Rfam 14: expanded coverage of metagenomic, viral and microRNA families von Kalvari, Ioanna, Nawrocki, Eric P, Ontiveros-Palacios, Nancy, Argasinska, Joanna, Lamkiewicz, Kevin, Marz, Manja, Griffiths-Jones, Sam, Toffano-Nioche, Claire, Gautheret, Daniel, Weinberg, Zasha, Rivas, Elena, Eddy, Sean R, Finn, Robert D, Bateman, Alex, Petrov, Anton I

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Skylign: a tool for creating informative, interactive logos representing sequence alignments and profile hidden Markov models von Wheeler, Travis J, Clements, Jody, Finn, Robert D

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A new genomic blueprint of the human gut microbiota von Almeida, Alexandre, Mitchell, Alex L., Boland, Miguel, Forster, Samuel C., Gloor, Gregory B., Tarkowska, Aleksandra, Lawley, Trevor D., Finn, Robert D.

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HMMER web server: interactive sequence similarity searching von Finn, Robert D., Clements, Jody, Eddy, Sean R.

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The EMBL-EBI search and sequence analysis tools APIs in 2019 von Madeira, Fábio, Park, Young Mi, Lee, Joon, Buso, Nicola, Gur, Tamer, Madhusoodanan, Nandana, Basutkar, Prasad, Tivey, Adrian R N, Potter, Simon C, Finn, Robert D, Lopez, Rodrigo

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HMMER web server: 2018 update von Potter, Simon C, Luciani, Aurélien, Eddy, Sean R, Park, Youngmi, Lopez, Rodrigo, Finn, Robert D

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A unified catalog of 204,938 reference genomes from the human gut microbiome von Almeida, Alexandre, Nayfach, Stephen, Boland, Miguel, Strozzi, Francesco, Beracochea, Martin, Shi, Zhou Jason, Pollard, Katherine S., Sakharova, Ekaterina, Parks, Donovan H., Hugenholtz, Philip, Segata, Nicola, Kyrpides, Nikos C., Finn, Robert D.

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Microbial abundance, activity and population genomic profiling with mOTUs2 von Milanese, Alessio, Mende, Daniel R, Paoli, Lucas, Salazar, Guillem, Ruscheweyh, Hans-Joachim, Cuenca, Miguelangel, Hingamp, Pascal, Alves, Renato, Costea, Paul I, Coelho, Luis Pedro, Schmidt, Thomas S. B., Almeida, Alexandre, Mitchell, Alex L, Finn, Robert D., Huerta-Cepas, Jaime, Bork, Peer, Zeller, Georg, Sunagawa, Shinichi

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The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database von Rawlings, Neil D, Barrett, Alan J, Thomas, Paul D, Huang, Xiaosong, Bateman, Alex, Finn, Robert D

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Pfam: The protein families database in 2021 von Mistry, Jaina, Chuguransky, Sara, Williams, Lowri, Qureshi, Matloob, Salazar, Gustavo A, Sonnhammer, Erik L L, Tosatto, Silvio C E, Paladin, Lisanna, Raj, Shriya, Richardson, Lorna J, Finn, Robert D, Bateman, Alex

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Massive expansion of human gut bacteriophage diversity von Camarillo-Guerrero, Luis F., Almeida, Alexandre, Rangel-Pineros, Guillermo, Finn, Robert D., Lawley, Trevor D.

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Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families von Kalvari, Ioanna, Argasinska, Joanna, Quinones-Olvera, Natalia, Nawrocki, Eric P, Rivas, Elena, Eddy, Sean R, Bateman, Alex, Finn, Robert D, Petrov, Anton I

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Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions von Mistry, Jaina, Finn, Robert D, Eddy, Sean R, Bateman, Alex, Punta, Marco

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The Dfam database of repetitive DNA families von Hubley, Robert, Finn, Robert D, Clements, Jody, Eddy, Sean R, Jones, Thomas A, Bao, Weidong, Smit, Arian F A, Wheeler, Travis J

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Estimating the quality of eukaryotic genomes recovered from metagenomic analysis with EukCC von Saary, Paul, Mitchell, Alex L., Finn, Robert D.

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Cache Domains That are Homologous to, but Different from PAS Domains Comprise the Largest Superfamily of Extracellular Sensors in Prokaryotes von Upadhyay, Amit A, Fleetwood, Aaron D, Adebali, Ogun, Finn, Robert D, Zhulin, Igor B

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MGnify: the microbiome analysis resource in 2020 von Mitchell, Alex L, Almeida, Alexandre, Beracochea, Martin, Boland, Miguel, Burgin, Josephine, Cochrane, Guy, Crusoe, Michael R, Kale, Varsha, Potter, Simon C, Richardson, Lorna J, Sakharova, Ekaterina, Scheremetjew, Maxim, Korobeynikov, Anton, Shlemov, Alex, Kunyavskaya, Olga, Lapidus, Alla, Finn, Robert D

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Predicting active site residue annotations in the Pfam database von Mistry, Jaina, Bateman, Alex, Finn, Robert D

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The European Bioinformatics Institute in 2016: Data growth and integration von Cook, Charles E, Bergman, Mary Todd, Finn, Robert D, Cochrane, Guy, Birney, Ewan, Apweiler, Rolf

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MGnify: the microbiome sequence data analysis resource in 2023 von Richardson, Lorna, Allen, Ben, Baldi, Germana, Beracochea, Martin, Bileschi, Maxwell L, Burdett, Tony, Burgin, Josephine, Caballero-Pérez, Juan, Cochrane, Guy, Colwell, Lucy J, Curtis, Tom, Escobar-Zepeda, Alejandra, Gurbich, Tatiana A, Kale, Varsha, Korobeynikov, Anton, Raj, Shriya, Rogers, Alexander B, Sakharova, Ekaterina, Sanchez, Santiago, Wilkinson, Darren J, Finn, Robert D

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