Department of Biosciences and Bioinformatics

Research output

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

• 385 Article
• 72 Review article
• 27 Conference Proceeding
• 14 Other contribution
• 60 More
  • 13 Chapter
  • 12 Meeting Abstract
  • 9 Patent
  • 8 Editorial
  • 7 Letter
  • 6 Comment/debate
  • 2 Book
  • 1 Anthology
  • 1 Paper
  • 1 Conference article

Research output per year

Research output per year

Search results

• 2025

  A fly CURE confers superior long-term retention of genetics skills than a traditional lab and lecture pairing

  Fendos, J. & Wei, Z., 2025, (In preparation) In: CBE Life Sciences Education.

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

• A plant CURE can decrease interest in botanical research, despite significant gains in lab competence

  Fendos, J. & Han, T., 2025, In: Journal of Experimental Education.

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

• A zebrafish developmental biology CURE improves student lab skills and appreciation for fish as a model organism

  Fendos, J. & Shen, H., 2025, (In preparation) In: Journal of Experimental Education.

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

• Biochemistry lab skill acquisition is task- and context-dependent, capable of supporting downstream learning outcomes

  Fendos, J. & Sun, Y., 2025, (In preparation) In: CBE Life Sciences Education.

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

• Cell biology lab skill acquisition is affected by task type, learning context, and iteration spacing

  Fendos, J. & Li, Y., 2025, (In preparation) In: International Journal of STEM Education.

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

• Enhancing student and teaching assistant performance in CUREs and microbiology lab courses via a gated preparatory training module

  Fendos, J. & Li, B., 2025, (In preparation) In: International Journal of STEM Education.

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

• Mouse lab skills are improved by a CURE, but with mixed results for improving appreciation of animal research

  Fendos, J. & Chen, H., 2025, (In preparation) In: Journal of Experimental Education.

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

• Neurotranscriptomic and behavioral effects of ISRIB, and its therapeutic effects in the traumatic brain injury model in zebrafish

  Ilyin, N. P., Shevlyakov, A. D., Boyko, G. A., Moskalenko, A. M., Ikrin, A. N., Galstyan, D. S., Kolesnikova, T. O., Katolikova, N. V., Chekrygin, S. A., Lim, L. W., Yang, L., De Abreu, M. S., Yenkoyan, K. B., Kaluev, A. & Demin, K. A., 1 Feb 2025, In: Brain Research. 1848, 149329.

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

  • Behavioral Effect 100%
  • Neurotrauma 100%
  • Traumatic Brain Injury 100%
  • Transcriptome 11%
  • Behavior (Neuroscience) 11%

• Science students exhibit a wide range of reasons for lecture absenteeism, with a policy-based intervention improving outcomes

  Fendos, J. & Song, Y., 2025, (In preparation) In: International Journal of STEM Education.

  Research output: Contribution to journal › Article › peer-review
• 2024

  Acute behavioral and neurochemical effects of sulpiride in adult zebrafish

  Kaluev, A., Sept 2024, In: Neurochemical Research.

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

• An adaptive block-wise prediction error-based (AdaBPE) reversible data hiding in encrypted images for medical image transmission

  Panchikkil, S., Manikandan, V. M., Pratim Roy, P., Wang, S. & Zhang, Y., 2024, (Accepted/In press) In: CAAI Transactions on Intelligence Technology.

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

  Open Access

  • Prediction Error 100%
  • Cloud Computing 33%

• A novel open-access artificial-intelligence-driven platform for CNS drug discovery utilizing adult zebrafish

  Lukovikov, D. A., Kolesnikova, T. O., Ikrin, A. N., Prokhorenko, N. O., Shevlyakov, A. D., Korotaev, A. A., Yang, L., Bley, V., de Abreu, M. S. & Kalueff, A. V., Nov 2024, In: Journal of Neuroscience Methods. 411, 110256.

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

  • In Vivo 100%
  • Drug Discovery 100%
  • Zebra Fish 100%
  • Cholinergic 50%
  • Locomotor Activity 50%

• A promising natural product in diffuse large B-cell lymphoma therapy by targeting PIM1

  Zhang, X., Su, Q., Zhang, Y., Rong, R., Chen, S., He, L., Zhuang, W. & Li, B., Aug 2024, In: Annals of Hematology. 103, 8, p. 2905-2915 11 p.

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

  • Diffuse Large B Cell Lymphoma 100%
  • Diffuse Large B-Cell Lymphoma 100%
  • PIM1 100%
  • B Cell Lymphoma 28%
  • Tucidinostat 14%

• A review of IoT applications in healthcare

  Li, C., Wang, J., Wang‎, S. & Zhang, Y., 14 Jan 2024, In: Neurocomputing. 565, 127017.

