Accelerated Profile HMM Searches

Cited by (1,027)

Items 301–400 of 1,027

1. Assessment of computational methods for predicting the effects of missense mutations in human cancers
   Florian Gnad, Albion Baucom, Kiran Mukhyala, Gerard Manning, Zemin Zhang · 2013 · BMC Genomics
2. The core root microbiome of sugarcanes cultivated under varying nitrogen fertilizer application
   Yun Kit Yeoh, Chanyarat Paungfoo‐Lonhienne, Paul G. Dennis, Nicole Robinson, Mark A. Ragan, Susanne Schmidt, Philip Hugenholtz · 2015 · Environmental Microbiology
3. Direct generation of protein conformational ensembles via machine learning
   Janson, Giacomo, Valdes-Garcia, Gilberto, Heo, Lim, Feig, Michael · 2023 · Nature Communications
4. MapZ marks the division sites and positions FtsZ rings in Streptococcus pneumoniae
   Aurore Fleurie, Christian Lesterlin, Sylvie Manuse, Chao Zhao, Caroline Cluzel, Jean-Pierre Lavergne, Mirita Franz‐Wachtel, Boris Maček, Christophe Combet, Erkin Kuru et al. · 2014 · Nature
5. De Novo Assembly of a New Solanum pennellii Accession Using Nanopore Sequencing
   Maximilian Schmidt, Alexander Vogel, Alisandra K. Denton, Benjamin Istace, Alexandra Wormit, Henri van de Geest, Marie Bolger, Saleh Alseekh, Janina Maß, Christian Pfaff et al. · 2017 · The Plant Cell
6. Recent development of antiSMASH and other computational approaches to mine secondary metabolite biosynthetic gene clusters
   Kai Blin, Hyun Uk Kim, Marnix H. Medema, Tilmann Weber · 2017 · Briefings in Bioinformatics
7. Comparison of normalization methods for the analysis of metagenomic gene abundance data
   Mariana Buongermino Pereira, Mikael Wallroth, Viktor Jönsson, Erik Kristiansson · 2018 · BMC Genomics
8. Akkermansia muciniphila Prevents Fatty Liver Disease, Decreases Serum Triglycerides, and Maintains Gut Homeostasis
   Sejeong Kim, Yewon Lee, Yujin Kim, Yeongeun Seo, Heeyoung Lee, Jimyeong Ha, Jeeyeon Lee, Yukyung Choi, Hyemin Oh, Yohan Yoon · 2020 · Applied and Environmental Microbiology
9. 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
10. Contrastive learning in protein language space predicts interactions between drugs and protein targets
    Rohit Singh, Samuel Sledzieski, Bryan D. Bryson, Lenore Cowen, Bonnie Berger · 2023 · Proceedings of the National Academy of Sciences
11. Detecting Nitrous Oxide Reductase ( nosZ ) Genes in Soil Metagenomes: Method Development and Implications for the Nitrogen Cycle
    Luis H. Orellana, Luis M. Rodriguez‐R, Steven Higgins, Joanne C. Chee‐Sanford, Robert A. Sanford, Kirsti M. Ritalahti, Frank E. Löffler, Konstantinos T. Konstantinidis · 2014 · mBio
12. Phylogenomic analysis of Apoidea sheds new light on the sister group of bees
    Manuela Sann, Oliver Niehuis, Ralph S. Peters, Christoph Mayer, Alexey M. Kozlov, Lars Podsiadłowski, Sarah Bank-Aubin, Karen Meusemann, Bernhard Y. Misof, Christoph Bleidorn et al. · 2018 · BMC Evolutionary Biology
13. ProteInfer, deep neural networks for protein functional inference
    Theo Sanderson, Maxwell L. Bileschi, David Belanger, Lucy J. Colwell · 2023 · eLife
14. Genome of the human hookworm Necator americanus
    Yat T. Tang, Xin Gao, Bruce A. Rosa, Sahar Abubucker, Kymberlie Hallsworth-Pepin, John C Martin, Rahul Tyagi, Esley M. Heizer, Xu Zhang, Veena Bhonagiri et al. · 2014 · Nature Genetics
15. A deep siamese neural network improves metagenome-assembled genomes in microbiome datasets across different environments
