Publikationen von Daniel M. Ibrahim

Michael-Florian Szalay , Blanka Majchrzycka, Ivana Jerković, Giacomo Cavalli, and Daniel M. Ibrahim, "Evolution and function of chromatin domains across the tree of life," Nature Structural & Molecular Biology 31 (12), 1824-1837 (2024).

Mai H. Q. Phan, Tobias Zehnder, Fiona Puntieri, Bai-Wei Lo, Boris Lenhard, Ferenc Mueller, Martin Vingron, and Daniel M. Ibrahim, "Conservation of Regulatory Elements with Highly Diverged Sequences Across Large Evolutionary Distances," bioRxiv (2024).

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

Xingfan Huang, Jana Henck, Chengxiang Qiu, Varun K. A. Sreenivasan, Saranya Balachandran, Oana V. Amarie, Martin Hrabě de Angelis, Rose Yinghan Behncke, Wing-Lee Chan, Alexandra Despang, Diane E. Dickel, Madeleine Duran, Annette Feuchtinger, Helmut Fuchs, Valerie Gailus-Durner, Natja Haag, Rene Hägerling, Nils Hansmeier, Friederike Hennig, Cooper Marshall, Sudha Rajderkar, Alessa Ringel, Michael I. Robson, Lauren M. Saunders, Patricia da Silva-Buttkus, Nadine Spielmann, Sanjay R. Srivatsan, Sascha Ulferts, Lars Wittler, Yiwen Zhu, Vera M. Kalscheuer, Daniel M. Ibrahim, Ingo Kurth, Uwe Kornak, Axel Visel, Len A. Pennacchio, David R. Beier, Cole Trapnell, Junyue Cao, Jay Shendure, and Malte Spielmann, "Single-cell, whole-embryo phenotyping of mammalian developmental disorders," Nature 623 (7988), 772-781 (2023).

Alessa Ringel, Quentin Szabo, Andrea M. Chiariello, Konrad Chudzik, Robert Schöpflin, Patricia Rothe, Alexandra L. Mattei, Tobias Zehnder, Dermot Harnett, Verena Laupert, Simona Bianco, Sara Hetzel, Juliane Glaser, Mai H. Q. Phan, Magdalena Schindler, Daniel M. Ibrahim, Christina Paliou, Andrea Esposito, César A. Prada-Medina, Stefan A. Haas, Peter Giere, Martin Vingron, Lars Wittler, Alexander Meissner, Mario Nicodemi, Giacomo Cavalli, Frédéric Bantignies, Stefan Mundlos, and Michael I. Robson, "Repression and 3D-restructuring resolves regulatory conflicts in evolutionarily rearranged genomes," Cell 185 (20), 3689-3704 (2022).

Shaon Basu, Sebastian Mackowiak, Henri Niskanen, Dora Knezevic, Vahid Asimi, Stefanie Grosswendt, Hylkje Geertsema, Salaheddine Ali, Ivana Jerković, Helge Ewers, Stefan Mundlos, Alexander Meissner, Daniel M. Ibrahim, and Denes Hnisz, "Unblending of Transcriptional Condensates in Human Repeat Expansion Disease," Cell 181 (5), 1062-1079 (2020).

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

Alexandra Despang, Robert Schöpflin, Martin Franke, Salaheddine Ali, Ivana Jerković, Christina Paliou, Wing-Lee Chan, Bernd Timmermann, Lars Wittler, Martin Vingron, Stefan Mundlos, and Daniel M. Ibrahim, "Functional dissection of the Sox9-Kcnj2 locus identifies nonessential and instructive roles of TAD architecture," Nature Genetics 51 (8), 1263-1271 (2019).

Katerina Kraft, Andreas Magg, Verena Heinrich, Christina Riemenschneider, Robert Schöpflin, Julia Markowski, Daniel Ibrahim, Rocío Acuna-Hidalgo, Alexandra Despang, Guillaume Andrey, Lars Wittler, Bernd Timmermann, Martin Vingron, and Stefan Mundlos, "Serial genomic inversions induce tissue-specific architectural stripes, gene misexpression and congenital malformations," Nature Cell Biology 21 (3), 305-310 (2019).

