UniRef: comprehensive and non-redundant UniProt reference clusters

Cited by (1,003)

Items 601–700 of 1,003

1. Computationally designed proteins mimic antibody immune evasion in viral evolution
   Noor Youssef, Sarah F. Gurev, Fadi Ghantous, Kelly P. Brock, Javier A. Jaimes, Nicole N. Thadani, Ann Dauphin, Amy C Sherman, Leonid Yurkovetskiy, Daria Soto et al. · 2025 · Immunity
2. The Microflora Danica atlas of Danish environmental microbiomes
   C. Singleton, T. Jensen, F. Delogu, K. Knudsen, E. Sørensen, V. Jørgensen, S. Karst, Y. Yang, M. Sereika, F. Petriglieri et al. · 2025 · Nature
3. Draft genome sequence and characterization of Desulfitobacterium hafniense PCE-S
   Tobias Goris, Bastian Hornung, Thomas Kruse, Anika Reinhold, Martin Westermann, Peter J. Schaap, Hauke Smidt, Gabriele B. Diekert · 2015 · Standards in Genomic Sciences
4. The first complete genomes of Metalmarks and the classification of butterfly families
   Qian Cong, Jinhui Shen, Wenlin Li, Dominika Borek, Zbyszek Otwinowski, Nick V. Grishin · 2017 · Genomics
5. Improved inter-protein contact prediction using dimensional hybrid residual networks and protein language models
   Si, Yunda, Yan, Chengfei · 2023 · Briefings in Bioinformatics
6. Sequencing delivers diminishing returns for homology detection: implications for mapping the protein universe
   Daniel Chubb, Benjamin R. Jefferys, Michael J.E. Sternberg, Lawrence A. Kelley · 2010 · Bioinformatics
7. The reduced genome of Candidatus Kinetoplastibacterium sorsogonicusi, the endosymbiont of Kentomonas sorsogonicus (Trypanosomatidae): loss of the haem-synthesis pathway
   Flávia Moraes Silva, Alexei Yu. Kostygov, Viktoria V. Spodareva, Anzhelika Butenko, Regis Tossou, Julius Lukeš, Vyacheslav Yurchenko, João M. P. Alves · 2018 · Parasitology
8. REC-1 and HIM-5 distribute meiotic crossovers and function redundantly in meiotic double-strand break formation in Caenorhabditis elegans
   George Chung, Ann M. Rose, Mark I.R. Petalcorin, Julie S. Martin, Zebulin Kessler, Luis Sanchez-Pulido, Chris P. Ponting, Judith L. Yanowitz, Simon J. Boulton · 2015 · Genes & Development
9. Metagenomics untangles potential adaptations of Antarctic endolithic bacteria at the fringe of habitability
   Claudia Coleine, Davide Albanese, Angelique E. Ray, Manuel Delgado‐Baquerizo, Jason Stajich, Timothy J. Williams, Stefano Larsen, Susannah Green Tringe, Christa Pennacchio, Belinda C. Ferrari et al. · 2024 · The Science of The Total Environment
10. Generative AI for the Design of Molecules: Advances and Challenges
    Yan Sun, Lianghong Chen, Zihao Jing, Yan Yi Li, Dongkyu Kim, Jing-Yan Gao, Reza Noroozi, Grace Y. Yi, Conrard Giresse Tetsassi Feugmo, Anna Klinkova et al. · 2025 · Journal of Chemical Information and Modeling
11. Computation-Aided Engineering of Cytochrome P450 for the Production of Pravastatin
    Mark A. Ashworth, Elvira Bombino, René M. de Jong, Hein J. Wijma, Dick B. Janssen, Kirsty J. McLean, Andrew W. Munro · 2022 · ACS Catalysis
12. Seasonality of biogeochemically relevant microbial genes in a coastal ocean microbiome
    Adrià Auladell, Isabel Ferrera, Lidia Montiel, Célio Dias Santos Júnior, Marta Sebastián, Ramiro Logares, Josep M. Gasol · 2023 · Environmental Microbiology
13. Molecular damage in F abry disease: Characterization and prediction of alpha‐galactosidase A pathological mutations
