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Quantitative Biology, Volume 12
Volume 12, Number 1, 2024
- Issue Information.
- Yazhen Song, Chenxi Feng, Difei Zhou, Zengxin Ma, Lian He, Cong Zhang, Guihong Yu, Yan Zhao, Song Yang, Xinhui Xing:
Constructing efficient bacterial cell factories to enable one-carbon utilization based on quantitative biology: A review. 1-14 - Yuhang Xia, Yongkang Wang, Zhiwei Wang, Wen Zhang:
A comprehensive review of molecular optimization in artificial intelligence-based drug discovery. 15-29 - Xinyue Li, Zhankun Xiong, Wen Zhang, Shichao Liu:
Deep learning for drug-drug interaction prediction: A comprehensive review. 30-52 - Mahsa Babaei, Soheila Kashanian, Huang-teck Lee, Frances Harding:
Proteomics techniques in protein biomarker discovery. 53-69 - Tianxing Ma, Zetong Zhao
, Haochen Li
NeoHunter: Flexible software for systematically detecting neoantigens from sequencing data. 70-84 - Siyu Li, Songming Tang, Yunchang Wang, Sijie Li, Yuhang Jia, Shengquan Chen:
Accurate cell type annotation for single-cell chromatin accessibility data via contrastive learning and reference guidance. 85-99 - Keran Sun, Jingyuan Ning, Keqi Jia, Xiaoqing Fan, Hongru Li, Jize Ma, Meiqi Meng, Cuiqing Ma, Lin Wei:
Role of ACLY in the development of gastric cancer under hyperglycemic conditions. 100-116 - Jiarui Ou
Re-examination of statistical relationships between dietary fats and other risk factors, and cardiovascular disease, based on two crucial datasets. 117-127
Volume 12, Number 2, 2024
- Chenrui Qin, Tong Xu, Xuejin Zhao, Yeqing Zong, Haoqian M. Zhang, Chunbo Lou, Qi Ouyang, Long Qian
Functional predictability of universal gene circuits in diverse microbial hosts. 129-140 - Yinfei Feng
GCARDTI: Drug-target interaction prediction based on a hybrid mechanism in drug SELFIES. 141-154 - Jiaming Su
DDI-Transform: A neural network for predicting drug-drug interaction events. 155-163 - Ji Lv
Measuring drug similarity using drug-drug interactions. 164-172 - Xiaomeng Xue
A feature extraction framework for discovering pan-cancer driver genes based on multi-omics data. 173-181 - Binyu Yang, Siying Liu, Jiemin Xie, Xi Tang, Pan Guan, Yifan Zhu, Xuemei Liu, Yunhui Xiong, Zuli Yang, Weiyao Li, Yonghua Wang, Wen Chen, Qingjiao Li, Li C. Xia:
Hierarchical learning of gastric cancer molecular subtypes by integrating multi-modal DNA-level omics data and clinical stratification. 182-196 - Yahan Li, Xinrui Cai, Junliang Shang, Yuanyuan Zhang, Jin-Xing Liu:
SimHOEPI: A resampling simulator for generating single nucleotide polymorphism data with a high-order epistasis model. 197-204 - Huamei Qi, Wenhui Yang
A clinical trial termination prediction model based on denoising autoencoder and deep survival regression. 205-214 - Jingxin Yang, Jin Chen, Luobin Zhang, Fangming Zhou, Xiaozhen Cui, Ruijun Tian, Ruilian Xu:
Plasma proteome profiling reveals biomarkers of chemotherapy resistance in patients with advanced colorectal cancer. 215-224 - Yuanli Gao
Toward predictable universal genetic circuit design. 225-229
Volume 12, Number 3, 2024
- Yuyang Wang, Yu Sun, Zeyu Liu, Bijia Chen, Hebing Chen, Chao Ren, Xuanwei Lin, Pengzhen Hu, Peiheng Jia, Xiang Xu
Effectiveness of machine learning at modeling the relationship between Hi-C data and copy number variation. 231-244 - Rui Xin, Limin Jiang, Hui Yu, Fengyao Yan, Jijun Tang, Yan Guo:
Comprehensive cross cancer analyses reveal mutational signature cancer specificity. 245-254 - Liangcheng Dong
A substructure-aware graph neural network incorporating relation features for drug-drug interaction prediction. 255-270 - Madhuri Gollapalli, Harsh Anand
Characterizing diseases using genetic and clinical variables: A data analytics approach. 271-285 - Ivan Krasnyakov:
Mathematical modeling of evolution of cell networks in epithelial tissues. 286-300 - Razieh Rezaei Adriani, Seyed Latif Mousavi Gargari, Hamid Bakherad, Jafar amani:
In silico designing and optimization of anti-epidermal growth factor receptor scaffolds by complementary-determining regions-grafting technique. 301-312 - Yang Li, Xiaonan Ren, Haochen Yu, Tao Sun, Shuangge Ma:
A penalized integrative deep neural network for variable selection among multiple omics datasets. 313-323 - Wenlong Zhao, Cecylia S. Lupala
Assessing the inhibition efficacy of clinical drugs against the main proteases of SARS-CoV-2 variants and other coronaviruses. 324-328 - Jianfeng Cao, Lihan Hu, Guoye Guan, Zelin Li
CShaperApp: Segmenting and analyzing cellular morphologies of the developing Caenorhabditis elegans embryo. 329-334
Volume 12, Number 4, 2024
- Issue Information. 1-4
- Christina V. Theodoris
Perspectives on benchmarking foundation models for network biology. 335-338 - Ziyu Chen, Lin Wei, Ge Gao:
Foundation models for bioinformatics. 339-344 - Jinge Wang, Zien Cheng, Qiuming Yao, Li Liu, Dong Xu, Gangqing Hu:
Bioinformatics and biomedical informatics with ChatGPT: Year one review. 345-359 - Muhammad Azam, Yibo Chen, Micheal Olaolu Arowolo, Haowang Liu, Mihail Popescu, Dong Xu:
A comprehensive evaluation of large language models in mining gene relations and pathway knowledge. 360-374 - Junjie Tang, Changhu Wang, Feiyi Xiao, Ruibin Xi
Single-cell gene regulatory network analysis for mixed cell populations. 375-388 - Yunjie Shi, Yun Cheng, Peiyu Chen, Lexiang Zhang, Fangfu Ye:
Integrated photothermal microcarriers for precise exosome-secreted microRNA profiling in breast cancer diagnosis. 389-399 - Gabor Kiss, Salissou Moutari, Cara Mctaggart, Lynsey Patterson, Frank Kee, Felicity Lamrock:
Deterministic modelling of asymptomatic spread and disease stage progression in vaccine preventable infectious diseases. 400-413 - Sarawoot Somin, Don Kulasiri
On electrostatic interactions of adenosine triphosphate-insulin-degrading enzyme revealed by quantum mechanics/molecular mechanics and molecular dynamics. 414-432 - Minsheng Hao, Lei Wei, Fan Yang, Jianhua Yao, Christina V. Theodoris
Current opinions on large cellular models. 433-443
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