Efficiency of DNA replication in the polymerase chain reaction
Open accessAbstract
A detailed quantitative kinetic model for the polymerase chain reaction (PCR) is developed, which allows us to predict the probability of replication of a DNA molecule in terms of the physical parameters involved in the system. The important issue of the determination of the number of PCR cycles during which this probability can be considered to be a constant is solved within the framework of the model. New phenomena of multimodality and scaling behavior in the distribution of the number of molecules after a given number of PCR cycles are presented. The relevance of the model for quantitative PCR is discussed, and a novel quantitative PCR technique is proposed.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
PCR is an exponential process, so small random variations early on in amplification can have a large impact on distribution.
“PCR is an exponential process, so small random variations early on in amplification can have a large impact on distribution18–24.”
From Quantifying Molecular Bias in DNA Data Storage (2019) · cites this paper as [19]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Molecular Cloning: A Laboratory Manual
Sambrook, J., Fritsch, E., & Maniatis, T. (1989) · UCLA - Biblioteca de Ciencias de la Salud · Cited by 133,589 · see citing works
Molecular cloning: A laboratory manual
Deininger, P. L. (1990) · Analytical Biochemistry · doi:10.1016/0003-2697(90)90595-z · Cited by 84,684 · see citing works
An introduction to probability theory and its applications
(1958) · Journal of the Franklin Institute · doi:10.1016/0016-0032(58)90688-4 · Cited by 29,620 · see citing works
Stochastic Processes in Physics and Chemistry
(2007) · Elsevier eBooks · doi:10.1016/b978-0-444-52965-7.x5000-4 · Cited by 9,070 · see citing works
An Introduction to Probability Theory and Its Applications.
Bharucha-Reid, A. T., & Feller, W. (1967) · American Mathematical Monthly · doi:10.2307/2314609 · Cited by 6,180 · see citing works
[21] Specific synthesis of DNA in vitro via a polymerase-catalyzed chain reaction
Mullis, K. B., & Faloona, F. (1987) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/0076-6879(87)55023-6 · Cited by 5,705 · see citing works
Molecular Computation of Solutions to Combinatorial Problems
Adleman, L. M. (1994) · Science · doi:10.1126/science.7973651 · Cited by 4,474 · see citing works
The Theory of Branching Processes
Ney, P. E., & Harris, T. E. (1965) · Technometrics · doi:10.2307/1266137 · Cited by 2,460 · see citing works
The Theory of Branching Processes
Harris, T. E. (1963) · Springer eBooks · doi:10.1007/978-3-642-51866-9 · Cited by 2,056 · see citing works
Athreya, K. B., & Ney, P. E. (1972) · Springer eBooks · doi:10.1007/978-3-642-65371-1 · Cited by 1,676 · see citing works
Gilliland, G. D., Perrin, S., Blanchard, K. L., & Bunn, H. F. (1990) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.87.7.2725 · Cited by 1,454 · see citing works
Transcription Against an Applied Force
Yin, H. Y., Wang, M. D., Svoboda, K., Landick, R. C., Block, S. M., & Gelles, J. (1995) · Science · doi:10.1126/science.270.5242.1653 · Cited by 592 · see citing works
Circuit Simulation of Genetic Networks
McAdams, H. H., & Shapiro, L. (1995) · Science · doi:10.1126/science.7624793 · Cited by 519 · see citing works
Patel, S. S., Wong, I., & Johnson, K. A. (1991) · Biochemistry · doi:10.1021/bi00216a029 · Cited by 500 · see citing works
