Publications since 2019

August 21, 2024
2024
  1. Batki, J., Hetzel, S., Schifferl, D., Bolondi, A., Walther, M., Wittler, L., Grosswendt, S., Herrmann, B. G., & Meissner, A. (2024). Extraembryonic gut endoderm cells undergo programmed cell death during development. Nat Cell Biol. https://doi.org/10.1038/s41556-024-01431-w
  2. Belicova, L., Bebelman, M., Gralinska, E., Jumel, T., Lahree, A., Shevchenko, A., Zatsepin, T., Kalaidzidis, Y., Vingron, M., & Zerial, M. (2024). Hepatocyte differentiation requires anisotropic expansion of bile canaliculi. bioRxiv, 2024.2002.2019.581065. https://doi.org/10.1101/2024.02.19.581065
  3. Campana, P. A., Prasse, P., Lienhard, M., Thedinga, K., Herwig, R., & Scheffer, T. (2024). Cancer drug sensitivity estimation using modular deep Graph Neural Networks. NAR Genomics and Bioinformatics,6(2). https://doi.org/10.1093/nargab/lqae043
  4. Dimartino, P., Zadorozhna, M., Yumiceba, V., Basile, A., Cani, I., Melo, U. S., Henck, J., Breur, M., Tonon, C., Lodi, R., Brusco, A., Pippucci, T., Koufi, F. D., Boschetti, E., Ramazzotti, G., Manzoli, L., Ratti, S., Pinto, E. V. F., Delatycki, M. B., . . . Giorgio, E. (2024). Structural Variants at the LMNB1 Locus: Deciphering Pathomechanisms in Autosomal Dominant Adult-Onset Demyelinating Leukodystrophy. Ann Neurol. https://doi.org/10.1002/ana.27038
  5. Guckelberger, P., Doughty, B. R., Munson, G., Rao, S. S. P., Tan, Y., Cai, X. S., Fulco, C. P., Nasser, J., Mualim, K. S., Bergman, D. T., Ray, J., Jagoda, E., Munger, C. J., Gschwind, A. R., Sheth, M. U., Tan, A. S., Pulido, S. G., Mitra, N., Weisz, D., . . . Engreitz, J. M. (2024). Cohesin-mediated 3D contacts tune enhancer-promoter regulation. bioRxiv, 2024.2007.2012.603288. https://doi.org/10.1101/2024.07.12.603288
  6. Hauswedell, H., Hetzel, S., Gottlieb, S. G., Kretzmer, H., Meissner, A., & Reinert, K. (2024). Lambda3: homology search for protein, nucleotide, and bisulfite-converted sequences. Bioinformatics, 40(3). https://doi.org/10.1093/bioinformatics/btae097
  7. Iyer*, D. P., Moyon*, L., Wittler, L., Cheng, C. Y., Ringeling, F. R., Canzar, S., Marsico, A., & Bulut-Karslioglu, A. (2024). Combinatorial microRNA activity is essential for the transition of pluripotent cells from proliferation into dormancy. Genome Res. https://doi.org/10.1101/gr.278662.123
  8. Jourdain, C., Eichstädt, B., & Schubert, D. (2024 (in press)). A protocol for using histone peptide arrays and testing protein-histone peptide interactions in vitro. In Springer (Ed.), Plant Chromatin Dynamics: Methods and Protocols.
  9. Kanata, E., Duffié, R., & Schulz, E. G. (2024). Establishment and maintenance of random monoallelic expression. Development, 151(10). https://doi.org/10.1242/dev.201741
  10. Martitz, A., & Schulz, E. G. (2024). Spatial orchestration of the genome: topological reorganisation during X-chromosome inactivation. Current Opinion in Genetics & Development, 86, 102198. https://doi.org/https://doi.org/10.1016/j.gde.2024.102198
  11. Mutzel, V., Schwämmle, T., Oeverdieck, S., Librenjak, L., Boesen, B., Bothe, M., Gjaltema, R. A., Dunkel, I., Noviello, G., & Schulz, E. G. (2024). Antisense transcription can induce expression memory via stable promoter repression. bioRxiv, 2024.2003.2006.583761. https://doi.org/10.1101/2024.03.06.583761
  12. Naderi, J., Magalhaes, A. P., Kibar, G., Stik, G., Zhang, Y., Mackowiak, S. D., Wieler, H. M., Rossi, F., Buschow, R., Christou-Kent, M., Alcoverro-Bertran, M., Graf, T., Vingron, M., & Hnisz, D. (2024). An activity-specificity trade-off encoded in human transcription factors. Nature Cell Biology. https://doi.org/10.1038/s41556-024-01411-0
  13. Raaz, L., Mendez, P. L., Mundlos, S., Knaus, P., & Jatzlau, J. (2024). Protocol for chromatin accessibility profiling of human endothelial cells cultured under fluid shear stress using ATAC-seq. STAR Protoc,5(1), 102859. https://doi.org/10.1016/j.xpro.2024.102859
  14. Rosebrock, D., Vingron, M., & Arndt, P. F. (2024). Modeling gene expression cascades during cell state transitions. iScience, 27(4), 109386. https://doi.org/10.1016/j.isci.2024.109386
  15. Schimunek, J., Seidl, P., Elez, K., Hempel, T., Le, T., Noe, F., Olsson, S., Raich, L., Winter, R., Gokcan, H., Gusev, F., Gutkin, E. M., Isayev, O., Kurnikova, M. G., Narangoda, C. H., Zubatyuk, R., Bosko, I. P., Furs, K. V., Karpenko, A. D., . . . Hermans, T. M. (2024). A community effort in SARS-CoV-2 drug discovery. Mol Inform, 43(1), e202300262. https://doi.org/10.1002/minf.202300262
  16. Schnitzler, G. R., Kang, H., Fang, S., Angom, R. S., Lee-Kim, V. S., Ma, X. R., Zhou, R., Zeng, T., Guo, K., Taylor, M. S., Vellarikkal, S. K., Barry, A. E., Sias-Garcia, O., Bloemendal, A., Munson, G., Guckelberger, P., Nguyen, T. H., Bergman, D. T., Hinshaw, S., . . . Engreitz, J. M. (2024). Convergence of coronary artery disease genes onto endothelial cell programs. Nature, 626(8000), 799-807. https://doi.org/10.1038/s41586-024-07022-x
  17. Stötzel, M., Cheng, C.-Y., Iiik, I. A., Kumar, A. S., Omgba, P. A., van der Weijden, V. A., Zhang, Y., Vingron, M., Meissner, A., Aktaş, T., Kretzmer, H., & Bulut-Karslioğlu, A. (2024). TET activity safeguards pluripotency throughout embryonic dormancy. Nature Structural & Molecular Biology. https://doi.org/10.1038/s41594-024-01313-7
  18. Ulicevic, J., Shao, Z., Jasnovidova, O., Bressin, A., Gajos, M., Ng, A. H., Annaldasula, S., Meierhofer, D., Church, G. M., Busskamp, V., & Mayer, A. (2024). Uncovering the dynamics and consequences of RNA isoform changes during neuronal differentiation. Mol Syst Biol. https://doi.org/10.1038/s44320-024-00039-4
