leeHom: adaptor trimming and merging for Illumina sequencing reads von Renaud, Gabriel, Stenzel, Udo, Kelso, Janet

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deML: robust demultiplexing of Illumina sequences using a likelihood-based approach von Renaud, Gabriel, Stenzel, Udo, Maricic, Tomislav, Wiebe, Victor, Kelso, Janet

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DNA analysis of an early modern human from Tianyuan Cave, China von Fu, Qiaomei, Meyer, Matthias, Gao, Xing, Stenzel, Udo, Burbano, Hernán A., Kelso, Janet, Pääbo, Svante

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Improved base calling for the Illumina Genome Analyzer using machine learning strategies von Kircher, Martin, Stenzel, Udo, Kelso, Janet

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A High-Coverage Genome Sequence from an Archaic Denisovan Individual von Meyer, Matthias, Kircher, Martin, Gansauge, Marie-Theres, Li, Heng, Racimo, Fernando, Mallick, Swapan, Schraiber, Joshua G., Jay, Flora, Prüfer, Kay, de Filippo, Cesare, Sudmant, Peter H., Alkan, Can, Fu, Qiaomei, Do, Ron, Rohland, Nadin, Tandon, Arti, Siebauer, Michael, Green, Richard E., Bryc, Katarzyna, Briggs, Adrian W., Stenzel, Udo, Dabney, Jesse, Shendure, Jay, Kitzman, Jacob, Hammer, Michael F., Shunkov, Michael V., Derevianko, Anatoli P., Patterson, Nick, Andrés, Aida M., Eichler, Evan E., Slatkin, Montgomery, Reich, David, Kelso, Janet, Pääbo, Svante

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Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA von Briggs, Adrian W, Stenzel, Udo, Meyer, Matthias, Krause, Johannes, Kircher, Martin, Pääbo, Svante

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Genetic history of an archaic hominin group from Denisova Cave in Siberia von Reich, David, Viola, Bence, Pääbo, Svante, Green, Richard E, Kircher, Martin, Krause, Johannes, Patterson, Nick, Durand, Eric Y, Briggs, Adrian W, Stenzel, Udo, Johnson, Philip L. F, Maricic, Tomislav, Good, Jeffrey M, Marques-Bonet, Tomas, Alkan, Can, Fu, Qiaomei, Mallick, Swapan, Li, Heng, Meyer, Matthias, Eichler, Evan E, Stoneking, Mark, Richards, Michael, Talamo, Sahra, Shunkov, Michael V, Derevianko, Anatoli P, Hublin, Jean-Jacques, Kelso, Janet, Slatkin, Montgomery

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Patterns of coding variation in the complete exomes of three Neandertals von Castellano, Sergi, Parra, Genís, Sánchez-Quinto, Federico A., Racimo, Fernando, Kuhlwilm, Martin, Kircher, Martin, Sawyer, Susanna, Fu, Qiaomei, Heinze, Anja, Nickel, Birgit, Dabney, Jesse, Siebauer, Michael, White, Louise, Burbano, Hernán A., Renaud, Gabriel, Stenzel, Udo, Lalueza-Fox, Carles, de la Rasilla, Marco, Rosas, Antonio, Rudan, Pavao, Brajković, Dejana, Kucan, Željko, Gušic, Ivan, Shunkov, Michael V., Derevianko, Anatoli P., Viola, Bence, Meyer, Matthias, Kelso, Janet, Andrés, Aida M., Pääbo, Svante

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Patterns of Damage in Genomic DNA Sequences from a Neandertal von Briggs, Adrian W., Stenzel, Udo, Johnson, Philip L. F., Green, Richard E., Kelso, Janet, Prüfer, Kay, Meyer, Matthias, Krause, Johannes, Ronan, Michael T., Lachmann, Michael, Pääbo, Svante

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Targeted Retrieval and Analysis of Five Neandertal mtDNA Genomes von Briggs, Adrian W, Good, Jeffrey M, Green, Richard E, Krause, Johannes, Maricic, Tomislav, Stenzel, Udo, Lalueza-Fox, Carles, Rudan, Pavao, Brajković, Dejana, Kućan, Željko, Gušić, Ivan, Schmitz, Ralf, Doronichev, Vladimir B, Golovanova, Liubov V, de la Rasilla, Marco, Fortea, Javier, Rosas, Antonio, Pääbo, Svante

