SignalP 6.0 predicts all five types of signal peptides using protein language models

BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding

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

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Cd-hit: Accelerated for clustering the next-generation sequencing data

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UniProt: a worldwide hub of protein knowledge

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Comparison of the predicted and observed secondary structure of T4 phage lysozyme

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Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences

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Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences

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ProtTrans: Toward Understanding the Language of Life Through Self-Supervised Learning

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UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches

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Unified rational protein engineering with sequence-based deep representation learning

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Bilingual language model for protein sequence and structure

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DeepLoc 2.1: multi-label membrane protein type prediction using protein language models

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Fine-tuning protein language models boosts predictions across diverse tasks

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Masked inverse folding with sequence transfer for protein representation learning

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Novel machine learning approaches revolutionize protein knowledge

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Disentangling the complex gene interaction networks between rice and the blast fungus identifies a new pathogen effector

Sugihara, Y., Abe, Y., Takagi, H., Abe, A., Shimizu, M., Ito, K., Kanzaki, E., Oikawa, K., Kourelis, J., Langner, T., et al. (2023) · PLOS Biology · doi:10.1371/journal.pbio.3001945 · Cited by 59

Feature Reuse and Scaling: Understanding Transfer Learning with Protein Language Models

Li, F.-Z., Amini, A. P., Yue, Y., Yang, K. K., & Lu, A. X. (2024) · doi:10.1101/2024.02.05.578959 · Cited by 51

Engineering Microbial Consortia as Living Materials: Advances and Prospectives

Wang, S., Zhan, Y., Jiang, X., & Lai, Y. (2024) · ACS Synthetic Biology · doi:10.1021/acssynbio.4c00313 · Cited by 50

Genetic and phenotypic assessment of the antimicrobial activity of three potential probiotic lactobacilli against human enteropathogenic bacteria

Kiousi, D. E., Efstathiou, C., Tzampazlis, V., Plessas, S., Panopoulou, M., Koffa, M., & Galanis, A. (2023) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2023.1127256 · Cited by 41

Interdigitated immunoglobulin arrays form the hyperstable surface layer of the extremophilic bacterium Deinococcus radiodurans

von Kügelgen, A., van Dorst, S., Yamashita, K., Sexton, D. L., Tocheva, E. I., Murshudov, G., Alva, V., & Bharat, T. A. M. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2215808120 · Cited by 35

Structural conservation of insulin/IGF signalling axis at the insulin receptors level in Drosophila and humans

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

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Cryo-EM structures of human magnesium channel MRS2 reveal gating and regulatory mechanisms

Lai, L. T. F., Balaraman, J., Zhou, F., & Matthies, D. (2023) · Nature Communications · doi:10.1038/s41467-023-42599-3 · Cited by 29

In situ structure of a bacterial flagellar motor at subnanometre resolution reveals adaptations for increased torque

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Protein embeddings predict binding residues in disordered regions

(2024) · doi:10.1038/s41598-024-64211-4 · Cited by 27

Architecture of the biofilm-associated archaic Chaperone-Usher pilus CupE from Pseudomonas aeruginosa

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Bacterial cell volume regulation and the importance of cyclic di-AMP

Foster, A. J., van den Noort, M., & Poolman, B. (2024) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00181-23 · Cited by 26

Evidence for a Widespread Third System for Bacterial Polysaccharide Export across the Outer Membrane Comprising a Composite OPX/β-Barrel Translocon

(2022) · doi:10.1128/mbio.02032-22 · Cited by 26

Parallel expansion and divergence of an adhesin family in pathogenic yeasts

Smoak, R. A., Snyder, L. F., Fassler, J. S., & He, B. Z. (2023) · GENETICS · doi:10.1093/genetics/iyad024 · Cited by 25

Molecular profiling of sponge deflation reveals an ancient relaxant-inflammatory response

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Proteomics Identifies Substrates and a Novel Component in hSnd2-Dependent ER Protein Targeting

Tirincsi, A., O’Keefe, S., Nguyen, D., Sicking, M., Dudek, J., Förster, F., Jung, M., Hadzibeganovic, D., Helms, V., High, S., et al. (2022) · Cells · doi:10.3390/cells11182925 · Cited by 20

Skin metatranscriptomics reveals a landscape of variation in microbial activity and gene expression across the human body

Chia, M., Ng, A. H. Q., Ravikrishnan, A., Mohamed Naim, A. N., Wearne, S., Common, J., & Nagarajan, N. (2026) · Nature Biotechnology · doi:10.1038/s41587-025-02797-4 · Cited by 18

