Shane McCarthy
Researcher Next ID · RN-027799
Researcher · Biochemistry, Genetics and Molecular Biology
Cambridge, United Kingdom
- Works count
- 214
- Citation count
- 110,403
- H-index
- 55
- i10-index
- 98
Research interests
Publications
Oatk: a de novo assembly tool for complex plant organelle genomes
Genome biology · 2025 · 10.1186/s13059-025-03676-6
MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads
BMC Bioinformatics · 2023 · https://doi.org/10.1186/s12859-023-05385-y
YaHS: yet another Hi-C scaffolding tool
Bioinformatics · 2022 · https://doi.org/10.1093/bioinformatics/btac808
MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio High Fidelity reads
bioRxiv (Cold Spring Harbor Laboratory) · 2022 · 10.1101/2022.12.23.521667
Twelve years of SAMtools and BCFtools
GigaScience · 2021 · https://doi.org/10.1093/gigascience/giab008
Towards complete and error-free genome assemblies of all vertebrate species
Nature · 2021 · https://doi.org/10.1038/s41586-021-03451-0
Insights into human genetic variation and population history from 929 diverse genomes
Science · 2020 · 10.1126/science.aay5012
Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression
Nature Communications · 2020 · 10.1038/s41467-020-14457-z
Identifying and removing haplotypic duplication in primary genome assemblies
Bioinformatics · 2020 · https://doi.org/10.1093/bioinformatics/btaa025
Common genetic variation drives molecular heterogeneity in human iPSCs
Nature · 2017 · 10.1038/nature22403
Genetic and Pharmacologic Inactivation of ANGPTL3 and Cardiovascular Disease
New England Journal of Medicine · 2017 · 10.1056/nejmoa1612790
BCFtools/csq: haplotype-aware variant consequences
Bioinformatics · 2017 · 10.1093/bioinformatics/btx100
Whole-Genome Sequencing Coupled to Imputation Discovers Genetic Signals for Anthropometric Traits
The American Journal of Human Genetics · 2017 · 10.1016/j.ajhg.2017.04.014
A reference panel of 64,976 haplotypes for genotype imputation
Nature Genetics · 2016 · https://doi.org/10.1038/ng.3643
Health and population effects of rare gene knockouts in adult humans with related parents
Science · 2016 · 10.1126/science.aac8624
An organelle-specific protein landscape identifies novel diseases and molecular mechanisms
Nature Communications · 2016 · 10.1038/ncomms11491
Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences
Nature Genetics · 2016 · 10.1038/ng.3559
Reference-based phasing using the Haplotype Reference Consortium panel
Nature Genetics · 2016 · 10.1038/ng.3679
An integrated map of structural variation in 2,504 human genomes
Nature · 2015 · https://doi.org/10.1038/nature15394
The UK10K project identifies rare variants in health and disease
Nature · 2015 · 10.1038/nature14962
Whole‐genome sequencing identifies EN1 as a determinant of bone density and fracture
Nature · 2015 · 10.1038/nature14878
Improved imputation of low-frequency and rare variants using the UK10K haplotype reference panel
Nature Communications · 2015 · 10.1038/ncomms9111
Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel
Nature Communications · 2014 · 10.1038/ncomms4934
Insights into hominid evolution from the gorilla genome sequence
Nature · 2012 · 10.1038/nature10842
Current projects
No projects listed.