Publications

MONTAGE: A Computation Framework to Identify Spatially Resolved Functional Enrichment Gradients in the Tissue Microenvironment via Spatial Communities. bioRxiv (2025)

Weiruo Zhang, Zinaida Good, Marc A. Baertsch, Guolan Lu, John W. Hickey, Rachel Hildebrand, Serena Chang, Andrew J. Gentles, John B. Sunwoo, Quynh-Thu Le, Christina S. Kong, Garry P. Nolan, Sylvia K. Plevritis.
https://www.biorxiv.org/content/10.1101/2025.04.30.651486v1

A quantitative spatial cell-cell colocalizations framework enabling comparisons between in vitro assembloids and pathological specimens. Nature Communications. 16: 1392 (2025)

Gina Bouchard, Weiruo Zhang, Ilayda Ilerten, Irene Li, Asmita Bhattacharya, Yuanyuan Li, Winston Trope, Joseph B. Shrager, Calvin Kuo, Michael G. Ozawa, Amato J. Giaccia, Lu Tian, Sylvia K. Plevritis. https://www.nature.com/articles/s41467-024-55129-6

The acid-sensing receptor GPR65 on tumor macrophages drives tumor growth in obesity. Science Immunology. Vol 9, Issue 100, (2024)

Sreya Bagchi, Robert Yuan, Han-Li Huang, Weiruo Zhang, David Kung-Chun Chiu, Hyungjoo Kim , Sophia L. Cha, Lorna Tolentino, Joshua Lowitz, Yilin Liu, Anna Moshnikova, Oleg Andreev, Sylvia Plevritis , and Edgar G. Engleman. https://www.science.org/doi/10.1126/sciimmunol.adg6453

Basal-to-inflammatory transition and tumor resistance via crosstalk with a pro-inflammatory stromal niche. Nature Communications. 15:8134 (2024)

Nancy Yanzhe Li, Weiruo Zhang, Daniel Haensel, Anna R. Jussila, Cory Pan, Sadhana Gaddam, Sylvia K. Plevritis, Anthony E. Oro.
https://www.nature.com/articles/s41467-024-52394-3

NFE2L2 Mutations Enhance Radioresistance in Head and Neck Cancer by Modulating Intratumoral Myeloid Cells. Cancer Research. 83 (6):861-874 (2023)

Li Guan, Dhanya K. Nambiar, Hongbin Cao, Vignesh Viswanathan, Shirley Kwok, Angela B. Hui, Yuan Hou, Rachel Hildebrand, Rie von Eyben, Brittany J. Holmes, Junfei Zhao, Christina S. Kong, Nathan Wamsley, Weiruo Zhang, Michael B. Major, Seung W. Seol, John B. Sunwoo, D. Neil Hayes, Maximilian Diehn, Quynh-Thu Le. https://doi.org/10.1158/0008-5472.CAN-22-1903

Organization of the human intestine at single-cell resolution. Nature. 619:7970 (2023)

John W Hickey, Winston R Becker, Stephanie A Nevins, Aaron Horning, Almudena Espin Perez, Chenchen Zhu, Bokai Zhu, Bei Wei, Roxanne Chiu, Derek C Chen, Daniel L Cotter, Edward D Esplin, Annika K Weimer, Chiara Caraccio, Vishal Venkataraaman, Christian M Schürch, Sarah Black, Maria Brbić , Kaidi Cao, Shuxiao Chen, Weiruo Zhang, Emma Monte, Nancy R Zhang, Zongming Ma, Jure Leskovec, Zhengyan Zhang, Shin Lin, Teri Longacre, Sylvia K Plevritis, Yiing Lin, Garry P Nolan, William J Greenleaf, Michael Snyder.
https://www.nature.com/articles/s41586-023-05915-x

Galectin-1 Mediates Chronic STING Activation in Tumors to Promote Metastasis through MDSC Recruitment. Cancer Research. 83 (19):3205-3219. (2023)

Dhanya K. Nambiar, Vignesh Viswanathan, Hongbin Cao, Weiruo Zhang, Li Guan, Manish Chamoli, Brittany Holmes, Christina Kong, Rachel Hildebrand, Amanda Jeanette Koong, Rie von Eyben, Sylvia Plevritis, Lingyin Li, Amato Giaccia, Edgar Engleman, Quynh Thu Le.
https://aacrjournals.org/cancerres/article-abstract/83/19/3205/729247/

Identification of cell types in multiplexed in situ images by combining protein expression and spatial information using CELESTA. Nature Methods. 19, 759-769 (2022)

