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Sean D. Hooper - Publications

Affiliations: 
Uppsala University, Uppsala, Uppsala län, Sweden 
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32 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2013 Jiao X, Hooper SD, Djureinovic T, Larsson C, Wärnberg F, Tellgren-Roth C, Botling J, Sjöblom T. Gene rearrangements in hormone receptor negative breast cancers revealed by mate pair sequencing. Bmc Genomics. 14: 165. PMID 23496902 DOI: 10.1186/1471-2164-14-165  0.363
2012 Hooper SD, Johansson AC, Tellgren-Roth C, Stattin EL, Dahl N, Cavelier L, Feuk L. Genome-wide sequencing for the identification of rearrangements associated with Tourette syndrome and obsessive-compulsive disorder. Bmc Medical Genetics. 13: 123. PMID 23253088 DOI: 10.1186/1471-2350-13-123  0.41
2012 Hooper SD, Jiao X, Sundström E, Rehman FL, Tellgren-Roth C, Sjöblom T, Cavelier L. Sequence based analysis of U-2973, a cell line established from a double-hit B-cell lymphoma with concurrent MYC and BCL2 rearrangements. Bmc Research Notes. 5: 648. PMID 23171647 DOI: 10.1186/1756-0500-5-648  0.36
2012 Mansouri L, Gunnarsson R, Sutton LA, Ameur A, Hooper SD, Mayrhofer M, Juliusson G, Isaksson A, Gyllensten U, Rosenquist R. Next generation RNA-sequencing in prognostic subsets of chronic lymphocytic leukemia. American Journal of Hematology. 87: 737-40. PMID 22674506 DOI: 10.1002/Ajh.23227  0.327
2011 Pavlopoulos GA, Hooper SD, Sifrim A, Schneider R, Aerts J. Medusa: A tool for exploring and clustering biological networks. Bmc Research Notes. 4: 384. PMID 21978489 DOI: 10.1186/1756-0500-4-384  0.336
2011 Jiao X, Rosenlund M, Hooper SD, Tellgren-Roth C, He L, Fu Y, Mangion J, Sjöblom T. Structural alterations from multiple displacement amplification of a human genome revealed by mate-pair sequencing. Plos One. 6: e22250. PMID 21799804 DOI: 10.1371/Journal.Pone.0022250  0.4
2011 Anderson I, Scheuner C, Göker M, Mavromatis K, Hooper SD, Porat I, Klenk HP, Ivanova N, Kyrpides N. Novel insights into the diversity of catabolic metabolism from ten haloarchaeal genomes. Plos One. 6: e20237. PMID 21633497 DOI: 10.1371/Journal.Pone.0020237  0.467
2011 Sutton L, Mansouri L, Gunnarsson R, Ameur A, Hooper S, Rasmussen M, Isaksson A, Gyllensten U, Rosenquist R. 1.12 Transcriptome Sequencing Reveals Novel Mutations and Differential Gene Expression in Stereotyped Subsets of Chronic Lymphocytic Leukemia Clinical Lymphoma Myeloma and Leukemia. 11: S148-S149. DOI: 10.1016/J.Clml.2011.09.013  0.348
2010 Pati A, Ivanova NN, Mikhailova N, Ovchinnikova G, Hooper SD, Lykidis A, Kyrpides NC. GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes. Nature Methods. 7: 455-7. PMID 20436475 DOI: 10.1038/Nmeth.1457  0.484
2010 Lykidis A, Pérez-Pantoja D, Ledger T, Mavromatis K, Anderson IJ, Ivanova NN, Hooper SD, Lapidus A, Lucas S, González B, Kyrpides NC. The complete multipartite genome sequence of Cupriavidus necator JMP134, a versatile pollutant degrader. Plos One. 5: e9729. PMID 20339589 DOI: 10.1371/Journal.Pone.0009729  0.458
2010 Hooper SD, Dalevi D, Pati A, Mavromatis K, Ivanova NN, Kyrpides NC. Estimating DNA coverage and abundance in metagenomes using a gamma approximation. Bioinformatics (Oxford, England). 26: 295-301. PMID 20008478 DOI: 10.1093/Bioinformatics/Btp687  0.376
2009 Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN, Kunin V, Goodwin L, Wu M, Tindall BJ, Hooper SD, Pati A, Lykidis A, Spring S, Anderson IJ, et al. A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature. 462: 1056-60. PMID 20033048 DOI: 10.1038/Nature08656  0.487
2009 Mavromatis K, Chu K, Ivanova N, Hooper SD, Markowitz VM, Kyrpides NC. Gene context analysis in the Integrated Microbial Genomes (IMG) data management system. Plos One. 4: e7979. PMID 19956731 DOI: 10.1371/Journal.Pone.0007979  0.544
2009 Anderson I, Ulrich LE, Lupa B, Susanti D, Porat I, Hooper SD, Lykidis A, Sieprawska-Lupa M, Dharmarajan L, Goltsman E, Lapidus A, Saunders E, Han C, Land M, Lucas S, et al. Genomic characterization of methanomicrobiales reveals three classes of methanogens. Plos One. 4: e5797. PMID 19495416 DOI: 10.1371/Journal.Pone.0005797  0.374
2009 Hooper SD, Mavromatis K, Kyrpides NC. Microbial co-habitation and lateral gene transfer: what transposases can tell us. Genome Biology. 10: R45. PMID 19393086 DOI: 10.1186/Gb-2009-10-4-R45  0.493
