Janet Kelso
Group leader
Abteilung für Evolutionäre Genetik
Max-Planck-Institut für evolutionäre Anthropologie
Deutscher Platz 6
04103 Leipzig
Curriculum Vitae
Biographical
| Name: | Janet Kelso |
| Nationality: | German |
| Email: | kelso@[>>> Please remove the text! <<<]eva.mpg.de |
Employment
| 2004-present | Group Leader of the Minerva Research Group for Bioinformatics Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany |
| 2003-2004 | Postdoctoral researcher. University of the Western Cape, Cape Town, South Africa |
Education
| 2003 | Ph.D. (Bioinformatics). University of the Western Cape, Cape Town, South Africa Advisor: Winston Hide |
| 2000 | M.Sc. (Med) (Chemical Pathology). University of Cape Town, Cape Town, South Africa |
| 1997 | B.Sc. (Med) (Hons) (Medical Biochemistry). University of Cape Town, Cape Town, South Africa |
| 1995 | B.Sc. (Biology). University of-Natal, Durban, South Africa. |
Grants, fellowships and awards
| 2017 | Chinese Academy of Sciences International Partnership Award for Young Scientists (with Qiaomei Fu) |
| 2016 | Elected Fellow of the International Society for Computational Biology (ISCB) |
| 2015 | DKFZ: Grant for sequencing of degraded DNA from FFPE samples in melanoma (with Matthias Meyer and Susanna Horn of the MPI-EVA) |
| 2012 | DFG Sonderforschungsbereich “Obesity Mechanisms” together with the SFB Consortium, University of Leipzig. |
| 2011 | EU COST Next generation sequencing data analysis network and training consortium. |
| 2011 | DKFZ: Grant for melanoma transcriptome analysis (together with Professor Manfred Kunz, University of Leipzig) |
| 2010 | AAAS Newcomb Cleveland Prize for the most outstanding paper in Science in 2010 (with co-authors) |
| 2004 | L'Oréal-UNESCO/DST fellowship for Women in Science: Young Scientist Award |
| 2003 | Merck Student Fellowship |
Scientific service
Editorial
| 2013 – present | Co-Executive Editor Bioinformatics (Oxford University Press) |
| 2011 – 2012 | Associate Editor Bioinformatics (Oxford University Press) |
| 2009 – present | Associate Editor Database (Oxford University Press) |
| 2014 – present | Editorial Board Genome Biology |
| 2007 – 2014 | Editor PLoS One |
| 2012 – present | Editorial Board Springer book series: Computational Biology |
International Society for Computational Biology (ISCB)
| 2011 – 2013, 2017-2019 | Vice-president, Executive Board |
| 2006 – 2011 | Secretary, Executive Board |
| 2006 – present | Conference Committee chair |
| 2005 – present | Member of Board of Directors |
Conference Organisation
| 2019 | Advances in Computational Biology / Bioinfo4Women. Conference co-chair (with Núria López-Bigas and Alison Kennedy) |
| 2015-2017 | CSHL 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 |
Advisory Boards/Review Panels (Selected)
| 2019 | Reviewer | Chinese Academy of Sciences Institute of Vertebrate Paleontology and Paleoanthropology |
| 2018- | Advisory Board | H3-Africa BioNet |
| 2016 | Review Panel | ERC Consolidator Grants |
| 2015-2017 | Review panel | Centre for Molecular Medicine (CeMM), Vienna |
| 2015 | Review panel | EBI-EMBL External Services |
| 2015 – present | Review board | H3-Africa/NIH Sickle Cell Disease Ontology Development |
| 2013 – present | Advisory Board | ELIXIR Scientific Advisory Board |
| 2013 – present | Advisory Board | NIH-H3Africa Wits-INDEPTH Centre |
| 2012, 2015 | Advisory Board | Genome Canada Bioinformatics & Computational Biology |
| 2014 – present | Review panel | Hercules Foundation/FWO for Belgian Research Infrastructure |
| 2009 – 2012 | Review panel | South African National Research Foundation |
| 2011 | Advisory Board | Genome Canada 4D Genomics Platform |
| 2010 | Review panel | Deutsche Forschungsgsgemeinschaft (DFG) Instrumentation |
| 2003 – 2011 | Advisory Board | Genome Canada Bioinformatics Platform |
Invited presentations and workshops (last 5 years)
| 2020 | Congress of the Spanish Society of Evolutionary Biology, Sevilla, Spain Human Genome Meeting, Perth, Australia (virtual presentation due to COVID-19) European Society of Human Genetics, Berlin, Germany (virtual presentation due to COVID-19) |
| 2019 | Cold Spring Harbor Genome Informatics, Cold Spring Harbor, USA SCAS Workshop, Uppsala University, Sweden ISMB-ECCB 2019 VarI-COSI, Basel, Switzerland |
| 2018 | Genome Informatics Workshop, Kunming, China XIV Symposium on Bioinformatics (JBI2018), Granada, Spain JBI2018 Student Symposium, Granada, Spain |
| 2017 | Human Evolution: Fossils, Ancient and Modern Genomes, Wellcome Trust Sanger Centre, UK Big Data Analyses in Evolutionary Biology, KAUST, Saudi Arabia 19th EMBL PhD Symposium: Bridging the Gaps - Interdisciplinary Approaches in Life Sciences, EMBL, Heidelberg, Germany Nordic-EMBL Partnership meeting, Helsinki, Finland |