    Shaojun Pan, Chengkai Zhu, Xing‐Ming Zhao, Luis Pedro Coelho · 2022 · Nature Communications
16. Genome Reduction and Co-evolution between the Primary and Secondary Bacterial Symbionts of Psyllids
    Daniel B. Sloan, Nancy A. Moran · 2012 · Molecular Biology and Evolution
17. Cache Domains That are Homologous to, but Different from PAS Domains Comprise the Largest Superfamily of Extracellular Sensors in Prokaryotes
    Amit A. Upadhyay, Aaron D. Fleetwood, Ogün Adebalı, Robert D. Finn, Igor B. Zhulin · 2016 · PLoS Computational Biology
18. Systematic discovery of natural CRISPR-Cas12a inhibitors
    Kyle E. Watters, Christof Fellmann, Hua Bai, Shawn M. Ren, Jennifer A. Doudna · 2018 · Science
19. Full‐length de novo assembly of RNA‐seq data in pea ( P isum sativum L.) provides a gene expression atlas and gives insights into root nodulation in this species
    Susete Alves Carvalho, Grégoire Aubert, Sébastien Carrère, Corinne Cruaud, Anne-Lise Brochot, Françoise Jacquin, Anthony Klein, Chantal Martin, Karen Boucherot, Jonathan Kreplak et al. · 2015 · The Plant Journal
20. The secondary metabolite bioinformatics portal: Computational tools to facilitate synthetic biology of secondary metabolite production
    Tilmann Weber, Hyun Uk Kim · 2016 · Synthetic and Systems Biotechnology
21. Distinct Polysaccharide Utilization Determines Interspecies Competition between Intestinal Prevotella spp.
    Eric J. C. Gálvez, Aida Iljazović, Lena Amend, Till Robin Lesker, Thibaud T. Renault, Sophie Thiemann, Lianxu Hao, Urmi Roy, Achim Gronow, Emmanuelle Charpentier et al. · 2020 · Cell Host & Microbe
22. Microbial mercury methylation in Antarctic sea ice
    Caitlin M. Gionfriddo, Michael T. Tate, Ryan R. Wick, Mark B. Schultz, Adam T Zemla, Michael P. Thelen, Robyn Schofield, David P. Krabbenhoft, Kathryn E. Holt, John W. Moreau · 2016 · Nature Microbiology
23. Proteomics and comparative genomics of Nitrososphaera viennensis reveal the core genome and adaptations of archaeal ammonia oxidizers
    Melina Kerou, Pierre Offre, Luís Valledor, Sophie S. Abby, Michael Melcher, Matthias Nagler, Wolfram Weckwerth, Christa Schleper · 2016 · Proceedings of the National Academy of Sciences
24. Genomics of Loa loa, a Wolbachia-free filarial parasite of humans
    Christopher A. Desjardins, Gustavo Cerqueira, Jonathan M. Goldberg, Julie C. Dunning Hotopp, Brian J. Haas, Jeremy Zucker, José M. C. Ribeiro, Sakina Saif, Joshua Z. Levin, Lin Fan et al. · 2013 · Nature Genetics
25. The genome of the jellyfish Clytia hemisphaerica and the evolution of the cnidarian life-cycle
    Lucas Leclère, Coralie Horin, Sandra Chevalier, Pascal Lapébie, Philippe Dru, Sophie Péron, Muriel Jager, Thomas Condamine, Karen Pottin, Séverine Romano et al. · 2019 · Nature Ecology & Evolution
26. Biodegradation as an important sink of aromatic hydrocarbons in the oceans
    B. González-Gaya, A. Martínez-Varela, M. Vila-Costa, Paulo Casal, Elena Cerro-Gálvez, N. Berrojálbiz, D. Lundin, M. Vidal, C. Mompeán, A. Bode et al. · 2019 · Nature Geoscience
27. Small-molecule ligand docking into comparative models with Rosetta
    Steven A. Combs, Samuel DeLuca, Stephanie H. DeLuca, Gordon Lemmon, David P. Nannemann, Elizabeth Dong Nguyen, Jordan R. Willis, Jonathan H. Sheehan, Jens Meiler · 2013 · Nature Protocols
