Combining metagenomics, metatranscriptomics and viromics to explore novel microbial interactions: towards a systems-level understanding of human microbiome

Fast and accurate short read alignment with Burrows-Wheeler transform

Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607

Gene Ontology: tool for the unification of biology

Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., et al. (2000) · Nature Genetics · doi:10.1038/75556 · Cited by 43,206

KEGG: Kyoto Encyclopedia of Genes and Genomes

Kanehisa, M. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.27 · Cited by 37,077

QIIME allows analysis of high-throughput community sequencing data

Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D., Costello, E. K., Fierer, N., Peña, A. G., Goodrich, J. K., Gordon, J. I., et al. (2010) · Nature Methods · doi:10.1038/nmeth.f.303 · Cited by 34,887

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P., Peplies, J., & Glöckner, F. O. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1219 · Cited by 33,055

KEGG: Kyoto Encyclopedia of Genes and Genomes

Ogata, H., Goto, S., Sato, K., Fujibuchi, W., Bono, H., & Kanehisa, M. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.1.29 · Cited by 31,232

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.

Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r25 · Cited by 21,849

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

Schloss, P. D., Westcott, S. L., Ryabin, T., Hall, J. R., Hartmann, M., Hollister, E. B., Lesniewski, R. A., Oakley, B. B., Parks, D. H., Robinson, C. J., et al. (2009) · Applied and Environmental Microbiology · doi:10.1128/aem.01541-09 · Cited by 21,481

Full-length transcriptome assembly from RNA-Seq data without a reference genome

Grabherr, M. G., Haas, B. J., Yassour, M., Levin, J. Z., Thompson, D. A., Amit, I., Adiconis, X., Fan, L., Raychowdhury, R., Zeng, Q., et al. (2011) · Nature Biotechnology · doi:10.1038/nbt.1883 · Cited by 21,201

Search and clustering orders of magnitude faster than BLAST

Edgar, R. C. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq461 · Cited by 21,098

Structure, function and diversity of the healthy human microbiome

The Human Microbiome Project Consortium (2012) · Nature · doi:10.1038/nature11234 · Cited by 11,726

A human gut microbial gene catalogue established by metagenomic sequencing

MetaHIT Consortium, Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K. S., Manichanh, C., Nielsen, T., Pons, N., Levenez, F., et al. (2010) · Nature · doi:10.1038/nature08821 · Cited by 11,624

Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB

DeSantis, T. Z., Hugenholtz, P., Larsen, N., Rojas, M., Brodie, E. L., Keller, K., Huber, T., Dalevi, D., Hu, P., & Andersen, G. L. (2006) · Applied and Environmental Microbiology · doi:10.1128/aem.03006-05 · Cited by 10,891

Diet rapidly and reproducibly alters the human gut microbiome

David, L. A., Maurice, C. F., Carmody, R. N., Gootenberg, D. B., Button, J. E., Wolfe, B. E., Ling, A. V., Devlin, A. S., Varma, Y., Fischbach, M. A., et al. (2014) · Nature · doi:10.1038/nature12820 · Cited by 10,100

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

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

Langille, M. G. I., Zaneveld, J., Caporaso, J. G., McDonald, D., Knights, D., Reyes, J. A., Clemente, J. C., Burkepile, D. E., Vega Thurber, R. L., Knight, R., et al. (2013) · Nature Biotechnology · doi:10.1038/nbt.2676 · Cited by 9,116

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

Caporaso, J. G., Lauber, C. L., Walters, W. A., Berg-Lyons, D., Huntley, J., Fierer, N., Owens, S. M., Betley, J., Fraser, L., Bauer, M., et al. (2012) · The ISME Journal · doi:10.1038/ismej.2012.8 · Cited by 8,839

Human gut microbes associated with obesity

Ley, R. E., Turnbaugh, P. J., Klein, S., & Gordon, J. I. (2006) · Nature · doi:10.1038/4441022a · Cited by 8,785

Enterotypes of the human gut microbiome

MetaHIT Consortium (additional members), Arumugam, M., Raes, J., Pelletier, E., Le Paslier, D., Yamada, T., Mende, D. R., Fernandes, G. R., Tap, J., Bruls, T., et al. (2011) · Nature · doi:10.1038/nature09944 · Cited by 7,548

Pfam: the protein families database

Finn, R. D., Bateman, A., Clements, J., Coggill, P., Eberhardt, R. Y., Eddy, S. R., Heger, A., Hetherington, K., Holm, L., Mistry, J., et al. (2014) · Nucleic Acids Research · doi:10.1093/nar/gkt1223 · Cited by 6,148

HMMER web server: interactive sequence similarity searching

Finn, R. D., Clements, J., & Eddy, S. R. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr367 · Cited by 5,952

Ribosomal Database Project: data and tools for high throughput rRNA analysis

Cole, J. R., Wang, Q., Fish, J. A., Chai, B., McGarrell, D. M., Sun, Y., Brown, C. T., Porras‐Alfaro, A., Kuske, C. R., & Tiedje, J. M. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt1244 · Cited by 4,480

Functional interactions between the gut microbiota and host metabolism

Tremaroli, V., & Bäckhed, F. (2012) · Nature · doi:10.1038/nature11552 · Cited by 4,387

Environmental genome shotgun sequencing of the sargasso sea

Venter, J. C., Remington, K., Heidelberg, J. F., Halpern, A. L., Rusch, D., Eisen, J. A., Wu, D., Paulsen, I., Nelson, K. E., Nelson, W., et al. (2004) · Science · doi:10.1126/science.1093857 · Cited by 4,376

SOAP2: an improved ultrafast tool for short read alignment

Li, R., Yu, C., Li, Y., Lam, T., Yiu, S., Kristiansen, K., & Wang, J. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp336 · Cited by 3,763

The impact of the gut microbiota on human health: an integrative view

Clemente, J. C., Ursell, L. K., Parfrey, L. W., & Knight, R. (2012) · Cell · doi:10.1016/j.cell.2012.01.035 · Cited by 3,710

The gut microbiota--masters of host development and physiology

Sommer, F., & Bäckhed, F. (2013) · Nature Reviews Microbiology · doi:10.1038/nrmicro2974 · Cited by 3,681

The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

Meyer, F., Paarmann, D., D'Souza, M., Olson, R., Glass, E., Kubal, M., Paczian, T., Rodriguez, A., Stevens, R. L., Wilke, A., et al. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-386 · Cited by 3,565

