KEGG: Kyoto Encyclopedia of Genes and Genomes

Post-Genome Informatics

Kanehisa, M. I. (2000) · doi:10.1093/oso/9780198503279.001.0001 · Cited by 157

DBGET/LinkDB: an integrated database retrieval system.

Fujibuchi, W., Goto, S., Migimatsu, H., et al. (1998) · PubMed · Cited by 109

Single-cell and spatial detection of senescent cells using DeepScence

Qu, Y., Ji, B., Dong, R., Gu, L., Chan, C., Xie, J., Glass, C., Wang, X.-F., Nixon, A. B., & Ji, Z. (2025) · Cell Genomics · doi:10.1016/j.xgen.2025.101035 · Cited by 30

Apolipoprotein J in Alzheimer’s disease: shedding light on its role with cell signaling pathway perspective and possible therapeutic approaches

Moezzi, S.-M.-I., Mozafari, N., Fazel-Hoseini, S.-M., Nadimi-Parashkoohi, S., Abbasi, H., Ashrafi, H., & Azadi, A. (2020) · ACS Chemical Neuroscience · doi:10.1021/acschemneuro.0c00637 · Cited by 13

CD300E+ macrophages facilitate liver regeneration after splenectomy in decompensated cirrhotic patients

Yang, T., Zhang, Y., Duan, C., Liu, H., Wang, D., Liang, Q., Chen, X., Ma, J., Cheng, K., Chen, Y., et al. (2025) · Experimental & Molecular Medicine · doi:10.1038/s12276-024-01371-3 · Cited by 11

Network spectra for drug-target identification in complex diseases: new guns against old foes

Rai, A., Shinde, P., & Jalan, S. (2018) · Applied Network Science · doi:10.1007/s41109-018-0107-y · Cited by 12

MicroRNA Profiling in Aging Brain of PSEN1/PSEN2 Double Knockout Mice

Ham, S., Kim, T. K., Lee, S., Tang, Y.-P., & Im, H.-I. (2018) · Molecular Neurobiology · doi:10.1007/s12035-017-0753-6 · Cited by 12

Molecular Mechanisms of Radiation Resistance in Breast Cancer: A Systematic Review of Radiosensitization Strategies

Mageau, E., Derbowka, R., Dickinson, N., Lefort, N., Kovala, A. T., Boreham, D. R., Tai, T. C., Thome, C., & Tharmalingam, S. (2025) · Current Issues in Molecular Biology · doi:10.3390/cimb47080589 · Cited by 12

Mechanosensitive ion channel-related genes in hepatocellular carcinoma: Unraveling prognostic genes and their roles in drug resistance and immune modulation

Huo, X., Jiang, S., Wu, S., Lian, Q., & Chen, H. (2025) · Liver Research · doi:10.1016/j.livres.2025.01.002 · Cited by 12

M3NetFlow: A multi-scale multi-hop graph AI model for integrative multi-omic data analysis

Zhang, H., Goedegebuure, S. P., Ding, L., DeNardo, D., Fields, R. C., Province, M., Chen, Y., Payne, P., & Li, F. (2025) · iScience · doi:10.1016/j.isci.2025.111920 · Cited by 12

Gene network centrality analysis identifies key regulators coordinating day-night metabolic transitions in Synechococcus elongatus PCC 7942 despite limited accuracy in predicting direct regulator-gene interactions

Johnson, Z., Anderson, D., Cheung, M. S., & Bohutskyi, P. (2025) · Frontiers in Microbiology · doi:10.3389/fmicb.2025.1569559 · Cited by 12

Bioinformatics analysis of microarray data to reveal the pathogenesis of brain ischemia

He, J., Gao, Y., Wu, G., Lei, X., Zhang, Y., Pan, W., & Yu, H. (2018) · Molecular Medicine Reports · doi:10.3892/mmr.2018.9000 · Cited by 11

Assessment of the safety and efficacy of an oral probiotic-based vaccine against Aspergillus infection in captive-bred Humboldt penguins (Spheniscus humboldti)

Thorel, M., Mateos-Hernandez, L., Mulot, B., Azzouni, M. N., Hodžić, A., Gaillot, H., Ruel, Y., Desoubeaux, G., Delaye, J.-B., Obregon, D., et al. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.897223 · Cited by 11

Short-Term Warming Induces Cyanobacterial Blooms and Antibiotic Resistance in Freshwater Lake, as Revealed by Metagenomics Analysis

Manna, B., Jay, E., Zhang, W., Zhou, X., Lyu, B., Thomas, G. M., & Singhal, N. (2024) · Water · doi:10.3390/w16182655 · Cited by 11

Using network extracted ontologies to identify novel genes with roles in appressorium development in the rice blast fungus magnaporthe oryzae

Ames, R. (2017) · Microorganisms · doi:10.3390/microorganisms5010003 · Cited by 10

Extracting reaction networks from databases—opening Pandora’s box

Fearnley, L. G., Davis, M. J., Ragan, M. A., & Nielsen, L. K. (2014) · Briefings in Bioinformatics · doi:10.1093/bib/bbt058 · Cited by 9

