定量生物学中心

ABHD6 suppresses colorectal cancer progression via AKT signaling pathway

Xiaoyu Xiong, Changjiang Yang, Yiteng Jin, Rui Zhang, Shuo Wang, Lin Gan, Sen Hou, Yudi Bao, Zexian Zeng, Yingjiang Ye, Zhidong Gao.

Molecular Carcinogenesis, 2024, 63(4), p. 647-662. [Html]

ACAT1 promotes proliferation and metastasis of bladder cancer via AKT/GSK3 β /c-Myc signaling pathway

Tingjun Wang, Gang Wang, Danni Shan, Yayun Fang, Fenfang Zhou, Mengxue Yu, Lingao Ju, Gang Li, Wan Xiang, Kaiyu Qian, Yi Zhang, Yu Xiao, Xinghuan Wang.

Journal of Cancer, 2024, 15(11), p. 3297-3312. [Html]

Acyl-coenzyme A: cholesterol acyltransferase inhibitor avasimibe suppresses tumorigenesis and induces G1-phase cell-cycle arrest by activating PPARγ signaling pathway in bladder cancer

Tianchen Peng, Kangping Xiong, Zhiwen He, Songtao Cheng, Siming Chen, Song Chen, Zhonghua Yang, Wan Xiang, Lingao Ju, Yi Zhang, Kaiyu Qian, Yu Xiao, Gang Wang.

Journal of Cancer, 2024, 15(2), p. 370-382. [Html]

AI for organic and polymer synthesis

Xin Hong, Qi Yang, Kuangbiao Liao, Jianfeng Pei, Mao Chen, Fanyang Mo, Hua Lu, Wen-Bin Zhang, Haisen Zhou, Jiaxiao Chen, Lebin Su, Shuo-Qing Zhang, Siyuan Liu, Xu Huang, Yi-Zhou Sun, Yuxiang Wang, Zexi Zhang, Zhunzhun Yu, Sanzhong Luo, Xue-Feng Fu, Shu-Li You.

Science China-Chemistry, 2024, 67(8), p. 2461-2496. [Html]

All-Atom Protein Sequence Design Based on Geometric Deep Learning

Jiale Liu, Zheng Guo, Hantian You, Changsheng Zhang, Luhua Lai.

Angewandte Chemie-International Edition, 2024, 63(50). [Html]

AMPK Attenuation of β-Adrenergic Receptor-Induced Cardiac Injury via Phosphorylation of β-Arrestin-1-ser330

Mingming Zhao, Ning Cao, Huijun Gu, Jiachao Xu, Wenli Xu, Di Zhang, Tong-You Wade Wei, Kang Wang, Ruiping Guo, Hongtu Cui, Xiaofeng Wang, Xin Guo, Zhiyuan Li, Kangmin He, Zijian Li, Youyi Zhang, John Y. J. Shyy, Erdan Dong, Han Xiao.

Circulation Research, 2024, 135(6), p. 651-667. [Html]

Application of AI in biological age prediction

Dawei Meng, Shiqiang Zhang, Yuanfang Huang, Kehang Mao, Jing-Dong J. Han.

Current Opinion in Structural Biology, 2024, 85. [Html]

Assessment of Two Restraint Potentials for Coarse-Grained Chemical-Cross-Link-Assisted Modeling of Protein Structures

Mateusz Lesniewski, Maciej Pyrka, Cezary Czaplewski, Nguyen Truong Co, Yida Jiang, Zhou Gong, Chun Tang, Adam Liwo.

Journal of Chemical Information and Modeling, 2024, 64(4), p. 1377-1393. [Html]

Asymmetrical calcium ions induced stress and remodeling in lipid bilayer membranes

Chang Liu, Qi Zhong, Kai Kang, Rui Ma, Chen Song.

Physical Chemistry Chemical Physics, 2024. [Html]

ATP promotes protein coacervation through conformational compaction

Yueling Zhu, Shiyan Lin, Lingshen Meng, Min Sun, Maili Liu, Jingyuan Li, Chun Tang, Zhou Gong.

Journal of molecular cell biology, 2024. [Html]

The backpropagation algorithm implemented on spiking neuromorphic hardware

Alpha Renner, Forrest Sheldon, Anatoly Zlotnik, Louis Tao, Andrew Sornborger.

Nature Communications, 2024, 15(1). [Html]

A biomimetic human disease model of bacterial keratitis using a cornea-on-a-chip system

Yudan Deng, Lingjun Li, Jian Xu, Yili Yao, Jiangtao Ding, Lei Wang, Chunxiong Luo, Wei Yang, Lingli Li.

Biomaterials Science, 2024, 12(20), p. 5239-5252. [Html]

Causal association of smoking, blood lipids, and bladder cancer: Insights from a multivariable and mediation mendelian randomization investigation

Houyi Wei, Xiangqun Cheng, Gang Wang, Zhilong Li, Wenzhi Du, Lingao Ju, Danni Shan, Mengxue Yu, Yayun Fang, Kaiyu Qian, Yi Zhang, Yu Xiao, Xinghuan Wang.

Journal of Cancer, 2024, 15(7), p. 1929-1939. [Html]

CCDC68 Maintains Mitotic Checkpoint Activation by Promoting CDC20 Integration into the MCC

Qi Li, Qingzhou Chen, Tao Zheng, Fulin Wang, Junlin Teng, Haining Zhou, Jianguo Chen.

