18.12.2014 - 13:29
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Publications

2014

Castellano, S., Parra, G., Sánchez-Quinto, F. A., Racimo, F., Kuhlwilm, M., Kircher, M., Sawyer, S., Fu, Q., Heinze, A., Nickel, B., Dabney, J., Siebauer, M. F., White, L., Burbano, H. A., Renaud, G., Stenzel, U., Lalueza-Fox, C., de la Rasilla, M., Rosas, A., Rudan, P., Brajković, D., Kucan, Ž., Gušic, I., Shunkov, M. V., Derevianko, A. P., Viola, B., Meyer, M., Kelso, J. F., Andrés, A. M., & Pääbo, S. (2014). Patterns of coding variation in the complete exomes of three Neandertals. Proceedings of the National Academy of Sciences of the United States of America, 111(18), 6666-6671. doi: 10.1073/pnas.1405138111
Fu, Q., Li, H., Moorjani, P., Jay, F., Slepchenko, S. M., Bondarev, A. A., Johnson, P. L. F., Ayinuer-Petri, A., Prüfer, K., de Filippo, C., Meyer, M., Zwyns, N., Salazar García, D. C., Kuzmin, Y. V., Keates, S. G., Kosintsev, P. A., Razhev, D. I., Richards, M. P., Peristov, N. V., Lachmann, M., Douka, K., Higham, T. F. G., Slatkin, M., Hublin, J.-J., Reich, D., Kelso, J. F., Viola, B., & Pääbo, S. (2014). Genome sequence of a 45,000-year-old modern human from western Siberia. Nature, 514, 445-449. doi: 10.1038/nature13810
Gokhman, D., Lavi, E., Prüfer, K., Fraga, M. F., Riancho, J. A., Kelso, J. F., Pääbo, S., Meshorer, E., & Carmel, L. (2014). Reconstructing the DNA methylation maps of the Neandertal and the Denisovan. Science, 344(6183), 523-527. doi: 10.1126/science.1250368
Heyn, P., Kircher, M., Dahl, A., Kelso, J. F., Tomancak, P., Kalinka, A. T., & Neugebauer, K. M. (2014). The earliest transcribed zygotic genes are short, newly evolved and different across species. Cell Reports, 6(2), 285-292. doi: 10.1016/j.celrep.2013.12.030
Khrameeva, E. E., Bozek, K., He, L., Yan, Z., Jiang, X., Wei, Y., Tang, K., Gelfand, M. S., Prüfer, K., Kelso, J. F., Pääbo, S., Giavalisco, P., Lachmann, M., & Khaitovich, P. (2014). Neanderthal ancestry drives evolution of lipid catabolism in contemporary Europeans. Nature Communications, 5: 3584. doi: 10.1038/ncomms4584
Lazaridis, I., Patterson, N., Mittnik, A., Renaud, G., Mallick, S., Kirsanow, K., Sudmant, P. H., Schraiber, J. G., Castellano, S., Lipson, M., Berger, B., Economou, C., Bollongino, R., Fu, Q., Bos, K. I., Nordenfelt, S., Li, H., de Filippo, C., Prüfer, K., Sawyer, S., Posth, C., Haak, W., Hallgren, F., Fornander, E., Rohland, N., Delsate, D., Francken, M., Guinet, J.-M., Wahl, J., Ayodo, G., Babiker, H. A., Bailliet, G., Balanovska, E., Balanovsky, O., Barrantes, R., Bedoya, G., Ben-Ami, H., Bene, J., Berrada, F., Bravi, C. M., Brisighelli, F., Busby, G. B. J., Cali, F., Churnosov, M., Cole, D. E. C., Corach, D., Damba, L., van Driem, G., Dryomov, S., Dugoujon, J.-M., Fedorova, S. A., Romero, I. G., Gubina, M., Hammer, M., Henn, B. M., Hervig, T., Hodoglugil, U., Jha, A. R., Karachanak-Yankova, S., Khusainova, R., Khusnutdinova, E., Kittles, R., Kivisild, T., Klitz, W., Kučinskas, V., Kushniarevich, A., Laredj, L., Litvinov, S., Loukidis, T., Mahley, R. W., Melegh, B., Metspalu, E., Molina, J., Mountain, J., Näkkäläjärvi, K., Nesheva, D., Nyambo, T., Osipova, L., Parik, J., Platonov, F., Posukh, O., Romano, V., Rothhammer, F., Rudan, I., Ruizbakiev, R., Sahakyan, H., Sajantila, A., Salas, A., Starikovskaya, E. B., Tarekegn, A., Toncheva, D., Turdikulova, S., Uktveryte, I., Utevska, O., Vasquez, R., Villena, M., Voevoda, M., Winkler, C. A., Yepiskoposyan, L., Zalloua, P., Zemunik, T., Cooper, A., Capelli, C., Thomas, M. G., Ruiz-Linares, A., Tishkoff, S. A., Singh, L., Thangaraj, K., Villems, R., Comas, D., Sukernik, R., Metspalu, M., Meyer, M., Eichler, E. E., Burger, J., Slatkin, M., Pääbo, S., Kelso, J. F., Reich, D., & Krause, J. (2014). Ancient human genomes suggest three ancestral populations for present-day Europeans. Nature, 513, 409-413. doi: 10.1038/nature13673
Lippold, S., Xu, H., Ko, A., Li, M., Renaud, G., Butthoff, A., Schröder, R., & Stoneking, M. (2014). Human paternal and maternal demographic histories: Insights from high-resolution Y chromosome and mtDNA sequences. Investigative Genetics, 5: 13. doi: 10.1186/2041-2223-5-13
Prüfer, K., Racimo, F., Patterson, N., Jay, F., Sankararaman, S., Sawyer, S., Heinze, A., Renaud, G., Sudmant, P. H., de Filippo, C., Li, H., Mallick, S., Dannemann, M., Fu, Q., Kircher, M., Kuhlwilm, M., Lachmann, M., Meyer, M., Ongyerth, M., Siebauer, M. F., Theunert, C., Tandon, A., Moorjani, P., Pickrell, J., Mullikin, J. C., Vohr, S. H., Green, R. E., Hellmann, I., Johnson, P. L. F., Blanche, H., Cann, H., Kitzman, J. O., Shendure, J., Eichler, E. E., Lein, E. S., Bakken, T. E., Golovanova, L. V., Doronichev, V. B., Shunkov, M. V., Derevianko, A. P., Viola, B., Slatkin, M., Reich, D., Kelso, J. F., & Pääbo, S. (2014). The complete genome sequence of a Neanderthal from the Altai Mountains. Nature, 505(7481), 43-49. doi: 10.1038/nature12886
Renaud, G., Stenzel, U., & Kelso, J. F. (2014). leeHom: adaptor trimming and merging for Illumina sequencing reads. Nucleic Acids Research (London), 42(18): e141. doi: 10.1093/nar/gku699
Renaud, G., Stenzel, U., Maricic, T., Wiebe, V., & Kelso, J. F. (2014). deML: Robust demultiplexing of Illumina sequences using a likelihood-based approach (advance online). Bioinformatics. doi: 10.1093/bioinformatics/btu719
Sankararaman, S., Mallick, S., Dannemann, M., Prüfer, K., Kelso, J. F., Pääbo, S., Patterson, N., & Reich, D. (2014). The genomic landscape of Neanderthal ancestry in present-day humans. Nature, 507, 354-357. doi: 10.1038/nature12961