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

  Open Access

  • Therapeutic Procedure 100%
  • Interpersonal Communication 100%
  • Researcher 100%
  • Adoption 100%
  • Patient Care 100%
  47 Citations (Scopus)

• 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%
  1 Citation (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)

• 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%
  1 Citation (Scopus)

• 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

  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., 30 Sept 2024, In: ACS Chemical Neuroscience.

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

• Decoding molecular bases of rodent social hetero-grooming behavior using in-silico analyses and bioinformatics tools

  Moskalenko, A., Ikrin, A., Kozlova, A., Mukhamadeev, R., de Abreu, M. S., Riga, V., Kolesnikova, T. & Kaluev, A., 30 Aug 2024, In: Neuroscience. 554, p. 146-155 10 p.

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

  • Synapsin 100%
  • Gene Linkage 100%

• Deep Fuzzy Multi-Teacher Distillation Network for Medical Visual Question Answering

  Liu, Y., Chen, B., Wang, S., Lu, G. & Zhang, Z., 2024, (Accepted/In press) In: IEEE Transactions on Fuzzy Systems. p. 1-15 15 p.

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

  • Visual Question Answering 100%
  • Medical Domain 25%
  3 Citations (Scopus)

• 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)

• 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%
  5 Citations (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%
  5 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

• Hepatitis B virus X protein contributes to hepatocellular carcinoma via upregulation of KIAA1429 methyltransferase and mRNA m6A hypermethylation of HSPG2/Perlecan.

  Sivasudhan, E., Zhou, J., Ma, J., Wang, Y., Liu, S., Khan, F. I., Lu, Z., Meng, J., Blake, N. & Rong, R., 2024, (Accepted/In press) In: Molecular Carcinogenesis.

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

  Open Access

  • HBx 100%
  • Hepatitis B Virus X Protein 100%
  • Upregulation 100%
  • Methyltransferase 100%
  • Messenger RNA 100%

• 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%
  3 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%
  2 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

• 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%

• 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%
  20 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%
  2 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%
  11 Citations (Scopus)

• MACFNet: Detection of Alzheimer's disease via multiscale attention and cross-enhancement fusion network

  Alzheimer's Disease Neuroimaging Initiative, Sept 2024, In: Computer Methods and Programs in Biomedicine. 254, 108259.

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

  Open Access

  • Classification Performance 100%
  • Alzheimer's Disease 100%
  • Receptive Field 100%
  • Deep Learning 100%
  • Related Feature 50%

• MAPFUNet: Multi-attention Perception-Fusion U-Net for Liver Tumor Segmentation

  Sun, J., Wang, B., Wu, X., Tang, C., Wang, S. & Zhang, Y., 18 Jun 2024, In: Journal of Bionic Engineering. 21, 5, p. 2515-2539 25 p.

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

  • Dice Value 100%
  • Position Information 100%
  • Sampling Process 50%

• Methylation of foreign DNA overcomes the restriction barrier of Flavobacterium psychrophilum and allows efficient genetic manipulation

  Sloboda, S., Ge, X., Jiang, D., Wiens, G., Su, L., Beveridge, C., Duchaud, E., McBride, M. J., Rochat, T. & Zhu, Y., 2 Aug 2024, (Submitted) In: Applied and Environmental Microbiology.

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

• MFISN: Modality Fuzzy Information Separation Network for Disease Classification

  Nan, F., Pu, B., Pan, J., Fan, Y., Yang, J., Dong, X., Xu, Z. & Wang, S., 2024, (Accepted/In press) In: IEEE Transactions on Fuzzy Systems. p. 1-12 12 p.

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

  • Information Common 100%
  • Medical Diagnosis 16%
  • Conventional Method 16%
  1 Citation (Scopus)

• Mfpenet: multistage foreground-perception enhancement network for remote-sensing scene classification

  Sun, J., Wang, C., Sima, H., Wu, X., Wang, S. & Zhang, Y., 2024, (Accepted/In press) In: Visual Computer.

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

  • Essential Property 100%

• Minocycline reduces neurobehavioral deficits evoked by chronic unpredictable stress in adult zebrafish

  Kaluev, A. & Yang, L., Aug 2024, In: Brain Research. 1845, 149209.

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

• Mixotrophic aerobic denitrification facilitated by denitrifying bacterial-fungal communities assisted with iron in micro-polluted water: Performance, metabolic activity, functional genes abundance, and community co-occurrence

  Ma, B., Chu, M., Zhang, H., Chen, K., Li, F., Liu, X., Kosolapov, D. B., Zhi, W., Chen, Z., Yang, J., Deng, Y., Sekar, R., Liu, T., Liu, X. & Huang, T., 5 Sept 2024, In: Journal of Hazardous Materials. 476, 135057.

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

  • Organic Carbon 100%
  1 Citation (Scopus)