ZFIN Lab: Mikut Lab

ZFIN ID: ZDB-LAB-140613-1

Mikut Lab

PI/Director:	Mikut, Ralf
Contact Person:	Mikut, Ralf
Email:	ralf.mikut@kit.edu
URL:	http://www.iai.kit.edu/www-extern/index.php?id=52&L=1
Address:	Karlsruhe Institute of Technology (KIT) Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen GERMANY
Country:	Germany
Phone:	+49 721 608 25731
Fax:	+49 721 608 25702
Line Designation:	None assigned

GENOMIC FEATURES ORIGINATING FROM THIS LAB No data available

STATEMENT OF RESEARCH INTERESTS

Image processing, data analysis, data mining, algorithms, software

LAB MEMBERS

ZEBRAFISH PUBLICATIONS OF LAB MEMBERS

Weger, M., Weger, B.D., Schink, A., Takamiya, M., Stegmaier, J., Gobet, C., Parisi, A., Kobitski, A.Y., Mertes, J., Krone, N., Strähle, U., Nienhaus, G.U., Mikut, R., Gachon, F., Gut, P., Dickmeis, T. (2020) MondoA regulates gene expression in cholesterol biosynthesis-associated pathways required for zebrafish epiboly. eLIFE. 9:

Takamiya, M., Stegmaier, J., Kobitski, A.Y., Schott, B., Weger, B.D., Margariti, D., Cereceda Delgado, A.R., Gourain, V., Scherr, T., Yang, L., Sorge, S., Otte, J.C., Hartmann, V., van Wezel, J., Stotzka, R., Reinhard, T., Schlunck, G., Dickmeis, T., Rastegar, S., Mikut, R., Nienhaus, G.U., Strähle, U. (2020) Pax6 organizes the anterior eye segment by guiding two distinct neural crest waves. PLoS Genetics. 16:e1008774

Schutera, M., Just, S., Gierten, J., Mikut, R., Reischl, M., Pylatiuk, C. (2019) Machine Learning Methods for Automated Quantification of Ventricular Dimensions. Zebrafish. 16(6):542-545

Gerber, V., Yang, L., Takamiya, M., Ribes, V., Gourain, V., Peravali, R., Stegmaier, J., Mikut, R., Reischl, M., Ferg, M., Rastegar, S., Strähle, U. (2019) The HMG box transcription factors Sox1a and b specify a new class of glycinergic interneurons in the spinal cord of zebrafish embryos. Development (Cambridge, England). 146(4):

Mattes, B., Dang, Y., Greicius, G., Kaufmann, L.T., Prunsche, B., Rosenbauer, J., Stegmaier, J., Mikut, R., Özbek, S., Nienhaus, G.U., Schug, A., Virshup, D.M., Scholpp, S. (2018) Wnt/PCP controls spreading of Wnt/β-catenin signals by cytonemes in vertebrates. eLIFE. 7:

Schott, B., Traub, M., Schlagenhauf, C., Takamiya, M., Antritter, T., Bartschat, A., Löffler, K., Blessing, D., Otte, J.C., Kobitski, A.Y., Nienhaus, G.U., Strähle, U., Mikut, R., Stegmaier, J. (2018) EmbryoMiner: A new framework for interactive knowledge discovery in large-scale cell tracking data of developing embryos. PLoS Computational Biology. 14:e1006128

Bedell, V., Buglo, E., Marcato, D., Pylatiuk, C., Mikut, R., Stegmaier, J., Scudder, W., Wray, M., Züchner, S., Strähle, U., Peravali, R., Dallman, J.E. (2018) Zebrafish: A Pharmacogenetic Model for Anesthesia. Methods in enzymology. 602:189-209

Stegmaier, J., Mikut, R. (2017) Fuzzy-based propagation of prior knowledge to improve large-scale image analysis pipelines. PLoS One. 12:e0187535

Etard, C., Joshi, S., Stegmaier, J., Mikut, R., Strähle, U. (2017) Tracking of Indels by DEcomposition is a Simple and Effective Method to Assess Efficiency of Guide RNAs in Zebrafish. Zebrafish. 14(6):586-588

Schutera, M., Dickmeis, T., Mione, M., Peravali, R., Marcato, D., Reischl, M., Mikut, R., Pylatiuk, C. (2016) Automated Phenotype Pattern Recognition of Zebrafish for High-throughput Screening. Bioengineered. 7(4):261-5

Shahid, M., Takamiya, M., Stegmaier, J., Middel, V., Gradl, M., Klüver, N., Mikut, R., Dickmeis, T., Scholz, S., Rastegar, S., Yang, L., Strähle, U. (2016) Zebrafish biosensor for toxicant induced muscle hyperactivity. Scientific Reports. 6:23768

Stegmaier, J., Amat, F., Lemon, W.C., McDole, K., Wan, Y., Teodoro, G., Mikut, R., Keller, P.J. (2016) Real-Time Three-Dimensional Cell Segmentation in Large-Scale Microscopy Data of Developing Embryos. Developmental Cell. 36:225-240

