Research Publications
Patient Mosaic has enabled a wide array of research; see the publications and datasets generated from this effort.
Patient Mosaic has enabled a wide array of research; see the publications and datasets generated from this effort.
2025
Pingjun Chen, Maria E. Salvatierra, Alejandra Serrano, Karina Pinao Gonzalez, Sara Ranjbar, Yasin Shokrollahi, Tanishq Gautam, B. Leticia Rodriguez, Patient Mosaic Team, Xiaoxi Pan, Luisa M. Solis Soto and Yinyin Yuan, Optimizing cell recognition in sarcoma multiplex immunohistochemistry images via pre-training strategies, International Symposium on Biomedical Imaging 2025, 06/12/2025, Manuscript 1571073780
Florentia Dimitriou, Ashish Damania, Priyadharsini Nagarajan, Sabitha Prabhakaran, Pranoti Sahasrabhojane, Yasmine Hoballah, Devarati Mitra, Roi Weiser, Shirley Y. Su, Ehab Y. Hanna, Bita Esmaeli, Travis T. Sims, Curtis Alvin Pettaway, Rodabe Navroze Amaria, Isabella Claudia Glitza, Nadim J. Ajami, Scott Eric Woodman, Jennifer Ann Wargo, Phillip Andrew Futreal, Jennifer Leigh McQuade , Delineating the role of the microbiome and tumor microenvironment interactions driving mucosal melanoma (MM) response and resistance to immune checkpoint inhibitor (ICI) treatment, American Society of Clinical Oncology 2025, 05/30/2025, Abstract 9561, doi: 10.1200/JCO.2025.43.16_suppl.9561
Fen Saj, Ashish Damania, Yasmine Hoballah, Pranoti Sahasrabhojane, Patient Mosaic Team, Felicity Namayanja, Quentin Kimana, Lianchun Xiao, Huda Elmehily, Sunyoung Lee, Zishuo Hu, Shubham Pant, Madhulika Eluri, Manal Hassan, Jennifer Wargo, Sabitha Prabhakaran, Milind Javle, Nadim Ajami, Association of gut microbiota with therapy efficacy and prognosis in biliary tract cancer, American Society of Clinical Oncology 2025, 05/22/2025, Abstract 4111, doi: 10.1200/JCO.2025.43.16_suppl.4111
Rosalba Minelli, Luigi Perelli, Benjamin J. Bivona, Sanjana Srinivasan, Desiree Catania, Bianca E. Amador, Frederick S. Robinson, Johnathon L. Rose, Christopher J. Terranova, Alejandro Hernandez Martinez, Charles E. Deckard, Courtney Le, Kuo-Shun Hsu, Michael Peoples, Aparna Subramaniam, Hannah C. Beird, Ningping Feng, Joseph R. Daniele, Christopher Vellano, Joseph Marszalek, Vinod Ravi, Alexander J. Lazar, Andrew Futreal, Timothy P. Heffernan, Giannicola Genovese, Virginia Giuliani, Development of advanced preclinical models for an in-depth characterization of cardiac angiosarcoma, American Association for Cancer Research 2025, 04/25/2025, Abstract 5167, doi: 10.1158/1538-7445.AM2025-5167
Yasin Shokrollahi, Tanishq Gautam, Alejandra Serrano, Simon P. Castillo, Pingjun Chen, Karina Pinao, Maria Esther Salvatierra, B. Leticia Rodriguez, Patient Mosaic Team, Luisa M. Solis Soto, Yinyin Yuan, Xiaoxi Pan, Artificial intelligence for predicting spatial proteomics using high-plex digital spatial profiling in carcinomas, American Association for Cancer Research 2025, 04/25/2025, Abstract 2428, doi: 10.1158/1538-7445.AM2025-2428