2013

Fu, Q., Meyer, M., Gao, X., Stenzel, U., Burbano, H. A., Kelso, J. F., & Pääbo, S. (2013). DNA analysis of an early modern human from Tianyuan Cave, China. Proceedings of the National Academy of Sciences of the United States of America, 110(6), 2223-2227. doi: 10.1073/pnas.1221359110
Kunz, M., Dannemann, M., & Kelso, J. (2013). High-throughput sequencing of the melanoma genome. Experimental Dermatology, 22(1), 10-17. doi: 10.1111/exd.12054
Maricic, T., Günther, V., Georgiev, O., Gehre, S., Ćurlin, M., Schreiweis, C., Naumann, R., Burbano, H. A., Meyer, M., Lalueza-Fox, C., de la Rasilla, M., Rosas, A., Gajović, S., Kelso, J. F., Enard, W., Schaffner, W., & Pääbo, S. (2013). A recent evolutionary change affects a regulatory element in the human FOXP2 gene. Molecular Biology and Evolution, 30(4), 844-852. doi: 10.1093/molbev/mss271
Renaud, G., Kircher, M., Stenzel, U., & Kelso, J. F. (2013). freeIbis: An efficient basecaller with calibrated quality scores for Illumina sequencers. Bioinformatics, 29(9), 1208-1209. doi: 10.1093/bioinformatics/btt117

