RESEARCH | biociphers

Research

Topics

Machine Learning
Computational Biology
Bioinformatics

Alternative splicing quantification
Post-transcriptional regulation
Regulatory elements modeling

Genetic variations effect on RNA processing
Personalized medicine based on clinical, genetic, and genomic profiling

Projects

The role of splicing variations in human disease

Multiple projects in the lab involve the role of splicing variations in disease such as cancer and neurodegeneration. We develop algorithms to detect these splicing variations from RNASeq, combine them with other data (multi-omics), experimentally validate those in relevant cell lines/primary tissues, and study their functional consequences

Lab member

Mathieu Quesnel-Vallieres, Matthew Gazzara, David Wang, Dina Issakova

In collaboration with

Kristen Lynch, Sara Cherry, Martin Carrol, Andrei Thomas-Tikhonenko, David Elliot, Elizabeth Bhoj

High-throughput assays development

We are developing new high-throughput assays for RNA processing.

Lab member

Kevin Yang, Nathaniel Islas, Danielle Gutman, Isaac Hoskins, Benjamin Wales-Mcgrath

In collaboration with

Peter Choi, Nick Hand

Quantification and Visualization of RNA splicing

A main focus is developing methods and tools for the community to address the computational challenges posed by high throughput data for accurately quantifying and visualizing splice variants and how these change across different conditions.

Lab member

Seong Han, San Jewell, Matthew Gazzara

RNA Processing Regulatory

Mechanisms

The lab iterates between computational modeling and experimental verifications of mechanisms involved in RNA processing

Lab member

Danielle Gutman, Farica Zhuang, Matthew Gazzara, Benjamin Wales-Mcgrath

In collaboration with

Kristen Lynch, Peter Choi, Nick Hand

Alternative Splicing Prediction

A major focus of the lab is developing algorithms and tools for predicting and analyzing splicing outcome under varying conditions.

Lab member