UniRef: comprehensive and non-redundant UniProt reference clusters

Cited by (1,003)

Items 701–800 of 1,003

1. Oral Microbiome in Nonsmoker Patients with Oral Cavity Squamous Cell Carcinoma, Defined by Metagenomic Shotgun Sequencing
   Ian Ganly, Yuhan Hao, Matthew Harry Rosenthal, Hongmei Wang, Jocelyn C. Migliacci, Bin Huang, Nora Katabi, Stuart M. Brown, Yi‐Wei Tang, Zhiheng Pei et al. · 2022 · Cancers
2. Enhanced meat chicken productivity in response to the probiotic Bacillus amyloliquefaciens H57 is associated with the enrichment of microbial amino acid and vitamin biosynthesis pathways
   Yadav Sharma Bajagai, Yun Kit Yeoh, Xiuhua Li, Dagong Zhang, Paul G. Dennis, D. Ouwerkerk, Peter J. Dart, Athol V. Klieve, W. L. Bryden · 2023 · Journal of Applied Microbiology
3. Oxygenolytic sulfoquinovose degradation by an iron-dependent alkanesulfonate dioxygenase
   Zonghua Ye, Yifeng Wei, Jiang Li, Yan Zhang · 2023 · iScience
4. Deciphering the protein landscape with ProtFlash, a lightweight language model
   Lei Wang, Hui Zhang, Wei Min Xu, Zhidong Xue, Yan Wang · 2023 · Cell Reports Physical Science
5. Accurate prediction of functional effect of single amino acid variants with deep learning
   Houssemeddine Derbel, Zhongming Zhao, Qian Liu · 2023 · Computational and Structural Biotechnology Journal
6. UmamiPreDL: Deep learning model for umami taste prediction of peptides using BERT and CNN
   Arun Pandiyan Indiran, Humaira Fatima, Sampriti Chattopadhyay, Sureshkumar Ramadoss, Yashwanth Radhakrishnan · 2024 · Computational Biology and Chemistry
7. Simple Porifera holobiont reveals complex interactions between the host, an archaeon, a bacterium, and a phage
   Alessandro N Garritano, Zhelun Zhang, Yunke Jia, Michelle A. Allen, Lilian J Hill, Unnikrishnan Kuzhiumparambil, Cora Hinkley, Jean‐Baptiste Raina, Raquel Silva Peixoto, Torsten Thomas · 2024 · The ISME Journal
8. De novo characterization of the Timema cristinae transcriptome facilitates marker discovery and inference of genetic divergence
   Aaron A. Comeault, Mathew Sommers, Tanja Schwander, C. Alex Buerkle, Timothy E. Farkas, Patrik Nosil, Thomas Lee Parchman · 2012 · Molecular Ecology Resources
9. Insights from the complete genome sequence of Clostridium tyrobutyricum provide a platform for biotechnological and industrial applications
   Qian Wu, Tingting Liu, Liying Zhu, He Huang, Ling Jiang · 2017 · Journal of Industrial Microbiology & Biotechnology
10. On the application of reverse vaccinology to parasitic diseases: a perspective on feature selection and ranking of vaccine candidates
    Stephen J. Goodswen, Paul J Kennedy, John Ellis · 2017 · International Journal for Parasitology
11. EUCANEXT: an integrated database for the exploration of genomic and transcriptomic data from Eucalyptus species
    Leandro Costa Nascimento, Marcela Mendes Salazar, Jorge Lepikson-Neto, Eduardo Leal Oliveira Camargo, Lucas Salera Parreiras, Gonçalo Amarante Guimarães Pereira, Marcelo Falsarella Carazzolle · 2017 · Database
12. Biochemical and structural investigation of sulfoacetaldehyde reductase from Klebsiella oxytoca
    Yan Zhou, Yifeng Wei, Lianyun Lin, Tong Xu, Ee Lui Ang, Huimin Zhao, Zhiguang Yuchi, Yan Zhang · 2019 · Biochemical Journal
13. Discovery of a New Genetic Variant of Methionine Aminopeptidase from Streptococci with Possible Post-Translational Modifications: Biochemical and Structural Characterization
    Tarun Arya, Chandan Kishor, Venkateshwarlu Saddanapu, Ravikumar Reddi, A. Addlagatta · 2013 · PLoS ONE
