KEGG: Kyoto Encyclopedia of Genes and Genomes

Kanehisa, M.·2000·Nucleic Acids Research
DOI 10.1093/nar/28.1.27

Cited by (416)

Items 301–400 of 416

  1. MicroRNome analysis generates a blood-based signature for endometriosis
    Bendifallah, Sofiane, Dabi, Yohann, Suisse, Stéphane, Jornea, Ludmila, Bouteiller, Delphine, Touboul, Cyril, Puchar, Anne, Daraï, Emile · 2022 · Scientific Reports
  2. Selective deletion of MyD88 signaling in α-SMA positive cells ameliorates experimental intestinal fibrosis via post-transcriptional regulation
    Zhao, Shuai, Dejanovic, Dina, Yao, Peng, Bhilocha, Shardul, Sadler, Tammy, Schirbel, Anja, West, Gail, Doyon, Genevieve, Lopez, Rocio, Mao, Ren et al. · 2020 · Mucosal Immunology
  3. Heat and drought induced transcriptomic changes in barley varieties with contrasting stress response phenotypes
    Mahalingam, Ramamurthy, Duhan, Naveen, Kaundal, Rakesh, Smertenko, Andrei, Nazarov, Taras, Bregitzer, Phil · 2022 · Frontiers in Plant Science
  4. Exome arrays capture polygenic rare variant contributions to schizophrenia
    Richards, A. L., Leonenko, G., Walters, J. T., Kavanagh, D. H., Rees, E. G., Evans, A., Chambert, K. D., Moran, J. L., Goldstein, J., Neale, B. M. et al. · 2016 · Human Molecular Genetics
  5. Environmental intervention as a therapy for adverse programming by ancestral stress
    McCreary, J. Keiko, Erickson, Zachary T., Hao, YongXin, Ilnytskyy, Yaroslav, Kovalchuk, Igor, Metz, Gerlinde A. S. · 2016 · Scientific Reports
  6. A cooperative strategy for parameter estimation in large scale systems biology models
    Villaverde, Alejandro F, Egea, Jose A, Banga, Julio R · 2012 · BMC Systems Biology
  7. Dissecting key regulators of transcriptome kinetics through scalable single-cell RNA profiling of pooled CRISPR screens
    Xu, Zihan, Sziraki, Andras, Lee, Jasper, Zhou, Wei, Cao, Junyue · 2024 · Nature Biotechnology
  8. Genetic analysis of biological pathway data through genomic randomization
    Yaspan, Brian L., Bush, William S., Torstenson, Eric S., Ma, Deqiong, Pericak-Vance, Margaret A., Ritchie, Marylyn D., Sutcliffe, James S., Haines, Jonathan L. · 2011 · Human Genetics
  9. Quantitative proteomics of a B<sub>12</sub>‐dependent alga grown in coculture with bacteria reveals metabolic tradeoffs required for mutualism
    Helliwell, Katherine E., Pandhal, Jagroop, Cooper, Matthew B., Longworth, Joseph, Kudahl, Ulrich Johan, Russo, David A., Tomsett, Eleanor V., Bunbury, Freddy, Salmon, Deborah L., Smirnoff, Nicholas et al. · 2018 · New Phytologist
  10. AlgaePath: comprehensive analysis of metabolic pathways using transcript abundance data from next-generation sequencing in green algae
    Zheng, Han-Qin, Chiang-Hsieh, Yi-Fan, Chien, Chia-Hung, Hsu, Bo-Kai Justin, Liu, Tsung-Lin, Chen, Ching-Nen Nathan, Chang, Wen-Chi · 2014 · BMC Genomics
  11. Breaking the paradigm: Dr Insight empowers signature-free, enhanced drug repurposing
    Chan, Jinyan, Wang, Xuan, Turner, Jacob A, Baldwin, Nicole E, Gu, Jinghua · 2019 · Bioinformatics
  12. Gut microbial metabolites in Parkinson's disease: Association with lifestyle, disease characteristics, and treatment status
