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Browse the 867 peer-reviewed publications enabled by 454 Sequencing technology.
Design of 16S rRNA gene primers for 454 pyrosequencing of the human foregut microbiome. Nossa CW, Oberdorf WE, Yang L, Aas JA, Paster BJ, Desantis TZ, Brodie EL, Malamud D, Poles MA, Pei Z. (2010) World J Gastroenterol 16(33): 4135-44. View Publication
The genome of the domesticated apple (Malus × domestica Borkh.) Velasco R et al. (2010) Nature Genetics ePub: View Publication
Gut microbial gene expression in mother-fed and formula-fed piglets. Poroyko V, White JR, Wang M, Donovan S, Alverdy J, Liu DC, Morowitz MJ. (2010) PLoS One 5(8): e12459. View Publication
Tracking the evolution of multiple in vitro HCV replicon variants under protease inhibitor selection pressure by 454 deep sequencing. Verbinnen T, Van Marck H, Vandenbroucke I, Vijgen L, Claes M, Lin TI, Simmen K, Neyts J, Fanning G, Lenz O. (2010) Journal of Virology ePub: View Publication
A comparative molecular analysis of water-filled limestone sinkholes in north-eastern Mexico. Sahl JW, Gary MO, Harris JK, Spear JR. (2010) Environ Microbiol ePub: View Publication
Reshaping the gut microbiome with bacterial transplantation and antibiotic intake. Manichanh C, Reeder J, Gibert P, Varela E, Llopis M, Antolin M, Guigo R, Knight R, Guarner F. (2010) Genome Research ePub: View Publication
Analysis of co-receptor usage of circulating viral and proviral HIV genome quasispecies by ultra-deep pyrosequencing in patients candidate to CCR5 antagonist treatment. Abbate I, Rozera G, Tommasi C, Bruselles A, Bartolini B, Chillemi G, Nicastri E, Narciso P, Ippolito G, Capobianchi MR. (2010) Clin Microbiol Infect ePub: View Publication
Characterization of Archaeal Community in Contaminated and Uncontaminated Surface Stream Sediments. Porat I, Vishnivetskaya TA, Mosher JJ, Brandt CC, Yang ZK, Brooks SC, Liang L, Drake MM, Podar M, Brown SD, Palumbo AV. (2010) Microbial Ecology ePub: View Publication
Evaluation of the bacterial diversity in the rumen and feces of cattle fed diets containing levels of dried distiller's grains plus solubles using bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP). Callaway TR, Dowd SE, Edrington TS, Anderson RC, Krueger N, Bauer N, Kononoff PJ, Nisbet DJ. (2010) J Anim Sci ePub: View Publication
A combined massively parallel sequencing - indicator species approach revealed significant association between sulfate-reducing bacteria and uranium-reducing microbial communities. Cardenas E, Wu WM, Leigh MB, Carley J, Carroll S, Gentry T, Luo J, Watson D, Gu B, Ginder-Vogel M, Kitanidis PK, Jardine PM, Zhou J, Criddle CS, Marsh TL, Tiedje JM. (2010) Appl Environ Microbiol ePub: View Publication
Horizon-specific bacterial community composition of German grassland soils as revealed by pyrosequencing-based analysis of 16S rRNA genes. Will C, Thürmer A, Wollherr A, Nacke H, Herold N, Schrumpf M, Gutknecht J, Wubet T, Buscot F, Daniel R. (2010) Appl Environ Microbiol ePub: View Publication
High-throughput SNP discovery and assay development in common bean. Hyten DL, Song Q, Fickus EW, Quigley CV, Lim JS, Choi IY, Hwang EY, Pastor-Corrales M, Cregan PB. (2010) BMC Genomics 11(1): 475. View Publication
Characterization of the horseweed (Conyza canadensis) transcriptome using GS-FLX 454 pyrosequencing and its application for expression analysis of candidate non-target herbicide resistance genes. Peng Y, Abercrombie LL, Yuan JS, Riggins CW, Sammons RD, Tranel PJ, Stewart CN Jr. (2010) Pest Manag Sci ePub: View Publication
A new dominant peroxiredoxin allele identified by whole-genome re-sequencing of random mutagenized yeast causes oxidant-resistance and premature aging. Timmermann B, Jarolim S, Rußmayer H, Kerick M, Michel S, Krüger A, Bluemlein K, Laun P, Grillari J, Lehrach H, Breitenbach M, Ralser M. (2010) Aging (Albany NY) ePub: View Publication
Bar-coded pyrosequencing of 16S rRNA gene amplicons reveals changes in ileal porcine bacterial communities due to high dietary zinc intake. Vahjen W, Pieper R, Zentek J. (2010) Appl Environ Microbiol ePub: View Publication
Endosymbiotic Gene Transfer and Transcriptional Regulation of Transferred Genes in Paulinella chromatophora. Nowack EC, Vogel H, Groth M, Grossman AR, Melkonian M, Glöckner G. (2010) Mol Biol Evol ePub: View Publication
A maraviroc-resistant HIV-1 with narrow cross-resistance to other CCR5 antagonists depends on both N-terminal and extracellular loop domains of drug-bound CCR5. Tilton JC, Wilen CB, Didigu CA, Sinha R, Harrison JE, Agrawal-Gamse C, Henning EA, Bushman FD, Martin JN, Deeks SG, Doms RW. (2010) Journal of Virology ePub: View Publication
Extreme positive selection on a new highly-expressed larval glycoprotein (LGP) gene in Galaxias fishes (Osmeriformes: Galaxiidae). Wallis LJ, Wallis GP. (2010) Mol Biol Evol ePub: View Publication
Analysis of human and animal fecal microbiota for microbial source tracking. Lee JE, Lee S, Sung J, Ko G. (2010) ISME Journal ePub: View Publication