Pingjun Chen, Alejandra Serrano, Tanishq Gautam, Sara Ranjbar, B. Leticia Rodriguez, Patient Mosaic Team, Luisa M. Solis Soto, Yinyin Yuan, Slide-level foundation models exhibit effective diagnostic and prognostic performance in H&E-stained histopathology, American Association for Cancer Research 2025, 04/25/2025, Abstract 2450, doi: 10.1158/1538-7445.AM2025-2450
Kyung Serk Cho, Yunhe Liu, Guangsheng Pei, Jianfeng Chen, Tieling Zhou, Khalida M. Wani, Alejandra G. Serrano, Sharia D. Hernandez, Akshaya S. Jadhav, Daiwei Zhang, Hannah C. Beird, Jiahui Jiang, Diana Shamsutdinova, Xinmiao Yan, Yibo Dai, Enyu Dai, Ashley L. Wilson, Anne Waldrep, Fuduan Peng, Wei Lu, Yang Liu, Jimin Min, Paola A. Guerrero, Idania C. Julio, Tong Yin, Shin Hsu Shi, Sabitha Prabhakaran, Scott E. Kopetz, Dipen M. Maru, Alexander Lazar, Amir A. Jazaeri, Michael Green, Mingyao Li, Catherine Sautes-Fridman, Wolf H. Fridman, Andrew Futreal, Luisa M. Soto, Humam Kadara, Anirban Maitra, Suet Yi Leung, Jianjun Gao, Linghua Wang, Pan-cancer spatial characterization of tertiary lymphoid structures, American Association for Cancer Research 2025, 04/15/2025, Abstract 3962, doi: 10.1158/1538-7445.AM2025-3962
Priya Nagarajan, Mark Knafl, Sharia Hernandez, Luisa Solis Soto, Mei Jiang,Scott Woodman, Pavandeep Gill, Michael Tetzlaff, Edwin Parra Cuentas, Bita Esmaeli, Conjunctival Melanoma: Correlation of Clinicopathologic Features and Tumor-Infiltrating Inflammatory Cells, United States and Canadian Academy of Pathology, 03/25/2025, Abstract 1529, doi: 10.1016/j.labinv.2024.103770
Tanishq Gautam, Karina Pinao, Pooja Shukla, Alex Lau, Caner Ercan, B. Leticia Rodriguez, Xiaoxi Pan, Lawrence Kwong, Pingjun Chen, Yinyin Yuan, Simon Castillo, AI-STORM- AI-guided Sampling Tissues for Optimal Representative Morphology, United States and Canadian Academy of Pathology, 03/22/2025, Abstract 1354, doi: 10.1016/j.labinv.2024.103592
2024
Ayse A Koksoy, Jacqueline Oliva, Katarzyna Tomczak, Michael D Stanford, Nathaniel Deboever, Renganayaki Pandurengan, Marina N Medina Rosales, Nejla Ozirmak Lermi, Chad Strange, Edwin R Parra, Annikka Weissferdt, Ken Chen, David C Rice, Jianjun Zhang, Luisa M Solis Soto, Boris Sepesi, Reza J Mehran, Mehmet Altan, Anne Tsao, Cara L Haymaker, Analysis of PD1+ T cells and lymphoid structure(TLS) presence in pleural mesothelioma using spatial and machine learning approaches, Journal for ImmunoTherapy of Cancer, 11/05/2024, Abstract 1219, doi: 10.1136/jitc-2024-SITC2024.1219