MEGAN analysis of metagenomic dataPreprint

Huson, D. H., Auch, A. F., Qi, J., & Schuster, S. C. (2007) · Genome Research · doi:10.1101/gr.5969107 · Cited by 3,294

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

Peng, Y., Leung, H. C. M., Yiu, S., & Chin, F. Y. L. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts174 · Cited by 2,998

A framework for human microbiome research

The Human Microbiome Project Consortium (2012) · Nature · doi:10.1038/nature11209 · Cited by 2,650

Commensal Host-Bacterial Relationships in the Gut

Hooper, L. V., & Gordon, J. I. (2001) · Science · doi:10.1126/science.1058709 · Cited by 2,362

Reduced diversity of faecal microbiota in Crohn’s disease revealed by a metagenomic approach

Manichanh, C., Rigottier-Gois, L., Bonnaud, E., Gloux, K., Pelletier, E., Frangeul, L., Nalin, R., Jarrin, C., Chardon, P., Marteau, P., et al. (2006) · Gut · doi:10.1136/gut.2005.073817 · Cited by 2,277

The NIH Human Microbiome ProjectPreprint

The NIH HMP Working Group, Peterson, J. L., Garges, S., Giovanni, M. Y., McInnes, P., Wang, L., Schloss, J. A., Bonazzi, V. R., McEwen, J. E., Wetterstrand, K. A., et al. (2009) · Genome Research · doi:10.1101/gr.096651.109 · Cited by 2,168

Artificial sweeteners induce glucose intolerance by altering the gut microbiota

Suez, J., Korem, T., Zeevi, D., Zilberman-Schapira, G., Thaiss, C. A., Maza, O., Israeli, D., Zmora, N., Gilad, S., Weinberger, A., et al. (2014) · Nature · doi:10.1038/nature13793 · Cited by 2,067 · cited 1×

The Intestinal Microbiota Modulates the Anticancer Immune Effects of Cyclophosphamide

Viaud, S., Saccheri, F., Mignot, G., Yamazaki, T., Daillère, R., Hannani, D., Enot, D. P., Pfirschke, C., Engblom, C., Pittet, M. J., et al. (2013) · Science · doi:10.1126/science.1240537 · Cited by 2,050

The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes

Overbeek, R. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki866 · Cited by 2,019

Metagenomic microbial community profiling using unique clade-specific marker genes

Segata, N., Waldron, L., Ballarini, A., Narasimhan, V., Jousson, O., & Huttenhower, C. (2012) · Nature Methods · doi:10.1038/nmeth.2066 · Cited by 1,776

Phages and the Evolution of Bacterial Pathogens: from Genomic Rearrangements to Lysogenic Conversion

Brüssow, H., Canchaya, C. A., & Hardt, W. (2004) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.68.3.560-602.2004 · Cited by 1,717

Reciprocal interactions of the intestinal microbiota and immune system

Maynard, C. L., Elson, C. O., Hatton, R. D., & Weaver, C. T. (2012) · Nature · doi:10.1038/nature11551 · Cited by 1,598 · cited 1×

The microglial sensome revealed by direct RNA sequencing

Hickman, S. E., Kingery, N. D., Ohsumi, T. K., Borowsky, M. L., Wang, L.-C., Means, T. K., & El Khoury, J. (2013) · Nature Neuroscience · doi:10.1038/nn.3554 · Cited by 1,511

Oases:robustde novoRNA-seq assembly across the dynamic range of expression levels

Schulz, M. H., Zerbino, D. R., Vingron, M., & Birney, E. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts094 · Cited by 1,470

Reduction in diversity of the colonic mucosa associated bacterial microflora in patients with active inflammatory bowel disease

Ott, S. J., Musfeldt, M., Wenderoth, D. F., Hampe, J., Brant, O., Fölsch, U. R., Timmis, K. N., & Schreiber, S. (2004) · Gut · doi:10.1136/gut.2003.025403 · Cited by 1,311

Disease-Specific Alterations in the Enteric Virome in Inflammatory Bowel Disease

Norman, J. M., Handley, S. A., Baldridge, M. T., Droit, L., Liu, C. Y., Keller, B. C., Kambal, A., Monaco, C. L., Zhao, G., Fleshner, P., et al. (2015) · Cell · doi:10.1016/j.cell.2015.01.002 · Cited by 1,285

Viruses in the faecal microbiota of monozygotic twins and their mothers

Reyes, A., Haynes, M. R., Hanson, N., Angly, F. E., Heath, A. C., Rohwer, F. L., & Gordon, J. I. (2010) · Nature · doi:10.1038/nature09199 · Cited by 1,230

Minireview: Gut microbiota: The neglected endocrine organ

Clarke, G., Stilling, R. M., Kennedy, P. J., Stanton, C., Cryan, J. F., & Dinan, T. G. (2014) · Molecular Endocrinology · doi:10.1210/me.2014-1108 · Cited by 1,192

Gut Microbiomes of Malawian Twin Pairs Discordant for Kwashiorkor

Smith, M. I., Yatsunenko, T., Manary, M. J., Trehan, I., Mkakosya, R., Cheng, J., Kau, A. L., Rich, S. S., Concannon, P., Mychaleckyj, J. C., et al. (2013) · Science · doi:10.1126/science.1229000 · Cited by 1,173

The human oral microbiome database: a web accessible resource for investigating oral microbe taxonomic and genomic information

Chen, T., Yu, W.-H., Izard, J., Baranova, O. V., Lakshmanan, A., & Dewhirst, F. E. (2010) · Database · doi:10.1093/database/baq013 · Cited by 1,162

A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria

Chakravorty, S., Helb, D., Burday, M., Connell, N. D., & Alland, D. (2007) · Journal of Microbiological Methods · doi:10.1016/j.mimet.2007.02.005 · Cited by 1,147

Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome

Abubucker, S., Segata, N., Goll, J. B., Schubert, A. M., Izard, J., Cantarel, B. L., Rodriguez-Mueller, B., Zucker, J., Thiagarajan, M., Henrissat, B., et al. (2012) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002358 · Cited by 1,076

De novo assembly and analysis of RNA-seq data

Robertson, G., Schein, J. E., Chiu, R., Corbett, R., Field, M. A., Jackman, S. D., Mungall, K. L., Lee, S. S., Okada, H. M., Qian, J. Q., et al. (2010) · Nature Methods · doi:10.1038/nmeth.1517 · Cited by 1,028

