October 5 -6, 2018
The 2018 Bioinformatics and Genomics retreat was held on October 5th and 6th. The one and a half day retreat featured Dr. Steven Brenner of University of California, Berkeley as the keynote speaker. There were a number of faculty and student talks as well as a workshop session on the October 6th.
Workshop
Machine Learning Tools for Visualization and Classification of Heterogenous Data. The workshop will use single cell RNA-sequencing data to explore visualization and classification of heterogenous data.
Agenda
| When | Who | What |
| Friday | ||
| 4:15-4:35 | Registration, coffee | |
| 4:35-4:40 | Jordan Hughey | Opening remarks |
| Session 1 | Moderator: Hillary Koch | |
| 4:40-5:00 | Student lightning talks | |
| 5:00-5:20 | Mingfu Shao | Efficient algorithms for transcript assembly |
| 5:20-5:40 | Lynn Lin | Unsupervised learning with uncertainty assessment |
| 5:40-6:00 | Rachel Herder | Intellectual Property Protection in the fields of Bioinformatics and Genomics: Current Trends and Penn State Resources |
| Brief 5 min break | ||
| Session 2 | Moderator: Scott Eckert | |
| 6:05-7:05 | Steven Brenner | Keynote: Interpreting newborn genomes |
| Saturday | ||
| 8:30-9:00 | Coffee and light refreshments | |
| Session 3 | Moderator: Jordan Hughey | |
| 9:00-9:20 | Student lightning talks | |
| 9:20-9:40 | Costas Maranas | Metabolic pathway design through uncharted biochemical spaces |
| 9:40-10:00 | Sarah Assmann | RNA structure and stress response in plants: from single molecules to ecological implications |
| 10:00-10:20 | Shaun Mahony | Characterizing the organization of regulatory complexes using ChIP-exo |
| 10:20-10:40 | Laura Carrel | Estimating inactive X expression from bulk RNAseq datasets to evaluate the X chromosome in gender-biased traits |
| 10:40-10:50 | Break | |
| Session 4 | Moderator: Ayaan Hossain | |
| 10:50-11:10 | Tejaswini Mishra | “The NASA Twins Study: A multi-omic, molecular and physiological analysis of a year-long human spaceflight”. |
| 11:10-12:10 | Anton Nekrutenko | Why genome analysis in academia is the only job you actually want |
| 12:20-2:00 | Lunch and poster session | |
| 2:00-4:30 | Divyanshi Srivastava and Mehreen Mughal | Workshop on Machine Learning |
Lightning Talks
| Friday | Talk title |
| Monika Cechova | Heterochromatic repeats in human trios |
| Jie Xu | Identification of structure variation and 3D genome disruption in cancer cells and leukemia samples |
| Xiaoheng Cheng | Detecting shared ancient balancing selection without trans-species polymorphisms |
| Debmalya Nandy | Covariate Information Number for Feature Screening in Ultrahigh-Dimensional Supervised Problems |
| Tarik Salameh | |
| Catherine Ambrosia Douds | Semi-empirical in vivo RNA structure prediction through motif constraining |
| Fan Song | A web-based browser for visualizing 3D genome organization and long-range chromatin interactions |
| Ana M Gonzalez | |
| Wilfried Guiblet | Non-B DNA structures affect polymerization fidelity |
| Saturday | Talk title |
| Bo Zhang | Epigenetic regulation in differentiation therapy |
| Molly Rathbun | Herpes simplex virus genomics reveals insights into clinical infection outcome. |
| Matthew Jensen | An interaction-based model for neuropsychiatric features of copy-number variants |
| Juan Cerda | Investigating convergent evolutionary trajectories of parasitism in plants |
| Sage Wright | Solving cancer breakpoints |
| Sarthok Rasique Rahman | Incremental BLAST: An "e-value-tionary" twist in BLAST searching |
| Vijay Kumar | New paradigm to explain phenotypic heterogeneity in autism |