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Joy A. Pai

ORCID: 0009-0000-3529-6671
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A5114731202
Research Areas
  • Cancer Immunotherapy and Biomarkers
  • Single-cell and spatial transcriptomics
  • Cancer Genomics and Diagnostics
  • Cytomegalovirus and herpesvirus research
  • Viral-associated cancers and disorders
  • Melanoma and MAPK Pathways
  • Cancer-related molecular mechanisms research
  • vaccines and immunoinformatics approaches

Stanford University
 2024

 Supplementary Figure 6 from Temporal Genomic Analysis of Homogeneous Tumor Models Reveals Key Regulators of Immune Evasion in Melanoma
OPENALEX - Publications 
Sapir Cohen Shvefel Joy A. Pai Yingying Cao Lipika R. Pal Osnat Bartok and 33 more Ronen Levy Marie J. Zemanek Chen Weller Ella Herzog Winnie Yao Kamir J. Hiam-Galvez Kuoyuan Cheng Yajie Yin Peter P. Du Colin J. Raposo Nofar Gumpert Michèle Welti Julia M. Martínez Gómez Federica Sella Elizabeta Yakubovich Irit Orr Shifra Ben‐Dor Roni Oren Liat Fellus-Alyagor Ofra Golani Ori Brenner Tomer‐Meir Salame Mirie Zerbib Inna Goliand Dean Ranmar Ilya Savchenko Nadav Ketrarou Alejandro A. Schäffer Rony Dahan Mitchell P. Levesque Eytan Ruppin Ansuman T. Satpathy Yardena Samuels

<p>Differential expression analysis of rejected vs. non-rejected tumor cells.</p>

10.1158/2159-8290.28522883 preprint EN cc-by 2025-03-03
 Supplementary Figure 8 from Temporal Genomic Analysis of Homogeneous Tumor Models Reveals Key Regulators of Immune Evasion in Melanoma
OPENALEX - Publications 
Sapir Cohen Shvefel Joy A. Pai Yingying Cao Lipika R. Pal Osnat Bartok and 33 more Ronen Levy Marie J. Zemanek Chen Weller Ella Herzog Winnie Yao Kamir J. Hiam-Galvez Kuoyuan Cheng Yajie Yin Peter P. Du Colin J. Raposo Nofar Gumpert Michèle Welti Julia M. Martínez Gómez Federica Sella Elizabeta Yakubovich Irit Orr Shifra Ben‐Dor Roni Oren Liat Fellus-Alyagor Ofra Golani Ori Brenner Tomer‐Meir Salame Mirie Zerbib Inna Goliand Dean Ranmar Ilya Savchenko Nadav Ketrarou Alejandro A. Schäffer Rony Dahan Mitchell P. Levesque Eytan Ruppin Ansuman T. Satpathy Yardena Samuels

<p>Supplementary data linked to the in vivo CRISPR screen.</p>

10.1158/2159-8290.28522877 preprint NL cc-by 2025-03-03
 Supplementary Figure 3 from Temporal Genomic Analysis of Homogeneous Tumor Models Reveals Key Regulators of Immune Evasion in Melanoma
OPENALEX - Publications 
Sapir Cohen Shvefel Joy A. Pai Yingying Cao Lipika R. Pal Osnat Bartok and 33 more Ronen Levy Marie J. Zemanek Chen Weller Ella Herzog Winnie Yao Kamir J. Hiam-Galvez Kuoyuan Cheng Yajie Yin Peter P. Du Colin J. Raposo Nofar Gumpert Michèle Welti Julia M. Martínez Gómez Federica Sella Elizabeta Yakubovich Irit Orr Shifra Ben‐Dor Roni Oren Liat Fellus-Alyagor Ofra Golani Ori Brenner Tomer‐Meir Salame Mirie Zerbib Inna Goliand Dean Ranmar Ilya Savchenko Nadav Ketrarou Alejandro A. Schäffer Rony Dahan Mitchell P. Levesque Eytan Ruppin Ansuman T. Satpathy Yardena Samuels

<p>Cell types from scRNA-seq of tumors mice inoculated with rejected or non-rejected SCCs.</p>

