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A Gene Expression High-Throughput Screen (GE-HTS) for Coordinated Detection of Functionally Similar Effectors in Cancer

Chaitra Rao, Dianna H. Huisman, Heidi M. Vieira, Danielle E. Frodyma, Beth K. Neilsen, Binita Chakraborty, Suzie K. Hight, Michael A. White, Kurt W. Fisher, Robert E. Lewis
2020 Cancers  
We have used FUSION to screen for functional analogues to Kinase suppressor of Ras 1 (KSR1), a scaffold protein downstream of Ras in the Raf-MEK-ERK kinase cascade, and biologically validated several proteins  ...  Challenges associated with FUSION and other high-content genome-wide screens include variation, batch effects, and controlling for potential off-target effects.  ...  Conflicts of Interest: The authors declare no conflict of interest. The funders had no role in the decision to publish or preparation of the manuscript.  ... 
doi:10.3390/cancers12113143 pmid:33120942 fatcat:bhezewhslzeh7kjvr67vsnzubi

RNA Interference (RNAi) Screening inDrosophila

Florian Heigwer, Fillip Port, Michael Boutros
2018 Genetics  
We will discuss available reagent libraries and cell lines, methodological approaches for cell-based assays, and computational methods for the analysis of high-throughput screens.  ...  In the last decade, RNA interference (RNAi), a cellular mechanism that uses RNA-guided degradation of messenger RNA transcripts, has had an important impact on identifying and characterizing gene function  ...  Research in the laboratory of M.B. was supported by a European Research Council advanced grant of the European Commission and a Drosophila RNAi Core (DRiC) infrastructure grant from the German Research  ... 
doi:10.1534/genetics.117.300077 pmid:29487145 pmcid:PMC5844339 fatcat:b3u5gda2fzhklfo3ghf4d6cbnu

Repurposing High-Throughput Image Assays Enables Biological Activity Prediction for Drug Discovery

Jaak Simm, Günter Klambauer, Adam Arany, Marvin Steijaert, Jörg Kurt Wegner, Emmanuel Gustin, Vladimir Chupakhin, Yolanda T. Chong, Jorge Vialard, Peter Buijnsters, Ingrid Velter, Alexander Vapirev (+6 others)
2018 Cell Chemical Biology  
We hypothesized that data from a single high-throughput imaging assay can be repurposed to predict the biological activity of compounds in other assays, even those targeting alternate pathways or biological  ...  Indeed, quantitative information extracted from a three-channel microscopy-based screen for glucocorticoid receptor translocation was able to predict assay-specific biological activity in two ongoing drug  ...  We used the average of the k folds as the evaluation metric for each model, and focused on models with an AUC-ROC > 0.9.  ... 
doi:10.1016/j.chembiol.2018.01.015 pmid:29503208 pmcid:PMC6031326 fatcat:oqhm2h3ojvakljwdxxnsfa6rsi

A cell-based high-throughput screening assay for radiation susceptibility using automated cell counting

Jasmina Hodzic, Ilse Dingjan, Mariëlle Maas, Ida H van der Meulen-Muileman, Renee X de Menezes, Stan Heukelom, Marcel Verheij, Winald R Gerritsen, Albert A Geldof, Baukelien van Triest, Victor W van Beusechem
2015 Radiation Oncology  
Compound and RNA interference high-throughput screening technologies allow comprehensive enterprises to identify new agents and targets for radiosensitization.  ...  In a high-throughput screening setting, using 4 Gy irradiated and control PC-3 cells, the effects of DNA-PKcs siRNA and non-targeting control siRNA could be clearly discriminated.  ...  Acknowledgements We thank André Elferink for his help with the irradiation procedure, Peter Sminia for expert advice and Conchita Vens for critically reading the manuscript.  ... 
doi:10.1186/s13014-015-0355-2 pmid:25888875 pmcid:PMC4355372 fatcat:qfsek2odube3lo2ocmsiufi3xi

