Patents

Leff, E., Tseng, A., Cheung, V., Gupte, R., Tabari, E., Vallania, F., Donnella, H., St. John, J., Lovejoy, A., Ulz, P. “Methods and systems for inferring gene expression using cell-free DNA fragments.” US Patent Application US20250305061A1, filed March 27, 2025, pending. Freenome Holdings, Inc.
Computational methods for inferring gene expression from cell-free DNA sequencing data.

Publications

* denotes equal contribution

2025

Reck, M., Gupte, R., Qing, T., Cheung, V., Tang, A.D., et al. “Machine learning classification of small cell lung cancer using plasma multiomics in IMPower133.” Annals of Oncology.

Cauwels, A.* , Levy, E.* , Tang, AD.* , __Cheung, V.__ , et al. “Plasma-based multimodal profiling of urothelial carcinoma to characterize tissue-based subtypes.” *Cancer Research 85(8_Supplement_1): 3679.

2024

Herault, A., Mak, J., de la Cruz-Chuh, J., Dillon, MA., Ellerman, D., Go, M., Cosino, E., Clark, R., Carson, E., Yeung, S., Pichery, M., Gador, M., Chiang, EY., Wu, J., Liang, Y., Modrusan, Z., Gampa, G., Sudhamsu, J., Kemball, CC., Cheung, V., Nguyen, TTT., Seshasayee, D., Piskol, R., Totpal, K., Yu, SF., Lee, G., Kozak, KR., Spiess, C., Walsh, KB, “NKG2D-bispecific enhances NK and CD8+ T cell antitumor immunity.” Cancer Immunology, Immunotherapy 73.10 (2024): 1-16.

Tang, AD.* , Gupte, R.* , Cheung, V.* , Qing, T. * , Cauwels, A., Leff, E., Walter, K., Tabari, E., Lovejoy, A., Lin, CHJ. “Noninvasive longitudinal monitoring of residual disease in chemotherapy-treated colorectal cancer patients.” Cancer Research 84(6): 6258.

Leff, E.* , Tseng, A.* , Cheung, V., Tabari, E., Walter, K., Lovejoy, A., Lin, CHJ. “Inference of gene expression using fragmentation patterns from targeted high-depth sequencing of cell-free DNA.” Cancer Research, 84(6_Supplement), 2024, 4788.

2023

Vallania, F.* , Cheung, V.* , Tripathi, A., Louie, M., Snyder, T., Lin, CHJ., Havenith, K., Qin, Y., Pantano, S., Wuerthner, J., van Berkel P.H.; “Discovery of plasma protein biomarkers associated with overall survival in R/R DLBCL patients treated with loncastuximab tesirine.” Cancer Res 1 April 2023; 83 (7_Supplement): 5387.

2022

Vallania, F., Cheung, V., Zamba, MD., Liu, J., Pasupathy, A., Donnella, H., Bailey, M., Louie, M., Lin, CHJ., Havenith, K., Qin, Y., Pantano, S., Wuerthner, J., van Berkel, PH.; “Identification of Predictive Biomarkers for Response of R/R DLBCL Patients Treated with Loncastuximab Tesirine Using Low Pass Whole-Genome Sequencing (WGS).” Blood 2022; 140 (Supplement 1): 3551–3552.

Cheung, V., Chung, P., and Feinberg, EH. (2022) “Transcriptional profiling of mouse projection neurons with VECTORseq” STAR Protocols, 3(3):101625

2021

Cheung, V., Chung, P., Bjorni, M.* , Shvareva, VA.* , Lopez, YC., and Feinberg, EH. (2021) “Virally Encoded Connectivity Transgenic Overlay RNA sequencing (VECTORseq) defines projection neurons involved in sensorimotor integration.” Cell Reports, 37(12):110131

2020

Cheung, V. “Predicting Acute Kidney Injury in Hospitalized Patients Using Machine Learning” Towards Data Science. Medium, 20 Jun. 2020. Web.

2014

Cheung, V., Mullins, O., Nguyen, P., Huberman, AD. “Extreme binocular plasticity and dynamic strategy implementation supports vision-dependent prey capture in cuttlefish.” Proceedings of the SACNAS National Conference, 2014, p. 1159.