Cited by 2,132Genomics and Phylogenetic StudiesAlgorithms and Data CompressionMicrobial Community Ecology and Physiology

The DOI matches its Crossref record; 12 of the 12 references it cites were found in a registry or an index.

PANDAseq: paired-end assembler for illumina sequences

Open access

Masella, Andre P, Bartram, Andrea K, Truszkowski, Jakub M, Brown, Daniel G, Neufeld, Josh D·2012·BMC Bioinformatics

DOI 10.1186/1471-2105-13-31PMC PMC3471323

Open this paper in CoChat — free account Open PDF

Abstract

BACKGROUND: Illumina paired-end reads are used to analyse microbial communities by targeting amplicons of the 16S rRNA gene. Publicly available tools are needed to assemble overlapping paired-end reads while correcting mismatches and uncalled bases; many errors could be corrected to obtain higher sequence yields using quality information. RESULTS: PANDAseq assembles paired-end reads rapidly and with the correction of most errors. Uncertain error corrections come from reads with many low-quality bases identified by upstream processing. Benchmarks were done using real error masks on simulated data, a pure source template, and a pooled template of genomic DNA from known organisms. PANDAseq assembled reads more rapidly and with reduced error incorporation compared to alternative methods. CONCLUSIONS: PANDAseq rapidly assembles sequences and scales to billions of paired-end reads. Assembly of control libraries showed a 4-50% increase in the number of assembled sequences over naïve assembly with negligible loss of "good" sequence.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Integrity signals

Registry

Crossref · 10.1186/1471-2105-13-31

Cites

12 of 12 references verified0 citation errors · 0 not checkable

Statistics

Figure 1 Schematic of paired-end assembly. Typical scenario: forward and reverse reads are overlapped and the primer regions are removed to reconstruct the sequences. Highly overlapping scenario: for short templates, the overlapping region may include the primer regions.CC BY · PubMed Central

Figure 2 Quality scores of assembled masked data. A perfect 16S rRNA sequence from Sinorhizobium meliloti was masked using real Illumina quality scores and the resulting paired-end sequences were assembled with PANDAseq. A histogram of quality scores for the assembled sequences is shown.CC BY · PubMed Central

Figure 3 Comparison of output of various assemblers. A scatter plot of the percentage of paired-end sequence assemblies from sequenced V3-region amplicons of Methylococcus capsulatus strain Bath against the average number of mismatching nucleotides between the assembled sequence and the reference sequence. The comparison was done between PANDAseq and three alternative assemblers (see text).CC BY · PubMed Central

Figure 4 Rank abundance curves for control libraries. Rank-abundance curves for defined multi-organism libraries [1] assembled at two different quality thresholds using PANDAseq and naïve assembly followed by clustering with CD-HIT into OTUs of 97% identity.CC BY · PubMed Central

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

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?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA
Muyzer, G., de Waal, E. C., & Uitterlinden, A. G. (1993) · Applied and Environmental Microbiology · doi:10.1128/aem.59.3.695-700.1993 · Cited by 11,490
A general method applicable to the search for similarities in the amino acid sequence of two proteins
Needleman, S. B., & Wunsch, C. D. (1970) · Journal of Molecular Biology · doi:10.1016/0022-2836(70)90057-4 · Cited by 11,288
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
Li, W.-Z., & Godzik, A. (2006) · Bioinform. · doi:10.1093/bioinformatics/btl158 · Cited by 10,996
Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample
Caporaso, J. G., Lauber, C. L., Walters, W. A., Berg-Lyons, D., Lozupone, C., Turnbaugh, P. J., Fierer, N., & Knight, R. D. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1000080107 · Cited by 9,944
The Ribosomal Database Project: improved alignments and new tools for rRNA analysis
Cole, J. R., Wang, Q., Cardenas, E., Fish, J., Chai, B., Farris, R. J., Kulam-Syed-Mohideen, A. S., McGarrell, D. M., Marsh, T. L., Garrity, G. M., et al. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn879 · Cited by 4,873
The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants
Cock, P., Fields, C. J., Goto, N., Heuer, M., & Rice, P. M. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp1137 · Cited by 1,896
The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data
Cole, J. R., Chai, B., Farris, R. J., Wang, Q., Kulam-Syed-Mohideen, A. S., McGarrell, D. M., Bandela, A. M., Cardenas, E., Garrity, G. M., & Tiedje, J. M. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl889 · Cited by 1,171
Generation of Multimillion-Sequence 16S rRNA Gene Libraries from Complex Microbial Communities by Assembling Paired-End Illumina Reads
Bartram, A. K., Lynch, M. D. J., Stearns, J. C., Moreno‐Hagelsieb, G., & Neufeld, J. D. (2011) · Applied and Environmental Microbiology · doi:10.1128/aem.02772-10 · Cited by 800
Self-citation
Illumina-based analysis of microbial community diversity
Degnan, P. H., & Ochman, H. (2011) · The ISME Journal · doi:10.1038/ismej.2011.74 · Cited by 422
Microbiome profiling by Illumina sequencing of combinatorial sequence-tagged PCR products
Gloor, G. B., Hummelen, R., Macklaim, J. M., Dickson, R. J., Fernandes, A. D., MacPhee, R., & Reid, G. (2010) · PLoS ONE · doi:10.1371/journal.pone.0015406 · Cited by 330

Show all 12 references

Research works printed but not linked: 1

Illumina, Inc: CASAVA Software Version 1.7 User Guide. Illumina, Inc; 2010.