    Casandra Riera, Sergio Lois, Carmen Domı́nguez, Israel Fernández‐Cadenas, Joan Montaner, Victor Rodríguez‐Sureda, Xavier de la Cruz · 2014 · Proteins Structure Function and Bioinformatics
14. Protein Bioinformatics Infrastructure for the Integration and Analysis of Multiple High-Throughput “omics” Data
    Chuming Chen, Peter B. McGarvey, Hongzhan Huang, Cathy H. Wu · 2010 · Advances in Bioinformatics
15. A Structured Loop Modulates Coupling between the Substrate-binding and Dimerization Domains in the Multidrug Resistance Transporter EmrE
    James R. Banigan, Anindita Gayen, Min‐Kyu Cho, Nathaniel J. Traaseth · 2014 · Journal of Biological Chemistry
16. Characterisation of Faba Bean (Vicia faba L.) Transcriptome Using RNA-Seq: Sequencing, De Novo Assembly, Annotation, and Expression Analysis
    Shivraj Braich, Shimna Sudheesh, John W. Forster, Sukhjiwan Kaur · 2017 · Agronomy
17. Protein–Protein Interaction Methods and Protein Phase Separation
    Castrense Savojardo, Pier Luigi Martelli, Rita Casadio · 2020 · Annual Review of Biomedical Data Science
18. Following the Footsteps of Chlamydial Gene Regulation
    Daryl Domman, Matthias Horn · 2015 · Molecular Biology and Evolution
19. Prediction of antibiotic resistance mechanisms using a protein language model
    Yagimoto, Kanami, Hosoda, Shion, Sato, Miwa, Hamada, Michiaki · 2024 · Bioinformatics
20. Bacteroidia and Clostridia are equipped to degrade a cascade of polysaccharides along the hindgut of the herbivorous fish Kyphosus sydneyanus
    César Toshio Facimoto, Kendall D. Clements, William Lindsey White, Kim M. Handley · 2024 · ISME Communications
21. The Historical Evolution and Significance of Multiple Sequence Alignment in Molecular Structure and Function Prediction
    Chenyue Zhang, Qinxin Wang, Yiyang Li, Anqi Teng, Gang Hu, Qiqige Wuyun, Wei Hui Zheng · 2024 · Biomolecules
22. Microbial methane production from calcium carbonate at moderately alkaline pH
    Nicole A. Fiore, Anthony J. Kohtz, Daniel N. Miller, Sanjay Antony‐Babu, Donald Pan, Caitlin Lahey, Xi Huang, Yongfeng Lu, Nicole R. Buan, Karrie A. Weber · 2025 · Communications Earth & Environment
23. DRAMMA: a multifaceted machine learning approach for novel antimicrobial resistance gene detection in metagenomic data
    Ella Rannon, Sagi Shaashua, David E Burstein · 2025 · Microbiome
24. Widespread Antibiotic, Biocide, and Metal Resistance in Microbial Communities Inhabiting a Municipal Waste Environment and Anthropogenically Impacted River
    A. Collins-Fairclough, R. Co, M. Ellis, L. Hug · 2018 · Msphere
25. Recovery of Lutacidiplasmatales archaeal order genomes suggests convergent evolution in Thermoplasmatota
    Paul O. Sheridan, Yiyu Meng, Tom A. Williams, Cécile Gubry‐Rangin · 2022 · Nature Communications
26. Comparative Genomics and Physiology of Akkermansia muciniphila Isolates from Human Intestine Reveal Specialized Mucosal Adaptation
    Ouwerkerk, Janneke P., Tytgat, Hanne L. P., Elzinga, Janneke, Koehorst, Jasper, Van den Abbeele, Pieter, Henrissat, Bernard, Gueimonde, Miguel, Cani, Patrice D., Van de Wiele, Tom, Belzer, Clara et al. · 2022 · Microorganisms
27. Nitrate-driven anaerobic oxidation of ethane and butane by bacteria
    Wu, Mengxiong, Li, Jie, Lai, Chun-Yu, Leu, Andy O, Sun, Shengjie, Gu, Rui, Erler, Dirk V, Liu, Lian, Li, Lin, Tyson, Gene W et al. · 2024 · The ISME Journal
28. De Novo Assembly and Characterization of Tall Fescue Transcriptome under Water Stress
    Shishir Kanti Talukder, Perumal Azhaguvel, Shreyartha Mukherjee, Carolyn A. Young, Yuhong Tang, Nick Krom, Malay C. Saha · 2015 · The Plant Genome
