RTG 3074 GönomiX

Publications

Start of the RTG is in 2026 – check again some years later!

  • Aguado, M.T., Ponz-Segrelles, G., Glasby, C., Rannyele P.R., Mayuko N., Kohei O., Akihito O., Hisanori K., Christian F., Yuji I., Naoto J., Toru M. Ramisyllis kingghidorahi n. sp., a new branching annelid from Japan. Organisms Diversity & Evolution. 2022. doi: 10.1007/s13127-021-00538-4
  • Ponz-Segrelles, G., Ribeiro, R.P., Aguado, M.T. Monsters reveal patterns: Bifurcated annelids and their implications for the study of development and evolution. Biological Reviews. 2022. doi: 10.1111/brv.12826
  • Ribeiro, R.P., Aguado, M.T. Effects of GSK3β inhibition in the regeneration of Syllis malaquini (Syllidae, Annelida). Development Genes and Evolution. 2021; 231:141–146. doi: 10.1007/s00427-021-00681-0
  • Ponz-Segrelles, G., Glasby, C.J., Helm, C., Beckers, P., Jammel, J.U., Ribeiro, R.P., Aguado, M.T. Integrative anatomical study of the branched annelid Ramisyllis multicaudata (Annelida, Syllidae). Journal of Morphology. 2021; 282(6):900-916. doi: 10.1002/jmor.21356
  • Ribeiro, R.P.; Egger, B.; Ponz-Segrelles, G., Aguado, M.T. Cellular proliferation dynamics during regeneration in Syllis malaquini (Syllidae, Annelida). Frontiers in Zoology. 2021, 18:27. doi: 10.1186/s12983-021-00396-y
  • Ponz-Segrelles, G., Ribeiro, R.P., G., Bleidorn, C., Aguado, M.T. Sex-specific gene expression differences in reproducing Syllis prolifera and Nudisyllis pulligera (Annelida, Syllidae). Marine Genomics. 2020; 54: 100772. doi: 10.1016/j.margen.2020.100772
  • Passos-Ribeiro, R., Ponz-Segrelles, G., Bleidorn, C., Aguado, M.T. Comparative transcriptomics in Syllidae (Annelida) indicates that posterior regeneration and regular growth are comparable, while anterior regeneration is a distinct process. BMC Genomics. 2019; 20: 855. doi: 10.1186/s12864-019-6223-y
  • Passos-Ribeiro, R., Bleidorn, C., Aguado, M.T. Regeneration mechanism in Syllidae (Annelida). Regeneration. 2018; 5:26-42. doi: 10.1002/reg2.98
  • Aguado, M.T., Glasby, C., Schroeder, P., Weigert, A., Bleidorn, C. 2015. The making of a branching annelid: an analysis of complete mitochondrial genome and ribosomal data of Ramisyllis multicaudata. Scientific reports. 2015; srep12072. doi: 10.1038/srep12072
  • Aguado, M.T., San Martín, G. & Siddall, M. Systematics and Evolution of syllids (Annelida, Syllidae). Cladistics. 2012, 28: 234-250. doi: 10.1111/j.1096-0031.2011.00377.x
  • Sahrhage M, Paul NB, Beißbarth T, Haubrock M. The importance of DNA sequence for nucleosome positioning in transcriptional regulation. Life Sci Alliance. 2024 Jun 3;7(8):e202302380. doi: 10.26508/lsa.202302380
  • Kornrumpf K, Kurz NS, Drofenik K, Krauß L, Schneider C, Koch R, Beißbarth T, Dönitz J. SeqCAT: Sequence Conversion and Analysis Toolbox. Nucleic Acids Res. 2024 May 27:gkae422. doi: 10.1093/nar/gkae422
  • Chereda H, Leha A, Beißbarth T. Stable feature selection utilizing Graph Convolutional Neural Network and Layer-wise Relevance Propagation for biomarker discovery in breast cancer. Artif Intell Med. 2024 May;151:102840. doi: 10.1016/j.artmed.2024.102840
  • Chereda H, Bleckmann A, Menck K, Perera-Bel J, Stegmaier P, Auer F, Kramer F, Leha A, Beißbarth T (2021) Explaining decisions of graph convolutional neural networks: patient-specific molecular subnetworks responsible for metastasis prediction in breast cancer. Genome Medicine, 13(1):42. doi: 10.1186/s13073-021-00845-7
  • Kalya M, Kel A, Wlochowitz D, Wingender E, Beißbarth T (2021). IGFBP2 Is a Potential Master Regulator Driving the Dysregulated Gene Network Responsible for Short Survival in Glioblastoma Multiforme. Front Genet, 12:670240. doi: 10.3389/fgene.2021.670240.