Bartschat, A., Hübner, E., Reischl, M., Mikut, R., Stegmaier, J. (2016) XPIWIT—an XML pipeline wrapper for the Insight Toolkit. Bioinformatics (Oxford, England). 32(2):315-7

Wittmann, C., Reischl, M., Shah, A.H., Kronfuss, E., Mikut, R., Liebel, U., Grabher, C. (2015) A Zebrafish Drug-Repurposing Screen Reveals sGC-Dependent and sGC-Independent Pro-Inflammatory Activities of Nitric Oxide. PLoS One. 10:e0137286

Kobitski, A.Y., Otte, J.C., Takamiya, M., Schäfer, B., Mertes, J., Stegmaier, J., Rastegar, S., Rindone, F., Hartmann, V., Stotzka, R., García, A., van Wezel, J., Mikut, R., Strähle, U., Nienhaus, G.U. (2015) An ensemble-averaged, cell density-based digital model of zebrafish embryo development derived from light-sheet microscopy data with single-cell resolution. Scientific Reports. 5:8601

Marcato, D., Alshut, R., Breitwieser, H., Mikut, R., Strahle, U., Pylatiuk, C., Peravali, R. (2015) An automated and high-throughput Photomotor Response platform for chemical screens. Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference. 2015:7728-7731

Pylatiuk, C., Sanchez, D., Mikut, R., Alshut, R., Reischl, M., Hirth, S., Rottbauer, W., Just, S. (2014) Automatic Zebrafish Heartbeat Detection and Analysis for Zebrafish Embryos. Zebrafish. 11(4):379-83

Stegmaier, J., Shahid, M., Takamiya, M., Yang, L., Rastegar, S., Reischl, M., Strähle, U., and Mikut, R. (2014) Automated prior knowledge-based quantification of neuronal patterns in the spinal cord of zebrafish. Bioinformatics (Oxford, England). 30(5):726-33

Stegmaier, J., Otte, J.C., Kobitski, A., Bartschat, A., Garcia, A., Nienhaus, G.U., Strähle, U., Mikut, R. (2014) Fast segmentation of stained nuclei in terabyte-scale, time resolved 3D microscopy image stacks. PLoS One. 9:e90036

Mikut, R., Dickmeis, T., Driever, W., Geurts, P., Hamprecht, F.A., Kausler, B.X., Ledesma-Carbayo, M.J., Marée, R., Mikula, K., Pantazis, P., Ronneberger, O., Santos, A., Stotzka, R., Strähle, U., and Peyriéras, N. (2013) Automated Processing of Zebrafish Imaging Data: A Survey. Zebrafish. 10(3):401-21

Armant, O., März, M., Schmidt, R., Ferg, M., Diotel, N., Ertzer, R., Bryne, J.C., Yang, L., Baader, I., Reischl, M., Legradi, J., Mikut, R., Stemple, D., Ijcken, W.V., van der Sloot, A., Lenhard, B., Strähle, U., and Rastegar, S. (2013) Genome-wide, whole mount in situ analysis of transcriptional regulators in zebrafish embryos. Developmental Biology. 380(2):351-62

Cavodeassi, F., Bene, F.D., Fürthauer, M., Grabher, C., Herzog, W., Lehtonen, S., Linker, C., Mercader, N., Mikut, R., Norton, W., Strähle, U., Tiso, N., and Foulkes, N.S. (2013) Report of the Second European Zebrafish Principal Investigator Meeting in Karlsruhe, Germany, March 21-24, 2012. Zebrafish. 10(1):119-23

Kokel, D., Dunn, T.W., Ahrens, M.B., Alshut, R., Cheung, C.Y., Saint-Amant, L., Bruni, G., Mateus, R., van Ham, T.J., Shiraki, T., Fukada, Y., Kojima, D., Yeh, J.R., Mikut, R., von Lintig, J., Engert, F., and Peterson, R.T. (2013) Identification of Nonvisual Photomotor Response Cells in the Vertebrate Hindbrain. The Journal of neuroscience : the official journal of the Society for Neuroscience. 33(9):3834-3843

Wittmann, C., Reischl, M., Shah, A.H., Mikut, R., Liebel, U., and Grabher, C. (2012) Facilitating Drug Discovery: An Automated High-content Inflammation Assay in Zebrafish. Journal of visualized experiments : JoVE. (65):e4203

Alshut, R., Legradi, J., Liebel, U., Yang, L., van Wezel, J., Strähle, U., Mikut, R., and Reischl, M. (2010) Methods for Automated High-Throughput Toxicity Testing Using Zebrafish Embryos. KI 2010: Advances in Artificial Intelligence. 6359:219-226

Alshut, R., Legradi, J., Mikut, R., Strähle, U., and Reischl, M. (2009) Robust Identification of Coagulated Zebrafish Eggs using Image Processing and Classification Techniques. Proceedings 19 Workshop Computational Intelligence. 50:9-21

Yang, L., Ho, N.Y., Alshut, R., Legradi, J., Weiss, C., Reischl, M., Mikut, R., Liebel, U., Müller, F., and Strähle, U. (2009) Zebrafish embryos as models for embryotoxic and teratological effects of chemicals. Reproductive toxicology (Elmsford, N.Y.). 28(2):245-253