José L. McFaline-Figueroa


Jose L. McFaline-Figueroa’s research focuses on defining the molecular changes induced in cancer cells after exposure to anti-cancer therapy, how those changes alter response to treatment and how they differ as a function of the genetic background of individual cancer cells.

Research Interests

Single-cell Genomics, Multiplex Molecular Screens, Genome Engineering, Cancer Biology, Computational Biology

The goal of the lab is to leverage these functional atlases of cellular response to arrive at novel treatments against cancer, with a particular focus on aggressive tumor types that frequently fail the current standard-of-care.

McFaline-Figueroa’s approach includes the development and application of tools centered around single-cell genomics, multiplex genome editing and chemical genetics. These techniques increase the scale at which we can determine how chemical and genetic perturbations alter molecular phenotypes and how those phenotypes vary due to the cellular heterogeneity observed between and within tumors.

José L. McFaline-Figueroa received his bachelor’s degree in Chemistry from the University of Puerto Rico at Mayagüez (2006) and his PhD in Biology from the Massachusetts Institute of Technology (2014). He was a postdoctoral fellow at the University of Washington (2015-2020).


  • Postdoctoral Fellow, University of Washington, 2015-2020


  • Assistant Professor of Biomedical Engineering, Columbia University, 2021-


  • NIH Ruth L. Kirschstein National Research Service Award


  • Srivatsan, S.*, McFaline-Figueroa, J.L.*, Ramani, V.*, Saunders, L., Cao, J., Packer, J., Pliner, H.A., Jackson, D., Daza, R., Christiansen, L., Zhang, F., Steemers, F., Shendure, J. and Trapnell, C. 2020. Massively multiplex chemical transcriptomics at single cell resolution. Science, 367(6473), p.45-51. doi: 10.1126/science.aax6234.
  • McFaline-Figueroa, J.L., Hill, A.J., Qiu, X., Jackson, D., Shendure, J. and Trapnell, C. 2019. A pooled single-cell genetic screen identifies regulatory barriers in the continuum of the epithelial to mesenchymal transition. Nature Genetics, 51, p. 1389-1398. doi: 10.1038/s41588-019-0489-5.
  • Gasperini, M., Hill, A.J., McFaline-Figueroa, J.L., Martin, B., Kim, S., Zhang, M.D., Jackson, D., Leith, A., Schreiber, J., Noble, W.S., Trapnell, C. Ahituv, N and Shendure, J. 2019. A genome-wide framework for mapping gene regulation via cellular genetic screens. Cell, 176(1-2), p. 377-390. doi: 10.1016/j.cell.2018.11.029.
  • Jean-Baptiste, K. McFaline-Figueroa, J.L., Alexandre, C.M., Dorrity, M.W., Saunders, L., Bubb, K.L., Trapnell, C. Fields, S., Queitsch, C. and Cuperus, J.T. 2019. Dynamics of Gene Expression in Single Root Cells of Arabidopsis thaliana. Plant Cell, 31(5), p. 993-1011. doi: 10.1105/tpc.18.00785.
  • Hill, A.J.*, McFaline-Figueroa, J.L.*, Starita, L.M., Gasperini, M.J., Matreyek, K.A., Packer, J., Jackson, D., Shendure, J. and Trapnell, C. 2018. On the design of CRISPR-based single-cell molecular screens. Nat Methods, 15(4), p. 271-274. doi: 10.1038/nmeth.4604.
  • Pliner, H., Packer, J., McFaline-Figueroa, J.L., Cusanovich, D., Daza, R., Aghamirzaie, D., Srivatsan, S., Qiu, X., Jackson, D., Minkina, A., Adey, A., Steemers, F., Shendure, J. and Trapnell, C. 2018. Cicero predicts cis-regulatory DNA interaction from single-cell chromatin accessibility data. Mol Cell, 71(5), p. 858-871. doi: 10.1016/j.molcel.2018.06.044.
  • McFaline-Figueroa, J.L., Braun, C., Stanciu, M., Nagel, Z., Mazzucato, P., Sangaraju, D., Cerniauskas, E., Barford, K., Vargas, A., Chen, Y., Tretyakova, N., Lees, J.A., Hemann, M.T., White, F.M. and Samson, L.D. 2015. Minor changes in expression of the mismatch repair protein MSH2 exert a major impact on glioblastoma response to temozolomide. 2015. Cancer Res, 75(15), p. 3127-3138. doi: 10.1158/0008-5472.CAN-14-3616.
  • Valiathan, C., McFaline, J.L., Samson, L.D. 2012. A Rapid survival assay to measure drug-induced cytotoxicity and cell cycle effects. DNA Repair. 11(1), p. 92-98. doi: 10.1016/j.dnarep.2011.11.002.