UniProt: the Universal Protein Knowledgebase in 2023

Database resources of the National Center for Biotechnology Information: update

Wheeler, D. L. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkh073 · Cited by 10,695

AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models

Varadi, M., Anyango, S., Deshpande, M., Nair, S., Natassia, C., Yordanova, G., Yuan, D., Stroe, O., Wood, G., Laydon, A., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkab1061 · Cited by 7,850 · cited 1×

UniProt: the universal protein knowledgebase in 2021

The UniProt Consortium, Bateman, A., Martin, M.-J., Orchard, S., Magrane, M., Agivetova, R., Ahmad, S., Alpi, E., Bowler-Barnett, E. H., Britto, R., et al. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkaa1100 · Cited by 6,372

Database resources of the national center for biotechnology information

Sayers, E. W., Bolton, E. E., Brister, J. R., Canese, K., Chan, J., Comeau, D. C., Connor, R., Funk, K., Kelly, C., Kim, S., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkab1112 · Cited by 2,812

InterPro in 2022

Paysan‐Lafosse, T., Blum, M., Chuguransky, S., Grego, T., Pinto, B. L., Salazar, G. A., Bileschi, M. L., Bork, P., Bridge, A. J., Colwell, L. J., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac993 · Cited by 2,457

Ensembl 2022

Cunningham, F., Allen, J. E., Allen, J., Alvarez-Jarreta, J., Amode, M. R., Armean, I. M., Austine-Orimoloye, O., Azov, A. G., Barnes, I., Bennett, R., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkab1049 · Cited by 1,923

RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences

Burley, S. K., Bhikadiya, C., Bi, C., Bittrich, S., Chen, L., Crichlow, G. V., Christie, C. H., Dalenberg, K., Di Costanzo, L., Duarte, J. M., et al. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkaa1038 · Cited by 1,581

ChEBI in 2016: Improved services and an expanding collection of metabolites

Hastings, J., Owen, G., Dekker, A., Ennis, M., Kale, N., Muthukrishnan, V., Turner, S., Swainston, N., Mendes, P., & Steinbeck, C. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1031 · Cited by 1,083

Metabolomics: A New Tool to Reveal the Nature of Diabetic Kidney Disease

Huang, G., Li, M., Li, Y. J., & Mao, Y. (2022) · Laboratory Medicine · doi:10.1093/labmed/lmac041 · Cited by 933

BioLiP: a semi-manually curated database for biologically relevant ligand–protein interactions

Yang, J., Roy, A., & Zhang, Y. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks966 · Cited by 749

Molecular annotation of G protein variants in a neurological disorder

Knight, K. M., Obarow, E. G., Wei, W., Mani, S., Esteller, M. I., Cui, M., Ma, N., Martin, S. A., Brinson, E., Hewitt, N., et al. (2023) · Cell Reports · doi:10.1016/j.celrep.2023.113462 · Cited by 22

Constructions of quorum sensing signaling network for activated sludge microbial community

Jin, Y., Chen, W., Hu, J. H., Wang, J., & Ren, H. (2024) · ISME Communications · doi:10.1093/ismeco/ycae018 · Cited by 22

ContScout: sensitive detection and removal of contamination from annotated genomes

Bálint, B., Merényi, Z., Hegedüs, B., Grigoriev, I. V., Hou, Z., Földi, C., & Nagy, L. G. (2024) · Nature Communications · doi:10.1038/s41467-024-45024-5 · Cited by 21

A widespread bacterial protein compartment sequesters and stores elemental sulfur

Benisch, R., Andreas, M. P., & Giessen, T. W. (2024) · Science Advances · doi:10.1126/sciadv.adk9345 · Cited by 22

CollaPPI: A Collaborative Learning Framework for Predicting Protein-Protein Interactions

Ma, W., Bi, X., Jiang, H., Zhang, S., & Wei, Z. (2024) · IEEE Journal of Biomedical and Health Informatics · doi:10.1109/jbhi.2024.3375621 · Cited by 22

The Functional Roles of the Src Homology 2 Domain-Containing Inositol 5-Phosphatases SHIP1 and SHIP2 in the Pathogenesis of Human Diseases

Müller, S., & Jücker, M. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms25105254 · Cited by 21