Advanced Science, 2024, 11(35). [Html]

Cereal genetics: Novel modulators of spikelet number and flowering time

Mingjiu Li, Yuling Jiao.

Current Biology, 2024, 34(11). [Html]

Challenging Complexity with Simplicity: Rethinking the Role of Single-Step Models in Computer-Aided Synthesis Planning

Junren Li, Kangjie Lin, Jianfeng Pei, Luhua Lai.

Journal of Chemical Information and Modeling, 2024, 64(14), p. 5470-5479. [Html]

Characterizing Cellular Physiological States with Three-Dimensional Shape Descriptors for Cell Membranes

Guoye Guan, Yixuan Chen, Hongli Wang, Qi Ouyang, Chao Tang.

Membranes, 2024, 14(6). [Html]

A chromosome-coupled ubiquitin-proteasome pathway is required for meiotic surveillance

Ruirui Zhang, Bohan Liu, Yuqi Tian, Mingyu Xin, Qian Li, Xiuhua Huang, Yuanyuan Liu, Li Zhao, Feifei Qi, Ruoxi Wang, Xiaoqian Meng, Jianguo Chen, Jun Zhou, Jinmin Gao.

Cell Death and Differentiation, 2024, 31(12), p. 1730-1745. [Html]

Connecting Protein Millisecond Conformational Dynamics to Protein Thermal Stability

Xue-Ni Hou, Bin Song, Chang Zhao, Wen-Ting Chu, Mei-Xia Ruan, Xu Dong, Ling-Shen Meng, Zhou Gong, Yu-Xiang Weng, Jie Zheng, Jin Wang, Chun Tang.

Jacs Au, 2024, 4(8), p. 3310-3320. [Html]

A conserved N-terminal motif of CUL3 contributes to assembly and E3 ligase activity of CRL3KLHL22

Weize Wang, Ling Liang, Zonglin Dai, Peng Zuo, Shang Yu, Yishuo Lu, Dian Ding, Hongyi Chen, Hui Shan, Yan Jin, Youdong Mao, Yuxin Yin.

Nature Communications, 2024, 15(1). [Html]

Continually adapting pre-trained language model to universal annotation of single-cell RNA-seq data

Hui Wan, Musu Yuan, Yiwei Fu, Minghua Deng.

Briefings in Bioinformatics, 2024, 25(2). [Html]

Coordinate-wise monotonic transformations enable privacy-preserving age estimation with 3D face point cloud

Xinyu Yang, Runhan Li, Xindi Yang, Yong Zhou, Yi Liu, Jing-Dong J. Han.

Science China-Life Sciences, 2024, 67(7), p. 1489-1501. [Html]

CShaperApp: Segmenting and analyzing cellular morphologies of the developing Caenorhabditis elegans embryo

Jianfeng Cao, Lihan Hu, Guoye Guan, Zelin Li, Zhongying Zhao, Chao Tang, Hong Yan.

Quantitative Biology, 2024, 12(3), p. 329-334. [Html]

Deciphering the molecular mechanism underlying morphology transition in two-component DNA-protein cophase separation

Cheng Li, Yunqiang Bian, Yiting Tang, Lingyu Meng, Peipei Yin, Ye Hong, Jun Cheng, Yuchen Li, Jie Lin, Chao Tang, Chunlai Chen, Wenfei Li, Zhi Qi.

Structure (London, England : 1993), 2024. [Html]

A designer synthetic chromosome fragment functions in moss

Lian-Ge Chen, Tianlong Lan, Shuo Zhang, Mengkai Zhao, Guangyu Luo, Yi Gao, Yuliang Zhang, Qingwei Du, Houze Lu, Bimeng Li, Bingke Jiao, Zhangli Hu, Yingxin Ma, Qiao Zhao, Ying Wang, Wenfeng Qian, Junbiao Dai, Yuling Jiao.

Nature Plants, 2024, 10(2). [Html]

Designing a synthetic moss genome using GenoDesigner

Wenfei Yu, Shuo Zhang, Shijun Zhao, Lian-ge Chen, Jie Cao, Hao Ye, Jianbin Yan, Qiao Zhao, Beixin Mo, Ying Wang, Yuling Jiao, Yixing Ma, Xiaoluo Huang, Wenfeng Qian, Junbiao Dai.

Nature Plants, 2024, 10(6). [Html]

The detection, biological function, and liquid biopsy application of extracellular vesicle-associated DNA

Shan Guo, Xin Wang, Danni Shan, Yu Xiao, Lingao Ju, Yi Zhang, Gang Wang, Kaiyu Qian.

Biomarker Research, 2024, 12(1). [Html]

DiffBindFR: an SE(3) equivariant network for flexible protein-ligand docking

Jintao Zhu, Zhonghui Gu, Jianfeng Pei, Luhua Lai.

Chemical Science, 2024, 15(21). [Html]

Dissecting diazirine photo-reaction mechanism for protein residue-specific cross-linking and distance mapping

Yida Jiang, Xinghe Zhang, Honggang Nie, Jianxiong Fan, Shuangshuang Di, Hui Fu, Xiu Zhang, Lijuan Wang, Chun Tang.

Nature Communications, 2024, 15(1). [Html]

Dual roles of CCDC102A in governing centrosome duplication and cohesion

Tianning Wang, Guiliang Fan, Yuqing Xia, Yuhong Zou, Yunjie Liu, Jiaxin Wang, Yingchun Hu, Junlin Teng, Ning Huang, Jianguo Chen.

