Publications
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^ denotes equal contribution,* denotes (co)-corresponding author(s), Mir lab members in bold
Preprints
45.Kapoor M and Mir M.* , Simulation of transcription factor clustering in nuclei from molecular kinetics, bioRxiv (2026) Download PDF
45. Fallacaro S., Kapoor M^, Encarnation L.^, Mukherjee A., Garcia H.G., Turner M.A., Mir M.* , Enhancer binding kinetics explain transcription factor hub formation, bioRxiv (2026, Under Review) Download PDF
44. Fallacaro S.^, Mukherjee A.^, Ratchasanmuang P.^, Zinski J.^, Haloush Y. I, Shankta K., Mir M.*, A fine kinetic balance of interactions directs transcription factor hubs to genes, bioRxiv (2024, in Revision) Download PDF
2026-
43. Porello E. A,, Wu. J, Fallacaro S., Dreispiel J., Trudeau R.T., Vidal J. A., Cesar N., Singh A., Mir M., Lim B.* , Enhancer Placement Impacts Transcriptional Dynamics in Drosophila Embryos, Nature Communications (2026, posted on bioRxiv 2025) Download PDF
42. Mukherjee A., Kapoor M^, Shankta K.^, Fallacaro S., Carter R.D., Hayward-Lara, G. Ratchasanmuang P., Haloush Y. I, Mir M.*, A single cluster of RNA Polymerase II molecules is stably associated with active genes, Nature Communications (2026, posted on bioRxiv 2025) Download PDF
41. D. Hwang, M. C. Erdman, S. Adhikari, R. Pantula, K. Epstein, P. Li, F. Costabile, P. Rotsides, C.S. Wang, S. M. Sun, H. Fazelinia, L. A. Spruce, T. Fugmann, T. Rrustemi, W. T. Soh, A. Farrel, M. Y. Want, A. Facciabene, M. Mir, J. M. Maris, N. G. Sgourakis*,HLA-Shuttle: A system for enhancing antigen presentation in immunologically cold tumors, Science Advances (2026) Download PDF
2020-2025
40. A. D. Guerra, S. Matkar, C. Acholla, C. Larmour, G. Li, M. Mazzeschi, K. Patel, K. Krytska, C. Chen, S. Balyasny, J. Kalna, P. Kamitsuka, M. Gerelus, G. Polkosnik, D. Groff, A. Mukherjee, C. Adams, G. Witek, A. Hamilton, D. Martinez, J. Pogoriler, Y. Li, P. Jung, D. Alvarado, M. Lauriola, J. Maris, A. Wolpaw, D. Dimitrov, M. Mir, D. V Zhelev, Y. P. Mossé*, A humanized anti-anaplastic lymphoma kinase (ALK)-directed antibody-drug conjugate CDX0239-PBD demonstrates potent cytotoxicity in ALK-expressing cancers, Nature Communications (2025) Download PDF
39. Fallacaro, S., Mukherjee, A., Gamauf, E., Mir, M.* (2025). Quantifying Transcription Factor Enrichment at Target Loci in Live Embryos. Zygotic Genome Activation. Methods in Molecular Biology, (2025) Download PDF
38. Mir M.*,Miller spreads and the power of observation, Nature Reviews Genetics (2024) Download PDF
37. Hayward-Lara G.^, Fischer M.D.^, Mir M.*, Dynamic microenvironments shape nuclear organization and gene expression,Current Opinion in Genetics & Development (2024) Download PDF
36. Gaskill M., Slouri I. V., Branks A. E., Boka A. P., Stadler M. R. , Vietor K. , Huang H. S. , Gibson T. J. , Mukherjee A., Mir M. , Blythe S. A. Harrison M. M.,* Localization of the pioneer factor GAF to subnuclear foci is driven by DNA binding and required to silence satellite repeat expression,, Developmental Cell (2023, posted on bioRxiv 2022) Download PDF
35. Song L., Yao X., Li H.. Peng B., Boka A. P., Liu Y.. Chen G., Liu Z., Mathias K. M., Xia L.. Li Q. Mir M., Li Y.*, Li H.*, Wan l.*, Hotspot mutations in the structured ENL YEATS domain link aberrant transcriptional condensates and cancer, Molecular Cell (2022) Download PDF
34. Boka, A.P., Mukherjee, A., Mir M.*, Single-molecule tracking technologies for quantifying the dynamics of gene regulation in cells, tissue, and embryos, Development, (2021) Download PDF
