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^ denotes equal contribution,* denotes corresponding author(s), lab members underlined

Publications: Publications

39. Mir M.*,Miller spreads and the power of observation, Nature Reviews Genetics (2024),   Download PDF

38. Mukheree A.^, Fallacaro S.^, Ratchasanmuang P.^, Zinski J.^, Boka A., Shankta K., Mir M.*, A fine kinetic balance of interactions directs transcription factor hubs to genes, bioRxiv (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,, Biorxiv (2022), Developmental Cell (2023),  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

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