Biology

Cells and multicellular organisms have long been recognized as sophisticated information processors. They sense and integrate external signals in order to adapt to environmental changes and to  communicate with other cells and organisms. To reach decisions, they process symbolic information according to logical rules, and as such can be compared to man-made computers. However, natural systems differ in design and function: biological systems are distributed probabilistic devices which compute information at multiple levels, ranging from single proteins to cellular networks. These features endow biological systems with superior robustness of function, conferring on them in particular an exceptional adaptability and the capacity to either exploit or filter out noise. Therefore, biological systems represent a rich source of inspiration for the future development of novel soft- and hardware architectures, as exemplified by biology-inspired neural network-based machine learning. However, the prerequisite is to fully understand the molecular and cellular hardware, the biological computational rules and the underlying algorithms. With recent advances in knowledge and technology in various key areas, such as the structure of the genome and proteome, as well as the availability of advanced imaging modalities and computational tools, we are now in the position to address this monumental challenge. Within this context, the aim is to decipher the molecular mechanisms of biological information processing in cells and cellular networks, and to bring this knowledge to the first proof-of-principle applications.

Publication list


2024
Drug retention after intradiscal administration
Rudnik-Jansen, I.; Du, J.; Karssemakers-Degen, N.; Tellegen, A. R.; Wadhwani, P.; Zuncheddu, D.; Meij, B. P.; Thies, J.; Emans, P.; Öner, F. C.; Mihov, G.; Garcia, J. P.; Ulrich, A. S.; Grad, S.; Tryfonidou, M. A.; Ingen, H. van; Creemers, L. B.
2024. Drug Delivery, 31 (1), Art.-Nr.: 2415579. doi:10.1080/10717544.2024.2415579
An open-source software for the simulation of fixational eye movements
Allgeier, S.; Anzlinger, F.; Bohn, S.; Mikut, R.; Neumann, O.; Reichert, K.-M.; Stachs, O.; Sperlich, K.
2024. Current Directions in Biomedical Engineering, 10 (4), 25–28. doi:10.1515/cdbme-2024-2007
Gene expression patterns of the LDL receptor and its inhibitor Pcsk9 in the adult zebrafish brain suggest a possible role in neurogenesis
Gence, L.; Morello, E.; Rastegar, S.; Apalama, M. L.; Meilhac, O.; Bascands, J.-L.; Diotel, N.
2024. European Journal of Neuroscience. doi:10.1111/ejn.16586
Context-aware composition of agent policies by Markov decision process entity embeddings and agent ensembles
Merkle, N.; Mikut, R.
2024. Semantic Web, 15 (4), 1443–1471. doi:10.3233/SW-233531
A self-supervised embedding of cell migration features for behavior discovery over cell populations
Molina-Moreno, M.; González-Díaz, I.; Mikut, R.; Díaz-de-María, F.
2024. Computer Methods and Programs in Biomedicine, 255, 108337. doi:10.1016/j.cmpb.2024.108337
Comparative insight into the regenerative mechanisms of the adult brain in zebrafish and mouse: highlighting the importance of the immune system and inflammation in successful regeneration
Chen, J.; Sanchez-Iranzo, H.; Diotel, N.; Rastegar, S.
2024. The FEBS Journal, 291 (19), 4193–4205. doi:10.1111/febs.17231
Fluorine and Bromine Dual-Doped Nanoporous Carbons: Preparation and Surface Chemistry Studies
Mussabek, G.; Baktygerey, S.; Taurbayev, Y.; Yermukhamed, D.; Zhylkybayeva, N.; Diyuk, V. E.; Zaderko, A.; Afonin, S.; Mariychuk, R.; Kaňuchová, M.; Lisnyak, V. V.
2024. ACS Omega, 9 (37), 38618–38628. doi:10.1021/acsomega.4c04179
Printing Green: Microalgae‐Based Materials for 3D Printing with Light
Vazquez-Martel, C.; Florido Martins, L.; Genthner, E.; Almeida, C.; Martel Quintana, A.; Bastmeyer, M.; Gómez Pinchetti, J. L.; Blasco, E.
2024. Advanced Materials, 36 (33), Art.-Nr.: 2402786. doi:10.1002/adma.202402786
The role of host response to chemotherapy: resistance, metastasis and clinical implications
Deo, A.; Sleeman, J. P.; Shaked, Y.
2024. Clinical and Experimental Metastasis, 41 (4), 495–507. doi:10.1007/s10585-023-10243-5
Flavin-induced charge separation in transmembrane model peptides
Wörner, S.; Rauthe, P.; Werner, J.; Afonin, S.; Ulrich, A. S.; Unterreiner, A.-N.; Wagenknecht, H.-A.
2024. Organic & Biomolecular Chemistry, 22 (29), 5930–5935. doi:10.1039/d4ob00932k
Insights into the mechanisms of neuron generation and specification in the zebrafish ventral spinal cord
Cucun, G.; Köhler, M.; Pfitsch, S.; Rastegar, S.
2024. The FEBS Journal, 291 (4), 646–662. doi:10.1111/febs.16913
Automated handling of biological objects with a flexible gripper for biodiversity research; [Automatisierte Handhabung biologischer Objekten mit einem flexiblen Greifer für die Biodiversitätsforschung]
Wührl, L.; Keller, L.; Klug, N.; Shirali, H.; Meier, R.; Pylatiuk, C.
2024. at - Automatisierungstechnik, 72 (7), 672–678. doi:10.1515/auto-2023-0238
Sporadic feeding regulates robust food entrainable circadian clocks in blind cavefish
Di Rosa, V.; Frigato, E.; Negrini, P.; Cristiano, W.; López-Olmeda, J. F.; Rétaux, S.; Sánchez-Vázquez, F. J.; Foulkes, N. S.; Bertolucci, C.
2024. iScience, 27 (7), 110171. doi:10.1016/j.isci.2024.110171
TRIM11 expression in non-small cell lung cancer is associated with poor prognosis
Kuempers, C.; Jagomast, T.; Paulsen, F. O.; Heidel, C.; Bohnet, S.; Schierholz, S.; Reischl, M.; Dreyer, E.; Olchers, T.; Reck, M.; Kirfel, J.; Perner, S.
2024. Histology and histopathology, 39, 437–446. doi:10.14670/HH-18-647
Towards global insect biomonitoring with frugal methods
Brydegaard, M.; Pedales, R. D.; Feng, V.; Yamoa, A. saint- doria; Kouakou, B.; Månefjord, H.; Wührl, L.; Pylatiuk, C.; Amorim, D. de S.; Meier, R.
2024. Philosophical Transactions of the Royal Society B: Biological Sciences, 379 (1904). doi:10.1098/rstb.2023.0103
Towards holistic insect monitoring: species discovery, description, identification and traits for all insects
Meier, R.; Hartop, E.; Pylatiuk, C.; Srivathsan, A.
2024. Philosophical transactions of the Royal Society of London / Series B, 379 (1904). doi:10.1098/rstb.2023.0120
A Versatile Microfluidic Platform for Extravasation Studies Based on DNA Origami—Cell Interactions
García-Chamé, M.; Wadhwani, P.; Pfeifer, J.; Schepers, U.; Niemeyer, C. M.; Domínguez, C. M.
2024. Angewandte Chemie International Edition, 63 (28), Art.-Nr.: e202318805. doi:10.1002/anie.202318805
High‐Throughput Miniaturized Synthesis of PROTAC‐Like Molecules
Tian, Y.; Seifermann, M.; Bauer, L.; Luchena, C.; Wiedmann, J. J.; Schmidt, S.; Geisel, A.; Afonin, S.; Höpfner, J.; Brehm, M.; Liu, X.; Hopf, C.; Popova, A. A.; Levkin, P. A.
2024. Small, 20 (26), Art.-Nr.: 2307215. doi:10.1002/smll.202307215
ObiWan-Microbi: OMERO-based integrated workflow for annotating microbes in the cloud
Seiffarth, J.; Scherr, T.; Wollenhaupt, B.; Neumann, O.; Scharr, H.; Kohlheyer, D.; Mikut, R.; Nöh, K.