2012

Burbano, H. A., Green, R. E., Maricic, T., Lalueza-Fox, C., de la Rasilla, M., Rosas, A., Kelso, J., Pollard, K. S., Lachmann, M., & Pääbo, S. (2012). Analysis of human accelerated DNA regions using archaic hominin genomes. PLoS One, 7(3): e32877. doi: 10.1371/journal.pone.0032877
Dannemann, M., Nickel, B., Lizano, E., Burbano, H., & Kelso, J. F. (2012). Annotation of primate miRNAs by high throughput sequencing of small RNA libraries. BMC Genomics, 13(Suppl. 3): 116. doi: 10.1186/1471-2164-13-116
Dannemann, M., Prüfer, K., Lizano, E., Nickel, B., Burbano, H. A., & Kelso, J. (2012). Transcription factors are targeted by differentially expressed miRNAs in primates. Genome biology and evolution, 4(4), 552-564. doi: 10.1093/gbe/evs033
Groß, A., Hartung, M., Prüfer, K., Kelso, J., & Rahm, E. (2012). Impact of ontology evolution on functional analyses. Bioinformatics, 28(20), 2671-2677. doi: 10.1093/bioinformatics/bts498
Meyer, M., Kircher, M., Gansauge, M.-T., Li, H., Racimo, F., Mallick, S., Schraiber, J. G., Jay, F., Prüfer, K., Filippo, C. d., Sudmant, P. H., Alkan, C., Fu, Q., Do, R., Rohland, N., Tandon, A., Siebauer, M., Green, R. E., Bryc, K., Briggs, A. W., Stenzel, U., Dabney, J., Shendure, J., Kitzman, J., Hammer, M. F., Shunkov, M. V., Derevianko, A. P., Patterson, N., Andrés, A. M., Eichler, E. E., Slatkin, M., Reich, D., Kelso, J., & Pääbo, S. (2012). A high-coverage genome sequence from an archaic Denisovan individual. Science, 338(6104), 222-226. doi: 10.1126/science.1224344
Prüfer, K., Munch, K., Hellmann, I., Akagi, K., Miller, J. R., Walenz, B., Koren, S., Sutton, G., Kodira, C., Winer, R., Knight, J. R., Mullikin, J. C., Meader, S. J., Ponting, C. P., Lunter, G., Higashino, S., Hobolth, A., Dutheil, J., Karakoç, E., Alkan, C., Sajjadian, S., Catacchio, C. R., Ventura, M., Marques-Bonet, T., Eichler, E. E., André, C., Atencia, R., Mugisha, L., Junhold, J., Patterson, N., Siebauer, M., Good, J. M., Fischer, A., Ptak, S. E., Lachmann, M., Symer, D. E., Mailund, T., Schierup, M. H., Andrés, A. M., Kelso, J., & Pääbo, S. (2012). The bonobo genome compared with the chimpanzee and human genomes. Nature, 486(7404), 527-531. doi: 10.1038/nature11128
Rost, B., Gaasterland, T., Lengauer, T., Linial, M., Markel, S., McKay, B. M., Schneider, R., Horton, P., & Kelso, J. F. (2012). Paving the future: finding suitable ISMB venues. Bioinformatics, 28(19), 2556-2559. doi: 10.1093/bioinformatics/bts420

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
Ranganathan, S., Schönbach, C., Kelso, J. F., Rost, B., Nathan, S., & Tan, T. W. (2011). Towards big data science in the decade ahead from ten years of InCoB and the 1st ISCB-Asia Joint Conference. BMC Bioinformatics, 12(Suppl. 13): S1. doi: 10.1186/1471-2105-12-S13-S1
Schönbach, C., Tan, T. W., Kelso, J. F., Rost, B., Nathan, S., & Ranganathan, S. (2011). InCoB celebrates its tenth anniversary as first joint conference with ISCB-Asia. BMC Genomics, 12(Suppl. 3): S1. doi: 10.1186/1471-2164-12-S3-S1

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., Bacher, J., Backhaus, M., Gregorio, S. E. J., Loebe, F., Pruefer, K., Uciteli, A., Visagie, J., Herre, H., & Kelso, J. F. (2009). BOWiki: an ontology-based wiki for annotation of data and integration of knowledge in biology. BMC Bioinformatics, 10: S5. doi: 10.1186/1471-2105-10-S5-S5
Download: [hoehndorf_2009.pdf]
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

