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Items: 1 to 50 of 58

1.

BioSAXS Measurements Reveal That Two Antimicrobial Peptides Induce Similar Molecular Changes in Gram-Negative and Gram-Positive Bacteria.

von Gundlach A, Ashby MP, Gani J, Lopez-Perez PM, Cookson AR, Ann Huws S, Rumancev C, Garamus VM, Mikut R, Rosenhahn A, Hilpert K.

Front Pharmacol. 2019 Sep 26;10:1127. doi: 10.3389/fphar.2019.01127. eCollection 2019.

2.

Machine Learning Methods for Automated Quantification of Ventricular Dimensions.

Schutera M, Just S, Gierten J, Mikut R, Reischl M, Pylatiuk C.

Zebrafish. 2019 Oct 3. doi: 10.1089/zeb.2019.1754. [Epub ahead of print]

PMID:
31536467
3.

Microfluidic Chips for Life Sciences-A Comparison of Low Entry Manufacturing Technologies.

Grösche M, Zoheir AE, Stegmaier J, Mikut R, Mager D, Korvink JG, Rabe KS, Niemeyer CM.

Small. 2019 Aug;15(35):e1901956. doi: 10.1002/smll.201901956. Epub 2019 Jul 15.

PMID:
31305015
4.

Quanfima: An open source Python package for automated fiber analysis of biomaterials.

Shkarin R, Shkarin A, Shkarina S, Cecilia A, Surmenev RA, Surmeneva MA, Weinhardt V, Baumbach T, Mikut R.

PLoS One. 2019 Apr 11;14(4):e0215137. doi: 10.1371/journal.pone.0215137. eCollection 2019.

5.

The HMG box transcription factors Sox1a and Sox1b specify a new class of glycinergic interneuron in the spinal cord of zebrafish embryos.

Gerber V, Yang L, Takamiya M, Ribes V, Gourain V, Peravali R, Stegmaier J, Mikut R, Reischl M, Ferg M, Rastegar S, Strähle U.

Development. 2019 Feb 20;146(4). pii: dev172510. doi: 10.1242/dev.172510.

6.

Cellular in vivo 3D imaging of the cornea by confocal laser scanning microscopy.

Bohn S, Sperlich K, Allgeier S, Bartschat A, Prakasam R, Reichert KM, Stolz H, Guthoff R, Mikut R, Köhler B, Stachs O.

Biomed Opt Express. 2018 May 1;9(6):2511-2525. doi: 10.1364/BOE.9.002511. eCollection 2018 Jun 1.

7.

Wnt/PCP controls spreading of Wnt/β-catenin signals by cytonemes in vertebrates.

Mattes B, Dang Y, Greicius G, Kaufmann LT, Prunsche B, Rosenbauer J, Stegmaier J, Mikut R, Özbek S, Nienhaus GU, Schug A, Virshup DM, Scholpp S.

Elife. 2018 Jul 31;7. pii: e36953. doi: 10.7554/eLife.36953.

8.

3D confocal laser-scanning microscopy for large-area imaging of the corneal subbasal nerve plexus.

Allgeier S, Bartschat A, Bohn S, Peschel S, Reichert KM, Sperlich K, Walckling M, Hagenmeyer V, Mikut R, Stachs O, Köhler B.

Sci Rep. 2018 May 10;8(1):7468. doi: 10.1038/s41598-018-25915-6.

9.

EmbryoMiner: A new framework for interactive knowledge discovery in large-scale cell tracking data of developing embryos.

Schott B, Traub M, Schlagenhauf C, Takamiya M, Antritter T, Bartschat A, Löffler K, Blessing D, Otte JC, Kobitski AY, Nienhaus GU, Strähle U, Mikut R, Stegmaier J.

PLoS Comput Biol. 2018 Apr 19;14(4):e1006128. doi: 10.1371/journal.pcbi.1006128. eCollection 2018 Apr.

10.

Correction: Fuzzy-based propagation of prior knowledge to improve large-scale image analysis pipelines.

Stegmaier J, Mikut R.

PLoS One. 2018 Mar 29;13(3):e0195394. doi: 10.1371/journal.pone.0195394. eCollection 2018.

