2022
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. bioRxiv 2022.10.20.513057 (2022). doi:10.1101/2022.10.20.513057 *equal contribution +co-corresponding author
Murphy, S. & Boettiger, A. N. Polycomb repression of Hox genes involves spatial feedback but not domain compaction or demixing. bioRxiv 2022.10.14.512199 (2022). doi:10.1101/2022.10.14.512199
Hafner, A. & Boettiger, A. The spatial organization of transcriptional control. Nat. Rev. Genet. (2022). doi:10.1038/s41576-022-00526-0
Hafner, A., Park, M., Berger, S. E., Nora, E. P. & Boettiger, A. N. Loop stacking organizes genome folding from TADs to chromosomes. bioRxiv 2022.07.13.499982 (2022). doi:10.1101/2022.07.13.499982
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). OpenAccess
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. OpenAccess
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. (2021) How subtle changes in 3D structure can create large changes in transcription. eLife doi: 10.7554/eLife.64320
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. TiG
Quantitative cytogenetics reveals molecular stoichiometry and longitudinal organization of meiotic chromosome axes and loops. PLoS biology 18 (8): e3000817 (2020). OpenAccess
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. PubMed
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). Nature
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. Science
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. Methods Mol Biol
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., and Zhuang X. (2016) Super-resolution imaging reveals distinct chromatin folding for different epigenetic domains. Nature. Nature
Wani A. H. *, Boettiger A. N. *, Shorderet P., Ergun A., Munger C., Sadreyev R. I., Zhuang X., Kingston R. E., and Francis N. J. Chromatin topology is coupled to Polycomb Group protein subnuclear organization. Nature Communications. (2016) *co-first author. OpenAccess
Moffitt J. R. , Pandey S., Boettiger A. N. , Wang S., and Zhuang X. (2016) Spatial organization shapes the turnover of a bacterial transcriptome. eLife 5, 1–22. OpenAccess
Chen K. H.*, Boettiger A. N.*, Moffitt J. M. *, Wang S., Zhuang X. (2015) Spatially resolved, highly multiplexed RNA profiling in single cells. Science. 348:412. *co-first author. Science
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