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Targeted high-throughput sequencing of tagged nucleic acid samples von Meyer, Matthias, Stenzel, Udo, Myles, Sean, Prüfer, Kay, Hofreiter, Michael

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A Complete Neandertal Mitochondrial Genome Sequence Determined by High-Throughput Sequencing von Green, Richard E., Malaspinas, Anna-Sapfo, Krause, Johannes, Briggs, Adrian W., Johnson, Philip L.F., Uhler, Caroline, Meyer, Matthias, Good, Jeffrey M., Maricic, Tomislav, Stenzel, Udo, Prüfer, Kay, Siebauer, Michael, Burbano, Hernán A., Ronan, Michael, Rothberg, Jonathan M., Egholm, Michael, Rudan, Pavao, Brajković, Dejana, Kućan, Željko, Gušić, Ivan, Wikström, Mårten, Laakkonen, Liisa, Kelso, Janet, Slatkin, Montgomery, Pääbo, Svante

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PatMaN: rapid alignment of short sequences to large databases von Prüfer, Kay, Stenzel, Udo, Dannemann, Michael, Green, Richard E., Lachmann, Michael, Kelso, Janet

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Parallel tagged sequencing on the 454 platform von Meyer, Matthias, Stenzel, Udo, Hofreiter, Michael

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The repertoire and structure of adhesion GPCR transcript variants assembled from publicly available deep-sequenced human samples von Kuhn, Christina Katharina, Stenzel, Udo, Berndt, Sandra, Liebscher, Ines, Schöneberg, Torsten, Horn, Susanne

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freeIbis: an efficient basecaller with calibrated quality scores for Illumina sequencers von Renaud, Gabriel, Kircher, Martin, Stenzel, Udo, Kelso, Janet

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Direct multiplex sequencing (DMPS)--a novel method for targeted high-throughput sequencing of ancient and highly degraded DNA von Stiller, Mathias, Knapp, Michael, Stenzel, Udo, Hofreiter, Michael, Meyer, Matthias

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Sequence variants in SLC16A11 are a common risk factor for type 2 diabetes in Mexico von Williams, Amy L, Jacobs, Suzanne B R, Moreno-Macías, Hortensia, Huerta-Chagoya, Alicia, Churchhouse, Claire, Márquez-Luna, Carla, García-Ortíz, Humberto, Gómez-Vázquez, María José, Burtt, Noël P, Aguilar-Salinas, Carlos A, González-Villalpando, Clicerio, Florez, Jose C, Orozco, Lorena, Haiman, Christopher A, Tusié-Luna, Teresa, Altshuler, David

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Draft Sequence of the Neandertal Genome von Green, Richard E, Krause, Johannes, Briggs, Adrian W, Maricic, Tomislav, Stenzel, Udo, Kircher, Martin, Patterson, Nick, Li, Heng, Zhai, Weiwei, Fritz, Markus Hsi-Yang, Hansen, Nancy F, Durand, Eric Y, Malaspinas, Anna-Sapfo, Jensen, Jeffrey D, Marques-Bonet, Tomas, Alkan, Can, Prüfer, Kay, Meyer, Matthias, Burbano, Hernán A, Good, Jeffrey M, Schultz, Rigo, Aximu-Petri, Ayinuer, Butthof, Anne, Höber, Barbara, Höffner, Barbara, Siegemund, Madlen, Weihmann, Antje, Nusbaum, Chad, Lander, Eric S, Russ, Carsten, Novod, Nathaniel, Affourtit, Jason, Egholm, Michael, Verna, Christine, Rudan, Pavao, Brajkovic, Dejana, Kucan, Željko, Gušic, Ivan, Doronichev, Vladimir B, Golovanova, Liubov V, Lalueza-Fox, Carles, de la Rasilla, Marco, Fortea, Javier, Rosas, Antonio, Schmitz, Ralf W, Johnson, Philip L.F, Eichler, Evan E, Falush, Daniel, Birney, Ewan, Mullikin, James C, Slatkin, Montgomery, Nielsen, Rasmus, Kelso, Janet, Lachmann, Michael, Reich, David, Pääbo, Svante

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Computational challenges in the analysis of ancient DNA von Prüfer, Kay, Stenzel, Udo, Hofreiter, Michael, Pääbo, Svante, Kelso, Janet, Green, Richard E

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