UniRef: comprehensive and non-redundant UniProt reference clusters
Suzek, Baris E., Huang, Hongzhan, McGarvey, Peter, Mazumder, Raja, Wu, Cathy H.·2007·Bioinformatics
Cited by (1,003)
Items 801–900 of 1,003
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- Hyperexpansion of genetic diversity and metabolic capacity of extremophilic bacteria and archaea in ancient Andean lake sedimentsMaría Ángeles Lezcano, T. Bornemann, L. Sánchez-García, D. Carrizo, P. Adam, S. Esser, N. Cabrol, Alexander J. Probst, V. Parro · 2024 · Microbiome
- Incorporating genetic load contributes to predicting Arabidopsis thaliana’s response to climate changeJuan Jiang, Jia‐Fu Chen, Xin-Tong Li, Li Wang, Jian‐Feng Mao, Baosheng Wang, Ya‐Long Guo · 2025 · Nature Communications
- MiFoDB, a workflow for microbial food metagenomic characterization, enables high-resolution analysis of fermented food microbial dynamicsElisa B. Caffrey, Matthew R. Olm, Caroline Isabel Kothe, Hannah Constance Wastyk, Joshua D. Evans, Justin Laine Sonnenburg · 2025 · mSystems
- UniProtKB amid the turmoil of plant proteomics researchMichel Schneider, Sylvain Poux · 2012 · Frontiers in Plant Science
- Classifying Proteins into Functional Groups Based on All-versus-All BLAST of 10 Million ProteinsNatali Kolker, Roger Higdon, William Broomall, Larissa I Stanberry, Dean Welch, Wei Lu, Winston A. Haynes, Roger Barga, Eugene Kolker · 2011 · OMICS A Journal of Integrative Biology
- M-ORBIS: Mapping of mOleculaR Binding sItes and SurfacesLaurent‐Philippe Albou, Olivier Poch, Dino Moras · 2010 · Nucleic Acids Research
- MScDB: A Mass Spectrometry-centric Protein Sequence Database for ProteomicsHarald Marx, Simone Lemeer, Susan Klaeger, Thomas Rattei, Bernhard Küster · 2013 · Journal of Proteome Research
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- Structural analysis of missense mutations occurring in the DNA-binding domain of HSF4 associated with congenital cataractsZaiyu Xiao, Ling Guo, Yang Zhang, Liwei Cui, Yujie Dai, Zhu Lan, Qinghua Zhang, Sheng Wang, Wei Liu · 2019 · Journal of Structural Biology X
- Exploring Mechanisms of Communication Switching in the Hsp90-Cdc37 Regulatory Complexes with Client Kinases through Allosteric Coupling of Phosphorylation Sites: Perturbation-Based Modeling and Hierarchical Community Analysis of Residue Interaction NetworksGabrielle Stetz, Lindy Astl, Gennady M. Verkhivker · 2020 · Journal of Chemical Theory and Computation
- Predicting the Disease Risk of Protein Mutation Sequences With Pre-training ModelKuan Li, Yue Zhong, Xuan Lin, Zhe Quan · 2020 · Frontiers in Genetics
- SPRoBERTa: protein embedding learning with local fragment modelingLijun Wu, Chengcan Yin, Jinhua Zhu, Zhen Wu, Liang He, Yingce Xia, Shufang Xie, Tao Qin, Tie‐Yan Liu · 2022 · Briefings in Bioinformatics
- Temporal disturbance of a model stream ecosystem by high microbial diversity from treated wastewaterTom Lennard Stach, Guido Sieber, Manan Shah, Sophie A. Simon, André Soares, Till L. V. Bornemann, Julia Plewka, Julian Künkel, Christian Becker, Folker Meyer et al. · 2023 · MicrobiologyOpen
- Detecting duplicate biological entities using Shortest Path Edit DistanceAlex Rudniy, Min Song, James Geller · 2010 · International Journal of Data Mining and Bioinformatics
- Renin mRNA is upregulated in testes and testicular cells in response to treatment with aflatoxin B1Kathleen J Austin, Rebecca Cockrum, A.M. Jons, Brenda M. Alexander, K. M. Cammack · 2011 · Theriogenology
- Single substitutions to closely related amino acids contribute to the functional diversification of an insect‐inducible, positively selected plant cystatinAsieh Rasoolizadeh, Marie‐Claire Goulet, Frank Sainsbury, Conrad Cloutier, Dominique Michaud · 2016 · FEBS Journal
