bold face – Boettiger-lab mentees and co-mentees
2026
Patel, A. L., Raja Venkatesh, A., Borjigin, T., Li, X., Levine, M. S. & Boettiger, A. N. Multiscale spatial analysis implicates chromosomal metaloops in gene patterning across the Drosophila brain. bioRxiv 2026.09.02.748911 (2026). doi:10.64898/2026.09.02.748911
Le, D. J.*, Hafner, A.*, Raja Venkatesh, A., Udomlumleart, T., Gaddam, S., Novacic, A., Wang, K. C. & Boettiger, A. N. Single-cell 3D genome imaging shows super-enhancer hubs are rare, nonspecific, and neither necessary nor sufficient for transcriptional bursting. Cell Genomics. 0, 101331 (2026). *equal contribution
Koska, M., Nagano, M., Swigut, T., Boettiger, A. N., Hansen, A. S. & Wysocka, J. Promoter strength and position govern promoter competition through transcript-dependent insulation. Nat. Genet. 58, 1928–1940 (2026).
Choppakatla, P., Patel, A. L., Borjigin, T., Udomlumleart, T., Hu, J., Gregor, T., Boettiger, A. N. & Levine, M. S. Loop extrusion accelerates long-range enhancer-promoter searches in living embryos. bioRxiv 2026.02.17.706355 (2026). doi:10.64898/2026.02.17.706355
Anderson, E. C., Rahmaninejad, H., Aljahani, A., Arnold, E. M., Adachi, A. S., Shah, R., Hansen, K. L., Cavka, I., Boettiger, A. N., Fudenberg, G. & Nora, E. P. The role of cohesin loading at enhancers in the flux of loop extrusion and long-range transcriptional control. bioRxiv (2026). doi:10.64898/2026.01.20.700462
Fujimori, T., Thurm, A. R., Gaudin, S., Rios-Martinez, C., Doughty, B. R., Hinks, M. M., Sinha, J., Le, D., Hafner, A., Greenleaf, W. J., Boettiger, A. N. & Bintu, L. Single-cell chromatin state transitions during epigenetic memory formation. Sci. Adv. 12, eaeb0060 (2026).
2025
Kraft, K.*, Murphy, S. E.*, Jones, M. G.*, Shi, Q., Bhargava-Shah, A., Luong, C., Hung, K. L., He, B. J., Li, R., Park, S. K., Montgomery, M. T., Weiser, N. E., Wang, Y., Luebeck, J., Bafna, V., Boeke, J. D., Mischel, P. S., Boettiger, A. N. & Chang, H. Y. Enhancer activation from transposable elements in extrachromosomal DNA. Nat. Cell Biol. 27, 1914–1924 (2025). *equal contribution
Huang, Y., Verstegen, M. J. A. M., Tjalsma, S. J. D., Krijger, P. H. L., Gupta, K., Park, M., Boettiger, A. & de Laat, W. Two unrelated distal genes activated by a shared enhancer benefit from localizing inside the same small topological domain. Genes Dev. 39, 348–363 (2025).
Koska, M., Swigut, T., Boettiger, A. N. & Wysocka, J. Promoter strength and position govern promoter competition. bioRxiv 2025.05.06.652547 (2025). doi:10.1101/2025.05.06.652547
2024
Jensen, C. L., Chen, L.-F., Swigut, T., Crocker, O. J., Yao, D., Bassik, M. C., Ferrell, J. E., Jr, Boettiger, A. N. & Wysocka, J. Long-range regulation of transcription scales with genomic distance in a gene-specific manner. Mol. Cell (2024). doi:10.1016/j.molcel.2024.10.021
Murphy, S. & Boettiger, A. N. Polycomb repression of Hox genes involves spatial feedback but not domain compaction or demixing. Nature Genetics, 56, 493–504 (2024).
Hung, T.-C., Kingsley, D. M. & Boettiger, A. Boundary stacking interactions enable cross-TAD enhancer-promoter communication during limb development. Nature Genetics. 56, 306–314 (2024).
Kraft, K.*, Murphy, S. E.*, Jones, M. G.*, Shi, Q., Bhargava-Shah, A., Luong, C., Hung, K. L., He, B. J., Li, R., Park, S. K., Weiser, N. E., Luebeck, J., Bafna, V., Boeke, J. D., Mischel, P. S., Boettiger, A. N. & Chang, H. Y. Enhancer activation from transposable elements in extrachromosomal DNA. bioRxiv 2024.09.04.611262 (2024). doi:10.1101/2024.09.04.611262 *equal contribution
Le, D. J., Hafner, A., Gaddam, S., Wang, K. C. & Boettiger, A. N. Super-enhancer interactomes from single cells link clustering and transcription. bioRxiv 2024.05.08.593251 (2024). doi:10.1101/2024.05.08.593251
2023
Dutta, S., Ghosh, A., Boettiger, A. N. & Spakowitz, A. J. Leveraging polymer modeling to reconstruct chromatin connectivity from live images. Biophys. J. (2023). doi:10.1016/j.bpj.2023.08.001
Dekker, J., Alber, F., Aufmkolk, S., Beliveau, B. J., Bruneau, B. G., Belmont, A. S., Bintu, L., Boettiger, A., Calandrelli, R., Disteche, C. M., Gilbert, D. M., Gregor, T., Hansen, A. S., Huang, B., Huangfu, D., Kalhor, R., Leslie, C. S., Li, W., Li, Y., Ma, J., Noble, W. S., Park, P. J., Phillips-Cremins, J. E., Pollard, K. S., Rafelski, S. M., Ren, B., Ruan, Y., Shav-Tal, Y., Shen, Y., Shendure, J., Shu, X., Strambio-De-Castillia, C., Vertii, A., Zhang, H. & Zhong, S. Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project. Molecular Cell 83, 2624–2640 (2023).
