Ibrahim Cissé

Ibrahim Cissé

Associate Professor of Physics and Biology

Ibrahim Cissé develops single-molecule and super-resolution approaches to study protein clustering, biomolecular condensation in transcription, and other processes in living cells.





Karen Sagna



Assistant Phone


  • PhD, 2009, University of Illinois at Urbana-Champaign
  • BS, 2004, Physics, North Carolina Central University

Research Summary

We leverage our expertise in single-molecule and super-resolution imaging in live mammalian cells to study collective behaviors (e.g., protein clustering), which emerge from weak or transient biomolecular interactions. We unveil, often for the first time, that these clusters exist in living cells, and expand on imaging approaches — as well as cellular and molecular biology techniques — to discover the biophysical mechanisms of action and their function in vivo. The Cissé will be moving to Caltech in 2021, and is no longer accepting students at MIT.


  • Vilcek Prize for Creative Promise in Biomedical Science, 2020
  • Everett Moor Baker Award for Excellence in Undergrad Teaching, 2019
  • Next Einstein Forum, Fellow, 2019
  • Science News (SN10) Scientist To Watch, 2018
  • Biomedical Scholar, PEW Charitable Trust, 2017
  • NIH Director’s New Innovator Award, 2014

Recent Publications

  1. The dynamic clustering of insulin receptor underlies its signaling and is disrupted in insulin resistance. Dall'Agnese, A, Platt, JM, Zheng, MM, Friesen, M, Dall'Agnese, G, Blaise, AM, Spinelli, JB, Henninger, JE, Tevonian, EN, Hannett, NM et al.. 2022. Nat Commun 13, 7522.
    doi: 10.1038/s41467-022-35176-7PMID:36473871
  2. Hijacking of transcriptional condensates by endogenous retroviruses. Asimi, V, Sampath Kumar, A, Niskanen, H, Riemenschneider, C, Hetzel, S, Naderi, J, Fasching, N, Popitsch, N, Du, M, Kretzmer, H et al.. 2022. Nat Genet 54, 1238-1247.
    doi: 10.1038/s41588-022-01132-wPMID:35864192
  3. A dual role for H2A.Z.1 in modulating the dynamics of RNA polymerase II initiation and elongation. Mylonas, C, Lee, C, Auld, AL, Cisse, II, Boyer, LA. 2021. Nat Struct Mol Biol 28, 435-442.
    doi: 10.1038/s41594-021-00589-3PMID:33972784
  4. RNA-Mediated Feedback Control of Transcriptional Condensates. Henninger, JE, Oksuz, O, Shrinivas, K, Sagi, I, LeRoy, G, Zheng, MM, Andrews, JO, Zamudio, AV, Lazaris, C, Hannett, NM et al.. 2021. Cell 184, 207-225.e24.
    doi: 10.1016/j.cell.2020.11.030PMID:33333019
  5. Mediator Condensates Localize Signaling Factors to Key Cell Identity Genes. Zamudio, AV, Dall'Agnese, A, Henninger, JE, Manteiga, JC, Afeyan, LK, Hannett, NM, Coffey, EL, Li, CH, Oksuz, O, Sabari, BR et al.. 2019. Mol Cell 76, 753-766.e6.
    doi: 10.1016/j.molcel.2019.08.016PMID:31563432
  6. Voices in methods development. Anikeeva, P, Boyden, E, Brangwynne, C, Cissé, II, Fiehn, O, Fromme, P, Gingras, AC, Greene, CS, Heard, E, Hell, SW et al.. 2019. Nat Methods 16, 945-951.
    doi: 10.1038/s41592-019-0585-6PMID:31562479
  7. Pol II phosphorylation regulates a switch between transcriptional and splicing condensates. Guo, YE, Manteiga, JC, Henninger, JE, Sabari, BR, Dall'Agnese, A, Hannett, NM, Spille, JH, Afeyan, LK, Zamudio, AV, Shrinivas, K et al.. 2019. Nature 572, 543-548.
    doi: 10.1038/s41586-019-1464-0PMID:31391587
  8. A first order phase transition mechanism underlies protein aggregation in mammalian cells. Narayanan, A, Meriin, A, Andrews, JO, Spille, JH, Sherman, MY, Cisse, II. 2019. Elife 8, .
    doi: 10.7554/eLife.39695PMID:30716021
  9. A CRISPR/Cas9 platform for MS2-labelling of single mRNA in live stem cells. Spille, JH, Hecht, M, Grube, V, Cho, WK, Lee, C, Cissé, II. 2019. Methods 153, 35-45.
    doi: 10.1016/j.ymeth.2018.09.004PMID:30217531
  10. Hsp70-Bag3 complex is a hub for proteotoxicity-induced signaling that controls protein aggregation. Meriin, AB, Narayanan, A, Meng, L, Alexandrov, I, Varelas, X, Cissé, II, Sherman, MY. 2018. Proc Natl Acad Sci U S A 115, E7043-E7052.
    doi: 10.1073/pnas.1803130115PMID:29987014
More Publications




Photo credit: Matt Staley (HHMI)