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Castellano, S., G. Parra, F.A. Sánchez-Quinto, F. Racimo, M. Kuhlwilm, M. Kircher, S. Sawyer, Q. Fu, A. Heinze, B. Nickel, J. Dabney, M. Siebauer, L. White, H.A. Burbano, G. Renaud, U. Stenzel, C. Lalueza-Fox, M. de la Rasilla, A. Rosas, P.Rudan, D. Brajković, Ž. Kucan, I. Gušic, M.V. Shunkov, A.P. Derevianko, B. Viola, M. Meyer, J. Kelso, A. Andrés and S. Pääbo: Patterns of coding variation in the complete exomes of three Neandertals. PNAS, in press (2014).

Heyn, P., M. Kircher, A. Dahl, J. Kelso, P. Tomancak, A.T. Kalinka and K.M. Neugebauer: The earliest transcribed zygotic genes are short, newly evolved and different across species. Cell Reports 6, 285-292 (2014).

Khrameeva, E.E., K.Bozek, L. He, Z. Yan, X. Jiang, Y. Wei, K. Tang, M.S. Gelfand, K. Prüfer, J. Kelso, S. Pääbo, P. Giavalisco, M. Lachmann and P. Khaitovich: Neanderthal ancestry drives evolution of lipid catabolism in contemporary Europeans. Nature Communications 5:3584, doi:10.1038/ncomms4584 (2014).

Prüfer, K., F. Racimo, N. Patterson, F. Jay, S. Sankararaman, S. Sawyer, A. Heinze, G. Renaud, P.H. Sudmant, C. de Filippo, H. Li, S. Mallick, M. Dannemann, Q. Fu, M. Kircher, M. Kuhlwilm, M. Lachmann, M. Meyer, M. Ongyerth, M. Siebauer, C. Theunert, A. Tandon, P. Moorjani, J. Pickrell, J.C. Mullikin, S.H. Vohr, R.E. Green, I. Hellmann, P.L.F. Johnson, H. Blanche, H. Cann, J.O. Kitzman, J. Shendure, E.E. Eichler, E.S. Lein, T.E. Bakken, L.V. Golovanova, V.B. Doronichev, M.V. Shunkov, A.P. Derevianko, B. Viola, M. Slatkin, D. Reich, J. Kelso and S. Pääbo: The complete genome sequence of a Neandertal from the Altai Mountains. Nature 505, 43-49 (2014). 


Fu Q, Meyer M, Gao X, Stenzel U, Burbano HA, Kelso J, Paabo S: DNA analysis of an early modern human from Tianyuan Cave, China. Proceedings of the National Academy of Sciences of the United States of America 2013, 110:2223-2227.

Kunz M, Dannemann M, Kelso J: High-throughput sequencing of the melanoma genome. Experimental dermatology 2013, 22:10-17.

Maricic T, Gunther V, Georgiev O, Gehre S, Curlin M, Schreiweis C, Naumann R, Burbano HA, Meyer M, Lalueza-Fox C, de la Rasilla M, Rosas A, Gajovic S, Kelso J, Enard W, Schaffner W, Paabo S: A Recent Evolutionary Change Affects a Regulatory Element in the Human FOXP2 Gene. Molecular biology and evolution 2013, 30:844-852.

Renaud G, Kircher M, Stenzel U, Kelso J: freeIbis: an efficient basecaller with calibrated quality scores for Illumina sequencers. Bioinformatics 2013.


Burbano HA, Green RE, Maricic T, Lalueza-Fox C, de la Rasilla M, Rosas A, Kelso J, Pollard KS, Lachmann M, Paabo S: Analysis of human accelerated DNA regions using archaic hominin genomes. PLoS One 2012, 7:e32877.

Dannemann M, Nickel B, Lizano E, Burbano HA, Kelso J: Annotation of primate miRNAs by high throughput sequencing of small RNA libraries. BMC genomics 2012, 13:116.

Dannemann M, Prüfer K, Lizano E, Nickel B, Burbano HA, Kelso J: Transcription factors are targeted by differentially expressed miRNAs in primates. Genome biology and evolution 2012, 4:552-564.

Gross A, Hartung M, Prüfer K, Kelso J, Rahm E: Impact of ontology evolution on functional analyses. Bioinformatics 2012, 28:2671-2677.

Meyer M, Kircher M, Gansauge MT, Li H, Racimo F, Mallick S, Schraiber JG, Jay F, Prüfer K, de Filippo C, Sudmant PH, Alkan C, Fu Q, Do R, Rohland N, Tandon A, Siebauer M, Green RE, Bryc K, Briggs AW, Stenzel U, Dabney J, Shendure J, Kitzman J, Hammer MF, Shunkov MV, Derevianko AP, Patterson N, Andres AM, Eichler EE, Slatkin M, Reich D, Kelso J, Paabo S: A High-Coverage Genome Sequence from an Archaic Denisovan Individual. Science 2012.

Prüfer K, Munch K, Hellmann I, Akagi K, Miller JR, Walenz B, Koren S, Sutton G, Kodira C, Winer R, Knight JR, Mullikin JC, Meader SJ, Ponting CP, Lunter G, Higashino S, Hobolth A, Dutheil J, Karakoc E, Alkan C, Sajjadian S, Catacchio CR, Ventura M, Marques-Bonet T, Eichler EE, Andre C, Atencia R, Mugisha L, Junhold J, Patterson N, Siebauer M, Good JM, Fischer A, Ptak SE, Lachmann M, Symer DE, Mailund T, Schierup MH, Andres AM, Kelso J, Paabo S: The bonobo genome compared with the chimpanzee and human genomes. Nature 2012, 486:527-531.

Rost B, Gaasterland T, Lengauer T, Linial M, Markel S, McKay BM, Schneider R, Horton P, Kelso J: Paving the future: finding suitable ISMB venues. Bioinformatics 2012.

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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).

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. Nucleic Acids Research 39, D7-D10, doi:10.1093/nar/gkq1173 (2011).

Herre, H., R. Hoehndorf, J. Kelso, F. Loebe and S. Schulz: OBML – Ontologies in biomedicine and life sciences. Journal of Biokmedical Semantics 2 (Suppl 4):I1 (2011).

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

Nagaraj, N., J.R. Wisniewski, T. Geiger, J. Cox, M. Kircher, J. Kelso, S. Pääbo and M. Mann: Deep proteome and transcriptome mapping of a human cancer cell line. Molecular Systems Biology 7, 548, doi:10.1038/msb.2011.81 (2011).

Ranganathan, S., C. Schönbach, J. Kelso, B. Rost, S. Nathan and T.W. Tan: 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 (2011).

Schönbach, C., T.W. Tan, J. Kelso, B. Rost, S. Nathan and S. Ranganathan: InCoB celebrates its tenth anniversary as first joint conference with ISCB-Asia. BMC Genomics 12 (Suppl 3):S1 (2011).

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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).

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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).

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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.

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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. [Read online]

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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.

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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.

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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).

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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.

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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.

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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

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