28. Verrucomicrobiota are specialist consumers of sulfated methyl pentoses during diatom blooms
    Luis H. Orellana, Ben Francis, Marcela Ferraro, Jan‐Hendrik Hehemann, Bernhard Maximilian Fuchs, Rudolf Amann · 2021 · The ISME Journal
29. Genome-wide identification and comparative analysis of the heat shock transcription factor family in Chinese white pear (Pyrus bretschneideri) and five other Rosaceae species
    Xin Qiao, Meng Li, Leiting Li, Hao Yin, Juyou Wu, Shaoling Zhang · 2015 · BMC Plant Biology
30. Draft Sequences of the Radish (Raphanus sativus L.) Genome
    Hiroyasu Kitashiba, Li Feng, Hideki Hirakawa, Takahiro Kawanabe, Zhongwei Zou, Yoichi Hasegawa, Kaoru Tonosaki, Sachiko Shirasawa, Aki Fukushima, Shuji Yokoi et al. · 2014 · DNA Research
31. CeMbio - The Caenorhabditis elegans Microbiome Resource
    Philipp Dirksen, Adrien Assié, Johannes Zimmermann, Fan Zhang, Adina-Malin Tietje, Sarah Marsh, Marie‐Anne Félix, Michael Shapira, Christoph Kaleta, Hinrich Schulenburg Y et al. · 2020 · G3 Genes Genomes Genetics
32. Divergent evolutionary trajectories of bryophytes and tracheophytes from a complex common ancestor of land plants
    Harris, Brogan J., Clark, James W., Schrempf, Dominik, Szöllősi, Gergely J., Donoghue, Philip C. J., Hetherington, Alistair M., Williams, Tom A. · 2022 · Nature Ecology & Evolution
33. Transcriptionally and post-transcriptionally regulated microRNAs in heat stress response in barley
    Katarzyna Kruszka, Andrzej Miroslaw Pacak, Aleksandra Świda-Barteczka, Przemysław Nuc, Sylwia Alaba, Zuzanna Wroblewska, Wojciech Maciej Karlowski, Artur Jarmołowski, Zofia Szweykowska-Kulińska · 2014 · Journal of Experimental Botany
34. Gene3D: Extensive prediction of globular domains in proteins
    Tony E. Lewis, I. Sillitoe, N. Dawson, S. Lam, Tristan Clarke, David A. Lee, C. Orengo, J. Lees · 2017 · Nucleic Acids Res.
35. Footprints of parasitism in the genome of the parasitic flowering plant Cuscuta campestris
    Alexander Vogel, Rainer Schwacke, Alisandra K. Denton, Björn Usadel, Julien Hollmann, Karsten Fischer, Anthony Bolger, Maximilian Schmidt, Marie Bolger, Heidrun Gundlach et al. · 2018 · Nature Communications
36. Carbohydrate Binding Modules: Diversity of Domain Architecture in Amylases and Cellulases From Filamentous Microorganisms
    Andika Sidar, Érica Dutra Albuquerque, Gerben P. Voshol, Arthur F. J. Ram, Erik Vijgenboom, Peter J. Punt · 2020 · Frontiers in Bioengineering and Biotechnology
37. A metagenomics roadmap to the uncultured genome diversity in hypersaline soda lake sediments
    Charlotte D. Vavourakis, Adrian‐Ștefan Andrei, Maliheh Mehrshad, Rohit Ghai, Dimitry Y. Sorokin, Gerard Muyzer · 2018 · Microbiome
38. In marine Bacteroidetes the bulk of glycan degradation during algae blooms is mediated by few clades using a restricted set of genes
    Karen Krüger, Meghan E. Chafee, Ben Francis, Tijana Glavina del Rio, Dörte Becher, Thomas Schweder, Rudolf Amann, Hanno Teeling · 2019 · The ISME Journal
39. Diversity, function and assembly of mangrove root-associated microbial communities at a continuous fine-scale
    Wei Zhuang, Xiaoli Yu, Ruiwen Hu, Zhiwen Luo, Xingyu Liu, Xiafei Zheng, Fanshu Xiao, Yisheng Peng, Qiang He, Yun Tian et al. · 2020 · npj Biofilms and Microbiomes
40. Language models generalize beyond natural proteins
    Verkuil, Robert, Kabeli, Ori, Du, Yilun, Wicky, Basile I. M., Milles, Lukas F., Dauparas, Justas, Baker, David, Ovchinnikov, Sergey, Sercu, Tom, Rives, Alexander · 2022