The ancient Z-DNA and Z-RNA specific Zα fold has evolved modern roles in immunity and transcription through the natural selection of flipons

Herbert, A. G. (2024) · Royal Society Open Science · doi:10.1098/rsos.240080 · Cited by 22

Direct prediction of intermolecular interactions driven by disordered regionsPreprint

Ginell, G. M., Emenecker, R. J., Lotthammer, J. M., Usher, E. T., & Holehouse, A. S. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.06.03.597104 · Cited by 22

MAVISp: A Modular Structure-Based Framework for Protein Variant Effects

Arnaudi, M., Utichi, M., Degn, K., Tiberti, M., Beltrame, L., Krzesińska, K., Sánchez-Izquierdo Besora, P., Kiachaki, E., Scrima, S., Bauer, L., et al. (2022) · doi:10.1101/2022.10.22.513328 · Cited by 20

Structural principles of peptide-centric chimeric antigen receptor recognition guide therapeutic expansion

Sun, Y., Florio, T. J., Gupta, S., Young, M. C., Marshall, Q. F., Garfinkle, S. E., Papadaki, G. F., Truong, H. V., Mycek, E., Li, P., et al. (2023) · Science Immunology · doi:10.1126/sciimmunol.adj5792 · Cited by 19

CURTAIN—A unique web-based tool for exploration and sharing of MS-based proteomics data

Phung, T. K., Berndsen, K., Shastry, R., Phan, T. L. C. H. B., Muqit, M. M. K., Alessi, D. R., & Nirujogi, R. S. (2024) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2312676121 · Cited by 18

Molecular signature of primate astrocytes reveals pathways and regulatory changes contributing to human brain evolution

Ciuba, K., Piotrowska, A., Chaudhury, D., Dehingia, B., Duński, E., Behr, R., Soroczyńska, K., Czystowska-Kuźmicz, M., Abbas, M., Bulanda, E., et al. (2025) · Cell Stem Cell · doi:10.1016/j.stem.2024.12.011 · Cited by 25

Metaproteomics in the One Health framework for unraveling microbial effectors in microbiomes

Heyer, R., Wolf, M., Benndorf, D., Uzzau, S., Seifert, J., Grenga, L., Pabst, M., Schmitt, H., Mesuere, B., Van Den Bossche, T., et al. (2025) · Microbiome · doi:10.1186/s40168-025-02119-5 · Cited by 22

Structural bioinformatics studies of serotonin, dopamine and norepinephrine transporters and their AlphaFold2 predicted water-soluble QTY variants and uncovering the natural mutations of L->Q, I->T, F->Y and Q->L, T->I and Y->F

Karagöl, T., Karagöl, A., & Zhang, S. (2024) · PLoS ONE · doi:10.1371/journal.pone.0300340 · Cited by 28

Microbiome modeling: a beginner's guide

Lange, E., Kranert, L., Krüger, J., Benndorf, D., & Heyer, R. (2024) · Frontiers in Microbiology · doi:10.3389/fmicb.2024.1368377 · Cited by 21

An integrative approach to protein sequence design through multiobjective optimization

Hong, L., & Kortemme, T. (2024) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1011953 · Cited by 25

Central role of SUMOylation in the regulation of chromatin interactions and transcriptional outputs of the androgen receptor in prostate cancer cells

Launonen, K., Varis, V., Aaltonen, N., Niskanen, E. A., Varjosalo, M. T., Paakinaho, V., & Palvimo, J. J. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae653 · Cited by 22

Drug-target interaction prediction with collaborative contrastive learning and adaptive self-paced sampling strategy

Tian, Z., Yu, Y., Ni, F., & Zou, Q. (2024) · BMC Biology · doi:10.1186/s12915-024-02012-x · Cited by 21

Discovering CRISPR-Cas system with self-processing pre-crRNA capability by foundation models

Li, W., Jiang, X., Wang, W., Hou, L., Cai, R., Li, Y., Gu, Q., Chen, Q., Ma, P., Tang, J., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-54365-0 · Cited by 21

Beyond AlphaFold2: The Impact of AI for the Further Improvement of Protein Structure Prediction

Genc, A. G., & McGuffin, L. J. (2024) · Methods in molecular biology · doi:10.1007/978-1-0716-4196-5_7 · Cited by 22

