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Alistair N. Boettiger - Publications

Affiliations: 
2011 Biophysics University of California, Berkeley, Berkeley, CA, United States 
 2016- Stanford School of Medicine, Palo Alto, CA, United States 
Website:
https://med.stanford.edu/profiles/alistair-boettiger
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37 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2025 Huang Y, Verstegen MJAM, Tjalsma SJD, Krijger PHL, 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 & Development. PMID 39870429 DOI: 10.1101/gad.352235.124  0.329
2024 Jensen CL, Chen LF, Swigut T, Crocker OJ, Yao D, Bassik MC, Ferrell JE, Boettiger AN, Wysocka J. Long-range regulation of transcription scales with genomic distance in a gene-specific manner. Molecular Cell. PMID 39626660 DOI: 10.1016/j.molcel.2024.10.021  0.334
2024 Jensen CL, Chen LF, Swigut T, Crocker OJ, Yao D, Bassik MC, Ferrell JE, Boettiger AN, Wysocka J. Long range regulation of transcription scales with genomic distance in a gene specific manner. Biorxiv : the Preprint Server For Biology. PMID 39071420 DOI: 10.1101/2024.07.19.604327  0.337
2024 Murphy SE, Boettiger AN. Polycomb repression of Hox genes involves spatial feedback but not domain compaction or phase transition. Nature Genetics. PMID 38361032 DOI: 10.1038/s41588-024-01661-6  0.333
2023 Dekker J, Alber F, Aufmkolk S, Beliveau BJ, Bruneau BG, Belmont AS, Bintu L, Boettiger A, Calandrelli R, Disteche CM, Gilbert DM, Gregor T, Hansen AS, Huang B, Huangfu D, et al. Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project. Molecular Cell. PMID 37419111 DOI: 10.1016/j.molcel.2023.06.018  0.408
2023 Hafner A, Park M, Berger SE, Murphy SE, Nora EP, Boettiger AN. Loop stacking organizes genome folding from TADs to chromosomes. Molecular Cell. 83: 1377-1392.e6. PMID 37146570 DOI: 10.1016/j.molcel.2023.04.008  0.312
2023 Chen LF, Long HK, Park M, Swigut T, Boettiger AN, Wysocka J. Structural elements promote architectural stripe formation and facilitate ultra-long-range gene regulation at a human disease locus. Molecular Cell. PMID 36996812 DOI: 10.1016/j.molcel.2023.03.009  0.331
2023 Chen LF, Lee J, Boettiger A. Recent progress and challenges in single-cell imaging of enhancer-promoter interaction. Current Opinion in Genetics & Development. 79: 102023. PMID 36854248 DOI: 10.1016/j.gde.2023.102023  0.338
2022 Hafner A, Boettiger A. The spatial organization of transcriptional control. Nature Reviews. Genetics. PMID 36104547 DOI: 10.1038/s41576-022-00526-0  0.331
2021 Xiao JY, Hafner A, Boettiger AN. How subtle changes in 3D structure can create large changes in transcription. Elife. 10. PMID 34240703 DOI: 10.7554/eLife.64320  0.315
2021 Xiao JY, Hafner A, Boettiger AN. How subtle changes in 3D structure can create large changes in transcription. Elife. 10. PMID 34240703 DOI: 10.7554/eLife.64320  0.315
2021 Rajpurkar AR, Mateo LJ, Murphy SE, Boettiger AN. Deep learning connects DNA traces to transcription to reveal predictive features beyond enhancer-promoter contact. Nature Communications. 12: 3423. PMID 34103507 DOI: 10.1038/s41467-021-23831-4  0.328
2020 Woglar A, Yamaya K, Roelens B, Boettiger A, Köhler S, Villeneuve AM. Quantitative cytogenetics reveals molecular stoichiometry and longitudinal organization of meiotic chromosome axes and loops. Plos Biology. 18: e3000817. PMID 32813728 DOI: 10.1371/Journal.Pbio.3000817  0.378
2020 Boettiger A, Murphy S. Advances in Chromatin Imaging at Kilobase-Scale Resolution. Trends in Genetics : Tig. PMID 32007290 DOI: 10.1016/J.Tig.2019.12.010  0.48
2019 Fazal FM, Han S, Parker KR, Kaewsapsak P, Xu J, Boettiger AN, Chang HY, Ting AY. Atlas of Subcellular RNA Localization Revealed by APEX-Seq. Cell. PMID 31230715 DOI: 10.1016/J.Cell.2019.05.027  0.334
2019 Mateo LJ, Murphy SE, Hafner A, Cinquini IS, Walker CA, Boettiger AN. Visualizing DNA folding and RNA in embryos at single-cell resolution. Nature. PMID 30886393 DOI: 10.1038/S41586-019-1035-4  0.477
2018 Bintu B, Mateo LJ, Su JH, Sinnott-Armstrong NA, Parker M, Kinrot S, Yamaya K, Boettiger AN, Zhuang X. Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells. Science (New York, N.Y.). 362. PMID 30361340 DOI: 10.1126/Science.Aau1783  0.712
2017 Beliveau BJ, Boettiger AN, Nir G, Bintu B, Yin P, Zhuang X, Wu CT. In Situ Super-Resolution Imaging of Genomic DNA with OligoSTORM and OligoDNA-PAINT. Methods in Molecular Biology (Clifton, N.J.). 1663: 231-252. PMID 28924672 DOI: 10.1007/978-1-4939-7265-4_19  0.691