Genomic analysis of uncultured marine viral communities

Breitbart, M., Salamon, P., Andresen, B., Mahaffy, J. M., Segall, A. M., Mead, D. A., Azam, F., & Rohwer, F. L. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.202488399 · Cited by 992

SSAHA: A Fast Search Method for Large DNA Databases

Ning, Z., Cox, A. J., & Mullikin, J. C. (2001) · Genome Research · doi:10.1101/gr.194201 · Cited by 965

The Marine Viromes of Four Oceanic Regions

Angly, F. E., Felts, B., Breitbart, M., Salamon, P., Edwards, R. A., Carlson, C. A., Chan, A. M., Haynes, M. R., Kelley, S. T., Liu, H., et al. (2006) · PLoS Biology · doi:10.1371/journal.pbio.0040368 · Cited by 954

Host lifestyle affects human microbiota on daily timescales

David, L. A., Materna, A. C., Friedman, J., Campos-Baptista, M. I., Blackburn, M. C., Perrotta, A., Erdman, S. E., & Alm, E. J. (2014) · Genome biology · doi:10.1186/gb-2014-15-7-r89 · Cited by 950 · cited 2×

The human gut virome: inter-individual variation and dynamic response to diet

Minot, S., Sinha, R., Chen, J., Li, H., Keilbaugh, S. A., Wu, G. D., Lewis, J. D., & Bushman, F. D. (2011) · Genome Research · doi:10.1101/gr.122705.111 · Cited by 935

The Earth Microbiome project: successes and aspirations

Gilbert, J. A., Jansson, J. K., & Knight, R. D. (2014) · BMC Biology · doi:10.1186/s12915-014-0069-1 · Cited by 917

Decreased Bacterial Diversity Characterizes the Altered Gut Microbiota in Patients With Psoriatic Arthritis, Resembling Dysbiosis in Inflammatory Bowel Disease

Scher, J. U., Úbeda, C., Artacho, A., Attur, M. G., Isaac, S., Reddy, S. M., Marmon, S., Neimann, A. L., Brusca, S. B., Patel, T., et al. (2014) · Arthritis & Rheumatology · doi:10.1002/art.38892 · Cited by 844

A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes

Dutilh, B. E., Cassman, N. A., McNair, K., Sanchez, S. E., Silva, A. E. T., Boling, L., Barr, J. J., Speth, D. R., Seguritan, V., Aziz, R. K., et al. (2014) · Nature Communications · doi:10.1038/ncomms5498 · Cited by 834

Metagenomic Analyses of an Uncultured Viral Community from Human Feces

Breitbart, M., Hewson, I., Felts, B., Mahaffy, J. M., Nulton, J., Salamon, P., & Rohwer, F. L. (2003) · Journal of Bacteriology · doi:10.1128/jb.185.20.6220-6223.2003 · Cited by 828

Fast Identification and Removal of Sequence Contamination from Genomic and Metagenomic Datasets

Schmieder, R., & Edwards, R. A. (2011) · PLoS ONE · doi:10.1371/journal.pone.0017288 · Cited by 765

Relating the metatranscriptome and metagenome of the human gut

Franzosa, E. A., Morgan, X. C., Segata, N., Waldron, L., Reyes, J. A., Earl, A. M., Giannoukos, G., Boylan, M. R., Ciulla, D., Gevers, D., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1319284111 · Cited by 731

Experimental and analytical tools for studying the human microbiome

Kuczynski, J., Lauber, C. L., Walters, W. A., Parfrey, L. W., Clemente, J. C., Gevers, D., & Knight, R. D. (2011) · Nature Reviews Genetics · doi:10.1038/nrg3129 · Cited by 729

Recombinant human DNase I reduces the viscosity of cystic fibrosis sputum.

Shak, S., Capon, D. J., Hellmiss, R., Marsters, S. A., & Baker, C. L. (1990) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.87.23.9188 · Cited by 707

Short pyrosequencing reads suffice for accurate microbial community analysis

Liu, Z., Lozupone, C., Hamady, M., Bushman, F. D., & Knight, R. D. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm541 · Cited by 692

NCBI Viral Genomes Resource

Brister, J. R., Ako-adjei, D., Bào, Y., & Blinkova, O. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku1207 · Cited by 673

MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads

Namiki, T., Hachiya, T., Tanaka, H. L., & Sakakibara, Y. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks678 · Cited by 669

Prophage Genomics

Canchaya, C. A., Proux, C., Fournous, G., Bruttin, A., & Brüssow, H. (2003) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.67.2.238-276.2003 · Cited by 663

Viruses manipulate the marine environment

Rohwer, F. L., & Thurber, R. L. V. (2009) · Nature · doi:10.1038/nature08060 · Cited by 651

Cleaning up with genomics: applying molecular biology to bioremediation

Lovley, D. R. (2003) · Nature Reviews Microbiology · doi:10.1038/nrmicro731 · Cited by 625

Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers

Liu, Z., DeSantis, T. Z., Andersen, G. L., & Knight, R. D. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn491 · Cited by 611

Laboratory procedures to generate viral metagenomes

Thurber, R. L. V., Haynes, M. R., Breitbart, M., Wegley, L., & Rohwer, F. L. (2009) · Nature Protocols · doi:10.1038/nprot.2009.10 · Cited by 600

A historical overview of bacteriophage therapy as an alternative to antibiotics for the treatment of bacterial pathogens

Wittebole, X., Roock, S. D., & Opal, S. M. (2013) · Virulence · doi:10.4161/viru.25991 · Cited by 599

Profound alterations of intestinal microbiota following a single dose of clindamycin results in sustained susceptibility to Clostridium difficile-induced colitis

Buffie, C. G., Jarchum, I., Equinda, M., Lipuma, L., Gobourne, A., Viale, A., Ubeda, C., Xavier, J., & Pamer, E. G. (2012) · Infection and Immunity · doi:10.1128/iai.05496-11 · Cited by 596

Ray Meta: scalable de novo metagenome assembly and profiling

Boisvert, S., Raymond, F., Godzaridis, É., Laviolette, F., & Corbeil, J. (2012) · Genome biology · doi:10.1186/gb-2012-13-12-r122 · Cited by 590

