UniRef: comprehensive and non-redundant UniProt reference clusters

Cited by (1,003)

Items 301–400 of 1,003

1. TemStaPro: protein thermostability prediction using sequence representations from protein language models
   Ieva Pudžiuvelytė, Kliment Olechnovič, Eglė Godliauskaitė, Kristupas Sermokas, Tomas Urbaitis, Giedrius Gasiūnas, Darius Kazlauskas · 2024 · Bioinformatics
2. Biosynthesis of Vitamins and Cofactors in Bacterium-Harbouring Trypanosomatids Depends on the Symbiotic Association as Revealed by Genomic Analyses
   Cecília C. Klein, João M. P. Alves, Myrna G. Serrano, Gregory A. Buck, Ana Tereza Ribeiro de Vasconcelos, Marie‐France Sagot, Marta M. G. Teixeira, Erney P. Camargo, María Cristina M. Motta · 2013 · PLoS ONE
3. Genome Evolution and Phylogenomic Analysis of Candidatus Kinetoplastibacterium, the Betaproteobacterial Endosymbionts of Strigomonas and Angomonas
   João M. P. Alves, Myrna G. Serrano, Flávia Maia da Silva, Logan J. Voegtly, Andrey V. Matveyev, Marta M. G. Teixeira, Erney P. Camargo, Gregory A. Buck · 2013 · Genome Biology and Evolution
4. Phylogenomic fingerprinting of tempo and functions of horizontal gene transfer within ochrophytes
   R. Dorrell, Adrien Villain, Benoît Perez-Lamarque, Guillemette Audren de Kerdrel, G. Mccallum, A. K. Watson, Ouardia Ait-Mohamed, A. Alberti, E. Corre, K. Frischkorn et al. · 2021 · Proceedings of the National Academy of Sciences of the United States of America
5. Interaction dynamics and virus–host range for estuarine actinophages captured by epicPCR
   Eric G. Sakowski, Keith Arora‐Williams, Funing Tian, Ahmed A. Zayed, Olivier Zablocki, Matthew B. Sullivan, Sarah Pacocha Preheim · 2021 · Nature Microbiology
6. Integrated Biophysical Modeling of the SARS-CoV-2 Spike Protein Binding and Allosteric Interactions with Antibodies
   Gennady M. Verkhivker, Luisa Di Paola · 2021 · The Journal of Physical Chemistry B
7. TCR signaling induces STAT3 phosphorylation to promote TH17 cell differentiation
   Zhen Qin, Ruining Wang, Ping Hou, Yuanyuan Zhang, Qianmu Yuan, Ying Wang, Yuedong Yang, Tao Xu · 2024 · The Journal of Experimental Medicine
8. PMAP: databases for analyzing proteolytic events and pathways
   Yoshinobu Igarashi, Emily Heureux, Kutbuddin S. Doctor, Priti Talwar, Svetlana I. Gramatikova, Kosi Gramatikoff, Ying Zhang, Michael L. Blinov, Salmaz S. Ibragimova, Sarah Elizabeth Boyd et al. · 2008 · Nucleic Acids Research
9. Global transcriptome analysis of Atlantic cod (Gadus morhua) liver after in vivo methylmercury exposure suggests effects on energy metabolism pathways
   Fekadu Yadetie, Odd André Karlsen, Anders Lanzén, Karin Berg, Pål A. Olsvik, Christer Högstrand, Anders Goksøyr · 2012 · Aquatic Toxicology
10. Diverse Genomic Traits Differentiate Sinking-Particle-Associated versus Free-Living Microbes throughout the Oligotrophic Open Ocean Water Column
    Andy O Leu, John M. Eppley, Andrew H. Burger, Edward F. DeLong · 2022 · mBio
11. Detection and Diversity of Fungal Nitric Oxide Reductase Genes ( p450nor ) in Agricultural Soils