2024. SoftwareX, 26, Article no: 101638. doi:10.1016/j.softx.2024.101638
Cell Shape and Forces in Elastic and Structured Environments: From Single Cells to Organoids
Link, R.; Weißenbruch, K.; Tanaka, M.; Bastmeyer, M.; Schwarz, U. S.
2024. Advanced Functional Materials, 34 (20), Art.-Nr.: 2302145. doi:10.1002/adfm.202302145
Spiropyran‐Based Photoisomerizable α‐Amino Acid for Membrane‐Active Peptide Modification
Hrebonkin, A.; Afonin, S.; Nikitjuka, A.; Borysov, O. V.; Leitis, G.; Babii, O.; Koniev, S.; Lorig, T.; Grage, S. L.; Nick, P.; Ulrich, A. S.; Jirgensons, A.; Komarov, I. V.
2024. Chemistry – A European Journal, 30 (22). doi:10.1002/chem.202400066
Reversible Influence of Hemipiperazine Photochromism on the Early Development of Zebrafish Embryo
Seliwjorstow, A.; Takamiya, M.; Rastegar, S.; Pianowski, Z.
2024. ChemBioChem, 25 (8), Article e202400143. doi:10.1002/cbic.202400143
Parenchymal cues define Vegfa-driven venous angiogenesis by activating a sprouting competent venous endothelial subtype
Préau, L.; Lischke, A.; Merkel, M.; Oegel, N.; Weissenbruch, M.; Michael, A.; Park, H.; Gradl, D.; Kupatt, C.; le Noble, F.
2024. Nature Communications, 15 (1), Art.-Nr.: 3118. doi:10.1038/s41467-024-47434-x
Modelling cell shape in 3D structured environments: A quantitative comparison with experiments
Link, R.; Jaggy, M.; Bastmeyer, M.; Schwarz, U. S.
2024. (P. Rangamani, Ed.) PLOS Computational Biology, 20 (4), Art.-Nr.: e1011412. doi:10.1371/journal.pcbi.1011412
Systematic acquisition of toxicity data in non-sentient models across animal phylogeny: implications for read-across and estimation of toxicity in humans
Hayot, G.; Massei, R.; Lloyd, G.; Keith, N.; Diwan, G.; Martínez López, R.; Barnard, M.; Cramer von Clausbruch, C. A.; Grasse, N.; Smoot, S.; Escher, B.; Tennessen, J.; Tindall, A.; Oliver, B.; Shaw, J.; Scholz, S.; Freedman, J.; Strähle, U.; Colbourne, J. K.; Weiss, C.; Dickmeis, T.
2024. Naunyn-Schmiedeberg’s archives of pharmacology, 397 (Suppl. 1), S17–69. doi:10.1007/s00210-024-02974-3
Surface-Patterned DNA Origami Rulers Reveal Nanoscale Distance Dependency of the Epidermal Growth Factor Receptor Activation
Mayer, I.; Karimian, T.; Gordiyenko, K.; Angelin, A.; Kumar, R.; Hirtz, M.; Mikut, R.; Reischl, M.; Stegmaier, J.; Zhou, L.; Ma, R.; Nienhaus, G. U.; Rabe, K. S.; Lanzerstorfer, P.; Domínguez, C. M.; Niemeyer, C. M.
2024. Nano Letters, 24 (5), 1611–1619. doi:10.1021/acs.nanolett.3c04272
Caveolae disassemble upon membrane lesioning and foster cell survival
Štefl, M.; Takamiya, M.; Middel, V.; Tekpınar, M.; Nienhaus, K.; Beil, T.; Rastegar, S.; Strähle, U.; Nienhaus, G. U.
2024. iScience, 27 (2), 108849. doi:10.1016/j.isci.2024.108849
A spheroid whole mount drug testing pipeline with machine-learning based image analysis identifies cell-type specific differences in drug efficacy on a single-cell level
Vitacolonna, M.; Bruch, R.; Schneider, R.; Jabs, J.; Hafner, M.; Reischl, M.; Rudolf, R.
2024. BMC Cancer, 24 (1), Art.-Nr.: 1542. doi:10.1186/s12885-024-13329-9
Development of a Benzophenone-Free Red Propolis Extract and Evaluation of Its Efficacy against Colon Carcinogenesis
Squarisi, I. S.; Ribeiro, V. P.; Ribeiro, A. B.; Souza, L. T. M. de; Junqueira, M. de M.; Oliveira, K. M. de; Hayot, G.; Dickmeis, T.; Bastos, J. K.; Veneziani, R. C. S.; Ambrósio, S. R.; Tavares, D. C.
2024. Pharmaceuticals, 17 (10), Art.-Nr.: 1340. doi:10.3390/ph17101340
Surface chemistry and catalytic activity in HO decomposition of pyrolytically fluoralkylated activated carbons
Mussabek, G.; Baktygerey, S.; Taurbayev, Y.; Yermukhamed, D.; Zhylkybayeva, N.; Zaderko, A. N.; Diyuk, V. E.; Afonin, S.; Yar-Mukhamedova, G.; Mariychuk, R. T.; Grishchenko, L. M.; Kaňuchová, M.; Lisnyak, V. V.
2024. RSC Advances, 14 (40), 29052–29071. doi:10.1039/d4ra04883k
Mapping the cellular expression patterns of vascular endothelial growth factor aa and bb genes and their receptors in the adult zebrafish brain during constitutive and regenerative neurogenesis
Fernezelian, D.; Pfitsch, S.; Rastegar, S.; Diotel, N.
2024. Neural Development, 19, Article no: 17. doi:10.1186/s13064-024-00195-1
Modular control of vertebrate axis segmentation in time and space
Seleit, A.; Brettell, I.; Fitzgerald, T.; Vibe, C.; Loosli, F.; Wittbrodt, J.; Naruse, K.; Birney, E.; Aulehla, A.
2024. The EMBO Journal, 43 (18), 4068–4091. doi:10.1038/s44318-024-00186-2
Image-based recognition of parasitoid wasps using advanced neural networks
Shirali, H.; Hübner, J.; Both, R.; Raupach, M.; Reischl, M.; Schmidt, S.; Pylatiuk, C.
2024. Invertebrate Systematics, 38, Article no: IS24011. doi:10.1071/IS24011
A multiparametric analysis including single-cell and subcellular feature assessment reveals differential behavior of spheroid cultures on distinct ultra-low attachment plate types
Vitacolonna, M.; Bruch, R.; Agaçi, A.; Nürnberg, E.; Cesetti, T.; Keller, F.; Padovani, F.; Sauer, S.; Schmoller, K. M.; Reischl, M.; Hafner, M.; Rudolf, R.
2024. Frontiers in Bioengineering and Biotechnology, 12. doi:10.3389/fbioe.2024.1422235
A comparative metabolomic investigation of different sections of Sicilian Citrus x limon (L.) Osbeck, characterization of bioactive metabolites, and evaluation of in vivo toxicity on zebrafish embryo
Pagliari, S.; Sicari, M.; Pansera, L.; Guidi Nissim, W.; Mhalhel, K.; Rastegar, S.; Germanà, A.; Cicero, N.; Labra, M.; Cannavacciuolo, C.; Montalbano, G.; Campone, L.
2024. Journal of Food Science, 89 (6), 3729–3744. doi:10.1111/1750-3841.17079
Reactive Oxygen Species Signaling and Oxidative Stress: Transcriptional Regulation and Evolution
Hong, Y.; Boiti, A.; Vallone, D.; Foulkes, N. S.
2024. Antioxidants, 13 (3), Art.-Nr.: 312. doi:10.3390/antiox13030312
Opto-fluidically multiplexed assembly and micro-robotics
Erben, E.; Liao, W.; Minopoli, A.; Maghelli, N.; Lauga, E.; Kreysing, M.
2024. Light: Science & Applications, 13 (1), 59. doi:10.1038/s41377-024-01406-4
Evaluating Toxicity of Chemicals using a Zebrafish Vibration Startle Response Screening System
Hayot, G.; Marcato, D.; Cramer von Clausbruch, C. A.; Pace, G.; Strähle, U.; Colbourne, J. K.; Pylatiuk, C.; Peravali, R.; Weiss, C.; Scholz, S.; Dickmeis, T.
