Cited by 252Genomics and Phylogenetic StudiesRNA and protein synthesis mechanismsFractal and DNA sequence analysis

The DOI matches its Crossref record.

SEPP: SATé-Enabled Phylogenetic Placement

MIRARAB, S., NGUYEN, N., WARNOW, T.·2011·Biocomputing 2012

Open this paper in CoChat — free account

Abstract

We address the problem of Phylogenetic Placement, in which the objective is to insert short molecular sequences (called query sequences) into an existing phylogenetic tree and alignment on full-length sequences for the same gene. Phylogenetic placement has the potential to provide information beyond pure "species identification" (i.e., the association of metagenomic reads to existing species), because it can also give information about the evolutionary relationships between these query sequences and to known species. Approaches for phylogenetic placement have been developed that operate in two steps: first, an alignment is estimated for each query sequence to the alignment of the full-length sequences, and then that alignment is used to find the optimal location in the phylogenetic tree for the query sequence. Recent methods of this type include HMMALIGN+EPA, HMMALIGN+pplacer, and PaPaRa+EPA.We report on a study evaluating phylogenetic placement methods on biological and simulated data. This study shows that these methods have extremely good accuracy and computational tractability under conditions where the input contains a highly accurate alignment and tree for the full-length sequences, and the set of full-length sequences is sufficiently small and not too evolutionarily diverse; however, we also show that under other conditions accuracy declines and the computational requirements for memory and time exceed acceptable limits. We present SEPP, a general "boosting" technique…

Integrity signals

Registry

Crossref · 10.1142/9789814366496_0024

Cites

Statistics

Recomputing p-values needs the paper’s full text.

Claims the paper makes

This paper’s full text isn’t openly available, so its claims and self-check weren’t run. The registry and citation checks still apply.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Still being checked.