41. DNA-binding specificity changes in the evolution of forkhead transcription factors
    So Nakagawa, Stephen S. Gisselbrecht, Julia M. Rogers, Daniel L. Hartl, Martha L. Bulyk · 2013 · Proceedings of the National Academy of Sciences
42. Marine biofilms constitute a bank of hidden microbial diversity and functional potential
    Weipeng Zhang, Wei Ding, Yong‐Xin Li, Chunkit Tam, Salim Bougouffa, Ruojun Wang, Bite Pei, Hoyin Chiang, Pok Man Leung, Yanhong Lu et al. · 2019 · Nature Communications
43. Niche partitioning of diverse sulfur-oxidizing bacteria at hydrothermal vents.
    Meier, Dimitri V, Pjevac, Petra, Bach, Wolfgang, Hourdez, Stephane, Girguis, Peter R, Vidoudez, Charles, Amann, Rudolf, Meyerdierks, Anke · 2017 · The ISME Journal
44. Phage-Plasmids Spread Antibiotic Resistance Genes through Infection and Lysogenic Conversion
    Eugen Pfeifer, Rémy A. Bonnin, Eduardo P. C. Rocha · 2022 · mBio
45. Comprehensive taxonomic identification of microbial species in metagenomic data using SingleM and Sandpiper
    Ben J. Woodcroft, Samuel T. N. Aroney, Rossen Zhao, Mitchell A. Cunningham, J. A. Mitchell, Rizky Nurdiansyah, Linda L. Blackall, Gene W. Tyson · 2025 · Nature Biotechnology
46. Microbial community structure and function on sinking particles in the North Pacific Subtropical Gyre
    Kristina M. Fontanez, John M. Eppley, Ty J. Samo, David M. Karl, Edward F. DeLong · 2015 · Frontiers in Microbiology
47. SAR202 Genomes from the Dark Ocean Predict Pathways for the Oxidation of Recalcitrant Dissolved Organic Matter
    Zachary Landry, Brandon K. Swan, Gerhard J. Herndl, Ramūnas Stepanauskas, Stephen J. Giovannoni · 2017 · mBio
48. A catalogue of biochemically diverse CRISPR-Cas9 orthologs
    Giedrius Gasiūnas, Joshua K. Young, Tautvydas Karvelis, Darius Kazlauskas, Tomas Urbaitis, Monika Jasnauskaitė, Mantvyda M. Grusyte, Sushmitha Paulraj, Po-Hao Wang, Zhenglin Hou et al. · 2020 · Nature Communications
49. Metabolomics and genomics in natural products research: complementary tools for targeting new chemical entities
    Lindsay K. Caesar, Rana Montaser, Nancy P. Keller, Neil L. Kelleher · 2021 · Natural Product Reports
50. A simple guide to de novo transcriptome assembly and annotation
    Venket Raghavan, Louis Kraft, Fantin Mesny, Linda Rigerte · 2021 · Briefings in Bioinformatics
51. MacSyFinder v2: Improved modelling and search engine to identify molecular systems in genomes
    Bertrand Néron, Rémi Denise, Charles Coluzzi, Marie Touchon, Eduardo P. C. Rocha, Sophie S. Abby · 2023 · Peer Community Journal
52. Metagenomic analysis of a Mexican ripened cheese reveals a unique complex microbiota
    Escobar-Zepeda, Alejandra, Sanchez-Flores, Alejandro, Quirasco Baruch, Maricarmen · 2016 · Food Microbiology
53. Phylogeny and physiology of candidate phylum ‘Atribacteria’ (OP9/JS1) inferred from cultivation-independent genomics
    Masaru Konishi Nobu, Jeremy A. Dodsworth, Senthil K. Murugapiran, Christian Rinke, Esther Gies, Gordon Webster, Patrick Schwientek, Peter Kille, Ronald John Parkes, Henrik Sass et al. · 2015 · The ISME Journal
54. Compact RNA editors with small Cas13 proteins
    Kannan, Soumya, Altae-Tran, Han, Jin, Xin, Madigan, Victoria J., Oshiro, Rachel, Makarova, Kira S., Koonin, Eugene V., Zhang, Feng · 2022 · Nature Biotechnology
