Highlights

Briefings in Bioinformatics

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scGO: interpretable deep neural network for cell status annotation and disease diagnosis

You Wu, Pengfei Xu, Liyuan Wang, Shuai Liu, Yingnan Hou, Hui Lu, Peng Hu*, Xiaofei Li*, Xiang Yu*(2025)

本研究提出了scGO，一种基于GO的深度学习框架，通过利用稀疏神经网络提高可解释性，精准注释单细胞RNA测序数据中的细胞状态。

Journal of Genetics and Genomics

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bmp10 maintains cardiac function by regulating iron homeostasis

Ruiqin Hu , Genfang Li , Peng Hu, Hongbo Niu , Wenhao Li , Shouwen Jiang , Guijun Guan , Qianghua Xu , Mingli Liu , Liangbiao Chen*(2024)

本研究揭示了BMP10在调节心脏铁稳态中的关键作用，突出了靶向BMP10-hepcidin-铁轴作为治疗铁相关心肌病的潜在策略。

Journal:iScience

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Identification of two miRNAs regulating cardiomyocyte proliferation in an Antarctic icefish

Qianghua Xu*, Ruonan Jia, Fei Yang, Peng Hu, Xue Li, Saiya Ge, Shouwen Jiang, Jiulin Chan, Wanying Zhai, Liangbiao Chen*(2024)

揭示了miR-458-3p和miR-144-5p通过调控骨形态发生蛋白-2（bmp2）在南极冰鱼的心脏增大和缺氧诱导的心脏重塑中发挥关键作用。

Journal:Aquaculture

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Integrated transcriptomic and epigenomic analyses to disclose the transcriptional regulatory mechanisms of lipid and energy metabolism under cold stress in grass carp

Songqian Huang, Chenyu Yan, Yuan Xu, He Jiao, Minghao Zhang, Jiangbo Cheng, Wenting Wang, Zongbin Cui, Liangbiao Chen, Peng Hu*, Qianghua Xu*(2024)

揭示了草鱼在寒冷应激下的脂质和能量代谢的转录调控机制，强调了Hnf1b和PPARa等关键转录因子的作用。

Journal:Biosensors & Bioelectronics

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A handheld isothermal fluorescence detector for duplex visualization of aquatic pathogens via enhanced one-pot LAMP-PfAgo assay

Feibiao Pang, Tao Zhang, Fengyi Dai, Kaizheng Wang, Tianjiao Jiao, Zuoying Zhang, Liyi Zhang, Mingli Liu, Peng Hu*, Jinzhao Song*(2024)

开发了一款先进的手持式等温核酸扩增设备（WeD-1），结合增强型的一锅法原核生物Argonaute基于核酸检测方法，实现了水生病原体的双重视觉检测。

Journal:Developmental Cell

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Sweat gland development requires an eccrine dermal niche and couples two epidermal programs

Heather L. Dingwall, Reiko R. Tomizawa, Adam Aharoni, Peng Hu, Qi Qiu, Blerina Kokalari, Serenity M. Martinez, Joan C. Donahue, Daniel Aldea, Meryl Mendoza, Ian A. Glass, Birth Defects Research Laboratory (BDRL), Hao Wu and Yana G.Kamberov*(2023)

揭示了分泌腺的发育需要EDEN，这是一种进化过程保守的皮肤生态位。

Journal:Nature Biotechnology

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Joint single-cell profiling resolves 5mC and 5hmC and reveals their distinct gene regulatory effects

Emily B. Fabyanic*,Hu P*, Qi Qiu, Kiara N. Berríos, Daniel R. Connolly, Tong Wang, Jennifer Flournoy, Zhaolan Zhou, Rahul M. Kohli & Hao Wu(2023)

这一技术为研究单细胞水平上的胞嘧啶羟甲基化5hmC修饰和真正的胞嘧啶甲基化5mC修饰提供了平台。

Journal:Molecular Cell

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Dissecting Cell-Type Composition and Activity-Dependent Transcriptional State in Mammalian Brains by Massively Parallel Single-Nucleus RNA-Seq

Hu P*, Fabyanic E*, Kwon DY, Tang S, Zhou Z, Wu H (2017)

第一批研发了单细胞核转录组测序技术，首次鉴定了戊四氮诱导痫癫痫小鼠模型中细胞类型特异的转录图谱。

Journal:Genes & Development

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Single-nucleus transcriptomic survey of cell diversity and functional maturation in postnatal mammalian hearts

Hu P*, Liu J*, Zhao J*, Wilkins BJ, Lupino K, Wu H, Pei L (2018)

应用研发的单细胞核转录组测序技术，首次描绘了出生后小鼠心脏发育的单细胞图谱。

Journal:Nature Methods

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Massively parallel and time-resolved single-cell RNA sequencing with scNT-Seq

Qiu Q*, Hu P*(共同第一), Qiu X, Govek KW, Camara PG, Wu H (2020)

开发了型新型的高通量单细胞新生转录本标记技术，准确定量单个细胞中“新”和“旧”的转录本，能准确用于追溯单细胞的轨迹。

Journal:Nucleic Acids Research

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Global identification of the genetic networks and cis-regulatory elements of the cold response in zebrafish

Hu P, Liu M, Zhang D, Wang J, Niu H, Liu Y, Wu Z, Han B, Zhai W, Shen Y, Chen L (2015)

