Shenzhen Bay Laboratory
Computational and Disease Genomics Lab
News
February, 2026
● Congratulations that our work has been accepted in principle by Nature Biomedical Engineering. Our study reveals a novel Engineering System (3′UTRCES) that can precisely manipulate mRNA 3′UTR length at the single-transcript level, uncovering an unexpected link between SPSB1 3′UTR shortening and cancer immune evasion, and establishing "3′UTR-targeted therapy" as a promising strategy to overcome immunotherapy resistance in prostate cancer.
December, 2025
● Our computational method MAAS has finally been accepted by Genome Medicine. MAAS
enables flexible and sensitive identification of clinically relevant tumor subpopulations using a
single scATAC-seq assay.
August, 2025
● Congratulations to Dr. Xudong Zou in our team for receiving the General Grant of the
National Natural Science Foundation of China. This grant will support him to develop
computational method for RNA-seq data.
● Congratulations to our postdoctoral associate Dr. Ting Zhang, who has been recevied the
Prestigious 2025 ASHG Trainee Research Excellence Award – Postdoctoral Semifinalist. This
year’s competition was exceptionally competitive, with more than 800 applicants, from which only
42 semifinalists were chosen. We are also proud to share that our student Hui has been awarded
the ASHG Travel Award. Cheers!
● We have two abstracts been ACCEPTED as platform (oral) presentations at the ASHG 2025 Annual
Meeting in Boston. There are less than 10% of abstracts can be selected as oral presentations.
Also Dr. Li was invited to moderate a platform session on Computational Tools for Precision
Therapeutics at ASHG. Cheers.
July, 2025
● Dr. Li was invited to give a talk at Harvard Medical School and the International
Conference on Intelligent Biology and Medicine (ICIBM) .
May, 2025
● Congratulations that our collaborative work with Dr. Mireya Plass has been accepted in
principle by Nature Communications. Our study reveals a novel computational
method SCALPEL that can accurately quantification of transcript isoforms at the
single-cell level.
March, 2025
● Professor Michael Snyder, Chair of the Department of Genetics at Stanford University
School of Medicine, visited our Lab and delivered a great presentation about precision
medicine. Prof. Snyder also had a nice discussions with our lab trainees.
February, 2025
● Congratulations to our trainee, Dr. Zeyang Wang, starting his independent lab as
an Associate Professor at Hainan Medical University! He is the third independent
faculty member from our lab. Cheers!
● Congratulations that our collaborative work with Dr. Yongsheng Shi has been
accepted in principle by Molecular Cell. Our study reveals a novel
"nuclear RNA degradation code" that triggers PAXT-mediated RNA decay.
January, 2025
● Our genetic basis of enhancer RNAs paper has finally been accepted by
Advanced Science. We constructed a comprehensive atlas of
eRNA-mediated genetic effects in 49 human normal tissues and 31 tumor types,
revealing a distinctive class of pan-cancer susceptibility eRNAs. Congratulations
to Wenyan, Zeyang and Yinuo and many co-authors in the lab.
● Congratulations that our collaborative work with Dr. Ruan Wei, Dr Eltzschig has
been accepted by Nature. Our study demonstrates that the
BMAL1/HIF2A heterodimer plays a crucial role in modulating the circadian
variations of myocardial injury. Cheers.
● Congratulations to our graduate student, Hui, for receiving the prestigious
Shenzhen Bay Laboratory Director’s Scholarship this year. We are honored
that our lab has been recognized with this award for three consecutive
years.
December, 2024
● Congratulations to our two trainees, Dr. Wenyan Chen and Dr. Ruofan Ding, on
their new faculty positions at Inner Mongolia University and Huizhou
University, respectively.
November, 2024
● Our alternative polyadenylation outliers (aOutliers) paper has finally
been accepted by Nature Communications. We conducted a
comprehensive cross-tissue analysis of aOutliers and discovered a unique
class of aOutliers-associated RVs with a large effect on disease.
Congratulations to Xudong.
August, 2024
● Congratulations to Dr. Ruofan Ding in our team for receiving the
Young Scientists Grant of the National Natural Science
Foundation of China. This grant will support him to develop
computational method for single cell sequencing data.
● Congratulations to our student Hui, who has received the Prestigious
2024 predoctoral Trainee Research Excellence Award. Also, Xudong
has received the Reviewers’ Choice Award as his abstract ranked
within the top 10% of all abstracts. Cheers!
