Antiviral stratagems against HIV-1 using RNA interference (RNAi) technology

Evolutionary Bioinformatics

Volumn 2013, Issue 9, 2013, Pages 203-213

  Vlachakis, Dimitrios ^a   Tsiliki, Georgia ^a   Pavlopoulou, Athanasia ^a   Roubelakis, Maria G ^a,b   Champeris Tsaniras, Spyridon ^c   Kossida, Sophia ^a  

^a BIOMEDICAL RESEARCH FOUNDATION   (Greece)

^b UNIVERSITY OF ATHENS MEDICAL SCHOOL   (Greece)

^c UNIVERSITY OF PATRAS   (Greece)

Author keywords

Antiviral therapy; HIV 1; MiRNA; RNA interference (RNAi); RNAi screens

Indexed keywords

ANTIRETROVIRUS AGENT; ANTISENSE OLIGONUCLEOTIDE; APTAMER; COMPLEMENTARY RNA; DOUBLE STRANDED DNA; HUMAN IMMUNODEFICIENCY VIRUS VACCINE; LENTIVIRUS VECTOR; MESSENGER RNA; MICRORNA; MICRORNA 125B; MICRORNA 150; MICRORNA 17 P; MICRORNA 223; MICRORNA 28; MICRORNA 29A; MICRORNA 382; NANOPARTICLE; SHORT HAIRPIN RNA; SINGLE STRANDED RNA; SMALL INTERFERING RNA; UNCLASSIFIED DRUG; VIRUS RNA;

ACQUIRED IMMUNE DEFICIENCY SYNDROME; ALGORITHM; BIOINFORMATICS; BIOSTATISTICS; BIOTECHNOLOGY; CD4+ T LYMPHOCYTE; CLINICAL PROTOCOL; DIZZINESS; DRUG DELIVERY SYSTEM; DRUG RESEARCH; HIGH THROUGHPUT SCREENING; HIGHLY ACTIVE ANTIRETROVIRAL THERAPY; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS 1 INFECTION; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; LIFE CYCLE; LIPODYSTROPHY; MICROBIAL ACTIVITY; MIGRAINE; MOLECULAR WEIGHT; NONHUMAN; REVIEW; RNA INTERFERENCE; RNA SEQUENCE; T CELL DEPLETION; TOXIC HEPATITIS; VIRAL GENETICS; VIROGENESIS; VIRUS CELL INTERACTION; VIRUS INHIBITION; VIRUS MUTANT; VIRUS REPLICATION; VIRUS RESISTANCE;

EID: 84878076945     PISSN: 11769343     EISSN: None     Source Type: Journal    
DOI: 10.4137/EBO.S11412     Document Type: Review

References (124)

