Publications of Daniel M. Ibrahim

Szalay , M.-F.; Majchrzycka, B.; Jerković, I.; Cavalli, G.; Ibrahim, D. M.: Evolution and function of chromatin domains across the tree of life. Nature Structural & Molecular Biology 31 (12), pp. 1824 - 1837 (2024)

Phan, M. H. Q.; Zehnder, T.; Puntieri, F.; Lo, B.-W.; Lenhard, B.; Mueller, F.; Vingron, M.; Ibrahim, D. M.: Conservation of Regulatory Elements with Highly Diverged Sequences Across Large Evolutionary Distances. bioRxiv (2024)

Ibrahim, D. M.: Enhancer contacts during embryonic development show diverse interaction modes and modest yet significant increases upon gene activation. Nature Genetics 56 (4), pp. 558 - 560 (2024)

Huang, X.; Henck, J.; Qiu, C.; Sreenivasan, V. K. A.; Balachandran, S.; Amarie, O. V.; de Angelis, M. H.; Behncke, R. Y.; Chan, W.-L.; Despang, A. et al.; Dickel, D. E.; Duran, M.; Feuchtinger, A.; Fuchs, H.; Gailus-Durner, V.; Haag, N.; Hägerling, R.; Hansmeier, N.; Hennig, F.; Marshall, C.; Rajderkar, S.; Ringel, A.; Robson, M. I.; Saunders, L. M.; da Silva-Buttkus, P.; Spielmann, N.; Srivatsan, S. R.; Ulferts, S.; Wittler, L.; Zhu, Y.; Kalscheuer, V. M.; Ibrahim, D. M.; Kurth, I.; Kornak, U.; Visel, A.; Pennacchio, L. A.; Beier, D. R.; Trapnell, C.; Cao, J.; Shendure, J.; Spielmann, M.: Single-cell, whole-embryo phenotyping of mammalian developmental disorders. Nature 623 (7988), pp. 772 - 781 (2023)

Ringel, A.; Szabo, Q.; Chiariello, A. M.; Chudzik, K.; Schöpflin, R.; Rothe, P.; Mattei, A. L.; Zehnder, T.; Harnett, D.; Laupert, V. et al.; Bianco, S.; Hetzel, S.; Glaser, J.; Phan, M. H. Q.; Schindler, M.; Ibrahim, D. M.; Paliou, C.; Esposito, A.; Prada-Medina, C. A.; Haas, S. A.; Giere, P.; Vingron, M.; Wittler, L.; Meissner, A.; Nicodemi, M.; Cavalli, G.; Bantignies, F.; Mundlos, S.; Robson, M. I.: Repression and 3D-restructuring resolves regulatory conflicts in evolutionarily rearranged genomes. Cell 185 (20), pp. 3689 - 3704 (2022)

Basu, S.; Mackowiak, S.; Niskanen, H.; Knezevic, D.; Asimi, V.; Grosswendt, S.; Geertsema, H.; Ali, S.; Jerković, I.; Ewers, H. et al.; Mundlos, S.; Meissner, A.; Ibrahim, D. M.; Hnisz, D.: Unblending of Transcriptional Condensates in Human Repeat Expansion Disease. Cell 181 (5), pp. 1062 - 1079 (2020)

Ibrahim, D. M.; Mundlos, S.: The role of 3D chromatin domains in gene regulation: a multi-facetted view on genome organization. Current Opinion in Genetics & Development 61, pp. 1 - 8 (2020)

Despang, A.; Schöpflin, R.; Franke, M.; Ali, S.; Jerković, I.; Paliou, C.; Chan, W.-L.; Timmermann, B.; Wittler, L.; Vingron, M. et al.; Mundlos, S.; Ibrahim, D. M.: Functional dissection of the Sox9-Kcnj2 locus identifies nonessential and instructive roles of TAD architecture. Nature Genetics 51 (8), pp. 1263 - 1271 (2019)

Kraft, K.; Magg, A.; Heinrich, V.; Riemenschneider, C.; Schöpflin, R.; Markowski, J.; Ibrahim, D.; Acuna-Hidalgo, R.; Despang, A.; Andrey, G. et al.; Wittler, L.; Timmermann, B.; Vingron, M.; Mundlos, S.: Serial genomic inversions induce tissue-specific architectural stripes, gene misexpression and congenital malformations. Nature Cell Biology 21 (3), pp. 305 - 310 (2019)

