Wenpin Hou

Publications

For a complete list of publications, see also Google Scholar.

Preprint / Submitted

  • Hou, W.*, Shang, X., and Ji, Z.*, 2025. Benchmarking large language models for genomic knowledge with GeneTuring. bioRxiv, 2025 January 5. In Journal Review.

  • Hou, W.*, Liu, Q., Ma, H., Qu, Y., and Ji, Z.*, 2024. Assessing large multimodal models for one-shot learning and interpretability in biomedical image classification. bioRxiv, 2025 January 4. In Journal Review.

  • Zhuang, H., Gai, X., Zhang, A.R., Hou, W., Ji, Z., and Shi, P.*, 2024. Trajectory-guided dimensionality reduction for multi-sample single-cell RNA-seq data reveals biologically relevant sample-level heterogeneity. bioRxiv, pp.2024-09. In Journal Review.

  • Jackson, C.*, Cherry, C., Bom, S., Dykema, A., Thompson, E., Zheng, M., Ji, Z., Hou, W., Li, R., Zhang, H., Choi, J., Rodriguez, F., Weingart, J., Yegnasubramanian, S., Lim, M., Bettegowda, C.*, Powell, J.*, Eliesseff, J.*, Ji, H.*, and Pardoll, D.*, 2023. Distinct myeloid-derived suppressor cell populations promote tumor aggression in glioblastoma. bioRxiv, 2023 January 1. In Journal Review.

  • Hou, W.* and Ji, Z.*, 2022. Decomposing spatial heterogeneity of cell trajectories with Paella. bioRxiv, pp.2022-09. Software package: Paella.

Published / Accepted

Application of GPT models
Single-cell genomics

  • Montagne, J.M., Mitchell, J.T., Tandurella, J.A., Christenson, E.S., Danilova, L.V., Deshpande, A., Melanie L., Sidiropoulos, D.N., Davis-Marcisak, E.,Bergman, D.R., Zhu, Q., Wang, H., Kagohara, L.T., Engle, L.L., Green, B.F., Favorov, A.V., Ho, W.J., Lim, S.J., Zhang, R., Li, P., Gai, J., Mo, G., Mitchell, S., Wang, R., Vaghasia, A., Hou, W., Xu, Y., Zimmerman, J.W., Elisseeff, J.H., Yegnasubramanian, S., Anders, R.A., Jaffee, E.M., Zheng, L. and Fertig, E.J.* CD137 agonism enhances anti-PD1 induced activation of clonally expanded CD8+ T cells in a neoadjuvant pancreatic cancer clinical trial. iScience.

  • Hou, W., Ji, Z., Chen, Z., Wherry, E.J., Hicks, S.*, and Ji, H.* A statistical framework for differential pseudotime analysis with multiple single-cell RNA-seq samples. Nature Communications 14, 7286 (2023). Software package: Lamian.

  • Wang, Y., Wang, W., Liu, D., Hou, W., Zhou, T.*, Ji, Z.* GeneSegNet: a deep learning framework for cell segmentation by integrating gene expression and imaging. Genome Biology 24, 235 (2023). Software package: GeneSegNet

  • Dykema, A.G., Zhang, J., Cheung, L.S., Connor, S., Zhang, B., Zeng, Z., Cherry, C.M., Li, T., Caushi, J.X., Nishimoto, M., Munoz, A.J., Ji, Z., Hou, W., Zhan, W., Singh, D., Zhang, T., Rashid, R., Mitchell-Flack, M., Bom, S., Tam, A., Ionta, N., Aye, T.H.K., Wang, Y., Sawosik, C.A., Tirado, L.E., Tomasovic, L.M., Spangler, J.B., Anagnostou, W., Yang, S., Spicer, J., Rayes, R., Taube, J., Brahmer, J.R., Forde, P.M., Yegnasubramanian, S.*, Ji, H.*, Pardoll, M.*, and Smith K.N.*(2023). Lung tumor–infiltrating Treg have divergent transcriptional profiles and function linked to checkpoint blockade response. Science Immunology, 8(87). PMID: 37713507.

  • Hou, W., Ji, Z.* (2022). Palo: spatially-aware color palette optimization for single-cell and spatial data. Bioinformatics, June 01, 2022. Software package: Palo. PMID: 35642896. PMCID: PMC9272793.