Sorted by citations

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
Katoh, K., & Standley, D. M. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst010 · Cited by 46,209
BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes
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 communal catalogue reveals Earth's multiscale microbial diversity
Thompson, L. R., Sanders, J. G., McDonald, D., Amir, A., Ladau, J., Locey, K. J., Prill, R. J., Tripathi, A., Gibbons, S. M., Ackermann, G., et al. (2017) · Nature · doi:10.1038/nature24621 · Cited by 2,684
Self-citation
BUSCO: Assessing Genomic Data Quality and Beyond
Manni, M., Berkeley, M., Seppey, M., & Zdobnov, E. M. (2021) · Current Protocols · doi:10.1002/cpz1.323 · Cited by 1,309
American Gut: an Open Platform for Citizen-Science Microbiome Research
McDonalda, D., Hyde, E., Debelius, J. W., Morton, J. T., Gonzalez, A., Ackermann, G., Aksenov, A. A., Behsaz, B., Brennan, C., Chen, Y., et al. (2018) · doi:10.1101/277970 · Cited by 878
Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0
Asnicar, F., Thomas, A. M., Beghini, F., Mengoni, C., Manara, S., Manghi, P., Zhu, Q., Bolzan, M., Cumbo, F., May, U., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-16366-7 · Cited by 869
Self-citation
Gut microbiota utilize immunoglobulin A for mucosal colonization
Donaldson, G. P., Ladinsky, M. S., Yu, K. B., Sanders, J. G., Yoo, B. B., Chou, W., Conner, M. E., Earl, A. M., Knight, R. D., Björkman, P. J., et al. (2018) · Science · doi:10.1126/science.aaq0926 · Cited by 650
Inflammation-induced IgA+ cells dismantle anti-liver cancer immunity
Shalapour, S., Lin, X.-J., Bastian, I. N., Brain, J., Burt, A. D., Aksenov, A. A., Vrbanac, A. F., Li, W., Perkins, A., Matsutani, T., et al. (2017) · Nature · doi:10.1038/nature24302 · Cited by 589
Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information
Janssen, S., McDonald, D., Gonzalez, A., Navas-Molina, J. A., Jiang, L., Xu, Z. Z., Winker, K., Kado, D. M., Orwoll, E., Manary, M., et al. (2018) · mSystems · doi:10.1128/msystems.00021-18 · Cited by 536
Self-citation
Comparative Analyses of Vertebrate Gut Microbiomes Reveal Convergence between Birds and Bats
Song, S. J., Sanders, J. G., Delsuc, F., Metcalf, J. L., Amato, K. R., Taylor, M. W., Mazel, F., Lutz, H. L., Winker, K., Graves, G. R., et al. (2020) · mBio · doi:10.1128/mbio.02901-19 · Cited by 523
MAFFT: Iterative Refinement and Additional Methods
Katoh, K., & Standley, D. M. (2013) · Methods in molecular biology · doi:10.1007/978-1-62703-646-7_8 · Cited by 520
Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?
Lücking, R., Aime, M. C., Robbertse, B., Miller, A. N., Ariyawansa, H. A., Aoki, T., Cardinali, G., Crous, P. W., Druzhinina, I. S., Geiser, D. M., et al. (2020) · IMA Fungus · doi:10.1186/s43008-020-00033-z · Cited by 541
Denoising the Denoisers: an independent evaluation of microbiome sequence error-correction approaches
Nearing, J. T., Douglas, G. M., Comeau, A., & Langille, M. G. I. (2018) · PeerJ · doi:10.7717/peerj.5364 · Cited by 368
A perspective on 16S rRNA operational taxonomic unit clustering using sequence similarity
Nguyen, N., Warnow, T. J., Pop, M., & White, B. A. (2016) · npj Biofilms and Microbiomes · doi:10.1038/npjbiofilms.2016.4 · Cited by 309
Self-citation
Characterization of the total and viable bacterial and fungal communities associated with the International Space Station surfaces
Sielaff, A. C., Urbaniak, C., Mohan, G. B. M., Stepanov, V. G., Tran, Q. T. T., Wood, J. M., Minich, J. J., McDonald, D. T., Mayer, T., Knight, R. D., et al. (2019) · Microbiome · doi:10.1186/s40168-019-0666-x · Cited by 273
Adding unaligned sequences into an existing alignment using MAFFT and LAST
Katoh, K., & Frith, M. C. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts578 · Cited by 242
Consumption of fermented foods is associated with systematic differences in the gut microbiome and metabolome
Taylor, B. C., Lejzerowicz, F., Poirel, M., Shaffer, J. P., Jiang, L., Aksenov, A., Litwin, N., Humphrey, G., Martino, C., Miller-Montgomery, S., et al. (2020) · mSystems · doi:10.1128/msystems.00901-19 · Cited by 203
Suppression of the gut microbiome ameliorates age‐related arterial dysfunction and oxidative stress in mice
Brunt, V. E., Gioscia‐Ryan, R. A., Richey, J. J., Zigler, M. C., Cuevas, L. M., Gonzalez, A., Vázquez‐Baeza, Y., Battson, M. L., Smithson, A. T., Gilley, A. D., et al. (2019) · The Journal of Physiology · doi:10.1113/jp277336 · Cited by 182
