KEGG: Kyoto Encyclopedia of Genes and Genomes

Cited by (419)

Items 101–200 of 419

1. Critical pathways in cellular senescence and immortalization revealed by gene expression profiling
   Fridman, A L, Tainsky, M A · 2008 · Oncogene
2. Global Functional Atlas of Escherichia coli Encompassing Previously Uncharacterized Proteins
   Hu, Pingzhao, Janga, Sarath Chandra, Babu, Mohan, Díaz-Mejía, J. Javier, Butland, Gareth, Yang, Wenhong, Pogoutse, Oxana, Guo, Xinghua, Phanse, Sadhna, Wong, Peter et al. · 2009 · PLoS Biology
3. Recommendations for the design and analysis of epigenome-wide association studies
   Michels, Karin B, Binder, Alexandra M, Dedeurwaerder, Sarah, Epstein, Charles B, Greally, John M, Gut, Ivo, Houseman, E Andres, Izzi, Benedetta, Kelsey, Karl T, Meissner, Alexander et al. · 2013 · Nature Methods
4. Postmortem Cortex Samples Identify Distinct Molecular Subtypes of ALS: Retrotransposon Activation, Oxidative Stress, and Activated Glia
   Tam, Oliver H., Rozhkov, Nikolay V., Shaw, Regina, Kim, Duyang, Hubbard, Isabel, Fennessey, Samantha, Propp, Nadia, Phatnani, Hemali, Kwan, Justin, Sareen, Dhruv et al. · 2019 · Cell Reports
5. Structural variation in the gut microbiome associates with host health
   Zeevi, David, Korem, Tal, Godneva, Anastasia, Bar, Noam, Kurilshikov, Alexander, Lotan-Pompan, Maya, Weinberger, Adina, Fu, Jingyuan, Wijmenga, Cisca, Zhernakova, Alexandra et al. · 2019 · Nature
6. Optical Pooled Screens in Human Cells
   Feldman, David, Singh, Avtar, Schmid-Burgk, Jonathan L., Carlson, Rebecca J., Mezger, Anja, Garrity, Anthony J., Zhang, Feng, Blainey, Paul C. · 2019 · Cell
7. Gut microbiome correlates of response and toxicity following anti-CD19 CAR T cell therapy
   Smith, Melody, Dai, Anqi, Ghilardi, Guido, Amelsberg, Kimberly V., Devlin, Sean M., Pajarillo, Raymone, Slingerland, John B., Beghi, Silvia, Herrera, Pamela S., Giardina, Paul et al. · 2022 · Nature Medicine
8. A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation
   Brylinski, Michal, Skolnick, Jeffrey · 2008 · Proceedings of the National Academy of Sciences
9. Microbial metabolites control the thymic development of mucosal-associated invariant T cells
   Legoux, François, Bellet, Déborah, Daviaud, Celine, El Morr, Yara, Darbois, Aurelie, Niort, Kristina, Procopio, Emanuele, Salou, Marion, Gilet, Jules, Ryffel, Bernhard et al. · 2019 · Science
10. Human skeletal muscle possesses an epigenetic memory of hypertrophy
    Seaborne, Robert A., Strauss, Juliette, Cocks, Matthew, Shepherd, Sam, O’Brien, Thomas D., van Someren, Ken A., Bell, Phillip G., Murgatroyd, Christopher, Morton, James P., Stewart, Claire E. et al. · 2018 · Scientific Reports
11. Index and biological spectrum of human DNase I hypersensitive sites
    Meuleman, Wouter, Muratov, Alexander, Rynes, Eric, Halow, Jessica, Lee, Kristen, Bates, Daniel, Diegel, Morgan, Dunn, Douglas, Neri, Fidencio, Teodosiadis, Athanasios et al. · 2020 · Nature
12. Morphological, cellular and molecular basis of brain infection in COVID-19 patients
    Crunfli, Fernanda, Carregari, Victor Corasolla, Veras, Flavio Protasio, Vendramini, Pedro Henrique, Valença, Aline Gazzola Fragnani, Antunes, André Saraiva Leão Marcelo, Brandão-Teles, Caroline, da Silva Zuccoli, Giuliana, Reis-de-Oliveira, Guilherme, Silva-Costa, Lícia C. et al. · 2020
13. Impact of Dietary Resistant Starch on the Human Gut Microbiome, Metaproteome, and Metabolome