    Voigt, Robin M., Wang, Zeneng, Brown, J. Mark, Engen, Phillip A., Naqib, Ankur, Goetz, Christopher G., Hall, Deborah A., Metman, Leo Verhagen, Shaikh, Maliha, Forsyth, Christopher B. et al. · 2022 · Neurobiology of Disease
  13. A functional selection model explains evolutionary robustness despite plasticity in regulatory networks
    Habib, Naomi, Wapinski, Ilan, Margalit, Hanah, Regev, Aviv, Friedman, Nir · 2012 · Molecular Systems Biology
  14. Sex-Specific Cross Tissue Meta-Analysis Identifies Immune Dysregulation in Women With Alzheimer’s Disease
    Paranjpe, Manish D., Belonwu, Stella, Wang, Jason K., Oskotsky, Tomiko, Gupta, Aarzu, Taubes, Alice, Zalocusky, Kelly A., Paranjpe, Ishan, Glicksberg, Benjamin S., Huang, Yadong et al. · 2021 · Frontiers in Aging Neuroscience
  15. Yeast metabolic innovations emerged via expanded metabolic network and gene positive selection
    Lu, Hongzhong, Li, Feiran, Yuan, Le, Domenzain, Iván, Yu, Rosemary, Wang, Hao, Li, Gang, Chen, Yu, Ji, Boyang, Kerkhoven, Eduard J et al. · 2021 · Molecular Systems Biology
  16. Genome-wide DNA methylation and gene expression patterns reflect genetic ancestry and environmental differences across the Indonesian archipelago
    Natri, Heini M., Bobowik, Katalina S., Kusuma, Pradiptajati, Crenna Darusallam, Chelzie, Jacobs, Guy S., Hudjashov, Georgi, Lansing, J. Stephen, Sudoyo, Herawati, Banovich, Nicholas E., Cox, Murray P. et al. · 2020 · PLoS Genetics
  17. Exploiting Conformational Ensembles in Modeling Protein–Protein Interactions on the Proteome Scale
    Kuzu, Guray, Gursoy, Attila, Nussinov, Ruth, Keskin, Ozlem · 2013 · Journal of Proteome Research
  18. Multi-omics integration strategies for animal epigenetic studies — A review
    Kim, Do-Young, Kim, Jun-Mo · 2021 · Animal Bioscience
  19. Gene expression alterations in bipolar disorder postmortem brains
    Chen, Haiming, Wang, Nulang, Zhao, Xin, Ross, Christopher A, O’Shea, K Sue, McInnis, Melvin G · 2013 · Bipolar Disorders
  20. Diet-induced obesity, energy metabolism and gut microbiota in C57BL/6J mice fed Western diets based on lean seafood or lean meat mixtures
    Holm, Jacob Bak, Rønnevik, Alexander, Tastesen, Hanne Sørup, Fjære, Even, Fauske, Kristin Røen, Liisberg, Ulrike, Madsen, Lise, Kristiansen, Karsten, Liaset, Bjørn · 2016 · The Journal of Nutritional Biochemistry
  21. Distinct gene clusters drive formation of ferrosome organelles in bacteria
    Grant, Carly R., Amor, Matthieu, Trujillo, Hector A., Krishnapura, Sunaya, Iavarone, Anthony T., Komeili, Arash · 2022 · Nature
  22. Gut microbiota-derived hexa-acylated lipopolysaccharides enhance cancer immunotherapy responses
    Sardar, Puspendu, Beresford-Jones, Benjamin S., Xia, Wangmingyu, Shabana, Omar, Suyama, Satoshi, Ramos, Ruben J. F., Soderholm, Amelia T., Tourlomousis, Panagiotis, Kuo, Paula, Evans, Alexander C. et al. · 2025 · Nature Microbiology
  23. Dysregulated FXR-FGF19 signaling and choline metabolism are associated with gut dysbiosis and hyperplasia in a novel pig model of pediatric NASH
    Hernandez, Gabriella V., Smith, Victoria A., Melnyk, Megan, Burd, Matthew A., Sprayberry, Kimberly A., Edwards, Mark S., Peterson, Daniel G., Bennet, Darin C., Fanter, Rob K., Columbus, Daniel A. et al. · 2020 · American Journal of Physiology-Gastrointestinal and Liver Physiology