- Databases for Wheat Genomics and Crop ImprovementYuxuan Yuan, Armin Scheben, Chon‐Kit Kenneth Chan, David Edwards · 2017 · Methods in molecular biology
- Unraveling the complex genome of Saccharum spontaneum using Polyploid Gene AssemblerLeandro Costa do Nascimento, Karina Yanagui, Juliana José, Eduardo Leal Oliveira Camargo, Maria Carolina B. Grassi, Camila Pinto da Cunha, José Antonio Bressiani, Guilherme Mendes Almeida Carvalho, Carlos Roberto Carvalho, Paula Favoretti Vital do Prado et al. · 2019 · DNA Research
- Genome profiling of sterol synthesis shows convergent evolution in parasites and guides chemotherapeutic attackMatthias A. Fügi, Kapila Gunasekera, Torsten Ochsenreiter, Xue Li Guan, Markus Rene Wenk, Pascal Mäser · 2014 · Journal of Lipid Research
- Unique and Universal Features of Epsilonproteobacterial Origins of Chromosome Replication and DnaA-DnaA Box InteractionsPawel Jaworski, Rafał Donczew, Thorsten Mielke, Marcel Thiel, Stanisław Ołdziej, Christoph Weigel, Anna Magdalena Zawilak-Pawlik · 2016 · Frontiers in Microbiology
- The high-throughput gene prediction of more than 1,700 eukaryote genomes using the software package EukMetaSanityChristopher J. Neely, Sarah K. Hu, Harriet Alexander, Benjamin Tully · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
- HMD-AMP: Protein Language-Powered Hierarchical Multi-label Deep Forest for Annotating Antimicrobial PeptidesQinze Yu, Zhihang Dong, Xingyu Fan, Licheng Zong, Yu Li · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
- Codon language embeddings provide strong signals for protein engineeringCarlos Outeiral, Charlotte Mary Deane · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
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- Streptococcus anginosus -derived methionine promotes gastric cancer progressionCheng‐Bei Zhou, Licong Zhao, Youwen Qin, Jingchen Yu, W. Li, Qianhui Feng, Xin Tong, Resalaiti Abuduaini, Shiyuan Lu, Huang Tang et al. · 2026 · Gut
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- The Bear Giant-Skipper genome suggests genetic adaptations to living inside yucca rootsQian Cong, Wenlin Li, Dominika Borek, Zbyszek Otwinowski, Nick V. Grishin · 2018 · Molecular Genetics and Genomics
- Analysis of host-pathogen gene association networks reveals patient-specific response to streptococcal and polymicrobial necrotising soft tissue infectionsSanjeevan Jahagirdar, Lorna Morris, Nirupama Benis, Oddvar Oppegaard, Mattias Svenson, Ole Hyldegaard, Steinar Skrede, Anna Norrby‐Teglund, INFECT Study group, Trond Bruun et al. · 2022 · BMC Medicine
- Analysis of the inter-domain orientation of tandem RRM domains with diverse linkers: connecting experimental with AlphaFold2 predicted modelsJoel Roca‐Martínez, Hyun-Seo Kang, Michael Sattler, Wim Vranken · 2024 · NAR Genomics and Bioinformatics
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- Is There an Optimal Substitution Matrix for Contact Prediction with Correlated Mutations?Pietro Di Lena, Piero Fariselli, Luciano Margara, Marco Vassura, Rita Casadio · 2010 · IEEE Transactions on Computational Biology and Bioinformatics
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- Novel search method for the discovery of functional relationshipsFidel Ramírez, Glenn Lawyer, Mario Albrecht · 2011 · Bioinformatics
- NrichD database: sequence databases enriched with computationally designed protein-like sequences aid in remote homology detectionRicha Mudgal, Sankaran Sandhya, Gayatri Kumar, Ramanathan Sowdhamini, Nagasuma R Chandra, Narayanaswamy Srinivasan · 2014 · Nucleic Acids Research
