Next Generation Sequencing and Bioinformatics
at the University of Edinburgh

GenePool Publications

76 2012Zhang, J. et al. Structure and Mechanism of the CMR Complex for CRISPR-Mediated Antiviral Immunity. Mol Cell (2012) 10.1016/j.molcel.2011.12.013.
75 2012Kumar, S., Koutsovoulos, G., Kaur, G. & Blaxter, M. Toward 959 nematode genomes. Worm 1, 0--1 (2012).
74 2012 Halliday, A.M. et al. Transcriptional changes in Teladorsagia circumcincta upon encountering host tissue of differing immune status. Parasitology, 1-19 (2012).
73 2011Walrad, P.B., Capewell, P., Fenn, K. & Matthews, K.R. The post-transcriptional trans-acting regulator, TbZFP3, co-ordinates transmission-stage enriched mRNAs in Trypanosoma brucei. Nucleic Acids Research (2011) 10.1093/nar/gkr1106.
72 2011Temperton, B. et al. Permanent draft genome sequence of Vibrio tubiashii strain NCIMB 1337 (ATCC19106). Stand Genomic Sci 4, 183 (2011).
71 2011Telford, A., O'Hare, M. & Cavers, S. Can genetic bar-coding be used to identify Aquatic Ranunculus L. subgenus Batrachium (DC) A. Gray? A test using some species from the British Isles. Aquatic Botany 95: 65-70 (2011).
70 2011Spurgin, L.G. et al. Gene conversion rapidly generates major histocompatibility complex diversity in recently founded bird populations. Molecular Ecology 20, 5213-5225 (2011).
69 2011Smith, D., McFadden, N., Blundell, R.J., Meredith, A. & Simmonds, P. Diversity of murine norovirus in wild rodent populations: species-specific associations suggest an ancient divergence. J Gen Virol (2011) 10.1099/vir.0.036392-0.
68 2011Siu, R.W.C. et al. Antiviral RNA interference responses induced by Semliki Forest virus infection of mosquito cells: characterization, origin, and frequency-dependent functions of virus-derived small interfering RNAs. J Virol 85, 2907-2917 (2011).
67 2011Sharp, C.P., Lail, A., Donfield, S., Gomperts, E.D. & Simmonds, P. Virologic and clinical features of primary infection with human parvovirus 4 in subjects with hemophilia: frequent transmission by virally inactivated clotting factor concentrates. Transfusion (2011) 10.1111/j.1537-2995.2011.03420.x.
66 2011Saunders, N.J. et al. Deep resequencing of serial sputum isolates of Mycobacterium tuberculosis during therapeutic failure due to poor compliance reveals stepwise mutation of key resistance genes on an otherwise stable genetic background. The Journal of infection 62, 212-217 (2011).
65 2011Sait, M. et al. Genome Sequence of the Chlamydophila abortus Variant Strain LLG. J Bacteriol 193, 4276-4277 (2011).
64 2011Russell, J.R. et al. Identification, utilisation and mapping of novel transcriptome-based markers from blackcurrant (Ribes nigrum). BMC Plant Biol 11, 147 (2011).
63 2011Rubasinghe, S.C.K., Milne, R., Forrest, L.L. & Long, D.G. Realignment of the genera of Cleveaceae (Marchantiopsida, Marchantiidae). The Bryologist 114, 116-127 (2011).
62 2011Rheindt, F.E. et al. Conflict between Genetic and Phenotypic Differentiation: The Evolutionary History of a ‘Lost and Rediscovered’ Shorebird. PLoS ONE 6, e26995 (2011).
61 2011Pemberton, J.M., Beraldi, D., Craig, B.H. & Hopkins, J. Digital gene expression analysis of gastrointestinal helminth resistance in Scottish blackface lambs. Molecular Ecology 20, 910-919 (2011).
60 2011Obbard, D., Jiggins, F. & Bradshaw, N. Recent and Recurrent Selective Sweeps of the Antiviral RNAi Gene Argonaute-2 in Three Species of Drosophila. Molecular biology and Evolution 2, 1043-1056 (2011).
59 2011Nadeau, N.J. et al. Genomic islands of divergence in hybridizing Heliconius butterflies identified by large-scale targeted sequencing. Philosophical Transactions of the Royal Society B: Biological Sciences 367, 343-353 (2011).