First transcriptomic analysis of the economically important parasitic nematode, Trichostrongylus colubriformis, using a next-generation sequencing approach. Cantacessi C, Mitreva M, Campbell BE, Hall RS, Young ND, Jex AR, Ranganathan S, Gasser RB. (2010) Infect Genet Evol ePub: View Publication
Pyrosequencing and characterization of immune response genes from the American dog tick, Dermacentor variabilis (L.). Jaworski DC, Zou Z, Bowen CJ, Wasala NB, Madden R, Wang Y, Kocan KM, Jiang H, Dillwith JW. (2010) Insect Mol Biol ePub: View Publication
Characterization of de novo transcriptome for waterhemp (Amaranthus tuberculatus) using GS-FLX 454 pyrosequencing and its application for studies of herbicide target-site genes. Riggins CW, Peng Y, Stewart CN Jr, Tranel PJ. (2010) Pest Management Science ePub: View Publication
Genome-wide high-throughput integrome analyses by nrLAM-PCR and next-generation sequencing. Paruzynski A, Arens A, Gabriel R, Bartholomae CC, Scholz S, Wang W, Wolf S, Glimm H, Schmidt M, von Kalle C. (2010) Nature Protocols 5(8): 1379-95. View Publication
Oral Bacterial Genome Sequencing Using the High-Throughput Roche Genome Sequencer FLX System. Heng NC, Stanton JA. (2010) Methods in Molecular Biology 666: 197-218. View Publication
Structure and dynamics of the microbial communities underlying the carboxylate platform for biofuel production. Hollister EB, Forrest AK, Wilkinson HH, Ebbole DJ, Malfatti SA, Tringe SG, Holtzapple MT, Gentry TJ. (2010) Appl Microbiol Biotechnol ePub: View Publication
An EST-based genome scan using 454 sequencing in the marine snail Littorina saxatilis. Galindo J, Grahame JW, Butlin RK. (2010) Journal of Evolutionary Biology ePub: View Publication
Diverse somatic mutation patterns and pathway alterations in human cancers. Kan Z et al. (2010) Nature ePub: View Publication
Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags. Wu GD, Lewis JD, Hoffmann C, Chen YY, Knight R, Bittinger K, Hwang J, Chen J, Berkowsky R, Nessel L, Li H, Bushman FD. (2010) BMC Microbiology 10(1): 206. View Publication
Comparative metagenomics of bathypelagic plankton and bottom sediment from the Sea of Marmara. Quaiser A, Zivanovic Y, Moreira D, López-García P. (2010) ISME Journal ePub: View Publication
Vertical stratification of microbial communities in the Red Sea revealed by 16S rDNA pyrosequencing. Qian PY, Wang Y, Lee OO, Lau SC, Yang J, Lafi FF, Al-Suwailem A, Wong TY. (2010) ISME Journal ePub: View Publication
Non PCR-amplified Transcripts and AFLP fragments as reduced representations of the quail genome for 454 Titanium sequencing. Leroux S, Feve K, Vignoles F, Bouchez O, Klopp C, Noirot C, Gourichon D, Richard S, Leterrier C, Beaumont C, Minvielle F, Vignal A, Pitel F. (2010) BMC Research Notes 3(1): 214. View Publication
Error correction of next-generation sequencing data and reliable estimation of HIV quasispecies. Zagordi O, Klein R, Däumer M, Beerenwinkel N. (2010) Nucleic Acids Research ePub: View Publication
Isolation of mixed subtypes of influenza A virus from a bald eagle (Haliaeetus leucocephalus). Goyal SM, Jindal N, Chander Y, Ramakrishnan MA, Redig PT, Sreevatsan S. (2010) Virology Journal 7: 174. View Publication
Reliable resequencing of the human dystrophin locus by universal long PCR and massive pyrosequencing. Bonnal RJ, Severgnini M, Castaldi A, Bordoni R, Iacono M, Trimarco A, Torella A, Piluso G, Aurino S, Condorelli G, De Bellis G, Nigro V. (2010) Analytical Biochemistry ePub: View Publication
The Landscape of C. elegans 3'UTRs. Mangone M et al. (2010) Science 329(5990): 432-435. View Publication
Genome-wide characterization of methylguanosine-capped and polyadenylated small RNAs in the rice blast fungus Magnaporthe oryzae. Gowda M, Nunes CC, Sailsbery J, Xue M, Chen F, Nelson CA, Brown DE, Oh Y, Meng S, Mitchell T, Hagedorn CH, Dean RA. (2010) Nucleic Acids Research ePub: View Publication
Viruses in the faecal microbiota of monozygotic twins and their mothers. Reyes A, Haynes M, Hanson N, Angly FE, Heath AC, Rohwer F, Gordon JI. (2010) Nature 466(7304): 334-8. View Publication
Phylogenetic and metabolic diversity of bacteria associated with cystic fibrosis. Guss AM, Roeselers G, Newton IL, Young CR, Klepac-Ceraj V, Lory S, Cavanaugh CM. (2010) ISME Journal ePub: View Publication
Bisulfite Patch PCR enables multiplexed sequencing of promoter methylation across cancer samples. Varley KE, Mitra RD. (2010) Genome Research ePub: View Publication
Evolutionary Genomics of Staphylococcus aureus Reveals Insights into the Origin and Molecular Basis of Ruminant Host Adaptation. Guinane CM, Ben Zakour NL, Tormo-Mas MA, Weinert LA, Lowder BV, Cartwright RA, Smyth DS, Smyth CJ, Lindsay JA, Gould KA, Witney A, Hinds J, Bollback JP, Rambaut A, Penadés JR, Fitzgerald JR. (2010) Genome Biol Evol 2: 454-66. View Publication
When Technology Meets Conservation: Increased Microsatellite Marker Production Using 454 Genome Sequencing on the Endangered Okaloosa Darter (Etheostoma okaloosae). Saarinen EV, Austin JD. (2010) J Hered ePub: View Publication
Global sequence characterization of rice centromeric satellite based on oligomer frequency analysis in large-scale sequencing data. Macas J, Neumann P, Novák P, Jiang J. (2010) Bioinformatics ePub: View Publication