| 2016 | 5th International Symposium on Regulators of Adaptive Immunity, Erlangen, Germany Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign EMBL, Heidelberg, Germany BioVis 2016, Orlando, Florida, USA |
Publications
Artikel
Peyrégne, S., Slon, V., & Kelso, J. (2023). More than a decade of genetic research on the Denisovans. Nature Reviews Genetics, 25(2), 83-103. |
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Essel, E., Zavala, E. I., Schulz-Kornas, E., Kozlikin, M. B., Fewlass, H., Vernot, B., Shunkov, M. V., Derevianko, A. P., Douka, K., Barnes, I., Soulier, M.-C., Schmidt, A., Szymanski, M., Tsanova, T., Sirakov, N., Endarova, E., McPherron, S. P., Hublin, J.-J., Kelso, J., Pääbo, S., Hajdinjak, M., Soressi, M., & Meyer, M. (2023). Ancient human DNA recovered from a Palaeolithic pendant. Nature, 618, 328-332. |
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Skov, L., Peyrégne, S., Popli, D. R., Iasi, L. N., Devièse, T., Slon, V., Zavala, E. I., Hajdinjak, M., Sümer, A., Grote, S., Bossoms Mesa, A., López Herráez, D., Nickel, B., Nagel, S., Richter, J., Essel, E., Gansauge, M.-T., Schmidt, A., Korlevic, P., Comeskey, D., Derevianko, A. P., Kharevich, A., Markin, S. V., Talamo, S., Douka, K., Krajcarz, M. T., Roberts, R. G., Higham, T., Viola, B., Krivoshapkin, A. I., Kolobova, K. A., Kelso, J., Meyer, M., Pääbo, S., & Peter, B. M. (2022). Genetic insights into the social organization of Neanderthals. Nature, 610, 519-525. |
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Peyrégne, S., Kelso, J., Peter, B. M., & Pääbo, S. (2022). The evolutionary history of human spindle genes includes back-and-forth gene flow with Neandertals. eLife, 11: e75464. |
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Kilpatrick, A. M., Rahman, F., Anjum, A., Shome, S., Andalib, K. M. S., Banik, S., Chowdhury, S. F., Coombe, P., Astroz, Y. C., Douglas, J. M., Eranti, P., Kiran, A. D., Kumar, S., Lim, H., Lorenzi, V., Lubiana, T., Mahmud, S., Puche, R., Rybarczyk, A., Sium, A., Muktadir, S., Twesigomwe, D., Zok, T., Orengo, C. A., Friedberg, I., Kelso, J., & Welch, L. (2022). Characterizing domain-specific open educational resources by linking ISCB Communities of Special Interest to Wikipedia. Bioinformatics, 38(Supplement_1), i19-i27. |
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Le Duc, D., Velluva, A., Cassatt-Johnstone, M., Olsen, R.-A., Baleka, S., Lin, C.-C., Lemke, J. R., Southon, J. R., Burdin, A., Wang, M.-S., Grunewald, S., Rosendahl, W., Joger, U., Rutschmann, S., Hildebrandt, T. B., Fritsch, G., Estes, J. A., Kelso, J., Dalén, L., Hofreiter, M., Shapiro, B., & Schöneberg, T. (2022). Genomic basis for skin phenotype and cold adaptation in the extinct Steller’s sea cow. Science Advances, 8(5). |
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Brown, S., Massilani, D., Kozlikin, M. B., Shunkov, M. V., Derevianko, A. P., Stoessel, A., Jope-Street, B., Meyer, M., Kelso, J., Pääbo, S., Higham, T., & Douka, K. (2022). The earliest Denisovans and their cultural adaptation. Nature Ecology & Evolution, 6, 28-35. |
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Jagoda, E., Xue, J. R., Reilly, S. K., Dannemann, M., Racimo, F., Huerta-Sanchez, E., Sankararaman, S., Kelso, J., Pagani, L., Sabeti, P. C., & Capellini, T. D. (2022). Detection of Neanderthal adaptively introgressed genetic variants that modulate reporter gene expression in human immune cells. Molecular Biology and Evolution, 39(1): msab304. |
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Alpaslan-Roodenberg, S., Anthony, D., Babiker, H., Bánffy, E., Booth, T., Capone, P., Deshpande-Mukherjee, A., Eisenmann, S., Fehren-Schmitz, L., Frachetti, M., Fujita, R., Frieman, C. J., Fu, Q., Gibbon, V., Haak, W., Hajdinjak, M., Hofmann, K. P., Holguin, B., Inomata, T., Kanzawa-Kiriyama, H., Keegan, W., Kelso, J., Krause, J., Kumaresan, G., Kusimba, C., Kusimba, S., Lalueza-Fox, C., Llamas, B., MacEachern, S., Mallick, S., Matsumura, H., Morales-Arce, A. Y., Matuzeviciute, G. M., Mushrif-Tripathy, V., Nakatsuka, N., Nores, R., Ogola, C., Okumura, M., Patterson, N., Pinhasi, R., Prasad, S. P. R., Prendergast, M. E., Punzo, J. L., Reich, D., Sawafuji, R., Sawchuk, E., Schiffels, S., Sedig, J., Shnaider, S., Sirak, K., Skoglund, P., Slon, V., Snow, M., Soressi, M., Spriggs, M., Stockhammer, P. W., Szécsényi-Nagy, A., Thangaraj, K., Tiesler, V., Tobler, R., Wang, C.-C., Warinner, C., Yasawardene, S., & Zahir, M. (2021). Ethics of DNA research on human remains: Five globally applicable guidelines. Nature, 599, 41-46. |
