Wenpin Hou

Publications

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

Preprint

  • Wu, J., Wan, C., Ji, Z.*, Zhou, Y.* and Hou, W.* 2025. EpiFoundation: A Foundation Model for Single-Cell ATAC-seq via Peak-to-Gene Alignment. bioRxiv, 2025 February 8. Model: EpiFoundation.

  • Huang, X., Liu, Q., Zhao, Y., Tang, X., Zhou, Y.* and Hou, W.*. 2025. MethylProphet: A Generalized Gene-Contextual Model for Inferring Whole-Genome DNA Methylation Landscape. bioRxiv, 2025 February 8. Model: Methylprophet.

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

  • Lo, E.K., Idrizi, A., Tryggvadottir, R., Zhou, W., Hou, W., Ji, H., Cahan, P. and Feinberg, A.P. 2024. DNA methylation memory of pancreatic acinar-ductal metaplasia transition state altering Kras-downstream PI3K and Rho GTPase signaling in the absence of Kras mutation. bioRxiv, pp.2024-10.

  • 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.

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

Published

Application of GPT models
Single-cell genomics

  • Jackson, C., Cherry, C., Bom, S., Dykema, A., Wang, R., Thompson, E., Zhang, M., Li, R., Ji, Z., Hou, W., Li, R., Zhang, H. and Choi, J., Rodriguez, F., Weingart, J., Yegnasubramanian, S., Lim, M., Bettegowda, C., Powell, J., Eliesseff, J., Ji, H., and Pardoll, D. 2025. Distinct myeloid derived suppressor cell populations promote tumor aggression in glioblastoma. Science, 387(6713).

  • 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.