29.10.2020 - 18:48
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Janet Kelso

 

Group leader of
The Minerva Research Group for Bioinformatics 

Max Planck Institute for Evolutionary Anthropology
Deutscher Platz 6
04103 Leipzig

tel: +49 341 3550 552
fax: +49 341 3550 555
e-mail: kelso@[>>> Please remove the brackets! <<<]eva.mpg.de

Curriculum Vitae
Publications
Gallery

Curriculum Vitae

Biographical

Name:Janet Kelso
Nationality:South African
Email:kelso@[>>> Please remove the brackets! <<<]eva.mpg.de

Employment

2004-presentBioinformatics research group leader / Minerva Professor
Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
2003-2004Postdoctoral researcher.
University of the Western Cape, Cape Town, South Africa

Education

2003Ph.D. (Bioinformatics). University of the Western Cape, Cape Town, South Africa
Advisor: Winston Hide
2000M.Sc. (Med) (Chemical Pathology). University of Cape Town, Cape Town, South Africa
1997B.Sc. (Med) (Hons) (Medical Biochemistry). University of Cape Town, Cape Town, South Africa
1995B.Sc. (Biology). University of-Natal, Durban, South Africa.

Fellowships and Awards

2016Elected Fellow of the International Society for Computational Biology (ISCB)
2010AAAS Newcomb Cleveland Prize for the most outstanding paper in Science in 2010 (with co-authors)
2004L'Oréal-UNESCO/DST fellowship for Women in Science: Young Scientist Award
2003Merck Student Fellowship

Scientific service

Editorial
2013 – presentCo-Executive Editor Bioinformatics (Oxford University Press)
2011 – 2012Associate Editor Bioinformatics (Oxford University Press)
2009 – presentAssociate Editor Database (Oxford University Press)
2014 – presentEditorial Board Genome Biology
2007 – 2014Editor PLoS One
2012 – presentEditorial Board Springer book series: Computational Biology
International Society for Computational Biology (ISCB)
2011 – 2013, 2017-Vice-president, Executive Board
2006 – 2011Secretary, Executive Board
2006 – presentConference Committee chair
2005 – presentMember of Board of Directors
Conference Organisation
2015-2017CSHL Genome Informatics Organiser (with Daniel McArthur, Mike Schatz, Aaron Quinlan and Melissa Wilson-Sayres)
2015, Dublin ISMB/ECCB Conference co-chair (with Alex Bateman and Des Higgins) 2014, Boston ISMB Conference co-chair (with Bonnie Berger) 
2014 CSHL Genome Informatics Session Chair (with Nick Loman)
2011 ISCB-Africa ASBCB Conference Co-Chair (with Nicola Mulder)
2006 – present Member of the ISMB Conference Steering Committee 2006 – 2013 Chair of ISMB Tutorials Programme
Max Planck Institute for Evolutionary Anthropology
2014 – presentDeputy Equal Opportunities Officer
Advisory Boards/Review Panels (Selected)
2018-Advisory Board H3-Africa BioNet
2016Review PanelERC Consolidator Grants
2015-2017Review panelCentre for Molecular Medicine (CeMM), Vienna
2015 Review panelEBI-EMBL External Services
2015 – presentReview boardH3-Africa/NIH Sickle Cell Disease Ontology Development
2013 – present Advisory BoardELIXIR Scientific Advisory Board
2013 – presentAdvisory BoardNIH-H3Africa Wits-INDEPTH Centre
2012, 2015Advisory BoardGenome Canada Bioinformatics & Computational Biology
2014 – presentReview panelHercules Foundation/FWO for Belgian Research Infrastructure
2009 – 2012Review panelSouth African National Research Foundation
2011 Advisory BoardGenome Canada 4D Genomics Platform
2010 Review panelDeutsche Forschungsgsgemeinschaft (DFG) Instrumentation
2003 – 2011Advisory BoardGenome Canada Bioinformatics Platform

Invited presentations and workshops (last 5 years)

2017

Human Evolution: Fossils, Ancient and Modern Genomes, Wellcome Trust Sanger Centre, UK
“The implications of admixture between modern and archaic humans”

Big Data Analyses in Evolutionary Biology, KAUST, Saudi Arabia
“The Impact of Admixture between Modern and Archaic Humans”

19th EMBL PhD Symposium: Bridging the Gaps - Interdisciplinary Approaches in Life Sciences, EMBL, Heidelberg, Germany
“What we have Learned from Ancient Genomes”

Nordic-EMBL Partnership meeting, Helsinki, Finland
“The impact of admixture between modern and archaic humans”

2016

5th International Symposium on Regulators of Adaptive Immunity, Erlangen, Germany
“The contributions of archaic humans to modern human immunity”

Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign
“Functional Implications of admixture with archaic humans”

EMBL, Heidelberg, Germany
“Implications of admixture with archaic humans”

BioVis 2016, Orlando, Florida, USA
“Visualization in Ancient Genomics”

2015

ISABS Conference on Forensic and Anthropologic Genetics, Brač, Croatia.
“Functional implications of admixture between modern and archaic humans”

Australian Genome Technologies Conference (AGTA), Hunter Valley, Australia
“What we have learned from sequencing ancient genomes”

