Database resources of the National Center for Biotechnology Information: update

Basic local alignment search tool

Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302

Gene Ontology: tool for the unification of biology

Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., et al. (2000) · Nature Genetics · doi:10.1038/75556 · Cited by 43,206

Gene Expression Omnibus: NCBI gene expression and hybridization array data repository

Edgar, R. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.1.207 · Cited by 13,288

A general method applicable to the search for similarities in the amino acid sequence of two proteins

Needleman, S. B., & Wunsch, C. D. (1970) · Journal of Molecular Biology · doi:10.1016/0022-2836(70)90057-4 · Cited by 11,288

BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes

Manni, M., Berkeley, M. R., Seppey, M., Simão, F. A., & Zdobnov, E. M. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab199 · Cited by 6,187

PubChem Substance and Compound databases

Kim, S., Thiessen, P. A., Bolton, E. E., Chen, J., Fu, G., Gindulyte, A., Han, L., He, J., He, S., Shoemaker, B. A., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv951 · Cited by 5,436

A gene expression atlas of the central nervous system based on bacterial artificial chromosomes

Gong, S., Zheng, C., Doughty, M. L., Losos, K., Didkovsky, N., Schambra, U. B., Nowak, N. J., Joyner, A., Leblanc, G., Hatten, M. E., et al. (2003) · Nature · doi:10.1038/nature02033 · Cited by 2,108

Reactome knowledgebase of human biological pathways and processes

Matthews, L., Gopinath, G., Gillespie, M., Caudy, M., Croft, D., de Bono, B., Garapati, P., Hemish, J., Hermjakob, H., Jassal, B., et al. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkn863 · Cited by 873

NCBI Reference Sequences: current status, policy and new initiatives

Pruitt, K. D., Tatusova, T., Klimke, W., & Maglott, D. R. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkn721 · Cited by 736

Molecular architecture of the autoinhibited kinesin-1 lambda particle

Weijman, J. F., Yadav, S. K. N., Surridge, K. J., Cross, J. A., Borucu, U., Mantell, J., Woolfson, D. N., Schaffitzel, C., & Dodding, M. P. (2022) · Science Advances · doi:10.1126/sciadv.abp9660 · Cited by 54

Gut microbiota mediated the therapeutic efficacies and the side effects of prednisone in the treatment of MRL/lpr mice

Wang, M., Zhu, Z., Lin, X., Li, H., Wen, C., Bao, J., & He, Z. (2021) · Arthritis Research & Therapy · doi:10.1186/s13075-021-02620-w · Cited by 52

Sharing Biomedical Data: Strengthening AI Development in Healthcare

Pereira, T., Morgado, J., Silva, F., Pelter, M. M., Dias, V. R., Barros, R., Freitas, C., Negrão, E., Flor de Lima, B., Correia da Silva, M., et al. (2021) · Healthcare · doi:10.3390/healthcare9070827 · Cited by 54

Phage tailspike modularity and horizontal gene transfer reveals specificity towards E. coli O-antigen serogroups

Pas, C., Latka, A., Fieseler, L., & Briers, Y. (2023) · Virology Journal · doi:10.1186/s12985-023-02138-4 · Cited by 52

A role for Rab11 in the homeostasis of the endosome-lysosomal pathway

Zulkefli, K. L., Houghton, F. J., Gosavi, P., & Gleeson, P. A. (2019) · Experimental Cell Research · doi:10.1016/j.yexcr.2019.04.010 · Cited by 52

Phylogenomics Identifies a New Major Subgroup of Apicomplexans, Marosporida class nov., with Extreme Apicoplast Genome Reduction

Mathur, V., Kwong, W. K., Husnik, F., Irwin, N. A. T., Kristmundsson, Á., Gestal, C., Freeman, M., & Keeling, P. J. (2021) · Genome Biology and Evolution · doi:10.1093/gbe/evaa244 · Cited by 50

Gut microbiota-derived hexa-acylated lipopolysaccharides enhance cancer immunotherapy responses

Sardar, P., Beresford-Jones, B. S., Xia, W., Shabana, O., Suyama, S., Ramos, R. J. F., Soderholm, A. T., Tourlomousis, P., Kuo, P., Evans, A. C., et al. (2025) · Nature Microbiology · doi:10.1038/s41564-025-01930-y · Cited by 49

Pressing needs of biomedical text mining in biocuration and beyond: opportunities and challenges

Singhal, A., Leaman, R., Catlett, N., Lemberger, T., McEntyre, J., Polson, S., Xenarios, I., Arighi, C., & Lu, Z. (2016) · Database · doi:10.1093/database/baw161 · Cited by 48

