Friday September 22-23, 2017
The 2017 Bioinformatics and Genomics retreat will be held on September 22nd and 23rd. The one and a half day retreat will feature Dr. Zhiping Weng from University of Massachusetts Medical School as the keynote speaker. There will also be a number of faculty and student talks as well as a workshop session on the September 23rd. The retreat is open to everyone and attendance is free, but everyone must register before September 15th.
Please be considerate while signing up for dinner (Friday), breakfast, and lunch (Saturday), because we need accurate headcount for ordering food and beverages.
Register for the retreat
Registration for this event is now closed.
Workshop
There will be a free hands-on workshop session entitled “Bioinformatics 101: Simple and Efficient Genomic Data Analysis” on Saturday afternoon.
Directions, Parking and Lodging
How to find us, where to park, and where to stay if attending the Bioinformatics and Genomics Retreat.
Directions and Parking
Friday parking is available in the East Parking Deck on Bigler road for $1 per hour.
Saturday parking is available in the Eisenhower Parking Deck for free. Directions to Eisenhower Parking Deck.
Eisenhower Parking Deck is conveniently located next to the Life Sciences Building.
Lodging
Participants are responsible for making their own accommodation arrangements.
Rooms are available at the Nittany Lion Inn on campus. There are also many other hotels in State College.
Agenda
Friday, Sept.22nd
| Time | Speaker | Topic | Location |
|---|---|---|---|
|
3:15-3:45PM 3:45 pm |
Ms. Divyanshi Srivastava
|
Regisration, Coffee Opening Remarks |
112 Forest Resource Building |
| Session 1 | |||
|
3:50 pm |
Moderator: Mr. Lin An Dr. Mark Shriver |
Evolutionary genetics of human facial feature variation |
112 Forest Resource Building |
|
4:10 pm |
Dr. Michael DeGiorgio |
Fast and robust detection of ancestral selective sweeps |
112 Forest Resource Building |
|
4:30 pm |
Dr. Feng Yue |
HiCPlus: A deep-learning framework for resolution enhancement of chromatin interaction data |
112 Forest Resource Building |
|
4:50 pm |
Dr. Kateryna Makova |
Non-B DNA affects polymerase progression and error rates in sequencers and living cells
|
112 Forest Resource Building |
|
5:10 pm |
Break |
112 Forest Resource Building |
|
|
5:20 pm |
Student Lightning Talks-I Moderator: Ms.Mehreen Mughal |
112 Forest Resource Building |
|
|
5:40 pm |
Dr. Kenneth Weiss (Moderator: Mr. Bruce Chen) |
How do we know what we (think we) know in genetics? |
112 Forest Resource Building |
|
6:40 pm |
Dinner and Poster |
Third Floor Bridge, Life Sciences Building |
|
Saturday, Sept.23rd
| Time | Speaker | Topic | Location |
|---|---|---|---|
| Session 2 | |||
|
9:00 am |
Moderator: Ms. Divyanshi Srivastava Dr. Molly Hall |
Emerging approaches for identifying complex associations predictive of common disease |
Berg Auditorium, 100 Life Sciences Building |
|
9:20 am |
Dr. Howard Salis |
Automated design of cellular sensors, circuits and pathways |
Berg Auditorium, 100 Life Sciences Building |
|
9:40 am |
Dr. Matthew Reimherr |
Functional regression models and applications |
Berg Auditorium, 100 Life Sciences Building |
|
10:00 am |
Dr. Dajiang Liu |
Understanding the genetic regulation and disease association for the inactive X chromosome from RNA seq data |
Berg Auditorium, 100 Life Sciences Building |
|
10:20 am |
Break |
Berg Auditorium, 100 Life Sciences Building |
|
| Session 3 | |||
|
10:40 am |
Moderator: Mr. Bruce Chen Dr. Qunhua Li |
Measuring reproducibility of Hi-C data |
Berg Auditorium, 100 Life Sciences Building |
|
11:00 am |
Dr. Yu Zhang |
Using functional annotations to map causal variants, tissues and target genes |