  • Perera-Bel J, Hutter B, Heining C, Bleckmann A, Fröhlich M, Fröhling S, Glimm H, Brors B, Beißbarth T (2018) From somatic variants towards precision oncology: Evidence-driven reporting of treatment options in molecular tumor boards. Genome Med,10(1):18. doi: 10.1186/s13073-018-0529-2
  • Wolff A, Bayerlová M, Gaedcke J, Kube D, Beißbarth T (2018). A comparative study of RNA-Seq and microarray data analysis on the two examples of rectal-cancer patients and Burkitt Lymphoma cells. PLoS One. 13(5):e0197162. doi: 10.1371/journal.pone.0197162
  • Bayerlová M, Klemm F, Kramer F, Pukrop T, Beißbarth T*, Bleckmann A (2015)*. Newly Constructed Network Models of Different WNT Signaling Cascades Applied to Breast Cancer Expression Data. PLoS One, 10(12):e0144014. doi: 10.1371/journal.pone.0144014
  • Wachter A, Beißbarth T (2015) pwOmics: An R package for pathway-based integration of time-series omics data using public database knowledge. Bioinformatics, 31(18):3072-4. doi: 10.1093/bioinformatics/btv323
  • Beißbarth T, Speed TP (2004). GOstat: Find statistically overrepresented Gene Ontologies within a group of genes. Bioinformatics, 20(9):1464-1465. doi: 10.1093/bioinformatics/bth088
  • Kaufholz F, Ulrich J, Hakeemi MS, Bucher G. Temporal control of RNAi reveals both robust and labile feedback loops in the segmentation clock of the red flour beetle. Proc Natl Acad Sci. 2024 Jun 18;121(25):e2318229121. doi: 10.1073//pnas.2318229121
  • Hakeemi MS*, Ansari S*, Teuscher M*, Weißkopf M*, Großmann D, Kessel T, …, Bucher G. Screens in fly and beetle reveal vastly divergent gene sets required for developmental processes. BMC Biol. 2022;20:38. doi: 10.1186/s12915-022-01231-4
  • Farnworth MS, Eckermann KN, Bucher G. Sequence heterochrony led to a gain of functionality in an immature stage of the central complex: A fly–beetle insight. PLOS Biol. 2020;18:e3000881. doi: 10.1371/journal.pbio.3000881
  • He B, Buescher M, Farnworth MS, Strobl F, Stelzer EH, Koniszewski ND, Mühlen D, Bucher G. An ancestral apical brain region contributes to the central complex under the control of foxQ2 in the beetle Tribolium. eLife. 2019;8. doi: 10.7554/eLife.49065
  • Ansari S, Troelenberg N, Dao VA, Richter T, Bucher G*, Klingler M*. Double abdomen in a short-germ insect: Zygotic control of axis formation revealed in the beetle Tribolium castaneum. Proc Natl Acad Sci U S A. 2018 Feb 20;115(8):1819-1824. doi: 10.1073/pnas.1716512115
  • Schmitt-Engel C, Schultheis D, Schwirz J, Ströhlein N, Troelenberg N, Majumdar U, Dao VA, Grossmann D, Richter T, Tech M, Dönitz J, Gerischer L, Theis M, Schild I, Trauner J, Koniszewski ND, Küster E, Kittelmann S, Hu Y, Lehmann S, Siemanowski J, Ulrich J, Panfilio KA, Schröder R, Morgenstern B, Stanke M, Buchhholz F, Frasch M, Roth S, Wimmer EA, Schoppmeier M*, Klingler M*, Bucher G*. The iBeetle large-scale RNAi screen reveals gene functions for insect development and physiology. Nat Commun. 2015 Jul 28;6:7822. doi: 10.1038/ncomms8822
  • Fu* J, Posnien* N, Bolognesi R, Fischer TD, Rayl P, Oberhofer G, Kitzmann P, Brown* SJ, Bucher* G. Asymmetrically expressed axin required for anterior development in Tribolium. Proc Natl Acad Sci USA. 2012;109:7782–6. doi: 10.1073/pnas.1116641109