  19. van der Weijden, V. A., Stotzel, M., Iyer, D. P., Fauler, B., Gralinska, E., Shahraz, M., Meierhofer, D., Vingron, M., Rulands, S., Alexandrov, T., Mielke, T., & Bulut-Karslioglu, A. (2024). FOXO1-mediated lipid metabolism maintains mammalian embryos in dormancy. Nat Cell Biol, 26(2), 181-193. https://doi.org/10.1038/s41556-023-01325-3
  20. Wang, L.-W., van der Toorn, W., Bohn, P., Hölzer, M., Smyth, R. P., & von Kleist, M. (2024). Sequencing accuracy and systematic errors of nanopore direct RNA sequencing. BMC Genomics, 25(1), 528. https://doi.org/10.1186/s12864-024-10440-w
  21. Wei, X., Rigopoulos, A., Lienhard, M., Pöhle-Kronawitter, S., Kotsaris, G., Franke, J., Berndt, N., Mejedo, J. O., Wu, H., Börno, S., Timmermann, B., Murgai, A., Glauben, R., & Stricker, S. (2024). Neurofibromin 1 controls metabolic balance and Notch-dependent quiescence of murine juvenile myogenic progenitors. Nature Communications, 15(1), 1393. https://doi.org/10.1038/s41467-024-45618-z
  22. Yan, M., Li, M., Wang, Y., Wang, X., Moeinzadeh, M. H., Quispe-Huamanquispe, D. G., Fan, W., Fang, Y., Wang, Y., Nie, H., Wang, Z., Tanaka, A., Heider, B., Kreuze, J. F., Gheysen, G., Wang, H., Vingron, M., Bock, R., & Yang, J. (2024). Haplotype-based phylogenetic analysis and population genomics uncover the origin and domestication of sweetpotato. Mol Plant, 17(2), 277-296. https://doi.org/10.1016/j.molp.2023.12.019
  23. Zhao, Y., Kohl, C., Rosebrock, D., Hu, Q., Hu, Y., & Vingron, M. (2024). CAbiNet: joint clustering and visualization of cells and genes for single-cell transcriptomics. Nucleic Acids Res. https://doi.org/10.1093/nar/gkae480
2023
  1. Abdullaev, E. T., Haridoss, D. A., & Arndt, P. F. (2023). Reconstruction of segmental duplication rates and associated genomic features by network analysis. bioRxiv, 2023.2003.2018.533287. https://doi.org/10.1101/2023.03.18.533287
  2. Basu*, S., Martinez-Cristobal*, P., Frigole-Vivas, M., Pesarrodona, M., Lewis, M., Szulc, E., Banuelos, C. A., Sanchez-Zarzalejo, C., Bielskute, S., Zhu, J., Pombo-Garcia, K., Garcia-Cabau, C., Zodi, L., Dockx, H., Smak, J., Kaur, H., Batlle, C., Mateos, B., Biesaga, M., . . . Salvatella, X. (2023). Rational optimization of a transcription factor activation domain inhibitor. Nat Struct Mol Biol, 30(12), 1958-1969. https://doi.org/10.1038/s41594-023-01159-5
  3. Bose, S., de Heus, C., Kennedy, M. E., Wang, F., Jentsch, T. J., Klumperman, J., & Stauber, T. (2023). Impaired Autophagic Clearance with a Gain-of-Function Variant of the Lysosomal Cl(-)/H(+) Exchanger ClC-7. Biomolecules, 13(12). https://doi.org/10.3390/biom13121799
  4. Bouabid, C., Rabhi, S., Thedinga, K., Barel, G., Tnani, H., Rabhi, I., Benkahla, A., Herwig, R., & Guizani-Tabbane, L. (2023). Host M-CSF induced gene expression drives changes in susceptible and resistant mice-derived BMdMs upon Leishmania major infection. Front Immunol, 14, 1111072. https://doi.org/10.3389/fimmu.2023.1111072
  5. Bressin, A., Jasnovidova, O., Arnold, M., Altendorfer, E., Trajkovski, F., Kratz, T. A., Handzlik, J. E., Hnisz, D., & Mayer, A. (2023). High-sensitive nascent transcript sequencing reveals BRD4-specific control of widespread enhancer and target gene transcription. Nat Commun, 14(1), 4971. https://doi.org/10.1038/s41467-023-40633-y
  6. Bryant, P., Kelkar, A., Guljas, A., Clementi, C., & Noé, F. (2023). Structure prediction of protein-ligand complexes from sequence information with Umol. bioRxiv, 2023.2011.2003.565471. https://doi.org/10.1101/2023.11.03.565471
  7. Charron, N. E., Musil, F., Guljas, A., Chen, Y., Bonneau, K., Pasos-Trejo, A. S., Venturin, J., Gusew, D., Zaporozhets, I., Krämer, A., Templeton, C., Kelkar, A., Durumeric, A. E. P., Olsson, S., Pérez, A., Majewski, M., Husic, B. E., Patel, A., De Fabritiis, G., . . . Clementi, C. (2023). Navigating protein landscapes with a machine-learned transferable coarse-grained model. ARXIV. https://doi.org/10.48550/arXiv.2310.18278
  8. Christou-Kent*, M., Cuartero*, S., Garcia-Cabau*, C., Ruehle, J., Naderi, J., Erber, J., Neguembor, M. V., Plana-Carmona, M., Alcoverro-Bertran, M., De Andres-Aguayo, L., Klonizakis, A., Julia-Vilella, E., Lynch, C., Serrano, M., Hnisz, D., Salvatella, X., Graf, T., & Stik, G. (2023). CEBPA phase separation links transcriptional activity and 3D chromatin hubs. Cell Rep, 42(8), 112897. https://doi.org/10.1016/j.celrep.2023.112897
  9. Dazzi, C., Mehl, J., Benamar, M., Gerhardt, H., Knaus, P., Duda, G. N., & Checa, S. (2023). External mechanical loading overrules cell-cell mechanical communication in sprouting angiogenesis during early bone regeneration. PLoS Comput Biol, 19(11), e1011647. https://doi.org/10.1371/journal.pcbi.1011647
  10. Durumeric, A. E. P., Charron, N. E., Templeton, C., Musil, F., Bonneau, K., Pasos-Trejo, A. S., Chen, Y., Kelkar, A., Noe, F., & Clementi, C. (2023). Machine learned coarse-grained protein force-fields: Are we there yet? Curr Opin Struct Biol, 79, 102533. https://doi.org/10.1016/j.sbi.2023.102533
  11. Eischer, N., Arnold, M., & Mayer, A. (2023). Emerging roles of BET proteins in transcription and co-transcriptional RNA processing. Wiley Interdiscip Rev RNA, 14(1), e1734. https://doi.org/10.1002/wrna.1734
  12. Gorriz, R. F., Volkenandt, S., & Imhof, P. (2023). Protonation-State Dependence of Hydration and Interactions in the Two Proton-Conducting Channels of Cytochrome c Oxidase. Int J Mol Sci, 24(13). https://doi.org/10.3390/ijms241310464
  13. Gralinska, E., & Vingron, M. (2023). Association Plots: visualizing cluster-specific associations in high-dimensional correspondence analysis biplots. Journal of the Royal Statistical Society Series C: Applied Statistics, 72(4), 1023-1040. https://doi.org/10.1093/jrsssc/qlad039
