Spring 2017

We're meeting Tuesdays at 10:00 AM in the lab. Here's the schedule of journal club presentations for this semester.

Date Person Paper
Feb 14 Kevin Legarreta The Lair
Feb 21 Angel Sanquiche diginorm
Feb 28 David Ortiz salmon
Mar 7 Ivan Jimenez Huang et al
Mar 14 Josefina Correa SHMlast
Mar 21 Student Assembly No Lab Meeting
Mar 28 Student strike
??? ?? Walter Baez kallisto
??? ?? Paola Figueroa cap3


The Lair
Pimentel, H., Sturmfels, P., Bray, N., Melsted, P., & Pachter, L. (2016). The Lair: a resource for exploratory analysis of published RNA-Seq data. BMC bioinformatics, 17(1), 490. https://dx.doi.org/10.1186/s12859-016-1357-2
A Reference-Free Algorithm for Computational Normalization of Shotgun Sequencing Data Brown CT, Howe AC, Zhang Q, Pyrkosz AB, Brom TH arXiv:1203.4802 [q-bio.GN] http://arxiv.org/abs/1203.4802
Salmon provides accurate, fast, and bias-aware transcript expression estimates using dual-phase inference Rob Patro, Geet Duggal, Michael I Love, Rafael A Irizarry, Carl Kingsford bioRxiv 021592; doi: https://doi.org/10.1101/021592
Huang et al
Huang, X., Chen, X. G., & Armbruster, P. A. (2016). Comparative performance of transcriptome assembly methods for non-model organisms. BMC genomics, 17(1), 523.
Scott, C. (2017). shmlast: An improved implementation of Conditional Reciprocal Best Hits with LAST and Python. The Journal of Open Source Software. 2(9). https://doi.org/10.21105/joss.00142
Bray, N. L., Pimentel, H., Melsted, P., & Pachter, L. (2016). Near-optimal probabilistic RNA-seq quantification. Nature biotechnology, 34(5), 525-527. https://dx.doi.org/10.1038/nbt.3519
Huang X, Madan A. CAP3: A DNA sequence assembly program. Genome Res. 1999 Sep;9(9):868-77. PubMed PMID: 10508846; PubMed Central PMCID: PMC310812. https://dx.doi.org/10.1101/gr.9.9.868