biOverlay

“Detecting and harmonizing scanner differences in the ABCD study - annual release 1.0” Dylan M Nielson, Francisco Pereira, Charles Y Zheng, Nino Migineishvili, John A Lee, Adam G Thomas, Peter A Bandettini bioRxiv 309260; doi: https://doi.org/10.1101/309260 I have selected the manuscript this article to be featured in biOverlay because it discusses an increasingly important topic of statistical issues involved in combining data from multiple sources. The authors used a large dataset produced by the ABCD consortium that spans multiple sites and scanners. »

Update: This paper has now been published at mBio “Analysis and Correction of Inappropriate Image Duplication: The Molecular and Cellular Biology Experience” by Arturo Casadevall, Elisabeth M Bik, Ferric C Fang, Amy Kullas, Roger J Davis. https://doi.org/10.1101/354621 [Ed note: we’re using the bioRxiv listing information because that’s what we sent for review, but the author order has changed on the published paper and on that Dr. Bik is first author.] »

Update: This paper has now been published in PLOS Comp Bio. “Mapping DNA sequence to transcription factor binding energy in vivo” by Stephanie L Barnes, Nathan M Belliveau, William T Ireland, Justin B Kinney and Robert Phillips https://doi.org/10.1101/331124 In this article, Barnes and colleagues constructed a libraries of strains in which GFP expression is controlled by a transcription factor, and the transcription factor (TF) binding sites were randomly mutated. Libraries were sorted by GFP fluorescence and sequenced to determine the likelihood that a given binding site corresponds to a range of fluroescence. »

Update: This paper has now been published at Nature Communications. “Single cell RNA-seq denoising using a deep count autoencoder” by Gokcen Eraslan, Lukas M. Simon (both first-authors contributed equally), Maria Mircea, Nikola S. Mueller, Fabian J. Theis. https://doi.org/10.1101/300681 I selected this article for review for two reasons: I work with single-cell RNA-Sequencing (scRNA-seq) data quite a bit and I have a general interest in methods that remove technical sources of variation from it. »

Update: This paper has now been published in PNAS. “The harmonic mean p-value for combining dependent tests” by Daniel J. Wilson. https://doi.org/10.1101/171751 I selected this article for review for the following reasons: Multiple testing approaches are extraordinarily important in modern science and I am personally interested in new developments in that area. The mathematical solution and the equivalency between the mean maximized likelihood and the harmonic mean p-values (HMP) seemed particularly elegant. »