McCarthy, Shane

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

YaHS: yet another Hi-C scaffolding tool

Zhou, C., McCarthy, S. A., & Durbin, R. (2023) · Bioinformatics

Genomics and Phylogenetic StudiesGenomics and Chromatin Dynamics

Cited by 2,440

An integrated map of structural variation in 2,504 human genomes

Sudmant, P. H., Rausch, T., Gardner, E. J., Handsaker, R. E., Abyzov, A., Huddleston, J., Zhang, Y., Ye, K., Jun, G., Hsi-Yang Fritz, M., et al. (2015) · Nature

Genomic variations and chromosomal abnormalitiesGenome Rearrangement Algorithms

Cited by 2,354

Reference-based phasing using the Haplotype Reference Consortium panel

Loh, P.-R., Danecek, P., Palamara, P. F., Fuchsberger, C., A Reshef, Y., K Finucane, H., Schoenherr, S., Forer, L., McCarthy, S., Abecasis, G. R., et al. (2016) · Nature Genetics

Genetic Associations and EpidemiologyGenomics and Phylogenetic Studies

Cited by 1,723

Insights into human genetic variation and population history from 929 diverse genomes

Bergström, A., McCarthy, S. A., Hui, R., Almarri, M. A., Ayub, Q., Danecek, P., Chen, Y., Felkel, S., Hallast, P., Kamm, J., et al. (2020) · Science

Forensic and Genetic ResearchGenetic diversity and population structure

Cited by 1,020

Common genetic variation drives molecular heterogeneity in human iPSCs

Kilpinen, H., Goncalves, A., Leha, A., Afzal, V., Alasoo, K., Ashford, S., Bala, S., Bensaddek, D., Casale, F. P., Culley, O. J., et al. (2017) · Nature

Pluripotent Stem Cells ResearchGenetic Associations and Epidemiology

Cited by 586

BCFtools/csq: haplotype-aware variant consequences

Danecek, P., & McCarthy, S. A. (2017) · Bioinformatics

Genomics and Rare DiseasesGenomics and Phylogenetic Studies

Cited by 468

Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression

Cuomo, A. S. E., Seaton, D. D., McCarthy, D. J., Martinez, I., Bonder, M. J., Garcia-Bernardo, J., Amatya, S., Madrigal, P., Isaacson, A., Buettner, F., et al. (2020) · Nature Communications

Pluripotent Stem Cells ResearchSingle-cell and spatial transcriptomics

Cited by 331

Health and population effects of rare gene knockouts in adult humans with related parents

Narasimhan, V. M., Hunt, K. A., Mason, D., Baker, C. L., Karczewski, K. J., Barnes, M. R., Barnett, A. H., Bates, C., Bellary, S., Bockett, N. A., et al. (2016) · Science

Genomics and Rare DiseasesGenetic Associations and Epidemiology

Cited by 286

An organelle-specific protein landscape identifies novel diseases and molecular mechanisms

Boldt, K., van Reeuwijk, J., Lu, Q., Koutroumpas, K., Nguyen, T.-M. T., Texier, Y., van Beersum, S. E. C., Horn, N., Willer, J. R., Mans, D. A., et al. (2016) · Nature Communications

Genetic and Kidney Cyst DiseasesCystic Fibrosis Research Advances

Cited by 240

Exploring the genetic architecture of inflammatory bowel disease by whole-genome sequencing identifies association at ADCY7

Luo, Y., de Lange, K. M., Jostins, L., Moutsianas, L., Randall, J., Kennedy, N. A., Lamb, C. A., McCarthy, S., Ahmad, T., Edwards, C., et al. (2017) · Nature Genetics

Inflammatory Bowel DiseaseGenetic Associations and Epidemiology

Cited by 162

Whole-genome sequence-based analysis of thyroid function

Taylor, P. N., Porcu, E., Chew, S., Campbell, P. J., Traglia, M., Brown, S. J., Mullin, B. H., Shihab, H. A., Min, J., Walter, K., et al. (2015) · Nature Communications

Genetic Associations and EpidemiologyThyroid Disorders and Treatments

Cited by 104

Genomic and genetic insights into speciation and pigment pattern diversification in Danio fishes

Lu, J., Podobnik, M., Huang, J., McCluskey, B. M., McCarthy, S. A., Wood, J., Collins, J., Torrance, J., Sims, Y., Gao, D., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory)

Developmental Biology and Gene RegulationZebrafish Biomedical Research Applications

Cited by 4

The genome sequence of the Dracula fish, Danionella dracula (Britz, Conway & Rüber, 2009)

Rüber, L., Britz, R., Conway, K., Bista, I., McCarthy, S., Wood, J., Smith, M., Oliver, K., Howe, K., & Durbin, R. (2024) · Wellcome Open Research

Genomics and Phylogenetic StudiesChromosomal and Genetic Variations

Cited by 3