454 Life Sciences

Gene-specific FACS sorting method for target selection in high-throughput amplicon sequencing.  Sandberg J, Neiman MG, Ahmadian A, Lundeberg J. (2010) BMC Genomics 11(1): 140.
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Metabolic streamlining in an open-ocean nitrogen-fixing cyanobacterium.  Tripp HJ, Bench SR, Turk KA, Foster RA, Desany BA, Niazi F, Affourtit JP, Zehr JP. (2010) Nature ePub:
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Ultra deep sequencing detects a low rate of mosaic mutations in tuberous sclerosis complex.  Qin W, Kozlowski P, Taillon BE, Bouffard P, Holmes AJ, Janne P, Camposano S, Thiele E, Franz D, Kwiatkowski DJ. (2010) Human Genetics ePub:
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High-throughput genome sequencing of two Listeria monocytogenes clinical isolates during a large foodborne outbreak.  Gilmour MW, Graham M, Van Domselaar G, Tyler S, Kent H, Trout-Yakel KM, Larios O, Allen V, Lee B, Nadon C. (2010) BMC Genomics 11(1): 120.
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Complete Khoisan and Bantu genomes from southern Africa.  Schuster SC et al. (2010) Nature 463(7283): 943-7.
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HIV Drug Resistance Surveillance Using Pooled Pyrosequencing.  Ji H, Massé N, Tyler S, Liang B, Li Y, Merks H, Graham M, Sandstrom P, Brooks J. (2010) PLoS One 5(2): e9263.
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Transcriptomic changes arising during light-induced sporulation in Physarum polycephalum.  Barrantes I, Glockner G, Meyer S, Marwan W. (2010) BMC Genomics 11(1): 115.
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Rapid interactome profiling by massive sequencing.  Di Niro R, Sulic AM, Mignone F, D'Angelo S, Bordoni R, Iacono M, Marzari R, Gaiotto T, Lavric M, Bradbury AR, Biancone L, Zevin-Sonkin D, De Bellis G, Santoro C, Sblattero D. (2010) Nucleic Acids Research ePub:
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Stressor exposure disrupts commensal microbial populations in the intestines and leads to increased colonization by Citrobacter rodentium.  Bailey MT, Dowd SE, Parry NM, Galley JD, Schauer DB, Lyte M. (2010) Infection and Immunity ePub:
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Development of a EST dataset and characterization of EST-SSRs in a traditional Chinese medicinal plant, Epimedium sagittatum (Sieb. Et Zucc.) Maxim.  Zeng S, Xiao G, Guo J, Fei Z, Xu Y, Roe BA, Wang Y. (2010) BMC Genomics 11(1): 94.
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Dynamics of Haplotype Frequency Change in a CD8+TL Epitope of Simian Immunodeficiency Virus.  Hughes AL, O'Connor S, Dudley DM, Burwitz BJ, Bimber BN, O'Connor D. (2010) Infect Genet Evol ePub:
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Nitrate-responsive miR393/AFB3 regulatory module controls root system architecture in Arabidopsis thaliana.  Vidal EA, Araus V, Lu C, Parry G, Green PJ, Coruzzi GM, Gutiérrez RA. (2010) PNAS ePub:
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Analysis of High-Throughput Sequencing and Annotation Strategies for Phage Genomes.  Henn MR, Sullivan MB, Stange-Thomann N, Osburne MS, Berlin AM, Kelly L, Yandava C, Kodira C, Zeng Q, Weiand M, Sparrow T, Saif S, Giannoukos G, Young SK, Nusbaum C, Birren BW, Chisholm SW. (2010) PLoS One 5(2): e9083.
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Gut Microbiota in Human Adults with Type 2 Diabetes Differs from Non-Diabetic Adults.  Larsen N, Vogensen FK, van den Berg FW, Nielsen DS, Andreasen AS, Pedersen BK, Al-Soud WA, Sørensen SJ, Hansen LH, Jakobsen M. (2010) PLoS One 5(2): e9085.
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A scalable, fully automated process for construction of sequence-ready barcoded libraries for 454.  Lennon NJ et al. (2010) Genome Biology 11(2): R15.
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Shifts in microbial community structure along an ecological gradient of hypersaline soils and sediments.  Hollister EB, Engledow AS, Hammett AJ, Provin TL, Wilkinson HH, Gentry TJ. (2010) ISME Journal ePub:
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Genomic and small RNA sequencing of Miscanthus x giganteus shows the utility of sorghum as a reference genome sequence for Andropogoneae grasses.  Swaminathan K, Alabady M, Varala K, De Paoli E, Ho I, Rokhsar DS, Ming R, Green PJ, Meyers BC, Moose SP, Hudson ME, Arumuganathan AK. (2010) Genome Biology 11(2): R12.
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The structure of bacterial communities in the western Arctic Ocean as revealed by pyrosequencing of 16S rRNA genes.  Kirchman DL, Cottrell MT, Lovejoy C. (2010) Environmental Microbiology ePub:
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High-throughput sequencing of retrotransposon integration provides a saturated profile of target activity in Schizosaccharomyces pombe.  Guo Y, Levin HL. (2010) Genome Research 20(2): 239-48.
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Interactions between gut microbiota, host genetics and diet relevant to development of metabolic syndromes in mice.  Zhang C, Zhang M, Wang S, Han R, Cao Y, Hua W, Mao Y, Zhang X, Pang X, Wei C, Zhao G, Chen Y, Zhao L. (2010) ISME Journal 4(2): 232-41.
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Bacterial communities of disease vectors sampled across time, space, and species.  Jones RT, Knight R, Martin AP.  (2010) ISME Journal 4(2): 223-31.
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Pyrosequencing the Manduca sexta larval midgut transcriptome: messages for digestion, detoxification and defence.  Pauchet Y, Wilkinson P, Vogel H, Nelson DR, Reynolds SE, Heckel DG, Ffrench-Constant RH. (2010) Insect Molecular Biology 19(1): 61-75.
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Fine-scale comparative genetic and physical mapping supports map-based cloning strategies for the self-incompatibility loci of perennial ryegrass (Lolium perenne L.).  Shinozuka H, Cogan NO, Smith KF, Spangenberg GC, Forster JW. (2010) Plant Mol Biol. 72(3): 343-55.
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QDD: a user-friendly program to select microsatellite markers and design primers from large sequencing projects.  Meglécz E, Costedoat C, Dubut V, Gilles A, Malausa T, Pech N, Martin JF. (2010) Bioinformatics 26(3): 403-4.
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Lens epithelium-derived growth factor fusion proteins redirect HIV-1 DNA integration.  Ferris AL, Wu X, Hughes CM, Stewart C, Smith SJ, Milne TA, Wang GG, Shun MC, Allis CD, Engelman A, Hughes SH. (2010) PNAS 107(7): 3135-40.
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Microindel detection in short-read sequence data.  Krawitz P, Rödelsperger C, Jäger M, Jostins L, Bauer S, Robinson PN. (2010) Bioinformatics ePub:
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Identification of Rhesus Macaque Genital Microbiota by 16S Pyrosequencing Shows Similarities to Human Bacterial Vaginosis: Implications for Use as an Animal Model for HIV Vaginal Infection.  Spear GT, Gilbert D, Sikaroodi M, Doyle L, Green L, Gillevet PM, Landay AL, Veazey RS. (2010) AIDS Res Hum Retroviruses 26(2): 193-200.
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Gene-targeted-metagenomics reveals extensive diversity of aromatic dioxygenase genes in the environment.  Iwai S, Chai B, Sul WJ, Cole JR, Hashsham SA, Tiedje JM. (2010) ISME Journal 4(2): 279-85.
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Pyrosequencing reveals contrasting seasonal dynamics of taxa within Baltic Sea bacterioplankton communities.  Andersson AF, Riemann L, Bertilsson S. (2010) ISME Journal 4(2): 171-81.
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Comparison of bisulfite sequencing PCR with pyrosequencing for measuring differences in DNA methylation.  Reed K, Poulin ML, Yan L, Parissenti AM. (2010) Analytical Biochemistry 397(1): 96-106.
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HIV Sequence Variation Associated With env Antisense Adoptive T-cell Therapy in the hNSG Mouse Model.  Mukherjee R, Plesa G, Sherrill-Mix S, Richardson MW, Riley JL, Bushman FD. (2010) Molecular Therapy ePub:
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Pyrosequencing of Mytilus galloprovincialis cDNAs: Tissue-Specific Expression Patterns.  Craft JA, Gilbert JA, Temperton B, Dempsey KE, Ashelford K, Tiwari B, Hutchinson TH, Chipman JK. (2010) PLoS One 5(1): e8875.
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The carnivorous Pale Pitcher Plant harbors diverse, distinct and temporally dependent bacterial communities.  Koopman MM, Fuselier DM, Hird S, Carstens BC. (2010) Applied Evironmental Microbiology ePub:
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Seasonally dynamic fungal communities in the Quercus macrocarpa phyllosphere differ between urban and nonurban environments.  Jumpponen A, Jones KL. (2010) New Phytologist ePub:
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Improving sequence assembly using machine learning and comparative genomics for overlap correction.  Palmer LE, Dejori M, Bolanos R, Fasulo D. (2010) BMC Bioinformatics 11(1): 33.
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One-step identification of conserved miRNAs, their targets, potential transcription factors and effector genes of complete secondary metabolism pathways after 454 pyrosequencing of calyx cDNAs from the Labiate Salvia sclarea L.  Legrand S, Valot N, Nicolé F, Moja S, Baudino S, Jullien F, Magnard JL, Caissard JC, Legendre L. (2010) Gene 450(1-2): 55-62.
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Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content.  Hughes JF, Skaletsky H, Pyntikova T, Graves TA, van Daalen SK, Minx PJ, Fulton RS, McGrath SD, Locke DP, Friedman C, Trask BJ, Mardis ER, Warren WC, Repping S, Rozen S, Wilson RK, Page DC. (2010) Nature 463(7280): 536-9.
