Publications

* Equal contribution

† Co-correspondence

Highlights

• Qin, Y., Huttlin, E. L., Winsnes, C. F., …, Yeo, G. W., Lafontaine, D. LJ., Lundberg, E.†, and Ideker, T. † (2021). A multi-scale map of cell structure fusing protein images and interactions. Nature.
  • Paper
  • Portal page
  • GitHub repo
  • In press

All Publications

• Walton, R. T., Qin, Y., Blainey, P. C. (2024). CROPseq-multi: a versatile solution for multiplexed perturbation and decoding in pooled CRISPR screens. bioRxiv.
• Kratz, A.*, Kim, M.*, Kelly, M., …, Qin, Y., …, Sobol, R. W. †, Krogan N. † & Ideker, T. † (2023). A multi-scale map of protein assemblies in the DNA damage response. Cell Systems.
• Qin, Y., Huttlin, E. L., Winsnes, C. F., …, Yeo, G. W., Lafontaine, D. LJ., Lundberg, E.† & Ideker, T. † (2021). A multi-scale map of cell structure fusing protein images and interactions. Nature.
• CSBC/PS-ON Image Analysis Working Group. (2022). A community-based approach to image analysis of cells, tissues and tumors. Computerized Medical Imaging and Graphics.
• Dang, J., Tiwari, S. K., …, Qin, Y., & Rana, T. M. (2021). Cellular diversity of human cerebral organoids revealed by single cell RNA-seq. Molecular Psychiatry.
• Dang, J.*, Tiwari, S. K.*, …, Qin, Y., & Rana, T. M. (2021). Glial cell diversity and metham-phetamine-induced neuroinflammation in human cerebral organoids. Molecular Psychiatry.
• Tiwari, S. K.*, Dang, J. W.*, Lin, N., Qin, Y., Wang, S., & Rana, T. M. (2020). Zika virus depletes neural stem cells and evades selective autophagy by suppressing the Fanconi anemia protein FANCC. EMBO Reports, 21(12), e49183.
• Carlin, D. E.*, Fong, S. H.*, Qin, Y., Jia, T., Huang, J. K., Bao, B., Zhang, C., & Ideker, T. (2019). A Fast and Flexible Framework for Network-Assisted Genomic Association. iScience.
• Fong, S. H., Carlin, D. E., Ozturk, K., …, Qin, Y., … & Ideker, T. (2019). Strategies for network GWAS evaluated using classroom crowd science. Cell Systems, 8(4), 275-280.
  • In press
• Chao, T.-C.*, Zhang, Q.*, …, Qin, Y., … & Rana, T. M. (2019). The Long Noncoding RNA HEAL Regulates HIV-1 Replication through Epigenetic Regulation of the HIV-1 Promoter. mBio.
• Dang, J. W., Tiwari, S. K., Qin, Y., & Rana, T. M. (2019). Genome-wide Integrative Analysis of Zika-Virus-Infected Neuronal Stem Cells Reveals Roles for MicroRNAs in Cell Cycle and Stemness. Cell Reports, 27(12), 3618–3628.e5.
• Zhang, Q.*, Chao, T.-C.*, Patil, V. S.*, Qin, Y., … & Rana, T. M. (2019). The long noncoding RNA ROCKI regulates inflammatory gene expression. The EMBO Journal, 38(8).
• Tiwari, S. K.*, Dang, J.*, Qin, Y., … & Rana, T. M. (2017). Zika virus infection reprograms global transcription of host cells to allow sustained infection. Emerging Microbes & Infections.
• Lichinchi, G.*, Zhao, B. S.*, Wu, Y., Lu, Z., Qin, Y., He, C., & Rana, T. M. (2016). Dynamics of human and viral RNA methylation during Zika virus infection. Cell Host & Microbe.
• Dang, J.*, Tiwari, S. K.*, Lichinchi, G., Qin, Y., Patil, V. S., Eroshkin, A. M., & Rana, T. M. (2016). Zika Virus Depletes Neural Progenitors in Human Cerebral Organoids through Activation of the Innate Immune Receptor TLR3. Cell Stem Cell, 19(2), 258–265.