29. Protein structure based prediction of catalytic residues
    Jorge Eduardo Fajardo, András Fiser · 2013 · BMC Bioinformatics
30. The Nuanced Interplay of Intrinsic Disorder and Other Structural Properties Driving Protein Evolution
    Joseph B. Ahrens, Helena Gomes Dos Santos, Jessica Siltberg-Liberles · 2016 · Molecular Biology and Evolution
31. Functional insights into the testis transcriptome of the edible sea urchin Loxechinus albus
    Juan Diego Gaitán‐Espitía, Roland Sánchez, Paulina Bruning, Leyla Cárdenas · 2016 · Scientific Reports
32. From Mechanistic Interpretability to Mechanistic Biology: Training, Evaluating, and Interpreting Sparse Autoencoders on Protein Language Models
    Etowah Adams, Liam Bai, Minji Lee, Yiyang Yu, Mohammed AlQuraishi · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
33. Interpreting Potts and Transformer Protein Models Through the Lens of Simplified Attention
    Bhattacharya, Nicholas, Thomas, Neil, Rao, Roshan, Dauparas, Justas, Koo, Peter K., Baker, David, Song, Yun S., Ovchinnikov, Sergey · 2021 · Biocomputing 2022
34. PHIStruct: improving phage–host interaction prediction at low sequence similarity settings using structure-aware protein embeddings
    Gonzales, Mark Edward M, Ureta, Jennifer C, Shrestha, Anish M S · 2024 · Bioinformatics
35. A high-quality genomic catalog of the human oral microbiome broadens its phylogeny and clinical insights
    Jun Hyung Cha, Nayeon Kim, Junyeong Ma, Sung-Ho Lee, Geon Koh, Sunmo Yang, Samuel Beck, Iksu Byeon, Byungwook Lee, Insuk Lee · 2025 · Cell Host & Microbe
36. Proteotyping of laboratory-scale biogas plants reveals multiple steady-states in community composition
    Fabian Kohrs, Robert Heyer, Thomas Bissinger, Robert Kottler, Kay Schallert, Sebastian Püttker, Alexander Behne, Erdmann Rapp, Dirk Benndorf, Udo Reichl · 2017 · Anaerobe
37. Diverse Microorganisms in Sediment and Groundwater Are Implicated in Extracellular Redox Processes Based on Genomic Analysis of Bioanode Communities
    T. Arbour, B. Gilbert, J. Banfield · 2020 · Frontiers in Microbiology
38. Improved protein contact prediction using dimensional hybrid residual networks and singularity enhanced loss function
    Yunda Si, Chengfei Yan · 2021 · Briefings in Bioinformatics
39. The male and female gonad transcriptome of the edible sea urchin, Paracentrotus lividus: Identification of sex-related and lipid biosynthesis genes
    André M. Machado, Sérgio Fernández-Boo, Manuel Nande, Rui Almeida Pinto, Benjamín Costas, L. Filipe C. Castro · 2021 · Aquaculture Reports
40. Possibilities of Using De Novo Design for Generating Diverse Functional Food Enzymes
    Xinglong Wang, Kangjie Xu, Yameng Tan, Song Liu, Jingwen Zhou · 2023 · International Journal of Molecular Sciences
41. Integrating Embeddings from Multiple Protein Language Models to Improve Protein O-GlcNAc Site Prediction
    Suresh Pokharel, Pawel Pratyush, Hamid D. Ismail, Junfeng Ma, Dukka B. KC · 2023 · International Journal of Molecular Sciences
42. ContScout: sensitive detection and removal of contamination from annotated genomes
    Balázs Bálint, Zsolt Merényi, Botond Hegedüs, Igor V. Grigoriev, Zhihao Hou, Csenge Földi, László G. Nagy · 2024 · Nature Communications
43. CollaPPI: A Collaborative Learning Framework for Predicting Protein-Protein Interactions
