COMBImage2: a parallel computational framework for higher-order drug combination analysis that includes automated plate design, matched filter based object counting and temporal data mining

BMC Bioinformatics
Efthymia ChantziMats G Gustafsson

Abstract

Pharmacological treatment of complex diseases using more than two drugs is commonplace in the clinic due to better efficacy, decreased toxicity and reduced risk for developing resistance. However, many of these higher-order treatments have not undergone any detailed preceding in vitro evaluation that could support their therapeutic potential and reveal disease related insights. Despite the increased medical need for discovery and development of higher-order drug combinations, very few reports from systematic large-scale studies along this direction exist. A major reason is lack of computational tools that enable automated design and analysis of exhaustive drug combination experiments, where all possible subsets among a panel of pre-selected drugs have to be evaluated. Motivated by this, we developed COMBImage2, a parallel computational framework for higher-order drug combination analysis. COMBImage2 goes far beyond its predecessor COMBImage in many different ways. In particular, it offers automated 384-well plate design, as well as quality control that involves resampling statistics and inter-plate analyses. Moreover, it is equipped with a generic matched filter based object counting method that is currently designed for apopto...Continue Reading

Associated Datasets

May 7, 2019·Efthymia Chantzi, Efthymia Chantzi
May 7, 2019·Efthymia Chantzi, Efthymia Chantzi
May 7, 2019·Efthymia Chantzi, Efthymia Chantzi

References

Dec 14, 2004·Nature Genetics·Daniel SegrèRoy Kishony
Aug 21, 2008·Nature Protocols·Elin LindhagenRolf Larsson
Jul 28, 2012·Critical Care : the Official Journal of the Critical Care Forum·Martin SchulzAchim Schmoldt
Apr 24, 2014·Molecular Cancer Therapeutics·Muhammad KashifMats G Gustafsson
Jun 14, 2014·Apoptosis : an International Journal on Programmed Cell Death·Obaid AftabMats G Gustafsson
Dec 20, 2014·Ecancermedicalscience·Pan PantziarkaVikas P Sukhatme
Feb 24, 2015·Drugs in R&D·Christine Roder, Melanie J Thomson
Aug 8, 2015·Journal of Laboratory Automation·Kristin BlomClaes R Andersson
May 7, 2016·Bioinformatics·Giovanni Y Di VeroliDuncan I Jodrell
Dec 16, 2016·Journal of the Royal Society, Interface·Casey BepplerPamela J Yeh
Dec 19, 2017·Bioinformatics·Kristina PreuerGünter Klambauer
May 15, 2018·Diabetes, Obesity & Metabolism·Clifford J Bailey
Sep 6, 2018·NPJ Systems Biology and Applications·Elif TekinPamela J Yeh
Oct 20, 2018·Frontiers in Pharmacology·Daniel J MasonAndreas Bender

❮ Previous
Next ❯

Citations


❮ Previous
Next ❯

Methods Mentioned

BETA
feature extraction

Software Mentioned

COMBImage2
ReDO
R
MF
MOD
MapReduce
MATLAB
Windows
Pick
Mine

Related Concepts

Related Feeds

Apoptosis in Cancer

Apoptosis is an important mechanism in cancer. By evading apoptosis, tumors can continue to grow without regulation and metastasize systemically. Many therapies are evaluating the use of pro-apoptotic activation to eliminate cancer growth. Here is the latest research on apoptosis in cancer.

Apoptosis

Apoptosis is a specific process that leads to programmed cell death through the activation of an evolutionary conserved intracellular pathway leading to pathognomic cellular changes distinct from cellular necrosis