2024. Journal of visualized experiments : JoVE, 203, Art.-Nr.: e66153. doi:10.3791/66153
Role of melanocortin system in the locomotor activity rhythms and melatonin secretion as revealed by agouti‐signalling protein ( asip1 ) overexpression in zebrafish
Godino-Gimeno, A.; Leal, E.; Chivite, M.; Tormos, E.; Rotllant, J.; Vallone, D.; Foulkes, N. S.; Míguez, J. M.; Cerdá-Reverter, J. M.
2024. Journal of Pineal Research, 76 (1), Art.-Nr.: e12939. doi:10.1111/jpi.12939
Rapid Flow Behavior Modeling of Thermal Interface Materials Using Deep Neural Networks
Baeuerle, S.; Gebhardt, M.; Barth, J.; Mikut, R.; Steimert, A.
2024. IEEE Access, 12, 17782–17792. doi:10.1109/ACCESS.2024.3359169
Entomoscope: An Open-Source Photomicroscope for Biodiversity Discovery
Wührl, L.; Rettenberger, L.; Meier, R.; Hartop, E.; Graf, J.; Pylatiuk, C.
2024. IEEE Access, 12, 11785–11794. doi:10.1109/ACCESS.2024.3355272
Reversible Host–Guest Crosslinks in Supramolecular Hydrogels for On‐Demand Mechanical Stimulation of Human Mesenchymal Stem Cells
Linke, P.; Munding, N.; Kimmle, E.; Kaufmann, S.; Hayashi, K.; Nakahata, M.; Takashima, Y.; Sano, M.; Bastmeyer, M.; Holstein, T.; Dietrich, S.; Müller-Tidow, C.; Harada, A.; Ho, A. D.; Tanaka, M.
2024. Advanced Healthcare Materials, 13 (10), Art.-Nr.: 2302607. doi:10.1002/adhm.202302607
Comparison of Decellularized Human Dermal Scaffolds versus Bovine Collagen/Elastin Matrices for Engineering of Soft-Tissue Flaps
Falkner, F.; Mayer, S. A.; Heuer, M.; Brune, J.; Helt, H.; Bigdeli, A. K.; Dimmler, A.; Heimel, P.; Thiele, W.; Sleeman, J. P.; Bergmeister, H.; Schneider, K. H.; Kneser, U.; Thomas, B.
2024. Plastic and Reconstructive Surgery, 153 (1), 130 – 141. doi:10.1097/PRS.0000000000010511
Probe-free optical chromatin deformation and measurement of differential mechanical properties in the nucleus
Seelbinder, B.; Wagner, S.; Jain, M.; Erben, E.; Klykov, S.; Stoev, I. D.; Krishnaswamy, V. R.; Kreysing, M.
2024. eLife, 13. doi:10.7554/eLife.76421
CoNIC Challenge: Pushing the frontiers of nuclear detection, segmentation, classification and counting
Graham, S.; Vu, Q. D.; Jahanifar, M.; Weigert, M.; Schmidt, U.; Zhang, W.; Zhang, J.; Yang, S.; Xiang, J.; Wang, X.; Rumberger, J. L.; Baumann, E.; Hirsch, P.; Liu, L.; Hong, C.; Aviles-Rivero, A. I.; Jain, A.; Ahn, H.; Hong, Y.; Azzuni, H.; Xu, M.; Yaqub, M.; Blache, M.-C.; Piégu, B.; Vernay, B.; Scherr, T.; Böhland, M.; Löffler, K.; Li, J.; Ying, W.; Wang, C.; Snead, D.; Raza, S. E. A.; Minhas, F.; Rajpoot, N. M.
2024. Medical Image Analysis, 92, Article no: 103047. doi:10.1016/j.media.2023.103047
On the reproducibility of extrusion-based bioprinting: round robin study on standardization in the field
Grijalva Garces, D.; Strauß, S.; Gretzinger, S.; Schmieg, B.; Jüngst, T.; Groll, J.; Meinel, L.; Schmidt, I.; Hartmann, H.; Schenke-Layland, K.; Brandt, N.; Selzer, M.; Zimmermann, S.; Koltay, P.; Southan, A.; Tovar, G. E. M.; Schmidt, S.; Weber, A.; Ahlfeld, T.; Gelinsky, M.; Scheibel, T.; Detsch, R.; Boccaccini, A. R.; Naolou, T.; Lee-Thedieck, C.; Willems, C.; Groth, T.; Allgeier, S.; Köhler, B.; Friedrich, T.; Briesen, H.; Buchholz, J.; Paulus, D.; von Gladiss, A.; Hubbuch, J.
2024. Biofabrication, 16 (1), Art.-Nr.: 015002. doi:10.1088/1758-5090/acfe3b
Exploring the Antibacterial Effects of Ozonated Oils in Medicine: A Study on Escherichia coli Inhibition
Petani, L.; Jung, A.-M.; Frietsch Musulin, R.-R.; Sturm, G.; Kaster, A.-K.; Pylatiuk, C.
2024. Ozone: Science & Engineering, 46 (2), 174–181. doi:10.1080/01919512.2023.2233746
Exploring Functional Photonic Devices made from a Chiral Metal–Organic Framework Material by a Multiscale Computational Method
Zerulla, B.; Li, C.; Beutel, D.; Oßwald, S.; Holzer, C.; Bürck, J.; Bräse, S.; Wöll, C.; Fernandez-Corbaton, I.; Heinke, L.; Rockstuhl, C.; Krstić, M.
2024. Advanced Functional Materials, 34 (20), Art.-Nr.: 2301093. doi:10.1002/adfm.202301093
2023
Congratulations to Prof. em. Garth L. Nicolson – co-founder of Clinical and Experimental Metastasis
Haier, J.; Sleeman, J.
2023. Clinical & Experimental Metastasis, 40 (6), 443–444. doi:10.1007/s10585-023-10239-1
Chromatic Swept-Source Laser Scanning - Konzept für eine zellauflösende konfokale Laserspaltlampe? [Chromatic Swept-Source Laser Scanning - Concept for a Cell-Resolving Confocal Laser Slit Lamp?]
Sperlich, K.; Bohn, S.; Reichert, K.-M.; Stolz, H.; Guthoff, R. F.; Stachs, O.; Allgeier, S.
2023. Klinische Monatsblätter für Augenheilkunde, 240 (12), 1375 – 1382. doi:10.1055/a-2184-9382
An AI-based segmentation and analysis pipeline for high-field MR monitoring of cerebral organoids
Deininger, L.; Jung-Klawitter, S.; Mikut, R.; Richter, P.; Fischer, M.; Karimian-Jazi, K.; Breckwoldt, M. O.; Bendszus, M.; Heiland, S.; Kleesiek, J.; Opladen, T.; Hübschmann, O. K.; Hübschmann, D.; Schwarz, D.
2023. Scientific Reports, 13, Art.-Nr.: 21231. doi:10.1038/s41598-023-48343-7
TRIM25 targets p300 for degradation
Elabd, S.; Pauletto, E.; Solozobova, V.; Eickhoff, N.; Padrao, N.; Zwart, W.; Blattner, C.
2023. Life Science Alliance, 6 (12), e202301980. doi:10.26508/lsa.202301980
Interlayer, gallery-engineered graphene oxide using selective protection of mono-Boc-ethylenediamine as anode for sodium ion batteries
Thushara, K. M.; Ponraj, M. R.; Mandal, S.; Peng, X.; Grage, S. L.; Kang, J. W.; Venkatesan, R.; Thavasi, V.; Kannan, A. M.; Liepmann, D.; Pillai, V. K.; Bhagavathsingh, J.
2023. Journal of Energy Storage, 73 (Part D), Art.-Nr.: 109237. doi:10.1016/j.est.2023.109237
Estrogenic regulation of claudin 5 and tight junction protein 1 gene expression in zebrafish: A role on blood-brain barrier?