    Steven Higgins, Allana K. Welsh, Luis H. Orellana, Konstantinos T. Konstantinidis, Joanne C. Chee‐Sanford, Robert A. Sanford, Christopher W. Schadt, Frank E. Löffler · 2016 · Applied and Environmental Microbiology
12. Analysis of five complete genome sequences for members of the class Peribacteria in the recently recognized Peregrinibacteria bacterial phylum
    Karthik Anantharaman, C. Brown, D. Burstein, C. Castelle, A. Probst, B. Thomas, K. Williams, J. Banfield · 2016 · PeerJ
13. Bayesian prediction of RNA translation from ribosome profiling
    Brandon Malone, Ilian Atanassov, Florian Aeschimann, Xinping Li, Helge Großhans, Christoph Dieterich · 2017 · Nucleic Acids Research
14. Long-term taxonomic and functional divergence from donor bacterial strains following fecal microbiota transplantation in immunocompromised patients
    Eli L. Moss, Shannon B. Falconer, Tkachenko Ei, Mingjie Wang, Hannah K. Systrom, Jasmin Mahabamunuge, David A. Relman, Elizabeth L. Hohmann, Ami Siddharth Bhatt · 2017 · PLoS ONE
15. Enhancing Protein Function Prediction Performance by Utilizing AlphaFold-Predicted Protein Structures
    Wenjian Ma, Shugang Zhang, Zhen Li, Mingjian Jiang, Shuang Wang, Weigang Lu, Xiangpeng Bi, Huasen Jiang, Henggui Zhang, Zhiqiang Wei · 2022 · Journal of Chemical Information and Modeling
16. Using the MEROPS Database for Proteolytic Enzymes and Their Inhibitors and Substrates
    Neil David Rawlings, A. John Barrett, Alex G. Bateman · 2014 · Current Protocols in Bioinformatics
17. Metagenomics of the Gut Microbiome in Parkinson's Disease: Prodromal Changes
    Palacios, Natalia, Wilkinson, Jeremy, Bjornevik, Kjetil, Schwarzschild, Michael A., McIver, Lauren, Ascherio, Alberto, Huttenhower, Curtis · 2023 · Annals of Neurology
18. Consistent signatures in the human gut microbiome of old- and young-onset colorectal cancer
    Youwen Qin, Xin Tong, Wei-Jian Mei, Yanshuang Cheng, Yuanqiang Zou, Kai Han, Jiehai Yu, Zhuye Jie, Tao Zhang, Shida Zhu et al. · 2024 · Nature Communications
19. Structure and Sequence Analyses of Clustered Protocadherins Reveal Antiparallel Interactions that Mediate Homophilic Specificity
    John M. Nicoludis, Sze-Yi Lau, Charlotta Schärfe, Debora S. Marks, Wilhelm Andreas Weihofen, Rachelle Gaudet · 2015 · Structure
20. mRNA-Seq Analysis of the Pseudoperonospora cubensis Transcriptome During Cucumber (Cucumis sativus L.) Infection
    Elizabeth A. Savory, Bishwo N. Adhikari, John P. Hamilton, Brieanne Vaillancourt, C. Robin Buell, Brad Day · 2012 · PLoS ONE
21. Minireview: Toward the Establishment of a Link between Melatonin and Glucose Homeostasis: Association of Melatonin MT2Receptor Variants with Type 2 Diabetes
    Angeliki Karamitri, Nicolas Renault, Nathalie Clément, Jean‐Luc Guillaume, Ralf Jockers · 2013 · Molecular Endocrinology
22. Machine learning for metagenomics: methods and tools
    Hayssam Soueidan, Macha Nikolski · 2016 · Metagenomics
23. Efficient mining of natural NADH-utilizing dehydrogenases enables systematic cofactor engineering of lysine synthesis pathway of Corynebacterium glutamicum
    Wenjun Wu, Ye Zhang, Dehua Liu, Zhen Chen · 2018 · Metabolic Engineering
