Is My Network Module Preserved and Reproducible?

Langfelder, Peter, Luo, Rui, Oldham, Michael C., Horvath, Steve·2011·PLoS Computational Biology

Cited by (1,002)

Items 501–600 of 1,002

  1. Coexpression and Cosplicing Network Approaches for the Study of Mammalian Brain Transcriptomes
    Ovidiu D. Iancu, Alexandre M. Colville, Priscila Darakjian, ROBERT J. HITZEMANN · 2014 · International review of neurobiology
  2. Integrating Genetic and Gene Co-expression Analysis Identifies Gene Networks Involved in Alcohol and Stress Responses
    Jie Luo, Pei Xu, Peijian Cao, Hongjian Wan, Xiaonan Lv, Shengchun Xu, Gangjun Wang, Melloni N. Cook, Byron C. Jones, Lu Lu et al. · 2018 · Frontiers in Molecular Neuroscience
  3. Co-expression Network Analysis Reveals Key Genes Related to Ankylosing spondylitis Arthritis Disease: Computational and Experimental Validation.
    Leila Najafzadeh, Mahdi Mahmoudi, Mostafa Ebadi, Marzieh Dehghan Shasaltaneh · 2021 · PubMed Central
  4. Coral: an integrated suite of visualizations for comparing clusterings
    Darya Filippova, Aashish Gadani, Carl Kingsford · 2012 · BMC Bioinformatics
  5. Do gene expression findings from mouse models of cocaine use recapitulate human cocaine use disorder in reward circuitry?
    Spencer B. Huggett, Jason A. Bubier, Elissa J. Chesler, Rohan H. C. Palmer · 2020 · Genes Brain & Behavior
  6. Putative contributions of the sex chromosome proteins SOX3 and SRY to neurodevelopmental disorders
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  7. Toxicogenomics Approaches to Address Toxicity and Carcinogenicity in the Liver
    Arun R. Pandiri, Scott S. Auerbach, J STEVENS, Eric A.G. Blomme · 2023 · Toxicologic Pathology
  8. Early life adversity is associated with differential gene expression in immune cells: A cluster-based analysis across an acute psychosocial stressor
    Laura C. Etzel, Abner T. Apsley, Waylon James Hastings, Qiaofeng Ye, Idan Shalev · 2024 · Brain Behavior and Immunity
  9. Identification of key genes associated with acute myocardial infarction using WGCNA and two-sample mendelian randomization study
    Xiaohe Yang, Yingtao Huang, Dadong Tang, Liangming Yue · 2024 · PLoS ONE
  10. Aberrant expression of collagen type X in solid tumor stroma is associated with EMT, immunosuppressive and pro-metastatic pathways, bone marrow stromal cell signatures, and poor survival prognosis
    Elliot H. H. Youth, Aryana Famili-Youth, Dongfang Yang, Ayesha Siddique, Elizabeth Yiru Wu, Wenguang Liu, Murray B. Resnick, Qian Chen, Alexander S. Brodsky · 2025 · BMC Cancer
  11. Hippo-vgll3 signaling may contribute to sex differences in Atlantic salmon maturation age via contrasting adipose dynamics
    Ehsan Pashay Ahi, Jukka‐Pekka Verta, Johanna Kurko, Annukka Ruokolainen, Paul V. Debes, Craig Robert Primmer · 2025 · Biology of Sex Differences
  12. RNAseq studies reveal distinct transcriptional response to vitamin A deficiency in small intestine versus colon, uncovering novel vitamin A-regulated genes
    Zhi Chai, Yafei Lyu, Qiuyan Chen, Cheng-Hsin Wei, Lindsay M. Snyder, Veronika C. Weaver, Aswathy Sebastian, Istvan U. Albert, Qunhua Li, Margherita T. Cantorna et al. · 2021 · The Journal of Nutritional Biochemistry
  13. Identification of atrial fibrillation-associated lncRNAs and exploration of their functions based on WGCNA and ceRNA network analyses
    Yanhong Liu, Xue Liang, Jianlong Wang, Yu Wang, Xing Liu, Wenfeng Shangguan, Shuai Miao, Yingwu Liu, Zhanquan Jiao · 2021 · General Physiology and Biophysics
  14. Discovery of Novel Drug Candidates for Alzheimer’s Disease by Molecular Network Modeling
    Jiaxin Zhou, Qingyong Li, Wensi Wu, Xiaojun Zhang, Zhiyi Zuo, Yanan Lu, Huiying Zhao, Zhi Wang · 2022 · Frontiers in Aging Neuroscience
