UniRef: comprehensive and non-redundant UniProt reference clusters

Suzek, Baris E., Huang, Hongzhan, McGarvey, Peter, Mazumder, Raja, Wu, Cathy H.·2007·Bioinformatics

DOI 10.1093/bioinformatics/btm098

Cited by (1,003)

Items 101–200 of 1,003

A fast method for large‐scale De Novo peptide and miniprotein structure prediction
Julien Maupetit, Philippe Derreumaux, Pierre Tufféry · 2009 · Journal of Computational Chemistry
Discovery of a novel methanogen prevalent in thawing permafrost
Rhiannon Mondav, Ben J. Woodcroft, Eun‐Hae Kim, Carmody Kathryn Mccalley, Suzanne B. Hodgkins, Patrick Crill, Jeffrey P. Chanton, Gregory B. Hurst, Nathan C. VerBerkmoes, SCOTT REID SALESKA et al. · 2014 · Nature Communications
Depth: a web server to compute depth, cavity sizes, detect potential small-molecule ligand-binding cavities and predict the pKa of ionizable residues in proteins
Kuan Pern Tan, Thanh Nguyen, Siddharth Patel, Raghavan Varadarajan, Mallur Srivatsan Madhusudhan · 2013 · Nucleic Acids Research
Learning functional properties of proteins with language models
Serbülent Ünsal, Heval Ataş, Muammer Albayrak, Kemal Turhan, Aybar C. Acar, Tunca Doğan · 2022 · Nature Machine Intelligence
VIROME: a standard operating procedure for analysis of viral metagenome sequences
K. Eric Wommack, Jaysheel Bhavsar, Shawn W. Polson, Jing Chen, Michael Dumas, Sharath Srinivasiah, Megan Furman, Sanchita Jamindar, Daniel J. Nasko · 2012 · Standards in Genomic Sciences
Genomic resolution of a cold subsurface aquifer community provides metabolic insights for novel microbes adapted to high CO2 concentrations
A. Probst, C. Castelle, Andrea Singh, C. Brown, Karthik Anantharaman, Itai Sharon, L. Hug, D. Burstein, J. Emerson, B. Thomas et al. · 2017 · Environmental Microbiology
The FTO (fat mass and obesity associated) gene codes for a novel member of the non-heme dioxygenase superfamily
Luis Sánchez‐Pulido, Miguel Angel Andrade-Navarro · 2007 · BMC Biochemistry
Draft Assembly of Elite Inbred Line PH207 Provides Insights into Genomic and Transcriptome Diversity in Maize
Candice N. Hirsch, Cory D. Hirsch, Alex B. Brohammer, Megan J. Bowman, Ilya Soifer, Omer Barad, Doron Shem‐Tov, Kobi Baruch, Fei Lü, Alvaro Gonzalo Hernandez et al. · 2016 · The Plant Cell
The MetaProteomeAnalyzer: A Powerful Open-Source Software Suite for Metaproteomics Data Analysis and Interpretation
Thilo Muth, Alexander Behne, Robert Heyer, Fabian Kohrs, Dirk Benndorf, Marcus Hoffmann, Miro Lehtevä, Udo Reichl, Lennart Martens, Erdmann Rapp · 2015 · Journal of Proteome Research
Structure-aware protein-protein interaction site prediction using deep graph convolutional network
Qianmu Yuan, Jian-Wen Chen, Hui-Ying Zhao, Yaoqi Zhou, Yuedong Yang · 2021 · Bioinform.
