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Search Results to Lihua Zhu PhD

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One or more keywords matched the following properties of Zhu, Lihua

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Academic Background

Lihua Julie Zhu obtained her Ph.D. in Nutritional Sciences from the University of Wisconsin-Madison in 1999, and her M.S. in Computer Science from DePaul University in Chicago in 2001. She joined the Bioinformatics Core of the Robert H. Lurie Comprehensive Cancer Center (RHLCCC) of Northwestern University in 2001, where she was the Director of Bioinformatics Consulting Core from 2003 to 2005 and the Director of Clinical Informatics Group from 2005 to 2007. She joined the University of Massachusetts Medical School (UMMS) as the head of Bioinformatics core of Program in Gene Function and Expression (PGFE) in 2007.  Dr. Zhu is currently a professor and the head of Bioinformatics Core in the Department of Molecular, Cell and Cancer Biology (MCCB) of UMMS.

Computational Biology and Bioinformatics

Photo: Julie Zhu, Ph.D.

We are interested in the understanding of gene regulation and cancer etiology, biomarker discovery, and development and application of genome editing technology by mining and integrating various high-throughput datasets such as ChIP-seq, RNA-seq, ATAC-seq, miRNA-seq, Hi-C, shRNA-seq, PAS-seq, NAD-seq and GUIDE-seq. Our expertise is algorithm and computational tool development. My group is an active contributor to the open-source open-development Bioconductor project. We have developed a dozen packages with various utilities, ranging from machine learning, peak calling, motif identification and alignment, quality assessment of ATACseq data, annotation, data integration, visualization, gRNA design and genome-wide offtargets identification in CRISPR genome editing studies.


One or more keywords matched the following items that are connected to Zhu, Lihua

Item TypeName
Academic Article Mining biomedical data using MetaMap Transfer (MMtx) and the Unified Medical Language System (UMLS).
Academic Article Annotating the human genome with Disease Ontology.
Academic Article ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data.
Academic Article Visual presentation as a welcome alternative to textual presentation of gene annotation information.
Academic Article Integrative analysis of ChIP-chip and ChIP-seq dataset.
Academic Article Interpreting microarray results with gene ontology and MeSH.
Academic Article FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system.
Academic Article Thrombopoietin/MPL participates in initiating and maintaining RUNX1-ETO acute myeloid leukemia via PI3K/AKT signaling.
Concept Data Interpretation, Statistical
Concept Database Management Systems
Concept Databases, Genetic
Concept Data Collection
Concept Molecular Sequence Data
Academic Article CRISPRseek: a bioconductor package to identify target-specific guide RNAs for CRISPR-Cas9 genome-editing systems.
Academic Article Global analysis of CPSF2-mediated alternative splicing: Integration of global iCLIP and transcriptome profiling data.
Academic Article Tead and AP1 Coordinate Transcription and Motility.
Academic Article GUIDEseq: a bioconductor package to analyze GUIDE-Seq datasets for CRISPR-Cas nucleases.
Academic Article ATACseqQC: a Bioconductor package for post-alignment quality assessment of ATAC-seq data.
Academic Article trackViewer: a Bioconductor package for interactive and integrative visualization of multi-omics data.
Academic Article OneStopRNAseq: A Web Application for Comprehensive and Efficient Analyses of RNA-Seq Data.
Academic Article dagLogo: An R/Bioconductor package for identifying and visualizing differential amino acid group usage in proteomics data.

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