系统性地鉴定了基因组中低温响应的顺式作用元件，绘制了模式动物斑马鱼低温响应的调控网络。

Journal:Protein & Cell

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Single cell transcriptomic analysis of the adult mouse pituitary reveals a novel multi-hormone cell cluster and physiologic demand-induced lineage plasticity

Ho Y*, Hu P*(共同第一), Peel MT, Chen S, Camara PG, Epstein DJ, Wu H, Liebhaber SA (2020)

通过单细胞转录组学分析技术，在小鼠脑垂体前叶中鉴定出了一种新的分泌多种激素的细胞类型，扩展了教科书的认知。

Molecular Biomedicine

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The vertebrate- and testis- specific transmembrane protein C11ORF94 plays a critical role in sperm-oocyte membrane binding

Hongying Hao, Baolu Shi, Jiacheng Zhang, Ao Dai, Wenhao Li, Haidi Chen, Wenya Ji, Chenjia Gong, Chang Zhang, Jing Li, Li Chen, Bin Yao, Peng Hu, Hao Yang, Juergen Brosius, Shanshan Lai, Qinghua Shi & Cheng Deng (2020.09)

Frontiers in Cell and Developmental Biology

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MiR-202-3p determines embryo viability during mid-blastula transition

Ruiqin Hu, Yanna Xu, Bingshe Han, Yi Chen, Wenhao Li, Guijun Guan, Peng Hu, Yan Zhou, Qianghua Xu, Liangbiao Chen(2020.8)

Nature

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Molecular landscapes of human hippocampal immature neurons across lifespan

Zhou Y, Su Y, Li S, Kennedy BC, Zhang DY, Bond AM, Sun Y, Jacob F, Lu L, Hu P, Viaene AN, Helbig I, Kessler SK, Lucas T, Salinas RD, Gu X, Chen HI, Wu H, Kleinman JE, Hyde TM, Nauen DW, Weinberger DR, Ming GL, Song H(2020.07)

Nature Communications

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Neuronal Yin Yang1 in the prefrontal cortex regulates transcriptional and behavioral responses to chronic stress in mice

Kwon DY, Xu B, Hu P, Zhao YT, Beagan JA, Nofziger JH, Cui Y, Phillips-Cremins JE, Blendy JA, Wu H, Zhou Z. (2020.01)

bioRxiv

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Quantitative single cell 5hmC sequencing reveals non-canonical gene regulation by non-CG hydroxymethylation

Emily B. Fabyanic, Peng Hu, Qi Qiu, Tong Wang, Kiara N. Berríos, Jennifer Flournoy, Daniel R. Connolly, Zhaolan Zhou, Rahul M. Kohil, Hao Wu (2021.03)

Fish & Shellfish Immunology

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Transcriptomic responses to low temperature stress in the Nile tilapia, Oreochromis niloticus

Zhou T, Gui L, Liu M, Li W, Hu P, Duarte DFC, Niu H, Chen L (2019.01)

Nature Biotechnology

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Nondestructive, base-resolution sequencing of 5-hydroxymethylcytosine using a DNA deaminase

Schutsky EK, DeNizio JE, Hu P, Liu MY, Nabel CS, Fabyanic EB, Hwang Y, Bushman FD, Wu H, Kohli RM.(2018.10)

BMC Genomics

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GC bias lead to increased small amino acids and random coils of proteins in cold-water fishes

Zhang D, Hu P, Liu T, Wang J, Jiang S, Xu Q, Chen L. (2018.5)

Biochemical Systematics and Ecology

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Divergent adaptation to Qinghai-Tibetan Plateau implicated from transciptome study of Gymnocypris dobula and Schizothorax nukiangensis

Mengchao Yu, Dongsheng Zhang, Peng Hu, Sihua Peng, Weiwen Li, Shunping He, Wanying Zhai, Qianghua Xu, Liangbiao Chen(2017.4)

G3: Genes, Genomes, Genetics

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Genetic Adaptation of Schizothoracine Fish to the Phased Uplifting of the Qinghai–Tibetan Plateau

Zhang D, Yu M, Hu P, Peng S, Liu Y, Li W, Wang C, He S, Zhai W, Xu Q, Chen L. (2017.4)

Journal of fishery sciences of China

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The role of dusp1 downregulation in apoptosis of zebrafish ZF4 cells under cold stress

Hongbo Niu, Peng Hu, Pengli Cheng, Xu Chu, Chunlan Hu, Liangbiao Chen. (2017.1)

Nature Communications

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Neofunctionalization of zona pellucida proteins enhances freeze-prevention in the eggs of Antarctic notothenioids

Cao L, Huang Q, Wu Z, Cao DD, Ma Z, Xu Q, Hu P, Fu Y, Shen Y, Chan J, Zhou CZ, Zhai W, Chen L. (2017.1)

Scientific Reports

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Transcriptome comparison reveals a genetic network regulating the lower temperature limit in fish

Hu P, Liu M, Liu Y, Wang J, Zhang D, Niu H, Jiang S, Wang J, Zhang D, Han B, Xu Q, Chen L. (2016.6)

Molecular Ecology

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Evolutionary suppression of erythropoiesis via the modulation of TGF‐β signalling in an Antarctic icefish

Xu Q, Cai C, Hu X, Liu Y, Guo Y, Hu P, Chen Z, Peng S, Zhang D, Jiang S, Wu Z, Chan J, Chen L. (2015.9)