passion for unraveling the complexities of cancer biology. After earning her master’s degree in translational biotechnology from the University of Southern California, Qian is now pursuing her Ph.D. under Dr. Carpten’s mentorship. Her research harnesses leading-edge spatial transcriptomics and integrative multi-omic profiling to explore tumor heterogeneity, immune–tumor interactions and the genomic alterations that influence therapeutic response. Qian seeks to uncover biomarkers that predict patient outcomes and guide precision therapies. Her goals are to improve treatment effectiveness and offer new hope for patients facing aggressive ovarian cancers.
Yuxin Jin, M.S., is a bioinformatician and genomic scientist
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Yuxin Jin, M.S., is a bioinformatician and genomic scientist specializing in computational cancer genomics, with a focus on multi-omics data integration and cancer heterogeneity. She received her master’s in translational biotechnology from the University of Southern California, where she cultivated research interests that included developing her initial genetic ancestry analysis pipeline. During this time, Jin gained extensive experience in next-generation sequencing data analysis and bioinformatics pipeline development. She later joined Dr. Carpten’s lab at City of Hope, where she provides bioinformatics support, conducts ancestry analysis for multiple collaborative projects and integrates large-scale multi-omics data. Her research focuses on ancestry-related genomic variation and molecular mechanisms underlying cancer heterogeneity across diverse cancer types.
Alex Wong serves as Chief of Staff for the Office of the Chief
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Alex Wong serves as Chief of Staff for the Office of the Chief Scientific Officer at City of Hope. In his role, he oversees and coordinates various aspects of research operations, including finance, human resources, research facilities, and other operational areas. He also helps establish connections among research faculty and staff to ensure that City of Hope teams have what they need to advance discoveries in the fight against cancer and diabetes.
Prior to joining City of Hope, Alex spent over a decade at the University of Southern California, where he served as an Administrative Program Director. He began his career at the University of California, San Diego, where he received his BA. He is on track to obtain an MBA from Arizona State University in Summer 2026.
Jian Ye, Ph.D., is an immuno-oncology scientist with a research
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Jian Ye, Ph.D., is an immuno-oncology scientist with a research focus on colorectal cancer. Dr. Ye earned his Ph.D. in developmental biology from Fudan University, where he studied T-cell development, and completed postdoctoral training in mucosal immunology at Northwestern University and the University of Florida. Based in the Department of Medical Oncology & Therapeutics Research, Dr. Ye collaborates closely with Dr. John Carpten and Dr. Marwan Fakih to connect discovery science with clinical investigation in colorectal cancer. His research integrates immunology with advanced multi-omics approaches to generate insights that drive innovation in precision immunotherapy and improve care for patients with colorectal cancer.
Resources and Downloads
The Carpten Lab offers several free software resources for researchers and scientists at City of Hope and beyond. These include:
- A collection of breast cancer tissues profiled by spatial transcriptomics in our lab is freely available for further analysis through the Gene Expression Omnibus as record GSE210616. This collection comprises 43 samples obtained from 22 patients. Access the data.
- stJoincount is an R package for application of join count analysis to spatial transcriptomics data. It is freely available through Bioconductor or at stJoincount.
Our Publications
Yao, S., Wei, L., Hu, Q., Liu, S., Manojlovic, Z., Fiorica, P. N., Long, M., Zirpoli, G. R., Cai, Q., Long, J., Ping, J., Barnard, M. E., Jin, Y., Murakami, M., Wang, J., Zhu, Q., Davis, W., Chen, J., Ondracek, R. P., Khoury, T., … Carpten, J. D.
Bassiouni R., Jin Y., Gibbs L.D., Qian J., Rotimi S.O., Miller H., Webb M.G., Rajpara S., Arias-Stella J., Craig D.W., Roman L., Carpten J.D.
Bassiouni, R., Idowu, M. O., Gibbs, L. D., Robila, V., Grizzard, P. J., Webb, M. G., Song, J., Noriega, A., Craig, D. W., & Carpten, J. D.
Latest Research News
Contact the John Carpten Lab
34.1291661, -117.9725847
Duarte, CA 91010