Sorted by citations

Items 501–600 of 1,002

Preferential suppression of Anopheles gambiae host sequences allows detection of the mosquito eukaryotic microbiome
Belda, E., Coulibaly, B., Fofana, A., Béavogui, A. H., Traore, S. F., Gohl, D. M., Vernick, K. D., & Riehle, M. M. (2017) · Scientific Reports · doi:10.1038/s41598-017-03487-1 · Cited by 59
High-Throughput Sequence Analyses of Bacterial Communities and Multi-Mycotoxin Profiling During Processing of Different Formulations of Kunu, a Traditional Fermented Beverage
Ezekiel, C. N., Ayeni, K. I., Ezeokoli, O. T., Sulyok, M., van Wyk, D. A. B., Oyedele, O. A., Akinyemi, M. O., Chibuzor‐Onyema, I. E., Adeleke, R. A., Nwangburuka, C. C., et al. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.03282 · Cited by 62
Clonify: unseeded antibody lineage assignment from next-generation sequencing data
Briney, B. S., Le, K. M., Zhu, J., & Burton, D. R. (2016) · Scientific Reports · doi:10.1038/srep23901 · Cited by 59
Genomic epidemiology of Cryptococcus yeasts identifies adaptation to environmental niches underpinning infection across an African HIV / AIDS cohort
Vanhove, M., Beale, M. A., Rhodes, J. L., Chanda, D. M., Lakhi, S., Kwenda, G., Molloy, S. F., Karunaharan, N., Stone, N. R. H., Harrison, T. S., et al. (2016) · Molecular Ecology · doi:10.1111/mec.13891 · Cited by 59
Influence of Library Composition on SourceTracker Predictions for Community-Based Microbial Source Tracking
Brown, C. M., Mathai, P. P., Lösekann, T., Staley, C. M., & Sadowsky, M. J. (2018) · Environmental Science & Technology · doi:10.1021/acs.est.8b04707 · Cited by 59
Plant functional diversity and soil properties control elevational diversity gradients of soil bacteria
Shigyo, N., Umeki, K., & Hirao, T. (2019) · FEMS Microbiology Ecology · doi:10.1093/femsec/fiz025 · Cited by 59
Comparative Analysis of Root Microbiomes of Rice Cultivars with High and Low Methane Emissions Reveals Differences in Abundance of Methanogenic Archaea and Putative Upstream Fermenters
Liechty, Z., Santos‐Medellín, C., Edwards, J. A., Nguyen, B., Mikhail, D., Eason, S., Phillips, G. C., & Sundaresan, V. (2020) · mSystems · doi:10.1128/msystems.00897-19 · Cited by 59
Gut Microbiota of Drosophila subobscura Contributes to Its Heat Tolerance and Is Sensitive to Transient Thermal Stress
Jaramillo, A., & Castañeda, L. E. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.654108 · Cited by 62
Biodiversity and technological-functional potential of lactic acid bacteria isolated from spontaneously fermented chia sourdough
Maidana, S. D., Ficoseco, C. A., Bassi, D., Cocconcelli, P. S., Puglisi, E., Savoy, G., Vignolo, G. M., & Fontana, C. A. (2019) · International Journal of Food Microbiology · doi:10.1016/j.ijfoodmicro.2019.108425 · Cited by 59
Valorization of food waste and economical treatment: Effect of inoculation methods
Shewa, W. A., Hussain, A., Chandra, R., Lee, J., Saha, S., & Lee, H. (2020) · Journal of Cleaner Production · doi:10.1016/j.jclepro.2020.121170 · Cited by 58
Analyses of Potential Driver and Passenger Bacteria in Human Colorectal Cancer
Wang, Y., Zhang, C., Hou, S., Wu, X., Liu, J., & Wan, X. (2020) · Cancer Management and Research · doi:10.2147/cmar.s275316 · Cited by 57
Naive human B cells engage the receptor binding domain of SARS-CoV-2, variants of concern, and related sarbecoviruses
Feldman, J. E., Bals, J., Altomare, C. G., Denis, K. S., Lam, E. C., Hauser, B. M., Ronsard, L., Sangesland, M., Moreno, T. B., Okonkwo, V., et al. (2021) · Science Immunology · doi:10.1126/sciimmunol.abl5842 · Cited by 60
Temporal Relationships Exist Between Cecum, Ileum, and Litter Bacterial Microbiomes in a Commercial Turkey Flock, and Subtherapeutic Penicillin Treatment Impacts Ileum Bacterial Community Establishment
Danzeisen, J. L., Clayton, J. B., Huang, H., Knights, D., McComb, B., Hayer, S. S., & Johnson, T. J. (2015) · Frontiers in Veterinary Science · doi:10.3389/fvets.2015.00056 · Cited by 58
Analysis of bacterial and fungal communities in Marcha and Thiat, traditionally prepared amylolytic starters of India
Sha, S. P., Jani, K., Sharma, A., Anupma, A., Pradhan, P., Shouche, Y. S., & Tamang, J. P. (2017) · Scientific Reports · doi:10.1038/s41598-017-11609-y · Cited by 58
β-Klotho deficiency protects against obesity through a crosstalk between liver, microbiota, and brown adipose tissue
Somm, E., Henry, H., Bruce, S. J., Aeby, S., Rosikiewicz, M., Sykiotis, G. P., Asrih, M., Jornayvaz, F. R., Denechaud, P., Albrecht, U., et al. (2017) · JCI Insight · doi:10.1172/jci.insight.91809 · Cited by 58
Distribution of bacterial polycyclic aromatic hydrocarbon (PAH) ring-hydroxylating dioxygenases genes in oilfield soils and mangrove sediments explored by gene-targeted metagenomics