Weiruo Zhang, Irene Li, Nathan E. Reticker-Flynn, Zinaida Good, Serena Chang, Nikolay Samusik, Saumyaa Saumyaa, Yuanyuan Li, Xin Zhou, Rachel Liang, Christina S. Kong, Quynh-Thu Le, Andrew J. Gentles, John B. Sunwoo, Garry P. Nolan, Edgar G. Engleman, Sylvia K. Plevritis.
https://www.nature.com/articles/s41592-022-01498-z

Lymph node colonization induces tumor-immune tolerance to promote distant metastasis. Cell. 185 (11) 1924-1942 (2022)

Nathan E. Reticker-Flynn, Weiruo Zhang, Julia A. Belk, Pamela A. Basto, Nichole K. Escalante, Genay O.W. Pilarowski, Alborz Bejnood, Maria M. Martins, Justin A. Kenkel, Ian L. Linde, Sreya Bagchi, Robert Yuan, Serena Chang, Matthew H. Spitzer, Yaron Carmi, Jiahan Cheng, Lorna L. Tolentino, Okmi Choi, Nancy Wu, Christina S. Kong, Andrew J. Gentles, John B. Sunwoo, Ansuman T. Satpathy, Sylvia K. Plevritis, Edgar G. Engleman.
10.1016/j.cell.2022.04.019

Multiomics Analysis of Spatially Distinct Stromal Cells Reveals Tumor-Induced O-Glycosylation of the CDK4–pRB Axis in Fibroblasts at the Invasive Tumor Edge. Cancer Research. 82 (4):648-664 (2021)

Gina Bouchard, Fernando Jose Garcia-Marques, Loukia Georgiou Karacosta, Weiruo Zhang, Abel Bermudez; Nicholas McIlvain Riley, Sushama Varma, Lindsey Catherine Mehl, Jalen Anthony Benson, Joseph B. Shrager; Carolyn Ruth Bertozzi, Sharon J. Pitteri, Amato J. Giaccia, Sylvia Katina Plevritis.
https://doi.org/10.1158/0008-5472.CAN-21-1705

A radiogenomic dataset of non-small cell lung cancer. Scientific Data. 5:180202 (2018)

Shaimaa Bakr, Olivier Gevaert, Sebastian Echegaray, Kelsey Ayers, Mu Zhou, Majid Shafiq, Hong Zheng, Jalen Anthony Benson, Weiruo Zhang, Ann N. C. Leung, Michael Kadoch, Chuong D. Hoang, Joseph Shrager, Andrew Quon, Daniel L. Rubin, Sylvia K. Plevritis, Sandy Napel.
https://www.nature.com/articles/sdata2018202

Studying tumor metabolic reprogramming through integration of metabolomics and transcriptomics. Cancer Research. 78: 13 (2018)

Weiruo Zhang, Sylvia Plevritis
https://doi.org/10.1158/1538-7445.AM2018-1297

GFPT2-Expressing Cancer-Associated Fibroblasts Mediate Metabolic Reprogramming in Human Lung Adenocarcinoma. Cancer Research. 78 (13):3445-3457. (2018)

Weiruo Zhang, Gina Bouchard, Alice Yu, Majid Shafiq, Mehran Jamali, Joseph B. Shrager, Kelsey Ayers, Shaimaa Bakr, Andrew J. Gentles, Maximilian Diehn, Andrew Quon, Robert B. West, Viswam Nair, Matt van de Rijn, Sandy Napel, Sylvia K. Plevritis.
https://doi.org/10.1158/0008-5472.CAN-17-2928

Towards in vivo estimation of reaction kinetics using high-throughput metabolomics data: a maximum likelihood approach. BMC Systems Biology. 9:66 (2015)

Weiruo Zhang, Ritesh Kolte, David L Dill.
10.1186/s12918-015-0214-7

Liquid chromatography/mass spectrometry methods for measuring dipeptide abundance in non-small-cell lung cancer. Rapid Communications in Mass Spectrometry. 27 (18):2091-2098 (2013)

Manhong Wu, Yue Xu, William L. Fitch, Ming Zheng, Robert E. Merritt, Joseph B. Shrager, Weiruo Zhang, David L. Dill, Gary Peltz, Chuong D. Hoang
https://doi.org/10.1002/rcm.6656

Identification of drug targets by chemogenomic and metabolomic profiling in yeast. Pharmacogenetics and Genomics. 22(12):p 877-886 (2012)

Manhong Wu, Ming Zheng, Weiruo Zhang, Sundari Suresh, Ulrich Schlecht, William L Fitch, Sofia Aronova, Stephan Baumann, Ronald Davis, Robert St.Onge, David Dill, Gary Peltz.
10.1097/FPC.0b013e32835aa888