1. WHO, UNAIDS & UNICEF. Global HIV/AIDS Response: Epidemic update and health sector progress towards Universal Access 2011. [Progress Report].
2. ter Hofstede HJ, Burger DM, Koopmans PP. Antiretroviral therapy in HIV patients: aspects of metabolic complications and mitochondrial toxicity. Neth J Med. 2003;61(12):393-403.
3. Rambaut A, Posada D, Crandall KA, Holmes EC. The causes and consequences of HIV evolution. Nat Rev Genet. 2004;5(1):52-61.
4. Hu WS, Pathak VK. Design of retroviral vectors and helper cells for gene therapy. Pharmacol Rev. 2000;52(4):493-511.
5. Porth CM. Essentials of Pathophysiology: Concepts of Altered Health States, 3rd ed. Philadelphia, PA: Lippincott Williams & Wilkins; 2010.
6. Levy JA. HIV and the Pathogenesis of AIDS, 3rd ed. Hoboken, NJ: Wiley-Blackwell; 2007.
7. Skripkin E, Paillart JC, Marquet R, Ehresmann B, Ehresmann C. Identification of the primary site of the human immunodeficiency virus type 1 RNA dimerization in vitro. Proc Natl Acad Sci U S A. 1994;91(11):4945-9.
8. St Louis DC, Gotte D, Sanders-Buell E, et al. Infectious molecular clones with the nonhomologous dimer initiation sequences found in different subtypes of human immunodeficiency virus type 1 can recombine and initiate a spreading infection in vitro. J Virol. 1998;72(5):3991-8.
9. Rossi JJ. The application of ribozymes to HIV infection. Curr Opin Mol Ther. 1999;1(3):316-22.
10. Browning CM, Cagnon L, Good PD, Rossi J, Engelke DR, Markovitz DM. Potent inhibition of human immunodeficiency virus type 1 (HIV-1) gene expression and virus production by an HIV-2 tat activation-response RNA decoy. J Virol. 1999;73(6):5191-5.
11. IAVI. Database of AIDS Vaccine Candidates in Clinical Trials. http://www.iavireport.org/Trials-Database/Pages/default.aspx.
12. Brass AL, Dykxhoorn DM, Benita Y, et al. Identification of host proteins required for HIV infection through a functional genomic screen. Science. 2008;319(5865):921-6.
13. Zhou H, Xu M, Huang Q, et al. Genome-scale RNAi screen for host factors required for HIV replication. Cell Host Microbe. 2008;4(5):495-504.
14. Leuschner PJ, Ameres SL, Kueng S, Martinez J. Cleavage of the siRNA passenger strand during RISC assembly in human cells. EMBO Rep. 2006;7(3):314-20.
15. Jinek M, Doudna JA. A three-dimensional view of the molecular machinery of RNA interference. Nature. 2009;457(7228):405-12.
16. Dykxhoorn DM, Novina CD, Sharp PA. Killing the messenger: short RNAs that silence gene expression. Nat Rev Mol Cell Biol. 2003;4(6):457-67.
17. Yu JY, DeRuiter SL, Turner DL. RNA interference by expression of short-interfering RNAs and hairpin RNAs in mammalian cells. Proc Natl Acad Sci U S A. 2002;99(9):6047-52.
18. Brummelkamp TR, Bernards R, Agami R. A system for stable expression of short interfering RNAs in mammalian cells. Science. 2002; 296(5567):550-3.
19. Siomi H, Siomi MC. On the road to reading the RNA-interference code. Nature. 2009;457(7228):396-404.
20. Klase Z, Houzet L, Jeang KT. MicroRNAs and HIV-1: complex interactions. J Biol Chem. 30 2012;287(49):40884-90.
21. Witwer KW, Watson AK, Blankson JN, Clements JE. Relationships of PBMC microRNA expression, plasma viral load, and CD4+ T-cell count in HIV-1-infected elite suppressors and viremic patients. Retrovirology. 2012;9:5.
22. Weiss B. Antisense Oligodeoxynucleotides and Antisense RNA: Novel Pharmacological and Therapeutic Agents. Boca Raton, FL: CRC Press; 1997.
23. Corbeau P. Interfering RNA and HIV: reciprocal interferences. PLoS Pathog. 2008;4(9):e1000162.
24. Houzet L, Klase Z, Yeung ML, et al. The extent of sequence complementarity correlates with the potency of cellular miRNA-mediated restriction of HIV-1. Nucleic Acids Res. 2012;40(22):11684-96.
25. Klase Z, Kale P, Winograd R, et al. HIV-1 TAR element is processed by Dicer to yield a viral micro-RNA involved in chromatin remodeling of the viral LTR. BMC Mol Biol. 2007;8:63.
