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


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
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
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
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: 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
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
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
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