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Berger, C., Heyne, H. O., Heiland, T., Dommel, S., Höfling, C., Guiu-Jurado, E., Lorenz, J., Roßner, S., Dannemann, M., Kelso, J., Kovacs, P., Blüher, M., & Klöting, N. (2021). A novel compound heterozygous leptin receptor mutation causes more severe obesity than in Lepr mice. Journal of Lipid Research, 62: 100105. |
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Vernot, B., Zavala, E. I., Gómez-Olivencia, A., Jacobs, Z., Slon, V., Mafessoni, F., Romagné, F., Pearson, A., Petr, M., Sala, N., Pablos, A., Aranburu, A., de Castro, J. M. B., Carbonell, E., Li, B., Krajcarz, M. T., Krivoshapkin, A. I., Kolobova, K. A., Kozlikin, M. B., Shunkov, M. V., Derevianko, A. P., Viola, B., Grote, S., Essel, E., López Herráez, D., Nagel, S., Nickel, B., Richter, J., Schmidt, A., Peter, B., Kelso, J., Roberts, R. G., Arsuaga, J.-L., & Meyer, M. (2021). Unearthing Neanderthal population history using nuclear and mitochondrial DNA from cave sediments. Science, eabf1667. |
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Hajdinjak, M., Mafessoni, F., Skov, L., Vernot, B., Hübner, A., Fu, Q., Essel, E., Nagel, S., Nickel, B., Richter, J., Moldovan, O. T., Constantin, S., Endarova, E., Zahariev, N., Spasov, R., Welker, F., Smith, G. M., Sinet-Mathiot, V., Paskulin, L., Fewlass, H., Talamo, S., Rezek, Z., Sirakova, S., Sirakov, N., McPherron, S. P., Tsanova, T., Hublin, J.-J., Peter, B., Meyer, M., Skoglund, P., Kelso, J., & Pääbo, S. (2021). Initial Upper Palaeolithic humans in Europe had recent Neanderthal ancestry. Nature, 592, 253-257. |
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Zavala, E. I., Jacobs, Z., Vernot, B., Shunkov, M. V., Kozlikin, M. B., Derevianko, A. P., Essel, E., de Filippo, C., Nagel, S., Richter, J., Romagné, F., Schmidt, A., Li, B., O’Gorman, K., Slon, V., Kelso, J., Pääbo, S., Roberts, R. G., & Meyer, M. (2021). Pleistocene sediment DNA reveals hominin and faunal turnovers at Denisova Cave. Nature, 595, 399-403. |
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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. (2020). Denisovan ancestry and population history of early East Asians. Science, 370(6516), 579-583. |
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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. (2020). Denisovan DNA in Late Pleistocene sediments from Baishiya Karst Cave on the Tibetan Plateau. Science, 370(6516), 584-587. |
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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 humans. 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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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. |
Open AccessBuchkapitel
Kelso, J., Hoehndorf, R., & Prüfer, K. (2010). Ontologies in biology. In R. Poli, M. Healy, & A. Kameas ( |
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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 ( |
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Kelso, J. (2004). EST resources, clone sets, and databases. In L. B. Jorde ( |
Poster
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. |
Meeting Abstracts
Zavala, E. I., Jacobs, Z., Vernot, B., Shunkov, M. V., Kozlikin, M. B., Derevianko, A. P., Essel, E., de Filippo, C., Nagel, S., Richter, J., Romagné, F., Schmidt, A., Li, B., O'Gorman, K., Slon, V., Kelso, J., Pääbo, S., Roberts, R. G., & Meyer, M. (2023). The occupational history of Denisova Cave. American Journal of Biological Anthropology, 180(S75), 199-200. |
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Velluva, A., Radtke, M., Horn, S., Platzer, K., Gjermeni, E., Lemke, J. R., Schöneberg, T., Kelso, J., Jamra, R. A., & Le Duc, D. (2022). Phenotype-Tissue expression and exploration (PTEE) facilitates RNA-seq-based Mendelian disease diagnosis. European Journal of Human Genetics, 30(Suppl. 1), 499. |
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Kelso, J. (2020). What ancient humans can teach us about modern genetic variation. European journal of human genetics, 28(Suppl.1), 7-8. |
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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 ( |
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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 ( |
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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 ( |
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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 ( |
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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. |
Gallery