  24. Transcriptomic Insights into the Growth Phase- and Sugar-Associated Changes in the Exopolysaccharide Production of a High EPS-Producing Streptococcus thermophilus ASCC 1275
    Padmanabhan, Aparna, Tong, Ying, Wu, Qinglong, Zhang, Jiangwen, Shah, Nagendra P. · 2018 · Frontiers in Microbiology
  25. The evolution and spread of sulfur cycling enzymes reflect the redox state of the early Earth
    Mateos, Katherine, Chappell, Garrett, Klos, Aya, Le, Bryan, Boden, Joanne, Stüeken, Eva, Anderson, Rika · 2023 · Science Advances
  26. Single-cell transcriptome and cell type-specific molecular pathways of human non-alcoholic steatohepatitis
    Fred, Rikard G., Steen Pedersen, Julie, Thompson, Jonatan J., Lee, Julie, Timshel, Pascal N., Stender, Stefan, Opseth Rygg, Marte, Gluud, Lise Lotte, Bjerregaard Kristiansen, Viggo, Bendtsen, Flemming et al. · 2022 · Scientific Reports
  27. Hal Is a Bacillus anthracis heme acquisition protein
    Balderas, Miriam A., Nobles, Christopher L., Honsa, Erin S., Alicki, Embriette R., Maresso, Anthony W. · 2012 · Journal of Bacteriology
  28. <i>PSMD12</i> haploinsufficiency in a neurodevelopmental disorder with autistic features
    Khalil, Raida, Kenny, Connor, Hill, R. Sean, Mochida, Ganeshwaran H., Nasir, Ramzi, Partlow, Jennifer N., Barry, Brenda J., Al‐Saffar, Muna, Egan, Chloe, Stevens, Christine R. et al. · 2018 · American Journal of Medical Genetics Part B: Neuropsychiatric Genetics
  29. Enhanced cerebellar myelination with concomitant iron elevation and ultrastructural irregularities following prenatal exposure to ambient particulate matter in the mouse
    Klocke, Carolyn, Sherina, Valeriia, Graham, Uschi M., Gunderson, Jakob, Allen, Joshua L., Sobolewski, Marissa, Blum, Jason L., Zelikoff, Judith T., Cory-Slechta, Deborah A. · 2018 · Inhalation Toxicology
  30. Tannin supplementation modulates the composition and function of ruminal microbiome in lambs infected with gastrointestinal nematodes
    Corrêa, Patricia Spoto, Mendes, Lucas William, Lemos, Leandro Nascimento, Crouzoulon, Pierre, Niderkorn, Vincent, Hoste, Hervé, Costa-Júnior, Livio Martins, Tsai, Siu Mui, Faciola, Antonio P, Abdalla, Adibe Luiz et al. · 2020 · FEMS Microbiology Ecology
  31. Combined chemosensitivity and chromatin profiling prioritizes drug combinations in CLL
    Schmidl, Christian, Vladimer, Gregory I., Rendeiro, André F., Schnabl, Susanne, Krausgruber, Thomas, Taubert, Christina, Krall, Nikolaus, Pemovska, Tea, Araghi, Mohammad, Snijder, Berend et al. · 2019 · Nature Chemical Biology
  32. Functional contribution of the intestinal microbiome in autism spectrum disorder, attention deficit hyperactivity disorder, and Rett syndrome: a systematic review of pediatric and adult studies
    Caputi, Valentina, Hill, Lee, Figueiredo, Melanie, Popov, Jelena, Hartung, Emily, Margolis, Kara Gross, Baskaran, Kanish, Joharapurkar, Papiha, Moshkovich, Michal, Pai, Nikhil · 2024 · Frontiers in Neuroscience
  33. Multiomics Implicate Gut Microbiota in Altered Lipid and Energy Metabolism in Parkinson’s Disease
    Pereira, Pedro A. B., Trivedi, Drupad K., Silverman, Justin, Duru, Ilhan Cem, Paulin, Lars, Auvinen, Petri, Scheperjans, Filip · 2022 · npj Parkinson s Disease