26. Ouellet DL, Plante I, Landry P, et al. Identification of functional microRNAs released through asymmetrical processing of HIV-1 TAR element. Nucleic Acids Res. 2008;36(7):2353-65.
27. Klase Z, Winograd R, Davis J, et al. HIV-1 TAR miRNA protects against apoptosis by altering cellular gene expression. Retrovirology. 2009;6:18.
28. Omoto S, Fujii YR. Regulation of human immunodeficiency virus 1 transcription by nef microRNA. J Gen Virol. 2005;86(Pt 3):751-5.
29. Omoto S, Ito M, Tsutsumi Y, et al. HIV-1 nef suppression by virally encoded microRNA. Retrovirology. 2004;1:44.
30. Hariharan M, Scaria V, Pillai B, Brahmachari SK. Targets for human encoded microRNAs in HIV genes. Biochem Biophys Res Commun. 2005;337(4):1214-8.
31. Nathans R, Chu CY, Serquina AK, Lu CC, Cao H, Rana TM. Cellular microRNA and P bodies modulate host-HIV-1 interactions. Mol Cell. 2009; 34(6):696-709.
32. Kulkarni M, Ozgur S, Stoecklin G. On track with P-bodies. Biochem Soc Trans. 2010;38(Pt 1):242-51.
33. Huang J, Wang F, Argyris E, et al. Cellular microRNAs contribute to HIV-1 latency in resting primary CD4+ T lymphocytes. Nat Med. 2007;13(10): 1241-7.
34. Bennasser Y, Le SY, Yeung ML, Jeang KT. HIV-1 encoded candidate micro-RNAs and their cellular targets. Retrovirology. 2004;1:43.
35. Bennasser Y, Le SY, Benkirane M, Jeang KT. Evidence that HIV-1 encodes an siRNA and a suppressor of RNA silencing. Immunity. 2005;22(5):607-19.
36. Qian S, Zhong X, Yu L, Ding B, de Haan P, Boris-Lawrie K. HIV-1 Tat RNA silencing suppressor activity is conserved across kingdoms and counteracts translational repression of HIV-1. Proc Natl Acad Sci U S A. 2009;106(2):605-10.
37. Bennasser Y, Jeang KT. HIV-1 Tat interaction with Dicer: requirement for RNA. Retrovirology. 2006;3:95.
38. Liu X, Houzet L, Jeang KT. Tombusvirus P19 RNA silencing suppressor (RSS) activity in mammalian cells correlates with charged amino acids that contribute to direct RNA-binding. Cell Biosci. 6 2012;2(1):41.
39. Bennasser Y, Yeung ML, Jeang KT. HIV-1 TAR RNA subverts RNA interference in transfected cells through sequestration of TAR RNA-binding protein, TRBP. J Biol Chem. 2006;281(38):27674-8.
40. Ludwig LB. RNA silencing and HIV: a hypothesis for the etiology of the severe combined immunodeficiency induced by the virus. Retrovirology. 2008;5:79.
41. Triboulet R, Mari B, Lin YL, et al. Suppression of microRNA-silencing pathway by HIV-1 during virus replication. Science. 2007;315(5818):1579-82.
42. Benkirane M, Chun RF, Xiao H, et al. Activation of integrated provirus requires histone acetyltransferase. p300 and P/CAF are coactivators for HIV-1 Tat. J Biol Chem. 1998;273(38):24898-905.
43. Zhang HS, Wu TC, Sang WW, Ruan Z. MiR-217 is involved in Tat-induced HIV-1 long terminal repeat (LTR) transactivation by down-regulation of SIRT1. Biochim Biophys Acta. 2012;1823(5):1017-23.
44. Vaquero A, Scher M, Lee D, Erdjument-Bromage H, Tempst P, Reinberg D. Human SirT1 interacts with histone H1 and promotes formation of facultative heterochromatin. Mol Cell. 2004;16(1):93-105.
45. Chiang K, Rice AP. Mini ways to stop a virus: microRNAs and HIV-1 replication. Future Virol. 2011;6(2):209-21.
46. Haasnoot J, Westerhout EM, Berkhout B. RNA interference against viruses: strike and counterstrike. Nat Biotechnol. 2007;25(12):1435-43.
47. Capodici J, Kariko K, Weissman D. Inhibition of HIV-1 infection by small interfering RNA-mediated RNA interference. J Immunol. 2002; 169(9):5196-201.
48. Coburn GA, Cullen BR. Potent and specific inhibition of human immunodeficiency virus type 1 replication by RNA interference. J Virol. 2002;76(18): 9225-31.
49. Jacque JM, Triques K, Stevenson M. Modulation of HIV-1 replication by RNA interference. Nature. 2002;418(6896):435-8.