Diatom modulation of select bacteria through use of two unique secondary metabolites
Ahmed A. Shibl, Ashley Isaac, Michael A. Ochsenkühn, Anny Cárdenas, Cong Fei, Gregory Behringer, Marc Arnoux, Nizar Drou, Miraflor Santos, Kristin C. Gunsalus et al. · 2020 · Proceedings of the National Academy of Sciences
Improved model quality assessment using ProQ2
Arjun Ray, Erik R. Lindahl, Björn Wallner · 2012 · BMC Bioinformatics
Comparative transcriptome analysis of developmental stages of the L imonium bicolor leaf generates insights into salt gland differentiation
Fang Yuan, Ming‐Ju Amy Lyu, Bingying Leng, Guangyong Zheng, ZHONG‐TAO FENG, PING‐HUA LI, Xin‐Guang Zhu, Baoshan Wang · 2015 · Plant Cell & Environment
Urban Transit System Microbial Communities Differ by Surface Type and Interaction with Humans and the Environment
Tiffany Y. Hsu, Regina Joice Cordy, Jose Vallarino, Galeb Abu-Ali, Erica Marie Hartmann, Afrah Shafquat, Casey R. DuLong, Catherine Baranowski, Dirk Gevers, Jessica L. Green et al. · 2016 · mSystems
The landscape of tolerated genetic variation in humans and primates
2023
A Comprehensive Analysis of the Global Human Gut Archaeome from a Thousand Genome Catalogue
Cynthia Maria Chibani, Alexander Mahnert, Guillaume Borrel, Alexandre Almeida, Almut Werner, Jean‐François Brugère, Simonetta Gribaldo, Robert D. Finn, Ruth A. Schmitz, Christine Moissl‐Eichinger · 2020 · Nature Microbiology
De Novo Transcriptome Sequence Assembly and Analysis of RNA Silencing Genes of Nicotiana benthamiana
Kenlee Nakasugi, Ross N. Crowhurst, Julia Bally, Craig C. Wood, Roger P. Hellens, Peter M. Waterhouse · 2016 · Figshare
Dietary fiber intake, the gut microbiome, and chronic systemic inflammation in a cohort of adult men
Wenjie Ma, Long H. Nguyen, Mingyang Song, Dong D. Wang, Eric A. Franzosa, Yin Cao, Amit D. Joshi, David A. Drew, Raaj S. Mehta, Kerry Lee Ivey et al. · 2021 · Genome Medicine
Microbial community successional patterns in beach sands impacted by the Deepwater Horizon oil spill
Luis M. Rodriguez‐R, Will A. Overholt, Christopher Hagan, Markus Huettel, Joel E. Kostka, Konstantinos T. Konstantinidis · 2015 · The ISME Journal
A simple guide to de novo transcriptome assembly and annotation
Venket Raghavan, Louis Kraft, Fantin Mesny, Linda Rigerte · 2021 · Briefings in Bioinformatics
Accurate multiple sequence alignment of transmembrane proteins with PSI-Coffee
Jia‐Ming Chang, Paolo Di Tommaso, Jean-François Taly, Cédric Notredame · 2012 · BMC Bioinformatics
Combining Transcriptome Assemblies from Multiple De Novo Assemblers in the Allo-Tetraploid Plant Nicotiana benthamiana
Kenlee Nakasugi, Ross N. Crowhurst, Julia Bally, Peter M. Waterhouse · 2014 · PLoS ONE
Genomic and functional analysis of Romboutsia ilealis CRIB T reveals adaptation to the small intestine
Jacoline Gerritsen, Bastian Hornung, B.A.M. Renckens, Sacha A. F. T. van Hijum, Vítor A. P. Martins dos Santos, Ger T. Rijkers, Peter J. Schaap, Willem M. de Vos, Hauke Smidt · 2017 · PeerJ
Drawing the line between commensal and pathogenic Gardnerella vaginalis through genome analysis and virulence studies