Liang, C., Huang, Y., Wang, Y., Ye, Q., Zhang, Z., & Wang, H. (2019) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-018-09613-x · Cited by 57
Bacterial diversity in Korean temple kimchi fermentation
Lee, M., Song, J. H., Park, J. M., & Chang, J. Y. (2019) · Food Research International · doi:10.1016/j.foodres.2019.108592 · Cited by 57
Iron deficiency anemia-related gut microbiota dysbiosis in infants and young children: A pilot study
Mulevičienė, A., D’Amico, F., Turroni, S., Candela, M., & Jankauskienė, A. (2018) · Acta Microbiologica et Immunologica Hungarica · doi:10.1556/030.65.2018.045 · Cited by 60
Evolution of a highly functional circular DNA aptamer in serum
Mao, Y., Gu, J., Chang, D., Wang, L., Yao, L., Ma, Q., Luo, Z., Qu, H., Li, Y., & Zheng, L. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa800 · Cited by 56
Effects of increasing dietary level of organic acids and nature-identical compounds on growth, intestinal cytokine gene expression and gut microbiota of rainbow trout (Oncorhynchus mykiss) reared at normal and high temperature
Pelusio, N. F., Rossi, B., Parma, L., Volpe, E., Ciulli, S., Piva, A., D’Amico, F., Scicchitano, D., Candela, M., Gatta, P. P., et al. (2020) · Fish & Shellfish Immunology · doi:10.1016/j.fsi.2020.10.021 · Cited by 56
Follicular T cells optimize the germinal center response to SARS-CoV-2 protein vaccination in mice
Cavazzoni, C. B., Hanson, B. L., Podestà, M. A., Bechu, E. D., Clement, R. L., Zhang, H., Daccache, J., Robles, T. R., Hett, E. C., Vora, K. A., et al. (2022) · Cell Reports · doi:10.1016/j.celrep.2022.110399 · Cited by 58
Probiotic Escherichia coli Nissle 1917 Expressing Elafin Protects Against Inflammation and Restores the Gut Microbiota
Teng, G., Li, H., Liu, Y., Wu, T., Dai, Y., Wang, H., & Wang, W. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.819336 · Cited by 56
Temporal changes in fungal communities associated with guts and appendages of Collembola as based on culturing and high-throughput sequencing
Anslan, S., Bahram, M., & Tedersoo, L. (2016) · Soil Biology and Biochemistry · doi:10.1016/j.soilbio.2016.02.006 · Cited by 56
Impact of Cropping Systems, Soil Inoculum, and Plant Species Identity on Soil Bacterial Community Structure
Ishaq, S. L., Johnson, S. P., Miller, Z. J., Lehnhoff, E. A., Olivo, S., Yeoman, C. J., & Menalled, F. D. (2016) · Microbial Ecology · doi:10.1007/s00248-016-0861-2 · Cited by 55
Effect of seasonal production on bacterial communities in Korean industrial kimchi fermentation
Lee, M., Song, J. H., Lee, S. H., Jung, M. Y., & Chang, J. Y. (2018) · Food Control · doi:10.1016/j.foodcont.2018.04.023 · Cited by 56
Human Activity Determines the Presence of Integron-Associated and Antibiotic Resistance Genes in Southwestern British Columbia
Uyaguari, M., Croxen, M. A., Luo, Z., Cronin, K. I., Chan, M., Baticados, W. N., Nesbitt, M. J., Li, S., Miller, K. M., Dooley, D., et al. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.00852 · Cited by 56
Gut Microbiota Dynamics during Chemotherapy in Epithelial Ovarian Cancer Patients Are Related to Therapeutic Outcome
D’Amico, F., Perrone, A. M., Rampelli, S., Coluccelli, S., Barone, M., Ravegnini, G., Fabbrini, M., Brigidi, P., Iaco, P. D., & Turroni, S. (2021) · Cancers · doi:10.3390/cancers13163999 · Cited by 57
Detection of minimal residual disease in NPM1-mutated acute myeloid leukemia by next-generation sequencing
Salipante, S. J., Fromm, J. R., Shendure, J., Wood, B. L., & Wu, D. (2014) · Modern Pathology · doi:10.1038/modpathol.2014.57 · Cited by 55
Characterization of bacterial communities associated with the pinewood nematode insect vector Monochamus alternatus Hope and the host tree Pinus massoniana
Guo, Y., Lin, Q., Chen, L., Carballar‐Lejarazú, R., Zhang, A., Shao, E., Liang, G., Hu, X., Wang, R., Xu, L., et al. (2020) · BMC Genomics · doi:10.1186/s12864-020-6718-6 · Cited by 55
Conventional and organic farms with more intensive management have lower soil functionality
van Rijssel, S. Q., Koorneef, G. J., Veen, G. F., Pulleman, M., de Goede, R. G. M., Comans, R. N. J., van der Putten, W. H., & Mason‐Jones, K. (2025) · Science · doi:10.1126/science.adr0211 · Cited by 55
Deciphering the pathogenesis of NSAID enteropathy using proton pump inhibitors and a hydrogen sulfide-releasing NSAID
Blackler, R. W., Palma, G. D., Mańko, A., Silva, G., Flannigan, K. L., Berčík, P., Surette, M. G., Buret, A. G., & Wallace, J. L. (2015) · American Journal of Physiology-Gastrointestinal and Liver Physiology · doi:10.1152/ajpgi.00066.2015 · Cited by 55
The Features of Fecal and Ileal Mucosa-Associated Microbiota in Dairy Calves during Early Infection with Mycobacterium avium Subspecies paratuberculosis
Derakhshani, H., Buck, J. D., Mortier, R. A. R., Barkema, H. W., Krause, D. O., & Khafipour, E. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.00426 · Cited by 57