  15. The applications of network analysis in fruit ripening
    Ching Ching Wee, Vijay Kumar Subbiah, Masanori Arita, Hoe‐Han Goh · 2022 · Scientia Horticulturae
  16. A conjoint analysis of bulk RNA-seq and single-nucleus RNA-seq for revealing the role of ferroptosis and iron metabolism in ALS
    Xiujuan Fu, Yizi He, Yongzhi Xie, Zuneng Lu · 2023 · Frontiers in Neuroscience
  17. Potential miRNA-gene interactions determining progression of various ATLL cancer subtypes after infection by HTLV-1 oncovirus
    Mohadeseh Zarei Ghobadi, Elaheh Afsaneh, Rahman Emamzadeh, Mona Soroush · 2023 · BMC Medical Genomics
  18. Longitudinal Lipidomic Profile of Hypertension in American Indians: Findings From the Strong Heart Family Study
    Mingjing Chen, Guanhong Miao, Ying Zhang, Jason G. Umans, Elisa T. Lee, Barbara V. Howard, Oliver Fiehn, Jinying Zhao · 2023 · Hypertension
  19. Identification of the susceptible genes and mechanism underlying the comorbid presence of coronary artery disease and rheumatoid arthritis: a network modularization analysis
    Siqi Zhang, Qikai Niu, Tong Lin, Sihong Liu, Pengqian Wang, Haiyu Xu, Bing Li, Huamin Zhang · 2023 · BMC Genomics
  20. Therapeutic effect of microRNA-21 on differentially expressed hub genes in gastric cancer based on systems biology
    Hesam Ghafouri Kalajahi, AmirHossein Yari, Mohammad Ali Amini, Tunç Çatal, Mahya Ahmadpour Youshanlui, Omid Pourbagherian, Çiğdem Sezer Zhmurov, Ahad Mokhtarzadeh · 2023 · Scientific Reports
  21. Identification of hub genes of pneumocyte senescence induced by thoracic irradiation using weighted gene co-expression network analysis
    Yonghua Xing, Junling Zhang, LU LU, Deguan Li, Yueying Wang, Song Mei Huang, Chengcheng Li, Zhubo D. Zhang, JIANGUO LI, Aimin Meng · 2015 · Molecular Medicine Reports
  22. A methodological study of genome-wide DNA methylation analyses using matched archival formalin-fixed paraffin embedded and fresh frozen breast tumors
    Allyson C. Espinal, Dan Wang, Li Yan, Song Liu, Li Tang, Qiang Hu, Carl D. Morrison, Christine B. Ambrosone, Michael J. Higgins, Lara E. Sucheston‐Campbell · 2017 · Oncotarget
  23. Different mating contexts lead to extensive rewiring of female brain coexpression networks in the guppy
    Natasha I. Bloch, Alberto Corral‐López, Severine Denise Buechel, Alexander Kotrschal, Niclas Kolm, Judith E. Mank · 2020 · Genes Brain & Behavior
  24. A longitudinal study of gene expression in first-episode schizophrenia; exploring relapse mechanisms by co-expression analysis in peripheral blood
    Patricia Gassó, Natàlia Rodríguez, Albert Martínez-Pinteño, Gisela Mezquida, M. Ribeiro, Javier González‐Peñas, Eric P. Zorrilla, Laura Martínez-Sadurní, Roberto Rodríguez–Jiménez, Iluminada Corripio et al. · 2021 · Translational Psychiatry
  25. Modular Screening Reveals Driver Induced Additive Mechanisms of Baicalin and Jasminoidin on Cerebral Ischemia Therapy
    Bing Li, Ying Wang, Hao Gu, Yanan Yu, Pengqian Wang, Jun Hong Liu, Yingying Zhang, Yinying Chen, Qikai Niu, Bo Wang et al. · 2022 · Frontiers in Cardiovascular Medicine
  26. Entropy-based divergent and convergent modular pattern reveals additive and synergistic anticerebral ischemia mechanisms
    Yanan Yu, Xiaoxu Zhang, Bing Li, Yingying Zhang, Jun Hong Liu, Haixia Li, Yinying Chen, Pengqian Wang, Ruixia Kang, Hongli Wu et al. · 2016 · Experimental Biology and Medicine
  27. Microbial production of short-chain fatty acids attenuates long-term neurologic impairment after traumatic brain injury
    Zujian Xiong, Brittany P. Dodson, Matthew Brian Rogers, Chaim T. Sneiderman, Keri L. Janesko‐Feldman, Vincent Vagni, Mioara D. Manole, Xuejun Li, Dhivyaa Rajasundaram, Robert S. B. Clark et al. · 2025 · Journal of Neuroinflammation