10.1158/2159-8290.28522892 preprint EN cc-by 2025-03-03
 Supplementary Figure 12 from Temporal Genomic Analysis of Homogeneous Tumor Models Reveals Key Regulators of Immune Evasion in Melanoma
OPENALEX - Publications 
Sapir Cohen Shvefel Joy A. Pai Yingying Cao Lipika R. Pal Osnat Bartok and 33 more Ronen Levy Marie J. Zemanek Chen Weller Ella Herzog Winnie Yao Kamir J. Hiam-Galvez Kuoyuan Cheng Yajie Yin Peter P. Du Colin J. Raposo Nofar Gumpert Michèle Welti Julia M. Martínez Gómez Federica Sella Elizabeta Yakubovich Irit Orr Shifra Ben‐Dor Roni Oren Liat Fellus-Alyagor Ofra Golani Ori Brenner Tomer‐Meir Salame Mirie Zerbib Inna Goliand Dean Ranmar Ilya Savchenko Nadav Ketrarou Alejandro A. Schäffer Rony Dahan Mitchell P. Levesque Eytan Ruppin Ansuman T. Satpathy Yardena Samuels

<p>Evaluation of Mif expression in stromal cells, and its effect on patient survival.</p>

10.1158/2159-8290.28522913 preprint EN cc-by 2025-03-03
 Supplementary Figure 11 from Temporal Genomic Analysis of Homogeneous Tumor Models Reveals Key Regulators of Immune Evasion in Melanoma
OPENALEX - Publications 
Sapir Cohen Shvefel Joy A. Pai Yingying Cao Lipika R. Pal Osnat Bartok and 33 more Ronen Levy Marie J. Zemanek Chen Weller Ella Herzog Winnie Yao Kamir J. Hiam-Galvez Kuoyuan Cheng Yajie Yin Peter P. Du Colin J. Raposo Nofar Gumpert Michèle Welti Julia M. Martínez Gómez Federica Sella Elizabeta Yakubovich Irit Orr Shifra Ben‐Dor Roni Oren Liat Fellus-Alyagor Ofra Golani Ori Brenner Tomer‐Meir Salame Mirie Zerbib Inna Goliand Dean Ranmar Ilya Savchenko Nadav Ketrarou Alejandro A. Schäffer Rony Dahan Mitchell P. Levesque Eytan Ruppin Ansuman T. Satpathy Yardena Samuels

<p>Analysis of tissue microarray biopsies from cancer patients.</p>

10.1158/2159-8290.28522916 preprint EN cc-by 2025-03-03
 Supplementary Figure 15 from Temporal Genomic Analysis of Homogeneous Tumor Models Reveals Key Regulators of Immune Evasion in Melanoma
OPENALEX - Publications 
Sapir Cohen Shvefel Joy A. Pai Yingying Cao Lipika R. Pal Osnat Bartok and 33 more Ronen Levy Marie J. Zemanek Chen Weller Ella Herzog Winnie Yao Kamir J. Hiam-Galvez Kuoyuan Cheng Yajie Yin Peter P. Du Colin J. Raposo Nofar Gumpert Michèle Welti Julia M. Martínez Gómez Federica Sella Elizabeta Yakubovich Irit Orr Shifra Ben‐Dor Roni Oren Liat Fellus-Alyagor Ofra Golani Ori Brenner Tomer‐Meir Salame Mirie Zerbib Inna Goliand Dean Ranmar Ilya Savchenko Nadav Ketrarou Alejandro A. Schäffer Rony Dahan Mitchell P. Levesque Eytan Ruppin Ansuman T. Satpathy Yardena Samuels

<p>CyTOF analysis comparing tumors derived from Mif WT and KO validating the scRNAseq findings.</p>

