Shapiro, Beth

Towards complete and error-free genome assemblies of all vertebrate species

Rhie, A., McCarthy, S. A., Fedrigo, O., Damas, J., Formenti, G., Koren, S., Uliano-Silva, M., Chow, W., Fungtammasan, A., Kim, J., et al. (2021) · Nature

Genomics and Phylogenetic StudiesChromosomal and Genetic Variations

Cited by 3,097

Towards complete and error-free genome assemblies of all vertebrate species

Rhie, A., McCarthy, S. A., Fedrigo, O., Damas, J., Formenti, G., Koren, S., Uliano-Silva, M., Chow, W., Fungtammasan, A., Gedman, G. L., et al. (2020) · Nature

Genomics and Phylogenetic StudiesChromosomal and Genetic Variations

Cited by 3,097

Whole-genome analyses resolve early branches in the tree of life of modern birds

Jarvis, E. D., Mirarab, S., Aberer, A. J., Li, B., Houde, P., Li, C., Ho, S. Y. W., Faircloth, B. C., Nabholz, B., Howard, J. T., et al. (2014) · Science

Genomics and Phylogenetic StudiesEvolution and Paleontology Studies

Cited by 1,901

Recalibrating equus evolution using the genome sequence of an early middle pleistocene horse

Orlando, L., Ginolhac, A., Zhang, G., Froese, D., Albrechtsen, A., Stiller, M., Schubert, M., Cappellini, E., Petersen, B., Moltke, I., et al. (2013) · Nature

Genomics and Phylogenetic StudiesVeterinary Equine Medical Research

Cited by 841

Dense sampling of bird diversity increases power of comparative genomics

Feng, S., Stiller, J., Deng, Y., Armstrong, J., Fang, Q., Reeve, A. H., Xie, D., Chen, G., Guo, C., Faircloth, B. C., et al. (2020) · Nature

Genomics and Phylogenetic StudiesChromosomal and Genetic Variations

Cited by 459

A comparative genomics multitool for scientific discovery and conservation

Zoonomia Consortium, Genereux, D. P., Serres, A., Armstrong, J., Johnson, J., Marinescu, V. D., Murén, E., Juan, D., Bejerano, G., Casewell, N. R., et al. (2020) · Nature

Genomics and Phylogenetic StudiesChromosomal and Genetic Variations

Cited by 373

Million-year-old DNA sheds light on the genomic history of mammoths

van der Valk, T., Pečnerová, P., Díez-del-Molino, D., Bergström, A., Oppenheimer, J., Hartmann, S., Xenikoudakis, G., Thomas, J. A., Dehasque, M., Sağlıcan, E., et al. (2021) · Nature

Pleistocene-Era Hominins and ArchaeologyGenetic diversity and population structure

Cited by 345

Prehistoric genomes reveal the genetic foundation and cost of horse domestication

Schubert, M., Jónsson, H., Chang, D., Der Sarkissian, C., Ermini, L., Ginolhac, A., Albrechtsen, A., Dupanloup, I., Foucal, A., Petersen, B., et al. (2014) · Proceedings of the National Academy of Sciences

Genetic and phenotypic traits in livestockForensic and Genetic Research

Cited by 324

863 genomes reveal the origin and domestication of chicken

Wang, M.-S., Thakur, M., Peng, M.-S., Jiang, Y., Frantz, L. A. F., Li, M., Zhang, J.-J., Wang, S., Peters, J., Otecko, N. O., et al. (2020) · Cell Research

Genetic and phenotypic traits in livestockLivestock and Poultry Management

Cited by 286

Mitochondrial DNA Analysis Shows a Near Eastern Neolithic Origin for Domestic Cattle and No Indication of Domestication of European Aurochs

Edwards, C. J., Bollongino, R., Scheu, A., Chamberlain, A., Tresset, A., Vigne, J.-D., Baird, J. F., Larson, G., Ho, S. Y. W., Heupink, T. H., et al. (2007) · Proceedings of the Royal Society B: Biological Sciences

Forensic and Genetic ResearchArchaeology and ancient environmental studies

Cited by 266

Conserving intraspecific variation for nature’s contributions to people

Des Roches, S., Pendleton, L. H., Shapiro, B., & Palkovacs, E. P. (2021) · Nature Ecology & Evolution

Land Use and Ecosystem ServicesEcology and Vegetation Dynamics Studies

Cited by 253

Ancient DNA analyses exclude humans as the driving force behind late Pleistocene musk ox ( Ovibos moschatus ) population dynamics

Campos, P. F., Willerslev, E., Sher, A., Orlando, L., Axelsson, E., Tikhonov, A., Aaris-Sørensen, K., Greenwood, A. D., Kahlke, R.-D., Kosintsev, P., et al. (2010) · Proceedings of the National Academy of Sciences

