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Analysis of cell-based RNAi screens
Michael Boutros, Lígia P Brás, Wolfgang Huber
Genome Biol. 2006; 7(7): R66. Published online 2006 July 25. doi: 10.1186/gb-2006-7-7-r66
PMCID:
PMC1779553
Abstract Full Text PDF–655K Supplementary Material
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 Is Cited by the Following 36 Articles in this Archive:
Normalizing for individual cell population context in the analysis of high-content cellular screens
Bettina Knapp, Ilka Rebhan, Anil Kumar, Petr Matula, Narsis A Kiani, Marco Binder, Holger Erfle, Karl Rohr, Roland Eils, Ralf Bartenschlager, Lars Kaderali
BMC Bioinformatics. 2011; 12: 485. Published online 2011 December 20. doi: 10.1186/1471-2105-12-485
PMCID:
PMC3259109
Abstract Full Text PDF–1.4M Supplementary Material
Extracting quantitative genetic interaction phenotypes from matrix combinatorial RNAi
Elin Axelsson, Thomas Sandmann, Thomas Horn, Michael Boutros, Wolfgang Huber , Bernd Fischer
BMC Bioinformatics. 2011; 12: 342. Published online 2011 August 17. doi: 10.1186/1471-2105-12-342
PMCID:
PMC3230910
Abstract Full Text PDF–580K Supplementary Material
Functional Viability Profiles of Breast Cancer
Rachel Brough, Jessica R. Frankum, David Sims, Alan Mackay, Ana M. Mendes-Pereira, Ilirjana Bajrami, Sara Costa-Cabral, Rumana Rafiq, Amar S. Ahmad, Maria Antonietta Cerone, Rachael Natrajan, Rachel Sharpe, Kai-Keen Shiu, Daniel Wetterskog, Konstantine J. Dedes, Maryou B. Lambros, Teeara Rawjee, Spiros Linardopoulos, Jorge S. Reis-Filho, Nicholas C. Turner, Christopher J. Lord, Alan Ashworth
Cancer Discov. Author manuscript; available in PMC 2012 February 1.
Published in final edited form as: Cancer Discov. 2011 August; 1(3): 260–273. doi: 10.1158/2159-8290.CD-11-0107
PMCID:
PMC3188379
Abstract Full Text PDF–4.2M Supplementary Material
Time-Resolved Human Kinome RNAi Screen Identifies a Network Regulating Mitotic-Events as Early Regulators of Cell Proliferation
Jitao David Zhang, Cindy Koerner, Stephanie Bechtel, Christian Bender, Ioanna Keklikoglou, Christian Schmidt, Anja Irsigler, Ute Ernst, Özgür Sahin, Stefan Wiemann, Ulrich Tschulena
PLoS One. 2011; 6(7): e22176. Published online 2011 July 13. doi: 10.1371/journal.pone.0022176
PMCID:
PMC3135613
Abstract Full Text PDF–489K Supplementary Material
Whole genome siRNA cell-based screen links mitochondria to Akt signaling network through uncoupling of electron transport chain
William T. Senapedis, Caleb J. Kennedy, Patrick M. Boyle, Pamela A. Silver
Mol Biol Cell. 2011 May 15; 22(10): 1791–1805. doi: 10.1091/mbc.E10-10-0854
PMCID:
PMC3093329
Abstract Full Text PDF–3.1M Supplementary Material
Role of Endosomes in Simian Virus 40 Entry and Infection
Sabrina Engel, Thomas Heger, Roberta Mancini, Fabian Herzog, Jürgen Kartenbeck, Arnold Hayer, Ari Helenius
J Virol. 2011 May; 85(9): 4198–4211. doi: 10.1128/JVI.02179-10
PMCID:
PMC3126231
Abstract Full Text PDF–5.5M Supplementary Material
HTSanalyzeR: an R/Bioconductor package for integrated network analysis of high-throughput screens
Xin Wang, Camille Terfve, John C. Rose, Florian Markowetz
Bioinformatics. 2011 March 15; 27(6): 879–880. Published online 2011 January 22. doi: 10.1093/bioinformatics/btr028
PMCID:
PMC3051329
Abstract Full Text PDF–133K
RNAi-based screening identifies the Mms22L–Nfkbil2 complex as a novel regulator of DNA replication in human cells