Cell Reports, 2024, 43(2). [Html]

Dual-objective two-photon microscope for volumetric imaging of dense scattering biological samples by bidirectional excitation and collection

Muyue Zhai, Jing Yu, Yanhui Hu, Hang Yu, Beichen Xie, Yi Yu, Dawei Li, Aimin Wang, Heping Cheng.

Photonics Research, 2024, 12(6), p. 1351-1361. [Html]

Dynamic processes of fate decision in inducible bistable systems

Sijing Chen, Yanhong Sun, Fengyu Zhang, Chunxiong Luo.

Biophysical Journal, 2024, 123(23), p. 4030-4041. [Html]

The dynamic-process characterization and prediction of synthetic gene circuits by dynamic delay model

Yanhong Sun, Fengyu Zhang, Qi Ouyang, Chunxiong Luo.

Iscience, 2024, 27(3). [Html]

Exploring the relationship among Alzheimer's disease, aging and cognitive scores through neuroimaging-based approach

Jinhui Sun, Jing-Dong J. Han, Weiyang Chen.

Scientific Reports, 2024, 14(1). [Html]

Feature sequence-based genome mining uncovers the hidden diversity of bacterial siderophore pathways

Shaohua Gu, Yuanzhe Shao, Karoline Rehm, Laurent Bigler, Di Zhang, Ruolin He, Ruichen Xu, Jiqi Shao, Alexandre Jousset, Ville-Petri Friman, Xiaoying Bian, Zhong Wei, Rolf Kummerli, Zhiyuan Li.

Elife, 2024, 13. [Html]

Feature sequence-based genome mining uncovers the hidden diversity of bacterial siderophore pathways

Shaohua Gu, Yuanzhe Shao, Karoline Rehm, Laurent Bigler, Di Zhang, Ruolin He, Ruichen Xu, Jiqi Shao, Alexandre Jousset, Ville-Petri Friman, Xiaoying Bian, Zhong Wei, Rolf Kummerli, Zhiyuan Li.

eLife, 2024, 13. [Html]

Fingering Instability Accelerates Population Growth of a Proliferating Cell Collective

Yiyang Ye, Jie Lin.

Physical Review Letters, 2024, 132(1). [Html]

A flexible, modular and versatile functional part assembly toolkit for gene cluster engineering in Streptomyces

Xuejin Zhao, Yeqing Zong, Qiuli Lou, Chenrui Qin, Chunbo Lou.

Synthetic and Systems Biotechnology, 2024, 9(1), p. 69-77. [Html]

Functional predictability of universal gene circuits in diverse microbial hosts

Chenrui Qin, Tong Xu, Xuejin Zhao, Yeqing Zong, Haoqian M. Zhang, Chunbo Lou, Qi Ouyang, Long Qian.

Quantitative Biology, 2024, 12(2), p. 129-140. [Html]

Germline loss in C. elegans enhances longevity by disrupting adhesion between niche and stem cells

Meng Liu, Jiehui Chen, Guizhong Cui, Yumin Dai, Mengjiao Song, Chunyu Zhou, Qingyuan Hu, Qingxia Chen, Hongwei Wang, Wanli Chen, Jingdong Jackie Han, Guangdun Peng, Naihe Jing, Yidong Shen.

Embo Journal, 2024, 43(18), p. 4000-4019. [Html]

Global Analysis of Natural Products Biosynthetic Diversity Encoded in Fungal Genomes

Shu Zhang, Guohui Shi, Xinran Xu, Xu Guo, Sijia Li, Zhiyuan Li, Qi Wu, Wen-Bing Yin.

Journal of Fungi, 2024, 10(9). [Html]

GRB7 Plays a Vital Role in Promoting the Progression and Mediating Immune Evasion of Ovarian Cancer

Liang Wen, Wei Hu, Sen Hou, Ce Luo, Yiteng Jin, Zexian Zeng, Zhe Zhang, Yuanguang Meng.

Pharmaceuticals, 2024, 17(8). [Html]

Heterogeneous elasticity drives ripening and controls bursting kinetics of transcriptional condensates

Lingyu Meng, Sheng Mao, Jie Lin.

Proceedings of the National Academy of Sciences of the United States of America, 2024, 121(12). [Html]

Homeostasis of mRNA concentrations through coupling transcription, export, and degradation

Qirun Wang, Jie Lin.

Iscience, 2024, 27(8). [Html]

How Do DNA Molecular Springs Modulate Protein-Protein Interactions: Experimental and Theoretical Results

Kecheng Zhang, Jingze Duan, Cong Li, Chen Song, Zhixing Chen.

Biochemistry, 2024, 63(24), p. 3369-3380. [Html]

COASY variant as a new genetic cause of riboflavin-responsive lipid storage myopathy

Yilei Zheng, Tongling Liufu, Bing Wen, Chao Zhou, Lingchun Liu, Yusen Qiu, Wenquan Zou, Wei Zhang, Yu Li, Jianfeng Pei, Yiheng Zeng, Wanjin Chen, Chunhua Zhang, Yun Yuan, Guochun Wang, Chuanzhu Yan, Xin Lu, Jianwen Deng, Zhaoxia Wang, Daojun Hong.

Cell Discovery, 2024, 10(1). [Html]

Switching Go-Martini for Investigating Protein Conformational Transitions and Associated Protein-Lipid Interactions

Song Yang, Chen Song.

