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OpenAlex Citation Counts

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OpenAlex is a bibliographic catalogue of scientific papers, authors and institutions accessible in open access mode, named after the Library of Alexandria. It's citation coverage is excellent and I hope you will find utility in this listing of citing articles!

If you click the article title, you'll navigate to the article, as listed in CrossRef. If you click the Open Access links, you'll navigate to the "best Open Access location". Clicking the citation count will open this listing for that article. Lastly at the bottom of the page, you'll find basic pagination options.

Requested Article:

DNAgenie: accurate prediction of DNA-type-specific binding residues in protein sequences
Jian Zhang, Sina Ghadermarzi, Akila Katuwawala, et al.
Briefings in Bioinformatics (2021) Vol. 22, Iss. 6
Closed Access | Times Cited: 27

Showing 1-25 of 27 citing articles:

EquiPNAS: improved protein–nucleic acid binding site prediction using protein-language-model-informed equivariant deep graph neural networks
Rahmatullah Roche, Bernard Moussad, Md Hossain Shuvo, et al.
Nucleic Acids Research (2024) Vol. 52, Iss. 5, pp. e27-e27
Open Access | Times Cited: 24
AlphaFold2-aware protein–DNA binding site prediction using graph transformer
Qianmu Yuan, Sheng Chen, Jiahua Rao, et al.
Briefings in Bioinformatics (2021) Vol. 23, Iss. 2
Open Access | Times Cited: 92
Deep learning in prediction of intrinsic disorder in proteins
Bi Zhao, Lukasz Kurgan
Computational and Structural Biotechnology Journal (2022) Vol. 20, pp. 1286-1294
Open Access | Times Cited: 41
HybridDBRpred: improved sequence-based prediction of DNA-binding amino acids using annotations from structured complexes and disordered proteins
Jian Zhang, Sushmita Basu, Lukasz Kurgan
Nucleic Acids Research (2023) Vol. 52, Iss. 2, pp. e10-e10
Open Access | Times Cited: 16
flDPnn2: Accurate and Fast Predictor of Intrinsic Disorder in Proteins
Kui Wang, Gang Hu, Sushmita Basu, et al.
Journal of Molecular Biology (2024) Vol. 436, Iss. 17, pp. 168605-168605
Closed Access | Times Cited: 6
Explainable Deep Multilevel Attention Learning for Predicting Protein Carbonylation Sites
Jian Zhang, Jingjing Qian, Pei Wang, et al.
Advanced Science (2025)
Open Access
A Comprehensive Review of Computational Methods for Protein-DNA Binding Site Prediction
Zi Liu, Wang-Ren Qiu, Yan Liu, et al.
Analytical Biochemistry (2025), pp. 115862-115862
Closed Access
Four classic “de novo” genes all have plausible homologs and likely evolved from retro-duplicated or pseudogenic sequences
Joseph Hannon Bozorgmehr
Molecular Genetics and Genomics (2024) Vol. 299, Iss. 1
Closed Access | Times Cited: 2
Recent Advances in Computational Prediction of Secondary and Supersecondary Structures from Protein Sequences
Jian Zhang, Jingjing Qian, Quan Zou, et al.
Methods in molecular biology (2024), pp. 1-19
Closed Access | Times Cited: 2
CoMemMoRFPred: Sequence-based Prediction of MemMoRFs by Combining Predictors of Intrinsic Disorder, MoRFs and Disordered Lipid-binding Regions
Sushmita Basu, Tamás Hegedűs, Lukasz Kurgan
Journal of Molecular Biology (2023) Vol. 435, Iss. 21, pp. 168272-168272
Closed Access | Times Cited: 6
Centromeric localization of KNL2 and CENP-C proteins in plants depends on their centromere-targeting domain and DNA-binding regions
Surya Prakash Yalagapati, Ulkar Ahmadli, Aditya Sinha, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2024)
Open Access | Times Cited: 1
Advances in the Application of Protein Language Modeling for Nucleic Acid Protein Binding Site Prediction
Bo Wang, Wenjin Li
Genes (2024) Vol. 15, Iss. 8, pp. 1090-1090
Open Access | Times Cited: 1
MERIT: Accurate prediction of multi ligand-binding residues with hybrid deep transformer network, evolutionary couplings and transfer learning
Jian Zhang, Sushmita Basu, Fuhao Zhang, et al.
Journal of Molecular Biology (2024), pp. 168872-168872
Closed Access | Times Cited: 1
SCAMPER: Accurate Type-Specific Prediction of Calcium-Binding Residues Using Sequence-Derived Features
Jian Zhang, Feng Zhou, Xingchen Liang, et al.
IEEE/ACM Transactions on Computational Biology and Bioinformatics (2022) Vol. 20, Iss. 2, pp. 1406-1416
Closed Access | Times Cited: 5
TSNAPred: predicting type-specific nucleic acid binding residues via an ensemble approach
Wenjuan Nie, Lei Deng
Briefings in Bioinformatics (2022) Vol. 23, Iss. 4
Closed Access | Times Cited: 5
EquiPNAS: improved protein-nucleic acid binding site prediction using protein-language-model-informed equivariant deep graph neural networks
Rahmatullah Roche, Bernard Moussad, Md Hossain Shuvo, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2023)
Open Access | Times Cited: 2
AlphaFold2-aware protein-DNA binding site prediction using graph transformer
Qianmu Yuan, Sheng Chen, Jiahua Rao, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2021)
Open Access | Times Cited: 4
Four classic “de novo” genes all have plausible homologs and likely evolved from retro-duplicated or pseudogenic sequences
Joseph Hannon Bozorgmehr
Research Square (Research Square) (2024)
Open Access
Prediction of Protein-DNA Binding Sites Based on Protein Language Model and Deep Learning
Kaixuan Shan, Xiankun Zhang, Chen Song
Lecture notes in computer science (2024), pp. 314-325
Closed Access
Advances in Computational Intelligence-Based Methods of Structure and Function Prediction of Proteins
Jian Zhang, Jingjing Qian
Biomolecules (2024) Vol. 14, Iss. 9, pp. 1083-1083
Open Access
Accurate Prediction of Protein-Binding Residues in Protein Sequences Using SCRIBER
Jian Zhang, Feng Zhou, Xingchen Liang, et al.
Methods in molecular biology (2024), pp. 247-260
Closed Access
Evaluation of Predictions of Disordered Binding Regions in the CAID2 Experiment
Fuhao Zhang, Lukasz Kurgan
Computational and Structural Biotechnology Journal (2024) Vol. 27, pp. 78-88
Open Access
A comprehensive review of protein-centric predictors for biomolecular interactions: from proteins to nucleic acids and beyond
Pengzhen Jia, Fuhao Zhang, Chaojin Wu, et al.
Briefings in Bioinformatics (2024) Vol. 25, Iss. 3
Open Access
Centromeric localization of αKNL2 and CENP-C proteins in plants depends on their centromere-targeting domain and DNA-binding regions
Surya Prakash Yalagapati, Ulkar Ahmadli, Aditya Sinha, et al.
Nucleic Acids Research (2024)
Open Access
Twenty years of advances in prediction of nucleic acid-binding residues in protein sequences
Sushmita Basu, Jing Yu, Daisuke Kihara, et al.
Briefings in Bioinformatics (2024) Vol. 26, Iss. 1
Open Access
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