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    Journal: Quant. Biol.

    Volume 11, Issue 4

    0 -- 0. Issue Information
    359 -- 362Michael Q. Zhang. Dialog between artificial intelligence & natural intelligence
    363 -- 375Feiran Li, Yu Chen, Johan Gustafsson, Hao Wang, Yi Wang, Chong Zhang, Xinhui Xing. Genome-scale metabolic models applied for human health and biopharmaceutical engineering
    376 -- 394Lu Peng, Zecheng Zhang, Xianyi Wang, Weiyi Qiu, Liqian Zhou, Hui Xiao, Chunxiuzi Liu, Shaohua Tang, Zhiwei Qin, Jiakun Jiang, Zengru Di, Yu Liu. Theoretical perspective on synthetic man-made life: Learning from the origin of life
    395 -- 404Chao Pang, Henry H. Y. Tong, Leyi Wei. Advanced deep learning methods for molecular property prediction
    405 -- 420Junqi Zhang, Zixuan You, Dingyuan Liu, Rui Tang, Chao Zhao, Yingxiu Cao, Feng Li, Hao Song. Conductive proteins-based extracellular electron transfer of electroactive microorganisms
    421 -- 433Dali Wang, Jiaxuan Li, Lei Wang, Yipeng Cao, Bo Kang, Xiangfei Meng, Sai Li, Chen Song. Toward atomistic models of intact severe acute respiratory syndrome coronavirus 2 via Martini coarse-grained molecular dynamics simulations
    434 -- 450Ke Feng, Hongyang Jiang 0002, Chaoyi Yin, Huiyan Sun. Gene regulatory network inference based on causal discovery integrating with graph neural network
    451 -- 470Hongfei Cui. Reorganizing heterogeneous information from host-microbe interaction reveals innate associations among samples
    471 -- 473Jianfeng Feng. Simulating the whole brain as an alternative way to achieve AGI

    Volume 11, Issue 3

    0 -- 0. Issue Information
    207 -- 213Xuegong Zhang, Lei Wei, Rui Jiang 0001, Xiaowo Wang, Jin Gu, Zhen Xie, Hairong Lv. Building digital life systems for future biology and medicine
    214 -- 230Chenfei Tian, Jianhua Li, Yong Wang. From qualitative to quantitative: the state of the art and challenges for plant synthetic biology
    231 -- 245Yan Yan, Liheng Yang, Leyuan Meng, Haochen Su, Cheng Zhou, Le Yu, Zhengtu Li, Xu Zhang, Huihua Cai, Juntao Gao. Introduction to bioimaging-based spatial multi-omic novel methods
    246 -- 259Xabier Martinez-de-morentin, Sumeer Ahmad Khan, Robert Lehmann 0002, Sally Sisi Qu, Alberto Maillo, Narsis A. Kiani, Felipe Prósper, Jesper Tegnér, David Gomez-Cabrero. LIBRA: an adaptative integrative tool for paired single-cell multi-omics data
    260 -- 274Qijin Yin, Rui Fan, Xusheng Cao, Qiao Liu, Rui Jiang 0001, Wanwen Zeng. DeepDrug: A general graph-based deep learning framework for drug-drug interactions and drug-target interactions prediction
    275 -- 286Yuanpeng Xiong, Xuan He, Dan Zhao, Tao Jiang 0001, Jianyang Zeng 0001. DeepRCI: predicting RNA-chromatin interactions via deep learning with multi-omics data
    287 -- 296Xiuquan Wang, Mian Umair Ahsan, Yunyun Zhou, Kai Wang. Transformer-based DNA methylation detection on ionic signals from Oxford Nanopore sequencing data
    297 -- 305Nan Miles Xi, Angelos Vasilopoulos. Tuning hyperparameters of doublet-detection methods for single-cell RNA sequencing data
    306 -- 319Doyoung Park. Use of artificial neural networks to identify and analyze polymerized actin-based cytoskeletal structures in 3D confocal images
    320 -- 331Qin Xie, Wei Ma, Jianhang Zhang, Shiliang Li, XiaoBing Deng, Youjun Xu, Weilin Zhang. Exploration on learning molecular docking with deep learning models
    332 -- 342Leandro R. Jones, Julieta M. Manrique. High-throughput metabarcoding of SAR11 assemblages from the southwest Atlantic shelf and arid Patagonia: richness and associated rank abundance distributions
    343 -- 358Elham Dalalbashi Esfahani, Esmaeil Ebrahimie, Ali Niazi, Manijeh Mohammadi Dehcheshmeh. Pattern discovery of long non-coding RNAs associated with the herbal treatments in breast and prostate cancers

