Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation

Toward Automatic Reconstruction of a Highly Resolved Tree of Life

Ciccarelli, F. D., Doerks, T., von Mering, C., Creevey, C. J., Snel, B., & Bork, P. (2006) · Science · doi:10.1126/science.1123061 · Cited by 1,663

Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells

Furusawa, Y., Obata, Y., Fukuda, S., Endo, T. A., Nakato, G., Takahashi, D., Nakanishi, Y., Uetake, C., Kato, K., Kato, T., et al. (2013) · Nature · doi:10.1038/nature12721 · Cited by 5,549

Indigenous bacteria from the gut microbiota regulate host serotonin biosynthesis

Yano, J. M., Yu, K., Donaldson, G. P., Shastri, G. G., Ann, P., Ma, L., Nagler, C. R., Ismagilov, R. F., Mazmanian, S. K., & Hsiao, E. Y. (2015) · Cell · doi:10.1016/j.cell.2015.02.047 · Cited by 3,614

Plant-derived exosomal MicroRNAs shape the gut microbiota

Teng, Y., Ren, Y., Sayed, M., Hu, X., Lei, C., Kumar, A., Hutchins, E., Mu, J., Deng, Z., Luo, C., et al. (2018) · Cell Host & Microbe · doi:10.1016/j.chom.2018.10.001 · Cited by 1,027

Systematic genome assessment of B-vitamin biosynthesis suggests co-operation among gut microbes

Magnúsdóttir, S., Ravcheev, D., de Crécy-Lagard, V., & Thiele, I. (2015) · Frontiers in Genetics · doi:10.3389/fgene.2015.00148 · Cited by 876

A systematic analysis of biosynthetic gene clusters in the human microbiome reveals a common family of antibiotics

Donia, M. S., Cimermancic, P., Schulze, C. J., Wieland Brown, L. C., Martin, J., Mitreva, M., Clardy, J., Linington, R. G., & Fischbach, M. A. (2014) · Cell · doi:10.1016/j.cell.2014.08.032 · Cited by 705

Massive expansion of human gut bacteriophage diversity

Camarillo-Guerrero, L. F., Almeida, A., Rangel-Pineros, G., Finn, R. D., & Lawley, T. D. (2021) · Cell · doi:10.1016/j.cell.2021.01.029 · Cited by 594

The oral microbiome and the immunobiology of periodontal disease and caries

Costalonga, M., & Herzberg, M. C. (2014) · Immunology Letters · doi:10.1016/j.imlet.2014.08.017 · Cited by 645

eggNOG: automated construction and annotation of orthologous groups of genes

Jensen, L. J., Julien, P., Kuhn, M., von Mering, C., Muller, J., Doerks, T., & Bork, P. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm796 · Cited by 547

Targeted restoration of the intestinal microbiota with a simple, defined bacteriotherapy resolves relapsing Clostridium difficile disease in mice

Lawley, T. D., Clare, S., Walker, A. W., Stares, M. D., Connor, T. R., Raisen, C., Goulding, D., Rad, R., Schreiber, F., Brandt, C., et al. (2012) · PLoS Pathogens · doi:10.1371/journal.ppat.1002995 · Cited by 540

The outer mucus layer hosts a distinct intestinal microbial niche

Li, H., Limenitakis, J. P., Fuhrer, T., Geuking, M. B., Lawson, M. A., Wyss, M., Brugiroux, S., Keller, I., Macpherson, J. A., Rupp, S., et al. (2015) · Nature Communications · doi:10.1038/ncomms9292 · Cited by 511

System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation

Rigbolt, K. T. G., Prokhorova, T. A., Akimov, V., Henningsen, J., Johansen, P. T., Kratchmarova, I., Kassem, M., Mann, M., Olsen, J. V., & Blagoev, B. (2011) · Science Signaling · doi:10.1126/scisignal.2001570 · Cited by 451

Widespread genetic switches and toxicity resistance proteins for fluoride

Baker, J. L., Sudarsan, N., Weinberg, Z., Roth, A., Stockbridge, R. B., & Breaker, R. R. (2012) · Science · doi:10.1126/science.1215063 · Cited by 438

Inteins: nature's gift to protein chemists

Shah, N. H., & Muir, T. W. (2014) · Chem. Sci. · doi:10.1039/c3sc52951g · Cited by 404

Sinus Microbiome Diversity Depletion and Corynebacterium tuberculostearicum Enrichment Mediates Rhinosinusitis

Abreu, N. A., Nagalingam, N. A., Song, Y., Roediger, F. C., Pletcher, S. D., Goldberg, A. N., & Lynch, S. V. (2012) · Science Translational Medicine · doi:10.1126/scitranslmed.3003783 · Cited by 415

Community characteristics of the gut microbiomes of competitive cyclists

Petersen, L. M., Bautista, E. J., Nguyen, H., Hanson, B. M., Chen, L., Lek, S. H., Sodergren, E., & Weinstock, G. M. (2017) · Microbiome · doi:10.1186/s40168-017-0320-4 · Cited by 377