Quantitative or semi-quantitative PCR: reality versus myth.Preprint
Ferre, F. (1992) · Genome Research · doi:10.1101/gr.2.1.1 · Cited by 351 · see citing works
Kinetic mechanism of DNA polymerase I (Klenow)
Kuchta, R. D., Mizrahi, V., Benkovic, P. A., Johnson, K. A., & Benkovic, S. J. (1987) · Biochemistry · doi:10.1021/bi00399a057 · Cited by 350 · see citing works
Quantitative PCR: Theoretical Considerations with Practical Implications
Raeymaekers, L. (1993) · Analytical Biochemistry · doi:10.1006/abio.1993.1542 · Cited by 230 · see citing works
Dahlberg, M. E., & Benkovic, S. J. (1991) · Biochemistry · doi:10.1021/bi00234a002 · Cited by 218 · see citing works
Capson, T. L., Peliska, J. A., Kaboord, B. F., Frey, M. W., Lively, C. R., Dahlberg, M. E., & Benkovic, S. J. (1992) · Biochemistry · doi:10.1021/bi00160a007 · Cited by 210 · see citing works
DNA amplification by the polymerase chain reaction
Gibbs, R. A. (1990) · Analytical Chemistry · doi:10.1021/ac00212a004 · Cited by 174 · see citing works
Quantitative PCR and RT-PCR in virology.Preprint
Clementi, M., Menzo, S., Bagnarelli, P., Manzin, A., Valenza, A., & Varaldo, P. E. (1993) · Genome Research · doi:10.1101/gr.2.3.191 · Cited by 148 · see citing works
The Polymerase Chain Reaction and Branching Processes
Sun, F. (1995) · Journal of Computational Biology · doi:10.1089/cmb.1995.2.63 · Cited by 90 · see citing works
Modeling the Polymerase Chain Reaction
Weiß, G., & von Haeseler, A. (1995) · Journal of Computational Biology · doi:10.1089/cmb.1995.2.49 · Cited by 56 · see citing works
Flagged first, then by citations
Research works printed but not linked: 3
- [3]Gestland R, Atkins J, editors. The RNA World. Plainview, NY: Cold Spring Harbor Lab. Press; 1993. [Google Scholar]
- [5]Kaplan P, Cecchi G, Libchaber A. In: Proceedings of the 2nd Annual Princeton Conference on DNA-Based Computation. Baum E, Boneh D, Kaplan P, Reif J, Seeman A, editors. Providence, RI: Am. Mathematical Soc.; 1996. in press. [Google Scholar]
- [10]Kuchta R D, Mizrahi V, Benkovic P A, Johnson K A, Benkovic S J. Biochemistry. 1987;26:8410–8417. doi: 10.1021/bi00399a057. [DOI] [PubMed] [Google Scholar] · DOI
Cited by
Sorted by citations
Amplification efficiency: linking baseline and bias in the analysis of quantitative PCR data
Ruijter, J. M., Ramakers, C., Hoogaars, W. M. H., Karlen, Y., Bakker, O., van den Hoff, M. J. B., & Moorman, A. F. M. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp045 · Cited by 3,043 · see citing works
Svec, D., Tichopad, A., Novosadova, V., Pfaffl, M. W., & Kubista, M. (2015) · Biomolecular Detection and Quantification · doi:10.1016/j.bdq.2015.01.005 · Cited by 601 · see citing works
Statistical significance of quantitative PCR
Karlen, Y., McNair, A., Perseguers, S., Mazza, C., & Mermod, N. (2007) · BMC Bioinformatics · doi:10.1186/1471-2105-8-131 · Cited by 373 · see citing works
Sources of PCR-induced distortions in high-throughput sequencing data sets
Kebschull, J. M., & Zador, A. M. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv717 · Cited by 300 · see citing works
Robust Quantification of Polymerase Chain Reactions Using Global Fitting
Carr, A. C., & Moore, S. D. (2012) · PLoS ONE · doi:10.1371/journal.pone.0037640 · Cited by 297 · see citing works