Bioinformatic Suggestions on MiSeq-Based Microbial Community Analysis
Unno, T. (2015) · Journal of Microbiology and Biotechnology · doi:10.4014/jmb.1409.09057 · Cited by 55
Faecal bacterial microbiota in patients with cirrhosis and the effect of lactulose administration
Sarangi, A. N., Goel, A., Singh, A., Sasi, A., & Aggarwal, R. (2017) · BMC Gastroenterology · doi:10.1186/s12876-017-0683-9 · Cited by 56
Evaluation of Oral Cavity DNA Extraction Methods on Bacterial and Fungal Microbiota
Rosenbaum, J., Usyk, M., Chen, Z., Zolnik, C. P., Jones, H. E., Waldron, L., Dowd, J. B., Thorpe, L. E., & Burk, R. D. (2019) · Scientific Reports · doi:10.1038/s41598-018-38049-6 · Cited by 57
Microbial Chain Elongation and Subsequent Fermentation of Elongated Carboxylates as H2-Producing Processes for Sustained Reductive Dechlorination of Chlorinated Ethenes
Robles, A., Yellowman, T. L., Joshi, S., Rangan, S. M., & Delgado, A. G. (2021) · Environmental Science & Technology · doi:10.1021/acs.est.1c01319 · Cited by 55
Enriched taxa were found among the gut microbiota of centenarians in East China
Wang, N., Li, R., Lin, H., Fu, C., Wang, X., Zhang, Y., Su, M., Huang, P., Qian, J., Jiang, F., et al. (2019) · PLoS ONE · doi:10.1371/journal.pone.0222763 · Cited by 55
Running after ghosts: are dead bacteria the dark matter of the human gut microbiota?
Bellali, S., Lagier, J., Million, M., Anani, H., Haddad, G., Francis, R., Yimagou, E. K., Khelaifia, S., Levasseur, A., Raoult, D., et al. (2021) · Gut Microbes · doi:10.1080/19490976.2021.1897208 · Cited by 54
Metagenomic and metatranscriptomic inventories of the lower Amazon River, May 2011
Satinsky, B. M., Fortunato, C. S., Doherty, M., Smith, C. B., Sharma, S., Ward, N. D., Krusche, A. V., Yager, P. L., Richey, J. E., Moran, M. A., et al. (2015) · Microbiome · doi:10.1186/s40168-015-0099-0 · Cited by 54
Fecal Microbiota Transplantation for Recurrent Clostridium difficile Infection in the Elderly: Long-Term Outcomes and Microbiota Changes
Girotra, M., Garg, S., Anand, R., Song, Y., & Dutta, S. (2016) · Digestive Diseases and Sciences · doi:10.1007/s10620-016-4229-8 · Cited by 56
Extraction and 16S rRNA Sequence Analysis of Microbiomes Associated with Rice Roots
Edwards, J. A., Santos‐Medellín, C., & Sundaresan, V. (2018) · BIO-PROTOCOL · doi:10.21769/bioprotoc.2884 · Cited by 54
Terminal restriction fragment length polymorphism is an “old school” reliable technique for swift microbial community screening in anaerobic digestion
Vrieze, J. D., Ijaz, U. Z., Saunders, A. M., & Theuerl, S. (2018) · Scientific Reports · doi:10.1038/s41598-018-34921-7 · Cited by 54
The maturity period is the main stage of antibiotic resistance genes reduction in aerobic composting process of swine manure in sub-scale farms
Guo, W., Huang, C., Xi, B., Tang, Z., Tan, W., Li, W., Zhang, Y., & Li, W. (2020) · Bioresource Technology · doi:10.1016/j.biortech.2020.124139 · Cited by 54
Correction: A Filtering Method to Generate High Quality Short Reads Using Illumina Paired-End Technology
Eren, A. M., Vineis, J. H., Morrison, H. G., & Sogin, M. L. (2013) · PLoS ONE · doi:10.1371/annotation/afa5c40d-c604-46ae-84c4-82cb92193a5e · Cited by 54
N2O Reduction by Gemmatimonas aurantiaca and Potential Involvement of Gemmatimonadetes Bacteria in N2O Reduction in Agricultural Soils
Oshiki, M., Toyama, Y., Suenaga, T., Terada, A., Kasahara, Y., Yamaguchi, T., & Araki, N. (2022) · Microbes and Environments · doi:10.1264/jsme2.me21090 · Cited by 54
Allelic polymorphism controls autoreactivity and vaccine elicitation of human broadly neutralizing antibodies against influenza virus
Sangesland, M., de la Peña, A. T., Boyoglu-Barnum, S., Ronsard, L., Mohamed, F. A. N., Moreno, T. B., Barnes, R. M., Rohrer, D., Lönberg, N., Ghebremichael, M. S., et al. (2022) · Immunity · doi:10.1016/j.immuni.2022.07.006 · Cited by 54
Coinfection of Fusobacterium nucleatum and Actinomyces israelii in Mastoiditis Diagnosed by Next-Generation DNA Sequencing
Salipante, S. J., Hoogestraat, D. R., Abbott, A. N., SenGupta, D. J., Cummings, L. A., Butler‐Wu, S. M., Stephens, K. G., Cookson, B. T., & Hoffman, N. G. (2014) · Journal of Clinical Microbiology · doi:10.1128/jcm.03133-13 · Cited by 53
Distinctive Tropical Forest Variants Have Unique Soil Microbial Communities, But Not Always Low Microbial Diversity
Tripathi, B. M., Song, W., Slik, F. J. W., Sukri, R. S., Jaafar, S. M., Dong, K., & Adams, J. M. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.00376 · Cited by 53
Microbial ecology involved in the ripening of naturally fermented llama meat sausages. A focus on lactobacilli diversity