Structural and Functional Characterization of a Multifunctional Alanine-Rich Peptide Analogue from Pleuronectes americanus

Migliolo, L., Silva, O. N., Silva, P. A., Costa, M. P., Costa, C. R., Nolasco, D. O., Barbosa, J. A. R. G., Silva, M. R. R., Bemquerer, M. P., Lima, L. M. P., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0047047 · Cited by 48

Integrated Metabolomic–Genomic Workflows Accelerate Microbial Natural Product Discovery

Avalon, N. E., Murray, A. E., & Baker, B. J. (2022) · Analytical Chemistry · doi:10.1021/acs.analchem.2c02245 · Cited by 47

Best Practices for Making Reproducible Biochemical Models

Porubsky, V. L., Goldberg, A. P., Rampadarath, A. K., Nickerson, D. P., Karr, J. R., & Sauro, H. M. (2020) · Cell Systems · doi:10.1016/j.cels.2020.06.012 · Cited by 45

Experimentally induced metamorphosis in highly regenerative axolotl (ambystoma mexicanum) under constant diet restructures microbiota

Demircan, T., Ovezmyradov, G., Yıldırım, B., Keskin, İ., İlhan, A. E., Fesçioğlu, E. C., Öztürk, G., & Yıldırım, S. (2018) · Scientific Reports · doi:10.1038/s41598-018-29373-y · Cited by 45

Antibacterial T6SS effectors with a VRR-Nuc domain are structure-specific nucleases

Hespanhol, J. T., Sanchez-Limache, D. E., Nicastro, G. G., Mead, L., Llontop, E. E., Chagas-Santos, G., Farah, C. S., de Souza, R. F., Galhardo, R. D. S., Lovering, A. L., et al. (2022) · eLife · doi:10.7554/elife.82437 · Cited by 45

Dysregulated FXR-FGF19 signaling and choline metabolism are associated with gut dysbiosis and hyperplasia in a novel pig model of pediatric NASH

Hernandez, G. V., Smith, V. A., Melnyk, M., Burd, M. A., Sprayberry, K. A., Edwards, M. S., Peterson, D. G., Bennet, D. C., Fanter, R. K., Columbus, D. A., et al. (2020) · American Journal of Physiology-Gastrointestinal and Liver Physiology · doi:10.1152/ajpgi.00344.2019 · Cited by 44

A FAIR guide for data providers to maximise sharing of human genomic data

Corpas, M., Kovalevskaya, N. V., McMurray, A., & Nielsen, F. G. G. (2018) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1005873 · Cited by 44

Integrative RNA-seq and microarray data analysis reveals GC content and gene length biases in the psoriasis transcriptome

Swindell, W. R., Xing, X., Voorhees, J. J., Elder, J. T., Johnston, A., & Gudjonsson, J. E. (2014) · Physiological Genomics · doi:10.1152/physiolgenomics.00022.2014 · Cited by 42

RNA Sequencing Revealed Numerous Polyketide Synthase Genes in the Harmful Dinoflagellate Karenia mikimotoi

Kimura, K., Okuda, S., Nakayama, K., Shikata, T., Takahashi, F., Yamaguchi, H., Skamoto, S., Yamaguchi, M., & Tomaru, Y. (2015) · PLOS ONE · doi:10.1371/journal.pone.0142731 · Cited by 39

Exploring human disease using the Rat Genome Database

Shimoyama, M., Laulederkind, S. J. F., De Pons, J., Nigam, R., Smith, J. R., Tutaj, M., Petri, V., Hayman, G. T., Wang, S.-J., Ghiasvand, O., et al. (2016) · Disease Models & Mechanisms · doi:10.1242/dmm.026021 · Cited by 37

Genomic insights into antibiotic resistance and mobilome of lactic acid bacteria and bifidobacteria

Rozman, V., Mohar Lorbeg, P., Treven, P., Accetto, T., Janežič, S., Rupnik, M., & Bogovič Matijašić, B. (2023) · Life Science Alliance · doi:10.26508/lsa.202201637 · Cited by 36

Sodium rutin extends lifespan and health span in mice including positive impacts on liver health

Li, S., Li, J., Pan, R., Cheng, J., Cui, Q., Chen, J., & Yuan, Z. (2022) · British Journal of Pharmacology · doi:10.1111/bph.15410 · Cited by 36

TransPTM: a transformer-based model for non-histone acetylation site prediction

Meng, L., Chen, X., Cheng, K., Chen, N., Zheng, Z., Wang, F., Sun, H., & Wong, K.-C. (2024) · Briefings in Bioinformatics · doi:10.1093/bib/bbae219 · Cited by 31