Journal of Chemical Theory and Computation, 2024, 20(6), p. 2618-2629. [Html]

Identification of the metaphyseal skeletal stem cell building trabecular bone

Guan Yang, Qi He, Xiaoxiao Guo, Rong-Yu Li, Jingting Lin, Yiming Lang, Wanyu Tao, Wenjia Liu, Huisang Lin, Shilai Xing, Yini Qi, Zhongliang Xie, Jing-Dong J. Han, Bin Zhou, Yan Teng, Xiao Yang.

Science Advances, 2024, 10(8). [Html]

In situ injectable hydrogel encapsulating Mn/NO-based immune nano-activator for prevention of postoperative tumor recurrence

Shengnan Huang, Chenyang Zhou, Chengzhi Song, Xiali Zhu, Mingsan Miao, Chunming Li, Shaofeng Duan, Yurong Hu.

Asian Journal of Pharmaceutical Sciences, 2024, 19(2). [Html]

Initial nutrient condition determines the recovery speed of quiescent cells in fission yeast

Qi Liu, Nan Sheng, Zhiwen Zhang, Chenjun He, Yao Zhao, Haoyuan Sun, Jianguo Chen, Xiaojing Yang, Chao Tang.

Heliyon, 2024, 10(5). [Html]

Insights into a functional synthetic plant genome

Fei Du, Junbiao Dai, Yuling Jiao.

New Phytologist, 2024, 244(1), p. 46-50. [Html]

Integrative Single Cell Atlas Revealed Intratumoral Heterogeneity Generation from an Adaptive Epigenetic Cell State in Human Bladder Urothelial Carcinoma

Yu Xiao, Wan Jin, Kaiyu Qian, Lingao Ju, Gang Wang, Kai Wu, Rui Cao, Luyuan Chang, Zilin Xu, Jun Luo, Liuying Shan, Fang Yu, Xintong Chen, Dongmei Liu, Hong Cao, Yejinpeng Wang, Xinyue Cao, Wei Zhou, Diansheng Cui, Ye Tian, Chundong Ji, Yongwen Luo, Xin Hong, Fangjin Chen, Minsheng Peng, Yi Zhang, Xinghuan Wang.

Advanced Science, 2024, 11(24). [Html]

An integrative temperature-controlled microfluidic system for budding yeast heat shock response analysis at the single-cell level

Jie Hong, Hao He, Yinjia Xu, Shujing Wang, Chunxiong Luo.

Lab on a Chip, 2024, 24(15). [Html]

IPEV: identification of prokaryotic and eukaryotic virus-derived sequences in virome using deep learning

Hengchuang Yin, Shufang Wu, Jie Tan, Qian Guo, Mo Li, Jinyuan Guo, Yaqi Wang, Xiaoqing Jiang, Huaiqiu Zhu.

Gigascience, 2024, 13. [Html]

Learning a generalized graph transformer for protein function prediction in dissimilar sequences

Yiwei Fu, Zhonghui Gu, Xiao Luo, Qirui Guo, Luhua Lai, Minghua Deng.

Gigascience, 2024, 13. [Html]

Learning spiking neuronal networks with artificial neural networks: neural oscillations

Ruilin Zhang, Zhongyi Wang, Tianyi Wu, Yuhang Cai, Louis Tao, Zhuo-Cheng Xiao, Yao Li.

Journal of Mathematical Biology, 2024, 88(6). [Html]

A logic-incorporated gene regulatory network deciphers principles in cell fate decisions

Gang Xue, Xiaoyi Zhang, Wanqi Li, Lu Zhang, Zongxu Zhang, Xiaolin Zhou, Di Zhang, Lei Zhang, Zhiyuan Li.

Elife, 2024, 12. [Html]

Mapping Full Conformational Transition Dynamics of Intrinsically Disordered Proteins Using a Single-Molecule Nanocircuit

Dongbao Yin, Ruoyao Xiong, Zhiheng Yang, Jianfei Feng, Wenzhe Liu, Shiyun Li, Mingyao Li, Hao Ruan, Jie Li, Lidong Li, Luhua Lai, Xuefeng Guo.

Acs Nano, 2024, 18(38), p. 25986-25996. [Html]

A mathematical framework for understanding the spontaneous emergence of complexity applicable to growing multicellular systems

Lu Zhang, Gang Xue, Xiaolin Zhou, Jiandong Huang, Zhiyuan Li.

PLoS computational biology, 2024, 20(6), p. e1011882-e1011882. [Html]

Mathematical modeling of viral infection and the immune response controlled by the circadian clock

Jiaxin Zhou, Hongli Wang, Qi Ouyang.

Journal of Biological Physics, 2024, 50(2), p. 197-214. [Html]

Mevalonate pathway inhibition reduces bladder cancer metastasis by modulating RhoB protein stability and integrin β1 localization

Gang Wang, Tianchen Peng, Liang Chen, Kangping Xiong, Lingao Ju, Kaiyu Qian, Yi Zhang, Yu Xiao, Xinghuan Wang.