Pellegrini, E.; Fernezelian, D.; Malleret, C.; Gueguen, M. M.; Patche-Firmin, J.; Rastegar, S.; Meilhac, O.; Diotel, N.
2023. The journal of comparative neurology, 531 (17), 1828–1845. doi:10.1002/cne.25543
Development and Validation of a New BAG-1L–Specific Antibody to Quantify BAG-1L Protein Expression in Advanced Prostate Cancer
Neeb, A.; Figueiredo, I.; Gurel, B.; Nava Rodrigues, D.; Rekowski, J.; Riisnaes, R.; Ferreira, A.; Miranda, S.; Crespo, M.; Westaby, D.; de Los Dolores Fenor de La Maza, M.; Guo, C.; Carmichael, J.; Grochot, R.; Tunariu, N.; Cato, A. C. B.; Plymate, S. R.; de Bono, J. S.; Sharp, A.
2023. Laboratory Investigation, 103 (11), Article no: 100245. doi:10.1016/j.labinv.2023.100245
Selected contributions from the Workshop “Computational Intelligence”
Mikut, R.; Kroll, A.; Schulte, H.
2023. at - Automatisierungstechnik, 71 (10), 817–819. doi:10.1515/auto-2023-0159
A fully automated touch-response behavior inspection pipeline on zebrafish larvae
Wang, Y.; Pylatiuk, C.; Mikut, R.; Peravali, R.; Reischl, M.
2023. at - Automatisierungstechnik, 71 (10), 845–852. doi:10.1515/auto-2023-0013
Cleavage furrow-directed cortical flows bias PAR polarization pathways to link cell polarity to cell division
Ng, K.; Hirani, N.; Bland, T.; Borrego-Pinto, J.; Wagner, S.; Kreysing, M.; Goehring, N. W.
2023. Current Biology, 33 (20), 4298–4311.e6. doi:10.1016/j.cub.2023.08.076
Establishment of cell lines from individual zebrafish embryos
Geyer, N.; Kaminsky, S.; Confino, S.; Livne, Z. B.-M.; Gothilf, Y.; Foulkes, N. S.; Vallone, D.
2023. Laboratory Animals, 57 (5), 518–528. doi:10.1177/00236772231157162
Amphiphiles Formed from Synthetic DNA-Nanomotifs Mimic the Stepwise Dispersal of Transcriptional Clusters in the Cell Nucleus
Tschurikow, X.; Gadzekpo, A.; Tran, M. P.; Chatterjee, R.; Sobucki, M.; Zaburdaev, V.; Göpfrich, K.; Hilbert, L.
2023. Nano Letters, 23 (17), 7815–7824. doi:10.1021/acs.nanolett.3c01301
Unsupervised GAN epoch selection for biomedical data synthesis
Böhland, M.; Bruch, R.; Löffler, K.; Reischl, M.
2023. Current Directions in Biomedical Engineering, 9 (1), 467–470. doi:10.1515/cdbme-2023-1117
A Lightweight Framework for Semantic Segmentation of Biomedical Images
Münke, F. R.; Rettenberger, L.; Popova, A.; Reischl, M.
2023. Current Directions in Biomedical Engineering, 9 (1), 190–193. doi:10.1515/cdbme-2023-1048
Mask R-CNN Outperforms U-Net in Instance Segmentation for Overlapping Cells
Rettenberger, L.; Münke, F. R.; Bruch, R.; Reischl, M.
2023. Current Directions in Biomedical Engineering, 9 (1), 335–338. doi:10.1515/cdbme-2023-1084
Systems toxicology of complex wood combustion aerosol reveals gaseous carbonyl compounds as critical constituents
Dilger, M.; Armant, O.; Ramme, L.; Mülhopt, S.; Sapcariu, S. C.; Schlager, C.; Dilger, E.; Reda, A.; Orasche, J.; Schnelle-Kreis, J.; Conlon, T. M.; Yildirim, A. Ö.; Hartwig, A.; Zimmermann, R.; Hiller, K.; Diabaté, S.; Paur, H.-R.; Weiss, C.
2023. Environment International, 179, Art.-Nr.: 108169. doi:10.1016/j.envint.2023.108169
”Iteratively nafionated water” in its solid phase at room temperature is in fact a mixture of lyophilized biological and non-biological contaminants
Greil, F.; Punampalam, R.; Walther, T. H.; Heißler, S.; Ulrich, A. S.
2023. Journal of Molecular Liquids, 385, Art.-Nr.: 122351. doi:10.1016/j.molliq.2023.122351
Self-Supervised Learning for Annotation Efficient Biomedical Image Segmentation
Rettenberger, L.; Schilling, M.; Elser, S.; Boehland, M.; Reischl, M.
2023. IEEE Transactions on Biomedical Engineering, 70 (9), 2519–2528. doi:10.1109/TBME.2023.3252889
Key Role of Choline Head Groups in Large Unilamellar Phospholipid Vesicles for the Interaction with and Rupture by Silica Nanoparticles
Leibe, R.; Fritsch-Decker, S.; Gussmann, F.; Wagbo, A. M.; Wadhwani, P.; Diabaté, S.; Wenzel, W.; Ulrich, A. S.; Weiss, C.
2023. Small, 19 (34), Artkl.Nr.: 2207593. doi:10.1002/smll.202207593
sox1a:eGFP transgenic line and single-cell transcriptomics reveal the origin of zebrafish intraspinal serotonergic neurons
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Smuggling on the Nanoscale—Fusogenic Liposomes Enable Efficient RNA-Transfer with Negligible Immune Response In Vitro and In Vivo
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Zebrafish: A Model Deciphering the Impact of Flavonoids on Neurodegenerative Disorders
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Mosaic vs. Single Image Analysis with Confocal Microscopy of the Corneal Nerve Plexus for Diagnosis of Early Diabetic Peripheral Neuropathy
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Loss of the Bardet-Biedl protein Bbs1 alters photoreceptor outer segment protein and lipid composition
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Droplet Microarray Based Screening Identifies Proteins for Maintaining Pluripotency of hiPSCs
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Abstractband DOG 2022; Utilizing static corneal landmarks to assess dynamic corneal nerve changes by in vivo large-area confocal microscopy
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Medaka as a model for seasonal plasticity: Photoperiod-mediated changes in behaviour, cognition, and hormones
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Room-temperature ferromagnetic wide bandgap semiconducting fluorinated Graphene-hBN vertical heterostructures
Sahoo, K. R.; Sharma, R.; Bawari, S.; Vivek, S.; Rastogi, P. K.; Nair, S. S.; Grage, S. L.; Narayanan, T. N.
2021. Materials today, 21, Art.Nr. 100547. doi:10.1016/j.mtphys.2021.100547
SemML: Facilitating development of ML models for condition monitoring with semantics
Zhou, B.; Svetashova, Y.; Gusmao, A.; Soylu, A.; Cheng, G.; Mikut, R.; Waaler, A.; Kharlamov, E.
2021. Web semantics, 71, Art.Nr. 100664. doi:10.1016/j.websem.2021.100664
Pilotstudie zur Evaluation einer medizinisch-beruflich orientierten Rehabilitation für Pflegekräfte
Wittmann, C.; Papst, L.; Reischl, M.; Welsch, K.; Käfer, M.; Köllner, V.
2021. Zeitschrift für psychosomatische Medizin und Psychotherapie, 68 (2), 128–140. doi:10.13109/zptm.2021.67.oa13
Evaluierung von Merkmalen zur Abbildung von Veränderungen in ungeordneten Bilddaten = Evaluating features to represent changes in unstructured image data
Münke, F. R.; Schilling, M. P.; Mikut, R.; Reischl, M.
2021. Automatisierungstechnik, 69 (10), 892–902. doi:10.1515/auto-2021-0038
CAD-to-real: enabling deep neural networks for 3D pose estimation of electronic control units – A transferable and automated approach for industrial use cases = CAD-to-real: Eine Methode zum Einsatz tiefer neuronaler Netze bei der 3D-Lageerkennung von elektronischen Steuergeräten - Ein transferierbarer und automatisierter Ansatz für industrielle Anwendungen
Bäuerle, S.; Böhland, M.; Barth, J.; Reischl, M.; Steimer, A.; Mikut, R.