Single-cell genomics reveals the lifestyle of Poribacteria, a candidate phylum symbiotically associated with marine sponges. Siegl A, Kamke J, Hochmuth T, Piel J, Richter M, Liang C, Dandekar T, Hentschel U. (2010) ISME Journal ePub: View Publication
Analysis of Oral Microbiota in Children with Dental Caries by PCR-DGGE and Barcoded Pyrosequencing. Analysis of Oral Microbiota in Children with Dental Caries by PCR-DGGE and Barcoded Pyrosequencing. (2010) Microbial Ecology ePub: View Publication
Structural shifts of gut microbiota as surrogate endpoints for monitoring host health changes induced by carcinogen exposure. Wei H, Dong L, Wang T, Zhang M, Hua W, Zhang C, Pang X, Chen M, Su M, Qiu Y, Zhou M, Yang S, Chen Z, Rantalainen M, Nicholson JK, Jia W, Wu D, Zhao L. (2010) FEMS Microbiol Ecol ePub: View Publication
Dynamics of HIV-1 Quasispecies during Antiviral Treatment Dissected Using Ultra-Deep Pyrosequencing. Hedskog C, Mild M, Jernberg J, Sherwood E, Bratt G, Leitner T, Lundeberg J, Andersson B, Albert J. (2010) PLoS One 5(7): e11345. View Publication
Next-Generation Sequencing: The Solution for High-Resolution, Unambiguous HLA Typing. Lind C, Ferriola D, Mackiewicz K, Heron S, Rogers M, Slavich L, Walker R, Hsiao T, McLaughlin L, D'Arcy M, Gai X, Goodridge D, Sayer D, Monos D. (2010) Human Immunology ePub: View Publication
Pyrosequencing Study of Fecal Microflora of Autistic and Control Children. Finegold SM, Dowd SE, Gontcharova V, Liu C, Henley KE, Wolcott RD, Youn E, Summanen PH, Granpeesheh D, Dixon D, Liu M, Molitoris DR, Green JA 3rd. (2010) Anaerobe ePub: View Publication
Contrasting seasonal niche separation between rare and abundant taxa conceals the extent of protist diversity. Nolte V, Pandey RV, Jost S, Medinger R, Ottenwälder B, Boenigk J, Schlötterer C. (2010) Molecular Ecology 19(14): 2908-15. View Publication
Resistance and resilience of benthic biofilm communities from a temperate saltmarsh to desiccation and rewetting. McKew BA, Taylor JD, McGenity TJ, Underwood GJ. (2010) ISME Journal ePub: View Publication
454 Pyrosequencing and Sanger sequencing of tropical mycorrhizal fungi provide similar results but reveal substantial methodological biases. Tedersoo L, Nilsson RH, Abarenkov K, Jairus T, Sadam A, Saar I, Bahram M, Bechem E, Chuyong G, Kõljalg U. (2010) New Phytologist ePub: View Publication
Comparison of gene order of GIGANTEA loci in yellow-poplar, monocots, and eudicots. Liang H, Barakat A, Schlarbaum SE, Mandoli DF, Carlson JE. (2010) Genome 53(7): 533-44. View Publication
Identification of GBV-D, a Novel GB-like Flavivirus from Old World Frugivorous Bats (Pteropus giganteus) in Bangladesh. Epstein JH, Quan PL, Briese T, Street C, Jabado O, Conlan S, Ali Khan S, Verdugo D, Hossain MJ, Hutchison SK, Egholm M, Luby SP, Daszak P, Lipkin WI. (2010) PLoS Pathogens 6: e10000972. View Publication
Microbes and Health Sackler Colloquium: Effect of broad- and narrow-spectrum antimicrobials on Clostridium difficile and microbial diversity in a model of the distal colon. Rea MC, Dobson A, O'Sullivan O, Crispie F, Fouhy F, Cotter PD, Shanahan F, Kiely B, Hill C, Ross RP. (2010) PNAS ePub: View Publication
Targeted next-generation sequencing of DNA regions proximal to a conserved GXGXXG signaling motif enables systematic discovery of tyrosine kinase fusions in cancer. Chmielecki J, Peifer M, Jia P, Socci ND, Hutchinson K, Viale A, Zhao Z, Thomas RK, Pao W. (2010) Nucleic Acids Research ePub: View Publication
Combining next-generation sequencing strategies for rapid molecular resource development from an invasive aphid species, Aphis glycines. Bai X, Zhang W, Orantes L, Jun TH, Mittapalli O, Mian MA, Michel AP. (2010) PLoS One 5(6): e11370. View Publication
Natural Mutagenesis of Human Genomes by Endogenous Retrotransposons. Iskow RC, McCabe MT, Mills RE, Torene S, Pittard WS, Neuwald AF, Van Meir EG, Vertino PM, Devine SE. (2010) Cell 141(7): 1253-1261. View Publication
Analysis of bacterial biofilm communities in water meters of a drinking water distribution system via pyrosequencing. Hong PY, Hwang C, Ling F, Andersen GL, Lechevallier MW, Liu WT. (2010) Appl Environ Microbiol. ePub: View Publication
Associations between Major Histocompatibility Complex genes and PUUV infection in Myodes glareolus are detected in wild populations but not from experimental infection data. Guivier E, Galan M, Malé PJ, Kallio ER, Voutilainen L, Henttonen H, Olsson G, Lundkvist A, Tersago K, Augot D, Cosson JF, Charbonnel N. (2010) Journal of General Virology ePub: View Publication
TagCleaner: Identification and removal of tag sequences from genomic and metagenomic datasets. Schmieder R, Lim YW, Rohwer F, Edwards R. (2010) BMC Bioinformatics 11: 341. View Publication
Heart transcriptome of the bank vole (Myodes glareolus): towards understanding the evolutionary variation in metabolic rate. Babik W, Stuglik M, Qi W, Kuenzli M, Kuduk K, Koteja P, Radwan J. (2010) BMC Genomics 11(1): 390. View Publication
Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Dominguez-Bello MG, Costello EK, Contreras M, Magris M, Hidalgo G, Fierer N, Knight R. (2010) PNAS 107(26): 11971-5. View Publication