55. Two MYB transcription factors regulate flavonoid biosynthesis in pear fruit (Pyrus bretschneideriRehd.)
    Rui Zhai, Zhimin Wang, Shiwei Zhang, Geng Meng, Linyan Song, Zhigang Wang, Pengmin Li, Fengwang Ma, Lingfei Xu · 2015 · Journal of Experimental Botany
56. Peatland Acidobacteria with a dissimilatory sulfur metabolism
    Bela Hausmann, Claus Pelikan, Craig William Herbold, Stephan Köstlbacher, Mads Albertsen, Stephanie A. Eichorst, Tijana Glavina del Rio, Martin Huemer, Per Halkjær Nielsen, Thomas Rattei et al. · 2018 · The ISME Journal
57. Chemical dispersants enhance the activity of oil- and gas condensate-degrading marine bacteria
    Julien Tremblay, Étienne Yergeau, Nathalie Y. Fortin, Susan E. Cobanli, Miria Elias, Thomas L. King, Kenneth Lee, Charles W. Greer · 2017 · The ISME Journal
58. Functional repertoire convergence of distantly related eukaryotic plankton lineages abundant in the sunlit ocean
    Delmont, Tom O., Gaia, Morgan, Hinsinger, Damien D., Frémont, Paul, Vanni, Chiara, Fernandez-Guerra, Antonio, Eren, A. Murat, Kourlaiev, Artem, d'Agata, Leo, Clayssen, Quentin et al. · 2022 · Cell Genomics
59. The whole genome sequence of the Mediterranean fruit fly, Ceratitis capitata (Wiedemann), reveals insights into the biology and adaptive evolution of a highly invasive pest species
    Alexie Papanicolaou, Marc F. Schetelig, Peter Arensburger, Peter W. Atkinson, Joshua B. Benoit, Kostas Bourtzis, Pedro Castañera, John P. Cavanaugh, Hsu Chao, Christopher P. Childers et al. · 2016 · Genome biology
60. Diversification of bacterial genome content through distinct mechanisms over different timescales
    Nicholas J. Croucher, Paul G. Coupland, Abbie E. Stevenson, Alanna Callendrello, Stephen D. Bentley, William Paul Hanage · 2014 · Nature Communications
61. Comparative Genomics Reveals the Origins and Diversity of Arthropod Immune Systems
    William J. Palmer, Francis M. Jiggins · 2015 · Molecular Biology and Evolution
62. Function, distribution, and annotation of characterized cellulases, xylanases, and chitinases from CAZy
    Stanley T. C. Nguyen, Hannah L. Freund, Joshua Kasanjian, Renaud Berlemont · 2018 · Applied Microbiology and Biotechnology
63. Phylogeny of the manta and devilrays (Chondrichthyes: mobulidae), with an updated taxonomic arrangement for the family
    William T. White, Shannon L. Corrigan, Lei Yang, Aaron C. Henderson, Adam L. Bazinet, David L. Swofford, Gavin J. P. Naylor · 2017 · Zoological Journal of the Linnean Society
64. Rapid evolutionary turnover of mobile genetic elements drives bacterial resistance to phages
    Fatima A. Hussain, Javier Dubert, Joseph Elsherbini, Mikayla Murphy, David VanInsberghe, Philip Arevalo, Kathryn M. Kauffman, Bruno K. Rodiño‐Janeiro, Hannah E. Gavin, Annika L. Gomez et al. · 2021 · Science
65. Comparative single-cell genomics reveals potential ecological niches for the freshwater acI Actinobacteria lineage
    Trevor Ghylin, Sarahi L. Garcia, Francisco Moya, Ben O. Oyserman, Patrick Schwientek, Katrina T. Forest, James P. Mutschler, Jeffrey R. Dwulit‐Smith, Leong‐Keat Chan, Manuel Martínez‐García et al. · 2014 · The ISME Journal