Idania Lubo, Wei Lu, Sharia D Hernandez, Khaja Khan, Ximing Tang, Junya Fujimoto, Edwin R Parra, Jacqueline Oliva, Katarzyna Tomczak, Michael D Stanford, Ayse A Koksoy, Marina N Medina Rosales, Nejla Ozirmak Lermi, Maria Gabriela Raso, Stephanie T Schmidt, Carmen Behrens, John V Heymach, Jianjun Zhang, Boris Sepesi, Annikka Weissferdt, David C Rice, Reza J Mehran, Mehmet Altan, Anne Tsao, Tina Cascone, Don L Gibbons, Ken Chen, Ignacio I Wistuba, Cara L Haymaker, and Luisa M Solis Soto., Utilization of a tissue-based PD1_PD-L1 in situ proximity ligation assay in lung adenocarcinoma (LUAD) and pleural mesothelioma, Society for Immunotherapy of Cancer 2024, 11/05/2024, Abstract 115, doi: 10.1136/jitc-2024-SITC2024.0115
Katarzyna Tomczak, Nejla Ozirmak Lermi, Nathaniel Deboever, Shumin Li, Sevinj Isgandarova, Michael D Stanford, Carlos Ramos, Jacqueline Oliva, Marina Nayeli Medina Rosales, Ayse A Koksoy, Chang-Jiun Wu, Chad Strange, Annikka Weissferdt, Ken Chen, David C Rice, Reza J Mehran, Jianjun Zhang, Boris Sepesi, Mehmet Altan, Anne Tsao, and Cara L Haymaker, An integrated tumor, immune and genetic landscape of pleural mesothelioma to unleash effective immunotherapy avenues, Society for Immunotherapy of Cancer 2024, 11/05/2024, Abstract 1413, doi: 10.1136/jitc-2024-SITC2024.1413
Jacqueline Oliva, Katarzyna Tomczak, Michael D Stanford, Hsinyi Lu, Nathaniel Deboever, Shumin Li, Marina Nayeli Medina Rosales, Ayse A Koksoy, Nejla Ozirmak Lermi, Chad Strange, Annikka Weissferdt, Ken Chen, David C Rice, Jianjun Zhang, Reza J Mehran, Mehmet Altan, Anne Tsao, Boris Sepesi, Cara L Haymaker, Functional and transcriptomic evaluation of pleural mesothelioma tumor expanded infiltrating lymphocytes and their TCR repertoire, Society for Immunotherapy of Cancer 2024, 11/05/2024, Abstract 456, doi: 10.1136/jitc-2024-SITC2024.0456
Florentia Dimitriou, Ashish V Damania, Priyadharsini Nagarajan, Sabitha Prabhakaran, Neus Bota, Randy Chu, Pranoti Sahasrabhojane, Yasmine Hoballah, Devarati Mitra, Roi Weiser, Shirley Y Su, Bita Esmaeli, Travis T Sims, Curtis A Pettaway, Rodabe N Amaria, Isabella C Glitza, Jillian Losh, Nadim J Ajami, Scott Woodman, Jennifer A Wargo, P. Andrew Futreal, Jennifer McQuade, Delineating the role of the microbiome and tumor microenvironment interactions driving mucosal melanoma response and resistance to immune checkpoint inhibitor treatment, Society for Immunotherapy of Cancer 2024, 11/05/2024, Abstract 1256, doi: 10.1136/jitc-2024-SITC2024.1256
Tanishq Gautam, Yasin Shokrollahi, Sara Ranjbar, Pingjun Chen, Letty Rodriguez, Simon Castillo, Xiaoxi Pan, Yinyin Yuan, Luisa M. Solis Soto MD, Karina B Pinao Gonzales MD, Maria Esther Salvatierra MD, Alejandra G. Serrano MD, Patient Mosaic Team, Immune-guided AI for Reproducible ROI Detection in Immunofluorescence Pathology, 27th International Conference on Medical Image Computing and Computer Assisted Intervention, 10/06/2024, Paper 3757, doi: 10.1007/978-3-031-72083-3_21
