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Prodigal: prokaryotic gene recognition and translation initiation site identification
Open accessAbstract
BACKGROUND: The quality of automated gene prediction in microbial organisms has improved steadily over the past decade, but there is still room for improvement. Increasing the number of correct identifications, both of genes and of the translation initiation sites for each gene, and reducing the overall number of false positives, are all desirable goals. RESULTS: With our years of experience in manually curating genomes for the Joint Genome Institute, we developed a new gene prediction algorithm called Prodigal (PROkaryotic DYnamic programming Gene-finding ALgorithm). With Prodigal, we focused specifically on the three goals of improved gene structure prediction, improved translation initiation site recognition, and reduced false positives. We compared the results of Prodigal to existing gene-finding methods to demonstrate that it met each of these objectives. CONCLUSION: We built a fast, lightweight, open source gene prediction program called Prodigal http://compbio.ornl.gov/prodigal/. Prodigal achieved good results compared to existing methods, and we believe it will be a valuable asset to automated microbial annotation pipelines.
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Basic local alignment search tool
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669
On the theory of dynamic programming
Bellman, R. (1952) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.38.8.716 · Cited by 998
Cited by
Manni, M., Berkeley, M. R., Seppey, M., Simão, F. A., & Zdobnov, E. M. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab199 · Cited by 6,187
A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life
Parks, D. H., Chuvochina, M., Waite, D. W., Rinke, C., Skarshewski, A., Chaumeil, P.-A., & Hugenholtz, P. (2018) · Nature Biotechnology · doi:10.1038/nbt.4229 · Cited by 3,603
Zheng, J., Wittouck, S., Salvetti, E., Franz, C. M. A. P., Harris, H. M. B., Mattarelli, P., O’Toole, P. W., Pot, B., Vandamme, P., Walter, J., et al. (2020) · International Journal of Systematic and Evolutionary Microbiology · doi:10.1099/ijsem.0.004107 · Cited by 3,313
Beghini, F., McIver, L. J., Blanco-Míguez, A., Dubois, L., Asnicar, F., Maharjan, S., Mailyan, A., Manghi, P., Scholz, M., Thomas, A. M., et al. (2021) · eLife · doi:10.7554/elife.65088 · Cited by 2,303
Gut bacteria selectively promoted by dietary fibers alleviate type 2 diabetes
Zhao, L., Zhang, F., Ding, X., Wu, G., Lam, Y. Y., Wang, X., Fu, H., Xue, X., Lu, C., Ma, J., et al. (2018) · Science · doi:10.1126/science.aao5774 · Cited by 2,304
Zheng, P., Zeng, B., Zhou, C., Liu, M., Fang, Z., Xu, X., Zeng, L., Chen, J., Fan, S., Du, X., et al. (2016) · Molecular Psychiatry · doi:10.1038/mp.2016.44 · Cited by 2,023
Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life
Parks, D. H., Rinke, C., Chuvochina, M., Chaumeil, P.-A., Woodcroft, B. J., Evans, P. N., Hugenholtz, P., & Tyson, G. W. (2017) · Nature Microbiology · doi:10.1038/s41564-017-0012-7 · Cited by 1,882