Genomic approaches to studying the human microbiota

Weinstock, G. M. (2012) · Nature · doi:10.1038/nature11553 · Cited by 558

The GEM mapper: fast, accurate and versatile alignment by filtration

Marco‐Sola, S., Sammeth, M., Guigó, R., & Ribeca, P. (2012) · Nature Methods · doi:10.1038/nmeth.2221 · Cited by 545

A simple, fast, and accurate method of phylogenomic inference

Wu, M., & Eisen, J. A. (2008) · Genome biology · doi:10.1186/gb-2008-9-10-r151 · Cited by 519

Chapter 12: Human Microbiome Analysis

Morgan, X. C., & Huttenhower, C. (2012) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002808 · Cited by 496

The role of the gut microbiome in the healthy adult status

D’Argenio, V., & Salvatore, F. (2015) · Clinica Chimica Acta · doi:10.1016/j.cca.2015.01.003 · Cited by 492

Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonizationPreprint

Sharon, I., Morowitz, M. J., Thomas, B. C., Costello, E. K., Relman, D. A., & Banfield, J. F. (2012) · Genome Research · doi:10.1101/gr.142315.112 · Cited by 481

Molecular analysis of the gut microbiota of identical twins with Crohn's disease

Dicksved, J., Halfvarson, J., Rosenquist, M., Järnerot, G., Tysk, C., Apajalahti, J., Engstrand, L. G., & Jansson, J. K. (2008) · The ISME Journal · doi:10.1038/ismej.2008.37 · Cited by 459

De Novo Assembly of Chickpea Transcriptome Using Short Reads for Gene Discovery and Marker Identification

Garg, R., Patel, R. K., Tyagi, A. K., & Jain, M. (2011) · DNA Research · doi:10.1093/dnares/dsq028 · Cited by 457

Direct RNA sequencing

Ozsolak, F., Platt, A. R., Jones, D. R., Reifenberger, J. G., Sass, L. E., McInerney, P., Thompson, J. F., Bowers, J., Jarosz, M., & Milos, P. M. (2009) · Nature · doi:10.1038/nature08390 · Cited by 448

Biodegradation of Polyester Polyurethane by Endophytic Fungi

Russell, J. R., Huang, J. R., Anand, P., Kucera, K., Sandoval, A., Dantzler, K. W., Hickman, D. A., Jee, J.-W., Kimovec, F. M., Koppstein, D., et al. (2011) · Applied and Environmental Microbiology · doi:10.1128/aem.00521-11 · Cited by 434

Sequencing genomes from single cells by polymerase cloning

Zhang, K., Martiny, A. C., Reppas, N. B., Barry, K., Malek, J. A., Chisholm, S. W., & Church, G. M. (2006) · Nature Biotechnology · doi:10.1038/nbt1214 · Cited by 412

De novo transcriptome assembly with ABySS

Birol, İ., Jackman, S. D., Nielsen, C. B., Qian, J. Q., Varhol, R., Stazyk, G., Morin, R. D., Zhao, Y., Hirst, M., Schein, J. E., et al. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp367 · Cited by 403

Deep sequencing of the Camellia sinensis transcriptome revealed candidate genes for major metabolic pathways of tea-specific compounds

Shi, C.-Y., Yang, H., Wei, C., Yu, O. S., Zhang, Z., Jiang, C., Sun, J., Li, Y., Chen, Q., Xia, T., et al. (2011) · BMC Genomics · doi:10.1186/1471-2164-12-131 · Cited by 399

Metatranscriptomic Approach to Analyze the Functional Human Gut Microbiota

Gosalbes, M. J., Durbán, A., Pignatelli, M., Abellan, J. J., Jiménez‐Hernández, N., Pérez‐Cobas, A. E., Latorre, A., & Moyá, A. (2011) · PLoS ONE · doi:10.1371/journal.pone.0017447 · Cited by 395

IMG/M: a data management and analysis system for metagenomes

Markowitz, V. M., Ivanova, N., Szeto, E., Palaniappan, K., Chu, K., Dalevi, D., Chen, I.-M. A., Grechkin, Y., Dubchak, I. L., Anderson, I., et al. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm869 · Cited by 392

Metatranscriptomics of the Human Oral Microbiome during Health and Disease

Jorth, P., Turner, K. H., Gumus, P., Nizam, N., Buduneli, N., & Whiteley, M. (2014) · mBio · doi:10.1128/mbio.01012-14 · Cited by 386 · cited 1×

The impact of prophages on bacterial chromosomes

Canchaya, C. A., Fournous, G., & Brüssow, H. (2004) · Molecular Microbiology · doi:10.1111/j.1365-2958.2004.04113.x · Cited by 373

Global Phage Diversity

Rohwer, F. L. (2003) · Cell · doi:10.1016/s0092-8674(03)00276-9 · Cited by 372

Metagenomic Analysis of Fever, Thrombocytopenia and Leukopenia Syndrome (FTLS) in Henan Province, China: Discovery of a New Bunyavirus

Xu, B., Liu, L., Huang, X., Ma, H., Zhang, Y., Du, Y., Wang, P., Tang, X., Wang, H., Kang, K., et al. (2011) · PLoS Pathogens · doi:10.1371/journal.ppat.1002369 · Cited by 356

The Microbiota Mediates Pathogen Clearance from the Gut Lumen after Non-Typhoidal Salmonella Diarrhea

Endt, K., Stecher, B., Chaffron, S., Slack, E. M. C., Tchitchek, N., Benecke, A., Maele, L. V., Sirard, J., Müller, A. J., Heikenwälder, M. F., et al. (2010) · PLoS Pathogens · doi:10.1371/journal.ppat.1001097 · Cited by 352

Molecular Characterization of the Fecal Microbiota in Patients with Nonalcoholic Steatohepatitis – A Longitudinal Study

Wong, V. W., Tse, C., Lam, T. T., Wong, G. L., Chim, A. M., Chu, C. W., Yeung, D. K., Law, P. T. W., Kwan, H. S., Yu, J. Q., et al. (2013) · PLoS ONE · doi:10.1371/journal.pone.0062885 · Cited by 350

The Pacific Ocean Virome (POV): A Marine Viral Metagenomic Dataset and Associated Protein Clusters for Quantitative Viral Ecology

Hurwitz, B. L., & Sullivan, M. B. (2013) · PLoS ONE · doi:10.1371/journal.pone.0057355 · Cited by 344

