Shane McCarthy

103.7k total citations · 4 hit papers
52 papers, 9.1k citations indexed

About

Shane McCarthy is a scholar working on Genetics, Molecular Biology and Pulmonary and Respiratory Medicine. According to data from OpenAlex, Shane McCarthy has authored 52 papers receiving a total of 9.1k indexed citations (citations by other indexed papers that have themselves been cited), including 17 papers in Genetics, 15 papers in Molecular Biology and 9 papers in Pulmonary and Respiratory Medicine. Recurrent topics in Shane McCarthy's work include Genomics and Phylogenetic Studies (9 papers), Genetic Associations and Epidemiology (5 papers) and Genomics and Rare Diseases (4 papers). Shane McCarthy is often cited by papers focused on Genomics and Phylogenetic Studies (9 papers), Genetic Associations and Epidemiology (5 papers) and Genomics and Rare Diseases (4 papers). Shane McCarthy collaborates with scholars based in United Kingdom, United States and Sweden. Shane McCarthy's co-authors include Petr Danecek, James Bonfield, Thomas Keane, Martin Pollard, John Marshall, Heng Li, Robert M. Davies, Andrew Whitwham, Valeriu Ohan and Jennifer Liddle and has published in prestigious journals such as Nature Communications, Nature Genetics and Bioinformatics.

In The Last Decade

Shane McCarthy

47 papers receiving 9.0k citations

Hit Papers

Twelve years of SAMtools and BCFtools 2016 2026 2019 2022 2021 2016 2020 2022 2.0k 4.0k 6.0k
What are hit papers?

Hit papers significantly outperform the citation benchmark for their cohort. A paper qualifies if it has ≥500 total citations, achieves ≥1.5× the top-1% citation threshold for papers in the same subfield and year (this is the minimum needed to enter the top 1%, not the average within it), or reaches the top citation threshold in at least one of its specific research topics.

  1. Twelve years of SAMtools and BCFtools
    2021 6.3k citations Petr Danecek, James Bonfield et al. GigaScience profile →
  2. Reference-based phasing using the Haplotype Reference Consortium panel
    2016 829 citations Petr Danecek, Shane McCarthy et al. profile →
  3. Identifying and removing haplotypic duplication in primary genome assemblies
    2020 636 citations Dengfeng Guan, Shane McCarthy et al. Bioinformatics profile →
  4. YaHS: yet another Hi-C scaffolding tool
    2022 265 citations Chenxi Zhou, Shane McCarthy et al. Bioinformatics profile →

Peers — A (Enhanced Table)

Peers by citation overlap · career bar shows stage (early→late) cites · hero ref

Name h Career Trend Papers Cites
Shane McCarthy United Kingdom 19 4.5k 2.9k 1.9k 1.0k 675 52 9.1k
James Bonfield United Kingdom 17 4.8k 1.1× 2.3k 0.8× 2.0k 1.1× 1.2k 1.2× 615 0.9× 19 9.2k
John Welsh United States 43 4.5k 1.0× 3.3k 1.1× 2.4k 1.2× 855 0.8× 588 0.9× 124 11.7k
Robert M. Davies United Kingdom 8 3.8k 0.8× 2.0k 0.7× 1.5k 0.8× 851 0.8× 569 0.8× 11 6.9k
Xiangyi Lu United States 25 4.8k 1.1× 3.4k 1.2× 2.2k 1.2× 597 0.6× 1.0k 1.5× 81 10.1k
Thomas Keane United Kingdom 37 6.3k 1.4× 3.0k 1.1× 2.5k 1.3× 1.4k 1.3× 886 1.3× 83 11.4k
Wen Wang China 55 5.7k 1.3× 2.6k 0.9× 3.2k 1.7× 905 0.9× 673 1.0× 298 10.5k
Andrew Whitwham United Kingdom 4 3.6k 0.8× 1.8k 0.6× 1.5k 0.8× 865 0.9× 553 0.8× 4 6.8k
Douglas M. Ruden United States 35 5.7k 1.3× 3.6k 1.2× 2.2k 1.2× 640 0.6× 1.1k 1.7× 104 12.3k
Ioana Cutcutache Singapore 10 5.4k 1.2× 2.1k 0.7× 2.9k 1.5× 1.5k 1.5× 705 1.0× 19 11.7k
Andreas Untergasser Germany 15 4.6k 1.0× 2.0k 0.7× 3.0k 1.6× 1.2k 1.2× 507 0.8× 17 10.1k

Countries citing papers authored by Shane McCarthy

Since Specialization
Citations

This map shows the geographic impact of Shane McCarthy's research. It shows the number of citations coming from papers published by authors working in each country. You can also color the map by specialization and compare the number of citations received by Shane McCarthy with the expected number of citations based on a country's size and research output (numbers larger than one mean the country cites Shane McCarthy more than expected).

Fields of papers citing papers by Shane McCarthy

Since Specialization
Physical SciencesHealth SciencesLife SciencesSocial Sciences

This network shows the impact of papers produced by Shane McCarthy. Nodes represent research fields, and links connect fields that are likely to share authors. Colored nodes show fields that tend to cite the papers produced by Shane McCarthy. The network helps show where Shane McCarthy may publish in the future.