50. Lee NS, Dohjima T, Bauer G, et al. Expression of small interfering RNAs targeted against HIV-1 rev transcripts in human cells. Nat Biotechnol. 2002;20(5):500-5.
51. Martinez MA, Clotet B, Esté JA. RNA interference of HIV replication. Trends Immunol. 2002;23(12):559-61.
52. Novina CD, Murray MF, Dykxhoorn DM, Beresford PJ, Riess J, Lee SK, et al. siRNA-directed inhibition of HIV-1 infection. Nat Med. Jul 8, 2002:681-6.
53. Krützfeldt J, Rajewsky N, Braich R, et al. Silencing of microRNAs in vivo with 'antagomirs'. Nature. 2005;438(7068):685-9.
54. Czech MP. MicroRNAs as therapeutic targets. N Engl J Med. 2006;354(11): 1194-5.
55. Scherr M, Venturini L, Battmer K, et al. Lentivirus-mediated antagomir expression for specific inhibition of miRNA function. Nucleic Acids Res. 2007;35(22):e149.
56. Grimm D, Streetz KL, Jopling CL, et al. Fatality in mice due to oversaturation of cellular microRNA/short hairpin RNA pathways. Nature. 2006;441(7092):537-41.
57. Song E, Zhu P, Lee SK, et al. Antibody mediated in vivo delivery of small interfering RNAs via cell-surface receptors. Nat Biotechnol. 2005;23(6): 709-17.
58. Das AT, Berkhout B. HIV-1 evolution: frustrating therapies, but disclosing molecular mechanisms. Philos Trans R Soc Lond B Biol Sci. 2010; 365(1548):1965-73.
59. Boden D, Pusch O, Lee F, Tucker L, Ramratnam B. Human immunodeficiency virus type 1 escape from RNA interference. J Virol. 2003;77(21):11531-5.
60. Das AT, Brummelkamp TR, Westerhout EM, et al. Human immunodeficiency virus type 1 escapes from RNA interference-mediated inhibition. J Virol. 2004;78(5):2601-5.
61. Sabariegos R, Giménez-Barcons M, Tàpia N, Clotet B, Martínez MA. Sequence homology required by human immunodeficiency virus type 1 to escape from short interfering RNAs. J Virol. 2006;80(2):571-7.
62. Westerhout EM, Ooms M, Vink M, Das AT, Berkhout B. HIV-1 can escape from RNA interference by evolving an alternative structure in its RNA genome. Nucleic Acids Res. 2005;33(2):796-804.
63. Anderson J, Akkina R. CXCR4 and CCR5 shRNA transgenic CD34+ cell derived macrophages are functionally normal and resist HIV-1 infection. Retrovirology. 2005;2:53.
64. Kim SS, Peer D, Kumar P, et al. RNAi-mediated CCR5 silencing by LFA-1-targeted nanoparticles prevents HIV infection in BLT mice. Mol Ther. 2010;18(2):370-6.
65. Kumar P, Ban HS, Kim SS, et al. T cell-specific siRNA delivery suppresses HIV-1 infection in humanized mice. Cell. 2008;134(4):577-86.
66. Liu S, Asparuhova M, Brondani V, Ziekau I, Klimkait T, Schümperli D. Inhibition of HIV-1 multiplication by antisense U7 snRNAs and siRNAs targeting cyclophilin A. Nucleic Acids Res. 2004;32:3752-9.
67. Sugiyama R, Habu Y, Ohnari A, Miyano-Kurosaki N, Takaku H. RNA interference targeted to the conserved dimerization initiation site (DIS) of HIV-1 restricts virus escape mutation. J Biochem. 2009;146(4):481-9.
68. Berkhout B. RNA interference as an antiviral approach: targeting HIV-1. Curr Opin Mol Ther. 2004;6(2):141-5.
69. Haasnoot PC, Cupac D, Berkhout B. Inhibition of virus replication by RNA interference. J Biomed Sci. 2003;10(6 Pt 1):607-16.
70. Knoepfel SA, Centlivre M, Liu YP, Boutimah F, Berkhout B. Selection of RNAi-based inhibitors for anti-HIV gene therapy. World Journal of Virology. 2012;1(3):79-90.
71. Liu YP, Haasnoot J, ter Brake O, Berkhout B, Konstantinova P. Inhibition of HIV-1 by multiple siRNAs expressed from a single microRNA polycistron. Nucleic Acids Res. 2008;36(9):2811-24.
72. ter Brake O, Konstantinova P, Ceylan M, Berkhout B. Silencing of HIV-1 with RNA interference: a multiple shRNA approach. Mol Ther. 2006;14(6):883-92.
73. Chung J, Zhang J, Li H, Ouellet D, Digiusto DL, Rossi JJ. Endogenous MCM7 microRNA cluster as a novel platform to multiplex small interfering and nucleolar RNAs for combinational HIV-1 gene therapy. Hum Gene Ther. 2012;23(11):1200-8.