Zmora, N., Zilberman-Schapira, G., Suez, J., Mor, U., Dori-Bachash, M., Bashiardes, S., Kotler, E., Zur, M., Regev-Lehavi, D., Brik, R. B.-Z., et al. (2018) · Cell · doi:10.1016/j.cell.2018.08.041 · Cited by 1,695
Chklovski, A., Parks, D. H., Woodcroft, B. J., & Tyson, G. W. (2023) · Nature Methods · doi:10.1038/s41592-023-01940-w · Cited by 1,705
A unified catalog of 204,938 reference genomes from the human gut microbiome
Almeida, A., Nayfach, S., Boland, M., Strozzi, F., Beracochea, M., Shi, Z. J., Pollard, K. S., Sakharova, E., Parks, D. H., Hugenholtz, P., et al. (2021) · Nature Biotechnology · doi:10.1038/s41587-020-0603-3 · Cited by 1,367
Complex archaea that bridge the gap between prokaryotes and eukaryotes
Spang, A., Saw, J. H., Jørgensen, S. L., Zaremba-Niedzwiedzka, K., Martijn, J., Lind, A. E., van Eijk, R., Schleper, C., Guy, L., & Ettema, T. J. G. (2015) · Nature · doi:10.1038/nature14447 · Cited by 1,324
A new genomic blueprint of the human gut microbiota
Almeida, A., Mitchell, A. L., Boland, M., Forster, S. C., Gloor, G. B., Tarkowska, A., Lawley, T. D., & Finn, R. D. (2019) · Nature · doi:10.1038/s41586-019-0965-1 · Cited by 1,314
Asgard archaea illuminate the origin of eukaryotic cellular complexity
Zaremba-Niedzwiedzka, K., Caceres, E. F., Saw, J. H., Bäckström, D., Juzokaite, L., Vancaester, E., Seitz, K. W., Anantharaman, K., Starnawski, P., Kjeldsen, K. U., et al. (2017) · Nature · doi:10.1038/nature21031 · Cited by 1,226
GABA-modulating bacteria of the human gut microbiota
Strandwitz, P., Kim, K. H., Terekhova, D., Liu, J. K., Sharma, A., Levering, J., McDonald, D., Dietrich, D., Ramadhar, T. R., Lekbua, A., et al. (2018) · Nature Microbiology · doi:10.1038/s41564-018-0307-3 · Cited by 1,170
Suez, J., Zmora, N., Zilberman-Schapira, G., Mor, U., Dori-Bachash, M., Bashiardes, S., Zur, M., Regev-Lehavi, D., Ben-Zeev Brik, R., Federici, S., et al. (2018) · Cell · doi:10.1016/j.cell.2018.08.047 · Cited by 1,184
Individual intestinal symbionts induce a distinct population of RORγ + regulatory T cells
Sefik, E., Geva-Zatorsky, N., Oh, S., Konnikova, L., Zemmour, D., McGuire, A. M., Burzyn, D., Ortiz-Lopez, A., Lobera, M., Yang, J., et al. (2015) · Science · doi:10.1126/science.aaa9420 · Cited by 879
Clustering huge protein sequence sets in linear time
Steinegger, M., & Söding, J. (2018) · Nature Communications · doi:10.1038/s41467-018-04964-5 · Cited by 875
Improving the coverage of the cyanobacterial phylum using diversity driven genome sequencing
Shih, P. M., Wu, D., Latifi, A., Axen, S. D., Fewer, D. P., Talla, E., Calteau, A., Cai, F., Tandeau de Marsac, N., Rippka, R., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1217107110 · Cited by 800
Massive expansion of human gut bacteriophage diversity
Camarillo-Guerrero, L. F., Almeida, A., Rangel-Pineros, G., Finn, R. D., & Lawley, T. D. (2021) · Cell · doi:10.1016/j.cell.2021.01.029 · Cited by 594
Novel bile acid biosynthetic pathways are enriched in the microbiome of centenarians
