History of Real-time PCR Miner

• First Real-time PCR experiment
  •  2003/09/03 at Russ Fernald's lab in Stanford.
  • Very bad, many mistakes, but improved little by little...
• Come up with the idea to make an algorithm without the need of standard curve.
  •  2004/06/01 Dr. Sabrina Burmeister (Thanks a lot) introduced me Peirson's paper (Peirson, S.N., Butler, J.N. and Foster, R.G. (2003) Nucleic Acids Res, 31, e73.) for individual efficiency calculation, which did not work for our machine (MyIQ).
  •  Start to make a better one.
• First Real-time PCR Miner 0.0
  •  Linear regression, still need baseline subtraction.
  • 2004/09/07 Patent / License application started (Patent / License reference number (pending): S04-261 at Stanford University Office of Technology Licensing).
  • 2004/09/15 Submitted the manuscript to Nuclear Acid Research ( rejected (2004/10/13 ),  sad,  but not bad since we got some good recommendations and questions from reviewers).
  •  2004/09/17 Website for Miner was opened.
  •  2004/10/16 Poster for Biomedical Computation at Stanford (BCATS) 2004
• Improved Real-time PCR Miner 0.9
  • Improved a lot, e.g. using non-linear regression, discard baseline subtraction, etc.
  • Almost done except that the calculation for weight is not assumption-free.
  •  2004/11/18 Talk for the Miner at Bio-Rad Real-time PCR seminar at Stanford.
  • 2004/12/21 Re-submitted the manuscript to Nuclear Acid Research ( rejected again (2004/12/29 ),  sad and  a little bit angry about the reviewer who tested Miner subjectively by data in wrong format and after baseline subtraction, but not too bad since we still got some good questions.).
  • 2004/12/21 Updated Patent / License application.
• Formal Real-time PCR Miner 1.0
  •  2005/01/01 Solved the problem of the weight calculation which make the whole algorithm totally objective (Cheers!).
  • 2005/05/12 The manuscript for Miner has been accepted by Journal of Computational Biology. Welcome to cite us:

  Sheng Zhao, Russell D. Fernald. Comprehensive algorithm for quantitative real-time polymerase chain reaction. J. Comput. Biol. 2005 Oct; 12(8):1045-62

  • 2005/05/13 Talk for Neurodev joint lab meeting at Stanford.
  • 2005/05/14 Introduced error detecting feature for the submitted data on Miner website. Less blockage will happen for the server in future.
  • 2005/10 Paper published and is available online now! Cheers!

    Sheng Zhao, Russell D. Fernald. Comprehensive algorithm for quantitative real-time polymerase chain reaction. J. Comput. Biol. 2005 Oct;12(8):1045-62. PubMed and PDF

  • 2005/11/23 Introduced more error detecting features for the submitted data on Miner website. Less blockage will happen for the server in future.
  • 2005/12/21 Improved Miner website for searching previous results and sending email with a link to the result page at both begining and end of the analysis. Also, several small improvements have been added into the algorithm.
  • 2006/01/06 Added a page for supporting the website as well as Google AdSense to help keeping this website running and updating. I also added a example for how to quantify the data by using the average efficiency of each gene and the average CT of replicates generated by Miner.
• Real-time PCR Miner 2.0
  • 2006/03/13 A new version of Miner (2.0) have been developed. Several improvements have been added into the new version and make Miner at least 10 times faster, more accurate, and more stable. Also, the new version is compatible with much larger sample data.
• Real-time PCR Miner 2.1
  • 2007/01/18 New features have been added to Miner 2.0 to allow user specify the basic options for Miner for particular experiment and samples with lower quality data.
• Real-time PCR Miner 2.2
  • 2009/05/16 An automatic recovering feature has been introduced on Miner website to detect and reset the blocking data automatically.
• Real-time PCR Miner 3.0
  • 2011/04/15 A high noise toleration feature has been introduced on Miner software, which make it more accurate, stable, and robust across different PCR platforms.
• Real-time PCR Miner 4.0
  • 2011/10/21 Introduced new codes for high noise sample at later cycles and corrected several bugs, making Miner more compatible with all PCR platforms.
  • 2013/01 A review paper has been published by original developers of curve analysis methods, including Miner, to compare and assess the algorithms’ precision, bias, and resolution.

    Jan M. Ruijter, Michael W. Pfaffl, Sheng Zhao, Andrej N. Spiess, Gregory Boggy, Jochen Blom, Robert G. Rutledge, Davide Sisti, Antoon Lievens, Katleen De Preter, Stefaan Derveaux, Jan Hellemans, Jo Vandesompele. Evaluation of qPCR curve analysis methods for reliable biomarker discovery: Bias, resolution, precision, and implications. Methods. 2013 Jan;59(1):32-46. doi: 10.1016/j.ymeth.2012.08.011. Epub 2012 Sep 3. PubMed and PDF

  • 2014/03 A third-part evaluation of Miner and other curve analysis methods by Dr. Joel Tellinghuisen and Dr. Andrej-Nikolai Spiess has been published.

    Joel Tellinghuisen, Andrej-Nikolai Spiess. Comparing real-time quantitative polymerase chain reaction analysis methods for precision, linearity, and accuracy of estimating amplification efficiency. Analytical Biochemistry 2014 Mar;449: 76-82. Science Direct and PDF

  • 2020/08 Ventura, a Turkey software company, included Realtime PCR Miner into their latest bioinformatic package (CAtenA).
• Other news, coming soon...

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