  14. Heise, V., Holman, C., Lo, H., Lyras, E. M., Adkins, M. C., Aquino, M. R. J., Bougioukas, K. I., Bray, K. O., Gajos, M., Guo, X., Hartling, C., Huerta-Gutierrez, R., Jindrova, M., Kenney, J. P. M., Kepinska, A. P., Kneller, L., Lopez-Rodriguez, E., Muhlensiepen, F., Richards, A., . . . Weissgerber, T. L. (2023). Ten simple rules for implementing open and reproducible research practices after attending a training course. PLoS Comput Biol, 19(1), e1010750. https://doi.org/10.1371/journal.pcbi.1010750
  15. Huang*, X., Henck*, J., Qiu*, C., Sreenivasan, V. K. A., Balachandran, S., Amarie, O. V., Hrabe de Angelis, M., Behncke, R. Y., Chan, W. L., Despang, A., Dickel, D. E., Duran, M., Feuchtinger, A., Fuchs, H., Gailus-Durner, V., Haag, N., Hagerling, R., Hansmeier, N., Hennig, F., . . . Spielmann, M. (2023). Single-cell, whole-embryo phenotyping of mammalian developmental disorders. Nature,623(7988), 772-781. https://doi.org/10.1038/s41586-023-06548-w
  16. Iyer*, D. P., Weijden*, V. A. v. d., Khoei, H. H., McCarthy, A., Rayon, T., Simon, C. S., Dunkel, I., Wamaitha, S. E., Elder, K., Snell, P., Christie, L., Schulz, E. G., Niakan, K. K., Rivron, N., & Bulut-Karslioglu, A. (2023). Delay of human early development via in vitro diapause. bioRxiv, 2023.2005.2029.541316. https://doi.org/10.1101/2023.05.29.541316
  17. Jatzlau, J., Burdzinski, W., Trumpp, M., Obendorf, L., Rossmann, K., Ravn, K., Hyvonen, M., Bottanelli, F., Broichhagen, J., & Knaus, P. (2023). A versatile Halo- and SNAP-tagged BMP/TGFbeta receptor library for quantification of cell surface ligand binding. Commun Biol, 6(1), 34. https://doi.org/10.1038/s42003-022-04388-4
  18. Jatzlau, J., Mendez*, P. L., Altay*, A., Raaz, L., Zhang, Y., Mahr, S., Sesver, A., Reichenbach, M., Mundlos, S., Vingron, M., & Knaus, P. (2023). Fluid shear stress-modulated chromatin accessibility reveals the mechano-dependency of endothelial SMAD1/5-mediated gene transcription. iScience, 26(9), 107405. https://doi.org/10.1016/j.isci.2023.107405
  19. Jia, J., Hilal, T., Bohnsack, K. E., Chernev, A., Tsao, N., Bethmann, J., Arumugam, A., Parmely, L., Holton, N., Loll, B., Mosammaparast, N., Bohnsack, M. T., Urlaub, H., & Wahl, M. C. (2023). Extended DNA threading through a dual-engine motor module of the activating signal co-integrator 1 complex. Nat Commun, 14(1), 1886. https://doi.org/10.1038/s41467-023-37528-3
  20. Kibar, G., & Vingron, M. (2023). Prediction of protein-protein interactions using sequences of intrinsically disordered regions. Proteins, 91(7), 980-990. https://doi.org/10.1002/prot.26486
  21. Klever, M. K., Strang, E., Hetzel, S., Jungnitsch, J., Dolnik, A., Schopflin, R., Schrezenmeier, J. F., Schick, F., Blau, O., Westermann, J., Rucker, F. G., Xia, Z., Dohner, K., Schrezenmeier, H., Spielmann, M., Meissner, A., Melo, U. S., Mundlos, S., & Bullinger, L. (2023). AML with complex karyotype: extreme genomic complexity revealed by combined long-read sequencing and Hi-C technology. Blood Adv, 7(21), 6520-6531. https://doi.org/10.1182/bloodadvances.2023010887
  22. Kohler, J., Chen, Y., Kramer, A., Clementi, C., & Noe, F. (2023). Flow-Matching: Efficient Coarse-Graining of Molecular Dynamics without Forces. J Chem Theory Comput, 19(3), 942-952. https://doi.org/10.1021/acs.jctc.3c00016
  23. Kotsaris, G., Qazi, T. H., Bucher, C. H., Zahid, H., Pohle-Kronawitter, S., Ugorets, V., Jarassier, W., Borno, S., Timmermann, B., Giesecke-Thiel, C., Economides, A. N., Le Grand, F., Vallecillo-Garcia, P., Knaus, P., Geissler, S., & Stricker, S. (2023). Odd skipped-related 1 controls the pro-regenerative response of fibro-adipogenic progenitors. NPJ Regen Med, 8(1), 19. https://doi.org/10.1038/s41536-023-00291-6
  24. Kramer, A., Durumeric, A. E. P., Charron, N. E., Chen, Y., Clementi, C., & Noe, F. (2023). Statistically Optimal Force Aggregation for Coarse-Graining Molecular Dynamics. J Phys Chem Lett, 14(17), 3970-3979. https://doi.org/10.1021/acs.jpclett.3c00444
  25. Kusova, A., Steinbachova, L., Prerovska, T., Drabkova, L. Z., Palecek, J., Khan, A., Rigoova, G., Gadiou, Z., Jourdain, C., Stricker, T., Schubert, D., Honys, D., & Schrumpfova, P. P. (2023). Completing the TRB family: newly characterized members show ancient evolutionary origins and distinct localization, yet similar interactions. Plant Mol Biol, 112(1-2), 61-83. https://doi.org/10.1007/s11103-023-01348-2
  26. Landshammer, A., Bolondi, A., Kretzmer, H., Much, C., Buschow, R., Rose, A., Wu, H. J., Mackowiak, S. D., Braendl, B., Giesselmann, P., Tornisiello, R., Parsi, K. M., Huey, J., Mielke, T., Meierhofer, D., Maehr, R., Hnisz, D., Michor, F., Rinn, J. L., & Meissner, A. (2023). T-REX17 is a transiently expressed non-coding RNA essential for human endoderm formation. eLife, 12. https://doi.org/10.7554/eLife.83077
  27. Luque, A. V., Savill, R., López-Anguita, N., Bolondi, A., Garai, S., Gassaloglu, S. I., Poddar, A., Bulut-Karslioglu, A., & Veenvliet, J. V. (2023). Integrated Molecular-Phenotypic Profiling Reveals Metabolic Control of Morphological Variation in Stembryos. bioRxiv, 2023.2012.2004.569921. https://doi.org/10.1101/2023.12.04.569921
  28. Mehringer*, S., Seiler*, E., Droop, F., Darvish, M., Rahn, R., Vingron, M., & Reinert, K. (2023). Hierarchical Interleaved Bloom Filter: enabling ultrafast, approximate sequence queries. Genome Biol,24(1), 131. https://doi.org/10.1186/s13059-023-02971-4