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CANGS: a user-friendly utility for processing and analyzing 454 GS-FLX data in biodiversity studies.  Pandey RV, Nolte V, Schlötterer C. (2010) BMC Research Notes 3(1): 3.
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Characterization of the oral fungal microbiome (mycobiome) in healthy individuals.  Ghannoum MA, Jurevic RJ, Mukherjee PK, Cui F, Sikaroodi M, Naqvi A, Gillevet PM. (2010) PLoS Pathogens 6(1): e1000713.
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Characterization of nucleotide misincorporation patterns in the iceman's mitochondrial DNA.  Olivieri C, Ermini L, Rizzi E, Corti G, Bonnal R, Luciani S, Marota I, De Bellis G, Rollo F. (2010) PLoS One 5(1): e8629.
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The effects of circumcision on the penis microbiome.  Price LB, Liu CM, Johnson KE, Aziz M, Lau MK, Bowers J, Ravel J, Keim PS, Serwadda D, Wawer MJ, Gray RH. (2010) PLoS One 5(1): e8422.
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Like will to like: abundances of closely related species can predict susceptibility to intestinal colonization by pathogenic and commensal bacteria.  Stecher B, Chaffron S, Käppeli R, Hapfelmeier S, Freedrich S, Weber TC, Kirundi J, Suar M, McCoy KD, von Mering C, Macpherson AJ, Hardt WD. (2010) PLoS Pathogens 6(1): e1000711.
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Complete genome sequence of the fire blight pathogen Erwinia pyrifoliae DSM 12163T and comparative genomic insights into plant pathogenicity.  Smits TH, Jaenicke S, Rezzonico F, Kamber T, Goesmann A, Frey JE, Duffy B. (2010) BMC Genomics 11(1): 2.
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Genomic characterization of the Yersinia genus.  Chen PE, Cook C, Stewart AC, Nagarajan N, Sommer DD, Pop M, Thomason B, Kiley MP, Lentz S, Nolan N, Sozhamannan S, Sulakvelidze A, Mateczun A, Du L, Zwick ME, Read TD. (2010) Genome Biology 11(1): R1.
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High throughput sequencing reveals a complex pattern of dynamic interrelationships among human T cell subsets.  Wang C, Sanders CM, Yang Q, Schroeder HW Jr, Wang E, Babrzadeh F, Gharizadeh B, Myers RM, Hudson JR Jr, Davis RW, Han J. (2010) PNAS 107(4): 1518-23.
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Discovery of chicken microRNAs associated with lipogenesis and cell proliferation.  Hicks JA, Trakooljul N, Liu HC. (2010) Physiological Genomics ePub:
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Effect of the herbicide glyphosate on glyphosate-tolerant maize rhizobacterial communities: a comparison with pre-emergency applied herbicide consisting of a combination of acetochlor and terbuthylazine.  Barriuso J, Marín S, Mellado RP. (2010) Environmental Microbiology ePub:
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Evolution at a High Imposed Mutation Rate: Adaptation Obscures the Load in Phage T7.  Springman R, Keller T, Molineux I, Bull JJ. (2010) Genetics 184(1): 221-32.
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The Tasmanian Devil Transcriptome Reveals Schwann Cell Origins of a Clonally Transmissible Cancer.  Murchison EP, Tovar C, Hsu A, Bender HS, Kheradpour P, Rebbeck CA, Obendorf D, Conlan C, Bahlo M, Blizzard CA, Pyecroft S, Kreiss A, Kellis M, Stark A, Harkins TT, Graves JA, Woods GM, Hannon GJ, Papenfuss AT. (2010) Science 327(5961): 84-87.
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Moussa virus: A new member of the Rhabdoviridae family isolated from Culex decens mosquitoes in Côte d'Ivoire.  Quan PL, Junglen S, Tashmukhamedova A, Conlan S, Hutchison SK, Kurth A, Ellerbrok H, Egholm M, Briese T, Leendertz FH, Lipkin WI. (2010) Virus Research 147(1): 17-24.
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Deep Sequencing of a DMSP-Degrading Gene (dmdA) Using PCR Primer Pairs Designed from Marine Metagenomic Data.  Varaljay VA, Howard EC, Sun S, Moran MA. (2010) Applied Environmental Microbiology 76(2): 609-17.
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DNA Sequence Capture and Enrichment by Microarray Followed by Next-Generation Sequencing for Targeted Resequencing: Neurofibromatosis Type 1 Gene as a Model.  Chou LS, Liu CS, Boese B, Zhang X, Mao R. (2010) Clinical Chemistry 56(1): 62-72.
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inGAP: an integrated next-generation genome analysis pipeline.  Qi J, Zhao F, Buboltz A, Schuster SC. (2010) Bioinformatics 26(1): 127-9.
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Intestinal Microbial Ecology in Premature Infants Assessed with Non-Culture-Based Techniques.  Mshvildadze M, Neu J, Shuster J, Theriaque D, Li N, Mai V. (2010) Journal of Pediatrics 156(1): 20-5.
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Differentially expressed alternatively spliced genes in Malignant Pleural Mesothelioma identified using massively parallel transcriptome sequencing.  Dong L, Jensen RV, De Rienzo A, Gordon GJ, Xu Y, Sugarbaker DJ, Bueno R. (2009) BMC Medical Genetics 10(1): 149.
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MicroRNA and tasiRNA diversity in mature pollen of Arabidopsis thaliana.  Grant-Downton R, Le Trionnaire G, Schmid R, Rodriguez-Enriquez J, Hafidh S, Mehdi S, Twell D, Dickinson H. (2009) BMC Genomics 10(1): 643.
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Photoperiod Modulates Gut Bacteria Composition in Male Siberian Hamsters (Phodopus sungorus).  Bailey MT, Walton JC, Dowd SE, Weil ZM, Nelson RJ. (2009) Brain Behav Immun ePub:
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Rumen Bacterial Diversity Dynamics Associated with Changing from Bermudagrass Hay to Grazed Winter Wheat Diets.  Pitta DW, Pinchak WE, Dowd SE, Osterstock J, Gontcharova V, Youn E, Dorton K, Yoon I, Min BR, Fulford JD, Wickersham TA, Malinowski DP. (2009) Microbial Ecology ePub:
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Sympatric ecological speciation meets pyrosequencing: sampling the transcriptome of the apple maggot Rhagoletis pomonella.  Schwarz D, Robertson HM, Feder JL, Varala K, Hudson ME, Ragland GJ, Hahn DA, Berlocher SH. (2009) BMC Genomics 10(1): 633.
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Next generation transcriptomes for next generation genomes using est2assembly.  Papanicolaou A, Stierli R, Ffrench-Constant RH, Heckel DG. (2009) BMC Bioinformatics 10(1): 447.
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Measurement and clinical monitoring of human lymphocyte clonality by massively parallel VDJ pyrosequencing.  Boyd SD, 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, Fire AZ. (2009) Science Translational Medicine 1(12): 12ra23.
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Genome-wide profiling of Populus small RNAs.  Klevebring D, Street NR, Fahlgren N, Kasschau KD, Carrington JC, Lundeberg J, Jansson S. (2009) BMC Genomics 10(1): 620.
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Next-generation phage display: integrating and comparing available molecular tools to enable cost-effective high-throughput analysis.  Dias-Neto E, Nunes DN, Giordano RJ, Sun J, Botz GH, Yang K, Setubal JC, Pasqualini R, Arap W. (2009) PLoS One 4(12): e8338.
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Exome sequencing of a multigenerational human pedigree.  Hedges D, Burges D, Powell E, Almonte C, Huang J, Young S, Boese B, Schmidt M, Pericak-Vance MA, Martin E, Zhang X, Harkins TT, Züchner S. (2009) PLoS One 4(12): e8232.
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Hydrography shapes bacterial biogeography of the deep Arctic Ocean.  Galand PE, Potvin M, Casamayor EO, Lovejoy C. (2009) ISME Journal ePub:
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Defining the healthy "core microbiome" of oral microbial communities.  Zaura E, Keijser BJ, Huse SM, Crielaard W. (2009) BMC Microbiology 9(1): 259.
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The Chloroplast Genome Sequence of Mungbean (Vigna radiata) Determined by High-throughput Pyrosequencing: Structural Organization and Phylogenetic Relationships.  Tangphatsornruang S, Sangsrakru D, Chanprasert J, Uthaipaisanwong P, Yoocha T, Jomchai N, Tragoonrung S. (2009) DNA Research 17(1): 11-22.
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Giant Marseillevirus highlights the role of amoebae as a melting pot in emergence of chimeric microorganisms.  Mickaël Boyera, Natalya Yutinb, Isabelle Pagniera, Lina Barrassia, Ghislain Fournousa, Leon Espinosaa, Catherine Roberta, Saïd Azzaa, Siyang Sunc, Michael G. Rossmannc, Marie Suzan-Montia, Bernard La Scolaa, Eugene V. Kooninb and Didier Raoulta (2009) PNAS 106(51): 21848-53.
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Deep sequencing analysis of the Methanosarcina mazei Go1 transcriptome in response to nitrogen availability.  Jäger D, Sharma CM, Thomsen J, Ehlers C, Vogel J, Schmitz RA. (2009) PNAS 106(51): 21878-82.
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Mining regulatory 5'UTRs from cDNA deep sequencing datasets.  Livny J, Waldor MK. (2009) Nucleic Acids Research ePub:
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Direct sequencing and expression analysis of a large number of miRNAs in Aedes aegypti and a multi-species survey of novel mosquito miRNAs.  Li S, Mead EA, Liang S, Tu Z. (2009) BMC Genomics 10(1): 581.
