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.
56. Eder M, Moene CJ, Dauban L, Magnitov M, Drayton J, de Haas M, Leemans C, Verkuilen M, de Wit E, Hansen AS, van Steensel B^. Functional maps of a genomic locus reveal confinement of an enhancer by its target gene. Science. 2025.
55. Nagano M, Hu B, Ogata K, Umemura F, Ishikura Y, Suzuki S, Katsifis CG, Yoshinaga M, Litos G, Nagasaka K, Tang W, Nosaka Y, Sasada H, Wang H, Kondo D, Katou Y, Mizuta K, Yabuta Y, Ohta H, de Luna Vitorino FN, Arima H, Ichikawa T, Gabriele M, Majewski J, Garcia BA, Takeuchi O, Yoshida S, Hansen AS, Peters JP, Ishihama Y, Saitou M^. The mitotic STAG3–cohesin complex shapes male germline nucleome. Nature Structural & Molecular Biology 2025
54. Zhang Z, Bao X, Jiang L, Luo X, Wang Y, Comai A, Waldhaus J, Hansen AS, Li W, Liu J^. Developing a general AI model for integrating diverse genomic modalities and comprehensive genomic knowledge. BioRxiv 2025.
53. Mazzocca M*, Narducci DN*, Grosse-Holz S*, Matthias J, Hansen AS^. Chromatin Dynamics are Highly Subdiffusive Across Seven Orders of Magnitude. BioRxiv 2025.
52. Hong CKY*, Feng F*, Ramanathan V, Liu J^, Hansen AS^. Genome structure mapping with high-resolution 3D genomics and deep learning. BioRxiv. 2025
50. Jusuf JM, Grosse-Holz S, Gabriele M, Mach P, Flyamer IM, Zechner C, Giorgetti L, Mirny L, Hansen AS^. Genome-wide absolute quantification of chromatin looping. BioRxiv 2025.
49. Goel VY, Aboreden NG, Jusuf JM, Zhang H, Mori L, Mirny LA, Blobel G, Banigan EJ^, Hansen AS^. Dynamics of microcompartment formation at the mitosis-to-G1 transition. Nature Structural and Molecular Biology 2025. BioRxiv 2024.
48. Aboreden NG, Lam JC, Goel VY, Wang S, Wang X, Midla SC, Quijano A, Keller CA, Giardine BM, Hardison RC, Zhang H, Hansen AS, Blobel GA^. LDB1 establishes multi-enhancer networks to regulate gene expression. Molecular Cell 2025. BioRxiv. 2024.
47. Nemsick S, Hansen AS. Molecular models of bidirectional promoter regulation. Current Opinion in Structural Biology. 2024.
46. Waterbury AL, Kwok HS, Lee C, Narducci DN, Freedy AM, Su C, Raval S, Reiter AH, Hawkins W, Lee K, Li J, Hoenig SM, Vinyard ME, Cole PA, Hansen AS, Carr SA, Papanastasiou M, Liau BB. An autoinhibitory switch of the LSD1 disordered region controls enhancer silencing. Molecular Cell. 2024.
45. Schlissel G, Meziane M, Narducci DN, Hansen AS, Li P+. Diffusion barriers imposed by tissue topology shape Hedgehog morphogen gradients.  PNAS 2024 BioRxiv 2024.
43. Kim KL, Rahme GJ, Goel VY, El Farran CA, Hansen AS, Bernstein BE. Dissection of a CTCF topological boundary uncovers principles of enhancer-oncogene regulation. Molecular Cell. 2024.
42. Yang JH, Hansen AS. Enhancer selectivity in space and time: from enhancer-promoter interactions to promoter activation. Nature Reviews Molecular Cell Biology 2024.
41. Do C*, Jiang G, Katsifis CC, Narducci DN, Yang J, Cova G, Sakellaropoulos T, Vidal R, Lhoumaud P, Regis FF, Kakabadze N, Nora EP, Noyes M, Chen X, Hansen AS, Skok JA+. Brain and cancer associated binding domain mutations provide insight into CTCF′s relationship with chromatin and its ability to act as a chromatin organizer.  Cell Genomics 2025. BioRxiv 2024.
40. Sept CE, Tak E, Cerda-Smith CG, Hutchinson HM, Goel VY, Blanchette M, Bhakta MS, Hansen AS, Joung JK, Johnstone SE, Eyler CE, Aryee MJ+. High-resolution CTCF footprinting reveals impact of chromatin state on cohesin extrusion dynamics. Nature Commenucations 2025. BioRxiv 2023.
39. Cerda-Smith C*, Hutchinson HM*, Liu A, Goel VY, Sept C, Kim H, Casaní-Galdón S, Burkman KG, Bassil CF, Hansen AS, Aryee MJ, Johnstone SE, Eyler CE+, Wood KC+. Integrative PTEN Enhancer Discovery Reveals a New Model of Enhancer Organization. BioRxiv 2023.
37. Drayton JA, Hansen AS^. Right on target:  Chromatin jets arise from targeted cohesin loading in wild-type cells. Molecular Cell. 2022. Volume 82, Issue 20, Pages 3769-3780.e5
35. Narducci D, Hansen, AS^. Reeling it in: how DNA topology drives loop extrusion by condensin. Nature Structural and Molecular Biology. 2022.
34. Mahadevan J, Jha A, Rudolph J, Bowerman S, Narducci D, Hansen AS, Luger K. Dynamics of endogenous PARP1 and PARP2 during DNA damage revealed by live-cell single-molecule imaging. iScience 2023. BioRxiv. 2022.
32. Gabriele M*, Brandão HB*, Grosse-Holz S*, Jha A, Dailey GM, Cattoglio C, Hsieh THS, Mirny L^, Zechner C^, Hansen AS^. Dynamics of CTCF and cohesin mediated chromatin looping revealed by live-cell imaging. Science, 2022. BioRxiv 2021
31. Yang HY, Brandão HB^, Hansen AS^. DNA double-strand break end synapsis by DNA loop extrusion. Nature Communications, 2023. BioRxiv 2021
30. Hsieh TSH*, Cattoglio C*, Slobodyanyuk E, Hansen AS, Darzacq X^, Tjian R^. Enhancer-promoter interactions and transcription are maintained upon 1 acute loss of CTCF, Cohesin, WAPL, and YY1. Nature Genetics 2022. BioRxiv, 2021
29. Brandão HB*, Gabriele M*,  Hansen AS^. Tracking and interpreting long-range chromatin interactions with super-resolution live-cell imaging. Current Opinion in Cell Biology. 2021, 70, 18–26.
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.
24.  Hansen AS^; Zechner C^. Promoters adopt distinct dynamic manifestations depending on transcription factor context. Molecular Systems Biology, 2021, e9821. BioRxiv 2019.
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. BioRxiv 2019
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. BioRxiv 2018
21. Hansen AS*; Amitai A*; Cattoglio C; Tjian R^; Darzacq X^. Guided nuclear exploration increases CTCF target search efficiency. Nature Chemical Biology, 2019. BioRxiv 2018
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. BioRxiv 2018
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. BioRxiv 2018
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. BioRxiv 2018.
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. BioRxiv 2018.
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. BioRxiv 2017.
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. BioRxiv 2016.
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. BioRxiv 2016.
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.