• Hou, W. and Ji, Z., (2023). Reference-free and cost-effective automated cell type annotation with GPT-4 in single-cell RNA-seq analysis. Preprint in bioRxiv, 2023 April 21Software package: GPTCelltype. In Revision for Nature Methods.
  • Hou, W. and Ji, Z. (2023) GeneTuring tests GPT models in genomics. Preprint in bioRxiv, 2023 March 13In 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 1In Journal Review.
  • Hou, W. and Ji, Z. (2022) Decomposing spatial heterogeneity of cell trajectories with Paella. Preprint in bioRxivSoftware package: PaellaIn Journal Review.


Single-cell genomics

  • 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, 2022Software package: Palo. PMID: 35642896. PMCID: PMC9272793.
  • Hou, W., Ji, Z.* (2022). Single-cell Unbiased Visualization with SCUBI. Cell Reports Methods, 100135, 2022Software 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: CodeTwitter.
  • 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: SCATESCATEData.

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.


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.



* Corresponding author.

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