14. What's that gene (or protein)? Online resources for exploring functions of genes, transcripts, and proteins
    James R. A. Hutchins · 2014 · Molecular Biology of the Cell
15. A generative artificial intelligence approach for antibiotic optimization
    Marcelo D. T. Torres, Yimeng Zeng, Fang Wan, Natalie Maus, Jacob R. Gardner, César de la Fuente‐Núñez · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
16. How artificial intelligence is reengineering protein engineering
    Jennifer Listgarten, Hanlun Jiang · 2026 · Science
17. Population-associated heterogeneity of the digestive Cys protease complement in Colorado potato beetle, Leptinotarsa decemlineata
    Asieh Rasoolizadeh, Marie‐Claire Goulet, Jean‐Frédéric Guay, Conrad Cloutier, Dominique Michaud · 2017 · Journal of Insect Physiology
18. Evolutionary Stabilization of Cooperative Toxin Production through a Bacterium-Plasmid-Phage Interplay
    Stefanie Spriewald, Eva Stadler, Burkhard A. Hense, Philipp C. Münch, Alice Carolyn McHardy, Anna S. Weiß, Nancy Obeng, Johannes Müller, Bärbel Stecher · 2020 · mBio
19. AggBERT: Best in Class Prediction of Hexapeptide Amyloidogenesis with a Semi-Supervised ProtBERT Model
    Ryann M. Perez, Xinning Li, Sam G. Giannakoulias, E. James Petersson · 2023 · Journal of Chemical Information and Modeling
20. Spatom: a graph neural network for structure-based protein–protein interaction site prediction
    Haonan Wu, Jiyun Han, Shizhuo Zhang, Gaojia Xin, Chaozhou Mou, Juntao Liu · 2023 · Briefings in Bioinformatics
21. Deep mutational scanning of hepatitis B virus reveals a mechanism for cis-preferential reverse transcription
    Yingpu Yu, Maximilian A. Kass, Mengyin Zhang, Noor Youssef, Catherine A. Freije, Kelly P. Brock, Lauren C. Aguado, Leon Louis Seifert, Sanjana Venkittu, Xupeng Hong et al. · 2024 · Cell
22. Metagenomic analysis demonstrates distinct changes in the gut microbiome of Kawasaki diseases children
    Linli Han, Xu Liu, Yue Lan, Y. Hua, Zhen-Xin Fan, Yi-Fei Li · 2024 · Frontiers in Immunology
23. Complete Genome Sequence of the Thermophilic Bacterium Thermus sp. Strain CCB_US3_UF1
    B. S. Teh, Amirah Rahman, J. Saito, Shaobin Hou, Mukhtar Alam · 2012 · Journal of Bacteriology
24. SCLpredT: Ab initio and homology-based prediction of subcellular localization by N-to-1 neural networks
    Alessandro Adelfio, Viola Volpato, Gianluca Pollastri · 2013 · SpringerPlus
25. Near complete genome sequence of the animal feed probiotic, Bacillus amyloliquefaciens H57
    Benjamin J. Schofield, Adam Skarshewski, Nancy Lachner, D. Ouwerkerk, Athol V. Klieve, Peter J. Dart, Philip Hugenholtz · 2016 · Standards in Genomic Sciences
26. Evolutionary coupling analysis identifies the impact of disease-associated variants at less-conserved sites
    Donghyo Kim, Seong Kyu Han, Kwanghwan Lee, Inhae Kim, JungHo Kong, Sanguk Kim · 2019 · Nucleic Acids Research
27. Temporal distribution of microbial community in an industrial wastewater treatment system following crash and during recovery periods
    Hana Barak, Asher Brenner, Alex Sivan, Ariel Kushmaro · 2020 · Chemosphere
28. The Lung Microbiome of Three Young Brazilian Patients With Cystic Fibrosis Colonized by Fungi
    Otávio Guilherme Gonçalves de Almeida, Carolina Paulino da Costa Capizzani, Ludmilla Tonani, Patrícia Helena Grizante Barião, Anderson Ferreira da Cunha, Elaine Cristina Pereira De Martinis, Lídia Alice Gomes Monteiro Marin Torres, Márcia Regina von Zeska Kress · 2020 · Frontiers in Cellular and Infection Microbiology