Evidence of a robust resident bacteriophage population revealed through analysis of the human salivary virome

Pride, D. T., Salzman, J., Haynes, M., Rohwer, F., Davis-Long, C., White, R. A., Loomer, P., Armitage, G. C., & Relman, D. A. (2012) · The ISME Journal · doi:10.1038/ismej.2011.169 · Cited by 335

Metagenomics: Read Length Matters

Wommack, K. E., Bhavsar, J., & Ravel, J. (2008) · Applied and Environmental Microbiology · doi:10.1128/aem.02181-07 · Cited by 331

Meta-IDBA: a de Novo assembler for metagenomic data

Peng, Y., Leung, H. C. M., Yiu, S., & Chin, F. Y. L. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr216 · Cited by 330

Mechanism of chimera formation during the Multiple Displacement Amplification reaction

Lasken, R. S., & Stockwell, T. B. (2007) · BMC Biotechnology · doi:10.1186/1472-6750-7-19 · Cited by 328

ACLAME: A CLAssification of Mobile genetic Elements, update 2010

Leplae, R., Lima‐Mendez, G., & Toussaint, A. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp938 · Cited by 326

Antibiotic‐induced SOS response promotes horizontal dissemination of pathogenicity island‐encoded virulence factors in staphylococci

Úbeda, C., Maiques, E., Knecht, E., Lasa, Í., Novick, R. P., & Penadés, J. R. (2005) · Molecular Microbiology · doi:10.1111/j.1365-2958.2005.04584.x · Cited by 324

Coevolution with viruses drives the evolution of bacterial mutation rates

Pál, C., Macia, M. D., Oliver, A., Schachar, I. H., & Buckling, A. G. J. (2007) · Nature · doi:10.1038/nature06350 · Cited by 324

Phage-Mediated Intergeneric Transfer of Toxin Genes

Chen, J. Y.-S., & Novick, R. P. (2009) · Science · doi:10.1126/science.1164783 · Cited by 314

The oral microbiome diversity and its relation to human diseases

He, J., Li, Y., Cao, Y., Xue, J., & Zhou, X. (2015) · Folia Microbiologica · doi:10.1007/s12223-014-0342-2 · Cited by 314

Diversity and population structure of a near–shore marine–sediment viral community

Breitbart, M., Felts, B., Kelley, S. T., Mahaffy, J. M., Nulton, J., Salamon, P., & Rohwer, F. L. (2004) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2003.2628 · Cited by 305

Effect of Primers Hybridizing to Different Evolutionarily Conserved Regions of the Small-Subunit rRNA Gene in PCR-Based Microbial Community Analyses and Genetic Profiling

Schmalenberger, A., Schwieger, F., & Tebbe, C. C. (2001) · Applied and Environmental Microbiology · doi:10.1128/aem.67.8.3557-3563.2001 · Cited by 289

Pathogenic Simian Immunodeficiency Virus Infection Is Associated with Expansion of the Enteric Virome

Handley, S. A., Thackray, L. B., Zhao, G., Presti, R. M., Miller, A. D., Droit, L., Abbink, P., Maxfield, L. F., Kambal, A., Duan, E., et al. (2012) · Cell · doi:10.1016/j.cell.2012.09.024 · Cited by 280

Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes

Giannoukos, G., Ciulla, D., Huang, K. H., Haas, B. J., Izard, J., Levin, J. Z., Livny, J., Earl, A. M., Gevers, D., Ward, D. V., et al. (2012) · Genome biology · doi:10.1186/gb-2012-13-3-r23 · Cited by 269

Movers and shakers

Mills, S., Shanahan, F., Stanton, C., Hill, C., Coffey, A., & Ross, R. P. (2013) · Gut Microbes · doi:10.4161/gmic.22371 · Cited by 263

The Gut Microbiome: A New Frontier in Autism Research

Mulle, J. G., Sharp, W. G., & Cubells, J. F. (2013) · Current Psychiatry Reports · doi:10.1007/s11920-012-0337-0 · Cited by 262

The role of gut microbiota in the development of type 1, type 2 diabetes mellitus and obesity

Tai, N., Wong, F. S., & Li, W. (2015) · Reviews in Endocrine and Metabolic Disorders · doi:10.1007/s11154-015-9309-0 · Cited by 260

A composite bacteriophage alters colonization by an intestinal commensal bacterium

Duerkop, B. A., Clements, C. V., Rollins, D., Rodrigues, J. L. M., & Hooper, L. V. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1206136109 · Cited by 259

Acetate-producing bifidobacteria protect the host from enteropathogenic infection via carbohydrate transporters

Fukuda, S., Toh, H., Taylor, T. D., Ohno, H., & Hattori, M. (2012) · Gut Microbes · doi:10.4161/gmic.21214 · Cited by 257

Alzheimer's disease and the microbiome

Bhattacharjee, S., & Lukiw, W. J. (2013) · Frontiers in Cellular Neuroscience · doi:10.3389/fncel.2013.00153 · Cited by 253

Multiple displacement amplification compromises quantitative analysis of metagenomes

Yilmaz, S., Allgaier, M., & Hugenholtz, P. (2010) · Nature Methods · doi:10.1038/nmeth1210-943 · Cited by 252

Scaling metagenome sequence assembly with probabilistic de Bruijn graphs

Jason, P., Hintze, A., Canino-Koning, R., Howe, A., Tiedje, J. M., & Brown, C. T. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1121464109 · Cited by 250

Environmental Whole-Genome Amplification To Access Microbial Populations in Contaminated Sediments

Abulencia, C. B., Wyborski, D. L., Garcia, J. A., Podar, M., Chen, W., Chang, S. H., Chang, H. W., Watson, D. B., Brodie, E., Hazen, T. C., et al. (2006) · Applied and Environmental Microbiology · doi:10.1128/aem.72.5.3291-3301.2006 · Cited by 240

Detection of a Novel Astrovirus in Brain Tissue of Mink Suffering from Shaking Mink Syndrome by Use of Viral Metagenomics

Blomström, A., Widén, F., Hammer, A., Belák, S., & Berg, M. (2010) · Journal of Clinical Microbiology · doi:10.1128/jcm.01040-10 · Cited by 238

