Eli Roberson (he/him)
Teresita Porter 🙋🏻♀️"Sexing From Seawater: Application of Environmental DNA Beyond Species Detection for Cetaceans"
devSJR 
Following #rstats packages were maintained and are back on #CRAN now thanks to Andrej Spiess
- #dpcR, 2025-06-18, Digital PCR Analysis <10.32614/CRAN.package.dpcR>
- #MBmca, 2025-06-11, Nucleic Acid Melting Curve Analysis (https://journal.r-project.org/articles/RJ-2013-024/)
- #qpcR, 2025-06-10, Modelling and Analysis of Real-Time PCR Data <doi10.1093/bioinformatics/btn227>
- #PCRedux, 2025-06-13, Quantitative #PCR (#qPCR) Data Mining and Machine Learning Toolkit as Described in <doi:10.21105/Joss.04407>
RoedigerRGOur paper "MIQE 2.0: Revision of the Minimum Information for Publication of Quantitative Real-Time PCR Experiments Guidelines" is now published in Clinical Chemistry! 📚🔬
This update addresses recent advances in qPCR technology, providing clear recommendations on sample handling, assay design, and data analysis. We emphasize transparency and reproducibility to enhance the reliability of qPCR research.
https://doi.org/10.1093/clinchem/hvaf043 #MIQE2_0 #MIQE #qPCR #ResearchIntegrity #ScientificMethodology 📊🔍
IL PhotonicsQuantitative polymerase chain reaction (#qPCR) is a variation of the traditional PCR methodology to not just rapidly amplify and copy a DNA sample but to count how much has been produced. Real-time qPCR is now considered to be the gold standard method in microarray analysis, which allows for the study of the expression levels of many #genes simultaneously. Learn more: https://ilphotonics.com/what-pcr-filter-challenges-affect-high-performance-qpcr-instruments/
For the next few months, Dr. Andrej-Nikolai Spiess (https://openalex.org/works?page=1&filter=authorships.author.id%3Aa5027948408&sort=publication_year%3Adesc) will be a guest in my working group.
We are working on a paper where we show that 29 % of papers in top journals like Science, Nature & PNAS were skewed by a single influential data point! Time to rethink our reliance on p-values and explore alternative measures like #dfstat. #reproducibilitycrisis #linearregression #rstats
Moreover, we will work on #qPCR related software like PCRedux (https://joss.theoj.org/papers/10.21105/joss.04407)
William PerryGreat to be involved in this lovely Water Research paper led by the brilliant Maggie Knight at Bangor University! The paper compares the pros and cons of #qPCR vs #metagenomic approaches for detecting antibiotic resistance genes in wastewater. The comprehensive dataset used in the study was from the the widespread Wales wastewater monitoring. Personally, I'm team metagenomic!
http://doi.org/10.1016/j.watres.2024.121989
http://doi.org/10.1016/j.watres.2024.121989
Most problems have been fixed in the #PCRedux package. There are still issues with the #rgl package and #Matrix is causing trouble on older platforms (especially #Ubuntu) 🤔. We're still figuring out how to solve the rgl problem, unfortunately it depends on the #qpcR package which calculates some of our key parameters 💡.
More work ahead of us.
NIOO-KNAWNew publication: Risk assessment of toxic #cyanobacterial blooms in recreational #waters: A comparative study of monitoring #methods. #microsystin #fluorometry #microscopy #qPCR
https://doi.org/10.1016/j.hal.2024.102683
https://doi.org/10.1016/j.hal.2024.102683
VictorExplaining the impact of mutations on quantification of SARS-CoV-2 in wastewater. #wastewater #SARS #COVID #wastewatersurveillance #diseasesurveillance #PCR #qPCR https://www.nature.com/articles/s41598-024-62659-y
Explaining the impact of mutations on quantification of SARS-CoV-2 in wastewater - Scientific Reports
Wastewater surveillance is an effective tool for monitoring community spread of COVID-19 and other diseases. Quantitative PCR (qPCR) analysis for wastewater surveillance is more susceptible to mutations in target genome regions than binary PCR analysis for clinical surveillance. The SARS-CoV-2 concentrations in wastewater estimated by N1 and N2 qPCR assays started to diverge around July 2022 in data from different sampling sites, analytical methods, and analytical laboratories in Japan. On the basis of clinical genomic surveillance data and experimental data, we demonstrate that the divergence is due to two mutations in the N1 probe region, which can cause underestimation of viral concentrations. We further show that this inaccuracy can be alleviated if the qPCR data are analyzed with the second derivative method or the Cy0 method instead of the crossing point method.