Cost-Effective, Species-Specific Microsatellite Development for the Endangered Dwarf Bulrush (Typha minima) Using Next-Generation Sequencing Technology. Csencsics D, Brodbeck S, Holderegger R. (2010) Journal of Heredity ePub: View Publication
Transcriptome sequencing and comparative analysis of cucumber flowers with different sex types. Guo S, Zheng Y, Joung JG, Liu S, Zhang Z, Crasta OR, Sobral BW, Xu Y, Huang S, Fei Z. (2010) BMC Genomics 11(1): 384. View Publication
VITCOMIC: visualization tool for taxonomic compositions of microbial communities based on 16S rRNA gene sequences. Mori H, Maruyama F, Kurokawa K. (2010) BMC Bioinformatics 11(1): 332. View Publication
Production of ectomycorrhizal mycelium peaks during canopy closure in Norway spruce forests. Wallander H, Johansson U, Sterkenburg E, Brandström Durling M, Lindahl BD. (2010) New Phytology ePub: View Publication
Multivariate Cutoff Level Analysis (MultiCoLA) of large community data sets. Gobet A, Quince C, Ramette A. (2010) Nucleic Acids Research ePub: View Publication
Detection of Cereal yellow dwarf virus using small interfering RNAs and enhanced infection rate with Cocksfoot streak virus in wild cocksfoot grass (Dactylis glomerata). Pallett DW, Ho T, Cooper I, Wang H. (2010) Journal of Virology Methods 168(1-2): 223-7. View Publication
Microbes and Health Sackler Colloquium: Metagenomic detection of phage-encoded platelet-binding factors in the human oral cavity. Willner D, Furlan M, Schmieder R, Grasis JA, Pride DT, Relman DA, Angly FE, McDole T, Mariella RP Jr, Rohwer F, Haynes M. (2010) PNAS ePub: View Publication
Reassociation kinetics-based approach for partial genome sequencing of the cattle tick, Rhipicephalus (Boophilus) microplus. Guerrero FD, Moolhuijzen P, Peterson DG, Bidwell S, Caler E, Bellgard M, Nene VM, Djikeng A. (2010) BMC Genomics 11: 374. View Publication
Rapid transcriptome and proteome profiling of a non-model marine invertebrate, Bugula neritina. Wang H, Zhang H, Wong YH, Voolstra C, Ravasi T, Bajic V, Qian PY. (2010) Proteomics ePub: View Publication
Endosymbiont DNA in endobacteria-free filarial nematodes indicates ancient horizontal genetic transfer. McNulty SN, Foster JM, Mitreva M, Dunning Hotopp JC, Martin J, Fischer K, Wu B, Davis PJ, Kumar S, Brattig NW, Slatko BE, Weil GJ, Fischer PU. (2010) PLoS One 5(6): e11029. View Publication
Pyrosequencing of the 16S rRNA gene to reveal bacterial pathogen diversity in biosolids. Bibby K, Viau E, Peccia J. (2010) Water Research 44(14): 4252-60. View Publication
De Novo assembly of the complete genome of an enhanced electricity-producing variant of Geobacter sulfurreducens using only short reads. Nagarajan H, Butler JE, Klimes A, Qiu Y, Zengler K, Ward J, Young ND, Methé BA, Palsson BØ, Lovley DR, Barrett CL. (2010) PLoS One 5(6): e10922. View Publication
Discovery of commonly existing anode biofilm microbes in two different wastewater treatment MFCs using FLX Titanium pyrosequencing. Lee TK, Van Doan T, Yoo K, Choi S, Kim C, Park J. (2010) Appl Microbiol Biotechnol 87(6): 2335-43. View Publication
Insights into shell deposition in the Antarctic bivalve Laternula elliptica: gene discovery in the mantle transcriptome using 454 pyroseqeuencing. Clark MS, Thorne MA, Vieira FA, Cardoso JC, Power DM, Peck LS. (2010) BMC Genomics 11(1): 362. View Publication
Effect of Dechlorination and Sulfate Reduction on the Microbial Community Structure in Denitrifying Membrane-Biofilm Reactors. Zhang H, Ziv-El M, Rittmann BE, Krajmalnik-Brown R. (2010) Environ Sci Technology 44(13): 5159-64. View Publication
Prevalence and clinical significance of HIV drug resistance mutations by ultra-deep sequencing in antiretroviral-naïve subjects in the CASTLE study. Lataillade M, Chiarella J, Yang R, Schnittman S, Wirtz V, Uy J, Seekins D, Krystal M, Mancini M, McGrath D, Simen B, Egholm M, Kozal M. (2010) PLoS One 5(6): e10952. View Publication
Postprandial remodeling of the gut microbiota in Burmese pythons. Costello EK, Gordon JI, Secor SM, Knight R. (2010) ISME Journal ePub: View Publication
Microbes and Health Sackler Colloquium: Vaginal microbiome of reproductive-age women. Ravel J, Gajer P, Abdo Z, Schneider GM, Koenig SS, McCulle SL, Karlebach S, Gorle R, Russell J, Tacket CO, Brotman RM, Davis CC, Ault K, Peralta L, Forney LJ. (2010) PNAS ePub: View Publication
Dynamics of gene-modified progenitor cells analyzed by tracking retroviral integration sites in a human SCID-X1 gene therapy trial. Wang GP, Berry CC, Malani N, Leboulch P, Fischer A, Hacein-Bey-Abina S, Cavazzana-Calvo M, Bushman FD. (2010) Blood 115(22): 4356-66. View Publication
Analyzing Endodontic Infections by Deep Coverage Pyrosequencing. Li L, Hsiao WW, Nandakumar R, Barbuto SM, Mongodin EF, Paster BJ, Fraser-Liggett CM, Fouad AF. (2010) Journal of Dental Research ePub: View Publication
Astrovirus encephalitis in boy with X-linked agammaglobulinemia. Quan PL, Wagner TA, Briese T, Torgerson TR, Hornig M, Tashmukhamedova A, Firth C, Palacios G, Baisre-De-Leon A, Paddock CD, Hutchison SK, Egholm M, Zaki SR, Goldman JE, Ochs HD, Lipkin WI. (2010) Emerg Infect Dis 16(6): 918-25. View Publication