66. Coupled anaerobic methane oxidation and reductive arsenic mobilization in wetland soils
    Ling-Dong Shi, Ting Guo, Pan-Long Lv, Zi-Fan Niu, Yujie Zhou, Xianjin Tang, Ping Zheng, Lizhong Zhu, Yong‐Guan Zhu, Andreas A. Kappler et al. · 2020 · Nature Geoscience
67. Long solids retention times and attached growth phase favor prevalence of comammox bacteria in nitrogen removal systems
    Irmarie Cotto, Zihan Dai, Linxuan Huo, Christopher L. Anderson, Katherine Jeanne Vilardi, Umer Zeeshan Ijaz, Wendell Khunjar, Chris Wilson, Haydée De Clippeleir, Kevin R. Gilmore et al. · 2019 · Water Research
68. Diversity and evolution of the animal virome
    Erin Harvey, Edward Charles Holmes · 2022 · Nature Reviews Microbiology
69. Orthograph: a versatile tool for mapping coding nucleotide sequences to clusters of orthologous genes
    Malte Petersen, Karen Meusemann, Alexander Donath, Daniel Dowling, Shanlin Liu, Ralph S. Peters, Lars Podsiadłowski, Alexandros Vasilikopoulos, Xin Yu Zhou, Bernhard Y. Misof et al. · 2017 · BMC Bioinformatics
70. MetaCHIP: community-level horizontal gene transfer identification through the combination of best-match and phylogenetic approaches
    Wei-Zhi Song, B. Wemheuer, Sha Zhang, Kerrin Steensen, T. Thomas · 2019 · Microbiome
71. Bacteria have numerous distinctive groups of phage–plasmids with conserved phage and variable plasmid gene repertoires
    Eugen Pfeifer, Jorge A. Moura de Sousa, Marie Touchon, Eduardo P. C. Rocha · 2021 · Nucleic Acids Research
72. Cyanate and urea are substrates for nitrification by Thaumarchaeota in the marine environment
    Katharina Kitzinger, Cory C. Padilla, Hannah K. Marchant, Philipp F. Hach, Craig William Herbold, Abiel T. Kidane, Martin Könneke, Sten Littmann, Maria Mooshammer, Jutta Niggemann et al. · 2018 · Nature Microbiology
73. Dominant Bacterial Phyla from the Human Gut Show Widespread Ability To Transform and Conjugate Bile Acids
    Lucas, L. N., Barrett, K., Kerby, R. L., Zhang, Q., Cattaneo, L. E., Stevenson, D., Rey, F. E., Amador-Noguez, D. · 2021 · mSystems
74. In-depth resistome analysis by targeted metagenomics
    Val F. Lanza, Fernando Baquero, José Luis Martínez, Ricardo Ramos, Bruno González‐Zorn, Antoine Andremont, Antonio Sánchez Valenzuela, Stanislav Dusko Ehrlich, Sean Kennedy, Étienne Ruppé et al. · 2018 · Microbiome
75. GraftM: a tool for scalable, phylogenetically informed classification of genes within metagenomes
    Joel A. Boyd, Ben J. Woodcroft, Gene W. Tyson · 2018 · Nucleic Acids Research
76. Extensive loss of cell-cycle and DNA repair genes in an ancient lineage of bipolar budding yeasts
    Steenwyk, Jacob L., Opulente, Dana A., Kominek, Jacek, Shen, Xing-Xing, Zhou, Xiaofan, Labella, Abigail L., Bradley, Noah P., Eichman, Brandt F., Čadež, Neža, Libkind, Diego et al. · 2019 · PLoS Biology
77. The Effect of Probiotics on Gut Microbiota during the Helicobacter pylori Eradication: Randomized Controlled Trial
    Bumjo Oh, Bong Soo Kim, Ji Won Kim, Jong S. Kim, Seong‐Joon Koh, Byeong Gwan Kim, Kook Lae Lee, Jongsik Chun · 2015 · Helicobacter