58 2011Magwire, M.M., Bayer, F., Webster, C.L., Cao, C. & Jiggins, F.M. Successive Increases in the Resistance of Drosophila to Viral Infection through a Transposon Insertion Followed by a Duplication. PLoS Genet 7, e1002337 (2011).
57 2011Longdon, B., Wilfert, L. & Osei-Poku, J. Host-switching by a vertically transmitted rhabdovirus in Drosophila. Biology Letters 7, 747-750 (2011).
56 2011Longdon, B., Wilfert, L., Obbard, D.J. & Jiggins, F.M. Rhabdoviruses in Two Species of Drosophila: Vertical Transmission and a Recent Sweep. Genetics 188, 141-150 (2011).
55 2011Lohse, K., Sharanowski, B., Blaxter, M., Nicholls, J.A. & Stone, G.N. Developing EPIC markers for chalcidoid Hymenoptera from EST and genomic data. Molecular Ecology Resources 11, 521-529 (2011).
54 2011Lepais, O. & Bacles, C.F.E. Comparison of random and SSR-enriched shotgun pyrosequencing for microsatellite discovery and single multiplex PCR optimization in Acacia harpophylla F. Muell. Ex Benth. Molecular Ecology Resources (2011).
53 2011Kirkham, A.R. et al. Basin-scale distribution patterns of photosynthetic picoeukaryotes along an Atlantic Meridional Transect. Environ Microbiol 13, 975-990 (2011).
52 2011Kelly, L.C. et al. Bacterial Diversity of Terrestrial Crystalline Volcanic Rocks, Iceland. Microbial Ecology 62, 69-79 (2011).
51 2011Joron, M. et al. Chromosomal rearrangements maintain a polymorphic supergene controlling butterfly mimicry. Nature, 1-6 (2011).
50 2011Hoffman, J.I. Gene discovery in the Antarctic fur seal (Arctocephalus gazella) skin transcriptome. Molecular Ecology Resources (2011).
49 2011Hewitson, J.P. et al. Proteomic analysis of secretory products from the model gastrointestinal nematode Heligmosomoides polygyrus reveals dominance of Venom Allergen-Like (VAL) proteins. Journal of Proteomics 74, 1573-1594 (2011).
48 2011Granneman, S., Petfalski, E. & Tollervey, D. A cluster of ribosome synthesis factors regulate pre-rRNA folding and 5.8S rRNA maturation by the Rat1 exonuclease. The EMBO journal, - (2011).
47 2011Gossner, A., Peers, A., Venturina, V. & Hopkins, J. Expressed gene sequences of two variants of sheep interleukin-25. Vet Immunol Immunopathol 139, 319-323 (2011).
46 2011Gkikopoulos, T. et al. A Role for Snf2-Related Nucleosome-Spacing Enzymes in Genome-Wide Nucleosome Organization. Science 333, 1758-1760 (2011).
45 2011Davey, J.W. et al. Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat Rev Genet 12, 499-510 (2011).
44 2011Colgan, T.J. et al. Polyphenism in social insects: Insights from a transcriptome-wide analysis of gene expression in the life stages of the key pollinator, Bombus terrestris. BMC genomics 12, 623 (2011).
43 2011Bergero, R. & Charlesworth, D. Preservation of the y transcriptome in a 10-million-year-old plant sex chromosome system. Current biology : CB 21, 1470-1474 (2011).
42 2011Baxter, S.W. et al. Linkage Mapping and Comparative Genomics Using Next-Generation RAD Sequencing of a Non-Model Organism. PLoS One 6, e19315 (2011).
41 2011Annavi, G., Dawson, D. & Horsburgh, G. Characterisation of twenty-one European badger (Meles meles) microsatellite loci facilitates the discrimination of second-order relatives. Conservation Genetics in press (2011).
40 2010Veitch, N.J. et al. Digital gene expression analysis of two life cycle stages of the human-infective parasite, Trypanosoma brucei gambiense reveals differentially expressed clusters of co-regulated genes. BMC genomics 11, 124 (2010).
39 2010van Koningsbruggen, S. et al. High-Resolution Whole-Genome Sequencing Reveals That Specific Chromatin Domains from Most Human Chromosomes Associate with Nucleoli. Molecular Biology of the Cell 21, 3735-3748 (2010).