Supplementation of Saturated Long-Chain Fatty Acids Maintains Intestinal Eubiosis and Reduces Ethanol-induced Liver Injury in Mice

Chen, P., Torralba, M., Tan, J., Embree, M., Zengler, K., Stärkel, P., van Pijkeren, J.-P., DePew, J., Loomba, R., Ho, S. B., et al. (2015) · Gastroenterology · doi:10.1053/j.gastro.2014.09.014 · Cited by 322

Changes in temperature alter the relationship between biodiversity and ecosystem functioning

García, F. C., Bestion, E., Warfield, R., & Yvon-Durocher, G. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1805518115 · Cited by 316

Early-branching gut fungi possess a large, comprehensive array of biomass-degrading enzymes

Solomon, K. V., Haitjema, C. H., Henske, J. K., Gilmore, S. P., Borges-Rivera, D., Lipzen, A., Brewer, H. M., Purvine, S. O., Wright, A. T., Theodorou, M. K., et al. (2016) · Science · doi:10.1126/science.aad1431 · Cited by 302

Ferritin is secreted via 2 distinct nonclassical vesicular pathways

Truman-Rosentsvit, M., Berenbaum, D., Spektor, L., Cohen, L. A., Belizowsky-Moshe, S., Lifshitz, L., Ma, J., Li, W., Kesselman, E., Abutbul-Ionita, I., et al. (2018) · Blood · doi:10.1182/blood-2017-02-768580 · Cited by 223

Targeted deletion of MyD88 in intestinal epithelial cells results in compromised antibacterial immunity associated with downregulation of polymeric immunoglobulin receptor, mucin-2, and antibacterial peptides

Frantz, A. L., Rogier, E. W., Weber, C. R., Shen, L., Cohen, D. A., Fenton, L. A., Bruno, M. E. C., & Kaetzel, C. S. (2012) · Mucosal Immunology · doi:10.1038/mi.2012.23 · Cited by 230

Histone deacetylase 10 structure and molecular function as a polyamine deacetylase

Hai, Y., Shinsky, S. A., Porter, N. J., & Christianson, D. W. (2017) · Nature Communications · doi:10.1038/ncomms15368 · Cited by 200

Deep Sequencing Analyses of Low Density Microbial Communities: Working at the Boundary of Accurate Microbiota Detection

Biesbroek, G., Sanders, E. A. M., Roeselers, G., Wang, X., Caspers, M. P. M., Trzciński, K., Bogaert, D., & Keijser, B. J. F. (2012) · PLoS ONE · doi:10.1371/journal.pone.0032942 · Cited by 196

Towards a comprehensive barcode library for arctic life—Ephemeroptera, Plecoptera, and Trichoptera of Churchill, Manitoba, Canada

Zhou, X., Adamowicz, S. J., Jacobus, L. M., DeWalt, R. E., & Hebert, P. D. (2009) · Frontiers in Zoology · doi:10.1186/1742-9994-6-30 · Cited by 153

Exploration of bacterial community classes in major human habitats

Zhou, Y., Mihindukulasuriya, K. A., Gao, H., La Rosa, P. S., Wylie, K. M., Martin, J. C., Kota, K., Shannon, W. D., Mitreva, M., Sodergren, E., et al. (2014) · Genome Biology · doi:10.1186/gb-2014-15-5-r66 · Cited by 149

Metabolic engineering of omega-3 long-chain polyunsaturated fatty acids in plants using an acyl-CoA Δ6-desaturase with ω3-preference from the marine microalga Micromonas pusilla

Petrie, J. R., Shrestha, P., Mansour, M. P., Nichols, P. D., Liu, Q., & Singh, S. P. (2010) · Metabolic Engineering · doi:10.1016/j.ymben.2009.12.001 · Cited by 132

A Global Survey of Mycobacterial Diversity in Soil

Walsh, C. M., Gebert, M. J., Delgado-Baquerizo, M., Maestre, F. T., & Fierer, N. (2019) · Applied and Environmental Microbiology · doi:10.1128/aem.01180-19 · Cited by 111

Identification and characterization of Rhodopseudomonas palustris TIE‐1 hopanoid biosynthesis mutants

WELANDER, P. V., DOUGHTY, D. M., WU, C. ‐., MEHAY, S., SUMMONS, R. E., & NEWMAN, D. K. (2012) · Geobiology · doi:10.1111/j.1472-4669.2011.00314.x · Cited by 101

Rumen methanogenic genotypes differ in abundance according to host residual feed intake phenotype and diet type

Carberry, C. A., Waters, S. M., Kenny, D. A., & Creevey, C. J. (2014) · Applied and Environmental Microbiology · doi:10.1128/aem.03131-13 · Cited by 100

A new analysis of archaea-bacteria domain separation: Variable phylogenetic distance and the tempo of early evolution