24. Complete genome of Pieris rapae, a resilient alien, a cabbage pest, and a source of anti-cancer proteins
    Jinhui Shen, Qian Cong, Lisa N. Kinch, Dominika Borek, Zbyszek Otwinowski, Nick V. Grishin · 2016 · F1000Research
25. Unusual Metabolism and Hypervariation in the Genome of a Gracilibacterium (BD1-5) from an Oil-Degrading Community
    C. Sieber, B. Paul, C. Castelle, Ping Hu, S. Tringe, D. Valentine, G. Andersen, J. Banfield · 2019 · mBio
26. Genome-Centric Analysis of Microbial Populations Enriched by Hydraulic Fracture Fluid Additives in a Coal Bed Methane Production Well
    Steven J. Robbins, Paul N. Evans, Donovan H. Parks, S. D. Golding, Gene W. Tyson · 2016 · Frontiers in Microbiology
27. A comprehensive review and comparison of existing computational methods for protein function prediction
    Baohui Lin, Xiaoling Luo, Yumeng Liu, Xiaopeng Jin · 2024 · Briefings in Bioinformatics
28. Crop root bacterial and viral genomes reveal unexplored species and microbiome patterns
    Rui Dai, Jingying Zhang, Fang Liu, Haoran Xu, Jing-Mei Qian, Shani Cheskis, Weidong Liu, Binglei Wang, Honghui Zhu, Lotte J. U. Pronk et al. · 2025 · Cell
29. Cultivar-specific kinetics of gene induction during downy mildew early infection in grapevine
    Andreia Figueiredo, Filipa Monteiro, Ana Margarida Fortes, Martina Rex, Eva Zyprian, Lisete Sousa, Maria Salomé Pais · 2012 · Functional & Integrative Genomics
30. Identification of MicroRNAs in the Coral Stylophora pistillata
    Yi Jin Liew, Manuel Aranda, Adrian R. Carr, Sebastian Baumgarten, Didier Zoccola, Sylvie Tambutté, Denis Allemand, Gos Micklem, Christian Robert Voolstra · 2014 · PLoS ONE
31. New Structural and Functional Contexts of the Dx[DN]xDG Linear Motif: Insights into Evolution of Calcium-Binding Proteins
    Daniel John Rigden, Duncan David Woodhead, Prudence W. H. Wong, Michael Y. Galperin · 2011 · PLoS ONE
32. MetaRef: a pan-genomic database for comparative and community microbial genomics
    Katherine H Huang, Arthur Brady, Anup Mahurkar, Owen R. White, Dirk Gevers, Curtis Huttenhower, Nicola Segata · 2013 · Nucleic Acids Research
33. A genome-wide 20 K citrus microarray for gene expression analysis
    Maria Ángeles Martínez-Godoy, Nuria Mauri, José Juárez, Maria Carmen Marqués, Julia Santiago, Javier Forment, José Gadea · 2008 · BMC Genomics
34. HoloVir: A Workflow for Investigating the Diversity and Function of Viruses in Invertebrate Holobionts
    Patrick W. Laffy, Elisha M. Wood‐Charlson, Dmitrij Turaev, Karen D. Weynberg, Emmanuelle S. Botté, Madeleine J. H. van Oppen, Nicole S. Webster, Thomas Rattei · 2016 · Frontiers in Microbiology
35. Diapause in a tropical oil-collecting bee: molecular basis unveiled by RNA-Seq
    Priscila Karla Ferreira Santos, Natália de Souza Araujo, Elaine Françoso, Alexandre Rizzo Zuntini, Maria Cristina Arias · 2018 · BMC Genomics
36. MYB24 orchestrates terpene and flavonol metabolism as light responses to anthocyanin depletion in variegated grape berries
