KEGG as a reference resource for gene and protein annotation

Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences

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UniProt: a hub for protein information

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KAAS: an automatic genome annotation and pathway reconstruction server

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Data, information, knowledge and principle: back to metabolism in KEGG

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Updated Functional Classification of β-Lactamases

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The ncbi taxonomy database

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NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy

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GenBank

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Update on RefSeq microbial genomes resources

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Fifty‐five years of enzyme classification: advances and difficulties

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KEGG: new perspectives on genomes, pathways, diseases and drugs

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The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets

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Genetic meta-analysis of diagnosed Alzheimer’s disease identifies new risk loci and implicates Aβ, tau, immunity and lipid processing

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Formation of propionate and butyrate by the human colonic microbiota

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Genomic atlas of the human plasma proteome

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Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors

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The neuroactive potential of the human gut microbiota in quality of life and depression

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Computational correction of copy number effect improves specificity of CRISPR-Cas9 essentiality screens in cancer cells

Meyers, R. M., Bryan, J. G., McFarland, J. M., Weir, B. A., Sizemore, A. E., Xu, H., Dharia, N. V., Montgomery, P. G., Cowley, G. S., Pantel, S., et al. (2017) · Nature Genetics · doi:10.1038/ng.3984 · Cited by 1,952

Species-level functional profiling of metagenomes and metatranscriptomes

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Common schizophrenia alleles are enriched in mutation-intolerant genes and in regions under strong background selection

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CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning

Chklovski, A., Parks, D. H., Woodcroft, B. J., & Tyson, G. W. (2023) · Nature Methods · doi:10.1038/s41592-023-01940-w · Cited by 1,705

Distinct Immune Cell Populations Define Response to Anti-PD-1 Monotherapy and Anti-PD-1/Anti-CTLA-4 Combined Therapy

Gide, T. N., Quek, C., Menzies, A. M., Tasker, A. T., Shang, P., Holst, J., Madore, J., Lim, S. Y., Velickovic, R., Wongchenko, M., et al. (2019) · Cancer Cell · doi:10.1016/j.ccell.2019.01.003 · Cited by 1,047

OpenCell: Endogenous tagging for the cartography of human cellular organization

Cho, N. H., Cheveralls, K. C., Brunner, A.-D., Kim, K., Michaelis, A. C., Raghavan, P., Kobayashi, H., Savy, L., Li, J. Y., Canaj, H., et al. (2022) · Science · doi:10.1126/science.abi6983 · Cited by 567

Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum

Shen, X.-X., Opulente, D. A., Kominek, J., Zhou, X., Steenwyk, J. L., Buh, K. V., Haase, M. A. B., Wisecaver, J. H., Wang, M., Doering, D. T., et al. (2018) · Cell · doi:10.1016/j.cell.2018.10.023 · Cited by 619

Dietary emulsifiers directly alter human microbiota composition and gene expression ex vivo potentiating intestinal inflammation

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Microbiota-Derived Metabolites Suppress Arthritis by Amplifying Aryl-Hydrocarbon Receptor Activation in Regulatory B Cells

Rosser, E. C., Piper, C. J. M., Matei, D. E., Blair, P. A., Rendeiro, A. F., Orford, M., Alber, D. G., Krausgruber, T., Catalan, D., Klein, N., et al. (2020) · Cell Metabolism · doi:10.1016/j.cmet.2020.03.003 · Cited by 579

MGnify: the microbiome analysis resource in 2020

Mitchell, A. L., Almeida, A., Beracochea, M., Boland, M., Burgin, J., Cochrane, G., Crusoe, M. R., Kale, V., Potter, S. C., Richardson, L. J., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz1035 · Cited by 562

Genome sequencing analysis identifies new loci associated with Lewy body dementia and provides insights into its genetic architecture

Chia, R., Sabir, M. S., Bandres-Ciga, S., Saez-Atienzar, S., Reynolds, R. H., Gustavsson, E., Walton, R. L., Ahmed, S., Viollet, C., Ding, J., et al. (2021) · Nature Genetics · doi:10.1038/s41588-021-00785-3 · Cited by 438

Cross-cohort gut microbiome associations with immune checkpoint inhibitor response in advanced melanoma

Lee, K. A., Thomas, A. M., Bolte, L. A., Björk, J. R., de Ruijter, L. K., Armanini, F., Asnicar, F., Blanco-Miguez, A., Board, R., Calbet-Llopart, N., et al. (2022) · Nature Medicine · doi:10.1038/s41591-022-01695-5 · Cited by 464