  • Hou, W., Ji, Z.* (2022). Single-cell Unbiased Visualization with SCUBI. Cell Reports Methods, 100135, 2022. Software package: scubi. PMID: 35224531. PMCID: PMC8871596

  • Caushi, J.X., Zhang, J., Ji, Z., Vaghasia, A., Zhang, B., Hsiue, E., Mog, B., Hou, W., Justesen, S., Blosser, R., Tam, A., Anagnostou, V., Cottrell, T.R., Guo, H., Chan, H., Singh, D., Thapa, S., Dykema, A., Choudhury, C., Aparicio, L., Cheung, L., Lanis, M., Belcaid, Z., Asmar, M.E., Illei, P., Brock, M., Ha, J., Bush, E., Park, B., Bott, M., Naidoo, J., Marrone, K.A., Reuss, J.E., Velculescu, V.E., Chaft, J.E., Kinzler, K.W., Zhou, S., Vogelstein, B., Taube, J.M., Merghoub, T., Brahmer, J.R., Hellmann, M.D., Forde, P.M., Yegnasubramanian, S.*, Ji, H.*, Pardoll, D.M.*, Smith, K.N.* (2021). Transcriptional programs of neoantigen-specific TIL in anti-PD-1-treated lung cancers. Nature, July 21, 2021. PMID: 34290408 PMCID: PMC8338555.

  • Hou, W., Ji, Z., Ji, H.* and Hicks, S.C.*, (2020). A Systematic Evaluation of Single-cell RNA-sequencing Imputation Methods. Genome Biology 21, 218 (2020), doi: 10.1186/s13059-020-02132-x. PMID: 32854757. PMCID: PMC7450705. Links to: Code, Twitter.

  • Ji, Z., Zhou, W., Hou, W. and Ji, H.*, (2020). SCATE: Single-cell ATAC-seq Signal Extraction and Enhancement. Genome Biology, 21,161 (2020). doi: 10.1186/s13059-020-02075-3. PMID: 32620137. PMCID: PMC7333383. Links to: Software package: SCATE, SCATEData.

Boolean networks

  • Hou, W., Ruan, P., Ching, W.K. and Akutsu, T.*, (2019). On the number of driver nodes for controlling a Boolean network when the targets are restricted to attractors. Journal of Theoretical Biology, 463, pp.1-11. doi:10.1016/j.jtbi.2018.12.012.

  • Hou, W., Tamura, T., Ching, W.K. and Akutsu, T.*, (2016). Finding and analyzing the minimum set of driver nodes in control of Boolean networks. Advances in Complex Systems, 19(03), p.1650006. doi: 10.1142/S0219525916500065.

Glycosylation networks
  • Hou, W., Qiu, Y., Hashimoto, N., Ching, W.K. and Aoki-Kinoshita, K.F.*, (2016). A systematic framework to derive N-glycan biosynthesis process and the automated construction of glycosylation networks. BMC Bioinformatics, 17(7), p.240. doi:10.1186/s12859-016-1094-6.
Epigenetics
Machine learning

  • Jiang, H., Qiu, Y., Hou, W., Cheng, X., Yim, M. and Ching, W.K.*, (2018). Drug side-effect profiles prediction: from empirical risk minimization to structural risk minimization. IEEE/ACM Transactions on Computational Biology and Bioinformatics. doi:10.1109/TCBB.2018.2850884.

  • Jiang, H.*, Ching, W.K., Cheung, W.S., Hou, W. and Yin, H., (2017). Hadamard kernel SVM with applications for breast cancer outcome predictions. BMC Systems Biology, 11(7), p.138. doi:10.1186/s12918-017-0514-1.

  • Jiang, H.*, Ching, W.K. and Hou, W., (2016). On orthogonal feature extraction model with applications in medical prognosis. Applied Mathematical Modelling, 40(19-20), pp.8766-8776. doi:10.1016/j.apm.2016.05.011.

  • Hou, W.*, Chen,Y. and Zhang, Y., (2012) Investigation of Heavy Metal Pollution on Urban Topsoil. Economic Life Digest (in Chinese), 15, pp.204-206. [ISSN1009 – 5535]

Obesity and maternal health

  • Hou, W.*, Zhang, M., Ji, Y., Hong, X., Wang, G., Xu, R., Liang, L., Saria, S. and Ji, H. (2022) A prospective birth cohort study of maternal prenatal cigarette smoking assessed by self-report and biomarkers on childhood risk of overweight or obesity. Precision Nutrition, 1(3), e00017, doi: 10.1097/PN9.0000000000000017.

  • Huang, W., Igusa, T., Wang, G., Buckley, J.P., Hong, X., Bind, E., Steffens, A., Mukherjee, J., Haltmeier, D., Ji, Y., Xu, R., Hou, W., Fan, Z., and Wang, X.* (2022) In-utero co-exposure to toxic metals and micronutrients on childhood risk of overweight or obesity: new insight on micronutrients counteracting toxic metals. International Journal of Obesity, 46, 1435–1445. PMID: 35589962. PMCID: PMC9329205.

Psychiatry

Posters

* Corresponding author.