Sato, Y., Atarashi, K., Plichta, D. R., Arai, Y., Sasajima, S., Kearney, S. M., Suda, W., Takeshita, K., Sasaki, T., Okamoto, S., et al. (2021) · Nature · doi:10.1038/s41586-021-03832-5 · Cited by 632
Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection
Hungate1000 project collaborators, Seshadri, R., Leahy, S. C., Attwood, G. T., Teh, K. H., Lambie, S. C., Cookson, A. L., Eloe-Fadrosh, E. A., Pavlopoulos, G. A., Hadjithomas, M., et al. (2018) · Nature Biotechnology · doi:10.1038/nbt.4110 · Cited by 624
Current challenges and best-practice protocols for microbiome analysis
Bharti, R., & Grimm, D. G. (2021) · Briefings in Bioinformatics · doi:10.1093/bib/bbz155 · Cited by 592
Sequence modeling and design from molecular to genome scale with Evo
Nguyen, E., Poli, M., Durrant, M. G., Kang, B., Katrekar, D., Li, D. B., Bartie, L. J., Thomas, A. W., King, S. H., Brixi, G., et al. (2024) · Science · doi:10.1126/science.ado9336 · Cited by 580
MGnify: the microbiome analysis resource in 2020
Mitchell, A. L., Almeida, A., Beracochea, M., Boland, M., Burgin, J., Cochrane, G., Crusoe, M. R., Kale, V., Potter, S. C., Richardson, L. J., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz1035 · Cited by 562
Olm, M. R., Crits-Christoph, A., Bouma-Gregson, K., Firek, B. A., Morowitz, M. J., & Banfield, J. F. (2021) · Nature Biotechnology · doi:10.1038/s41587-020-00797-0 · Cited by 537
Tett, A., Huang, K. D., Asnicar, F., Fehlner-Peach, H., Pasolli, E., Karcher, N., Armanini, F., Manghi, P., Bonham, K., Zolfo, M., et al. (2019) · Cell Host & Microbe · doi:10.1016/j.chom.2019.08.018 · Cited by 476
Profiling the human intestinal environment under physiological conditions
Shalon, D., Culver, R. N., Grembi, J. A., Folz, J., Treit, P. V., Shi, H., Rosenberger, F. A., Dethlefsen, L., Meng, X., Yaffe, E., et al. (2023) · Nature · doi:10.1038/s41586-023-05989-7 · Cited by 484
Protein-level assembly increases protein sequence recovery from metagenomic samples manyfold
Steinegger, M., Mirdita, M., & Söding, J. (2019) · Nature Methods · doi:10.1038/s41592-019-0437-4 · Cited by 445
Accurate and complete genomes from metagenomes
Chen, L.-X., Anantharaman, K., Shaiber, A., Eren, A. M., & Banfield, J. F. (2020) · Genome Research · doi:10.1101/gr.258640.119 · Cited by 401
Deep mitochondrial origin outside the sampled alphaproteobacteria
Martijn, J., Vosseberg, J., Guy, L., Offre, P., & Ettema, T. J. G. (2018) · Nature · doi:10.1038/s41586-018-0059-5 · Cited by 378
Mills, R. H., Dulai, P. S., Vázquez-Baeza, Y., Sauceda, C., Daniel, N., Gerner, R. R., Batachari, L. E., Malfavon, M., Zhu, Q., Weldon, K., et al. (2022) · Nature Microbiology · doi:10.1038/s41564-021-01050-3 · Cited by 385
Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes
Heintz-Buschart, A., May, P., Laczny, C. C., Lebrun, L. A., Bellora, C., Krishna, A., Wampach, L., Schneider, J. G., Hogan, A., de Beaufort, C., et al. (2016) · Nature Microbiology · doi:10.1038/nmicrobiol.2016.180 · Cited by 316
Bifidobacterium adolescentis as a key member of the human gut microbiota in the production of GABA
