Department of Biosciences and Bioinformatics

Research output

Research output per year 1993 2019 2020 2021 2022 2023 2024 2025

• 418 Article
• 78 Review article
• 29 Conference Proceeding
• 18 Chapter
• 68 More
  • 14 Other contribution
  • 13 Meeting Abstract
  • 9 Comment/debate
  • 9 Editorial
  • 9 Patent
  • 7 Letter
  • 3 Book
  • 2 Paper
  • 1 Anthology
  • 1 Conference article

Research output per year

Research output per year

Search results

• 2024

  Aspartyl protease in the secretome of honey bee trypanosomatid parasite contributes to infection of bees

  Yuan, X., Sun, J. & Kadowaki, T., 10 Feb 2024, In: Parasites and Vectors. 17, 1, 60.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Bee 100%
  • Secretome 100%
  • Insect 40%
  • Host Cell 20%
  • Leishmania 20%
  2 Citations (Scopus)

• Bat algorithm based on kinetic adaptation and elite communication for engineering problems

  Yuan, C., Zhao, D., Heidari, A. A., Liu, L., Wang, S., Chen, H. & Zhang, Y., 2024, (Accepted/In press) In: CAAI Transactions on Intelligence Technology.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Bat Algorithm 100%
  • Engineering Problem 100%
  • Optimization Problem 50%
  • Metaheuristic Optimization 50%
  • Optimization Technique 25%

• BCL6 confers resistance to HDAC inhibitors in DLBCL

  Fan, G., Zhang, Y., Li, Q., Rong, R., Chen, S., He, L., Li, B. & Zhuang, W., Sept 2024, In: Biochemical Pharmacology. 227, 116466.

  Research output: Contribution to journal › Article › peer-review

  • BCL6 100%
  • Histone Deacetylase 100%
  • Mitogen-Activated Protein Kinase 7%
  • Drug Resistance 7%
  • Deep Sequencing 7%
  1 Citation (Scopus)

• Breast cancer diagnosis: A systematic review

  Wen, X., Guo, X., Wang, S., Lu, Z. & Zhang, Y., 1 Jan 2024, In: Biocybernetics and Biomedical Engineering. 44, 1, p. 119-148 30 p.

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  • Breast Cancer 100%
  • Cancer Diagnosis 100%
  • Systematic Review 100%
  • Learning 80%
  • Development 40%
  15 Citations (Scopus)

• Broad-spectrum ginsentides are principal bioactives in unraveling the cure-all effects of ginseng

  Loo, S., Kam, A., Dutta, B., Zhang, X., Feng, N., Sze, S. K., Liu, C. F., Wang, X. & Tam, J. P., Feb 2024, In: Acta Pharmaceutica Sinica B. 14, 2, p. 653-666 14 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Adrenergic Receptor 100%
  • Adenosine Diphosphate 100%
  • Epinephrine 100%
  2 Citations (Scopus)

• Can we gain translational insights into the functional roles of cerebral cortex from acortical rodent and naturally acortical zebrafish models?

  Kaluev, A., Zabegalov, K. N., Costa, F. V., Kolesnikova, T. O., de Abreu, M. S., Elena V, P. & Yenkoyan, K. B., 8 Jun 2024, In: Progress in Neuro-Psychopharmacology and Biological Psychiatry.

  Research output: Contribution to journal › Article › peer-review

• CD39+ tumor infiltrating T cells from colorectal cancers exhibit dysfunctional phenotype

  Feng, Y., Xu, X., Zhang, J., Sanderson, C., Xia, J., Bu, Z., Yang, Y., Yang, P. & Lu, Z., 15 Mar 2024, In: American Journal of Cancer Research. 14, 2, p. 585-600 16 p.

