2017 Annual Retreat

Friday September 22-23, 2017

The 2017 Bioinformatics and Genomics retreat was held on September 22nd and 23rd. The one and a half day retreat featured Dr. Zhiping Weng from the University of Massachusetts Medical School as the keynote speaker. There were also a number of faculty and student talks as well as a workshop session on the September 23rd.

Register for the retreat

Registration for this event is now closed.


There will be a free hands-on workshop session entitled “Bioinformatics 101: Simple and Efficient Genomic Data Analysis” on Saturday afternoon.


Friday, Sept.22nd

Time Speaker Topic Location


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


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


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


Bioinformatics 101:

Simple and Efficient Genomic Data Analysis

Berg Auditorium, 100 Life Sciences Building

Lightning Talks

There were two sessions of lightning talks by graduate students. Each talk was of 90 second duration. Students were allowed one PowerPoint slide.

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
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