Co-authorship network of co-authors of Shane McCarthy

This figure shows the co-authorship network connecting the top 25 collaborators of Shane McCarthy. A scholar is included among the top collaborators of Shane McCarthy based on the total number of citations received by their joint publications. Widths of edges represent the number of papers authors have co-authored together. Node borders signify the number of papers an author published with Shane McCarthy. Shane McCarthy is excluded from the visualization to improve readability, since they are connected to all nodes in the network.

All Works

20 of 20 papers shown
1.
Zhou, Chenxi, Claudia Weber, Emmelien Vancaester, et al.. (2025). Forty new genomes shed light on sexual reproduction and the origin of tetraploidy in Microsporidia. PLoS Biology. 23(10). e3003446–e3003446.
2.
Zhou, Chenxi, Max R. Brown, Mark Blaxter, Shane McCarthy, & Richard Durbin. (2025). Oatk: a de novo assembly tool for complex plant organelle genomes. Genome biology. 26(1). 235–235. 5 indexed citations
3.
Lefoulon, Emilie, Kimberlee B. Beckmen, Jennifer L. Malmberg, et al.. (2024). A footworm in the door: revising Onchocerca phylogeny with previously unknown cryptic species in wild North American ungulates. International Journal for Parasitology. 55(1). 59–68. 1 indexed citations
4.
Zhang, Xiao, Mark Blaxter, Jonathan Wood, et al.. (2024). Temporal genomics in Hawaiian crickets reveals compensatory intragenomic coadaptation during adaptive evolution. Nature Communications. 15(1). 5001–5001. 5 indexed citations
5.
McCarthy, Shane, Emily A. Hornett, Matthew Gemmell, et al.. (2024). The Hypolimnas misippus Genome Supports a Common Origin of the W Chromosome in Lepidoptera. Genome Biology and Evolution. 16(10). 1 indexed citations
6.
Pardo‐Díaz, Carolina, Gabriela Montejo‐Kovacevich, W. Owen McMillan, et al.. (2024). Genomic evidence reveals three W-autosome fusions in Heliconius butterflies. PLoS Genetics. 20(7). e1011318–e1011318. 2 indexed citations
7.
8.
Ovchinnikov, Vladimir, Marcela Uliano‐Silva, Mark Wilkinson, et al.. (2023). Caecilian Genomes Reveal the Molecular Basis of Adaptation and Convergent Evolution of Limblessness in Snakes and Caecilians. Molecular Biology and Evolution. 40(5). 9 indexed citations
9.
10.
Kwon, Young Mi, Iliana Bista, Jonathan Wood, et al.. (2022). Genomic consequences of domestication of the Siamese fighting fish. Science Advances. 8(10). eabm4950–eabm4950. 23 indexed citations
11.
Zhou, Chenxi, Shane McCarthy, & Richard Durbin. (2022). YaHS: yet another Hi-C scaffolding tool. Bioinformatics. 39(1). 265 indexed citations breakdown →
12.
McCarthy, Shane, Ian A. Warren, Jonathan Wood, et al.. (2021). A high-quality, chromosome-level genome assembly of the Black Soldier Fly ( Hermetia illucens L.). G3 Genes Genomes Genetics. 11(5). 57 indexed citations
13.
Danecek, Petr, James Bonfield, Jennifer Liddle, et al.. (2021). Twelve years of SAMtools and BCFtools. GigaScience. 10(2). 6307 indexed citations breakdown →
14.
Guan, Dengfeng, Shane McCarthy, Jonathan Wood, et al.. (2020). Identifying and removing haplotypic duplication in primary genome assemblies. Bioinformatics. 36(9). 2896–2898. 636 indexed citations breakdown →
15.
McCarthy, Shane, Juan A. Galarza, Sarah Pelan, et al.. (2020). A haplotype-resolved, de novo genome assembly for the wood tiger moth ( Arctia plantaginis ) through trio binning. GigaScience. 9(8). 18 indexed citations
16.
Bonfield, James, Shane McCarthy, & Richard Durbin. (2018). Crumble: reference free lossy compression of sequence quality values. Bioinformatics. 35(2). 337–339. 18 indexed citations
17.
Danecek, Petr & Shane McCarthy. (2017). BCFtools/csq: haplotype-aware variant consequences. Bioinformatics. 33(13). 2037–2039. 255 indexed citations
18.
Bergström, Anders, Nano Nagle, Yuan Chen, et al.. (2016). Deep Roots for Aboriginal Australian Y Chromosomes. Current Biology. 26(6). 809–813. 43 indexed citations
19.
Weyden, Louise van der, Alistair G. Rust, Rebecca E. McIntyre, et al.. (2012). Jdp2 downregulates Trp53 transcription to promote leukaemogenesis in the context of Trp53 heterozygosity. Oncogene. 32(3). 397–402. 19 indexed citations
20.
McCarthy, Shane, et al.. (2011). Path to fracture in granular flows: Dynamics of contact networks. Physical Review E. 83(6). 61303–61303. 30 indexed citations

Rankless uses publication and citation data sourced from OpenAlex, an open and comprehensive bibliographic database. While OpenAlex provides broad and valuable coverage of the global research landscape, it—like all bibliographic datasets—has inherent limitations. These include incomplete records, variations in author disambiguation, differences in journal indexing, and delays in data updates. As a result, some metrics and network relationships displayed in Rankless may not fully capture the entirety of a scholar's output or impact.

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