2021. Automatisierungstechnik, 69 (10), 880–891. doi:10.1515/auto-2021-0020
Ausgewählte Beiträge aus dem GMA-Fachausschuss 5.14 „Computational Intelligence“ [Editorial]
Mikut, R.; Kroll, A.; Schulte, H.
2021. Automatisierungstechnik, 69 (10), 817–819. doi:10.1515/auto-2021-0124
O to bR transition in bacteriorhodopsin occurs through a proton hole mechanism
Maag, D.; Mast, T.; Elstner, M.; Cui, Q.; Kubař, T.
2021. Proceedings of the National Academy of Sciences of the United States of America, 118 (39), Art.-Nr. e2024803118. doi:10.1073/pnas.2024803118
Diarylethene-Based Photoswitchable Inhibitors of Serine Proteases
Babii, O.; Afonin, S.; Diel, C.; Huhn, M.; Dommermuth, J.; Schober, T.; Koniev, S.; Hrebonkin, A.; Nesterov-Mueller, A.; Komarov, I. V.; Ulrich, A. S.
2021. Angewandte Chemie - International Edition, 60 (40), 21789–21794. doi:10.1002/anie.202108847
Development of a Benzothiazole Scaffold-Based Androgen Receptor N-Terminal Inhibitor for Treating Androgen-Responsive Prostate Cancer
Kuznik, N. C.; Solozobova, V.; Jung, N.; Gräßle, S.; Lei, Q.; Lewandowski, E. M.; Munuganti, R.; Zoubeidi, A.; Chen, Y.; Bräse, S.; Cato, A. C. B.
2021. ACS Chemical Biology, 16 (11), 2103–2108. doi:10.1021/acschembio.1c00390
Designing Inherently Photodegradable Cell‐Adhesive Hydrogels for 3D Cell Culture
Rosenfeld, A.; Göckler, T.; Kuzina, M.; Reischl, M.; Schepers, U.; Levkin, P. A.
2021. Advanced healthcare materials, 10 (16), Art.Nr. 2100632. doi:10.1002/adhm.202100632
Geometry dependence of excitonic couplings and the consequences for configuration-space sampling
Schieschke, N.; Bold, B. M.; Dohmen, P. M.; Wehl, D.; Hoffmann, M.; Dreuw, A.; Elstner, M.; Höfener, S.
2021. Journal of Computational Chemistry, 42 (20), 1402–1418. doi:10.1002/jcc.26552
Impact of Nanocomposite Combustion Aerosols on A549 Cells and a 3D Airway Model
Hufnagel, M.; May, N.; Wall, J.; Wingert, N.; Garcia-Käufer, M.; Arif, A.; Hübner, C.; Berger, M.; Mülhopt, S.; Baumann, W.; Weis, F.; Krebs, T.; Becker, W.; Gminski, R.; Stapf, D.; Hartwig, A.
2021. Nanomaterials, 11 (7), Art. Nr.: 1685. doi:10.3390/nano11071685
Impact of the interplay between stemness features, p53 and pol iota on replication pathway choices
Ihle, M.; Biber, S.; Schroeder, I. S.; Blattner, C.; Deniz, M.; Damia, G.; Gottifredi, V.; Wiesmüller, L.
2021. Nucleic acids research, 49 (13), 7457–7475. doi:10.1093/nar/gkab526
DNA-Directed Assembly of a Cell-Responsive Biohybrid Interface for Cargo Release
Sun, P.; Scharnweber, T.; Wadhwani, P.; Rabe, K. S.; Niemeyer, C. M.
2021. Small Methods, 5 (7), Art-Nr. 2001049. doi:10.1002/smtd.202001049
Correlation between Macroscopic Elasticity and Chain Dynamics of Natural Rubber during Vulcanization as Determined by a Unique Rheo-NMR Combination
Nie, S.; Ratzsch, K.-F.; Grage, S. L.; Keller, J.; Ulrich, A. S.; Lacayo-Pineda, J.; Wilhelm, M.
2021. Macromolecules, 54 (13), 6090–6100. doi:10.1021/acs.macromol.1c00354
TRIMming Down Hormone-Driven Cancers: The Biological Impact of TRIM Proteins on Tumor Development, Progression and Prognostication
Pauletto, E.; Eickhoff, N.; Padrão, N.; Blattner, C.; Zwart, W.
2021. Cells, 10 (6), Art.-Nr.: 1517. doi:10.3390/cells10061517
Long photoperiod impairs learning in male but not female medaka
López-Olmeda, J. F.; Zhao, H.; Reischl, M.; Pylatiuk, C.; Lucon-Xiccato, T.; Loosli, F.; Foulkes, N. S.
2021. iScience, 24 (7), Art. Nr.: 102784. doi:10.1016/j.isci.2021.102784
Simulation and evaluation of a body energy harvesting device for arm and leg swing motions
Petani, L.; Essig, S.; Zeilfelder, J.; Kortenhaus, M.; Pylatiuk, C.
2021. AIP Advances, 11 (6), 065201. doi:10.1063/5.0050424
Evaluation of four point cloud similarity measures for the use in autonomous driving
Berens, F.; Elser, S.; Reischl, M.
2021. Automatisierungstechnik, 69 (6), 499–510. doi:10.1515/auto-2020-0140
Chirality Remote Control in Nanoporous Materials by Circularly Polarized Light
Kanj, A. B.; Bürck, J.; Vankova, N.; Li, C.; Mutruc, D.; Chandresh, A.; Hecht, S.; Heine, T.; Heinke, L.
2021. Journal of the American Chemical Society, 143 (18), 7059–7068. doi:10.1021/jacs.1c01693
Photoreceptor Diversification Accompanies the Evolution of Anthozoa
Gornik, S. G.; Bergheim, B. G.; Benoit, M.; Stamatakis, A.; Foulkes, N. S.; Guse, A.
2021. Molecular biology and evolution, 38 (5), 1744–1760. doi:10.1093/molbev/msaa304
Enhancing deep-learning training for phase identification in powder X-ray diffractograms
Schuetzke, J.; Benedix, A.; Mikut, R.; Reischl, M.
2021. IUCrJ, 8 (3). doi:10.1107/S2052252521002402
Analytical Time-Dependent Long-Range Corrected Density Functional Tight Binding (TD-LC-DFTB) Gradients in DFTB+: Implementation and Benchmark for Excited-State Geometries and Transition Energies
Sokolov, M.; Bold, B. M.; Kranz, J. J.; Höfener, S.; Niehaus, T. A.; Elstner, M.
2021. Journal of Chemical Theory and Computation, 17 (4), 2266–2282. doi:10.1021/acs.jctc.1c00095
Regulation of ddb2 expression in blind cavefish and zebrafish reveals plasticity in the control of sunlight-induced DNA damage repair
Zhao, H.; Li, H.; Du, J.; Di Mauro, G.; Lungu-Mitea, S.; Geyer, N.; Vallone, D.; Bertolucci, C.; Foulkes, N. S.
2021. PLoS Genetics, 17 (2), Art.-Nr. e1009356. doi:10.1371/JOURNAL.PGEN.1009356
Cell Proliferation and Collective Cell Migration During Zebrafish Lateral Line System Development Are Regulated by Ncam/Fgf-Receptor Interactions
Dries, R.; Lange, A.; Heiny, S.; Berghaus, K. I.; Bastmeyer, M.; Bentrop, J.
2021. Frontiers in Cell and Developmental Biology, 8, Art.-Nr.: 591011. doi:10.3389/fcell.2020.591011
Parkinson’s disease with restless legs syndrome - an in vivo corneal confocal microscopy study
Andréasson, M.; Lagali, N.; Badian, R. A.; Utheim, T. P.; Scarpa, F.; Colonna, A.; Allgeier, S.; Bartschat, A.; Köhler, B.; Mikut, R.; Reichert, K.-M.; Solders, G.; Samuelsson, K.; Zetterberg, H.; Blennow, K.; Svenningsson, P.
