Vizardous: interactive analysis of microbial populations with single cell resolution

Helfrich S, Azzouzi CE, Probst C, Seiffarth J, Grünberger A, Wiechert W, Kohlheyer D, Nöh K (2015)
Bioinformatics 31(23): 3875-3877.

Download
Es wurde kein Volltext hochgeladen. Nur Publikationsnachweis!
Zeitschriftenaufsatz | Veröffentlicht | Englisch
Autor
; ; ; ; ; ; ;
Abstract / Bemerkung
Motivation: Single cell time-lapse microscopy is a powerful method for investigating heterogeneous cell behavior. Advances in microfluidic lab-on-a-chip technologies and live-cell imaging render the parallel observation of the development of individual cells in hundreds of populations possible. While image analysis tools are available for cell detection and tracking, biologists are still confronted with the challenge of exploring and evaluating this data. Results: We present the software tool Vizardous that assists scientists with explorative analysis and interpretation tasks of single cell data in an interactive, configurable and visual way. With Vizardous, lineage tree drawings can be augmented with various, time-resolved cellular characteristics. Associated statistical moments bridge the gap between single cell and the population-average level. Availability and implementation: The software, including documentation and examples, is available as executable Java archive as well as in source form at https://github.com/modsim/vizardous. Contact:k.noeh@fz-juelich.de Supplementary information:Supplementary data are available at Bioinformatics online.
Erscheinungsjahr
Zeitschriftentitel
Bioinformatics
Band
31
Ausgabe
23
Seite(n)
3875-3877
eISSN
PUB-ID

Zitieren

Helfrich S, Azzouzi CE, Probst C, et al. Vizardous: interactive analysis of microbial populations with single cell resolution. Bioinformatics. 2015;31(23):3875-3877.
Helfrich, S., Azzouzi, C. E., Probst, C., Seiffarth, J., Grünberger, A., Wiechert, W., Kohlheyer, D., et al. (2015). Vizardous: interactive analysis of microbial populations with single cell resolution. Bioinformatics, 31(23), 3875-3877. doi:10.1093/bioinformatics/btv468
Helfrich, S., Azzouzi, C. E., Probst, C., Seiffarth, J., Grünberger, A., Wiechert, W., Kohlheyer, D., and Nöh, K. (2015). Vizardous: interactive analysis of microbial populations with single cell resolution. Bioinformatics 31, 3875-3877.
Helfrich, S., et al., 2015. Vizardous: interactive analysis of microbial populations with single cell resolution. Bioinformatics, 31(23), p 3875-3877.
S. Helfrich, et al., “Vizardous: interactive analysis of microbial populations with single cell resolution”, Bioinformatics, vol. 31, 2015, pp. 3875-3877.
Helfrich, S., Azzouzi, C.E., Probst, C., Seiffarth, J., Grünberger, A., Wiechert, W., Kohlheyer, D., Nöh, K.: Vizardous: interactive analysis of microbial populations with single cell resolution. Bioinformatics. 31, 3875-3877 (2015).
Helfrich, Stefan, Azzouzi, Charaf E., Probst, Christopher, Seiffarth, Johannes, Grünberger, Alexander, Wiechert, Wolfgang, Kohlheyer, Dietrich, and Nöh, Katharina. “Vizardous: interactive analysis of microbial populations with single cell resolution”. Bioinformatics 31.23 (2015): 3875-3877.

6 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Coarse-graining bacteria colonies for modelling critical solute distributions in picolitre bioreactors for bacterial studies on single-cell level.
Westerwalbesloh C, Grünberger A, Wiechert W, Kohlheyer D, von Lieres E., Microb Biotechnol 10(4), 2017
PMID: 28371389
Taking control over microbial populations: Current approaches for exploiting biological noise in bioprocesses.
Delvigne F, Baert J, Sassi H, Fickers P, Grünberger A, Dusny C., Biotechnol J 12(7), 2017
PMID: 28544731
Homogenizing bacterial cell factories: Analysis and engineering of phenotypic heterogeneity.
Binder D, Drepper T, Jaeger KE, Delvigne F, Wiechert W, Kohlheyer D, Grünberger A., Metab Eng 42(), 2017
PMID: 28645641
Image-Based Single Cell Profiling: High-Throughput Processing of Mother Machine Experiments.
Sachs CC, Grünberger A, Helfrich S, Probst C, Wiechert W, Kohlheyer D, Nöh K., PLoS One 11(9), 2016
PMID: 27661996
Modeling and CFD simulation of nutrient distribution in picoliter bioreactors for bacterial growth studies on single-cell level.
Westerwalbesloh C, Grünberger A, Stute B, Weber S, Wiechert W, Kohlheyer D, von Lieres E., Lab Chip 15(21), 2015
PMID: 26345659

19 References

Daten bereitgestellt von Europe PubMed Central.