29. Identification of functional motions in the adenylate kinase (ADK) protein family by computational hybrid approaches
    Dagoberto Armenta‐Medina, Ernesto Pérez‐Rueda, Lorenzo Segovia · 2011 · Proteins Structure Function and Bioinformatics
30. Expression of the mevalonate pathway enzymes in the Lutzomyia longipalpis (Diptera: Psychodidae) sex pheromone gland demonstrated by an integrated proteomic approach
    Natalia González-Caballero, Andrés Rodríguez-Vega, Geovane Dias-Lopes, Jesus Gilberto Valenzuela, José M. C. Ribeiro, Paulo C. Carvalho, Richard Hemmi Valente, Reginaldo Peçanha Brazil, Patrícia Cuervo · 2013 · Journal of Proteomics
31. Filling-in Void and Sparse Regions in Protein Sequence Space by Protein-Like Artificial Sequences Enables Remarkable Enhancement in Remote Homology Detection Capability
    Richa Mudgal, Ramanathan Sowdhamini, Nagasuma R Chandra, Narayanaswamy Srinivasan, Sankaran Sandhya · 2013 · Journal of Molecular Biology
32. Efficient Distributed Smith-Waterman Algorithm Based on Apache Spark
    Bo Xu, Changlong Li, Hang Zhuang, Jiali Wang, Qingfeng Wang, Xuehai Zhou · 2017 · IEEE ... International Conference on Cloud Computing
33. Microevolutionary selection dynamics acting on immune genes of the green‐veined white butterfly, Pieris napi
    Naomi L. P. Keehnen, Jason A. Hill, Sören Nylin, Christopher West Wheat · 2018 · Molecular Ecology
34. Bioinformatic approaches to identifying orthologs and assessing evolutionary relationships
    Eric J. Vallender · 2009 · Methods
35. FastBLAST: Homology Relationships for Millions of Proteins
    Morgan N. Price, Paramvir Dehal, Adam P. Arkin · 2008 · PLoS ONE
36. Differential Effects of CSF-1R D802V and KIT D816V Homologous Mutations on Receptor Tertiary Structure and Allosteric Communication
    Priscila da Silva Figueiredo Celestino Gomes, Nicolas Panel, Élodie Laine, Pedro G. Pascutti, Éric Solary, Luba Tchertanov · 2014 · PLoS ONE
37. Association of distinct microbial and metabolic signatures with microscopic colitis
    Sheng-Yin Chen, Hanseul Kim, Étienne Nzabarushimana, Jiaxian Shen, Katherine Williams, Jenny Gurung, Jessica McGoldrick, Kristin E. Burke, Joseph Carl Yarze, Long H. Nguyen et al. · 2025 · Nature Communications
38. A common root for coevolution and substitution rate variability in protein sequence evolution
    Francesca Rizzato, Stefano Zamuner, Andrea Pagnani, Alessandro Laio · 2019 · Scientific Reports
39. Bacteroides thetaiotaomicron, a Model Gastrointestinal Tract Species, Prefers Heme as an Iron Source, Yields Protoporphyrin IX as a Product, and Acts as a Heme Reservoir
    Margaux Meslé, Chase R. Gray, Mensur Dlakić, Jennifer L. DuBois · 2023 · Microbiology Spectrum
40. The claim of primacy of human gut Bacteroides ovatus in dietary cellobiose degradation
    Meixia Li, Yeqing Wang, Ciliang Guo, Sheng Wang, Liangzhen Zheng, Yifan Bu, Kan Ding · 2023 · Gut Microbes
41. Multi-label classification and features investigation of antimicrobial peptides with various functional classes
    Chia‐Ru Chung, Jhen-Ting Liou, Li-Ching Wu, Jorng‐Tzong Horng, Tzong-Yi Lee · 2023 · iScience
42. Ceftiofur treatment of sows results in long-term alterations in the nasal microbiota of the offspring that can be ameliorated by inoculation of nasal colonizers
    Miguel Blanco-Fuertes, Marina Sibila, Giovanni Franzo, Pau Obregón-Gutierrez, Francesc Illas, Florencia Correa‐Fiz, Virginia Aragón · 2023 · Animal Microbiome