    Maier, Tanja V., Lucio, Marianna, Lee, Lang Ho, VerBerkmoes, Nathan C., Brislawn, Colin J., Bernhardt, Jörg, Lamendella, Regina, McDermott, Jason E., Bergeron, Nathalie, Heinzmann, Silke S. et al. · 2017 · mBio
14. Chronic stress-induced gut dysfunction exacerbates Parkinson's disease phenotype and pathology in a rotenone-induced mouse model of Parkinson's disease
    Dodiya, Hemraj B., Forsyth, Christopher B., Voigt, Robin M., Engen, Phillip A., Patel, Jinal, Shaikh, Maliha, Green, Stefan J., Naqib, Ankur, Roy, Avik, Kordower, Jeffrey H. et al. · 2020 · Neurobiology of Disease
15. Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae
    Reguly, Teresa, Breitkreutz, Ashton, Boucher, Lorrie, Breitkreutz, Bobby-Joe, Hon, Gary C, Myers, Chad L, Parsons, Ainslie, Friesen, Helena, Oughtred, Rose, Tong, Amy et al. · 2006 · Journal of Biology
16. Bread Affects Clinical Parameters and Induces Gut Microbiome-Associated Personal Glycemic Responses
    Korem, Tal, Zeevi, David, Zmora, Niv, Weissbrod, Omer, Bar, Noam, Lotan-Pompan, Maya, Avnit-Sagi, Tali, Kosower, Noa, Malka, Gal, Rein, Michal et al. · 2017 · Cell Metabolism
17. Single-cell transcriptomics identifies an effectorness gradient shaping the response of CD4+ T cells to cytokines
    Cano-Gamez, Kiki, Soskic, Blagoje, Roumeliotis, Theodoros I., So, Ernest, Smyth, Deborah J., Baldrighi, Marta, Willé, David, Nakic, Nikolina, Esparza-Gordillo, Jorge, Larminie, Christopher G. C. et al. · 2020 · Nature Communications
18. Novel Entries in a Fungal Biofilm Matrix Encyclopedia
    Zarnowski, Robert, Westler, William M., Lacmbouh, Ghislain Ade, Marita, Jane M., Bothe, Jameson R., Bernhardt, Jörg, Lounes-Hadj Sahraoui, Anissa, Fontaine, Joël, Sanchez, Hiram, Hatfield, Ronald D. et al. · 2014 · mBio
19. The signature of maternal rearing in the methylome in rhesus macaque prefrontal cortex and T cells
    Provençal, Nadine, Suderman, Matthew J., Guillemin, Claire, Massart, Renaud, Ruggiero, Angela, Wang, Dongsha, Bennett, Allyson J., Pierre, Peter J., Friedman, David P., Côté, Sylvana M. et al. · 2012 · The Journal of Neuroscience
20. Identification of genetic variants associated with Huntington's disease progression: a genome-wide association study
    Moss, Davina J Hensman, Pardiñas, Antonio F, Langbehn, Douglas, Lo, Kitty, Leavitt, Blair R, Roos, Raymund, Durr, Alexandra, Mead, Simon, Coleman, A, Santos, R Dar et al. · 2017 · The Lancet Neurology
21. Association between fatty acid metabolism in the brain and Alzheimer disease neuropathology and cognitive performance: A nontargeted metabolomic study
    Snowden, Stuart G., Ebshiana, Amera A., Hye, Abdul, An, Yang, Pletnikova, Olga, O’Brien, Richard, Troncoso, John, Legido-Quigley, Cristina, Thambisetty, Madhav · 2017 · PLOS Medicine
22. Gene regulatory networks and their applications: understanding biological and medical problems in terms of networks
    Emmert-Streib, Frank, Dehmer, Matthias, Haibe-Kains, Benjamin · 2014 · Frontiers in Cell and Developmental Biology
23. Proteogenomic Characterization of Human Early-Onset Gastric Cancer
    Mun, Dong-Gi, Bhin, Jinhyuk, Kim, Sangok, Kim, Hyunwoo, Jung, Jae Hun, Jung, Yeonjoo, Jang, Ye Eun, Park, Jong Moon, Kim, Hokeun, Jung, Yeonhwa et al. · 2019 · Cancer Cell
24. Birth mode is associated with earliest strain-conferred gut microbiome functions and immunostimulatory potential