  29. Mensah, M. A., Niskanen, H., Magalhaes, A. P., Basu, S., Kircher, M., Sczakiel, H. L., Reiter, A. M. V., Elsner, J., Meinecke, P., Biskup, S., Chung, B. H. Y., Dombrowsky, G., Eckmann-Scholz, C., Hitz, M. P., Hoischen, A., Holterhus, P. M., Hulsemann, W., Kahrizi, K., Kalscheuer, V. M., . . . Hnisz, D. (2023). Aberrant phase separation and nucleolar dysfunction in rare genetic diseases. Nature, 614(7948), 564-571. https://doi.org/10.1038/s41586-022-05682-1
  30. Nabavizadeh*, N., Bressin*, A., Shboul, M., Moreno Traspas, R., Chia, P. H., Bonnard, C., Szenker-Ravi, E., Saribas, B., Beillard, E., Altunoglu, U., Hojati, Z., Drutman, S., Freier, S., El-Khateeb, M., Fathallah, R., Casanova, J. L., Soror, W., Arafat, A., Escande-Beillard, N., . . . Reversade, B. (2023). A progeroid syndrome caused by a deep intronic variant in TAPT1 is revealed by RNA/SI-NET sequencing. EMBO Mol Med, 15(2), e16478. https://doi.org/10.15252/emmm.202216478
  31. Preussner, M., Smith, H. L., Hughes, D., Zhang, M., Emmerichs, A. K., Scalzitti, S., Peretti, D., Swinden, D., Neumann, A., Haltenhof, T., Mallucci, G. R., & Heyd, F. (2023). ASO targeting RBM3 temperature-controlled poison exon splicing prevents neurodegeneration in vivo. EMBO Mol Med, 15(5), e17157. https://doi.org/10.15252/emmm.202217157
  32. Ravid Lustig, L., Sampath Kumar, A., Schwämmle, T., Dunkel, I., Noviello, G., Limberg, E., Weigert, R., Pacini, G., Buschow, R., Ghauri, A., Stötzel, M., Wittler, L., Meissner, A., & Schulz, E. G. (2023).GATA transcription factors drive initial Xist upregulation after fertilization through direct activation of long-range enhancers. Nat Cell Biol, 25(11), 1704-1715. https://doi.org/10.1038/s41556-023-01266-x
  33. Sampath Kumar, A., Tian, L., Bolondi, A., Hernández, A. A., Stickels, R., Kretzmer, H., Murray, E., Wittler, L., Walther, M., Barakat, G., Haut, L., Elkabetz, Y., Macosko, E. Z., Guignard, L., Chen, F., & Meissner, A. (2023). Spatiotemporal transcriptomic maps of whole mouse embryos at the onset of organogenesis. Nature Genetics, 55(7), 1176-1185. https://doi.org/10.1038/s41588-023-01435-6
  34. Schmidt, D., Duport, Y., Kollan, C., Marcus, U., Iannuzzi, S., & von Kleist, M. (2023). Dynamics of HIV Prep Use and Coverage During and after Covid-19 in Germany. SSRN (preprint). https://doi.org/10.2139/ssrn.4611490
  35. Sreenivasan, V. K. A., Dore, R., Resch, J., Maier, J., Dietrich, C., Henck, J., Balachandran, S., Mittag, J., & Spielmann, M. (2023). Single-cell RNA-based phenotyping reveals a pivotal role of thyroid hormone receptor alpha for hypothalamic development. Development, 150(3). https://doi.org/10.1242/dev.201228
  36. Ugorets, V., Mendez, P.-L., Zagrebin, D., Russo, G., Kerkhoff, Y., Herpelinck, T., Kotsaris, G., Jatzlau, J., Stricker, S., & Knaus, P. (2023). Reorganization of Septin structures regulates early myogenesis. bioRxiv, 2023.2008.2024.554594. https://doi.org/10.1101/2023.08.24.554594
  37. Volkenandt, S., & Imhof, P. (2023). Comparison of Empirical Zn2+ Models in Protein–DNA Complexes. Biophysica, 3(1), 214-230. https://www.mdpi.com/2673-4125/3/1/14
  38. Wang, L.-W., van der Toorn, W., Bohn, P., Hölzer, M., Smyth, R., & von Kleist, M. (2023). Sequencing accuracy and systematic errors of nanopore direct RNA sequencing. bioRxiv, 2023.2003.2029.534691. https://doi.org/10.1101/2023.03.29.534691
  39. Weigert*, R., Hetzel*, S., Bailly, N., Haggerty, C., Ilik, I. A., Yung, P. Y. K., Navarro, C., Bolondi, A., Kumar, A. S., Anania, C., Brandl, B., Meierhofer, D., Lupianez, D. G., Muller, F. J., Aktas, T., Elsasser, S. J., Kretzmer, H., Smith, Z. D., & Meissner, A. (2023). Dynamic antagonism between key repressive pathways maintains the placental epigenome. Nat Cell Biol, 25(4), 579-591. https://doi.org/10.1038/s41556-023-01114-y
  40. Zhang*, L., Iannuzzi*, S., Chaturvedula, A., Irungu, E., Haberer, J. E., Hendrix, C. W., & von Kleist, M. (2023). Model-based predictions of protective HIV pre-exposure prophylaxis adherence levels in cisgender women. Nat Med, 29(11), 2753-2762. https://doi.org/10.1038/s41591-023-02615-x
2022
  1. Altenburg, T., Giese, S. H., Wang, S., Muth, T., & Renard, B. Y. (2022). Ad hoc learning of peptide fragmentation from mass spectra enables an interpretable detection of phosphorylated and cross-linked peptides. Nature Machine Intelligence, 4(4), 378-388. https://doi.org/10.1038/s42256-022-00467-7
  2. Altendorfer, E., Mochalova, Y., & Mayer, A. (2022). BRD4: a general regulator of transcription elongation. Transcription, 13(1-3), 70-81. https://doi.org/10.1080/21541264.2022.2108302
  3. Asimi, V., Sampath Kumar, A., Niskanen, H., Riemenschneider, C., Hetzel, S., Naderi, J., Fasching, N., Popitsch, N., Du, M., Kretzmer, H., Smith, Z. D., Weigert, R., Walther, M., Mamde, S., Meierhofer, D., Wittler, L., Buschow, R., Timmermann, B., Cisse, II, . . . Hnisz, D. (2022). Hijacking of transcriptional condensates by endogenous retroviruses. Nat Genet, 54(8), 1238-1247. https://doi.org/10.1038/s41588-022-01132-w
  4. Beierlein, F., Volkenandt, S., & Imhof, P. (2022). Oxidation Enhances Binding of Extrahelical 5-Methyl-Cytosines by Thymine DNA Glycosylase. J Phys Chem B, 126(6), 1188-1201. https://doi.org/10.1021/acs.jpcb.1c09896
  5. Bothe, M., & Schulz, E. G. (2022). Evaluation of Sadagopan et al.: X chromosome inactivation in male cancers. Cell Syst, 13(11), 857-858. https://doi.org/10.1016/j.cels.2022.10.007
  6. Cifuentes-Fontanals, L., Tonello, E., & Siebert, H. (2022). Control in Boolean Networks With Model Checking [Original Research]. Frontiers in Applied Mathematics and Statistics, 8. https://doi.org/10.3389/fams.2022.838546