78. Sulfonate-based networks between eukaryotic phytoplankton and heterotrophic bacteria in the surface ocean
    Bryndan P. Durham, Angela K. Boysen, Laura Truxal Carlson, Ryan D. Groussman, Katherine R. Heal, Kelsy Cain, Rhonda L. Morales, Sacha Coesel, Robert M. Morris, Anitra E. Ingalls et al. · 2019 · Nature Microbiology
79. New targets acquired: Improving locus recovery from the Angiosperms353 probe set
    Todd G. B. McLay, Joanne L. Birch, Bee F. Gunn, Weixuan Ning, Jennifer A. Tate, Lars Nauheimer, Elizabeth Joyce, Lalita Simpson, Nicholas Weigner, Alexander N. Schmidt‐Lebuhn et al. · 2021 · Applications in Plant Sciences
80. Neural networks to learn protein sequence–function relationships from deep mutational scanning data
    Sam Gelman, Sarah A. Fahlberg, Pete Heinzelman, Philip A. Romero, Anthony Gitter · 2021 · Proceedings of the National Academy of Sciences
81. MARVEL, a Tool for Prediction of Bacteriophage Sequences in Metagenomic Bins
    Deyvid Amgarten, Lucas P. P. Braga, Aline Maria da Silva, João Carlos Setúbal · 2018 · Frontiers in Genetics
82. Long-term colonisation with donor bacteriophages following successful faecal microbial transplantation
    Lorraine A. Draper, Feargal J. Ryan, Muireann K. Smith, Jonna Jalanka, E. Mattila, Perttu Arkkila, R. Paul Ross, Reetta M. Satokari, Colin Hill · 2018 · Microbiome
83. A new mitofusin topology places the redox-regulated C terminus in the mitochondrial intermembrane space
    Sevan Mattie, Jan Riemer, Jeremy G. Wideman, Heidi May McBride · 2017 · The Journal of Cell Biology
84. The Ocean Gene Atlas: exploring the biogeography of plankton genes online
    Émilie Villar, Thomas Vannier, Caroline Vernette, Magali Lescot, Miguelangel Cuenca V., Aurélien Alexandre, Paul Bachelerie, Thomas Rosnet, Éric Pelletier, Shinichi Sunagawa et al. · 2018 · Nucleic Acids Research
85. Evolutionary Genetics of Cytoplasmic Incompatibility Genes cifA and cifB in Prophage WO of Wolbachia
    Amelia R. I. Lindsey, Danny W. Rice, Sarah R. Bordenstein, Andrew Brooks, Seth R. Bordenstein, Irene L. G. Newton · 2018 · Genome Biology and Evolution
86. Widespread endogenization of giant viruses shapes genomes of green algae
    Mohammad Moniruzzaman, Alaina Weinheimer, Carolina A. Martínez-Gutiérrez, Frank O. Aylward · 2020 · Nature
87. Mitochondrial genome annotation with MFannot: a critical analysis of gene identification and gene model prediction
    Bernd Franz Lang, Natacha Beck, Samuel Prince, Matt Sarrasin, Pierre Rioux, Gertraud Burger · 2023 · Frontiers in Plant Science
88. Assembly of the 373k gene space of the polyploid sugarcane genome reveals reservoirs of functional diversity in the world's leading biomass crop
    Gláucia Mendes Souza, Marie‐Anne Van Sluys, Carolina Gimiliani Lembke, Hayan Lee, Gabriel Rodrigues Alves Margarido, Carlos Takeshi Hotta, Jonas Weissmann Gaiarsa, Augusto Lima Diniz, Mauro de Medeiros Oliveira, Sávio Siqueira Ferreira et al. · 2019 · GigaScience
89. Re-assessing the diversity of negative strand RNA viruses in insects