Ruijter, J. M., Pfaffl, M. W., Zhao, S., Spiess, A., Boggy, G. J., Blom, J., Rutledge, R. G., Sisti, D., Lievens, A., Preter, K. D., et al. (2012) · Methods · doi:10.1016/j.ymeth.2012.08.011 · Cited by 258 · see citing works
Felske, A., Akkermans, A. D. L., & de Vos, W. M. (1998) · Applied and Environmental Microbiology · doi:10.1128/aem.64.11.4581-4587.1998 · Cited by 233 · see citing works
Validating TrueAllele ® DNA Mixture Interpretation* ,†
Perlin, M. W., Legler, M. M., Spencer, C. E., Smith, J. L., Allan, W. P., Belrose, J. L., & Duceman, B. W. (2011) · Journal of Forensic Sciences · doi:10.1111/j.1556-4029.2011.01859.x · Cited by 228 · see citing works
Gill, P. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki205 · Cited by 137 · see citing works
Analysis of Forensic DNA Mixtures with Artefacts
Cowell, R. G., Graversen, T., Lauritzen, S. L., & Mortera, J. (2014) · Journal of the Royal Statistical Society Series C (Applied Statistics) · doi:10.1111/rssc.12071 · Cited by 132 · see citing works
Bustin, S., & Nolan, T. (2017) · European Journal of Clinical Investigation · doi:10.1111/eci.12801 · Cited by 113 · see citing works
Quantifying Molecular Bias in DNA Data Storage
Chen, Y.-J., Takahashi, C. N., Organick, L., Stewart, K., Ang, S. D., Weiss, P., Peck, B., Seelig, G., Ceze, L., & Strauss, K. (2019) · doi:10.1101/566554 · Cited by 109 · see citing works
A New Method for Quantitative Real-Time Polymerase Chain Reaction Data Analysis
Rao, X., Lai, D., & Huang, X. (2013) · Journal of Computational Biology · doi:10.1089/cmb.2012.0279 · Cited by 107 · see citing works
Best, K., Oakes, T., Heather, J., Shawe-Taylor, J. S., & Chain, B. (2015) · Scientific Reports · doi:10.1038/srep14629 · Cited by 103 · see citing works
Christopoulos, T. K. (1999) · Analytical Chemistry · doi:10.1021/a19900161 · Cited by 95 · see citing works
An Information Gap in DNA Evidence Interpretation
Perlin, M. W., & Sinelnikov, A. (2009) · PLoS ONE · doi:10.1371/journal.pone.0008327 · Cited by 71 · see citing works
Evaluation of loss of heterozygosity/allelic imbalance scoring in tumor DNA
Skotheim, R. I., Diep, C. B., Kraggerud, S. M., Jakobsen, K. S., & Lothe, R. A. (2001) · Cancer Genetics and Cytogenetics · doi:10.1016/s0165-4608(00)00433-7 · Cited by 71 · see citing works
Validation of kinetics similarity in qPCR
Bar, T., Kubista, M., & Tichopád, A. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr778 · Cited by 60 · see citing works
Alveolar macrophage dynamics in murine lung regeneration
Chamoto, K., Gibney, B. C., Ackermann, M., Lee, G. S., Lin, M., Konerding, M. A., Tsuda, A., & Mentzer, S. J. (2011) · Journal of Cellular Physiology · doi:10.1002/jcp.24009 · Cited by 55 · see citing works
A kinetic model of quantitative real‐time polymerase chain reaction
Mehra, S., & Hu, W. (2005) · Biotechnology and Bioengineering · doi:10.1002/bit.20555 · Cited by 51 · see citing works
White, J. A., Kufera, J. T., Bachmann, N., Dai, W., Simonetti, F. R., Armstrong, C., Lai, J., Beg, S. A., Siliciano, J. D., & Siliciano, R. F. (2022) · PLoS Pathogens · doi:10.1371/journal.ppat.1010845 · Cited by 47 · see citing works
Mátyás, G., Giunta, C., Steinmann, B. U., Hossle, J. P., & Hellwig, R. (2001) · Human Mutation · doi:10.1002/humu.10013 · Cited by 48 · see citing works
Evaluation of SYBR Green real time PCR for detecting SARS-CoV-2 from clinical samples
Pereira-Gómez, M., Fajardo, Á., Echeverría, N., Tort, L. F. L., Perbolianachis, P., Costábile, A., Aldunate, F., Moreno, P., & Moratorio, G. (2020) · Journal of Virological Methods · doi:10.1016/j.jviromet.2020.114035 · Cited by 47 · see citing works