The Arabidopsis SAC9 enzyme is enriched in a cortical population of early endosomes and restricts PI(4,5)P2 at the plasma membrane

Lebecq, A., Doumane, M., Fangain, A., Bayle, V., Leong, J. X., Rozier, F., Marques-Bueno, M. D., Armengot, L., Boisseau, R., Simon, M. L., et al. (2022) · eLife · doi:10.7554/elife.73837 · Cited by 31

A bird-like genome from a frog: Mechanisms of genome size reduction in the ornate burrowing frog, Platyplectrum ornatum

Lamichhaney, S., Catullo, R., Keogh, J. S., Clulow, S., Edwards, S. V., & Ezaz, T. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2011649118 · Cited by 31

Motif oriented high-resolution analysis of ChIP-seq data reveals the topological order of CTCF and cohesin proteins on DNA

Nagy, G., Czipa, E., Steiner, L., Nagy, T., Pongor, S., Nagy, L., & Barta, E. (2016) · BMC Genomics · doi:10.1186/s12864-016-2940-7 · Cited by 27

Discovery of a novel insecticidal protein from Chromobacterium piscinae, with activity against Western Corn Rootworm, Diabrotica virgifera virgifera

Sampson, K., Zaitseva, J., Stauffer, M., Vande Berg, B., Guo, R., Tomso, D., McNulty, B., Desai, N., & Balasubramanian, D. (2017) · Journal of Invertebrate Pathology · doi:10.1016/j.jip.2016.10.004 · Cited by 30

Simultaneous proteome localization and turnover analysis reveals spatiotemporal features of protein homeostasis disruptions

Currie, J., Manda, V., Robinson, S. K., Lai, C., Agnihotri, V., Hidalgo, V., Ludwig, R. W., Zhang, K., Pavelka, J., Wang, Z. V., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-46600-5 · Cited by 29

Congenital Thyrotropin Deficiency-From Discovery to Molecular Biology, Postgenome and Preventive Medicine-

MIYAI, K. (2007) · Endocrine Journal · doi:10.1507/endocrj.kr-107 · Cited by 28

The Disease Portals, disease-gene annotation and the RGD disease ontology at the Rat Genome Database

Hayman, G. T., Laulederkind, S. J. F., Smith, J. R., Wang, S.-J., Petri, V., Nigam, R., Tutaj, M., De Pons, J., Dwinell, M. R., & Shimoyama, M. (2016) · Database · doi:10.1093/database/baw034 · Cited by 27

Modeling the Orthosteric Binding Site of the G Protein-Coupled Odorant Receptor OR5K1

Nicoli, A., Haag, F., Marcinek, P., He, R., Kreißl, J., Stein, J., Marchetto, A., Dunkel, A., Hofmann, T., Krautwurst, D., et al. (2023) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.2c00752 · Cited by 28

The Birth-and-Death Evolution of Cytochrome P450 Genes in Bees

Darragh, K., Nelson, D. R., & Ramírez, S. R. (2021) · Genome Biology and Evolution · doi:10.1093/gbe/evab261 · Cited by 27

Functionally conserved enhancers with divergent sequences in distant vertebrates

Yang, S., Oksenberg, N., Takayama, S., Heo, S.-J., Poliakov, A., Ahituv, N., Dubchak, I., & Boffelli, D. (2015) · BMC Genomics · doi:10.1186/s12864-015-2070-7 · Cited by 27

PAGER 2.0: an update to the pathway, annotated-list and gene-signature electronic repository for Human Network Biology

Yue, Z., Zheng, Q., Neylon, M. T., Yoo, M., Shin, J., Zhao, Z., Tan, A. C., & Chen, J. Y. (2018) · Nucleic Acids Research · doi:10.1093/nar/gkx1040 · Cited by 27

A novel RNA sequencing data analysis method for cell line authentication

Fasterius, E., Raso, C., Kennedy, S., Rauch, N., Lundin, P., Kolch, W., Uhlén, M., & Al-Khalili Szigyarto, C. (2017) · PLoS ONE · doi:10.1371/journal.pone.0171435 · Cited by 26

Molecular Characterization of Probiotics and Their Influence on Children with Autism Spectrum Disorder

Meguid, N. A., Mawgoud, Y. I. A., Bjørklund, G., Mehanne, N. S., Anwar, M., Effat, B. A. E.-K., Chirumbolo, S., & Elrahman, M. M. A. (2022) · Molecular Neurobiology · doi:10.1007/s12035-022-02963-8 · Cited by 24

Metabolite Damage and Damage Control in a Minimal Genome

(2022) · doi:10.1128/mbio.01630-22 · Cited by 24

Structural implications of BK polyomavirus sequence variations in the major viral capsid protein Vp1 and large T-antigen: a computational study

