Publications

For the most up-to-date list, please see our Google Scholar page. "*" denotes co-first authors and "^" denotes corresponding or co-corresponding authors.
25. Xie L*; Dong P*; Qi Y; Hsieh THS; De Marzio M; Chen X; Banala S; Legant WR; English BP; Hansen AS; Schulmann A; Lavis LD; Betzig E; Casellas R; Chang HY; Zhang B^; Tjian R^; Liu Z^. 3D ATAC-PALM: super-resolution imaging of the accessible genome. Nature Methods, 2020.
23. Hsieh THS; Cattoglio C; Slobodyanyuk E; Hansen AS; Rando OL; Tjian R^; Darzacq X^. Resolving the 3D landscape of transcription-linked mammalian chromatin folding. Molecular Cell, 2020. (Preprint)
22. Hansen AS*; Hsieh THS*; Cattoglio C*; Pustova I; Saldana-Meyer R; Reinberg D; Darzacq X^; Tjian R^. Distinct Classes of Chromatin Loops Revealed by Deletion of an RNA-Binding Region in CTCF. Molecular Cell, 2019, DOI:https://doi.org/10.1016/j.molcel.2019.07.039.
21. Hansen AS*; Amitai A*; Cattoglio C; Tjian R^; Darzacq X^. Guided nuclear exploration increases CTCF target search efficiency. Nature Chemical Biology, 2019, doi:10.1038/s41589-019-0422-3. (Preprint)
20. Cattoglio C; Pustova I; Walther N; Ho JJ; Hantsche-Grininger M; Inouye CJ; Hossain MJ; Dailey GM; Ellenberg J; Darzacq X; Tjian R; Hansen AS^: Determining cellular CTCF and cohesin abundances to constrain 3D genome models. eLife 2019, 40164.
19. McSwiggen DT; Hansen AS; Marie-Nelly H; Teves SS; Heckert A; Hao Y; Umemoto K; Dugast-Darzacq C; Tjian R^; Darzacq X^. Evidence for DNA-mediated nuclear compartmentalization distinct from phase separation. eLife 2019, e47098.
18. Oomen ME; Hansen AS; Liu Y; Darzacq X; Dekker J^. CTCF sites display cell cycle dependent dynamics in factor binding and nucleosome positioning. Genome Research 2019 29, 236-249
17. Boehning M; Dugast-Darzacq C; Rankovic M; Hansen AS; Yu TK; Marie-Nelly H; Kokic G; Dailey GM; Cramer P^; Darzacq X^;  Zweckstetter M^. RNA polymerase II clustering through carboxy-terminal domain phase separation. Nature Structural and Molecular Biology 2018 25, 833–840.
16. Lu H; Yu D; Hansen AS; Ganguly S; Liu R; Heckert A; Darzacq X; Zhou Q^; 2018. Phase-separation mechanism for C-terminal  hyperphosphorylation of RNA polymerase II. Nature 2018 558, 318–323
15. Mir M; Reimer A; Stadler M; Tangara A; Hansen AS; Hockemeyer D; Eisen MB; Garcia H; Darzacq X^; Single molecule imaging in live embryos using lattice light-sheet microscopy. Methods in Molecular Biology. Nanoscale Imaging. 2018
14. Hansen AS*^; Woringer M*; Grimm J; Lavis LD; Tjian R^; Darzacq X^. Robust model-based analysis of single-particle tracking experiments with Spot-On. eLife 2018 e33125
13. Hansen AS^; Cattoglio C; Darzacq X; Tjian R. Recent evidence that TADs and chromatin loops are dynamic structures. Nucleus 2018, 20-32.
12. Dekker J^ et al.. The 4D Nucleome Project. Nature 2017. 549, 219–226
11. Hansen AS; Pustova I; Cattoglio C; Tjian R^; Darzacq X^. CTCF and Cohesin Regulate Chromatin Loop Stability with Distinct Dynamics. eLife 2017. e25776
10. Teves SS; An L; Hansen AS; Xie L; Darzacq X^; Tjian R^. A dynamic mode of mitotic bookmarking by transcription factors. eLife 2016. e22280
9. Huang L; Pauleve L; Zechner C; Unger M; Hansen AS; Koeppl H^. Reconstructing dynamic molecular states from single-cell time series. Journal of The Royal Society Interface 2016, 13(122).
8. Hansen AS; O’Shea EK^. Encoding four gene expression programs in the activation dynamics of a single transcription factor. Current Biology 2016, 26(7), R269-271
7. Hansen AS; O’Shea EK^. Cis-determinants of promoter threshold and activation timescale. Cell Reports 2015, 12(8), 1226-1233.
6. Hansen AS; Hao N; O’Shea EK^. High-throughput microfluidics to control and measure signaling dynamics in single yeast cells. Nature Protocols 2015, 10(8), 1181-1197.
3. Wang Y; Jimenez M; Hansen AS; Raiber EA; Schreiber SL^; Young DW^. Control of olefin geometry in macrocyclic ring-closing metathesis using a removable silyl group. Journal of the American Chemical Society 2011, 133, 9196-9.
2. Thalhammer A; Hansen AS; El-Sagheer AH; Brown T; Schofield CJ^. Hydroxylation of methylated CpG dinucleotides reverses stabilisation of DNA duplexes by cytosine 5-methylation. Chemical Communications 2011, 47, 5325-7.
1. Hansen AS; Thalhammer A; El-Sagheer AH; Brown T; Schofield CJ^. Improved synthesis of 5-hydroxymethyl-2′-deoxycytidine phosphoramidite using a 2′-deoxyuridine to 2′-deoxycytidine conversion without temporary protecting groups. Bioorganic and Medicinal Chemistry Letters 2011, 21, 1181-4.