Florentia Dimitriou, Ashish Damania, Priyadharsini Nagarajan, Sabitha Prabhakaran, Neus Bota, Mark Knafl, Randy A. Chu, Pranoti Sahasrabhojane, Yasmine M. Hoballah, Devarati Mitra, Roi Weiser, Shirley Y. Su, Ehab Y. Hanna, Bita Esmaeli, Travis T. Sims, Curtis A. Pettaway, Rodabe Amaria, Isabella C. Glitza, Tim P. Heffernan, Virginia Giuliani, Christopher P. Vellano, Jillian S. Losh, Nadim J. Ajami, Scott E. Woodman, Jennifer A. Wargo, Andrew Futreal, Jennifer McQuade, Delineating germline, molecular and microbiome factors driving mucosal melanoma risk and immunotherapy response, 21st International Congress of the Society for Melanoma Research, 10/01/2024, Poster e13218, doi: 10.1111/pcmr.13218
Yasin Shokrollahi, Karina Pinao Gonzales, Maria Esther Salvatierra, Tanishq Gautam, Pingjun Chen, Simon Castillo, Patient Mosaic Team, Luisa Solis Soto, Yinyin Yuan, Xiaoxi Pan, Advancing Multiplex Immunofluorescence Imaging Cell Detection using a Semi-Supervised Approach with Pseudo-Labeling, Medical Imaging with Deep Learning 2024, 07/01/2024, Article #184
Afsaneh Amouzegar, Xiaogang Wu, James Long, Justin W. Wong, Sabitha Prabhakaran, Latasha Little, Curtis Gumbs, Jared Malke, Julie Simon, Jianhua Zhang, Jennifer Wargo, Priyadharsini Nagarajan, Paul Scheet, Jennifer L. McQuade, Andrew Futreal, The Genetic Risk Architecture of Mucosal Melanoma, American Society of Clinical Oncology 2024, 05/29/2024, Abstract 10595, doi: 10.1200/JCO.2024.42.16_suppl.10595
Alicia A. Gingrich, Hannah Beird, Rossana Lazcano, Ryan Denu, Michael Nakazawa, Rare Tumor Initiative Team, Patient Mosaic Team, Ravin Ratan, J. Andrew Livingston, M Alex Zarzour, Anthony Conley, Neeta Somaiah, Dejka Araujo, Shreyaskumar Patel, Christina L. Roland, P. Andrew Futreal, Alexander J. Lazar, Emily Z. Keung, Elise F Nassif Haddad, Immune infiltrate analysis to reveal distinct immune classes for leiomyosarcomas, ASCO 2024, 05/29/2024, Abstract 11546, doi: 10.1200/JCO.2024.42.16_suppl.11546
Florentia Dimitriou, Priyadharsini Nagarajan, Sabitha Prabhakaran, Neus Bota, Mark Knafl, Randy Chu, Ashish Damania, Pranoti V Sahasrabhojane, Yasmine Hoballah, Jillian Losh, Nadim J Ajami, Scott E Woodman, Andrew Futreal, Jennifer A Wargo, Jennifer L McQuade, Gut microbiota profiles in mucosal melanoma (MM) patients treated with neoadjuvant immune checkpoint inhibitors (ICIs), Society for Immunotherapy of Cancer, 04/10/2024
Afsaneh Amouzegar, Xiaogang Wu, James Long, Sabitha Prabhakaran, Latasha Little, Curtis Gumbs, Jared Malke, Julie Simon, Jianhua Zhang, Jennifer Wargo, Paul Scheet, Justin W. Wong, Priyadharsini Nagarajan, Jennifer L. McQuade, Andrew Futreal, Germline mutations in cancer susceptibility genes in patients with mucosal melanoma, American Association for Cancer Research 2024, 04/05/2024, Abstract 7334, doi: 10.1158/1538-7445.AM2024-7334
Florentia Dimitriou, Priyadharsini Nagarajan, Sabitha Prabhakaran, Neus Bota, Mark Knafl, Randy Chu, Ashish Damania, Pranoti V Sahasrabhojane, Yasmine Hoballah, Jillian Losh, Nadim J Ajami, Scott E Woodman, Jennifer A Wargo, Andrew Futreal, Jennifer L McQuade, Delineating germline, tumor and extrinsic factors driving mucosal melanoma (MM) risk and response to immune checkpoint inhibitor (ICI) treatment, American Association for Cancer Research 2024, 04/05/2024, Abstract 6699, doi: 10.1158/1538-7445.AM2024-6699