MetAMOS: a modular and open source metagenomic assembly and analysis pipeline

Treangen, T. J., Koren, S., Sommer, D. D., Liu, B., Astrovskaya, I., Ondov, B., Darling, A. E., Phillippy, A. M., & Pop, M. (2013) · Genome biology · doi:10.1186/gb-2013-14-1-r2 · Cited by 232

Rapid 16S rRNA Next-Generation Sequencing of Polymicrobial Clinical Samples for Diagnosis of Complex Bacterial Infections

Salipante, S. J., SenGupta, D. J., Rosenthal, C. A., Costa, G. L., Spangler, J., Sims, E. H., Jacobs, M. A., Miller, S. I., Hoogestraat, D. R., Cookson, B. T., et al. (2013) · PLoS ONE · doi:10.1371/journal.pone.0065226 · Cited by 226

CRISPR targeting reveals a reservoir of common phages associated with the human gut microbiomePreprint

Stern, A., Mick, E., Tirosh, I., Sagy, O., & Sorek, R. (2012) · Genome Research · doi:10.1101/gr.138297.112 · Cited by 218

The origin of DNA associated with mucus glycoproteins in cystic fibrosis sputum

Lethem, M. I., James, S., Marriott, C., & Burke, J. F. (1990) · European Respiratory Journal · doi:10.1183/09031936.93.03010019 · Cited by 215

De novo assembly of highly diverse viral populations

Yang, X. Q., Charlebois, P., Gnerre, S., Coole, M. G., Lennon, N. J., Levin, J. Z., Qu, J., Ryan, E. M., Zody, M. C., & Henn, M. R. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-475 · Cited by 210

Next Generation Sequence Assembly with AMOS

Treangen, T. J., Sommer, D. D., Angly, F. E., Koren, S., & Pop, M. (2011) · Current Protocols in Bioinformatics · doi:10.1002/0471250953.bi1108s33 · Cited by 205

PHACCS, an online tool for estimating the structure and diversity of uncultured viral communities using metagenomic information

Angly, F. E., Rodriguez-Brito, B., Bangor, D., McNairnie, P., Breitbart, M., Salamon, P., Felts, B., Nulton, J., Mahaffy, J. M., & Rohwer, F. L. (2005) · BMC Bioinformatics · doi:10.1186/1471-2105-6-41 · Cited by 203

Assembly of Viral Metagenomes from Yellowstone Hot Springs

Schoenfeld, T. W., Patterson, M., Richardson, P. M., Wommack, K. E., Young, M., & Mead, D. A. (2008) · Applied and Environmental Microbiology · doi:10.1128/aem.02598-07 · Cited by 203

Hypervariable loci in the human gut virome

Minot, S. S., Grunberg, S., Wu, G. D., Lewis, J. D., & Bushman, F. D. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1119061109 · Cited by 195

Microbiota diversity and gene expression dynamics in human oral biofilms

Benítez‐Páez, A., Belda‐Ferre, P., Simón‐Soro, Á., & Mira, Á. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-311 · Cited by 193

Evaluation of methods to concentrate and purify ocean virus communities through comparative, replicated metagenomics

Hurwitz, B. L., Deng, L., Poulos, B. T., & Sullivan, M. B. (2012) · Environmental Microbiology · doi:10.1111/j.1462-2920.2012.02836.x · Cited by 191

Species-level classification of the vaginal microbiome

Fettweis, J. M., Serrano, M. G., Sheth, N. U., Mayer, C. M., Glascock, A. L., Brooks, J. P., Jefferson, K. K., & Buck, G. A. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-s8-s17 · Cited by 187

Bacteriophages: an underestimated role in human and animal health?

Paepe, M. D., Leclerc, M., Tinsley, C. R., & Petit, M. (2014) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2014.00039 · Cited by 186

The involvement of gut microbiota in inflammatory bowel disease pathogenesis: Potential for therapy

Cammarota, G., Ianiro, G., Cianci, R., Bibbò, S., Gasbarrini, A., & Currò, D. (2015) · Pharmacology & Therapeutics · doi:10.1016/j.pharmthera.2014.12.006 · Cited by 184

Oral microbiome profiles: 16S rRNA pyrosequencing and microarray assay comparison

Ahn, J., Yang, L., Paster, B. J., Ganly, I., Morris, L., Pei, Z., & Hayes, R. B. (2011) · PLoS ONE · doi:10.1371/journal.pone.0022788 · Cited by 183

Cell-free cloning using φ29 DNA polymerase

Hutchison, C. A., Smith, H. O., Pfannkoch, C. M., & Venter, J. C. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0508809102 · Cited by 181

Amplification of Uncultured Single-Stranded DNA Viruses from Rice Paddy Soil

Kim, K., Chang, H.-W., Nam, Y., Roh, S. W., Kim, M., Sung, Y., Jeon, C. O., Oh, H., & Bae, J. (2008) · Applied and Environmental Microbiology · doi:10.1128/aem.01275-08 · Cited by 179

Exploiting gut bacteriophages for human health

Dalmasso, M., Hill, C., & Ross, R. P. (2014) · Trends in Microbiology · doi:10.1016/j.tim.2014.02.010 · Cited by 177

Molecular Bases and Role of Viruses in the Human Microbiome

Abeles, S. R., & Pride, D. T. (2014) · Journal of Molecular Biology · doi:10.1016/j.jmb.2014.07.002 · Cited by 171

Human oral viruses are personal, persistent and gender-consistent

Abeles, S. R., Robles‐Sikisaka, R., Ly, M., Lum, A. G., Salzman, J., Boehm, T. K., & Pride, D. T. (2014) · The ISME Journal · doi:10.1038/ismej.2014.31 · Cited by 170

Virus Identification in Unknown Tropical Febrile Illness Cases Using Deep Sequencing

Yozwiak, N. L., Skewes-Cox, P., Stenglein, M. D., Balmaseda, Á., Harris, E., & DeRisi, J. L. (2012) · PLoS neglected tropical diseases · doi:10.1371/journal.pntd.0001485 · Cited by 169

Unbiased Parallel Detection of Viral Pathogens in Clinical Samples by Use of a Metagenomic Approach

Yang, J., Yang, F., Ren, L., Xiong, Z., Wú, Z., Dong, J., Sun, L., Zhang, T., Hu, Y., Du, J., et al. (2011) · Journal of Clinical Microbiology · doi:10.1128/jcm.00273-11 · Cited by 162