- 3gClust: Human Protein Cluster AnalysisAnup Kumar Halder, Piyali Chatterjee, Mita Nasipuri, Dariusz Plewczyński, Subhadip Basu · 2018 · IEEE Transactions on Computational Biology and Bioinformatics
- Comparative Analysis of Homologous Sequences of Saccharum officinarum and Saccharum spontaneum Reveals Independent Polyploidization EventsAnupma Sharma, Jinjin Song, Qingfan Lin, Ratnesh Kumar Singh, Ninfa Ramos, Kai Wang, Jisen Zhang, Ray Ming, Qingyi Yu · 2018 · Frontiers in Plant Science
- Quantitative proteome-based guidelines for intrinsic disorder characterizationMichael P. Vincent, Mark E. Whidden, Santiago D. Schnell · 2016 · Biophysical Chemistry
- lncRNADetector: a bioinformatics pipeline for long non-coding RNA identification and MAPslnc: a repository of medicinal and aromatic plant lncRNAsBhaskar Shukla, Sanchita Gupta, Gaurava Srivastava, Ashok Kumar Sharma, Ashutosh K. Shukla, Ajit Kumar Shasany · 2021 · RNA Biology
- Anaerobic Hydroxyproline Degradation Involving C–N Cleavage by a Glycyl Radical EnzymeYongxu Duan, Yifeng Wei, Meining Xing, Jiayi Liu, Li Jiang, Qiang Lü, Xumei Liu, Yanhong Liu, Ee Lui Ang, Rong‐Zhen Liao et al. · 2022 · Journal of the American Chemical Society
- Discovery of the ATPase Activity of a Cobalt-Type Nitrile Hydratase Activator and Its Promoting Effect on Enzyme MaturationYuanyuan Xia, Zhongyi Cheng, Chen Hou, Łukasz Pepłowski, Zhemin Zhou, Xianzhong Chen · 2022 · Biochemistry
- Multi-omics analysis reveals the host–microbe interactions in aged rhesus macaquesJue Xu, Yue Lan, Xinqi Wang, Ke Shang, Xu Liu, Jiao Wang, Jing Li, Bisong Yue, Meiying Shao, Zhenxin Fan · 2022 · Frontiers in Microbiology
- Protein language models meet reduced amino acid alphabetsIoan Ieremie, Rob M. Ewing, Mahesan Niranjan · 2024 · Bioinformatics
- Missing microbial eukaryotes and misleading meta-omic conclusionsArianna I. Krinos, Margaret Mars Brisbin, Sarah K. Hu, Natalie R. Cohen, Tatiana A. Rynearson, Michael J. Follows, Frederik Schulz, Harriet Alexander · 2024 · Nature Communications
- FHY3/FAR1 transposable elements generate adaptive genetic variation in the Bassia scoparia genomeNathan D. Hall, Jacob S. Montgomery, Jinyi Chen, Christopher A. Saski, Maor Matzrafi, Philip H. Westra, Todd Adam Gaines, Eric L. Patterson · 2025 · Pest Management Science
- Flavonoid supplementation affects the expression of genes involved in cell wall formation and lignification metabolism and increases sugar content and saccharification in the fast-growing eucalyptus hybrid E. urophylla x E. grandisJorge Lepikson-Neto, Leandro Costa do Nascimento, Marcela M Salazar, Eduardo Leal Oliveira Camargo, João Paulo L. Franco Cairo, Paulo José Pereira Lima Teixeira, Wesley Leoricy Marques, Fabio Marcio Squina, Piotr A. Mieczkowski, Ana Carolina Deckmann et al. · 2014 · BMC Plant Biology
- Uncovering hidden duplicated content in public transcriptomics dataMarta Rosikiewicz, Aurélie Comte, Anne Niknejad, Marc Robinson‐Rechavi, Frederic Bastian · 2013 · Database
- N-Terminal Domains in Two-Domain Proteins Are Biased to Be Shorter and Predicted to Fold Faster Than Their C-Terminal CounterpartsEtai Jacob, Ron Unger, Amnon Horovitz · 2013 · Cell Reports
- EPTool: A New Enhancing PSSM Tool for Protein Secondary Structure PredictionYuzhi Guo, Jiaxiang Wu, Hehuan Ma, Sheng Wang, Junzhou Huang · 2020 · Journal of Computational Biology
- Coordinated Diel Gene Expression of Cyanobacteria and Their MicrobiomeKai Wang, Xiaozhen Mou · 2021 · Microorganisms
- Calcineurin B‐like domains in the large regulatory α/β subunits of phosphorylase kinaseCathelène Carrière, Jean‐Paul Mornon, Catherine Vénien‐Bryan, Nicolas Boisset, Isabelle Callebaut · 2008 · Proteins Structure Function and Bioinformatics