43. Protein–protein interaction and site prediction using transfer learning
    Tuoyu Liu, Han Gao, Xiaopu Ren, Guoshun Xu, Bo Liu, Ningfeng Wu, Huiying Luo, Yuan Wang, Tao Tu, Bin Yao et al. · 2023 · Briefings in Bioinformatics
44. Dancing the Nanopore limbo – Nanopore metagenomics from small DNA quantities for bacterial genome reconstruction
    Sophie A. Simon, Katharina Schmidt, Lea Griesdorn, André Soares, Till L. V. Bornemann, Alexander J. Probst · 2023 · BMC Genomics
45. Red pandas with different diets and environments exhibit different gut microbial functional composition and capacity
    Yunwei LU, Liang Zhang, Xu Liu, Yue Lan, Lixia WU, Jiao Wang, Kongju Wu, Chaojie YANG, Ruiqing Lv, Dejiao Yi et al. · 2024 · Integrative Zoology
46. BLANNOTATOR: enhanced homology-based function prediction of bacterial proteins
    Matti Kankainen, Teija Ojala, Liisa Holm · 2012 · BMC Bioinformatics
47. Analysis of the tryptic search space in UniProt databases
    Emanuele Alpi, Johannes Griss, Alan Sousa da Silva, Benoît Bely, Ricardo Antunes, Hermann Zellner, Daniel Ríos, Claire O’Donovan, Juan Antonio Vizcaíno, Maria Jesus Martin · 2014 · PROTEOMICS
48. Lncident: A Tool for Rapid Identification of Long Noncoding RNAs Utilizing Sequence Intrinsic Composition and Open Reading Frame Information
    Siyu Han, Yanchun Liang, Ying Li, Wei Du · 2016 · International Journal of Genomics
49. Nature of Long-Range Evolutionary Constraint in Enzymes: Insights from Comparison to Pseudoenzymes with Similar Structures
    Avital Sharir‐Ivry, Yu Xia · 2018 · Molecular Biology and Evolution
50. Surface patches on recombinant erythropoietin predict protein solubility: engineering proteins to minimise aggregation
    M. Alejandro Carballo-Amador, Edward A. McKenzie, Alan J. Dickson, J. Warwicker · 2019 · BMC Biotechnology
51. Molecular replacement using structure predictions from databases
    Adam J. Simpkin, Jens M. H. Thomas, Felix Šimkovic, Ronan M. Keegan, Daniel John Rigden · 2019 · Acta Crystallographica Section D Structural Biology
52. Performance of Five Metagenomic Classifiers for Virus Pathogen Detection Using Respiratory Samples from a Clinical Cohort
    Ellen C. Carbo, Igor A. Sidorov, Anneloes L. van Rijn, Nikolaos Pappas, Sander van Boheemen, Hailiang Mei, Pieter Sicco Hiemstra, Tomas Eagan, Eric C. J. Claas, Aloys C.M. Kroes et al. · 2022 · Pathogens
53. Labellum transcriptome reveals alkene biosynthetic genes involved in orchid sexual deception and pollination-induced senescence
    Filipa Monteiro, Mónica Sebastiana, Andreia Figueiredo, Lisete Sousa, Helena C. Cotrim, Maria Salomé Pais · 2012 · Functional & Integrative Genomics
54. Transcriptional profiling in burbot (Lota lota) from Lake Mjøsa—A Norwegian Lake contaminated by several organic pollutants
    Pål A. Olsvik, Vidar Berg, Jan Ludvig Lyche · 2013 · Ecotoxicology and Environmental Safety
55. Dynamic changes in the transcriptome of Populus hopeiensis in response to abscisic acid
    Zhong Chen, Lexiang Ji, Jia Wang, Jinpu Jin, Xiaoyu Yang, Pian Rao, Kai Gao, Weihua Liao, Meixia Ye, Xinmin An · 2017 · Scientific Reports
56. Computational crystallization
    Irem Altan, Patrick Charbonneau, Edward H. Snell · 2016 · Archives of Biochemistry and Biophysics
57. Nature of Protein Family Signatures: Insights from Singular Value Analysis of Position-Specific Scoring Matrices
    Akira R. Kinjo, Haruki Nakamura · 2008 · PLoS ONE