Deciphering metabolic differentiation during Bacillus subtilis sporulation

Tibocha‐Bonilla, J. D., Lyda, J. A., Riley, E. P., Pogliano, K., & Zengler, K. (2025) · Nature Communications · doi:10.1038/s41467-024-55586-z · Cited by 20

Comparative analysis of glycoproteomic software using a tailored glycan database

Hogan, R. A., Pepi, L. E., Riley, N. M., & Chalkley, R. J. (2025) · Analytical and Bioanalytical Chemistry · doi:10.1007/s00216-025-05780-9 · Cited by 21

FOXM1 expression reverts aging chromatin profiles through repression of the senescence-associated pioneer factor AP-1

Ferreira, F. J., Galhardo, M., Nogueira, J. M., Teixeira, J., Logarinho, E., & Bessa, J. (2025) · Nature Communications · doi:10.1038/s41467-025-57503-4 · Cited by 27

Leveraging AI to explore structural contexts of post-translational modifications in drug binding

Medvedev, K. E., Schaeffer, R. D., & Grishin, N. V. (2025) · Journal of Cheminformatics · doi:10.1186/s13321-025-01019-y · Cited by 25

Data- and knowledge-derived functional landscape of human solute carriers

Goldmann, U., Wiedmer, T., Garofoli, A., Sedlyarov, V., Bichler, M., Haladik, B., Wolf, G., Christodoulaki, E., Inglés‐Prieto, Á., Ferrada, E., et al. (2025) · Molecular Systems Biology · doi:10.1038/s44320-025-00108-2 · Cited by 25

Large language models for bioinformatics

Ruan, W., Lyu, Y., Zhang, J., Cai, J., Shu, P., Yang, G., Lu, Y., Gao, S., Wang, Y., Wang, P., et al. (2025) · Quantitative Biology · doi:10.1002/qub2.70014 · Cited by 37

Exome sequencing of families from Ghana reveals known and candidate hearing impairment genes

Wonkam, A., Adadey, S. M., Schrauwen, I., Aboagye, E. T., Wonkam‐Tingang, E., Esoh, K. K., Popel, K., Manyisa, N. R., Jonas, M., de Kock, C. A., et al. (2022) · Communications Biology · doi:10.1038/s42003-022-03326-8 · Cited by 22

Combination of size‐exclusion chromatography and ion exchange adsorption for improving the proteomic analysis of plasma‐derived extracellular vesicles

Wang, Y., Zhang, Y., Li, Z., Wei, S., Chi, X., Yan, X., Lv, H., Zhao, L., & Zhao, L. (2023) · PROTEOMICS · doi:10.1002/pmic.202200364 · Cited by 21

Day–night fluctuations in choroid plexus transcriptomics and cerebrospinal fluid metabolomics

Edelbo, B. L., Andreassen, S. N., Steffensen, A. B., & MacAulay, N. (2023) · PNAS Nexus · doi:10.1093/pnasnexus/pgad262 · Cited by 20

N-linked glycosylation is essential for anti-tumor activities of KIAA1324 in gastric cancer

Yun, R., Hong, E., Kim, J., Park, B., Kim, S. J., Lee, B., Song, Y. S., Kim, S., Park, S., & Kang, J. M. (2023) · Cell Death and Disease · doi:10.1038/s41419-023-06083-6 · Cited by 21

Identifying G protein-coupled receptors involved in adipose tissue function using the innovative RNA-seq database FATTLAS

Kaczmarek, I., Wower, I., Ettig, K., Kuhn, C. K., Kraft, R., Landgraf, K., Körner, A., Schöneberg, T., Horn, S., & Thor, D. (2023) · iScience · doi:10.1016/j.isci.2023.107841 · Cited by 24

Structure of the voltage-gated potassium channel K V 1.3: Insights into the inactivated conformation and binding to therapeutic leads

Chandy, K. G., Sanches, K., & Norton, R. S. (2023) · Channels · doi:10.1080/19336950.2023.2253104 · Cited by 24

MDverse, shedding light on the dark matter of molecular dynamics simulations

Tiemann, J. K. S., Szczuka, M., Bouarroudj, L., Oussaren, M., Garcia, S., Howard, R. J., Delemotte, L., Lindahl, E. R., Baaden, M., Lindorff‐Larsen, K., et al. (2023) · eLife · doi:10.7554/elife.90061 · Cited by 42

