Viral metagenomics

Molecular cloning: A laboratory manual

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Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

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Genome sequencing in microfabricated high-density picolitre reactors

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Isolation of a cDNA cLone Derived from a Blood-Borne Non-A, Non-B Viral Hepatitis Genome

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Identification of Herpesvirus-Like DNA Sequences in AIDS-Sssociated Kaposi's Sarcoma

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CAP3: A DNA Sequence Assembly Program

Huang, X., & Madan, A. (1999) · Genome Research · doi:10.1101/gr.9.9.868 · Cited by 5,261

Fingerprinting genomes using PCR with arbitrary primers

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Emerging Infectious Diseases of Wildlife-- Threats to Biodiversity and Human Health

Daszak, P., Cunningham, A. A., & Hyatt, A. D. (2000) · Science · doi:10.1126/science.287.5452.443 · Cited by 4,885

Marine viruses and their biogeochemical and ecological effects

Fuhrman, J. A. (1999) · Nature · doi:10.1038/21119 · Cited by 2,249

A newly discovered human pneumovirus isolated from young children with respiratory tract disease

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Identification of a new human coronavirus

van der Hoek, L., Pyrc, K., Jebbink, M. F., Vermeulen-Oost, W., Berkhout, R. J. M., Wolthers, K. C., Wertheim-van Dillen, P. M. E., Kaandorp, J., Spaargaren, J., & Berkhout, B. (2004) · Nature Medicine · doi:10.1038/nm1024 · Cited by 1,886

Fruit bats as reservoirs of Ebola virus

Leroy, E. M., Kumulungui, B., Pourrut, X., Rouquet, P., Hassanin, A., Yaba, P., Délicat, A., Paweska, J. T., Gonzalez, J.-P., & Swanepoel, R. (2005) · Nature · doi:10.1038/438575a · Cited by 1,606

Origin of the West Nile Virus Responsible for an Outbreak of Encephalitis in the Northeastern United States

Lanciotti, R. S., Roehrig, J. T., Deubel, V., Smith, J., Parker, M., Steele, K., Crise, B., Volpe, K. E., Crabtree, M. B., Scherret, J. H., et al. (1999) · Science · doi:10.1126/science.286.5448.2333 · Cited by 1,593

Cloning of a human parvovirus by molecular screening of respiratory tract samples

Allander, T., Tammi, M. T., Eriksson, M., Bjerkner, A., Tiveljung-Lindell, A., & Andersson, B. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0504666102 · Cited by 1,580

Severe acute respiratory syndrome coronavirus-like virus in Chinese horseshoe bats

Lau, S. K. P., Woo, P. C. Y., Li, K. S. M., Huang, Y., Tsoi, H.-W., Wong, B. H. L., Wong, S. S. Y., Leung, S.-Y., Chan, K.-H., & Yuen, K.-Y. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0506735102 · Cited by 1,544

Comprehensive human genome amplification using multiple displacement amplification

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Accurate Multiplex Polony Sequencing of an Evolved Bacterial Genome

Shendure, J., Porreca, G. J., Reppas, N. B., Lin, X., McCutcheon, J. P., Rosenbaum, A. M., Wang, M. D., Zhang, K., Mitra, R. D., & Church, G. M. (2005) · Science · doi:10.1126/science.1117389 · Cited by 1,402

Molecular Cloning and Disease Association of Hepatitis G Virus: A Transfusion-Transmissible Agent

Linnen, J., Wages, J., Zhang-Keck, Z.-Y., Fry, K. E., Krawczynski, K. Z., Alter, H., Koonin, E., Gallagher, M., Alter, M., Hadziyannis, S., et al. (1996) · Science · doi:10.1126/science.271.5248.505 · Cited by 1,359

Cloning the Differences Between Two Complex Genomes

Lisitsyn, N., Lisitsyn, N., & Wigler, M. (1993) · Science · doi:10.1126/science.8438152 · Cited by 1,285

A Novel DNA Virus (TTV) Associated with Elevated Transaminase Levels in Posttransfusion Hepatitis of Unknown Etiology

Nishizawa, T., Okamoto, H., Konishi, K., Yoshizawa, H., Miyakawa, Y., & Mayumi, M. (1997) · Biochemical and Biophysical Research Communications · doi:10.1006/bbrc.1997.7765 · Cited by 1,234

Genetic Identification of a Hantavirus Associated with an Outbreak of Acute Respiratory Illness

Nichol, S. T., Spiropoulou, C. F., Morzunov, S., Rollin, P. E., Ksiazek, T. G., Feldmann, H., Sanchez, A., Childs, J., Zaki, S., & Peters, C. J. (1993) · Science · doi:10.1126/science.8235615 · Cited by 1,129