  Research output: Contribution to journal › Article › peer-review

  • Cytokine Release 100%

• Chronic Behavioral and Neurochemical Effects of Four Novel N-Benzyl-2-phenylethylamine Derivatives Recently Identified as “Psychoactive” in Adult Zebrafish Screens

  Ilyin, N. P., Nabiullin, A. D., Kozlova, A. D., Kupriyanova, O. V., Shevyrin, V. A., Gloriozova, T., Filimonov, D., Lagunin, A., Galstyan, D. S., Kolesnikova, T. O., Mor, M. S., Efimova, E. V., Poroikov, V., Yenkoyan, K. B., de Abreu, M. S., Demin, K. A. & Kalueff, A. V., 15 May 2024, In: ACS Chemical Neuroscience. 15, 10, p. 2006-2017 12 p.

  Research output: Contribution to journal › Article › peer-review

  • Zebra Fish 100%
  • Neurochemical 100%
  • Phenethylamine 100%
  • Behavior (Neuroscience) 33%
  • Norepinephrine 33%
  1 Citation (Scopus)

• Chronic exposure to polycyclic aromatic hydrocarbons alters skin virome composition and virus-host interactions

  Du, S., Tong, X., Leung, M. H. Y., Betts, R. J., Woo, A. C., Bastien, P., Misra, N., Aguilar, L., Clavaud, C. & Lee, P. K. H., 25 Oct 2024, In: The ISME journal. 18, 1, wrae218.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Polycyclic Aromatic Hydrocarbon 100%
  • Microbiome 22%
  • Biodegradation 22%
  • Cheek 16%
  • Skin Flora 11%

• Classics in Chemical Neuroscience: Deliriant Antihistaminic Drugs

  Kaluev, A., Nerush, M. O., Shevyrin, V. A., Golushko, N. I., Moskalenko, A. M., Rosemberg, D. B., de Abreu, M. S., Yang, L., Galstyan, D. S., Lim, L. W. & Demin, K. A., 30 Sept 2024, In: ACS Chemical Neuroscience.

  Research output: Contribution to journal › Article › peer-review

• Comparing Business, Innovation, and Platform Ecosystems: A Systematic Review of the Literature

  Liu, Z., Li, Z., Zhang, Y., Mutukumira, A. N., Feng, Y., Cui, Y., Wang, S., Wang, J. & Wang, S., Apr 2024, In: Biomimetics. 9, 4, 216.

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  • Content Analysis 100%
  • Bibliology 100%
  • Systematic Review 100%
  • Business Innovation 100%
  • Business Ecosystem 100%
  2 Citations (Scopus)

• Current trends of computational tools and artificial intelligence in geriatric medicine

  Awuah, W. A., Ou Yong, B. M., Mikhailova, T., Ng, J. C., Abdul-Rahman, T., Yarlagadda, R., Tedeschi, A. J., Miteu, G. D., Garg, T., David, L., Lansiaux, E., Huang, H., Nansubuga, E. P., Anand, A., Sikora, K., Isik, A., Debnath, S., Pramanik, S., Seth, D., Mukerjee, N., & 5 othersNarli, F., Sharma, R., Ghosh, A., Md Ashraf, G. & Alexiou, Α., 1 Jan 2024, Essential Guide to Neurodegenerative Disorders: Mechanistic, Diagnostic and Therapeutic Advances. Elsevier, p. 363-374 12 p.

  Research output: Chapter in Book or Report/Conference proceeding › Chapter › peer-review

  • Neurodegenerative Disorder 100%
  • Gerontology 100%
  • Natural Language Processing 50%
  • Language Processing 50%
  • Treatment Classification 50%

• Deciphering the genetic interplay between depression and dysmenorrhea: a Mendelian randomization study

  Liu, S., Wei, Z., Carr, D. F. & Moraros, J., 27 Nov 2024, In: Briefings in Bioinformatics. 26, 1

  Research output: Contribution to journal › Article › peer-review

  Open Access

• Deep Fuzzy Multiteacher Distillation Network for Medical Visual Question Answering

  Liu, Y., Chen, B., Wang, S., Lu, G. & Zhang, Z., 2024, In: IEEE Transactions on Fuzzy Systems. 32, 10, p. 5413-5427 15 p.