2014

Genome Informatics Workshop / ISCB-Asia, Tokyo, Japan
“An Early Modern Human from Ust’-Ishim”

Colloquium Series Centre for Bioinformatics, Saarbrücken, Germany
Reconstructing ancient human genomes

Genome Informatics, Cambridge, UK
“Archaic Genomes”

ISCB-Latin America x-Meeting on Bioinformatics, Belo Horizonte, Brazil
“Insights from the sequencing of ancient genomes”

Seminar Series of the Research Center for Molecular Medicine (CEMM), Vienna, Austria
“The genome of a Neandertal from the Altai Mountains”

Genome Informatics Workshop / ISCB-Asia, Tokyo, Japan
“What we have learned from sequencing archaic human genomes”

School of Biological Anthropology, Zagreb, Croatia
“The genome of a 45,000 year-old modern human from Eurasia”

2013

The Next NGS Challenge, Valencia, Spain
“Sequencing ancient human genomes”

Beyond the Genome 2013, San Francisco, USA.
“Sequencing ancient human genomes”

Publications

Print version (PDF)

Articles

Massilani, D., Skov, L., Hajdinjak, M., Gunchinsuren, B., Tseveendorj, D., Yi, S., Lee, J., Nagel, S., Nickel, B., Devièse, T., Higham, T., Meyer, M., Kelso, J., Peter, B., & Pääbo, S. (in press). Denisovan ancestry and population history of early East Asians. Science.