GraftM: a tool for scalable, phylogenetically informed classification of genes within metagenomes
Boyd, J. A., Woodcroft, B. J., & Tyson, G. W. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky174 · Cited by 162
Ultra-large alignments using phylogeny-aware profiles
Nguyen, N., Mirarab, S., Kumar, K., & Warnow, T. J. (2015) · Genome biology · doi:10.1186/s13059-015-0688-z · Cited by 142
Self-citation
Analytical Tools and Databases for Metagenomics in the Next-Generation Sequencing Era
Kim, M., Lee, K.-H., Yoon, S.-W., Kim, B. S., Chun, J., & Yi, H. (2013) · Genomics & Informatics · doi:10.5808/gi.2013.11.3.102 · Cited by 146
Skmer: assembly-free and alignment-free sample identification using genome skims
Sarmashghi, S., Bohmann, K., Gilbert, M. T. P., Bafna, V., & Mirarab, S. (2019) · Genome biology · doi:10.1186/s13059-019-1632-4 · Cited by 128
Self-citation
Intermittent Hypoxia and Hypercapnia, a Hallmark of Obstructive Sleep Apnea, Alters the Gut Microbiome and Metabolome
Tripathi, A., Melnik, A. V., Xue, J., Poulsen, O., Meehan, M. J., Humphrey, G., Jiang, L., Ackermann, G. L., McDonald, D. T., Zhou, D., et al. (2018) · mSystems · doi:10.1128/msystems.00020-18 · Cited by 135
Gut microbiota and fecal short chain fatty acids differ with adiposity and country of origin: the METS-microbiome study
Ecklu-Mensah, G., Choo-Kang, C., Maseng, M. G., Donato, S., Bovet, P., Viswanathan, B., Bedu-Addo, K., Plange‐Rhule, J., Boateng, P. O., Forrester, T., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-40874-x · Cited by 147
Taxonomic binning of metagenome samples generated by next-generation sequencing technologies
Dröge, J., & McHardy, A. C. (2012) · Briefings in Bioinformatics · doi:10.1093/bib/bbs031 · Cited by 126
Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm
Löytynoja, A., Vilella, A. J., & Goldman, N. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts198 · Cited by 123
Assessing the variation within the oral microbiome of healthy adults
Nearing, J. T., DeClercq, V., Van Limbergen, J., & Langille, M. G. I. (2020) · mSphere · doi:10.1128/msphere.00451-20 · Cited by 117
Effects of ‘Healthy’ Fecal Microbiota Transplantation against the Deterioration of Depression in Fawn-Hooded Rats
Hu, B., Das, P., Lv, X., Shi, M., Aa, J., Wang, K., Duan, L., Gilbert, J. A., Nie, Y., & Wu, X. (2022) · mSystems · doi:10.1128/msystems.00218-22 · Cited by 116
Effects of the microalgae Chlamydomonas on gastrointestinal health
Fields, F. J., Lejzerowicz, F., Schroeder, D., Ngoi, S. M., Tran, M., McDonald, D., Jiang, L., Chang, J. T., Knight, R., & Mayfield, S. (2020) · Journal of Functional Foods · doi:10.1016/j.jff.2019.103738 · Cited by 104
PASTA: Ultra-Large Multiple Sequence Alignment
Mirarab, S., Nguyen, N., & Warnow, T. J. (2014) · Lecture notes in computer science · doi:10.1007/978-3-319-05269-4_15 · Cited by 103
Self-citation
Repeated sleep disruption in mice leads to persistent shifts in the fecal microbiome and metabolome
Bowers, S. J., Vargas, F., González, A., He, S., Jiang, P., Dorrestein, P. C., Knight, R. D., Wright, K. P., Lowry, C. A., Fleshner, M., et al. (2020) · PLoS ONE · doi:10.1371/journal.pone.0229001 · Cited by 99
Differential Activation of Hepatic Invariant NKT Cell Subsets Plays a Key Role in Progression of Nonalcoholic Steatohepatitis
Maricic, I., Marrero, I., Eguchi, A., Nakamura, R., Johnson, C. D., Dasgupta, S., Hernandez, C. D., Nguyen, P. S., Swafford, A. D., Knight, R., et al. (2018) · The Journal of Immunology · doi:10.4049/jimmunol.1800614 · Cited by 92
Environmental genes and genomes: understanding the differences and challenges in the approaches and software for their analyses
Mendoza, M. L. Z., Sicheritz‐Pontén, T., & Gilbert, M. T. P. (2015) · Briefings in Bioinformatics · doi:10.1093/bib/bbv001 · Cited by 92
Integrative analysis reveals associations between oral microbiota dysbiosis and host genetic and epigenetic aberrations in oral cavity squamous cell carcinoma
Cai, L., Zhu, H., Mou, Q., Wong, P. Y., Lan, L., Ng, C. W. K., Pu, L., Cheung, M. K., Wang, D., Wong, E. W. Y., et al. (2024) · npj Biofilms and Microbiomes · doi:10.1038/s41522-024-00511-x · Cited by 97
Convergence of human and Old World monkey gut microbiomes demonstrates the importance of human ecology over phylogeny
Amato, K. R., Mallott, E. K., McDonald, D. T., Dominy, N. J., Goldberg, T. L., Lambert, J. E., Swedell, L., Metcalf, J. L., Gomez, A. M., Britton, G. A. O., et al. (2019) · Genome biology · doi:10.1186/s13059-019-1807-z · Cited by 89