    Chen Zhang, Zhanwu Dai, Thilia Ferrier, Luis Orduña, Antonio Santiago, Arnau Peris-Cuesta, Darren C. J. Wong, Christian Kappel, Stefania Savoi, Rodrigo Loyola et al. · 2023 · The Plant Cell
37. Generative models for protein sequence modeling: recent advances and future directions
    Mehrsa Mardikoraem, Zirui Wang, Nathaniel Pascual, Daniel Woldring · 2023 · Briefings in Bioinformatics
38. Gene-level metagenomic architectures across diseases yield high-resolution microbiome diagnostic indicators
    Braden T. Tierney, Yingxuan Tan, Aleksandar David Kostic, Chirag J. Patel · 2021 · Nature Communications
39. O2 partitioning of sulfur oxidizing bacteria drives acidity and thiosulfate distributions in mining waters
    Kelly J. Whaley-Martin, Lin-Xing Chen, Tara Colenbrander Nelson, Jennifer Gordon, Rose S. Kantor, Lauren E. Twible, Stephanie Marshall, Sam McGarry, Laura Rossi, Benoit Bessette et al. · 2023 · Nature Communications
40. Accurate prediction of protein enzymatic class by N-to-1 Neural Networks
    Viola Volpato, Alessandro Adelfio, Gianluca Pollastri · 2013 · BMC Bioinformatics
41. Genome resolved analysis of a premature infant gut microbial community reveals a Varibaculum cambriense genome and a shift towards fermentation-based metabolism during the third week of life
    Christopher T. Brown, Itai Sharon, Brian C. Thomas, Cindy J. Castelle, Michael J. Morowitz, Jillian F. Banfield · 2013 · Microbiome
42. Systematic identification of phosphorylation-mediated protein interaction switches
    Matthew J. Betts, Oliver Wichmann, Mathias Utz, Timon André, Evangelia Petsalaki, Pablo Mínguez, Luca Parca, Frederick P. Roth, Anne‐Claude Gavin, Peer Bork B et al. · 2017 · PLoS Computational Biology
43. Plastid establishment did not require a chlamydial partner
    Domman, Daryl, Horn, Matthias, Embley, T. Martin, Williams, Tom A. · 2015 · Nature Communications
44. BioT5: Enriching Cross-modal Integration in Biology with Chemical Knowledge and Natural Language Associations
    Qizhi Pei, Wei Zhang, Jinhua Zhu, Kehan Wu, Kaiyuan Gao, Lijun Wu, Yingce Xia, Rui Yan · 2023 · Conference on Empirical Methods in Natural Language Processing (EMNLP)
45. Gene Duplication and Divergence of Long Wavelength-Sensitive Opsin Genes in the Guppy, Poecilia reticulata
    Corey T. Watson, Suzanne M. Gray, Margarete Hoffmann, Krzysztof P. Lubieniecki, Jeffrey B. Joy, Benjamin A. Sandkam, Detlef Weigel, Ellis R. Loew, Christine Dreyer, William S. Davidson et al. · 2010 · Journal of Molecular Evolution
46. Complete Genome Sequence of Multidrug-Resistant Acinetobacter baumannii Strain 1656-2, Which Forms Sturdy Biofilm
    Jin Yeol Park, Shukho Kim, Sung‐Min Kim, Sun Ho Cha, Si‐Kyu Lim, Jungmin Kim · 2011 · Journal of Bacteriology
47. Complete genomes of Hairstreak butterflies, their speciation and nucleo-mitochondrial incongruence
    Qian Cong, Jinhui Shen, Dominika Borek, Robert K. Robbins, Zbyszek Otwinowski, Nick V. Grishin · 2016 · Scientific Reports
48. ProT-VAE: Protein Transformer Variational AutoEncoder for functional protein design