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Zhang, D., Xia, H., Chen, F., Li, B., Slon, V., Cheng, T., Yang, R., Jacobs, Z., Dai, Q., Massilani, D., Shen, X., Wang, J., Feng, X., Cao, P., Yang, M. A., Yao, J., Yang, J., Madsen, D. B., Han, Y., Ping, W., Liu, F., Perreault, C., Chen, X., Meyer, M., Kelso, J., Pääbo, S., & Fu, Q. (in press). Denisovan DNA in Late Pleistocene sediments from Baishiya Karst Cave on the Tibetan Plateau. Science.
Petr, M., Hajdinjak, M., Fu, Q., Essel, E., Rougier, H., Crevecoeur, I., Semal, P., Golovanova, L. V., Doronichev, V. B., Lalueza-Fox, C., de la Rasilla, M., Rosas, A., Shunkov, M. V., Kozlikin, M. B., Derevianko, A. P., Vernot, B., Meyer, M., & Kelso, J. (2020). The evolutionary history of Neanderthal and Denisovan Y chromosomes. Science,369(6511), 1653-1656.
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Zeberg, H., Dannemann, M., Sahlholm, K., Tsuo, K., Maricic, T., Wiebe, V., Hevers, W., Robinson, H. P., Kelso, J., & Pääbo, S. (2020). A Neandertal sodium channel increases pain sensitivity in present-day. Current Biology,30(17), 3465-3469.
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Dannemann, M., He, Z., Heide, C., Vernot, B., Sidow, L., Kanton, S., Weigert, A., Treutlein, B., Pääbo, S., Kelso, J., & Camp, J. G. (2020). Human stem cell resources are an inroad to Neandertal DNA functions. Stem Cell Reports,15, 214-225.
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Mafessoni, F., Grote, S., de Filippo, C., Slon, V., Kolobova, K. A., Viola, B., Markin, S. V., Chintalapati, M., Peyrégne, S., Skov, L., Skoglund, P., Krivoshapkin, A. I., Derevianko, A. P., Meyer, M., Kelso, J., Peter, B., Prüfer, K., & Pääbo, S. (2020). A high-coverage Neandertal genome from Chagyrskaya Cave. Proceedings of the National Academy of Sciences,117(26), 15132-15136.
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Zeberg, H., Kelso, J., & Pääbo, S. (2020). The Neandertal progesterone receptor. Molecular Biology and Evolution,37(9): msaa119, pp. 2655-2660.
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Zeberg, H., Dannemann, M., Sahlholm, K., Tsuo, K., Maricic, T., Wiebe, V., Hevers, W., Robinson, H. P., Kelso, J., & Pääbo, S. (2020). A Neanderthal sodium channel increases pain sensitivity in present-day humans. Current Biology,30(17), 3465-3469.e4.
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Wren, J. D., Valencia, A., & Kelso, J. (2019). Reviewer-coerced citation: Case report, update on journal policy and suggestions for future prevention. Bioinformatics,35(18), 3217-3218.
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Petr, M., Vernot, B., & Kelso, J. (2019). admixr – R package for reproducible analyses using ADMIXTOOLS. Bioinformatics,35(17): btz030, pp. 3194-3195.
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Bokelmann, L., Hajdinjak, M., Peyrégne, S., Brace, S., Essel, E., de Filippo, C., Glocke, I., Grote, S., Mafessoni, F., Nagel, S., Kelso, J., Prüfer, K., Vernot, B., Barnes, I., Pääbo, S., Meyer, M., & Stringer, C. (2019). A genetic analysis of the Gibraltar Neanderthals. Proceedings of the National Academy of Sciences,116(31), 15610-15615.
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Peyrégne, S., Slon, V., Mafessoni, F., de Filippo, C., Hajdinjak, M., Nagel, S., Nickel, B., Essel, E., Le Cabec, A., Wehrberger, K., Conard, N. J., Kind, C. J., Posth, C., Krause, J., Abrams, G., Bonjean, D., Di Modica, K., Toussaint, M., Kelso, J., Meyer, M., Pääbo, S., & Prüfer, K. (2019). Nuclear DNA from two early Neandertals reveals 80,000 years of genetic continuity in Europe. Science Advances,5(6): eaaw5873.
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Douka, K., Slon, V., Jacobs, Z., Ramsey, C. B., Shunkov, M. V., Derevianko, A. P., Mafessoni, F., Kozlikin, M. B., Li, B., Grün, R., Comeskey, D., Devièse, T., Brown, S., Viola, B., Kinsley, L., Buckley, M., Meyer, M., Roberts, R. G., Pääbo, S., Kelso, J., & Higham, T. (2019). Age estimates for hominin fossils and the onset of the Upper Palaeolithic at Denisova Cave. Nature,565(7741), 640-644.
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Petr, M., Pääbo, S., Kelso, J., & Vernot, B. (2019). Limits of long-term selection against Neandertal introgression. Proceedings of the National Academy of Sciences,116(5), 1639-1644.
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Gunz, P., Tilot, A. K., Wittfeld, K., Teumer, A., Shapland, C. Y., van Erp, T. G. M., Dannemann, M., Vernot, B., Neubauer, S., Guadalupe, T., Fernández, G., Brunner, H. G., Enard, W., Fallon, J., Hosten, N., Völker, U., Profico, A., Di Vincenzo, F., Manzi, G., Kelso, J., St. Pourcain, B., Hublin, J.-J., Franke, B., Pääbo, S., Macciardi, F., Grabe, H. J., & Fisher, S. E. (2019). Neandertal introgression sheds light on modern human endocranial globularity. Current Biology,29(1), 120-127.e5.
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Reher, D., Key, F. M., Andrés, A. M., & Kelso, J. (2019). Immune gene diversity in archaic and present-day humans. Genome Biology and Evolution,11(1), 232-241.
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Lamnidis, T. C., Majander, K., Jeong, C., Salmela, E., Wessman, A., Moiseyev, V., Khartanovich, V., Balanovsky, O., Ongyerth, M., Weihmann, A., Sajantila, A., Kelso, J., Pääbo, S., Onkamo, P., Haak, W., Krause, J., & Schiffels, S. (2018). Ancient Fennoscandian genomes reveal origin and spread of Siberian ancestry in Europe. Nature Communications,9: 5018.
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Slon, V., Mafessoni, F., Vernot, B., de Filippo, C., Grote, S., Viola, T. B., Hajdinjak, M., Peyrégne, S., Nagel, S., Brown, S., Douka, K., Higham, T., Kozlikin, M. B., Shunkov, M. V., Derevianko, A. P., Kelso, J., Meyer, M., Prüfer, K., & Pääbo, S. (2018). The genome of the offspring of a Neanderthal mother and a Denisovan father. Nature,561(7721), 113-116.