The gut microbiota manages host metabolism

Cani, P. D. (2013) · Nature Reviews Endocrinology · doi:10.1038/nrendo.2013.240 · Cited by 161

Identification of mixed bacterial DNA contamination in broad-range PCR amplification of 16S rDNA V1 and V3 variable regions by pyrosequencing of cloned amplicons

Grahn, N., Olofsson, M., Ellnebo‐Svedlund, K., Monstein, H.-J. ⁄. R., & Jonasson, J. (2003) · FEMS Microbiology Letters · doi:10.1016/s0378-1097(02)01190-4 · Cited by 143

Study of the Viral and Microbial Communities Associated With Crohn's Disease: A Metagenomic Approach

Pérez‐Brocal, V., García-López, R., Vázquez-Castellanos, J. F., Nos, P., Beltrán, B., Latorre, A., & Moyá, A. (2013) · Clinical and Translational Gastroenterology · doi:10.1038/ctg.2013.9 · Cited by 132

METAREP: JCVI metagenomics reports—an open source tool for high-performance comparative metagenomics

Goll, J. B., Rusch, D. B., Tanenbaum, D. M., Thiagarajan, M., Li, K., Methé, B. A., & Yooseph, S. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq455 · Cited by 131

Experimental coevolution with bacteria and phage

Brockhurst, M. A., Morgan, A. D., Fenton, A., & Buckling, A. G. J. (2007) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2007.01.005 · Cited by 128

Metagenomic Exploration of Viruses throughout the Indian Ocean

Williamson, S. J., Allen, L. Z., Lorenzi, H., Fadrosh, D. W., Brami, D., Thiagarajan, M., McCrow, J. P., Tovchigrechko, A., Yooseph, S., & Venter, J. C. (2012) · PLoS ONE · doi:10.1371/journal.pone.0042047 · Cited by 125

The Gut Microbiome in Health and Disease

Owyang, C., & Wu, G. D. (2014) · Gastroenterology · doi:10.1053/j.gastro.2014.03.032 · Cited by 118

De novo sequence assembly and characterization of the floral transcriptome in cross- and self-fertilizing plants

Ness, R. W., Siol, M., & Barrett, S. C. H. (2011) · BMC Genomics · doi:10.1186/1471-2164-12-298 · Cited by 108

The role played by viruses in the evolution of their hosts: a view based on informational protein phylogenies

Filée, J., Forterre, P., & Laurent, J. (2003) · Research in Microbiology · doi:10.1016/s0923-2508(03)00066-4 · Cited by 106

Virulent Bacteriophages Can Target O104:H4 Enteroaggregative Escherichia coli in the Mouse Intestine

Maura, D., Galtier, M., Bouguénec, C. L., & Debarbieux, L. (2012) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.00602-12 · Cited by 104

Viral metagenome analysis to guide human pathogen monitoring in environmental samples

Bibby, K. J., Viau, E. J., & Peccia, J. (2011) · Letters in Applied Microbiology · doi:10.1111/j.1472-765x.2011.03014.x · Cited by 102

Antibiotic Treatment of Pregnant Non‐Obese Diabetic Mice Leads to Altered Gut Microbiota and Intestinal Immunological Changes in the Offspring

Tormo-Badia, N., Håkansson, Å., Vasudevan, K., Molin, G., Ahrné, S., & Cilio, C. (2014) · Scandinavian Journal of Immunology · doi:10.1111/sji.12205 · Cited by 102

Novel transcriptome assembly and improved annotation of the whiteleg shrimp (Litopenaeus vannamei), a dominant crustacean in global seafood mariculture

Ghaffari, N., Sánchez‐Flores, A., Doan, R. N., García‐Orozco, K. D., Chen, P. L., Ochoa‐Leyva, A., López-Zavala, A. A., Carrasco, J. S., Hong, C., Brieba, L. G., et al. (2014) · Scientific Reports · doi:10.1038/srep07081 · Cited by 99

Association between living environment and human oral viral ecology

Robles‐Sikisaka, R., Ly, M., Boehm, T. K., Naidu, M., Salzman, J., & Pride, D. T. (2013) · The ISME Journal · doi:10.1038/ismej.2013.63 · Cited by 96

Childhood Obesity: A Role for Gut Microbiota?

Sánchez, M., Panahi, S., & Tremblay, A. (2014) · International Journal of Environmental Research and Public Health · doi:10.3390/ijerph120100162 · Cited by 90

Comparison of different assembly and annotation tools on analysis of simulated viral metagenomic communities in the gut

Vázquez-Castellanos, J. F., García-López, R., Pérez‐Brocal, V., Pignatelli, M., & Moyá, A. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-37 · Cited by 88

Metatranscriptomic array analysis of ‘ Candidatus Accumulibacter phosphatis’‐enriched enhanced biological phosphorus removal sludge

He, S., Kunin, V., Haynes, M. R., Martín, H. G., Ivanova, N., Rohwer, F. L., Hugenholtz, P., & McMahon, K. D. (2010) · Environmental Microbiology · doi:10.1111/j.1462-2920.2010.02163.x · Cited by 86

De-novo assembly of mango fruit peel transcriptome reveals mechanisms of mango response to hot water treatment

Luria, N., Sela, N., Yaari, M., Feygenberg, O., Kobiler, I., Lers, A., & Prusky, D. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-957 · Cited by 84

Windshield splatter analysis with the Galaxy metagenomic pipelinePreprint

Pond, S. K., Wadhawan, S., Chiaromonte, F., Ananda, G., Chung, W.-Y., Taylor, J., Nekrutenko, A., & The Galaxy Team (2009) · Genome Research · doi:10.1101/gr.094508.109 · Cited by 74

Harnessing the power of the human microbiome

Blaser, M. J. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1002112107 · Cited by 68

Isolation of bacteriophages from the oral cavity

Hitch, G., Pratten, J. R., & Taylor, P. W. (2004) · Letters in Applied Microbiology · doi:10.1111/j.1472-765x.2004.01565.x · Cited by 65

Single‐molecule direct RNA sequencing without cDNA synthesis

Ozsolak, F., & Milos, P. M. (2011) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.84 · Cited by 63

Reference-independent comparative metagenomics using cross-assembly: crAss

Dutilh, B. E., Schmieder, R., Nulton, J., Felts, B., Salamon, P., Edwards, R. A., & Mokili, J. L. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts613 · Cited by 60