Lalam, N., Jacob, C., & Jagers, P. (2004) · Advances in Applied Probability · doi:10.1239/aap/1086957587 · Cited by 46 · see citing works
Ballantyne, J., Hanson, E., & Perlin, M. W. (2012) · Science & Justice · doi:10.1016/j.scijus.2012.04.004 · Cited by 44 · see citing works
Estimation of the reaction efficiency in polymerase chain reaction
Lalam, N. (2006) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2006.06.001 · Cited by 41 · see citing works
Stochastic sampling effects in STR typing: Implications for analysis and interpretation
Timken, M. D., Klein, S. B., & Buoncristiani, M. R. (2014) · Forensic Science International Genetics · doi:10.1016/j.fsigen.2014.03.015 · Cited by 40 · see citing works
Milanović, V., Osimani, A., Roncolini, A., Garofalo, C., Aquilanti, L., Pasquini, M., Tavoletti, S., Vignaroli, C., Canonico, L., Ciani, M., et al. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.03036 · Cited by 39 · see citing works
Efficiency of the polymerase chain reaction
Booth, C. S., Pienaar, E., TerMaat, J. R., Whitney, S. E., Louw, T. M., & Viljoen, H. J. (2010) · Chemical Engineering Science · doi:10.1016/j.ces.2010.05.046 · Cited by 38 · see citing works
So FAR: Software for Fully Automatic Evaluation of Real-Time PCR Data
Wilhelm, J., Pingoud, A. M., & Hahn, M. (2003) · BioTechniques · doi:10.2144/03342rr03 · Cited by 36 · see citing works
Validating TrueAllele® Interpretation of DNA Mixtures Containing up to Ten Unknown Contributors
Bauer, D. W., Butt, N. A., Hornyak, J. M., & Perlin, M. W. (2019) · Journal of Forensic Sciences · doi:10.1111/1556-4029.14204 · Cited by 34 · see citing works
Designer DNA biomolecules as a defined biomaterial for 3D bioprinting applications
Budharaju, H., Zennifer, A., Sethuraman, S., Paul, A., & Sundaramurthi, D. (2021) · Materials Horizons · doi:10.1039/d1mh01632f · Cited by 34 · see citing works
Perlin, M. W., Dormer, K., Hornyak, J. M., Schiermeier‐Wood, L., & Greenspoon, S. A. (2014) · PLoS ONE · doi:10.1371/journal.pone.0092837 · Cited by 33 · see citing works
Computational challenges in combinatorial library design for protein engineering
Moore, G. L., & Maranas, C. D. (2004) · AIChE Journal · doi:10.1002/aic.10025 · Cited by 34 · see citing works
Migration of CD11b+ accessory cells during murine lung regeneration
Chamoto, K., Gibney, B. C., Lee, G. S., Ackermann, M., Konerding, M. A., Tsuda, A., & Mentzer, S. J. (2013) · Stem Cell Research · doi:10.1016/j.scr.2012.12.006 · Cited by 31 · see citing works
Validation of an STR peak area model
Cowell, R. G. (2009) · Forensic Science International Genetics · doi:10.1016/j.fsigen.2009.01.006 · Cited by 30 · see citing works
Hansson, O., Egeland, T., & Gill, P. (2016) · International Journal of Legal Medicine · doi:10.1007/s00414-016-1453-x · Cited by 29 · see citing works
Polymerase chain reaction in natural convection systems: A convection-diffusion-reaction model
Yariv, E., Ben-Dov, G., & Dorfman, K. D. (2005) · Europhysics Letters (EPL) · doi:10.1209/epl/i2005-10171-6 · Cited by 28 · see citing works
Angiogenesis gene expression in murine endothelial cells during post-pneumonectomy lung growth
Lin, M., Chamoto, K., Gibney, B. C., Lee, G. S., Simpson, D. C., Houdek, J. P., Konerding, M. A., Tsuda, A., & Mentzer, S. J. (2011) · Respiratory Research · doi:10.1186/1465-9921-12-98 · Cited by 26 · see citing works