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Klotz, B., Kneitz, S., Regensburger, M., Hahn, L., Dannemann, M., Kelso, J., Nickel, B., Lu, Y., Boswell, W., Postlethwait, J., Warren, W., Kunz, M., Walter, R. B., & Schartl, M. (2018). Expression signatures of early-stage and advanced medaka melanomas. Comparative Biochemistry and Physiology Part C: Toxicology & Pharmacology,208, 20-28.
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Hajdinjak, M., Fu, Q., Hübner, A., Petr, M., Mafessoni, F., Grote, S., Skoglund, P., Narasimham, V., Rougier, H., Crevecoeur, I., Semal, P., Soressi, M., Talamo, S., Hublin, J.-J., Gušic, I., Kucan, Ž., Rudan, P., Golovanova, L. V., Doronichev, V. B., Posth, C., Krause, J., Korlevic, P., Nagel, S., Nickel, B., Slatkin, M., Patterson, N., Reich, D., Prüfer, K., Meyer, M., Pääbo, S., & Kelso, J. (2018). Reconstructing the genetic history of late Neanderthals. Nature,555(7698), 652-656.
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Prüfer, K., Filippo, C. d., Grote, S., Mafessoni, F., Korlevic, P., Hajdinjak, M., Vernot, B., Skov, L., Hsieh, P., Peyrégne, S., Reher, D., Hopfe, C., Nagel, S., Maricic, T., Fu, Q., Theunert, C., Rogers, R., Skoglund, P., Chintalapati, M., Dannemann, M., Nelson, B. J., Key, F. M., Rudan, P., Kucan, Ž., Gušic, I., Golovanova, L. V., Doronichev, V. B., Patterson, N., Reich, D., Eichler, E. E., Slatkin, M., Schierup, M. H., Andrés, A. M., Kelso, J., Meyer, M., & Pääbo, S. (2017). A high-coverage Neandertal genome from Vindija Cave in Croatia. Science,358(6363), 655-658.
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Dannemann, M., & Kelso, J. (2017). The contribution of Neanderthals to phenotypic variation in modern humans. The American Journal of Human Genetics,101(4), 578-589.
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Yang, M. A., Gao, X., Theunert, C., Tong, H., Ayinuer-Petri, A., Nickel, B., Slatkin, M., Meyer, M., Pääbo, S., Kelso, J., & Fu, Q. (2017). 40,000-year-old individual from Asia provides insight into early population structure in Eurasia. Current Biology,27(20), 3202-3208.
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Kelso, J., Kovats, D. E., Leard, S., & Orengo, C. (2017). ISMB/ECCB 2017 proceedings paper comitee. Bioinformatics,33, I3-I4.
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Slon, V., Viola, B., Renaud, G., Gansauge, M.-T., Benazzi, S., Sawyer, S., Hublin, J.-J., Shunkov, M. V., Derevianko, A. P., Kelso, J., Prüfer, K., Meyer, M., & Pääbo, S. (2017). A fourth Denisovan individual. Science Advances,3(7): e1700186.
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Slon, V., Hopfe, C., Weiß, C. L., Mafessoni, F., de la Rasilla, M., Lalueza-Fox, C., Rosas, A., Soressi, M., Knul, M. V., Miller, R., Stewart, J. R., Derevianko, A. P., Jacobs, Z., Li, B., Roberts, R. G., Shunkov, M. V., de Lumley, H., Perrenoud, C., Gušic, I., Kucan, Ž., Rudan, P., Ayinuer-Petri, A., Essel, E., Nagel, S., Nickel, B., Schmidt, A., Prüfer, K., Kelso, J., Burbano, H. A., Pääbo, S., & Meyer, M. (2017). Neandertal and Denisovan DNA from Pleistocene sediments. Science,356(6338), 605-608.
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Dannemann, M., Prüfer, K., & Kelso, J. (2017). Functional implications of Neandertal introgression in modern humans. Genome Biology,18: 61.
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Welker, F., Hajdinjak, M., Talamo, S., Jaouen, K., Dannemann, M., David, F., Julien, M., Meyer, M., Kelso, J., Barnes, I., Braces, S., Kamminga, P., Fischer, R., Kessler, B., Stewart, J. R., Pääbo, S., Collins, M. J., & Hublin, J.-J. (2016). Palaeoproteomic evidence identifies archaic hominins associated with the Châtelperronian at the Grotte du Renne. Proceedings of the National Academy of Sciences of the United States of America,113(44), 11162-11167.
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Quach, H., Rotival, M., Pothlichet, J., Loh, Y.-H.-E., Dannemann, M., Zidane, N., Laval, G., Patin, E., Harmant, C., Lopez, M., Deschamps, M., Naffakh, N., Duffy, D., Coen, A., Leroux-Roels, G., Clément, F., Boland, A., Deleuze, J.-F., Kelso, J., Albert, M. L., & Quintana-Murci, L. (2016). Genetic adaptation and neandertal admixture shaped the immune system of human populations. Cell,167(3), 643-656.
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Grote, S., Prüfer, K., Kelso, J., & Dannemann, M. (2016). ABAEnrichment: An R package to test for gene set expression enrichment in the adult and developing human brain. Bioinformatics,32(20), 3201-3203.
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Mallick, S., Li, H., Lipson, M., Mathieson, I., Gymrek, M., Racimo, F., Zhao, M., Chennagiri, N., Nordenfelt, S., Tandon, A., Skoglund, P., Lazaridis, I., Sankararaman, S., Fu, Q., Rohland, N., Renaud, G., Erlich, Y., Willems, T., Gallo, C., Spence, J. P., Song, Y. S., Poletti, G., Balloux, F., van Driem, G., de Knijff, P., Romero, I. G., Jha, A. R., Behar, D. M., Bravi, C. M., Capelli, C., Hervig, T., Moreno-Estrada, A., Posukh, O. L., Balanovska, E., Balanovsky, O., Karachanak-Yankova, S., Sahakyan, H., Toncheva, D., Yepiskoposyan, L., Tyler-Smith, C., Xue, Y., Abdullah, M. S., Ruiz-Linares, A., Beall, C. M., Rienzo, A. D., Jeong, C., Starikovskaya, E. B., Metspalu, E., Parik, J., Villems, R., Henn, B. M., Hodoglugil, U., Mahley, R., Sajantila, A., Stamatoyannopoulos, G., Wee, J. T. S., Khusainova, R., Khusnutdinova, E., Litvinov, S., Ayodo, G., Comas, D., Hammer, M. F., Kivisild, T., Klitz, W., Winkler, C. A., Labuda, D., Bamshad, M., Jorde, L. B., Tishkoff, S. A., Watkins, W. S., Metspalu, M., Dryomov, S., Sukernik, R., Singh, L., Thangaraj, K., Pääbo, S., Kelso, J., Patterson, N., & Reich, D. (2016). The Simons Genome Diversity Project: 300 genomes from 142 diverse populations. Nature,538(7624), 201-206.