Duranti, S., Ruiz, L., Lugli, G. A., Tames, H., Milani, C., Mancabelli, L., Mancino, W., Longhi, G., Carnevali, L., Sgoifo, A., et al. (2020) · Scientific Reports · doi:10.1038/s41598-020-70986-z · Cited by 341
The revisited genome of Pseudomonas putida KT2440 enlightens its value as a robust metabolic chassis
Belda, E., van Heck, R. G. A., José Lopez‐Sanchez, M., Cruveiller, S., Barbe, V., Fraser, C., Klenk, H., Petersen, J., Morgat, A., Nikel, P. I., et al. (2016) · Environmental Microbiology · doi:10.1111/1462-2920.13230 · Cited by 338
Duranti, S., Lugli, G. A., Mancabelli, L., Armanini, F., Turroni, F., James, K., Ferretti, P., Gorfer, V., Ferrario, C., Milani, C., et al. (2017) · Microbiome · doi:10.1186/s40168-017-0282-6 · Cited by 327
Pérez-Cobas, A. E., Gomez-Valero, L., & Buchrieser, C. (2020) · Microbial Genomics · doi:10.1099/mgen.0.000409 · Cited by 314
The reductive glycine pathway allows autotrophic growth of Desulfovibrio desulfuricans
Sánchez-Andrea, I., Guedes, I. A., Hornung, B., Boeren, S., Lawson, C. E., Sousa, D. Z., Bar-Even, A., Claassens, N. J., & Stams, A. J. M. (2020) · Nature Communications · doi:10.1038/s41467-020-18906-7 · Cited by 306
Mobile genes in the human microbiome are structured from global to individual scales
Brito, I. L., Yilmaz, S., Huang, K., Xu, L., Jupiter, S. D., Jenkins, A. P., Naisilisili, W., Tamminen, M., Smillie, C. S., Wortman, J. R., et al. (2016) · Nature · doi:10.1038/nature18927 · Cited by 288
1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life
Mukherjee, S., Seshadri, R., Varghese, N. J., Eloe-Fadrosh, E. A., Meier-Kolthoff, J. P., Göker, M., Coates, R. C., Hadjithomas, M., Pavlopoulos, G. A., Paez-Espino, D., et al. (2017) · Nature Biotechnology · doi:10.1038/nbt.3886 · Cited by 267
Large-Scale Analyses of Human Microbiomes Reveal Thousands of Small, Novel Genes
Sberro, H., Fremin, B. J., Zlitni, S., Edfors, F., Greenfield, N., Snyder, M. P., Pavlopoulos, G. A., Kyrpides, N. C., & Bhatt, A. S. (2019) · Cell · doi:10.1016/j.cell.2019.07.016 · Cited by 237
Vollmers, J., Wiegand, S., & Kaster, A.-K. (2017) · PLoS ONE · doi:10.1371/journal.pone.0169662 · Cited by 240
Kent, A. G., Vill, A. C., Shi, Q., Satlin, M. J., & Brito, I. L. (2020) · Nature Communications · doi:10.1038/s41467-020-18164-7 · Cited by 216
Drivers and determinants of strain dynamics following fecal microbiota transplantation
Schmidt, T. S. B., Li, S. S., Maistrenko, O. M., Akanni, W., Coelho, L. P., Dolai, S., Fullam, A., Glazek, A. M., Hercog, R., Herrema, H., et al. (2022) · Nature Medicine · doi:10.1038/s41591-022-01913-0 · Cited by 233
Brooks, B., Olm, M. R., Firek, B. A., Baker, R., Thomas, B. C., Morowitz, M. J., & Banfield, J. F. (2017) · Nature Communications · doi:10.1038/s41467-017-02018-w · Cited by 226
Metagenomics uncovers a new group of low GC and ultra-small marine Actinobacteria
Ghai, R., Mizuno, C. M., Picazo, A., Camacho, A., & Rodriguez-Valera, F. (2013) · Scientific Reports · doi:10.1038/srep02471 · Cited by 224
Codiversification of gut microbiota with humans
Suzuki, T. A., Fitzstevens, J. L., Schmidt, V. T., Enav, H., Huus, K. E., Mbong Ngwese, M., Grießhammer, A., Pfleiderer, A., Adegbite, B. R., Zinsou, J. F., et al. (2022) · Science · doi:10.1126/science.abm7759 · Cited by 210