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Metagenomic islands of hyperhalophiles: the case of Salinibacter ruber.  Pasic L, Rodriguez-Mueller B, Martin-Cuadrado AB, Mira A, Rohwer F, Rodriguez-Valera F. (2009) BMC Genomics 10(1): 570.
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A Subtle Alternative Splicing Event of the Na(V)1.8 Voltage-Gated Sodium Channel is Conserved in Human, Rat, and Mouse.  Schirmeyer J, Szafranski K, Leipold E, Mawrin C, Platzer M, Heinemann SH. (2009) Journal of Molecular Neuroscience ePub:
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454 pyrosequencing based transcriptome analysis of Zygaena filipendulae with focus on genes involved in biosynthesis of cyanogenic glucosides.  Zagrobelny M, Scheibye-Alsing K, Bjerg Jensen N, Lindberg Moller B, Gorodkin J, Bak S. (2009) BMC Genomics 10(1): 574.
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Phylogenetic Analysis of Population-Based and Deep Sequencing Data to Identify Coevolving Sites in the nef Gene of HIV-1.  Poon AF, Swenson LC, Dong WW, Deng W, Kosakovsky Pond SL, Brumme ZL, Mullins JI, Richman DD, Harrigan PR, Frost SD. (2009) Molecular Biology and Evolution ePub:
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Single nucleotide polymorphism discovery in rainbow trout by deep sequencing of a reduced representation library.  Castano-Sanchez C, Smith TP, Wiedmann RT, Vallejo RL, Salem M, Yao J, Rexroad CE 3rd. (2009) BMC Genomics 10(1): 559.
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Characterization of microsatellites and gene contents from genome shotgun sequences of mungbean (Vigna radiata (L.)Wilczek).  Tangphatsornruang S, Somta P, Uthaipaisanwong P, Chanprasert J, Sangsrakru D, Seehalak W, Sommanas W, Tragoonrung S, Srinives P. (2009) BMC Plant Biology 9(1): 137.
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Combining next-generation pyrosequencing with microarray for large scale expression analysis in non-model species.  Bellin D, Ferrarini A, Chimento A, Kaiser O, Levenkova N, Bouffard P, Delledonne M. (2009) BMC Genomics 10(1): 555.
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De novo 454 sequencing of barcoded BAC pools for comprehensive gene survey and genome analysis in the complex genome of barley.  Steuernagel B, Taudien S, Gundlach H, Seidel M, Ariyadasa R, Schulte D, Petzold A, Felder M, Graner A, Scholz U, Mayer KF, Platzer M, Stein N. (2009) BMC Genomics 10(1): 547.
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Disclosing arbuscular mycorrhizal fungal biodiversity in soil through a land-use gradient using a pyrosequencing approach.  Lumini E, Orgiazzi A, Borriello R, Bonfante P, Bianciotto V. (2009) Environmental Microbiology ePub:
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The Effect of Diet on the Human Gut Microbiome: A Metagenomic Analysis in Humanized Gnotobiotic Mice.  Peter J. Turnbaugh, Vanessa K. Ridaura, Jeremiah J. Faith, Federico E. Rey, Rob Knight and Jeffrey I. Gordon (2009) Science Translational Medicine 1(6):
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High diversity of the viral community from an Antarctic lake.  López-Bueno A, Tamames J, Velázquez D, Moya A, Quesada A, Alcamí A. (2009) Science 326(5954): 858-61.
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High-throughput sequencing of microdissected chromosomal regions.  Weise A, Timmermann B, Grabherr M, Werber M, Heyn P, Kosyakova N, Liehr T, Neitzel H, Konrat K, Bommer C, Dietrich C, Rajab A, Reinhardt R, Mundlos S, Lindner TH, Hoffmann K. (2009) European Journal of Human Genetics ePub:
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Massively parallel tag sequencing reveals the complexity of anaerobic marine protistan communities.  Stoeck T, Behnke A, Christen R, Amaral-Zettler L, Rodriguez-Mora MJ, Chistoserdov A, Orsi W, Edgcomb VP. (2009) BMC Biology 7(1): 72.
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Microdroplet-based PCR enrichment for large-scale targeted sequencing.  Tewhey R, Warner JB, Nakano M, Libby B, Medkova M, David PH, Kotsopoulos SK, Samuels ML, Hutchison JB, Larson JW, Topol EJ, Weiner MP, Harismendy O, Olson J, Link DR, Frazer KA. (2009) Nature Biotechnology 27(11): 1025-31.
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High-resolution, high-throughput HLA genotyping by next-generation sequencing.  Bentley G, Higuchi R, Hoglund B, Goodridge D, Sayer D, Trachtenberg EA, Erlich HA. (2009) Tissue Antigens 74(5): 393-403.
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Precise determination of the diversity of a combinatorial antibody library gives insight into the human immunoglobulin repertoire.  Glanville J, Zhai W, Berka J, Telman D, Huerta G, Mehta GR, Ni I, Mei L, Sundar PD, Day GM, Cox D, Rajpal A, Pons J. (2009) PNAS 106(48): 21216-21.
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Evaluation of the bacterial diversity among and within individual venous leg ulcers using bacterial tag-encoded FLX and Titanium amplicon pyrosequencing and metagenomic approaches.  Wolcott RD, Gontcharova V, Sun Y, Dowd SE. (2009) BMC Microbiology 9: 226.
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Generalized antifungal activity and 454-screening of Pseudonocardia and Amycolatopsis bacteria in nests of fungus-growing ants.  Sen R, Ishak HD, Estrada D, Dowd SE, Hong E, Mueller UG. (2009) PNAS 106(42): 17805-10.
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Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli.  Mendoza-Vargas A, Olvera L, Olvera M, Grande R, Vega-Alvarado L, Taboada B, Jimenez-Jacinto V, Salgado H, Juárez K, Contreras-Moreira B, Huerta AM, Collado-Vides J, Morett E. (2009) PLoS One 4(10): e7526.
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Transcription analysis of central metabolism genes in Escherichia coli. Possible roles of sigma38 in their expression, as a response to carbon limitation.  Olvera L, Mendoza-Vargas A, Flores N, Olvera M, Sigala JC, Gosset G, Morett E, Bolívar F. (2009) PLoS One 40(10): e7466.
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Diversity and population structure of sewage-derived microorganisms in wastewater treatment plant influent.  McLellan SL, Huse SM, Mueller-Spitz SR, Andreishcheva EN, Sogin ML. (2009) Environmental Microbiology ePub:
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Major histocompatibility complex genotyping with massively parallel pyrosequencing.  Wiseman RW, Karl JA, Bimber BN, O'Leary CE, Lank SM, Tuscher JJ, Detmer AM, Bouffard P, Levenkova N, Turcotte CL, Szekeres E Jr, Wright C, Harkins T, O'Connor DH. (2009) Nature Medicine 15(11): 1322-6.
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Global characterization of Artemisia annua glandular trichome transcriptome using 454 pyrosequencing.  Wang W, Wang Y, Zhang Q, Qi Y, Guo D. (2009) BMC Genomics 10: 465.
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Metagenomic analysis of respiratory tract DNA viral communities in cystic fibrosis and non-cystic fibrosis individuals.  Willner D, Furlan M, Haynes M, Schmieder R, Angly FE, Silva J, Tammadoni S, Nosrat B, Conrad D, Rohwer F. (2009) PLoS One 4(10): e7370.
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Windshield splatter analysis with the Galaxy metagenomic pipeline.  Kosakovsky Pond S, Wadhawan S, Chiaromonte F, Ananda G, Chung WY, Taylor J, Nekrutenko A; The Galaxy Team. (2009) Genome Research 19(11): 2144-53
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Novel software package for cross-platform transcriptome analysis (CPTRA).  Zhou X, Su Z, Sammons RD, Peng Y, Tranel PJ, Stewart CN Jr, Yuan JS. (2009) BMC Bioinformatics 10 Suppl 11: S16.
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Genome structure of a Saccharomyces cerevisiae strain widely used in bioethanol production.  Argueso et al. (2009) Genome Research 19(12): 2258-70.
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Characterization of marine isoprene-degrading communities.  Alvarez LA, Exton DA, Timmis KN, Suggett DJ, McGenity TJ. (2009) Environmental Microbiology 11(12): 3280-91.
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DLA-Based Strategies for Cloning Insertion Mutants: Cloning the gl4 Locus of Maize Using Mu Transposon Tagged Alleles.  Liu S, Dietrich CR, Schnable PS. (2009) Genetics 183(4): 1215-25.
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Introducing mothur: Open Source, Platform-independent, Community-supported Software for Describing and Comparing Microbial Communities.  Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF. (2009) Applied Environmental Microbiology 75(23): 7537-41.
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Phylogenetic diversity and metabolic potential encoded by a glacial ice metagenome.  Simon C, Wiezer A, Strittmatter AW, Daniel R. (2009) Applied Environmental Microbiology 75(23): 7519-26.
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The effect of the macrolide antibiotic tylosin on microbial diversity in the canine small intestine as demonstrated by massive parallel 16S rRNA gene sequencing.  Suchodolski JS, Dowd SE, Westermarck E, Steiner JM, Wolcott RD, Spillmann T, Harmoinen JA. (2009) BMC Microbiology 9: 210.
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Personalized copy number and segmental duplication maps using next-generation sequencing.  Alkan C, Kidd JM, Marques-Bonet T, Aksay G, Antonacci F, Hormozdiari F, Kitzman JO, Baker C, Malig M, Mutlu O, Sahinalp SC, Gibbs RA, Eichler EE. (2009) Nature Genetics 41(10): 1061-7.
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Confirmation of the Sequence of 'Candidatus Liberibacter asiaticus' and Assessment of Microbial Diversity in Huanglongbing-Infected Citrus Phloem Using a Metagenomic Approach.  Tyler HL, Roesch LF, Gowda S, Dawson WO, Triplett EW. (2009) Molecular Plant Microbial Interactions 22(12): 1624-34.
