Spring 2023

We're meeting Mondays at 11:30 AM as schedules permit. Here's the schedule of journal club presentations for this semester.

Date Person Paper
Aug 28 Dharsy sparser
Sep 8 Juan binarized
Sep 11 Miguel noise
Sep 18 Ian specious
Sep 25 Ricardo stringtie


The rise of sparser single-cell RNAseq datasets; consequences and opportunities. Gerard A. Bouland, Ahmed Mahfouz, Marcel J.T. Reinders bioRxiv 2022.05.20.492823; doi: https://doi.org/10.1101/2022.05.20.492823
Gerard A Bouland, Ahmed Mahfouz, Marcel J T Reinders, Differential analysis of binarized single-cell RNA sequencing data captures biological variation, NAR Genomics and Bioinformatics, Volume 3, Issue 4, December 2021, lqab118, https://doi.org/10.1093/nargab/lqab118
Varabyou A, Salzberg SL, Pertea M. Effects of transcriptional noise on estimates of gene and transcript expression in RNA sequencing experiments. Genome Res. 2020 Dec 23;31(2):301–8. doi: https://dx.doi.org/10.1101/gr.266213.120. Epub ahead of print. PMID: 33361112; PMCID: PMC7849408.
Chari T, Pachter L (2023) The specious art of single-cell genomics. PLoS Comput Biol 19(8): e1011288. https://doi.org/10.1371/journal.pcbi.1011288
Pertea, M., Pertea, G., Antonescu, C. et al. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol 33, 290–295 (2015). https://doi.org/10.1038/nbt.3122