Nagata, N., Nishijima, S., Kojima, Y., Hisada, Y., Imbe, K., Miyoshi-Akiyama, T., Suda, W., Kimura, M., Aoki, R., Sekine, K., et al. (2022) · Gastroenterology · doi:10.1053/j.gastro.2022.03.054 · Cited by 209
Delmont, T. O., Gaia, M., Hinsinger, D. D., Frémont, P., Vanni, C., Fernandez-Guerra, A., Eren, A. M., Kourlaiev, A., d'Agata, L., Clayssen, Q., et al. (2022) · Cell Genomics · doi:10.1016/j.xgen.2022.100123 · Cited by 173
Bile salt hydrolase/aminoacyltransferase shapes the microbiome
Guzior, D., Okros, M., Hernandez, C. M., Shivel, M., Armwald, B., Hausinger, R., & Quinn, R. (2022) · doi:10.21203/rs.3.rs-2050406/v1 · Cited by 187
Nagata, N., Nishijima, S., Miyoshi-Akiyama, T., Kojima, Y., Kimura, M., Aoki, R., Ohsugi, M., Ueki, K., Miki, K., Iwata, E., et al. (2022) · Gastroenterology · doi:10.1053/j.gastro.2022.06.070 · Cited by 178
Oliver, A., Chase, A. B., Weihe, C., Orchanian, S. B., Riedel, S. F., Hendrickson, C. L., Lay, M., Sewall, J. M., Martiny, J. B. H., & Whiteson, K. (2021) · mSystems · doi:10.1128/msystems.00115-21 · Cited by 171
Maguire, F., Jia, B., Gray, K. L., Lau, W. Y. V., Beiko, R. G., & Brinkman, F. S. L. (2020) · Microbial Genomics · doi:10.1099/mgen.0.000436 · Cited by 152
Leonard, M. M., Valitutti, F., Karathia, H., Pujolassos, M., Kenyon, V., Fanelli, B., Troisi, J., Subramanian, P., Camhi, S., Colucci, A., et al. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2020322118 · Cited by 162
Bridge RNAs direct programmable recombination of target and donor DNA
Durrant, M. G., Perry, N. T., Pai, J. J., Jangid, A. R., Athukoralage, J. S., Hiraizumi, M., McSpedon, J. P., Pawluk, A., Nishimasu, H., Konermann, S., et al. (2024) · Nature · doi:10.1038/s41586-024-07552-4 · Cited by 163
Arnoriaga-Rodríguez, M., Mayneris-Perxachs, J., Burokas, A., Contreras-Rodríguez, O., Blasco, G., Coll, C., Biarnés, C., Miranda-Olivos, R., Latorre, J., Moreno-Navarrete, J.-M., et al. (2020) · Cell Metabolism · doi:10.1016/j.cmet.2020.09.002 · Cited by 157
Brown, S. D., Nagaraju, S., Utturkar, S., De Tissera, S., Segovia, S., Mitchell, W., Land, M. L., Dassanayake, A., & Köpke, M. (2014) · Biotechnology for Biofuels · doi:10.1186/1754-6834-7-40 · Cited by 145
Self-citationProbiotics synergized with conventional regimen in managing Parkinson’s disease
Sun, H., Zhao, F., Liu, Y., Ma, T., Jin, H., Quan, K., Leng, B., Zhao, J., Yuan, X., Li, Z., et al. (2022) · npj Parkinson's Disease · doi:10.1038/s41531-022-00327-6 · Cited by 136
Unifying the known and unknown microbial coding sequence space
Vanni, C., Schechter, M. S., Acinas, S. G., Barberán, A., Buttigieg, P. L., Casamayor, E. O., Delmont, T. O., Duarte, C. M., Eren, A. M., Finn, R. D., et al. (2022) · eLife · doi:10.7554/elife.67667 · Cited by 134
Meta-analysis of cheese microbiomes highlights contributions to multiple aspects of quality
Walsh, A. M., Macori, G., Kilcawley, K. N., & Cotter, P. D. (2020) · Nature Food · doi:10.1038/s43016-020-0129-3 · Cited by 133