Comparisons of clustered regularly interspaced short palindromic repeats and viromes in human saliva reveal bacterial adaptations to salivary viruses

Pride, D. T., Salzman, J., & Relman, D. A. (2012) · Environmental Microbiology · doi:10.1111/j.1462-2920.2012.02775.x · Cited by 60

Conceptualizing Human Microbiota: From Multicelled Organ to Ecological Community

Foxman, B., Goldberg, D. E., Murdock, C. C., Xi, C., & Gilsdorf, J. R. (2008) · Interdisciplinary Perspectives on Infectious Diseases · doi:10.1155/2008/613979 · Cited by 47

Quantitative comparison of EST libraries requires compensation for systematic biases in cDNA generation

Liu, D., & Graber, J. H. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-77 · Cited by 46

The impact of bacteriophages on probiotic bacteria and gut microbiota diversity

Ventura, M., Sozzi, T., Turroni, F., Matteuzzi, D., & van Sinderen, D. (2010) · Genes & Nutrition · doi:10.1007/s12263-010-0188-4 · Cited by 42

Computational identification of functional RNA homologs in metagenomic data

Nawrocki, E. P., & Eddy, S. R. (2013) · RNA Biology · doi:10.4161/rna.25038 · Cited by 41

Production of Shotgun Libraries Using Random Amplification

Rohwer, F. L., Seguritan, V., Choi, D. H., Segall, A. M., & Azam, F. (2001) · BioTechniques · doi:10.2144/01311rr02 · Cited by 38

Xenobiotics and the Human Gut Microbiome: Metatranscriptomics Reveal the Active Players

Ursell, L. K., & Knight, R. D. (2013) · Cell Metabolism · doi:10.1016/j.cmet.2013.02.013 · Cited by 37

Pyrosequencing assessment of prokaryotic and eukaryotic diversity in biofilm communities from a F rench river

Bricheux, G., Morin, L., Moal, G. L., Coffe, G., Balestrino, D., Charbonnel, N., Bohatier, J., & Forestier, C. (2013) · MicrobiologyOpen · doi:10.1002/mbo3.80 · Cited by 37

AN ORFOME ASSEMBLY APPROACH TO METAGENOMICS SEQUENCES ANALYSIS

Ye, Y., & Tang, H. (2009) · Journal of Bioinformatics and Computational Biology · doi:10.1142/s0219720009004151 · Cited by 36

Host-Associated and Free-Living Phage Communities Differ Profoundly in Phylogenetic Composition

Caporaso, J. G., Knight, R. D., & Kelley, S. T. (2011) · PLoS ONE · doi:10.1371/journal.pone.0016900 · Cited by 30

Estimation of viral richness from shotgun metagenomes using a frequency count approach

Allen, H. K., Bunge, J., Foster, J. A., Bayles, D. O., & Stanton, T. B. (2013) · Microbiome · doi:10.1186/2049-2618-1-5 · Cited by 26

Detection of novel viruses in porcine fecal samples from China

Yu, J., Li, J., Ao, Y., & Duan, Z.-J. (2013) · Virology Journal · doi:10.1186/1743-422x-10-39 · Cited by 17

Genomic Library Screening for Viruses from the Human Dental Plaque Revealed Pathogen-Specific Lytic Phage Sequences

Aljarbou, A. N. (2011) · Current Microbiology · doi:10.1007/s00284-011-0025-z · Cited by 13

Pulsed field gel electrophoresis of bacterial DNA isolated directly from patients' sputa

Breitenstein, S., Tümmler, B., & Römling, U. (1995) · Nucleic Acids Research · doi:10.1093/nar/23.4.722 · Cited by 9

Best practices for analysing microbiomes

Knight, R., Vrbanac, A., Taylor, B. C., Aksenov, A., Callewaert, C., Debelius, J., Gonzalez, A., Kosciolek, T., McCall, L.-I., McDonald, D., et al. (2018) · Nature Reviews Microbiology · doi:10.1038/s41579-018-0029-9 · Cited by 2,030

The oral microbiome – an update for oral healthcare professionals

Kilian, M., Chapple, I. L. C., Hannig, M., Marsh, P. D., Meuric, V., Pedersen, A. M. L., Tonetti, M. S., Wade, W. G., & Zaura, E. (2016) · British Dental Journal · doi:10.1038/sj.bdj.2016.865 · Cited by 1,269

The oral microbiome: Role of key organisms and complex networks in oral health and disease

Sedghi, L., DiMassa, V., Harrington, A., Lynch, S. V., & Kapila, Y. L. (2021) · Periodontology 2000 · doi:10.1111/prd.12393 · Cited by 755

Bacterial Communities: Interactions to Scale

Stubbendieck, R. M., Vargas-Bautista, C., & Straight, P. D. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.01234 · Cited by 582

Optimizing methods and dodging pitfalls in microbiome research

Kim, D. J., Hofstaedter, C. E., Zhao, C., Mattei, L. M., Tanes, C., Clarke, E., Lauder, A. P., Sherrill-Mix, S. A., Chehoud, C., Kelsen, J. R., et al. (2017) · Microbiome · doi:10.1186/s40168-017-0267-5 · Cited by 557

Human Microbiome Acquisition and Bioinformatic Challenges in Metagenomic Studies

D’Argenio, V. (2018) · International Journal of Molecular Sciences · doi:10.3390/ijms19020383 · Cited by 56

Understanding human health through metatranscriptomics

Ojala, T., Kankuri, E. M., & Kankainen, M. (2023) · Trends in Molecular Medicine · doi:10.1016/j.molmed.2023.02.002 · Cited by 113

Studying the Human Gut Microbiota in the Trans-Omics Era - Focus on Metagenomics and Metabonomics

Tuohy, K. M., Gougoulias, C., Shen, Q., Walton, G., Fava, F., & Ramnani, P. (2009) · Current Pharmaceutical Design · doi:10.2174/138161209788168182 · Cited by 77

Metagenomics approaches for studying the human microbiome

Eskeziyaw, B. M., & Mengistu, D. Y. (2024) · All Life · doi:10.1080/26895293.2024.2350166 · Cited by 9

Current concepts, advances, and challenges in deciphering the human microbiota with metatranscriptomics

Ojala, T., Häkkinen, A.-E., Kankuri, E. M., & Kankainen, M. (2023) · Trends in Genetics · doi:10.1016/j.tig.2023.05.004 · Cited by 81