  28. Are the 50’s, the transition decade, in choroid plexus aging?
    Ana Carolina Tahira, Fernanda Marques, Bianca Cristina Garcia Lisbôa, Arthur Sant’Anna Feltrin, Amilton de Lima Barbosa, Katia C. Oliveira, Carlos Alberto de Bragança Pereira, Renata Elaine Paraízo Leite, Lea T. Grinberg, Cláudia Kimie Suemoto et al. · 2021 · GeroScience
  29. Gene expression in male and female stickleback from populations with convergent and divergent throat coloration
    Jeffrey S. McKinnon, William Burns Newsome, Christopher N. Balakrishnan · 2022 · Ecology and Evolution
  30. Differential co-expression network analysis with DCoNA reveals isomiR targeting aberrations in prostate cancer
    Anton Zhiyanov, Narek Engibaryan, Stepan A. Nersisyan, M. Yu. Shkurnikov, Alexander Tonevitsky · 2023 · Bioinformatics
  31. Domestication over Speciation in Allopolyploid Cotton Species: A Stronger Transcriptomic Pull
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  32. A WGCNA-based cancer-associated fibroblast risk signature in colorectal cancer for prognosis and immunotherapy response
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  33. Transcriptomic meta-analysis reveals ERRα-mediated oxidative phosphorylation is downregulated in Fuchs’ endothelial corneal dystrophy
    Xunzhi Zhang, Ashwani Kumar, Adwait Amod Sathe, V. Vinod Mootha, Chao Xing · 2023 · PLoS ONE
  34. Re-wiring and gene expression changes of AC025034.1 and ATP2B1 play complex roles in early-to-late breast cancer progression
    Samane Khoshbakht, Majid Mokhtari, Sayyed Sajjad Moravveji, Sadegh Azimzadeh Jamalkandi, Ali Masoudi‐Nejad · 2022 · BMC Genomic Data
  35. DNA methylation mediates a randomized controlled trial home-visiting intervention during pregnancy and the Bayley infant’s cognitive scores at 12 months of age
    Veronica Luiza Vale Euclydes, Vinícius Daguano Gastaldi, Arthur Sant’Anna Feltrin, Daniël J. Hoffman, Gisele Rodrigues Gouveia, Hugo Cogo, Aloísio Felipe-Silva, Rossana Pulcineli Vieira, Eurı́pedes Constantino Miguel, Guilherme V. Polanczyk et al. · 2022 · Journal of Developmental Origins of Health and Disease
  36. Research on a Weighted Gene Co-expression Network Analysis method for mining pathogenic genes in thyroid cancer
    Bo Wang, Wei I. Jiang, Xiaodong Zheng, Yu Han, Runjie Liu · 2022 · PLoS ONE
  37. Multi-omic integration reveals cell-type-specific regulatory networks of insulin resistance in distinct ancestry populations
    Peng Xu, Minghui Wang, Neeraj Sharma, Mary E. Comeau, Martin Wabitsch, Carl D. Langefeld, Mete Civelek, Bin Zhang, Swapan K. Das · 2023 · Cell Systems
  38. Contrasting patterns of divergence at the regulatory and sequence level in European Daphnia galeata natural populations
    Suda Parimala Ravindran, Maike Herrmann, Mathilde Cordellier · 2019 · Ecology and Evolution
  39. LGALS4 as a Prognostic Factor in Urothelial Carcinoma of Bladder Affects Cell Functions
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  40. miR-142-3p regulates cortical oligodendrocyte gene co-expression networks associated with tauopathy
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  41. Transcriptional Analysis of Nuclear-Encoded Mitochondrial Genes in Eight Neurodegenerative Disorders: The Analysis of Seven Diseases in Reference to Friedreich’s Ataxia
    Muhammad Elsadany, Reem A. Elghaish, Aya S. Khalil, Alaa S. Ahmed, Rana H. Mansour, Eman Badr, Menattallah Elserafy · 2021 · Frontiers in Genetics
  42. Glacial snow and ice Contribute Differentially to the dissolved organic matter in the runoff of Qiangyong Glacier, Tibetan Plateau
    Bixi Guo, Yongqin Liu, Pengfei Liu, Ruanhong Cai, Qiang Zheng, Quan Shi, Chen He · 2024 · Journal of Hydrology