OMERO: flexible, model-driven data management for experimental biology.
Allan C, Burel JM, Moore J, Blackburn C, Linkert M, Loynton S, Macdonald D, Moore WJ, Neves C, Patterson A, Porter M, Tarkowska A, Loranger B, Avondo J, Lagerstedt I, Lianas L, Leo S, Hands K, Hay RT, Patwardhan A, Best C, Kleywegt GJ, Zanetti G, Swedlow JR., Nat. Methods 9(3), 2012
PMID: 22373911
Bacterial persistence as a phenotypic switch.
Balaban NQ, Merrin J, Chait R, Kowalik L, Leibler S., Science 305(5690), 2004
PMID: 15308767
Light-responsive control of bacterial gene expression: precise triggering of the lac promoter activity using photocaged IPTG.
Binder D, Grunberger A, Loeschcke A, Probst C, Bier C, Pietruszka J, Wiechert W, Kohlheyer D, Jaeger KE, Drepper T., Integr Biol (Camb) 6(8), 2014
PMID: 24894989
A constant size extension drives bacterial cell size homeostasis.
Campos M, Surovtsev IV, Kato S, Paintdakhi A, Beltran B, Ebmeier SE, Jacobs-Wagner C., Cell 159(6), 2014
PMID: 25480302
Single-cell microfluidics: opportunity for bioprocess development.
Grunberger A, Wiechert W, Kohlheyer D., Curr. Opin. Biotechnol. 29(), 2014
PMID: 24642389
phyloXML: XML for evolutionary biology and comparative genomics.
Han MV, Zmasek CM., BMC Bioinformatics 10(), 2009
PMID: 19860910
Stochasticity of metabolism and growth at the single-cell level.
Kiviet DJ, Nghe P, Walker N, Boulineau S, Sunderlikova V, Tans SJ., Nature 514(7522), 2014
PMID: 25186725
Functional roles of pulsing in genetic circuits.
Levine JH, Lin Y, Elowitz MB., Science 342(6163), 2013
PMID: 24311681
Using movies to analyse gene circuit dynamics in single cells.
Locke JC, Elowitz MB., Nat. Rev. Microbiol. 7(5), 2009
PMID: 19369953
Analysis of SOS-induced spontaneous prophage induction in Corynebacterium glutamicum at the single-cell level.
Nanda AM, Heyer A, Kramer C, Grunberger A, Kohlheyer D, Frunzke J., J. Bacteriol. 196(1), 2013
PMID: 24163339

AUTHOR UNKNOWN, 0
Following evolution of bacterial antibiotic resistance in real time.
Rosenthal AZ, Elowitz MB., Nat. Genet. 44(1), 2011
PMID: 22200772
The present and future role of microfluidics in biomedical research.
Sackmann EK, Fulton AL, Beebe DJ., Nature 507(7491), 2014
PMID: 24622198
Cell-size control and homeostasis in bacteria.
Taheri-Araghi S, Bradde S, Sauls JT, Hill NS, Levin PA, Paulsson J, Vergassola M, Jun S., Curr. Biol. 25(3), 2014
PMID: 25544609
Robust growth of Escherichia coli.
Wang P, Robert L, Pelletier J, Dang WL, Taddei F, Wright A, Jun S., Curr. Biol. 20(12), 2010
PMID: 20537537
Measuring single-cell gene expression dynamics in bacteria using fluorescence time-lapse microscopy.
Young JW, Locke JC, Altinok A, Rosenfeld N, Bacarian T, Swain PS, Mjolsness E, Elowitz MB., Nat Protoc 7(1), 2011
PMID: 22179594

Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®

Quellen

PMID: 26261223
PubMed | Europe PMC

Suchen in

Google Scholar