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Deep sequencing reveals exceptional diversity and modes of transmission for bacterial sponge symbionts.  Webster NS, Taylor MW, Behnam F, Lücker S, Rattei T, Whalan S, Horn M, Wagner M. (2009) Environmental Microbiology ePub:
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Comparative genome and phenotypic analysis of Clostridium difficile 027 strains provides insight into the evolution of a hypervirulent bacterium.  Stabler RA, He M, Dawson L, Martin M, Valiente E, Corton C, Lawley TD, Sebaihia M, Quail MA, Rose G, Gerding DN, Gibert M, Popoff MR, Parkhill J, Dougan G, Wren BW. (2009) Genome Biology 10(9): R102.
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Identification of novel MHC class I sequences in pig-tailed macaques by amplicon pyrosequencing and full-length cDNA cloning and sequencing.  O'Leary CE, Wiseman RW, Karl JA, Bimber BN, Lank SM, Tuscher JJ, O'Connor DH. (2009) Immunogenetics 61(10): 689-701.
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Ancient DNA Reveals Lack of Continuity between Neolithic Hunter-Gatherers and Contemporary Scandinavians.  Helena Malmström, M.Thomas P. Gilbert, Mark G. Thomas, Mikael Brandström, Jan Storå, Petra Molnar, Pernille K. Andersen, Christian Bendixen, Gunilla Holmlund, Anders Götherström , and Eske Willerslev (2009) Current Biology 19(20): 1758-62.
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Comparative SNP diversity among four Eucalyptus species for genes from secondary metabolite biosynthetic pathways.  Külheim C, Yeoh SH, Maintz J, Foley WJ, Moran GF. (2009) BMC Genomics 10: 452.
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Community proteogenomics reveals insights into the physiology of phyllosphere bacteria.  Delmotte N, Knief C, Chaffron S, Innerebner G, Roschitzki B, Schlapbach R, von Mering C, Vorholt JA. (2009) PNAS 106(38): 16428-33.
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Eukaryote-to-eukaryote gene transfer events revealed by the genome sequence of the wine yeast Saccharomyces cerevisiae EC1118.  Novo M, Bigey F, Beyne E, Galeote V, Gavory F, Mallet S, Cambon B, Legras JL, Wincker P, Casaregola S, Dequin S. (2009) PNAS 106(38): 16333-8.
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The novel polysaccharide deacetylase homolog Pdi contributes to virulence of the aquatic pathogen Streptococcus iniae.  Milani CJ, Aziz RK, Locke JB, Dahesh S, Nizet V, Buchanan JT. (2009) Microbiology 156(Pt 2): 543-54.
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Repertoire and evolution of miRNA genes in four divergent nematode species.  de Wit E, Linsen SE, Cuppen E, Berezikov E. (2009) Genome Research 19(11): 2064-74.
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Genomic Diversity and Evolution of Mycobacterium ulcerans Revealed by Next-Generation Sequencing.  Weihong Qi, Michael Käser, Katharina Röltgen, Dorothy Yeboah-Manu, Gerd Pluschke (2009) PLoS Pathogens 5(9): e10000580.
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Photosystem I gene cassettes are present in marine virus genomes.  Sharon I, Alperovitch A, Rohwer F, Haynes M, Glaser F, Atamna-Ismaeel N, Pinter RY, Partensky F, Koonin EV, Wolf YI, Nelson N, Béjà O. (2009) Nature 461(7261): 258-62.
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Recognition and coupling of A-to-I edited sites are determined by the tertiary structure of the RNA.  Ensterö M, Daniel C, Wahlstedt H, Major F, Ohman M. (2009) Nucleic Acids Research 37(20): 6916-26.
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Minority Variants Associated with Transmitted and Acquired HIV-1 Nonnucleoside Reverse Transcriptase Inhibitor Resistance: Implications for the Use of Second-Generation Nonnucleoside Reverse Transcriptase Inhibitors.  Varghese V, Shahriar R, Rhee SY, Liu T, Simen BB, Egholm M, Hanczaruk B, Blake LA, Gharizadeh B, Babrzadeh F, Bachmann MH, Fessel WJ, Shafer RW. (2009) AIDS 52(3): 309-15.
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Whole genome amplification and de novo assembly of single bacterial cells.  Rodrigue S, Malmstrom RR, Berlin AM, Birren BW, Henn MR, Chisholm SW. (2009) PLoS One 4(9): e6864.
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De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data.  Diguistini S, Liao NY, Platt D, Robertson G, Seidel M, Chan SK, Docking TR, Birol I, Holt RA, Hirst M, Mardis E, Marra MA, Hamelin RC, Bohlmann J, Breuil C, Jones SJ. (2009) Genome Biology 10(9): R94.
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Fast mapping of short sequences with mismatches, insertions and deletions using index structures.  Hoffmann S, Otto C, Kurtz S, Sharma CM, Khaitovich P, Vogel J, Stadler PF, Hackermüller J. (2009) PLoS Computational Biology 5(9): e1000502.
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Use of massive parallel pyrosequencing for near full-length characterization of a unique HIV Type 1 BF recombinant associated with a fatal primary infection.  Bruselles A, Rozera G, Bartolini B, Prosperi M, Del Nonno F, Narciso P, Capobianchi MR, Abbate I. (2009) AIDS Research and Human Retroviruses 25(9): 937-42.
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A database of expressed genes from Cochliomyia hominivorax (Diptera: Calliphoridae).  Guerrero FD, Dowd SE, Djikeng A, Wiley G, Macmil S, Saldivar L, Najar F, Roe BA. (2009) Journal of Medical Entomology 46(5): 1109-16.
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Identification and expression analysis of infectious laryngotracheitis virus encoding microRNAs.  Rachamadugu R, Lee JY, Wooming A, Kong BW. (2009) Virus Genes ePub:
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Highly dynamic and sex-specific expression of microRNAs during early ES cell differentiation.  Ciaudo C, Servant N, Cognat V, Sarazin A, Kieffer E, Viville S, Colot V, Barillot E, Heard E, Voinnet O. (2009) PLoS Genetics 5(8): e1000620.
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Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data.  Hamady M, Lozupone C, Knight R. (2009) ISME Journal ePub:
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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.
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PAVE: Program for assembling and viewing ESTs.  Soderlund CA, Johnson E, Bomhoff M, Descour A. (2009) BMC Genomics 10(1): 400.
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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.
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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.
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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.
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Draft genome sequencing of giardia intestinalis assemblage B isolate GS: is human giardiasis caused by two different species?  Franzén O, Jerlström-Hultqvist J, Castro E, Sherwood E, Ankarklev J, Reiner DS, Palm D, Andersson JO, Andersson B, Svärd SG. (2009) PLos Pathogens 5(8): 31000560.
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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.
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Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine.  Claesson MJ, O'Sullivan O, Wang Q, Nikkilä J, Marchesi JR, Smidt H, de Vos WM, Ross RP, O'Toole PW. (2009) PLoS One 4(8): e6669.
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Characterisation of circulating DNA by parallel tagged sequencing on the 454 platform.  van der Vaart M, Semenov DV, Kuligina EV, Richter VA, Pretorius PJ. (2009) Clinical Chemistry Acta 409(1-2): 21-7.
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Gene content and virtual gene order of barley chromosome 1H.  Mayer KF, Taudien S, Martis M, Simkova H, Suchankova P, Gundlach H, Wicker T, Petzold A, Felder M, Steuernagel B, Scholz U, Graner A, Platzer M, Dolezel J, Stein N. (2009) Plant Physiology 151(2): 496-505.
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Tracking the past: interspersed repeats in an extinct Afrotherian mammal, Mammuthus primigenius.  Zhao F, Qi J, Schuster SC. (2009) Genome Research 19(8): 1384-92.
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What can you do with 0.1x genome coverage? A case study based on a genome survey of the scuttle fly Megaselia scalaris (Phoridae).  David A Rasmussen and Mohamed AF Noor (2009) BMC Genomics 10: 382.
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Microbial community structure in a biofilm anode fed with a fermentable substrate: The significance of hydrogen scavengers.  Parameswaran P, Zhang H, Torres CI, Rittmann BE, Krajmalnik-Brown R. (2009) Biotechnology and Bioengineering 105(1): 69-78.
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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.
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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.
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Massively parallel 454 sequencing indicates hyperdiverse fungal communities in temperate Quercus macrocarpa phyllosphere.  Jumpponen A, Jones KL. (2009) New Phytologist 184(2): 438-48.
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Deep-sequencing of plant viral small RNAs reveals effective and widespread targeting of viral genomes.  Donaire L, Wang Y, Gonzalez-Ibeas D, Mayer KF, Aranda MA, Llave C. (2009) Virology 392(2): 203-14.
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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.
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Focused-Pulsed sludge pre-treatment increases the bacterial diversity and relative abundance of acetoclastic methanogens in a full-scale anaerobic digester.  Zhang H, Banaszak JE, Parameswaran P, Alder J, Krajmalnik-Brown R, Rittmann BE. (2009) Water Research 43(18): 4517-26.
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Brucella microti: the genome sequence of an emerging pathogen.  Audic S, Lescot M, Claverie JM, Scholz HC. (2009) BMC Genomics 10(1): 352.
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Comparison of next generation sequencing technologies for transcriptome characterization.  Wall PK, Leebens-Mack J, Chanderbali AS, Barakat A, Wolcott E, Liang H, Landherr L, Tomsho LP, Hu Y, Carlson JE, Ma H, Schuster SC, Soltis DE, Soltis PS, Altman N, Depamphilis CW. (2009) BMC Genomics 10(1): 347.
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Bacterial diversity in surgical site infections: not just aerobic cocci any more.  Wolcott RD, Gontcharova V, Sun Y, Zischakau A, Dowd SE. (2009) Journal of Wound Care 18(8): 317-23.