11.

Zebrafish: A Pharmacogenetic Model for Anesthesia.

Bedell V, Buglo E, Marcato D, Pylatiuk C, Mikut R, Stegmaier J, Scudder W, Wray M, Züchner S, Strähle U, Peravali R, Dallman JE.

Methods Enzymol. 2018;602:189-209. doi: 10.1016/bs.mie.2018.02.004. Epub 2018 Mar 15.

PMID:
29588029
12.

The rumen microbiome: an underexplored resource for novel antimicrobial discovery.

Oyama LB, Girdwood SE, Cookson AR, Fernandez-Fuentes N, Privé F, Vallin HE, Wilkinson TJ, Golyshin PN, Golyshina OV, Mikut R, Hilpert K, Richards J, Wootton M, Edwards JE, Maresca M, Perrier J, Lundy FT, Luo Y, Zhou M, Hess M, Mantovani HC, Creevey CJ, Huws SA.

NPJ Biofilms Microbiomes. 2017 Dec 1;3:33. doi: 10.1038/s41522-017-0042-1. eCollection 2017.

13.

Fuzzy-based propagation of prior knowledge to improve large-scale image analysis pipelines.

Stegmaier J, Mikut R.

PLoS One. 2017 Nov 2;12(11):e0187535. doi: 10.1371/journal.pone.0187535. eCollection 2017. Erratum in: PLoS One. 2018 Mar 29;13(3):e0195394.

14.

An objective comparison of cell-tracking algorithms.

Ulman V, Maška M, Magnusson KEG, Ronneberger O, Haubold C, Harder N, Matula P, Matula P, Svoboda D, Radojevic M, Smal I, Rohr K, Jaldén J, Blau HM, Dzyubachyk O, Lelieveldt B, Xiao P, Li Y, Cho SY, Dufour AC, Olivo-Marin JC, Reyes-Aldasoro CC, Solis-Lemus JA, Bensch R, Brox T, Stegmaier J, Mikut R, Wolf S, Hamprecht FA, Esteves T, Quelhas P, Demirel Ö, Malmström L, Jug F, Tomancak P, Meijering E, Muñoz-Barrutia A, Kozubek M, Ortiz-de-Solorzano C.

Nat Methods. 2017 Dec;14(12):1141-1152. doi: 10.1038/nmeth.4473. Epub 2017 Oct 30.

15.

Tracking of Indels by DEcomposition is a Simple and Effective Method to Assess Efficiency of Guide RNAs in Zebrafish.

Etard C, Joshi S, Stegmaier J, Mikut R, Strähle U.

Zebrafish. 2017 Dec;14(6):586-588. doi: 10.1089/zeb.2017.1454. Epub 2017 Aug 2.

PMID:
28767326
16.

Screening and Optimizing Antimicrobial Peptides by Using SPOT-Synthesis.

López-Pérez PM, Grimsey E, Bourne L, Mikut R, Hilpert K.

Front Chem. 2017 Apr 12;5:25. doi: 10.3389/fchem.2017.00025. eCollection 2017. Review.

17.

[In vivo imaging of the corneal nerve plexus : From single image to large scale map].

Köhler B, Allgeier S, Bartschat A, Guthoff RF, Bohn S, Reichert KM, Stachs O, Winter K, Mikut R.

Ophthalmologe. 2017 Jul;114(7):601-607. doi: 10.1007/s00347-017-0464-4. Review. German.

PMID:
28283769
18.

A New Feedback-Based Method for Parameter Adaptation in Image Processing Routines.

Khan AU, Mikut R, Reischl M.

PLoS One. 2016 Oct 20;11(10):e0165180. doi: 10.1371/journal.pone.0165180. eCollection 2016.

19.

Use of Peptide Libraries for Identification and Optimization of Novel Antimicrobial Peptides.

Ashby M, Petkova A, Gani J, Mikut R, Hilpert K.

Curr Top Med Chem. 2017;17(5):537-553. Review.

PMID:
27411326
20.

Automated phenotype pattern recognition of zebrafish for high-throughput screening.

Schutera M, Dickmeis T, Mione M, Peravali R, Marcato D, Reischl M, Mikut R, Pylatiuk C.