Evidence for phylogenetically and catabolically diverse active diazotrophs in deep-sea sediment
Kapili, B. J., Barnett, S. E., Buckley, D. H., & Dekas, A. (2020) · The ISME Journal · doi:10.1038/s41396-019-0584-8 · Cited by 87
Evaluation of the Effect of Storage Methods on Fecal, Saliva, and Skin Microbiome Composition
Marotz, C. A., Cavagnero, K. J., Song, S. J., McDonald, D. T., Wandro, S., Humphrey, G. C., Bryant, M., Ackermann, G. L., Diaz, E., & Knight, R. D. (2021) · mSystems · doi:10.1128/msystems.01329-20 · Cited by 80
A Format for Phylogenetic Placements
Matsen, F. A., IV, Hoffman, N. G., Gallagher, A., & Stamatakis, A. (2012) · PLoS ONE · doi:10.1371/journal.pone.0031009 · Cited by 76
Early life gut microbiota is associated with rapid infant growth in Hispanics from Southern California
Alderete, T. L., Jones, R. B., Shaffer, J. P., Holzhausen, E. A., Patterson, W. B., Kazemian, E., Chatzi, L., Knight, R. D., Plows, J. F., Berger, P. K., et al. (2021) · Gut Microbes · doi:10.1080/19490976.2021.1961203 · Cited by 68
Eukaryotic Biodiversity and Spatial Patterns in the Clarion-Clipperton Zone and Other Abyssal Regions: Insights From Sediment DNA and RNA Metabarcoding
Lejzerowicz, F., GOODAY, A. J., Angeles, I. B., Cordier, T., Morard, R., Apothéloz‐Perret‐Gentil, L., Lins, L., Menot, L., Brandt, A., Levin, L. A., et al. (2021) · Frontiers in Marine Science · doi:10.3389/fmars.2021.671033 · Cited by 67
Metagenomic Analysis Using Phylogenetic Placement—A Review of the First Decade
Czech, L., Stamatakis, A., Dunthorn, M., & Barbera, P. (2022) · Frontiers in Bioinformatics · doi:10.3389/fbinf.2022.871393 · Cited by 69
Trace Evidence Potential in Postmortem Skin Microbiomes: From Death Scene to Morgue
Kodama, W. A., Xu, Z. Z., Metcalf, J. L., Song, S. J., Harrison, N., Knight, R. D., Carter, D. O., & Happy, C. B. (2018) · Journal of Forensic Sciences · doi:10.1111/1556-4029.13949 · Cited by 62
SCNIC: Sparse correlation network investigation for compositional data
Shaffer, M., Thurimella, K., Sterrett, J. D., & Lozupone, C. (2022) · Molecular Ecology Resources · doi:10.1111/1755-0998.13704 · Cited by 68
The influence of carbon dioxide on fermentation products, microbial community, and functional gene in food waste fermentation with uncontrol pH
Pan, X.-R., Shang-Guan, P.-K., Li, S., Zhang, C.-H., Lou, J.-M., Guo, L., Liu, L., & Lu, Y. (2024) · Environmental Research · doi:10.1016/j.envres.2024.120645 · Cited by 60
Bacterial Communities in Concrete Reflect Its Composite Nature and Change with Weathering
Kiledal, E. A., Keffer, J. L., & Maresca, J. A. (2021) · mSystems · doi:10.1128/msystems.01153-20 · Cited by 59
Beyond the gut: Skin microbiome compositional changes are associated with BMI
Brandwein, M., Katz, I., Katz, A., & Kohen, R. (2019) · Human Microbiome Journal · doi:10.1016/j.humic.2019.100063 · Cited by 58
Microbiome preterm birth DREAM challenge: Crowdsourcing machine learning approaches to advance preterm birth research
Golob, J. L., Oskotsky, T., Tang, A., Roldan, A., Chung, V., Ha, C. W. Y., Wong, R. J., Flynn, K. J., Chai, R., Dubin, C., et al. (2023) · Cell Reports Medicine · doi:10.1016/j.xcrm.2023.101350 · Cited by 53
SARS-CoV-2 does not have a strong effect on the nasopharyngeal microbial composition
Braun, T., Halevi, S., Hadar, R., Efroni, G., Saar, E. G., Keller, N., Amir, A., Amit, S., & Haberman, Y. (2021) · Scientific Reports · doi:10.1038/s41598-021-88536-6 · Cited by 48
Efficient computation of Faith's phylogenetic diversity with applications in characterizing microbiomesPreprint
Armstrong, G., Cantrell, K., Huang, S. W., McDonald, D. T., Haiminen, N., Carrieri, A. P., Zhu, Q., González, A., McGrath, I., Beck, K. L., et al. (2021) · Genome Research · doi:10.1101/gr.275777.121 · Cited by 48
Origin and functional diversification of PAS domain, a ubiquitous intracellular sensor
Xing, J., Gumerov, V. M., & Zhulin, I. B. (2023) · Science Advances · doi:10.1126/sciadv.adi4517 · Cited by 44
Phylogenetics and the Human Microbiome
Matsen, F. A., IV (2014) · Systematic Biology · doi:10.1093/sysbio/syu053 · Cited by 47
Skin inflammation activates intestinal stromal fibroblasts and promotes colitis
Dokoshi, T., Seidman, J. S., Cavagnero, K. J., Li, F., Liggins, M. C., Taylor, B. C., Olvera, J. G., Knight, R. D., Chang, J. T., Salzman, N. H., et al. (2021) · Journal of Clinical Investigation · doi:10.1172/jci147614 · Cited by 43