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Ultradeep pyrosequencing detects complex patterns of CD8+ T-lymphocyte escape in simian immunodeficiency virus-infected macaques.  Bimber BN, Burwitz BJ, O'Connor S, Detmer A, Gostick E, Lank SM, Price DA, Hughes A, O'Connor D. (2009) Journal of Virology 83(16): 8247-53.
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The sea lamprey Petromyzon marinus genome reveals the early origin of several chemosensory receptor families in the vertebrate lineage.  Libants S, Carr K, Wu H, Teeter JH, Chung-Davidson YW, Zhang Z, Wilkerson C, Li W. (2009) BMC Evolutionary Biology 9(1): 180.
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Community analysis of chronic wound bacteria using 16S rRNA gene-based pyrosequencing: impact of diabetes and antibiotics on chronic wound microbiota.  Price LB, Liu CM, Melendez JH, Frankel YM, Engelthaler D, Aziz M, Bowers J, Rattray R, Ravel J, Kingsley C, Keim PS, Lazarus GS, Zenilman JM. (2009) PLoS One 4(7): e6462.
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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. ePub:
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Characterization of the Zoarces viviparus liver transcriptome using massively parallel pyrosequencing.  Kristiansson E, Asker N, Forlin L, Larsson DG. (2009) BMC Genomics 10(1): 345.
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Mapping accuracy of short reads from massively parallel sequencing and the implications for quantitative expression profiling.  Palmieri N, Schlötterer C. (2009) PLoS One 4(7): e6323.
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Community-wide response of gut microbiota to enteropathogenic Citrobacter infection revealed by deep sequencing.  Hoffmann C, Hill DA, Minkah N, Kirn T, Troy A, Artis D, Bushman F. (2009) Infection and Immunity 77(10): 4668-78.
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A method for studying protistan diversity using massively parallel sequencing of V9 hypervariable regions of small-subunit ribosomal RNA genes.  Amaral-Zettler LA, McCliment EA, Ducklow HW, Huse SM. (2009) PLoS One 4(7): e6372.
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Microbial community structure in the North Pacific ocean.  Brown MV, Philip GK, Bunge JA, Smith MC, Bissett A, Lauro FM, Fuhrman JA, Donachie SP. (2009) ISME Journal ePub:
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Mutation discovery in the mouse using genetically guided array capture and resequencing.  D'Ascenzo M, Meacham C, Kitzman J, Middle C, Knight J, Winer R, Kukricar M, Richmond T, Albert TJ, Czechanski A, Donahue LR, Affourtit J, Jeddeloh JA, Reinholdt L. (2009) Mammalian Genome 20(7): 424-36.
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Targeted retrieval and analysis of five Neandertal mtDNA genomes.  Briggs AW, Good JM, Green RE, Krause J, Maricic T, Stenzel U, Lalueza-Fox C, Rudan P, Brajkovic D, Kucan Z, Gusic I, Schmitz R, Doronichev VB, Golovanova LV, de la Rasilla M, Fortea J, Rosas A, Pääbo S. (2009) Science 325(5938): 318-21.
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The value of avian genomics to the conservation of wildlife.  Romanov et al. (2009) BMC Genomics 10 Suppl 2: S10.
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Experimental induction of proventricular dilatation disease in cockatiels (Nymphicus hollandicus) inoculated with brain homogenates containing avian bornavirus 4.  Gancz AY, Kistler AL, Greninger AL, Farnoushi Y, Mechani S, Perl S, Berkowitz A, Perez N, Clubb S, Derisi JL, Ganem D, Lublin A. (2009) Journal of Virology 6(1): 100.
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Investigation of archaeal and bacterial diversity in fermented seafood using barcoded pyrosequencing.  Roh SW, Kim KH, Nam YD, Chang HW, Park EJ, Bae JW. (2009) ISME Journal ePub:
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Universal DNA-based methods for assessing the diet of grazing livestock and wildlife from feces.  Pegard A, Miquel C, Valentini A, Coissac E, Bouvier F, François D, Taberlet P, Engel E, Pompanon F. (2009) J Agric Food Chem 57(13): 5700-6.
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Regulation of myocardial ketone body metabolism by the gut microbiota during nutrient deprivation.  Crawford PA, Crowley JR, Sambandam N, Muegge BD, Costello EK, Hamady M, Knight R, Gordon JI. (2009) PNAS 106(27): 11276-81.
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Deep sampling of the Palomero maize transcriptome by a high throughput strategy of pyrosequencing.  Vega-Arreguin JC, Ibarra-Laclette E, Jimenez-Moraila B, Martinez O, Vielle-Calzada JP, Herrera-Estrella L, Herrera-Estrella A. (2009) BMC Genomics 10(1): 299.
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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.
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Next-generation sequencing and metagenomic analysis: a universal diagnostic tool in plant virology.  Adams IP, Glover RH, Monger WA, Mumford R, Jackeviciene E, Navalinskiene M, Samuitiene M, Boonham N. (2009) Molecular Plant Pathology 10(4): 537-45.
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Integrating sequencing technologies in personal genomics: optimal low cost reconstruction of structural variants.  Du J, Bjornson RD, Zhang ZD, Kong Y, Snyder M, Gerstein MB. (2009) PLoS Computational Biology 5(7): e1000432.
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Large-Scale Discovery of Gene-Enriched SNPs.  Gore M, Wright M, Ersoz E, Bouffard P, Szekeres E, Jarvie T, Hurwitz B, Narechania A, Harkins T, Grills G, Ware D and Buckler E. (2009) The Plant Genome 2: 121-133.
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Frameshift detection in prokaryotic genomic sequences.  Kislyuk A, Lomsadze A, Lapidus AL, Borodovsky M. (2009) Int J Bioinform Res Appl. 5(4): 458-77.
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Low-abundance HIV drug-resistant viral variants in treatment-experienced persons correlate with historical antiretroviral use.  Le T, Chiarella J, Simen BB, Hanczaruk B, Egholm M, Landry ML, Dieckhaus K, Rosen MI, Kozal MJ. (2009) PLoS One 4(6): e6079.
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High-resolution profiling and discovery of planarian small RNAs.  Marc R. Friedländera, Catherine Adamidia, Ting Hanb, Svetlana Lebedevaa, Thomas A. Isenbargerc, Martin Hirstd, Marco Marrad, Chad Nusbaume, William L. Leee, James C. Jenkinf, Alejandro Sánchez Alvaradof, John K. Kimb and Nikolaus Rajewskya (2009) PNAS 106(28): 11546-51.
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Assessment of bias associated with incomplete extraction of microbial DNA from soil.  Feinstein LM, Sul WJ, Blackwood CB. (2009) Appl Environ Microbiol 75(16): 5428-33.
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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.
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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.
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Shedding light on an extremophile lifestyle through transcriptomics.  Dassanayake M, Haas JS, Bohnert HJ, Cheeseman JM. (2009) New Phytologist 183(3): 764-75.
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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.
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VarScan: Variant detection in massively parallel sequencing of individual and pooled samples.  Koboldt DC, Chen K, Wylie T, Larson DE, McLellan MD, Mardis ER, Weinstock GM, Wilson RK, Ding L. (2009) Bioinformatics 25(17): 2283-5.
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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.
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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.
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Novel TET2 Mutations Associated With UPD4q24 in Myelodysplastic Syndrome.  Mohamedali AM, Smith AE, Gaken J, Lea NC, Mian SA, Westwood NB, Strupp C, Gattermann N, Germing U, Mufti GJ. (2009) Journal of Clinical Oncology. 27(24): 4002-6.
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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.
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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.
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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.
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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.
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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.
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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.
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Allelic imbalance sequencing reveals that single-nucleotide polymorphisms frequently alter microRNA-directed repression.  Kim J, Bartel DP. (2009) Nature Biotechnology 27(5): 472-7.
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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.
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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.
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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.
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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.
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Complete genome sequence of Lactobacillus plantarum JDM1.  Zhang Z, Liu C, Zhu Y, Zhong Y, Zhu Y, Zheng H, Zhao GP, Wang SY, Guo X. (2009) Journal of Bacteriology 191(15): 5020-1.
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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.
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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
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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Bioinformatics analysis suggests base modifications of tRNAs and miRNAs in Arabidopsis thaliana.  Iida K, Jin H, Zhu JK. (2009) BMC Genomics 10: 155.
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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.
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Orphelia: predicting genes in metagenomic sequencing reads.  Hoff KJ, Lingner T, Meinicke P, Tech M. (2009) Nucleic Acids Research 37: W101-5.
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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.
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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.
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Sim4cc: a cross-species spliced alignment program.  Zhou L, Pertea M, Delcher AL, Florea L. (2009) Nucleic Acids Research 37(11): e80.
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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.
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Large-scale mRNA sequencing determines global regulation of RNA editing during brain development.  Wahlstedt H, Daniel C, Ensterö M, Ohman M. (2009) Genome Research 19(6): 978-86.
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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.
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ESPRIT: estimating species richness using large collections of 16S rRNA pyrosequences.  Sun Y, Cai Y, Liu L, Yu F, Farrell ML, McKendree W, Farmerie W. (2009) Nucleic Acids Research 37(10): e76.
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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.
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Whole genome assembly from 454 sequencing output via modified DNA graph concept.  Blazewicz J, Bryja M, Figlerowicz M, Gawron P, Kasprzak M, Kirton E, Platt D, Przybytek J, Swiercz A, Szajkowski L. (2009) Comput Biol Chem. 33(3): 224-30.
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Comparative analysis of human saliva microbiome diversity by barcoded pyrosequencing and cloning approaches.  Nasidze I, Quinque D, Li J, Li M, Tang K, Stoneking M. (2009) Analytical Biochemistry 391(1): 64-8.
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16SrRNA bacterial tag-encoded amplicons pyrosequencing for rapid deciphering of the microbiome of fermented foods: the case of fermented pearl-millet slurries.  Humblot C, Guyot JP. (2009) Applied Environmental Microbiology 75(13): 4354-61.