(2024) · doi:10.1128/msphere.00799-23 · Cited by 23

Diversification of molecular pattern recognition in bacterial NLR-like proteins

(2024) · doi:10.1038/s41467-024-54214-0 · Cited by 23

Lactic acid bacteria and bifidobacteria deliberately introduced into the agro-food chain do not significantly increase the antimicrobial resistance gene pool

Rozman, V., Mohar Lorbeg, P., Treven, P., Accetto, T., Golob, M., Zdovc, I., & Bogovič Matijašić, B. (2022) · Gut Microbes · doi:10.1080/19490976.2022.2127438 · Cited by 21

ZccE is a Novel P-type ATPase That Protects Streptococcus mutans Against Zinc Intoxication

(2022) · doi:10.1371/journal.ppat.1010477 · Cited by 20

Practical implications of erythromycin resistance gene diversity on surveillance and monitoring of resistance

Choi, J., Rieke, E. L., Moorman, T. B., Soupir, M. L., Allen, H. K., Smith, S. D., & Howe, A. (2018) · FEMS Microbiology Ecology · doi:10.1093/femsec/fiy006 · Cited by 19

Exploring a diverse world of effector domains and amyloid signaling motifs in fungal NLR proteins

Wojciechowski, J. W., Tekoglu, E., Gąsior-Głogowska, M., Coustou, V., Szulc, N., Szefczyk, M., Kopaczyńska, M., Saupe, S. J., & Dyrka, W. (2022) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1010787 · Cited by 19

The implications of APOBEC3-mediated C-to-U RNA editing for human disease

(2024) · doi:10.1038/s42003-024-06239-w · Cited by 16

A Noncoding A-to-U Kozak Site Change Related to the High Transmissibility of Alpha, Delta, and Omicron VOCs

Yang, J., Cui, Y., Yu, D., Zhang, G., Cao, R., Gu, Z., Dai, G., Wu, X., Ling, Y., Yi, C., et al. (2023) · Molecular Biology and Evolution · doi:10.1093/molbev/msad142 · Cited by 15

Deep mining reveals the diversity of endogenous viral elements in vertebrate genomes

(2024) · doi:10.1038/s41564-024-01825-4 · Cited by 15

cazy_webscraper: local compilation and interrogation of comprehensive CAZyme datasets

Hobbs, E. E. M., Gloster, T. M., & Pritchard, L. (2023) · Microbial Genomics · doi:10.1099/mgen.0.001086 · Cited by 15

An integrated systems biology approach reveals differences in formate metabolism in the genus Methanothermobacter

Casini, I., McCubbin, T., Esquivel-Elizondo, S., Luque, G. G., Evseeva, D., Fink, C., Beblawy, S., Youngblut, N. D., Aristilde, L., Huson, D. H., et al. (2023) · iScience · doi:10.1016/j.isci.2023.108016 · Cited by 14

Cloning and Characterization of hoxH Genes from Arthrospira and Spirulina and Application in Phylogenetic Study

Zhang, X., Zhang, X., Shiraiwa, Y., Mao, Y., Sui, Z., & Liu, J. (2005) · Marine Biotechnology · doi:10.1007/s10126-004-3127-9 · Cited by 13

Unveiling the molecular complexity of proliferative diabetic retinopathy through scRNA-seq, AlphaFold 2, and machine learning

Wang, J., Sun, H., Mou, L., Lu, Y., Wu, Z., Pu, Z., & Yang, M.-M. (2024) · Frontiers in Endocrinology · doi:10.3389/fendo.2024.1382896 · Cited by 13

Uncultured prokaryotic genomes in the spotlight: An examination of publicly available data from metagenomics and single-cell genomics

Arikawa, K., & Hosokawa, M. (2023) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2023.09.010 · Cited by 13

Cek1 regulates ß(1,3)-glucan exposure through calcineurin effectors in Candida albicans

Wagner, A. S., Lumsdaine, S. W., Mangrum, M. M., King, A. E., Hancock, T. J., Sparer, T. E., & Reynolds, T. B. (2022) · PLOS Genetics · doi:10.1371/journal.pgen.1010405 · Cited by 12

VirtuousPocketome: a computational tool for screening protein–ligand complexes to identify similar binding sites

Pallante, L., Cannariato, M., Androutsos, L., Zizzi, E. A., Bompotas, A., Hada, X., Grasso, G., Kalogeras, A., Mavroudi, S., Di Benedetto, G., et al. (2024) · Scientific Reports · doi:10.1038/s41598-024-56893-7 · Cited by 12

The intrinsically disordered transcriptional activation domain of CIITA is functionally tuneable by single substitutions: An exception or a new paradigm?