Extremotolerant tardigrade genome and improved radiotolerance of human cultured cells by tardigrade-unique protein

Hashimoto, T., Horikawa, D. D., Saito, Y., Kuwahara, H., Kozuka-Hata, H., Shin-I, T., Minakuchi, Y., Ohishi, K., Motoyama, A., Aizu, T., et al. (2016) · Nature Communications · doi:10.1038/ncomms12808 · Cited by 394

Unraveling gut microbiota in Parkinson's disease and atypical parkinsonism

Barichella, M., Severgnini, M., Cilia, R., Cassani, E., Bolliri, C., Caronni, S., Ferri, V., Cancello, R., Ceccarani, C., Faierman, S., et al. (2019) · Movement Disorders · doi:10.1002/mds.27581 · Cited by 393

Tubular cell and keratinocyte single-cell transcriptomics applied to lupus nephritis reveal type I IFN and fibrosis relevant pathways

the Accelerating Medicines Partnership Rheumatoid Arthritis and Systemic Lupus Erythematosus (AMP RA/SLE) Consortium, Der, E., Suryawanshi, H., Morozov, P., Kustagi, M., Goilav, B., Ranabothu, S., Izmirly, P., Clancy, R., Belmont, H. M., et al. (2019) · Nature Immunology · doi:10.1038/s41590-019-0386-1 · Cited by 403

An engineered E. coli Nissle improves hyperammonemia and survival in mice and shows dose-dependent exposure in healthy humans

Kurtz, C. B., Millet, Y. A., Puurunen, M. K., Perreault, M., Charbonneau, M. R., Isabella, V. M., Kotula, J. W., Antipov, E., Dagon, Y., Denney, W. S., et al. (2019) · Science Translational Medicine · doi:10.1126/scitranslmed.aau7975 · Cited by 399

High-confidence structural annotation of metabolites absent from spectral libraries

Hoffmann, M. A., Nothias, L.-F., Ludwig, M., Fleischauer, M., Gentry, E. C., Witting, M., Dorrestein, P. C., Dührkop, K., & Böcker, S. (2022) · Nature Biotechnology · doi:10.1038/s41587-021-01045-9 · Cited by 388

The Gut Microbiome Is Associated with Clinical Response to Anti–PD-1/PD-L1 Immunotherapy in Gastrointestinal Cancer

Peng, Z., Cheng, S., Kou, Y., Wang, Z., Jin, R., Hu, H., Zhang, X., Gong, J.-F., Li, J., Lu, M., et al. (2020) · Cancer Immunology Research · doi:10.1158/2326-6066.cir-19-1014 · Cited by 361

Human skeletal muscle possesses an epigenetic memory of hypertrophy

Seaborne, R. A., Strauss, J., Cocks, M., Shepherd, S., O’Brien, T. D., van Someren, K. A., Bell, P. G., Murgatroyd, C., Morton, J. P., Stewart, C. E., et al. (2018) · Scientific Reports · doi:10.1038/s41598-018-20287-3 · Cited by 334

The ketogenic diet influences taxonomic and functional composition of the gut microbiota in children with severe epilepsy

Lindefeldt, M., Eng, A., Darban, H., Bjerkner, A., Zetterström, C. K., Allander, T., Andersson, B., Borenstein, E., Dahlin, M., & Prast-Nielsen, S. (2019) · npj Biofilms and Microbiomes · doi:10.1038/s41522-018-0073-2 · Cited by 310

Time of exercise specifies the impact on muscle metabolic pathways and systemic energy homeostasis

Sato, S., Basse, A. L., Schönke, M., Chen, S., Samad, M., Altıntaş, A., Laker, R. C., Dalbram, E., Barrès, R., Baldi, P., et al. (2019) · Cell Metabolism · doi:10.1016/j.cmet.2019.03.013 · Cited by 298

Candida albicans biofilm–induced vesicles confer drug resistance through matrix biogenesis

Zarnowski, R., Sanchez, H., Covelli, A. S., Dominguez, E., Jaromin, A., Bernhardt, J., Mitchell, K. F., Heiss, C., Azadi, P., Mitchell, A., et al. (2018) · PLOS Biology · doi:10.1371/journal.pbio.2006872 · Cited by 260

Gut Microbiota Features in Young Children With Autism Spectrum Disorders

Coretti, L., Paparo, L., Riccio, M. P., Amato, F., Cuomo, M., Natale, A., Borrelli, L., Corrado, G., De Caro, C., Comegna, M., et al. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.03146 · Cited by 266

Structure of the bacterial ribosome at 2 Å resolution

Watson, Z. L., Ward, F. R., Méheust, R., Ad, O., Schepartz, A., Banfield, J. F., & Cate, J. H. (2020) · eLife · doi:10.7554/elife.60482 · Cited by 263

Insect-based diet, a promising nutritional source, modulates gut microbiota composition and SCFAs production in laying hens.