    Wampach, Linda, Heintz-Buschart, Anna, Fritz, Joëlle V., Ramiro-Garcia, Javier, Habier, Janine, Herold, Malte, Narayanasamy, Shaman, Kaysen, Anne, Hogan, Angela H., Bindl, Lutz et al. · 2018 · Nature Communications
25. Wnt-Pathway Activation in Two Molecular Classes of Hepatocellular Carcinoma and Experimental Modulation by Sorafenib
    Lachenmayer, Anja, Alsinet, Clara, Savic, Radoslav, Cabellos, Laia, Toffanin, Sara, Hoshida, Yujin, Villanueva, Augusto, Minguez, Beatriz, Newell, Philippa, Tsai, Hung-Wen et al. · 2012 · Clinical Cancer Research
26. WITHDRAWN—a resource for withdrawn and discontinued drugs
    Siramshetty, Vishal B., Nickel, Janette, Omieczynski, Christian, Gohlke, Bjoern-Oliver, Drwal, Malgorzata N., Preissner, Robert · 2016 · Nucleic Acids Research · Retracted
27. Slow TCA flux and ATP production in primary solid tumours but not metastases
    Bartman, Caroline R., Weilandt, Daniel R., Shen, Yihui, Lee, Won Dong, Han, Yujiao, TeSlaa, Tara, Jankowski, Connor S. R., Samarah, Laith, Park, Noel R., da Silva-Diz, Victoria et al. · 2023 · Nature
28. De novo sequencing and analysis of the American ginseng root transcriptome using a GS FLX Titanium platform to discover putative genes involved in ginsenoside biosynthesis
    Sun, Chao, Li, Ying, Wu, Qiong, Luo, Hongmei, Sun, Yongzhen, Song, Jingyuan, Lui, Edmund MK, Chen, Shilin · 2010 · BMC Genomics
29. In silico method for modelling metabolism and gene product expression at genome scale
    Lerman, Joshua A., Hyduke, Daniel R., Latif, Haythem, Portnoy, Vasiliy A., Lewis, Nathan E., Orth, Jeffrey D., Schrimpe-Rutledge, Alexandra C., Smith, Richard D., Adkins, Joshua N., Zengler, Karsten et al. · 2012 · Nature Communications
30. Time of exercise specifies the impact on muscle metabolic pathways and systemic energy homeostasis
    Sato, Shogo, Basse, Astrid Linde, Schönke, Milena, Chen, Siwei, Samad, Muntaha, Altıntaş, Ali, Laker, Rhianna C., Dalbram, Emilie, Barrès, Romain, Baldi, Pierre et al. · 2019 · Cell Metabolism
31. Reconstructing organisms in silico: genome-scale models and their emerging applications
    Fang, Xin, Lloyd, Colton J., Palsson, Bernhard O. · 2020 · Nature Reviews Microbiology
32. Diverse Genome-wide Association Studies Associate the IL12/IL23 Pathway with Crohn Disease
    Wang, Kai, Zhang, Haitao, Kugathasan, Subra, Annese, Vito, Bradfield, Jonathan P., Russell, Richard K., Sleiman, Patrick M.A., Imielinski, Marcin, Glessner, Joseph, Hou, Cuiping et al. · 2009 · The American Journal of Human Genetics
33. Disease severity-specific neutrophil signatures in blood transcriptomes stratify COVID-19 patients
    German COVID-19 Omics Initiative (DeCOI), Aschenbrenner, Anna C., Mouktaroudi, Maria, Krämer, Benjamin, Oestreich, Marie, Antonakos, Nikolaos, Nuesch-Germano, Melanie, Gkizeli, Konstantina, Bonaguro, Lorenzo, Reusch, Nico et al. · 2021 · Genome Medicine
34. Inhibition of mTOR induces a paused pluripotent state
    Bulut-Karslioglu, Aydan, Biechele, Steffen, Jin, Hu, Macrae, Trisha A., Hejna, Miroslav, Gertsenstein, Marina, Song, Jun S., Ramalho-Santos, Miguel · 2016 · Nature
35. Candida albicans biofilm–induced vesicles confer drug resistance through matrix biogenesis
    Zarnowski, Robert, Sanchez, Hiram, Covelli, Antonio S., Dominguez, Eddie, Jaromin, Anna, Bernhardt, Jörg, Mitchell, Kaitlin F., Heiss, Christian, Azadi, Parastoo, Mitchell, Aaron et al. · 2018 · PLOS Biology
