{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,11]],"date-time":"2025-11-11T12:55:29Z","timestamp":1762865729700,"version":"3.38.0"},"reference-count":44,"publisher":"Oxford University Press (OUP)","issue":"18","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2220,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: Detecting human proteins that are involved in virus entry and replication is facilitated by modern high-throughput RNAi screening technology. However, hit lists from different laboratories have shown only little consistency. This may be caused by not only experimental discrepancies, but also not fully explored possibilities of the data analysis. We wanted to improve reliability of such screens by combining a population analysis of infected cells with an established dye intensity readout.<\/jats:p><jats:p>Results: Viral infection is mainly spread by cell\u2013cell contacts and clustering of infected cells can be observed during spreading of the infection in situ and in vivo. We employed this clustering feature to define knockdowns which harm viral infection efficiency of human Hepatitis C Virus. Images of knocked down cells for 719 human kinase genes were analyzed with an established point pattern analysis method (Ripley's K-function) to detect knockdowns in which virally infected cells did not show any clustering and therefore were hindered to spread their infection to their neighboring cells. The results were compared with a statistical analysis using a common intensity readout of the GFP-expressing viruses and a luciferase-based secondary screen yielding five promising host factors which may suit as potential targets for drug therapy.<\/jats:p><jats:p>Conclusion: We report of an alternative method for high-throughput imaging methods to detect host factors being relevant for the infection efficiency of viruses. The method is generic and has the potential to be used for a large variety of different viruses and treatments being screened by imaging techniques.<\/jats:p><jats:p>Contact: \u00a0r.eils@dkfz.de; r.koenig@dkfz.de<\/jats:p><jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq398","type":"journal-article","created":{"date-parts":[[2010,9,7]],"date-time":"2010-09-07T17:41:46Z","timestamp":1283881306000},"page":"i653-i658","source":"Crossref","is-referenced-by-count":15,"title":["Detecting host factors involved in virus infection by observing the clustering of infected cells in siRNA screening images"],"prefix":"10.1093","volume":"26","author":[{"given":"Apichat","family":"Suratanee","sequence":"first","affiliation":[{"name":"1 Department of Bioinformatics and Functional Genomics, Institute of Pharmacy and Molecular Biotechnology, Bioquant, University of Heidelberg, INF 267, 2Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), INF 280, 3The Department for Infectious Diseases, Molecular Virology, University of Heidelberg, INF 345 and 4Viroquant Research Group Modeling, Bioquant, University of Heidelberg, INF 267, 69120 Heidelberg, Germany"},{"name":"1 Department of Bioinformatics and Functional Genomics, Institute of Pharmacy and Molecular Biotechnology, Bioquant, University of Heidelberg, INF 267, 2Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), INF 280, 3The Department for Infectious Diseases, Molecular Virology, University of Heidelberg, INF 345 and 4Viroquant Research Group Modeling, Bioquant, University of Heidelberg, INF 267, 69120 Heidelberg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ilka","family":"Rebhan","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics and Functional Genomics, Institute of Pharmacy and Molecular Biotechnology, Bioquant, University of Heidelberg, INF 267, 2Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), INF 280, 3The Department for Infectious Diseases, Molecular Virology, University of Heidelberg, INF 345 and 4Viroquant Research Group Modeling, Bioquant, University of Heidelberg, INF 267, 69120 Heidelberg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Petr","family":"Matula","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics and Functional Genomics, Institute of Pharmacy and Molecular Biotechnology, Bioquant, University of Heidelberg, INF 267, 2Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), INF 280, 3The Department for Infectious Diseases, Molecular Virology, University of Heidelberg, INF 345 and 4Viroquant Research Group Modeling, Bioquant, University of Heidelberg, INF 267, 69120 Heidelberg, Germany"},{"name":"1 Department of Bioinformatics and Functional Genomics, Institute of Pharmacy and Molecular Biotechnology, Bioquant, University of Heidelberg, INF 267, 2Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), INF 280, 3The Department for Infectious Diseases, Molecular Virology, University of Heidelberg, INF 345 and 4Viroquant Research Group Modeling, Bioquant, University of Heidelberg, INF 267, 69120 Heidelberg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anil","family":"Kumar","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics and Functional Genomics, Institute of Pharmacy and Molecular Biotechnology, Bioquant, University of Heidelberg, INF 267, 2Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), INF 280, 3The Department for Infectious Diseases, Molecular Virology, University of Heidelberg, INF 345 and 4Viroquant Research Group Modeling, Bioquant, University of Heidelberg, INF 267, 69120 Heidelberg, 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Diseases, Molecular Virology, University of Heidelberg, INF 345 and 4Viroquant Research Group Modeling, Bioquant, University of Heidelberg, INF 267, 69120 Heidelberg, Germany"},{"name":"1 Department of Bioinformatics and Functional Genomics, Institute of Pharmacy and Molecular Biotechnology, Bioquant, University of Heidelberg, INF 267, 2Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), INF 280, 3The Department for Infectious Diseases, Molecular Virology, University of Heidelberg, INF 345 and 4Viroquant Research Group Modeling, Bioquant, University of Heidelberg, INF 267, 69120 Heidelberg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ralf","family":"Bartenschlager","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics and Functional Genomics, Institute of Pharmacy and Molecular Biotechnology, Bioquant, University of Heidelberg, INF 267, 2Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), INF 280, 3The Department for Infectious Diseases, Molecular Virology, University of Heidelberg, INF 345 and 4Viroquant Research Group Modeling, Bioquant, University of Heidelberg, INF 267, 69120 Heidelberg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Roland","family":"Eils","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics and Functional Genomics, Institute of Pharmacy and Molecular Biotechnology, Bioquant, University of Heidelberg, INF 267, 2Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), INF 280, 3The Department for Infectious Diseases, Molecular Virology, University of Heidelberg, INF 345 and 4Viroquant Research Group Modeling, Bioquant, University of Heidelberg, INF 267, 69120 Heidelberg, Germany"},{"name":"1 Department of Bioinformatics and Functional Genomics, Institute of Pharmacy and Molecular Biotechnology, Bioquant, University of Heidelberg, INF 267, 2Division of Theoretical 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