  34. Spatiotemporal localization of proteins in mycobacteria
    Zhu, Junhao, Wolf, Ian D., Dulberger, Charles L., Won, Harim I., Kester, Jemila C., Judd, Julius A., Wirth, Samantha E., Clark, Ryan R., Li, Yawei, Luo, Yuan et al. · 2021 · Cell Reports
  35. Construction of a Genome-Scale Metabolic Model of Arthrospira platensis NIES-39 and Metabolic Design for Cyanobacterial Bioproduction
    Yoshikawa, Katsunori, Aikawa, Shimpei, Kojima, Yuta, Toya, Yoshihiro, Furusawa, Chikara, Kondo, Akihiko, Shimizu, Hiroshi · 2015 · PLOS ONE
  36. Differential Gene Expression in Liver Tissues of Streptozotocin-Induced Diabetic Rats in Response to Resveratrol Treatment
    Sadi, Gökhan, Baloğlu, Mehmet Cengiz, Pektaş, Mehmet Bilgehan · 2015 · PLOS ONE
  37. 14q32 and let-7 microRNAs regulate transcriptional networks in fetal and adult human erythroblasts
    Lessard, Samuel, Beaudoin, Mélissa, Orkin, Stuart H, Bauer, Daniel E, Lettre, Guillaume · 2018 · Human Molecular Genetics
  38. Interactions of the hindgut mucosa-associated microbiome with its host regulate shedding of Escherichia coli O157:H7 by cattle
    Wang, Ou, McAllister, Tim A., Plastow, Graham, Stanford, Kim, Selinger, Brent, Guan, Le Luo · 2018 · Applied and Environmental Microbiology
  39. Conservation Genomics in a Changing Arctic
    Colella, Jocelyn P., Talbot, Sandra L., Brochmann, Christian, Taylor, Eric B., Hoberg, Eric P., Cook, Joseph A. · 2020 · Trends in Ecology &amp; Evolution
  40. Safety and functional enrichment of gut microbiome in healthy subjects consuming a multi-strain fermented milk product: a randomised controlled trial
    Alvarez, Anne-Sophie, Tap, Julien, Chambaud, Isabelle, Cools-Portier, Stéphanie, Quinquis, Laurent, Bourlioux, Pierre, Marteau, Philippe, Guillemard, Eric, Schrezenmeir, Juergen, Derrien, Muriel · 2020 · Scientific Reports
  41. Cold stress tolerance of the intertidal red alga Neoporphyra haitanensis
    Zhu, Shanshan, Gu, Denghui, Lu, Caiping, Zhang, Caixia, Chen, Juanjuan, Yang, Rui, Luo, Qijun, Wang, Tiegan, Zhang, Peng, Chen, Haimin · 2022 · BMC Plant Biology
  42. High-throughput transcriptomics of 409 bacteria–drug pairs reveals drivers of gut microbiota perturbation
    Ricaurte, Deirdre, Huang, Yiming, Sheth, Ravi U., Gelsinger, Diego Rivera, Kaufman, Andrew, Wang, Harris H. · 2024 · Nature Microbiology
  43. Prokaryotic and viral genomes recovered from 787 Japanese gut metagenomes revealed microbial features linked to diets, populations, and diseases
    Tomofuji, Yoshihiko, Kishikawa, Toshihiro, Maeda, Yuichi, Ogawa, Kotaro, Otake-Kasamoto, Yuriko, Kawabata, Shuhei, Nii, Takuro, Okuno, Tatsusada, Oguro-Igashira, Eri, Kinoshita, Makoto et al. · 2022 · Cell Genomics
  44. Single-Cell Transcriptomics Reveals Heterogeneity and Drug Response of Human Colorectal Cancer Organoids
    Chen, Kai-Yuan, Srinivasan, Tara, Lin, Christopher, Tung, Kuei-Ling, Gao, Ziyang, Hsu, David S., Lipkin, Steven M., Shen, Xiling · 2018 · 2018 40th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)
  45. RAPPPID: towards generalizable protein interaction prediction with AWD-LSTM twin networks
    Szymborski, Joseph, Emad, Amin · 2022 · Bioinformatics