  7. Cifuentes-Fontanals, L., Tonello, E., & Siebert, H. (2022). Computing trap space-based control strategies for Boolean networks using answer set programming. AIP Conference Proceedings, 2611(1). https://doi.org/10.1063/5.0122073
  8. Darvish, M., Seiler, E., Mehringer, S., Rahn, R., & Reinert, K. (2022). Needle: a fast and space-efficient prefilter for estimating the quantification of very large collections of expression experiments. Bioinformatics, 38(17), 4100-4108. https://doi.org/10.1093/bioinformatics/btac492
  9. Gralinska, E., Kohl, C., Sokhandan Fadakar, B., & Vingron, M. (2022). Visualizing Cluster-specific Genes from Single-cell Transcriptomics Data Using Association Plots. J Mol Biol, 434(11), 167525. https://doi.org/10.1016/j.jmb.2022.167525
  10. Hetzel, S., Mattei, A. L., Kretzmer, H., Qu, C., Chen, X., Fan, Y., Wu, G., Roberts, K. G., Luger, S., Litzow, M., Rowe, J., Paietta, E., Stock, W., Mardis, E. R., Wilson, R. K., Downing, J. R., Mullighan, C. G., & Meissner, A. (2022). Acute lymphoblastic leukemia displays a distinct highly methylated genome. Nat Cancer, 3(6), 768-782. https://doi.org/10.1038/s43018-022-00370-5
  11. Kleinert, P., & Kircher, M. (2022). A framework to score the effects of structural variants in health and disease. Genome Research, 32(4), 766-777. https://doi.org/10.1101/gr.275995.121
  12. Knaust, M., Seiler, E., Reinert, K., & Steinke, T. (2022). Co-Design for Energy Efficient and Fast Genomic Search Proceedings of the 2022 ACM/SIGDA International Symposium on Field-Programmable Gate Arrays, Virtual Event, USA. https://doi.org/10.1145/3490422.3502366
  13. Kroon, C., Breuer, L., Jones, L., An, J., Akan, A., Mohamed Ali, E. A., Busch, F., Fislage, M., Ghosh, B., Hellrigel-Holderbaum, M., Kazezian, V., Koppold, A., Moreira Restrepo, C. A., Riedel, N., Scherschinski, L., Urrutia Gonzalez, F. R., & Weissgerber, T. L. (2022). Blind spots on western blots: Assessment of common problems in western blot figures and methods reporting with recommendations to improve them. PLoS Biol, 20(9), e3001783. https://doi.org/10.1371/journal.pbio.3001783
  14. Lopez-Anguita, N., Gassaloglu*, S. I., Stotzel*, M., Bolondi, A., Conkar, D., Typou, M., Buschow, R., Veenvliet, J. V., & Bulut-Karslioglu, A. (2022). Hypoxia induces an early primitive streak signature, enhancing spontaneous elongation and lineage representation in gastruloids. Development, 149(20). https://doi.org/10.1242/dev.200679
  15. Los, B., Preussner, M., Eschke, K., Vidal, R. M., Abdelgawad, A., Olofsson, D., Keiper, S., Paulo-Pedro, M., Grindel, A., Meinke, S., Trimpert, J., & Heyd, F. (2022). Body temperature variation controls pre-mRNA processing and transcription of antiviral genes and SARS-CoV-2 replication. Nucleic Acids Res,50(12), 6769-6785. https://doi.org/10.1093/nar/gkac513
  16. Ly, L. H., & Vingron, M. (2022). Effect of imputation on gene network reconstruction from single-cell RNA-seq data. Patterns (N Y), 3(2), 100414. https://doi.org/10.1016/j.patter.2021.100414
  17. Malysheva, N., Wang, J., & von Kleist, M. (2022). S̲tochastic S̲imulation A̲lgorithm For Effective Spreading Dynamics On T̲ime-Evolving A̲daptive N̲etworX̲ (SSATAN-X)*. Math. Model. Nat. Phenom., 17, 35. https://doi.org/10.1051/mmnp/2022035
  18. Mendez, P. L., Obendorf, L., Jatzlau, J., Burdzinski, W., Reichenbach, M., Nageswaran, V., Haghikia, A., Stangl, V., Hiepen, C., & Knaus, P. (2022). Atheroprone fluid shear stress-regulated ALK1-Endoglin-SMAD signaling originates from early endosomes. BMC Biol, 20(1), 210. https://doi.org/10.1186/s12915-022-01396-y
  19. Meyer, F., Fritz, A., Deng, Z. L., Koslicki, D., Lesker, T. R., Gurevich, A., Robertson, G., Alser, M., Antipov, D., Beghini, F., Bertrand, D., Brito, J. J., Brown, C. T., Buchmann, J., Buluc, A., Chen, B., Chikhi, R., Clausen, P., Cristian, A., . . . McHardy, A. C. (2022). Critical Assessment of Metagenome Interpretation: the second round of challenges. Nat Methods, 19(4), 429-440. https://doi.org/10.1038/s41592-022-01431-4
  20. Ostwaldt, F., Los, B., & Heyd, F. (2022). In silico analysis of alternative splicing events implicated in intracellular trafficking during B-lymphocyte differentiation. Front Immunol, 13, 1030409. https://doi.org/10.3389/fimmu.2022.1030409
  21. Prasse, P., Iversen, P., Lienhard, M., Thedinga, K., Bauer, C., Herwig, R., & Scheffer, T. (2022). Matching anticancer compounds and tumor cell lines by neural networks with ranking loss. NAR Genom Bioinform, 4(1), lqab128. https://doi.org/10.1093/nargab/lqab128
  22. Prasse, P., Iversen, P., Lienhard, M., Thedinga, K., Herwig, R., & Scheffer, T. (2022). Pre-Training on In Vitro and Fine-Tuning on Patient-Derived Data Improves Deep Neural Networks for Anti-Cancer Drug-Sensitivity Prediction. Cancers (Basel), 14(16). https://doi.org/10.3390/cancers14163950
  23. Randall*, R. S., Jourdain*, C., Nowicka*, A., Kaduchova*, K., Kubova*, M., Ayoub, M. A., Schubert, V., Tatout, C., Colas, I., Kalyanikrishna, Desset, S., Mermet, S., Boulaflous-Stevens, A., Kubalova, I., Mandakova, T., Heckmann, S., Lysak, M. A., Panatta, M., Santoro, R., . . . Baroux, C. (2022). Image analysis workflows to reveal the spatial organization of cell nuclei and chromosomes. Nucleus, 13(1), 277-299. https://doi.org/10.1080/19491034.2022.2144013
  24. Ringel, A. R., Szabo, Q., Chiariello, A. M., Chudzik, K., Schopflin, R., Rothe, P., Mattei, A. L., Zehnder, T., Harnett, D., Laupert, V., Bianco, S., Hetzel, S., Glaser, J., Phan, M. H. Q., Schindler, M., Ibrahim, D. M., Paliou, C., Esposito, A., Prada-Medina, C. A., . . . Robson, M. I. (2022). Repression and 3D-restructuring resolves regulatory conflicts in evolutionarily rearranged genomes. Cell, 185(20), 3689-3704 e3621. https://doi.org/10.1016/j.cell.2022.09.006