Isolation of novel virus-like sequences associated with human hepatitis

Simons, J. N., Leary, T. P., Dawson, G. J., Pilot-Matias, T. J., Muerhoff, A. S., Schlauder, G. G., Desai, S. M., & Mushahwar, I. K. (1995) · Nature Medicine · doi:10.1038/nm0695-564 · Cited by 1,129

Metagenomics: Genomic Analysis of Microbial Communities

Riesenfeld, C. S., Schloss, P. D., & Handelsman, J. (2004) · Annual Review of Genetics · doi:10.1146/annurev.genet.38.072902.091216 · Cited by 1,129

Evolution and Taxonomy of Positive-Strand RNA Viruses: Implications of Comparative Analysis of Amino Acid Sequences

Koonin, E. V., Dolja, V. V., & Morris, T. J. (1993) · Critical Reviews in Biochemistry and Molecular Biology · doi:10.3109/10409239309078440 · Cited by 1,094

Rapid Amplification of Plasmid and Phage DNA Using Phi29 DNA Polymerase and Multiply-Primed Rolling Circle Amplification

Dean, F. B., Nelson, J. R., Giesler, T. L., & Lasken, R. S. (2001) · Genome Research · doi:10.1101/gr.180501 · Cited by 1,067

Genomic analysis of uncultured marine viral communities

Breitbart, M., Salamon, P., Andresen, B., Mahaffy, J. M., Segall, A. M., Mead, D., Azam, F., & Rohwer, F. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.202488399 · Cited by 994

Chimpanzee Reservoirs of Pandemic and Nonpandemic HIV-1

Keele, B. F., Van Heuverswyn, F., Li, Y., Bailes, E., Takehisa, J., Santiago, M. L., Bibollet-Ruche, F., Chen, Y., Wain, L. V., Liegeois, F., et al. (2006) · Science · doi:10.1126/science.1126531 · Cited by 957

A Giant Virus in Amoebae

Scola, B. L., Audic, S., Robert, C., Jungang, L., de Lamballerie, X., Drancourt, M., Birtles, R., Claverie, J.-M., & Raoult, D. (2003) · Science · doi:10.1126/science.1081867 · Cited by 893

Isolation of a cDNA from the Virus Responsible for Enterically Transmitted Non-A, Non-B Hepatitis

Reyes, G. R., Purdy, M. A., Kim, J., Luk, K.-C., Young, L. M., Fry, K. E., & Bradley, D. W. (1990) · Science · doi:10.1126/science.2107574 · Cited by 867

Here a virus, there a virus, everywhere the same virus?

Breitbart, M., & Rohwer, F. (2005) · Trends in Microbiology · doi:10.1016/j.tim.2005.04.003 · Cited by 854

Transmission of H7N7 avian influenza A virus to human beings during a large outbreak in commercial poultry farms in the Netherlands

Koopmans, M., Wilbrink, B., Conyn, M., Natrop, G., van der Nat, H., Vennema, H., Meijer, A., van Steenbergen, J., Fouchier, R., Osterhaus, A., et al. (2004) · The Lancet · doi:10.1016/s0140-6736(04)15589-x · Cited by 837

Detection and analysis of diverse herpesviral species by consensus primer PCR

VanDevanter, D. R., Warrener, P., Bennett, L., Schultz, E. R., Coulter, S., Garber, R. L., & Rose, T. M. (1996) · Journal of Clinical Microbiology · doi:10.1128/jcm.34.7.1666-1671.1996 · Cited by 831

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. (2003) · Journal of Bacteriology · doi:10.1128/jb.185.20.6220-6223.2003 · Cited by 830

Viral metagenomics

Edwards, R. A., & Rohwer, F. (2005) · Nature Reviews Microbiology · doi:10.1038/nrmicro1163 · Cited by 820

Microarray-based detection and genotyping of viral pathogens

Wang, D., Coscoy, L., Zylberberg, M., Avila, P. C., Boushey, H. A., Ganem, D., & DeRisi, J. L. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.242579699 · Cited by 810

RNA Viral Community in Human Feces: Prevalence of Plant Pathogenic Viruses

Zhang, T., Breitbart, M., Lee, W. H., Run, J.-Q., Wei, C. L., Soh, S. W. L., Hibberd, M. L., Liu, E. T., Rohwer, F., & Ruan, Y. (2005) · PLoS Biology · doi:10.1371/journal.pbio.0040003 · Cited by 805

Multiple Ebola Virus Transmission Events and Rapid Decline of Central African Wildlife

Leroy, E. M., Rouquet, P., Formenty, P., Souquière, S., Kilbourne, A., Froment, J.-M., Bermejo, M., Smit, S., Karesh, W., Swanepoel, R., et al. (2004) · Science · doi:10.1126/science.1092528 · Cited by 794

The ancient Virus World and evolution of cells.