2021. npj Parkinson’s Disease, 7 (1), Art.-Nr. 4. doi:10.1038/s41531-020-00148-5
Cancer microenvironment and genomics: evolution in process
Leong, S. P.; Witz, I. P.; Sagi-Assif, O.; Izraely, S.; Sleeman, J.; Piening, B.; Fox, B. A.; Bifulco, C. B.; Martini, R.; Newman, L.; Davis, M.; Sanders, L. M.; Haussler, D.; Vaske, O. M.; Witte, M.
2021. Clinical & experimental metastasis, 39, 85–99. doi:10.1007/s10585-021-10097-9
In Vitro and In Vivo Toxicity Evaluation of Natural Products with Potential Applications as Biopesticides
Sangermano, F.; Masi, M.; Kumar, A.; Peravali, R.; Tuzi, A.; Cimmino, A.; Vallone, D.; Giamundo, G.; Conte, I.; Evidente, A.; Calabrò, V.
2021. Toxins, 13 (11), Art. Nr.: 805. doi:10.3390/toxins13110805
Methylmercury-induced hair cell loss requires hydrogen peroxide production and leukocytes in zebrafish embryos
Luo, Z.; Guo, S.; Ho, N. Y.; Takamiya, M.; Strähle, U.; Yang, L.
2021. Toxicology Letters, 356, 151–160. doi:10.1016/j.toxlet.2021.12.012
Tough, Transparent, 3D printable and Self‐healing Polyethylene Glycol‐Gel (PEGgel)
Wang, Z.; Cui, H.; Liu, M.; Grage, S. L.; Hoffmann, M.; Sedghamiz, E.; Wenzel, W.; Levkin, P. A.
2021. Advanced materials, 34 (11), 2107791. doi:10.1002/adma.202107791
Antibiotic Potential and Biophysical Characterization of Amphipathic β-Stranded [XZ]n Peptides With Alternating Cationic and Hydrophobic Residues
Strandberg, E.; Wadhwani, P.; Ulrich, A. S.
2021. Frontiers in Medical Technology, 3. doi:10.3389/fmedt.2021.622096
Remarkably high solvatochromism in the circular dichroism spectra of the polyproline-II conformation: limitations or new opportunities?
Kubyshkin, V.; Bürck, J.; Babii, O.; Budisa, N.; Ulrich, A. S.
2021. Physical chemistry, chemical physics, 23 (47), 26931–26939. doi:10.1039/d1cp04551b
Rational Designed Hybrid Peptides Show up to a 6-Fold Increase in Antimicrobial Activity and Demonstrate Different Ultrastructural Changes as the Parental Peptides Measured by BioSAXS
Hilpert, K.; Gani, J.; Rumancev, C.; Simpson, N.; Lopez-Perez, P. M.; Garamus, V. M.; Gundlach, A. R. von; Markov, P.; Scocchi, M.; Mikut, R.; Rosenhahn, A.
2021. Frontiers in pharmacology, 12, Article no: 769739. doi:10.3389/fphar.2021.769739
Membrane-Mediated Activity of Local Anesthetics
Grage, S. L.; Culetto, A.; Ulrich, A. S.; Weinschenk, S.
2021. Molecular pharmacology, 100 (5), 502–512. doi:10.1124/molpharm.121.000252
Electrostatic interactions contribute to the control of intramolecular thiol-disulfide isomerization in a protein
Maag, D.; Putzu, M.; Gómez-Flores, C. L.; Gräter, F.; Elstner, M.; Kubař, T.
2021. Physical Chemistry Chemical Physics, 23 (46), 26366–26375. doi:10.1039/d1cp03129e
Machine learning methods for automated classification of tumors with papillary thyroid carcinoma-like nuclei : A quantitative analysis
Böhland, M.; Tharun, L.; Scherr, T.; Mikut, R.; Hagenmeyer, V.; Thompson, L. D. R.; Perner, S.; Reischl, M.
2021. PLOS ONE, 16 (9), e0257635. doi:10.1371/journal.pone.0257635
Toxicology and Biocompatibility of Nanomaterials : Editorial
Weiss, C.; Diabaté, S.
2021. Nanomaterials, 11 (11), Art.-Nr.: 3110. doi:10.3390/nano11113110
A Core Response to the CDX2 Homeoprotein During Development and in Pathologies
Gourain, V.; Duluc, I.; Domon-Dell, C.; Freund, J.-N.
2021. Frontiers in Genetics, 12, Art.Nr. 744165. doi:10.3389/fgene.2021.744165
Quantitative detection of disseminated melanoma cells by trp-1 transcript analysis reveals stochastic distribution of pulmonary metastases
Kyjacova, L.; Saup, R.; Rothley, M.; Schmaus, A.; Wagner, T.; Boßerhoff, A.; Garvalov, B. K.; Thiele, W.; Sleeman, J. P.
2021. Journal of Clinical Medicine, 10 (22), Art.Nr. 5459. doi:10.3390/jcm10225459
Classification of Bundle Branch Blocks with QRS Templates Extracted from 12-lead ECGs
Welle, H.; Nagel, C.; Loewe, A.; Mikut, R.; Dössel, O.
2021. Biomedical engineering, 66 (s1), S228–S233. doi:10.1515/bmt-2021-6033
Influence of contact cap design on large-area imaging of the subbasal nerve plexus
Bohn, S.; Sperlich, K.; Allgeier, S.; Bartschat, A.; Reichert, K.-M.; Kornelius, L.; Mikut, R.; Köhler, B.; Stachs, O.
2021. Biomedical engineering, 66 (s1), S124. doi:10.1515/bmt-2021-6018
A software framework for real-time image mosaicking of the corneal subbasal nerve plexus
Köhler, B.; Kornelius, L.; Bartschat, A.; Bohn, S.; Mikut, R.; Reichert, K.-M.; Sperlich, K.; Stachs, O.; Allgeier, S.
2021. Biomedical engineering, 66 (s1), S121
Strain-Specific Liver Metabolite Profiles in Medaka
Soergel, H.; Loosli, F.; Muhle-Goll, C.
2021. Metabolites, 11 (11), Art.-Nr.: 744. doi:10.3390/metabo11110744
Neuron-Radial Glial Cell Communication via BMP/Id1 Signaling Is Key to Long-Term Maintenance of the Regenerative Capacity of the Adult Zebrafish Telencephalon
Zhang, G.; Lübke, L.; Chen, F.; Beil, T.; Takamiya, M.; Diotel, N.; Strähle, U.; Rastegar, S.
2021. Cells, 10 (10), Art.-Nr.: 2794. doi:10.3390/cells10102794
Systematic assessment of the biocompatibility of materials for inkjet-printed ozone sensors for medical therapy
Petani, L.; Wehrheim, V.; Koker, L.; Reischl, M.; Ungerer, M.; Gengenbach, U.; Pylatiuk, C.
2021. Flexible and printed electronics, 6 (4), Art.-Nr.: 043003. doi:10.1088/2058-8585/ac32ab
IER2-induced senescence drives melanoma invasion through osteopontin
Kyjacova, L.; Saup, R.; Rönsch, K.; Wallbaum, S.; Dukowic-Schulze, S.; Foss, A.; Scherer, S. D.; Rothley, M.; Neeb, A.; Grau, N.; Thiele, W.; Thaler, S.; Cremers, N.; Sticht, C.; Gretz, N.; Garvalov, B. K.; Utikal, J.; Sleeman, J. P.
2021. Oncogene, 40, 6494–6412. doi:10.1038/s41388-021-02027-6
Is There a Connection Between Gut Microbiome Dysbiosis Occurring in COVID-19 Patients and Post-COVID-19 Symptoms?
Hilpert, K.; Mikut, R.
2021. Frontiers in Microbiology, 12, Art.-Nr.: 732838. doi:10.3389/fmicb.2021.732838
Micro-scaffolds as synthetic cell niches: recent advances and challenges
Weißenbruch, K.; Lemma, E. D.; Hippler, M.; Bastmeyer, M.