MMPatho: Leveraging Multilevel Consensus and Evolutionary Information for Enhanced Missense Mutation Pathogenic Prediction

Ge, F., Arif, M., Yan, Z., Alahmadi, H., Worachartcheewan, A., Yu, D., & Shoombuatong, W. (2023) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.3c00950 · Cited by 21

Computational Chemistry in Structure-Based Solute Carrier Transporter Drug Design: Recent Advances and Future Perspectives

Tu, G., Fu, T., Zheng, G., Xu, B., Gou, R., Luo, D., Wang, P., & Xue, W. (2024) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.3c01736 · Cited by 23

Nuclear pore dysfunction and disease: a complex opportunity

Fare, C. M., & Rothstein, J. D. (2024) · Nucleus · doi:10.1080/19491034.2024.2314297 · Cited by 21

High-throughput prediction of enzyme promiscuity based on substrate–product pairs

Xing, H., Cai, P., Liu, D., Han, M., Liu, J., Le, Y., Zhang, D., & Hu, Q. (2024) · Briefings in Bioinformatics · doi:10.1093/bib/bbae089 · Cited by 20

Gastric digestion of the sweet-tasting plant protein thaumatin releases bitter peptides that reduce H. pylori induced pro-inflammatory IL-17A release via the TAS2R16 bitter taste receptor

Richter, P., Sebald, K., Fischer, K., Schnieke, A., Jlilati, M., Mittermeier-Kleßinger, V. K., & Somoza, V. (2024) · Food Chemistry · doi:10.1016/j.foodchem.2024.139157 · Cited by 21

Mitochondrial remodeling underlying age-induced skeletal muscle wasting: let’s talk about sex

Moreira‐Pais, A., Vitorino, R. M. P., Sousa-Mendes, C., Neuparth, M. J., Nuccio, A., Luparello, C., Attanzio, A., Novák, P., Loginov, D. S., Nogueira‐Ferreira, R., et al. (2024) · Free Radical Biology and Medicine · doi:10.1016/j.freeradbiomed.2024.04.005 · Cited by 23

Protein persulfidation in plants: mechanisms and functions beyond a simple stress response

Moseler, A., Wagner, S., & Meyer, A. J. (2024) · Biological Chemistry · doi:10.1515/hsz-2024-0038 · Cited by 21

Metaproteomics Beyond Databases: Addressing the Challenges and Potentials of De Novo Sequencing

Bossche, T. V. D., Beslic, D., van Puyenbroeck, S., Suomi, T., Holstein, T., Martens, L., Elo, L. L., & Muth, T. (2025) · PROTEOMICS · doi:10.1002/pmic.202400321 · Cited by 21

Pooled Tagging and Hydrophobic Targeting of Endogenous Proteins for Unbiased Mapping of Unfolded Protein Responses

Sansbury, S. E., Serebrenik, Y. V., Lapidot, T., Smith, D. G., Burslem, G. M., & Shalem, O. (2023) · Molecular Cell · doi:10.1016/j.molcel.2025.04.002 · Cited by 22

The MIGenAS integrated bioinformatics toolkit for web-based sequence analysis

Rampp, M., Soddemann, T., & Lederer, H. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl254 · Cited by 21

Long-read genomics reveal extensive nuclear-specific evolution and allele-specific expression in a dikaryotic fungusPreprint

Tam, R., Möller, M., Luo, R., Luo, Z., Jones, A., Periyannan, S. K., Rathjen, J. P., & Schwessinger, B. (2025) · Genome Research · doi:10.1101/gr.280359.124 · Cited by 19

Defining the Cell Surface Cysteinome Using Two-Step Enrichment Proteomics

(2023) · doi:10.1021/jacsau.3c00707 · Cited by 21

Evaluation of AlphaFold3 for the fatty acids docking to human fatty acid-binding proteins

Nam, K. H. (2024) · Journal of Molecular Graphics and Modelling · doi:10.1016/j.jmgm.2024.108872 · Cited by 21

Bioprospecting and marine ‘omics’: surfing the deep blue sea for novel bioactive proteins and peptides

Cabral, I. M., Gonçalves, C., Grosso, A. R., & Costa, P. M. (2024) · Frontiers in Marine Science · doi:10.3389/fmars.2024.1362697 · Cited by 31

