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Siqi Chen
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Journal Articles

Abstract 1205: Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics

Cong Ma, Metin Balaban, Jingxian Liu, Siqi Chen, Li Ding, Benjamin J. Raphael
Journal: Cancer Research
Cancer Res (2024) 84 (6_Supplement): 1205.
https://doi.org/10.1158/1538-7445.AM2024-1205
Published: 22 March 2024
View article titled, Abstract 1205: Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics
Journal Articles

Abstract 1773: Deciphering the roles of germline predisposition variants and somatic mutations on breast cancer cells and the tumor microenvironment

Fernanda Martins Rodrigues, Kelsey Gallant, Reyka Jayasinghe, Michael Iglesia, Andrew Houston, Siqi Chen, Preet Lal, Ryan Fields, William Gillanders, Feng Chen, Li Ding
Journal: Cancer Research
Cancer Res (2024) 84 (6_Supplement): 1773.
https://doi.org/10.1158/1538-7445.AM2024-1773
Published: 22 March 2024
View article titled, Abstract 1773: Deciphering the roles of germline predisposition variants and somatic mutations on breast cancer cells and the tumor microenvironment
Journal Articles

Abstract 2341: Morph: A feature extraction toolset for spatial transcriptomics

André Luiz N. Targino da Costa, Jingxian Liu, Chia-Kuei Mo, Erik Storrs, Austin N. Southard-Smith, Reyka G. Jayasinghe, Julia T. Wang, Michael D. Iglesia, Michael Wendl, Siqi Chen, Andrew Houston, Alla Karpova, Yize Li, Li Ding
Journal: Cancer Research
Cancer Res (2024) 84 (6_Supplement): 2341.
https://doi.org/10.1158/1538-7445.AM2024-2341
Published: 22 March 2024
View article titled, Abstract 2341: Morph: A feature extraction toolset for spatial transcriptomics
Journal Articles

Abstract 5367: Single cell resolution spatial transcriptomics reveals genetic driver and TME interaction in clear cell renal cell carcinoma

Ilya Strunilin, Wagma Caravan, Atieh Abedin-Do, Andrew Houston, Yize Li, Yizhe Song, Song Cao, Chia-Kuei Mo, Siqi Chen, Russel Pachynski, Feng Chen, Li Ding
Journal: Cancer Research
Cancer Res (2024) 84 (6_Supplement): 5367.
https://doi.org/10.1158/1538-7445.AM2024-5367
Published: 22 March 2024
View article titled, Abstract 5367: Single cell resolution spatial transcriptomics reveals genetic driver and TME interaction in clear cell renal cell carcinoma
Journal Articles

Abstract 5670: CRISPR-Mediated knockout of Ceruloplasmin (CP) and UCHL1 reveals angiogenic role in renal cell carcinoma (RCC) cell survival and proliferation

Wagma Caravan, Yige Wu, Preet Lal, Kazu Sato, Yize Li, Nataly Naser Al Deen, Siqi Chen, Ateih Abedin, Feng Chen, Li Ding
Journal: Cancer Research
Cancer Res (2024) 84 (6_Supplement): 5670.
https://doi.org/10.1158/1538-7445.AM2024-5670
Published: 22 March 2024
View article titled, Abstract 5670: CRISPR-Mediated knockout of Ceruloplasmin (CP) and UCHL1 reveals angiogenic role in renal cell carcinoma (RCC) cell survival and proliferation
Journal Articles

Abstract 1157: Molecular signatures associated with the progression from DCIS to IDC

Siqi Chen, Alla Karpova, Preet Lal, Erik Storrs, Reyka Jayasinghe, Michael Iglesia, Andrew Houston, Yanyan Zhao, Andrew Shinkle, Chia-Kuei Mo, John Herndon, Feng Chen, William Gillanders, Li Ding
Journal: Cancer Research
Cancer Res (2024) 84 (6_Supplement): 1157.
https://doi.org/10.1158/1538-7445.AM2024-1157
Published: 22 March 2024
View article titled, Abstract 1157: Molecular signatures associated with the progression from DCIS to IDC
Journal Articles

Abstract 2627: PanCancer epigenetic regulators of lymphocyte activation states

Alla Karpova, Nadezhda V. Terekhanova, Siqi Chen, Reyka G. Jayasinghe, Andrew Houston, Wagma Caravan, Ryan C. Fields, Li Ding
Journal: Cancer Research
Cancer Res (2024) 84 (6_Supplement): 2627.
https://doi.org/10.1158/1538-7445.AM2024-2627
Published: 22 March 2024
View article titled, Abstract 2627: PanCancer epigenetic regulators of lymphocyte activation states
Journal Articles

