Brief Research Biograph
Yaqiang started his college education in bioengineering, but he discovered his passion for mathematical
modeling and coding while participating in competitions such as CUMCM. This led him to the field of computational biology, where he
earned his PhD from the CAS-MPG Partner Institute for
Computational Biology with Dr. Jing-Dong Jackie Han. Currently, he works as a bioinformatics
postdoc with Dr.Keji Zhao at the NHLBI/NIH, where he studies the chromatin interaction landscapes of
human and mouse immune cells, specifically T cells.
Yaqiang is a bioinformatics expert with over ten years of experience in utilizing and interpreting deep
sequencing technologies, including RNA-seq, ChIP-seq, DNase-seq, ATAC-seq, MNase-seq, Hi-C, Hi-TrAC, STARR-seq, 10X
scRNA-seq,
and etc, to study transcription regulation across various biological processes. During his Ph.D.
studies, he focused on investigating the epigenetic roles of human transposable elements. Currently, he
is working on unraveling the chromatin interaction patterns of human and mouse cells, with a focus on T
cells. By closely collaborating with his wet-lab colleagues, Yaqiang analyzes and integrates sequencing
data to gain new biological insights, and develops cutting-edge analysis methods for new chromatin 1D
and 3D profiling sequencing protocols.
Yaqiang's early research interests centered on data mining, machine learning from large-scale sequencing
data, and developing bioinformatics tools while working in Dr. Han's lab. During his postdoctoral
training with Dr. Zhao, his focus shifted towards developing sequencing-based methodologies and studying
T-cell immunology.
Yaqiang has published several research articles as the first or co-first author in prominent journals,
including Immunity (2024 & 2023[cover]), Nature Cell Biology (2024), Nucleic Acids Research (2023, 2022, 2020),
Nature Communications (2022), Blood (2020[Plenary Paper]), Bioinformatics (2020),
and Genome Research (2019). Additionally, he has contributed to several other impactful research
papers as a collaborator, published in prestigious journals such as Science (2022), Immunity
(2022a and b), Nature Cell Biology (2022), Nature Metabolism (2020), Science
Advances (2020), Cell Reports (2019), and Cell Research (2015).
Yaqiang actively reviews for several journals, focusing on the topics of bioinformatics and epigenetics, including Bioinformatics, Frontiers in
Immunology/Oncology/Bioinformatics/Pharmacology/Genetics, Communication Biology, BMC Genomics,
F1000Research, and others, and is
dedicated to serving the scientific community.
Yaqiang actively develops and maintains open-source bioinformatics software (cLoops, cLoops2, astroBoy) for NGS data analysis and visualization, gaining wide recognition.
Outside of work, Yaqiang enjoys exploring sports and spending time with family.
Experience and Education Background
-
[2024.04 - ] National Heart, Lung, and Blood Institute (NHLBI), NIH, Postdoc (Research Fellow), with
Dr. Keji Zhao,
Maryland, US.
[2019.04 - 2024.04] National Heart, Lung, and Blood Institute (NHLBI), NIH, Postdoc (Visiting
Fellow), with Dr. Keji
Zhao,
Maryland, US.
-
[2012.09 - 2018.12] CAS-MPG Partner Insitute for Computational Biology, Ph.D. of Computational
Biology, with Dr. Jing-Dong Jackie Han, Shanghai,
China.
-
[2008.09 - 2012.06] East China University of Science and Technology, Bachelor of Bioengineering,
Shanghai, China.
Research Interests
gene expression regulation, epigenetics, bioinformatics, next-generation sequencing, chromatin 3D
structures, T-cell immunology
Research Publications (full
list)
bioRxiv first or co-first preprint
-
First/co-first Author Papers
Bioinformatics Algorithms/Tools
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Cao, Yaqiang, et al. "cLoops2: a full-stack comprehensive analytical tool for chromatin interactions."
Nucleic Acids Research 50.1 (2022): 57-71.
LINK
-
Cao, Yaqiang, et al. “Accurate loop calling for 3D genomic data with cLoops.”
Bioinformatics 36.3
(2020): 666-675.
LINK
Biological Questions Orientated Data Mining
-
Ma, Fei, et al. Three-dimensional chromatin reorganization regulates B cell development during ageing Nature Cell Biology, 2024
LINK
-
Liu, Shuai, et al. Regulation of T helper cell differentiation by the interplay between histone
modification and chromatin interaction Immunity, 2024, ISSN 1074-7613
LINK
- Cao, Yaqiang, et al. "Hi-TrAC detects active sub-TADs and reveals internal organizations of
super-enhancers"
Nucleic Acids Research (2023): gkad378. LINK
-
Cui, Kairong, et al. Restraint of IFN-γ expression through a distal silencer CNS–28 for tissue
homeostasis Immunity, 56.5 (2023): 944-958.
LINK,
selected
as cover, Preview: To loop or not to loop?