  Research output: Contribution to journal › Article › peer-review

  • Fuzzy Mathematics 100%
  4 Citations (Scopus)

• Deep Learning for Image Classification: A Review

  Wu, M., Zhou, J., Peng, Y., Wang, S. & Zhang, Y., 2024, Proceedings of 2023 International Conference on Medical Imaging and Computer-Aided Diagnosis (MICAD 2023) - Medical Imaging and Computer-Aided Diagnosis. Su, R., Zhang, Y-D. & Frangi, A. F. (eds.). Springer Science and Business Media Deutschland GmbH, p. 352-362 11 p. (Lecture Notes in Electrical Engineering; vol. 1166 LNEE).

  Research output: Chapter in Book or Report/Conference proceeding › Conference Proceeding › peer-review

  • Image Classification 100%
  • Deep Learning 100%
  • Learning Approach 83%
  • Scalability 20%
  • Learning System 20%
  4 Citations (Scopus)

• Deep learning on medical image analysis

  Wang, J., Wang, S. & Zhang, Y., 2024, (Accepted/In press) In: CAAI Transactions on Intelligence Technology. 10, 1, p. 1-35 35 p.

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  • Image Analysis 100%
  • Deep Learning 100%
  • Neural Network 100%
  • Learning Strategy 100%
  • Convolutional Neural Network 50%

• Developing Peripheral Biochemical Biomarkers of Brain Disorders: Insights from Zebrafish Models

  Kaluev, A., Ilyin, N. P., Elena V, P., Kolesnikova, T. O., Demin, K. A., Khatsko, S. L. & Apuhtin, K. V., 8 Feb 2024, In: Biochemistry (Moscow).

  Research output: Contribution to journal › Article › peer-review

• Diverse and specialized metabolic capabilities of microbes in oligotrophic built environments

  Tong, X., Luo, D., Leung, M. H. Y., Lee, J. Y. Y., Shen, Z., Jiang, W., Mason, C. E. & Lee, P. K. H., 17 Oct 2024, In: Microbiome. 12, 1, 198.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Metagenome 100%
  • Propionibacterium acnes 33%
  • Denitrification 33%
  • Micrococcus luteus 33%
  • Phylum 33%

• Domain-knowledge enabled ensemble learning of 5-formylcytosine (f5C) modification sites

  Huang, J., Wang, X., Xia, R., Yang, D., Liu, J., Lv, Q., Yu, X., Meng, J., Chen, K., Song, B. & Wang, Y., Dec 2024, In: Computational and Structural Biotechnology Journal. 23, p. 3175-3185 11 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • RNA Translation 100%
  • Saccharomyces cerevisiae 100%

• EAFP-Med: An efficient adaptive feature processing module based on prompts for medical image detection

  Li, X., Lan, L., Lahza, H., Yang, S., Wang, S., Yang, W., Liu, H. & Zhang, Y., 1 Aug 2024, In: Expert Systems with Applications. 247, 123334.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Preprocessing Module 100%
  • Dynamic Parameter 100%
  1 Citation (Scopus)

• Editorial: Novel biomarkers in tumor immunity and immunotherapy

  Matsutani, T., Akbay, E. & Elkord, E., 8 Apr 2024, In: Frontiers in Immunology. 15, 1405082.

  Research output: Contribution to journal › Editorial

  Open Access

• Editorial: Computational drug discovery of medicinal compounds for cancer management, volume II

  Ahmad, K., Shaikh, S., Khan, F. & Khan, M. E., 24 Jun 2024, In: Frontiers in Chemistry. 12, 1446510.

  Research output: Contribution to journal › Editorial

  Open Access

• Effects of 1H-1,2,3-Triazole Derivatives of 3-O-Acetyl-11-Keto-Beta-Boswellic Acid from Boswellia sacra Resin on T-Cell Proliferation and Activation

  Elkord, E., 8 Dec 2024, In: Pharmaceuticals.

  Research output: Contribution to journal › Article › peer-review

• Effects of chronic fluoxetine on zebrafish behavior – Comment on Pinto et al., (2024)

  Kaluev, A., 5 Sept 2024, In: Chemosphere.