  46. Influence of microbiota-associated metabolic reprogramming on clinical outcome in patients with melanoma from the randomized adjuvant dendritic cell-based MIND-DC trial
    Alves Costa Silva, Carolina, Piccinno, Gianmarco, Suissa, Déborah, Bourgin, Mélanie, Schreibelt, Gerty, Durand, Sylvère, Birebent, Roxanne, Fidelle, Marine, Sow, Cissé, Aprahamian, Fanny et al. · 2024 · Nature Communications
  47. A genome-scale database and reconstruction of Caenorhabditis elegans metabolism
    Gebauer, Juliane, Gentsch, Christoph, Mansfeld, Johannes, Schmeißer, Kathrin, Waschina, Silvio, Brandes, Susanne, Klimmasch, Lukas, Zamboni, Nicola, Zarse, Kim, Schuster, Stefan et al. · 2016 · Cell Systems
  48. Prioritizing cancer-related key miRNA-target interactions by integrative genomics
    Xiao, Yun, Guan, Jinxia, Ping, Yanyan, Xu, Chaohan, Huang, Teng, Zhao, Hongying, Fan, Huihui, Li, Yiqun, Lv, Yanling, Zhao, Tingting et al. · 2012 · Nucleic Acids Research
  49. The Intestinal Microbiome in Nonalcoholic Fatty Liver Disease
    Puri, Puneet, Sanyal, Arun J. · 2018 · Clinics in Liver Disease
  50. Advanced stoichiometric analysis of metabolic networks of mammalian systems
    Orman, Mehmet A., Berthiaume, Francois, Androulakis, Ioannis P., Ierapetritou, Marianthi G. · 2011 · Critical Reviews™ in Biomedical Engineering
  51. Berberine-microbiota interplay: orchestrating gut health through modulation of the gut microbiota and metabolic transformation into bioactive metabolites
    Dehau, Tessa, Cherlet, Marc, Croubels, Siska, Van De Vliet, Michiel, Goossens, Evy, Van Immerseel, Filip · 2023 · Frontiers in Pharmacology
  52. Exome Sequencing Identified NRG3 as a Novel Susceptible Gene of Hirschsprung’s Disease in a Chinese Population
    Yang, Jun, Duan, Shengyu, Zhong, Rong, Yin, Jieyun, Pu, Jiarui, Ke, Juntao, Lu, Xuzai, Zou, Li, Zhang, Hongmei, Zhu, Zhidong et al. · 2013 · Molecular Neurobiology
  53. Identification of MicroRNAs as Potential Biomarkers in Ovarian Endometriosis
    Gu, Cheng-lei, Zhang, Zhe, Fan, Wen-sheng, Li, Li-an, Ye, Ming-xia, Zhang, Qian, Zhang, Ni-na, Li, Zhen, Meng, Yuan-guang · 2020 · Reproductive Sciences
  54. Sniffing out the hypoxia volatile metabolic signature of <i>Aspergillus fumigatus</i>
    Rees, Christiaan A, Stefanuto, Pierre-Hugues, Beattie, Sarah R, Bultman, Katherine M, Cramer, Robert A, Hill, Jane E · 2017 · Journal of Breath Research
  55. libAnnotationSBML: a library for exploiting SBML annotations
    Swainston, Neil, Mendes, Pedro · 2009 · Bioinformatics
  56. SDGCCA: Supervised Deep Generalized Canonical Correlation Analysis for Multi-Omics Integration
    Moon, Sehwan, Hwang, Jeongyoung, Lee, Hyunju · 2022 · Journal of Computational Biology
  57. Comparative and integrative metabolomics reveal that S-nitrosation inhibits physiologically relevant metabolic enzymes
    Bruegger, Joel J., Smith, Brian C., Wynia-Smith, Sarah L., Marletta, Michael A. · 2018 · Journal of Biological Chemistry
  58. A transcriptome-based human universal senescence index (hUSI) robustly predicts cellular senescence under various conditions
    Wang, Jing, Zhou, Xiaolan, Yu, Peng, Yao, Jun, Guo, Pengfei, Xu, Qiushi, Zhao, Yuqi, Wang, Guanlong, Li, Qianru, Zhu, Xiaofeng et al. · 2025 · Nature Aging