  43. Complex Networks, Gene Expression and Cancer Complexity: A Brief Review of Methodology and Applications
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  44. Developing a transcriptomic framework for testing testosterone-mediated handicap hypotheses
    Daniel Newhouse, Ben J. Vernasco · 2019 · General and Comparative Endocrinology
  45. Inferring miRNA sponge modules across major neuropsychiatric disorders
    Rami Balasubramanian, Palakkad Krishnan Unni Vinod · 2022 · Frontiers in Molecular Neuroscience
  46. Weighted gene co-expression network analysis identifies key hub genes and pathways in acute myeloid leukemia
    Xinfeng Wang, Akhilesh Kumar Bajpai, Qingqing Gu, David George Ashbrook, Athena Starlard‐Davenport, Lu Lu · 2023 · Frontiers in Genetics
  47. Maternal Serum Metabolomics in Mid-Pregnancy Identifies Lipid Pathways as a Key Link to Offspring Obesity in Early Childhood
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  48. Gene Network Construction from Microarray Data Identifies a Key Network Module and Several Candidate Hub Genes in Age-Associated Spatial Learning Impairment
    Raihan Uddin, Shiva M. Singh · 2017 · Frontiers in Systems Neuroscience
  49. Pathways of topological rank analysis (PoTRA): a novel method to detect pathways involved in hepatocellular carcinoma
    Chaoxing Li, Li Liu, Valentin Dinu · 2018 · PeerJ
  50. Cell Type-Specific Gene Network-Based Analysis Depicts the Heterogeneity of Autism Spectrum Disorder
    Jinting Guan, Yiping Lin, Guoli Ji · 2020 · Frontiers in Cellular Neuroscience
  51. Network Preservation Analysis Reveals Dysregulated Synaptic Modules and Regulatory Hubs Shared Between Alzheimer’s Disease and Temporal Lobe Epilepsy
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  52. Multicopper oxidases GbAO and GbSKS are involved in the Verticillium dahliae resistance in Gossypium barbadense
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  53. Co-Expression Network Analysis of AMPK and Autophagy Gene Products during Adipocyte Differentiation
    Mahmoud Ahmed, Jin Seok Hwang, Trang Huyen Lai, Sahib Zada, Huynh Quoc Nguyen, Trang Minh Pham, Miyong Yun, Deok Ryong Kim · 2018 · International Journal of Molecular Sciences
  54. A Comprehensive Survey of Immune Cytolytic Activity-Associated Gene Co-Expression Networks across 17 Tumor and Normal Tissue Types
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  55. Lung Transcriptomics Link Emphysema to Barrier Dysfunction and Macrophage Subpopulations
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  56. Spatial and development responses in the wheat leaf highlight the loss of chloroplast protein homeostasis during salt stress
    Samalka Wijeweera, Owen Duncan, A. Harvey Millar · 2025 · Journal of Proteomics
  57. Integrating explainable machine learning and transcriptomics data reveals cell-type specific immune signatures underlying macular degeneration
    Khang Ma, Hosei Nakajima, Nipa Basak, Arko Barman, Rinki Ratnapriya · 2025 · npj Genomic Medicine
  58. Mepolizumab alters gene regulatory networks of nasal airway type-2 and epithelial inflammation in urban children with asthma
    Courtney L. Gaberino, R. Max Segnitz, Kimberly A. Dill‐McFarland, Leonard B. Bacharier, Agustin Calatroni, Michelle Ann Gill, Jeffrey R. Stokes, Andrew H. Liu, Robyn T. Cohen, Rajesh Kumar et al. · 2025 · Nature Communications
  59. RETRACTED: In-depth systems biological evaluation of bovine alveolar macrophages suggests novel insights into molecular mechanisms underlying Mycobacterium bovis infection
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  60. Identification of disease-related genes and construction of a gene co-expression database in non-alcoholic fatty liver disease