Fontana, C. A., Bassi, D., Lopez, C. M., Pisacane, V., Otero, M. C., Puglisi, E., Rebecchi, A., Cocconcelli, P. S., & Vignolo, G. M. (2016) · International Journal of Food Microbiology · doi:10.1016/j.ijfoodmicro.2016.07.002 · Cited by 54
Acetylcholine-producing T cells in the intestine regulate antimicrobial peptide expression and microbial diversity.
Dhawan, S., Palma, G. D., Willemze, R., Hilbers, F., Verseijden, C., Luyer, M., Nuding, S., Wehkamp, J., Souwer, Y., de Jong, E. C., et al. (2016) · American Journal of Physiology - Gastrointestinal and Liver Physiology · doi:10.1152/ajpgi.00114.2016 · Cited by 48
Evolution of microbial communities growing with carbon monoxide, hydrogen, and carbon dioxide
Esquivel‐Elizondo, S., Delgado, A. G., & Krajmalnik‐Brown, R. (2017) · FEMS Microbiology Ecology · doi:10.1093/femsec/fix076 · Cited by 53
Cervical microbiome is altered in cervical intraepithelial neoplasia after loop electrosurgical excision procedure in china
Zhang, H., Lu, J., Lü, Y., Cai, Q., Liu, H., & Xu, C. (2018) · Scientific Reports · doi:10.1038/s41598-018-23389-0 · Cited by 53
Effect of High versus Low Dairy Consumption on the Gut Microbiome: Results of a Randomized, Cross-Over Study
Swarte, J. C., Eelderink, C., Douwes, R. M., Said, M. Y., Hu, S., Post, A., Westerhuis, R., Bakker, S. J. L., & Harmsen, H. J. M. (2020) · Nutrients · doi:10.3390/nu12072129 · Cited by 53
Revealing Cues for Fungal Interplay in the Plant–Air Interface in Vineyards
Abdelfattah, A., Sanzani, S. M., Wisniewski, M., Berg, G., Cacciola, S. O., & Schena, L. (2019) · Frontiers in Plant Science · doi:10.3389/fpls.2019.00922 · Cited by 56
A 45-Amino-Acid Scaffold Mined from the PDB for High-Affinity Ligand Engineering
Kruziki, M. A., Bhatnagar, S., Woldring, D., Duong, V. T., & Hackel, B. J. (2015) · Chemistry & Biology · doi:10.1016/j.chembiol.2015.06.012 · Cited by 57
In vitro selection of RNA-cleaving DNAzymes for bacterial detection
Zhang, W., Feng, Q., Chang, D., Tram, K., & Li, Y. (2016) · Methods · doi:10.1016/j.ymeth.2016.03.018 · Cited by 52
Barite encrustation of benthic sulfur‐oxidizing bacteria at a marine cold seep
Stevens, E., Bailey, J. V., Flood, B. E., Jones, D. S., Gilhooly, W., Joye, S. B., Teske, A., & Mason, O. U. (2015) · Geobiology · doi:10.1111/gbi.12154 · Cited by 51
The draft genome of Corchorus olitorius cv. JRO-524 (Navin)
Sarkar, D., Mahato, A. K., Satya, P., Kundu, A., Singh, S., Jayaswal, P. K., Singh, A. K., Bahadur, K., Pattnaik, S., Singh, N., et al. (2017) · Genomics Data · doi:10.1016/j.gdata.2017.05.007 · Cited by 51
Comparing Rock-inhabiting Microbial Communities in Different Rock Types from a High Arctic Polar Desert
Choe, Y., Kim, M., Woo, J., Lee, M. J., Lee, J. I., Lee, E. J., & Lee, Y. K. (2018) · FEMS Microbiology Ecology · doi:10.1093/femsec/fiy070 · Cited by 54
Characteristics of the rhizosphere bacterial community across different cultivation years in saline–alkaline paddy soils of Songnen Plain of China
Cui, J., Li, Y., Wang, C., Kim, K. S., Wang, T., & Liu, S. (2018) · Canadian Journal of Microbiology · doi:10.1139/cjm-2017-0752 · Cited by 51
PEMA: a flexible Pipeline for Environmental DNA Metabarcoding Analysis of the 16S/18S ribosomal RNA, ITS, and COI marker genes
Zafeiropoulos, H., Ha, Q. V., Vasileiadou, K., Potirakis, A., Arvanitidis, C., Topalis, P., Pavloudi, C., & Pafilis, E. (2020) · GigaScience · doi:10.1093/gigascience/giaa022 · Cited by 54
Lactobacillus sakei ADM14 Induces Anti-Obesity Effects and Changes in Gut Microbiome in High-Fat Diet-Induced Obese Mice
Won, S., Chen, S., Lee, S. Y., Lee, K. E., Park, K. W., & Yoon, J. (2020) · Nutrients · doi:10.3390/nu12123703 · Cited by 53
Multi-scale ecological filters shape the crayfish microbiome
Skelton, J., Geyer, K. M., Lennon, J. T., Creed, R. P., & Brown, B. L. (2016) · Symbiosis · doi:10.1007/s13199-016-0469-9 · Cited by 50
Environmental filtering: A case of bacterial community assembly in soil
Yan, Y., Klinkhamer, P. G. L., van Veen, J. A., & Kuramae, E. E. (2019) · Soil Biology and Biochemistry · doi:10.1016/j.soilbio.2019.107531 · Cited by 50
Enhancing the plants growth and arsenic uptake from soil using arsenite-oxidizing bacteria
Dębiec-Andrzejewska, K., Krucoń, T., Piatkowska, K., & Drewniak, Ł. (2020) · Environmental Pollution · doi:10.1016/j.envpol.2020.114692 · Cited by 50
Characteristics of Gut Microbiota in Patients with GH-Secreting Pituitary Adenoma
Lin, B. C., Wang, M., Gao, R., Ye, Z., Yu, Y., He, W., Qiao, N., Ma, Z., Ji, C., Shi, C., et al. (2022) · Microbiology Spectrum · doi:10.1128/spectrum.00425-21 · Cited by 49
A Single-Granule-Level Approach Reveals Ecological Heterogeneity in an Upflow Anaerobic Sludge Blanket Reactor
Kuroda, K., Nobu, M. K., Mei, R., Narihiro, T., Bocher, B. T. W., Yamaguchi, T., & Liu, W. (2016) · PLoS ONE · doi:10.1371/journal.pone.0167788 · Cited by 50
Vertical distribution of fungi in hollows and hummocks of boreal peatlands