DEPP: Deep Learning Enables Extending Species Trees using Single Genes
Jiang, Y., Balaban, M., Zhu, Q., & Mirarab, S. (2022) · Systematic Biology · doi:10.1093/sysbio/syac031 · Cited by 45
Self-citation
Fast and accurate distance‐based phylogenetic placement using divide and conquer
Balaban, M., Jiang, Y., Roush, D., Zhu, Q., & Mirarab, S. (2021) · Molecular Ecology Resources · doi:10.1111/1755-0998.13527 · Cited by 38
Self-citation
Abrupt perturbation and delayed recovery of the vaginal ecosystem following childbirth
Costello, E. K., DiGiulio, D. B., Robaczewska, A., Symul, L., Wong, R. J., Shaw, G. M., Stevenson, D. K., Holmes, S., Kwon, D. S., & Relman, D. A. (2023) · Nature Communications · doi:10.1038/s41467-023-39849-9 · Cited by 41
Methods for automatic reference trees and multilevel phylogenetic placement
Czech, L., Barbera, P., & Stamatakis, A. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty767 · Cited by 41
Phylogeny Estimation Given Sequence Length Heterogeneity
Smirnov, V. M., & Warnow, T. J. (2020) · Systematic Biology · doi:10.1093/sysbio/syaa058 · Cited by 37
Self-citation
Intermittent Hypoxia and Hypercapnia Reproducibly Change the Gut Microbiome and Metabolome across Rodent Model Systems
Tripathi, A., Xu, Z. Z., Xue, J., Poulsen, O., Gonzalez, A., Humphrey, G., Meehan, M. J., Melnik, A. V., Ackermann, G. L., Zhou, D., et al. (2019) · mSystems · doi:10.1128/msystems.00058-19 · Cited by 36
Investigating prenatal and perinatal factors on meconium microbiota: a systematic review and cohort study
Turunen, J., Tejesvi, M. V., Paalanne, N., Pokka, T. M.-L., Amatya, S. B., Mishra, S., Kaisanlahti, A., Reunanen, J., & Tapiainen, T. (2023) · Pediatric Research · doi:10.1038/s41390-023-02783-z · Cited by 34
Is there convergence of gut microbes in blood-feeding vertebrates?
Song, S. J., Sanders, J. G., Baldassarre, D. T., Chaves, J. A., Johnson, N. S., Piaggio, A. J., Stuckey, M. J., Nováková, E., Metcalf, J. L., Chomel, B. B., et al. (2019) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2018.0249 · Cited by 35
Investigating the oral microbiome in retrospective and prospective cases of prostate, colon, and breast cancer
Nearing, J. T., DeClercq, V., & Langille, M. G. I. (2023) · npj Biofilms and Microbiomes · doi:10.1038/s41522-023-00391-7 · Cited by 31
A phased chromosome-level genome and full mitochondrial sequence for the dikaryotic myrtle rust pathogen, Austropuccinia psidiiPreprint
Edwards, R. J., Dong, C., Park, R., & Tobias, P. A. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.04.22.489119 · Cited by 31
Hematophagy and tick-borne Rickettsial pathogen shape the microbial community structure and predicted functions within the tick vector, Amblyomma maculatum
Adegoke, A., Kumar, D., Budachetri, K., & Karim, S. (2022) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2022.1037387 · Cited by 29
Convergent dysbiosis of upper aerodigestive microbiota between patients with esophageal and oral cavity squamous cell carcinoma
Zhu, H., Yip, H. C., Cheung, M. K., Chan, H. C., Ng, C. W. K., Lau, E. H. L., Yeung, Z. W. C., Wong, E. W. Y., Leung, L. L., Qu, X., et al. (2023) · International Journal of Cancer · doi:10.1002/ijc.34460 · Cited by 33
INSTRAL: Discordance-Aware Phylogenetic Placement Using Quartet Scores
Rabiee, M., & Mirarab, S. (2019) · Systematic Biology · doi:10.1093/sysbio/syz045 · Cited by 31
Self-citation
The microbiome of fly organs and fly-human microbial transfer during decomposition
Deel, H. L., Montoya, S., King, K., Emmons, A. L., Huhn, C., Lynne, A. M., Metcalf, J. L., & BUCHELI, S. R. (2022) · Forensic Science International · doi:10.1016/j.forsciint.2022.111425 · Cited by 26
Host-Adapted Strains of Spodoptera frugiperda Hold and Share a Core Microbial Community Across the Western Hemisphere
de Oliveira, N. C., Rodrigues, P. A. P., & Cônsoli, F. L. (2022) · Microbial Ecology · doi:10.1007/s00248-022-02008-6 · Cited by 26
A Prebiotic Diet Alters the Fecal Microbiome and Improves Sleep in Response to Sleep Disruption in Rats
Bowers, S. J., Summa, K. C., Thompson, R. S., González, A., Vargas, F., Olker, C. J., Jiang, P., Lowry, C. A., Dorrestein, P. C., Knight, R. D., et al. (2022) · Frontiers in Neuroscience · doi:10.3389/fnins.2022.889211 · Cited by 29
The Sputum Microbiome in Pulmonary Tuberculosis and Its Association With Disease Manifestations: A Cross-Sectional Study