Viral nucleic acids in live-attenuated vaccines: detection of minority variants and an adventitious virus. Victoria JG, Wang C, Jones MS, Jaing C, McLoughlin K, Gardner S, Delwart EL. (2010) Journal of Virology 84(12): 6033-40. View Publication
Viral and microbial community dynamics in four aquatic environments. Rodriguez-Brito B et al. (2010) ISME Journal 4(6): 739-51. View Publication
The ecology of the phyllosphere: geographic and phylogenetic variability in the distribution of bacteria on tree leaves. Redford AJ, Bowers RM, Knight R, Linhart Y, Fierer N. (2010) Environmental Microbiology ePub: View Publication
Assessment of soil fungal communities using pyrosequencing. Lim YW, Kim BK, Kim C, Jung HS, Kim BS, Lee JH, Chun J. (2010) Journal of Microbiology 48(3): 284-9. View Publication
Analysis of expressed sequence tags from a significant livestock pest, the stable fly (Stomoxys calcitrans), identifies transcripts with a putative role in chemosensation and sex determination. Olafson PU, Lohmeyer KH, Dowd SE. (2010) Arch Insect Biochem Physiol 74(3): 179-204. View Publication
Comparison of normalization methods for construction of large, multiplex amplicon pools for next-generation sequencing. Harris JK, Sahl JW, Castoe TA, Wagner BD, Pollock DD, Spear JR. (2010) Applied Environmental Microbiology 76(12): 3863-8. View Publication
Hepatitis C virus transmission bottlenecks analyzed by deep sequencing. Wang GP, Sherrill-Mix SA, Chang KM, Quince C, Bushman FD. (2010) Journal of Virology 84(12): 6218-28. View Publication
Host-interactive genes in Amerindian Helicobacter pylori diverge from their Old World homologs and mediate inflammatory responses. Mane SP, Dominguez-Bello MG, Blaser MJ, Sobral BW, Hontecillas R, Skoneczka J, Mohapatra SK, Crasta OR, Evans C, Modise T, Shallom S, Shukla M, Varon C, Mégraud F, Maldonado-Contreras AL, Williams KP, Bassaganya-Riera J. (2010) Journal of Bacteriology 192(12): 3078-92. View Publication
The waddlia genome: a window into chlamydial biology. Bertelli C, Collyn F, Croxatto A, Rückert C, Polkinghorne A, Kebbi-Beghdadi C, Goesmann A, Vaughan L, Greub G. (2010) PLoS One 5(5): e10890. View Publication
Improved Detection of CXCR4-Using HIV by V3 Genotyping: Application of Population-Based and "Deep" Sequencing to Plasma RNA and Proviral DNA. Swenson LC, Moores A, Low AJ, Thielen A, Dong W, Woods C, Jensen MA, Wynhoven B, Chan D, Glascock C, Harrigan PR. (2010) Journal of AIDS 54(5): 506-10. View Publication
Transcriptome sequencing and comparative transcriptome analysis of the scleroglucan producer Sclerotium rolfsii. Schmid J, Muller-Hagen D, Bekel T, Funk L, Stahl U, Sieber V, Meyer V. (2010) BMC Genomics 11(1): 329. View Publication
Uncovering the evolutionary origin of plant molecular processes: comparison of Coleochaete (Coleochaetales) and Spirogyra (Zygnematales) transcriptomes. Timme RE, Delwiche CF. (2010) BMC Plan Biology 10(1): 96. View Publication
The complete genome sequence of Canna yellow streak virus. Monger WA, Adams IP, Glover RH, Barrett B. (2010) Arch Virol ePub: View Publication
A catalog of reference genomes from the human microbiome. Human Microbiome Jumpstart Reference Strains Consortium (2010) Science 328(5981): 994-9. View Publication
Bayesian analysis of molecular variance in pyrosequences quantifies population genetic structure across the genome of Lycaeides butterflies. Gompert Z, Forister ML, Fordyce JA, Nice CC, Williamson RJ, Alex Buerkle C. (2010) Molecular Ecollogy 19(12): 2455-73. View Publication
Individual Variation in the Germline Ig Gene Repertoire Inferred from Variable Region Gene Rearrangements. Boyd SD, Gaëta BA, Jackson KJ, Fire AZ, Marshall EL, Merker JD, Maniar JM, Zhang LN, Sahaf B, Jones CD, Simen BB, Hanczaruk B, Nguyen KD, Nadeau KC, Egholm M, Miklos DB, Zehnder JL, Collins AM. (2010) Journal of Immunology 184(12): 6986-92. View Publication
Analysing 454 amplicon resequencing experiments using the modular and database oriented Variant Identification Pipeline. De Schrijver JM, De Leeneer K, Lefever S, Sabbe N, Pattyn F, Van Nieuwerburgh F, Coucke P, Deforce D, Vandesompele J, Bekaert S, Hellemans J, Van Criekinge W. (2010) BMC Bioinformatics 11(1): 269. View Publication
RNA deep sequencing of the Atlantic cod transcriptome. Johansen SD, Karlsen BO, Furmanek T, Andreassen M, Jørgensen TE, Bizuayehu TT, Breines R, Emblem A, Kettunen P, Luukko K, Edvardsen RB, Nordeide JT, Coucheron DH, Moum T. (2010) Comp Biochem Physiol Part D Genomics Proteomics ePub: View Publication
Paradigm for industrial strain improvement identifies sodium acetate tolerance loci in Zymomonas mobilis and Saccharomyces cerevisiae. Yang S, Land ML, Klingeman DM, Pelletier DA, Lu TY, Martin SL, Guo HB, Smith JC, Brown SD. (2010) PNAS 107(23): 10395-400. View Publication
SNP discovery performance of two second-generation sequencing platforms in the NOD2 gene region. Melum E, May S, Schilhabel MB, Thomsen I, Karlsen TH, Rosenstiel P, Schreiber S, Franke A. (2010) Human Mutation 31(7): 875-85. View Publication
Population-level transcriptome sequencing of nonmodel organisms Erynnis propertius and Papilio zelicaon. O'Neil ST, Dzurisin JD, Carmichael RD, Lobo NF, Emrich SJ, Hellmann JJ. (2010) BMC Genomics 11(1): 310. View Publication