58. The passenger‐associated transport repeat promotes virulence factor secretion efficiency and delineates a distinct autotransporter subtype
    Matthew Thomas Doyle, Elizabeth Ngoc Hoa Tran, Renato Morona · 2015 · Molecular Microbiology
59. Discovering the nuclear localization signal universe through a deep learning model with interpretable attention units
    Li, Yi-Fan, Pan, Xiaoyong, Shen, Hong-Bin · 2025 · Patterns
60. Key role of Desulfobacteraceae in C/S cycles of marine sediments is based on congeneric catabolic-regulatory networks
    Lars Wöhlbrand, Marvin Dörries, Roberto Siani, Arturo Medrano-Soto, Vanessa Schnaars, Julian Schumacher, Christina Hilbers, Daniela Thies, Michael Kube, Richard Reinhardt et al. · 2025 · Science Advances
61. Using metagenomic data to boost protein structure prediction and discovery
    Qingzhen Hou, Fabrizio Pucci, Fengming Pan, Fuzhong Xue, Marianne J. Rooman, Qiang Feng · 2022 · Computational and Structural Biotechnology Journal
62. An Improved 1.5-Gigabase Draft Assembly of Massospora cicadina (Zoopagomycota), an Obligate Fungal Parasite of 13- and 17-Year Cicadas
    Jason Stajich, Brian Lovett, Cassandra L. Ettinger, Derreck Carter-House, Tania Kurbessoian, Matt T. Kasson · 2022 · Microbiology Resource Announcements
63. Ocean-wide comparisons of mesopelagic planktonic community structures
    Janaína Rigonato, Marko Budinich, Alejandro A. Murillo, Manoela C. Brandão, Juan José Pierella Karlusich, Yawouvi Dodji Soviadan, Ann Gregory, Hisashi Endo, Florian Volmer Martin Kokoszka, Dean R. Vik et al. · 2023 · ISME Communications
64. Inferring the Effects of Protein Variants on Protein–Protein Interactions with Interpretable Transformer Representations
    Zhe Liu, Wei Qian, Wenxiang Cai, Weichen Song, Weidi Wang, Dhruba Tara Maharjan, Wenhong Cheng, Jue Chen, Han Wang, Dong He Xu et al. · 2023 · Research
65. DeepNeoAG: Neoantigen epitope prediction from melanoma antigens using a synergistic deep learning model combining protein language models and multi-window scanning convolutional neural networks
    Cheng-Che Chuang, Yuchen Liu, Yu‐Yen Ou · 2024 · International Journal of Biological Macromolecules
66. Large language models transform biological research: from architecture to utilization
    Wang, Tao, Luo, Zeyu · 2025 · Science China Information Sciences
67. SARITA: a large language model for generating the S1 subunit of the SARS-CoV-2 spike protein
    Simone Rancati, Giovanna Nicora, Laura Bergomi, Tommaso Mario Buonocore, Daniel M. Czyż, Enea Parimbelli, Riccardo Bellazzi, Marco Salemi, Mattia Prosperi, Simone Marini · 2025 · Briefings in Bioinformatics
68. A reproducible approach to high-throughput biological data acquisition and integration
    Daniela Börnigen, Yo Sup Moon, Ali Rahnavard, Levi Waldron, Lauren J. McIver, Afrah Shafquat, Eric A. Franzosa, Larissa Miropolsky, Christopher J. Sweeney, Xochitl C. Morgan et al. · 2015 · PeerJ
69. Characterisation and Analysis of the Aegilops sharonensis Transcriptome, a Wild Relative of Wheat in the Sitopsis Section
    Costas Bouyioukos, Matthew Moscou, Nicolas Champouret, Inmaculada Hernández‐Pinzón, Eric R. Ward, Brande B. H. Wulff · 2013 · PLoS ONE
70. miRNA Repertoires of Demosponges Stylissa carteri and Xestospongia testudinaria
    Yi Jin Liew, Taewoo Ryu, Manuel Aranda, Timothy Ravasi · 2016 · PLoS ONE
71. RNA-Seq analysis of soft rush (Juncus effusus): transcriptome sequencing, de novo assembly, annotation, and polymorphism identification