  Research output: Contribution to journal › Letter › peer-review

• Emerging nanotechnologies in drug delivery: Insights and regulatory challenges

  Debnath, S., Pramanik, S., Seth, D., Mukerjee, N., Ng, J. C., Awuah, W. A., Abdul-Rahman, T., Lansiaux, E., Nazir, A., Tenkorang, P. O., Mustapha, M. J., Kalmanovich, J., Sikora, K., Narli, F., Sharma, R., Ghosh, A., Ashraf, G. M. & Alexiou, A., 1 Jan 2024, Essential Guide to Neurodegenerative Disorders: Mechanistic, Diagnostic and Therapeutic Advances. Elsevier, p. 377-395 19 p.

  Research output: Chapter in Book or Report/Conference proceeding › Chapter › peer-review

  • Malignant Neoplasm 100%
  • Nanoparticle 100%
  • Polysaccharide 100%
  • Nanocarrier 60%
  • Phytochemical 60%

• Epidemiology of neuropsychiatric complications in HIV

  Chaudhary, S. A., Chaudhary, S. S., Rawat, S., Deshmukh, S., Perveen, A. & Ashraf, G. M., 1 Jan 2024, Neuropsychiatric Complications of HIV: a Challenging Health Concern. Elsevier, p. 77-99 23 p.

  Research output: Chapter in Book or Report/Conference proceeding › Chapter › peer-review

  • Human immunodeficiency virus 100%

• Erratum: Correction: A fully human IgG1 antibody targeting connexin 32 extracellular domain blocks CMTX1 hemichannel dysfunction in an in vitro model (Cell communication and signaling : CCS (2024) 22 1 DOI: 10.1186/s12964-024-01969-0)

  Tettey-Matey, A., Donati, V., Cimmino, C., Pietro, C. D., Buratto, D., Panarelli, M., Reale, A., Calistri, A., Fornaini, M. V., Zhou, R., Yang, G., Zonta, F., Marazziti, D. & Mammano, F., 12 Dec 2024, In: Cell Communication and Signaling. 22, 1, p. 591 1 p.

  Research output: Contribution to journal › Comment/debate

  Open Access

• Evaluating the Reliability of Machine Learning Predictors in m6A-SNP Association Analysis: A Comparative Study Using m6A-QTL Data

  Mao, Z. & Wei, Z., 2024, (Accepted/In press) In: Current Bioinformatics.

  Research output: Contribution to journal › Article › peer-review

• Excitation energy transfer in proteoliposomes reconstituted with LH2 and RC-LH1 complexes from Rhodobacter sphaeroides

  Huang, X., Vasilev, C., Swainsbury, D. & Hunter, C. N., 29 Feb 2024, In: Bioscience Reports. 44, 2, BSR20231302.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Rhodobacter Sphaeroides 100%
  • Carotenoid 40%
  • Phototrophic Bacteria 20%
  2 Citations (Scopus)

• Experimental design skills are improved by a modular guided inquiry method

  Fendos, J., 1 Sept 2024, (Submitted) In: CBE Life Sciences Education.

  Research output: Contribution to journal › Article › peer-review

  • Skill Acquisition 100%
  • Targeted Manner 100%

• Exploring simple triplet representation learning

  Ren, Z., Lan, Q., Zhang, Y. & Wang, S., Dec 2024, In: Computational and Structural Biotechnology Journal. 23, p. 1510-1521 12 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Representation Learning 100%
  • Supervised Learning 100%
  • Image Analysis 66%
  • Unlabeled Data 66%
  • Training Instance 33%
  14 Citations (Scopus)

• FDA-approved drugs as PIM-1 kinase inhibitors: A drug repurposed approach for cancer therapy

  Rathi, A., Noor, S., Sulaimani, M. N., Ahmed, S., Taiyab, A., AlAjmi, M. F., Khan, F. I., Hassan, M. I. & Haque, M. M., 23 Dec 2024, In: International Journal of Biological Macromolecules. 292, 139107.

