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Publications

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2011

Gaudet, P., Bairoch, A., Field, D., Sansone, S.-A., Taylor, C., Attwood, T. K., Bateman, A., Blake, J. A., Bult, C. J., Cherry, J. M., Chrisholm, R. L., Cochrane, G., Cook, C. E., Eppig, J. T., Galperin, M. Y., Gentleman, R., Goble, C. A., Gojobori, T., Hancock, J. M., Howe, D. G., Imanishi, T., Kelso, J., Landsman, D., Lewis, S. E., Karsch-Mizrachi, I., Orchard, S., Ouellette, B. F. F., Ranganathan, S., Richardson, L., Rocca-Serra, P., Schofield, P. N., Smedley, D., Southan, C., Tan, T. W., Tatusova, T., Whetzel, P. L., White, O., & Yamasaki, C. (2011). Towards BioDBcore: a community-defined information specification for biological databases. Nucleic Acids Research, 39(Suppl. 1). doi: 10.1093/nar/gkq1173
Gaudet, P., Bairoch, A., Field, D., Sansone, S.-A., Taylor, C., Attwood, T. K., Bateman, A., Blake, J. A., Bult, C. J., Cherry, J. M., Chrisholm, R. L., Cochrane, G., Cook, C. E., Eppig, J. T., Galperin, M. Y., Gentleman, R., Goble, C. A., Gojobori, T., Hancock, J. M., Howe, D. G., Imanishi, T., Kelso, J., Landsman, D., Lewis, S. E., Mizrachi, I. K., Orchard, S., Ouellette, B. F. F., Ranganathan, S., Richardson, L., Rocca-Serra, P., Schofield, P. N., Smedley, D., Southan, C., Tan, T. W., Tatusova, T., Whetzel, P. L., White, O., & Yamasaki, C. (2011). Towards BioDBcore: a community-defined information specification for biological databases. Database: the Journal of Biological Databases and Curation, 2011: baq027, pp. 1-6. doi: 10.1093/database/baq027
Herre, H., Hoehndorf, R., Kelso, J., Loebe, F., & Schulz, S. (2011). OBML – Ontologies in biomedicine and life sciences. Journal of Biomedical Semantics, 2(Suppl. 4): I1, pp. 1-6. doi: 10.1186/2041-1480-2-S4-I1
Kircher, M., Heyn, P., & Kelso, J. (2011). Addressing challenges in the production and analysis of illumina sequencing data. BMC Genomics, 12: 382. doi: 10.1186/1471-2164-12-382
Nagaraj, N., Wisniewski, J. R., Geiger, T., Cox, J., Kircher, M., Kelso, J., Pääbo, S., & Mann, M. (2011). Deep proteome and transcriptome mapping of a human cancer cell line. Molecular Systems Biology, 7: 548. doi: 10.1038/msb.2011.81