Wojciech Piwko, Michael H Olma, Michael Held, Julien N Bianco, Patrick G A Pedrioli, Kay Hofmann, Philippe Pasero, Daniel W Gerlich, Matthias Peter
EMBO J. 2010 December 15; 29(24): 4210–4222. Published online 2010 November 26. doi: 10.1038/emboj.2010.304
PMCID:
PMC3018799
Abstract Full Text PDF–2.1M Supplementary Material
RNAi Screen Indicates Widespread Biological Function for Human Natural Antisense Transcripts
Mohammad Ali Faghihi, Jannet Kocerha, Farzaneh Modarresi, Pär G. Engström, Alistair M. Chalk, Shaun P. Brothers, Eric Koesema, Georges St. Laurent, III, Claes Wahlestedt
PLoS One. 2010; 5(10): e13177. Published online 2010 October 4. doi: 10.1371/journal.pone.0013177
PMCID:
PMC2949395
Abstract Full Text PDF–1.6M Supplementary Material
A Multi-Parameter, High-Content, High-Throughput Screening Platform to Identify Natural Compounds that Modulate Insulin and Pdx1 Expression
Jessica A. Hill, Marta Szabat, Corinne A. Hoesli, Blair K. Gage, Yu Hsuan C. Yang, David E. Williams, Michael J. Riedel, Dan S. Luciani, Tatyana B. Kalynyak, Kevin Tsai, Ziliang Ao, Raymond J. Andersen, Garth L. Warnock, James M. Piret, Timothy J. Kieffer, James D. Johnson
PLoS One. 2010; 5(9): e12958. Published online 2010 September 23. doi: 10.1371/journal.pone.0012958
PMCID:
PMC2944895
Abstract Full Text PDF–1.4M Supplementary Material
Large-scale data integration framework provides a comprehensive view on glioblastoma multiforme
Kristian Ovaska, Marko Laakso, Saija Haapa-Paananen, Riku Louhimo, Ping Chen, Viljami Aittomäki, Erkka Valo, Javier Núñez-Fontarnau, Ville Rantanen, Sirkku Karinen, Kari Nousiainen, Anna-Maria Lahesmaa-Korpinen, Minna Miettinen, Lilli Saarinen, Pekka Kohonen, Jianmin Wu, Jukka Westermarck, Sampsa Hautaniemi
Genome Med. 2010; 2(9): 65. Published online 2010 September 7. doi: 10.1186/gm186
PMCID:
PMC3092116
Abstract Full Text PDF–1.3M Supplementary Material
Detecting host factors involved in virus infection by observing the clustering of infected cells in siRNA screening images
Apichat Suratanee, Ilka Rebhan, Petr Matula, Anil Kumar, Lars Kaderali, Karl Rohr, Ralf Bartenschlager, Roland Eils, Rainer König
Bioinformatics. 2010 September 15; 26(18): i653–i658. Published online 2010 September 4. doi: 10.1093/bioinformatics/btq398
PMCID:
PMC2935410
Abstract Full Text PDF–338K Supplementary Material
Screensaver: an open source lab information management system (LIMS) for high throughput screening facilities
Andrew N Tolopko, John P Sullivan, Sean D Erickson, David Wrobel, Su L Chiang, Katrina Rudnicki, Stewart Rudnicki, Jennifer Nale, Laura M Selfors, Dara Greenhouse, Jeremy L Muhlich, Caroline E Shamu
BMC Bioinformatics. 2010; 11: 260. Published online 2010 May 18. doi: 10.1186/1471-2105-11-260
PMCID:
PMC3001403
Abstract Full Text PDF–10M
web cellHTS2: A web-application for the analysis of high-throughput screening data
Oliver Pelz, Moritz Gilsdorf, Michael Boutros
BMC Bioinformatics. 2010; 11: 185. Published online 2010 April 12. doi: 10.1186/1471-2105-11-185
PMCID:
PMC3098057
Abstract Full Text PDF–702K
A siRNA Screen of Genes Involved in DNA Repair Identifies Tumour Specific Radiosensitisation by POLQ Knockdown
Geoff S Higgins, Remko Prevo, Yin-Fai Lee, Thomas Helleday, Ruth J Muschel, Steve Taylor, Michio Yoshimura, Ian D Hickson, Eric J Bernhard, W Gillies McKenna
Cancer Res. Author manuscript; available in PMC 2010 October 1.