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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.
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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
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Tiny RNAs associated with transcription start sites in animals.  Taft, Glazov, Cloonan, Simons, Stephen, Faulkner, Lassmann , Forrest, Grimmond, Schroder, Irvine, Arakawa, Nakamura, Kubosaki, Hayashida, Kawazu, Murata, Nishiyori, Fukuda, Kawai, Daub, Hume, Suzuki, Orlando, Carninci, Hayashizaki, Mattick. (2009) Nature Genetics 41(5): 572-8
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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.
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Flow cytometry for enrichment and titration in massively parallel DNA sequencing.  Sandberg J, Ståhl PL, Ahmadian A, Bjursell MK, Lundeberg J. (2009) Nucleic Acids Research 37(8): e63.
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Pyrosequencing of the chaperonin-60 (cpn60) universal target as a tool for determining the composition of microbial communities.  Schellenberg J, Links MG, Hill JE, Dumonceaux TJ, Peters GA, Tyler S, Ball TB, Severini A, Plummer FA. (2009) Applied Environmental Microbiology 75(9): 2889-98.
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Metagenomic Analyses of Viruses in Stool Samples from Children with Acute Flaccid Paralysis.  Victoria JG, Kapoor A, Li L, Blinkova O, Slikas B, Wang C, Naeem A, Zaidi S, Delwart E. (2009) Journal of Virology 83(9): 4642-51
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Targeted single nucleotide polymorphism (SNP) discovery in a highly polyploid plant species using 454 sequencing.  Bundock PC, Eliott FG, Ablett G, Benson AD, Casu RE, Aitken KS, Henry RJ. (2009) Plant Biotechnol Journal 7(4): 347-54
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Culture-independent identification of gut bacteria correlated with the onset of diabetes in a rat model.  Roesch LF, Lorca GL, Casella G, Giongo A, Naranjo A, Pionzio AM, Li N, Mai V, Wasserfall CH, Schatz D, Atkinson MA, Neu J, Triplett EW. (2009) ISME Journal 3(5): 536-48
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Ultra-Deep Pyrosequencing of Hepatitis B Virus Quasispecies from Nucleoside and Nucleotide Reverse-Transcriptase Inhibitor (NRTI)-Treated Patients and NRTI-Naive Patients.  Margeridon-Thermet S, Shulman NS, Ahmed A, Shahriar R, Liu T, Wang C, Holmes SP, Babrzadeh F, Gharizadeh B, Hanczaruk B, Simen BB, Egholm M, Shafer RW. (2009) Journal of Infectious Disease 199(9): 1275-85.
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Analysis of Australian fur seal diet by pyrosequencing prey DNA in faeces.  Deagle BE, Kirkwood R, Jarman SN. (2009) Molecular Ecology 18(9): 2022-38.
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Comparative genomic characterization of Francisella tularensis strains belonging to low and high virulence subspecies.  Champion MD, Zeng Q, Nix EB, Nano FE, Keim P, Kodira CD, Borowsky M, Young S, Koehrsen M, Engels R, Pearson M, Howarth C, Larson L, White J, Alvarado L, Forsman M, Bearden SW, Sjöstedt A, Titball R, Michell SL, Birren B, Galagan J. (2009) PLoS Pathogens 5(5): e1000459.
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The regulated retrotransposon transcriptome of mammalian cells.  Faulkner GJ, Kimura Y, Daub CO, Wani S, Plessy C, Irvine KM, Schroder K, Cloonan N, Steptoe AL, Lassmann T, Waki K, Hornig N, Arakawa T, Takahashi H, Kawai J, Forrest AR, Suzuki H, Hayashizaki Y, Hume DA, Orlando V, Grimmond SM, Carninci P. (2009) Nature Genetics 41(5): 563-71.
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Meta-analysis of small RNA-sequencing errors reveals ubiquitous post-transcriptional RNA modifications.  Ebhardt HA, Tsang HH, Dai DC, Liu Y, Bostan B, Fahlman RP. (2009) Nucleic Acids Research 37(8): 2461-70.
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The ITS region as a target for characterization of fungal communities using emerging sequencing technologies.  Nilsson RH, Ryberg M, Abarenkov K, Sjökvist E, Kristiansson E. (2009) FEMS Microbiol Letter ePub.:
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Genomic analysis of "Elusimicrobium minutum," the first cultivated representative of the phylum "Elusimicrobia" (formerly termite group 1).  Herlemann DP, Geissinger O, Ikeda-Ohtsubo W, Kunin V, Sun H, Lapidus A, Hugenholtz P, Brune A. (2009) Applied Environmental Microbiology 75(9): 2841-9.
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Effects of experimental choices and analysis noise on surveys of the "rare biosphere".  Hamp TJ, Jones WJ, Fodor AA. (2009) Applied Environmental Microbiology 75(10): 3263-70.
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Analysis of lentiviral vector integration in HIV+ study subjects receiving autologous infusions of gene modified CD4+ T cells.  Wang GP, Levine BL, Binder GK, Berry CC, Malani N, McGarrity G, Tebas P, June CH, Bushman FD. (2009) Molecular Therapy 17(5): 844-50.
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The polyadenylation site of Mimivirus transcripts obeys a stringent "hairpin rule".  Byrne D, Grzela R, Lartigue A, Audic S, Chenivesse S, Encinas S, Claverie JM, Abergel C. (2009) Genome Research 19(7): 1233-42.
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Next-generation pyrosequencing of gonad transcriptomes in the polyploid lake sturgeon (Acipenser fulvescens): the relative merits of normalization and rarefaction in gene discovery.  Hale MC, McCormick CR, Jackson JR, Dewoody JA. (2009) Genome Research 10(1): 203
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Parallel DNA pyrosequencing unveils new zebrafish microRNAs.  Soares AR, Pereira PM, Santos B, Egas C, Gomes AC, Arrais J, Oliveira JL, Moura GR, Santos MA. (2009) BMC Genomics 10(1): 195.
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The first genome-level transcriptome of the wood-degrading fungus Phanerochaete chrysosporium grown on red oak.  Sato S, Feltus FA, Iyer P, Tien M. (2009) Current Genetics 55(3): 273-86.
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Assembling the marine metagenome, one cell at a time.  Woyke T, Xie G, Copeland A, González JM, Han C, Kiss H, Saw JH, Senin P, Yang C, Chatterji S, Cheng JF, Eisen JA, Sieracki ME, Stepanauskas R. (2009) PLoS ONE 4(4): e5299.
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Repertoire of microRNAs in epithelial ovarian cancer as determined by next generation sequencing of small RNA cDNA libraries.  Wyman SK, Parkin RK, Mitchell PS, Fritz BR, O'Briant K, Godwin AK, Urban N, Drescher CW, Knudsen BS, Tewari M. (2009) PLoS ONE 4(4): e5311
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Metagenomic analysis of stressed coral holobionts.  Thurber RV, Willner-Hall D, Rodriguez-Mueller B, Desnues C, Edwards RA, Angly F, Dinsdale E, Kelly L, Rohwer F. (2009) Environmental Microbiology 11(8): 2148-63.
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Comparative metagenomics of Daphnia symbionts.  Qi W, Nong G, Preston JF, Ben-Ami F, Ebert D. (2009) BMC Genomics 10: 172.
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Pyrosequencing analysis of endosymbiont population structure: co-occurrence of divergent symbiont lineages in a single vesicomyid host clam.  Stewart FJ, Cavanaugh CM. (2009) Environmental Microbiology 11(8): 2136-47.
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A transcriptional sketch of a primary human breast cancer by 454 deep sequencing.  Guffanti A, Iacono M, Pelucchi P, Kim N, Solda G, Croft LJ, Taft RJ, Rizzi E, Askarian-Amiri M, Bonnal RJ, Callari M, Mignone F, Pesole G, Bertalot G, Rossi Bernardi L, Albertini A, Lee C, Mattick JS, Zucchi I, De Bellis G. (2009) BMC Genomics 10(1): 163
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The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line.  The FANTOM Consortium, Riken Omics Science Center (2009) Nature Genetics 41: 553-562.
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Comparison of the complete genome sequences of Bifidobacterium animalis subsp. lactis DSM 10140 and Bl-04.  Barrangou R, Briczinski EP, Traeger LL, Loquasto JR, Richards M, Horvath P, Coûté-Monvoisin AC, Leyer G, Rendulic S, Steele JL, Broadbent JR, Oberg T, Dudley EG, Schuster S, Romero DA, Roberts RF. (2009) Journal of Bacteriology 191(13): 4144-51.
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Massive parallel bisulfite sequencing of CG-rich DNA fragments reveals that methylation of many X-chromosomal CpG islands in female blood DNA is incomplete.  Zeschnigk M, Martin M, Betzl G, Kalbe A, Sirsch C, Buiting K, Gross S, Fritzilas E, Frey B, Rahmann S, Horsthemke B. (2009) Human Molecular Genetics 18(8): 1439-48.
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Pyrosequencing of the midgut transcriptome of the poplar leaf beetle Chrysomela tremulae reveals new gene families in Coleoptera.  Pauchet Y, Wilkinson P, van Munster M, Augustin S, Pauron D, Ffrench-Constant RH. (2009) Insect Biochem Mol Biol. 39(5-6): 403-13.
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The mitochondrial genome sequence of the arbuscular mycorrhizal fungus Glomus intraradices isolate 494 and implications for the phylogenetic placement of Glomus.  Lee J, Young JP. (2009) New Phytol 183(1): 200-11
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Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla.  Mahowald MA, Rey FE, Seedorf H, Turnbaugh PJ, Fulton RS, Wollam A, Shah N, Wang C, Magrini V, Wilson RK, Cantarel BL, Coutinho PM, Henrissat B, Crock LW, Russell A, Verberkmoes NC, Hettich RL, Gordon JI. (2009) PNAS 106(14): 5859-64.