38 2010Tota Maharaj, K., Scholz, M., Ahmed, T., French, C. & Pagaling, E. The synergy of permeable pavements and geothermal heat pumps for stormwater treatment and reuse. Environmental Technology 31, 1517-1531 (2010).
37 2010Stanton, R.J. et al. Reconstruction of the complete human cytomegalovirus genome in a BAC reveals RL13 to be a potent inhibitor of replication. The Journal of Clinical Investigation 120, 3191-3208 (2010).
36 2010Simmer, F. et al. Hairpin RNA induces secondary small interfering RNA synthesis and silencing in trans in fission yeast. EMBO reports 11, 112-118 (2010).
35 2010Sharp, C.P. et al. Widespread Infection with Homologues of Human Parvoviruses B19, PARV4, and Human Bocavirus of Chimpanzees and Gorillas in the Wild. The Journal of Virology 84, 10289 (2010).
34 2010Rota-Stabelli, O. et al. Ecdysozoan mitogenomics: evidence for a common origin of the legged invertebrates, the Panarthropoda. Genome Biol Evol 2, 425-440 (2010).
33 2010Nicholls, J.A. et al. Community impacts of anthropogenic disturbance: natural enemies exploit multiple routes in pursuit of invading herbivore hosts. BMC Evol Biol 10, 322 (2010).
32 2010Lee, E.-K. et al. Cultured cambial meristematic cells as a source of plant natural products. Nat Biotechnol 28, 1213-1217 (2010).
31 2010Kumar, S. & Blaxter, M.L. Comparing de novo assemblers for 454 transcriptome data. BMC genomics 11, 571 (2010).
30 2010Kegel, J.U. et al. Transcriptional host-virus interaction of Emiliania huxleyi (Haptophyceae) and EhV-86 deduced from
29 2010Jardillier, L., Zubkov, M.V., Pearman, J. & Scanlan, D.J. Significant CO2 fixation by small prymnesiophytes in the subtropical and tropical northeast Atlantic Ocean. Isme J 4, 1180-1192 (2010).
28 2010Hunt, P. et al. Experimental evolution, genetic analysis and genome re-sequencing reveal the mutation conferring artemisinin resistance in an isogenic lineage of malaria parasites. BMC genomics 11, 499 (2010).
27 2010Green, S. et al. Comparative Genome Analysis Provides Insights into the Evolution and Adaptation of Pseudomonas syringae pv. aesculi on Aesculus hippocastanum. PLoS ONE 5, e10224 (2010).
26 2010Granneman, S., Petfalski, E., Swiatkowska, A. & Tollervey, D. Cracking pre-40S ribosomal subunit structure by systematic analyses of RNA-protein cross-linking. The EMBO journal 29, 2026-2036 (2010).
25 2010Fonseca, V.G. et al. Second-generation environmental sequencing unmasks marine metazoan biodiversity. Nat Commun 1, 98 (2010).
24 2010Ferguson, L. et al. Characterization of a hotspot for mimicry: assembly of a butterfly wing transcriptome to genomic sequence at the HmYb/Sb locus. Molecular Ecology 19 Suppl 1, 240-254 (2010).
23 2010Davey, J.L. & Blaxter, M.W. RADSeq: next-generation population genetics. Briefings in functional genomics 9, 416-423 (2010).
22 2010Cunningham, C. et al. Sequences of complete human cytomegalovirus genomes from infected cell cultures and clinical specimens. J Gen Virol 91, 605-615 (2010).
21 2010Creer, S. et al. Ultrasequencing of the meiofaunal biosphere: practice, pitfalls and promises. Molecular Ecology 19 Suppl 1, 4-20 (2010).
20 2010Chieochansin, T., Simmonds, P. & Poovorawan, Y. Determination and analysis of complete coding sequence regions of new discovered human bocavirus types 2 and 3. Arch Virol 155, 2023-2028 (2010).
19 2010Acs, Z. et al. Phylogeny and DNA barcoding of inquiline oak gallwasps (Hymenoptera: Cynipidae) of the Western Palaearctic. Mol Phylogenet Evol 55, 210-225 (2010).