    Simon Käfer, Sofia Paraskevopoulou, Florian Zirkel, Nicolas Wieseke, Alexander Donath, Malte Petersen, Terry C. Jones, Shanlin Liu, Xin Yu Zhou, Martin Middendorf et al. · 2019 · PLoS Pathogens
90. Plasmid Flux in Escherichia coli ST131 Sublineages, Analyzed by Plasmid Constellation Network (PLACNET), a New Method for Plasmid Reconstruction from Whole Genome Sequences
    Val F. Lanza, María de Toro, Maria Pilar Garcillán-Barcia, Azucena Mora, Jorge Blanco, Teresa M. Coque, Fernando de la Cruz · 2014 · PLoS Genetics
91. Comparative Transcriptome Analyses Reveal Core Parasitism Genes and Suggest Gene Duplication and Repurposing as Sources of Structural Novelty
    Zhenzhen Yang, Eric K. Wafula, Loren A. Honaas, Huiting Zhang, Malay Das, Mónica Fernández‐Aparicio, Kan Huang, P. C. G. Bandaranayake, Biao Wu, Joshua P. Der et al. · 2014 · Molecular Biology and Evolution
92. Reciprocal genomic evolution in the ant–fungus agricultural symbiosis
    Sanne Nygaard, Haofu Hu, Cai Li, Morten Schiøtt, Zhensheng Chen, Zhikai Yang, Qiaolin Xie, Chunyu Ma, Yuan Deng, Rebecca B. Dikow et al. · 2016 · Nature Communications
93. Finding Protein and Nucleotide Similarities with FASTA
    William R. Pearson · 2016 · Current Protocols in Bioinformatics
94. FlaGs and webFlaGs: discovering novel biology through the analysis of gene neighbourhood conservation
    Chayan Kumar Saha, Rodrigo Sanches Pires, Harald Brolin, Maxence Delannoy, Gemma Catherine Atkinson · 2020 · Bioinformatics
95. Phylogenetic Analysis of SARS-CoV-2 Data Is Difficult
    Benoit Morel, Pierre Barbera, Lucas Czech, Ben Bettisworth, Lukáš Hübner, Sarah Lutteropp, Dora Serdari, Evangelia Georgia Kostaki, Ioannis Mamais, Alexey M. Kozlov et al. · 2020 · Molecular Biology and Evolution
96. Diversification of giant and large eukaryotic dsDNA viruses predated the origin of modern eukaryotes
    Julien Guglielmini, Anthony C. Woo, Mart Krupovìč, Patrick Forterre, Morgan Gaïa · 2019 · Proceedings of the National Academy of Sciences
97. Evaluating the usefulness of alignment filtering methods to reduce the impact of errors on evolutionary inferences
    Arnaud Di Franco, Raphaël Poujol, Denis Baurain, Hervé Philippe · 2019 · BMC Evolutionary Biology
98. Complementary Roles of Wood-Inhabiting Fungi and Bacteria Facilitate Deadwood Decomposition
    Vojtěch Tláskal, Vendula Brabcová, Tomáš Větrovský, Mayuko Jomura, Rubén López‐Mondéjar, Lummy Maria Oliveira Monteiro, J. Saraiva, Zander Rainier Human, Tomáš Cajthaml, Ulisses Nunes da Rocha et al. · 2021 · mSystems
99. Uncovering new families and folds in the natural protein universe
    Janani Durairaj, Andrew Mark Waterhouse, Toomas Mets, Tetiana Brodiazhenko, Minhal Abdullah, Gabriel Studer, Gerardo Tauriello, Mehmet Akdel, Antonina E. Andreeva, Alex G. Bateman et al. · 2023 · Nature
100. GIPSy: Genomic island prediction software
     Siomar de Castro Soares, Hakan Geyik, Rommel Thiago Jucá Ramos, Pablo Henrique Caracciolo Gomes de Sá, Eudes G. V. Barbosa, Jan Baumbach, Henrique César Pereira Figueiredo, Anderson Miyoshi, Andreas Tauch, Artur Silva et al. · 2015 · Journal of Biotechnology