Fluorescent RNA Aptamers as a Tool to Study RNA-Modifying Enzymes

Nina Svensen, Samie R. Jaffrey
2016 Cell Chemical Biology  
We describe a high-throughput screen for FTO inhibitors using the fluorogenic methylated Broccoli substrate HTS assay performs robustly with a Z'-factor > 0.8 in the LOPAC1280 library.  ...  This allowed the identification of novel high-affinity FTO inhibitors.  ...  ) for FTO plasmid, and Fraser Glickman and Jeanne Chiaravalli at The Rockefeller University High Throughput and Spectroscopy Resource Center for providing assay guidance, instrumentation and infrastructure  ... 
doi:10.1016/j.chembiol.2015.11.018 pmid:26877022 pmcid:PMC4800036 fatcat:sxiiafa4xjhg7e4iuedklgtwra

Next-Generation Sequencing in Clinical Molecular Diagnostics of Cancer: Advantages and Challenges

Rajyalakshmi Luthra, Hui Chen, Sinchita Roy-Chowdhuri, R. Singh
2015 Cancers  
Massively parallel sequencing capabilities of NGS provide a much-needed alternative for mutation screening in multiple genes with a single low investment of DNA.  ...  Here, we have reviewed approaches for validation of NGS technology for routine screening of tumors.  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/cancers7040874 pmid:26473927 pmcid:PMC4695874 fatcat:w5oq3qy6kbccxfx2edfzp3iot4

ScreenBEAM: a novel meta-analysis algorithm for functional genomics screens via Bayesian hierarchical modeling

Jiyang Yu, Jose Silva, Andrea Califano
2015 Bioinformatics  
Method: We use large RNAi and CRISPR repositories that are publicly available to evaluate a novel meta-analysis approach for FG screens via Bayesian hierarchical modeling, Screening Bayesian Evaluation  ...  Indeed, rigorous statistical analysis of high-throughput FG screening data remains challenging, particularly when integrative analyses are used to combine multiple sh/sgRNAs targeting the same gene in  ...  Acknowledgements The authors thank all the members of the Califano and Silva labs for helpful discussions, Dr. Aaron Diaz for sharing data, Dr. Barbara Weir for Achilles data access.  ... 
doi:10.1093/bioinformatics/btv556 pmid:26415723 pmcid:PMC4907394 fatcat:wlghp2dfufhldcwd3no5vtvpvq

A pair of new statistical parameters for quality control in RNA interference high-throughput screening assays

Xiaohua Douglas Zhang
2007 Genomics  
To obtain high-quality HTS assays, there is a strong need for an easily interpretable and theoretically based quality control (QC) metric.  ...  RNA interference (RNAi) high-throughput screening (HTS) enables massive parallel gene silencing and is increasingly being used to reveal novel connections between genes and disease-relevant phenotypes.  ...  Acknowledgments The author thanks Daniel Holder, Keith Soper, and Joseph Heyse for their supports in this research; Daniel Holder, Jason Liao at Merck, and Xiaohua Shu at Temple University for their helpful  ... 
doi:10.1016/j.ygeno.2006.12.014 pmid:17276655 fatcat:mwme7kbcjrh33arvykfx4lktua

A novel phenotypic dissimilarity method for image-based high-throughput screens

Xian Zhang, Michael Boutros
2013 BMC Bioinformatics  
Conclusions: PhenoDissim is a novel analysis method for image-based high-throughput screen, relying on two parameters which can be automatically optimized without a priori knowledge.  ...  Such image-based high-throughput RNAi screening studies have facilitated the discovery of novel components of gene networks and their interactions.  ...  We acknowledge two anonymous reviewers for their review and comments on the manuscript. XZ was supported by a DKFZ postdoctoral fellowship.  ... 
doi:10.1186/1471-2105-14-336 pmid:24256072 pmcid:PMC4225524 fatcat:t4vfjswxzffklez235a4mque54

High-throughput RNA interference screens integrative analysis: Towards a comprehensive understanding of the virus-host interplay

Sandeep Amberkar
2013 World Journal of Virology  
High-throughput RNA interference screens integrative analysis: Towards a comprehensive understanding of the virus-host interplay.  ...  Figure 1 A 1 Figure 1 A schematic workflow for the analysis of high-throughput RNA interference screens to identify host cell regulators of viral life cycle. Amberkar S et al .  ...  To this end, the establishment of platforms enabling genome-wide high-throughput RNA interference (HT-RNAi) screens has led to the identification of several key factors involved in the viral life cycle  ... 
doi:10.5501/wjv.v2.i2.18 pmid:24175227 pmcid:PMC3785050 fatcat:jpltfxygnrekvhigej6phqobyu