Yan, M., Treu, L., Campanaro, S., Tian, H., Zhu, X., Khoshnevisan, B., Tsapekos, P., Angelidaki, I., & Fotidis, I. A. (2020) · Chemical Engineering Journal · doi:10.1016/j.cej.2020.126159 · Cited by 128
Viromes of one year old infants reveal the impact of birth mode on microbiome diversity
McCann, A., Ryan, F. J., Stockdale, S. R., Dalmasso, M., Blake, T., Ryan, C. A., Stanton, C., Mills, S., Ross, P. R., & Hill, C. (2018) · PeerJ · doi:10.7717/peerj.4694 · Cited by 129
Genotypic and Phenotypic Diversity among Human Isolates of Akkermansia muciniphila
Becken, B., Davey, L., Middleton, D. R., Mueller, K. D., Sharma, A., Holmes, Z. C., Dallow, E., Remick, B., Barton, G. M., David, L. A., et al. (2021) · mBio · doi:10.1128/mbio.00478-21 · Cited by 125
Huber-Ruano, I., Calvo, E., Mayneris-Perxachs, J., Rodríguez-Peña, M.-M., Ceperuelo-Mallafré, V., Cedó, L., Núñez-Roa, C., Miro-Blanch, J., Arnoriaga-Rodríguez, M., Balvay, A., et al. (2022) · Microbiome · doi:10.1186/s40168-022-01306-y · Cited by 122
Karcher, N., Pasolli, E., Asnicar, F., Huang, K. D., Tett, A., Manara, S., Armanini, F., Bain, D., Duncan, S. H., Louis, P., et al. (2020) · Genome Biology · doi:10.1186/s13059-020-02042-y · Cited by 116
Mirusviruses link herpesviruses to giant viruses
Gaïa, M., Meng, L., Pelletier, E., Forterre, P., Vanni, C., Fernandez-Guerra, A., Jaillon, O., Wincker, P., Ogata, H., Krupovic, M., et al. (2023) · Nature · doi:10.1038/s41586-023-05962-4 · Cited by 108
Metabolic independence drives gut microbial colonization and resilience in health and disease
Watson, A. R., Füssel, J., Veseli, I., DeLongchamp, J. Z., Silva, M., Trigodet, F., Lolans, K., Shaiber, A., Fogarty, E., Runde, J. M., et al. (2023) · Genome Biology · doi:10.1186/s13059-023-02924-x · Cited by 92
Asgard archaea shed light on the evolutionary origins of the eukaryotic ubiquitin-ESCRT machinery
Hatano, T., Palani, S., Papatziamou, D., Salzer, R., Souza, D. P., Tamarit, D., Makwana, M., Potter, A., Haig, A., Xu, W., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-30656-2 · Cited by 104
Bandyopadhyay, A., Elvitigala, T., Welsh, E., Stöckel, J., Liberton, M., Min, H., Sherman, L. A., & Pakrasi, H. B. (2011) · mBio · doi:10.1128/mbio.00214-11 · Cited by 102
Deeply-sourced formate fuels sulfate reducers but not methanogens at lost City hydrothermal field
Lang, S. Q., Früh-Green, G. L., Bernasconi, S. M., Brazelton, W. J., Schrenk, M. O., & McGonigle, J. M. (2018) · Scientific Reports · doi:10.1038/s41598-017-19002-5 · Cited by 100
Mobile antimicrobial resistance genes in probiotics
Tóth, A. G., Csabai, I., Judge, M. F., Maróti, G., Becsei, Á., Spisák, S., & Solymosi, N. (2021) · doi:10.1101/2021.05.04.442546 · Cited by 97
IMG/PR: a database of plasmids from genomes and metagenomes with rich annotations and metadata
Camargo, A. P., Call, L., Roux, S., Nayfach, S., Huntemann, M., Palaniappan, K., Ratner, A., Chu, K., Mukherjeep, S., Reddy, T. B. K., et al. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkad964 · Cited by 87
Kirmiz, N., Galindo, K., Cross, K. L., Luna, E., Rhoades, N., Podar, M., & Flores, G. E. (2020) · Applied and Environmental Microbiology · doi:10.1128/aem.02117-19 · Cited by 94