36. Mesenchymal stem cell-derived exosomes: a new therapeutic approach to osteoarthritis?
    Mianehsaz, Elaheh, Mirzaei, Hamid Reza, Mahjoubin-Tehran, Maryam, Rezaee, Alireza, Sahebnasagh, Roxana, Pourhanifeh, Mohammad Hossein, Mirzaei, Hamed, Hamblin, Michael R. · 2019 · Stem Cell Research & Therapy
37. Comparative genome-scale modelling of <i>Staphylococcus aureus</i> strains identifies strain-specific metabolic capabilities linked to pathogenicity
    Bosi, Emanuele, Monk, Jonathan M., Aziz, Ramy K., Fondi, Marco, Nizet, Victor, Palsson, Bernhard Ø. · 2016 · Proceedings of the National Academy of Sciences
38. Genomic diversity and evolution of the head crest in the rock pigeon
    Shapiro, Michael D., Kronenberg, Zev, Li, Cai, Domyan, Eric T., Pan, Hailin, Campbell, Michael, Tan, Hao, Huff, Chad D., Hu, Haofu, Vickrey, Anna I. et al. · 2013 · Science
39. Combining metagenomics, metatranscriptomics and viromics to explore novel microbial interactions: towards a systems-level understanding of human microbiome
    Bikel, Shirley, Valdez-Lara, Alejandra, Cornejo-Granados, Fernanda, Rico, Karina, Canizales-Quinteros, Samuel, Soberón, Xavier, Del Pozo-Yauner, Luis, Ochoa-Leyva, Adrián · 2015 · Computational and Structural Biotechnology Journal
40. TimeDelay-ARACNE: reverse engineering of gene networks from time-course data by an information theoretic approach
    Zoppoli, Pietro, Morganella, Sandro, Ceccarelli, Michele · 2010 · BMC Bioinformatics
41. Prolonged hypernutrition impairs TREM2-dependent efferocytosis to license chronic liver inflammation and NASH development
    Wang, Xiaochen, He, Qifeng, Zhou, Chuanli, Xu, Yueyuan, Liu, Danhui, Fujiwara, Naoto, Kubota, Naoto, Click, Arielle, Henderson, Polly, Vancil, Janiece et al. · 2023 · Immunity
42. Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models
    Heckmann, David, Lloyd, Colton J., Mih, Nathan, Ha, Yuanchi, Zielinski, Daniel C., Haiman, Zachary B., Desouki, Abdelmoneim Amer, Lercher, Martin J., Palsson, Bernhard O. · 2018 · Nature Communications
43. Bacteria Boost Mammalian Host NAD Metabolism by Engaging the Deamidated Biosynthesis Pathway
    Shats, Igor, Williams, Jason G., Liu, Juan, Makarov, Mikhail V., Wu, Xiaoyue, Lih, Fred B., Deterding, Leesa J., Lim, Chaemin, Xu, Xiaojiang, Randall, Thomas A. et al. · 2020 · Cell Metabolism
44. A Systems Biology Approach for the Investigation of the Heparin/Heparan Sulfate Interactome
    Ori, Alessandro, Wilkinson, Mark C., Fernig, David G. · 2011 · Journal of Biological Chemistry
45. Guidance for RNA-seq co-expression network construction and analysis: safety in numbers
    Ballouz, S., Verleyen, W., Gillis, J. · 2015 · Bioinformatics
46. Genomic epidemiology of the UK outbreak of the emerging human fungal pathogen <i>Candida auris</i>
    Rhodes, Johanna, Abdolrasouli, Alireza, Farrer, Rhys A., Cuomo, Christina A., Aanensen, David M., Armstrong-James, Darius, Fisher, Matthew C., Schelenz, Silke · 2018 · Emerging Microbes &amp; Infections
47. Human Cancer Protein-Protein Interaction Network: A Structural Perspective
    Kar, Gozde, Gursoy, Attila, Keskin, Ozlem · 2009 · PLoS Computational Biology
