PLA技術原理之參考文獻(2011/3/22更新) 時間: 2011-03-22 05:58:00
Additional related publications of Assay:
1. Paulsson J, Lindh MB, Jarvius M, Puputti M, Nistér M, Nupponen NN, Paulus W, Söderberg O, Dresemann G, von Deimling A, Joensuu H, Ostman A, Hasselblatt M. Prognostic but not predictive role of platelet-derived growth factor receptors in patients with recurrent glioblastoma. Int J Cancer. 2010 Jun 29. [Epub ahead of print]
2. Weibrecht I, Leuchowius KJ, Clausson CM, Conze T, Jarvius M, Howell WM, Kamali-Moghaddam M, Söderberg O. Proximity ligation assays: a recent addition to the proteomics toolbox. Expert Rev Proteomics. 2010 Jun;7(3):401-9.
3. Schlingemann J, Leijon M, Yacoub A, Schlingemann H, Zohari S, Matyi-Tóth A, Kiss I, Holmquist G, Nordengrahn A, Landegren U, Ekström B, Belák S. Novel means of viral antigen identification: improved detection of avian influenza viruses by proximity ligation. J Virol Methods. 2010 Jan;163(1):116-22.
4. Spears M, Bartlett JM. Human epidermal growth factor receptor dimerization analysis in breast cancer diagnosis: potential for improving testing accuracy and treatment selection. Mol Diagn Ther. 2009 Dec 1;13(6):359-65.
5. Söderberg O, Gullberg M, Jarvius M, Ridderstråle K, Leuchowius KJ, Jarvius J, Wester K, Hydbring P, Bahram F, Larsson LG, Landegren U. Direct observation of individual endogenous protein complexes in situ by proximity ligation. Nat. Methods. 2006 Dec;3(12):995-1000.
6. Jarvius J, Melin J, Göransson J, Stenberg J, Fredriksson S, Gonzalez-Rey C, Bertilsson S, Nilsson M. Digital quantification using amplified single-molecule detection. Nat Methods. 2006 Sep;3(9):725-7.
7. Jarvius M, Paulsson J, Weibrecht I, Leuchowius KJ, Andersson AC, Wählby C, Gullberg M, Botling J, Sjöblom T, Markova B, Ostman A, Landegren U, Söderberg O. In situ detection of phosphorylated platelet-derived growth factor receptor beta using a generalized proximity ligation method. Mol. Cell Proteomics, 2007 Sep;6(9):1500-9.

Multiplex PLA:
1. Fredriksson S, Dixon W, Ji H, Koong AC, Mindrinos M, Davis RW: Multiplexed protein detection by proximity ligation for cancer biomarker validation. Nat Methods 2007, 4(4):327-329.
2. Söderberg O, Leuchowius KJ, Kamali-Moghaddam M, Jarvius M, Gustafsdottir S, Schallmeiner E, Gullberg M, Jarvius J, Landegren U: Proximity ligation: a specific and versatile tool for the proteomic era. Genet Eng (N Y) 2007, 28:85-93.

In solution PLA for pathogen detection:
1. Gustafsdottir SM, Nordengrahn A, Fredriksson S, Wallgren P, Rivera E, Schallmeiner E, Merza M, Landegren U: Detection of individual microbial pathogens by proximity ligation Clin Chem 2006, 52(6):1152-1160
2. Gustafsdottir SM, Schallmeiner E, Fredriksson S, Gullberg M, Soderberg O, Jarvius M, Jarvius J, Howell M, Landegren U: Proximity ligation assays for sensitive and specific protein analyses Anal Biochem, 2005, 345(1):2-9
3. Zhu, L, Koistinen, H, Wu, P, Narvanen, A, Schallmeiner, E, Fredriksson, S, Landegren, U & Stenman, U H, A sensitive proximity ligation assay for active PSA Biol Chem, 2006, 387, 769-72