  • Posnien N, Koniszewski NDB, Hein HJ, Bucher G. Candidate Gene Screen in the Red Flour Beetle Tribolium Reveals Six3 as Ancient Regulator of Anterior Median Head and Central Complex Development. PLoS Genet. 2011;7:e1002418. doi: 10.1371/journal.pgen.1002416
  • Park Y, Hauschild AC. The effect of data transformation on low-dimensional integration of single-cell RNA-seq. BMC Bioinformatics 25, 171 (2024). doi: 10.1186/s12859-024-05788-5
  • Metsch JM J, Saranti A, Angerschmid A, Pfeifer B, Klemt V, Holzinger A, Hauschild AC. CLARUS: An Interactive Explainable AI Platform for Manual Counterfactuals in graph neural networks. Journal of Biomedical Informatics. 2024 Jan 30:104600. doi: 10.1016/j.jbi.2024.104600
  • Park Y, Muttray NP, Hauschild AC. Species-Agnostic Transfer Learning for Cross-species Transcriptomics Data Integration without Gene Orthology. Briefings in Bioinformatics, 25(2), 2024. doi: 10.1093/bib/bbae004
  • Pfeifer B, Chereda H, Martin R, Saranti A, Clemens S, Hauschild AC, Beißbarth T, Holzinger A, Heider D. EnsembleGNN: federated ensemble learning with graph neural networks for disease module discovery and classification. Bioinformatics, Volume 39, Issue 11, November 2023. doi: 10.1093/bioinformatics/btad703
  • Bender T, Beinecke JM, Krefting D, Müller C, Dathe H, Seidler T, Spicher N, Hauschild AC. (2022). Analysis of a Deep Learning Model for 12-Lead ECG Classification Reveals Learned Features Similar to Diagnostic Criteria. IEEE, Journal of Biomedical and Health Informatics 2023. doi: 10.1109/JBHI.2023.3271858
  • Hauschild AC, Pastrello C., Ekaputeri GKA, Waddell DB, Abovsky M, Ahmed Z, Kotlyar M, Lu R, Jurisica I. (2022). MirDIP 5.2 tissue context annotation and novel microRNA curation. Nucleic Acids Research 2022. doi: 10.1093/nar/gkac1070
  • Hauschild AC, Lemanczyk M, Matschinske J, Frisch T, Zolotareva O, Holzinger A, Baumbach J, Heider D (2022) Federated Random Forests can improve local performance of predictive models for various health care applications. Bioinformatics 38(8):2278-2286. doi: 10.1093/bioinformatics/btac065
  • Beinecke JM, Anders P, Schurrat T, Heider D, Luster M, Librizzi D, Hauschild AC (2022) Evaluation of machine learning strategies for imaging confirmed prostate cancer recurrence prediction on electronic health records. Comput Biol Med 143:105263. doi: 10.1016/j.compbiomed.2022.105263
  • Park Y, Hauschild AC, Heider D (2021) Transfer learning compensates limited data, batch effects and technological heterogeneity in single-cell sequencing. NAR Genom Bioinform 3(4):lqab104. doi: 10.1093/nargab/lqab104
  • Jackson D.J.^*, Cerveau, N.^, Posnien, N.^*. De novo assembly of transcriptomes and differential gene expression analysis using short-read data from emerging model organisms – a brief guide. Front Zool. 2024 Jun 20;21(1):17. doi: 10.1186/s12983-024-00538-y
  • Simmons, M., Horbelt, N., Sverko, T., Scoppola, E., Jackson, D.J.*, Harrington, M.J.* (2023). Invasive mussels fashion silk-like byssus via mechanical processing of massive horizontally acquired coiled coils. PNAS. e2311901120. doi:10.1073/pnas.2311901120