Koonin, E. V., Senkevich, T. G., & Dolja, V. V. (2006) · Biology Direct · doi:10.1186/1745-6150-1-29 · Cited by 745

Dinucleotide relative abundance extremes: a genomic signature

Kariin, S., & Burge, C. (1995) · Trends in Genetics · doi:10.1016/s0168-9525(00)89076-9 · Cited by 701

Consensus-degenerate hybrid oligonucleotide primers for amplification of distantly related sequences

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Metagenomics to Paleogenomics: Large-Scale Sequencing of Mammoth DNA

Poinar, H. N., Schwarz, C., Qi, J., Shapiro, B., MacPhee, R. D. E., Buigues, B., Tikhonov, A., Huson, D. H., Tomsho, L. P., Auch, A., et al. (2006) · Science · doi:10.1126/science.1123360 · Cited by 616

A previously undescribed coronavirus associated with respiratory disease in humans

Fouchier, R. A. M., Hartwig, N. G., Bestebroer, T. M., Niemeyer, B., de Jong, J. C., Simon, J. H., & Osterhaus, A. D. M. E. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0400762101 · Cited by 598

Identification of two flavivirus-like genomes in the GB hepatitis agent.

Simons, J. N., Pilot-Matias, T. J., Leary, T. P., Dawson, G. J., Desai, S. M., Schlauder, G. G., Muerhoff, A. S., Erker, J. C., Buijk, S. L., & Chalmers, M. L. (1995) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.92.8.3401 · Cited by 551

Using pyrosequencing to shed light on deep mine microbial ecology

Edwards, R. A., Rodriguez-Brito, B., Wegley, L., Haynes, M., Breitbart, M., Peterson, D. M., Saar, M. O., Alexander, S., Alexander, E. C., & Rohwer, F. (2006) · BMC Genomics · doi:10.1186/1471-2164-7-57 · Cited by 484

Biased biological functions of horizontally transferred genes in prokaryotic genomes

Nakamura, Y., Itoh, T., Matsuda, H., & Gojobori, T. (2004) · Nature Genetics · doi:10.1038/ng1381 · Cited by 480

Nipah Virus Infection in Bats (Order Chiroptera) in Peninsular Malaysia

Yob, J. M., Field, H., Rashdi, A. M., Morrissy, C., van der Heide, B., Rota, P., bin Adzhar, A., White, J., Daniels, P., Jamaluddin, A., et al. (2001) · Emerging Infectious Diseases · doi:10.3201/eid0703.017312 · Cited by 475

The Human Polyomavirus, JCV, Uses Serotonin Receptors to Infect Cells

Elphick, G. F., Querbes, W., Jordan, J. A., Gee, G. V., Eash, S., Manley, K., Dugan, A., Stanifer, M., Bhatnagar, A., Kroeze, W. K., et al. (2004) · Science · doi:10.1126/science.1103492 · Cited by 475

Viral Discovery and Sequence Recovery Using DNA Microarrays

Wang, D., Urisman, A., Liu, Y.-T., Springer, M., Ksiazek, T. G., Erdman, D. D., Mardis, E. R., Hickenbotham, M., Magrini, V., Eldred, J., et al. (2003) · PLoS Biology · doi:10.1371/journal.pbio.0000002 · Cited by 465

Emergence of unique primate T-lymphotropic viruses among central African bushmeat hunters

Wolfe, N. D., Heneine, W., Carr, J. K., Garcia, A. D., Shanmugam, V., Tamoufe, U., Torimiro, J. N., Prosser, A. T., LeBreton, M., Mpoudi-Ngole, E., et al. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0501734102 · Cited by 453

Naturally acquired simian retrovirus infections in central African hunters

Wolfe, N. D., Switzer, W. M., Carr, J. K., Bhullar, V. B., Shanmugam, V., Tamoufe, U., Prosser, A. T., Torimiro, J. N., Wright, A., Mpoudi-Ngole, E., et al. (2004) · The Lancet · doi:10.1016/s0140-6736(04)15787-5 · Cited by 439

In Search of Encephalitis Etiologies: Diagnostic Challenges in the California Encephalitis Project, 1998–2000

Glaser, C. A., Gilliam, S., Schnurr, D., Forghani, B., Honarmand, S., Khetsuriani, N., Fischer, M., Cossen, C. K., & Anderson, L. J. (2003) · Clinical Infectious Diseases · doi:10.1086/367841 · Cited by 434