Luis Rodrigo Hernandez-Miranda, Daniel Ibrahim, Pierre-Louis Ruffault, Madeleine Larrosa, Kira Balueva, Thomas Müller, Willemien de Weerd, Irene Stolte-Dijkstra, Robert M. W. Hostra, Jean-François Brunet, Gilles Fortin, Stefan Mundlos, and Carmen Birchmeier, "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), 13021-13026 (2018).

Pedro Vallecillo-García, Mickael Orgeur, Sophie vom Hofe-Schneider, Jürgen Stumm, Verena Kappert, Daniel Ibrahim, Stefan T. Börno, Shinichiro Hayashi, Frédéric Relaix, Katrin Hildebrandt, Gerhard Sengle, Manuel Koch, Bernd Timmermann, Giovanna Marazzi, David A. Sassoon, Delphine Duprez, and Sigmar Stricker, "Odd skipped-related 1 identifies a population of embryonic fibro-adipogenic progenitors regulating myogenesis during limb development," Nature Communications 8 (1), 1218 (2017).

Guillaume Andrey, Robert Schöpflin, Ivana Jerković, Verena Heinrich, Daniel Ibrahim, Christina Paliou, Myriam Hochradel, Bernd Timmermann, Stefan Haas, Martin Vingron, and Stefan Mundlos, "Characterization of hundreds of regulatory landscapes in developing limbs reveals two regimes of chromatin folding," Genome Research 27 (2), 223-233 (2017).

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

Martin Franke, Daniel Ibrahim, Guillaume Andrey, Wibke Schwarzer, Verena Heinrich, Robert Schöpflin, Katerina Kraft, Rieke Kempfer, Ivana Jerković, Wing-Lee Chan, Malte Spielmann, Bernd Timmermann, Lars Wittler, Ingo Kurth, Paola Cambiaso, Orsetta Zuffardi, Gunnar Houge, Lindsay Lambie, Francesco Brancati, Ana Pombo, Martin Vingron, Francois Spitz, and Stefan Mundlos, "Formation of novel chromatin domains determines pathogenicity of genomic duplications," Nature 538 (7624), 265-269 (2016).

Daniel Ibrahim, Naeimeh Tayebi, Alexej Knaus, Asita Carola Stiege, Afsaneh Sahebzamani, Jochen Hecht, Stefan Mundlos, and Malte Spielmann, "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), 615-621 (2016).

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

Daniel Ibrahim, Peter Hansen, Christian Rödelsperger, Asita C. Stiege, Sandra C. Doelken, Denise Horn, Marten Jäger, Catrin Janetzki, Peter Krawitz, Gundula Leschik, Florian Wagner, Till Scheuer, Mareen Schmidt-von Kegler, Petra Seemann, Bernd Timmermann, Peter N. Robinson, Stefan Mundlos, and Jochen Hecht, "Distinct global shifts in genomic binding profiles of limb malformation associated HOXD13 mutations," Genome Research 23 (12), 2091-2102 (2013).

Robert Schöpflin, Guillaume Andrey, Verena Heinrich, Martin Franke, Daniel Ibrahim, Christina Paliou, Stefan Mundlos, and Martin Vingron, "Identification of potential regulatory elements in Capture-C interaction profiles", in Genome Regulation in 3D, (Weizmann Institute, Rehovot, Israel, 2015).

Daniel Ibrahim and Darío García Lupiáñez, "LilBUBome - Why would you crowdfund a cute cat?", (2016).

Daniel Ibrahim, ChIP-seq Reveals Mutation-Specific Pathomechanismus of HOXD13 Missense Mutations, PhD Thesis, Humboldt University, FB Mathemathik, 2014.