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Fu, Q., Posth, C., Hajdinjak, M., Petr, M., Mallick, S., Fernandes, D., Furtwängler, A., Haak, W., Meyer, M., Mittnik, A., Nickel, B., Peltzer, A., Rohland, N., Slon, V., Talamo, S., Lazaridis, I., Lipson, M., Mathieson, I., Schiffels, S., Skoglund, P., Derevianko, A. P., Drozdov, N., Slavinsky, V., Tsybankov, A., Cremonesi, R. G., Mallegni, F., Gély, B., Vacca, E., Morales, M. R. G., Straus, L. G., Neugebauer-Maresch, C., Teschler-Nicola, M., Constantin, S., Moldovan, O. T., Benazzi, S., Peresani, M., Coppola, D., Lari, M., Ricci, S., Ronchitelli, A., Valentin, F., Thevenet, C., Wehrberger, K., Grigorescu, D., Rougier, H., Crevecoeur, I., Flas, D., Semal, P., Mannino, M. A., Cupillard, C., Bocherens, H., Conard, N. J., Harvati, K., Moiseyev, V., Drucker, D. G., Svoboda, J., Richards, M. P., Caramelli, D., Pinhasi, R., Kelso, J., Patterson, N., Krause, J., Pääbo, S., & Reich, D. (2016). The genetic history of Ice Age Europe. Nature,534(7606), 200-205.
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Vernot, B., Tucci, S., Kelso, J., Schraiber, J., Wolf, A., Gittelman, R., Dannemann, M., Grote, S., McCoy, R., Norton, H., Scheinfeldt, L., Merriwether, D., Koki, G., Friedlaender, J., Wakefield, J., Pääbo, S., & Akey, J. (2016). Excavating Neandertal and Denisovan DNA from the genomes of Melanesian individuals. Science,352(6282), 235-239.
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Meyer, M., Arsuaga, J.-L., de Filippo, C., Nagel, S., Aximu-Petri, A., Nickel, B., Martínez, I., Gracia, A., Bermúdez de Castro, J. M., Carbonell, E., Viola, B., Kelso, J., Prüfer, K., & Pääbo, S. (2016). Nuclear DNA sequences from the Middle Pleistocene Sima de los Huesos hominins. Nature,531(7595), 504-507.
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Dannemann, M., Andrés, A. M., & Kelso, J. (2016). Introgression of Neandertal- and Denisovan-like haplotypes contributes to adaptive variation in human toll-like receptors. The American Journal of Human Genetics,98(1), 22-33.
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Carmody, R. N., Dannemann, M., Briggs, A. W., Nickel, B., Groopman, E. E., Wrangham, R. W., & Kelso, J. (2016). Genetic evidence of human adaptation to a cooked diet. Genome biology and evolution,8(4), 1091-1103.
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Sawyer, S., Renaud, G., Viola, B., Hublin, J.-J., Gansauge, M.-T., Shunkov, M. V., Derevianko, A. P., Prüfer, K., Kelso, J., & Pääbo, S. (2015). Nuclear and mitochondrial DNA sequences from two Denisovan individuals. Proceedings of the National Academy of Sciences of the United States of America,112(51), 15696-15700.
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Renaud, G., Slon, V., Duggan, A. T., & Kelso, J. (2015). Schmutzi: Estimation of contamination and endogenous mitochondrial consensus calling for ancient DNA. Genome Biology,16: 224.
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Fu, Q., Hajdinjak, M., Moldovan, O., Constantin, S., Mallick, S., Skoglund, P., Patterson, N., Rohland, N., Lazaridis, I., Nickel, B., Viola, B., Prüfer, K., Meyer, M., Kelso, J., Reich, D., & Pääbo, S. (2015). An early modern human from Romania with a recent Neanderthal ancestor. Nature,524(7564), 216-219.
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Ronke, C., Dannemann, M., Halbwax, M., Fischer, A., Helmschrodt, C., Brügel, M., André, C., Atencia, R., Mugisha, L., Scholz, M., Ceglarek, U., Thiery, J., Pääbo, S., Prüfer, K., & Kelso, J. (2015). Lineage-specific changes in biomarkers in great apes and humans. PLoS One,10(8): e0134548.
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Le Duc, D., Renaud, G., Krishnan, A., Almén, M. S., Huynen, L., Prohaska, S. J., Ongyerth, M., Bitarello, B. D., Schiöth, H. B., Hofreiter, M., Stadler, P. F., Prüfer, K., Lambert, D., Kelso, J., & Schöneberg, T. (2015). Kiwi genome provides insights into evolution of a nocturnal lifestyle. Genome Biology,16: 147.
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Florio, M., Albert, M., Taverna, E., Namba, T., Brandl, H., Lewitus, E., Haffner, C., Sykes, A., Wong, F. K., Peters, J., Guhr, E., Klemroth, S., Prüfer, K., Kelso, J., Naumann, R., Nüsslein, I., Dahl, A., Lachmann, R., Pääbo, S., & Huttner, W. B. (2015). Human-specific gene ARHGAP11B promotes basal progenitor amplification and neocortex expansion. Science,347(6229), 1465-1470.
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Renaud, G., Stenzel, U., Maricic, T., Wiebe, V., & Kelso, J. (2015). deML: Robust demultiplexing of Illumina sequences using a likelihood-based approach. Bioinformatics,31(5), 770-772.
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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., Viola, B., & Pääbo, S. (2014). Genome sequence of a 45,000-year-old modern human from western Siberia. Nature,514(7523), 445-449.
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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., Kucinskas, 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., Reich, D., & Krause, J. (2014). Ancient human genomes suggest three ancestral populations for present-day Europeans. Nature,513(7518), 409-413.
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Gokhman, D., Lavi, E., Prüfer, K., Fraga, M. F., Riancho, J. A., Kelso, J., Pääbo, S., Meshorer, E., & Carmel, L. (2014). Reconstructing the DNA methylation maps of the Neandertal and the Denisovan. Science,344(6183), 523-527.
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Khrameeva, E. E., Bozek, K., He, L., Yan, Z., Jiang, X., Wei, Y., Tang, K., Gelfand, M. S., Prüfer, K., Kelso, J., Pääbo, S., Giavalisco, P., Lachmann, M., & Khaitovich, P. (2014). Neanderthal ancestry drives evolution of lipid catabolism in contemporary Europeans. Nature Communications,5: 3584.