Discovering the nuclear localization signal universe through a deep learning model with interpretable attention units

Li, Y.-F., Pan, X., & Shen, H.-B. (2025) · Patterns · doi:10.1016/j.patter.2025.101262 · Cited by 18

Mapping the ultrastructural topology of the corynebacterial cell surface

Isbilir, B., Yeates, A., Alva, V., & Bharat, T. A. M. (2025) · PLOS Biology · doi:10.1371/journal.pbio.3003130 · Cited by 18

A cytoplasmic chemoreceptor and reactive oxygen species mediate bacterial chemotaxis to copper

Louis, G., Cherry, P., Michaux, C., Rahuel-Clermont, S., Dieu, M., Tilquin, F., Maertens, L., Van Houdt, R., Renard, P., Perpete, E., et al. (2023) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2023.105207 · Cited by 17

Comparative Structure Analysis of the Multi-Domain, Cell Envelope Proteases of Lactic Acid Bacteria

Christensen, L. F., Høie, M. H., Bang-Berthelsen, C. H., Marcatili, P., & Hansen, E. B. (2023) · Microorganisms · doi:10.3390/microorganisms11092256 · Cited by 17

Predicting Metal-binding Proteins and Structures Through Integration of Evolutionary-scale and Physics-based Modeling

(2025) · doi:10.1016/j.jmb.2025.168962 · Cited by 17

The signal peptide of yeast killer toxin K2 confers producer self-protection and allows conversion into a modular toxin-immunity system

(2024) · doi:10.1016/j.celrep.2024.114449 · Cited by 17

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

Multiplex and multimodal mapping of variant effects in secreted proteins via MultiSTEP

Popp, N. A., Powell, R. L., Wheelock, M. K., Holmes, K. J., Zapp, B. D., Sheldon, K. M., Fletcher, S. N., Wu, X., Fayer, S., Rubin, A. F., et al. (2025) · Nature Structural & Molecular Biology · doi:10.1038/s41594-025-01582-w · Cited by 15

Saccharibacteria deploy two distinct type IV pili, driving episymbiosis, host competition, and twitching motility

Grossman, A. S., Lei, L., Botting, J. M., Liu, J., Nahar, N., Liu, J., McLean, J. S., He, X., & Bor, B. (2025) · The ISME Journal · doi:10.1093/ismejo/wraf119 · Cited by 14

Unveiling the evolution of antimicrobial peptides in gut microbes via foundation-model-powered framework

Li, W., Huang, B., Guo, M., Zeng, Z., Cai, T., Feng, L., Zhang, X., Guo, L., Jiang, X., Yin, Y., et al. (2025) · Cell Reports · doi:10.1016/j.celrep.2025.115773 · Cited by 13

High-affinity PQQ import is widespread in Gram-negative bacteria

Munder, F., Voutsinos, M., Hantke, K., Venugopal, H., & Grinter, R. (2025) · Science Advances · doi:10.1126/sciadv.adr2753 · Cited by 12

Painting Peptides With Antimicrobial Potency Through Deep Reinforcement Learning

Dong, R., Cao, Q., & Song, C. (2025) · Advanced Science · doi:10.1002/advs.202506332 · Cited by 11

Duplication and neofunctionalization of a horizontally transferred xyloglucanase as a facet of the Red Queen coevolutionary dynamic

Attah, V., Milner, D. S., Fang, Y., Yan, X., Leonard, G., Heitman, J., Talbot, N. J., & Richards, T. A. (2024) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2218927121 · Cited by 11

Plant-associated fungi co-opt ancient antimicrobials for host manipulation

Mesny, F., Wolf, V., López-Moral, A., Kraege, A., Punt, W., Liu, S., Zhu, J., Park, J., Sato, Y., & Thomma, B. P. H. J. (2026) · Science Advances · doi:10.1126/sciadv.aec1406 · Cited by 11

High-throughput nanopore sequencing of Treponema pallidum tandem repeat genes arp and tp0470 reveals clade-specific patterns and recapitulates global whole genome phylogeny

Lieberman, N. A. P., Armstrong, T. D., Chung, B., Pfalmer, D., Hennelly, C. M., Haynes, A., Romeis, E., Wang, Q.-Q., Zhang, R.-L., Kou, C.-X., et al. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.1007056 · Cited by 10

