BIOL 5496/CSE 7800: Computational Molecular Biology Journal Club

Welcome to the home page for BIOL 5496/CSE 7800, the Computational Molecular Biology Journal Club. The Journal Club meets Tuesdays at 10:00 AM on Zoom. Please see our Canvas site or the compgen-disc mailing list for the Zoom link.

Your course masters are Jeremy Buhler and Gary Stormo.

Participants in the Journal Club present recent published research in the areas of computational molecular biology, systems biology, and bioinformatics. Every student receiving credit for participation must present a paper at one meeting of the Journal Club and must otherwise participate as described in the course overview. Other students, postdocs, faculty, and staff are welcome to attend and participate.

Announcements of upcoming meetings will be made via the mailing list Please ask one of the course masters if you want to join the list.

Schedule of Presentations for Spring 2022

Date Presenter Topic/Reading
Jan 18 Organizational Meeting
Jan 25 Emily Benedict C Farrell, M Thompson, A Tosevska, A Oyetunde, and M Pellegrini. BiSulfite Bolt: a bisulfite sequencing analysis platform. GigaScience 10(5):giab033, 2021.
Feb 1 Bridget Phillips M. Wöste, E Leitão, S Laurentino, B Horsthemke, S Rahmann, and C Schröder. wg-blimp: an end-to-end analysis pipeline for whole genome bisulfite sequencing data. BMC Bioinformatics 21:169, 2020.
Feb 8 Prashant Kuntala Q Liu, L Fang, G Yu, D Wang, C-L Xiao, and K Wang. "Detection of DNA base modifications by deep recurrent neural network on Oxford Nanopore sequencing data." Nature Communications 10:2449, 2019.
Feb 15 Ling Liao N Liang, B Li, Z Jia, C Wang, P Wu, et al. "Ultrasensitive detection of circulating tumour DNA via deep methylation sequencing aided by machine learning." Nature Biomedical Engineering 5:568-599, 2021.
Feb 22 Colin McCornack E Zhao, MR Stone, X Ren, J Guenthoer, KS Smythe, et al. "Spatial transcriptomics at subspot resolution with BayesSpace." Nature Biotechnology 39:1375-1384, 2021.
Mar 1 Juanru Guo and Clara Liu M Elosua-Bayes, P Nieto, E Mereu, I Gut, and H Heyn. "SPOTlight: seeded NMF regression to deconvolute spatial transcriptomics spots with single-cell transcriptomes." Nucleic Acids Research 49(9):e50, 2021.
Mar 8 Chia-Jung Lee Q Song and J Su. "DSTG: deconvoluting spatial transcriptomics data through graph-based artificial intelligence." Briefings in Bioinformatics 22(5):bbaa414, 2021.
Mar 15 Spring Break -- no meeting
Mar 22 Megan Burkhalter C Shengquan, Z Boheng, C Xiaoyang, Z Xuegong, and J Rui. "stPlus: a reference-based method fo rthe accurate enhancement of spatial transcriptomics." Bioinformatics 37s1:i299-i307, 2021.
Mar 29 Douglas Abrams T Risom, DR Glass, I Averbukh, GA Colditz, RB West, et al. "Transition to invasive breast cancer is associated with progressive changes in the structure and composition of tumor stroma." Cell 185(2):299-310.E18, 2022.
Apr 5 Shane Canfield and Emily King SV Pageon, PR Nicovich, M Mollazade, T Tabarin, and K Gaus. "Clus-DoC: a combined cluster detection and colocalization analysis for single-molecule localization microscopy data." Molecular Biology of the Cell 27(22):3627-3636, 2016.
Apr 12 John Wildenthal and Borna Novak MA Kennedy, WA Hofstadter, IM Cristea. "TRANSPIRE: a computational pipeline to elucidate intracellular protein movements from spatial proteomics data sets." J. of American Society of Mass Spectrometry 31(7):1422-1439, 2020.
Apr 19 Wenjin Zhang F Levet, G Julien, R Galland, C Butler, et al. "A tesselation-based colocalization analysis approach for single-molecule localization microscopy." Nature Communications 10:2379, 2019.
Apr 26 Dian Li DJ Williamson, GL Burn, S Simoncelli, J Griffie, et al. "Machine learning for cluster analysis of localization microscopy data." Nature Communications 11:1493, 2020.

Some Prior Editions of the Journal Club