Asemaninejad, A., Thorn, R. G., & Lindo, Z. (2017) · Fungal ecology · doi:10.1016/j.funeco.2017.02.002 · Cited by 52
Tropical forest conversion to rubber plantation in southwest China results in lower fungal beta diversity and reduced network complexity
Song, H., Singh, D., Tomlinson, K. W., Yang, X., Ogwu, M. C., Slik, F. J. W., & Adams, J. M. (2019) · FEMS Microbiology Ecology · doi:10.1093/femsec/fiz092 · Cited by 56
Response of bacterial communities in coastal mudflat saline soil to sewage sludge amendment
Bai, Y., Mei, L., Zuo, W., Zhang, Y., Gu, C., Shan, Y., Hu, J., & Dai, Q. (2019) · Applied Soil Ecology · doi:10.1016/j.apsoil.2019.07.007 · Cited by 50
Interaction of bacterial communities and indicators of water quality in shoreline sand, sediment, and water of Lake Michigan
Nevers, M. B., Byappanahalli, M. N., Nakatsu, C. H., Kinzelman, J. L., Phanikumar, M. S., Shively, D. A., & Spoljaric, A. M. (2020) · Water Research · doi:10.1016/j.watres.2020.115671 · Cited by 50
Proteobacteria Overgrowth and Butyrate-Producing Taxa Depletion in the Gut Microbiota of Glycogen Storage Disease Type 1 Patients
Ceccarani, C., Bassanini, G., Montanari, C., Casiraghi, M. C., Ottaviano, E., Morace, G., Biasucci, G., Paci, S., Borghi, E., & Verduci, E. (2020) · Metabolites · doi:10.3390/metabo10040133 · Cited by 52
Changes in Soil Fungal Community Structure with Increasing Disturbance Frequency
Cho, H., Kim, M., Tripathi, B. M., & Adams, J. M. (2017) · Microbial Ecology · doi:10.1007/s00248-016-0919-1 · Cited by 50
In Vitro Fermentation Characteristics and Fiber-Degrading Enzyme Kinetics of Cellulose, Arabinoxylan, β-Glucan and Glucomannan by Pig Fecal Microbiota
Bai, Y., Zhou, X., Li, N., Zhao, J., Ye, H., Zhang, S., Yang, H., Pi, Y., Tao, S., Han, D., et al. (2021) · Microorganisms · doi:10.3390/microorganisms9051071 · Cited by 55
The hidden effects of agrochemicals on plant metabolism and root-associated microorganisms
Cesco, S., Lucini, L., Miras‐Moreno, B., Borruso, L., Mimmo, T., Pii, Y., Puglisi, E., Spini, G., Taskin, E., Tiziani, R., et al. (2021) · Plant Science · doi:10.1016/j.plantsci.2021.111012 · Cited by 49
β-Glucan-Induced Immuno-Modulation: A Role for the Intestinal Microbiota and Short-Chain Fatty Acids in Common Carp
Petit, J., de Bruijn, I., Goldman, M. R. G., van den Brink, E., Pellikaan, W. F., Forlenza, M., & Wiegertjes, G. F. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2021.761820 · Cited by 47
Soil microbial diversity and community composition during conversion from conventional to organic agriculture
van Rijssel, S. Q., Veen, G. F., Koorneef, G. J., Bakx‐Schotman, J. M. T., ten Hooven, F. C., Geisen, S., & van der Putten, W. H. (2022) · Molecular Ecology · doi:10.1111/mec.16571 · Cited by 49
Association of gut microbiota with sort-chain fatty acids and inflammatory cytokines in diabetic patients with cognitive impairment: A cross-sectional, non-controlled study
Du, Y., Li, X., An, Y., Song, Y., & Lu, Y. (2022) · Frontiers in Nutrition · doi:10.3389/fnut.2022.930626 · Cited by 49
Most azole resistance mutations in the Candida albicans drug target confer cross-resistance without intrinsic fitness cost
Bédard, C., Gagnon‐Arsenault, I., Boisvert, J., Plante, S., Dubé, A. K., Pageau, A., Fijarczyk, A., Sharma, J., Maroc, L., Shapiro, R. S., et al. (2024) · Nature Microbiology · doi:10.1038/s41564-024-01819-2 · Cited by 50
Reutericyclin producing Lactobacillus reuteri modulates development of fecal microbiota in weanling pigs
Yang, Y., Zhao, X., Le, M. H. A., Zijlstra, R. T., & Gänzle, M. G. (2015) · Frontiers in Microbiology · doi:10.3389/fmicb.2015.00762 · Cited by 49
AmpliconDuo: A Split-Sample Filtering Protocol for High-Throughput Amplicon Sequencing of Microbial Communities
Lange, A., Jost, S., Heider, D., Böck, C., Budeus, B., Schilling, E., Strittmatter, A. W., Boenigk, J., & Hoffmann, D. E. (2015) · PLoS ONE · doi:10.1371/journal.pone.0141590 · Cited by 51
AXIOME: automated exploration of microbial diversity
Lynch, M. D. J., Masella, A. P., Hall, M., Bartram, A. K., & Neufeld, J. D. (2013) · GigaScience · doi:10.1186/2047-217x-2-3 · Cited by 49
Self-citation
Surveying wood-inhabiting fungi: Most molecularly detected polypore species form fruit-bodies within short distances
Runnel, K., Tamm, H., & Lõhmus, A. (2015) · Fungal ecology · doi:10.1016/j.funeco.2015.08.008 · Cited by 49
High-Throughput Ligand Discovery Reveals a Sitewise Gradient of Diversity in Broadly Evolved Hydrophilic Fibronectin Domains
Woldring, D., Holec, P. V., Zhou, H., & Hackel, B. J. (2015) · PLoS ONE · doi:10.1371/journal.pone.0138956 · Cited by 52
Intestinal microbiome disruption in patients in a long-term acute care hospital: A case for development of microbiome disruption indices to improve infection prevention