Large language models improve annotation of prokaryotic viral proteins
Flamholz, Z. N., Biller, S. J., & Kelly, L. (2024) · Nature Microbiology · doi:10.1038/s41564-023-01584-8 · Cited by 92
Phelps, C. M., Willis, N. B., Duan, T., Lee, A. H., Zhang, Y., Rodriguez J, D. M., Pandey, S. P., Laughlin, C. R., Rosen, A. B. I., McPherson, A. C., et al. (2025) · Cell · doi:10.1016/j.cell.2025.06.018 · Cited by 91
Parsons, C., Stüeken, E. E., Rosen, C. J., Mateos, K., & Anderson, R. E. (2021) · Geobiology · doi:10.1111/gbi.12419 · Cited by 91
Hendriksen, R. S., Leekitcharoenphon, P., Lukjancenko, O., Lukwesa-Musyani, C., Tambatamba, B., Mwaba, J., Kalonda, A., Nakazwe, R., Kwenda, G., Jensen, J. D., et al. (2015) · Journal of Clinical Microbiology · doi:10.1128/jcm.02026-14 · Cited by 90
Genome-wide analysis of the Firmicutes illuminates the diderm/monoderm transition
Taib, N., Megrian, D., Witwinowski, J., Adam, P., Poppleton, D., Borrel, G., Beloin, C., & Gribaldo, S. (2020) · Nature Ecology & Evolution · doi:10.1038/s41559-020-01299-7 · Cited by 82
Microbial hitchhikers harbouring antimicrobial-resistance genes in the riverine plastisphere
Zadjelovic, V., Wright, R. J., Borsetto, C., Quartey, J., Cairns, T. N., Langille, M. G. I., Wellington, E. M. H., & Christie-Oleza, J. A. (2023) · Microbiome · doi:10.1186/s40168-023-01662-3 · Cited by 87
Calabrese, F. M., Ameur, H., Nikoloudaki, O., Celano, G., Vacca, M., Junior, W. J., Manzari, C., Vertè, F., Di Cagno, R., Pesole, G., et al. (2022) · Microbiome · doi:10.1186/s40168-022-01301-3 · Cited by 85
Poehlein, A., Cebulla, M., Ilg, M. M., Bengelsdorf, F. R., Schiel-Bengelsdorf, B., Whited, G., Andreesen, J. R., Gottschalk, G., Daniel, R., & Dürre, P. (2015) · mBio · doi:10.1128/mbio.01168-15 · Cited by 80
Dietary- and host-derived metabolites are used by diverse gut bacteria for anaerobic respiration
Little, A. S., Younker, I. T., Schechter, M. S., Bernardino, P. N., Méheust, R., Stemczynski, J., Scorza, K., Mullowney, M. W., Sharan, D., Waligurski, E., et al. (2024) · Nature Microbiology · doi:10.1038/s41564-023-01560-2 · Cited by 80
An archaeal origin of the Wood–Ljungdahl H4MPT branch and the emergence of bacterial methylotrophy
Adam, P. S., Borrel, G., & Gribaldo, S. (2019) · Nature Microbiology · doi:10.1038/s41564-019-0534-2 · Cited by 76
Yinda, C. K., Vanhulle, E., Conceição-Neto, N., Beller, L., Deboutte, W., Shi, C., Ghogomu, S. M., Maes, P., Van Ranst, M., & Matthijnssens, J. (2019) · mSphere · doi:10.1128/msphere.00585-18 · Cited by 75
Xu, F., Jerlström-Hultqvist, J., Einarsson, E., Ástvaldsson, Á., Svärd, S. G., & Andersson, J. O. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004053 · Cited by 74
Pervasive translation in Mycobacterium tuberculosis
Smith, C., Canestrari, J. G., Wang, A. J., Champion, M. M., Derbyshire, K. M., Gray, T. A., & Wade, J. T. (2022) · eLife · doi:10.7554/elife.73980 · Cited by 71
Viroid-like colonists of human microbiomes
