Julie Zhu, Ph.D.


Professor Julie Zhu, Ph.D.
   
Ph.D., 1999, Nutritional Sciences, University of Wisconsin-Madison 
M.S., 2001, Computer Science, DePaul University, Chicago 
   
Office: University of Massachusetts Medical School
364 Plantation Street, LRB-613
Worcester, MA 01605
Phone: 508-856-5256
Email: Julie.Zhu@umassmed.edu

Research

We develop and apply algorithms and computational tools to analyze, annotate and integrate various datasets, including those generated from high-throughput experiments such as ChIP-seq, ChIP-chip, RNA-seq, PAS-seq, GUIDE-seq, ATAC-seq, NAD-seq, Cut&Run, Exome sequencing, shRNA and CRISPR screening. My group is an active contributor to the open-source open-development Bioconductor project. We have developed more than a dozen packages with various utilities, ranging from applications of machine learning, peak caller, annotation, to visualization. Among them, one of the widely downloaded and cited packages ChIPpeakAnno is for mining and annotating ChIP-seq, ChIP-chip dataset or any type of dataset consisting of a list of genomic coordinates .  In addition, we have also developed two packages for designing and evaluating gRNAs for the genome editing technology using engineered CRISPR-Cas9 nucleases: CRISPRseek is for designing target-specific and efficient gRNAs; and GUIDEseq is for evaluating the specificity of gRNAs using GUIDE-seq technology. Additional information on software packages developed by the Bioinformatics Core of MCCB is available at http://www.umassmed.edu/mccb/bioinformatics-core/software/.

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