Abstract 1203: Mushroom: a tool for identification of 3D cellular neighborhoods in multi-modal spatial datasets

Erik Storrs, Siqi Chen, Chia-Kuei Mo, Andrew Houston, Andrew Shinkle, Austin Southard-Smith, Faria Simin, Andre Targino, Xiang Li, Ateih Abedin, Reyka Jayasinghe, Alla Karpova, Jingxian Liu, John Herndon, David Fenyo, Feng Chen, Ryan Fields, Tao Ju, Ben Raphael, Li Ding
Journal: Cancer Research
Cancer Res (2024) 84 (6_Supplement): 1203.
https://doi.org/10.1158/1538-7445.AM2024-1203
Published: 22 March 2024
View article titled, Abstract 1203: Mushroom: a tool for identification of 3D cellular neighborhoods in multi-modal spatial datasets
Journal Articles

Combining the Tyrosine Kinase Inhibitor Cabozantinib and the mTORC1/2 Inhibitor Sapanisertib Blocks ERK Pathway Activity and Suppresses Tumor Growth in Renal Cell Carcinoma

Yige Wu, Siqi Chen, Xiaolu Yang, Kazuhito Sato, Preet Lal, Yuefan Wang, Andrew T. Shinkle, Michael C. Wendl, Tina M. Primeau, Yanyan Zhao, Alanna Gould, Hua Sun, Jacqueline L. Mudd, Jeremy Hoog, R. Jay Mashl, Matthew A. Wyczalkowski, Chia-Kuei Mo, Ruiyang Liu, John M. Herndon, Sherri R. Davies, Di Liu, Xi Ding, Yvonne A. Evrard, Bryan E. Welm, David Lum, Mei Yee Koh, Alana L. Welm, Jeffrey H. Chuang, Jeffrey A. Moscow, Funda Meric-Bernstam, Ramaswamy Govindan, Shunqiang Li, James Hsieh, Ryan C. Fields, Kian-Huat Lim, Cynthia X. Ma, Hui Zhang, Li Ding, Feng Chen
Journal: Cancer Research
Cancer Res (2023) 83 (24): 4161–4178.
https://doi.org/10.1158/0008-5472.CAN-23-0604
Published: 15 December 2023
View article titled, Combining the Tyrosine Kinase Inhibitor Cabozantinib and the mTORC1/2 Inhibitor Sapanisertib Blocks ERK Pathway Activity and Suppresses Tumor Growth in Renal Cell Carcinoma
Open the PDF for Combining the Tyrosine Kinase Inhibitor Cabozantinib and the mTORC1/2 Inhibitor Sapanisertib Blocks ERK Pathway Activity and Suppresses Tumor Growth in Renal Cell Carcinoma in another window
Includes: Supplementary data
Journal Articles

Single-Cell Discovery and Multiomic Characterization of Therapeutic Targets in Multiple Myeloma

Lijun Yao, Julia T. Wang, Reyka G. Jayasinghe, Julie O'Neal, Chia-Feng Tsai, Michael P. Rettig, Yizhe Song, Ruiyang Liu, Yanyan Zhao, Omar M. Ibrahim, Mark A. Fiala, Julie M. Fortier, Siqi Chen, Leah Gehrs, Fernanda Martins Rodrigues, Michael C. Wendl, Daniel Kohnen, Andrew Shinkle, Song Cao, Steven M. Foltz, Daniel Cui Zhou, Erik Storrs, Matthew A. Wyczalkowski, Smrithi Mani, Scott R. Goldsmith, Ying Zhu, Mark Hamilton, Tao Liu, Feng Chen, Ravi Vij, Li Ding, John F. DiPersio
Journal: Cancer Research
Cancer Res (2023) 83 (8): 1214–1233.
https://doi.org/10.1158/0008-5472.CAN-22-1769
Published: 14 April 2023
View article titled, Single-Cell Discovery and Multiomic Characterization of Therapeutic Targets in Multiple Myeloma
Open the PDF for Single-Cell Discovery and Multiomic Characterization of Therapeutic Targets in Multiple Myeloma in another window
Includes: Supplementary data
Journal Articles

Abstract 2936: Multi-omic characterization of transitional cell populations in breast cancer