Rolling circle amplification revolutionizes diagnosis and genomics of geminiviruses

Haible, D., Kober, S., & Jeske, H. (2006) · Journal of Virological Methods · doi:10.1016/j.jviromet.2006.01.017 · Cited by 424

CODEHOP (COnsensus-DEgenerate Hybrid Oligonucleotide Primer) PCR primer design

Rose, T. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg524 · Cited by 414

Frequent detection of human rhinoviruses, paramyxoviruses, coronaviruses, and bocavirus during acute respiratory tract infections

Arden, K. E., McErlean, P., Nissen, M. D., Sloots, T. P., & Mackay, I. M. (2006) · Journal of Medical Virology · doi:10.1002/jmv.20689 · Cited by 410

Unbiased Whole-Genome Amplification Directly From Clinical Samples

Hosono, S., Faruqi, A. F., Dean, F. B., Du, Y., Sun, Z., Wu, X., Du, J., Kingsmore, S. F., Egholm, M., & Lasken, R. S. (2003) · Genome Research · doi:10.1101/gr.816903 · Cited by 410

Extensive Set of 16S rRNA-Based Probes for Detection of Bacteria in Human Feces

Harmsen, H. J. M., Raangs, G. C., He, T., Degener, J. E., & Welling, G. W. (2002) · Applied and Environmental Microbiology · doi:10.1128/aem.68.6.2982-2990.2002 · Cited by 401

Association between a Novel Human Coronavirus and Kawasaki Disease

Esper, F., Shapiro, E. D., Weibel, C., Ferguson, D., Landry, M. L., & Kahn, J. S. (2005) · The Journal of Infectious Diseases · doi:10.1086/428291 · Cited by 397

TETRA: a web-service and a stand-alone program for the analysis and comparison of tetranucleotide usage patterns in DNA sequences

Teeling, H., Waldmann, J., Lombardot, T., Bauer, M., & Glöckner, F. O. (2004) · BMC Bioinformatics · doi:10.1186/1471-2105-5-163 · Cited by 396

The Association of Newly Identified Respiratory Viruses with Lower Respiratory Tract Infections in Korean Children, 2000–2005

Choi, E. H., Lee, H. J., Kim, S. J., Eun, B. W., Kim, N. H., Lee, J. A., Lee, J. H., Song, E. K., Kim, S. H., Park, J. Y., et al. (2006) · Clinical Infectious Diseases · doi:10.1086/506350 · Cited by 396

New DNA Viruses Identified in Patients with Acute Viral Infection Syndrome

Jones, M. S., Kapoor, A., Lukashov, V. V., Simmonds, P., Hecht, F., & Delwart, E. (2005) · Journal of Virology · doi:10.1128/jvi.79.13.8230-8236.2005 · Cited by 386

Type C Retrovirus Released from Porcine Primary Peripheral Blood Mononuclear Cells Infects Human Cells

Wilson, C. A., Wong, S., Muller, J., Davidson, C. E., Rose, T. M., & Burd, P. (1998) · Journal of Virology · doi:10.1128/jvi.72.4.3082-3087.1998 · Cited by 382

Metagenomic Analysis of Coastal RNA Virus Communities

Culley, A. I., Lang, A. S., & Suttle, C. A. (2006) · Science · doi:10.1126/science.1127404 · Cited by 374

A virus discovery method incorporating DNase treatment and its application to the identification of two bovine parvovirus species

Allander, T., Emerson, S. U., Engle, R. E., Purcell, R. H., & Bukh, J. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.211424698 · Cited by 373

Endogenous circulating DNA in systemic lupus erythematosus. Occurrence as multimeric complexes bound to histone.

Rumore, P. M., & Steinman, C. R. (1990) · Journal of Clinical Investigation · doi:10.1172/jci114716 · Cited by 361

Evidence of human coronavirus HKU1 and human bocavirus in Australian children

SLOOTS, T., MCERLEAN, P., SPEICHER, D., ARDEN, K., NISSEN, M., & MACKAY, I. (2006) · Journal of Clinical Virology · doi:10.1016/j.jcv.2005.09.008 · Cited by 360

Protein sequence similarity searches using patterns as seeds

Zhang, Z. (1998) · Nucleic Acids Research · doi:10.1093/nar/26.17.3986 · Cited by 342

Bats as a continuing source of emerging infections in humans

Wong, S., Lau, S., Woo, P., & Yuen, K. (2007) · Reviews in Medical Virology · doi:10.1002/rmv.520 · Cited by 321

Quantitation of genomic DNA in plasma and serum samples: higher concentrations of genomic DNA found in serum than in plasma

Lee, T., Montalvo, L., Chrebtow, V., & Busch, M. P. (2001) · Transfusion · doi:10.1046/j.1537-2995.2001.41020276.x · Cited by 311

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

Breitbart, M., Felts, B., Kelley, S., Mahaffy, J. M., Nulton, J., Salamon, P., & Rohwer, F. (2004) · Proceedings of the Royal Society of London. Series B: Biological Sciences · doi:10.1098/rspb.2003.2628 · Cited by 304

Fidelity of phi 29 DNA polymerase. Comparison between protein-primed initiation and DNA polymerization.