Communications Biology, 2024, 7(1). [Html]

The Microbiome Protocols eBook initiative: Building a bridge to microbiome research

Yunyun Gao, Kai Peng, Defeng Bai, Xiao-Ye Bai, Yujing Bi, Anqi Chen, Baodong Chen, Feng Chen, Juan Chen, Lei Chen, Tong Chen, Wei Chen, Xu Cheng, Yanfen Cheng, Jie Cui, Jingjing Dai, Junbiao Dai, Zhaolai Dai, Ye Deng, Yi-Zhen Deng, Wei Ding, Zhencheng Fang, Wei Fu, Hanbing Gao, Shaohua Gu, Xue Guo, Xuguang Guo, Dongfei Han, Lele He, Yatao He, Hui-Yu Hou, Baolei Jia, Gengjie Jia, Shuo Jiao, Wei Jin, Feng Ju, Zhicheng Ju, Siyuan Kong, Canhui Lan, Bing Li, Da Li, Diyan Li, Jingdi Li, Meng Li, Qi Li, Qiang Li, Wen-Jun Li, Xiaofang Li, Xuemeng Li, Yahui Li, You-Gui Li, Zhibin Liang, Ning Ling, Fufeng Liu, Qing Liu, Shuang-Jiang Liu, Hongye Lu, Qi Lu, Guangwe Luo, Hao Luo, Yuheng Luo, Hujie Lyu, Chuang Ma, Liyuan Ma, Tengfei Ma, Jinfeng Ni, Ziqin Pang, Xiaojing Qiang, Yuan Qin, Qingyue Qu, Chao Ran, Shuqiang Ren, Haitao Shang, Luyang Song, Linyang Sun, Weimin Sun, Liping Tang, Jian Tian, Kai Wang, Mengzhi Wang, Ming-Ke Wang, Tao Wang, Xiao-Yan Wang, Yao Wang, Yiwen Wang, Youshan Wang, Hailei Wei, Hong Wei, Zhong Wei, Tao Wen, Jiqiu Wu, Linhuan Wu, Linkun Wu, Jiao Xi, Bo Xie, Guofang Xu, Jun Xu, Shanshan Xu, Qing Xue, Liping Yan, Haifei Yang, Jun Yang, Junbo Yang, Ruifu Yang, Yalin Yang, Ying-Jie Yang, Xiaofang Yao, Yanpo Yao, Salsabeel Yousuf, Ke Yu, Zhengrong Yuan, Zhilin Yuan, Dong Zhang, Tianyuan Zhang, Weipeng Zhang, Yunzeng Zhang, Zhaonan Zhang, Zhen Zhang, Zhi-Feng Zhang, Shengguo Zhao, Wei Zhao, Maosheng Zheng, Ziqiang Zheng, Xin Zhou, Yuanping Zhou, Zhigang Zhou, Mo Zhu, Yong-Guan Zhu, Haiyan Chu, Yang Bai, Yong-Xin Liu.

Imeta, 2024, 3(2). [Html]

Modulating cell proliferation by asymmetric division: A conserved pattern in the early embryogenesis of nematode species

Guoye Guan, Ce Luo, Lei-Han Tang, Chao Tang.

microPublication biology, 2024, 2024. [Html]

A multilayer microfluidic system for studies of the dynamic responses of cellular proteins to oxygen switches at the single-cell level

Wei Fu, Shujing Wang, Qi Ouyang, Chunxiong Luo.

Integrative Biology, 2024, 16. [Html]

Multiomics Analyses With Stool-Type Stratification in Patient Cohorts and Blautia Identification as a Potential Bacterial Modulator in Type 2 Diabetes Mellitus

Qian Guo, Zezheng Gao, Linhua Zhao, Han Wang, Zhen Luo, Doris Vandeputte, Lisha He, Mo Li, Sha Di, Yanwen Liu, Jiaheng Hou, Xiaoqing Jiang, Huaiqiu Zhu, Xiaolin Tong.

Diabetes, 2024, 73(3). [Html]

Nanoscale one-dimensional close packing of interfacial alkali ions driven by water-mediated attraction

Ye Tian, Yizhi Song, Yijie Xia, Jiani Hong, Yupeng Huang, Runze Ma, Sifan You, Dong Guan, Duanyun Cao, Mengze Zhao, Ji Chen, Chen Song, Kaihui Liu, Li-Mei Xu, Yi Qin Gao, En-Ge Wang, Ying Jiang.

Nature Nanotechnology, 2024, 19(4). [Html]

Natural diversifying evolution of nonribosomal peptide synthetases in a defensive symbiont reveals nonmodular functional constraints

Zhiyuan Li, Laura P. Ioca, Ruolin He, Mohamed S. Donia.

Pnas Nexus, 2024, 3(9). [Html]

Near telomere-to-telomere genome of the model plant Physcomitrium patens

Guiqi Bi, Shijun Zhao, Jiawei Yao, Huan Wang, Mengkai Zhao, Yuanyuan Sun, Xueren Hou, Fabian B. Haas, Deepti Varshney, Michael Prigge, Stefan A. Rensing, Yuling Jiao, Yingxin Ma, Jianbin Yan, Junbiao Dai.

Nature Plants, 2024, 10(2). [Html]

Non-image-forming photoreceptors improve visual orientation selectivity and image perception

Yiming Shi, Jiaming Zhang, Xingyi Li, Yuchong Han, Jiangheng Guan, Yilin Li, Jiawei Shen, Tzvetomir Tzvetanov, Dongyu Yang, Xinyi Luo, Yichuan Yao, Zhikun Chu, Tianyi Wu, Zhiping Chen, Ying Miao, Yufei Li, Qian Wang, Jiaxi Hu, Jianjun Meng, Xiang Liao, Yifeng Zhou, Louis Tao, Yuqian Ma, Jutao Chen, Mei Zhang, Rong Liu, Yuanyuan Mi, Jin Bao, Zhong Li, Xiaowei Chen, Tian Xue.

