Citizen Science

Nuclei Ninja

In order to train a computer to recognize 3D nuclei in tissue cleared images of brains, we are starting a citizen science project called Nuclei Ninja (https://www.nucleininja.org/) together with Guorong Wu, David Borland, and Minjeong Kim. Check out the project at the website above and see how you can get involved!

Teaching Materials

Introduction to Imaging Genetics 2018

Here are the lecture slides from the Introduction to Imaging Genetics educational day course at the Organization for Human Brain Mapping 2018 meeting in Singapore.

A brief history of imaging genetics - Jason Stein, UNC Chapel Hill
The genetic influences on neuropsychiatric disease risk - Sven Cichon, Universitat Basel, Switzerland
The effect of common genetic variation on human brain structure - Paul Thompson, USC
The effect of rare variation on human brain structure - Carrie Bearden, UCLA
Connecting genetic variation to gene regulation - Bernard Ng, University of British Columbia

Introduction to Imaging Genetics 2017

Here are the lecture slides from the Introduction to Imaging Genetics educational day course at the Organization for Human Brain Mapping 2017 meeting in Vancouver, Canada.

A brief history of imaging genetics - JB Poline, UC Berkley
The modern day endophenotype - Roberto Toro, Institut Pasteur
Utilizing big datasets in imaging-genetics - Derrek Hibar, Janssen Pharmaceuticals
Imaging Epigenetics - Sylvane Desrivieres, King's College London
Networks of gene expression and brain function - Vilas Menon, HHMI Janelia Research Campus
Rare variant associations - David Glahn, Yale
After the association - Jason Stein, UNC Chapel Hill

Computational Tools

RRHO

The RRHO package was written in collaboration with Jonathan Rosenblatt and is available as part of the Bioconductor suite to be used with the R statistical package.  The package compares the degree and significance of overlap between two ranked lists of same length. The function was originally proposed by Plaisier et al. and implemented in our work (Stein et al., 2014), among others.

Context

The CoNTExT package was written in collaboration with Luis de la Torre Ubieta in the Geschwind lab. The package evaluates the fidelity of neural stem cell differentiation. A publication describing this tools is available here (Stein et al., 2014).

TALENSeek

The TALENSeek package was written in collaboration with Joshua Grimley at the Allen Institute for Brain Science.  This tool is used to identify TALEN binding sites in the human and mouse genome.  A publication describing this tool and its application is available here (Martinez et al., 2015).