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  61. Neural circuit-wide analysis of changes to gene expression during deafening-induced birdsong destabilization
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  62. Identification of novel N7-methylguanine-related gene signatures associated with ulcerative colitis and the association with biological therapy
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  63. Sex-Differential Gene Expression in Developing Human Cortex and Its Intersection With Autism Risk Pathways
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  64. Deciphering molecular landscape of breast cancer progression and insights from functional genomics and therapeutic explorations followed by in vitro validation
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  65. Discovering Perturbation of Modular Structure in HIV Progression by Integrating Multiple Data Sources Through Non-Negative Matrix Factorization
    Sumanta Ray, Ujjwal Maulik · 2016 · IEEE Transactions on Computational Biology and Bioinformatics
  66. Erosion of Gene Co-expression Networks Reveal Deregulation of Immune System Processes in Late-Onset Alzheimer’s Disease
    John Stephen Malamon, Andres Kriete · 2020 · Frontiers in Neuroscience
  67. Interactive Gene Expression Patterns of Susceptible and Resistant Lens ervoides Recombinant Inbred Lines and the Necrotroph Ascochyta lentis
    Zhe Cao, Karan Kapoor, Li Li, Sabine Banniza · 2020 · Frontiers in Microbiology
  68. Metabolite Profiles of the Relationship between Body Mass Index (BMI) Milestones and Metabolic Risk during Early Adolescence
    Wei Perng, Mohammad Lutfar Rahman, Izzuddin M. Aris, Gregory Alexander Michelotti, Joanne E. Sordillo, Jorge E. Chavarro, Emily Oken, Marie‐France Hivert · 2020 · Metabolites
  69. Identification of the potential novel biomarkers as susceptibility gene for Wilms tumor
    Li Liu, Zhe Song, Xudong Gao, Xian Chen, Xiaobin Wu, Mi Wang, Yude Hong · 2021 · BMC Cancer
  70. Changes in the Coexpression of Innate Immunity Genes During Persistent Islet Autoimmunity Are Associated With Progression of Islet Autoimmunity: Diabetes Autoimmunity Study in the Young (DAISY)
    Patrick M. Carry, Kathleen Waugh, Lauren A. Vanderlinden, Randi K. Johnson, Teresa Buckner, Marian Rewers, Andrea K. Steck, Ivana V. Yang, Tasha E. Fingerlin, Katerina J. Kechris et al. · 2022 · Diabetes
  71. Sensory conflict disrupts circadian rhythms in the sea anemone Nematostella vectensis
    Cory A. Berger, Ann M. Tarrant · 2023 · eLife
  72. A Systems Approach Implicates a Brain Mitochondrial Oxidative Homeostasis Co-expression Network in Genetic Vulnerability to Alcohol Withdrawal
    Nicole A. R. Walter, Deaunne L. Denmark, Laura B. Kozell, Kari Johnson Buck · 2017 · Frontiers in Genetics
  73. Gene network variation and alternative paths to convergent evolution in turtles
    Gerardo A. Cordero, Haibo Liu, Kokulapalan Wimalanathan, Rachel Weber, Kevin Quinteros, Fredric J. Janzen · 2018 · Evolution & Development
  74. Network analysis of drug effect on triglyceride-associated DNA methylation
    Elise Lim, Hanfei Xu, Peitao Wu, Daniel C. Posner, Jiayi Wu, Gina Marie Peloso, Achilleas Pitsillides, Anita L. DeStefano, L. Adrienne Cupples, Ching‐Ti Liu · 2018 · BMC Proceedings
  75. Integrated systems‐genetic analyses reveal a network target for delaying glioma progression
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  76. HPC framework for in-silico trials on 3D virtual human cardiac population to assess drug-induced arrhythmic risk
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  77. Key gene modules and hub genes associated with pyrethroid and organophosphate resistance in Anopheles mosquitoes: a systems biology approach