Michael D. Harwich, João M. P. Alves, Gregory A. Buck, Jerome F. Strauss, Jennifer Patterson, Aminat T. Oki, Philippe H. Girerd, Kimberly K. Jefferson · 2010 · BMC Genomics
Genomic characterization of theBacillus cereussensu lato species: Backdrop to the evolution ofBacillus anthracis
Michael E. Zwick, Sandeep J. Joseph, Xavier Didelot, Peter E. Chen, Kimberly A. Bishop‐Lilly, Andrew C. Stewart, Kristin M. Willner, Nichole M. E. Nolan, Shannon M. Lentz, Maureen Kiley Thomason et al. · 2012 · Genome Research
iSeeRNA: identification of long intergenic non-coding RNA transcripts from transcriptome sequencing data
Kun Sun, Xiaona Chen, Peiyong Jiang, Xiaofeng Song, Huating Wang, Hao Sun · 2013 · BMC Genomics
LncFinder: an integrated platform for long non-coding RNA identification utilizing sequence intrinsic composition, structural information and physicochemical property
Siyu Han, Yanchun Liang, Qin Ma, Yangyi Xu, Yu Zhang, Wei Du, Cankun Wang, Ying Li · 2018 · Briefings in Bioinformatics
Taxonomer: an interactive metagenomics analysis portal for universal pathogen detection and host mRNA expression profiling
Flygare, Steven, Simmon, Keith, Miller, Chase, Qiao, Yi, Kennedy, Brett, Di Sera, Tonya, Graf, Erin H., Tardif, Keith D., Kapusta, Aurélie, Rynearson, Shawn et al. · 2016 · Genome Biology
Development of Transcriptomic Resources for Interrogating the Biosynthesis of Monoterpene Indole Alkaloids in Medicinal Plant Species
Elsa Góngora‐Castillo, Kevin L. Childs, Greg Fedewa, John P. Hamilton, David K. Liscombe, Maria Magallanes‐Lundback, Kranthi Kiran Mandadi, Ezekiel Nims, Weerawat Runguphan, Brieanne Vaillancourt et al. · 2012 · PLoS ONE
Adaptation of soil microbial community structure and function to chronic metal contamination at an abandoned Pb-Zn mine
Lur Epelde, Anders Lanzén, Fernando Blanco, Tim Urich, Carlos Garbisu · 2014 · FEMS Microbiology Ecology
The impact of AlphaFold2 one year on
David T. Jones, Janet M. Thornton · 2022 · Nature Methods
Maize (Zea mays L.) Genome Diversity as Revealed by RNA-Sequencing
Candice N. Hansey, Brieanne Vaillancourt, Rajandeep S. Sekhon, Natalia de León, Shawn M. Kaeppler, C. Robin Buell · 2012 · PLoS ONE
Development of a set of SNP markers present in expressed genes of the apple
David Chagné, Ksenija Gašić, Ross N. Crowhurst, Yuepeng Han, Heather C. M. Bassett, Deepa R. Bowatte, Timothy J. Lawrence, Erik H. A. Rikkerink, Susan E. Gardiner, Schuyler Safi Korban · 2008 · Genomics
Chemotaxis shapes the microscale organization of the ocean’s microbiome
Jean‐Baptiste Raina, Bennett Lambert, Donovan H. Parks, Christian Rinke, Nachshon Siboni, Anna R. Bramucci, Martin D. Ostrowski, Bethany Signal, Adrian Lutz, Himasha Mendis et al. · 2022 · Nature
Chimeric origins of ochrophytes and haptophytes revealed through an ancient plastid proteome
Dorrell, Richard G, Gile, Gillian, McCallum, Giselle, Méheust, Raphaël, Bapteste, Eric P, Klinger, Christen M, Brillet-Guéguen, Loraine, Freeman, Katalina D, Richter, Daniel J, Bowler, Chris · 2017 · eLife
Genomic sequence analysis and characterization of Sneathia amnii sp. nov