Metabolic network segmentation: a probabilistic graphical modeling approach to identify the sites and sequential order of metabolic regulation from non-targeted metabolomics data

Kuehne, A., Mayr, U., Sévin, D. C., Claassen, M., & Zamboni, N. (2017) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1005577 · Cited by 9

Whole genome analysis and in vivo safety assessment of probiotic candidate Lactobacillus acidophilus L177

Liu, Y., Zheng, H., Wang, J., Xin, J., Wu, R., Zhang, J., Zhong, Z., Liu, H., Huang, Y., Fu, H., et al. (2025) · BMC Microbiology · doi:10.1186/s12866-025-04099-w · Cited by 9

Identification of functionally connected multi-omic biomarkers for Alzheimer’s disease using modularity-constrained Lasso

Xie, L., Varathan, P., Nho, K., Saykin, A. J., Salama, P., & Yan, J. (2020) · PLOS ONE · doi:10.1371/journal.pone.0234748 · Cited by 9

Correlation between gut dysbiosis, metabolite alterations and erosive hand osteoarthritis – An observational study within the community-based Xiangya Osteoarthritis (XO) cohort

Xie, D., Wang, Y., Li, J., Yang, T., Zhang, Y., Zhang, W., Doherty, M., Zhu, Y., Yang, Z., Wang, Y., et al. (2025) · Osteoarthritis and Cartilage · doi:10.1016/j.joca.2025.07.004 · Cited by 8

Comparison of Transcriptomic Profiles of MiaPaCa-2 Pancreatic Cancer Cells Treated with Different Statins

Rimpelová, S., Kolář, M., Strnad, H., Ruml, T., Vítek, L., & Gbelcová, H. (2021) · Molecules · doi:10.3390/molecules26123528 · Cited by 8

Autophagy-associated biomarkers ULK2, UVRAG, and miRNAs miR-21, miR-126, and miR-374: Prognostic significance in glioma patients

Amin, W., Enam, S. A., Sufiyan, S., Ghias, K., Bajwa, M. H., Ilyas, S., Laghari, A. A., Naeem, S., Abidi, S. H., & Mughal, N. (2024) · PLOS ONE · doi:10.1371/journal.pone.0311308 · Cited by 8

Resource constrained flux balance analysis predicts selective pressure on the global structure of metabolic networks

Abedpour, N., & Kollmann, M. (2015) · BMC Systems Biology · doi:10.1186/s12918-015-0232-5 · Cited by 7

CHEK2 knockout is a therapeutic target for TP53-mutated hepatocellular carcinoma

Chen, Y., Zhu, Z., Wu, X., Li, H., Guan, W., & Ren, H. (2024) · Cell Death Discovery · doi:10.1038/s41420-023-01777-4 · Cited by 6

Metabolomic alterations in mammary glands from pubertal mice fed a high-fat diet

Yan, L., Rust, B. M., Sundaram, S., & Bukowski, M. R. (2023) · Nutrition and Metabolic Insights · doi:10.1177/11786388221148858 · Cited by 6

Neurocellular Stress Response to Mojave Type A Rattlesnake Venom: Study of Molecular Mechanisms Using Human iPSC-Derived Neural Stem Cell Model

Kumar, S., Aceves, M., Granados, J., Guerra, L., Juarez, F., Novilla, E., C. Leandro, A., Leandro, M., Peralta, J., Williams-Blangero, S., et al. (2025) · Biomolecules · doi:10.3390/biom15030381 · Cited by 6

Integrated multi omics and machine learning reveal mitochondrial immunometabolic networks in sepsis associated encephalopathy

Zhang, Z., Qiu, X., Zeng, X., Liu, X., Lu, J., Xu, C., Huang, J., Zhao, C., & Zhan, Y. (2025) · Scientific Reports · doi:10.1038/s41598-025-18650-2 · Cited by 6

scGraph2Vec: a deep generative model for gene embedding augmented by graph neural network and single-cell omics data

Lin, S., & Jia, P. (2024) · GigaScience · doi:10.1093/gigascience/giae108 · Cited by 4

Chromosome-level genome assembly of the glass catfish (Kryptopterus vitreolus) reveals molecular clues to its transparent phenotype

Bian, C., 深圳大学生命与海洋科学学院水产基因组学实验室, 广. 深. 5., Laboratory of Aquatic Genomics, C. O. L. S. A. O., Li, R.-H., Ruan, Z.-Q., Chen, W.-T., Huang, Y., Liu, L.-Y., Zhou, H.-L., Chong, C.-M., et al. (2024) · Zoological Research · doi:10.24272/j.issn.2095-8137.2023.396 · Cited by 4

Whole-genome sequencing and genomic analysis of four Akkermansia strains newly isolated from human feces

Lu, W., Zha, B., Lyu, J., LingHu, C., Chen, J., Deng, S., Zhang, X., Li, L., & Wang, G. (2024) · Frontiers in Microbiology · doi:10.3389/fmicb.2024.1500886 · Cited by 4

AI-powered Immune Cell Knowledge Graph (ICKG) with granular immune contexts enables immune program interpretation

