Welcome to CAB at St. Jude

The Transcriptomics Group focuses on transcriptome-wide analysis of differential gene expression and differential splicing of mRNAs including bulk gene expression, single-cell gene expression, translation (the translatome). We also integrate RNA-seq data with other high throughput sequencing data such as epigenomics data to better understand the biology. In addition, the group is interested in establishing analytic/visualization pipelines to support the work of St. Jude investigators.


We are expereinced in data analysis on areas related to:

  • Cancer Biology
  • Cancer Immunotherapy
  • Developmental Biology

We categorized Transcriptomics Analyses into three major topics:

  1. Differential gene expression: Identify differentially expressed gene using high thoughput data such as RNA-seq at both bulk and single cell level.
  2. splicing and fusion detection: Identify alternative splicing and fusion events using RNA-seq.
  3. Data integation: Integrate RNA-seq data with epigenomics data such as DNA methylation to better understand the biology.

Technologies and methods

The CAB transcriptomics is primarily a bioinformatic group that uses a wide range of genomic, bioinformatic, and statistical methods to analyze biological data. The main platforms are:

  • RNA-Seq/SLAM-Seq/scRNA
  • ChIP-Seq
  • ATAC-Seq/scATAC
  • WGBS

Joining St. Jude

If you are interested in joining please go to the recruitment page.

Funding

We are grateful for funding from the National Cancer Institute at National Institute of Health

News

Oct 19th 2021

New paper! Wang et al. 2021 published in Life Sci. Alliance: PROSER1 mediates TET2 O-GlcNAcylation to regulate DNA demethylation on UTX-dependent enhancers and CpG islands. Kudo to Wojciech, first co-first author with St. Jude PIs

Aug 24th 2021

New paper! Xu et al. 2021 published in Genome Bio.: Acute depletion of CTCF rewires genome-wide chromatin accessibility. Press Release

Jun 8th 2021

New paper! Montefiori et al. 2021 published in Cancer Discov.: Enhancer Hijacking Drives Oncogenic BCL11B Expression in Lineage Ambiguous Stem Cell Leukemia

Jun 4th 2021

New paper! Zong et al. 2021 published in J. Exp. Med.: Foxp3 Enhancers Synergize to Maximize Regulatory T Cell Suppressive Capacity

Apr 5th 2021

New paper! Chen et al. 2021 published in Nat Genet, Dr. Mohamed Nadhir Djekidel(co-first) deciphers the Mysterious Roles of PRC Complexes in Histone Modification

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