Michael D. Harwich, Myrna G. Serrano, Jennifer M. Fettweis, João M. P. Alves, Mark A. Reimers, Gregory A. Buck, Kimberly K. Jefferson · 2012 · BMC Genomics
Diterpene cyclases and the nature of the isoprene fold
Rong Cao, Yonghui Zhang, Francis M. Mann, Cancan Huang, Dushyant Mukkamala, Michael P. Hudock, Matthew E. Mead, Sladjana Prišić, Ke Wang, Fu‐Yang Lin et al. · 2010 · Proteins Structure Function and Bioinformatics
Stable isotope informed genome-resolved metagenomics reveals that Saccharibacteria utilize microbially-processed plant-derived carbon
Evan P. Starr, Sheng-Jing Shi, S. Blazewicz, A. Probst, D. Herman, M. Firestone, J. Banfield · 2017 · Microbiome
Evolutionary velocity with protein language models predicts evolutionary dynamics of diverse proteins
Brian Hie, Kevin Yang, Peter S. Kim · 2022 · Cell Systems
Efficient algorithms for accurate hierarchical clustering of huge datasets: tackling the entire protein space
Yaniv Loewenstein, Elon Portugaly, Menachem Fromer, Michal Linial B · 2008 · Bioinformatics
Genome-Resolved Metagenomic Analysis Reveals Roles for Candidate Phyla and Other Microbial Community Members in Biogeochemical Transformations in Oil Reservoirs
Ping Hu, L. Tom, Andrea Singh, B. Thomas, B. Baker, Y. Piceno, G. Andersen, J. Banfield · 2016 · mBio
Upcoming progress of transcriptomics studies on plants: An overview
Parul Tyagi, Deeksha Singh, Shivangi Mathur, Ayushi Singh, Rajiv Ranjan · 2022 · Frontiers in Plant Science
A comprehensive review and comparison of different computational methods for protein remote homology detection
Junjie Chen, Mingyue Guo, Xiaolong Wang, Bin Liu · 2016 · Briefings in Bioinformatics
Protein sequence design with deep generative models
Zachary Wu, Kadina E. Johnston, Frances H. Arnold, Kevin Yang · 2021 · Current Opinion in Chemical Biology
Potential for microbial H2 and metal transformations associated with novel bacteria and archaea in deep terrestrial subsurface sediments
Alex W Hernsdorf, Y. Amano, Kazuya Miyakawa, K. Ise, Yohey Suzuki, Karthik Anantharaman, A. Probst, D. Burstein, B. Thomas, J. Banfield · 2017 · The ISME Journal
Metatranscriptomics of the marine sponge Geodia barretti : tackling phylogeny and function of its microbial community
Regina Radax, Thomas Rattei, Anders Lanzén, Christoph Bayer, Hans Tore Rapp, Tim Urich, Christa Schleper · 2012 · Environmental Microbiology
A Metagenomic Framework for the Study of Airborne Microbial Communities
Shibu Yooseph, Cynthia M. Andrews-Pfannkoch, Aaron E. Tenney, Jeffrey B. McQuaid, Shannon J. Williamson, Mathangi Thiagarajan, Daniel Brami, Lisa Zeigler Allen, Jeff Hoffman, Johannes B. Goll et al. · 2013 · PLoS ONE
The IGS Standard Operating Procedure for Automated Prokaryotic Annotation
Kevin Galens, Joshua Orvis, Sean C. Daugherty, Heather H. Creasy, Samuel V. Angiuoli, Owen R. White, Jennifer Russo Wortman, Anup Mahurkar, Michelle Gwinn Giglio · 2011 · Standards in Genomic Sciences
Exploration of databases and methods supporting drug repurposing: a comprehensive survey
Tanoli, Ziaurrehman, Seemab, Umair, Scherer, Andreas, Wennerberg, Krister, Tang, Jing, Vähä-Koskela, Markus · 2021 · Briefings in Bioinformatics