Borrelli, L., Coretti, L., Dipineto, L., Bovera, F., Menna, F., Chiariotti, L., Nizza, A., Lembo, F., & Fioretti, A. (2017) · Scientific Reports · doi:10.1038/s41598-017-16560-6 · Cited by 263

Integrative modeling of gene and genome evolution roots the archaeal tree of life

Williams, T. A., Szöllősi, G. J., Spang, A., Foster, P. G., Heaps, S. E., Boussau, B., Ettema, T. J. G., & Embley, T. M. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1618463114 · Cited by 233

Large-scale plasma proteomic analysis identifies proteins and pathways associated with dementia risk

Walker, K. A., Chen, J., Zhang, J., Fornage, M., Yang, Y., Zhou, L., Grams, M. E., Tin, A., Daya, N., Hoogeveen, R. C., et al. (2021) · Nature Aging · doi:10.1038/s43587-021-00064-0 · Cited by 212

Genetic Screen for Cell Fitness in High or Low Oxygen Highlights Mitochondrial and Lipid Metabolism

Jain, I. H., Calvo, S. E., Markhard, A. L., Skinner, O. S., To, T.-L., Ast, T., & Mootha, V. K. (2020) · Cell · doi:10.1016/j.cell.2020.03.029 · Cited by 224

The BRENDA enzyme information system–From a database to an expert system

Schomburg, I., Jeske, L., Ulbrich, M., Placzek, S., Chang, A., & Schomburg, D. (2017) · Journal of Biotechnology · doi:10.1016/j.jbiotec.2017.04.020 · Cited by 222

Impact of CHO Metabolism on Cell Growth and Protein Production: An Overview of Toxic and Inhibiting Metabolites and Nutrients

Pereira, S., Kildegaard, H. F., & Andersen, M. R. (2018) · Biotechnology Journal · doi:10.1002/biot.201700499 · Cited by 214

Trem2 promotes anti-inflammatory responses in microglia and is suppressed under pro-inflammatory conditions

Liu, W., Taso, O., Wang, R., Bayram, S., Graham, A. C., Garcia-Reitboeck, P., Mallach, A., Andrews, W. D., Piers, T. M., Botia, J. A., et al. (2020) · Human Molecular Genetics · doi:10.1093/hmg/ddaa209 · Cited by 214

Essential metabolism for a minimal cell

Breuer, M., Earnest, E. E., Merryman, C., Wise, K. S., Sun, L., Lynott, M. R., Hutchison, C. A., Smith, H. O., Lapek, J. D., Gonzalez, D. J., et al. (2019) · eLife · doi:10.7554/elife.36842 · Cited by 190

Characterization of gut microbiota composition and functions in patients with chronic alcohol overconsumption

Bjørkhaug, S. T., Aanes, H., Neupane, S. P., Bramness, J. G., Malvik, S., Henriksen, C., Skar, V., Medhus, A. W., & Valeur, J. (2019) · Gut Microbes · doi:10.1080/19490976.2019.1580097 · Cited by 205

Longitudinal multi-omics analyses link gut microbiome dysbiosis with recurrent urinary tract infections in women

Worby, C. J., Schreiber, H. L., Straub, T. J., van Dijk, L. R., Bronson, R. A., Olson, B. S., Pinkner, J. S., Obernuefemann, C. L. P., Muñoz, V. L., Paharik, A. E., et al. (2022) · Nature Microbiology · doi:10.1038/s41564-022-01107-x · Cited by 188

A network medicine approach to investigation and population-based validation of disease manifestations and drug repurposing for COVID-19

Zhou, Y., Hou, Y., Shen, J., Mehra, R., Kallianpur, A., Culver, D. A., Gack, M. U., Farha, S., Zein, J., Comhair, S., et al. (2020) · PLoS Biology · doi:10.1371/journal.pbio.3000970 · Cited by 180

Potential and active functions in the gut microbiota of a healthy human cohort

Tanca, A., Abbondio, M., Palomba, A., Fraumene, C., Manghina, V., Cucca, F., Fiorillo, E., & Uzzau, S. (2017) · Microbiome · doi:10.1186/s40168-017-0293-3 · Cited by 172