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Genomic fingerprinting using arbitrarily primed PCR and a matrix of pairwise combinations of primers

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Genetic characterization of new West African simian immunodeficiency virus SIVsm: geographic clustering of household-derived SIV strains with human immunodeficiency virus type 2 subtypes and genetically diverse viruses from a single feral sooty mangabey troop

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Genome Sequence of a Polydnavirus: Insights into Symbiotic Virus Evolution

Espagne, E., Dupuy, C., Huguet, E., Cattolico, L., Provost, B., Martins, N., Poirié, M., Periquet, G., & Drezen, J. M. (2004) · Science · doi:10.1126/science.1103066 · Cited by 264

Whole Genome Analysis of Genetic Alterations in Small DNA Samples Using Hyperbranched Strand Displacement Amplification and Array–CGH

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Does Blood of Healthy Subjects Contain Bacterial Ribosomal DNA?

Nikkari, S., McLaughlin, I. J., Bi, W., Dodge, D. E., & Relman, D. A. (2001) · Journal of Clinical Microbiology · doi:10.1128/jcm.39.5.1956-1959.2001 · Cited by 258

Infectious Diseases: Preparing for the Future

King, D. A., Peckham, C., Waage, J. K., Brownlie, J., & Woolhouse, M. E. J. (2006) · Science · doi:10.1126/science.1129134 · Cited by 251

Human Bocavirus: Prevalence and Clinical Spectrum at a Children’s Hospital

Arnold, J. C., Singh, K. K., Spector, S. A., & Sawyer, M. H. (2006) · Clinical Infectious Diseases · doi:10.1086/505399 · Cited by 246

Human Bocavirus Infection, Canada

Bastien, N., Brandt, K., Dust, K., Ward, D., & Li, Y. (2006) · Emerging Infectious Diseases · doi:10.3201/eid1205.051424 · Cited by 243

Detection of Human Bocavirus in Japanese Children with Lower Respiratory Tract Infections

Ma, X., Endo, R., Ishiguro, N., Ebihara, T., Ishiko, H., Ariga, T., & Kikuta, H. (2006) · Journal of Clinical Microbiology · doi:10.1128/jcm.44.3.1132-1134.2006 · Cited by 230

Frequent Simian Foamy Virus Infection in Persons Occupationally Exposed to Nonhuman Primates

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High diversity of unknown picorna-like viruses in the sea

Culley, A. I., Lang, A. S., & Suttle, C. A. (2003) · Nature · doi:10.1038/nature01886 · Cited by 219

Evidence of a Novel Human Coronavirus That Is Associated with Respiratory Tract Disease in Infants and Young Children

Esper, F., Weibel, C., Ferguson, D., Landry, M. L., & Kahn, J. S. (2005) · The Journal of Infectious Diseases · doi:10.1086/428138 · Cited by 219

Nanofiltration of plasma‐derived biopharmaceutical products

Burnouf, T., & Radosevich, M. (2003) · Haemophilia · doi:10.1046/j.1365-2516.2003.00701.x · Cited by 214

Use of Ultrafiltration To Isolate Viruses from Seawater Which Are Pathogens of Marine Phytoplankton

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Identification of two homologs of the Kaposi's sarcoma-associated herpesvirus (human herpesvirus 8) in retroperitoneal fibromatosis of different macaque species

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Torque teno virus (TTV): current status

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Detection of genome-scale ordered RNA structure (GORS) in genomes of positive-stranded RNA viruses: Implications for virus evolution and host persistence

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Sequence-independent, single-primer amplification (SISPA) of complex DNA populations

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A method for the rapid sequence-independent amplification of microdissected chromosomal material

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A Sequence-Independent Strategy for Detection and Cloning of Circular DNA Virus Genomes by Using Multiply Primed Rolling-Circle Amplification

Rector, A., Tachezy, R., & Van Ranst, M. (2004) · Journal of Virology · doi:10.1128/jvi.78.10.4993-4998.2004 · Cited by 179

Frequent detection of bocavirus DNA in German children with respiratory tract infections

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