Kircher, Martin

A general framework for estimating the relative pathogenicity of human genetic variants

Kircher, M., Witten, D. M., Jain, P., O'Roak, B. J., Cooper, G. M., & Shendure, J. (2014) · Nature Genetics

Genomics and Rare DiseasesGenetic Associations and Epidemiology

Cited by 6,183

A draft sequence of the Neandertal genome

Green, R. E., Krause, J., Briggs, A. W., Maricic, T., Stenzel, U., Kircher, M., Patterson, N., Li, H., Zhai, W., Fritz, M. H.-Y., et al. (2010) · Science

Pleistocene-Era Hominins and ArchaeologyForensic and Genetic Research

Cited by 4,318

CADD: predicting the deleteriousness of variants throughout the human genome

Rentzsch, P., Witten, D., Cooper, G. M., Shendure, J., & Kircher, M. (2019) · Nucleic Acids Research

Genomics and Rare DiseasesGenetic Associations and Epidemiology

Cited by 3,534

The complete genome sequence of a Neanderthal from the Altai Mountains

Prüfer, K., Racimo, F., Patterson, N., Jay, F., Sankararaman, S., Sawyer, S., Heinze, A., Renaud, G., Sudmant, P. H., de Filippo, C., et al. (2014) · Nature

Pleistocene-Era Hominins and ArchaeologyForensic and Genetic Research

Cited by 2,254

Genetic history of an archaic hominin group from Denisova Cave in Siberia

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., et al. (2010) · Nature

Pleistocene-Era Hominins and ArchaeologyForensic and Genetic Research

Cited by 1,991

A high-coverage genome sequence from an archaic denisovan individual

Meyer, M., Kircher, M., Gansauge, M.-T., Li, H., Racimo, F., Mallick, S., Schraiber, J. G., Jay, F., Prüfer, K., de Filippo, C., et al. (2012) · Science

Pleistocene-Era Hominins and ArchaeologyForensic and Genetic Research

Cited by 1,967

The evolution of gene expression levels in mammalian organs

Brawand, D., Soumillon, M., Necsulea, A., Julien, P., Csárdi, G., Harrigan, P., Weier, M., Liechti, A., Aximu-Petri, A., Kircher, M., et al. (2011) · Nature

Genomics and Phylogenetic StudiesChromosomal and Genetic Variations

Cited by 1,248

Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform

Kircher, M., Sawyer, S., & Meyer, M. (2012) · Nucleic Acids Research

Genomics and Phylogenetic StudiesGenomics and Rare Diseases

Cited by 1,106

Deep proteome and transcriptome mapping of a human cancer cell line

Nagaraj, N., Wisniewski, J. R., Geiger, T., Cox, J., Kircher, M., Kelso, J., Pääbo, S., & Mann, M. (2011) · Molecular Systems Biology

Advanced Proteomics Techniques and ApplicationsBioinformatics and Genomic Networks

Cited by 979

Denisova Admixture and the First Modern Human Dispersals into Southeast Asia and Oceania

Reich, D., Patterson, N., Kircher, M., Delfin, F., Nandineni, M. R., Pugach, I., Ko, A. M.-S., Ko, Y.-C., Jinam, T. A., Phipps, M. E., et al. (2011) · The American Journal of Human Genetics

Pleistocene-Era Hominins and ArchaeologyForensic and Genetic Research

Cited by 656

The Genetic Basis of Mendelian Phenotypes: Discoveries, Challenges, and Opportunities

Chong, J. X., Buckingham, K. J., Jhangiani, S. N., Boehm, C., Sobreira, N., Smith, J. D., Harrell, T. M., McMillin, M. J., Wiszniewski, W., Gambin, T., et al. (2015) · The American Journal of Human Genetics

Genomics and Rare DiseasesGenetic Associations and Epidemiology

Cited by 643

CADD-Splice—improving genome-wide variant effect prediction using deep learning-derived splice scores

