Analysis of High-Throughput Ancient DNA Sequencing Data von Kircher, Martin

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CADD-Splice-improving genome-wide variant effect prediction using deep learning-derived splice scores von Rentzsch, Philipp, Schubach, Max, Shendure, Jay, Kircher, Martin

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CADD: predicting the deleteriousness of variants throughout the human genome von Rentzsch, Philipp, Witten, Daniela, Cooper, Gregory M, Shendure, Jay, Kircher, Martin

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High-throughput DNA sequencing - concepts and limitations von Kircher, Martin, Kelso, Janet

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Addressing challenges in the production and analysis of illumina sequencing data von Kircher, Martin, Heyn, Patricia, Kelso, Janet

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Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX von Schubert, Mikkel, Ermini, Luca, Sarkissian, Clio Der, Jónsson, Hákon, Ginolhac, Aurélien, Schaefer, Robert, Martin, Michael D, Fernández, Ruth, Kircher, Martin, McCue, Molly, Willerslev, Eske, Orlando, Ludovic

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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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Saturation mutagenesis of twenty disease-associated regulatory elements at single base-pair resolution von Kircher, Martin, Xiong, Chenling, Martin, Beth, Schubach, Max, Inoue, Fumitaka, Bell, Robert J. A., Costello, Joseph F., Shendure, Jay, Ahituv, Nadav

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Deep proteome and transcriptome mapping of a human cancer cell line von Nagaraj, Nagarjuna, Wisniewski, Jacek R, Geiger, Tamar, Cox, Juergen, Kircher, Martin, Kelso, Janet, Pääbo, Svante, Mann, Matthias

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A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity von Inoue, Fumitaka, Kircher, Martin, Martin, Beth, Cooper, Gregory M, Witten, Daniela M, McManus, Michael T, Ahituv, Nadav, Shendure, Jay

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The evolution of gene expression levels in mammalian organs von Brawand, David, Soumillon, Magali, Necsulea, Anamaria, Julien, Philippe, Csárdi, Gábor, Harrigan, Patrick, Weier, Manuela, Liechti, Angélica, Aximu-Petri, Ayinuer, Kircher, Martin, Albert, Frank W., Zeller, Ulrich, Khaitovich, Philipp, Grützner, Frank, Bergmann, Sven, Nielsen, Rasmus, Pääbo, Svante, Kaessmann, Henrik

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HemoMIPs—Automated analysis and result reporting pipeline for targeted sequencing data von Kleinert, Philip, Martin, Beth, Kircher, Martin

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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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Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform von Kircher, Martin, Sawyer, Susanna, Meyer, Matthias

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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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The impact of different negative training data on regulatory sequence predictions von Krützfeldt, Louisa-Marie, Schubach, Max, Kircher, Martin

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Boosting tissue-specific prediction of active cis-regulatory regions through deep learning and Bayesian optimization techniques von Cappelletti, Luca, Petrini, Alessandro, Gliozzo, Jessica, Casiraghi, Elena, Schubach, Max, Kircher, Martin, Valentini, Giorgio

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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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Machine learning dissection of human accelerated regions in primate neurodevelopment von Whalen, Sean, Inoue, Fumitaka, Ryu, Hane, Fair, Tyler, Markenscoff-Papadimitriou, Eirene, Keough, Kathleen, Kircher, Martin, Martin, Beth, Alvarado, Beatriz, Elor, Orry, Laboy Cintron, Dianne, Williams, Alex, Hassan Samee, Md. Abul, Thomas, Sean, Krencik, Robert, Ullian, Erik M., Kriegstein, Arnold, Rubenstein, John L., Shendure, Jay, Pollen, Alex A., Ahituv, Nadav, Pollard, Katherine S.

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A Complete mtDNA Genome of an Early Modern Human from Kostenki, Russia von Krause, Johannes, Briggs, Adrian W., Kircher, Martin, Maricic, Tomislav, Zwyns, Nicolas, Derevianko, Anatoli, Pääbo, Svante

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