Hafner, A., Park, M., Berger, S. E., Nora, E. P. & Boettiger, A. N. Loop stacking organizes genome folding from TADs to chromosomes. Molecular Cell 83(9):1377-1392.e6 (2023).
Chen, L.-F.*, Long, H. K.*, Park, M., Swigut, T., Boettiger, A. N.+ & Wysocka, J.+ Structural elements facilitate extreme long-range gene regulation at a human disease locus. Molecular Cell 83(9):1446-1461.e6 (2023). *equal contribution +co-corresponding author
Chen, L.-F., Lee, J. & Boettiger, A. Recent progress and challenges in single-cell imaging of enhancer-promoter interaction. Curr. Opin. Genet. Dev. 79, 102023 (2023).
Hafner, A. & Boettiger, A. The spatial organization of transcriptional control. Nature Reviews Genetics 24, 53–68 (2023).
Fujimori, T., Rios-Martinez, C., Thurm, A. R., Hinks, M. M., Doughty, B. R., Sinha, J., Le, D., Hafner, A., Greenleaf, W. J., Boettiger, A. N. & Bintu, L. Single-cell chromatin state transitions during epigenetic memory formation. bioRxiv 2023.10.03.560616 (2023). doi:10.1101/2023.10.03.560616
2022
Llimos, G., Gardeux, V., Koch, U., Kribelbauer, J. F., Hafner, A., Alpern, D., Pezoldt, J., Litovchenko, M., Russeil, J., Dainese, R., Moia, R., Mahmoud, A. M., Rossi, D., Gaidano, G., Plass, C., Lutsik, P., Gerhauser, C., Waszak, S. M., Boettiger, A., Radtke, F. & Deplancke, B. A leukemia-protective germline variant mediates chromatin module formation via transcription factor nucleation. Nature Communications. 13, 2042 (2022).
Kraft, K., Yost, K. E., Murphy, S. E., Magg, A., Long, Y., Corces, M. R., Granja, J. M., Wittler, L., Mundlos, S., Cech, T. R., Boettiger, A. N. & Chang, H. Y. (2022). Polycomb-mediated genome architecture enables long-range spreading of H3K27 methylation. Proc. Natl. Acad. Sci. U. S. A. 119, e2201883119.
2021
Rajpurkar, A.R., Mateo, L.J., Murphy, S.E., Boettiger, A.N. (2021) Deep learning connects DNA traces to transcription to reveal predictive features beyond enhancer–promoter contact. Nature Communications. 12(1):3423
Mateo, L. J., Sinnott-Armstrong, N., Boettiger, A. N. (2021) Tracing DNA paths and RNA profiles in cultured cells and tissues with ORCA. Nature protocols. 16:1647-1713.
Xiao, J. Y., Hafner, A. & Boettiger, A. N. How subtle changes in 3D structure can create large changes in transcription. Elife 10, (2021).
Weber, C.M., Hafner, A., Braun, M.G.S., Boettiger, A.N., and Crabtree, G.R. (2021). mSWI/SNF promotes Polycomb repression both directly and through genome-wide redistribution. Nature structural & molecular biology. 28(6): 501-511.
2020
Boettiger, A.*, Murphy, S. Advances in chromatin imaging at kilobase-scale resolution. Trends in Genetics. 10.1016/j.tig.2019.12.010 (2020). *corresponding author.
Woglar, A., Yamaya, K., Roelens, B., Boettiger, A., Köhler, S., Villeneuve, A. M. Quantitative cytogenetics reveals molecular stoichiometry and longitudinal organization of meiotic chromosome axes and loops. PLoS biology 18 (8): e3000817 (2020).
2019
Fazal F.M*, Han S.*, Kaewsapsak P., Parker K.R., Xu J., Boettiger A.N., Chang H.Y.+, Ting A.Y.+ Atlas of Subcellular RNA Localization Revealed by APEX-seq. Cell 178(2):473-490 (2019). *equal contribution +co-corresponding author.
Mateo L. J, Murphy S. E., Hafner A., Cinquini I. S., Walker C. A., Boettiger A.N. Visualizing DNA folding and RNA in embryos at single-cell resolution. Nature 568, 49-54 (2019).
