Wenpin Hou

Publications

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

Preprint / Submitted

  • Hou, W., and Ji, Z., 2024. A systematic evaluation of large language models for generating programming code. Preprint in arXiv, 2024 March 1. In Journal Review.

  • Hou, W., and Ji, Z., 2024. GPT-4V exhibits human-like performance in biomedical image classification. Preprint in bioRxiv, 2024 January 1. In Journal Review.

  • Hou, W. and Ji, Z., 2023 GeneTuring tests GPT models in genomics. Preprint in bioRxiv, 2023 March 13. In Journal Review.

  • Jackson, C., Cherry, C., Bom, S., Dykema, A., Thompson, E., Zheng, M., 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., 2023. Distinct myeloid derived suppressor cell populations promote tumor aggression in glioblastoma. Preprint in bioRxiv, 2023 Jan 1. In Journal Review.

  • Hou, W. and Ji, Z., 2022. Decomposing spatial heterogeneity of cell trajectories with Paella. Preprint in bioRxiv. Software package: Paella. In Journal Review.

Published / Accepted

Single-cell genomics

  • Hou, W.* and Ji, Z.*, 2023. Reference-free and cost-effective automated cell type annotation with GPT-4 in single-cell RNA-seq analysis. Nature Methods, 2024 March 25. Software package: GPTCelltype. Featured in Columbia News Spotlight, Columbia MSPH News, Science Daily, The Medical News, Health Tech World, and 6 other news outlets. It ranked the top #1 when comparing to 69 others from the same source and published within six weeks.

  • 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.