    Muhammad Arslan, Upendra Kumar Devisetty, Martin Porsch, Ivo Große, Jochen A. Müller, Stefan G. Michalski · 2019 · BMC Genomics
72. HMMvar-func: a new method for predicting the functional outcome of genetic variants
    Mingming Liu, Layne T. Watson, Liqing Zhang · 2015 · BMC Bioinformatics
73. The midgut of Aedes albopictus females expresses active trypsin-like serine peptidases
    Leonardo Saboia Vahia, Patrícia Cuervo, André Borges-Veloso, Nathalia Pinho, Constança Britto, Geovane Dias-Lopes, José Batista de Jesus · 2014 · Parasites & Vectors
74. Parameter advising for multiple sequence alignment
    Dan DeBlasio, John D. Kececioglu · 2015 · BMC Bioinformatics
75. A clustering package for nucleotide sequences using Laplacian Eigenmaps and Gaussian Mixture Model
    Marine Bruneau, Thierry Mottet, Serge Moulin, Maël Kerbiriou, Franz Chouly, Stéphane Chrétien, Christophe Guyeux · 2017 · Computers in Biology and Medicine
76. Large-Scale Analyses of Site-Specific Evolutionary Rates across Eukaryote Proteomes Reveal Confounding Interactions between Intrinsic Disorder, Secondary Structure, and Functional Domains
    Joseph B. Ahrens, Jordon Rahaman, Jessica Siltberg-Liberles · 2018 · Genes
77. Bioinformatic prediction of G protein-coupled receptor encoding sequences from the transcriptome of the foreleg, including the Haller’s organ, of the cattle tick, Rhipicephalus australis
    Sergio Munoz, Felix David Guerrero, Anastasia Kellogg, Andrew M. Heekin, Ming‐Ying Leung · 2017 · PLoS ONE
78. Now What Sequence? Pre-trained Ensembles for Bayesian Optimization of Protein Sequences
    Ziyue Yang, Katarina A. Milas, Andrew D. White · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
79. Whole-genome prediction of bacterial pathogenic capacity on novel bacteria using protein language models with PathogenFinder2
    Ferrer Florensa, Alfred, Almagro Armenteros, Jose Juan, Kaas, Rolf Sommer, Clausen, Philip Thomas Lanken Conradsen, Nielsen, Henrik, Rost, Burkhard, Aarestrup, Frank Møller · 2026 · Bioinformatics
80. Response of the gut microbiome and metabolome to dietary fiber in healthy dogs
    Amrisha Bhosle, Matthew Irick Jackson, Aaron M. Walsh, Eric A. Franzosa, Dayakar V. Badri, Curtis Huttenhower · 2024 · mSystems
81. Challenging AlphaFold in predicting proteins with large-scale allosteric transitions
    Brooks H. Perkins-Jechow, Juan Pablo Iglesias Ahualli, Huyen Thuc Nhu, Alireza Omidi, Chunchao Li, Jorge A. Holguin-Cruz, Daeahn Cho, Dokyun Na, Nawar Malhis, Jennifer M. Bui et al. · 2025 · Communications Chemistry
82. A Variant of the Sulfoglycolytic Transketolase Pathway for the Degradation of Sulfoquinovose into Sulfoacetate
    Ruoxing Chu, Yifeng Wei, Jiayi Liu, Boran Li, Jianing Zhang, Yan Zhou, Yunfei Du, Yan Zhang · 2023 · Applied and Environmental Microbiology
83. Running ahead of evolution—AI-based simulation for predicting future high-risk SARS-CoV-2 variants
    Jie Chen, Zhiwei Nie, Yu Wang, Kai Wang, Fan Xu, Zhiheng Hu, Bing Zheng, Zhennan Wang, Guoli Song, Jingyi Zhang et al. · 2023 · The International Journal of High Performance Computing Applications
84. SOFB is a comprehensive ensemble deep learning approach for elucidating and characterizing protein-nucleic-acid-binding residues
    Bin Zhang, Zilong Hou, Yuning Yang, Ka‐Chun Wong, Haoran Zhu, Xiangtao Li · 2024 · Communications Biology
85. Gut microbiome structure and function in asymptomatic diverticulosis
    Xinwei Hua, Jessica McGoldrick, Nour Nakrour, Kyle D. Staller, Daniel C. Chung, Ramnik J. Xavier, Hamed Khalili · 2024 · Genome Medicine