  25. Rosebrock*, D., Arora*, S., Mutukula, N., Volkman, R., Gralinska, E., Balaskas, A., Aragones Hernandez, A., Buschow, R., Brandl, B., Muller, F. J., Arndt, P. F., Vingron, M., & Elkabetz, Y. (2022). Enhanced cortical neural stem cell identity through short SMAD and WNT inhibition in human cerebral organoids facilitates emergence of outer radial glial cells. Nat Cell Biol, 24(6), 981-995. https://doi.org/10.1038/s41556-022-00929-5
  26. Smajic, S., Prada-Medina, C. A., Landoulsi, Z., Ghelfi, J., Delcambre, S., Dietrich, C., Jarazo, J., Henck, J., Balachandran, S., Pachchek, S., Morris, C. M., Antony, P., Timmermann, B., Sauer, S., Pereira, S. L., Schwamborn, J. C., May, P., Grunewald, A., & Spielmann, M. (2022). Single-cell sequencing of human midbrain reveals glial activation and a Parkinson-specific neuronal state. Brain, 145(3), 964-978. https://doi.org/10.1093/brain/awab446
  27. Sreenivasan, V. K. A., Henck, J., & Spielmann, M. (2022). Single-cell sequencing: promises and challenges for human genetics. Medizinische Genetik, 34(4), 261-273. https://doi.org/doi:10.1515/medgen-2022-2156
  28. Thedinga, K., & Herwig, R. (2022). Gradient tree boosting and network propagation for the identification of pan-cancer survival networks. STAR Protoc, 3(2), 101353. https://doi.org/10.1016/j.xpro.2022.101353
  29. Thedinga, K., & Herwig, R. (2022). A gradient tree boosting and network propagation derived pan-cancer survival network of the tumor microenvironment. iScience, 25(1), 103617. https://doi.org/10.1016/j.isci.2021.103617
  30. Walker, K., Kalra, D., Lowdon, R., Chen, G., Molik, D., Soto, D. C., Dabbaghie, F., Khleifat, A. A., Mahmoud, M., Paulin, L. F., Raza, M. S., Pfeifer, S. P., Agustinho, D. P., Aliyev, E., Avdeyev, P., Barrozo, E. R., Behera, S., Billingsley, K., Chong, L. C., . . . Busby, B. (2022). The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms. F1000Res, 11, 530. https://doi.org/10.12688/f1000research.110194.1
  31. Weijden, V. A. v. d., Stoetzel, M., Fauler, B., Iyer, D. P., Shahraz, M., Meierhofer, D., Rulands, S., Alexandrov, T., Mielke, T., & Bulut-Karslioglu, A. (2022). Metabolic enhancement of mammalian developmental pausing. bioRxiv, 2022.2008.2022.504730. https://doi.org/10.1101/2022.08.22.504730
  32. Wittig*, A., Miranda*, F., Hölzer, M., Altenburg, T., Bartoszewicz, J. M., Beyvers, S., Dieckmann, M. A., Genske, U., Giese, S. H., Nowicka, M., Richard, H., Schiebenhoefer, H., Schmachtenberg, A.-J., Sieben, P., Tang, M., Tembrockhaus, J., Renard, B. Y., & Fuchs, S. (2022). CovRadar: continuously tracking and filtering SARS-CoV-2 mutations for genomic surveillance. Bioinformatics, 38(17), 4223-4225. https://doi.org/10.1093/bioinformatics/btac411
2021
  1. Abdullaev, E. T., Umarova, I. R., & Arndt, P. F. (2021). Modelling segmental duplications in the human genome. BMC Genomics, 22(1), 496. https://doi.org/10.1186/s12864-021-07789-7
  2. Arnold*, M., Bressin*, A., Jasnovidova, O., Meierhofer, D., & Mayer, A. (2021). A BRD4-mediated elongation control point primes transcribing RNA polymerase II for 3'-processing and termination. Mol Cell, 81(17), 3589-3603 e3513. https://doi.org/10.1016/j.molcel.2021.06.026
  3. Annaldasula, S., Gajos, M., & Mayer, A. (2021). IsoTV: processing and visualizing functional features of translated transcript isoforms. Bioinformatics, 37(18), 3070-3072. https://doi.org/10.1093/bioinformatics/btab103
  4. Azouz, N. P., Klingler, A. M., Callahan, V., Akhrymuk, I. V., Elez, K., Raich, L., Henry, B. M., Benoit, J. L., Benoit, S. W., Noe, F., Kehn-Hall, K., & Rothenberg, M. E. (2021). Alpha 1 Antitrypsin is an Inhibitor of the SARS-CoV-2-Priming Protease TMPRSS2. Pathog Immun, 6(1), 55-74. https://doi.org/10.20411/pai.v6i1.408
  5. Belicova, L., Repnik, U., Delpierre, J., Gralinska, E., Seifert, S., Valenzuela, J. I., Morales-Navarrete, H. A., Franke, C., Raagel, H., Shcherbinina, E., Prikazchikova, T., Koteliansky, V., Vingron, M., Kalaidzidis, Y. L., Zatsepin, T., & Zerial, M. (2021). Anisotropic expansion of hepatocyte lumina enforced by apical bulkheads. J Cell Biol, 220(10). https://doi.org/10.1083/jcb.202103003
  6. Bose, S., He, H., & Stauber, T. (2021). Neurodegeneration Upon Dysfunction of Endosomal/Lysosomal CLC Chloride Transporters. Front Cell Dev Biol, 9, 639231. https://doi.org/10.3389/fcell.2021.639231
  7. Bothe, M., Buschow, R., & Meijsing, S. H. (2021). Glucocorticoid signaling induces transcriptional memory and universally reversible chromatin changes. Life Sci Alliance, 4(10). https://doi.org/10.26508/lsa.202101080
  8. Chen, Y., Kramer, A., Charron, N. E., Husic, B. E., Clementi, C., & Noe, F. (2021). Machine learning implicit solvation for molecular dynamics. J Chem Phys, 155(8), 084101. https://doi.org/10.1063/5.0059915
  9. Enervald, E., Powell, L. M., Boteva, L., Foti, R., Blanes Ruiz, N., Kibar, G., Piszczek, A., Cavaleri, F., Vingron, M., Cerase, A., & Buonomo, S. B. C. (2021). RIF1 and KAP1 differentially regulate the choice of inactive versus active X chromosomes. Embo j, 40(24), e105862. https://doi.org/10.15252/embj.2020105862
  10. Gajos, M., Jasnovidova, O., van Bommel, A., Freier, S., Vingron, M., & Mayer, A. (2021). Conserved DNA sequence features underlie pervasive RNA polymerase pausing. Nucleic Acids Res, 49(8), 4402-4420. https://doi.org/10.1093/nar/gkab208
