Daifeng Wang, PhD

Position title: H.I. Romnes Associate Professor, Biostatistics & Medical Informatics, Computer Sciences

PhD, University of Texas – Austin
Postdoc, Yale University
Core Director, Data Science

Contact Information

Waisman Center
1500 Highland Avenue
Room 517
Madison, WI 53705
daifeng.wang@wisc.edu
Daifeng Lab

Research Statement

Daifeng’s lab develops machine learning and artificial intelligence (ML/AI) approaches and bioinformatics tools to bridge computation and biology for mechanistic insights into neurodevelopmental and neurodegenerative diseases. His applications focus on functional genomics, gene regulation, cell dynamics and neural circuits.

Selected Publications

Pubmed

West, N. R., Arachchilage, K. H., Knaack, S., MacGregor, S., Hosseini, M., Risgaard, R. D., Kumarage, P., Martinez, J. L., Zhang, S. C., Wang, D., Sousa, A. M. M., & Bhattacharyya, A. (2025). Single-nucleus analysis reveals oxidative stress in Down syndrome basal forebrain neurons at birth. Alzheimer’s & dementia : the journal of the Alzheimer’s Association, 21(7), e70445. https://doi.org/10.1002/alz.70445
Risgaard, R. D., Arachchilage, K. H., Knaack, S. A., Hosseini, M., Chen, R. J., Kumarage, P., Schmidt, D. K., Huang, X., Sheng, J., Wang, C. J., Giusti, E., Liu, S., Zhang, S. C., Wang, D., Bhattacharyya, A., & Sousa, A. M. M. (2025). Molecular and cellular processes disrupted in the early postnatal Down syndrome prefrontal cortex. bioRxiv : the preprint server for biology, 2025.06.30.662385. https://doi.org/10.1101/2025.06.30.662385
Gao, Y., Dong, Q., Arachchilage, K. H., Risgaard, R., Sheng, J., Syed, M., Schmidt, D. K., Jin, T., Liu, S., Knaack, S. A., Doherty, D., Glass, I., Levine, J. E., Wang, D., Chang, Q., Zhao, X., & Sousa, A. M. (2025). Multimodal analyses reveal genes driving electrophysiological maturation of neurons in the primate prefrontal cortex. Neuron, S0896-6273(25)00308-3. Advance online publication. https://doi.org/10.1016/j.neuron.2025.04.025
Choi, J. J., Svaren, J., & Wang, D. (2025). CoTF-reg reveals cooperative transcription factors in oligodendrocyte gene regulation using single-cell multi-omics. Communications biology, 8(1), 181. https://doi.org/10.1038/s42003-025-07570-6
Huang, X., Kumarage, P., Sandoval, S., Zhao, X., & Wang, D. (2024). Protocol for comparative gene expression data analysis between brains and organoids using a cloud-based web app. STAR protocols, 5(4), 103375. https://doi.org/10.1016/j.xpro.2024.103375
Khullar, S., Huang, X., Ramesh, R., Svaren, J., & Wang, D. (2024). NetREm: Network Regression Embeddings reveal cell-type transcription factor coordination for gene regulation. Bioinformatics advances, 5(1), vbae206. https://doi.org/10.1093/bioadv/vbae206
Huang, X., Kalafut, N. C., Alatkar, S., Li, A. Z., Dong, Q., Chang, Q., & Wang, D. (2024). NeuroTD: A Time-Frequency Based Multimodal Learning Approach to Analyze Time Delays in Neural Activities. bioRxiv : the preprint server for biology, 2024.10.28.620662. https://doi.org/10.1101/2024.10.28.620662
Shen, M., Sirois, C. L., Guo, Y., Li, M., Dong, Q., Méndez-Albelo, N. M., Gao, Y., Khullar, S., Kissel, L., Sandoval, S. O., Wolkoff, N. E., Huang, S. X., Xu, Z., Bryan, J. E., Contractor, A. M., Korabelnikov, T., Glass, I. A., Doherty, D., Birth Defects Research Laboratory, Levine, J. E., … Zhao, X. (2023). Species-specific FMRP regulation of RACK1 is critical for prenatal cortical development. Neuron, 111(24), 3988–4005.e11. https://doi.org/10.1016/j.neuron.2023.09.014
