Li Lab

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Recent News

. 09/2020: Jie's DORGE cancer driver gene paper was accepted in Science Advances

. 08/2020: Jianfeng's CHALM methylation paper was accepted in Nature Communications

. 08/2020: Cui Ya's NG-Circos paper was accepted in NAR Genomics and Bioinformatics

. 01/2020: Our lab has moved to University of California Irvine

. 01/2020: Lei's paper w/ Ryan Potts was accepted in Molecular Cell

. 10/2019: Collaborative work with David Allis and Wen Hong was accepted in Nature;

. 10/2019: Collaborative work with Suming Huang was accepted in Cancer Cell;

. 9/2019: Collaborative work with Costa-Mattioli's group was accepted in Science;

. 05/2019: Collaborative work with Paolo Sassone-Corsi at UCI was published in Cell

. 02/2019: Our new 5-year NCI R01 grant regarding DNA methylation canyon was funded.

. 07/2018: Jianzhong's DNA methylation canyon paper was accepted to Genome Biology.

. 06/2018: Jiejun’s paper was accepted to Nature Cell Biology.

. 06/2018: Xueqiu's DNMT3A binding paper was accepted to Genome Biology

. 03/2018: HJ Park's papers were accepted to PLOS Computational Biology and Cell Reports, respectively.

. 01/2018: HJ Park's 3'UTR vs ceRNA paper was finally accepted to Nature Genetics after 1.5 years and 3 rounds of revisions/appeals. A good start of the new year!


News Archive

Our lab is focused on the design and application of bioinformatics algorithms to elucidate global regulatory mechanisms in normal development and diseases such as cancer. We have a solid track record in large-scale genomics data analysis, and in developing widely used open-source bioinformatics software, such as MACS (>7,000 citations) for ChIP-seq and RSeqQC (>800 citations) for RNA-seq. In collaboration with experimental biologists, we have used bioinformatics to gain novel biological insights into development, aging, stem cell, neurologic disorders, and various cancers. Our areas of expertise include 1) DNA methylation using Bisulfite-seq; 2) Epigenetic regulation using ChIP-seq; 3) Alternative Polyadenylation (APA); 4) Non-coding RNA; 5) Nucleosome organization using MNase-seq. Since establishing our own bioinformatics lab in early 2008, we have (as of Febuary 2020)

  • Published 143 peer-reviewed papers through solid methodology development and extensive collaboration research, including 20 senior-author papers in Nature and Cell series.
  • Been well-funded with total external funding >$1.0 million per year, including 4 PI grants from NIH: NIH R01HG007538 (2013-2020), R01CA193466 (2015-2020), R01CA228140 (2019-2024) and U54CA217297 (2017-2022).
  • Mentored the first 7 postdoc trainees to start their tenure track faculty positions in prestigious research institutions in the US (6) and China (1).

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