Eran Mukamel, PI

Dr. Dominic Burrows

Dominic is interested in studying the organizing principles of brain cells at the microscale in health and disease. He is focusing on the epigenetic regulation of cell fate throughout the lifespan, and also on the development of new computational methods to study spatial patterns of gene expression throughout the brain.

Twitter | Git | Google scholar

Jo-Fan Chien

Jo-Fan is working on genomic variation in brain cell types and their epigenomes. She is also interested in how disease or sensory input affect cells' transcriptome and epigenome properties.

Mike Cuoco

Mike is interested in the causes and consequences transposable element activity in the developing, healthy, and aging brain. In his current work, Mike uses novel molecular and computational techniques to measure and perturb transposable element activity in neurons.

Alon Gelber

Alon is interested in the development of computational methods for the analysis of single-cell omics data, and the application of these methods to answer questions about the molecular underpinnings of behavior. He is currently working on transcriptomic sex differences in the cortex.

Abbey Green

Abbey is interested in the field of biomedical informatics and is currently working to elucidate the relationship between aging and mitochondrial DNA methylation in the brain

Dr. Junhao Li

Research Scientist
contact: jul307 [at] ucsd [dot] edu

Junhao is interested in finding non-coding RNAs related to neuroepigenetics from large-scale next-generation sequencing data, and investigating their implications for neurodevelopment and neurological disorders.

Heng Xu

PhD Candidate in Bioinformatics and Systems Biology
University of California, San Diego
Contact: hex002 [at] ucsd [dot] edu

Heng is engaged in the field of genomics, specifically focusing on DNA methylation. His aim is to unravel the mechanisms that interconnect DNA sequences, epigenomics, and transcriptomes, through machine learning/deep learning techniques.

Alumni

Dr. Fangming Xie

Ph.D. in Physics; currently Postdoctoral Fellow at UCLA
University of California, San Diego
contact: f7xie [at] ucsd [dot] edu

Fangming is interested in differentiating DNAs from their mixture of different tissue origins, with applications to detection of neurodegenerative disease.

Russell Li

High school student,
St. John's School in Houston
Contact: rli [at] sjs [dot] org

Russell is a high school senior at St. John's School in Houston. His research interests include using deep learning to analyze epigenomic sequencing data and uncovering the connection between the patterns and aberrations in such data and various neurological disorders.

Ethan Armand

UCSD Cognitive Science
contact: earmand [at] ucsd [dot] edu

Ethan is now a Ph.D. student in the Bioinformatics and Systems Biology program at UCSD.

Lily Tran

Bioinformatics Programmer
University of California, San Diego
Contact: lit008 [at] ucsd [dot] edu

Lily is interested in database engineering and applying machine learning algorithms to next-generation sequencing data.

Aditya Chandrasekar

UCSD BS in Computer Science with specialization in Bioinformatics; Mathematics minor
University of California, San Diego
contact: adc041 [at] ucsd [dot] edu

Aditya is interested in applying software and bioinformatics tools for understanding large-scale genomic data, as well as the role of the epigenetic profile of the brain in development and disease. He is currently hoping to write software for the lab, especially across web portal development.

Christopher Keown

Ph.D. Candidate in Cognitive Science
University of California, San Diego
website: http://www.chriskeown.com
contact: christopher.keown [at] gmail [dot] com

Chris is interested in examining genome-wide DNA methylation patterns in the brain to understand how methylation markers differ across cell types and the functional implications of this; how changes in methylation may support cognition; and whether methylation differences may be implicated in disorders such as schizophrenia and autism.

Dr. Wayne Doyle

Postdoctoral Fellow
University of California, San Diego
contact: widoyle [at] ucsd [dot] edu

Now at Active Motif

Krystyna Kolodziej

Ph.D. Candidate in Biomedical Sciences
University of California, San Diego
contact: kkolodzi [at] ucsd [dot] edu

Han Li

UCSD CSE
University of California, San Diego
contact: h5li [at] ucsd [dot] edu

Dr. Urvashi Bhattacharyya

Shweta Patkar

Research Associate, Summer 2017
contact: shwetapatkar96 [at] gmail [dot] com

Tianhao Xiao

Research Associate, Summer 2017

Diego Zamora Rodriguez

Research Associate, Summer 2017
B.A. candidate, Computer Science
Tecnologico de Monterrey, Campus Guadalajara (ITESM), Mexico

Michael Hatch

B.S. candidate in Cognitive Science
University of California, San Diego
contact: mjhatch [at] ucsd [dot] edu

Alex Jorjorian

B.S. candidate in Bioengineering Biotechnology
University of California, San Diego
contact: ajorjori [at] ucsd [dot] edu

Tomo Ishihara

We are recruiting students and postdocs interested in getting involved with our work on computational analysis and modeling of neural dynamics and epigenomics data sets. If you are interested, email us at lab [at] brainome [dot] ucsd [dot] edu.

Postdoctoral position in Computational Neuro-Epigenomics

The UCSD Computational Neural Data and Dynamics Lab, led by Prof. Eran Mukamel, is seeking applications for a funded postdoctoral research position as part of our group's studies of epigenomic regulation in brain cells. Our lab in the University of California, San Diego (UCSD) Cognitive Science department uses tools from bioinformatics and machine learning to analyze a variety of neural epigenetic processes. We have identified unique forms of DNA methylation in neurons and glial cells, and we are working to understand the distribution, development and potential function of these epigenomic marks. Our theoretical and computational research group has close ties with experimental neurobiology and genomics labs in San Diego. More information about the lab is at http://brainome.ucsd.edu.

Applicants should hold a Ph.D. (or expect to receive one shortly) and have a strong background in computational biology (e.g. computational neuroscience, bioinformatics), or physical science or engineering (e.g. math, physics, computer science, bioengineering) as well as a strong interest in fundamental genomic processes underlying neural development and cognition. Previous experience with genomic or epigenomic data analysis is an advantage, but not necessary.

To apply, please send the following to Prof. Mukamel (emukamel@ucsd.edu):

• A cover letter describing your background, research interests and how they fit with our lab
• Curriculum vitae
• Contact information for 2-3 references
• If available, a sample of the applicant's work, e.g. a manuscript, thesis, or other work product
Salary will be commensurate with NIH rates. For inquiries or more information, please contact Eran Mukamel at the address above.

Contact