    Wenjian Ma, Xiangpeng Bi, Huasen Jiang, Shugang Zhang, Zhiqiang Wei · 2024 · IEEE Journal of Biomedical and Health Informatics
44. A novel genetic selection system for PLP-dependent threonine aldolases
    Lars Giger, Miguel Duarte Toscano, Madeleine Bouzon, Philippe Marlière, Donald Hilvert · 2012 · Tetrahedron
45. A Plasma Membrane Association Module in Yeast Amino Acid Transporters
    Dušan Popov‐Čeleketić, Frans Bianchi, Stephanie J. Ruiz, Febrina Meutiawati, Bert Poolman · 2016 · Journal of Biological Chemistry
46. Analysis of global human gut metagenomes shows that metabolic resilience potential for short-chain fatty acid production is strongly influenced by lifestyle
    David K. Jacobson, Tanvi P. Honap, Andrew T. Ozga, Nicolas Méda, Thérèse Kagone, Hélène Carabin, Paul Spicer, Raul Yhossef Tito, Alexandra J. Obregón-Tito, Luis Marin-Reyes et al. · 2021 · Scientific Reports
47. Redβ177 annealase structure reveals details of oligomerization and λ Red-mediated homologous DNA recombination
    Newing, Timothy P., Brewster, Jodi L., Fitschen, Lucy J., Bouwer, James C., Johnston, Nikolas P., Yu, Haibo, Tolun, Gökhan · 2022 · Nature Communications
48. Spatio-temporal dynamics of the human small intestinal microbiome and its response to a synbiotic
    Ran An, Ellen Wilms, Jacoline Gerritsen, Hye Kyong Kim, Celia Segui‐Perez, Isolde Besseling-van der Vaart, Daisy M.A.E. Jonkers, Ger T. Rijkers, Willem M. de Vos, Ad Masclee et al. · 2024 · Gut Microbes
49. Recent advances in deep learning and language models for studying the microbiome
    Binghao Yan, Yunbi Nam, Lingyao Li, Rebecca A. Deek, Hongzhe Li, Siyuan Ma · 2025 · Frontiers in Genetics
50. A combination of fecal calprotectin and human beta-defensin 2 facilitates diagnosis and monitoring of inflammatory bowel disease
    Ranko Gaćeša, Arnau Vich Vila, Valerie Collij, Zlatan Mujagic, Alexander Kurilshikov, M.D. Voskuil, Eleonora Anna Margaretha Festen, Cisca Wijmenga, Daisy M.A.E. Jonkers, Gerard D. H. Dijkstra et al. · 2021 · Gut Microbes
51. Machine Learning for Protein Engineering
    Kadina E. Johnston, Clara Fannjiang, Bruce J. Wittmann, Brian Hie, Kevin Yang, Zachary Wu · 2023 · Challenges and advances in computational chemistry and physics
52. Accurately clustering biological sequences in linear time by relatedness sorting
    Erik S. Wright · 2024 · Nature Communications
53. Complete Genome Sequence of Bacillus anthracis H9401, an Isolate from a Korean Patient with Anthrax
    Jeong‐Hoon Chun, Kee‐Jong Hong, Sun Ho Cha, Minhee Cho, Kwang Jun Lee, Duck Hee Jeong, Cheon‐Kwon Yoo, Gi‐eun Rhie · 2012 · Journal of Bacteriology
54. A novel compound heterozygous genotype associated with aromatic amino acid decarboxylase deficiency: Clinical aspects and biochemical studies
    Riccardo Montioli, Roberta Battini, Alessandro Paiardini, Manuela Tolve, Mariarita Bertoldi, Carla Carducci, Vincenzo Leuzzi, Carla Borri Voltattorni · 2019 · Molecular Genetics and Metabolism
55. Intraspecific Diversity in the Cold Stress Response of Transposable Elements in the Diatom Leptocylindrus aporus
    Aikaterini Pargana, Francesco Musacchia, Remo Sanges, Monia Teresa Russo, Maria Immacolata Ferrante, Chris Bowler, Adriana Zingone · 2019 · Genes
56. Bagging MSA Learning: Enhancing Low-Quality PSSM with Deep Learning for Accurate Protein Structure Property Prediction
    Yuzhi Guo, Jiaxiang Wu, Hehuan Ma, Sheng Wang, Junzhou Huang · 2020 · Lecture notes in computer science