Exploring biology with small organic molecules

Brent R. Stockwell
2004 Nature  
Acknowledgements B.R.S. is supported in part by a Career Award at the Scientific Interface from the Burroughs Wellcome Fund.  ...  In a high-throughput screen, many different chemicals (or other test reagents) are evaluated in the same biological test for their effects on a protein or cellular process.  ...  Finally, a large collection of RNAi reagents can be a useful tool for high-throughput screens 9 .  ... 
doi:10.1038/nature03196 pmid:15602550 pmcid:PMC3165172 fatcat:cp6zd7zhtrbgphu4m2wb3bpbdi

Transcriptomics in Toxicogenomics, Part I: Experimental Design, Technologies, Publicly Available Data, and Regulatory Aspects

Pia Anneli Sofia Kinaret, Angela Serra, Antonio Federico, Pekka Kohonen, Penny Nymark, Irene Liampa, My Kieu Ha, Jang-Sik Choi, Karolina Jagiello, Natasha Sanabria, Georgia Melagraki, Luca Cattelani (+8 others)
2020 Nanomaterials  
The increasing development of novel materials and chemical compounds dictates the need for a better understanding of the molecular changes occurring in exposed biological systems.  ...  In this review, we summarize the recent advancements in the design and analysis of DNA microarray, RNA sequencing (RNA-Seq), and single-cell RNA-Seq (scRNA-Seq) data.  ...  Acknowledgments: The authors would like to thank David Winkler for critical comments to the manuscript. Conflicts of Interest: The authors declare no conflicts of interest.  ... 
doi:10.3390/nano10040750 pmid:32326418 fatcat:yibinmlorvfvbh7i7mggzy2d5i

RNA G-quadruplexes (rG4s): genomics and biological functions

Kaixin Lyu, Eugene Yui-Ching Chow, Xi Mou, Ting-Fung Chan, Chun Kit Kwok
2021 Nucleic Acids Research  
In this review, we will summarize the innovative high-throughput methods recently developed to detect rG4s on a transcriptome-wide scale, highlight the many novel and important functions of rG4 being discovered  ...  Compared to DNA G4s (dG4s), the study of RNA G4s (rG4s) has received less attention until recently.  ...  Sunny Yang for a generous donation.  ... 
doi:10.1093/nar/gkab187 pmid:33772593 fatcat:ukkuhgnjybd6jhrczbu7indyhu

Genome-scale measurement of off-target activity using Cas9 toxicity in high-throughput screens

David W. Morgens, Michael Wainberg, Evan A. Boyle, Oana Ursu, Carlos L. Araya, C. Kimberly Tsui, Michael S. Haney, Gaelen T. Hess, Kyuho Han, Edwin E. Jeng, Amy Li, Michael P. Snyder (+3 others)
2017 Nature Communications  
Our results demonstrate a simple strategy for high-throughput evaluation of target specificity and nuclease toxicity in Cas9 screens.  ...  CRISPR-Cas9 screens are powerful tools for high-throughput interrogation of genome function, but can be confounded by nuclease-induced toxicity at both on-and off-target sites, likely due to DNA damage  ...  in high-throughput screens.  ... 
doi:10.1038/ncomms15178 pmid:28474669 pmcid:PMC5424143 fatcat:j2l3ylfnkfhh7aprgtjqixm4pe

High throughput toxicity screening and intracellular detection of nanomaterials

Andrew R. Collins, Balasubramanyam Annangi, Laura Rubio, Ricard Marcos, Marco Dorn, Carolin Merker, Irina Estrela-Lopis, Mihaela Roxana Cimpan, Mohamed Ibrahim, Emil Cimpan, Melanie Ostermann, Alexander Sauter (+21 others)
2016 Wiley Interdisciplinary Reviews: Nanomedicine and Nanobiotechnology  
assay, High throughput in vitro micronucleus assay, and γH2AX assay.  ...  The adoption of high throughput screening (HTS) and high content analysis (HCA) for NM toxicity testing allows the testing of numerous materials at different concentrations and on different types of cells  ...  useful as high throughput techniques for NM screening.  ... 
doi:10.1002/wnan.1413 pmid:27273980 pmcid:PMC5215403 fatcat:cyo37xrmsndibcquoldjnlxlnu
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