CNS-28 is the answer
-
Zeng, Yingying, et al. “Characterization of functional transposable element enhancers in acute myeloid
leukemia.” Science China Life Sciences 63.5 (2020): 675-687.
LINK
-
Cao, Yaqiang, et al. “Widespread roles of enhancer-like transposable elements in cell identity and
long-range genomic interactions.” Genome research 29.1 (2019): 40-52.
LINK
Sequencing-Based Methods Development
-
Liu, Shuai, et al. Hi-TrAC reveals division of labor of transcription factors in
organizing chromatin loops. Nat Commun 13, 6679 (2022).
LINK
Sequencing Data Analysis Collaboration
-
Zhen, Tao, et al. "RUNX1 and CBFβ-SMMHC transactivate target genes together in abnormal myeloid
progenitors for leukemia development." Blood 136.21 (2020): 2373-2385.
LINK,
selected as Plenary Paper, editor's
comment
-
Han, Mengmeng, et al. "A role for LSH in facilitating DNA methylation by DNMT1 through enhancing UHRF1
chromatin association." Nucleic Acids Research 48.21 (2020): 12116-12134.
LINK
-
Huang, Fei, et al. “BMP2 signalling activation enhances bone metastases of non‐small cell lung cancer.”
J Cell Mol Med. 2020; 00: 1– 17.
LINK
-
Wang, Lu, et al. “Activin/Smad2-induced histone H3 Lys-27 trimethylation (H3K27me3) reduction is crucial
to initiate mesendoderm differentiation of human embryonic stem cells.” Journal of Biological
Chemistry 292.4 (2017): 1339-1350.
LINK
Contribution Publications
-
Zhang, Xiaoli, et al. "KCNQ1OT1 promotes genome-wide transposon repression by guiding
RNA–DNA
triplexes and HP1 binding." Nature Cell Biology (2022):1-13.
LINK
-
Lin, Xueqiu, et al. "Nested epistasis enhancer networks for robust genome regulation."
Science (2022): eabk3512.
LINK
-
Ren, Gang, et al. "Transcription factors TCF-1 and GATA3 are key factors for the epigenetic
priming of early innate lymphoid progenitors toward distinct cell fates."
Immunity
55.8 (2022): 1402-1413.
LINK
-
Pan, Lixia, et al. “scPCOR-seq enables co-profiling of chromatin occupancy and RNAs in
single
cells.”
Communications Biology 5.1 (2022): 1-9.
LINK
-
Fang, Difeng, et al. “Differential regulation of transcription factor T-bet induction during
NK
cell
development and T helper-1 cell differentiation.” Immunity (2022):
S1074-7613(22)00128-5.
LINK
-
Huang, Fei, et al. “PNMA5 promotes bone metastasis of non-small-cell lung cancer as a target
of
BMP2
signaling.” Frontiers in cell and developmental biology 9 (2021).
LINK
-
Ku, Wai Lim, et al. “Profiling single-cell histone modifications using indexing chromatin
immunocleavage
sequencing.” Genome Research (2021): gr-260893.
LINK
-
Xia, Xian, et al. “Three-dimensional facial-image analysis to predict heterogeneity of the
human
ageing
rate and the impact of lifestyle.” Nature Metabolism (2020): 1-12.
LINK
-
Qiu, Xiang, et al. "Altered 3D chromatin structure permits inversional recombination at the
IgH
locus."
Science advances 6.33 (2020): eaaz8850.
LINK
-
Chen, Xingwei, et al. “Immune cell types and secreted factors contributing to
inflammation-to-cancer
transition and immune therapy response.” Cell reports 26.7 (2019): 1965-1977.
LINK
-
Xu, Chi, et al. “Accurate Drug Repositioning through Non-tissue-Specific Core Signatures
from
Cancer
Transcriptomes.” Cell reports 29.4 (2019): 1055.
LINK
-
Huang, Yi, et al. “Single-cell-level spatial gene expression in the embryonic neural
differentiation
niche.” Genome research 25.4 (2015): 570-581.
LINK
-
Chen, Weiyang, et al. “Three-dimensional human facial morphologies as robust aging markers.”
Cell
research 25.5 (2015): 574-587.
LINK
|
Softwares
-
astroBoy: streamlined NGS data automatic processing web
service for in-house/local data and public data from GEO database, in-house service within NIH since
December 2022
-
cLoops2: full stack analysis tool for chromatin
interaction data such as Hi-TrAC (released in 2021)
-
cLoops: accurate and flexible loops calling tool
for 3D genomic data (released in 2017)
Editorial Services
Peer Reviewer Services
Awards
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2024 NHLBI Director's Awards of Innovation: For discovering the first negative
regulatory element for interferon-gamma expression and elucidating its mechanism of
function in preventing enhancer-promoter interaction through long-distance chromatin
interactions.