Michael D. Iglesia, Reyka G. Jayasinghe, Daniel Cui Zhou, Nadezhda V. Terekhanova, John Herndon, Alla Karpova, Siqi Chen, Nataly Naser Al Deen, Kazuhito Sato, Feng Chen, Deborah J. Veis, Ryan C. Fields, William E. Gillanders, Li Ding
Journal: Cancer Research
Cancer Res (2022) 82 (12_Supplement): 2936.
https://doi.org/10.1158/1538-7445.AM2022-2936
Published: 15 June 2022
View article titled, Abstract 2936: Multi-omic characterization of transitional cell populations in breast cancer
Journal Articles

Abstract 3873: Profiling the tumor microenvironment within clear cell renal cell carcinoma by single-nuclei RNA-Seq

Ruiyang Liu, Ilya Strunilin, Yige Wu, Alla Karpova, Siqi Chen, Chia-Kuei Mo, Yize Li, Feng Chen, Li Ding
Journal: Cancer Research
Cancer Res (2022) 82 (12_Supplement): 3873.
https://doi.org/10.1158/1538-7445.AM2022-3873
Published: 15 June 2022
View article titled, Abstract 3873: Profiling the tumor microenvironment within clear cell renal cell carcinoma by single-nuclei RNA-Seq
Journal Articles

Abstract 2025: Spatial transcriptomic profiling of progression markers in clear cell renal cell carcinoma

Chia-Kuei Mo, Yige Wu, Terekhanova Nadezhda, Caravan Wagma, Preet Lal, Siqi Chen, Nataly Naser AL Deen, Ruiyang Liu, Yanyan Zhao, Kazuhito Sato, Lijun Yao, Mamatha Serasanambati, Andrew Shinkle, Reyka G. Jayasinghe, Li Ding, Feng Chen
Journal: Cancer Research
Cancer Res (2022) 82 (12_Supplement): 2025.
https://doi.org/10.1158/1538-7445.AM2022-2025
Published: 15 June 2022
View article titled, Abstract 2025: Spatial transcriptomic profiling of progression markers in clear cell renal cell carcinoma
Journal Articles

Abstract 1710: Spatial transcriptomics and multiplexed imaging to explore tumor heterogeneity and immune complexity

Siqi Chen, Andrew Shinkle, Yanyan Zhao, Chia-Kuei Mo, Andrew Houston, Preet Lal, John M. Herndon, Ryan C. Fields, William Gillanders, Feng Chen, Li Ding
Journal: Cancer Research
Cancer Res (2022) 82 (12_Supplement): 1710.
https://doi.org/10.1158/1538-7445.AM2022-1710
Published: 15 June 2022
View article titled, Abstract 1710: Spatial transcriptomics and multiplexed imaging to explore tumor heterogeneity and immune complexity
Journal Articles

Abstract 2648: Hypoxia-induced NADPH oxidase 5 (NOX5) promotes tumor growth of head and neck squamous cell carcinoma through HIF-2á signaling

Siqi Chen, Wei Gao, Jimmy Yu-Wai Chan, Thian-Sze Wong
Journal: Cancer Research
Cancer Res (2019) 79 (13_Supplement): 2648.
https://doi.org/10.1158/1538-7445.AM2019-2648
Published: 01 July 2019
View article titled, Abstract 2648: Hypoxia-induced NADPH oxidase 5 (NOX5) promotes tumor growth of head and neck squamous cell carcinoma through HIF-2á signaling
Journal Articles

Abstract 4758: Sensitization of nasopharyngeal carcinoma to radiotherapy by targeting GFPT1/TGF-β1 signaling pathways

Siqi Chen, Wei Gao, Jimmy Yu-Wai Chan, Thian-Sze Wong
Journal: Cancer Research
Cancer Res (2017) 77 (13_Supplement): 4758.
https://doi.org/10.1158/1538-7445.AM2017-4758
Published: 01 July 2017
View article titled, Abstract 4758: Sensitization of nasopharyngeal carcinoma to radiotherapy by targeting GFPT1/TGF-β1 signaling pathways
Journal Articles

Host miR155 Promotes Tumor Growth through a Myeloid-Derived Suppressor Cell–Dependent Mechanism

Siqi Chen, Long Wang, Jie Fan, Cong Ye, Donye Dominguez, Yi Zhang, Tyler J. Curiel, Deyu Fang, Timothy M. Kuzel, Bin Zhang
Journal: Cancer Research
Cancer Res (2015) 75 (3): 519–531.
https://doi.org/10.1158/0008-5472.CAN-14-2331
Published: 01 February 2015
View article titled, Host miR155 Promotes Tumor Growth through a Myeloid-Derived Suppressor Cell–Dependent Mechanism
Open the PDF for Host miR155 Promotes Tumor Growth through a Myeloid-Derived Suppressor Cell–Dependent Mechanism in another window
Includes: Supplementary data