A formal perturbation equation between genotype and phenotype determines the evolutionary action of protein-coding variations on fitness
Katsonis, Panagiotis, Lichtarge, Olivier · 2014 · Genome Research
AlphaFold2-aware protein–DNA binding site prediction using graph transformer
Yuan, Qianmu, Chen, Sheng, Rao, Jiahua, Zheng, Shuangjia, Zhao, Huiying, Yang, Yuedong · 2022 · Briefings in Bioinformatics
Biology of a widespread uncultivated archaeon that contributes to carbon fixation in the subsurface
Probst, Alexander J., Weinmaier, Thomas, Raymann, Kasie, Perras, Alexandra, Emerson, Joanne B., Rattei, Thomas, Wanner, Gerhard, Klingl, Andreas, Berg, Ivan A., Yoshinaga, Marcos et al. · 2014 · Nature Communications
Metatranscriptomics for the Human Microbiome and Microbial Community Functional Profiling
Yancong Zhang, Kelsey N. Thompson, Tobyn A. Branck, Yan Yan, Long Hoang Nguyen, Eric A. Franzosa, Curtis Huttenhower · 2021 · Annual Review of Biomedical Data Science
The Basic Leucine Zipper Transcription Factor ABSCISIC ACID RESPONSE ELEMENT-BINDING FACTOR2 Is an Important Transcriptional Regulator of Abscisic Acid-Dependent Grape Berry Ripening Processes
Philippe Nicolas, David Lecourieux, Christian Kappel, Stéphanie Cluzet, Grant R. Cramer, Serge Delrot, Fatma Lecourieux · 2013 · PLANT PHYSIOLOGY
Proteome-Wide Discovery of Evolutionary Conserved Sequences in Disordered Regions
Alex N. Nguyen Ba, Brian J. Yeh, Dewald van Dyk, Alan R. Davidson, Brenda Andrews, Eric L. Weiss, Alan M Moses · 2012 · Science Signaling
RubisCO of a nucleoside pathway known from Archaea is found in diverse uncultivated phyla in bacteria
K. Wrighton, C. Castelle, V. Varaljay, S. Satagopan, C. Brown, M. Wilkins, B. Thomas, Itai Sharon, K. Williams, F. Tabita et al. · 2016 · The ISME Journal
Large freshwater phages with the potential to augment aerobic methane oxidation
Lin-Xing Chen, R. Méheust, A. Crits-Christoph, K. McMahon, T. Nelson, Gregory F. Slater, L. Warren, J. Banfield · 2020 · Nature Microbiology
Characterization of interactions of dietary cholesterol with the murine and human gut microbiome
Henry H. Le, Min-Ting Lee, Kevin R. Besler, Janine M. C. Comrie, Elizabeth L. Johnson · 2022 · Nature Microbiology
The Genome Sequence of Leishmania (Leishmania) amazonensis: Functional Annotation and Extended Analysis of Gene Models
Fernando Real, Ramon Oliveira Vidal, Marcelo Falsarella Carazzolle, Jorge Maurı́cio Costa Mondego, Gustavo G.L. Costa, Roberto H. Herai, M. Wurtele, Leandro Machado de Carvalho, Renata C. Ferreira, Renato A. Mortara et al. · 2013 · DNA Research
A fast Peptide Match service for UniProt Knowledgebase
Chuming Chen, Zhiwen Li, Hongzhan Huang, Barış Ethem Süzek, Cathy H. Wu · 2013 · Bioinformatics
Strain-specific gut microbial signatures in type 2 diabetes identified in a cross-cohort analysis of 8,117 metagenomes
Zhendong Mei, Fenglei Wang, Amrisha Bhosle, Danyue Dong, Raaj S. Mehta, Andrew R. Ghazi, Yancong Zhang, Yuxi Liu, Ehud Rinott, Siyuan Ma et al. · 2024 · Nature Medicine
Scientific Large Language Models: A Survey on Biological & Chemical Domains