He, S., Tan, Y., Ye, Q., M Gubin, M., Dede, M., Rafei, H., Peng, W., Rezvani, K., Mohanty, V., & Chen, K. (2026) · npj Artificial Intelligence · doi:10.1038/s44387-025-00060-4 · Cited by 3

GRouNdGAN: GRN-guided simulation of single-cell RNA-seq data using causal generative adversarial networks

Zinati, Y., Takiddeen, A., & Emad, A. (2023) · doi:10.1101/2023.07.25.550225 · Cited by 36

Transcriptomic Signatures of Single-Suture Craniosynostosis Phenotypes

Lapehn, S., Gustafson, J. A., Timms, A. E., Cunningham, M. L., & Paquette, A. G. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24065353 · Cited by 3

MicroRNA Transcriptomes Reveal Prevalence of Rare and Species-Specific Arm Switching Events During Zebrafish Ontogenesis

Oliveira, A. C. D., Bovolenta, L. A., Figueiredo, L., Ribeiro, A. D. O., Pereira, B. J. A., de Almeida, T. R. A., Campos, V. F., Patton, J. G., & Pinhal, D. (2024) · Evolutionary Bioinformatics · doi:10.1177/11769343241263230 · Cited by 2

Gene Expression Analysis of Yeast Strains with a Nonsense Mutation in the eRF3-Coding Gene Highlights Possible Mechanisms of Adaptation

Maksiutenko, E. M., Barbitoff, Y. A., Danilov, L. G., Matveenko, A. G., Zemlyanko, O. M., Efremova, E. P., Moskalenko, S. E., & Zhouravleva, G. A. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms25126308 · Cited by 2

miR-21 as a diagnostic and prognostic biomarker in glioma: tissue and serum expression analysis in a Pakistani cohort

Laghari, A. A., Sufiyan, S., Amin, W., Ilyas, S., Naeem, S., Adnan, U., Abidi, S. H., Uddin, S., Enam, S. A., & Mughal, N. (2026) · Journal of Neuro-Oncology · doi:10.1007/s11060-025-05287-4 · Cited by 1

APOE4 reduces hippocampal expression of phosphoglycerate kinase 1 and sodium potassium pump to enhance seizure susceptibility in mice

Singh, T., Bridgeman, E., Baker, A. J., Noblet, H. A., Yang, K. Y., Kang, S., Lim, K. H., Lee, S. S., Amundsen, N. M., Lee, Y., et al. (2026) · Neurobiology of Disease · doi:10.1016/j.nbd.2025.107246 · Cited by 1

TFXcan reveals transcription factor programs driving GWAS loci

Adeluwa, T., Salazar-Magaña, S., Sumner, S., Gona, S., Nyasimi, F., Carbonetto, P., Baca, S. C., Freedman, M., Gusev, A., Liu, B., et al. (2026) · Cell Genomics · doi:10.1016/j.xgen.2026.101398

SenolyticSynergy: An Attention-Based Network for Discovering Novel Senolytic Combinations via Human Aging Genomics

Ye, Y., Su, T., Gao, J., & Ming, D. (2025) · International Journal of Molecular Sciences · doi:10.3390/ijms26189004

MetabolEx: Platform for Small-Molecule Metabolites Generation and Metabolic Pathway Prediction

Lunghini, F., Agazzi, G., Tazzari, V., Fava, A., Vittorio, S., Macorano, A., Vistoli, G., & Beccari, A. R. (2026) · ACS Measurement Science Au · doi:10.1021/acsmeasuresciau.6c00019

Improving the annotation of the Heterorhabditis bacteriophora genomePreprint

McLean, F., Berger, D., Laetsch, D. R., et al. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/225904 · Cited by 1

Improving the annotation of the Heterorhabditis bacteriophora genome

McLean, F., Berger, D., Laetsch, D. R., Schwartz, H. T., & Blaxter, M. (2018) · GigaScience · doi:10.1093/gigascience/giy034 · Cited by 26

Identification of a unique library of complex, but ordered, arrays of repetitive elements in the human genome and implication of their potential involvement in pathobiology

Lee, K.-H., Lee, Y.-K., Kwon, D.-N., Chiu, S., Chew, V. W., Rah, H., Kujawski, G., Melhem, R., Hsu, K. J., Chung, C. J., et al. (2011) · Experimental and Molecular Pathology · doi:10.1016/j.yexmp.2011.02.007 · Cited by 5

Toward Chromosome-Level Comparative Analysis of Vertebrate Genomes

Murakami, K., Noguchi, H., Totoki, Y., et al. (2001) · Proceedings Genome Informatics Workshop/Genome informatics · doi:10.11234/gi1990.12.411

Genome sequence analysis of the Vibrio parahaemolyticus lytic bacteriophage VPMS1

Ramírez-Orozco, M., Serrano‐Pinto, V., Ochoa-Álvarez, N. A., Makarov, R., & Martínez‐Díaz, S. F. (2013) · Archives of Virology · doi:10.1007/s00705-013-1726-3 · Cited by 11