    Emre Sevgen, Joshua Moller, Adrian Lange, John Parker, Sean D. Quigley, Jeff Mayer, Poonam Srivastava, Sitaram Gayatri, David J. Hosfield, Clayton M. Dilks et al. · 2025 · Proceedings of the National Academy of Sciences
49. A full-length enriched cDNA library and expressed sequence tag analysis of the parasitic weed, Striga hermonthica
    Satoko Yoshida, Juliane Karine Ishida, Nasrein Mohamed Kamal, Abdelbagi Mukhtar Ali, Shigetou NAMBA, Ken Shirasu · 2010 · BMC Plant Biology
50. De novo assembly of Aureococcus anophagefferens transcriptomes reveals diverse responses to the low nutrient and low light conditions present during blooms
    Kyle R. Frischkorn, Matthew J. Harke, Christopher J. Gobler, Sonya T. Dyhrman · 2014 · Frontiers in Microbiology
51. Genome-resolved metagenomics of sugarcane vinasse bacteria
    Noriko A. Cassman, Késia Silva Lourenço, Janaína Braga do Carmo, Heitor Cantarella, Eiko E. Kuramae · 2018 · Biotechnology for Biofuels
52. Are Deep Learning Structural Models Sufficiently Accurate for Free-Energy Calculations? Application of FEP+ to AlphaFold2-Predicted Structures
    Beuming, Thijs, Martín, Helena, Díaz-Rovira, Anna M., Díaz, Lucía, Guallar, Victor, Ray, Soumya S. · 2022 · Journal of Chemical Information and Modeling
53. Reaching alignment-profile-based accuracy in predicting protein secondary and tertiary structural properties without alignment
    Jaspreet Singh, Kuldip K. Paliwal, Thomas Litfin, Jaswinder Singh, Yaoqi Zhou · 2022 · Scientific Reports
54. Microbial polyphenol metabolism is part of the thawing permafrost carbon cycle
    Bridget B. McGivern, Dylan R. Cronin, Jared Ellenbogen, Mikayla Borton, Eleanor Knutson, Viviana Freire-Zapata, John A. Bouranis, Lukas Bernhardt, Alma I. Hernandez, Rory M. Flynn et al. · 2024 · Nature Microbiology
55. A tree-based conservation scoring method for short linear motifs in multiple alignments of protein sequences
    Claudia Chica, Alberto Labarga, Cathryn M. Gould, Rodrigo López, Toby J. Gibson · 2008 · BMC Bioinformatics
56. Calf Diarrhea Caused by Prolonged Expansion of Autochthonous Gut Enterobacteriaceae and Their Lytic Bacteriophages
    Tae Woong Whon, Hyun Sik Kim, Na‐Ri Shin, Hojun Sung, Min‐Soo Kim, Joon Yong Kim, Woorim Kang, Pil Soo Kim, Dong‐Wook Hyun, Hoon Je Seong et al. · 2021 · mSystems
57. HydRA: Deep-learning models for predicting RNA-binding capacity from protein interaction association context and protein sequence
    Jin, Wenhao, Brannan, Kristopher W., Kapeli, Katannya, Park, Samuel S., Tan, Hui Qing, Gosztyla, Maya L., Mujumdar, Mayuresh, Ahdout, Joshua, Henroid, Bryce, Rothamel, Katherine et al. · 2023 · Molecular Cell
58. Antibody design using deep learning: from sequence and structure design to affinity maturation
    Sara Joubbi, Alessio Micheli, Paolo Milazzo, Giuseppe Maccari, Giorgio Ciano, Dario Cardamone, Duccio Medini · 2024 · Briefings in Bioinformatics
59. Why are polar residues within the membrane core evolutionary conserved?
    Kristoffer Illergård, Anni Kauko, Arne Elofsson · 2010 · Proteins Structure Function and Bioinformatics
60. Structural Requirements for Interaction of Peroxisomal Targeting Signal 2 and Its Receptor PEX7