Qiang Zhang, Keyan Ding, Tianwen Lv, Xinda Wang, Qingyu Yin, Yiwen Zhang, Yu Jing, Yuhao Wang, Xiaotong Li, Zhuoyi Xiang et al. · 2025 · ACM Computing Surveys
Porter, PaleAle 4.0: high-accuracy prediction of protein secondary structure and relative solvent accessibility
Claudio Mirabello, Gianluca Pollastri · 2013 · Bioinformatics
Identical bacterial populations colonize premature infant gut, skin, and oral microbiomes and exhibit different in situ growth rates
Matthew R. Olm, Christopher T. Brown, Brandon Brooks, Brian Firek, Robyn Baker, David Burstein, Karina Soenjoyo, Brian C. Thomas, Michael Morowitz, JF Banfield · 2017 · Genome Research
Lifestyle Evolution in Cyanobacterial Symbionts of Sponges
Ilia Burgsdorf, Beate M. Slaby, Kim M. Handley, Markus Haber, Jochen Blom, C. W. Marshall, Jack A. Gilbert, Ute Hentschel, Laura Steindler · 2015 · mBio
Simulation of Deepwater Horizon oil plume reveals substrate specialization within a complex community of hydrocarbon degraders
Ping Hu, Eric A. Dubinsky, Alexander J. Probst, Jian Wang, Christian M. K. Sieber, Lauren M. Tom, Piero R. Gardinali, Jillian F. Banfield, Ronald M. Atlas, Gary L. Andersen · 2017 · Proceedings of the National Academy of Sciences
AMP‐BERT : Prediction of antimicrobial peptide function based on a BERT model
Hansol Lee, Songyeon Lee, Ingoo Lee, Hojung Nam · 2022 · Protein Science
<i>In planta</i> anthocyanin degradation by a vacuolar class <scp>III</scp> peroxidase in <i>Brunfelsia calycina</i> flowers
Zipor, Gadi, Duarte, Patrícia, Carqueijeiro, Inês, Shahar, Liat, Ovadia, Rinat, Teper‐Bamnolker, Paula, Eshel, Dani, Levin, Yishai, Doron‐Faigenboim, Adi, Sottomayor, Mariana et al. · 2015 · New Phytologist
Evolution and host-specific adaptation ofPseudomonas aeruginosa
Aaron Weimann, Adam M. Dinan, Christopher Ruis, Audrey Bernut, Stéphane Pont, Karen Brown, Judy Ryan, L. Santos, Louise Ellison, E.-F. Ukor et al. · 2024 · Science
Functional Sites Induce Long-Range Evolutionary Constraints in Enzymes
Benjamin R. Jack, Austin G. Meyer, Julián Echave, Claus O. Wilke · 2016 · PLoS Biology
Genomic characterization of the Yersinia genus
Peter E. Chen, Christopher Cook, Andrew C Stewart, Niranjan Nagarajan, Dan D. Sommer, Mihai Pop, Brendan Thomason, Maureen Kiley, Shannon M. Lentz, Nichole M. E. Nolan et al. · 2010 · Genome biology
The Universal Protein Resource (UniProt)
Whitehaven St · 2008
Genome and secretome analysis of the hemibiotrophic fungal pathogen, Moniliophthora roreri, which causes frosty pod rot disease of cacao: mechanisms of the biotrophic and necrotrophic phases
Lyndel W. Meinhardt, Gustavo G.L. Costa, Daniela Paula de Toledo Thomazella, Paulo José Pereira Lima Teixeira, Marcelo Falsarella Carazzolle, Stephan Christoph Schuster, John E. Carlson, Mark J. Guiltinan, Piotr A. Mieczkowski, Andrew D Farmer et al. · 2014 · BMC Genomics
Robust enzyme discovery and engineering with deep learning using CataPro
Ze-Chen Wang, Dongqi Xie, Dong Wu, Xiao-Zhou Luo, Sheng Wang, Yangyang Li, Yan-Mei Yang, Wei-Feng Li, Liang-Zhen Zheng · 2025 · Nature Communications