Bioengineered. 2016 Jul 3;7(4):261-5. doi: 10.1080/21655979.2016.1197710.

21.

Zebrafish biosensor for toxicant induced muscle hyperactivity.

Shahid M, Takamiya M, Stegmaier J, Middel V, Gradl M, Klüver N, Mikut R, Dickmeis T, Scholz S, Rastegar S, Yang L, Strähle U.

Sci Rep. 2016 Mar 31;6:23768. doi: 10.1038/srep23768.

22.

Real-Time Three-Dimensional Cell Segmentation in Large-Scale Microscopy Data of Developing Embryos.

Stegmaier J, Amat F, Lemon WC, McDole K, Wan Y, Teodoro G, Mikut R, Keller PJ.

Dev Cell. 2016 Jan 25;36(2):225-40. doi: 10.1016/j.devcel.2015.12.028.

23.

An automated and high-throughput Photomotor Response platform for chemical screens.

Marcato D, Alshut R, Breitwieser H, Mikut R, Strahle U, Pylatiuk C, Peravali R.

Conf Proc IEEE Eng Med Biol Soc. 2015;2015:7728-31. doi: 10.1109/EMBC.2015.7320183.

PMID:
26738083
24.

Small angle X-ray scattering as a high-throughput method to classify antimicrobial modes of action.

von Gundlach AR, Garamus VM, Gorniak T, Davies HA, Reischl M, Mikut R, Hilpert K, Rosenhahn A.

Biochim Biophys Acta. 2016 May;1858(5):918-25. doi: 10.1016/j.bbamem.2015.12.022. Epub 2015 Dec 28.

25.

Improving short antimicrobial peptides despite elusive rules for activity.

Mikut R, Ruden S, Reischl M, Breitling F, Volkmer R, Hilpert K.

Biochim Biophys Acta. 2016 May;1858(5):1024-33. doi: 10.1016/j.bbamem.2015.12.013. Epub 2015 Dec 11.

26.

Steer by ear: Myoelectric auricular control of powered wheelchairs for individuals with spinal cord injury.

Schmalfuß L, Rupp R, Tuga MR, Kogut A, Hewitt M, Meincke J, Klinker F, Duttenhoefer W, Eck U, Mikut R, Reischl M, Liebetanz D.

Restor Neurol Neurosci. 2015;34(1):79-95. doi: 10.3233/RNN-150579.

PMID:
26599475
27.

A Zebrafish Drug-Repurposing Screen Reveals sGC-Dependent and sGC-Independent Pro-Inflammatory Activities of Nitric Oxide.

Wittmann C, Reischl M, Shah AH, Kronfuss E, Mikut R, Liebel U, Grabher C.

PLoS One. 2015 Oct 7;10(10):e0137286. doi: 10.1371/journal.pone.0137286. eCollection 2015.

28.

XPIWIT--an XML pipeline wrapper for the Insight Toolkit.

Bartschat A, Hübner E, Reischl M, Mikut R, Stegmaier J.

Bioinformatics. 2016 Jan 15;32(2):315-7. doi: 10.1093/bioinformatics/btv559. Epub 2015 Sep 28.

PMID:
26415725
29.

Optimization of oncocin for antibacterial activity using a SPOT synthesis approach: extending the pathogen spectrum to Staphylococcus aureus.

Knappe D, Ruden S, Langanke S, Tikkoo T, Ritzer J, Mikut R, Martin LL, Hoffmann R, Hilpert K.

Amino Acids. 2016 Jan;48(1):269-80. doi: 10.1007/s00726-015-2082-2. Epub 2015 Sep 3.

PMID:
26334348
30.

Interaction of blood components with cathelicidins and their modified versions.

Yu K, Lai BF, Gani J, Mikut R, Hilpert K, Kizhakkedathu JN.

Biomaterials. 2015 Nov;69:201-11. doi: 10.1016/j.biomaterials.2015.08.003. Epub 2015 Aug 6.

PMID:
26295533
31.

A Benchmark Data Set to Evaluate the Illumination Robustness of Image Processing Algorithms for Object Segmentation and Classification.