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Bias in assessments of marine microbial biodiversity in fosmid libraries as evaluated by pyrosequencing.  Temperton B, Field D, Oliver A, Tiwari B, Mühling M, Joint I, Gilbert JA. (2009) ISME Journal 3(7): 792-6.
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An oligarchic microbial assemblage in the anoxic bottom waters of a volcanic subglacial lake.  Gaidos E, Marteinsson V, Thorsteinsson T, Jóhannesson T, Rúnarsson AR, Stefansson A, Glazer B, Lanoil B, Skidmore M, Han S, Miller M, Rusch A, Foo W. (2009) ISME Journal 3(4): 486-97.
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Experimental discovery of sRNAs in Vibrio cholerae by direct cloning, 5S/tRNA depletion and parallel sequencing.  Liu JM, Livny J, Lawrence MS, Kimball MD, Waldor MK, Camilli A. (2009) Nucleic Acids Research 37(6): e46
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Identification of novel Epstein-Barr virus microRNA genes from nasopharyngeal carcinomas.  Zhu JY, Pfuhl T, Motsch N, Barth S, Nicholls J, Grässer F, Meister G. (2009) Journal of Virology 83(7): 3333-41
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Methods for generating shotgun and mixed shotgun/paired-end libraries for the 454 DNA sequencer.  Wiley G, Macmil S, Qu C, Wang P, Xing Y, White D, Li J, White JD, Domingo A, Roe BA. (2009) Current Protocols Human Genetics Chapter18: Unit18.1.
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DIYA: a bacterial annotation pipeline for any genomics lab.  Stewart AC, Osborne B, Read TD. (2009) Bioinformatics 25(7): 962-3
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A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses.  Jones RT, Robeson MS, Lauber CL, Hamady M, Knight R, Fierer N. (2009) ISME Journal 3(4): 442-53
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Complete genome sequence of the anaerobic, protein-degrading hyperthermophilic crenarchaeon Desulfurococcus kamchatkensis.  Ravin NV, Mardanov AV, Beletsky AV, Kublanov IV, Kolganova TV, Lebedinsky AV, Chernyh NA, Bonch-Osmolovskaya EA, Skryabin KG. (2009) Journal of Bacteriology 191(7): 2371-9
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Transcriptome Analysis of the Circadian Regulatory Network in the Coral Acropora millepora.  Vize PD. (2009) Biological Bulletin 216(2): 131-7.
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Whole-genome-based phylogeny and divergence of the genus Brucella.  Foster JT, Beckstrom-Sternberg SM, Pearson T, Beckstrom-Sternberg JS, Chain PS, Roberto FF, Hnath J, Brettin T, Keim P. (2009) Journal of Bacteriology 191(8): 2864-70.
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Evidence that the intra-amoebal Legionella drancourtii acquired a sterol reductase gene from eukaryotes.  Moliner C, Raoult D, Fournier PE. (2009) BMC Research Notes 2: 51.
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A transposon-based genetic screen in mice identifies genes altered in colorectal cancer.  Starr TK, Allaei R, Silverstein KA, Staggs RA, Sarver AL, Bergemann TL, Gupta M, O'Sullivan MG, Matise I, Dupuy AJ, Collier LS, Powers S, Oberg AL, Asmann YW, Thibodeau SN, Tessarollo L, Copeland NG, Jenkins NA, Cormier RT, Largaespada DA. (2009) Science 323(5922): 1747-50.
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Unique archaeal assemblages in the Arctic Ocean unveiled by massively parallel tag sequencing.  Galand PE, Casamayor EO, Kirchman DL, Potvin M, Lovejoy C. (2009) The ISME Journal ePub:
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Influence of fecal sample storage on bacterial community diversity.  Roesch LF, Casella G, Simell O, Krischer J, Wasserfall CH, Schatz D, Atkinson MA, Neu J, Triplett EW. (2009) Open Microbiology Journal 3: 40-6
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Reproducible Community Dynamics of the Gastrointestinal Microbiota Following Antibiotic Perturbation.  Antonopoulos DA, Huse SM, Morrison HG, Schmidt TM, Sogin ML, Young VB. (2009) Infection and Immunity 77(6): 2367-75.
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Digital PCR provides sensitive and absolute calibration for high throughput sequencing.  White RA 3rd, Blainey PC, Fan HC, Quake SR. (2009) BMC Genomics 10: 116.
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Metagenomic signatures of 86 microbial and viral metagenomes.  Willner D, Thurber RV, Rohwer F. (2009) Environmental Microbiology ePub:
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High-throughput detection of induced mutations and natural variation using KeyPoint technology.  Rigola D, van Oeveren J, Janssen A, Bonné A, Schneiders H, van der Poel HJ, van Orsouw NJ, Hogers RC, de Both MT, van Eijk MJ. (2009) PLoS ONE 4(3): e4761
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CLIP: Construction of cDNA libraries for high-throughput sequencing from RNAs cross-linked to proteins in vivo.  Wang Z, Tollervey J, Briese M, Turner D, Ule J. (2009) Methods 48(3): 287-93.
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Transcriptome sequencing to detect gene fusions in cancer.  Maher C, Kumar-Sinha C, Cao X, Kalyana-Sundaram S, Han B, Jing X, Sam L, Barrette T, Palanisamy N & Chinnaiyan AM. (2009) Nature 458: 97-101
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De novo next generation sequencing of plant genomes.  Steve Rounsley, Pradeep Reddy Marri, Yeisoo Yu, Ruifeng He, Nick Sisneros, Jose Luis Goicoechea, So Jeong Lee, Angelina Angelova, Dave Kudrna, Meizhong Luo, Jason Affourtit, Brian Desany, James Knight, Faheem Niazi, Michael Egholm and Rod A. Wing (2009) Rice 2(1): 35-43
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The TRIM-NHL protein TRIM32 activates microRNAs and prevents self-renewal in mouse neural progenitors.  Schwamborn JC, Berezikov E, Knoblich JA. (2009) Cell 136(5): 913-25
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CNV-seq, a new method to detect copy number variation using high-throughput sequencing.  Xie C, Tammi MT. (2009) BMC Bioinformatics 10: 80.
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Genome sequence of the pathogenic intestinal spirochete brachyspira hyodysenteriae reveals adaptations to its lifestyle in the porcine large intestine.  Bellgard MI, Wanchanthuek P, La T, Ryan K, Moolhuijzen P, Albertyn Z, Shaban B, Motro Y, Dunn DS, Schibeci D, Hunter A, Barrero R, Phillips ND, Hampson DJ. (2009) PLoS ONE 4(3): e4641
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Rare Variants of IFIH1, a Gene Implicated in Antiviral Responses, Protect Against Type 1 Diabetes.  Nejentsev S, Walker N, Riches D, Egholm M, Todd JA. (2009) Science 324(5925): 387-9.
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Improved strategies for sequence-independent amplification and sequencing of viral double-stranded RNA genomes.  Potgieter AC, Page NA, Liebenberg J, Wright IM, Landt O, van Dijk AA. (2009) J Gen Virology 90(Pt 6): 1423-32.
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Identification of microsatellites from an extinct moa species using high-throughput (454) sequence data.  Allentoft M, Schuster S, Holdaway R, Hale M, McLay E, Oskam C, Gilbert MT, Spencer P, Willerslev E, Bunce M. (2009) Biotechniques 46(3): 195-200
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The complete mitochondrial genome of the large yellow croaker, Larimichthys crocea (Perciformes, Sciaenidae): Unusual features of its control region and the phylogenetic position of the Sciaenidae.  Cui Z, Liu Y, Li CP, You F, Chu KH. (2009) Gene 432(1-2): 33-43
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Molecular Diversity of a North Carolina Wastewater Treatment Plant As Revealed by Pyrosequencing.  Sanapareddy N, Hamp TJ, Gonzalez LC, Hilger HA, Fodor AA, Clinton SM. (2009) Applied Environmental Microbiology 75(6): 1688-96
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Simple, sensitive, and swift sequencing of complete Avian Influenza H5N1 genomes.  D. Hoper, B. Hoffmann, and M. Beer (2009) Journal of Clinical Microbiology 47(3): 674-9
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Simultaneous mutation and copy number variation (CNV) detection by multiplex PCR-based GS-FLX sequencing.  Goossens D, Moens LN, Nelis E, Lenaerts AS, Glassee W, Kalbe A, Frey B, Kopal G, Jonghe PD, Rijk PD, Del-Favero J. (2009) Human Mutations 30(3): 472-6
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Microarray analysis of female- and larval-specific gene expression in the horn fly (Diptera: Muscidae).  Guerrero FD, Dowd SE, Sun Y, Saldivar L, Wiley GB, Macmil SL, Najar F, Roe BA, Foil LD. (2009) J Med Entomol 46(2): 257-70.
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A conditional transposon-based insertional mutagenesis screen for genes associated with mouse hepatocellular carcinoma.  Keng VW, Villanueva A, Chiang DY, Dupuy AJ, Ryan BJ, Matise I, Silverstein KA, Sarver A, Starr TK, Akagi K, Tessarollo L, Collier LS, Powers S, Lowe SW, Jenkins NA, Copeland NG, Llovet JM, Largaespada DA. (2009) Nature Biotechnology 27(3): 264-74.
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Fast, cost-effective development of species-specific microsatellite markers by genomic sequencing.  Abdelkrim J, Robertson B, Stanton JA, Gemmell N. (2009) Biotechniques 46(3): 185-92
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Identification of yeast in chronic wounds using new pathogen-detection technologies.  Leake JL, Dowd SE, Wolcott RD, Zischkau AM. (2009) Journal of Wound Care 18(3): 103-8
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Purification of DNA from the cell-associated herpesvirus Marek's disease virus for 454 pyrosequencing using micrococcal nuclease digestion and polyethylene glycol precipitation.  Volkening JD, Spatz SJ. (2009) Journal of Virology Methods 157(1): 55-61
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Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts.  Sanford JR, Wang X, Mort M, Vanduyn N, Cooper DN, Mooney SD, Edenberg HJ, Liu Y. (2009) Genome Research 19(3): 381-94.