  Research output: Contribution to journal › Article › peer-review

  • Rifaximin 100%
  • Telmisartan 25%
  • Stanozolol 25%
  • Alfaxalone 25%
  1 Citation (Scopus)

• FG-HFS: A feature filter and group evolution hybrid feature selection algorithm for high-dimensional gene expression data

  Xu, Z., Yang, F., Tang, C., Wang, H., Wang, S., Sun, J. & Zhang, Y., 1 Jul 2024, In: Expert Systems with Applications. 245, 123069.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Algorithms 100%
  • Feature Selection 100%
  • Gene Expression Data 100%
  • Accuracy 11%
  • Correlation 11%
  10 Citations (Scopus)

• From sequence to mechanobiology? Promises and challenges for AlphaFold 3

  Zonta, F. & Pantano, S., 1 Sept 2024, In: Mechanobiology in Medicine. 2, 3

  Research output: Contribution to journal › Review article › peer-review

  3 Citations (Scopus)

• Gaussian Backbone-Based Spherical Evolutionary Algorithm with Cross-search for Engineering Problems

  Li, Y., Zhao, D., Heidari, A. A., Wang, S., Chen, H. & Zhang, Y., Mar 2024, In: Journal of Bionic Engineering. 21, 2, p. 1055-1091 37 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Engineering Design Problem 100%
  • Industrial Engineering 49%
  • Real Application 25%
  1 Citation (Scopus)

• Gender-different effect of Src family kinases antagonism on photophobia and trigeminal ganglion activity

  Huang, Z., Yao, J., Nie, L., Nie, X., Xiong, X., Koks, S., Quinn, J. P., Kanhere, A. & Wang, M., Oct 2024, In: Journal of Headache and Pain.

  Research output: Contribution to journal › Article › peer-review

  Open Access
  1 Citation (Scopus)

• Global and regional burden of bloodstream infections caused by carbapenem-resistant Gram-negative bacteria in 2019: A systematic analysis from the MICROBE database

  Zha, L., Li, S., Guo, J., Hu, Y., Pan, L., Wang, H., Zhou, Y., Xu, Q., Lu, Z., Kong, X., Tong, X. & Cheng, Y., 24 Dec 2024, In: International Journal of Infectious Diseases. 153, p. 1 8 p., 107769.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Carbapenem 100%
  • Bloodstream Infection 100%
  • Carbapenem Resistance 33%
  • Infection Control 16%
  • Klebsiella pneumoniae 16%
  1 Citation (Scopus)

• Glymphotherapeutics for Alzheimer's disease: Time to move the needle

  MohanaSundaram, A. S., Mofatteh, M., Ashraf, G. M. & Praticò, D., Nov 2024, In: Ageing Research Reviews. 101, 102478.

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  • Aquaporin 4 100%
  • Encephalitis 100%
  • Meningitis 100%
  • Disease Modifying Therapy 100%
  • Aducanumab 100%

• Holistic approaches to healthy longevity. Handbook on Longevity Medicine: The Road Map.

  Rattan, S., Bartke, A., Rose, M. R., Lim, L. W., Caruso, C., Ulfhake, B. & Olovnikov, A., 11 Aug 2024, European Wellness Academy.

  Research output: Book/Report/Edited volume › Book › peer-review

• Hybrid Parallel Fuzzy CNN Paradigm: Unmasking Intricacies for Accurate Brain MRI Insights

  Iqbal, S., Qureshi, A. N., Aurangzeb, K., Alhussein, M., Wang, S., Anwar, M. S. & Khan, F., 4 Mar 2024, In: IEEE Transactions on Fuzzy Systems. p. 1-17 17 p.

