2018 Annual Retreat

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.


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.


4:15-4:35 Registration, coffee
4:35-4:40Jordan HugheyOpening remarks
Session 1Moderator: Hillary Koch
4:40-5:00 Student lightning talks
5:00-5:20Mingfu ShaoEfficient algorithms for transcript assembly
5:20-5:40Lynn LinUnsupervised learning with uncertainty assessment
5:40-6:00Rachel HerderIntellectual Property Protection in the fields of Bioinformatics and Genomics: Current Trends and Penn State Resources
Brief 5 min break
Session 2Moderator: Scott Eckert
6:05-7:05Steven BrennerKeynote: Interpreting newborn genomes
8:30-9:00 Coffee and light refreshments
Session 3Moderator: Jordan Hughey
9:00-9:20 Student lightning talks
9:20-9:40Costas MaranasMetabolic pathway design through uncharted biochemical spaces
9:40-10:00Sarah AssmannRNA structure and stress response in plants: from single molecules to ecological implications
10:00-10:20Shaun MahonyCharacterizing the organization of regulatory complexes using ChIP-exo
10:20-10:40Laura CarrelEstimating inactive X expression from bulk RNAseq datasets to evaluate the X chromosome in gender-biased traits
10:40-10:50 Break
Session 4Moderator: Ayaan Hossain
10:50-11:10Tejaswini Mishra“The NASA Twins Study: A multi-omic, molecular and physiological analysis of a year-long human spaceflight”.
11:10-12:10Anton NekrutenkoWhy genome analysis in academia is the only job you actually want
12:20-2:00 Lunch and poster session
2:00-4:30Divyanshi Srivastava and Mehreen MughalWorkshop on Machine Learning

Lightning Talks

FridayTalk title
Monika CechovaHeterochromatic repeats in human trios
Jie XuIdentification of structure variation and 3D genome disruption in cancer cells and leukemia samples
Xiaoheng ChengDetecting shared ancient balancing selection without trans-species polymorphisms
Debmalya NandyCovariate Information Number for Feature Screening in Ultrahigh-Dimensional Supervised Problems
Tarik Salameh
Catherine Ambrosia DoudsSemi-empirical in vivo RNA structure prediction through motif constraining
Fan SongA web-based browser for visualizing 3D genome organization and long-range chromatin interactions
Ana M Gonzalez
Wilfried GuibletNon-B DNA structures affect polymerization fidelity

SaturdayTalk title
Bo ZhangEpigenetic regulation in differentiation therapy
Molly RathbunHerpes simplex virus genomics reveals insights into clinical infection outcome.
Matthew JensenAn interaction-based model for neuropsychiatric features of copy-number variants
Juan CerdaInvestigating convergent evolutionary trajectories of parasitism in plants
Sage WrightSolving cancer breakpoints
Sarthok Rasique RahmanIncremental BLAST: An "e-value-tionary" twist in BLAST searching
Vijay KumarNew paradigm to explain phenotypic heterogeneity in autism