Published in final edited form as: Cancer Res. 2010 April 1; 70(7): 2984–2993. Published online 2010 March 16. doi: 10.1158/0008-5472.CAN-09-4040
PMCID:
PMC2848966
Abstract Full Text PDF–538K Supplementary Material
Systematic analysis of off-target effects in an RNAi screen reveals microRNAs affecting sensitivity to TRAIL-induced apoptosis
Ian Sudbery, Anton J Enright, Andrew G Fraser, Ian Dunham
BMC Genomics. 2010; 11: 175. Published online 2010 March 15. doi: 10.1186/1471-2164-11-175
PMCID:
PMC2996961
Abstract Full Text PDF–374K Supplementary Material
How to Understand the Cell by Breaking It: Network Analysis of Gene Perturbation Screens
Florian Markowetz
PLoS Comput Biol. 2010 February; 6(2): e1000655. Published online 2010 February 26. doi: 10.1371/journal.pcbi.1000655
PMCID:
PMC2829042
Full Text PDF–323K
Automated microscopy for high-content RNAi screening
Christian Conrad, Daniel W. Gerlich
J Cell Biol. 2010 February 22; 188(4): 453–461. doi: 10.1083/jcb.200910105
PMCID:
PMC2828931
Abstract Full Text PDF–3.0M
Enhanced CellClassifier: a multi-class classification tool for microscopy images
Benjamin Misselwitz, Gerhard Strittmatter, Balamurugan Periaswamy, Markus C Schlumberger, Samuel Rout, Peter Horvath, Karol Kozak, Wolf-Dietrich Hardt
BMC Bioinformatics. 2010; 11: 30. Published online 2010 January 14. doi: 10.1186/1471-2105-11-30
PMCID:
PMC2821321
Abstract Full Text PDF–1.3M Supplementary Material
GenomeRNAi: a database for cell-based RNAi phenotypes. 2009 update
Moritz Gilsdorf, Thomas Horn, Zeynep Arziman, Oliver Pelz, Evgeny Kiner, Michael Boutros
Nucleic Acids Res. 2010 January; 38(Database issue): D448–D452. Published online 2010 January. doi: 10.1093/nar/gkp1038
PMCID:
PMC2808900
Abstract Full Text PDF–3.1M
A global survey identifies novel upstream components of the Ath5 neurogenic network
Marcel Souren, Juan Ramon Martinez-Morales, Panagiota Makri, Beate Wittbrodt, Joachim Wittbrodt
Genome Biol. 2009; 10(9): R92. Published online 2009 September 7. doi: 10.1186/gb-2009-10-9-r92
PMCID:
PMC2768981
Abstract Full Text PDF–5.6M Supplementary Material
Knowledge based identification of essential signaling from genome-scale siRNA experiments
Armand Bankhead, III, Iliana Sach, Chester Ni, Nolwenn LeMeur, Mark Kruger, Marc Ferrer, Robert Gentleman, Carol Rohl
BMC Syst Biol. 2009; 3: 80. Published online 2009 August 5. doi: 10.1186/1752-0509-3-80
PMCID:
PMC2731733
Abstract Full Text PDF–828K
Statistical Methods for Analysis of High-Throughput RNA Interference Screens
Amanda Birmingham, Laura M. Selfors, Thorsten Forster, David Wrobel, Caleb J. Kennedy, Emma Shanks, Javier Santoyo-Lopez, Dara J. Dunican, Aideen Long, Dermot Kelleher, Queta Smith, Roderick L. Beijersbergen, Peter Ghazal, Caroline E. Shamu
Nat Methods. Author manuscript; available in PMC 2010 February 1.