In solution PLA using antibodies:
1. Gullberg, M, Gustafsdottir, S M, Schallmeiner, E, Jarvius, J, Bjarnegard, M, Betsholtz, C, Landegren, U & Fredriksson, S, Cytokine detection by antibody-based proximity ligation Proc Natl Acad Sci U S A, 2004, 101, 8420-4
2. Bjarnegard, M, Enge, M, Norlin, J, Gustafsdottir, S, Fredriksson, S, Abramsson, A, Takemoto, M, Gustafsson, E, Fassler, R & Betsholtz, C, Endothelium-specific ablation of PDGFB leads to pericyte loss and glomerular, cardiac and placental abnormalities Development, 2004, 131, 1847-57
3. Landegren, U, Nilsson, M, Gullberg, M, Soderberg, O, Jarvius, M, Larsson, C & Jarvius, J, Prospects for in situ analyses of individual and complexes of DNA, RNA, and protein molecules with padlock and proximity probes Methods Cell Biol, 2004, 75, 787-97
4. Lindblom, P, Gerhardt, H, Liebner, S, Abramsson, A, Enge, M, Hellstrom, M, Backstrom, G, Fredriksson, S, Landegren, U, Nystrom, H C, Bergstrom, G, Dejana, E, Ostman, A, Lindahl, P & Betsholtz, C, Endothelial PDGF-B retention is required for proper investment of pericytes in the microvessel wall Genes Dev, 2003, 17, 1835-40
5. Rollman, O, Jensen, U B, Ostman, A, Bolund, L, Gustafsdottir, S M & Jensen, T G, Platelet derived growth factor (PDGF) responsive epidermis formed from human keratinocytes transduced with the PDGF beta receptor gene J Invest Dermatol, 2003, 120, 742-9

In solution PLA using aptamers:
1. Fredriksson, S, Gullberg, M, Jarvius, J, Olsson, C, Pietras, K, Gustafsdottir, S M, Ostman, A & Landegren, U, Protein detection using proximity-dependent DNA ligation assays Nat Biotechnol, 2002, 20, 473-7


DNA-Protein interactions:
1. Gustafsdottir SM, Schlingemann J, Rada-Iglesias A, Schallmeiner E, Kamali-Moghaddam M, Wadelius C, Landegren U: In vitro analysis of DNA-protein interactions by proximity ligation. Proc Natl Acad Sci U S A 2007, 104(9):3067-3072.
2. Schallmeiner E, Oksanen E, Ericsson O, Spangberg L, Eriksson S, Stenman UH, Pettersson K, Landegren U: Sensitive protein detection via triple-binder proximity ligation assays. Nat Methods 2007, 4(2):135-137.

Selector Technology
1. Stenberg, J, Dahl, F, Landegren, U & Nilsson, M, PieceMaker: selection of DNA fragments for selector-guided multiplex amplification Nucleic Acids Res, 2005, 33, e72
2. Dahl, F, Stenberg, J, Fredriksson, S, Welch, K, Zhang, M, Nilsson, M, Bicknell, D, Bodmer, WF, Davis, RW & Ji, H Multigene amplification and massively parallel sequencing for cancer mutation discovery Proc Natl Acad Sci USA104, 9387-9392 (2007)
3. Isaksson, M, Stenberg, J, Dahl, F, Thuresson, A-C, Bondeson, M-L & Nilsson, M MLGA - a rapid and cost-efficient assay for gene copy-number analysis Nucleic Acids Res35, e115 (2007)
4. Salmon Hillbertz, NHC, Isaksson, M, Karlsson, EK, Hellmen, E, Rosengren Pilgren, G, Savolainen, P, Wade, CM, von Euler, H, Gustafson, U, Hedhammar, Nilsson, M, Lindblad-Toh, K, Andersson, L & Andersson, G A duplication of FGF3, FGF4, FGF9 and ORAOV1 causes the hair ridge and predisposes to dermoid sinus in Ridgeback dogs Nat Genet39, 1318-1320 (2007)
ProbeMaker Software for oligonucleotide design:
1. Stenberg, J, Nilsson, M & Landegren, U, ProbeMaker: an extensible framework for design of sets of oligonucleotide probes BMC Bioinformatics, 2005, 6:229
DNA amplification and detection
1. Jarvius, J, Melin, J, Goransson, J, Stenberg, J, Fredriksson, S, Gonzalez-Rey, C, Bertilsson, S & Nilsson, M, Digital quantification using amplified single-molecule detection Nat Methods, 2006, 3, 725-7
2. Melin, J, Jarvius, J, Göransson, J & Nilsson, M Homogenous amplified single-molecule detection - Characterization of key parameters Anal Biochem368, 230-238 (2007)
3. Blab, G A, Schmidt, T & Nilsson, M, Homogeneous detection of single rolling circle replication products Anal Chem, 2004, 76, 495-8

Circle-to-Circle amplification:
1. Dahl, F, Baner, J, Gullberg, M, Mendel-Hartvig, M, Landegren, U & Nilsson, M, Circle-to-circle amplification for precise and sensitive DNA analysis Proc Natl Acad Sci U S A, 2004, 101, 4548-53

