Fall 2019

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

Date Person Paper
Aug 30 Roberto Herrera DeNovo Congenital Heart Disease
Sep 6 No meeting
Sep 13 Briknie Baez Deepfinder
Sep 20 Luis Mieses Gene experession
Sep 27 Roberto Deep learning RNA-seq
Oct 4 Miguel denoising autoencoders
Oct 11 BSides meeting
Oct 18 No meeting
Oct 25 Briknie seq-seq-pan


DeNovo Congenital Heart Disease
Zaidi, Samir, Murim Choi, Hiroko Wakimoto, Lijiang Ma, Jianming Jiang, John D. Overton, Angela Romano-Adesman et al. "De novo mutations in histone-modifying genes in congenital heart disease." Nature 498, no. 7453 (2013): 220. https://www.nature.com/doifinder/10.1038/nature12141
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
Nung Kion Lee, Farah Liyana Azizan, Yu Shiong Wong & Norshafarina Omar (2018) DeepFinder: An integration of feature-based and deep learning approach for DNA motif discovery, Biotechnology & Biotechnological Equipment, 32:3, 759-768, DOI: https://dx.doi.org/10.1080/13102818.2018.1438209
Gene expression
Chen, Yifei, Yi Li, Rajiv Narayan, Aravind Subramanian, and Xiaohui Xie. "Gene expression inference with deep learning." Bioinformatics 32, no. 12 (2016): 1832-1839. https://dx.doi.org/10.1093/bioinformatics/btw074
Deep learning RNA-Seq
Urda, Daniel, Julio Montes-Torres, Fernando Moreno, Leonardo Franco, and José M. Jerez. "Deep learning to analyze RNA-seq gene expression data." In International Work-Conference on Artificial Neural Networks, pp. 50-59. Springer, Cham, 2017. https://core.ac.uk/download/pdf/132743527.pdf
Denoising autoencoders
Jie Tan, Matthew Ung, Chao Cheng, and Casey S Greene. Unsupervised feature construc-tion and knowledge extraction from genome-wide assays of breast cancer with denoising autoencoders. In Pacific Symposium on Biocomputing Co-Chairs, pages 132–143. WorldScientific, 2014. https://doi.org/10.1142/9789814644730_0014
Jandrasits, C., Dabrowski, P. W., Fuchs, S., & Renard, B. Y. (2018). seq-seq-pan: Building a computational pan-genome data structure on whole genome alignment. BMC genomics, 19(1), 47. https://doi.org/10.1186/s12864-017-4401-3