MDRepo—an open data warehouse for community-contributed molecular dynamics simulations of proteins

Roy, A., Ward, E., Choi, I., Cosi, M., Edgin, T., Hughes, T., Islam, M. S., Khan, A. M., Kolekar, A., Rayl, M. L., et al. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae1109 · Cited by 25

FungiFun3: systemic gene set enrichment analysis for fungal species

López, A. G., Albrecht-Eckardt, D., Panagiotou, G., & Schäuble, S. (2024) · Bioinformatics · doi:10.1093/bioinformatics/btae620 · Cited by 18

Cleavage of Cartilage Oligomeric Matrix Protein (COMP) by ADAMTS4 generates a neoepitope associated with osteoarthritis and other forms of degenerative joint disease

de Groot, R., Folgado, P. B., Yamamoto, K., Martin, D. R., Koch, C. D., Debruin, D. A., Blagg, S., Minns, A. F., Bhutada, S., Ahnström, J., et al. (2024) · Matrix Biology · doi:10.1016/j.matbio.2024.12.005 · Cited by 21

A plasmid-chromosome crosstalk in multidrug resistant enterobacteria

Toribio-Celestino, L., Calvo‐Villamañán, A., Herencias, C., Valle, A. A.-D., Sastre-Domínguez, J., Quesada, S., Mazel, D., Rocha, E. P. C., Fernández-Calvet, A., & Millán, Á. S. (2024) · Nature Communications · doi:10.1038/s41467-024-55169-y · Cited by 20

The Combination of Neurotropic Vitamins B1, B6, and B12 Enhances Neural Cell Maturation and Connectivity Superior to Single B Vitamins

Cuyubamba, O., Braga, C., Swift, D. D., Stickney, J. T., & Viel, C. (2025) · Cells · doi:10.3390/cells14070477 · Cited by 20

Integrating ESM-2 and Graph Neural Networks with AlphaFold-2 Structures for Enhanced Protein Function Prediction

Nguyen, T.-T., Jiang, Z., Nguyen, V., Le, N. Q. K., & Chua, M. C. H. (2025) · ACS Omega · doi:10.1021/acsomega.5c05484 · Cited by 24

Molecular Details of the Frataxin–Scaffold Interaction during Mitochondrial Fe–S Cluster Assembly

Campbell, C. J., Pall, A. E., Naik, A. R., Thompson, L., & Stemmler, T. L. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22116006 · Cited by 21

Towards Marker-Assisted Breeding for Black Rot Bunch Resistance: Identification of a Major QTL in the Grapevine Cultivar ‘Merzling’

Bettinelli, P., Nicolini, D., Costantini, L., Stefanini, M., Hausmann, L., & Vezzulli, S. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24043568 · Cited by 20

Proteome-wide quantitative analysis of redox cysteine availability in the Drosophila melanogaster eye reveals oxidation of phototransduction machinery during blue light exposure and age

Stanhope, S. C., Brandwine-Shemmer, T., Blum, H. R., Doud, E. H., Jannasch, A., Mosley, A. L., Minke, B., & Weake, V. M. (2023) · Redox Biology · doi:10.1016/j.redox.2023.102723 · Cited by 20

Proteomics Approach to Differentiate Protein Extraction Methods in Sugar Beet Leaves

Goktayoglu, E., Öztop, M. H., & Özcan, S. (2023) · Journal of Agricultural and Food Chemistry · doi:10.1021/acs.jafc.2c09190 · Cited by 20

Structural basis of regioselective tryptophan dibromination by the single-component flavin-dependent halogenase AetF

Gäfe, S., & Niemann, H. H. (2023) · Acta Crystallographica Section D Structural Biology · doi:10.1107/s2059798323004254 · Cited by 21

Inhibition of DNMT1 methyltransferase activity via glucose-regulated O-GlcNAcylation alters the epigenome

Shin, H., Leung, A., Costello, K. R., Senapati, P., Kato, H., Moore, R. E., Lee, M., Lin, D., Tang, X., Pirrotte, P., et al. (2023) · eLife · doi:10.7554/elife.85595 · Cited by 19

A random forest model for predicting exosomal proteins using evolutionary information and motifs

