MegaProbe Lab Spring 2019
We're meeting Fridays at 9:00 AM in the lab. Here's the schedule of journal club presentations for this semester.
| Date | Person | Paper |
|---|---|---|
| Feb 8 | Angel Sanquiche | Axolotl |
| Feb 15 | cancelled | |
| Feb 22 | Louis Gil / Roberto Lopez | Oshlack / Streams |
| Mar 1 | Israel Dilan | Next-gen Sequence Assembly |
| Mar 8 | Walter Baez | kalisto / Yanagi |
| Mar 15 | Briknie / Omar | Kmers / Kevlar |
| Mar 22 | Holiday (abolition of slavery) | |
| Mar 29 | Humberto | OMH |
| Apr 5 | Miguel | mapping |
| Apr 12 | Postponed: UCSC Genome browser | |
| Apr 19 | Spring break | |
| Apr 26 | Heriberto | subspace |
Papers
- Yanagi
- Fast and interpretable alternative splicing and differential gene-level expression analysis using transcriptome segmentation with Yanagi. Mohamed K Gunady, Steve Mount, Hector Corrada Bravo. bioRxiv 364281; doi: https://doi.org/10.1101/364281
- Axolotl
- Stewart R, Rascón CA, Tian S, Nie J, Barry C, et al. (2013). Comparative RNA-seq Analysis in the Unsequenced Axolotl: The Oncogene Burst Highlights Early Gene Expression in the Blastema. PLOS Computational Biology 9(3): e1002936. https://doi.org/10.1371/journal.pcbi.1002936
- Oshlack
- Fast and accurate differential transcript usage by testing equivalence class counts. Marek Cmero, Nadia Davidson, Alicia Oshlack. bioRxiv 501106; doi: https://doi.org/10.1101/501106
- Streams
- Zhang Q, Awad S, Brown CT. 2015. Crossing the streams: a framework for streaming analysis of short DNA sequencing reads. PeerJ PrePrints 3:e890v1 https://doi.org/10.7287/peerj.preprints.890v1
- Next-Generation Sequence Assembly
- El-Metwally S, Hamza T, Zakaria M, Helmy M (2013) Next-Generation Sequence Assembly: Four Stages of Data Processing and Computational Challenges. PLoS Comput Biol 9(12): e1003345. https://doi.org/10.1371/journal.pcbi.1003345
- Kevlar
- Kevlar: a mapping-free framework for accurate discovery of de novo variants Daniel S Standage, C Titus Brown, Fereydoun Hormozdiari bioRxiv 549154; doi: https://doi.org/10.1101/549154
- kmers
- Zhang, Q., Pell, J., Canino-Koning, R., Howe, A. C., & Brown, C. T. (2014). These are not the k-mers you are looking for: efficient online k-mer counting using a probabilistic data structure. PloS one, 9(7), e101271. https://doi.org/10.1371/journal.pone.0101271
- mapping
- Rahman, A., Hallgrímsdóttir, I., Eisen, M., & Pachter, L. (2018). Association mapping from sequencing reads using k-mers. eLife, 7, e32920 https://dx.doi.org/10.7554%2FeLife.32920
- order min hash
- Locality sensitive hashing for the edit distance Guillaume Marcais, Dan DeBlasio, Prashant Pandey, Carl Kingsford bioRxiv 534446; doi: https://doi.org/10.1101/534446
- subspace
- Lakhina, Anukool, Mark Crovella, and Christiphe Diot. "Characterization of network-wide anomalies in traffic flows." Proceedings of the 4th ACM SIGCOMM conference on Internet measurement. ACM, 2004. https://doi.org/10.1145/1028788.1028813