10.1158/2159-8290.28522901 preprint EN cc-by 2025-03-03
 Supplementary Figure 10 from Temporal Genomic Analysis of Homogeneous Tumor Models Reveals Key Regulators of Immune Evasion in Melanoma
OPENALEX - Publications 
Sapir Cohen Shvefel Joy A. Pai Yingying Cao Lipika R. Pal Osnat Bartok and 33 more Ronen Levy Marie J. Zemanek Chen Weller Ella Herzog Winnie Yao Kamir J. Hiam-Galvez Kuoyuan Cheng Yajie Yin Peter P. Du Colin J. Raposo Nofar Gumpert Michèle Welti Julia M. Martínez Gómez Federica Sella Elizabeta Yakubovich Irit Orr Shifra Ben‐Dor Roni Oren Liat Fellus-Alyagor Ofra Golani Ori Brenner Tomer‐Meir Salame Mirie Zerbib Inna Goliand Dean Ranmar Ilya Savchenko Nadav Ketrarou Alejandro A. Schäffer Rony Dahan Mitchell P. Levesque Eytan Ruppin Ansuman T. Satpathy Yardena Samuels

<p>Highest Mif expression was found in tumor cells, compared to other cell types.</p>

10.1158/2159-8290.28522922 preprint EN cc-by 2025-03-03
 Supplementary Figure 2 from Temporal Genomic Analysis of Homogeneous Tumor Models Reveals Key Regulators of Immune Evasion in Melanoma
OPENALEX - Publications 
Sapir Cohen Shvefel Joy A. Pai Yingying Cao Lipika R. Pal Osnat Bartok and 33 more Ronen Levy Marie J. Zemanek Chen Weller Ella Herzog Winnie Yao Kamir J. Hiam-Galvez Kuoyuan Cheng Yajie Yin Peter P. Du Colin J. Raposo Nofar Gumpert Michèle Welti Julia M. Martínez Gómez Federica Sella Elizabeta Yakubovich Irit Orr Shifra Ben‐Dor Roni Oren Liat Fellus-Alyagor Ofra Golani Ori Brenner Tomer‐Meir Salame Mirie Zerbib Inna Goliand Dean Ranmar Ilya Savchenko Nadav Ketrarou Alejandro A. Schäffer Rony Dahan Mitchell P. Levesque Eytan Ruppin Ansuman T. Satpathy Yardena Samuels

<p>Immunopeptidomics and TCR sequencing analyses showed similar results for the rejected non-rejected SCCs.</p>

10.1158/2159-8290.28522895 preprint EN cc-by 2025-03-03
 Data from Temporal Genomic Analysis of Homogeneous Tumor Models Reveals Key Regulators of Immune Evasion in Melanoma
OPENALEX - Publications 
Sapir Cohen Shvefel Joy A. Pai Yingying Cao Lipika R. Pal Osnat Bartok and 33 more Ronen Levy Marie J. Zemanek Chen Weller Ella Herzog Winnie Yao Kamir J. Hiam-Galvez Kuoyuan Cheng Yajie Yin Peter P. Du Colin J. Raposo Nofar Gumpert Michèle Welti Julia M. Martínez Gómez Federica Sella Elizabeta Yakubovich Irit Orr Shifra Ben‐Dor Roni Oren Liat Fellus-Alyagor Ofra Golani Ori Brenner Tomer‐Meir Salame Mirie Zerbib Inna Goliand Dean Ranmar Ilya Savchenko Nadav Ketrarou Alejandro A. Schäffer Rony Dahan Mitchell P. Levesque Eytan Ruppin Ansuman T. Satpathy Yardena Samuels

<div>Abstract<p>Low intratumor heterogeneity correlates with increased patient survival and immunotherapy response. However, even highly homogeneous tumors are variably aggressive, the immunologic factors impacting aggressiveness remain understudied. In this study, we analyzed mechanisms underlying immune escape in murine low heterogeneity. We used immunophenotyping single-cell RNA sequencing to compare temporal growth of <i>in vivo</i> transplanted, genetically...