One-step N-Terminomics Based on Isolation of Protein N-Terminal Peptides From LysargiNase Digests by Tip-Based Strong Cation Exchange Chromatography

(2024) · doi:10.1016/j.mcpro.2024.100820 · Cited by 10

Protein language models uncover carbohydrate-active enzyme function in metagenomics

Thurimella, K., Mohamed, A. M. T., Li, C., Vatanen, T., Graham, D. B., Owens, R. M., La Rosa, S. L., Plichta, D. R., Bacallado, S., & Xavier, R. J. (2025) · BMC Bioinformatics · doi:10.1186/s12859-025-06286-y · Cited by 9

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 AMP deaminase of the mollusk Helix pomatia is an unexpected member of the adenosine deaminase-related growth factor (ADGF) family

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Human cytokine and coronavirus nucleocapsid protein interactivity using large-scale virtual screens

Tomezsko, P. J., Ford, C. T., Meyer, A. E., Michaleas, A. M., & Jaimes, R. (2024) · Frontiers in Bioinformatics · doi:10.3389/fbinf.2024.1397968 · Cited by 9

A seven-transmembrane methyltransferase catalysing N-terminal histidine methylation of lytic polysaccharide monooxygenases

Batth, T. S., Simonsen, J. L., Hernández-Rollán, C., Brander, S., Morth, J. P., Johansen, K. S., Nørholm, M. H. H., Hoof, J. B., & Olsen, J. V. (2023) · Nature Communications · doi:10.1038/s41467-023-39875-7 · Cited by 9

WIV, a protein domain found in a wide number of arthropod viruses, which probably facilitates infection

Karlin, D. G. (2024) · Journal of General Virology · doi:10.1099/jgv.0.001948 · Cited by 8

Burkholderia pseudomallei Complex Subunit and Glycoconjugate Vaccines and Their Potential to Elicit Cross-Protection to Burkholderia cepacia Complex

Badten, A. J., & Torres, A. G. (2024) · Vaccines · doi:10.3390/vaccines12030313 · Cited by 8

Conservation of Three-Dimensional Structure of Lepidoptera and Trichoptera L-Fibroins for 290 Million Years

Stewart, R. J., Frandsen, P. B., Pauls, S. U., & Heckenhauer, J. (2022) · Molecules · doi:10.3390/molecules27185945 · Cited by 8

Novel Galectins Purified from the Sponge Chondrilla australiensis: Unique Structural Features and Cytotoxic Effects on Colorectal Cancer Cells Mediated by TF-Antigen Binding

Hayashi, R., Kamata, K., Gerdol, M., Fujii, Y., Hayashi, T., Onoda, Y., Kobayashi, N., Furushima, S., Ishiwata, R., Ohkawa, M., et al. (2024) · Marine Drugs · doi:10.3390/md22090400 · Cited by 7

Confidence-based prediction of antibiotic resistance at the patient level

Inda-Díaz, J. S., Johnning, A., Hessel, M., Sjöberg, A., Lokrantz, A., Helldal, L., Jirstrand, M., Svensson, L., & Kristiansson, E. (2026) · mBio · doi:10.1128/mbio.03431-25 · Cited by 7

Involvement of ArlI, ArlJ, and CirA in archaeal type IV pilin-mediated motility regulation

Chatterjee, P., Garcia, M. A., Cote, J. A., Yun, K., Legerme, G. P., Habib, R., Tripepi, M., Young, C., Kulp, D., Dyall-Smith, M., et al. (2024) · Journal of Bacteriology · doi:10.1128/jb.00089-24 · Cited by 7

CryoRhodopsins: A comprehensive characterization of a group of microbial rhodopsins from cold environments

Lamm, G. H. U., Marin, E., Alekseev, A., Schellbach, A. V., Stetsenko, A., Haro-Moreno, J. M., Bourenkov, G., Borshchevskiy, V., Asido, M., Agthe, M., et al. (2025) · Science Advances · doi:10.1126/sciadv.adv1015 · Cited by 7

Proteomics identifies substrates and a novel component in hSnd2-dependent ER protein targeting

Tirincsi, A., O’Keefe, S., Nguyen, D., Sicking, M., Dudek, J., Förster, F., Jung, M., Hadzibeganovic, D., Helms, V., High, S., et al. (2022) · doi:10.1101/2022.04.27.489649 · Cited by 7