Rentzsch, P., Schubach, M., Shendure, J., & Kircher, M. (2021) · Genome Medicine

Genomics and Rare DiseasesRNA Research and Splicing

Cited by 640

Ancient gene flow from early modern humans into Eastern Neanderthals

Kuhlwilm, M., Gronau, I., Hubisz, M. J., de Filippo, C., Prado-Martinez, J., Kircher, M., Fu, Q., Burbano, H. A., Lalueza-Fox, C., de la Rasilla, M., et al. (2016) · Nature

Pleistocene-Era Hominins and ArchaeologyForensic and Genetic Research

Cited by 577

Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA

Briggs, A. W., Stenzel, U., Meyer, M., Krause, J., Kircher, M., & Pääbo, S. (2010) · Nucleic Acids Research

Forensic and Genetic ResearchPleistocene-Era Hominins and Archaeology

Cited by 491

CADD v1.7: Using protein language models, regulatory CNNs and other nucleotide-level scores to improve genome-wide variant predictions

Schubach, M., Maass, T., Nazaretyan, L., Röner, S., & Kircher, M. (2024) · Nucleic Acids Research

Genomics and Rare DiseasesGenetic Associations and Epidemiology

Cited by 455

Multiplex assessment of protein variant abundance by massively parallel sequencing

Matreyek, K. A., Starita, L. M., Stephany, J. J., Martin, B., Chiasson, M. A., Gray, V. E., Kircher, M., Khechaduri, A., Dines, J. N., Hause, R. J., et al. (2018) · Nature Genetics

Genomics and Rare DiseasesCancer Genomics and Diagnostics

Cited by 436

Somatic mutations in cerebral cortical malformations

Jamuar, S. S., Lam, A.-T. N., Kircher, M., D’Gama, A. M., Wang, J., Barry, B. J., Zhang, X., Hill, R. S., Partlow, J. N., Rozzo, A., et al. (2014) · New England Journal of Medicine

Fetal and Pediatric Neurological DisordersGenomics and Rare Diseases

Cited by 392

Transcriptomes of germinal zones of human and mouse fetal neocortex suggest a role of extracellular matrix in progenitor self-renewal

Fietz, S. A., Lachmann, R., Brandl, H., Kircher, M., Samusik, N., Schröder, R., Lakshmanaperumal, N., Henry, I., Vogt, J., Riehn, A., et al. (2012) · Proceedings of the National Academy of Sciences

Neurogenesis and neuroplasticity mechanismsDevelopmental Biology and Gene Regulation

Cited by 337

A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity

Inoue, F., Kircher, M., Martin, B., Cooper, G. M., Witten, D. M., McManus, M. T., Ahituv, N., & Shendure, J. (2017) · Genome Research

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 331

Patterns of coding variation in the complete exomes of three Neandertals

Castellano, S., Parra, G., Sánchez-Quinto, F. A., Racimo, F., Kuhlwilm, M., Kircher, M., Sawyer, S., Fu, Q., Heinze, A., Nickel, B., et al. (2014) · Proceedings of the National Academy of Sciences

Pleistocene-Era Hominins and ArchaeologyForensic and Genetic Research

Cited by 247

Analysis of High-Throughput Ancient DNA Sequencing Data

Kircher, M. (2012) · Methods in Molecular Biology

Genomics and Phylogenetic StudiesForensic and Genetic Research

Cited by 236

Saturation mutagenesis of twenty disease-associated regulatory elements at single base-pair resolution

Kircher, M., Xiong, C., Martin, B., Schubach, M., Inoue, F., Bell, R. J. A., Costello, J. F., Shendure, J., & Ahituv, N. (2019) · Nature Communications

Genomics and Chromatin DynamicsGenetic Associations and Epidemiology

Cited by 234

A systematic evaluation of the design and context dependencies of massively parallel reporter assays

Klein, J. C., Agarwal, V., Inoue, F., Keith, A., Martin, B., Kircher, M., Ahituv, N., & Shendure, J. (2020) · Nature Methods

Genomics and Chromatin DynamicsCRISPR and Genetic Engineering

Cited by 226

Massively parallel characterization of transcriptional regulatory elements

Agarwal, V., Inoue, F., Schubach, M., Penzar, D., Martin, B. K., Dash, P. M., Keukeleire, P., Zhang, Z., Sohota, A., Zhao, J., et al. (2025) · Nature

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 146