18 2009Tsakiridis, A. et al. Expression-independent gene trap vectors for random and targeted mutagenesis in embryonic stem cells. Nucleic Acids Research 37, e129-e129 (2009).
17 2009Obbard, D.J., Welch, J.J., Kim, K.-W. & Jiggins, F.M. Quantifying adaptive evolution in the Drosophila immune system. PLoS Genet 5, e1000698 (2009).
16 2009Lowder, B.V. et al. Recent human-to-poultry host jump, adaptation, and pandemic spread of Staphylococcus aureus. Proc Natl Acad Sci U S A 106, 19545-19550 (2009).
15 2009Lepere, C., Vaulot, D. & Scanlan, D.J. Photosynthetic picoeukaryote community structure in the South East Pacific Ocean encompassing the most oligotrophic waters on Earth. Environ Microbiol 11, 3105-3117 (2009).
14 2009Küpper, C. et al. Kentish versus Snowy Plover: Phenotypic and Genetic Analyses of Charadrius alexandrinusReveal Divergence of Eurasian and American Subspecies. The Auk 126, 839-852 (2009).
13 2009Keightley, P.D. et al. Analysis of the genome sequences of three Drosophila melanogaster spontaneous mutation accumulation lines. Genome research 19, 1195-1201 (2009).
12 2009Herrera, A. et al. A cryptoendolithic community in volcanic glass. Astrobiology 9, 369-381 (2009).
11 2009Granneman, S., Kudla, G., Petfalski, E. & Tollervey, D. Identification of protein binding sites on U3 snoRNA and pre-rRNA by UV cross-linking and high-throughput analysis of cDNAs. Proceedings of the National Academy of Sciences 106, 9613-9618 (2009).
10 2009Fraser, R.M., Keszenman-Pereyra, D., Simmen, M.W. & Allan, J. High-resolution mapping of sequence-directed nucleosome positioning on genomic DNA. Journal of Molecular Biology 390, 292-305 (2009).
9 2009Fedorovich, V. et al. Novel Electrochemically Active Bacterium Phylogenetically Related to Arcobacter butzleri, Isolated from a Microbial Fuel Cell. Appl Environ Microbiol 75, 7326 (2009).
8 2009Bradley, A.J. et al. High-throughput sequence analysis of variants of human cytomegalovirus strains Towne and AD169. J Gen Virol 90, 2375-2380 (2009).
7 2008A'Hara, S.W., Hancock, M., Piertney, S.B. & Cottrell, J.E. The Development of a Molecular Assay to Distinguish Droppings of Black Grouse Tetrao tetrixfrom those of Capercaillie Tetrao urogallus and Red Grouse Lagopus Lagopus Scoticus. Wildlife Biology 15, 328-337 (2009).
6 2008Wasmuth, J., Schmid, R., Hedley, A. & Blaxter, M. On the extent and origins of genic novelty in the phylum nematoda. PLoS Negl Trop Dis 2, e258 (2008).
5 2008Vali, L., Davies, S.E., Lai, L.L.G., Dave, J. & Amyes, S.G.B. Frequency of biocide resistance genes, antibiotic resistance and the effect of chlorhexidine exposure on clinical methicillin-resistant Staphylococcus aureus isolates. Journal of Antimicrobial Chemotherapy 61, 524-532 (2008).
4 2008Svendsen, C. et al. Comparative transcriptomic responses to chronic cadmium, fluoranthene, and atrazine exposure in Lumbricus rubellus. Environ Sci Technol 42, 4208-4214 (2008).
3 2008Sekimoto, S. et al. The Development, Ultrastructural Cytology, and Molecular Phylogeny of the Basal Oomycete Eurychasma dicksonii, Infecting the Filamentous Phaeophyte Algae Ectocarpus siliculosus and Pylaiella littoralis. Protist 159, 299-318 (2008).
2 2008Owen, J. et al. Transcriptome profiling of developmental and xenobiotic responses in a keystone soil animal, the oligochaete annelid Lumbricus rubellus. BMC Genomics 9, 266 (2008).
1 2008Herrera, A. et al. Bacterial colonization and weathering of terrestrial obsidian in Iceland. Geomicrobiology 25, 25-37 (2008).


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School of Biological Sciences
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This is version 2.2 of the GenePool website (July 2009).