Isolated communities of Epsilonproteobacteria in hydrothermal vent fluids of the Mariana Arc seamounts. Huber JA, Cantin HV, Huse SM, Mark Welch DB, Sogin ML, Butterfield DA. (2010) FEMS Microbiol Ecol ePub: View Publication
Second generation sequencing of the mesothelioma tumor genome. Bueno R, De Rienzo A, Dong L, Gordon GJ, Hercus CF, Richards WG, Jensen RV, Anwar A, Maulik G, Chirieac LR, Ho KF, Taillon BE, Turcotte CL, Hercus RG, Gullans SR, Sugarbaker DJ. (2010) PLoS One 5(5): e10612. View Publication
Transcriptomic analysis of a marine bacterial community enriched with dimethylsulfoniopropionate. Vila-Costa M, Rinta-Kanto JM, Sun S, Sharma S, Poretsky R, Moran MA. (2010) ISME Journal ePub: View Publication
Massively parallel pyrosequencing-based transcriptome analyses of small brown planthopper (Laodelphax striatellus), a vector insect transmitting rice stripe virus (RSV). Zhang F, Guo H, Zheng H, Zhou T, Zhou Y, Wang S, Fang R, Qian W, Chen X. (2010) BMC Genomics 11(1): 303. View Publication
Deep sequencing reveals highly complex dynamics of human cytomegalovirus genotypes in transplant patients over time. Görzer I, Guelly C, Trajanoski S, Puchhammer-Stöckl E. (2010) Journal of Virology 84(14): 7195-203. View Publication
A 454 multiplex sequencing method for rapid and reliable genotyping of highly polymorphic genes in large-scale studies. Galan M, Guivier E, Caraux G, Charbonnel N, Cosson JF. (2010) BMC Genomics 11(1): 296. View Publication
Soil bacterial and fungal communities across a pH gradient in an arable soil. Rousk J, Bååth E, Brookes PC, Lauber CL, Lozupone C, Caporaso JG, Knight R, Fierer N. (2010) ISME Journal ePub: View Publication
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Comparative 454 pyrosequencing of transcripts from two olive genotypes during fruit development. Alagna F, D'Agostino N, Torchia L, Servili M, Rao R, Pietrella M, Giuliano G, Chiusano ML, Baldoni L, Perrotta G. (2009) BMC Genomics 10(1): 399. View Publication
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A genome-wide analysis of nonribosomal peptide synthetase gene clusters and their peptides in a Planktothrix rubescens strain. Rounge TB, Rohrlack T, Nederbragt AJ, Kristensen T, Jakobsen KS. (2009) BMC Genomics 10(1): 396. View Publication
Rapid High-throughput HLA Typing by Massively-parallel Pyrosequencing for High-Resolution Allele Identification. Gabriel C, Danzer M, Hackl C, Kopal G, Hufnagl P, Hofer K, Polin H, Stabentheiner S, Pröll J. (2009) Human Immunology 70(11): 960-4. View Publication
454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity. Buée M, Reich M, Murat C, Morin E, Nilsson RH, Uroz S, Martin F. (2009) New Phytologist 184(2): 449-56. View Publication
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Analysing diet of small herbivores: the efficiency of DNA barcoding coupled with high-throughput pyrosequencing for deciphering the composition of complex plant mixtures. Soininen EM, Valentini A, Coissac E, Miquel C, Gielly L, Brochmann C, Brysting AK, Sonstebo JH, Ims RA, Yoccoz NG, Taberlet P. (2009) Frontiers in Zooology 6(1): 16. View Publication
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A 454 sequencing approach for large-scale phylogenomic analysis of the Common Emperor Scorpion (Pandinus imperator). Roeding F, Borner J, Kube M, Klages S, Reinhardt R, Burmester T. (2009) Mol Phylogenet Evol 53(3): 826-34. View Publication
Identification of a novel astrovirus (Astrovirus VA1) associated with an outbreak of acute gastroenteritis. Finkbeiner SR, Li Y, Ruone S, Conrardy C, Gregoricus N, Toney D, Virgin HW, Anderson LJ, Vinjé J, Wang D, Tong S. (2009) Journal of Virology 83(20): 10836-9. View Publication
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Design of a high density SNP genotyping assay in the pig using SNPs identified and characterized by next generation sequencing technology. Ramos et al. (2009) PLoS One 4(8): e6524. View Publication
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The seasonal structure of microbial communities in the Western English Channel. Gilbert JA, Field D, Swift P, Newbold L, Oliver A, Smyth T, Somerfield PJ, Huse S, Joint I. (2009) Environmental Microbiology. 11(12): 3132-9. View Publication
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The complete genome of Teredinibacter turnerae T7901: an intracellular endosymbiont of marine wood-boring bivalves (shipworms). Yang et al. (2009) PLoS One 4(7): e6085. View Publication
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A Comparative study of species richness estimates obtained using nearly complete fragments and simulated pyrosequencing-generated fragments in 16S rRNA gene-based environmental surveys. Youssef N, Sheik CS, Krumholz LR, Najar FZ, Roe BA, Elshahed MS. (2009) Appl Environ Microbiol 75(16): 5227-36. View Publication
Large-scale parallel 454 sequencing reveals host ecological group specificity of arbuscular mycorrhizal fungi in a boreonemoral forest. Opik M, Metsis M, Daniell TJ, Zobel M, Moora M. (2009) New Phytology 184(2): 424-37. View Publication