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The SIGMA Type 2 Diabetes Consortium, including authors, Prüfer, K., Sawyer, S., Stenzel, U., Kelso, J., Pääbo, S., & and others (2014). Sequence variants in SLC16A11 are a common risk factor for type 2 diabetes in Mexico. Nature,506, 97-101.
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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., & Pääbo, S. (2014). The complete genome sequence of a Neanderthal from the Altai Mountains. Nature,505(7481), 43-49.
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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., Brajkovic, D., Kucan, Ž., Gušic, I., Shunkov, M. V., Derevianko, A. P., Viola, B., Meyer, M., Kelso, J., 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.
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Heyn, P., Kircher, M., Dahl, A., Kelso, J., 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.
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Kelso, J., & Prüfer, K. (2014). Ancient humans and the origin of modern humans. Current Opinion in Genetics & Development,29, 133-138.
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Renaud, G., Stenzel, U., & Kelso, J. (2014). leeHom: adaptor trimming and merging for Illumina sequencing reads. Nucleic Acids Research (London),42(18): e141.
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Sankararaman, S., Mallick, S., Dannemann, M., Prüfer, K., Kelso, J., Pääbo, S., Patterson, N., & Reich, D. (2014). The genomic landscape of Neanderthal ancestry in present-day humans. Nature,507(7492), 354-357.
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Renaud, G., Kircher, M., Stenzel, U., & Kelso, J. (2013). freeIbis: An efficient basecaller with calibrated quality scores for Illumina sequencers. Bioinformatics,29(9), 1208-1209.
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Maricic, T., Günther, V., Georgiev, O., Gehre, S., Curlin, M., Schreiweis, C., Naumann, R., Burbano, H. A., Meyer, M., Lalueza-Fox, C., de la Rasilla, M., Rosas, A., Gajovic, S., Kelso, J., 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.
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Fu, Q., Meyer, M., Gao, X., Stenzel, U., Burbano, H. A., Kelso, J., & 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.
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Kunz, M., Dannemann, M., & Kelso, J. (2013). High-throughput sequencing of the melanoma genome. Experimental Dermatology,22(1), 10-17.
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Groß, A., Hartung, M., Prüfer, K., Kelso, J., & Rahm, E. (2012). Impact of ontology evolution on functional analyses. Bioinformatics,28(20), 2671-2677.
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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.
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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.
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Dannemann, M., Nickel, B., Lizano, E., Burbano, H., & Kelso, J. (2012). Annotation of primate miRNAs by high throughput sequencing of small RNA libraries. BMC Genomics,13(Suppl. 3): 116.
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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.
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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.
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Rost, B., Gaasterland, T., Lengauer, T., Linial, M., Markel, S., McKay, B. M., Schneider, R., Horton, P., & Kelso, J. (2012). Paving the future: finding suitable ISMB venues. Bioinformatics,28(19), 2556-2559.
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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).
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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.
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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.
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Kircher, M., Heyn, P., & Kelso, J. (2011). Addressing challenges in the production and analysis of illumina sequencing data. BMC Genomics,12: 382.
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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.
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Ranganathan, S., Schönbach, C., Kelso, J., 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.
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Schönbach, C., Tan, T. W., Kelso, J., 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.
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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.
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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.
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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.
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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.
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Kircher, M., & Kelso, J. (2010). High-throughput DNA sequencing - concepts and limitations. BioEssays,32(6), 524-536.
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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.
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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.
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Hoehndorf, R., Bacher, J., Backhaus, M., Gregorio, S. E. J., Loebe, F., Pruefer, K., Uciteli, A., Visagie, J., Herre, H., & Kelso, J. (2009). BOWiki: An ontology-based wiki for annotation of data and integration of knowledge in biology. BMC Bioinformatics,10: S5.
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Hoehndorf, R., Kelso, J., & Herre, H. (2009). The ontology of biological sequences. BMC Bioinformatics,10: 377.