2016 Moffitt JR, Pandey S, Boettiger AN, Wang S, Zhuang X. Spatial organization shapes the turnover of a bacterial transcriptome. Elife. 5. PMID 27198188 DOI: 10.7554/Elife.13065  0.49
2016 Boettiger AN, Bintu B, Moffitt JR, Wang S, Beliveau BJ, Fudenberg G, Imakaev M, Mirny LA, Wu CT, Zhuang X. Super-resolution imaging reveals distinct chromatin folding for different epigenetic states. Nature. PMID 26760202 DOI: 10.1038/Nature16496  0.722
2016 Wani AH, Boettiger AN, Schorderet P, Ergun A, Münger C, Sadreyev RI, Zhuang X, Kingston RE, Francis NJ. Chromatin topology is coupled to Polycomb group protein subnuclear organization. Nature Communications. 7: 10291. PMID 26759081 DOI: 10.1038/Ncomms10291  0.498
2016 Moffitt JR, Pandey S, Boettiger AN, Wang S, Zhuang X. Author response: Spatial organization shapes the turnover of a bacterial transcriptome Elife. DOI: 10.7554/Elife.13065.029  0.463
2015 Beliveau BJ, Boettiger AN, Avendaño MS, Jungmann R, McCole RB, Joyce EF, Kim-Kiselak C, Bantignies F, Fonseka CY, Erceg J, Hannan MA, Hoang HG, Colognori D, Lee JT, Shih WM, et al. Single-molecule super-resolution imaging of chromosomes and in situ haplotype visualization using Oligopaint FISH probes. Nature Communications. 6: 7147. PMID 25962338 DOI: 10.1038/Ncomms8147  0.517
2015 Chen KH, Boettiger AN, Moffitt JR, Wang S, Zhuang X. RNA imaging. Spatially resolved, highly multiplexed RNA profiling in single cells. Science (New York, N.Y.). 348: aaa6090. PMID 25858977 DOI: 10.1126/Science.Aaa6090  0.544
2013 Boettiger AN. Analytic approaches to stochastic gene expression in multicellular systems. Biophysical Journal. 105: 2629-40. PMID 24359735 DOI: 10.1016/J.Bpj.2013.10.033  0.387
2013 Boettiger AN, Levine M. Rapid transcription fosters coordinate snail expression in the Drosophila embryo. Cell Reports. 3: 8-15. PMID 23352665 DOI: 10.1016/J.Celrep.2012.12.015  0.548
2011 Perry MW, Boettiger AN, Levine M. Multiple enhancers ensure precision of gap gene-expression patterns in the Drosophila embryo. Proceedings of the National Academy of Sciences of the United States of America. 108: 13570-5. PMID 21825127 DOI: 10.1073/Pnas.1109873108  0.684
2011 Boettiger AN, Ralph PL, Evans SN. Transcriptional regulation: effects of promoter proximal pausing on speed, synchrony and reliability. Plos Computational Biology. 7: e1001136. PMID 21589887 DOI: 10.1371/Journal.Pcbi.1001136  0.417
2010 Perry MW, Boettiger AN, Bothma JP, Levine M. Shadow enhancers foster robustness of Drosophila gastrulation. Current Biology : Cb. 20: 1562-7. PMID 20797865 DOI: 10.1016/J.Cub.2010.07.043  0.676
2010 Bothma JP, Levine M, Boettiger A. Morphogen gradients: limits to signaling or limits to measurement? Current Biology : Cb. 20: R232-4. PMID 20219171 DOI: 10.1016/J.Cub.2010.01.040  0.475
2009 Perry MW, Cande JD, Boettiger AN, Levine M. Evolution of insect dorsoventral patterning mechanisms. Cold Spring Harbor Symposia On Quantitative Biology. 74: 275-9. PMID 19843594 DOI: 10.1101/Sqb.2009.74.021  0.709
2009 Boettiger AN, Levine M. Synchronous and stochastic patterns of gene activation in the Drosophila embryo. Science (New York, N.Y.). 325: 471-3. PMID 19628867 DOI: 10.1126/Science.1173976  0.551
2009 Boettiger A, Ermentrout B, Oster G. The neural origins of shell structure and pattern in aquatic mollusks. Proceedings of the National Academy of Sciences of the United States of America. 106: 6837-42. PMID 19351900 DOI: 10.1073/Pnas.0810311106  0.306
2008 Coppey M, Boettiger AN, Berezhkovskii AM, Shvartsman SY. Nuclear trapping shapes the terminal gradient in the Drosophila embryo. Current Biology : Cb. 18: 915-9. PMID 18571412 DOI: 10.1016/J.Cub.2008.05.034  0.578
2008 Coppey M, Berezhkovskii AM, Kim Y, Boettiger AN, Shvartsman SY. Corrigendum to "Modeling the bicoid gradient: Diffusion and reversible nuclear trapping of a stable protein" [Dev. Biol. 312 (2007) 623-630] (DOI:10.1016/j.ydbio.2007.09.058) Developmental Biology. 316: 548. DOI: 10.1016/J.Ydbio.2008.02.002  0.496
2007 Coppey M, Berezhkovskii AM, Kim Y, Boettiger AN, Shvartsman SY. Modeling the bicoid gradient: diffusion and reversible nuclear trapping of a stable protein. Developmental Biology. 312: 623-30. PMID 18001703 DOI: 10.1016/J.Ydbio.2007.09.058  0.537
2006 Nikolić DL, Boettiger AN, Bar-Sagi D, Carbeck JD, Shvartsman SY. Role of boundary conditions in an experimental model of epithelial wound healing. American Journal of Physiology. Cell Physiology. 291: C68-75. PMID 16495370 DOI: 10.1152/Ajpcell.00411.2005  0.512
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