Chandrashekar, P. B., Alatkar, S., Wang, J., Hoffman, G. E., He, C., Jin, T., Khullar, S., Bendl, J., Fullard, J. F., Roussos, P., & Wang, D. (2023). DeepGAMI: deep biologically guided auxiliary learning for multimodal integration and imputation to improve genotype-phenotype prediction. Genome medicine, 15(1), 88. https://doi.org/10.1186/s13073-023-01248-6
Alatkar, S. A., & Wang, D. (2023). CMOT: Cross-Modality Optimal Transport for multimodal inference. Genome biology, 24(1), 163. https://doi.org/10.1186/s13059-023-02989-8
Guo, Y., Shen, M., Dong, Q., Méndez-Albelo, N. M., Huang, S. X., Sirois, C. L., Le, J., Li, M., Jarzembowski, E. D., Schoeller, K. A., Stockton, M. E., Horner, V. L., Sousa, A. M. M., Gao, Y., Birth Defects Research Laboratory, Levine, J. E., Wang, D., Chang, Q., & Zhao, X. (2023). Elevated levels of FMRP-target MAP1B impair human and mouse neuronal development and mouse social behaviors via autophagy pathway. Nature communications, 14(1), 3801. https://doi.org/10.1038/s41467-023-39337-0
Lear, B. P., Thompson, E. A. N., Rodriguez, K., Arndt, Z. P., Khullar, S., Klosa, P. C., Lu, R. J., Morrow, C. S., Risgaard, R., Peterson, E. R., Teefy, B. B., Bhattacharyya, A., Sousa, A. M. M., Wang, D., Benayoun, B. A., & Moore, D. L. (2023). Age-maintained human neurons demonstrate a developmental loss of intrinsic neurite growth ability. bioRxiv : the preprint server for biology, 2023.05.23.541995. https://doi.org/10.1101/2023.05.23.541995
He, C., Kalafut, N. C., Sandoval, S. O., Risgaard, R., Sirois, C. L., Yang, C., Khullar, S., Suzuki, M., Huang, X., Chang, Q., Zhao, X., Sousa, A. M. M., & Wang, D. (2023). BOMA, a machine-learning framework for comparative gene expression analysis across brains and organoids. Cell reports methods, 3(2), 100409. https://doi.org/10.1016/j.crmeth.2023.100409
Gandal, M. J., Haney, J. R., Wamsley, B., Yap, C. X., Parhami, S., Emani, P. S., Chang, N., Chen, G. T., Hoftman, G. D., de Alba, D., Ramaswami, G., Hartl, C. L., Bhattacharya, A., Luo, C., Jin, T., Wang, D., Kawaguchi, R., Quintero, D., Ou, J., Wu, Y. E., … Geschwind, D. H. (2022). Broad transcriptomic dysregulation occurs across the cerebral cortex in ASD. Nature, 611(7936), 532–539. https://doi.org/10.1038/s41586-022-05377-7
Gupta, C., Xu, J., Jin, T., Khullar, S., Liu, X., Alatkar, S., Cheng, F., & Wang, D. (2022). Single-cell network biology characterizes cell type gene regulation for drug repurposing and phenotype prediction in Alzheimer’s disease. PLoS Computational Biology, 18(7), e1010287. https://doi.org/10.1371/journal.pcbi.1010287
Giffin-Rao, Y., Sheng, J., Strand, B., Xu, K., Huang, L., Medo, M., Risgaard, K. A., Dantinne, S., Mohan, S., Keshan, A., Daley, R. A., Jr, Levesque, B., Amundson, L., Reese, R., Sousa, A., Tao, Y., Wang, D., Zhang, S. C., & Bhattacharyya, A. (2022). Altered patterning of trisomy 21 interneuron progenitors. Stem cell reports, 17(6), 1366–1379. https://doi.org/10.1016/j.stemcr.2022.05.001