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NA-Seq: a discovery tool for the analysis of chromatin structure and dynamics during differentiation.  Gargiulo G, Levy S, Bucci G, Romanenghi M, Fornasari L, Beeson KY, Goldberg SM, Cesaroni M, Ballarini M, Santoro F, Bezman N, Frigè G, Gregory PD, Holmes MC, Strausberg RL, Pelicci PG, Urnov FD, Minucci S. (2009) Dev Cell 16(3): 466-81.
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Integration target site selection by a resurrected human endogenous retrovirus.  Brady T, Lee YN, Ronen K, Malani N, Berry CC, Bieniasz PD, Bushman FD. (2009) Genes & Development 23(5): 633-42.
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SNP frequency estimation using massively parallel sequencing of pooled DNA.  Ingman M, Gyllensten U. (2009) European Journal of Human Genetics 17(3): 383-6
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PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data.  Korbel JO, Abyzov A, Mu XJ, Carriero N, Cayting P, Zhang Z, Snyder M, Gerstein MB. (2009) Genome Biology 10(2): R23.
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In situ transcriptomic analysis of the globally important keystone N(2)-fixing taxon Crocosphaera watsonii.  Hewson I, Poretsky RS, Beinart RA, White AE, Shi T, Bench SR, Moisander PH, Paerl RW, Tripp HJ, Montoya JP, Moran MA, Zehr JP. (2009) ISME Journal 3(5): 618-31.
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Human gut microbiota in obesity and after gastric bypass.  Zhang H, Dibaise JK, Zuccolo A, Kudrna D, Braidotti M, Yu Y, Parameswaran P, Crowell MD, Wing R, Rittmann BE, Krajmalnik-Brown R. (2009) PNAS 106(7): 2365-70
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Massively parallel pyrosequencing highlights minority variants in the HIV-1 env quasispecies deriving from lymphomonocyte sub-populations.  Rozera G, Abbate I, Bruselles A, Vlassi C, D'Offizi G, Narciso P, Chillemi G, Prosperi M, Ippolito G, Capobianchi MR. (2009) Retrovirology 6(1): 15
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Low-Abundance Drug-Resistant Viral Variants in Chronically HIV-Infected, Antiretroviral Treatment–Naive Patients Significantly Impact Treatment Outcomes.  Simen B, Simons J, Hullsiek K, Novak R, MacArthur R, Baxter J, Huang C, Lubeski C, Turenchalk G, Braverman M, Desany B, Rothberg J, Egholm M, and Kozal M. (2009) Journal of Infectious Diseases 199(5): 693-701
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Long-term control of HIV by CCR5 Delta32/Delta32 stem-cell transplantation.  Hütter G, Nowak D, Mossner M, Ganepola S, Müssig A, Allers K, Schneider T, Hofmann J, Kücherer C, Blau O, Blau IW, Hofmann WK, Thiel E. (2009) New England Journal of Medicine 360(7): 692-8.
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The mitochondrial genomes of Ancylostoma caninum and Bunostomum phlebotomum--two hookworms of animal health and zoonotic importance.  Jex AR, Waeschenbach A, Hu M, van Wyk JA, Beveridge I, Littlewood DT, Gasser RB. (2009) BMC Genomics 10: 79.
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Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases.  Brulc JM, Antonopoulos DA, Miller ME, Wilson MK, Yannarell AC, Dinsdale EA, Edwards RE, Frank ED, Emerson JB, Wacklin P, Coutinho PM, Henrissat B, Nelson KE, White BA. (2009) PNAS 106(6): 1948-53
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Transcriptome-guided characterization of genomic rearrangements in a breast cancer cell line.  Zhao Q, Caballero OL, Levy S, Stevenson BJ, Iseli C, de Souza SJ, Galante PA, Busam D, Leversha MA, Chadalavada K, Rogers YH, Venter JC, Simpson AJ, Strausberg RL. (2009) PNAS 106(6): 1886-91
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Identification of bacillus anthracis spore component antigens conserved across diverse bacillus cereus sensu lato strains.  Mukhopadhyay S, Akmal A, Stewart AC, Hsia RC, Read TD. (2009) Molecular & Cellular Proteomics 8(6): 1174-91.
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Comparative day/night metatranscriptomic analysis of microbial communities in the North Pacific subtropical gyre.  Poretsky RS, Hewson I, Sun S, Allen AE, Zehr JP, Moran MA. (2009) Environmental Microbiology ePub:
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The deep evolution of metazoan microRNAs.  Wheeler BM, Heimberg AM, Moy VN, Sperling EA, Holstein TW, Heber S, Peterson KJ. (2009) Evolution & Development 11(1): 50-68
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Microsatellite discovery by deep sequencing of enriched genomic libraries.  Santana Q, Coetzee M, Steenkamp E, Mlonyeni O, Hammond G, Wingfield M, Wingfield B. (2009) Biotechniques 46(30: 217-23
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Use of massively parallel ultradeep pyrosequencing to characterize the genetic diversity of hepatitis B virus in drug-resistant and drug-naive patients and to detect minor variants in reverse transcriptase and hepatitis B S antigen.  Solmone M, Vincenti D, Prosperi MC, Bruselles A, Ippolito G, Capobianchi MR. (2009) Journal of Virology 83(4): 1718-26
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De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae.  Reinhardt JA, Baltrus DA, Nishimura MT, Jeck WR, Jones CD, Dangl JL. (2009) Genome Research 19(2): 294-305
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Comparison of the Diversity of the Vaginal Microbiota in HIV-Infected and HIV-Uninfected Women with or without Bacterial Vaginosis.  Spear GT, Sikaroodi M, Zariffard MR, Landay AL, French AL, Gillevet PM. (2008) Journal of Infectious Disease 198: 1131-40
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A Metagenomic Survey of Microbes in Honey Bee Colony Collapse Disorder  Diana L. Cox-Foster, Sean Conlan, Edward C. Holmes, Gustavo Palacios, Jay D. Evans, Nancy A. Moran, Phenix-Lan Quan, Thomas Briese, Mady Hornig, David M. Geiser, Vince Martinson, Dennis vanEngelsdorp, Abby L. Kalkstein, Andrew Drysdale, Jeffrey Hui, Junhui Zhai,2Liwang Cui, StephenK. Hutchison, Jan Fredrik Simons, Michael Egholm, Jeffery S. Pettis, W. Ian Lipkin (2007) Science :
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The Genome of a Non-01 Vibrio cholerae NRT36S Demonstrates the Presence of Pathogenic Mechanisms that are Distinct from 01 Vibrio cholerae  Yuansha Chen, Judith A. Johnson, Gordon D. Pusch, J. Glenn Morris, Jr., and O. Colin Stine (2007) Infection and Immunity 10: 01317-13106
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Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach   Matthew N. Bainbridge, René L. Warren, Martin Hirst, Tammy Romanuik, Thomas Zeng, Anne Go, Allen Delaney, Malachi Griffith, Matthew Hickenbotham, Vincent Magrini, Elaine R. Mardis, Marianne D. Sadar, Asim S. Siddiqui, Marco A. Marra, Steven J.M. Jones (2006) BMC Genomics 7: 246-256
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Marek's Disease Virus Encodes MicroRNAs That Map to meq and the Latency-Associated Transcript  Joan Burnside, Erin Bernberg, Amy Anderson, Cheng Lu, Blake C. Meyers, Pamela J. Green, Neeta Jain, Grace Isaacs, and Robin W. Morgan (2006) Journal of Virology 80: 8778-8786
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Unique Features of a Highly Pathogenic Campylobacter jejuni Strain  Dirk Hofreuter, Jennifer Tsai, Robert O. Watson, Veronica Novik, Bill Altman, Michelle Benitez, Christina Clark, Clotilde Perbost, Thomas Jarvie, Lei Du, and Jorge E. Galán (2006) Infection and Immunity 74: 4694-4707
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Characterization of the piRNA Complex from Rat Testes  Nelson C. Lau, Anita G. Seto, Jinkuk Kim, Satomi Kuramochi-Miyagawa, Toru Nakano, David P. Bartel, Robert E. Kingston (2006) Science 313: 363-367
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Finding novel genes in bacterial communities isolated from the environment   Lutz Krause, Naryttza N. Diaz, Daniela Bartels, Robert A. Edwards, Alfred Puhler, Forest Rohwer, Folker Meyer and Jens Stoye  (2006) Bioinformatics 22: 281-289
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Dissecting Arabidopsis thaliana DICER function in small RNA processing, gene silencing and DNA methylation patterning  Ian R Henderson, Xiaoyu Zhang, Cheng Lu, Lianna Johnson, Blake C Meyers, Pamela J Green & Steven E Jacobsen (2006) Nature Genetics 38: 721-725
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Comprehensive mutation identification in an evolved bacterial cooperator and its cheating ancestor  Gregory J. Velicer, Gunter Raddatz, Heike Keller, Silvia Deiss, Christa Lanz, Iris Dinkelacker, and Stephan C. Schuster (2006) PNAS  103: 8107–8112
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Using pyrosequencing to shed light on deep mine microbial ecology   Robert A. Edwards, Beltran Rodriguez-Brito, Linda Wegley, Matthew Haynes, Mya Breitbart, Dean M. Peterson, Martin O. Saar, Scott Alexander, E. Calvin Alexander, Jr., Forest Rohwer (2006) BMC Genomics 7: 57
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A Diarylquinoline Drug Active on the ATP Synthase of Mycobacterium tuberculosis  Andries, K. et. al.  (2005) Science 307: 223-227
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