Burek, P., Höhndorf, R., Loebe, F., Visagie, J., Herre, H., & Kelso, J. (2006). A top-level ontology of functions and its application in the Open Biomedical Ontologies. Bioinformatics, 22(14), e66-e73. doi: 10.1093/bioinformatics/btl266
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

Carninci, P., Kasukawa, T., Katayama, S., Gough, J., Frith, M. C., Maeda, N., Oyama, R., Ravasi, T., Lenhard, B., Wells, C., Kodzius, R., Shimokawa, K., Bajic, V. B., Brenner, S. E., Batalov, S., Forrest, A. R. R., Zavolan, M., Davis, M. J., Wilming, L. G., Aidinis, V., Allen, J. E., Ambesi-Impiombato, A., Apweiler, R., Aturaliya, R. N., Bailey, T. L., Bansal, M., Baxter, L., Beisel, K. W., Bersano, T., Bono, H., Chalk, A. M., Chiu, K. P., Choudhary, V., Christoffels, A., Clutterbuck, D. R., Crowe, M. L., Dalla, E., Dalrymple, B. P., de Bono, B., Gatta, G. D., Bernardo, D. d., Down, T., Engstrom, P., Fagiolini, M., Faulkner, G., Fletcher, C. F., Fukushima, T., Furuno, M., Futaki, S., Gariboldi, M., Georgii-Hemming, P., Gingeras, T. R., Gojobori, T., Green, R. E., Gustincich, S., Harbers, M., Hayashi, Y., Hensch, T. K., Hirokawa, N., Hill, D., Huminiecki, L., Iacono, M., Ikeo, K., Iwama, A., Ishikawa, T., Jakt, M., Kanapin, A., Katoh, M., Kawasawa, Y., Kelso, J. F., Kitamura, H., Kitano, H., Kollias, G., Krishnan, S. P. T., Kruger, A., Kummerfeld, S. K., Kurochkin, I. V., Lareau, L. F., Lazarevic, D., Lipovich, L., Liu, J., Liuni, S., McWilliam, S., Babu, M. M., Madera, M., Marchionni, L., Matsuda, H., Matsuzawa, S., Miki, H., Mignone, F., Miyake, S., Morris, K., Mottagui-Tabar, S., Mulder, N., Nakano, N., Nakauchi, H., Ng, P., Nilsson, R., Nishiguchi, S., Nishikawa, S., Nori, F., Ohara, O., Okazaki, Y., Orlando, V., Pang, K. C., Pavan, W. J., Pavesi, G., Pesole, G., Petrovsky, N., Piazza, S., Reed, J., Reid, J. F., Ring, B. Z., Ringwald, M., Rost, B., Ruan, Y., Salzberg, S. L., Sandelin, A., Schneider, C., Schönbach, C., Sekiguchi, K., Semple, C. A. M., Seno, S., Sessa, L., Sheng, Y., Shibata, Y., Shimada, H., Shimada, K., Silva, D., Sinclair, B., Sperling, S., Stupka, E., Sugiura, K., Sultana, R., Takenaka, Y., Taki, K., Tammoja, K., Tan, S. L., Tang, S., Taylor, M. S., Tegner, J., Teichmann, S. A., Ueda, H. R., van Nimwegen, E., Verardo, R., Wei, C. L., Yagi, K., Yamanishi, H., Zabarovsky, E., Zhu, S., Zimmer, A., Hide, W., Bult, C., Grimmond, S. M., Teasdale, R. D., Liu, E. T., Brusic, V., Quackenbush, J., Wahlestedt, C., Mattick, J. S., Hume, D. A., Kai, C., Sasaki, D., Tomaru, Y., Fukuda, S., Kanamori-Katayama, M., Suzuki, M., Aoki, J., Arakawa, T., Iida, J., Imamura, K., Itoh, M., Kato, T., Kawaji, H., Kawagashira, N., Kawashima, T., Kojima, M., Kondo, S., Konno, H., Nakano, K., Ninomiya, N., Nishio, T., Okada, M., Plessy, C., Shibata, K., Shiraki, T., Suzuki, S., Tagami, M., Waki, K., Watahiki, A., Okamura-Oho, Y., Suzuki, H., Kawai, J., Hayashizaki, Y., FANTOM Consortium, & RIKEN Genome Exploration Research Group and Genome Science Group (Genome Network Project Core Group) (2005). The transcriptional landscape of the mammalian genome. Science, 309(5740), 1559-1563. doi: 10.1126/science.1112014
Tanino, M., Debily, M.-A., Tamura, T., Hishiki, T., Ogasawara, O., Murakawa, K., Kawamoto, S., Itoh, K., Watanabe, S., de Souza, S. J., Imbeaud, S., Graudens, E., Eveno, E., Hilton, P., Sudo, Y., Kelso, J. F., Ikeo, K., Imanishi, T., Gojobori, T., Auffray, C., Hide, W., & Okubo, K. (2005). The Human Anatomic Gene Expression Library (H-ANGEL), the H-Inv integrative display of human gene expression across disparate technologies and platforms. Nucleic Acids Research (London), 33(Suppl. 1 Database Issue), D567-D572. doi: 10.1093/nar/gki104
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

