John B Hogenesch

MetaCycle: an integrated R package to evaluate periodicity in large scale data

MetaCycle evaluates periodicity in time-series data by integrating ARSER, JTK_CYCLE, and Lomb-Scargle algorithms.

Benchmark Analysis of Algorithms for Determining and Quantifying Full-length mRNA Splice Forms from RNA-Seq Data

This study benchmarks algorithms for determining full-length mRNA splice forms from RNA-Seq data, finding most methods inaccurate even with idealized data and failing under real-world conditions.

Modeling of RNA-seq fragment sequence bias reduces systematic errors in transcript abundance estimation

The paper introduces a method to correct RNA-seq transcript abundance estimates by modeling fragment sequence bias, reducing false positives related to alternative isoform usage.

Assessing the prevalence of mycoplasma contamination in cell culture via a survey of NCBI’s RNA-seq archive

This study assesses mycoplasma contamination in cell culture using NCBI RNA-seq data, finding 11% of samples contaminated and 61 host genes significantly associated with contamination.

IVT-seq reveals extreme bias in RNA-sequencing

IVT-seq identifies significant technical biases in RNA-seq library preparation and sequencing, revealing coverage inconsistencies and rRNA depletion as major contributors.