Duffy, K. R., Gurram, N., Peters, K. C., Wellner, G. A., & Grgicak, C. M. (2016) · Electrophoresis · doi:10.1002/elps.201600385 · Cited by 25 · see citing works
Savonnet, M., Aubret, M., Laurent, P., Roupioz, Y., Cubizolles, M., & Buhot, A. (2022) · Biosensors · doi:10.3390/bios12050346 · Cited by 24 · see citing works
Elelu, N., Ferrolho, J., Couto, J., Domingos, A., & Eisler, M. C. (2016) · Experimental and Applied Acarology · doi:10.1007/s10493-016-0081-y · Cited by 22 · see citing works
Braun, P. R., Nguyen, M. D.-T., Walter, M. C., & Grass, G. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms222212224 · Cited by 20 · see citing works
Kinetic characterisation of primer mismatches in allele-specific PCR: a quantitative assessment
Waterfall, C. M., Eisenthal, R., & Cobb, B. D. (2002) · Biochemical and Biophysical Research Communications · doi:10.1016/s0006-291x(02)02750-x · Cited by 19 · see citing works
Principles of rapid polymerase chain reactions: mathematical modeling and experimental verification
Whitney, S. E., Alugupally, S., Nelson, R. M., & Viljoen, H. J. (2004) · Computational Biology and Chemistry · doi:10.1016/j.compbiolchem.2004.03.001 · Cited by 20 · see citing works
Lamberton, P. H. L., Cheke, R., Walker, M., Winskill, P., Crainey, J. L., Boakye, D. A., Osei-Atweneboana, M. Y., Tirados, I., Wilson, M. D., Tetteh-Kumah, A., et al. (2016) · Parasites & Vectors · doi:10.1186/s13071-016-1703-2 · Cited by 19 · see citing works
Peng, X., & Dorman, K. S. (2023) · Bioinformatics · doi:10.1093/bioinformatics/btad002 · Cited by 17 · see citing works
Ligation-Based High-Performance Mimetic Enzyme Sensing Platform for Nucleic Acid Detection
Yan, X., Yang, P., Qiu, D., Chen, D., Pan, J., Zhang, X., Ju, H., & Zhou, J. (2023) · Analytical Chemistry · doi:10.1021/acs.analchem.3c04417 · Cited by 18 · see citing works
Simulation and real-time monitoring of polymerase chain reaction for its higher efficiency
Lee, J. Y., Lim, H., Yoo, S.-I., Zhang, B., & Park, T. H. (2005) · Biochemical Engineering Journal · doi:10.1016/j.bej.2005.02.023 · Cited by 18 · see citing works
Alveolar Epithelial Dynamics in Postpneumonectomy Lung Growth
Chamoto, K., Gibney, B. C., Ackermann, M., Lee, G. S., Konerding, M. A., Tsuda, A., & Mentzer, S. J. (2013) · The Anatomical Record · doi:10.1002/ar.22659 · Cited by 16 · see citing works
Polymerase Chain Reaction: A Markov Process Approach
Velikanov, M. V., & Kapral, R. (1999) · Journal of Theoretical Biology · doi:10.1006/jtbi.1999.1031 · Cited by 15 · see citing works
Real-time cdPCR opens a window into events occurring in the first few PCR amplification cycles
Duewer, D. L., Kline, M. C., & Romsos, E. L. (2015) · Analytical and Bioanalytical Chemistry · doi:10.1007/s00216-015-9073-8 · Cited by 14 · see citing works
Kourkouli, A., Τhomaidis, Ν. S., Dasenaki, M. E., & Markou, A. N. (2024) · Molecules · doi:10.3390/molecules29081820 · Cited by 14 · see citing works
Figdor, D., & Brundin, M. (2016) · Journal of Endodontics · doi:10.1016/j.joen.2016.04.015 · Cited by 14 · see citing works
Weng, Z., Li, J., Wu, Y., Xiu, X., Wang, F., Zuo, X., Song, P., & Fan, C. (2025) · Nature Communications · doi:10.1038/s41467-025-55986-9 · Cited by 15 · see citing works
Sequence-Dependent Biophysical Modeling of DNA Amplification
Marimuthu, K., Jing, C., & Chakrabarti, R. (2014) · Biophysical Journal · doi:10.1016/j.bpj.2014.08.019 · Cited by 13 · see citing works