Ticlla, M., Hella, J., Hiza, H. C., Sasamalo, M., Mhimbira, F., Rutaihwa, L. K., Droz, S., Schaller, S., Reither, K., Hilty, M., et al. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.633396 · Cited by 28
Phenology-dependent root bacteria enhance yield of Brassica napus
Mamet, S. D., Helgason, B. L., Lamb, E. G., McGillivray, A., Stanley, K. G., Robinson, S. J., Aziz, S. U., Vail, S. L., & Siciliano, S. D. (2021) · Soil Biology and Biochemistry · doi:10.1016/j.soilbio.2021.108468 · Cited by 25
Chromosome‐level de novo genome assembly of Telopea speciosissima (New South Wales waratah) using long‐reads, linked‐reads and Hi‐C
Chen, S. H., Rossetto, M., van der Merwe, M. M., Lu‐Irving, P., Yap, J. S., Sauquet, H., Bourke, G., Amos, T. G., Bragg, J. G., & Edwards, R. J. (2022) · Molecular Ecology Resources · doi:10.1111/1755-0998.13574 · Cited by 26
Large-Scale Multiple Sequence Alignment and Tree Estimation Using SATé
Liu, K., & Warnow, T. J. (2013) · Methods in molecular biology · doi:10.1007/978-1-62703-646-7_15 · Cited by 25
Self-citation
Determination of Effect Sizes for Power Analysis for Microbiome Studies Using Large Microbiome Databases
Rahman, G., McDonald, D. T., González, A., Vázquez‐Baeza, Y., Jiang, L., Casals‐Pascual, C., Hakim, D., Dilmore, A. H., Nowinski, B., Peddada, S., et al. (2023) · Genes · doi:10.3390/genes14061239 · Cited by 23
HIPPI: highly accurate protein family classification with ensembles of HMMs
Nguyen, N., Nute, M., Mirarab, S., & Warnow, T. J. (2016) · BMC Genomics · doi:10.1186/s12864-016-3097-0 · Cited by 23
Self-citation
Diversity and structure of sparids external microbiota (Teleostei) and its link with monogenean ectoparasites
Scheifler, M., Sanchez-Brosseau, S., Magnanou, É., & Desdevises, Y. (2022) · Animal Microbiome · doi:10.1186/s42523-022-00180-1 · Cited by 22
Long-Term Effects of Developmental Exposure to Oxycodone on Gut Microbiota and Relationship to Adult Behaviors and Metabolism
Lyu, Z., Schmidt, R., Martin, R. E., Green, M. T., Kinkade, J. A., Mao, J., Bivens, N. J., Joshi, T., & Rosenfeld, C. S. (2022) · mSystems · doi:10.1128/msystems.00336-22 · Cited by 22
Composition of mucus- and digesta-associated bacteria in growing pigs with and without diarrhea differed according to the presence of colonic inflammation
Panah, F. M., Lauridsen, C., Højberg, O., Jensen, H. E., & Nielsen, T. S. (2023) · BMC Microbiology · doi:10.1186/s12866-023-02874-1 · Cited by 22
Metabolite-based inter-kingdom communication controls intestinal tissue recovery following chemotherapeutic injury
Anderson, C. J., Boeckaerts, L., Chin, P., Cardás, J. B., Xie, W., Gonçalves, A. C., Blancke, G., Benson, S., Rogatti, S., Simpson, M. S., et al. (2024) · Cell Host & Microbe · doi:10.1016/j.chom.2024.07.026 · Cited by 22
Isolated Grauer's gorilla populations differ in diet and gut microbiome
Michel, A., Minocher, R., Niehoff, P.-P., Li, Y., Nota, K., Gadhvi, M. A., Su, J., Iyer, N., Porter, A. M., Ngobobo, U., et al. (2022) · Molecular Ecology · doi:10.1111/mec.16663 · Cited by 19
Chromosomal-level genome assembly of the semi-dwarf rice Taichung Native 1, an initiator of Green Revolution
Panibe, J. P., Wang, L., Li, J.-Y., Li, M., Lee, Y., Wang, C., Ku, M. S. B., Lu, M. J., & Li, W. (2021) · Genomics · doi:10.1016/j.ygeno.2021.06.006 · Cited by 20
Freeze-drying can replace cold-chains for transport and storage of fecal microbiome samples
Bensch, H. M., Tolf, C., Waldenström, J., Lundin, D., & Zöttl, M. (2022) · PeerJ · doi:10.7717/peerj.13095 · Cited by 20
Large-Scale Multiple Sequence Alignment and Phylogeny Estimation
Warnow, T. J. (2013) · Computational biology · doi:10.1007/978-1-4471-5298-9_6 · Cited by 22
Self-citation
TADA: phylogenetic augmentation of microbiome samples enhances phenotype classification
Sayyari, E., Kawas, B., & Mirarab, S. (2019) · Bioinformatics · doi:10.1093/bioinformatics/btz394 · Cited by 20
Self-citation
SCAMPP: Scaling Alignment-Based Phylogenetic Placement to Large Trees
Wedell, E., Cai, Y., & Warnow, T. (2022) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbb.2022.3170386 · Cited by 19
Self-citation
Prolonged dysbiosis and altered immunity under nutritional intervention in a physiological mouse model of severe acute malnutrition
Hidalgo-Villeda, F., Million, M., Defoort, C., Vannier, T., Svilar, L., Lagier, M., Wagner, C., Arroyo-Portilla, C., Chasson, L., Luciani, C., et al. (2023) · iScience · doi:10.1016/j.isci.2023.106910 · Cited by 19