Neuron, 2024. [Html]

Parallel molecular data storage by printing epigenetic bits on DNA

Cheng Zhang, Ranfeng Wu, Fajia Sun, Yisheng Lin, Yuan Liang, Jiongjiong Teng, Na Liu, Qi Ouyang, Long Qian, Hao Yan.

Nature, 2024, 634(8035). [Html]

Parkin inhibits proliferation and migration of bladder cancer via ubiquitinating Catalase

Renjie Zhang, Wenyu Jiang, Gang Wang, Yi Zhang, Wei Liu, Mingxing Li, Jingtian Yu, Xin Yan, Fenfang Zhou, Wenzhi Du, Kaiyu Qian, Yu Xiao, Tongzu Liu, Lingao Ju, Xinghuan Wang.

Communications Biology, 2024, 7(1). [Html]

PDX1+cell budding morphogenesis in a stem cell-derived islet spheroid system

Jia Zhao, Shenghui Liang, Haoning Howard Cen, Yanjun Li, Robert K. Baker, Balwinder Ruprai, Guang Gao, Chloe Zhang, Huixia Ren, Chao Tang, Liangyi Chen, Yanmei Liu, Francis C. Lynn, James D. Johnson, Timothy J. Kieffer.

Nature Communications, 2024, 15(1). [Html]

Photoaffinity labeling coupled with proteomics identify PDI-ADAM17 module is targeted by (-)-vinigrol to induce TNFR1 shedding and ameliorate rheumatoid arthritis in mice

Yinhua Zhu, Lu Wang, Jing Li, Yuan Zhao, Xuerong Yu, Ping Liu, Xiaobing Deng, Jingjing Liu, Fan Yang, Yini Zhang, Jiaojiao Yu, Luhua Lai, Chu Wang, Zhanguo Li, Lei Wang, Tuoping Luo.

Cell Chemical Biology, 2024, 31(3). [Html]

pi-HuB: the proteomic navigator of the human body

Fuchu He, Ruedi Aebersold, Mark S. Baker, Xiuwu Bian, Xiaochen Bo, Daniel W. Chan, Cheng Chang, Luonan Chen, Xiangmei Chen, Yu-Ju Chen, Heping Cheng, Ben C. Collins, Fernando Corrales, Jurgen Cox, Weinan E, Jennifer E. Van Eyk, Jia Fan, Pouya Faridi, Daniel Figeys, George Fu Gao, Wen Gao, Zu-Hua Gao, Keisuke Goda, Wilson Wen Bin Goh, Dongfeng Gu, Changjiang Guo, Tiannan Guo, Yuezhong He, Albert J. R. Heck, Henning Hermjakob, Tony Hunter, Narayanan Gopalakrishna Iyer, Ying Jiang, Connie R. Jimenez, Lokesh Joshi, Neil L. Kelleher, Ming Li, Yang Li, Qingsong Lin, Cui Hua Liu, Fan Liu, Guang-Hui Liu, Yansheng Liu, Zhihua Liu, Teck Yew Low, Ben Lu, Matthias Mann, Anming Meng, Robert L. Moritz, Edouard Nice, Guang Ning, Gilbert S. Omenn, Christopher M. Overall, Giuseppe Palmisano, Yaojin Peng, Charles Pineau, Terence Chuen Wai Poon, Anthony W. Purcell, Jie Qiao, Roger R. Reddel, Phillip J. Robinson, Paola Roncada, Chris Sander, Jiahao Sha, Erwei Song, Sanjeeva Srivastava, Aihua Sun, Siu Kwan Sze, Chao Tang, Liujun Tang, Ruijun Tian, Juan Antonio Vizcaino, Chanjuan Wang, Chen Wang, Xiaowen Wang, Xinxing Wang, Yan Wang, Tobias Weiss, Mathias Wilhelm, Robert Winkler, Bernd Wollscheid, Limsoon Wong, Linhai Xie, Wei Xie, Tao Xu, Tianhao Xu, Liying Yan, Jing Yang, Xiao Yang, John Yates, Tao Yun, Qiwei Zhai, Bing Zhang, Hui Zhang, Lihua Zhang, Lingqiang Zhang, Pingwen Zhang, Yukui Zhang, Yu Zi Zheng, Qing Zhong, Yunping Zhu, B. Consortium pi-Hu.

Nature, 2024, 636(8042), p. 322-331. [Html]

Plant regeneration in the new era: from molecular mechanisms to biotechnology applications

Chunli Chen, Yuxin Hu, Momoko Ikeuchi, Yuling Jiao, Kalika Prasad, Ying Hua Su, Jun Xiao, Lin Xu, Weibing Yang, Zhong Zhao, Wenkun Zhou, Yun Zhou, Jian Gao, Jia-Wei Wang.

Science China-Life Sciences, 2024, 67(7), p. 1338-1367. [Html]

Prediagnosis recognition of acute ischemic stroke by artificial intelligence from facial images

Yiyang Wang, Yunyan Ye, Shengyi Shi, Kehang Mao, Haonan Zheng, Xuguang Chen, Hanting Yan, Yiming Lu, Yong Zhou, Weimin Ye, Jing Ye, Jing-Dong J. Han.

Aging Cell, 2024, 23(8). [Html]

Promoter DNA methylation and transcription factor condensation are linked to transcriptional memory in mammalian cells

Shenqi Fan, Liang Ma, Chengzhi Song, Xu Han, Bijunyao Zhong, Yihan Lin.