Genetic diversity and population structureForensic and Genetic Research

Cited by 239

Genomic evidence for island population conversion resolves conflicting theories of polar bear evolution

Cahill, J. A., Green, R. E., Fulton, T. L., Stiller, M., Jay, F., Ovsyanikov, N., Salamzade, R., St. John, J., Stirling, I., Slatkin, M., et al. (2013) · PLoS Genetics

Genetic diversity and population structureForensic and Genetic Research

Cited by 221

Integrating gene annotation with orthology inference at scale

Kirilenko, B. M., Munegowda, C., Osipova, E., Jebb, D., Sharma, V., Blumer, M., Morales, A. E., Ahmed, A.-W., Kontopoulos, D.-G., Hilgers, L., et al. (2023) · Science

Genomics and Phylogenetic StudiesChromosomal and Genetic Variations

Cited by 209

Museum Genomics

Card, D. C., Shapiro, B., Giribet, G., Moritz, C., & Edwards, S. V. (2021) · Annual Review of Genetics

Research Data Management PracticesEnvironmental DNA in Biodiversity Studies

Cited by 151

Three-dimensional genome rewiring in loci with human accelerated regions

Keough, K. C., Whalen, S., Inoue, F., Przytycki, P. F., Fair, T., Deng, C., Steyert, M., Ryu, H., Lindblad-Toh, K., Karlsson, E., et al. (2023) · Science

Genomics and Chromatin DynamicsChromosomal and Genetic Variations

Cited by 113

An ancestral recombination graph of human, Neanderthal, and Denisovan genomes

Schaefer, N. K., Shapiro, B., & Green, R. E. (2021) · Science Advances

Pleistocene-Era Hominins and ArchaeologyForensic and Genetic Research

Cited by 106

Ancient and modern genomes unravel the evolutionary history of the rhinoceros family

Liu, S., Westbury, M. V., Dussex, N., Mitchell, K. J., Sinding, M.-H. S., Heintzman, P. D., Duchêne, D. A., Kapp, J. D., von Seth, J., Heiniger, H., et al. (2021) · Cell

Genetic diversity and population structureEvolution and Paleontology Studies

Cited by 101

Reference genomes for conservation

Paez, S., Kraus, R. H. S., Shapiro, B., Gilbert, M. T. P., Jarvis, E. D., Vertebrate Genomes Project Conservation Group, Al-Ajli, F. O., Ceballos, G., Crawford, A. J., Fedrigo, O., et al. (2022) · Science

Genomics and Phylogenetic StudiesGenetic diversity and population structure

Cited by 83

Is amino acid racemization a useful tool for screening for ancient DNA in bone?

Collins, M. J., Penkman, K. E. H., Rohland, N., Shapiro, B., Dobberstein, R. C., Ritz-Timme, S., & Hofreiter, M. (2009) · Proceedings of the Royal Society B: Biological Sciences

Forensic and Genetic ResearchArchaeology and ancient environmental studies

Cited by 82

A Reference Genome Assembly of Simmental Cattle, Bos taurus taurus

Heaton, M. P., Smith, T. P. L., Bickhart, D. M., Vander Ley, B. L., Kuehn, L. A., Oppenheimer, J., Shafer, W. R., Schuetze, F. T., Stroud, B., McClure, J. C., et al. (2021) · Journal of Heredity

Genetic and phenotypic traits in livestockGenomics and Phylogenetic Studies

Cited by 52

Unravelling reference bias in ancient DNA datasets

Dolenz, S., van der Valk, T., Jin, C., Oppenheimer, J., Sharif, M. B., Orlando, L., Shapiro, B., Dalén, L., & Heintzman, P. D. (2024) · Bioinformatics

Genomics and Phylogenetic StudiesForensic and Genetic Research

Cited by 33

Demographic reconstruction from ancient DNA supports rapid extinction of the great auk

Thomas, J. E., Carvalho, G. R., Haile, J., Rawlence, N. J., Martin, M. D., Ho, S. Y., Sigfússon, A. Þ., Jósefsson, V. A., Frederiksen, M., Linnebjerg, J. F., et al. (2019) · eLife

Genetic diversity and population structureForensic and Genetic Research

Cited by 29

Early Pleistocene enamel proteome sequences from Dmanisi resolve Stephanorhinus phylogeny

Cappellini, E., Welker, F., Pandolfi, L., Madrigal, J. R., Fotakis, A. K., Lyon, D., Moreno Mayar, V. J., Bukhsianidze, M., Jersie-Christensen, R. R., Mackie, M., et al. (2018) · bioRxiv (Cold Spring Harbor Laboratory)

Evolution and Paleontology StudiesPleistocene-Era Hominins and Archaeology

Cited by 20