    Markus Kunze, Georg Neuberger, Sebastian Maurer‐Stroh, Jianmin Ma, Thomas Eck, Nancy Braverman, Johannes A. Schmid, Frank Eisenhaber, Johannes Berger · 2011 · Journal of Biological Chemistry
61. SmCL3, a Gastrodermal Cysteine Protease of the Human Blood Fluke Schistosoma mansoni
    Jan Dvořák, Susan T. Mashiyama, Mohammed Sajid, Bryony Braschi, Melaine Delcroix, Eric L. Schneider, Wilson McKerrow, Mahmoud Mohamed Bahgat, Elizabeth J. Hansell, Patricia Clement Babbitt et al. · 2009 · PLoS neglected tropical diseases
62. Genomic Approaches for Interrogating the Biochemistry of Medicinal Plant Species
    Elsa Góngora‐Castillo, Greg Fedewa, Yunsoo Yeo, Joe Chappell, DellaPenna Dean, C. Robin Buell · 2012 · Methods in enzymology on CD-ROM/Methods in enzymology
63. Ethephon induced oxidative stress in the olive leaf abscission zone enables development of a selective abscission compound
    Shiri Goldental-Cohen, C. Burstein, Iris Biton, S. Ben Sasson, Asaf Sadeh, Yair Many, Adi Doron‐Faigenboim, Hanita Zemach, Y. Mugira, Doron Schneider et al. · 2017 · BMC Plant Biology
64. How Many Protein Sequences Fold to a Given Structure? A Coevolutionary Analysis
    Pengfei Tian, Robert B. Best · 2017 · Biophysical Journal
65. SPOT-Contact-LM: improving single-sequence-based prediction of protein contact map using a transformer language model
    Jaspreet Singh, Thomas Litfin, Jaswinder Singh, Kuldip K. Paliwal, Yaoqi Zhou · 2022 · Bioinformatics
66. Microbial metabolic networks in a complex electrogenic biofilm recovered from a stimulus-induced metatranscriptomics approach
    Shun’ichi Ishii, Shino Suzuki, Aaron E. Tenney, Trina M. Norden‐Krichmar, Kenneth H. Nealson, Orianna Bretschger · 2015 · Scientific Reports
67. Bakta Web – rapid and standardized genome annotation on scalable infrastructures
    Sebastian Beyvers, Lukas Jelonek, Alexander Goesmann, Oliver Schwengers · 2025 · Nucleic Acids Research
68. Genome Annotation of a Model Diatom Phaeodactylum tricornutum Using an Integrated Proteogenomic Pipeline
    Mingkun Yang, Xiaohuang Lin, Xin Liu, Jia Zhang, Feng Ge · 2018 · Molecular Plant
69. Does Quorum Sensing play a role in microbial shifts along spontaneous fermentation of cocoa beans? An in silico perspective
    Otávio Guilherme Gonçalves de Almeida, Uelinton Manoel Pinto, Claudia Matos, Diego Araújo Frazilio, V.F. Braga, Márcia Regina von Zeska Kress, Elaine Cristina Pereira De Martinis · 2020 · Food Research International
70. Concept and application of a computational vaccinology workflow
    Johannes Söllner, Andreas Heinzel, Georg Summer, Raul Fechete, László Stipkovits, Susan Szathmáry, Bernd Mayer · 2010 · Immunome Research
71. Mobilizable antibiotic resistance genes are present in dust microbial communities
    Sarah Ben Maamar, Adam J. Glawe, Taylor K. Brown, Nancy Hellgeth, Jinglin Hu, Ji-Ping Wang, Curtis Huttenhower, Erica Marie Hartmann · 2020 · PLoS Pathogens
72. A 20 Residues Motif Delineates the Furin Cleavage Site and its Physical Properties May Influence Viral Fusion
    Sun Tian · 2009 · Biochemistry Insights
73. Unraveling the Complexities of Life Sciences Data