A landscape of metabolic variation across tumor types

Reznik, E., Luna, A., Aksoy, B. A., Liu, E. M., La, K., Ostrovnaya, I., Creighton, C. J., Hakimi, A. A., & Sander, C. (2018) · Cell Systems · doi:10.1016/j.cels.2017.12.014 · Cited by 172

Formulation, construction and analysis of kinetic models of metabolism: A review of modelling frameworks

Saa, P. A., & Nielsen, L. K. (2017) · Biotechnology Advances · doi:10.1016/j.biotechadv.2017.09.005 · Cited by 166

Extensive loss of cell-cycle and DNA repair genes in an ancient lineage of bipolar budding yeasts

Steenwyk, J. L., Opulente, D. A., Kominek, J., Shen, X.-X., Zhou, X., Labella, A. L., Bradley, N. P., Eichman, B. F., Čadež, N., Libkind, D., et al. (2019) · PLoS Biology · doi:10.1371/journal.pbio.3000255 · Cited by 162

A Transcriptomic Method to Determine Airway Immune Dysfunction in T2-High and T2-Low Asthma

Peters, M. C., Ringel, L., Dyjack, N., Herrin, R., Woodruff, P. G., Rios, C., O’Connor, B., Fahy, J. V., & Seibold, M. A. (2019) · American Journal of Respiratory and Critical Care Medicine · doi:10.1164/rccm.201807-1291oc · Cited by 151

Proteomics analysis of plasma from middle-aged adults identifies protein markers of dementia risk in later life

Walker, K. A., Chen, J., Shi, L., Yang, Y., Fornage, M., Zhou, L., Schlosser, P., Surapaneni, A., Grams, M. E., Duggan, M. R., et al. (2023) · Science Translational Medicine · doi:10.1126/scitranslmed.adf5681 · Cited by 148

DNA methylation across the genome in aged human skeletal muscle tissue and muscle-derived cells: The role of HOX genes and physical activity

Turner, D. C., Gorski, P. P., Maasar, M. F., Seaborne, R. A., Baumert, P., Brown, A. D., Kitchen, M. O., Erskine, R. M., Dos-Remedios, I., Voisin, S., et al. (2020) · Scientific Reports · doi:10.1038/s41598-020-72730-z · Cited by 139

Neuronal APOE4 removal protects against tau-mediated gliosis, neurodegeneration and myelin deficits

Koutsodendris, N., Blumenfeld, J., Agrawal, A., Traglia, M., Grone, B., Zilberter, M., Yip, O., Rao, A., Nelson, M. R., Hao, Y., et al. (2023) · Nature Aging · doi:10.1038/s43587-023-00368-3 · Cited by 132

Menopause Is Associated with an Altered Gut Microbiome and Estrobolome, with Implications for Adverse Cardiometabolic Risk in the Hispanic Community Health Study/Study of Latinos

Peters, B. A., Lin, J., Qi, Q., Usyk, M., Isasi, C. R., Mossavar-Rahmani, Y., Derby, C. A., Santoro, N., Perreira, K. M., Daviglus, M. L., et al. (2022) · mSystems · doi:10.1128/msystems.00273-22 · Cited by 130

Extending the small-molecule similarity principle to all levels of biology with the Chemical Checker

Duran-Frigola, M., Pauls, E., Guitart-Pla, O., Bertoni, M., Alcalde, V., Amat, D., Juan-Blanco, T., & Aloy, P. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0502-7 · Cited by 126

A Circadian Genomic Signature Common to Ketamine and Sleep Deprivation in the Anterior Cingulate Cortex

Orozco-Solis, R., Montellier, E., Aguilar-Arnal, L., Sato, S., Vawter, M. P., Bunney, B. G., Bunney, W. E., & Sassone-Corsi, P. (2017) · Biological Psychiatry · doi:10.1016/j.biopsych.2017.02.1176 · Cited by 119

Metagenomic analysis identified microbiome alterations and pathological association between intestinal microbiota and polycystic ovary syndrome

Chu, W., Han, Q., Xu, J., Wang, J., Sun, Y., Li, W., Chen, Z.-J., & Du, Y. (2020) · Fertility and Sterility · doi:10.1016/j.fertnstert.2020.01.027 · Cited by 121

The APOE-R136S mutation protects against APOE4-driven tau pathology, neurodegeneration, and neuroinflammation

Nelson, M. R., Liu, P., Agrawal, A., Yip, O., Blumenfeld, J., Traglia, M., Kim, M. J., Koutsodendris, N., Rao, A., Grone, B., et al. (2023) · Nature Neuroscience · doi:10.1038/s41593-023-01480-8 · Cited by 120

Differential Content of Proteins, mRNAs, and miRNAs Suggests that MDSC and Their Exosomes May Mediate Distinct Immune Suppressive Functions