74. Zhang T, Cheng T, Wei L, et al. Efficient inhibition of HIV-1 replication by an artificial polycistronic miRNA construct. Virol J. 2012;9:118.
75. Wheeler LA, Trifonova R, Vrbanac V, et al. Inhibition of HIV transmission in human cervicovaginal explants and humanized mice using CD4 aptamer-siRNA chimeras. J Clin Invest. 2011;121(6):2401-12.
76. Zhou J, Neff CP, Swiderski P, et al. Functional in vivo delivery of multiplexed anti-HIV-1 siRNAs via a chemically synthesized aptamer with a sticky bridge. Mol Ther. 2013;21(1):192-200.
77. Zhou J, Neff CP, Liu X, et al. Systemic administration of combinatorial dsiRNAs via nanoparticles efficiently suppresses HIV-1 infection in humanized mice. Mol Ther. 2011;19(12):2228-38.
78. Zeller SJ, Kumar P. RNA-based gene therapy for the treatment and prevention of HIV: from bench to bedside. Yale J Biol Med. 2011;84(3):301-9.
79. DiGiusto DL, Krishnan A, Li L, et al. RNA-based gene therapy for HIV with lentiviral vector-modified CD34(+) cells in patients undergoing transplantation for AIDS-related lymphoma. Sci Transl Med. 2010;2(36):36-43.
80. Levine BL, Humeau LM, Boyer J, et al. Gene transfer in humans using a conditionally replicating lentiviral vector. Proc Natl Acad Sci U S A. 2006;103(46):17372-7.
81. Amado RG, Mitsuyasu RT, Rosenblatt JD, et al. Anti-human immunodeficiency virus hematopoietic progenitor cell-delivered ribozyme in a phase I study: myeloid and lymphoid reconstitution in human immunodeficiency virus type-1-infected patients. Hum Gene Ther. 2004;15(3):251-62.
82. Kim VN. MicroRNA precursors in motion: exportin-5 mediates their nuclear export. Trends Cell Biol. 2004;14(4):156-9.
83. Zeng Y, Cullen BR. Structural requirements for pre-microRNA binding and nuclear export by Exportin 5. Nucleic Acids Res. 2004;32(16):4776-85.
84. Lagos-Quintana M, Rauhut R, Lendeckel W, Tuschl T. Identification of novel genes coding for small expressed RNAs. Science. 2001;294(5543):853-8.
85. Lau NC, Lim LP, Weinstein EG, Bartel DP. An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science. 2001;294:858-62.
86. Bartel DP. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell. 2004;116(2):281-97.
87. Lim LP, Glasner ME, Yekta S, Burge CB, Bartel DP. Vertebrate microRNA genes. Science. 2003;299(5612):1540.
88. Lim LP, Lau NC, Weinstein EG, et al. The microRNAs of Caenorhabditis elegans. Genes Dev. 2003;17(8):9911008.
89. Wang X, Zhang J, Li F, et al. MicroRNA identification based on sequence and structure alignment. Bioinformatics. 2005;21(18):3610-4.
90. Grad Y, Aach J, Hayes GD, et al. Computational and experimental identification of C. elegans microRNAs. Mol Cell. 2003;11(5):1253-63.
91. Lai EC, Tomancak P, Williams RW, Rubin GM. Computational identification of Drosophila microRNA genes. Genome Biol. 2003;4(7):R42.
92. Bentwich I, Avniel A, Karov Y, et al. Identification of hundreds of conserved and nonconserved human microRNAs. Nat Genet. 2005;37(7):766-70.
93. Thomassen GO, Røsok O, Rognes T. Computational prediction of microRNAs encoded in viral and other genomes. J Biomed Biotechnol. 2006; 2006(4):95270.
94. Xue C, Li F, He T, Liu GP, Li Y, Zhang X. Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine. BMC Bioinformatics. 2005;6:310.
95. Kumar S, Ansari FA, Scaria V. Prediction of viral microRNA precursors based on human microRNA precursor sequence and structural features. Virol J. 2009;6:129.
96. Sullivan CS, Grundhoff AT, Tevethia S, Pipas JM, Ganem D. SV40-encoded microRNAs regulate viral gene expression and reduce susceptibility to cytotoxic T cells. Nature. 2005;435(7042):682-6.
97. Hofacker IL. Vienna RNA secondary structure server. Nucleic Acids Res. 2003;31(13):3429-31.
98. Lindow M, Gorodkin J. Principles and limitations of computational microRNA gene and target finding. DNA Cell Biol. 2007;26(5):339-51.