    Roger Higdon, Winston A. Haynes, Larissa I Stanberry, Elizabeth Stewart, Gregory Yandl, Chris Howard, William Broomall, Natali Kolker, Eugene Kolker · 2012 · Big Data
74. Deciphering the complex leaf transcriptome of the allotetraploid species Nicotiana tabacum: a phylogenomic perspective
    Aureliano Bombarely, Kieron D. Edwards, J. P. Sanchez-Tamburrino, Lukas A. Mueller · 2012 · BMC Genomics
75. Whole-Genome Sequence Accuracy Is Improved by Replication in a Population of Mutagenized Sorghum
    Charles Addo‐Quaye, Mitchell R. Tuinstra, Nicola Carraro, Clifford F. Weil, Brian P. Dilkes · 2018 · G3 Genes Genomes Genetics
76. Dental Calculus as a Tool to Study the Evolution of the Mammalian Oral Microbiome
    Jaelle C. Brealey, Henrique G. Leitão, Tom van der Valk, Wenbo Xu, Katia Bougiouri, Love Dalén, Katerina Guschanski · 2020 · Molecular Biology and Evolution
77. DEEPCON: protein contact prediction using dilated convolutional neural networks with dropout
    Badri Adhikari · 2019 · Bioinformatics
78. ProtoNet 6.0: organizing 10 million protein sequences in a compact hierarchical family tree
    Nadav Rappoport, Solange Karsenty, A. Stern, Nathan Linial, Michal Linial B · 2011 · Nucleic Acids Research
79. Gut transcriptome of replete adult female cattle ticks, Rhipicephalus (Boophilus) microplus, feeding upon a Babesia bovis-infected bovine host
    Andrew M. Heekin, Felix David Guerrero, Kylie G. Bendele, Leo Saldivar, Glen A. Scoles, Scot E. Dowd, Cedric Gondro, Vishvanath M. Nene, Appolinaire Djikeng, Kelly A. Brayton · 2013 · Parasitology Research
80. A new method for decontamination of de novo transcriptomes using a hierarchical clustering algorithm
    Joël Lafond‐Lapalme, Marc‐Olivier Duceppe, Shengrui Wang, Peter Moffett, Benjamin Mimee · 2016 · Bioinformatics
81. Genomic adaptations enabling Acidithiobacillus distribution across wide-ranging hot spring temperatures and pHs
    Chanenath Sriaporn, Kathleen A. Campbell, Martin Julian Van Kranendonk, Kim M. Handley · 2021 · Microbiome
82. Diverse Viruses Carrying Genes for Microbial Extremotolerance in the Atacama Desert Hyperarid Soil
    Yunha Hwang, Janina Rahlff, Dirk Schulze‐Makuch, Michael Schloter, Alexander J. Probst · 2021 · mSystems
83. Convergent evolution and horizontal gene transfer in Arctic Ocean microalgae
    R. Dorrell, A. Kuo, Z. Füssy, Elisabeth H. Richardson, A. Salamov, Nikola Zarevski, Nastasia J. Freyria, Federico M. Ibarbalz, J. Jenkins, J. P. Pierella Karlusich et al. · 2022 · Life Science Alliance
84. Anaerobic methanotroph ‘Candidatus Methanoperedens nitroreducens’ has a pleomorphic life cycle
    Simon Jon McIlroy, Andy O Leu, Xueqin Zhang, Rhys Newell, Ben J. Woodcroft, Zhiguo Yuan, Shihu Hu, Gene W. Tyson · 2023 · Nature Microbiology
85. Complete sequencing of Novosphingobium sp. PP1Y reveals a biotechnologically meaningful metabolic pattern
    Valeria D’Argenio, Eugenio Notomista, Mauro Petrillo, Piergiuseppe Cantiello, Valeria Cafaro, Viviana Izzo, Barbara Naso, Luca Cozzuto, Lorenzo Durante, Luca Troncone et al. · 2014 · BMC Genomics