Cell Systems, 2024, 15(9). [Html]

Quantitative Characterization of Gene Regulatory Circuits Associated With Fungal Secondary Metabolism to Discover Novel Natural Products

Xinran Xu, Yanhong Sun, Anxin Zhang, Sijia Li, Shu Zhang, Sijing Chen, Chunbo Lou, Lei Cai, Yihua Chen, Chunxiong Luo, Wen-Bing Yin.

Advanced Science, 2024. [Html]

Reacon: a template- and cluster-based framework for reaction condition prediction

Zihan Wang, Kangjie Lin, Jianfeng Pei, Luhua Lai.

Chemical Science, 2024. [Html]

Readily releasable β cells with tight Ca2+-exocytosis coupling dictate biphasic glucose-stimulated insulin secretion

Xiaohong Peng, Huixia Ren, Lu Yang, Shiyan Tong, Renjie Zhou, Haochen Long, Yunxiang Wu, Lifen Wang, Yi Wu, Yongdeng Zhang, Jiayu Shen, Junwei Zhang, Guohua Qiu, Jianyong Wang, Chengsheng Han, Yulin Zhang, Mengxuan Zhou, Yiwen Zhao, Tao Xu, Chao Tang, Zhixing Chen, Huisheng Liu, Liangyi Chen.

Nature Metabolism, 2024, 6(2), p. 238-+. [Html]

Remodeling ceramide homeostasis promotes functional maturation of human pluripotent stem cell-derived (3 cells

Huijuan Hua, Yaqi Wang, Xiaofeng Wang, Shusen Wang, Yunlu Zhou, Yinan Liu, Zhen Liang, Huixia Ren, Sufang Lu, Shuangshuang Wu, Yong Jiang, Yue Pu, Xiang Zheng, Chao Tang, Zhongyang Shen, Cheng Li, Yuanyuan Du, Hongkui Deng.

Cell Stem Cell, 2024, 31(6). [Html]

Revealing excited states of rotational Bose-Einstein condensates

Jianyuan Yin, Zhen Huang, Yongyong Cai, Qiang Du, Lei Zhang.

Innovation, 2024, 5(1). [Html]

The scale of zebrafish pectoral fin buds is determined by intercellular K+ levels and consequent Ca2+-mediated signaling via retinoic acid regulation of Rcan2 and Kcnk5b

Xiaowen Jiang, Kun Zhao, Yi Sun, Xinyue Song, Chao Yi, Tianlong Xiong, Sen Wang, Yi Yu, Xiduo Chen, Run Liu, Xin Yan, Christopher L. Antos.

Plos Biology, 2024, 22(3). [Html]

scBOL: a universal cell type identification framework for single-cell and spatial transcriptomics data

Yuyao Zhai, Liang Chen, Minghua Deng.

Briefings in Bioinformatics, 2024, 25(3). [Html]

scEVOLVE: cell-type incremental annotation without forgetting for single-cell RNA-seq data

Yuyao Zhai, Liang Chen, Minghua Deng.

Briefings in Bioinformatics, 2024, 25(2). [Html]

scPLAN: a hierarchical computational framework for single transcriptomics data annotation, integration and cell-type label refinement

Qirui Guo, Musu Yuan, Lei Zhang, Minghua Deng.

Briefings in Bioinformatics, 2024, 25(4). [Html]

Securin acetylation prevents precocious separase activation and premature sister chromatid separation

Tianning Wang, Yuhong Zou, Hui Meng, Pengli Zheng, Junlin Teng, Ning Huang, Jianguo Chen.

Current Biology, 2024, 34(6). [Html]

SIDERITE: Unveiling hidden siderophore diversity in the chemical space through digital exploration

Ruolin He, Shaohua Gu, Jiazheng Xu, Xuejian Li, Haoran Chen, Zhengying Shao, Fanhao Wang, Jiqi Shao, Wen-Bing Yin, Long Qian, Zhong Wei, Zhiyuan Li.

Imeta, 2024, 3(2). [Html]

Siderophore interactions drive the ability of Pseudomonas spp. consortia to protect tomato against Ralstonia solanacearum

Zhengying Shao, Shaohua Gu, Xiaoni Zhang, Jiao Xue, Tao Yan, Saisai Guo, Thomas Pommier, Alexandre Jousset, Tianjie Yang, Yangchun Xu, Qirong Shen, Zhong Wei.

Horticulture Research, 2024, 11(09). [Html]

Single-cell omics: experimental workflow, data analyses and applications

Fengying Sun, Haoyan Li, Dongqing Sun, Shaliu Fu, Lei Gu, Xin Shao, Qinqin Wang, Xin Dong, Bin Duan, Feiyang Xing, Jun Wu, Minmin Xiao, Fangqing Zhao, Jing-Dong J. Han, Qi Liu, Xiaohui Fan, Chen Li, Chenfei Wang, Tieliu Shi.

Science China-Life Sciences, 2024. [Html]

Single-cell senescence identification reveals senescence heterogeneity, trajectory, and modulators

Wanyu Tao, Zhengqing Yu, Jing-Dong J. Han.

Cell Metabolism, 2024, 36(5). [Html]

SPANN: annotating single-cell resolution spatial transcriptome data with scRNA-seq data

Musu Yuan, Hui Wan, Zihao Wang, Qirui Guo, Minghua Deng.

Briefings in Bioinformatics, 2024, 25(2). [Html]

Spatially resolved profiling of protein conformation and interactions by biocompatible chemical cross-linking in living cells

Lili Zhao, Yuxin An, Nan Zhao, Hang Gao, Weijie Zhang, Zhou Gong, Xiaolong Liu, Baofeng Zhao, Zhen Liang, Chun Tang, Lihua Zhang, Yukui Zhang, Qun Zhao.