Halpin, A. L., de Man, T. J. B., Kraft, C. S., Perry, K. A., Chan, A. W., Lieu, S., Mikell, J., Limbago, B. M., & McDonald, L. C. (2016) · American Journal of Infection Control · doi:10.1016/j.ajic.2016.01.003 · Cited by 49
The Variable Influence of Dispersant on Degradation of Oil Hydrocarbons in Subarctic Deep-Sea Sediments at Low Temperatures (0–5 °C)
Ferguson, R., Gontikaki, E., Anderson, J. A., & Witte, U. F. M. (2017) · Scientific Reports · doi:10.1038/s41598-017-02475-9 · Cited by 50
Transient influence of blood meal and natural environment on blacklegged tick bacterial communities
Zolnik, C. P., Falco, R. C., Daniels, T. J., & Kolokotronis, S. (2018) · Ticks and Tick-borne Diseases · doi:10.1016/j.ttbdis.2018.01.007 · Cited by 49
Faecal bacterial communities from Mediterranean loggerhead sea turtles ( Caretta caretta )
Biagi, E., D’Amico, F., Soverini, M., Angelini, V., Barone, M., Turroni, S., Rampelli, S., Pari, S., Brigidi, P., & Candela, M. (2018) · Environmental Microbiology Reports · doi:10.1111/1758-2229.12683 · Cited by 49
Free-Living Nematodes Together With Associated Microbes Play an Essential Role in Apple Replant Disease
Kanfra, X., Liu, B., Beerhues, L., Sørensen, S. J., & Heuer, H. (2018) · Frontiers in Plant Science · doi:10.3389/fpls.2018.01666 · Cited by 49
Deep microbial community profiling along the fermentation process of pulque, a biocultural resource of Mexico
Rocha-Arriaga, C., Espinal‐Centeno, A., Martínez-Sánchez, S., Caballero-Pérez, J., Alcaraz, L. D., & Cruz‐Ramírez, A. (2020) · Microbiological Research · doi:10.1016/j.micres.2020.126593 · Cited by 52
Ciliates (Alveolata, Ciliophora) as bioindicators of environmental pressure: A karstic river case
Kulaš, A., Gulin, V., Kepčija, R. M., Žutinić, P., Perić, M. S., Orlić, S., Kajan, K., Stoeck, T., Lentendu, G., Čanjevac, I., et al. (2021) · Ecological Indicators · doi:10.1016/j.ecolind.2021.107430 · Cited by 49
Changes in gut microbiota composition and diversity associated with post-cholecystectomy diarrhea
Li, Y., Liu, B.-N., Zhao, S., Zhou, Y., Bai, L., & Liu, E. (2021) · World Journal of Gastroenterology · doi:10.3748/wjg.v27.i5.391 · Cited by 50
Pollutant removal, electricity generation and microbial community in an electrochemical membrane bioreactor during co-treatment of sewage and landfill leachate
Pierangeli, G. M. F., Ragio, R. A., Benassi, R. F., Gregoracci, G. B., & Subtil, E. L. (2021) · Journal of environmental chemical engineering · doi:10.1016/j.jece.2021.106205 · Cited by 49
Oral Bacteriome and Mycobiome across Stages of Oral Carcinogenesis
Heng, W., Wang, W., Dai, T., Jiang, P., Lu, Y., Li, R., Zhang, M., Xie, R., Zhou, Y., Zhao, M., et al. (2022) · Microbiology Spectrum · doi:10.1128/spectrum.02737-22 · Cited by 48
Multi-omics gut microbiome signatures in obese women: role of diet and uncontrolled eating behavior
Barone, M., Garelli, S., Rampelli, S., Agostini, A., Matysik, S., D’Amico, F., Krautbauer, S., Mazza, R., Salituro, N., Fanelli, F., et al. (2022) · BMC Medicine · doi:10.1186/s12916-022-02689-3 · Cited by 56
High-throughput characterization of HLA-E-presented CD94/NKG2x ligands reveals peptides which modulate NK cell activation
Huisman, B. D., Guan, N., Rückert, T., Garner, L. I., Singh, N. K., McMichael, A. J., Gillespie, G. M. A., Romagnani, C., & Birnbaum, M. E. (2023) · Nature Communications · doi:10.1038/s41467-023-40220-1 · Cited by 48
Bioreactor Scalability: Laboratory-Scale Bioreactor Design Influences Performance, Ecology, and Community Physiology in Expanded Granular Sludge Bed Bioreactors
Connelly, S., Shin, S. G., Dillon, R. J., Ijaz, U. Z., Quince, C., Sloan, W. T., & Collins, G. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.00664 · Cited by 48
Identification of sympatric cryptic species of Aedes albopictus subgroup in Vietnam: new perspectives in phylosymbiosis of insect vector
Minard, G., Van, V. T., Tran, F. H., Melaun, C., Klimpel, S., Koch, L. K., Kim, K. L. H., Thuy, T. H. T., Ngọc, H. T., Potier, P., et al. (2017) · Parasites & Vectors · doi:10.1186/s13071-017-2202-9 · Cited by 48
Reactivation of Intestinal Inflammation Is Suppressed by Catestatin in a Murine Model of Colitis via M1 Macrophages and Not the Gut Microbiota
Rabbi, M. F., Eissa, N., Munyaka, P. M., Kermarrec, L., Elgazzar, O., Khafipour, E., Bernstein, C. N., & Ghia, J. (2017) · Frontiers in Immunology · doi:10.3389/fimmu.2017.00985 · Cited by 48
Structural and compositional mismatch between captive and wild Atlantic salmon ( Salmo salar ) parrs’ gut microbiota highlights the relevance of integrating molecular ecology for management and conservation methods
Lavoie, C., Courcelle, M., Redivo, B., & Derôme, N. (2018) · Evolutionary Applications · doi:10.1111/eva.12658 · Cited by 48