Berkemer, S. J., & McGlynn, S. E. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msaa089 · Cited by 52

The DUF59 containing protein SufT is involved in the maturation of iron–sulfur (FeS) proteins during conditions of high FeS cofactor demand in Staphylococcus aureus

Mashruwala, A. A., Bhatt, S., Poudel, S., Boyd, E. S., & Boyd, J. M. (2016) · PLoS Genetics · doi:10.1371/journal.pgen.1006233 · Cited by 53

The genomic epidemiology of multi-drug resistant invasive non-typhoidal Salmonella in selected sub-Saharan African countries

Park, S. E., Pham, D. T., Pak, G. D., Panzner, U., Maria Cruz Espinoza, L., von Kalckreuth, V., Im, J., Mogeni, O. D., Schütt-Gerowitt, H., Crump, J. A., et al. (2021) · BMJ Global Health · doi:10.1136/bmjgh-2021-005659 · Cited by 50

A Truncated Singleton NLR Causes Hybrid Necrosis in Arabidopsis thaliana

Barragan, A. C., Collenberg, M., Wang, J., Lee, R. R. Q., Cher, W. Y., Rabanal, F. A., Ashkenazy, H., Weigel, D., & Chae, E. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msaa245 · Cited by 46

Disease Association and Druggability of WD40 Repeat Proteins

Song, R., Wang, Z.-D., & Schapira, M. (2017) · Journal of Proteome Research · doi:10.1021/acs.jproteome.7b00451 · Cited by 45

Comparative genomics reveals diversified CRISPR-Cas systems of globally distributed Microcystis aeruginosa, a freshwater bloom-forming cyanobacterium

Yang, C., Lin, F., Li, Q., Li, T., & Zhao, J. (2015) · Frontiers in Microbiology · doi:10.3389/fmicb.2015.00394 · Cited by 44

The evolution of the dystroglycan complex, a major mediator of muscle integrity

Adams, J. C., & Brancaccio, A. (2015) · Biology Open · doi:10.1242/bio.012468 · Cited by 35

Structural screens identify candidate human homologs of insect chemoreceptors and cryptic Drosophila gustatory receptor-like proteins

(2023) · doi:10.7554/elife.85537 · Cited by 28

Insights into the genomic plasticity of Pseudomonas putida KF715, a strain with unique biphenyl‐utilizing activity and genome instability properties

Suenaga, H., Fujihara, H., Kimura, N., Hirose, J., Watanabe, T., Futagami, T., Goto, M., Shimodaira, J., & Furukawa, K. (2017) · Environmental Microbiology Reports · doi:10.1111/1758-2229.12561 · Cited by 26

Transporter engineering for the development of cyanobacteria as cell factories: A text analytics guided survey

Sengupta, S., Sahasrabuddhe, D., & Wangikar, P. P. (2022) · Biotechnology Advances · doi:10.1016/j.biotechadv.2021.107816 · Cited by 16

Viruses of sulfur oxidizing phototrophs encode genes for pigment, carbon, and sulfur metabolisms

Hesketh-Best, P. J., Bosco-Santos, A., Garcia, S. L., O’Beirne, M. D., Werne, J. P., Gilhooly, W. P., & Silveira, C. B. (2023) · Communications Earth & Environment · doi:10.1038/s43247-023-00796-4 · Cited by 16

DDRprot: a database of DNA damage response-related proteins

Andrés-León, E., Cases, I., Arcas, A., & Rojas, A. M. (2016) · Database · doi:10.1093/database/baw123 · Cited by 12

Identification of sequence determinants for the ABHD14 enzymes

Vaidya, K., Rodrigues, G., Gupta, S., Devarajan, A., Yeolekar, M., Madhusudhan, M. S., & Kamat, S. S. (2025) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.26632 · Cited by 9

Using of DNA-Barcoding, SCoT and SDS-PAGE Protein to Assess Soma-Clonal Variation in Micro-Propagated Fig (Ficus carica L.) Plant

O. Attia, A., A. Ismail, I., S. Dessoky, E. D., & S. Aljuaid, B. (2022) · Pakistan Journal of Biological Sciences · doi:10.3923/pjbs.2022.415.425 · Cited by 6

Bioinformatics Analysis Identifies Sequence Determinants of Enzymatic Activity for the PHARC-Associated Lipase ABHD12

Chakraborty, A., Devarajan, A., Kumar, K., C. S., R., Madhusudhan, M. S., Ratnaparkhi, G. S., & Kamat, S. S. (2025) · Biochemistry · doi:10.1021/acs.biochem.4c00865 · Cited by 4

AcrIF11 is a potent CRISPR-specific ADP-ribosyltransferase encoded by phage and plasmid

Chen, D. F., Roe, L. T., Yuping, L., Borges, A. L., Zhang, J. Y., Babbar, P., Maji, S., Stevens, M. G. V., Correy, G. J., Diolaiti, M. E., et al. (2025) · mBio · doi:10.1128/mbio.01698-25 · Cited by 4