Rosalba Minelli, Luigi Perelli, Benjamin J. Bivona, Sanjana Srinivasan, Desiree Catania, Bianca E. Amador, Frederick S. Robinson, Johnathon L. Rose, Christopher T. Terranova, Alejandro Hernandez Martinez, Charles E. Deckard, Courtney N. Le, Kuo-Shun Hsu, Michael Peoples, Aparna Subramaniam, Hannah C. Beird, Ningping Feng, Joseph R. Daniele, Christopher Vellano, Joseph Marszalek, Vinod Ravi, Alexander J. Lazar, Andrew Futreal, Timothy P. Heffernan, Giannicola Genovese, Virginia Giuliani, Development of advanced preclinical modeling for a comprehensive characterization of cardiac angiosarcoma biology, American Association for Cancer Research 2024, 03/22/2024, Abstract 1447, doi: 10.1158/1538-7445.AM2024-1447
2023
Alicia Gingrich, Hannah Beird, Randy Chu, Ray Traweek, Brandon Cope, Emily Z. Keung, Chris P. Scally, Kelly K. Hunt, Keila E. Torres, Christina L. Roland, Rare Tumor Initiative Team, Patient Mosaic Team, P. Andrew Futreal, Andrew Bishop, B. Ashleigh Guadagnolo, Devarati Mitra, Ahsan Farooqi, Dejka Araujo, M. Alejandra Zarzour, J. Andrew Livingston, Anthony Conley, Shreyaskumar Patel, Vinod Ravi, Neetah Somaiah, Alexander J. Lazar, Ravin Ratan, Elise F Nassif , Leiomyosarcoma intratumoral macrophage infiltrates are associated with different clinical and genomic presentations, Connective Tissue Oncology Society 2023, 11/01/2023, Poster P394
Elise F. Nassif, Hannah Beird, Akash Mitra, Bin Liu, Kevin McBride, Wei-Lien Wang, Davis Ingram, Khalida Wani, Emily Z. Keung, Rare Tumor Initiative Team, Patient Mosaic Team, Alex Zarzour, Anthony Conley, Dejka Araujo, J. Andrew Livingston, Ravin Ratan, Shreyaskumar Patel, Vinod Ravi, Robert Benjamin, Alexander J. Lazar, Christina L. Roland, P. Andrew Futreal, Neeta Somaiah, Histology specific intratumoral B-cell biology in alveolar soft-part sarcomas (ASPS) in response to durvalumab-tremelimumab (D-T), Connective Tissue Oncology Society 2023, 11/01/2023, Poster P100
Elise Nassif Haddad , Rossana Lazcano, R Morey, Davis Ingram, Khalida Wani, Alicia Gingrich, Michael Nakazawa, Ryan Denu, Christina Roland, Neetah Somaiah, Andrew Livingston, Alex Zarzour, Anthony Conley , Dejka Araujo, Joseph Ludwig, Shreyaskumar Patel, Robert Benjamin, Vinod Ravi, Ravin Ratan, Emily Z Keung, Alexander J Lazar, Patterns of Expression of Immune Biomarkers in Leiomyosarcomas (LMS), NCI Strategic Advances in Sarcoma Science, 09/01/2023
2022
Sharia Hernandez, Rossana Lazcano Alejandra Serrano, Steven Powell, Larissa Kostousov, Jay Mehta, Khaja Khan, Wei Lu, Luisa M. Solis, Challenges and Opportunities for Immunoprofiling Using a Spatial High-Plex Technology: The NanoString GeoMx® Digital Spatial Profiler, Frontiers in Oncology, 06/28/2022, PMC9277770, doi: 10.3389/fonc.2022.890410