86. A web-based bioinformatics interface applied to the GENOSOJA project: databases and pipelines
    Leandro Costa do Nascimento, Gustavo G.L. Costa, Eliseu Binneck, Gonçalo Amarante Guimarães Pereira, Marcelo Falsarella Carazzolle · 2012 · Genetics and Molecular Biology
87. Comparative Analysis of Sequence Clustering Methods for Deduplication of Biological Databases
    Qingyu Chen, Yu Wan, Xiuzhen Zhang, Yang Lei, Justin Zobel, Karin M. Verspoor · 2017 · Journal of Data and Information Quality
88. Cytidine deaminases catalyze the conversion of N ( S , O ) 4 -substituted pyrimidine nucleosides
    Nina Urbelienė, Matas Tiškus, Giedrė Tamulaitienė, Renata Gasparavičiūtė, Ringailė Lapinskaitė, Vykintas Jauniškis, Jurgis Sūdžius, Rita Meškienė, Daiva Tauraitė, Emilija Skrodenytė et al. · 2023 · Science Advances
89. TMFoldRec: a statistical potential-based transmembrane protein fold recognition tool
    Dániel Kozma, Gábor Tusnády · 2015 · BMC Bioinformatics
90. Identification of a Cyclosporine-Specific P450 Hydroxylase Gene through Targeted Cytochrome P450 Complement (CYPome) Disruption in Sebekia benihana
    Mi-Jin Lee, Hyun-Bum Kim, Yeo Joon Yoon, Kyuboem Han, Eung‐Soo Kim · 2013 · Applied and Environmental Microbiology
91. Charting online OMICS resources: A navigational chart for clinical researchers
    Juan Antonio Vizcaíno, Michael Mueller, Henning Hermjakob, Lennart Martens · 2008 · PROTEOMICS - CLINICAL APPLICATIONS
92. The Pokeweed Leaf mRNA Transcriptome and Its Regulation by Jasmonic Acid
    Kira C. M. Neller, Alexander Klenov, Katalin A. Hudak · 2016 · Frontiers in Plant Science
93. Characterization of a male reproductive transcriptome for Peromyscus eremicus (Cactus mouse)
    Lauren L. Kordonowy, Matthew D. MacManes · 2016 · PeerJ
94. De novo transcriptome sequencing and comparative analysis of midgut tissues of four non-model insects pertaining to Hemiptera, Coleoptera, Diptera and Lepidoptera
    Rajesh Kumar Gazara, Christiane Cardoso, Daniel Bellieny Rabelo, Clélia Ferreira, Walter Ribeiro Terra, Thiago M. Venâncio · 2017 · Gene
95. Family-specific analysis of variant pathogenicity prediction tools
    Jan Maciej Zaucha, Michael Heinzinger, Svetlana I. Tarnovskaya, Burkhard Rost, Dmitrij Frishman · 2020 · NAR Genomics and Bioinformatics
96. Phylogenomic and Domain Analysis of Iterative Polyketide Synthases in Aspergillus Species
    Shu-Hsi Lin, Miwa Yoshimoto, Pingchiang C. Lyu, Chuan Yi Tang, Masanori Arita · 2012 · Evolutionary Bioinformatics
97. Evolutionary Constraints Acting on DDX3X Protein Potentially Interferes with Rev-Mediated Nuclear Export of HIV-1 RNA
    Deepak Sharma, Jayanta Bhattacharya · 2010 · PLoS ONE
98. RAFTS3: Rapid Alignment-Free Tool for Sequence Similarity Search
    Ricardo A. Vialle, Fábio de Oliveira Pedrosa, Vinícius Almir Weiss, Dieval Guizelini, Juliana Helena Tibães, Jeroniza Nunes Marchaukoski, Emanuel Maltempi de Souza, Roberto Tadeu Raittz · 2016 · bioRxiv (Cold Spring Harbor Laboratory)
99. PEFT-SP: Parameter-Efficient Fine-Tuning on Large Protein Language Models Improves Signal Peptide Prediction
    Shuai Zeng, Duolin Wang, Dong He Xu · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
100. A generative artificial intelligence approach for peptide antibiotic optimization
     Marcelo D. T. Torres, Yimeng Zeng, Fangping Wan, Natalie Maus, Jacob R. Gardner, César de la Fuente‐Núñez · 2026 · Nature Machine Intelligence