  11. Hempel*, T., Elez*, K., Kruger*, N., Raich, L., Shrimp, J. H., Danov, O., Jonigk, D., Braun, A., Shen, M., Hall, M. D., Pohlmann, S., Hoffmann, M., & Noe, F. (2021). Synergistic inhibition of SARS-CoV-2 cell entry by otamixaban and covalent protease inhibitors: pre-clinical assessment of pharmacological and molecular properties. Chem Sci, 12(38), 12600-12609. https://doi.org/10.1039/d1sc01494c
  12. Hetzel, S., Giesselmann, P., Reinert, K., Meissner, A., & Kretzmer, H. (2021). RLM: fast and simplified extraction of read-level methylation metrics from bisulfite sequencing data. Bioinformatics, 37(21), 3934-3935. https://doi.org/10.1093/bioinformatics/btab663
  13. Iannuzzi, S., & von Kleist, M. (2021). Mathematical Modelling of the Molecular Mechanisms of Interaction of Tenofovir with Emtricitabine against HIV. Viruses, 13(7). https://doi.org/10.3390/v13071354
  14. Klarner, H., Tonello, E., Cifuentes-Fontanals, L., Janody, F., Chaouiya, C., & Siebert, H. (2021). Detection of markers for discrete phenotypes The 12th International Conference on Computational Systems-Biology and Bioinformatics, Virtual, Thailand. https://doi.org/10.1145/3486713.3486729
  15. Kulik, M., Bothe, M., Kibar, G., Fuchs, A., Schone, S., Prekovic, S., Mayayo-Peralta, I., Chung, H. R., Zwart, W., Helsen, C., Claessens, F., & Meijsing, S. H. (2021). Androgen and glucocorticoid receptor direct distinct transcriptional programs by receptor-specific and shared DNA binding sites. Nucleic Acids Res, 49(7), 3856-3875. https://doi.org/10.1093/nar/gkab185
  16. Mc Cartney, A. M., Mahmoud, M., Jochum, M., Agustinho, D. P., Zorman, B., Al Khleifat, A., Dabbaghie, F., R, K. K., Smolka, M., Dawood, M., Albin, D., Aliyev, E., Almabrazi, H., Arslan, A., Balaji, A., Behera, S., Billingsley, K., D, L. C., Daw, J., . . . F, J. S. (2021). An international virtual hackathon to build tools for the analysis of structural variants within species ranging from coronaviruses to vertebrates. F1000Res, 10, 246. https://doi.org/10.12688/f1000research.51477.2
  17. Mendez, P. L., Obendorf, L., & Knaus, P. (2021). Visualization and Quantification of TGFbeta/BMP/SMAD Signaling under Different Fluid Shear Stress Conditions using Proximity-Ligation-Assay. J Vis Exp(175). https://doi.org/10.3791/62608
  18. Pacini, G., Dunkel, I., Mages, N., Mutzel, V., Timmermann, B., Marsico, A., & Schulz, E. G. (2021). Integrated analysis of Xist upregulation and X-chromosome inactivation with single-cell and single-allele resolution. Nat Commun, 12(1), 3638. https://doi.org/10.1038/s41467-021-23643-6
  19. Reichenbach, M., Mendez, P. L., da Silva Madaleno, C., Ugorets, V., Rikeit, P., Boerno, S., Jatzlau, J., & Knaus, P. (2021). Differential Impact of Fluid Shear Stress and YAP/TAZ on BMP/TGF-beta Induced Osteogenic Target Genes. Adv Biol (Weinh), 5(2), e2000051. https://doi.org/10.1002/adbi.202000051
  20. Rossler, U., Hennig, A. F., Stelzer, N., Bose, S., Kopp, J., Soe, K., Cyganek, L., Zifarelli, G., Ali, S., von der Hagen, M., Strassler, E. T., Hahn, G., Pusch, M., Stauber, T., Izsvak, Z., Gossen, M., Stachelscheid, H., & Kornak, U. (2021). Efficient generation of osteoclasts from human induced pluripotent stem cells and functional investigations of lethal CLCN7-related osteopetrosis. J Bone Miner Res, 36(8), 1621-1635. https://doi.org/10.1002/jbmr.4322
  21. Rossmann, M. P., Hoi, K., Chan, V., Abraham, B. J., Yang, S., Mullahoo, J., Papanastasiou, M., Wang, Y., Elia, I., Perlin, J. R., Hagedorn, E. J., Hetzel, S., Weigert, R., Vyas, S., Nag, P. P., Sullivan, L. B., Warren, C. R., Dorjsuren, B., Greig, E. C., . . . Zon, L. I. (2021). Cell-specific transcriptional control of mitochondrial metabolism by TIF1gamma drives erythropoiesis. Science, 372(6543), 716-721. https://doi.org/10.1126/science.aaz2740
  22. Sbailò, L., Dibak, M., & Noé, F. (2021). Neural mode jump Monte Carlo. The Journal of Chemical Physics, 154(7). https://doi.org/10.1063/5.0032346
  23. Schulte-Sasse, R., Budach, S., Hnisz, D., & Marsico, A. (2021). Integration of multiomics data with graph convolutional networks to identify new cancer genes and their associated molecular mechanisms. Nature Machine Intelligence, 3(6), 513-526. https://doi.org/10.1038/s42256-021-00325-y
  24. Seiler, E., Mehringer, S., Darvish, M., Turc, E., & Reinert, K. (2021). Raptor: A fast and space-efficient pre-filter for querying very large collections of nucleotide sequences. iScience, 24(7), 102782. https://doi.org/10.1016/j.isci.2021.102782
  25. Volkenandt, S., Beierlein, F., & Imhof, P. (2021). Interaction of Thymine DNA Glycosylase with Oxidised 5-Methyl-cytosines in Their Amino- and Imino-Forms. Molecules, 26(19). https://doi.org/10.3390/molecules26195728
2020
  1. Bagherpoor Helabad, M., Volkenandt, S., & Imhof, P. (2020). Molecular Dynamics Simulations of a Chimeric Androgen Receptor Protein (SPARKI) Confirm the Importance of the Dimerization Domain on DNA Binding Specificity. Front Mol Biosci, 7, 4. https://doi.org/10.3389/fmolb.2020.00004
  2. Barel, G., & Herwig, R. (2020). NetCore: a network propagation approach using node coreness. Nucleic Acids Research, 48(17), e98-e98. https://doi.org/10.1093/nar/gkaa639
  3. Basu*, S., Mackowiak*, S. D., Niskanen, H., Knezevic, D., Asimi, V., Grosswendt, S., Geertsema, H., Ali, S., Jerkovic, I., Ewers, H., Mundlos, S., Meissner, A., Ibrahim, D. M., & Hnisz, D. (2020). Unblending of Transcriptional Condensates in Human Repeat Expansion Disease. Cell, 181(5), 1062-1079 e1030. https://doi.org/10.1016/j.cell.2020.04.018
  4. Cifuentes Fontanals, L., Tonello, E., & Siebert, H. (2020). Control Strategy Identification via Trap Spaces in Boolean Networks. In A. Abate, T. Petrov, & V. Wolf, Computational Methods in Systems Biology Cham.