Published in final edited form as: Nat Methods. 2009 August; 6(8): 569–575. doi: 10.1038/nmeth.1351
PMCID:
PMC2789971
Abstract Full Text PDF–680K Supplementary Material
Mapping Identifiers for the Integration of Genomic Datasets with the R/Bioconductor package biomaRt
Steffen Durinck, Paul T. Spellman, Ewan Birney, Wolfgang Huber
Nat Protoc. Author manuscript; available in PMC 2011 August 22.
Published in final edited form as: Nat Protoc. 2009; 4(8): 1184–1191. Published online 2009 July 23. doi: 10.1038/nprot.2009.97
PMCID:
PMC3159387
Abstract Full Text PDF–984K Supplementary Material
A network-based integrative approach to prioritize reliable hits from multiple genome-wide RNAi screens in Drosophila
Li Wang, Zhidong Tu, Fengzhu Sun
BMC Genomics. 2009; 10: 220. Published online 2009 May 12. doi: 10.1186/1471-2164-10-220
PMCID:
PMC2697172
Abstract Full Text PDF–551K Supplementary Material
Dietary flavonoid fisetin induces a forced exit from mitosis by targeting the mitotic spindle checkpoint
Anna-Leena Salmela, Jeroen Pouwels, Asta Varis, Anu M. Kukkonen, Pauliina Toivonen, Pasi K. Halonen, Merja Perälä, Olli Kallioniemi, Gary J. Gorbsky, Marko J. Kallio
Carcinogenesis. 2009 June; 30(6): 1032–1040. Published online 2009 April 24. doi: 10.1093/carcin/bgp101
PMCID:
PMC2691139
Abstract Full Text PDF–862K Supplementary Material
Integrated Functional, Gene Expression and Genomic Analysis for the Identification of Cancer Targets
Elizabeth Iorns, Christopher J. Lord, Anita Grigoriadis, Sarah McDonald, Kerry Fenwick, Alan MacKay, Charles A. Mein, Rachael Natrajan, Kay Savage, Narinder Tamber, Jorge S. Reis-Filho, Nicholas C. Turner, Alan Ashworth
PLoS ONE. 2009; 4(4): e5120. Published online 2009 April 9. doi: 10.1371/journal.pone.0005120
PMCID:
PMC2663812
Abstract Full Text PDF–605K Supplementary Material
PDGF/VEGF signaling controls cell size in Drosophila
David Sims, Peter Duchek, Buzz Baum
Genome Biol. 2009; 10(2): R20. Published online 2009 February 12. doi: 10.1186/gb-2009-10-2-r20
PMCID:
PMC2688285
Abstract Full Text PDF–6.2M Supplementary Material
RNA interference screening demystified
C J Lord, S A Martin, A Ashworth
J Clin Pathol. 2009 March; 62(3): 195–200. Published online 2009 January 6. doi: 10.1136/jcp.2008.058735
PMCID:
PMC2652024
Abstract Full Text PDF–494K
CellProfiler Analyst: data exploration and analysis software for complex image-based screens
Thouis R Jones, In Han Kang, Douglas B Wheeler, Robert A Lindquist, Adam Papallo, David M Sabatini, Polina Golland, Anne E Carpenter
BMC Bioinformatics. 2008; 9: 482. Published online 2008 November 15. doi: 10.1186/1471-2105-9-482
PMCID:
PMC2614436
Abstract Full Text PDF–5.3M Supplementary Material
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