Khan AU, Mikut R, Reischl M.

PLoS One. 2015 Jul 20;10(7):e0131098. doi: 10.1371/journal.pone.0131098. eCollection 2015.

32.

Clinical and molecular implications of MED15 in head and neck squamous cell carcinoma.

Shaikhibrahim Z, Offermann A, Halbach R, Vogel W, Braun M, Kristiansen G, Bootz F, Wenzel J, Mikut R, Lengerke C, Reischl M, Schröck A, Perner S.

Am J Pathol. 2015 Apr;185(4):1114-22. doi: 10.1016/j.ajpath.2014.12.010. Epub 2015 Mar 16.

PMID:
25791637
33.

An ensemble-averaged, cell density-based digital model of zebrafish embryo development derived from light-sheet microscopy data with single-cell resolution.

Kobitski AY, Otte JC, 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 GU.

Sci Rep. 2015 Feb 25;5:8601. doi: 10.1038/srep08601.

34.

Mosaicking the subbasal nerve plexus by guided eye movements.

Allgeier S, Maier S, Mikut R, Peschel S, Reichert KM, Stachs O, Köhler B.

Invest Ophthalmol Vis Sci. 2014 Aug 26;55(9):6082-9. doi: 10.1167/iovs.14-14698.

PMID:
25159207
35.

Automatic zebrafish heartbeat detection and analysis for zebrafish embryos.

Pylatiuk C, Sanchez D, Mikut R, Alshut R, Reischl M, Hirth S, Rottbauer W, Just S.

Zebrafish. 2014 Aug;11(4):379-83. doi: 10.1089/zeb.2014.1002. Epub 2014 Jul 8.

36.

Fast segmentation of stained nuclei in terabyte-scale, time resolved 3D microscopy image stacks.

Stegmaier J, Otte JC, Kobitski A, Bartschat A, Garcia A, Nienhaus GU, Strähle U, Mikut R.

PLoS One. 2014 Feb 27;9(2):e90036. doi: 10.1371/journal.pone.0090036. eCollection 2014.

37.

Automated prior knowledge-based quantification of neuronal patterns in the spinal cord of zebrafish.

Stegmaier J, Shahid M, Takamiya M, Yang L, Rastegar S, Reischl M, Strähle U, Mikut R.

Bioinformatics. 2014 Mar 1;30(5):726-33. doi: 10.1093/bioinformatics/btt600. Epub 2013 Oct 17.

PMID:
24135262
38.

Which functional impairments are the main contributors to pelvic anterior tilt during gait in individuals with cerebral palsy?

Wolf SI, Mikut R, Kranzl A, Dreher T.

Gait Posture. 2014;39(1):359-64. doi: 10.1016/j.gaitpost.2013.08.014. Epub 2013 Sep 2.

PMID:
24054350
39.

Concept of a Co-Adaptive Training Environment for Human-Machine Interfaces Based on EMG-Control.

Tuga MR, Rupp R, Liebetanz D, Mikut R, Reischl M.

Biomed Tech (Berl). 2013 Aug;58 Suppl 1. pii: /j/bmte.2013.58.issue-s1-P/bmt-2013-4388/bmt-2013-4388.xml. doi: 10.1515/bmt-2013-4388. Epub 2013 Sep 7. No abstract available.

PMID:
24043103
40.

Automated processing of zebrafish imaging data: a survey.

Mikut R, Dickmeis T, Driever W, Geurts P, Hamprecht FA, Kausler BX, Ledesma-Carbayo MJ, Marée R, Mikula K, Pantazis P, Ronneberger O, Santos A, Stotzka R, Strähle U, Peyriéras N.

Zebrafish. 2013 Sep;10(3):401-21. doi: 10.1089/zeb.2013.0886. Epub 2013 Jun 12. Review.

41.

Genome-wide, whole mount in situ analysis of transcriptional regulators in zebrafish embryos.

Armant O, März M, Schmidt R, Ferg M, Diotel N, Ertzer R, Bryne JC, Yang L, Baader I, Reischl M, Legradi J, Mikut R, Stemple D, van IJcken W, van der Sloot A, Lenhard B, Strähle U, Rastegar S.