2021. Current Opinion in Biotechnology, 73, 290–299. doi:10.1016/j.copbio.2021.08.016
RNA polymerase II clusters form in line with surface condensation on regulatory chromatin
Pancholi, A.; Klingberg, T.; Zhang, W.; Prizak, R.; Mamontova, I.; Noa, A.; Sobucki, M.; Kobitski, A. Y.; Nienhaus, G. U.; Zaburdaev, V.; Hilbert, L.
2021. Molecular Systems Biology, 17 (9), Art.Nr. e10272. doi:10.15252/msb.202110272
Membrane interactions of latarcins: Antimicrobial peptides from spider venom
Wadhwani, P.; Sekaran, S.; Strandberg, E.; Bürck, J.; Chugh, A.; Ulrich, A. S.
2021. International Journal of Molecular Sciences, 22 (18), Art.-Nr.: 10156. doi:10.3390/ijms221810156
Period 2: A Regulator of Multiple Tissue-Specific Circadian Functions
Ruggiero, G.; Ben-Moshe Livne, Z.; Wexler, Y.; Geyer, N.; Vallone, D.; Gothilf, Y.; Foulkes, N. S.
2021. Frontiers in Molecular Neuroscience, 14, Art.Nr. 718387. doi:10.3389/fnmol.2021.718387
A Systematic Analysis of Metal and Metalloid Concentrations in Eight Zebrafish Recirculating Water Systems
Langa, X.; Neuhaus, P.; Lains, D.; Stewart, T. J.; Borel, N.; Certal, A. C.; Monteiro, J. F.; Aleström, P.; Diaz, E.; Piragyte, I.; Bräutigam, L.; Vázquez, R.; Hlushchuk, R.; Gfeller, L.; Mestrot, A.; Bigalke, M.; Varga, Z. M.; Mercader, N.
2021. Zebrafish, 18 (4), 252–264. doi:10.1089/zeb.2020.1970
The Combinatorial Fusion Cascade to Generate the Standard Genetic Code
Nesterov-Mueller, A.; Popov, R.
2021. Life, 11 (9), Art.-Nr.: 975. doi:10.3390/life11090975
A graph-based cell tracking algorithm with few manually tunable parameters and automated segmentation error correction
Löffler, K.; Scherr, T.; Mikut, R.
2021. PLOS ONE, 16 (9), e0249257. doi:10.1371/journal.pone.0249257
An Automated Experimentation System for the Touch-Response Quantification of Zebrafish Larvae
Wang, Y.; Marcato, D.; Tirumalasetty, V.; Kanagaraj, N. K.; Pylatiuk, C.; Mikut, R.; Peravali, R.; Reischl, M.
2021. IEEE transactions on automation science and engineering, 19 (4), 3007–3019. doi:10.1109/TASE.2021.3104507
Distinct roles of nonmuscle myosin ii isoforms for establishing tension and elasticity during cell morphodynamics
Weißenbruch, K.; Grewe, J.; Hippler, M.; Fladung, M.; Tremmel, M.; Stricker, K.; Schwarz, U. S.; Bastmeyer, M.
2021. eLife, 10, e71888. doi:10.7554/ELIFE.71888
Chiral Resolution of Spin-Crossover Active Iron(II) [2x2] Grid Complexes
Suryadevara, N.; Pausch, A.; Moreno-Pineda, E.; Mizuno, A.; Bürck, J.; Baksi, A.; Hochdörffer, T.; Šalitroš, I.; Ulrich, A. S.; Kappes, M. M.; Schünemann, V.; Klopper, W.; Ruben, M.
2021. Chemistry - A European Journal, 27 (61), 15172–15180. doi:10.1002/chem.202101432
Fungal phytochrome chromophore biosynthesis at mitochondria
Streng, C.; Hartmann, J.; Leister, K.; Krauß, N.; Lamparter, T.; Frankenberg-Dinkel, N.; Weth, F.; Bastmeyer, M.; Yu, Z.; Fischer, R.
2021. EMBO Journal, 40 (17), Art.-Nr.: e108083. doi:10.15252/embj.2021108083
Order and disorder - An integrative structure of the full-length human growth hormone receptor
Kassem, N.; Araya-Secchi, R.; Bugge, K.; Barclay, A.; Steinocher, H.; Khondker, A.; Wang, Y.; Lenard, A. J.; Bürck, J.; Sahin, C.; Ulrich, A. S.; Landreh, M.; Pedersen, M. C.; Rheinstädter, M. C.; Pedersen, P. A.; Lindorff-Larsen, K.; Arleth, L.; Kragelund, B. B.
2021. Science Advances, 7 (27), Art.-Nr.: eabh3805. doi:10.1126/sciadv.abh3805
CDX2 expression in the hematopoietic lineage promotes leukemogenesis via TGFβ inhibition
Galland, A.; Gourain, V.; Habbas, K.; Güler, Y.; Martin, E.; Ebel, C.; Tavian, M.; Vallat, L.; Chenard, M.-P.; Mauvieux, L.; Freund, J.-N.; Duluc, I.; Domon-Dell, C.
2021. Molecular Oncology, 15 (9), 2318–2329. doi:10.1002/1878-0261.12982
In Vivo Behavior of the Antibacterial Peptide Cyclo[RRRWFW], Explored Using a 3-Hydroxychromone-Derived Fluorescent Amino Acid
Afonin, S.; Koniev, S.; Préau, L.; Takamiya, M.; Strizhak, A. V.; Babii, O.; Hrebonkin, A.; Pivovarenko, V. G.; Dathe, M.; Noble, F. le; Rastegar, S.; Strähle, U.; Ulrich, A. S.; Komarov, I. V.
2021. Frontiers in Chemistry, 9, Art. Nr.: 688446. doi:10.3389/fchem.2021.688446
The LIM domain protein nTRIP6 modulates the dynamics of myogenic differentiation
Norizadeh Abbariki, T.; Gonda, Z.; Kemler, D.; Urbanek, P.; Wagner, T.; Litfin, M.; Wang, Z.-Q.; Herrlich, P.; Kassel, O.
2021. Scientific Reports, 11 (1), Art.Nr. 12904. doi:10.1038/s41598-021-92331-8
Regulation of p53 by E3s
Pan, M.; Blattner, C.
2021. Cancers, 13 (4), Art.Nr. 745. doi:10.3390/cancers13040745
Structural analysis of a genetically encoded fret biosensor by SAXS and MD simulations
Reinartz, I.; Sarter, M.; Otten, J.; Höfig, H.; Pohl, M.; Schug, A.; Stadler, A. M.; Fitter, J.
2021. Sensors, 21 (12), Art.Nr. 4144. doi:10.3390/s21124144
I-care-an interaction system for the individual activation of people with dementia
Schultz, T.; Putze, F.; Steinert, L.; Mikut, R.; Depner, A.; Kruse, A.; Franz, I.; Gaerte, P.; Dimitrov, T.; Gehrig, T.; Lohse, J.; Simon, C.
2021. Geriatrics (Switzerland), 6 (2), 51. doi:10.3390/geriatrics6020051
Droplet microarrays for cell culture: effect of surface properties and nanoliter culture volume on global transcriptomic landscape
Chakraborty, S.; Gourain, V.; Benz, M.; Scheiger, J. M.; Levkin, P. A.; Popova, A. A.
2021. Materials Today Bio, 11, Art.-Nr.: 100112. doi:10.1016/j.mtbio.2021.100112
Multi-Dimensional Transcriptome Analysis Reveals Modulation of Cholesterol Metabolism as Highly Integrated Response to Brain Injury
Gourain, V.; Armant, O.; Lübke, L.; Diotel, N.; Rastegar, S.; Strähle, U.
2021. Frontiers in neuroscience, 15, Article no: 671249. doi:10.3389/fnins.2021.671249
Overlapping Properties of the Short Membrane-Active Peptide BP100 With (i) Polycationic TAT and (ii) α-helical Magainin Family Peptides
Mink, C.; Strandberg, E.; Wadhwani, P.; Melo, M. N.; Reichert, J.; Wacker, I.; Castanho, M. A. R. B.; Ulrich, A. S.