Sreenivasan, S., Heffren, P., Suh, K., Rodnin, M. V., Kosa, E., Fenton, A. W., Ladokhin, A. S., Smith, P. E., Fontes, J. D., & Swint‐Kruse, L. (2024) · Protein Science · doi:10.1002/pro.4863 · Cited by 11

Helical reconstruction of VP39 reveals principles for baculovirus nucleocapsid assembly

(2024) · doi:10.1038/s41467-023-44596-y · Cited by 10

The Origin and Evolution of Sex Peptide and Sex Peptide Receptor Interactions

Peng, J., Svetec, N., Molina, H., & Zhao, L. (2024) · Molecular Biology and Evolution · doi:10.1093/molbev/msae065 · Cited by 9

The Escherichia coli replication initiator DnaA is titrated on the chromosome

Olivi, L., Köstlbacher, S., Ludwig, C., Langendoen, M., Claassens, N. J., Ettema, T. J. G., van der Oost, J., ten Wolde, P. R., Hohlbein, J., & Staals, R. H. J. (2025) · Nature Communications · doi:10.1038/s41467-025-63147-1 · Cited by 7

Tool for filtering PubMed search results by sample size.

Baladrón, C., Santos-Lozano, A., Aguiar, J. M., Lucia, A., & Martín-Hernández, J. (2018) · Journal of the American Medical Informatics Association · doi:10.1093/jamia/ocx155 · Cited by 6

Evolutionary plasticity and functional repurposing of the essential metabolic enzyme MoeA

Megrian, D., Martinez, M., Alzari, P. M., & Wehenkel, A. M. (2025) · Communications Biology · doi:10.1038/s42003-025-07476-3 · Cited by 6

Comparison of insect and human cytochrome b561 proteins: Insights into candidate ferric reductases in insects

Holst, J. D., Murphy, L. G., Gorman, M. J., & Ragan, E. J. (2023) · PLOS ONE · doi:10.1371/journal.pone.0291564 · Cited by 6

Analysis of Arabidopsis non-reference accessions reveals high diversity of metabolic gene clusters and discovers new candidate cluster members

(2023) · doi:10.3389/fpls.2023.1104303 · Cited by 5

SEQUENCE SLIDER: integration of structural and genetic data to characterize isoforms from natural sources

Borges, R. J., Salvador, G. H. M., Pimenta, D. C., dos Santos, L. D., Fontes, M. R. M., & Usón, I. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac029 · Cited by 5

Evolution and phylogenetic distribution of endo -α-mannosidase

Sobala, Ł. F. (2023) · Glycobiology · doi:10.1093/glycob/cwad041 · Cited by 5

Dynamic Birth and Death of Argonaute Gene Family Functional Repertoire Across Caenorhabditis Nematodes

(2025) · doi:10.1093/gbe/evaf106 · Cited by 5

Post-transcriptional control drives Aurora kinase A expression in human cancers

Cacioppo, R., Rad, D., Pagani, G., Gandellini, P., & Lindon, C. (2024) · PLOS ONE · doi:10.1371/journal.pone.0310625 · Cited by 3

New groups of highly divergent proteins in families as old as cellular life with important biological functions in the ocean

Sussfeld, D., Lannes, R., Corel, E., Bernard, G., Martin, P., Bapteste, E., Pelletier, E., & Lopez, P. (2025) · Environmental Microbiome · doi:10.1186/s40793-025-00697-3 · Cited by 3

Fucose as a nutrient ligand for Dikarya and a building block of early diverging lineages

(2023) · doi:10.1186/s43008-023-00123-8 · Cited by 3

Genetic analysis of the X-linked Adrenoleukodystrophy ABCD1 gene in Drosophila uncovers a role in Peroxisomal dynamics

Manor, J., Jangam, S. V., Chung, H.-L., Bhagwat, P., Andrews, J., Chester, H., Kondo, S., Srivastav, S., Botas, J., Moser, A. B., et al. (2024) · doi:10.1101/2024.09.23.614586 · Cited by 2

Xanthomonas immunity proteins protect against the cis-toxic effects of their cognate T4SS effectors

(2024) · doi:10.1038/s44319-024-00060-6 · Cited by 1

Proteomic analysis of the effect of the polyphenol pentagalloyl glucose on proteins involved in neurodegenerative diseases in activated BV‑2 microglial cells

Mendonca, P., Taka, E., & Soliman, K. (2019) · Molecular Medicine Reports · doi:10.3892/mmr.2019.10400 · Cited by 1