86. Development of SNP and InDel markers via de novo transcriptome assembly in Sesamum indicum L.
    Libin Wei, Hongmei Miao, Chun Li, Yinghui Duan, Jiaojiao Niu, Tide Zhang, Qiongyi Zhao, Haiyang Zhang · 2014 · Molecular Breeding
87. Functional Identification of Valerena-1,10-diene Synthase, a Terpene Synthase Catalyzing a Unique Chemical Cascade in the Biosynthesis of Biologically Active Sesquiterpenes in Valeriana officinalis
    Yunsoo Yeo, Stephen Eric Nybo, Amar Gopal Chittiboyina, Aruna Dharmapriya Weerasooriya, Yan-Hong Wang, Elsa Góngora‐Castillo, Brieanne Vaillancourt, C. Robin Buell, Dean DellaPenna, Mary Dawn Celiz et al. · 2012 · Journal of Biological Chemistry
88. A pilot study demonstrating the altered gut microbiota functionality in stable adults with Cystic Fibrosis
    Fiona Fouhy, Nicola J. Ronan, Órla O’Sullivan, Yvonne McCarthy, Aaron M. Walsh, Desmond M. Murphy, M. Daly, Evelyn Flanagan, C. Fleming, Melissa M. McCarthy et al. · 2017 · Scientific Reports
89. An expanded database and analytical toolkit for identifying bacterial virulence factors and their associations with chronic diseases
    Wanting Dong, X. Fan, Yaqiong Guo, Siyi Wang, Shulei Jia, Na Lv, Yuan Tao, Yuanlong Pan, Yong Xue, Xi Chen et al. · 2024 · Nature Communications
90. Rapid transcriptome sequencing of an invasive pest, the brown marmorated stink bug Halyomorpha halys
    Panagiotis Ioannidis, Yong Lu, Nikhil Kumar, Todd H. Creasy, Sean C. Daugherty, Marcus C. Chibucos, Joshua Orvis, Amol Carl Shetty, Sandra H. Ott, Melissa Flowers et al. · 2014 · BMC Genomics
91. Experimental metagenomics and ribosomal profiling of the human skin microbiome
    Pamela Ferretti, Stefania Farina, Mario Cristofolini, Giampiero Girolomoni, Adrian Tett, Nicola Segata · 2016 · Experimental Dermatology
92. Profiling of adhesive-related genes in the freshwater cnidarian Hydra magnipapillata by transcriptomics and proteomics
    Marcelo Rodrigues, Thomas Ostermann, Leopold Kremeser, Herbert H. Lindner, Christian Beisel, Eugène Berezikov, Bert Hobmayer, Peter Ladurner · 2016 · Biofouling
93. De novo transcriptome assembly for the spiny mouse (Acomys cahirinus)
    Jared Mamrot, Roxane Legaie, Stacey J. Ellery, Trevor Wilson, Torsten Seemann, David Powell, David K. Gardner, David W. Walker, Peter D. Temple-Smith, Anthony T. Papenfuss et al. · 2017 · Scientific Reports
94. Microaerobic conditions caused the overwhelming dominance of Acinetobacter spp. and the marginalization of Rhodococcus spp. in diesel fuel/crude oil mixture-amended enrichment cultures
    Fruzsina Révész, Perla Abigail Figueroa-Gonzalez, A. Probst, B. Kriszt, Sinchan Banerjee, S. Szoboszlay, G. Maróti, A. Táncsics · 2019 · Archives of Microbiology
95. Toward generalizable prediction of antibody thermostability using machine learning on sequence and structure features
    Ameya Harmalkar, Roshan Rao, Yuxuan Richard Xie, Jonas Honer, Wibke Deisting, Jonas Anlahr, Anja Hoenig, Julia Czwikla, Eva Sienz-Widmann, Doris Rau et al. · 2023 · mAbs
96. Anaerobic degradation of 1-methylnaphthalene by a member of the Thermoanaerobacteraceae contained in an iron-reducing enrichment culture
    Sviatlana Marozava, Housna Mouttaki, Hubert Müller, Nidal Abu Laban, Alexander J. Probst, Rainer U. Meckenstock · 2017 · Biodegradation
97. Lipid analysis of CO2-rich subsurface aquifers suggests an autotrophy-based deep biosphere with lysolipids enriched in CPR bacteria
    A. Probst, F. Elling, C. Castelle, Qing-Zeng Zhu, M. Elvert, G. Birarda, H. Holman, Katherine R. Lane, B. Ladd, M. Ryan et al. · 2018 · The ISME Journal
98. Early computational detection of potential high-risk SARS-CoV-2 variants
    2023
99. Anaerobic oxidation of propane coupled to nitrate reduction by a lineage within the class Symbiobacteriia
    Mengxiong Wu, Jie Li, Andy O Leu, Dirk V. Erler, Terra Stark, Gene W. Tyson, Zhiguo Yuan, Simon Jon McIlroy, Jianhua Guo · 2022 · Nature Communications
100. ULDNA: integrating unsupervised multi-source language models with LSTM-attention network for high-accuracy protein–DNA binding site prediction
     Yi-Heng Zhu, Zi Liu, Yan Liu, Zhi-Wei Ji, Dong-Jun Yu · 2024 · Briefings Bioinform.