Geis-Asteggiante, L., Belew, A. T., Clements, V. K., Edwards, N. J., Ostrand-Rosenberg, S., El-Sayed, N. M., & Fenselau, C. (2018) · Journal of Proteome Research · doi:10.1021/acs.jproteome.7b00646 · Cited by 104

Neuronal Apolipoprotein E4 Expression Results in Proteome-Wide Alterations and Compromises Bioenergetic Capacity by Disrupting Mitochondrial Function

Orr, A. L., Kim, C., Jimenez-Morales, D., Newton, B. W., Johnson, J. R., Krogan, N. J., Swaney, D. L., & Mahley, R. W. (2019) · Journal of Alzheimer's Disease · doi:10.3233/jad-181184 · Cited by 103

A Population Genomics Approach to Assessing the Genetic Basis of Within-Host Microevolution Underlying Recurrent Cryptococcal Meningitis Infection

Rhodes, J., Beale, M. A., Vanhove, M., Jarvis, J. N., Kannambath, S., Simpson, J. A., Ryan, A., Meintjes, G., Harrison, T. S., Fisher, M. C., et al. (2017) · G3 Genes|Genomes|Genetics · doi:10.1534/g3.116.037499 · Cited by 100

Genotyping by PCR and high-throughput sequencing of commercial probiotic products reveals composition biases

Morovic, W., Hibberd, A. A., Zabel, B., Barrangou, R., & Stahl, B. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.01747 · Cited by 99

Identification of a myofibroblast-specific expression signature in skin wounds

Bergmeier, V., Etich, J., Pitzler, L., Frie, C., Koch, M., Fischer, M., Rappl, G., Abken, H., Tomasek, J. J., & Brachvogel, B. (2018) · Matrix Biology · doi:10.1016/j.matbio.2017.07.005 · Cited by 87

Extensive accumulation of misfolded protein aggregates during natural aging and senescence

Cuanalo-Contreras, K., Schulz, J., Mukherjee, A., Park, K.-W., Armijo, E., & Soto, C. (2023) · Frontiers in Aging Neuroscience · doi:10.3389/fnagi.2022.1090109 · Cited by 92

A Caenorhabditis elegans genome-scale metabolic network model

Yilmaz, L. S., & Walhout, A. J. M. (2016) · Cell Systems · doi:10.1016/j.cels.2016.04.012 · Cited by 88

Metabolomics of Childhood Exposure to Perfluoroalkyl Substances: A Cross-Sectional Study

Kingsley, S. L., Walker, D. I., Calafat, A. M., Chen, A., Papandonatos, G. D., Xu, Y., Jones, D. P., Lanphear, B. P., Pennell, K. D., & Braun, J. M. (2019) · Metabolomics · doi:10.1007/s11306-019-1560-z · Cited by 90

Fermentation Conditions that Affect Clavulanic Acid Production in Streptomyces clavuligerus: A Systematic Review

Ser, H.-L., Law, J. W.-F., Chaiyakunapruk, N., Jacob, S. A., Palanisamy, U. D., Chan, K.-G., Goh, B.-H., & Lee, L.-H. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.00522 · Cited by 90

Taxa-function robustness in microbial communities

Eng, A., & Borenstein, E. (2018) · Microbiome · doi:10.1186/s40168-018-0425-4 · Cited by 89

Altered miRNA expression network in locus coeruleus of depressed suicide subjects

Roy, B., Wang, Q., Palkovits, M., Faludi, G., & Dwivedi, Y. (2017) · Scientific Reports · doi:10.1038/s41598-017-04300-9 · Cited by 86

Microbial hitchhikers harbouring antimicrobial-resistance genes in the riverine plastisphere

Zadjelovic, V., Wright, R. J., Borsetto, C., Quartey, J., Cairns, T. N., Langille, M. G. I., Wellington, E. M. H., & Christie-Oleza, J. A. (2023) · Microbiome · doi:10.1186/s40168-023-01662-3 · Cited by 87

Lactobacillus supports Clostridiales to restrict gut colonization by multidrug-resistant Enterobacteriaceae

Djukovic, A., Garzón, M. J., Canlet, C., Cabral, V., Lalaoui, R., García-Garcerá, M., Rechenberger, J., Tremblay-Franco, M., Peñaranda, I., Puchades-Carrasco, L., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-33313-w · Cited by 85

Interpretation of cancer mutations using a multiscale map of protein systems

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Caloric restriction promotes functional changes involving short-chain fatty acid biosynthesis in the rat gut microbiota

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