Authors: Masella, A. P., Bartram, A. K., Truszkowski, J. M., Brown, D. G., & Neufeld, J. D.
Affiliations: University of Waterloo (CA)
Corresponding author: Neufeld, Josh D
ORCID: Truszkowski, Jakub M
Brown, Daniel G
Neufeld, Josh D
Venue: BMC Bioinformatics
Publisher: Springer Science and Business Media LLC
Published: 2012-02-14
Volume: 13
Issue: 1
Pages: 31-31
ISSN: 1471-2105 (ISSN-L)
DOI: 10.1186/1471-2105-13-31
PMC: PMC3471323
OpenAlex: W2132548846
Cited by: 2,132
References: 12
Citations by year: 2026: 61 · 2025: 89 · 2024: 90 · 2023: 115 · 2022: 187 · 2021: 254 · 2020: 277 · 2019: 264 · 2018: 251 · 2017: 204 · 2016: 152 · 2015: 108 · 2014: 56 · 2013: 21 · 2012: 3
FWCI: 24.15
Type: journal article
Language: en
Open access: gold
doi.org
Licence: cc-by
Locations: BMC Bioinformatics (publishedVersion, cc-by)
Europe PMC (PubMed Central) (publishedVersion, cc-by)
PubMed Central (publishedVersion, cc-by)
PubMed (publishedVersion)
DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders: Government of Ontario
Natural Sciences and Engineering Research Council of Canada
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Physical Sciences › Mathematics › Theoretical Computer Science › Algorithms and Data Compression
Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
Keywords: 16S rRNA gene, microbial community analysis, error correction, amplicon sequencing, sequencing errors
MeSH terms: Bacteria, RNA, Bacterial, RNA, Ribosomal, 16S, Software, 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

PANDAseq: paired-end assembler for illumina sequences

Abstract

Overview

Integrity signals

Figures

Verification

Claims the paper makes

Claims other papers make about this one

Self-check

Citations

Cites

Cited by

Related

Metadata

Record

About these checks