2021. Frontiers in Cellular and Infection Microbiology, 11, Art.-Nr.: 609542. doi:10.3389/fcimb.2021.609542
Performance of Different Diagnostic PD-L1 Clones in Head and Neck Squamous Cell Carcinoma
Ribbat-Idel, J.; Dressler, F. F.; Krupar, R.; Watermann, C.; Paulsen, F.-O.; Kuppler, P.; Klapper, L.; Offermann, A.; Wollenberg, B.; Rades, D.; Laban, S.; Reischl, M.; Bruchhage, K.-L.; Idel, C.; Perner, S.
2021. Frontiers in Medicine, 8, Art.-Nr.: 640515. doi:10.3389/fmed.2021.640515
Nature of Fast Relaxation Processes and Spectroscopy of a Membrane-Active Peptide Modified with Fluorescent Amino Acid Exhibiting Excited State Intramolecular Proton Transfer and Efficient Stimulated Emission
Shaydyuk, Y. O.; Bashmakova, N. V.; Dmytruk, A. M.; Kachkovsky, O. D.; Koniev, S.; Strizhak, A. V.; Komarov, I. V.; Belfield, K. D.; Bondar, M. V.; Babii, O.
2021. ACS Omega, 6 (15), 10119–10128. doi:10.1021/acsomega.1c00193
Burst of corneal dendritic cells during Trastuzumab and Paclitaxel treatment
Sterenczak, K. A.; Stache, N.; Bohn, S.; Allgeier, S.; Köhler, B.; Bartschat, A.; George, C.; Guthoff, R. F.; Stachs, O.; Stachs, A.
2021. Diagnostics, 11 (5), Art.Nr. 838. doi:10.3390/diagnostics11050838
The hierarchical packing of euchromatin domains can be described as multiplicative cascades
Noa, A.; Kuan, H.-S.; Aschmann, V.; Zaburdaev, V.; Hilbert, L.
2021. PLoS Computational Biology, 17 (5), e1008974. doi:10.1371/journal.pcbi.1008974
Functional characterization of circulating tumor cells (CTCs) from metastatic ER+/HER2− breast cancer reveals dependence on HER2 and FOXM1 for endocrine therapy resistance and tumor cell survival: Implications for treatment of ER+/HER2− breast cancer
Roßwag, S.; Cotarelo, C. L.; Pantel, K.; Riethdorf, S.; Sleeman, J. P.; Schmidt, M.; Thaler, S.
2021. Cancers, 13 (8), Art.-Nr.: 1810. doi:10.3390/cancers13081810
Multiscale QM/MM molecular dynamics simulations of the trimeric major light-harvesting complex II
Maity, S.; Daskalakis, V.; Elstner, M.; Kleinekathöfer, U.
2021. Physical Chemistry Chemical Physics, 23 (12), 7407–7417. doi:10.1039/d1cp01011e
Interplay of structural dynamics and electronic effects in an engineered assembly of pentacene in a metal–organic framework
Haldar, R.; Kozlowska, M.; Ganschow, M.; Ghosh, S.; Jakoby, M.; Chen, H.; Ghalami, F.; Xie, W.; c; Tsutsui, Y.; Freudenberg, J.; Seki, S.; Howard, I. A.; Richards, B. S.; Bunz, U. H. F.; Elstner, M.; Wenzel, W.; Wöll, C.
2021. Chemical science, 12 (12), 4477–4483. doi:10.1039/d0sc07073d
Finding Nemo’s clock reveals switch from nocturnal to diurnal activity
Schalm, G.; Bruns, K.; Drachenberg, N.; Geyer, N.; Foulkes, N. S.; Bertolucci, C.; Gerlach, G.
2021. Scientific Reports, 11 (1), Art.-Nr.: 6801. doi:10.1038/s41598-021-86244-9
Cellular Mechanisms Participating in Brain Repair of Adult Zebrafish and Mammals after Injury
Ghaddar, B.; Lübke, L.; Couret, D.; Rastegar, S.; Diotel, N.
2021. Cells, 10 (2), 391. doi:10.3390/cells10020391
Substitutional landscape of a split fluorescent protein fragment using high-density peptide microarrays
Antonescu, O. N.; Rasmussen, A.; Damm, N. A. M.; Heidemann, D. F.; Popov, R.; Nesterov-Mueller, A.; Johansson, K. E.; Winther, J. R.
2021. PLOS ONE, 16 (2), Article: e0241461. doi:10.1371/journal.pone.0241461
Boron-rich, cytocompatible block copolymer nanoparticles by polymerization-induced self-assembly
Huang, L. C. S.; Le, D.; Hsiao, I. L.; Fritsch-Decker, S.; Hald, C.; Huang, S.-C.; Chen, J.-K.; Hwu, J. R.; Weiss, C.; Hsu, M.-H.; Delaittre, G.
2021. Polymer chemistry, 12 (1), 50–56. doi:10.1039/d0py00710b
Atypical cellular elements of unknown origin in the subbasal nerve plexus of a diabetic cornea diagnosed by large-area confocal laser scanning microscopy
Sterenczak, K. A.; Stachs, O.; Marfurt, C.; Matuszewska-Iwanicka, A.; Stratmann, B.; Sperlich, K.; Guthoff, R. F.; Hettlich, H.-J.; Allgeier, S.; Stahnke, T.
2021. Diagnostics, 11 (2), Article no: 154. doi:10.3390/diagnostics11020154
Effects of incremental endosulfan sulfate exposure and high fat diet on lipid metabolism, glucose homeostasis and gut microbiota in mice
Yan, J.; Wang, D.; Meng, Z.; Yan, S.; Teng, M.; Jia, M.; Li, R.; Tian, S.; Weiss, C.; Zhou, Z.; Zhu, W.
2021. Environmental pollution, 268 (A), Art.-Nr.: 115697. doi:10.1016/j.envpol.2020.115697
Cancer therapy_andrew catoAmadeus Bramsiepe (KIT)
Novel Approaches for Cancer Therapy

Prostate and breast cancer can become resistant to established hormone treatments, in particular due to mutations in the hormone receptor regions. Researchers at the Karlsruhe Institute of Technology (KIT) are pursuing an innovative approach that could help to circumvent the resistance of tumor cells to hormone treatments: They are finding inhibitors that do not act directly on the receptors, but on other proteins and influence their activity.

 

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2021_Hilbert-NienhausWorking groups Nienhaus and Hilbert, KIT
How Cells Correctly Choose Active Genes

It is essential for cells to control precisely which of the many genes of their genetic material they use. This is done in so-called transcription factories, molecular clusters in the nucleus. Researchers of Karlsruhe Institute of Technology (KIT), Friedrich-Alexander-Universität Erlangen-Nuremberg (FAU), and Max Planck Center for Physics and Medicine (MPZPM) have now found that the formation of transcription factories resembles the condensation of liquids. Their findings will improve the understanding of causes of diseases and advance the development of DNA-based data storage systems. The scientists report in Molecular Systems Biology (10.15252/msb.202110272).

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Zwei Tage alte Zebrafischembryonen in der EihülleGiuseppina Pace (KIT)
Health protection: More safety from hazardous substances

Chemicals can cause health problems even in small quantities if you are exposed to them for a longer period of time. Protecting people from hazardous substances is the goal of the EU project PrecisionTox, in which the Karlsruhe Institute of Technology (KIT) plays a major role. KIT is responsible for the work package "Comparative Toxicology" and contributes its extensive experience in molecular toxicology, zebrafish research, and high-throughput microscopy. With the aid of bioinformatic analysis, computer modeling and artificial intelligence, the data will reveal the mode of action of a wide variety of substances on complex biological processes and thus allow predictions about the biological effects of chemicals. In the future, harmful substances should be identified more quickly and reliably before they reach the market and the environment.

EU project PrecisionTox
Microphase separation in the cell nucleus (KIT / IBCS-BIP)KIT / IBCS-BIP
Microphase Separation In The Cell Nucleus

Lennart Hilbert has contributed to a study that addresses how active and inactive genes are separated inside the cell nucleus. The according article ’Transcription organizes euchromatin via microphase separation' was recently published in the journal Nature Communications (DOI: 10.1038/s41467-021-21589-3).

Source: KIT / ICBS-BIP