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  78. Estradiol-mediated enhancement of the human ectocervical epithelial barrier correlates with desmoglein-1 expression in the follicular menstrual phase
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  79. Computational Systems Biology Methods for Cross‐Disease Comparison of Omics Data
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  80. Cheminformatics and Bioinformatics at the Interface with Systems Biology
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  82. Large-scale integrative analysis of juvenile idiopathic arthritis for new insight into its pathogenesis
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  83. DNA methylation patterns in the frontal lobe white matter of multiple system atrophy, Parkinson’s disease, and progressive supranuclear palsy: a cross-comparative investigation
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  84. Gene Expression Shifts in Emperor Penguin Adaptation to the Extreme Antarctic Environment
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  85. Utilizing rat kidney gene co-expression networks to enhance safety assessment biomarker identification and human translation
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  86. Late‐Stage Skeletal Muscle Transcriptome in Duchenne Muscular Dystrophy Shows a BMP4‐Induced Molecular Signature
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  87. Integrating Tumor Stroma Biomarkers With Clinical Indicators for Colon Cancer Survival Stratification
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  88. Rewired Pathways and Disrupted Pathway Crosstalk in Schizophrenia Transcriptomes by Multiple Differential Coexpression Methods
    Hui Yu, Yan Ping Guo, Jingchun Chen, Xiangning Chen, Peilin Jia, Zhongming Zhao · 2021 · Genes
  89. Neuroimaging Examination of Driving Mode Switching Corresponding to Changes in the Driving Environment
    Ryu Ohata, Kenji Ogawa, Hiroshi Imamizu · 2022 · Frontiers in Human Neuroscience
  90. S100A9 and SOCS3 as diagnostic biomarkers of acute myocardial infarction and their association with immune infiltration
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  91. Impact of 5HydroxyMethylCytosine (5hmC) on reverse/direct association of cell-cycle, apoptosis, and extracellular matrix pathways in gastrointestinal cancers
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  93. Global analysis of iron metabolism‐related genes identifies potential mechanisms of gliomagenesis and reveals novel targets
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  94. Disentangling specific and unspecific components of innate immune memory in a copepod–tapeworm system
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  95. An Integrative Transcriptomic Analysis of Systemic Juvenile Idiopathic Arthritis for Identifying Potential Genetic Markers and Drug Candidates
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  96. Identification of key immune regulatory genes in HIV-1 progression
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  97. Proteomics and Phosphoproteomics Profiling of Drug-Addicted BRAFi-Resistant Melanoma Cells
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  98. Optimizing miRNA-module diagnostic biomarkers of gastric carcinoma via integrated network analysis
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  99. Bioinformatics analysis of common key genes and pathways of intracranial, abdominal, and thoracic aneurysms
    Siwei Bi, Ruiqi Liu, Linfeng He, Jingyi Li, Jun Gu · 2021 · BMC Cardiovascular Disorders
  100. Reference Module-Based Analysis of Ovarian Cancer Transcriptome Identifies Important Modules and Potential Drugs
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