2004

Imanishi, T., Itoh, T., Suzuki, Y., O'Donovan, C., Fukuchi, S., Koyanagi, K. O., Barrero, R. A., Tamura, T., Yamaguchi-Kabata, Y., Tanino, M., Yura, K., Miyazaki, S., Ikeo, K., Homma, K., Kasprzyk, A., Nishikawa, T., Hirakawa, M., Thierry-Mieg, J., Thierry-Mieg, D., Ashurst, J., Jia, L., Nakao, M., Thomas, M. A., Mulder, N., Karavidopoulou, Y., Jin, L., Kim, S., Yasuda, T., Lenhard, B., Eveno, E., Suzuki, Y., Yamasaki, C., Takeda, J.-i., Gough, C., Hilton, P., Fujii, Y., Sakai, H., Tanaka, S., Amid, C., Bellgard, M., de Bonaldo, M. F., Bono, H., Bromberg, S. K., Brookes, A. J., Bruford, E., Carninci, P., Chelala, C., Couillault, C., de Souza, S. J., Debily, M.-A., Devignes, M.-D., Dubchak, I., Endo, T., Estreicher, A., Eyras, E., Fukami-Kobayashi, K., Gopinath, G. R., Graudens, E., Hahn, Y., Han, M., Han, Z.-G., Hanada, K., Hanaoka, H., Harada, E., Hashimoto, K., Hinz, U., Hirai, M., Hishiki, T., Hopkinson, I., Imbeaud, S., Inoko, H., Kanapin, A., Kaneko, Y., Kasukawa, T., Kelso, J. F., Kersey, P., Kikuno, R., Kimura, K., Korn, B., Kuryshev, V., Makalowska, I., Makino, T., Mano, S., Mariage-Samson, R., Mashima, J., Matsuda, H., Mewes, H.-W., Minoshima, S., Nagai, K., Nagasaki, H., Nagata, N., Nigam, R., Ogasawara, O., Ohara, O., Ohtsubo, M., Okada, N., Okido, T., Oota, S., Ota, M., Ota, T., Otsuki, T., Piatier-Tonneau, D., Poustka, A., Ren, S.-X., Saitou, N., Sakai, K., Sakamoto, S., Sakate, R., Schupp, I., Servant, F., Sherry, S., Shiba, R., Shimizu, N., Shimoyama, M., Simpson, A. J., Soares, B., Steward, C., Suwa, M., Suzuki, M., Takahashi, A., Tamiya, G., Tanaka, H., Taylor, T., Terwilliger, J. D., Unneberg, P., Veeramachaneni, V., Watanabe, S., Wilming, L., Yasuda, N., Yoo, H.-S., Stodolsky, M., Makalowski, W., Go, M., Nakai, K., Takagi, T., Kanehisa, M., Sakaki, Y., Quackenbush, J., Okazaki, Y., Hayashizaki, Y., Hide, W., Chakraborty, R., Nishikawa, K., Sugawara, H., Tateno, Y., Chen, Z., Oishi, M., Tonellato, P., Apweiler, R., Okubo, K., Wagner, L., Wiemann, S., Strausberg, R. L., Isogai, T., Auffray, C., Nomura, N., Gojobori, T., & Sugano, S. (2004). Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biology, 2(6): e162. doi: 10.1371/journal.pbio.0020162
Kelso, J. F. (2004). EST resources, clone sets, and databases. In L. B. Jorde (Ed.), Encyclopedia of genetics, genomics, proteomics and bioinformatics. Wiley. doi: 10.1002/047001153X.g207210
Nembaware, V., Wolfe, K. H., Bettoni, F., Kelso, J. F., & Seoighe, C. (2004). Allele-specific transcript isoforms in human. FEBS Letters, 577(1-2), 233-238. doi: 10.1016/j.febslet.2004.10.018

