2011

Gaudet, P, A. Bairoch, D. Field, S.-A. Sansone, C. Taylor, T.K. Attwood, A. Bateman, J.A. Blake, C.J. Bult, J.M. Cherry, R.L. Chisholm, G. Cochrane, C.E. Cook, J.T. Eppig, M.Y. Galperin, R. Gentleman, C.A. Goble, T. Gojobori, J.M. Hancock, D.G. Howe, T. Imanishi, J. Kelso, D. Landsman, S.E. Lewis, I.K. Mizrachi, S. Orchard, B.F. Ouellette, S. Ranganathan, L. Richardson, P. Rocca-Serra, P.N. Schofield, D. Smedley, C. Southan, T.W. Tan, T. Tatusova, P.L. Whetzel, O. White, C. Yamasaki, BioDBCore Working Group: Towards BioDBcore: a community-definded information specification for biological databases. Database baq027, doi:10.1093/database/baq027 (2011).

Kircher, M., P. Heyn and J. Kelso: Addressing challenges in the production and analysis of illumina sequencing data. BMC Genomics 12:382 (2011).

2010

Green, R.E., J. Krause, A.W. Briggs, T. Maricic, U. Stenzel, M. Kircher, N. Patterson, H. Li, W. Zhai, M.H.-Y. Fritz, N.F. Hansen, E.Y. Durand, A.-S. Malaspinas, J.D. Jensen, T. Marques-Bonet, C. Alkan, K. Prüfer, M. Meyer, H.A. Burbano, J.M. Good, R. Schultz, A. Aximu-Petri, A. Butthof, B. Höber, B. Höffner, M. Siegemund, A. Weihmann, C. Nusbaum, E.S. Lander, C. Russ, N. Novod, J. Affourtit, M. Egholm, C. Verna, P. Rudan, D. Brajković, Ž. Kućan, I. Gušić, V.B. Doronichev, L.V. Golovanova, C. Lalueza-Fox, M. de la Rasilla, J. Fortea, A. Rosas, R.W. Schmitz, P.L.F. Johnson, E.E. Eichler, D. Falush, E. Birney, J.C. Mullikin, M. Slatkin, R. Nielsen, J. Kelso, M. Lachmann, D. Reich and S. Pääbo: A draft sequence of the Neandertal genome. Science 328, 710-722 (2010).

Hoehndorf, R., A.-C. Ngonga Ngomo and J. Kelso: Applying the functional abnormality ontology pattern to anatomical functions. Journal of Biomedical Semantics, 1:4 (2010).

Hoehndorf, R., A.-C. Ngonga Ngomo, M. Dannemann and J. Kelso: Statistical tests for associations between two directed acyclic graphs. PLoS ONE 5 (6), e10996 (2010).

Hoehndorf, R., A. Oellrich, M. Dumontier, J. Kelso, D. Rebholz-Schuhmann and H. Herre: Relations as patterns: bridging the gap between OBO and OWL. BMC Bioinformatics 11, 441 (2010).

Kelso, J., R. Hoehndorf and K. Prüfer: Ontologies in biology. In: Theory and Applications of Ontologies. Second Volume. Ontology: The Information-science Stance. (Eds) M. Healey, A. Kameas and R. Poli, Springer-Verlag, 347-371 (2010).

Kircher, M. and J. Kelso: High-throughput DNA sequencing – concepts and limitations. Bioessays 32, 524-536 (2010).

Prüfer, K., U. Stenzel, M. Hofreiter, S. Pääbo, J. Kelso, R.E. Green: Computational challenges in the analysis of ancient DNA. Genome Biology 11, R47 (2010).

Reich, D., R.E. Green, M. Kircher, J. Krause, N. Patterson, E.Y. Durand, B. Viola, A.W. Briggs, U. Stenzel, P.L.F. Johnson, T. Maricic, J.M. Good, T. Marques-Bonet, C. Alkan, Q. Fu, S. Mallick, H. Li, M. Meyer, E.E. Eichler, M. Stoneking, M. Richards, S. Talamo, M.V. Shunkov, A.P. Derevianko, J.-J. Hublin, J. Kelso, M. Slatkin and S. Pääbo: Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature 468, 1053-60 (2010).

2009

Hoehndorf, R., J. Kelso and H. Herre: The ontology of biological sequences. BMC Bioinformatics 10, 377 (2009).

Hoehndorf, R., J. Bacher, M. Backhaus, S.E. Gregorio, Jr., F. Loebe, K. Prüfer, A. Uciteli, J. Visagie, H. Herre and J. Kelso: BOWiki: An ontology-based wiki for annotation of data and integration of knowledge in biology. BMC Bioinformatics 10, S5 (2009).

Kircher, M., U. Stenzel and J. Kelso: Improved base calling for the Illumina Genome Analyzer using machine learning strategies. Genome Biology 10, R83 (2009).

Landsman, D., R. Gentleman, J. Kelso and B.F. Francis Ouellette: DATABASE: A new forum for biological databases and curation. Database bap002, doi:10.1093/database/bap002 (2009).