  Research output: Contribution to journal › Article › peer-review

  • Network Paradigm 100%
  • Magnetic Resonance Imaging 100%
  • Class Activation Mapping 25%
  • Confusion 20%
  • Backpropagation 20%
  4 Citations (Scopus)

• Industrial and agricultural land uses affected the water quality and shaped the bacterial communities in the inflow rivers of Taihu Lake

  Liu, S., Lu, J., Adriaenssens, E. M., Wang, J., McCarthy, A. J. & Sekar, R., 29 Jan 2024, In: Frontiers in Environmental Science. 12, 1340875.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Community 100%
  • Land Use 100%
  • Farmland 100%
  • Inflow 100%
  • Lake 100%
  4 Citations (Scopus)

• Ketamine modulates the exploratory dynamics and homebase-related behaviors of adult zebrafish

  Kaluev, A., 2 Oct 2024, In: Pharmacology Biochemistry and Behavior.

  Research output: Contribution to journal › Article › peer-review

• Large Foundation Model for Cancer Segmentation

  Ren, Z., Zhang, Y. & Wang, S., 1 Jan 2024, In: Technology in Cancer Research and Treatment. 23

  Research output: Contribution to journal › Editorial

  Open Access

  • Tasks 100%
  • Potential Benefit 100%
  • Computervision 100%
  • Natural Language Processing 100%
  4 Citations (Scopus)

• Letter to Editor: Effects of chronic fluoxetine on zebrafish behavior - Comment on Pinto et al., (2024)

  Kaluev, A. & de Abreu, M. S., 3 Oct 2024, In: Chemosphere. 366

  Research output: Contribution to journal › Letter › peer-review

• Low Iodine Nutrition Knowledge in Chinese Breastfeeding Women despite Adequate Iodine Status

  Liu, S., Sharp, A., Lane, S., Villanueva, E. V., Lu, Z. & Ma, Z. F., 8 Feb 2024, In: Nutrients. 16, 4, p. 491 14 p., 491.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Breastfeeding 100%
  • Iodine 100%
  • Nutrition Knowledge 100%
  • Lactation 31%
  • Iodine Deficiency 6%

• Lymphocyte-activation gene 3 in cancer immunotherapy: function, prognostic biomarker and therapeutic potentials

  Ren, K., Hamdy, H., Meyiah, A. & Elkord, E., 2024, In: Frontiers in Immunology. 15, 1501613.

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  • Biological Marker 100%
  • Malignant Neoplasm 100%
  • Neoplasm 100%
  • Immunotherapy 100%
  • Cancer Immunotherapy 100%
  1 Citation (Scopus)

• m 6 A-Atlas v2.0: updated resources for unraveling the N 6 -methyladenosine (m 6 A) epitr anscript ome among multiple species

  Liang, Z., Ye, H., Ma, J., Wei, Z., Wang, Y., Zhang, Y., Huang, D., Song, B., Meng, J., Rigden, D. J. & Chen, K., 5 Jan 2024, In: Nucleic Acids Research. 52, D1, p. D194-D202

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Post-Transcriptional Modification 100%
  • Interactions with RNA 100%
  26 Citations (Scopus)

• M6ACali: Machine learning-powered calibration for accurate m6A detection in MeRIP-Seq

  Ye, H., Li, T., Rigden, D. J. & Wei, Z., 22 May 2024, In: Nucleic Acids Research. 52, 9, p. 4830-4842 13 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Sequence Motif 100%
  3 Citations (Scopus)

• m6AConquer: a Data Resource for Unified Quantification and Integration of m6A Detection Techniques

  Zhao, X., Ye, H., Li, T., Rigden, D. J. & Wei, Z., Sept 2024, In: bioRxiv.

  Research output: Contribution to journal › Article

• m7GHub V2.0: an updated database for decoding the N7-methylguanosine (m 7 G) epitr anscript ome

  Wang, X., Zhang, Y., Chen, K., Liang, Z., Ma, J., Xia, R., de Magalhães, J. P., Rigden, D. J., Meng, J. & Song, B., 5 Jan 2024, In: Nucleic Acids Research. 52, D1, p. D203-D212

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Species 100%
  • database 100%
  • RNA 33%
  • Single Nucleotide Polymorphism 33%
  • Epitranscriptome 33%
  17 Citations (Scopus)