MegaProbe Lab 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 |
Papers
- 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
- diginorm
- 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
- 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.
- SHMLast
- 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
- kallisto
- 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
- cap3
- 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