Publications

2019

Fazal F.M*, Han S.*, Kaewsapsak P., Parker K.R., Xu J., Boettiger A.N., Chang H.Y.+, Ting A.Y.+ Principles of Subcellular RNA Localization Revealed by APEX-seq. Cell (in press). *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). 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

2016

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

2015

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

 

Alistair’s earlier work:

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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