48. Blood microRNA changes in depressed patients during antidepressant treatment
    Bocchio-Chiavetto, Luisella, Maffioletti, Elisabetta, Bettinsoli, Paola, Giovannini, Caterina, Bignotti, Stefano, Tardito, Daniela, Corrada, Dario, Milanesi, Luciano, Gennarelli, Massimo · 2013 · European Neuropsychopharmacology
49. Variation in Rural African Gut Microbiota Is Strongly Correlated with Colonization by Entamoeba and Subsistence
    Morton, Elise R., Lynch, Joshua, Froment, Alain, Lafosse, Sophie, Heyer, Evelyne, Przeworski, Molly, Blekhman, Ran, Ségurel, Laure · 2015 · PLOS Genetics
50. New applications of synthetic biology tools for cyanobacterial metabolic engineering
    Santos-Merino, María, Singh, Amit K., Ducat, Daniel C. · 2019 · Frontiers in Bioengineering and Biotechnology
51. MyCompoundID: using an evidence-based metabolome library for metabolite identification
    Li, Liang, Li, Ronghong, Zhou, Jianjun, Zuniga, Azeret, Stanislaus, Avalyn E., Wu, Yiman, Huan, Tao, Zheng, Jiamin, Shi, Yi, Wishart, David S. et al. · 2013 · Analytical Chemistry
52. Toward better drug discovery with knowledge graph
    Zeng, Xiangxiang, Tu, Xinqi, Liu, Yuansheng, Fu, Xiangzheng, Su, Yansen · 2022 · Current Opinion in Structural Biology
53. Genome-Wide Meta-Analysis Identifies Regions on 7p21 (AHR) and 15q24 (CYP1A2) As Determinants of Habitual Caffeine Consumption
    Cornelis, Marilyn C., Monda, Keri L., Yu, Kai, Paynter, Nina, Azzato, Elizabeth M., Bennett, Siiri N., Berndt, Sonja I., Boerwinkle, Eric, Chanock, Stephen, Chatterjee, Nilanjan et al. · 2011 · PLoS Genetics
54. Remnants of an Ancient Metabolism without Phosphate
    Goldford, Joshua E., Hartman, Hyman, Smith, Temple F., Segrè, Daniel · 2017 · Cell
55. Biological aging and the human gut microbiota
    Maffei, Vincent J, Kim, Sangkyu, Blanchard, Eugene, Luo, Meng, Jazwinski, S Michal, Taylor, Christopher M, Welsh, David A · 2017 · The Journals of Gerontology Series A
56. Guild-based analysis for understanding gut microbiome in human health and diseases
    Wu, Guojun, Zhao, Naisi, Zhang, Chenhong, Lam, Yan Y., Zhao, Liping · 2021 · Genome Medicine
57. MSNovelist: de novo structure generation from mass spectra
    Stravs, Michael A., Dührkop, Kai, Böcker, Sebastian, Zamboni, Nicola · 2022 · Nature Methods
58. Diverse human extracellular RNAs are widely detected in human plasma
    Freedman, Jane E., Gerstein, Mark, Mick, Eric, Rozowsky, Joel, Levy, Daniel, Kitchen, Robert, Das, Saumya, Shah, Ravi, Danielson, Kirsty, Beaulieu, Lea et al. · 2016 · Nature Communications
59. Systematic determination of the mitochondrial proportion in human and mice tissues for single-cell RNA-sequencing data quality control
    Osorio, Daniel, Cai, James J · 2021 · Bioinformatics
60. Transcriptional characterizations of differences between eutopic and ectopic endometrium
    Wu, Yan, Kajdacsy-Balla, André, Strawn, Estil, Basir, Zainab, Halverson, Gloria, Jailwala, Parthav, Wang, Yuedong, Wang, Xujing, Ghosh, Soumitra, Guo, Sun-Wei · 2006 · Endocrinology
61. Novel loci and pathways significantly associated with longevity
    Zeng, Yi, Nie, Chao, Min, Junxia, Liu, Xiaomin, Li, Mengmeng, Chen, Huashuai, Xu, Hanshi, Wang, Mingbang, Ni, Ting, Li, Yang et al. · 2016 · Scientific Reports