  • Cerveau, N., Jackson, D. J.* (2021). A survey of miRNAs involved in biomineralization and shell repair in the freshwater gastropod Lymnaea stagnalis. Discover Materials. 1:7. doi.org/10.1007/s43939-021-00007-x
  • Jackson, D. J.* (2021). Mantle modularity underlies the plasticity of the molluscan shell: supporting data from Cepaea nemoralis. Frontiers in Genetics 12:622400. doi: 10.3389/fgene.2021.622400
  • Affenzeller, S., Wolkenstein, K., Frauendorf, H., Jackson, D.J.* (2020). Challenging the concept that eumelanin is the polymorphic brown banded pigment in Cepaea nemoralis. Scientific Reports. 10. 2442. doi: 10.1038/s41598-020-59185-y
  • Affenzeller, S., Wolkenstein, K.*, Frauendorf, H., Jackson, D.J.*, (2019). Eumelanin and pheomelanin pigmentation in mollusc shells may be less common than expected: insights from mass spectrometry. Frontiers in Zoology 16:47. doi: 10.1186/s12983-019-0346-5
  • Herlitze, I., Marie, B., Marin, F., Jackson, D. J.* (2018). Molecular modularity and asymmetry of the molluscan mantle revealed by a gene expression atlas. Gigascience 7. doi: 10.1093/gigascience/giy056
  • Jackson, D. J.*, Bernard M. Degnan. (2016). The importance of Evo-Devo to an integrated understanding of molluscan biomineralisation. Journal of Structural Biology, 196(2): 67-74. doi: 10.1016/j.jsb.2016.01.005
  • Jackson, D. J.*, Macis, L., Reitner, J., Wörheide, G. (2011). A horizontal gene transfer supported the evolution of an early metazoan biomineralization strategy. BMC Evolutionary Biology, 11(1): 238. doi: 10.1186/1471-2148-11-238
  • Jentoft I M A, Bäuerlein F J B, Welp L M, Cooper B H, Petrovic A, So C, Penir S M, Politi A Z, Horokhovskyi Y, Takala I, Eckel H, Moltrecht R, Lénárt P, Cavazza T, Liepe J, Brose N, Urlaub H, Fernández-Busnadiego R, Schuh M. Mammalian oocytes store proteins for the early embryo on cytoplasmic lattices. Cell. 2023 Nov 22;186(24):5308-5327.e25. doi: 10.1016/j.cell.2023.10.003
  • Wesolowska N, Avilov I, Machado P, Geiss C, Kondo H, Mori M, Lénárt P. Actin assembly ruptures the nuclear envelope by prying the lamina away from nuclear pores and nuclear membranes in starfish oocytes. Elife. 2020 Jan 28;9. pii: e49774. doi: 10.7554/eLife.49774
  • Burdyniuk M, Callegari A, Mori M, Nedelec F, Lénárt P. F-Actin nucleated on chromosomes coordinates their capture by microtubules in oocyte meiosis. J Cell Biol. 2018 Aug 6;217(8):2661-2674. doi: 10.1083/jcb.201802080
  • Bun P, Dmitrieff S, Belmonte JM, Nédélec FJ, Lénárt P. A disassembly-driven mechanism explains F-actin-mediated chromosome transport in starfish oocytes. Elife. 2018 Jan 19;7. pii: e31469. doi: 10.7554/eLife.31469
  • Bischof J, Brand CA, Somogyi K, Májer I, Thome S, Mori M, Schwarz US, Lénárt P. A cdk1 gradient guides surface contraction waves in oocytes. Nat Commun. 2017 Oct 11;8(1):849. doi: 10.1038/s41467-017-00979-6
  • Borrego-Pinto J, Somogyi K, Karreman M, König J, Müller-Reichert T, Bettencourt-Dias M, Gönczy P, Schwab Y, Lénárt, P. Distinct mechanisms eliminate mother and daughter centrioles in meiosis of starfish oocytes. J. Cell Biol. 2016 Mar 28;212(7):815-27. doi: 10.1083/jcb.201510083