10.1158/2159-8290.c.7700576 preprint EN 2025-03-03
 Supplementary Figure 1 from Temporal Genomic Analysis of Homogeneous Tumor Models Reveals Key Regulators of Immune Evasion in Melanoma
OPENALEX - Publications 
Sapir Cohen Shvefel Joy A. Pai Yingying Cao Lipika R. Pal Osnat Bartok and 33 more Ronen Levy Marie J. Zemanek Chen Weller Ella Herzog Winnie Yao Kamir J. Hiam-Galvez Kuoyuan Cheng Yajie Yin Peter P. Du Colin J. Raposo Nofar Gumpert Michèle Welti Julia M. Martínez Gómez Federica Sella Elizabeta Yakubovich Irit Orr Shifra Ben‐Dor Roni Oren Liat Fellus-Alyagor Ofra Golani Ori Brenner Tomer‐Meir Salame Mirie Zerbib Inna Goliand Dean Ranmar Ilya Savchenko Nadav Ketrarou Alejandro A. Schäffer Rony Dahan Mitchell P. Levesque Eytan Ruppin Ansuman T. Satpathy Yardena Samuels

<p>Clinical data and characterization of the single-cell clones.</p>

10.1158/2159-8290.28522925 preprint EN cc-by 2025-03-03
 Supplementary Figure 4 from Temporal Genomic Analysis of Homogeneous Tumor Models Reveals Key Regulators of Immune Evasion in Melanoma
OPENALEX - Publications 
Sapir Cohen Shvefel Joy A. Pai Yingying Cao Lipika R. Pal Osnat Bartok and 33 more Ronen Levy Marie J. Zemanek Chen Weller Ella Herzog Winnie Yao Kamir J. Hiam-Galvez Kuoyuan Cheng Yajie Yin Peter P. Du Colin J. Raposo Nofar Gumpert Michèle Welti Julia M. Martínez Gómez Federica Sella Elizabeta Yakubovich Irit Orr Shifra Ben‐Dor Roni Oren Liat Fellus-Alyagor Ofra Golani Ori Brenner Tomer‐Meir Salame Mirie Zerbib Inna Goliand Dean Ranmar Ilya Savchenko Nadav Ketrarou Alejandro A. Schäffer Rony Dahan Mitchell P. Levesque Eytan Ruppin Ansuman T. Satpathy Yardena Samuels

<p>Opal and CODEX multiplexed tissue imaging data shows infiltration of proliferative CD8+ T-cells to the rejected SCCs.</p>

10.1158/2159-8290.28522889 preprint EN cc-by 2025-03-03
 Supplementary Figure 13 from Temporal Genomic Analysis of Homogeneous Tumor Models Reveals Key Regulators of Immune Evasion in Melanoma
OPENALEX - Publications 
Sapir Cohen Shvefel Joy A. Pai Yingying Cao Lipika R. Pal Osnat Bartok and 33 more Ronen Levy Marie J. Zemanek Chen Weller Ella Herzog Winnie Yao Kamir J. Hiam-Galvez Kuoyuan Cheng Yajie Yin Peter P. Du Colin J. Raposo Nofar Gumpert Michèle Welti Julia M. Martínez Gómez Federica Sella Elizabeta Yakubovich Irit Orr Shifra Ben‐Dor Roni Oren Liat Fellus-Alyagor Ofra Golani Ori Brenner Tomer‐Meir Salame Mirie Zerbib Inna Goliand Dean Ranmar Ilya Savchenko Nadav Ketrarou Alejandro A. Schäffer Rony Dahan Mitchell P. Levesque Eytan Ruppin Ansuman T. Satpathy Yardena Samuels

<p>scRNA-seq characterization of Mif KO tumor clones.</p>

10.1158/2159-8290.28522907 preprint EN cc-by 2025-03-03
 Supplementary Figure 14 from Temporal Genomic Analysis of Homogeneous Tumor Models Reveals Key Regulators of Immune Evasion in Melanoma
OPENALEX - Publications 
Sapir Cohen Shvefel Joy A. Pai Yingying Cao Lipika R. Pal Osnat Bartok and 33 more Ronen Levy Marie J. Zemanek Chen Weller Ella Herzog Winnie Yao Kamir J. Hiam-Galvez Kuoyuan Cheng Yajie Yin Peter P. Du Colin J. Raposo Nofar Gumpert Michèle Welti Julia M. Martínez Gómez Federica Sella Elizabeta Yakubovich Irit Orr Shifra Ben‐Dor Roni Oren Liat Fellus-Alyagor Ofra Golani Ori Brenner Tomer‐Meir Salame Mirie Zerbib Inna Goliand Dean Ranmar Ilya Savchenko Nadav Ketrarou Alejandro A. Schäffer Rony Dahan Mitchell P. Levesque Eytan Ruppin Ansuman T. Satpathy Yardena Samuels