33. Chong. S* and Mir M., Towards Decoding the Sequence-Based Grammar Governing the Functions of Intrinsically Disordered Protein Regions, Journal of Molecular Biology, (2021) Download PDF
Mustafa's Postdoc Work
32. McSwiggen D. T., Mir M., Darzacq X.*, Tjian R.*, Evaluating phase separation in live cells: diagnosis, caveats, and functional consequences, Genes Dev, (2019) Download PDF
31. M. W. Parker, M. Bell, M. Mir, J. A. Kao, X. Darzacq, M. R. Botchan*, J. M. Berger*, A new class of disordered elements controls DNA replication through initiator self-assembly, eLife 8:e48562, (2019) Download PDF
30. M. Mir*, W. Bickmore, E. E. M. Furlong, G. J. Narlikar, Chromatin topology, condensates, and gene regulation: shifting paradigms or just a phase? Development, 146,dev182766 (2019) Download PDF
29. M. Mir^, M. R. Stadler^, S.A. Ortiz, X. Darzacq*, M. B. Eisen*, Dynamic Multifactor hubs transiently interact with sites of active transcription in Drosophila embryos, eLife, 7:e40497, (2018) Download PDF
28. M. Mir, A. Reimer, M. Stadler, A. Tangara, A. S. Hansen, D. Hockemeyer, M. B. Eisen, H. Garcia, X. Darzacq*, Chapter 32 – Single Molecule Imaging in Live Embryos using Lattice Light-Sheet Microscopy, Methods in Molecular Biology, Nanoscale Imaging: Methods and Protocols, Volume 1814, Ed: Y. L. Lyubchenko, Springer, pp 541-559 (2018) Download PDF
27. M. Mir, A. Reimer, J. E. Haines, X.-Y. Li, M. Stadler, H. Garcia, M. B. Eisen, X. Darzacq*, Dense Bicoid hubs accentuate binding along the morphogen gradient, Genes Dev., 31, 1784-1794 (2017) Download PDF
26. A. R. Strom, A. V. Emelyanov, M. Mir, D. V. Fyodorov, X. Darzacq, and G. Karpen*, Phase separation drives heterochromatin domain formation, Nature, doi:10.1038/nature22989 (2017) Download PDF
25. S. M. Wichner, V. R. Mann, A. S. Powers, M. A. Segal, M. Mir, J. N. Bandaria, M. A. DeWitt, X. Darzacq, A. Yildiz*, and B. E. Cohen*, Covalent protein labeling and improved single molecule optical properties of aqueous CdSe/CdS Quantum Dots, ACS Nano, 11(7), 6773-6781 (2017) Download PDF
24. M. Woringer, X. Darzacq, C. Zimmer, and M. Mir*, Faster and less phototoxic 3D fluorescence microscopy using a versatile compressed sensing scheme, Optics Express, 25(12), 13668-13683, (2017) Download PDF
23. P. Qin, M. Parlak, C. Kuscu, J. Bandaria, M. Mir, K. Szlachta, R. Singh, X. Darzacq, A. Yildiz*, and M. Adli*, Live cell imaging of low- and non- repetitive chromosome loci using CRISPR-Cas9, Nature Communications, 8, 14725, (2017) Download PDF
22. S. Abrahamsson, R. Ilic, J. Wisniewski, B. Mehl, L. Yu, L. Chen, M. Davanco, L. Oudjedi, J. Fiche, B. Hajj, X. Jin, J. Pulupa, C. Cho, M. Mir, M. Beheiry, X. Darzacq, M. Nollmann, M. Dahan, C. Wu, T. Lionnet, J. Liddle, and C. Bargmann*, Multifocus microscopy with precise color multi-phase diffractive optics applied in functional neuronal imaging, Biomedical Optics Express, 7 (3), 855-869 (2016) Download PDF
Mustafa's Graduate Work
21. L. Ma, G. Rajshekhar, B. Bhaduri, S. Sridharan, M. Mir, A. Chakraborty, R. Iyer, S. Prasant, L. Millet, M. U. Gilette, and G. Popescu*, Phase correlation imaging of unlabeled cell dynamics, Scientific Reports, 6, 32702, (2016) Download PDF
20. H. Majeed, S. Sridharan, M. Mir, L. Ma, E. Min, W. Jung, and G. Popescu*, Quantitative phase imaging for medical diagnosis, Journal of Biophotonics, (2016) Download PDF
19. R. Raman, B. Bhaduri, M. Mir, A. Shkumatov, M. K. Lee, G. Popescu, H. J. Kong, R. Bashir*, High-Resolution Projection Micro-Stereolithography for patterning of Neovasculature, Advanced Healthcare Materials, 5 (5), 610-619 (2015) Download PDF