  • Mori M, Somogyi K, Kondo H, Monnier N, Falk HJ, Machado P, Bathe M, Nédélec F, Lénárt P. An Arp2/3 nucleated F-actin shell fragments nuclear membranes at nuclear envelope breakdown in starfish oocytes. Curr Biol. 2014 Jun 16;24(12):1421-8. doi: 10.1016/j.cub.2014.05.019
  • Žumer K*, Ochmann M, Aljahani A, Zheenbekova A, Devadas A, Maier KC, Rus P, Neef U, Oudelaar AM*, Cramer P* (2024) FACT maintains chromatin architecture and thereby stimulates RNA polymerase II pausing during transcription in vivo. Molecular Cell 84, 1-17. doi: 10.1016/j.molcel.2024.05.003
  • Oberbeckmann E*, Quililan K, Cramer P, Oudelaar AM* (2024) In vitro reconstitution of chromatin domains shows a role for nucleosome positioning in 3D genome organization. Nature Genetics 56, 483-492. doi: 10.1038/s41588-023-01649-8
  • Ramasamy S, Aljahani A, Karpinska MA, Cao NTB, Cruz JN, Oudelaar AM* (2023) The Mediator complex regulates enhancer-promoter interactions. Nature Structural and Molecular Biology 30, 991-1000. doi: 10.1038/s41594-023-01027-2
  • Karpinska MA and Oudelaar AM* (2023) The role of loop extrusion in enhancer-mediated gene activation. Current Opinion in Genetics & Development 79, 102022. doi: 10.1016/j.gde.2023.102022
  • Aljahani A, Hua P, Karpinska MA, Quililan K, Davies JOJ*, Oudelaar AM* (2022) Analysis of sub-kilobase chromatin topology reveals nano-scale regulatory interactions with variable dependence on cohesin and CTCF. Nature Communications 13, 2139. doi: 10.1038/s41467-022-29696-5
  • Downes DJ, Smith AL, Karpinska MA, Velychko T, Rue-Albrecht K, Sims D, Milne TA, Davies JOJ, Oudelaar AM*, Hughes JR* (2022) Capture-C: a modular and flexible approach for high-resolution chromosome conformation capture. Nature Protocols 17, 445-475. doi: 10.1038/s41596-021-00651-w
  • Oudelaar AM* and Higgs DR* (2021) The relationship between genome structure and function. Nature Reviews Genetics 22, 154-168. doi: 101038/s41576-020-00303-x
  • Ebrar Erdoğan DE*, Karimifard S*, Khodadadi M, Ling L, Linke L, Catalán A, Doublet V, Glaser-Schmitt A, Niehuis O, Nowick K, Soro A, Turetzek N#, Feldmeyer B#, Posnien N# (2025). ATAC-seq in Emerging Model Organisms: Challenges and Strategies. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, 2025; 1–21. doi: 10.1002/jez.b.23305
  • Torres-Oliva M*, Buchberger E*, Buffry AD*, Kittelmann M, Sumner-Rooney L, Gaspar PMC, Bullinger GC, Guerrero G, Casares F, Arif S#, Posnien N#, Nunes DDS#, McGregor AP#, Almudi I# (2025). Differences in orthodenticle expression promote ommatidial size variation between Drosophila species. BMC Biology, (2025) 23:34. doi: 10.1186/s12915‑025‑02136‑8
  • Wiegleb G, Reinhardt S, Dahl A, Posnien N (2022). Tissue dissociation for single-cell and single-nuclei RNA sequencing for low amounts of input material. Frontiers in Zoology 19:27. doi: 10.1186/s12983-022-00472-x
  • Buchberger E, Bilen A, Ayaz S, Salamanca D, Matas de las Heras C, Niksic A, Almudi I, Torres-Oliva M, Casares F, Posnien N (2021). Variation in pleiotropic hub gene expression is associated with interspecific differences in head shape and eye size in Drosophila. Molecular Biology and Evolution Volume 38, Issue 5, May 2021, p 1924–1942. doi: 10.1093/molbev/msaa335