57. Systems Integration of Biodefense Omics Data for Analysis of Pathogen-Host Interactions and Identification of Potential Targets
    Peter B. McGarvey, Hongzhan Huang, Raja Mazumder, Jian Zhang, Yongxing Chen, Chengdong Zhang, Stephen A. Cammer, Rebecca Will, Margie Odle, Bruno Sobral et al. · 2009 · PLoS ONE
58. A Large-Scale Foundation Model for RNA Function and Structure Prediction
    Shuxian Zou, Tianhua Tao, Sazan Mahbub, Caleb N. Ellington, Robin Algayres, Dian Li, Yonghao Zhuang, Hongyi Wang, Le Song, Eric P. Xing · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
59. Recent advances in generative biology for biotherapeutic discovery
    Marissa L. Mock, CHRISTOPHER JAMES LANGMEAD, Peter J. Grandsard, Suzanne C. Edavettal, Alan J. Russell · 2024 · Trends in Pharmacological Sciences
60. Positive selection of digestive Cys proteases in herbivorous Coleoptera
    Juan Vorster, Asieh Rasoolizadeh, Marie‐Claire Goulet, Conrad Cloutier, Frank Sainsbury, Dominique Michaud · 2015 · Insect Biochemistry and Molecular Biology
61. Gram-negative outer-membrane proteins with multiple β-barrel domains
    Ron Solan, Joana Pereira, Andrei N. Lupas, Rachel Kolodny, Nir Ben‐Tal · 2021 · Proceedings of the National Academy of Sciences
62. Microcoleus (Cyanobacteria) form watershed‐wide populations without strong gradients in population structure
    Keith Bouma‐Gregson, Alexander Crits‐Christoph, Matthew R. Olm, Mary E. Power, Jillian F. Banfield · 2021 · Molecular Ecology
63. Challenges in describing the conformation and dynamics of proteins with ambiguous behavior
    Joel Roca‐Martínez, Tamás Lázár, Jose Gavaldá-García, David Bickel, Rita Pancsa, Bhawna Dixit, Konstantina Tzavella, Pathmanaban Ramasamy, Maite Sanchez-Fornaris, Isel Grau et al. · 2022 · Frontiers in Molecular Biosciences
64. PITHIA: Protein Interaction Site Prediction Using Multiple Sequence Alignments and Attention
    Seyedmohsen Hosseini, Lucian Ilie · 2022 · International Journal of Molecular Sciences
65. Fast and accurate protein intrinsic disorder prediction by using a pretrained language model
    Yidong Song, Qianmu Yuan, Sheng Chen, Ken Chen, Yaoqi Zhou, Yuedong Yang · 2023 · Briefings in Bioinformatics
66. FastRNABindR: Fast and Accurate Prediction of Protein-RNA Interface Residues
    Yasser EL‐Manzalawy, Mostafa M Abbas, Qutaibah Marwan Malluhi, Vasant Honavar · 2016 · PLoS ONE
67. Getting to Know Your Neighbor: Protein Structure Prediction Comes of Age with Contextual Machine Learning
    Jack Hanson, Kuldip K. Paliwal, Thomas Litfin, Yuedong Yang, Yaoqi Zhou · 2019 · Journal of Computational Biology
68. N-GlycoGo: Predicting Protein N-Glycosylation Sites on Imbalanced Data Sets by Using Heterogeneous and Comprehensive Strategy
    Ching-Hsuan Chien, Chi‐Chang Chang, Shih-Huan Lin, Chi-Wei Chen, Zong-Han Chang, Yen-Wei Chu · 2020 · IEEE Access
69. Ultra-deep Sequencing of Hadza Hunter-Gatherers Recovers Vanishing Gut Microbes
    Bryan Douglas Merrill, Matthew M. Carter, Matthew R. Olm, Dylan Dahan, Surya Mani Tripathi, Sean Paul Spencer, Feiqiao Brian Yu, Sunit Jain, Norma F Neff, Aashish R. Jha et al. · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
70. Distance-AF improves predicted protein structure models by AlphaFold2 with user-specified distance constraints
    Zhang, Yuanyuan, Zhang, Zicong, Kagaya, Yuki, Terashi, Genki, Zhao, Bowen, Xiong, Yi, Kihara, Daisuke · 2025 · Communications Biology
71. Variants in ZFX are associated with an X-linked neurodevelopmental disorder with recurrent facial gestalt