RNA-seq-Based Gene Annotation and Comparative Genomics of Four Fungal Grass Pathogens in the GenusZymoseptoriaIdentify Novel Orphan Genes and Species-Specific Invasions of Transposable Elements
Jonathan Grandaubert, Amitava Bhattacharyya, Eva H. Stukenbrock · 2015 · G3 Genes Genomes Genetics
Biostimulation induces syntrophic interactions that impact C, S and N cycling in a sediment microbial community
Kim M. Handley, Nathan C. VerBerkmoes, Carl I. Steefel, Kenneth Hurst Williams, Itai Sharon, Christopher S. Miller, Kyle R. Frischkorn, Karuna Chourey, Brian C. Thomas, Manesh B. Shah et al. · 2012 · The ISME Journal
Proteogenomic analyses indicate bacterial methylotrophy and archaeal heterotrophy are prevalent below the grass root zone
Cristina N. Butterfield, Zhou Li, Peter F Andeer, Susan E. Spaulding, Brian C. Thomas, Andrea Singh, Robert L. Hettich, K. Blake Suttle, Alexander J. Probst, Susannah Green Tringe et al. · 2016 · PeerJ
Metagenomic analysis of a high carbon dioxide subsurface microbial community populated by chemolithoautotrophs and bacteria and archaea from candidate phyla
Joanne Emerson, Brian C. Thomas, Walter C. Alvarez, Jillian F. Banfield · 2015 · Environmental Microbiology
Sequencing and assembly of low copy and genic regions of isolated Triticum aestivum chromosome arm 7DS
Paul J. Berkman, Adam Skarshewski, Michał T. Lorenc, Kaitao Lai, Chris Duran, Edmund Y. S. Ling, Jiri Stiller, Lars Smits, Michael Imelfort, Sahana Manoli et al. · 2011 · Plant Biotechnology Journal
Surprising Prokaryotic and Eukaryotic Diversity, Community Structure and Biogeography of Ethiopian Soda Lakes
Anders Lanzén, Addis Simachew, Amare Gessesse, Dominika Chmolowska, Inge Jonassen, Lise Øvreås · 2013 · PLoS ONE
Insights on variant analysis in silico tools for pathogenicity prediction
Felipe Antônio de Oliveira Garcia, Edilene Santos de Andrade, Edenir Inêz Palmero · 2022 · Frontiers in Genetics
Epiphytic common core bacteria in the microbiomes of co-located green (Ulva), brown (Saccharina) and red (Grateloupia, Gelidium) macroalgae
De‐Chen Lu, Fengqing Wang, Rudolf Amann, Hanno Teeling, Zong‐Jun Du · 2023 · Microbiome
Prediction of Membrane Transport Proteins and Their Substrate Specificities Using Primary Sequence Information
Nitish K. Mishra, Junil Chang, Patrick Xuechun Zhao · 2014 · PLoS ONE
RBP2GO: a comprehensive pan-species database on RNA-binding proteins, their interactions and functions
Maïwen Caudron‐Herger, R. Jansen, Elsa Wassmer, Sven Diederichs · 2020 · Nucleic Acids Research
Back from the dead; the curious tale of the predatory cyanobacterium Vampirovibrio chlorellavorus
R. Soo, B. Woodcroft, D. Parks, G. Tyson, P. Hugenholtz · 2015 · PeerJ
Predicting protein function from domain content
Sofia Kirke Forslund, Erik L. L. Sonnhammer · 2008 · Bioinformatics
Bayesian analysis of molecular variance in pyrosequences quantifies population genetic structure across the genome of Lycaeides butterflies
Zachariah Gompert, Matthew L. Forister, James A. Fordyce, Chris C. Nice, ROBERT J. WILLIAMSON, C. Alex Buerkle · 2010 · Molecular Ecology
Evolutionary Dynamics of Complete Campylobacter Pan-Genomes and the Bacterial Species Concept
