Journal of Bioinformatics and Computational Biology, Volume 22 (original) (raw)

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Volume 22, Number 1, February 2024

Research Paper

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    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
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    Jujuan Zhuang, Wanquan Gao, Rui Su:
    EnAMP: A novel deep learning ensemble antibacterial peptide recognition algorithm based on multi-features. 2450001:1-2450001:16
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    Meizhen Sheng, Yanpeng Qi, Zhenbo Gao, Xiaohui Lin:
    Analyzing omics data based on sample network. 2450002:1-2450002:16
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    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

Research Paper

In Silico Studies

Critical Comments

Volume 22, Number 3, June 2024

Research Paper

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    Xinling Li, Peng Qiu:
    Gene representation bias in spatial transcriptomics. 2450007:1-2450007:14
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    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
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    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
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    Alexander V. Spirov, Ekaterina M. Myasnikova, David M. Holloway:
    Body plan evolvability: The role of variability in gene regulatory networks. 2450011:1-2450011:24
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    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
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    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
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    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

Research Paper

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    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
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    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
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    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
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    Jia Gao, Yun Xu:
    DNA sequences alignment method using sparse index on pan-genome graph. 2450019:1-2450019:14
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    Zhou Yi, Minzhu Xie:
    Polypharmacy side effect prediction based on semi-implicit graph variational auto-encoder. 2450020:1-2450020:15
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    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

Research Paper

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    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
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    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
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    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
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    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
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    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

Research Paper

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    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
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    Chao Li, Xiaoran Huang, Xiao Luo, Xiaohui Lin:
    Gene regulatory network inference based on modified adaptive lasso. 2450026:1-2450026:19
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    Li-Ping Wu, Li Yong, Xiang Cheng, Yang Zhou:
    Research on similarity retrieval method based on mass spectral entropy. 2450027:1-2450027:18
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    Weibin Ding, Shaohua Jiang, Ting Xu, Zhijian Lyu:
    ASAP-DTA: Predicting drug-target binding affinity with adaptive structure aware networks. 2450028:1-2450028:16
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    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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