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Quantitative Biology, Volume 11
Volume 11, Number 1, 2023
- Quan Cheng, Xuan Wang, Xian-En Zhang, Chengchen Xu, Feng Li:
Quantitative functionalization of biosynthetic caged protein materials. 1 - Huan Du, Meng Li
, Yang Liu:
Towards applications of genome-scale metabolic model-based approaches in designing synthetic microbial communities. 15 - Limin Jiang, Hui Yu, Yan Guo:
Modeling the relationship between gene expression and mutational signature. 31 - Luciana I. Escobar, Andres M. Alonso, Jorge R. Ronderos, Luis Diambra
Distal nucleotides affect the rate of stop codon read-through. 44 - Darren Wethington, Sayak Mukherjee, Jayajit Das:
McSNAC: A software to approximate first-order signaling networks from mass cytometry data. 59 - Mingwei 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. 72 - Rashmi Panigrahi, Senthilkumar Kailasam:
Mapping allosteric pathway in NIa-Pro using computational approach. 82 - Xian-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. 94
Volume 11, Number 2, June 2023
- Evelyn Shue, Li Liu, Bingxin Li, Zifeng Feng
Empowering beginners in bioinformatics with ChatGPT. 105-108 - Junting Wang
3D genomic organization in cancers. 109-121 - Haiyan Gong
Computational methods for identifying enhancer-promoter interactions. 122-142 - Huawei Zhu
Light-driven synthetic microbial consortia: playing with an oxygen dilemma. 143-154 - Mateusz Chilinski
Prediction of chromatin looping using deep hybrid learning (DHL). 155-162 - Yuwei 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. 163-174 - Kh Shahriya Zaman
Secure and efficient implementation of facial emotion detection for smart patient monitoring system. 175-182 - Ali Tarihi, Mojtaba Tarihi, Taki Tiraihi:
Cell-based allometry: an approach for evaluation of complexity in morphogenesis. 183-203 - Dong Xu:
ChatGPT opens a new door for bioinformatics. 204-206
Volume 11, Number 3, September 2023
- Issue Information.
- Xuegong Zhang, Lei Wei, Rui Jiang, Xiaowo Wang, Jin Gu, Zhen Xie, Hairong Lv:
Building digital life systems for future biology and medicine. 207-213 - Chenfei Tian, Jianhua Li, Yong Wang:
From qualitative to quantitative: the state of the art and challenges for plant synthetic biology. 214-230 - Yan 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. 231-245 - Xabier Martinez-de-morentin, Sumeer Ahmad Khan, Robert Lehmann, Sally Sisi Qu, Alberto Maillo, Narsis A. Kiani, Felipe Prósper, Jesper Tegnér
LIBRA: an adaptative integrative tool for paired single-cell multi-omics data. 246-259 - Qijin Yin, Rui Fan, Xusheng Cao, Qiao Liu, Rui Jiang, Wanwen Zeng:
DeepDrug: A general graph-based deep learning framework for drug-drug interactions and drug-target interactions prediction. 260-274 - Yuanpeng Xiong, Xuan He, Dan Zhao, Tao Jiang, Jianyang Zeng:
DeepRCI: predicting RNA-chromatin interactions via deep learning with multi-omics data. 275-286 - Xiuquan Wang, Mian Umair Ahsan
Transformer-based DNA methylation detection on ionic signals from Oxford Nanopore sequencing data. 287-296 - Nan Miles Xi, Angelos Vasilopoulos:
Tuning hyperparameters of doublet-detection methods for single-cell RNA sequencing data. 297-305 - Doyoung Park:
Use of artificial neural networks to identify and analyze polymerized actin-based cytoskeletal structures in 3D confocal images. 306-319 - Qin Xie, Wei Ma
Exploration on learning molecular docking with deep learning models. 320-331 - Leandro 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. 332-342 - Elham Dalalbashi Esfahani
Pattern discovery of long non-coding RNAs associated with the herbal treatments in breast and prostate cancers. 343-358
Volume 11, Number 4, December 2023
- Issue Information.
- Michael Q. Zhang:
Dialog between artificial intelligence & natural intelligence. 359-362 - Feiran Li
Genome-scale metabolic models applied for human health and biopharmaceutical engineering. 363-375 - Lu Peng
Theoretical perspective on synthetic man-made life: Learning from the origin of life. 376-394 - Chao Pang, Henry H. Y. Tong, Leyi Wei:
Advanced deep learning methods for molecular property prediction. 395-404 - Junqi Zhang, Zixuan You, Dingyuan Liu, Rui Tang, Chao Zhao, Yingxiu Cao, Feng Li, Hao Song:
Conductive proteins-based extracellular electron transfer of electroactive microorganisms. 405-420 - Dali Wang, Jiaxuan Li, Lei Wang, Yipeng Cao, Bo Kang, Xiangfei Meng, Sai Li
Toward atomistic models of intact severe acute respiratory syndrome coronavirus 2 via Martini coarse-grained molecular dynamics simulations. 421-433 - Ke Feng, Hongyang Jiang, Chaoyi Yin, Huiyan Sun:
Gene regulatory network inference based on causal discovery integrating with graph neural network. 434-450 - Hongfei Cui:
Reorganizing heterogeneous information from host-microbe interaction reveals innate associations among samples. 451-470 - Jianfeng Feng:
Simulating the whole brain as an alternative way to achieve AGI. 471-473
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