99. Min H, Yoon S. Got target? Computational methods for microRNA target prediction and their extension. Exp Mol Med. 2010;42(4):233-44.
100. Enright AJ, John B, Gaul U, Tuschl T, Sander C, Marks DS. MicroRNA targets in Drosophila. Genome Biol. 2003;5(1):R1.
101. John B, Enright AJ, Aravin A, Tuschl T, Sander C, Marks DS. Human MicroRNA targets. PLoS Biol. 2004;2(11):e363.
102. Lewis BP, Shih IH, Jones-Rhoades MW, Bartel DP, Burge CB. Prediction of mammalian microRNA targets. Cell. 2003;115(7):787-98.
103. Grun D, Wang YL, Langenberger D, Gunsalus KC, Rajewsky N. microRNA target predictions across seven Drosophila species and comparison to mammalian targets. PLoS Comput Biol. 2005;1(1):e13.
104. Krek A, Grün D, Poy MN, et al. Combinatorial microRNA target predictions. Nat Genet. 2005;37(5):495-500.
105. Krüger J, Rehmsmeier M. RNAhybrid: microRNA target prediction easy, fast and flexible. Nucleic Acids Res. 2006;34(Web Server Issue):W451-4.
106. Rehmsmeier M, Steffen P, Hochsmann M, Giegerich R. Fast and effective prediction of microRNA/target duplexes. RNA. 2004;10(10):1507-17.
107. Kertesz M, Iovino N, Unnerstall U, Gaul U, Segal E. The role of site accessibility in microRNA target recognition. Nat Genet. 2007;39(10):1278-84.
108. Birmingham A, Selfors LM, Forster T, et al. Statistical methods for analysis of high-throughput RNA interference screens. Nat Methods. 2009;6(8):569-75.
109. Echeverri CJ, Perrimon N. High-throughput RNAi screening in cultured cells: a user's guide. Nat Rev Genet. 2006;7(5):373-84.
110. Gordon EJ. Small-molecule screening: it takes a village. ACS Chem Biol. 2007;2(1):9-16.
111. Rieber N, Knapp B, Eils R, Kaderali L. RNAither, an automated pipeline for the statistical analysis of high-throughput RNAi screens. Bioinformatics. 2009;25(5):678-9.
112. Mohr S, Bakal C, Perrimon N. Genomic screening with RNAi: results and challenges. Annu Rev Biochem. 2010;79:37-64.
113. Zhang XD, Ferrer M, Espeseth AS, et al. The use of strictly standardized mean difference for hit selection in primary RNA interference high-throughput screening experiments. J Biomol Screen. 2007;12(4):497-509.
114. Buehler E, Khan AA, Marine S, et al. siRNA off-target effects in genome-wide screens identify signaling pathway members. Sci Rep. 2012;2:428.
115. Han L, Wang Y, Bryant SH. Developing and validating predictive decision tree models from mining chemical structural fingerprints and high-throughput screening data in PubChem. BMC Bioinformatics. 2008;9:401.
116. Klekota J, Roth FP. Chemical substructures that enrich for biological activity. Bioinformatics. 2008;24(21):2518-25.
117. Mohr J, Jain B, Sutter A, et al. A maximum common subgraph kernel method for predicting the chromosome aberration test. J Chem Inf Model. 2010;50(10):1821-38.
118. Rosenbaum L, Hinselmann G, Jahn A, Zell A. Interpreting linear support vector machine models with heat map molecule coloring. J Cheminform. 2011;3(1):11.
119. Gonzalez O, Zimmer R. Contextual analysis of RNAi-based functional screens using interaction networks. Bioinformatics. 2011;27(19):2707-13.
120. Walter T, Held M, Neumann B, et al. Automatic identification and clustering of chromosome phenotypes in a genome wide RNAi screen by time-lapse imaging. J Struct Biol. 2010;170(1):1-9.
121. Noble WS. How does multiple testing correction work? Nat Biotechnol. 2009;27(12):1135-7.
122. Zhang XD, Kuan PF, Ferrer M, et al. Hit selection with false discovery rate control in genome-scale RNAi screens. Nucleic Acids Res. 2008;36(14): 4667-79.
123. Zhang XD, Marine SD, Ferrer M. Error rates and powers in genome-scale RNAi screens. J Biomol Screen. 2009;14(3):230-8.
124. Pan WJ, Chen CW, Chu YW. siPRED: Predicting siRNA efficacy using various characteristic methods. PLoS One. 2011;6(11):e27602.