EnDeep4mC predicts DNA N4-methylcytosine sites using a dual-adaptive feature encoding framework in deep ensembles Shuyu Zhang, Quan Zou, Mengting Niu, Zhibin Lv, Antony Stalin, et al. Genome Research, 2026 DNA N 4 -methylcytosine (4mC), a key epigenetic modification regulating DNA repair and replication, requires efficient computational detection methods due to experimental limitations. Although machine learning predictors have been proposed, their performance could be enhanced through systematic optimization of feature encoding schemes. Here, we propose EnDeep4mC, a dual-adaptive framework integrating species-specific modeling with ensemble deep learning architectures to systematically optimize feature encoding schemes. Evaluated across six species, EnDeep4mC demonstrates commendable prediction performance and significantly outperforms current state-of-the-art predictors. Cross-species validation confirms its robust transferability from animal to microbe groups. Evolutionary analysis further uncovers the functional differentiation of 4mC sequences in biological evolution: Prokaryotic 4mC relies on stable patterns, whereas eukaryotes achieve regulatory plasticity through dynamic sequence combinations, which provides experimental evidence for species-adaptive encoding strategies.
hERG Channel Blockade and Antagonistic Interactions of Three Steroidal Alkaloids from Fritillaria Species Hui Lu, Tingting Hao, Zixuan Zhang, Chenxin Jiang, Jianwei Xu, et al. Molecules, 2025 The bulb of Fritillaria species called “Bei Mu” is a well-known traditional Chinese medicine. We have reported some potential off-target effects of “Bei Mu” due to peimine’s blockade of hERG (human Ether-a-go-go-Related Gene) channels. This research investigated the modulatory effects of three major alkaloid analogs of “Bei Mu” and their cooperative effects on hERG channels using manual whole-cell patch-clamp techniques. Results showed that peiminine and sipeimine blocked hERG currents with IC50s of 36.8 ± 2.5 μM and 47.6 ± 9.8 μM, which were close to that of peimine (26.1 ± 3.5 μM). Peiminine-induced blockade increased with increasing depolarizing strengths, durations, and frequencies, which suggested a preferential binding to open or inactivated states. The reduced blockade by the less inactivating S631A mutation supported peiminine‘s inactivation preference. Molecular docking and dynamics simulations confirmed the hERG-blocking activities of the three alkaloids and provided further insight into potential mechanisms. We also discovered antagonistic effects of the three alkaloids at nearly all concentrations tested, which might help reduce potential cardiotoxicities. To our knowledge, this is the first study to investigate combination effects of chemicals from one herb on hERG channels. In conclusion, peiminine and sipeimine can block hERG channels in a way similar to peimine, but antagonistic effects exist among them.
Gold Nanoparticles: Clinical Applications Sheikdawood Parveen, T. Sathiyapriya, D. Tharani, S. U. Mohammed Riyaz, Rakshi Anuja Dinesh, et al. Engineering Materials, 2023
In silico docking analysis to explore the proapoptotic and anti cell proliferative potential of ferulic acid Indian Journal of Biochemistry and Biophysics, 2016