62. Genomic insights into population history and biological adaptation in Oceania
    Choin, Jeremy, Mendoza-Revilla, Javier, Arauna, Lara R., Cuadros-Espinoza, Sebastian, Cassar, Olivier, Larena, Maximilian, Ko, Albert Min-Shan, Harmant, Christine, Laurent, Romain, Verdu, Paul et al. · 2021 · Nature
63. Regulators of gut motility revealed by a gnotobiotic model of diet-microbiome interactions related to travel
    Dey, Neelendu, Wagner, Vitas E., Blanton, Laura V., Cheng, Jiye, Fontana, Luigi, Haque, Rashidul, Ahmed, Tahmeed, Gordon, Jeffrey I. · 2015 · Cell
64. Gene2Vec: Distributed Representation of Genes Based on Co-Expression
    Du, Jingcheng, Jia, Peilin, Dai, Yulin, Tao, Cui, Zhao, Zhongming, Zhi, Degui · 2018
65. Spatial sorting enables comprehensive characterization of liver zonation
    Ben-Moshe, Shani, Shapira, Yonatan, Moor, Andreas E., Halpern, Keren Bahar, Itzkovitz, Shalev · 2019
66. Spatial sorting enables comprehensive characterization of liver zonation
    Ben-Moshe, Shani, Shapira, Yonatan, Moor, Andreas E., Manco, Rita, Veg, Tamar, Bahar Halpern, Keren, Itzkovitz, Shalev · 2019 · Nature Metabolism
67. Cooperative Metabolic Adaptations in the Host Can Favor Asymptomatic Infection and Select for Attenuated Virulence in an Enteric Pathogen
    Sanchez, Karina K., Chen, Grischa Y., Schieber, Alexandria M. Palaferri, Redford, Samuel E., Shokhirev, Maxim N., Leblanc, Mathias, Lee, Yujung M., Ayres, Janelle S. · 2018 · Cell
68. Mining the Unknown: A Systems Approach to Metabolite Identification Combining Genetic and Metabolic Information
    Krumsiek, Jan, Suhre, Karsten, Evans, Anne M., Mitchell, Matthew W., Mohney, Robert P., Milburn, Michael V., Wägele, Brigitte, Römisch-Margl, Werner, Illig, Thomas, Adamski, Jerzy et al. · 2012 · PLoS Genetics
69. Insights into TREM2 biology by network analysis of human brain gene expression data
    Forabosco, Paola, Ramasamy, Adaikalavan, Trabzuni, Daniah, Walker, Robert, Smith, Colin, Bras, Jose, Levine, Adam P., Hardy, John, Pocock, Jennifer M., Guerreiro, Rita et al. · 2013 · Neurobiology of Aging
70. Atlas of exercise metabolism reveals time-dependent signatures of metabolic homeostasis
    Sato, Shogo, Dyar, Kenneth A., Treebak, Jonas T., Jepsen, Sara L., Ehrlich, Amy M., Ashcroft, Stephen P., Trost, Kajetan, Kunzke, Thomas, Prade, Verena M., Small, Lewin et al. · 2022 · Cell Metabolism
71. Dysbiosis in the inflamed intestine: Chance favors the prepared microbe
    Winter, Sebastian E, Bäumler, Andreas J · 2014 · Gut Microbes
72. Single cell molecular alterations reveal target cells and pathways of concussive brain injury
    Arneson, Douglas, Zhang, Guanglin, Ying, Zhe, Zhuang, Yumei, Byun, Hyae Ran, Ahn, In Sook, Gomez-Pinilla, Fernando, Yang, Xia · 2018 · Nature Communications
73. The Mouse Gastrointestinal Bacteria Catalogue enables translation between the mouse and human gut microbiotas via functional mapping
    Beresford-Jones, Benjamin S., Forster, Samuel C., Stares, Mark D., Notley, George, Viciani, Elisa, Browne, Hilary P., Boehmler, Daniel J., Soderholm, Amelia T., Kumar, Nitin, Vervier, Kevin et al. · 2022 · Cell Host &amp; Microbe