Javadi, S., Li, Y., Sheng, J., Zhao, L., Fu, Y., Wang, D., & Zhao, X. (2022). Sustained correction of hippocampal neurogenic and cognitive deficits after a brief treatment by Nutlin-3 in a mouse model of fragile X syndrome. BMC medicine, 20(1), 163. https://doi.org/10.1186/s12916-022-02370-9
Gupta, C., Chandrashekar, P., Jin, T., He, C., Khullar, S., Chang, Q., & Wang, D. (2022). Bringing machine learning to research on intellectual and developmental disabilities: taking inspiration from neurological diseases. Journal of neurodevelopmental disorders, 14(1), 28. https://doi.org/10.1186/s11689-022-09438-w
Fathi, A., Mathivanan, S., Kong, L., Petersen, A. J., Harder, C., Block, J., Miller, J. M., Bhattacharyya, A., Wang, D., & Zhang, S. C. (2022). Chemically induced senescence in human stem cell-derived neurons promotes phenotypic presentation of neurodegeneration. Aging cell, 21(1), e13541. https://doi.org/10.1111/acel.13541
Lin, C. X., Li, H. D., Deng, C., Liu, W., Erhardt, S., Wu, F. X., Zhao, X. M., Guan, Y., Wang, J., Wang, D., Hu, B., & Wang, J. (2022). An integrated brain-specific network identifies genes associated with neuropathologic and clinical traits of Alzheimer’s disease. Briefings in bioinformatics, 23(1), bbab522. https://doi.org/10.1093/bib/bbab522
Nguyen, N. D., Huang, J., & Wang, D. (2022). A deep manifold-regularized learning model for improving phenotype prediction from multi-modal data. Nature computational science, 2(1), 38–46. https://doi.org/10.1038/s43588-021-00185-x
Huang, J., Sheng, J., & Wang, D. (2021). Manifold learning analysis suggests strategies to align single-cell multimodal data of neuronal electrophysiology and transcriptomics. Communications biology, 4(1), 1308. https://doi.org/10.1038/s42003-021-02807-6
Shen, M., Guo, Y., Dong, Q., Gao, Y., Stockton, M. E., Li, M., Kannan, S., Korabelnikov, T., Schoeller, K. A., Sirois, C. L., Zhou, C., Le, J., Wang, D., Chang, Q., Sun, Q. Q., & Zhao, X. (2021). FXR1 regulation of parvalbumin interneurons in the prefrontal cortex is critical for schizophrenia-like behaviors. Molecular psychiatry, 26(11), 6845–6867. https://doi.org/10.1038/s41380-021-01096-z
Nguyen, N. D., Jin, T., & Wang, D. (2021). Varmole: a biologically drop-connect deep neural network model for prioritizing disease risk variants and genes. Bioinformatics (Oxford, England), 37(12), 1772–1775. https://doi.org/10.1093/bioinformatics/btaa866
Jin, T., Rehani, P., Ying, M., Huang, J., Liu, S., Roussos, P., & Wang, D. (2021). scGRNom: a computational pipeline of integrative multi-omics analyses for predicting cell-type disease genes and regulatory networks. Genome medicine, 13(1), 95. https://doi.org/10.1186/s13073-021-00908-9
Jin, T., Nguyen, N. D., Talos, F., & Wang, D. (2021). ECMarker: interpretable machine learning model identifies gene expression biomarkers predicting clinical outcomes and reveals molecular mechanisms of human disease in early stages. Bioinformatics (Oxford, England), 37(8), 1115–1124. https://doi.org/10.1093/bioinformatics/btaa935
Huang, K., Wu, Y., Shin, J., Zheng, Y., Siahpirani, A. F., Lin, Y., Ni, Z., Chen, J., You, J., Keles, S., Wang, D., Roy, S., & Lu, Q. (2021). Transcriptome-wide transmission disequilibrium analysis identifies novel risk genes for autism spectrum disorder. PLoS genetics, 17(2), e1009309. https://doi.org/10.1371/journal.pgen.1009309