Novel natural therapies for infectious diseases using computational and pharmacological approaches A Stalin, P Saravana Kumar, C Ferrante, AEL Hesham, S Ignacimuthu, ... Frontiers in Pharmacology 17, 1826975 , 2026 2026
EnDeep4mC predicts DNA N4-methylcytosine sites using a dual-adaptive feature encoding framework in deep ensembles S Zhang, Q Zou, M Niu, Z Lv, A Stalin, X Luo Genome Research 36 (3), 589 , 2026 2026
Natural medicines for metabolic diseases–computational and pharmacological approaches, Volume II A Stalin, C Sunil, AEL Hesham, S Ignacimuthu, Q Zou, Y Wang Frontiers in Pharmacology 17, 1799670 , 2026 2026
Musizin from Rhamnus wightii and Its Derivatives Attenuate Non-Alcoholic Fatty Liver Disease in Palmitate Oleate-Induced HepG2 Hepatocytes TRW Raja, A Stalin, V Duraipandiyan, K Balakrishna, S Ignacimuthu, ... REVISTA BRASILEIRA DE FARMACOGNOSIA-BRAZILIAN JOURNAL OF PHARMACOGNOSY 36 (1) , 2026 2026
Musizin from Rhamnus wightii and Its Derivatives Attenuate Non-Alcoholic Fatty Liver Disease in Palmitate Oleate–Induced HepG2 Hepatocytes TR William Raja, A Stalin, V Duraipandiyan, K Balakrishna, S Ignacimuthu, ... Revista Brasileira de Farmacognosia 36 (1), 21 , 2026 2026
Photoprotective effects of deinoxanthin against UVA-Induced oxidative damage: an integrative computational and cellular analysis K Balamurugan, A Stalin, CS Pawar, NR Prasad Archives of Dermatological Research 318 (1), 57 , 2026 2026
The preference for ammonium may be attributed to a hyperpolarized membrane potential via TWIK-1 channels L Pan, B Zhu, SL Vu, A Stalin, A Winters, Q Gong, Y Chen Brain Research, 150109 , 2025 2025
hERG Channel Blockade and Antagonistic Interactions of Three Steroidal Alkaloids from Fritillaria Species H Lu, T Hao, Z Zhang, C Jiang, J Xu, A Stalin, W Zhao Molecules 30 (19), 3882 , 2025 2025
In silico molecular docking analysis on acetylcholinesterase (AChE) inhibition activity on Aedes aegypti and Culex quinquefasciatus by β-isocostic acid A Yagoo, MCJ Milton, J Vilvest, A Stalin Journal of Asia-Pacific Entomology 28 (3), 102433 , 2025 2025 Citations: 2
Integrating bulk and single cell sequencing data to identify prognostic biomarkers and drug candidates in HBV associated hepatocellular carcinoma Y Zhong, A Stalin, Y Dai, Z He, S Yang, R Zou, A Zhai, F Li, H Hu Scientific Reports 15 (1), 26038 , 2025 2025 Citations: 4
Effects of host age and size on progeny production and different foods on the adult longevity of Spalangia nigroaenea Curtis (Hymenoptera: Pteromalidae) reared on puparia … N Velayudham, I Hari, A Stalin, MK Dharmalingam Jothinathan, ... Biocontrol Science and Technology 35 (7), 740-754 , 2025 2025 Citations: 1
Identifying the DNA methylation preference of transcription factors using ProtBERT and SVM Y Li, Q Zou, Q Dai, A Stalin, X Luo PLOS Computational Biology 21 (5), e1012513 , 2025 2025 Citations: 4
Exploration of the regulatory mechanism of norcantharidin on sine oculis homeobox homolog 4 in colon cancer using transcriptome sequencing and bioinformatic F Zhang, C Wu, J Zhang, Z Huang, A Stalin, Y Zhai, S Liu, J Wu Journal of Traditional Chinese Medical Sciences 12 (2), 259-276 , 2025 2025
Activity of Essential Oils From Pentanema indicum (L.) Y. Ling and Chromolaena odorata (L.) R.M.King & H. Rob Against Three Mosquito Species P Ganesan, J Selvakumaran, S Ignacimuthu, B Aldahmash, A Rady, ... Entomological Research 55 (2), e70016 , 2025 2025 Citations: 1