  59. Identifying miRNA-mRNA regulation network of major depressive disorder in ovarian cancer patients.
    Wu, Chengjiang, Zhao, Yangjing, Liu, Yuefang, Yang, Xinxin, Yan, Meina, Min, Yujiao, Pan, Zihui, Qiu, Shali, Xia, Sheng, Yu, Jun et al. · 2018 · Oncology Letters
  60. Mathiomica: an integrative platform for dynamic omics
    Mias, George I., Yusufaly, Tahir, Roushangar, Raeuf, Brooks, Lavida R. K., Singh, Vikas V., Christou, Christina · 2016 · Scientific Reports
  61. Systematic permutation testing in GWAS pathway analyses: identification of genetic networks in dilated cardiomyopathy and ulcerative colitis
    Backes, Christina, Rühle, Frank, Stoll, Monika, Haas, Jan, Frese, Karen, Franke, Andre, Lieb, Wolfgang, Wichmann, H-Erich, Weis, Tanja, Kloos, Wanda et al. · 2014 · BMC Genomics
  62. RNAseq based transcriptomics study of SMCs from carotid atherosclerotic plaque: BMP2 and IDs proteins are crucial regulators of plaque stability
    Alloza, Iraide, Goikuria, Haize, Idro, Juan Luis, Triviño, Juan Carlos, Fernández Velasco, José María, Elizagaray, Elena, García-Barcina, María, Montoya-Murillo, Genoveva, Sarasola, Esther, Vega Manrique, Reyes et al. · 2017 · Scientific Reports
  63. Predictive Biomarkers of Age-Related Macular Degeneration Response to Anti-VEGF Treatment
    Oca, Ana I., Pérez-Sala, Álvaro, Pariente, Ana, Ochoa, Rodrigo, Velilla, Sara, Peláez, Rafael, Larráyoz, Ignacio M. · 2021 · Journal of Personalized Medicine
  64. Long-Term Artificial Selection of Hanwoo (Korean) Cattle Left Genetic Signatures for the Breeding Traits and Has Altered the Genomic Structure
    Seo, Dongwon, Lee, Doo Ho, Jin, Shil, Won, Jung Il, Lim, Dajeong, Park, Mina, Kim, Tae Hun, Lee, Hak Kyo, Kim, Sidong, Choi, Inchul et al. · 2022 · Scientific Reports
  65. 3D heterospecies spheroids of pancreatic stroma and cancer cells demonstrate key phenotypes of pancreatic ductal adenocarcinoma
    Liu, Xinyuan, Gündel, Beate, Li, Xidan, Liu, Jianping, Wright, Anthony, Löhr, Matthias, Arvidsson, Gustav, Heuchel, Rainer · 2021 · Translational Oncology
  66. Data integration across conditions improves turnover number estimates and metabolic predictions
    Wendering, Philipp, Arend, Marius, Razaghi-Moghadam, Zahra, Nikoloski, Zoran · 2023 · Nature Communications
  67. Identification of viral-mediated pathogenic mechanisms in neurodegenerative diseases using network-based approaches
    Onisiforou, Anna, Spyrou, George M · 2021 · Briefings in Bioinformatics
  68. Gut Microbiota–Related Biomarkers in Immuno-Oncology
    Silva, Carolina Alves Costa, Fidelle, Marine, Almonte, Andrew A., Derosa, Lisa, Zitvogel, Laurence · 2025 · Annual Review of Pharmacology and Toxicology
  69. Integrated Microbiome and Host Transcriptome Profiles Link Parkinson’s Disease to Blautia Genus: Evidence From Feces, Blood, and Brain
    Guo, Xingzhi, Tang, Peng, Hou, Chen, Chong, Li, Zhang, Xin, Liu, Peng, Chen, Li, Liu, Yue, Zhang, Lina, Li, Rui · 2022 · Frontiers in Microbiology
  70. In-depth profiling and quantification of the lysine acetylome in hepatocellular carcinoma with a trapped ion mobility mass spectrometer
    Xu, Jia, Guan, Xinyu, Jia, Xiaodong, Li, Hongyan, Chen, Ruibing, Lu, Yinying · 2022 · Molecular &amp; Cellular Proteomics
  71. <i>Proteus mirabilis</i> UreR coordinates cellular functions required for urease activity
    Fitzgerald, Madison J., Pearson, Melanie M., Mobley, Harry L. T. · 2024 · Journal of Bacteriology
  72. Positive and negative feedback regulation of the TGF-β1 explains two equilibrium states in skin aging