18. M. Mir^, T. Kim†, A. Majumder, M. Xiang, R. Wang, S. C. Liu, M. U. Gillette, S. Stice and G. Popescu, Label-Free Characterization of Emerging Human Neuronal Networks” Scientific Reports, 4, 4434 (2014) Download PDF
17. M. Mir, A. Bergamaschi, B.S. Katzenellenbogen and G. Popescu*, Highly sensitive quantitative imaging for single cancer cell growth kinetics and drug response, PLoS ONE, 9 (2), e89000 (2014) Download PDF
16. T. Kim^, R. Zhou^, M. Mir, S. D. Babacan, P. S. Carney, L. L. Goddard, and G. Popescu*, White light diffraction tomography of unlabelled live cells, Nature Photonics, (2014) Download PDF
15. G. Popescu, K. Park^, M. Mir^, and R. Bashir*, New technologies for measuring single cell mass, Lab on a Chip, 14, 646-652 (2014) Download PDF
14. R. Wang, T. W. Kim, M. Mir, and G. Popescu*, Nanoscale Fluctuations and Surface Tension Measurements in droplets using Phase-resolved Low-coherence Interferometry , Applied Optics, 52 (1), A177-A181 (2013) Download PDF
13. M. Mir, B. Bhaduri, R. Wang, R. Zhu, G. Popescu*, Chapter 3 - Quantitative Phase Imaging, Progress in Optics, Ed: W. Emil, Elsevier, Volume 57, pp. 133-217 (2012) Download PDF
12. M. Mir^*, D. Babacan†, M. Bednarz, I. Golding and G. Popescu, Three Dimensional Deconvolution Spatial Light Interference Tomography for studying Subcellular Structure in E. coli , PLoS ONE, 7 (6), e38916 (2012) Download PDF
11. B. Bhaduri, H. Pham, M. Mir, and G. Popescu, Diffraction Phase Microscopy with White Light, Optics Letters, 37 (6), (2012): 1094-1096 Download PDF
10. M. Mir*, K. Tangella and G. Popescu, Blood Testing at the Single Cell Level using Quantitative Phase and Amplitude Microscopy, Biomedical Optics Express, 2 (12),3259-3266 (2011) Download PDF
9. S. Sridharan, M. Mir, and G. Popescu*, Simultaneous Optical Measurements of Cell Motility and Growth, Biomedical Optics Express, 2 (10), 285-2820 (2011) Download PDF
8. J. Lim, H. Ding, M. Mir, R. Zhu, K. Tangella and G. Popescu*, Born Approximation Model Light Scattering by Red Blood Cells, Biomedical Optics Express, 2 (10), (2011): 2784-2791 Download PDF
7. M. Mir^, Z. Wang^, Z. Shen, M. Bednarz, R. Bashir, I. Golding and G. Popescu*, Optical Measurement of Cell Cycle Dependent Growth, Proceedings of the National Academies of Sciences (PNAS), 108 (32), 13124-13129 (2011) Download PDF
6. R. Wang, H. Ding, M. Mir, K. Tangella and G. Popescu*, Effective 3D Viscoelasticity of Red Blood Cells Measured by Diffraction Phase Microscopy, Biomedical Optics Express, 2 (3), : 485-490, (2011) Download PDF
5. Z. Wang, L. Millet, M. Mir, H. Ding, S. Unarunotai, J. Rogers, M. Gillette, and G. Popescu*, Spatial Light Interference Microscopy, Optics Express, 19 (2), (2011): 1016-1026 Download PDF
4. M. Mir, H. Ding, Z. Wang, J. Reedy, K. Tangella and G. Popescu*, Blood Screening using Diffraction Phase Cytometry, Journal of Biomedical Optics, 15 (2), (2010): 027016 Download PDF
3. M. Mir, Z. Wang, K. Tangella and G. Popescu*, Diffraction Phase Cytometry: Blood on a CD-ROM, Optics Express, 17 (4), (2009): 2579-2585 Download PDF
Mustafa's Undergraduate Work
2. U. Mirsaidov, J. Scrimgeour, W. Timp, K. Beck, M. Mir, P. Matsudaira and G. Timp*, Live Cell Lithography: Using Optical Tweezers to Create Synthetic Tissue, Lab on a Chip, 8 (12), (2008): 2174-2181 Download PDF
1. U. Mirsaidov, W. Timp, K. Timp, M. Mir, P. Matsudaira and G. Timp*, Optimal Optical Trap for Bacterial Viability, Physics Review E, 78 (2), (2008): 021910 Download PDF