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ORCIDJournal of Bioinformatics and Computational Biology, Volume 22
Volume 22, Number 1, February 2024
- Min Gao
, Shaohua Jiang, Weibin Ding, Ting Xu, Zhijian Lyu:
Learning long- and short-term dependencies for improving drug-target binding affinity prediction using transformer and edge contraction pooling. 2350030:1-2350030:17 - Jujuan Zhuang, Wanquan Gao, Rui Su:
EnAMP: A novel deep learning ensemble antibacterial peptide recognition algorithm based on multi-features. 2450001:1-2450001:16 - Meizhen Sheng, Yanpeng Qi, Zhenbo Gao, Xiaohui Lin:
Analyzing omics data based on sample network. 2450002:1-2450002:16 - Seloua Hadiby, Yamina Mohamed Ben Ali:
Integrating pharmacophore model and deep learning for activity prediction of molecules with BRCA1 gene. 2450003:1-2450003:21
Volume 22, Number 2, April 2024
- Yiqian Zhang, Changjian Zhou:
PfgPDI: Pocket feature-enabled graph neural network for protein-drug interaction prediction. 2450004:1-2450004:20 - Rajiv Karbhal, Sangeeta Sawant, Urmila Kulkarni-Kale:
iCEED: Integrated customized extraction of enzyme data. 2450005:1-2450005:16 - Chun Fang, Jiasheng He, Hayato Yamana:
MoRF_ESM: Prediction of MoRFs in disordered proteins based on a deep transformer protein language model. 2450006:1-2450006:17
- Hayeon Kim, Junghwan Lee, Mikyeong Je, Myeongji Cho, Hyeon S. Son:
Utilization of systematic error-assessment software to improve phylogenetic accuracy. 2450008:1-2450008:15
- Chowdhury Rafeed Rahman, Limsoon Wong:
How much can ChatGPT really help computational biologists in programming? 2471001:1-2471001:18
Volume 22, Number 3, June 2024
- Xinling Li, Peng Qiu:
Gene representation bias in spatial transcriptomics. 2450007:1-2450007:14 - Rituparna Sinha, Rajat Kumar Pal, Rajat Kumar De:
A novel method addressing NGS-based mappability bias for sensitive detection of DNA alterations. 2450009:1-2450009:18 - Hayat Ali Shah, Juan Liu, Zhihui Yang:
Gtie-Rt: A comprehensive graph learning model for predicting drugs targeting metabolic pathways in human. 2450010:1-2450010:21 - Alexander V. Spirov, Ekaterina M. Myasnikova, David M. Holloway:
Body plan evolvability: The role of variability in gene regulatory networks. 2450011:1-2450011:24 - V. Abinas, U. Abhinav, E. M. Haneem, A. Vishnusankar, K. A. Abdul Nazeer:
Integration of autoencoder and graph convolutional network for predicting breast cancer drug response. 2450013:1-2450013:25 - Yupeng Ma, Yongzhen Pei:
NDMNN: A novel deep residual network based MNN method to remove batch effects from scRNA-seq data. 2450015:1-2450015:17 - Hiroya Oka, Takaaki Kojima, Ryuji Kato, Kunio Ihara, Hideo Nakano:
Construction of transcript regulation mechanism prediction models based on binding motif environment of transcription factor AoXlnR in Aspergillus oryzae. 2450017:1-2450017:17
Volume 22, Number 4, August 2024
- Min Li, Zhifang Qi, Liang Liu, Mingzhu Lou, Shaobo Deng:
PCA-constrained multi-core matrix fusion network: A novel approach for cancer subtype identification. 2450014:1-2450014:22 - Xia Li, Xuetong Zhao, Xinjian Yu, Jianping Zhao, Xiangdong Fang:
Construction of a multi-tissue compound-target interaction network of Qingfei Paidu decoction in COVID-19 treatment based on deep learning and transcriptomic analysis. 2450016:1-2450016:28 - C. M. Salooja, Arjun Sanker, K. Deepthi, A. S. Jereesh:
An ensemble approach for circular RNA-disease association prediction using variational autoencoder and genetic algorithm. 2450018:1-2450018:29 - Jia Gao, Yun Xu:
DNA sequences alignment method using sparse index on pan-genome graph. 2450019:1-2450019:14 - Zhou Yi, Minzhu Xie:
Polypharmacy side effect prediction based on semi-implicit graph variational auto-encoder. 2450020:1-2450020:15 - Aikaterini G. Chatziargyri, Evangelia A. Stasi, Konstantinos D. Tsirigos, Zoi I. Litou, Vassiliki A. Iconomidou, Pantelis G. Bagos:
CW-PRED: Prediction of C-terminal surface anchoring sorting signals in bacteria and Archaea. 2450021:1-2450021:18
Volume 22, Number 5, October 2024
- Andrejs Sizovs, Gatis Melkus, Peteris Rucevskis, Sandra Silina, Lelde Lace, Edgars Celms, Juris Viksna:
A technique for preserving network structure in randomized Hi-C data. 2440001:1-2440001:14 - Leili Irankhah, Babak Khorsand, Mahmoud Naghibzadeh, Abdorreza Savadi:
Analyzing the performance of short-read classification tools on metagenomic samples toward proper diagnosis of diseases. 2450012:1-2450012:24 - Yan Li, Boran Wang, Zengding Wu, Shiliang Ji, Shi Xu, Caiyi Fei:
SAKit: An all-in-one analysis pipeline for identifying novel proteins resulting from variant events at both large and small scales. 2450022:1-2450022:23 - Rahim Berahmand, Masoumeh Emadpour, Mokhtar Jalali Javaran, Kaveh Haji-Allahverdipoor, Ali Akbarabadi:
Molecular dynamics simulations of ribosome-binding sites in theophylline-responsive riboswitch associated with improving the gene expression regulation in chloroplasts. 2450023:1-2450023:16 - Baozhong Zhu, Runhua Zhang, Tengsheng Jiang, Zhiming Cui, Jing Chen, Hongjie Wu:
Improving drug-target interaction prediction through dual-modality fusion with InteractNet. 2450024:1-2450024:19
Volume 22, Number 6, December 2024
- Dehua Chen, Yongsheng Yang, Dongdong Shi, ZhenHua Zhang, Mei Wang, Qiao Pan, Jianwen Su, Zhen Wang:
The use of 4D data-independent acquisition-based proteomic analysis and machine learning to reveal potential biomarkers for stress levels. 2450025:1-2450025:19 - Chao Li, Xiaoran Huang, Xiao Luo, Xiaohui Lin:
Gene regulatory network inference based on modified adaptive lasso. 2450026:1-2450026:19 - Li-Ping Wu, Li Yong, Xiang Cheng, Yang Zhou:
Research on similarity retrieval method based on mass spectral entropy. 2450027:1-2450027:18 - Weibin Ding, Shaohua Jiang, Ting Xu, Zhijian Lyu:
ASAP-DTA: Predicting drug-target binding affinity with adaptive structure aware networks. 2450028:1-2450028:16 - Mateusz Twardawa, Kaja Gutowska, Piotr Formanowicz:
Exploring relationship between hypercholesterolemia and instability of atherosclerotic plaque - An approach based on a matrix population model. 2450029:1-2450029:18
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