2010

Green, R. E., Krause, J., Briggs, A. W., Maricic, T., Stenzel, U., Kircher, M., Patterson, N., Li, H., Zhai, W., Fritz, M.-H.-Y., Hansen, N. F., Durand, E. Y., Malaspinas, A.-S., Jensen, J. D., Marques-Bonet, T., Alkan, C., Prüfer, K., Meyer, M., Burbano, H. A., Good, J. M., Schultz, R., Aximu-Petri, A., Butthoff, A., Höber, B., Höffner, B., Siegemund, M., Weihmann, A., Nusbaum, C., Lander, E. S., Russ, C., Novod, N., Affourtit, J., Egholm, M., Verna, C., Rudan, P., Brajkovic, D., Kucan, Z., Gusic, I., Doronichev, V. B., Golovanova, L. V., Lalueza-Fox, C., Rasilla, M. d. l., Fortea, J., Rosas, A., Schmitz, R. W., Johnson, P. L. F., Eichler, E. E., Falush, D., Birney, E., Mullikin, J. C., Slatkin, M., Nielsen, R., Kelso, J., Lachmann, M., Reich, D., & Pääbo, S. (2010). A draft sequence of the Neandertal genome. Science, 328(5979), 710-722. doi: 10.1126/science.1188021
Hoehndorf, R., Ngonga Ngomo, A.-C., & Kelso, J. (2010). Applying the functional abnormality ontology pattern to anatomical functions. Journal of biomedical semantics, 1(1): 4, pp. 1-15. doi: 10.1186/2041-1480-1-4
Hoehndorf, R., Ngonga Ngomo, A.-C., Dannemann, M., & Kelso, J. (2010). Statistical tests for associations between two directed acyclic graphs. PLoS ONE, 5(6): e10996, pp. 1-8. doi: 10.1371/journal.pone.0010996
Hoehndorf, R., Oellrich, A., Dumontier, M., Kelso, J., Rebholz-Schuhmann, D., & Herre, H. (2010). Relations as patterns: bridging the gap between OBO and OWL. BMC Bioinformatics, 11: 441. doi: 10.1186/1471-2105-11-441
Download: [Hoehndorf_2010.pdf]
Kelso, J., Hoehndorf, R., & Prüfer, K. (2010). Ontologies in biology. In R. Poli, M. Healy, & A. Kameas (Eds.), Theory and applications of ontology: Computer applications (pp. 347-371). New York [u.a.]: Springer. doi: 10.1007/978-90-481-8847-5_15
Kircher, M., & Kelso, J. (2010). High-throughput DNA sequencing - concepts and limitations. BioEssays, 32(6), 524-536. doi: 10.1002/bies.200900181
Prüfer, K., Stenzel, U., Hofreiter, M., Pääbo, S., Kelso, J., & Green, R. E. (2010). Computational challenges in the analysis of ancient DNA. Genome Biology, 11(5): R47, pp. 1-15. doi: 10.1186/gb-2010-11-5-r47
Reich, D., Green, R. E., Kircher, M., Krause, J., Patterson, N., Durand, E. Y., Viola, B., Briggs, A. W., Stenzel, U., Johnson, P. L. F., Maricic, T., Good, J. M., Marques-Bonet, T., Alkan, C., Fu, Q., Mallick, S., Li, H., Meyer, M., Eichler, E. E., Stoneking, M., Richards, M., Talamo, S., Shunkov, M. V., Derevianko, A. P., Hublin, J.-J., Kelso, J., Slatkin, M., & Pääbo, S. (2010). Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature, 468(7327), 1053-1060. doi: 10.1038/nature09710

2009

Hoehndorf, R., Kelso, J. F., & Herre, H. (2009). The ontology of biological sequences. BMC Bioinformatics, 10: 377. doi: 10.1186/1471-2105-10-377
Download: [Hoehndorf_2009.pdf]
Kircher, M., Stenzel, U., & Kelso, J. F. (2009). Improved base calling for the Illumina Genome Analyzer using machine learning strategies. Genome Biology, 10(8): R83, pp. 1-9. doi: 10.1186/gb-2009-10-8-r83
Landsman, D., Gentleman, R., Kelso, J., & Ouellette, B. F. F. (2009). DATABASE: A new forum for biological databases and curation. Database: the Journal of Biological Databases and Curation, 2009: bap002, pp. 1-2. doi: 10.1093/database/bap002
Somel, M., Franz, H., Yan, Z., Lorenc, A., Guo, S., Giger, T., Kelso, J. F., Nickel, B., Dannemann, M., Bahn, S., Webster, M. J., Weickert, C. S., Pääbo, S., & Khaitovich, P. (2009). Transcriptional neoteny in the human brain. PNAS - Proceedings of the National Academy of Sciences, 106(14), 5743-5748. doi: 10.1073/pnas.0900544106