2003

Brentani, H., Caballero, O. L., Camargo, A. A., da Silva, A. M., da Silva, W. A., Neto, E. D., Grivet, M., Gruber, A., Guimaraes, P. E. M., Hide, W., Iseli, C., Jongeneel, C. V., Kelso, J. F., Nagai, M. A., Ojopi, E. P. B., Osorio, E. C., Reis, E. M. R., Riggins, G. J., Simpson, A. J. G., de Souza, S., Stevenson, B. J., Strausberg, R. L., Tajara, E. H., Verjovski-Almeida, S., The Human Cancer Genome Project Cancer Genome Anatomy Project Annotation Consortium, & The Human Cancer Genome Project Sequencing Consortium (2003). The generation and utilization of a cancer-oriented representation of the human transcriptome by using expressed sequence tags. Proceedings of the National Academy of Sciences of the United States of America, 100(23), 13418-13423. doi: 10.1073/pnas.1233632100
Hide, W., Smedley, D., McCarthy, M., & Kelso, J. F. (2003). Application of eVOC: Controlled vocabularies for unifying gene expression data. Comptes Rendus Biologies, 326(10-11), 1089-1096. doi: 10.1016/j.crvi.2003.09.030
Kelso, J. F., Visagie, J., Theiler, G., Christoffels, A., Bardien, S., Smedley, D., Otgaar, D., Greyling, G., Jongeneel, C. V., McCarthy, M. I., Hide, T., & Hide, W. (2003). eVOC: A controlled vocabulary for unifying gene expression data. Genome Research, 13(6a), 1222-1230. doi: 10.1101/gr.985203
Sharov, A. A., Piao, Y., Matoba, R., Dudekula, D. B., Qian, Y., VanBuren, V., Falco, G., Martin, P. R., Stagg, C. A., Bassey, U. C., Wang, Y., Carter, M. G., Hamatani, T., Aiba, K., Akutsu, H., Sharova, L., Tanaka, T. S., Kimber, W. L., Yoshikawa, T., Jaradat, S. A., Pantano, S., Nagaraja, R., Boheler, K. R., Taub, D., Hodes, R. J., Longo, D. L., Schlessinger, D., Keller, J., Klotz, E., Kelsoe, G., Umezawa, A., Vescovi, A. L., Rossant, J., Kunath, T., Hogan, B. L. M., Curci, A., D'Urso, M., Kelso, J. F., Hide, W., & Ko, M. S. H. (2003). Transcriptome analysis of mouse stem cells and early embryos. PLoS Biology, 1(3): e74. doi: 10.1371/journal.pbio.0000074

2002

Kelso, J. F. (2002). Transcript reconstruction and analysis using STACKdb and stackPACK. EMBnet.news, 8(1), 8-11. Retrieved from http://journal.embnet.org/index.php/embnetnews/article/view/106/132.
Nembaware, V., Crum, K., Kelso, J. F., & Seoighe, C. (2002). Impact of the presence of paralogs on sequence divergence in a set of mouse-human orthologs. Genome Research, 12(9), 1370-1376. doi: 10.1101/gr.270902
VanBuren, V., Piao, Y., Dudekula, D. B., Qian, Y., Carter, M. G., Martin, P. R., Stagg, C. A., Bassey, U. C., Aiba, K., Hamatani, T., Kargul, G. J., Luo, A. G., Kelso, J. F., Hide, W., & Ko, M. S. (2002). Assembly, verification, and initial annotation of the NIA mouse 7.4K cDNA clone set. Genome Research, 12(12), 1999-2003. doi: 10.1101/gr.633802

2001

Hide, W. A., Babenko, V. N., van Heusden, P. A., Seoighe, C., & Kelso, J. F. (2001). The contribution of exon-skipping events on chromosome 22 to protein coding diversity. Genome Research, 11(11), 1848-1853. doi: 10.1101/gr.188001
Hide, W., Mizrahi, V., Venkatesh, B., Brenner, S., Simpson, A., Blatch, G., Soodyall, H., Denby, K., Wingfield, M., Wingfield, B., van Helden, P., Ramesar, R., Dorrington, R., Kelso, J. F., Oppon, E., Goyvaerts, E., Ramsay, M., de Villiers, E., van Heerden, C., Allsopp, B., & Seoighe, C. (2001). A platform for genomics in South Africa. South African Medical Journal, 91(12), 1006-1007. Retrieved from http://archive.samj.org.za/2001%20VOL%2091%20Jan-Dec/Articles/12%20December/1.1%20LETTERS.pdf.