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
PresenterTalk 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
PresenterTalk 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