    Volume 11, Issue 2

    105 -- 108Evelyn Shue, Li Liu, Bingxin Li, Zifeng Feng, Xin Li, Gangqing Hu. Empowering beginners in bioinformatics with ChatGPT
    109 -- 121Junting Wang, Huan Tao, Hao Li, Xiaochen Bo, Hebing Chen. 3D genomic organization in cancers
    122 -- 142Haiyan Gong, Zhengyuan Chen, Yuxin Tang, Minghong Li, Sichen Zhang, Xiaotong Zhang, Yang Chen. Computational methods for identifying enhancer-promoter interactions
    143 -- 154Huawei Zhu, Yin Li. Light-driven synthetic microbial consortia: playing with an oxygen dilemma
    155 -- 162Mateusz Chilinski, Anup Kumar Halder, Dariusz Plewczynski. Prediction of chromatin looping using deep hybrid learning (DHL)
    163 -- 174Yuwei Huang, Huidan Chang, Xiaoyi Chen, Jiayue Meng, Mengyao Han, Tao Huang, Liyun Yuan, Guoqing Zhang. A cell marker-based clustering strategy (cmCluster) for precise cell type identification of scRNA-seq data
    175 -- 182Kh Shahriya Zaman, Mamun Bin Ibne Reaz. Secure and efficient implementation of facial emotion detection for smart patient monitoring system
    183 -- 203Ali Tarihi, Mojtaba Tarihi, Taki Tiraihi. Cell-based allometry: an approach for evaluation of complexity in morphogenesis
    204 -- 206Dong Xu. ChatGPT opens a new door for bioinformatics

    Volume 11, Issue 1

    1 -- 0Quan Cheng, Xuan Wang, Xian-En Zhang, Chengchen Xu, Feng Li. Quantitative functionalization of biosynthetic caged protein materials
    15 -- 0Huan Du, Meng Li, Yang Liu. Towards applications of genome-scale metabolic model-based approaches in designing synthetic microbial communities
    31 -- 0Limin Jiang, Hui Yu, Yan Guo. Modeling the relationship between gene expression and mutational signature
    44 -- 0Luciana I. Escobar, Andres M. Alonso, Jorge R. Ronderos, Luis Diambra. Distal nucleotides affect the rate of stop codon read-through
    59 -- 0Darren Wethington, Sayak Mukherjee, Jayajit Das. McSNAC: A software to approximate first-order signaling networks from mass cytometry data
    72 -- 0Mingwei Li, Guanglin Chen, Zhiyong Zhang. Structural and dynamic properties of the YTH domain in complex with N$lt;sup$gt;6$lt;/sup$gt;-methyladenosine RNA studied by accelerated molecular dynamics simulations
    82 -- 0Rashmi Panigrahi, Senthilkumar Kailasam. Mapping allosteric pathway in NIa-Pro using computational approach
    94 -- 0Xian-Fang Wang, Zhi-Yong Du, Qi-Meng Li, Yi-Feng Liu, Shao-Hui Ma, Jui-Wei Cui. Network pharmacology research of mechanism of Maxing Shigan Decoction in treating COVID-19
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