Padlock Probe Technology
2. Nilsson, M., Dahl, F., Larsson, C., Gullberg, M. & Stenberg, J., Analyzing genes using closing and replicating circles. Trends Biotechnol, 2006, 24, 83-8.
3. Baner, J., Marits, P., Nilsson, M., Winqvist, O. & Landegren, U., Analysis of T-cell receptor V beta gene repertoires after immune stimulation and in malignancy by use of padlock probes and microarrays. Clin Chem, 2005, 51, 768-75.
4. Stenberg, J., Nilsson, M. & Landegren, U., ProbeMaker: an extensible framework for design of sets of oligonucleotide probes. BMC Bioinformatics, 2005, 6, 229.
5. Szemes, M., Bonants, P., de Weerdt, M., Baner, J., Landegren, U. & Schoen, C. D., Diagnostic application of padlock probes--multiplex detection of plant pathogens using universal microarrays. Nucleic Acids Res, 2005, 33, e70.
6. Landegren, U., Nilsson, M., Gullberg, M., Soderberg, O., Jarvius, M., Larsson, C. & Jarvius, J., Prospects for in situ analyses of individual and complexes of DNA, RNA, and protein molecules with padlock and proximity probes. Methods Cell Biol, 2004, 75, 787-97.
7. Baner, J., Isaksson, A., Waldenstrom, E., Jarvius, J., Landegren, U. & Nilsson, M., Parallel gene analysis with allele-specific padlock probes and tag microarrays. Nucleic Acids Res, 2003, 31, e103.
8. Baner, J., Gyarmati, P., Yacoub, A., Hakhverdyan, M., Stenberg, J., Ericsson, O., Nilsson, M., Landegren, U. & Belak, S. Microarray-based molecular detection of Foot-and-mouth disease, Vesicular stomatitis and Swine vesicular disease viruses, using padlock probes. J. Vir. Methods 143, 200-206 (2007).
9. Gyarmati, P., Conze, T., Zohari, S., Leblanc, N., Nilsson, M., Landegren, U., Baner, J. & Belak, S. Simultaneous genotyping of all hemagglutinin and neuraminidase subtypes of avian influenza viruses using padlock probes. J Clin Microbiol In press(2008).Â

In situ Genotyping:
1. Nilsson, M., Krejci, K., Koch, J., Kwiatkowski, M., Gustavsson, P. & Landegren, U., Padlock probes reveal single-nucleotide differences, parent of origin and in situ distribution of centromeric sequences in human chromosomes 13 and 21. Nat Genet, 1997, 16, 252-5.
2. Larsson, C., Koch, J., Nygren, A., Janssen, G., Raap, A. K., Landegren, U. & Nilsson, M., In situ genotyping individual DNA molecules by target-primed rolling-circle amplification of padlock probes. Nat Methods, 2004, 1, 227-32.
3. Antson, D. O., Mendel-Hartvig, M., Landegren, U. & Nilsson, M., PCR-generated padlock probes distinguish homologous chromosomes through quantitative fluorescence analysis. Eur J Hum Genet, 2003, 11, 357-63.
4. Nilsson, M., Lock and roll: single-molecule genotyping in situ using padlock probes and rolling-circle amplification. Histochem Cell Biol, 2006, 126, 159-64.
5. Shaposhnikov, S., Larsson, C., Henriksson, S., Collins, A. & Nilsson, M., Detections of Alu sequences and mtDNA in comets using padlock probes. Mutagenesis, 2006, 21, 243-247.

Inversion probes:
1. Hardenbol, P., Baner, J., Jain, M., Nilsson, M., Namsaraev, E. A., Karlin-Neumann, G. A., Fakhrai-Rad, H., Ronaghi, M., Willis, T. D., Landegren, U. & Davis, R. W., Multiplexed genotyping with sequence-tagged molecular inversion probes. Nat Biotechnol, 2003, 21, 673-8.

Padlock Probes on RNA:
1. Nilsson, M., Antson, D. O., Barbany, G. & Landegren, U., RNA-templated DNA ligation for transcript analysis. Nucleic Acids Res, 2001, 29, 578-81.
2. Nilsson, M., Barbany, G., Antson, D. O., Gertow, K. & Landegren, U., Enhanced detection and distinction of RNA by enzymatic probe ligation. Nat Biotechnol, 2000, 18, 791-3.

Padlock Probes and Rolling Circle Amplification:
1. Baner, J., Nilsson, M., Mendel-Hartvig, M. & Landegren, U., Signal amplification of padlock probes by rolling circle replication. Nucleic Acids Res, 1998, 26, 5073-8.
2. Nilsson, M., Gullberg, M., Dahl, F., Szuhai, K. & Raap, A.K. Real-time monitoring of rolling-circle amplification using a modified molecular beacon design. Nucleic Acids Res. 30, E66 (2002).

Original Paper on Padlock Probes:
1. Nilsson, M., Malmgren, H., Samiotaki, M., Kwiatkowski, M., Chowdhary, B. P. & Landegren, U., Padlock probes: circularizing oligonucleotides for localized DNA detection. Science, 1994, 265, 2085-8.