    Haga, Masatoshi, Iida, Keita, Okada, Mariko · 2024 · iScience
  73. JDSNMF: Joint Deep Semi-Non-Negative Matrix Factorization for Learning Integrative Representation of Molecular Signals in Alzheimer’s Disease
    Moon, Sehwan, Lee, Hyunju · 2021 · Journal of Personalized Medicine
  74. Deep proteomic analysis on biobanked paraffine-archived melanoma with prognostic/predictive biomarker read-out
    Szadai, Leticia, Velasquez, Erika, Szeitz, Beáta, Almeida, Natália Pinto de, Domont, Gilberto, Betancourt, Lazaro Hiram, Gil, Jeovanis, Marko-Varga, Matilda, Oskolas, Henriett, Jánosi, Ágnes Judit et al. · 2021 · Cancers
  75. Unraveling the Phenotypic and Genomic Background of Behavioral Plasticity and Temperament in North American Angus Cattle
    Alvarenga, Amanda B., Oliveira, Hinayah R., Turner, Simon P., Garcia, Andre, Retallick, Kelli J., Miller, Stephen P., Brito, Luiz F. · 2023 · Genetics Selection Evolution
  76. Single-cell and machine learning approaches uncover intrinsic immune-evasion genes in the prognosis of hepatocellular carcinoma
    Wang, Jiani, Chen, Xiaopeng, Wu, Donghao, Jia, Changchang, Lian, Qinghai, Pan, Yuhang, Yang, Jiumei · 2024 · Liver Research
  77. Genomic and functional diversity of the human-derived isolates of Faecalibacterium
    Li, Wenxi, Lin, Xiaoqian, Liang, Hewei, Wu, Zhinan, Wang, Mengmeng, Sun, Jingxi, Li, Xiaofang, He, Wenxin, Gao, Xiaowei, Hu, Tongyuan et al. · 2024 · Frontiers in Microbiology
  78. Tremorgenic effects and functional metabolomics analysis of lolitrem B and its biosynthetic intermediates
    Reddy, Priyanka, Rochfort, Simone, Read, Elizabeth, Deseo, Myrna, Jaehne, Emily, Van Den Buuse, Maarten, Guthridge, Kathryn, Combs, Martin, Spangenberg, German, Quinn, Jane · 2019 · Scientific Reports
  79. Global profiling of lysine acetylation in human histoplasmosis pathogen Histoplasma capsulatum
    Xie, Longxiang, Fang, Wenjie, Deng, Wanyan, Yu, Zhaoxiao, Li, Juan, Chen, Min, Liao, Wanqing, Xie, Jianping, Pan, Weihua · 2016 · The International Journal of Biochemistry &amp; Cell Biology
  80. Metabolites Associated with Early Cognitive Changes Implicated in Alzheimer’s Disease
    Darst, Burcu F., Huo, Zhiguang, Jonaitis, Erin M., Koscik, Rebecca L., Clark, Lindsay R., Lu, Qiongshi, Kremen, William S., Franz, Carol E., Rana, Brinda, Lyons, Michael J. et al. · 2021 · Journal of Alzheimer’s Disease
  81. Evidence for corrin biosynthesis in the last universal common ancestor
    Modjewski, Luca D., Karavaeva, Val, Mrnjavac, Natalia, Knopp, Michael, Martin, William F., Sousa, Filipa L. · 2025 · The FEBS Journal
  82. Genome-Scale Metabolic Model Reconstruction and Investigation into the Fluxome of the Fast-Growing Cyanobacterium <i>Synechococcus</i> sp. PCC 11901
    Ravindran, Somdutt, Hajinajaf, Nima, Kundu, Pritam, Comes, Jackson, Nielsen, David R., Varman, Arul M., Ghosh, Amit · 2024 · ACS Synthetic Biology
  83. csuWGCNA: a combination of signed and unsigned WGCNA to capture negative correlations
    Dai, Rujia, Xia, Yan, Liu, Chunyu, Chen, Chao · 2018
  84. Effects of Functional Bias on Supervised Learning of a Gene Network Model
    Lee, Insuk, Marcotte, Edward M. · 2009 · Methods in Molecular Biology
  85. Network-Free Inference of Knockout Effects in Yeast
    Peleg, Tal, Yosef, Nir, Ruppin, Eytan, Sharan, Roded · 2010 · PLoS Computational Biology
  86. Pathway Analysis Integrating Genome-Wide and Functional Data Identifies <i>PLCG2</i> as a Candidate Gene for Age-Related Macular Degeneration