Arora, A., Patiyal, S., Sharma, N., Naorem, L. D., Kaur, D., & Raghava, G. P. S. (2023) · PROTEOMICS · doi:10.1002/pmic.202300231 · Cited by 20

Scrutinizing the human TEX genes in the context of human male infertility

Sieper, M. H., Gaikwad, A., Fros, M., Weber, P., Persio, S. D., Oud, M. S., Kliesch, S., Neuhaus, N., Stallmeyer, B., Tüttelmann, F., et al. (2023) · Andrology · doi:10.1111/andr.13511 · Cited by 20

Plastid-localized xanthorhodopsin increases diatom biomass and ecosystem productivity in iron-limited surface oceans

Strauss, J., Deng, L., Gao, S., Toseland, A., Bachy, C., Zhang, C., Kirkham, A. R., Hopes, A., Utting, R., Joest, E. F., et al. (2023) · Nature Microbiology · doi:10.1038/s41564-023-01498-5 · Cited by 20

Proteomic insights into mental health status: plasma markers in young adults

Afonin, A. М., Piironen, A., Maciel, I. D. S., Ivanova, M., Alatalo, A., Whipp, A. M., Pulkkinen, L., Rose, R. J., KAMP, I. V., Kaprio, J. A., et al. (2024) · Translational Psychiatry · doi:10.1038/s41398-024-02751-z · Cited by 24

CyanoCyc cyanobacterial web portal

Moore, L. R., Caspi, R., Campbell, D. A., Casey, J. R., Crévecoeur, S., Lea‐Smith, D. J., Long, B., Omar, N. M., Paley, S., Schmelling, N. M., et al. (2024) · Frontiers in Microbiology · doi:10.3389/fmicb.2024.1340413 · Cited by 20

MIBPred: Ensemble Learning-Based Metal Ion-Binding Protein Classifier

Zhang, H., Liu, S., Li, R., Yu, J.-W., Ye, D.-X., Yuan, S.-S., Lin, H., Cheng-bing, H., & Tang, H. (2024) · ACS Omega · doi:10.1021/acsomega.3c09587 · Cited by 20

Vagus nerve stimulation enhances remyelination and decreases innate neuroinflammation in lysolecithin-induced demyelination

Bachmann, H., Vandemoortele, B., Vermeirssen, V., Carrette, E., Vonck, K. E. J., Boon, P., Raedt, R., & Laureys, G. (2024) · Brain stimulation · doi:10.1016/j.brs.2024.04.012 · Cited by 24

CLIPPER 2.0: Peptide-Level Annotation and Data Analysis for Positional Proteomics

Kalogeropoulos, K., Haack, A. M., Madzharova, E., Lorenzo, A. D., Hanna, R., Schoof, E. M., & Keller, U. A. D. (2024) · Molecular & Cellular Proteomics · doi:10.1016/j.mcpro.2024.100781 · Cited by 18

High-Throughput Proteomics and Phosphoproteomics of Rat Tissues Using Microflow Zeno SWATH

Humphries, E. M., Xavier, D., Ashman, K., Hains, P. G., & Robinson, P. J. (2024) · Journal of Proteome Research · doi:10.1021/acs.jproteome.4c00010 · Cited by 19

Multi-omic analysis tools for microbial metabolites prediction

Wu, S., Zhou, H., Chen, D., Lu, Y., Li, Y., & Qiao, J. (2024) · Briefings in Bioinformatics · doi:10.1093/bib/bbae264 · Cited by 19

Mass Spectrometry Structural Proteomics Enabled by Limited Proteolysis and Cross‐Linking

Lu, H., Zhu, Z., Fields, L. G., Zhang, H., & Li, L. (2024) · Mass Spectrometry Reviews · doi:10.1002/mas.21908 · Cited by 28

The Developmental Transcriptome of Bagworm, Metisa plana (Lepidoptera: Psychidae) and Insights into Chitin Biosynthesis Genes

Rahmat, N. L., Zifruddin, A. N., Abidin, C. M. R. Z., Muhammad, N. A. N., & Hassan, M. (2020) · Genes · doi:10.3390/genes12010007 · Cited by 20

