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.
28. Goel VY, Hansen AS. The macro and micro of chromosome conformation capture. WIREs Developmental Biology. 2020.
27. Agbleke AA, Amitai A, Buenrostro JD, Chakrabarti A, Chu L, Hansen AS, Koenig KM, Labade AS, Liu S, Nozaki T, Ovchinnikov S. Advances in Chromatin and Chromosome Research: Perspectives from Multiple Fields. Molecular Cell. 2020.
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.