July, 2024
● Hui’s abstract has been ACCEPTED as a oral presentation at
the ASHG 2024 Annual Meeting. There are less than 10% of abstracts
can be selected as oral presentations. Cheers!
June, 2024
● Our cancer alternative tandem TSS paper has finally been
accepted by Science Advances. We have developed a
new computational method (DATTSS) and demonstrated the widespread
dysregulation of tandem TSS usage in tumors. Our findings suggest
dysregulated tandem TSS usage represents an additional layer of
cancer-associated transcriptome alterations.
March, 2024
● Our PhD Candidate Hui was invited to give a presentation at
National Genome Informatics Conference (NGlC) 2024 in Wuhan,
China.
February, 2024
● Our cancer susceptibility genes paper has finally been
accepted by Nature Communications. We have
demonstrated a distinct class of cancer susceptibility genes
revealed by alternative polyadenylation
transcriptome-wide association study. Congratulations to Hui
and Dr. Wang and also other lab
members.
January, 2024
● Congratulations to our student Qixuan for being awarded
the Shenzhen Bay Laboratory (SZBL)
Director's Scholarship by Prof. Nieng Yan, Director of the
SZBL.
● Our RBBP6 collaborative work with Qi Xie’s Group has been
finally accepted by Cell
Discovery. We identified that E3 ligase RBBP6
is essential for glioblastoma stem cell
maintenance and regulates MYC expression. Congratulations to
Wenyan. Cheers!
December, 2023
● Dr. Li was invited to present in the 12th National
Ribonucleic Acid (RNA) Academic Meeting in
Shanghai.
November, 2023
● Our xQTLbiolinks paper has been accepted by
Briefings in Bioinformatics. We described
the xQTLbiolinks, as an end-to-end bioinformatic tool for
mining and analyzing bulk and single-cell
xQTL data for discovering disease susceptibility genes.
Congratulations to Dr. Ding and other lab
members.
● Our immune-response alternative polyadenylation has been
finally accepted by Nature
Communications. We have demonstrated the atlas
of responsive 3′aQTLs (raQTLs), i.e.,
genetic variants associated with APA of target genes upon
immune stimulations. Congratulations to Dr.
Ma and other lab members.
October, 2023
● Welcome Dr. Xixian Ma joins our lab as a Postdoctoral
Associate, Dr. Ma received his PhD in
Computational Biology from PICB (Partner Institute for
Computational Biology) under the supervision of
Prof. Shuhua Xu. Additionally, also we congratulate our
student on being awarded the prestigious
National Scholarship for Graduate Excellence.
September, 2023
● Our scQTLbase paper has been accepted by Nucleic
Acids Research. We described an
integrated human single-cell eQTL portal, which features 304
datasets across 57 cell types and 95 cell
states. Congratulations to Dr. Ding, Qixuan, Lihai and other
lab members!
August, 2023
● We received a new NSFC award for the next four years to
study computational modeling of intronic
polyadenylation in human cancers. Cheers!
● Xudong's abstract has been ACCEPTED as a platform (oral)
presentation at the ASHG 2023 Annual
Meeting. There are less than 10% of abstracts can be
selected as oral presentations.
Cheers!
June, 2023
● Dr. Li was invited to present at the Biological Data
Science, AI&Medicine Workshop.
April, 2023
● We had a lab retreat in Shanghai and visit Dr. Ting Ni’s
lab in Fudan Univerisity.
● Dr. Li was invited to give a talk in the Chinese Academic
Conference on Tumor Biomarker.
December, 2022
● Congratulation our student Qixuan awarded the most
prestigious Shenzhen Bay Principal's
Award.
● Welcome visiting student Zhaozhao Zhao from Fudan
University and HuiHui Yang from Central South
University visit our lab.
November, 2022
● Welcome Dr. Zeyang Wang from University of Munich to join
our lab as a postdoctoral fellow. His
research focus on functional characterization of the
regulatory activities of non-coding
elements.
● Congrats! We co-organized the first Shenzhen
bioinformatics symposium.
September, 2022
● Welcome Dr. Ting Zhang from Northwest A&F University to
join our lab as a postdoctoral fellow. His
research focus on single-cell method development.