Berg Auditorium, 100 Life Sciences Building |
|
11:20 am |
Dr. Forrest Briscoe |
Genomic privacy and security: a perspective from organization science |
Berg Auditorium, 100 Life Sciences Building |
|
11:40 am |
Student Lightning Talks-II Moderator: Ms. Mehreen Mughal |
Berg Auditorium, 100 Life Sciences Building |
|
|
12:00 pm |
Short Break |
||
|
12:10 pm |
Keynote Speaker Dr. Zhiping Weng, Professor, University of Massachussets Medical School, Worcester, MA Moderator: Mr. Lin An |
ENCODE Encyclopedia: Featuring a Registry of Candidate Regulatory Elements and the Visualization Tool SCREEN for Searching Them |
Berg Auditorium, 100 Life Sciences Building |
|
1:15 pm |
Lunch and Poster |
Third Floor Bridge, Life Sciences Building |
|
|
2:30 pm |
Workshop |
Bioinformatics 101: Simple and Efficient Genomic Data Analysis |
Berg Auditorium, 100 Life Sciences Building |
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!
Presenters of posters at the 2017 Bioinformatics and Genomics Retreat: make sure you read this information about how to prepare and when to put up your poster.
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 begins at 6:40 pm on Friday, and at 1:15 pm on Saturday.
When do you need to hang your poster?
Please hang your poster by 2:30 pm at the latest on Friday .
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
There will be two sessions of lightning talks by graduate students. Each talk is of 90 sec duration. You will be allowed one power point slide. If interested in presenting your work in this format, register here.
| Friday | |
|---|---|
| Presenter | Talk Title |
| Naomi Yamada | Discovery and characterization of binding sub-types in ChIP-exo |
| Divyanshi Srivastava | Prior Chromatin State Determines Transcription Factor Binding |
| Rahulsimham Vegesna | Copy number and expression variation in ampliconic genes on the Y chromosome |
| Samarth Rangavittal | DiscoverY: a fast & lightweight method to isolate Y-sequences |
| Theodora Kaiser | Transcriptionally active CrERV modulate mule deer gene expression |
| Sarthok R Rahman | How did bumblebees get their colors? The genetic mechanism of mimetic coloration in bumblebees |
| Matthew Jensen | Gene discoveries in autism are biased towards intellectual disability |
| Binglan Li | Data Integration towards Comprehensive Models of Complex Diseases |
| Xinyuan Zhang | Simulation Study on Different Case-Control Sample Sizes for Rare-Variant Association Analysis |
| Alex Harris | Detection of selective sweeps from unphased genotypes |
| Hillary Koch | An extreme value spliced mixture model for the clone size distribution of the immune repertoire |
| Saturday | |
| Presenter | Talk Title |
| Nabeel Ahmed | Evolutionarily-encoded Translation Kinetics Coordinate Co-translational Ssb Chaperone Binding in Yeast |
| Bruce Chen | Dynamic Landscape of L1 Transposition Revealed with Functional Data Analysis |
| Fan Song | An Integrative Detection and Analysis of Structural Variations in Cancer Genomes |
| Monika Cechova | Heterochromatin variation among great apes |
| Yafei Lyu | A screening procedure for fused graphical lasso |
| Tao Yang | Deeprimer: Predicting the AmpliSeq performance |
| Tarik Salameh | SNP-based drug response modeling: A summary of goals, challenges, and advancements in pharmacogenomics |
| Robert Nichols | The Who, What, and Where of the microbiome, Combining metagenomics, 16S sequencing and metabolomics to get a clear picture of systematic effects of environmental toxins and novel drugs |
| Bo Zhang | Epigenetic regulation in T-ALL by Ikaros |
| Di Wu | Intraspecies variation in green ash response to an invasive insect |