October 5 -6, 2018
The 2018 Bioinformatics and Genomics retreat will be held on October 5th and 6th. The one and a half day retreat will feature Dr. Steven Brenner, University of California, Berkeley l as the keynote speaker. There will also be a number of faculty and student talks as well as a workshop session on the October 6th. The retreat is open to everyone and attendance is free, but everyone must register before September 28th.
Please be considerate while signing up for breakfast and lunch (Saturday) because we need accurate headcount for ordering food and beverages.
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.
Register for the retreat
Registration for this event is now closed.
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 |
Poster session
Students in the Bioinformatics and Genomics program are required to present a poster.
This is a great opportunity to discuss your research with faculty and students in the Bioinformatics and Genomics community at Penn State as well as with our distinguished keynote speaker!
Who can present a poster?
Anyone who registered for the Bioinformatics and Genomics PhD program are particularly encouraged to present. This is a great chance for you to discuss your research with faculty, keynote speakers and other experienced researchers.
When will poster sessions be held?
The poster session is held during lunch on Saturday (12:20-2:00PM)
When do you need to hang your poster?
You may hang posters after 3:30PM on Friday and latest by 11AM on Saturday
Thumbtacks will be provided.
How big should posters be?
Poster boards are 4 foot high by 4 foot wide (120 x 120 cm). Please do not present a poster larger than this.
What information should be included on posters?
- Information about your research
- Title
- List of authors and their affiliations
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 |