Simulation of between Repeat Variability in Real Time PCR Reactions
Lievens, A., Aelst, S. V., den Bulcke, M. V., & Goetghebeur, E. J. T. (2012) · PLoS ONE · doi:10.1371/journal.pone.0047112 · Cited by 11 · see citing works
Modeling bias and variation in the stochastic processes of small RNA sequencing
Argyropoulos, C., Etheridge, A., Sakhanenko, N. A., & Galas, D. J. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx199 · Cited by 11 · see citing works
Felske, A., Pauling, B. V., von Canstein, H., Li, Y., Lauber, J., Buer, J., & Wagner‐Döbler, I. (2001) · BioTechniques · doi:10.2144/01301rr02 · Cited by 10 · see citing works
Perlin, M. W. (2015) · Journal of Pathology Informatics · doi:10.4103/2153-3539.168525 · Cited by 9 · see citing works
Elnaggar, J. H., Ardizzone, C. M., Cerca, N., Toh, E. C., Łaniewski, P., Lillis, R., Herbst‐Kralovetz, M. M., Quayle, A. J., Muzny, C. A., & Taylor, C. M. (2023) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2023.1198113 · Cited by 9 · see citing works
Empirical insights into the stochasticity of small RNA sequencing
Qin, L., Tuschl, T., & Singer, S. (2016) · Scientific Reports · doi:10.1038/srep24061 · Cited by 8 · see citing works
Stimulation of voltage-dependent Ca2+channels by NO at rat myenteric neurons
Sitmo, M., Rehn, M., & Diener, M. (2007) · American Journal of Physiology-Gastrointestinal and Liver Physiology · doi:10.1152/ajpgi.00124.2007 · Cited by 8 · see citing works
Emulsion PCR (ePCR) as a Tool to Improve the Power of DGGE Analysis for Microbial Population Studies
Iacumin, L., Cecchini, F., Vendrame, M., & Comi, G. (2020) · Microorganisms · doi:10.3390/microorganisms8081099 · Cited by 8 · see citing works
Emergence of fractals in aggregation with stochastic self-replication
Hassan, M. K., Hassan, M. Z., & Islam, N. (2013) · Physical Review E · doi:10.1103/physreve.88.042137 · Cited by 8 · see citing works
Milanović, V., Cardinali, F., Belleggia, L., Garofalo, C., Pasquini, M., Tavoletti, S., Riolo, P., Ruschioni, S., Isidoro, N., Osimani, A., et al. (2021) · Journal of Functional Foods · doi:10.1016/j.jff.2021.104490 · Cited by 7 · see citing works
Sueiro, R. A., Lamas, J., Palenzuela, O. R., Guliás, P., Díez‐Vives, C., García-Ulloa, A., & Leiro, J. M. (2022) · Aquaculture · doi:10.1016/j.aquaculture.2022.738303 · Cited by 6 · see citing works
Dynamics and control of DNA sequence amplification
Marimuthu, K., & Chakrabarti, R. (2014) · The Journal of Chemical Physics · doi:10.1063/1.4899053 · Cited by 6 · see citing works
Lalam, N., & Jacob, C. (2007) · Mathematical Population Studies · doi:10.1080/08898480701298418 · Cited by 6 · see citing works
Smith, S. E., Swan, E. R., & Furber, K. L. (2024) · Biochemistry and Cell Biology · doi:10.1139/bcb-2024-0088 · Cited by 5 · see citing works
Experimental validation of a fundamental model for PCR efficiency
Louw, T. M., Booth, C. S., Pienaar, E., TerMaat, J. R., Whitney, S. E., & Viljoen, H. J. (2011) · Chemical Engineering Science · doi:10.1016/j.ces.2011.01.029 · Cited by 5 · see citing works
Limits of Performance of Quantitative Polymerase Chain Reaction Systems
Vikalo, H., Hassibi, B., & Hassibi, A. (2010) · IEEE Transactions on Information Theory · doi:10.1109/tit.2009.2037088 · Cited by 5 · see citing works
A quantitative approach for polymerase chain reactions based on a hidden Markov model