August, 2022
● Our paper has been accepted by
Nucleic Acids Research, we described
the first atlas of intronic polyadenylation
quantitative trait loci. Congratulations to Dr. Ma, Shumin
and other lab members!
● Our collaboration paper with Dr. Jingyi Jessica Li from
the University of California, Los Angeles
has been accepted by Genome Biology.
We found that PCA outperforms popular
hidden variable inference methods for molecular QTL
mapping.
June, 2022
● Our research is featured in Nature Spotlight
on Precision medicine
● Welcome Ruilong Zhou from University of Chinese Academy of
Sciences join our group. He is interested
in developing deep learning and machine learning approaches
to analyze single cell data.
● Our paper has been accepted in principle by STAR
Protocols (Cell Press), Congratulations
to Dr. Zou, Dr. Ding!
May, 2022
● Welcome Kewei Xiong join our group, his interest is
focused on single cell algorithm development.
March, 2022
● Our paper have been featured on the cover of first issue
of Quantitative
Biology this year. Congrats to Dr. Zou
and
also Xiangli for the cover design.
December, 2021
● Dr. Li was invited to give a talk on Chinese Academic
Conference on Tumor Biomarker.
● Welcome Prof. Jianzhong Su, Dr. Liangde Xu, Dr. Meng Zhou
from Wenzhou Medical University and
Professor Yushan Qiu from Shenzhen University visit our lab
and give a talk in Shenzhen Bay
Laboratory.
November, 2021
● Congratulations! Our Lab received a open grant from
SZBL to study breast cancer.
October, 2021
● Dr. Li was invited to give presentations on Young
Bioinformatics PI Workshop and National
Congress of Bioinformatics and Systems Biology.
● Welcome Prof. Wenfei Jin from Southern University of
Science and Technology visit our lab and
give a talk in Shenzhen Bay Laboratory.
September, 2021
● Dr. Li was invited to visit and gave a
presentation in Key Laboratory of Molecular
Biophysics Ministry of Education
(Huazhong University of Science and Technology)
● Dr. Ruofan Ding, a bioinformatics PhD from the
Xiamen University, joined the lab as a
postdoc.
Aguest, 2021
● Congratulations! Our collaboration paper with
Prof.Shang about SNP rs4971059 was accepted
in The EMBO
Journal.
● Hui Chen, a master graduate from South China
University of Technology, will join the lab as
a RA.
● Congratulations! Our collaboration work about
3′aQTL-atlas was accepted in Nucleic Acids
Research.
July, 2021
● Dr. Li delivered a keynote presentation in the
1st Zhejiang-Sichuan Bioinformatics
conference.
● Qixuan Wang from Soochow University joined the
lab as a graduate student.
June, 2021
● Congratulations! Our Nature Genetics paper
have been previewed in Trends in
Genetics.
● Congratulations! Our collaboration paper with Dr.
Qian about Nuclear m6A Reader YTHDC1 was
accepted in Blood.
● Dr. Xuelian Ma, a bioinformatics PhD from the
China Agricultural University, will join the
lab as a postdoc.
● Dr. Li attended the International Symposium on
Big-Data, Non-coding RNA and Precision
Medicine.
● Congratulations! Our collaboration paper about
Pan-cancer characterization of TIL-lncRNAs
was accepted in npj Precision
Oncology.
May, 2021
● Dr. Yangmei Qin, a bioinformatics PhD from the
Xiamen University, will join the lab as a
postdoc.
● Dr. Wenyan Chen, a bioinformatics PhD from the
University of Chinese Academy of Sciences,
will join the lab as a postdoc.
March, 2021
● Liucheng Shi and Wenhao Gou, first year master's
student of Columbia University the lab as
visiting scholar.
● Our work on the development of new algorithms
(scDaPars) for APA analysis from single-cell
RNA-seq was accepted in Genome
Research, cheers !
● Xudong's abstract have been selected as
prerecorded poster presentation and will be
featured in the coming NHLBI Systems Biology
Symposium.
February, 2021
● Our work about Genetic Basis of Alternative
Polyadenylation was accepted in Nature
Genetics, cheers !
● Our work about Summary and Outlook on Alternative
Polyadenylation was accepted in Quantitative
Biology, cheers!
● Dr. Xudong Zou, a bioinformatics PhD from Peking
University, joined the lab as an assistant
researcher.
● Our Computing and Disease Genomics Research Lab
was established, cheers!