Somel, M., H. Franz, Z. Yan, A. Lorenc, S. Guo, T. Giger, J. Kelso, B. Nickel, M. Dannemann, S. Bahn, M.J. Webster, C.S. Weickert, M. Lachmann, S. Pääbo and P. Khaitovich: Transcriptional neoteny in the human brain. PNAS 106, 5743-48 (2009).

2008

Giger T, Excoffier L, Amstutz U, Day PJ, Champigneulle A, Hansen MM, Kelso J, Largiadèr CR. Population transcriptomics of life-history variation in the genus Salmo. Mol Ecol.  2008.

Green, R.E., A.-S. Malaspinas, J. Krause, A.W. Briggs, P.L.F. Johnson, C. Uhler, M. Meyer, J.M. Good, T. Maricic, U. Stenzel, K. Prüfer, M. Siebauer, H.A. Burbano, M. Ronan, J.M. Rothberg, M. Egholm, P. Rudan, D. Brajković, Ž. Kućan, I. Gušić, M. Wikström, L. Laakkonen, J. Kelso, M. Slatkin and S. Pääbo: A complete Neandertal mitochondrial genome sequence determined by high-throughput sequencing. Cell 134, 416-426 (2008).

Hoehndorf, R., F. Loebe, R. Poli, H. Herre and J. Kelso: GFO-Bio: A biological core ontology. Applied Ontology 3, 219-227 (2008).

Prüfer K, Stenzel U, Dannemann M, Green RE, Lachmann M, Kelso J. PatMaN: rapid alignment of short sequences to large databases. Bioinformatics. 2008.

Myles S, Tang K, Somel M, Green RE, Kelso J, Stoneking M. Identification and analysis of genomic regions with large between-population differentiation in humans. Ann Hum Genet. 2008. 72(1):99-110.

Kelso, J, Prüfer K and Hoehndorf, R.  Book Chapter. Ontologies in Biology. in Theory and Application of Ontologies. Volume II: Ontology: the Information-science stance. Editors: Michael Healy, Achilles Kameas, Roberto Poli. In Press.

2007

Hoehndorf R, Loebe F, Kelso J, Herre H. Representing default knowledge in biomedical ontologies: application to the integration of anatomy and phenotype ontologies. BMC Bioinformatics. 2007. 8:377.

Adrian W. Briggs, Udo Stenzel, Philip L.F. Johnson, Richard E. Green, Janet Kelso, Kay Prüfer, Matthias Meyer, Johannes Krause, Michael T. Ronan, Michael Lachmann and Svante Pääbo. Patterns of damage in genomic DNA sequences from a Neandertal. PNAS. 2007. 104(37):14616-21

Fu N., Drinnenberg I., Kelso J., Wu J.R., Paabo S., Zeng R., Khaitovich P., Comparison of protein and mRNA expression evolution in humans and chimpanzees. PLoS ONE. 2007. 2:e216.

Lizano E, Schuster J, Muller M, Kelso J, Morl M.  A splice variant of the human CCA-adding enzyme with modified activity. J. Mol. Biol. 2007 366(4):1258-65.

2006

Khaitovich, P.*, Kelso, J.*, Franz, H.*, Visagie, J., Giger, T., Joerchel, S., Petzold, E., Green, R.E., Lachmann, M., Paabo, S.  Functionality of intergenic transcription: an evolutionary comparison.  PLoS Genet. 2006.  2 (10):

Myles, S., Somel, M., Tang, K., Kelso, J., Stoneking, M. Identifying genes underlying skin pigmentation differences among human populations. Human Genetics. 2006.

Tiffin, N., Kelso, J.F., Powell, A.R., Pan, H., Bajic, V.B., and Hide, W.A. Integration of Text- and Data-Mining Using Ontologies Successfully Identifies Disease Gene Candidates. IMIA Yearbook of Medical Informatics 2006.

Patryk Burek, Robert Hoehndorf, Frank Loebe, Kay Prüfer, Johann Visagie, Heinrich Herre, Janet Kelso. Ontology of biological functions. Bioinformatics. 2006. 22(14):

Khaitovich, P., K. Tang, H. Franz, J. Kelso, I. Hellmann, W. Enard, M. Lachmann and S. Pääbo: Positive selection on gene expression in the human brain. Current Biology. 2006. 16: 356-358.

2005

Carninci P, et. al.  FANTOM Consortium; RIKEN Genome Exploration Research Group and Genome Science Group (Genome Network Project Core Group).
The transcriptional landscape of the mammalian genome. Science. 2005. 309(5740):1559-63.

Tiffin, N., Kelso, J.F., Powell, A.R., Pan, H., Bajic, V.B., and Hide, W.A.
Integration of Text- and Data-Mining Using Ontologies Successfully Identifies Disease Gene Candidates.  Nucleic Acids Research. 2005. 33(5):1544-52.

Tanino M, Debily MA, Tamura T, Hishiki T, Ogasawara O, Murakawa K, Kawamoto S, Itoh K, Watanabe S, de Souza SJ, Imbeaud S, Graudens E, Eveno E, Hilton P, Sudo Y, Kelso J, Ikeo K, Imanishi T, Gojobori T, Auffray C, Hide W, Okubo K.
The Human Anatomic Gene Expression Library (H-ANGEL), the H-Inv integrative display of human gene expression across disparate technologies and platforms.
Nucleic Acids Res. 2005. 1;33(Database Issue):D567-D572.

