List of publications

Klimm, F.; Jones, N. S.; Schaub, M. T.: Modularity Maximization for Graphons. SIAM Journal on Applied Mathematics 82 (6), pp. 1930 - 1952 (2022)

Klimm, F.: Quantifying the 'end of history' through a Bayesian Markov-chain approach. Royal Society Open Science 9 (11), 221131 (2022)

Schöpflin, R.; Melo, U. S.; Moeinzadeh, M. H.; Heller, D.; Laupert, V.; Hertzberg, J.; Holtgrewe, M.; Alavi, N.; Klever, M.-K.; Jungnitsch, J. et al.; Comak, E.; Türkmen, S.; Horn, D.; Duffourd, Y.; Faivre, L.; Callier, P.; Sanlaville, D.; Zuffardi, O.; Tenconi, R.; Kurtas, N. E.; Giglio, S.; Prager, B.; Latos-Bielenska, A.; Vogel, I.; Bugge, M.; Tommerup, N.; Spielmann, M.; Vitobello, A.; Kalscheuer, V. M.; Vingron, M.; Mundlos, S.: Integration of Hi-C with short and long-read genome sequencing reveals the structure of germline rearranged genomes. Nature Communications 13 (1), 6470 (2022)

Schindler, M.; Osterwalder, M.; Harabula, I.; Wittler, L.; Tzika, A. C.; Dechmann, D.; Vingron, M.; Visel, A.; Haas, S.; Real, F. M.: Co-option of the transcription factor SALL1 in mole ovotestis formation. bioRxiv, 514220 (2022)

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)

Pevzner, P.; Vingron, M.; Reidys, C.; Sun, F.; Istrail, S.: Michael Waterman's Contributions to Computational Biology and Bioinformatics. Journal of Computational Biology 29 (7), pp. 601 - 615 (2022)

Klimm, F.: Topological data analysis of truncated contagion maps. Chaos 32, 073108 (2022)

Baranasic, D.; Hörtenhuber, M.; Balwierz, P.; Zehnder, T.; Mukarram, A. K.; Nepal, C.; Varnai, C.; Hadzhiev, Y.; Jimenez- Gonzalez, A.; Li, N. et al.; Wragg, J.; D’Orazio, F.; Díaz, N.; Hernández- Rodríguez, B.; Chen, Z.; Stoiber, M.; Dong, M.; Stevens, I.; Ross, S. E.; Eagle, A.; Martin, R.; Obasaju, P.; Rastegar, S.; McGarvey, A. C.; Kopp, W.; Chambers, E.; Wang, D.; Kim, H. R.; Acemel, R. D.; Naranjo, S.; Lapinski, M.; Chong, V.; Mathavan, S.; Peers, B.; Sauka-Spengler, T.; Vingron, M.; Carninci, P.; Ohler, U.; Lacadie, S. A.; Burgess, S.; Winata, C.; van Eeden, F.; Vaquerizas, J. M.; Gómez-Skarmeta, J. L.; Onichtchouk, D.; Brown, B. J.; Bogdanovic, O.; Westerfield, M.; Wardle, F. C.; Daub, C. O.; Lenhard, B.; Müller, F.: Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements. Nature Genetics 54 (7), pp. 1037 - 1050 (2022)

Rosebrock, D.; Arora, S.; Mutukula, N.; Volkman, R.; Gralinska, E.; Balaskas, A.; Aragonés Hernández, A.; Buschow, R.; Brändl, B.; Müller, F.-J. et al.; Arndt, P. F.; Vingron, M.; Elkabetz, Y.: Enhanced cortical neural stem cell identity through short SMAD and WNT inhibition in human cerebral organoids facilitates emergence of outer radial glial cells. Nature Cell Biology 24, pp. 981 - 995 (2022)

Li, Y.; Chen, S.; Rapakoulia, T.; Kuwahara, H.; Yip, K. Y.; Gao, X.: Deep learning identifies and quantifies recombination hotspot determinants. Bioinformatics 38 (10), pp. 2683 - 2691 (2022)

Gralinska, E.; Kohl, C.; Fadakar, S.; Vingron, M.: Visualizing Cluster-specific Genes from Single-cell Transcriptomics Data Using Association Plots. Journal of Molecular Biology 434 (11), 167525 (2022)

Hertzberg, J.; Mundlos, S.; Vingron, M.; Gallone, G.: TADA – a Machine Learning Tool for Functional Annotation based Prioritisation of Putative Pathogenic CNVs. Genome Biology 23 (1), 67 (2022)

Ly, L.-H.: Deciphering cellular heterogeneity by single-cell transcriptome analysis. Dissertation, xiii, 131 pp. (2022)

Kleinert, P.: Computational interpretation of disease-causing, structural, and non-coding human genetic variants. Dissertation, 118 pp. (2022)

Gajos, M.: Analysis of the determinants of Pol II pausing. Dissertation, vi, 125 pp. (2022)

Abdullaev, E.: Dynamical Aspects of the Evolution of Segmental Duplications in the Human Genome. Dissertation, xiii, 129 pp. (2022)

Gralinska, E.: Association Plots visualize cluster-specific genes from high-dimensional transcriptomics data. Dissertation, vi, 108 pp. (2022)

Alavi, N.: An Unsupervised Learning Approach For Understanding Biases In Structural Variant Detection. Master (2022)