74. A general model to predict small molecule substrates of enzymes based on machine and deep learning
    Kroll, Alexander, Ranjan, Sahasra, Engqvist, Martin K. M., Lercher, Martin J. · 2023 · Nature Communications
75. Childhood abuse is associated with methylation of multiple loci in adult DNA
    Suderman, Matthew, Borghol, Nada, Pappas, Jane J, Pinto Pereira, Snehal M, Pembrey, Marcus, Hertzman, Clyde, Power, Chris, Szyf, Moshe · 2014 · BMC Medical Genomics
76. Turnover number predictions for kinetically uncharacterized enzymes using machine and deep learning
    Kroll, Alexander, Rousset, Yvan, Hu, Xiao-Pan, Liebrand, Nina A., Lercher, Martin J. · 2023 · Nature Communications
77. Phenol-Explorer 2.0: a major update of the Phenol-Explorer database integrating data on polyphenol metabolism and pharmacokinetics in humans and experimental animals
    Rothwell, J. A., Urpi-Sarda, M., Boto-Ordonez, M., Knox, C., Llorach, R., Eisner, R., Cruz, J., Neveu, V., Wishart, D., Manach, C. et al. · 2012 · Database
78. Neuronal ApoE upregulates MHC-I expression to drive selective neurodegeneration in Alzheimer’s disease
    Zalocusky, Kelly A., Najm, Ramsey, Taubes, Alice L., Hao, Yanxia, Yoon, Seo Yeon, Koutsodendris, Nicole, Nelson, Maxine R., Rao, Antara, Bennett, David A., Bant, Jason et al. · 2021 · Nature Neuroscience
79. A Comprehensive Mouse Transcriptomic BodyMap across 17 Tissues by RNA-seq
    Li, Bin, Qing, Tao, Zhu, Jinhang, Wen, Zhuo, Yu, Ying, Fukumura, Ryutaro, Zheng, Yuanting, Gondo, Yoichi, Shi, Leming · 2017 · Scientific Reports
80. Reconciled rat and human metabolic networks for comparative toxicogenomics and biomarker predictions
    Blais, Edik M., Rawls, Kristopher D., Dougherty, Bonnie V., Li, Zhuo I., Kolling, Glynis L., Ye, Ping, Wallqvist, Anders, Papin, Jason A. · 2017 · Nature Communications
81. Profiling senescent cells in human brains reveals neurons with CDKN2D/p19 and tau neuropathology
    Dehkordi, Shiva Kazempour, Walker, Jamie, Sah, Eric, Bennett, Emma, Atrian, Farzaneh, Frost, Bess, Woost, Benjamin, Bennett, Rachel E., Orr, Timothy C., Zhou, Yingyue et al. · 2021 · Nature Aging
82. Oil accumulation mechanisms of the oleaginous microalga Chlorella protothecoides revealed through its genome, transcriptomes, and proteomes
    Gao, Chunfang, Wang, Yun, Shen, Yue, Yan, Dong, He, Xi, Dai, Junbiao, Wu, Qingyu · 2014 · BMC Genomics
83. Heterogeneous Network Edge Prediction: A Data Integration Approach to Prioritize Disease-Associated Genes
    Himmelstein, Daniel S., Baranzini, Sergio E. · 2015 · PLOS Computational Biology
84. Probiotic Bifidobacterium longum alters gut luminal metabolism through modification of the gut microbial community
    Sugahara, Hirosuke, Odamaki, Toshitaka, Fukuda, Shinji, Kato, Tamotsu, Xiao, Jin-zhong, Abe, Fumiaki, Kikuchi, Jun, Ohno, Hiroshi · 2015 · Scientific Reports
85. Characterizing acetogenic metabolism using a genome-scale metabolic reconstruction of Clostridium ljungdahlii
    Nagarajan, Harish, Sahin, Merve, Nogales, Juan, Latif, Haythem, Lovley, Derek R, Ebrahim, Ali, Zengler, Karsten · 2013 · Microbial Cell Factories