Nature communications, 2024, 15(1), p. 8331-8331. [Html]

Structural insights into VAChT neurotransmitter recognition and inhibition

Yang Zhang, Fei Dai, Nanhao Chen, Dong Zhou, Chia-Hsueh Lee, Chen Song, Yixiao Zhang, Zhe Zhang.

Cell Research, 2024, 34(9), p. 665-668. [Html]

Structure-Based Screening and Optimization of PafA Inhibitors with Potent Anti-Tuberculosis Activity

Hewei Jiang, Jin Xie, Lei Wang, Hong Chen, Yunxiao Zheng, Xuening Wang, Shujuan Guo, Tao Wang, Jing Bi, Xuelian Zhang, Jianfeng Pei, Shengce Tao.

International Journal of Molecular Sciences, 2024, 25(23). [Html]

Study of non-equilibrium statistical physics of protein machine by cryogenic electron microscopy

Yang Tian, Ouyang Qi.

Acta Physica Sinica, 2024, 73(13). [Html]

Substrate and drug recognition mechanisms of SLC19A3

Yu Dang, Tianyi Zhang, Shabareesh Pidathala, Guopeng Wang, Yijie Wang, Nanhao Chen, Chen Song, Chia-Hsueh Lee, Zhe Zhang.

Cell Research, 2024, 34(6), p. 458-461. [Html]

Target-Specific De Novo Peptide Binder Design with DiffPepBuilder

Fanhao Wang, Yuzhe Wang, Laiyi Feng, Changsheng Zhang, Luhua Lai.

Journal of Chemical Information and Modeling, 2024. [Html]

Thermal facial image analyses reveal quantitative hallmarks of aging and metabolic diseases

Zhengqing Yu, Yong Zhou, Kehang Mao, Bo Pang, Kai Wang, Tang Jin, Haonan Zheng, Haotian Zhai, Yiyang Wang, Xiaohan Xu, Hongxiao Liu, Yi Wang, Jing-Dong J. Han.

Cell Metabolism, 2024, 36(7). [Html]

The ticking of aging clocks

Jing-Dong J. Han.

Trends in Endocrinology and Metabolism, 2024, 35(1), p. 11-22. [Html]

Tissue-specific profiling of age-dependent miRNAomic changes in Caenorhabditis elegans

Xueqing Wang, Quanlong Jiang, Hongdao Zhang, Zhidong He, Yuanyuan Song, Yifan Chen, Na Tang, Yifei Zhou, Yiping Li, Adam Antebi, Ligang Wu, Jing-Dong J. Han, Yidong Shen.

Nature Communications, 2024, 15(1). [Html]

TRAIP suppresses bladder cancer progression by catalyzing K48-linked polyubiquitination of MYC

Jingtian Yu, Mingxing Li, Lingao Ju, Fenfang Zhou, Yejinpeng Wang, Yi Zhang, Renjie Zhang, Wenzhi Du, Ruoyu Huang, Kaiyu Qian, Gang Wang, Yu Xiao, Xinghuan Wang.

Oncogene, 2024, 43(7), p. 470-483. [Html]

Transformation gap from research findings to large-scale commercialized products in microfluidic field

Yuqi Ma, Xiaoyi Sun, Ziwei Cai, Mengjing Tu, Yugang Wang, Qi Ouyang, Xueqing Yan, Gaoshan Jing, Gen Yang.

Materials Today Bio, 2024, 29. [Html]

Tuning the diffusion constant to optimize the readout of positional information of spatial concentration patterns

Ka Kit Kong, Chunxiong Luo, Feng Liu.

Chinese Physics B, 2024, 33(8). [Html]

Unraveling aging from transcriptomics

Yuanfang Huang, Shouxuan Zhu, Shuai Yao, Haotian Zhai, Chenyang Liu, Jing-Dong J. Han.

Trends in genetics : TIG, 2024. [Html]

Unveiling the association between HMG-CoA reductase inhibitors and bladder cancer: a comprehensive analysis using Mendelian randomization, animal models, and transcriptomics

Houyi Wei, Zhilong Li, Kaiyu Qian, Wenzhi Du, Lingao Ju, Danni Shan, Mengxue Yu, Yayun Fang, Yi Zhang, Yu Xiao, Gang Wang, Xinghuan Wang.

Pharmacogenomics Journal, 2024, 24(5). [Html]

UPP1 enhances bladder cancer progression and gemcitabine resistance through AKT

Wenzhi Du, Sheng Tu, Wenxiu Zhang, Yi Zhang, Wei Liu, Kangping Xiong, Fenfang Zhou, Na Li, Renjie Zhang, Jingtian Yu, Mingxing Li, Wan Xiang, Kaiyu Qian, Gang Wang, Yu Xiao, Xinghuan Wang, Lingao Ju.

International Journal of Biological Sciences, 2024, 20(4), p. 1389-1409. [Html]

USP43 stabilizes c-Myc to promote glycolysis and metastasis in bladder cancer

Mingxing Li, Jingtian Yu, Lingao Ju, Yejinpeng Wang, Wan Jin, Renjie Zhang, Wan Xiang, Meng Ji, Wenzhi Du, Gang Wang, Kaiyu Qian, Yi Zhang, Yu Xiao, Xinghuan Wang.

Cell Death & Disease, 2024, 15(1). [Html]