Dev Biol. 2013 Aug 15;380(2):351-62. doi: 10.1016/j.ydbio.2013.05.006. Epub 2013 May 14.

42.

Report of the Second European Zebrafish Principal Investigator Meeting in Karlsruhe, Germany, March 21-24, 2012.

Cavodeassi F, Del Bene F, Fürthauer M, Grabher C, Herzog W, Lehtonen S, Linker C, Mercader N, Mikut R, Norton W, Strähle U, Tiso N, Foulkes NS.

Zebrafish. 2013 Mar;10(1):119-23. doi: 10.1089/zeb.2012.0829. Epub 2013 Mar 26.

PMID:
23530760
43.

Targeting Mycobacterium tuberculosis and other microbial pathogens using improved synthetic antibacterial peptides.

Ramón-García S, Mikut R, Ng C, Ruden S, Volkmer R, Reischl M, Hilpert K, Thompson CJ.

Antimicrob Agents Chemother. 2013 May;57(5):2295-303. doi: 10.1128/AAC.00175-13. Epub 2013 Mar 11.

44.

Identification of nonvisual photomotor response cells in the vertebrate hindbrain.

Kokel D, Dunn TW, Ahrens MB, Alshut R, Cheung CY, Saint-Amant L, Bruni G, Mateus R, van Ham TJ, Shiraki T, Fukada Y, Kojima D, Yeh JR, Mikut R, von Lintig J, Engert F, Peterson RT.

J Neurosci. 2013 Feb 27;33(9):3834-43. doi: 10.1523/JNEUROSCI.3689-12.2013.

45.

Facilitating drug discovery: an automated high-content inflammation assay in zebrafish.

Wittmann C, Reischl M, Shah AH, Mikut R, Liebel U, Grabher C.

J Vis Exp. 2012 Jul 16;(65):e4203. doi: 10.3791/4203.

46.

Frequency and clinicopathologic correlates of KRAS amplification in non-small cell lung carcinoma.

Wagner PL, Stiedl AC, Wilbertz T, Petersen K, Scheble V, Menon R, Reischl M, Mikut R, Rubin MA, Fend F, Moch H, Soltermann A, Weder W, Altorki NK, Perner S.

Lung Cancer. 2011 Oct;74(1):118-23. doi: 10.1016/j.lungcan.2011.01.029. Epub 2011 Apr 8.

PMID:
21477882
47.

SOX2 gene amplification and protein overexpression are associated with better outcome in squamous cell lung cancer.

Wilbertz T, Wagner P, Petersen K, Stiedl AC, Scheble VJ, Maier S, Reischl M, Mikut R, Altorki NK, Moch H, Fend F, Staebler A, Bass AJ, Meyerson M, Rubin MA, Soltermann A, Lengerke C, Perner S.

Mod Pathol. 2011 Jul;24(7):944-53. doi: 10.1038/modpathol.2011.49. Epub 2011 Apr 1.

48.

SOX2 amplification is a common event in squamous cell carcinomas of different organ sites.

Maier S, Wilbertz T, Braun M, Scheble V, Reischl M, Mikut R, Menon R, Nikolov P, Petersen K, Beschorner C, Moch H, Kakies C, Protzel C, Bauer J, Soltermann A, Fend F, Staebler A, Lengerke C, Perner S.

Hum Pathol. 2011 Aug;42(8):1078-88. doi: 10.1016/j.humpath.2010.11.010. Epub 2011 Feb 21.

PMID:
21334718
49.

Gait analysis may help to distinguish hereditary spastic paraplegia from cerebral palsy.

Wolf SI, Braatz F, Metaxiotis D, Armbrust P, Dreher T, Döderlein L, Mikut R.

Gait Posture. 2011 Apr;33(4):556-61. doi: 10.1016/j.gaitpost.2011.01.009. Epub 2011 Feb 16.

PMID:
21330136
50.

Computer-based analysis, visualization, and interpretation of antimicrobial peptide activities.

Mikut R.

Methods Mol Biol. 2010;618:287-99. doi: 10.1007/978-1-60761-594-1_18.

PMID:
20094871

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