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An unprecedented view of gene regulation

Posted
May 8, 2023

MIT engineers’ new technique analyzes the 3D organization of the genome at a resolution 100 times higher than before.

Image: Melanie Gonick/MIT

Much of the human genome is made of regulatory regions that control which genes are expressed at a given time within a cell. Those regulatory elements can be located near a target gene or up to 2 million base pairs away from the target.

To enable those interactions, the genome loops itself in a 3D structure that brings distant regions close together. Using a new technique, MIT researchers have shown that they can map these interactions with 100 times higher resolution than has previously been possible.

“Using this method, we generate the highest-resolution maps of the 3D genome that have ever been generated, and what we see are a lot of...

Bioengineering and Neuroengineering
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Event

CSB Thesis Defense

Posted
May 3, 2023

 Ph.D. Candidate: Alexander Wu

Advisor: Prof. Bonnie Berger (MATH, EECS)

Title: Towards causality in gene regulatory network inference

Abstract: 

Understanding the coordination of biomolecules that underlies gene regulation is key to gaining

mechanistic insights into cellular functions, phenotypes, and diseases. Advances in single-cell

technologies promise to unveil mechanisms of gene regulation at unprecedented resolution by

enabling measurements of genomic and/or epigenetic features for individual cells. However,

unlocking insights from single-cell data requires algorithmic innovations.

This thesis introduces a series of methods for uncovering gene regulatory relationships

underlying cellular identity and function from single-cell data. Firstly, we present a framework for

enhancing the detection of statistical associations in small...

CSB Thesis Defense
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Event

CSB Theis Defense

Posted
May 1, 2023

CSB PhD Candidate: Adam Atanas

Advisor: Prof. Steven Flavell

Title: "Brain-wide representations of behavior spanning multiple timescales and states in C. elegans"

Abstract: "Changes in an animal’s behavior and internal state are accompanied by widespread changes in activity across its brain. However, how neurons across the brain encode behavior and how this is impacted by state is poorly understood. We recorded brain-wide activity and the diverse motor programs of freely-moving C. elegans and built probabilistic models that explain how eachneuron encodes quantitative features of the animal’s behavior. By determining the identities of the recorded neurons, we created, for the first time, an atlas of how the defined neuron classes in the C. elegans connectome encode behavior. Many neuron classes have conjunctivere presentations of multiple behaviors. Moreover, while many neurons encode current...

Bioengineering and Neuroengineering | CSB Thesis Defense
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Event

CSB Student Seminar Series

Posted
April 14, 2023

The April CSB seminar is scheduled for Tuesday, April 18th at 1 PM in 68-180. The seminar will be catered with pizza from OTTO (with vegan and GF options). We will have three speakers present their work on a variety of topics. 

 

Hannah Jacobs | Burge and Karczewski Labs 

Title: Using beta binomial models to understand widespread diversity of splicing in humans

 

Pablo Cardenas Ramirez | Niles Lab 

Title: Genomic models describe epidemiological determinants of pathogen evolution

 

Nicolas Romeo | Dunkel Group 

Title: Dynamics, scaling behavior, and control of nuclear wrinkling

 

 

 

CSB Student Seminars
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