2018
Bintu B.*, Mateo L. J*, Su J.-H., Sinnott-Armstrong N. A., Parker M., Kinrot S., Yamaya K., Boettiger A.N.*+ Zhuang X.*+ (2018) Super-resolution chromatin tracing reveals chromatin domains and cooperative high-order interactions in single cells. Science. 362(6413): 419. *equal contribution +co-corresponding author.
2017
Beliveau B. J.*, Boettiger A.N.*, Nir G.*, Bintu B.*, Yin P., Zhuang X., and Wu C.-T. (2017) In situ super-resolution imaging of genomic DNA with oligoSTORM and oligoDNA-PAINT. Methods in Mol. Bio. 1663. *co-first author.
Alistair’s pre-Stanford work
Boettiger, A. N., Bintu, B., Moffitt, J. R., Wang, S., Beliveau, B. J., Fudenberg, G., Imakaev, M., Mirny, L. A., Wu, C.-T. & Zhuang, X. Super-resolution imaging reveals distinct chromatin folding for different epigenetic states. Nature 529, 418–422 (2016).
Wani, A. H.*, Boettiger, A. N.*, Schorderet, P., Ergun, A., Münger, C., Sadreyev, R. I., Zhuang, X., Kingston, R. E. & Francis, N. J. Chromatin topology is coupled to Polycomb group protein subnuclear organization. Nat. Commun. 7, 10291 (2016). *co-first author.
Moffitt, J. R., Pandey, S., Boettiger, A. N., Wang, S. & Zhuang, X. Spatial organization shapes the turnover of a bacterial transcriptome. Elife 5, 1–22 (2016).
Chen, K. H.*, Boettiger, A. N.*, Moffitt, J. R.*, Wang, S. & Zhuang, X. Spatially resolved, highly multiplexed RNA profiling in single cells. Science 348, 412 (2015). *co-first author.
Beliveau B. J., Boettiger A. N., Avendaño M. S., Jungmann R., McCole R. B., Joyce E. F., Kim-Kiselak C., Bantignies F., Fonseka C. Y., Erceg J., Hannan M. A., Hoang H. G., Colognori D., Lee J. T., Shih W. M., Yin P., Zuang X., Wu C. (2015) Single-molecule super-resolution imaging of chromosomes and in situ haplotype visualization using Oligopaint FISH probes. Nature Communications. 6:7147. OpenAccess
Boettiger, A. N. (2013) Analytic Approaches to Stochastic Gene Expression in Multicellular Systems. Biophysical Journal 105(12) pp. 2629 – 2640. BioPhysJ
Boettiger, A. N., Levine, M. (2013) Rapid Transcription Fosters Coordinate snail Expression in the Drosophila Embryo. Cell Reports 3, 8–15. OpenAccess.
Perry M. W., Boettiger A. N., Levine M. (2011) Multiple Enhancers Ensure Precision of Gap Gene Expression Patterns in the Drosophila Embryo. PNAS. 108(33):13570-5. PubMed
Boettiger A. N.*, Ralph P. L.*, Evans S. N.* (2011) Transcriptional regulation: Effects of promoter proximal pausing on speed, synchrony and reliability. PLoS Computational Biology. 7(5):e1001136 *equal contribution. OpenAccess
Boettiger A. N.*, Wittemyer G.*, Starfield R,. Volrath F., Douglas-Hamilton I., Getz W. M. (2011) Inferring ecological and behavioral drivers of African elephant movement using a linear filtering approach. Ecology 92(8): 1648-1657. *equal contribution PubMed
Perry M. W.*, Boettiger A. N.*, Bothma J. P., Levine M. (2010) Shadow Enhancers Foster Robustness of Drosophila Gastrulation. Current Biology 20: 1562-7. *equal contribution PubMed
Boettiger A. N., Levine M. (2009) Synchronous and stochastic patterns of gene activation in the early Drosophila embryo. Science. 325:471-3. PubMed
Perry M.W., Cande J.D., Boettiger A. N., Levine M. (2009) Evolution of Insect Dorsoventral Patterning Mechanisms. Cold Spring Harb Symp Quant Biol. Epub Oct 20. PubMed
Boettiger A. N., Oster G. (2009) Emergent complexity in simple neural systems. Communicative & Integrative Biology. 2(6). PubMedOpenAccess
Boettiger A, Ermentrout B, Oster G. (2009) The neural origins of shell structure and pattern in aquatic mollusks. PNAS. 106:6837-42. PubMed
Coppey M., Boettiger A. N., Berezhkovskii A. M., and Shvartsman S. Y. (2008) Nuclear trapping shapes the terminal gradient in the Drosophila embryo. Current Biology. 18:915-9. PubMed
Coppey M., Berezhkovskii A. M., Kim Y., Boettiger A. N., and Shvartsman S. Y. (2007) Modeling the bicoid gradient: diffusion and reversible nuclear trapping of a stable protein. Developmental Biology. 312(2):623-30. PubMed
Nikolić D. L., Boettiger A. N., Bar-Sagi D., Carbeck J. D., and Shvartsman S. Y. (2006) Role of boundary conditions in an experimental model of epithelial wound healing. Am J Physiol Cell Physiol. 291:68-75. PubMed
