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Kashif, Mohammad, 2010. Algorithms offering kinetic analysis of drug induced proteasome inhibition and cell clump formation from time lapsed microscopy. Second cycle, A2E. Uppsala: SLU, Dept. of Animal Breeding and Genetics (until 231231)



High content screening (HCS) has potential to transform many biological fields, ranging from drug discovery to gene function discovery. HCS with time lapsed microscopy provide valuable insight information about live cells experiments that are usually lost during manual end point experiments. By means of novel bioinformatics algorithms, huge amount of phenotypic data might become available by these techniques which can be used to understand effects of chemical compounds on the cells and profile phenotypically both cell line and chemical compounds. The resultant data can also be compared with other experiments to find out the efficiency and affectivity of the different compounds under same conditions. Recent results also demonstrate that phenotypic profiles can be used to infer specific gene perturbations.
In this thesis, novel algorithms for such phenotypic profiling were implemented and demonstrated to be very useful revealing unknown kinetic information regarding two proteasome inhibitors (Bortezomib and CB3) as well as about cell clump formation during cell line growth on honeycomb nanoculture plates. The novel algorithms include specialized solutions both for phase contrast microscopy and fluorescent microscopy and are based on the publicly available cell image processing package Cell Profiler from Broad Institute.

Main title:Algorithms offering kinetic analysis of drug induced proteasome inhibition and cell clump formation from time lapsed microscopy
Authors:Kashif, Mohammad
Supervisor:Gustafsson, Mats and Bongcam-Rudloff, Erik
Examiner:Larsson, Rolf
Series:Examensarbete / SLU, Institutionen för husdjursgenetik
Volume/Sequential designation:326
Year of Publication:2010
Level and depth descriptor:Second cycle, A2E
Student's programme affiliation:Other
Supervising department:(VH) > Dept. of Animal Breeding and Genetics (until 231231)
Keywords:Image processing, time lapsed microscopy, kinetic studies, cell clumps, proteasome inhibition
Permanent URL:
Subject. Use of subject categories until 2023-04-30.:Life sciences
Human medicine, health, and safety
Additional Information:One-Year Master's Programme in Biology - Bioinformatics
Deposited On:25 Apr 2013 13:53
Metadata Last Modified:23 Oct 2013 23:15

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