Gao Y, Shen M, Gonzalez JC, Dong Q, Kannan S, Hoang JT, Eisinger BE, Pandey J, Javadi S, Chang Q, Wang D, Overstreet-Wadiche L, Zhao X. (2020). RGS6 Mediates Effects of Voluntary Running on Adult Hippocampal Neurogenesis. Cell Reports, 32(5):107997. doi: 10.1016/j.celrep.2020.107997.
Nguyen ND, Wang D. (2020). Multiview learning for understanding functional multiomics. PLoS Computational Biology, 16(4):e1007677. doi: 10.1371/journal.pcbi.1007677.
Yan KK, Wang D, Xiong K, Gerstein M. (2020). Comparing Technological Development and Biological Evolution from a Network Perspective. Cell Systems, 10(3):219-222. doi: 10.1016/j.cels.2020.02.004.
Nguyen ND, Blaby IK, Wang D. (2019). ManiNetCluster: a novel manifold learning approach to reveal the functional links between gene networks. BMC Genomics. 2019 Dec 30;20(Suppl 12):1003. doi: 10.1186/s12864-019-6329-2.
Gandal MJ, Zhang P, Hadjimichael E, Walker RL, Chen C, Liu S, Won H, van Bakel H, Varghese M, Wang Y, Shieh AW, Haney J, Parhami S, Belmont J, Kim M, Moran Losada P, Khan Z, Mleczko J, Xia Y, Dai R, Wang D, Yang YT, Xu M, Fish K, Hof PR, Warrell J, Fitzgerald D, White K, Jaffe AE; PsychENCODE Consortium, Peters MA, Gerstein M, Liu C, Iakoucheva LM, Pinto D, Geschwind DH. (2018). Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder. Science, 362(6420). pii: eaat8127. doi: 10.1126/science.aat8127.
Wang D, Liu S, Warrell J, Won H, Shi X, Navarro FCP, Clarke D, Gu M, Emani P, Yang YT, Xu M, Gandal MJ, Lou S, Zhang J, Park JJ, Yan C, Rhie SK, Manakongtreecheep K, Zhou H, Nathan A, Peters M, Mattei E, Fitzgerald D, Brunetti T, Moore J, Jiang Y, Girdhar K, Hoffman GE, Kalayci S, Gümüş ZH, Crawford GE; PsychENCODE Consortium, Roussos P, Akbarian S, Jaffe AE, White KP, Weng Z, Sestan N, Geschwind DH, Knowles JA, Gerstein MB. (2018). Comprehensive functional genomic resource and integrative model for the human brain. Science, 362(6420). pii: eaat8464. doi: 10.1126/science.aat8464.
Wang D, He F, Maslov S, Gerstein M. (2016). DREISS: Using State-Space Models to Infer the Dynamics of Gene Expression Driven by External and Internal Regulatory Networks. PLoS Computational Biology, 12(10):e1005146. doi: 10.1371/journal.pcbi.1005146.
Wang D, Yan KK, Rozowsky J, Pan E, Gerstein M. (2016). Temporal Dynamics of Collaborative Networks in Large Scientific Consortia. Trends in Genetics, 32(5):251-253. doi: 10.1016/j.tig.2016.02.006.
Yan KK, Wang D, Sethi A, Muir P, Kitchen R, Cheng C, Gerstein M. (2016). Cross-Disciplinary Network Comparison: Matchmaking Between Hairballs. Cell Systems, 23;2(3):147-157.
Wang D, Yan KK, Sisu C, Cheng C, Rozowsky J, Meyerson W, Gerstein MB. (2015). Loregic: a method to characterize the cooperative logic of regulatory factors. PLoS Computational Biology, 11(4):e1004132. doi: 10.1371/journal.pcbi.1004132.
Comparative analysis of regulatory information and circuits across distant species. (2014). Boyle AP, Araya CL, Brdlik C, Cayting P, Cheng C, Cheng Y, Gardner K, Hillier LW, Janette J, Jiang L, Kasper D, Kawli T, Kheradpour P, Kundaje A, Li JJ, Ma L, Niu W, Rehm EJ, Rozowsky J, Slattery M, Spokony R, Terrell R, Vafeados D, Wang D, Weisdepp P, Wu YC, Xie D, Yan KK, Feingold EA, Good PJ, Pazin MJ, Huang H, Bickel PJ, Brenner SE, Reinke V, Waterston RH, Gerstein M, White KP, Kellis M, Snyder M. Nature, 512(7515):453-6. doi: 10.1038/nature13668.