Kelso, J. Invited Chapter. EST resources, clone sets, and databases. in Encyclopedia of Genomics, Proteomics and Bioinformatics. Dunn, M., Jorde, L., Little, P., Subramaniam, S. (eds). John Wiley & Sons Ltd. Chichester, UK. Selected for advance online pre-publication  (http://www.wiley.com//legacy/wileychi/ggpb/) 2004.
Print publication 2005.

2004

Nembaware V, Wolfe KH, Bettoni F, Kelso J, Seoighe C.
Allele-specific transcript isoforms in human.
FEBS Letters. 2004. 577(1-2):233-8.

Imanishi T, et al.
Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones.
Public Library of Science: Biology. 2004.2 (6).

2003

Alexei A. Sharov, Yulan Piao, Ryo Matoba, Dawood B. Dudekula, Yong Qian, Vincent VanBuren, Geppino Falco, Patrick R. Martin, Carole A. Stagg, Uwem C. Bassey, Yuxia Wang, Mark G. Carter, Toshio Hamatani, Kazuhiro Aiba, Hidenori Akutsu, Lioudmila Sharova, Tetsuya S. Tanaka, Wendy L. Kimber, Toshiyuki Yoshikawa, Saied A. Jaradat, Serafino Pantano, Ramaiah Nagaraja, Kenneth R. Boheler, Dennis Taub, Richard J. Hodes, Dan L. Longo, David Schlessinger, Jonathan Keller, Emily Klotz, Garnett Kelsoe, Akihiro Umezawa, Angelo L. Vescovi, Janet Rossant, Tilo Kunath, Brigid L.M. Hogan Anna Curci, Michele D’Urso, Janet Kelso, Winston Hide, and Minoru S.H. Ko  Transcriptome analysis of mouse stem cells and early embryos. Public Library of Science: Biology 2003. 1 (3).

Hide, W. and Kelso, J. (2003). Application of eVOC: controlled vocabularies for unifying gene expression data. Comptes rendus – Biologies. 2003. 326: 1086-1096.

Helena Brentani, Ota´via L. Caballero, Anamaria A. Camargo, Aline M. da Silva, Wilson Arau´jo da Silva, Jr., Emmanuel Dias Neto, Marco Grivet, Arthur Gruber, Pedro Edson Moreira Guimaraes, Winston Hide, Christian Iseli, C. Victor Jongeneel, Janet Kelso, Maria Aparecida Nagai, Elida Paula Benquique Ojopi, Elisson C. Osorio, Eduardo M. R. Reis, Gregory J. Riggins, Andrew John George Simpson, Sandro de Souza, Brian J. Stevenson, Robert L. Strausberg, Eloiza H. Tajara, Sergio Verjovski-Almeida, The generation and utilization of a cancer-oriented representation of the human transcriptome, by using expressed sequence tags. Proc Natl Acad Sci U S A. 2003. 100(23):13418-13423.

2002

Kelso, J., Visagie, J., Theiler, G., Christoffels, A., Bardien, S., Smedley, D., Otgaar, D., Greyling, G., Jongeneel, C.V., McCarthy, M.I., Hide, T., Hide, W. eVOC:          A Controlled Vocabulary for Unifying Gene Expression Data. Genome Research 200313: 1222-1230.

Vincent VanBuren, Yulan Piao, Dawood B. Dudekula, Yong Qian, Mark G. Carter, Patrick R. Martin, Carole A. Stagg, Uwem C. Bassey, Kazuhiro Aiba, Toshio Hamatani, George J. Kargul, Amber G. Luo, Janet Kelso, Winston Hide, and Minoru S.H. Ko. Assembly, Verification, and Initial Annotation of the NIA Mouse 7.4K cDNA Clone Set. Genome Research  2002. 12(12): 1999-2003.

Nembaware, V., Crum, K., Kelso, J and Seoighe, C. Impact of the Presence of Paralogs on Sequence Divergence in a Set of Mouse-Human Orthologs. Genome Research 2002. 12:1370-1376

Kelso, J. (2002) Transcript reconstruction and analysis using STACKdb and stackPACK. EMBnetNews.

2001

Win Hide, Valerie Mizrahi, B. Venkatesh, Sydney Brenner, Andrew Simpson, Greg Blatch, Himla Soodyall, Katherine Denby, Mike Wingfield, Brenda Wingfield, Paul van Helden, Raj Ramesar, Rosemary Dorrington, Janet Kelso, Ekow Oppon, Elizabeth Goyvaerts, Michele Ramsay, Etienne de Villiers, Carel van Heerden, Basil Allsopp and Cathal Seoighe. The National Genome Initiative. S.A Medical Journal.  2001.  91 (12): 1006-1007

Winston A.Hide, Vladimir N. Babenko, Peter A. van Heusden, Cathal Seoighe, and Janet F. Kelso. The contribution of exon-skipping events on Chromosome 22 to Protein Coding Diversity. Genome Research 2001. 11:1848-1853