- A Case Study for Large-Scale Human Microbiome Analysis Using JCVI’s Metagenomics Reports (METAREP)Johannes B. Goll, Mathangi Thiagarajan, Sahar Abubucker, Curtis Huttenhower, Shibu Yooseph, Barbara A. Methé · 2012 · PLoS ONE
- Crystal Structure of the Substrate-Binding Domain from Listeria monocytogenes Bile-Resistance Determinant BilEStephanie J. Ruiz, Gea K. Schuurman‐Wolters, Bert Poolman · 2016 · Crystals
- De novo assembly of a transcriptome from the eggs and early embryos of Astropecten aranciacusFrancesco Musacchia, Filip Vasilev, Marco Borra, Elio Biffali, Remo Sanges, Luigia Santella, Jong Tai Chun · 2017 · PLoS ONE
- Computing the Pathogenicity of Wilson’s Disease ATP7B Mutations: Implications for Disease PrevalenceNing Tang, Thomas Damgaard Sandahl, Peter Ott, Kasper P. Kepp · 2019 · Journal of Chemical Information and Modeling
- Profiling novel lateral gene transfer events in the human microbiomeTiffany Y. Hsu, Étienne Nzabarushimana, Dennis H.-J. Wong, Chengwei Luo, Robert Gerald Beiko, Morgan G. I. Langille, Curtis Huttenhower, Long H. Nguyen, Eric A. Franzosa · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
- Molecular and physiological characterization of grapevine rootstock adaptation to droughtAnthony Peccoux · 2011 · Oskar-Bordeaux (Universite de Bordeaux)
- Diffusion Models at the Drug Discovery Frontier: A Review on Generating Small Molecules Versus Therapeutic PeptidesYiquan Wang, Yahui Ma, Yu-Han Chang, Jiayao Yan, Jialin Zhang, Ming-Yi Cai, Kai Wei · 2025 · Biology
- Gut Phage Biobank: a collection of bacteriophages targeting human commensal bacteriaBo Xing, Cong Liu, Wantong Chen, Zhuoran Li, Xiaohuan Jing, Chao‐Liang Wu, Ruixin Liu, Xiuqin Zhang, Xun Xu, Junhua Li et al. · 2025 · Nature Communications
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- Comprehensive Assessment of BERT-Based Methods for Predicting Antimicrobial PeptidesW J Gao, Jun Wei Zhao, Jianfeng Gui, Zehan Wang, Jie Chen, Zhenyu Yue · 2024 · Journal of Chemical Information and Modeling
- In silico prediction of variant effects: promises and limitations for precision plant breedingJanek Sendrowski, Thomas M Bataillon, Guillaume P. Ramstein · 2025 · Theoretical and Applied Genetics
- Protein language model identifies disordered, conserved motifs implicated in phase separationZhang, Yumeng, Zheng, Jared, Zhang, Bin · 2025 · eLife
- Transfer learning on protein language models improves antimicrobial peptide classificationElias Georgoulis, Michaela Areti Zervou, Yannis Pantazis · 2025 · Scientific Reports
- Structure- and context-based analysis of the GxGYxYP family reveals a new putative class of Glycoside HydrolaseDaniel John Rigden, Ruth Y. Eberhardt, Harry John Gilbert, Qingping Xu, Yuanyuan Chang, Adam Godzik · 2014 · BMC Bioinformatics
- Computational Investigation of Growth Hormone Receptor Trp169Arg Heterozygous Mutation in a Child With Short StatureWilliam Farias Porto, Felipe Albuquerque Marques, Huri Brito Pogue, Maria Teresinha de Oliveira Cardoso, Maria Gabriela Rodrigues do Vale, Állan da Silva Pires, Octávio Luiz Franco, Sérgio Amorim de Alencar, Robert Edward Pogue · 2017 · Journal of Cellular Biochemistry
- Predicting the functional impact of KCNQ1 variants with artificial neural networksSaksham Phul, Georg Kuenze, Carlos G. Vanoye, Charles R. Sanders, Alfred L. George, Jens Meiler · 2022 · PLoS Computational Biology
- Amphicarpic development in Cardamine chenopodiifoliaAurélia Emonet, Miguel Pérez‐Antón, Ulla Neumann, Sonja Dunemann, Bruno Hüettel, Robert Koller, Angela Hay · 2024 · New Phytologist
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