Enhanced Bioactivity of Streptomycin Bioconjugated Metal Nanoparticles Against Streptomycin Resistant Bacillus Sp N Ramasami, M Dhayalan, M Selvaraj, SUM Riyaz, P Perumal, ... Indian Journal of Microbiology 64 (4), 1787-1804 , 2024 2024 Citations: 2
Anticancer effects of rutin from Fagopyrum tataricum (tartary buckwheat) against osteosarcoma cell line D Soosai, R Ramalingam, E Perumal, K Veeramani, C Pancras, ... Molecular biology reports 51 (1), 312 , 2024 2024 Citations: 19
Antimycobacterial activity of plant compounds against extensively drug resistant (XDR-TB) Mycobacterium tuberculosis D Veeramuthu, I Savarimuthu, IA Khan, HA Alodaini, AA Hatamleh, ... Journal of King Saud University-Science 36 (9), 103351 , 2024 2024 Citations: 8
Exploring the antiviral inhibitory activity of Niloticin against the NS2B/NS3 protease of Dengue virus (DENV2) A Stalin, J Han, AD Reegan, S Ignacimuthu, S Liu, X Yao, Q Zou International Journal of Biological Macromolecules 277, 133791 , 2024 2024 Citations: 5
Herbal medical products Q Zou¹, S Ignacimuthu Herbal Medical Products for Metabolic Diseases-New Integrated … , 2024 2024
Herbal medical products for metabolic diseases-new integrated pharmacological approaches A Stalin, AEL Hesham, A Mishra, Q Zou, S Ignacimuthu Frontiers in Pharmacology 15, 1464176 , 2024 2024 Citations: 4
MOST CITED SCHOLAR PUBLICATIONS
Gallic acid attenuates high-fat diet fed-streptozotocin-induced insulin resistance via partial agonism of PPARγ in experimental type 2 diabetic rats and enhances glucose uptake … GR Gandhi, G Jothi, PJ Antony, K Balakrishna, MG Paulraj, S Ignacimuthu, ... European journal of pharmacology 745, 201-216 , 2014 2014 Citations: 235
Insulin sensitization via partial agonism of PPARγ and glucose uptake through translocation and activation of GLUT4 in PI3K/p-Akt signaling pathway by embelin in type 2 … GR Gandhi, A Stalin, K Balakrishna, S Ignacimuthu, MG Paulraj, R Vishal Biochimica et Biophysica Acta (BBA)-General Subjects 1830 (1), 2243-2255 , 2013 2013 Citations: 138
Wearable flexible electronics based cardiac electrode for researcher mental stress detection system using machine learning models on single lead electrocardiogram signal MB Bin Heyat, F Akhtar, SJ Abbas, M Al-Sarem, A Alqarafi, A Stalin, ... Biosensors 12 (6), 427 , 2022 2022 Citations: 130
Protective effects of Ficus carica leaves on glucose and lipids levels, carbohydrate metabolism enzymes and β-cells in type 2 diabetic rats S Stephen Irudayaraj, S Christudas, S Antony, V Duraipandiyan, ... Pharmaceutical biology 55 (1), 1074-1081 , 2017 2017 Citations: 119
Molecular docking of γ-sitosterol with some targets related to diabetes R Balamurugan, A Stalin, S Ignacimuthu European journal of medicinal chemistry 47, 38-43 , 2012 2012 Citations: 107
Antioxidant, antilipidemic and antidiabetic effects of ficusin with their effects on GLUT4 translocation and PPARγ expression in type 2 diabetic rats SS Irudayaraj, A Stalin, C Sunil, V Duraipandiyan, NA Al-Dhabi, ... Chemico-biological interactions 256, 85-93 , 2016 2016 Citations: 80
Myoinositol ameliorates high-fat diet and streptozotocin-induced diabetes in rats through promoting insulin receptor signaling PJ Antony, GR Gandhi, A Stalin, K Balakrishna, E Toppo, K Sivasankaran, ... Biomedicine & Pharmacotherapy 88, 1098-1113 , 2017 2017 Citations: 73