Zheludev, I. N., Edgar, R. C., Lopez-Galiano, M. J., de la Peña, M., Babaian, A., Bhatt, A. S., & Fire, A. Z. (2024) · Cell · doi:10.1016/j.cell.2024.09.033 · Cited by 73
Viroid-like colonists of human microbiomes
Zheludev, I. N., Edgar, R. C., Lopez-Galiano, M. J., de la Peña, M., Babaian, A., Bhatt, A. S., & Fire, A. Z. (2024) · doi:10.1101/2024.01.20.576352 · Cited by 73
Protein structure-informed bacteriophage genome annotation with Phold
Bouras, G., Grigson, S. R., Mirdita, M., Heinzinger, M., Papudeshi, B., Mallawaarachchi, V., Green, R., Kim, R. S., Mihalia, V., Psaltis, A. J., et al. (2026) · Nucleic Acids Research · doi:10.1093/nar/gkaf1448 · Cited by 71
Stokke, R., Dahle, H., Roalkvam, I., Wissuwa, J., Daae, F. L., Tooming‐Klunderud, A., Thorseth, I. H., Pedersen, R. B., & Steen, I. H. (2015) · Environmental Microbiology · doi:10.1111/1462-2920.12970 · Cited by 63
Pervasive generation of non-canonical subgenomic RNAs by SARS-CoV-2
Nomburg, J., Meyerson, M., & DeCaprio, J. A. (2020) · Genome Medicine · doi:10.1186/s13073-020-00802-w · Cited by 63
Lecoeuvre, A., Ménez, B., Cannat, M., Chavagnac, V., & Gérard, E. (2021) · The ISME Journal · doi:10.1038/s41396-020-00816-7 · Cited by 62
Durham, B. P., Grote, J., Whittaker, K. A., Bender, S. J., Luo, H., Grim, S. L., Brown, J. M., Casey, J. R., Dron, A., Florez-Leiva, L., et al. (2014) · Standards in Genomic Sciences · doi:10.4056/sigs.4998989 · Cited by 62
Transposon-encoded nucleases use guide RNAs to promote their selfish spread
Meers, C., Le, H. C., Pesari, S. R., Hoffmann, F. T., Walker, M. W. G., Gezelle, J., Tang, S., & Sternberg, S. H. (2023) · Nature · doi:10.1038/s41586-023-06597-1 · Cited by 60
Vitamin B12 is a limiting factor for induced cellular plasticity and tissue repair
Kovatcheva, M., Melendez, E., Chondronasiou, D., Pietrocola, F., Bernad, R., Caballe, A., Junza, A., Capellades, J., Holguín-Horcajo, A., Prats, N., et al. (2023) · Nature Metabolism · doi:10.1038/s42255-023-00916-6 · Cited by 58
Unexpected complexity of the ammonia monooxygenase in archaea
(2023) · doi:10.1038/s41396-023-01367-3 · Cited by 58
De novo gene synthesis by an antiviral reverse transcriptase
Tang, S., Conte, V., Zhang, D. J., Žedaveinytė, R., Lampe, G. D., Wiegand, T., Tang, L. C., Wang, M., Walker, M. W. G., George, J. T., et al. (2024) · Science · doi:10.1126/science.adq0876 · Cited by 58
Comparative genome analysis of the Lactobacillus brevis species
Feyereisen, M., Mahony, J., Kelleher, P., Roberts, R. J., O’Sullivan, T., Geertman, J.-M. A., & van Sinderen, D. (2019) · BMC Genomics · doi:10.1186/s12864-019-5783-1 · Cited by 57
Danchin, A., Ouzounis, C., Tokuyasu, T., & Zucker, J. (2018) · Microbial Biotechnology · doi:10.1111/1751-7915.13284 · Cited by 56
Metadata
- Authors
- Hyatt, D., Chen, G.-L., LoCascio, P. F., Land, M. L., Larimer, F. W., & Hauser, L. J.
- Venue
- BMC Bioinformatics
- Published
- 2010-03-08
- Volume
- 11
- Issue
- 1
- Pages
- 119-119
- ISSN
- 1471-2105 (ISSN-L)
- OpenAlex
- W2143485490
- Cited by
- 12,587
- References
- 2
- FWCI
- 63.80
- Type
- journal article
- Language
- en
- Open access
- gold
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.