Shedding light on an extremophile lifestyle through transcriptomics. Dassanayake M, Haas JS, Bohnert HJ, Cheeseman JM. (2009) New Phytologist 183(3): 764-75. View Publication
HIV integration site distributions in resting and activated CD4+ T cells infected in culture. Brady T, Agosto LM, Malani N, Berry CC, Doherty U, Bushman F. (2009) AIDS 23(12): 1461-71. View Publication
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The complete genome of klassevirus- a novel picornavirus in pediatric stool. Greninger AL, Runckel C, Chiu CY, Haggerty T, Parsonnet J, Ganem D, DeRisi JL (2009) Virology Journal 6: 79. View Publication
The Mycoplasma conjunctivae genome sequencing, annotation and analysis. Calderon-Copete SP, Wigger G, Wunderlin C, Schmidheini T, Frey J, Quail MA, Falquet L. (2009) BMC Bioinformatics Suppl 6: S7. View Publication
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Transcriptome sequencing of the Microarray Quality Control (MAQC) RNA reference samples using next generation sequencing. Mane SP, Evans C, Cooper KL, Crasta OR, Folkerts O, Hutchison SK, Harkins TT, Thierry-Mieg D, Thierry-Mieg J, Jensen RV. (2009) BMC Genomics 10(1): 264. View Publication
Identification and analysis of miRNAs in human breast cancer and teratoma samples using deep sequencing. Nygaard S, Jacobsen A, Lindow M, Eriksen J, Balslev E, Flyger H, Tolstrup N, Moller S, Krogh A, Litman T. (2009) BMC Medical Genomics 2(1): 35. View Publication
Closing gaps in the human genome using sequencing by synthesis. Garber M, Zody MC, Arachchi HM, Berlin A, Gnerre S, Green LM, Lennon N, Nusbaum C. (2009) Genome Biology 10(6): R60. View Publication
Genetic detection and characterization of Lujo virus, a new hemorrhagic fever-associated arenavirus from southern Africa. Briese T, Paweska JT, McMullan LK, Hutchison SK, Street C, Palacios G, Khristova ML, Weyer J, Swanepoel R, Egholm M, Nichol ST, Lipkin WI. (2009) PLoS Pathogens 5(5): e1000455. View Publication
Phylogenetic characterization of a biogas plant microbial community integrating clone library 16S-rDNA sequences and metagenome sequence data obtained by 454-pyrosequencing. Kröber M, Bekel T, Diaz NN, Goesmann A, Jaenicke S, Krause L, Miller D, Runte KJ, Viehöver P, Pühler A, Schlüter A. (2009) Journal of Biotechnology 142(1): 38-49. View Publication
Genome sequence of the recombinant protein production host Pichia pastoris. De Schutter K, Lin YC, Tiels P, Van Hecke A, Glinka S, Weber-Lehmann J, Rouzé P, Van de Peer Y, Callewaert N. (2009) Nature Biotechnology 27(6): 561-6. View Publication
Allelic imbalance sequencing reveals that single-nucleotide polymorphisms frequently alter microRNA-directed repression. Kim J, Bartel DP. (2009) Nature Biotechnology 27(5): 472-7. View Publication
Genome sequence of the anaerobic, thermophilic, and cellulolytic bacterium "Anaerocellum thermophilum" DSM 6725. Kataeva IA, Yang SJ, Dam P, Poole FL 2nd, Yin Y, Zhou F, Chou WC, Xu Y, Goodwin L, Sims DR, Detter JC, Hauser LJ, Westpheling J, Adams MW. (2009) Journal of Bacteriology 191(11): 3760-1. View Publication
Genomic analyses of the microsporidian Nosema ceranae, an emergent pathogen of honey bees. Cornman RS, Chen YP, Schatz MC, Street C, Zhao Y, Desany B, Egholm M, Hutchison S, Pettis JS, Lipkin WI, Evans JD. (2009) PLoS Pathogens 5(6): e1000466. View Publication
A high-throughput splinkerette-PCR method for the isolation and sequencing of retroviral insertion sites. Uren AG, Mikkers H, Kool J, van der Weyden L, Lund AH, Wilson CH, Rance R, Jonkers J, van Lohuizen M, Berns A, Adams DJ. (2009) Nature Protocols 4(5): 789-98. View Publication
Quantitative deep sequencing reveals dynamic HIV-1 escape and large population shifts during CCR5 antagonist therapy in vivo. Tsibris AM, Korber B, Arnaout R, Russ C, Lo CC, Leitner T, Gaschen B, Theiler J, Paredes R, Su Z, Hughes MD, Gulick RM, Greaves W, Coakley E, Flexner C, Nusbaum C, Kuritzkes DR. (2009) PLoS ONE 4(5): e5683. View Publication
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Phylogenetic classification of Escherichia coli O157:H7 strains of human and bovine origin using a novel set of nucleotide polymorphisms. Clawson ML, Keen JE, Smith TP, Durso LM, McDaneld TG, Mandrell RE, Davis MA, Bono JL. (2009) Genome Biology 10(5): R56. View Publication
Paleogenomics in a temperate environment: shotgun sequencing from an extinct mediterranean caprine. Ramírez O, Gigli E, Bover P, Alcover JA, Bertranpetit J, Castresana J, Lalueza-Fox C. (2009) PLoS ONE 4(5): e5670 View Publication
Whole genome sequencing of a natural recombinant Toxoplasma gondii strain reveals chromosome sorting and local allelic variants. Lindstrom Bontell I, Hall N, Ashelford KE, Dubey JP, Boyle JP, Lindh J, Smith JE. (2009) Genome Biology 10(5): R53. View Publication
Gene discovery using massively parallel pyrosequencing to develop ESTs for the flesh fly Sarcophaga crassipalpis. Hahn DA, Ragland GJ, Shoemaker DD, Denlinger DL. (2009) BMC Genomics 10(1): 234. View Publication
Microbial diversity in the sputum of a cystic fibrosis patient studied with 16S rDNA pyrosequencing. Armougom F, Bittar F, Stremler N, Rolain JM, Robert C, Dubus JC, Sarles J, Raoult D, La Scola B. (2009) Eur J Clin Microbiol Infect Dis. 28(9): 1151-4. View Publication