  • Reis M, Wiegleb G, Claude J, Lata R, Horchler B, Ha N-T, Reimer C, Vieira CP, Vieira J, Posnien N (2020). Multiple loci linked to inversions are associated with eye size variation in species of the Drosophila virilis phylad. Scientific Reports 10, 12832. doi: 10.1038/s41598-020-69719-z
  • Torres-Oliva M, Schneider J, Wiegleb G, Kaufholz F, Posnien N (2018). Dynamic genome wide expression profiling of Drosophila head development reveals a novel role of Hunchback in retinal glia cell development and blood-brain barrier integrity. PLoS Genet 14(1):e1007180. doi: 10.1371/journal.pgen.1007180
  • Schwager EE, […], Posnien N+, Richards S+, McGregor AP+ (2017). The house spider genome reveals a whole genome duplication during arachnid evolution. BMC Biology 15, 62. doi: 10.1186/s12915-017-0399-x
  • Torres-Oliva M, Almudí I, McGregor AP, Posnien N (2016). A robust (re-)annotation approach to generate unbiased mapping references for RNA-seq-based analyses of differential expression across closely related species. BMC Genomics 17, 392. doi: 10.1186/s12864-016-2646-x
  • Hall RN, Weill U, Drees L, Leal-Ortiz S, Li H, Khariton M, Chai C, Xue Y, Rosental B, Quake SR, Sánchez Alvarado A, Melosh NA, Fire AZ, Rink JC, Wang B. Heterologous reporter expression in the planarian Schmidtea mediterranea through somatic mRNA transfection. Cell Rep Methods. 2022 Sep 20;2(10):100298. doi: 10.1016/j.crmeth.2022.100298
  • Thommen A., Werner S., Frank O., Alt N., Richter J., Philipp J., Knittelfelder O., Quek Y., Fahmy K., Shevchenko A., Friedrich BM., Jülicher F., Rink JC. (2019). Body size-dependent energy storage causes Kleiber’s law scaling in planarians. eLife, 8:e38187. doi: 10.7554/eLife.38187
  • Thi-Kim Vu H., Mansour S., Blasse C., Kuecken M., Basquin C., Azimzadeh J., Myers G., Brusch L., Rink JC. (2019). Multi-scale coordination of planar cell polarity in planarians. DevCell 51(4):526-542. doi: 10.1101/324822
  • Liu SY, Rink JC. 2018. Total RNA Isolation from Planarian Tissues. Methods Mol Biol.1774:259-265. doi: 10.1007/978-1-4939-7802-1_6
  • Grohme M., Schloissnig S., Rozanski A., Pippel M., Young G., Winkler S., Brandl H., Henry, I., Dahl A., Powell S., Hiller M., Myers E., Rink JC. (2018). The genome of S. mediterranea and the evolution of cellular core mechanisms. Nature, 554(7690):56-61. doi: 10.1038/nature25473
  • Boothe T., Hilbert L., Heide M., Berninger L., Huttner WB., Zaburdaev V., Vastenhouw NL., Myers E., Drechsel DN., Rink JC. (2017). A tunable refractive index matching medium for live imaging cells, tissues and model organisms. eLife, 6:e27240. doi: 10.7554/eLife.27240
  • Stückemann T., Cleland JP., Werner S., Thi-Kim Vu, H., Bayersdorf R., Liu SY., Friedrich B., Jülicher F., Rink JC. (2017). Antagonistic Self-Organizing Patterning Systems Control Maintenance and Regeneration of the Anteroposterior Axis in Planarians. Dev Cell, 40(3):248-263. doi: 10.1016/j.devcel.2016.12.024
  • Liu SY., Selck C., Friedrich B., Lutz R., Vila-Farré M., Dahl A., Brandl H., Lakshmanaperumal N., Henry I., Rink JC. (2013). Reactivating head regrowth in a regeneration-deficient planarian species. Nature, 500(7460):81-4. doi: 10.1038/nature12414