Fall 2016

Here's the schedule of journal club presentations for this semester.

Date Person Paper
Sep 2 Humberto Ortiz-Zuazaga khmer
Sep 9 Grace Rodriguez Anomalies in IPv6 (poster)
Sep 16 Walter Baez stacks
Sep 23 Travel to Washington DC
Sep 30 Posponed
Oct 7 David Ortiz edgeR
Oct 14 Christopher de Jesus BRO
Oct 21 Angel Sanquiche trinity
Oct 28 Kevin Legarreta mutual
Nov 4 Ivan Jimenez cufflinks
Nov 11 Josefina Correa pepino


Crusoe MR, Alameldin HF, Awad S et al. The khmer software package: enabling efficient nucleotide sequence analysis [version 1; referees: 2 approved, 1 approved with reservations]. F1000Research 2015, 4:900 (doi: 10.12688/f1000research.6924.1)
Fu S, Tarone AM, Sze SH. (2015) Heuristic pairwise alignment of de Bruijn graphs to facilitate simultaneous transcript discovery in related organisms from RNA-Seq data. BMC Genomics 16:S5. article
Grabherr MG, Haas BJ, Yassour M, et al. Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data. Nature biotechnology. 2011;29(7):644-652. doi:10.1038/nbt.1883. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3571712/
Mashanov VS, Zueva OR, García-Arrarás JE. Transcriptomic changes during regeneration of the central nervous system in an echinoderm. BMC Genomics. 2014 May 12;15:357. doi: 10.1186/1471-2164-15-357. PubMed PMID: 24886271; PubMed Central PMCID: PMC4229883. http://dx.doi.org/10.1186/1471-2164-15-357
Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26(1):139-140. doi:10.1093/bioinformatics/btp616. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2796818/
CATCHEN J, HOHENLOHE PA, BASSHAM S, AMORES A, CRESKO WA. Stacks: an analysis tool set for population genomics. Molecular ecology. 2013;22(11):3124-3140. doi:10.1111/mec.12354. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3936987/
Roberts A, Trapnell C, Donaghey J, Rinn JL, Pachter L. Improving RNA-Seq expression estimates by correcting for fragment bias. Genome Biology. 2011;12(3):R22. doi:10.1186/gb-2011-12-3-r22 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3129672/