Lalam, N. (2008) · Journal of Mathematical Biology · doi:10.1007/s00285-008-0238-3 · Cited by 5 · see citing works
Huang, Y., Chen, X., Li, X., Shu, P., Wang, H., Hou, T., Wang, Y., Song, F., & Zhang, J. (2021) · Forensic Science International Genetics · doi:10.1016/j.fsigen.2021.102609 · Cited by 5 · see citing works
Coagulation and self-duplication processes of a chain-shaped polymer system
Jian-Hong, K., Zheng, Y., Lin, Z., & Chen, X. (2007) · Physics Letters A · doi:10.1016/j.physleta.2007.03.087 · Cited by 4 · see citing works
Crissman, J. W., Lin, Y., Separa, K., Duquette, M., Cohen, M., Velasquez, C., & Cujec, T. P. (2020) · PLoS ONE · doi:10.1371/journal.pone.0241803 · Cited by 4 · see citing works
Validation and Estimation of Parameters for a General Probabilistic Model of the PCR Process
Saha, N., Watson, L. T., Kafadar, K., Ramakrishnan, N., Onufriev, A. V., Mane, S. P., & Vásquez-Robinet, C. (2007) · Journal of Computational Biology · doi:10.1089/cmb.2006.0123 · Cited by 4 · see citing works
Reducing Bias and Quantifying Uncertainty in Fluorescence Produced by PCR
DeJaco, R. F., Roberts, M. J., Romsos, E. L., Vallone, P. M., & Kearsley, A. J. (2023) · Bulletin of Mathematical Biology · doi:10.1007/s11538-023-01182-z · Cited by 3 · see citing works
Molecular quantification of genes encoding for green-fluorescent proteins
Felske, A., Vandieken, V., Pauling, B. V., von Canstein, H., & Wagner‐Döbler, I. (2003) · Journal of Microbiological Methods · doi:10.1016/s0167-7012(02)00184-7 · Cited by 3 · see citing works
ML Estimation of DNA Initial Copy Number in Polymerase Chain Reaction (PCR) Processes
Vikalo, H., Hassibi, B., & Hassibi, A. (2007) · IEEE International Conference on Acoustics Speech and Signal Processing · doi:10.1109/icassp.2007.366705 · Cited by 3 · see citing works
A general probabilistic model of the PCR process
Saha, N., Watson, L. T., Kafadar, K., Onufriev, A. V., Ramakrishnan, N., Vásquez-Robinet, C., & Watkinson, J. I. (2006) · Applied Mathematics and Computation · doi:10.1016/j.amc.2006.01.092 · Cited by 3 · see citing works
Monitoring the Persistence of Pseudomonas sivasensis Strain CF10PS3 in Cereal Fields
Delitte, M., Dubois, B., Mahillon, J., Debode, F., & Bragard, C. (2024) · MicrobiologyOpen · doi:10.1002/mbo3.70005 · Cited by 2 · see citing works
A two stage model for quantitative PCRPreprint
Stone, E., Goldes, J., & Garlick, M. (2006) · arXiv (Cornell University) · doi:10.48550/arxiv.q-bio/0603004 · Cited by 2 · see citing works
Kinetics of catalytically activated duplication in aggregation growth
Haifeng, W., Zhen-Quan, L., Gao, Y. L., & Xu, C. (2009) · Chinese Physics B · doi:10.1088/1674-1056/18/8/074 · Cited by 2 · see citing works
On joint maximum-likelihood estimation of PCR efficiency and initial amount of target
Vikalo, H., Hassibi, B., & Hassibi, A. (2006) · IEEE International Workshop on Genomic Signal Processing and Statistics · doi:10.1109/gensips.2006.353149 · Cited by 2 · see citing works
Deep learning uncovers sequence-specific amplification bias in multi-template PCRPreprint
Gimpel, A. L., Fan, B., Chen, D., Wölfle, L. O. D., Horn, M., Meng-Papaxanthos, L., Antkowiak, P. L., Stark, W. J., Christen, B., Borgwardt, K. M., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.09.20.614030 · Cited by 2 · see citing works
Salter, I., Brandner, M. M., Djurhuus, A., Præbel, K., & Wangensteen, O. S. (2026) · Environmental DNA · doi:10.1002/edn3.70253 · Cited by 1 · see citing works