    James L. Shepherdson, Katie Hutchison, Dilan Wellalage Don, George McGillivray, Tae‐Ik Choi, Carolyn A Allan, David J. Amor, Siddharth Banka, Donald Basel, Laura D. Buch et al. · 2024 · The American Journal of Human Genetics
72. Zero-shot transfer of protein sequence likelihood models to thermostability prediction
    Shawn Reeves, Subha Kalyaanamoorthy · 2024 · Nature Machine Intelligence
73. Evaluation of a Machine Learning Duplicate Detection Method for Bioinformatics Databases
    Qingyu Chen, Justin Zobel, Karin M. Verspoor · 2015 · Data and Text Mining in Bioinformatics
74. The role of monovalent cations in the ATPase reaction of DNA gyrase
    Stephen James Hearnshaw, Terence Chung, C.E.M. Stevenson, Anthony Maxwell, David M. Lawson · 2015 · Acta Crystallographica Section D Biological Crystallography
75. Pyrosequencing-Based Transcriptome Analysis of the Asian Rice Gall Midge Reveals Differential Response during Compatible and Incompatible Interaction
    D. Sinha, J. Nagaraju, A. Tomar, J. Bentur, S. Nair · 2012 · International Journal of Molecular Sciences
76. Trichodesmium physiological ecology and phosphate reduction in the western tropical South Pacific
    Kyle R. Frischkorn, Andreas Krupke, Cécile Guieu, Justine Louis, Mónica Rouco, Andrés E. Salazar Estrada, Benjamin A. S. Van Mooy, Sonya T. Dyhrman · 2018 · Biogeosciences
77. Insights into mechanism and functional consequences of heme binding to hemolysin-activating lysine acyltransferase HlyC from Escherichia coli
    Sandra Peherstorfer, Hans Henning Brewitz, Ajay Abisheck Paul George, Amelie Wißbrock, Jana Maria Adam, Lutz Schmitt, Diana Imhof · 2018 · Biochimica et Biophysica Acta (BBA) - General Subjects
78. Comparative genomics of the family Vibrionaceae reveals the wide distribution of genes encoding virulence-associated proteins
    Timothy Lilburn, Jianying Gu, Hong Cai, Yufeng Wang · 2010 · BMC Genomics
79. Microarray analysis of genes and gene functions in disc degeneration
    Yanchun Tang, Shaokun Wang, Ying Liu, XUYUN WANG · 2013 · Experimental and Therapeutic Medicine
80. A Guide to UniProt for Protein Scientists
    Claire O’Donovan, Rolf Apweiler · 2010 · Methods in molecular biology
81. CloVR-16S: Phylogenetic microbial community composition analysis based on 16S ribosomal RNA amplicon sequencing – standard operating procedure, version1.0
    James Robert White, Cesar Arze, Malcolm N. Matalka, The CloVR Team, Samuel V. Angiuoli, W. Florian Fricke · 2011 · Nature Precedings
82. Protein Representation Learning via Knowledge Enhanced Primary Structure Modeling
    Hong-Yu Zhou, Yunxiang Fu, Zhicheng Zhang, Cheng Bian, Yizhou Yu · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
83. Analyses on clustering of the conserved residues at protein-RNA interfaces and its application in binding site identification
    Zhen Yang, Xueqing Deng, Yang Liu, Weikang Gong, Chunhua Li · 2020 · BMC Bioinformatics
84. Evaluating the relevance of sequence conservation in the prediction of pathogenic missense variants
    Emidio Capriotti, Piero Fariselli · 2022 · Human Genetics
85. ProB-Site: Protein Binding Site Prediction Using Local Features
    Sharzil Haris Khan, Hilal Tayara, Kil To Chong · 2022 · Cells
86. Comparison of Methods for Biological Sequence Clustering
    Ze‐Gang Wei, Xu Chen, Xiao-Dan Zhang, Hao Zhang, Xing-Guo Fan, Hongyan Gao, Fei Liu, Yu Peng Qian · 2023 · IEEE Transactions on Computational Biology and Bioinformatics