Evolution of the Growth Hormone Gene Duplication in Passerine Birds

Rasband, S. A., Bolton, P. E., Fang, Q., Johnson, P. L. F., & Braun, M. J. (2023) · Genome Biology and Evolution · doi:10.1093/gbe/evad033 · Cited by 7

Protein Language Models Uncover Carbohydrate-Active Enzyme Function in Metagenomics

Thurimella, K., Mohamed, A. M. T., Graham, D. B., Owens, R. M., La Rosa, S. L., Plichta, D. R., Bacallado, S., & Xavier, R. J. (2023) · doi:10.1101/2023.10.23.563620 · Cited by 7

The carRS-ompV-virK operon of Vibrio cholerae senses antimicrobial peptides and activates the expression of multiple resistance systems

(2025) · doi:10.1038/s41598-025-98217-3 · 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

Biophysical characterization of high-confidence, small human proteins

Whited, A. M., Jungreis, I., Allen, J., Cleveland, C. L., Mudge, J. M., Kellis, M., Rinn, J. L., & Hough, L. E. (2024) · Biophysical Reports · doi:10.1016/j.bpr.2024.100167 · Cited by 5

Evolution and phylogenetic distribution of endo -α-mannosidase

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

Genetic analysis reveals a robust and hierarchical recruitment of the LolA chaperone to the LolCDE lipoprotein transporter

(2024) · doi:10.1128/mbio.03039-23 · Cited by 5

Structure-guided secretome analysis of gall-forming microbes offers insights into effector diversity and evolution

Mukhopadhyay, S., Javed, M. A., Wu, J., & Perez-Lopez, E. (2025) · eLife · doi:10.7554/elife.105185 · Cited by 5

Convergent evolution of viral-like Borg archaeal extrachromosomal elements and giant eukaryotic viruses

Banfield, J. F., Valentin-Alvarado, L. E., Shi, L.-D., Robinson, C. M., Bamert, R. S., Coulibaly, F., Barth, Z. K., Aylward, F. O., Schoelmerich, M. C., Lei, S., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-65646-7 · Cited by 4

Identification and Characterization of a Bacterial Periplasmic Solute Binding Protein That Binds l -Amino Acid Amides

(2024) · doi:10.1021/acs.biochem.4c00096 · Cited by 4

TMVisDB: Annotation and 3D-visualization of Transmembrane Proteins

Olenyi, T., Marquet, C., Grekova, A., Houri, L., Heinzinger, M., Dallago, C., & Rost, B. (2025) · Journal of Molecular Biology · doi:10.1016/j.jmb.2025.168997 · Cited by 4

Implementing N-terminomics and machine learning to probe Nt-arginylation

Ju, S., Nawale, L., Lee, S., Kim, J. G., Lee, H., Park, N., Kim, D. H., Cha-Molstad, H., & Lee, C. (2025) · Nature Communications · doi:10.1038/s41467-025-66883-6 · Cited by 3

Cell wall‐resident proteins with internal repeats ( PIR s) show an inverted architecture in Neurospora crassa , but maintain their role as wall stabilizers

Montaño‐Silva, P., Callejas‐Negrete, O. A., Pereira‐Santana, A., & Verdín, J. (2025) · The FEBS Journal · doi:10.1111/febs.70020 · Cited by 3

Bridge protein-mediated viral targeting of cells expressing endogenous μ-opioid G protein-coupled receptors in the mouse and monkey brain

Kamaguchi, R., Amemori, S., Amemori, K.-I., & Osakada, F. (2025) · Neuroscience Research · doi:10.1016/j.neures.2025.02.007 · Cited by 2

Sulfated mannan of diatoms selects host-specific microbiota in the sunlit ocean

Krull, J., Sidhu, C., Solanki, V., Bligh, M., Rößler, L., Singh, R. K., Huang, G., Robb, C. S., Teeling, H., Seeberger, P. H., et al. (2026) · Microbiome · doi:10.1186/s40168-026-02379-9 · 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

Jasmonic acid signalling is targeted by a smut fungal Tin2-fold effector

(2025) · doi:10.1093/jxb/eraf381 · Cited by 1

A functional interleukin-4 homolog is encoded in the genome of infectious laryngotracheitis virus: Unveiling a novel virulence factor

Volkening, J. D., Spatz, S. J., Garcia, M., Ross, T. A., Maekawa, D. A., Rosenthal, K. S., Zamora, A. C., Skipper, A., Blakey, J. R., & Paudel, R. (2025) · PLOS Pathogens · doi:10.1371/journal.ppat.1013219 · Cited by 1