2008

Giger, T., Excoffier, L., Amstutz, U., Day, P. J. R., Champigneulle, A., Hansen, M. M., Kelso, J. F., & Largiadèr, C. R. (2008). Population transcriptomics of life-history variation in the genus Salmo. Molecular Ecology, 17(13), 3095-3108. doi: 10.1111/j.1365-294X.2008.03820.x
Green, R. E., Malaspinas, A.-S., Krause, J., Briggs, A. W., Johnson, P. L. F., Uhler, C., Meyer, M., Good, J. M., Maricic, T., Stenzel, U., Prüfer, K., Siebauer, M., Burbano, H. A., Ronan, M. T., Rothberg, J. M., Egholm, M., Rudan, P., Brajkovic, D., Kucan, Z., Gusic, I., Wikström, M., Laakkonen, L., Kelso, J. F., Slatkin, M., & Pääbo, S. (2008). A complete Neandertal mitochondrial genome sequence determined by high-throughput sequencing. Cell, 134(3), 416-426. doi: 10.1016/j.cell.2008.06.021
Hoehndorf, R., Loebe, F., Poli, R., Herre, H., & Kelso, J. F. (2008). GFO-Bio: A biological core ontology. Applied ontology, 3(4), 219-227. doi: 10.3233/AO-2008-0055
Myles, S., Tang, K., Somel, M., Green, R. E., Kelso, J. F., & Stoneking, M. (2008). Identification and analysis of genomic regions with large between-population differentiation in humans. Annals of Human Genetics, 72(1), 99-110. doi: 10.1111/j.1469-1809.2007.00390.x
Prüfer, K., Stenzel, U., Dannemann, M., Green, R. E., Lachmann, M., & Kelso, J. F. (2008). PatMaN: rapid alignment of short sequences to large databases. Bioinformatics, 24(13), 1530-1533. doi: 10.1093/bioinformatics/btn223

2007

Briggs, A. W., Stenzel, U., Johnson, P. L. F., Green, R. E., Kelso, J. F., Prüfer, K., Meyer, M., Krause, J., Ronan, M. T., Lachmann, M., & Pääbo, S. (2007). Patterns of damage in genomic DNA sequences from a Neandertal. Proceedings of the National Academy of Sciences of the United States of America, 104(37), 14616-14621. doi: 10.1073/pnas.0704665104
Fu, N., Drinnenberg, I., Kelso, J. F., Wu, J.-R., Pääbo, S., Zeng, R., & Khaitovich, P. (2007). Comparison of protein and mRNA expression evolution in humans and chimpanzees. PLoS One, 2(2): e216, pp. e216. doi: 10.1371/journal.pone.0000216
Hoehndorf, R., Loebe, F., Kelso, J. F., & Herre, H. (2007). Representing default knowledge in biomedical ontologies: Application to the integration of anatomy and phenotype ontologies. BMC Bioinformatics, 8: 377. doi: 10.1186/1471-2105-8-377
Download: [Hoehndorf_2007.pdf]
Lizano, E., Schuster, M., Müller, M., Kelso, J. F., & Mörl, M. (2007). A splice variant of the human CCA-adding enzyme with modified activity. Journal of Molecular Biology (London), 366, 1258-1265. doi: 10.1016/j.jmb.2006.2006.12.016
Myles, S., Somel, M., Tang, K., Kelso, J. F., & Stoneking, M. (2007). Identifying genes underlying skin pigmentation differences among human populations. Human Genetics, 120(5), 613-621. doi: 10.1007/s00439-006-0256-4

2006

Khaitovich, P., Kelso, J. F., Franz, H., Visagie, J., Giger, T., Joerchel, S., Petzold, E., Green, R. E., Lachmann, M., & Pääbo, S. (2006). Functionality of intergenic transcription: An evolutionary comparison. PLoS Genetics, 2(10): e171, pp. 1590-1598. doi: 10.1371/journal.pgen.0020171
Khaitovich, P., Tang, K., Franz, H., Kelso, J. F., Hellmann, I., Enard, W., Lachmann, M., & Pääbo, S. (2006). Positive selection on gene expression in the human brain. Current Biology, 16(10), R356-R358. doi: 10.1016/j.cub.2006.03.082

2005

Tiffin, N., Kelso, J. F., Powell, A. R., Hong, P., Bajic, V. B., & Hide, W. A. (2005). Integration of text- and data-mining using ontologies successfully selects disease gene candidates. Nucleic Acids Research, 33(5), 1544-1552. doi: 10.1093/nar/gki296