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


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.


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

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). OpenAccess


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


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


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


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