  5. Gorgulla, C., Boeszoermenyi, A., Wang, Z.-F., Fischer, P. D., Coote, P. W., Padmanabha Das, K. M., Malets, Y. S., Radchenko, D. S., Moroz, Y. S., Scott, D. A., Fackeldey, K., Hoffmann, M., Iavniuk, I., Wagner, G., & Arthanari, H. (2020). An open-source drug discovery platform enables ultra-large virtual screens. Nature, 580(7805), 663-668. https://doi.org/10.1038/s41586-020-2117-z
  6. Grosswendt*, S., Kretzmer*, H., Smith*, Z. D., Kumar, A. S., Hetzel, S., Wittler, L., Klages, S., Timmermann, B., Mukherji, S., & Meissner, A. (2020). Epigenetic regulator function through mouse gastrulation. Nature, 584(7819), 102-108. https://doi.org/10.1038/s41586-020-2552-x
  7. Heller, D., & Vingron, M. (2020). SVIM-asm: structural variant detection from haploid and diploid genome assemblies. Bioinformatics, 36(22-23), 5519-5521. https://doi.org/10.1093/bioinformatics/btaa1034
  8. Hickey, G., Heller, D., Monlong, J., Sibbesen, J. A., Siren, J., Eizenga, J., Dawson, E. T., Garrison, E., Novak, A. M., & Paten, B. (2020). Genotyping structural variants in pangenome graphs using the vg toolkit. Genome Biol, 21(1), 35. https://doi.org/10.1186/s13059-020-1941-7
  9. Hiepen, C., Mendez, P. L., & Knaus, P. (2020). It Takes Two to Tango: Endothelial TGFbeta/BMP Signaling Crosstalk with Mechanobiology. Cells, 9(9). https://doi.org/10.3390/cells9091965
  10. Husic, B. E., Charron, N. E., Lemm, D., Wang, J., Perez, A., Majewski, M., Kramer, A., Chen, Y., Olsson, S., de Fabritiis, G., Noe, F., & Clementi, C. (2020). Coarse graining molecular dynamics with graph neural networks. J Chem Phys, 153(19), 194101. https://doi.org/10.1063/5.0026133
  11. Ilik, I. A., Malszycki*, M., Luebke*, A. K., Schade, C., Meierhofer, D., & Aktas, T. (2020). SON and SRRM2 are essential for nuclear speckle formation. eLife, 9. https://doi.org/10.7554/eLife.60579
  12. Kleinert, P., Martin, B., & Kircher, M. (2020). HemoMIPs—Automated analysis and result reporting pipeline for targeted sequencing data. PLOS Computational Biology, 16(6), e1007956. https://doi.org/10.1371/journal.pcbi.1007956
  13. Kupke*, S. Y., Ly, L. H., Borno*, S. T., Ruff, A., Timmermann, B., Vingron, M., Haas, S., & Reichl, U. (2020). Single-Cell Analysis Uncovers a Vast Diversity in Intracellular Viral Defective Interfering RNA Content Affecting the Large Cell-to-Cell Heterogeneity in Influenza A Virus Replication. Viruses, 12(1). https://doi.org/10.3390/v12010071
  14. Moeinzadeh, M. H., Yang, J., Muzychenko, E., Gallone, G., Heller, D., Reinert, K., Haas, S., & Vingron, M. (2020). Ranbow: A fast and accurate method for polyploid haplotype reconstruction. PLoS Comput Biol, 16(5), e1007843. https://doi.org/10.1371/journal.pcbi.1007843
  15. Morselli Gysi, D., de Miranda Fragoso, T., Zebardast, F., Bertoli, W., Busskamp, V., Almaas, E., & Nowick, K. (2020). Whole transcriptomic network analysis using Co-expression Differential Network Analysis (CoDiNA). PLoS One, 15(10), e0240523. https://doi.org/10.1371/journal.pone.0240523
  16. Piro, V. C., Dadi, T. H., Seiler, E., Reinert, K., & Renard, B. Y. (2020). ganon: precise metagenomics classification against large and up-to-date sets of reference sequences. Bioinformatics, 36(Suppl_1), i12-i20. https://doi.org/10.1093/bioinformatics/btaa458
  17. Pockrandt, C., Alzamel, M., Iliopoulos, C. S., & Reinert, K. (2020). GenMap: ultra-fast computation of genome mappability. Bioinformatics, 36(12), 3687-3692. https://doi.org/10.1093/bioinformatics/btaa222
  18. Real, F. M., Haas, S. A., Franchini, P., Xiong, P., Simakov, O., Kuhl, H., Schopflin, R., Heller, D., Moeinzadeh, M. H., Heinrich, V., Krannich, T., Bressin, A., Hartmann, M. F., Wudy, S. A., Dechmann, D. K. N., Hurtado, A., Barrionuevo, F. J., Schindler, M., Harabula, I., . . . Lupianez, D. G. (2020). The mole genome reveals regulatory rearrangements associated with adaptive intersexuality. Science,370(6513), 208-214. https://doi.org/10.1126/science.aaz2582
  19. Richter, A. M., Possling, A., Malysheva, N., Yousef, K. P., Herbst, S., von Kleist, M., & Hengge, R. (2020). Local c-di-GMP Signaling in the Control of Synthesis of the E. coli Biofilm Exopolysaccharide pEtN-Cellulose. Journal of Molecular Biology, 432(16), 4576-4595.https://doi.org/https://doi.org/10.1016/j.jmb.2020.06.006
2019
  1. Barros de Andrade e Sousa, L., Jonkers, I., Syx, L., Dunkel, I., Chaumeil, J., Picard, C., Foret, B., Chen, C.-J., Lis, J. T., Heard, E., Schulz, E. G., & Marsico, A. (2019). Kinetics of Xist-induced gene silencing can be predicted from combinations of epigenetic and genomic features. Genome Research, 29(7), 1087-1099. https://doi.org/10.1101/gr.245027.118
  2. Bressin*, A., Schulte-Sasse*, R., Figini, D., Urdaneta, E. C., Beckmann, B. M., & Marsico, A. (2019). TriPepSVM: de novo prediction of RNA-binding proteins based on short amino acid motifs. Nucleic Acids Research, 47(9), 4406-4417. https://doi.org/10.1093/nar/gkz203
  3. Giesselmann, P., Hetzel, S., Muller, F. J., Meissner, A., & Kretzmer, H. (2019). Nanopype: a modular and scalable nanopore data processing pipeline. Bioinformatics, 35(22), 4770-4772. https://doi.org/10.1093/bioinformatics/btz461
  4. Han, H., Wu, G., Li, Y., & Zi, Z. (2019). eDetect: A Fast Error Detection and Correction Tool for Live Cell Imaging Data Analysis. iScience, 13, 1-8. https://doi.org/https://doi.org/10.1016/j.isci.2019.02.004
  5. Heller, D., & Vingron, M. (2019). SVIM: structural variant identification using mapped long reads. Bioinformatics, 35(17), 2907-2915. https://doi.org/10.1093/bioinformatics/btz041
  6. Kopp, W., & Vingron, M. (2019). DNA Motif Match Statistics Without Poisson Approximation. Journal of Computational Biology, 26(8), 846-865. https://doi.org/10.1089/cmb.2018.0144
  7. Nowicka, M., & Siebert, H. (2019). Designing Distributed Cell Classifier Circuits Using a Genetic Algorithm. In L. Bortolussi & G. Sanguinetti, Computational Methods in Systems Biology Cham.
  8. Ramisch, A., Heinrich, V., Glaser, L. V., Fuchs, A., Yang, X., Benner, P., Schöpflin, R., Li, N., Kinkley, S., Römer-Hillmann, A., Longinotto, J., Heyne, S., Czepukojc, B., Kessler, S. M., Kiemer, A. K., Cadenas, C., Arrigoni, L., Gasparoni, N., Manke, T., . . . Vingron, M. (2019). CRUP: a comprehensive framework to predict condition-specific regulatory units. Genome Biology, 20(1), 227. https://doi.org/10.1186/s13059-019-1860-7
  9. Schulte-Sasse, R., Budach, S., Hnisz, D., & Marsico, A. (2019). Graph Convolutional Networks Improve the Prediction of Cancer Driver Genes. In I. V. Tetko, V. Kůrková, P. Karpov, & F. Theis, Artificial Neural Networks and Machine Learning – ICANN 2019: Workshop and Special Sessions Cham.
  10. Seiler, E., Trappe, K., & Renard, B. Y. (2019). Where did you come from, where did you go: Refining metagenomic analysis tools for horizontal gene transfer characterisation. PLoS Comput Biol, 15(7), e1007208. https://doi.org/10.1371/journal.pcbi.1007208
  11. Thormann, V., Glaser, L. V., Rothkegel, M. C., Borschiwer, M., Bothe, M., Fuchs, A., & Meijsing, S. H. (2019). Expanding the repertoire of glucocorticoid receptor target genes by engineering genomic response elements. Life Sci Alliance, 2(2). https://doi.org/10.26508/lsa.201800283
  12. Zehnder, T., Benner, P., & Vingron, M. (2019). Predicting enhancers in mammalian genomes using supervised hidden Markov models. BMC Bioinformatics, 20(1), 157. https://doi.org/10.1186/s12859-019-2708-6

 

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