Hernandez-Miranda, L. R.; Ibrahim, D.; Ruffault, P.-L.; Larrosa, M.; Balueva, K.; Müller, T.; Weerd, W. d.; Stolte-Dijkstra, I.; Hostra, R. M. W.; Brunet, J.-F. et al.; Fortin, G.; Mundlos, S.; Birchmeier, C.: Mutation in LBX1/Lbx1 precludes transcription factor cooperativity and causes congenital hypoventilation in humans and mice. Proceedings of the National Academy of Sciences of the United States of America 115 (51), pp. 13021 - 13026 (2018)

Vallecillo-García, P.; Orgeur, M.; vom Hofe-Schneider, S.; Stumm, J.; Kappert, V.; Ibrahim, D.; Börno, S. T.; Hayashi, S.; Relaix, F.; Hildebrandt, K. et al.; Sengle, G.; Koch, M.; Timmermann, B.; Marazzi, G.; Sassoon, D. A.; Duprez, D.; Stricker, S.: Odd skipped-related 1 identifies a population of embryonic fibro-adipogenic progenitors regulating myogenesis during limb development. Nature Communications 8 (1), 1218 (2017)

Andrey, G.; Schöpflin, R.; Jerković, I.; Heinrich, V.; Ibrahim, D.; Paliou, C.; Hochradel, M.; Timmermann, B.; Haas, S.; Vingron, M. et al.; Mundlos, S.: Characterization of hundreds of regulatory landscapes in developing limbs reveals two regimes of chromatin folding. Genome Research 27 (2), pp. 223 - 233 (2017)

Jerković, I.; Ibrahim, D.; Andrey, G.; Haas, S.; Hansen, P.; Janetzki, C.; Gonzalez Navarrete, I.; Robinson, P. N.; Hecht, J.; Mundlos, S.: Genome-Wide Binding of Posterior HOXA/D Transcription Factors Reveals Subgrouping and Association with CTCF. PLoS Genetics 13 (1), e1006567 (2017)

Franke, M.; Ibrahim, D.; Andrey, G.; Schwarzer, W.; Heinrich, V.; Schöpflin, R.; Kraft, K.; Kempfer, R.; Jerković, I.; Chan, W.-L. et al.; Spielmann, M.; Timmermann, B.; Wittler, L.; Kurth, I.; Cambiaso, P.; Zuffardi, O.; Houge, G.; Lambie, L.; Brancati, F.; Pombo, A.; Vingron, M.; Spitz, F.; Mundlos, S.: Formation of novel chromatin domains determines pathogenicity of genomic duplications. Nature 538 (7624), pp. 265 - 269 (2016)

Ibrahim, D.; Tayebi, N.; Knaus, A.; Stiege, A. C.; Sahebzamani, A.; Hecht, J.; Mundlos, S.; Spielmann, M.: A homozygous HOXD13 missense mutation causes a severe form of synpolydactyly with metacarpal to carpal transformation. American Journal of Medical Genetics Part A 170 (3), pp. 615 - 621 (2016)

Kraft, K.; Geuer, S.; Will, A. J.; Chan, W. L.; Paliou, C.; Borschiwer, M.; Harabula, I.; Wittler, L.; Franke, M.; Ibrahim, D. et al.; Kragesteen, B. K.; Spielmann, M.; Mundlos, S.; Lupianez, D. G.; Andrey, G.: Deletions, Inversions, Duplications: Engineering of Structural Variants using CRISPR/Cas in Mice. Cell Reports 10 (5), pp. 833 - 839 (2015)

Ibrahim, D.; Hansen, P.; Rödelsperger, C.; Stiege, A. C.; Doelken, S. C.; Horn, D.; Jäger, M.; Janetzki, C.; Krawitz, P.; Leschik, G. et al.; Wagner, F.; Scheuer, T.; Schmidt-von Kegler, M.; Seemann, P.; Timmermann, B.; Robinson, P. N.; Mundlos, S.; Hecht, J.: Distinct global shifts in genomic binding profiles of limb malformation associated HOXD13 mutations. Genome Research 23 (12), pp. 2091 - 2102 (2013)

Schöpflin, R.; Andrey, G.; Heinrich, V.; Franke, M.; Ibrahim, D.; Paliou, C.; Mundlos, S.; Vingron, M.: Identification of potential regulatory elements in Capture-C interaction profiles. In: Genome Regulation in 3D. Genome Regulation in 3D, Rehovot, Israel, June 28, 2015 - June 30, 2015. Weizmann Institute, Rehovot, Israel (2015)

Ibrahim, D.; Lupiáñez, D. G.: LilBUBome - Why would you crowdfund a cute cat? Open Science Days 2016, Berlin (2016)

Ibrahim, D.: ChIP-seq Reveals Mutation-Specific Pathomechanismus of HOXD13 Missense Mutations. Dissertation, Humboldt University, FB Mathemathik, Berlin (2014)