2009 Anderson IJ, Dharmarajan L, Rodriguez J, Hooper S, Porat I, Ulrich LE, Elkins JG, Mavromatis K, Sun H, Land M, Lapidus A, Lucas S, Barry K, Huber H, Zhulin IB, et al. The complete genome sequence of Staphylothermus marinus reveals differences in sulfur metabolism among heterotrophic Crenarchaeota. Bmc Genomics. 10: 145. PMID 19341479 DOI: 10.1186/1471-2164-10-145  0.378
2009 Pavlopoulos GA, Pafilis E, Kuhn M, Hooper SD, Schneider R. OnTheFly: a tool for automated document-based text annotation, data linking and network generation. Bioinformatics (Oxford, England). 25: 977-8. PMID 19223449 DOI: 10.1093/Bioinformatics/Btp081  0.561
2009 Hooper SD, Anderson IJ, Pati A, Dalevi D, Mavromatis K, Kyrpides NC. Integration of phenotypic metadata and protein similarity in Archaea using a spectral bipartitioning approach. Nucleic Acids Research. 37: 2096-104. PMID 19223325 DOI: 10.1093/Nar/Gkp075  0.453
2009 Mavromatis K, Ivanova N, Anderson I, Lykidis A, Hooper SD, Sun H, Kunin V, Lapidus A, Hugenholtz P, Patel B, Kyrpides NC. Genome analysis of the anaerobic thermohalophilic bacterium Halothermothrix orenii. Plos One. 4: e4192. PMID 19145256 DOI: 10.1371/Journal.Pone.0004192  0.484
2008 Dalevi D, Ivanova NN, Mavromatis K, Hooper SD, Szeto E, Hugenholtz P, Kyrpides NC, Markowitz VM. Annotation of metagenome short reads using proxygenes. Bioinformatics (Oxford, England). 24: i7-13. PMID 18689842 DOI: 10.1093/bioinformatics/btn276  0.349
2008 Hooper SD, Raes J, Foerstner KU, Harrington ED, Dalevi D, Bork P. A molecular study of microbe transfer between distant environments. Plos One. 3: e2607. PMID 18612393 DOI: 10.1371/Journal.Pone.0002607  0.686
2007 Hooper SD, Boué S, Krause R, Jensen LJ, Mason CE, Ghanim M, White KP, Furlong EE, Bork P. Identification of tightly regulated groups of genes during Drosophila melanogaster embryogenesis. Molecular Systems Biology. 3: 72. PMID 17224916 DOI: 10.1038/Msb4100112  0.636
2006 Gavin AC, Aloy P, Grandi P, Krause R, Boesche M, Marzioch M, Rau C, Jensen LJ, Bastuck S, Dümpelfeld B, Edelmann A, Heurtier MA, Hoffman V, Hoefert C, Klein K, ... ... Hooper S, et al. Proteome survey reveals modularity of the yeast cell machinery. Nature. 440: 631-6. PMID 16429126 DOI: 10.1038/Nature04532  0.656
2005 Foerstner KU, von Mering C, Hooper SD, Bork P. Environments shape the nucleotide composition of genomes. Embo Reports. 6: 1208-13. PMID 16200051 DOI: 10.1038/Sj.Embor.7400538  0.661
2005 Hooper SD, Bork P. Medusa: a simple tool for interaction graph analysis. Bioinformatics (Oxford, England). 21: 4432-3. PMID 16188923 DOI: 10.1093/Bioinformatics/Bti696  0.433
2005 Korbel JO, Doerks T, Jensen LJ, Perez-Iratxeta C, Kaczanowski S, Hooper SD, Andrade MA, Bork P. Systematic association of genes to phenotypes by genome and literature mining. Plos Biology. 3: e134. PMID 15799710 DOI: 10.1371/Journal.Pbio.0030134  0.654
2005 von Mering C, Jensen LJ, Snel B, Hooper SD, Krupp M, Foglierini M, Jouffre N, Huynen MA, Bork P. STRING: known and predicted protein-protein associations, integrated and transferred across organisms. Nucleic Acids Research. 33: D433-7. PMID 15608232 DOI: 10.1093/Nar/Gki005  0.682
2003 Hooper SD, Berg OG. Duplication is more common among laterally transferred genes than among indigenous genes. Genome Biology. 4: R48. PMID 12914657 DOI: 10.1186/Gb-2003-4-8-R48  0.477
2003 Hooper SD, Berg OG. On the nature of gene innovation: duplication patterns in microbial genomes. Molecular Biology and Evolution. 20: 945-54. PMID 12716994 DOI: 10.1093/Molbev/Msg101  0.497
2002 Hooper SD, Berg OG. Gene Import or Deletion: A Study of the Different Genes in Escherichia coli Strains K12 and O157:H7. Journal of Molecular Evolution. 55: 734-44. PMID 12486532 DOI: 10.1007/S00239-002-2369-2  0.372
2002 Hooper SD, Berg OG. Detection of genes with atypical nucleotide sequence in microbial genomes. Journal of Molecular Evolution. 54: 365-75. PMID 11847562 DOI: 10.1007/S00239-001-0051-8  0.507
2000 Hooper SD, Berg OG. Gradients in nucleotide and codon usage along Escherichia coli genes. Nucleic Acids Research. 28: 3517-23. PMID 10982871 DOI: 10.1093/Nar/28.18.3517  0.376
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