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Kircher, M., Stenzel, U., & Kelso, J. (2009). Improved base calling for the Illumina Genome Analyzer using machine learning strategies. Genome Biology,10(8): R83, pp. 1-9.
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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.
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Somel, M., Franz, H., Yan, Z., Lorenc, A., Guo, S., Giger, T., Kelso, J., 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.
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Giger, T., Excoffier, L., Amstutz, U., Day, P. J. R., Champigneulle, A., Hansen, M. M., Kelso, J., & Largiadèr, C. R. (2008). Population transcriptomics of life-history variation in the genus Salmo. Molecular Ecology,17(13), 3095-3108.
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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., Slatkin, M., & Pääbo, S. (2008). A complete Neandertal mitochondrial genome sequence determined by high-throughput sequencing. Cell,134(3), 416-426.
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Hoehndorf, R., Loebe, F., Poli, R., Herre, H., & Kelso, J. (2008). GFO-Bio: A biological core ontology. Applied ontology,3(4), 219-227.
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Myles, S., Tang, K., Somel, M., Green, R. E., Kelso, J., & Stoneking, M. (2008). Identification and analysis of genomic regions with large between-population differentiation in humans. Annals of Human Genetics,72(1), 99-110.
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Prüfer, K., Stenzel, U., Dannemann, M., Green, R. E., Lachmann, M., & Kelso, J. (2008). PatMaN: Rapid alignment of short sequences to large databases. Bioinformatics,24(13), 1530-1533.
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Briggs, A. W., Stenzel, U., Johnson, P. L. F., Green, R. E., Kelso, J., 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.
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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.
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Hoehndorf, R., Loebe, F., Kelso, J., & Herre, H. (2007). Representing default knowledge in biomedical ontologies: Application to the integration of anatomy and phenotype ontologies. BMC Bioinformatics,8: 377.
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Lizano, E., Schuster, M., Müller, M., Kelso, J., & Mörl, M. (2007). A splice variant of the human CCA-adding enzyme with modified activity. Journal of Molecular Biology (London),366, 1258-1265.
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Myles, S., Somel, M., Tang, K., Kelso, J., & Stoneking, M. (2007). Identifying genes underlying skin pigmentation differences among human populations. Human Genetics,120(5), 613-621.
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Burek, P., Hoehndorf, 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.
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Khaitovich, P., Kelso, J., 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.
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Khaitovich, P., Tang, K., Franz, H., Kelso, J., Hellmann, I., Enard, W., Lachmann, M., & Pääbo, S. (2006). Positive selection on gene expression in the human brain. Current Biology,16(10), R356-R358.
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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., 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.
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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., 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.
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Tiffin, N., Kelso, J., 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.
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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., 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.
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Nembaware, V., Wolfe, K. H., Bettoni, F., Kelso, J., & Seoighe, C. (2004). Allele-specific transcript isoforms in human. FEBS Letters,577(1-2), 233-238.
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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., 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.
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Hide, W., Smedley, D., McCarthy, M., & Kelso, J. (2003). Application of eVOC: Controlled vocabularies for unifying gene expression data. Comptes Rendus Biologies,326(10-11), 1089-1096.
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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. (2003). eVOC: A controlled vocabulary for unifying gene expression data. Genome Research,13(6a), 1222-1230.
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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., Hide, W., & Ko, M. S. H. (2003). Transcriptome analysis of mouse stem cells and early embryos. PLoS Biology,1(3): e74.
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Kelso, J. (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.
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Nembaware, V., Crum, K., Kelso, J., & 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.
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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., 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.
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Hide, W. A., Babenko, V. N., van Heusden, P. A., Seoighe, C., & Kelso, J. (2001). The contribution of exon-skipping events on chromosome 22 to protein coding diversity. Genome Research,11(11), 1848-1853.
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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., 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.
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Book Chapters