86. Dissection of Regulatory Networks that Are Altered in Disease via Differential Co-expression
    Amar, David, Safer, Hershel, Shamir, Ron · 2013 · PLoS Computational Biology
87. Prolonged use of a proton pump inhibitor reduces microbial diversity: implications for Clostridium difficile susceptibility
    Seto, Charlie T, Jeraldo, Patricio, Orenstein, Robert, Chia, Nicholas, DiBaise, John K · 2014 · Microbiome
88. Mitochondrial CoQ deficiency is a common driver of mitochondrial oxidants and insulin resistance
    Fazakerley, Daniel J, Chaudhuri, Rima, Yang, Pengyi, Maghzal, Ghassan J, Thomas, Kristen C, Krycer, James R, Humphrey, Sean J, Parker, Benjamin L, Fisher-Wellman, Kelsey H, Meoli, Christopher C et al. · 2018 · eLife
89. Systematic review and analysis of human proteomics aging studies unveils a novel proteomic aging clock and identifies key processes that change with age
    Johnson, Adiv A., Shokhirev, Maxim N., Wyss-Coray, Tony, Lehallier, Benoit · 2020 · Ageing Research Reviews
90. Elimination of p19ARF-expressing cells enhances pulmonary function in mice
    Hashimoto, Michihiro, Asai, Azusa, Kawagishi, Hiroyuki, Mikawa, Ryuta, Iwashita, Yuji, Kanayama, Kazuki, Sugimoto, Kazushi, Sato, Tadashi, Maruyama, Mitsuo, Sugimoto, Masataka · 2016 · JCI Insight
91. Dietary heme induces gut dysbiosis, aggravates colitis, and potentiates the development of adenomas in mice
    Constante, Marco, Fragoso, Gabriela, Calvé, Annie, Samba-Mondonga, Macha, Santos, Manuela M. · 2017 · Frontiers in Microbiology
92. Meta-analytic support vector machine for integrating multiple omics data
    Kim, SungHwan, Jhong, Jae-Hwan, Lee, JungJun, Koo, Ja-Yong · 2017 · BioData Mining
93. CowPI: a rumen microbiome focussed version of the PICRUSt functional inference software
    Wilkinson, Toby J., Huws, Sharon A., Edwards, Joan E., Kingston-Smith, Alison H., Siu-Ting, Karen, Hughes, Martin, Rubino, Francesco, Friedersdorff, Maximillian, Creevey, Christopher J. · 2018 · Frontiers in Microbiology
94. Genetic Determinants of Depression: Recent Findings and Future Directions
    Dunn, Erin C., Brown, Ruth C., Dai, Yael, Rosand, Jonathan, Nugent, Nicole R., Amstadter, Ananda B., Smoller, Jordan W. · 2015 · Harvard Review of Psychiatry
95. GWAS for executive function and processing speed suggests involvement of the CADM2 gene
    Ibrahim-Verbaas, C A, Bressler, J, Debette, S, Schuur, M, Smith, A V, Bis, J C, Davies, G, Trompet, S, Smith, J A, Wolf, C et al. · 2016 · Molecular Psychiatry
96. A clinician's guide to microbiome analysis
    Claesson, Marcus J., Clooney, Adam G., O'Toole, Paul W. · 2017 · Nature Reviews Gastroenterology &amp; Hepatology
97. Obesity impairs short-term and working memory through gut microbial metabolism of aromatic amino acids
    Arnoriaga-Rodríguez, María, Mayneris-Perxachs, Jordi, Burokas, Aurelijus, Contreras-Rodríguez, Oren, Blasco, Gerard, Coll, Clàudia, Biarnés, Carles, Miranda-Olivos, Romina, Latorre, Jèssica, Moreno-Navarrete, José-Maria et al. · 2020 · Cell Metabolism
98. Development of an in vitro human liver system for interrogating nonalcoholic steatohepatitis
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