The Empusa code generator and its application to GBOL, an extendable ontology for genome annotation

van Dam, J. C. J., Koehorst, J. J., Vik, J. O., dos Santos, V. A. P. M., Schaap, P. J., & Diez, M. S. (2019) · Scientific Data · doi:10.1038/s41597-019-0263-7 · Cited by 20

Proteus mirabilis UreR coordinates cellular functions required for urease activity

Fitzgerald, M. J., Pearson, M. M., & Mobley, H. L. T. (2024) · Journal of Bacteriology · doi:10.1128/jb.00031-24 · Cited by 18

Systematic Analysis of Covalent and Allosteric Protein Kinase Inhibitors

Xerxa, E., Laufkötter, O., & Bajorath, J. (2023) · Molecules · doi:10.3390/molecules28155805 · Cited by 16

PeposX-Exhaust: A lightweight and efficient tool for identification of short peptides

Liu, W., Zhao, M., Gan, L., Sun, B., He, S., Liu, Y., Liu, L., Li, W., Chen, J., Liu, Y., et al. (2024) · Food Chemistry X · doi:10.1016/j.fochx.2024.101249 · Cited by 19

Diversification of the Rho transcription termination factor in bacteria

Moreira, S. M., Chyou, T., Wade, J. T., & Brown, C. M. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae582 · Cited by 19

A metagenome-assembled genome inventory for children reveals early-life gut bacteriome and virome dynamics

Peng, Y., Zhu, J., Wang, S., Liu, Y., Liu, X., DeLeon, O., Zhu, W., Xu, Z., Zhang, X., Zhao, S., et al. (2024) · Cell Host & Microbe · doi:10.1016/j.chom.2024.10.017 · Cited by 21

Cell type and dynamic state govern genetic regulation of gene expression in heterogeneous differentiating cultures

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Alzheimer's disease‐associated CD83(+) microglia are linked with increased immunoglobulin G4 and human cytomegalovirus in the gut, vagal nerve, and brain

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Disruption of G3BP1 granules promotes mammalian CNS and PNS axon regeneration

Sahoo, P. K., Agrawal, M., Hanovice, N. J., Ward, P. J., Desai, M., Smith, T. P., SiMa, H., Dulin, J. N., Vaughn, L. S., Tuszynski, M. H., et al. (2025) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2411811122 · Cited by 19

Therapeutic potential of curcuminoids in type 2 diabetes mellitus (T2DM): Insights from network pharmacology, molecular docking, and dynamics simulations

Ankit, P., Chong, K. T., & Tayara, H. (2025) · Food Bioscience · doi:10.1016/j.fbio.2025.106406 · Cited by 19

A structural perspective on enzymes and their catalytic mechanisms

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Top‐Down Proteomics: Why and When?

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Keratin 6A promotes skin inflammation through JAK1-STAT3 activation in keratinocytes

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RBPseg: Toward a complete phage tail fiber structure atlas

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Of Revolutions and Roadblocks: The Emerging Role of Machine Learning in Biocatalysis

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Prevalence of loss-of-function, gain-of-function and dominant-negative mechanisms across genetic disease phenotypes

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Tousled-like kinase 2 targets ASF1 histone chaperones through client mimicry

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Ribosome profiling reveals multiple roles of SecA in cotranslational protein export

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Saliva changes in composition associated to COVID-19: a preliminary study

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A method for Boolean analysis of protein interactions at a molecular level

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New approaches in developing medicinal herbs databases

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Elucidating the functional roles of prokaryotic proteins using big data and artificial intelligence

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Targeting the I7L Protease: A Rational Design for Anti-Monkeypox Drugs?

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A tRNA modification in Mycobacterium tuberculosis facilitates optimal intracellular growth

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Mechanisms of Primed Defense: Plant Immunity Induced by Endophytic Colonization of a Mycovirus-Induced Hypovirulent Fungal Pathogen

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Plasma proteomics discovery of mental health risk biomarkers in adolescents

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Multi-Omics Analysis of Circulating Exosomes in Adherent Long-Term Treated OSA Patients

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SPDB: a comprehensive resource and knowledgebase for proteomic data at the single-cell resolution

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Medication-Related Osteonecrosis of the Jaw: A Systematic Review and a Bioinformatic Analysis

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UniProt: the Universal Protein Knowledgebase in 2025

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doi:10.1093/nar/gkj161 The Universal Protein Resource (UniProt): an expanding universe of protein information

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