<p>Transcriptional changes in the Mif KO compared to WT tumors.</p>

10.1158/2159-8290.28522904 preprint EN cc-by 2025-03-03
 Supplementary Figure 7 from Temporal Genomic Analysis of Homogeneous Tumor Models Reveals Key Regulators of Immune Evasion in Melanoma
OPENALEX - Publications 
Sapir Cohen Shvefel Joy A. Pai Yingying Cao Lipika R. Pal Osnat Bartok and 33 more Ronen Levy Marie J. Zemanek Chen Weller Ella Herzog Winnie Yao Kamir J. Hiam-Galvez Kuoyuan Cheng Yajie Yin Peter P. Du Colin J. Raposo Nofar Gumpert Michèle Welti Julia M. Martínez Gómez Federica Sella Elizabeta Yakubovich Irit Orr Shifra Ben‐Dor Roni Oren Liat Fellus-Alyagor Ofra Golani Ori Brenner Tomer‐Meir Salame Mirie Zerbib Inna Goliand Dean Ranmar Ilya Savchenko Nadav Ketrarou Alejandro A. Schäffer Rony Dahan Mitchell P. Levesque Eytan Ruppin Ansuman T. Satpathy Yardena Samuels

<p>Rejection and non-rejection gene sets identified in the scRNA sequencing analysis can stratify patients with high/low ITH hot/cold tumor annotations.</p>

10.1158/2159-8290.28522880 preprint EN cc-by 2025-03-03
 Supplementary Figure 5 from Temporal Genomic Analysis of Homogeneous Tumor Models Reveals Key Regulators of Immune Evasion in Melanoma
OPENALEX - Publications 
Sapir Cohen Shvefel Joy A. Pai Yingying Cao Lipika R. Pal Osnat Bartok and 33 more Ronen Levy Marie J. Zemanek Chen Weller Ella Herzog Winnie Yao Kamir J. Hiam-Galvez Kuoyuan Cheng Yajie Yin Peter P. Du Colin J. Raposo Nofar Gumpert Michèle Welti Julia M. Martínez Gómez Federica Sella Elizabeta Yakubovich Irit Orr Shifra Ben‐Dor Roni Oren Liat Fellus-Alyagor Ofra Golani Ori Brenner Tomer‐Meir Salame Mirie Zerbib Inna Goliand Dean Ranmar Ilya Savchenko Nadav Ketrarou Alejandro A. Schäffer Rony Dahan Mitchell P. Levesque Eytan Ruppin Ansuman T. Satpathy Yardena Samuels

<p>CyTOF analysis confirms high M2-like macrophage infiltration and T-cell exhaustion in non-rejected single-cell clones.</p>

10.1158/2159-8290.28522886 preprint EN cc-by 2025-03-03
 Supplementary Figure 16 from Temporal Genomic Analysis of Homogeneous Tumor Models Reveals Key Regulators of Immune Evasion in Melanoma
OPENALEX - Publications 
Sapir Cohen Shvefel Joy A. Pai Yingying Cao Lipika R. Pal Osnat Bartok and 33 more Ronen Levy Marie J. Zemanek Chen Weller Ella Herzog Winnie Yao Kamir J. Hiam-Galvez Kuoyuan Cheng Yajie Yin Peter P. Du Colin J. Raposo Nofar Gumpert Michèle Welti Julia M. Martínez Gómez Federica Sella Elizabeta Yakubovich Irit Orr Shifra Ben‐Dor Roni Oren Liat Fellus-Alyagor Ofra Golani Ori Brenner Tomer‐Meir Salame Mirie Zerbib Inna Goliand Dean Ranmar Ilya Savchenko Nadav Ketrarou Alejandro A. Schäffer Rony Dahan Mitchell P. Levesque Eytan Ruppin Ansuman T. Satpathy Yardena Samuels

<p>CD8+ T cell depletion data. Supplemental figure to Figure 6F.</p>

10.1158/2159-8290.28522898 preprint IT cc-by 2025-03-03
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