87. Intestinal Epithelial Inactivity of Dual Oxidase 2 Results in Microbiome-Mediated Metabolic Syndrome
    Hajar Hazime, Gloria Michelle Ducasa, Ana M. Santander, Nivis Brito, Eddy Ernesto Gonzalez-Horta, Yuguang J. Ban, Jonathan D. Kaunitz, Yasutada Akiba, Irina Fernández, Juan F. Burgueño et al. · 2023 · Cellular and Molecular Gastroenterology and Hepatology
88. Advancing Antibody Engineering through Synthetic Evolution and Machine Learning
    Edward B. Irvine, Sai T. Reddy · 2024 · The Journal of Immunology
89. Signatures of Adaptation and Purifying Selection in Highland Populations of Dasiphora fruticosa
    Fu‐Sheng Yang, Min Liu, Xing Guo, Chao Xu, Juan Jiang, Weixue Mu, Dongming Fang, Yong‐Chao Xu, Fu‐Min Zhang, Yinghui Wang et al. · 2024 · Molecular Biology and Evolution
90. Reconstruction and Validation of RefRec: A Global Model for the Yeast Molecular Interaction Network
    Tommi Aho, Henrikki Almusa, Jukka Matilainen, Antti Larjo, Pekka Ruusuvuori, Kaisa-Leena Aho, Thomas E. Wilhelm, Harri J Lähdesmäki, Andreas Beyer, Manu Harju et al. · 2010 · PLoS ONE
91. EST resources and establishment and validation of a 16k cDNA microarray from Atlantic cod (Gadus morhua)
    Rolf B. Edvardsen, Ketil Malde, Christian Mittelholzer, Geir Lasse Taranger, Frank Nilsen · 2010 · Comparative Biochemistry and Physiology Part D Genomics and Proteomics
92. Functional proteomics-aided selection of protease inhibitors for herbivore insect control
    Asieh Rasoolizadeh, Aurélie Munger, Marie‐Claire Goulet, Frank Sainsbury, Conrad Cloutier, Dominique Michaud · 2016 · Scientific Reports
93. Complete Genome Sequence of Akkermansia glycaniphila Strain Pyt T , a Mucin-Degrading Specialist of the Reticulated Python Gut
    Janneke P. Ouwerkerk, Jasper J. Koehorst, Peter J. Schaap, Jarmo Ritari, Lars G. Paulin, Clara Belzer, Willem M. de Vos · 2017 · Genome Announcements
94. MarkUs: a server to navigate sequence-structure-function space
    M. Fischer, Qiangfeng Cliff Zhang, Fabian Dey, Brian Yuan Chen, Barry H. Honig, Donald S. Petrey · 2011 · Nucleic Acids Research
95. A general approach for predicting protein epitopes targeted by antibody repertoires using whole proteomes
    Michael L. Paull, Tim Johnston, Kelly N. Ibsen, Joel D. Bozekowski, Patrick S. Daugherty · 2019 · PLoS ONE
96. Gene content of the fish-hunting cone snail Conus consors
    Reidar Andreson, Märt Roosaare, Lauris Kaplinski, Silja Laht, Triinu Kõressaar, Maarja Lepamets, Age Brauer, Viktorija Kukuškina, Maido Remm · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
97. uBin – a manual refining tool for metagenomic bins designed for educational purposes
    T. Bornemann, S. Esser, T. Stach, Tim Burg, A. Probst · 2020 · bioRxiv
98. Paddy Soil Flooding and Nonflooding Affect the Transcriptional Activity of Arsenic Methylation and Demethylation Communities
    Ziyu Gao, Xin-Di Zhao, Chuan Chen, Fangjie J. Zhao, Siyu Zhang · 2025 · Environmental Science & Technology
99. From machine learning to multimodal models: The AI revolution in enzyme engineering
    Ziyan Shi, Shicheng Xu, Sihan Xue, Kaiming Chen, Yifan Lu, Feiyue Wang, Siyu Long, Yannan Tian, Peng Zhang, Jianing Wang et al. · 2025 · BioDesign Research
100. Protein complex structure prediction powered by multiple sequence alignments of interologs from multiple taxonomic ranks and AlphaFold2
     Yunda Si, Chengfei Yan · 2022 · Briefings in Bioinformatics