Publications

The following publications were published exclusively under the affiliation of the Max Planck Society. For publications by the principal investigator outside of the Max Planck Society, see the links on the lower left.

Journal Article (12)

Journal Article

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

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Journal Article

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

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publisher-version

Journal Article

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)

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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)

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pre-print

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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)

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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)

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Klimm, F.: Topological data analysis of truncated contagion maps. Chaos 32 (7), Article 073108 (2022)

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Journal Article

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)

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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 (6), pp. 981 - 995 (2022)

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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)

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supplementary-material

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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)

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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)

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Thesis - PhD (5)

Thesis - PhD

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

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Thesis - PhD

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

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Thesis - PhD

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

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Thesis - PhD

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

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Thesis - PhD

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

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Thesis - Master (1)

Thesis - Master

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

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