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.
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Hoehndorf, R., Prüfer, K., Backhaus, M., Herre, H., Kelso, J., Loebe, F., & Visagie, J. (2006). A proposal for a gene functions wiki. In R. Meersman, Z. Tari, & P. Herrero (Eds.), On the move to meaningful internet systems 2006: OTM 2006 workshops (pp. 669-678). New York [u.a.]: Springer.
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Kelso, J. (2004). EST resources, clone sets, and databases. In L. B. Jorde (Ed.), Encyclopedia of genetics, genomics, proteomics and bioinformatics. Wiley.
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Posters

Hajdinjak, M., Korlević, P., Gansauge, M.-T., Dabney, J., Slon, V., Glocke, I., Sawyer, S., Nickel, B., Nagel, S., Gerber, T., Hopfe, C., Stenzel, U., Renaud, G., Andrés, A. M., Castellano, S., Kelso, J., Prüfer, K., Meyer, M., & Pääbo, S. (2014).Neandertal genetic diversity. Poster presented at XVII World UISPP Congress, Burgos, Spain.
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Meeting Abstracts

Jagoda, E., Xue, J., Reilly, S., Dannemann, M., Racimo, F., Huerta-Huerta-Sanchez, E., Sankararaman, S., Kelso, J., Pagani, L., Sabeti, P., & Capellini, T. D. (2020). Direct Identification of Neanderthal Introgressed Genetic Variation Affecting Gene Expression in Modern Human Immune Cell Lines. American Journal of Physical Anthropology,171(S69), 130-130.
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Higham, T., Douka, K., Slon, V., Jacobs, Z., Ramsey, C., Mafessoni, F., Kozlikin, B. L., Comeskey, D., Deviese, T., Brown, S., Viola, B., Buckley, M., Meyer, M., Roberts, R., Pääbo, S., Derevianko, A., Shunkov, M., & Kelso, J. (2019). Age estimates for hominin fossils and the onset of the Upper Palaeolithic at Denisova Cave. American Journal of Physical Anthropology,168(S68), 103-103.
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Douka, K., Slon, V., Jacobs, Z., Ramsey, C. B., Shunkov, M. V., Derevianko, A. P., Kozlikin, M. B., Li, B., Comeskey, D., Devièse, T., Brown, S., Viola, B., Buckley, M., Meyer, M., Roberts, R. G., Pääbo, S., Kelso, J., & Higham, T. (2018). Age estimates for hominin fossils and the onset of the Upper Palaeolithic at Denisova Cave. In T. A. Klimenkova (Ed.), The origins of the Upper Paleolithic in Eurasia and the evolution of the genus Homo: Proceedings of the International Symposium (Denisova Cave, Altai, Russia, July 2-8, 2018) (pp. 22-23). Novosibirsk: IAET SB RAS Publishing.
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Mafessoni, F., de Filippo, C., Slon, V., Grote, S., Chintalapati, M., Peter, B., Viola, B., Markin, S. V., Vasilyev, S. K., Rudaya, N. A., Kolobova, K. A., Shunkov, M. V., Derevianko, A. P., Kelso, J., Meyer, M., Prüfer, K., & Pääbo, S. (2018). A high-coverage Neandertal genome from Chagyrskaya Cave. In T. A. Klimenkova (Ed.), The origins of the Upper Paleolithic in Eurasia and the evolution of the genus Homo: Proceedings of the International Symposium (Denisova Cave, Altai, Russia, July 2-8, 2018) (pp. 51-55). Novosibirsk: IAET SB RAS Publishing.
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Slon, V., Mafessoni, F., Vernot, B., de Filippo, C., Grote, S., Viola, B., Hajdinjak, M., Peyrégne, S., Nagel, S., Brown, S., Douka, K., Higham, T., Kozlikin, M. B., Shunkov, M. V., Derevianko, A. P., Kelso, J., Meyer, M., Prüfer, K., & Pääbo, S. (2018). Denisova 11: The daughter of a Neandertal and a Denisovan. In T. A. Klimenkova (Ed.), The origins of the Upper Paleolithic in Eurasia and the evolution of the genus Homo: Proceedings of the International Symposium (Denisova Cave, Altai, Russia, July 2-8, 2018) (pp. 82-86). Novosibirsk: IAET SB RAS Publishing.
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Kunz, M., Dannemann, M., Dose, G., Kelso, J., Hoffmann, S., Landsberg, J., Tuting, T., Zigrino, P., Mauch, C., Kottek, T., Utikal, J., Schulze, H., Ziemer, M., Simon, J., Bosserhoff, A., & Schartl, M. (2017). RNA-Seq analysis of benign melanocytic nevi and primary melanomas. Experimental Dermatology,26(3), E86-E86.
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Hajdinjak, M., Fu, Q., Stenzel, U., Hübner, A., Petr, M., Mafessoni, F., Grote, S., Rougier, H., Crevecoeur, I., Semal, P., Soressi, M., Talamo, S., Hublin, J.-J., Gušić, I., Kućan, Ž., Rudan, P., Golovanova, L. V., Doronichev, V. B., Posth, C., Krause, J., Korlević, P., Nagel, S., Nickel, B., Prüfer, K., Kelso, J., Meyer, M., & Pääbo, S. (2017). Population history of late Neandertals. In Proceedings of the European Society for the study of Human Evolution (PESHE) (6, pp. 83).
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Andrés, A. M., Dannemann, M., Teixeira, J. C., & Kelso, J. (2016). Balancing selection and adaptive introgression as sources of advantageous genetic diversity in populations. American Journal of Physical Anthropology,159(S62), 80-81.
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Kelso, J., & Dannemann, M. (2016). What we have learned from Neanderthals about genes involved in energy metabolism and adiposity. Neuropeptides,55, 9.
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Gokhman, D., Prüfer, K., Lavi, E., Kelso, J., Pääbo, S., Meshorer, E., & Carmel, L. (2013). Paleoepigenetics: Reconstructing the DNA methylation maps of archaic hominins. In European Society for the study of Human Evolution (Ed.), Proceedings of the European Society for the study of Human Evolution 2 (PESHE 2) (pp. 97-97). Retrieved from http://eshe.eu/static/eshe/files/ESHE_Vienna_2013_Abstracts.pdf.
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Krause, J., Green, R. E., Briggs, A. W., Stenzel, U., Prüfer, K., Maricic, T., Kichner, M., Kelso, J. F., Reich, D., Mullikin, J. C., Egholm, M., & Pääbo, S. (2009). Insights from sequencing the Neanderthal genome. American Journal of Physical Anthropology,138(S48), 170-170.
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