Detecting host responses to microbial stimulation using primary epithelial organoids

Bornholdt, J., Müller, C. V., Nielsen, M. J., Strickertsson, J., Rago, D., Chen, Y., Maciag, G., Skov, J., Wellejus, A., Schweiger, P. J., Hansen, S. L., Broholm, C., Gögenur, I., Maimets, M., Sloth, S., Hendel, J., Baker, A., Sandelin, A. & Jensen, K. B., 2023, In: Gut Microbes. 15, 2, 16 p., 2281012.

Research output: Contribution to journal › Journal article › Research › peer-review

Transcriptional and epigenomic profiling identifies YAP signaling as a key regulator of intestinal epithelium maturation

Pikkupeura, L. M., Bressan, R. B., Guiu, J., Chen, Y., Maimets, M., Mayer, D., Schweiger, P. J., Hansen, S. L., Maciag, G. J., Larsen, H. L., Lõhmussaar, K., Pedersen, M. T., Teves, J. M. Y., Bornholdt, J., Benes, V., Sandelin, A. & Jensen, K. B., 2023, In: Science Advances. 9, 28, 16 p., eadf9460.

Research output: Contribution to journal › Journal article › Research › peer-review

PAMP-triggered genetic reprogramming involves widespread alternative transcription initiation and an immediate transcription factor wave

Thieffry, A., López-Márquez, D., Bornholdt, J., Gholami Malekroudi, M., Bressendorff, S., Barghetti, A., Sandelin, A. & Brodersen, P., 2022, In: The Plant Cell. 34, 7, 23 p.

Research output: Contribution to journal › Journal article › Research › peer-review

Promoter sequence and architecture determine expression variability and confer robustness to genetic variants

Einarsson, H., Salvatore, M., Vaagenso, C., Alcaraz, N., Lange, J. B., Rennie, S. & Andersson, R., 2022, In: eLife. 2022, 36 p.

Research output: Contribution to journal › Journal article › Research › peer-review

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Grapotte, M., Saraswat, M., Bessière, C., Menichelli, C., Ramilowski, J. A., Severin, J., Hayashizaki, Y., Itoh, M., Tagami, M., Murata, M., Kojima-Ishiyama, M., Noma, S., Noguchi, S., Kasukawa, T., Hasegawa, A., Suzuki, H., Nishiyori-Sueki, H., Frith, M. C., Abugessaisa, I. & Aitken, S. & 31 others, Aken, B. L., Alam, I., Alam, T., Alasiri, R., Alhendi, A. M. N., Alinejad-Rokny, H., Alvarez, M. J., Andersson, R., Arakawa, T., Araki, M., Arbel, T., Bornholdt, J., Boyd, M., Chen, Y., Coskun, M., Dalby, M., Ienasescu, H., Jørgensen, M., Kaczkowski, B., Kere, J., Li, K., Lilje, B., Nepal, C., Nguyen, Q. H., Nielsen, L. K., Rennie, S., Sandelin, A., Valen, E., Vitezic, M., Vitting-Seerup, K. & FANTOM Consortium, 2021, In: Nature Communications. 12, 18 p., 3297.

Research output: Contribution to journal › Journal article › Research › peer-review

Characterization of Arabidopsis thaliana Promoter Bidirectionality and Antisense RNAs by Inactivation of Nuclear RNA Decay Pathways

Thieffry, A., Vigh, M. L., Bornholdt, J., Ivanov, M., Brodersen, P. & Sandelin, A., 2020, In: The Plant Cell. 32, 6, p. 1845-1867 23 p.

Research output: Contribution to journal › Journal article › Research › peer-review

Personalized B cell response to the Lactobacillus rhamnosus GG probiotic in healthy human subjects: a randomized trial

Bornholdt, J., Chen, Y., Rago, A., Sloth, S., Hendel, J., Melsæther, C., Müller, C. V., Juul Nielsen, M., Strickertsson, J., Engelholm, L., Vitting-Seerup, K., Jensen, K. B., Baker, A. & Sandelin, A., 9 Nov 2020, In: Gut Microbes. 12, 1, p. 1-14 14 p.

Research output: Contribution to journal › Journal article › Research › peer-review