    Waksmunski, Andrea R., Grunin, Michelle, Kinzy, Tyler G., Igo, Robert P., Haines, Jonathan L., Cooke Bailey, Jessica N., for the International Age-Related Macular Degeneration Genomics Consortium · 2019 · Investigative Opthalmology &amp; Visual Science
  87. Single-cell and spatial detection of senescent cells using DeepScence
    Qu, Yilong, Ji, Beijie, Dong, Runze, Gu, Liangcai, Chan, Cliburn, Xie, Jichun, Glass, Carolyn, Wang, Xiao-Fan, Nixon, Andrew B., Ji, Zhicheng · 2025 · Cell Genomics
  88. CD300E+ macrophages facilitate liver regeneration after splenectomy in decompensated cirrhotic patients
    Yang, Tao, Zhang, Yuan, Duan, Chujun, Liu, Hui, Wang, Dong, Liang, Qingshan, Chen, Xiao, Ma, Jingchang, Cheng, Kun, Chen, Yong et al. · 2025 · Experimental &amp; Molecular Medicine
  89. Network spectra for drug-target identification in complex diseases: new guns against old foes
    Rai, Aparna, Shinde, Pramod, Jalan, Sarika · 2018 · Applied Network Science
  90. MicroRNA Profiling in Aging Brain of PSEN1/PSEN2 Double Knockout Mice
    Ham, Suji, Kim, Tae Kyoo, Lee, Sangjoon, Tang, Ya-Ping, Im, Heh-In · 2018 · Molecular Neurobiology
  91. Molecular Mechanisms of Radiation Resistance in Breast Cancer: A Systematic Review of Radiosensitization Strategies
    Mageau, Emma, Derbowka, Ronan, Dickinson, Noah, Lefort, Natalie, Kovala, A. Thomas, Boreham, Douglas R., Tai, T. C., Thome, Christopher, Tharmalingam, Sujeenthar · 2025 · Current Issues in Molecular Biology
  92. Mechanosensitive ion channel-related genes in hepatocellular carcinoma: Unraveling prognostic genes and their roles in drug resistance and immune modulation
    Huo, Xinyan, Jiang, Shiyu, Wu, Sihuang, Lian, Qinghai, Chen, Hui · 2025 · Liver Research
  93. 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, Zachary, Anderson, David, Cheung, Margaret S., Bohutskyi, Pavlo · 2025 · Frontiers in Microbiology
  94. Bioinformatics analysis of microarray data to reveal the pathogenesis of brain ischemia
    He, Jiaxuan, Gao, Ya, Wu, Gang, Lei, Xiaoming, Zhang, Yong, Pan, Weikang, Yu, Hui · 2018 · Molecular Medicine Reports
  95. Assessment of the safety and efficacy of an oral probiotic-based vaccine against Aspergillus infection in captive-bred Humboldt penguins (Spheniscus humboldti)
    Thorel, Milan, Mateos-Hernandez, Lourdes, Mulot, Baptiste, Azzouni, Mouna Naila, Hodžić, Adnan, Gaillot, Hugues, Ruel, Yannick, Desoubeaux, Guillaume, Delaye, Jean-Baptiste, Obregon, Dasiel et al. · 2022 · Frontiers in Immunology
  96. Short-Term Warming Induces Cyanobacterial Blooms and Antibiotic Resistance in Freshwater Lake, as Revealed by Metagenomics Analysis
    Manna, Bharat, Jay, Emma, Zhang, Wensi, Zhou, Xueyang, Lyu, Boyu, Thomas, Gevargis Muramthookil, Singhal, Naresh · 2024 · Water
  97. Using network extracted ontologies to identify novel genes with roles in appressorium development in the rice blast fungus magnaporthe oryzae
    Ames, Ryan · 2017 · Microorganisms
  98. 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
  99. Metabolic network segmentation: a probabilistic graphical modeling approach to identify the sites and sequential order of metabolic regulation from non-targeted metabolomics data
    Kuehne, Andreas, Mayr, Urs, Sévin, Daniel C., Claassen, Manfred, Zamboni, Nicola · 2017 · PLoS Computational Biology
  100. Whole genome analysis and in vivo safety assessment of probiotic candidate Lactobacillus acidophilus L177
    Liu, Yunjiang, Zheng, Haohong, Wang, Jiali, Xin, Jialiang, Wu, Ruihu, Zhang, Jingyi, Zhong, Zhijun, Liu, Haifeng, Huang, Yixin, Fu, Hualin et al. · 2025 · BMC Microbiology