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.


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.


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

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

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