High diversity of picornaviruses in rats from different continents revealed by deep sequencing
Hansen, T. A., Mollerup, S., Nguyen, N., White, N. E., Coghlan, M. L., Alquezar‐Planas, D. E., Joshi, T., Jensen, R. H., Fridholm, H., Kjartansdóttir, K. R., et al. (2016) · Emerging Microbes & Infections · doi:10.1038/emi.2016.90 · Cited by 19
Self-citation
PPIT: an R package for inferring microbial taxonomy from nifH sequences
Kapili, B. J., & Dekas, A. (2021) · Bioinformatics · doi:10.1093/bioinformatics/btab100 · Cited by 15
Characterizing the Cattle Gut Microbiome in Farms with a High and Low Prevalence of Shiga Toxin Producing Escherichia coli
Vasco, K. A., Nohomovich, B., Singh, P., Venegas-Vargas, C., Mosci, R. E., Rust, S. R., Bartlett, P. C., Norby, B., Grooms, D. L., Zhang, L., et al. (2021) · Microorganisms · doi:10.3390/microorganisms9081737 · Cited by 19
MAGUS+eHMMs: improved multiple sequence alignment accuracy for fragmentary sequences
Shen, C., Zaharias, P., & Warnow, T. J. (2021) · Bioinformatics · doi:10.1093/bioinformatics/btab788 · Cited by 18
Self-citation
New microbiological insights from the Bowland shale highlight heterogeneity of the hydraulically fractured shale microbiome
Hernández-Becerra, N., Cliffe, L., Xiu, W., Boothman, C., Lloyd, J. R., & Nixon, S. L. (2023) · Environmental Microbiome · doi:10.1186/s40793-023-00465-1 · Cited by 20
Differential effects of antiretroviral treatment on immunity and gut microbiome composition in people living with HIV in rural versus urban Zimbabwe
Colorado, A. S. B., Lazzaro, A., Neff, C. P., Nusbacher, N. M., Boyd, K., Fiorillo, S. P., Martin, C. G., Siebert, J., Campbell, T., Borok, M. Z., et al. (2024) · Microbiome · doi:10.1186/s40168-023-01718-4 · Cited by 18
Evaluation of the gut microbiome in association with biological signatures of inflammation in murine polytrauma and shock
Appiah, S. A., Foxx, C. L., Langgartner, D., Palmer, A., Zambrano, C. A., Braumüller, S. T., Schaefer, E. J., Wachter, U. A., Elam, B. L., Radermacher, P., et al. (2021) · Scientific Reports · doi:10.1038/s41598-021-85897-w · Cited by 18
Pubertal consumption of R. badensis subspecies acadiensis modulates LPS-induced immune responses and gut microbiome dysbiosis in a sex-specific manner
Yahfoufi, N., Kadamani, A. K., Aly, S., Sharani, S. A., Liang, J., Butcher, J., Stintzi, A., Matar, C., & Ismail, N. (2022) · Brain Behavior and Immunity · doi:10.1016/j.bbi.2022.09.013 · Cited by 17
Untangling the complex interactions between turtle ants and their microbial partners
Ramalho, M. O., & Moreau, C. S. (2023) · Animal Microbiome · doi:10.1186/s42523-022-00223-7 · Cited by 16
Polyaniline-Derived Nitrogen-Containing Carbon Nanostructures with Different Morphologies as Anode Modifier in Microbial Fuel Cells
Lascu, I., Locovei, C., Bradu, C., Gheorghiu, C. C., Tănase, A., & Dumitru, A. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms231911230 · Cited by 17
The hidden Markov model and its applications in bioinformatics analysis
Ma, Y., Chen, H., Kang, J., Guo, X., Sun, C., Xu, J., Tao, J., Wei, S., Dong, Y., Tian, H., et al. (2025) · Genes & Diseases · doi:10.1016/j.gendis.2025.101729 · Cited by 20
App-SpaM: phylogenetic placement of short reads without sequence alignment
Blanke, M., & Morgenstern, B. (2021) · Bioinformatics Advances · doi:10.1093/bioadv/vbab027 · Cited by 16
The Effect of Oral Iron Supplementation on Gut Microbial Composition: a Secondary Analysis of a Double-Blind, Randomized Controlled Trial among Cambodian Women of Reproductive Age
Finlayson-Trick, E. C., Nearing, J. T., Fischer, J. A. J., Ma, Y., Wang, S., Kroeun, H., Goldfarb, D. A., & Karakochuk, C. D. (2023) · Microbiology Spectrum · doi:10.1128/spectrum.05273-22 · Cited by 16
Gut Microbes Are Associated with the Vascular Beneficial Effects of Dietary Strawberry on Metabolic Syndrome‐Induced Vascular Inflammation
Miller, J. C., Babu, A. K. S., Petersen, C., Wankhade, U. D., Robeson, M. S., Putich, M. N., Mueller, J. E., O'Farrell, A. S., Cho, J. M., Chintapalli, S. V., et al. (2022) · Molecular Nutrition & Food Research · doi:10.1002/mnfr.202200112 · Cited by 17
Exploring the diversity and potential interactions of bacterial and fungal endophytes associated with different cultivars of olive (Olea europaea) in Brazil
de Oliveira, A. A., Ramalho, M. O., Moreau, C. S., Campos, A. E. D. C., Harakava, R., & Bueno, O. C. (2022) · Microbiological Research · doi:10.1016/j.micres.2022.127128 · Cited by 15