Integrated analysis of single-cell RNA-seq and bulk RNA-seq unravels T cell-related prognostic risk model and tumor immune microenvironment modulation in triple-negative breast … S Guo, X Liu, J Zhang, Z Huang, P Ye, J Shi, A Stalin, C Wu, S Lu, ... Computers in biology and medicine 161, 107066 , 2023 2023 Citations: 69
Hypoglycemic activity of 6-bromoembelin and vilangin in high-fat diet fed-streptozotocin-induced type 2 diabetic rats and molecular docking studies A Stalin, SS Irudayaraj, GR Gandhi, K Balakrishna, S Ignacimuthu, ... Life sciences 153, 100-117 , 2016 2016 Citations: 50
γ-sitosterol a potent hypolipidemic agent: In silico docking analysis JHK Rangachari Balamurugan, Antony Stalin, Adithan Aravinthan Medicinal Chemistry Research 24 (Issue 1), 124-130 , 2014 2014 Citations: 47
Advances in functional lipid nanoparticles: from drug delivery platforms to clinical applications M Dhayalan, W Wang, SUM Riyaz, RA Dinesh, J Shanmugam, ... 3 Biotech 14 (2), 57 , 2024 2024 Citations: 46
A network pharmacology approach to reveal the pharmacological targets and biological mechanism of compound kushen injection for treating pancreatic cancer based on WGCNA and in … C Wu, ZH Huang, ZQ Meng, XT Fan, S Lu, YY Tan, LM You, JQ Huang, ... Chinese Medicine 16 (1), 121 , 2021 2021 Citations: 44
Geranii Herba as a Potential Inhibitor of SARS-CoV-2 Main 3CL pro , Spike RBD, and Regulation of Unfolded Protein Response: An In Silico Approach S Arokiyaraj, A Stalin, BS Kannan, H Shin Antibiotics 9 (12), 863 , 2020 2020 Citations: 44
T cell-related prognostic risk model and tumor immune environment modulation in lung adenocarcinoma based on single-cell and bulk RNA sequencing J Zhang, X Liu, Z Huang, C Wu, F Zhang, A Han, A Stalin, S Lu, S Guo, ... Computers in biology and medicine 152, 106460 , 2023 2023 Citations: 42
Biocontrol and non-target effect of fractions and compound isolated from Streptomyces rimosus on the immature stages of filarial vector Culex quinquefasciatus Say (Diptera … P Ganesan, A Stalin, MG Paulraj, K Balakrishna, S Ignacimuthu, ... Ecotoxicology and environmental safety 161, 120-128 , 2018 2018 Citations: 40
Curative effect of arjunolic acid from Terminalia arjuna in non-alcoholic fatty liver disease models E Toppo, SS Darvin, S Esakkimuthu, K Buvanesvaragurunathan, ... Biomedicine & Pharmacotherapy 107, 979-988 , 2018 2018 Citations: 36
Antihyperlipidemic and hepatoprotective effects of Gardenin A in cellular and high fat diet fed rodent models E Toppo, SS Darvin, S Esakkimuthu, A Stalin, K Balakrishna, ... Chemico-biological interactions 269, 9-17 , 2017 2017 Citations: 35
Polyphenols-rich Cyamopsis tetragonoloba (L.) Taub. beans show hypoglycemic and β-cells protective effects in type 2 diabetic rats GR Gandhi, P Vanlalhruaia, A Stalin, SS Irudayaraj, S Ignacimuthu, ... Food and chemical toxicology 66, 358-365 , 2014 2014 Citations: 34
Data mining combines bioinformatics discover immunoinfiltration-related gene SERPINE1 as a biomarker for diagnosis and prognosis of stomach adenocarcinoma Y Zhai, X Liu, Z Huang, J Zhang, A Stalin, Y Tan, F Zhang, M Chen, R Shi, ... Scientific reports 13 (1), 1373 , 2023 2023 Citations: 33
Structure and pharmacological activities of polysaccharides from Anoectochilus roxburghii (Wall.) Lindl T Wu, S Li, Y Huang, Z He, Y Zheng, A Stalin, Q Shao, D Lin Journal of Functional Foods 87, 104815 , 2021 2021 Citations: 31