Lefébure Tristan, Paulina D. Pavinski Bitar, Haruo Suzuki, Michael J. Stanhope · 2010 · Genome Biology and Evolution
Forest floor community metatranscriptomes identify fungal and bacterial responses to N deposition in two maple forests
Cedar N. Hesse, Rebecca Mueller, Momchilo Vuyisich, La Verne Gallegos‐Graves, Cheryl D. Gleasner, Donald R. Zak, Cheryl R. Kuske · 2015 · Frontiers in Microbiology
Viruses interact with hosts that span distantly related microbial domains in dense hydrothermal mats
Yunha Hwang, Simon Roux, Clément Coclet, Sebastian J. E. Krause, Peter R. Girguis · 2023 · Nature Microbiology
ProQ3: Improved model quality assessments using Rosetta energy terms
Karolis Uziela, N. Shu, B. Wallner, A. Elofsson · 2016 · Scientific Reports
Genetic manipulation of Patescibacteria provides mechanistic insights into microbial dark matter and the epibiotic lifestyle
Wang, Yaxi, Gallagher, Larry A., Andrade, Pia A., Liu, Andi, Humphreys, Ian R., Turkarslan, Serdar, Cutler, Kevin J., Arrieta-Ortiz, Mario L., Li, Yaqiao, Radey, Matthew C. et al. · 2023 · Cell
Aquifer environment selects for microbial species cohorts in sediment and groundwater
Laura A. Hug, Brian C. Thomas, Christopher T. Brown, Kyle R. Frischkorn, Kenneth Hurst Williams, Susannah Green Tringe, Jillian F. Banfield · 2015 · The ISME Journal
Bioreactor microbial ecosystems for thiocyanate and cyanide degradation unravelled with genome‐resolved metagenomics
Rose S. Kantor, Andries W. van Zyl, Robert P. van Hille, Brian C. Thomas, Susan T.L. Harrison, Jillian F. Banfield · 2015 · Environmental Microbiology
Metaproteomics of complex microbial communities in biogas plants
Robert Heyer, Fabian Kohrs, Udo Reichl, Dirk Benndorf · 2015 · Microbial Biotechnology
Unusual respiratory capacity and nitrogen metabolism in a Parcubacterium (OD1) of the Candidate Phyla Radiation
C. Castelle, C. Brown, B. Thomas, K. Williams, J. Banfield · 2017 · Scientific Reports
Multiple sequence alignment-based RNA language model and its application to structural inference
Zhang, Yikun, Lang, Mei, Jiang, Jiuhong, Gao, Zhiqiang, Xu, Fan, Litfin, Thomas, Chen, Ke, Singh, Jaswinder, Huang, Xiansong, Song, Guoli et al. · 2024 · Nucleic Acids Research
The genome sequence of Propionibacterium acidipropionici provides insights into its biotechnological and industrial potential
Lucas Pedersen Parizzi, Maria Carolina B. Grassi, Luige Armando Llerena Calderón, Marcelo Falsarella Carazzolle, Verônica L. Queiroz, Inês Lunardi, Ane F Zeidler, Paulo José Pereira Lima Teixeira, Piotr A. Mieczkowski, Johana Rincones et al. · 2012 · BMC Genomics
Transcriptome responses to Ralstonia solanacearum infection in the roots of the wild potato Solanum commersonii
Paola Zuluaga, Montserrat Solé, Haibin Lu, Elsa Góngora‐Castillo, Brieanne Vaillancourt, Núria S. Coll, C. Robin Buell, Marc Valls · 2015 · BMC Genomics
Gut microbial β-glucuronidases regulate host luminal proteases and are depleted in irritable bowel syndrome
Edwinson, Adam L., Yang, Lu, Peters, Stephanie, Hanning, Nikita, Jeraldo, Patricio, Jagtap, Pratik, Simpson, Joshua B., Yang, Tzu-Yi, Kumar, Praveen, Mehta, Subina et al. · 2022 · Nature Microbiology