Authors: MIRARAB, S., NGUYEN, N., & WARNOW, T.
Affiliations: The University of Texas at Austin (US)
ORCID: MIRARAB, S.
NGUYEN, N.
WARNOW, T.
Venue: Biocomputing 2012
Publisher: WORLD SCIENTIFIC
Published: 2011-12
Pages: 247-258
DOI: 10.1142/9789814366496_0024
OpenAlex: W2033900229
Cited by: 251
References: 0
Citations by year: 2026: 13 · 2025: 34 · 2024: 27 · 2023: 37 · 2022: 43 · 2021: 26 · 2020: 14 · 2019: 11 · 2018: 17 · 2017: 3 · 2016: 4 · 2015: 4 · 2014: 4 · 2013: 8 · 2012: 6
FWCI: 21.13
Type: conference paper
Language: en
Open access: closed
Locations: Pacific Symposium on Biocomputing (PSB) (publishedVersion)
PubMed (publishedVersion)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fractal and DNA sequence analysis
Keywords: phylogenetic placement, sate, boosting, computational tractability
MeSH terms: Algorithms, Bacteria, Phylogeny, RNA, Bacterial, RNA, Ribosomal, 16S, Software, Sequence Alignment, Evolution, Molecular, Computational Biology, Databases, Nucleic Acid, Metagenome, Metagenomics

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 ›

Are you an author, or do you see a problem with this page? Request a review

SEPP: SATé-Enabled Phylogenetic Placement

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Claims other papers make about this one

Citations

Cites

Cited by

Related

Metadata

Record

About these checks