Complete genome sequence of Aggregatibacter (Haemophilus) aphrophilus NJ8700. Di Bonaventura MP, Desalle R, Pop M, Nagarajan N, Figurski D, Fine DH, Kaplan J, Planet P. (2009) Journal of Bacteriology 191(14): 4693-4. View Publication
Complete sequence determination of a novel reptile iridovirus isolated from soft-shelled turtle and evolutionary analysis of Iridoviridae. Huang Y, Huang X, Hong L, Gong J, Ouyang Z, Cui H, Cao J, Zhao Y, Wang X, Jiang Y, Qin Q. (2009) BMC Genomics 10: 224. View Publication
Genome sequencing of linezolid-resistant Streptococcus pneumoniae mutants reveals novel mechanisms of resistance. Feng J, Lupien A, Gingras H, Wasserscheid J, Dewar K, Légaré D, Ouellette M. (2009) Genome Research 19(7): 1214-23. View Publication
Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column. Yanmei Shi, Gene W. Tyson, Edward F. DeLong (2009) Nature 459: 266-269. View Publication
PanGEA: Identification of allele specific gene expression using the 454 technology. Kofler R, Torres TT, Lelley T, Schlotterer C. (2009) BMC Bioinformatics 10(1): 143. View Publication
SOrt-ITEMS : Sequence Orthology based approach for Improved Taxonomic Estimation of Metagenomic Sequences. Monzoorul HM, Tarini S, Dinakar K, Sharmila S M. (2009) Bioinformatics 25(14): 1722-30. View Publication
Sequencing and de novo analysis of a coral larval transcriptome using 454 GS-FLX. Meyer E, Aglyamova GV, Wang S, Buchanan-Carter J, Abrego D, Colbourne JK, Willis BL, Matz MV (2009) BMC Genomics 10: 219. View Publication
A whole-genome snapshot of 454 sequences exposes the composition of the barley genome and provides evidence for parallel evolution of genome size in wheat and barley. Wicker T, Taudien S, Houben A, Keller B, Graner A, Platzer M, Stein N. (2009) Plant Journal 59(5): 712-22. View Publication
Deep sequencing analysis of RNAs from a grapevine showing Syrah decline symptoms reveals a multiple virus infection that includes a novel virus. Al Rwahnih M, Daubert S, Golino D, Rowhani A. (2009) Virology 387(2): 395-401. View Publication
Bioinformatics analysis suggests base modifications of tRNAs and miRNAs in Arabidopsis thaliana. Iida K, Jin H, Zhu JK. (2009) BMC Genomics 10: 155. View Publication
High-Throughput Sequencing of the Zebrafish Antibody Repertoire. Joshua A. Weinstein, Ning Jiang, Richard A. White, III, Daniel S. Fisher, Stephen R. Quake (2009) Science 324(5928): 807-810. View Publication
Orphelia: predicting genes in metagenomic sequencing reads. Hoff KJ, Lingner T, Meinicke P, Tech M. (2009) Nucleic Acids Research 37: W101-5. View Publication
Phylogenetic analysis of three genes of Penguinpox virus corresponding to Vaccinia virus G8R (VLTF-1), A3L (P4b) and H3L reveals that it is most closely related to Turkeypox virus, Ostrichpox virus and Pigeonpox virus. Carulei O, Douglass N, Williamson AL. (2009) Virology Journal 6: 52. View Publication
Barcoded Pyrosequencing Reveals Shared Bacterial Community Properties along Two Alkaline Hot Spring Temperature Gradients in Yellowstone National Park. Miller SR, Strong AL, Jones KL, Ungerer MC. (2009) Applied Environmental Microbiology 75(13): 4565-72. View Publication
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Comparison of the transcriptomes of American chestnut (Castanea dentata) and Chinese chestnut (Castanea mollissima) in response to the chestnut blight infection. Barakat A, Diloreto DS, Zhang Y, Smith C, Baier K, Powell WA, Wheeler N, Sederoff R, Carlson JE. (2009) BMC Plant Biology 9(1): 51. View Publication
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Detection of low-frequency pretherapy chemokine (CXC motif) receptor 4 (CXCR4)-using HIV-1 with ultra-deep pyrosequencing. Archer J, Braverman MS, Taillon BE, Desany B, James I, Harrigan PR, Lewis M, Robertson DL. (2009) AIDS 23(10): 1209-18. View Publication
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Evaluating high-throughput sequencing as a method for metagenomic analysis of nematode diversity. Porazinska et al. (2009) Molecular Ecology Resources 9(6): 1439-1450. View Publication
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Diet-induced metabolic improvements in a hamster model of hypercholesterolemia are strongly linked to alterations of the gut microbiota. Martínez I, Wallace G, Zhang C, Legge R, Benson AK, Carr TP, Moriyama EN, Walter J. (2009) Applied Environmental Microbiology 75(12): 4175-84. View Publication
Reduced genomic potential for secreted plant cell-wall-degrading enzymes in the ectomycorrhizal fungus Amanita bisporigera, based on the secretome of Trichoderma reesei. Nagendran S, Hallen-Adams HE, Paper JM, Aslam N, Walton JD. (2009) Fungal Genetic Biology 46(5): 427-35 View Publication
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The Expansion of the Microbiological Spectrum of Brain Abscesses with Use of Multiple 16S Ribosomal DNA Sequencing. Al Masalma M, Armougom F, Scheld WM, Dufour H, Roche PH, Drancourt M, Raoult D. (2009) Clinical Infectious Diseases 48(9): 1169-78. View Publication
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