The reliability and reporting of DNA match strength for uncertain genotype evidence
Perlin, M. W., Allan, W. P., Bracamontes, J. M., & Legler, M. M. (2026) · Heliyon · doi:10.1016/j.heliyon.2026.e44753 · Cited by 1 · see citing works
Supercritical branching processes and the role of fluctuations under exponential population growth
Manrubia, S. C., Arribas, M., & Lázaro, E. (2003) · Journal of Theoretical Biology · doi:10.1016/s0022-5193(03)00294-7 · Cited by 1 · see citing works
Efficiency of polymerase chain reaction processes: A stochastic model
Hassibi, A., & Sharif, M. (2006) · IEEE International Workshop on Genomic Signal Processing and Statistics · doi:10.1109/gensips.2006.353143 · Cited by 1 · see citing works
Gill, P., Bleka, Ø., Hansson, O., Benschop, C. C. G., & Haned, H. (2020) · Elsevier eBooks · doi:10.1016/b978-0-12-820562-4.00012-2 · Cited by 1 · see citing works
On the relation between input and output distributions of scRNA-seq experiments
Schwabe, D., & Falcke, M. (2021) · Bioinformatics · doi:10.1093/bioinformatics/btab841 · Cited by 1 · see citing works
Welch, R. D., Anderson, I., & Gorski, J. (1999) · Analytical Biochemistry · doi:10.1006/abio.1998.3055 · Cited by 1 · see citing works
Maximum a posteriori (MAP) estimator for polymerase chain reaction (PCR) processes
Kakavand, H., O'Brien, D., Hassibi, A., & Lee, T. H. (2005) · Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC) · doi:10.1109/iembs.2004.1403854 · Cited by 1 · see citing works
A Bayesian Approach to the Quantitative Polymerase Chain Reaction
Lalam, N., & Jacob, C. (2007) · Birkhäuser Boston eBooks · doi:10.1007/978-0-8176-4556-4_27
Technological Aspects of Molecular Diagnosis of Bacterial Infectious Diseases
Booth, C. S. (2012) · Lincoln (University of Nebraska)
Bayesian estimation for quantification by real-time Polymerase Chain Reaction
Lalam, N., & Jacob, C. (2005) · TU/e Research Portal
SURVEY AND SUMMARY Validation of kinetics similarity in qPCR
Bar, T., Kubista, M., Tichopád, A., & Benes, E. (2011)
Statistical Applications in Genetics and Molecular Biology
Lalam, N. (2007)
A NONLINEAR RESPONSE MODEL FOR SINGLE NUCLEOTIDE POLYMORPHISM DETECTION ASSAYS
Kouri, D. (2008) · OhioLink ETD Center (Ohio Library and Information Network)
- Authors
- Stolovitzky, G., & Cecchi, G.
- Affiliations
- Rockefeller University (US)
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 1996-11-12
- Volume
- 93
- Issue
- 23
- Pages
- 12947-12952
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC24026
- OpenAlex
- W2004803703
- Cited by
- 112
- References
- 23
- Citations by year
- 2026: 3 · 2025: 2 · 2024: 5 · 2023: 4 · 2022: 3 · 2021: 8 · 2020: 8 · 2019: 1 · 2018: 2 · 2017: 2 · 2016: 7 · 2015: 5 · 2014: 5 · 2013: 4 · 2012: 5
- FWCI
- 0.50
- Type
- journal article
- Language
- en
- Open access
- green
- europepmc.org
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Molecular Biology Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
- Physical Sciences › Mathematics › Mathematical Physics › Stochastic processes and statistical mechanics
- Keywords
- PCR, DNA replication, kinetic model, PCR cycle number, multimodality, scaling behavior, real-time PCR
- MeSH terms
- DNA Replication, Kinetics, Models, Theoretical, Probability, Time Factors, Reproducibility of Results, Polymerase Chain Reaction
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
