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OpenAlex Citation Counts

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OpenAlex is a bibliographic catalogue of scientific papers, authors and institutions accessible in open access mode, named after the Library of Alexandria. It's citation coverage is excellent and I hope you will find utility in this listing of citing articles!

If you click the article title, you'll navigate to the article, as listed in CrossRef. If you click the Open Access links, you'll navigate to the "best Open Access location". Clicking the citation count will open this listing for that article. Lastly at the bottom of the page, you'll find basic pagination options.

Requested Article:

matOptimize: a parallel tree optimization method enables online phylogenetics for SARS-CoV-2
Cheng Ye, Bryan Thornlow, Angie S. Hinrichs, et al.
Bioinformatics (2022) Vol. 38, Iss. 15, pp. 3734-3740
Open Access | Times Cited: 27

Showing 1-25 of 27 citing articles:

Genomic assessment of invasion dynamics of SARS-CoV-2 Omicron BA.1
Joseph L.-H. Tsui, John T. McCrone, Ben Lambert, et al.
Science (2023) Vol. 381, Iss. 6655, pp. 336-343
Open Access | Times Cited: 41
Maximum likelihood pandemic-scale phylogenetics
Nicola De Maio, Prabhav Kalaghatgi, Yatish Turakhia, et al.
Nature Genetics (2023) Vol. 55, Iss. 5, pp. 746-752
Open Access | Times Cited: 37
MAST: Phylogenetic Inference with Mixtures Across Sites and Trees
Thomas K. F. Wong, Caitlin Cherryh, Allen G. Rodrigo, et al.
Systematic Biology (2024) Vol. 73, Iss. 2, pp. 375-391
Open Access | Times Cited: 5
Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny
Martin Hunt, Angie S. Hinrichs, D.P. Anderson, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2024)
Open Access | Times Cited: 5
CompactTree: a lightweight header-only C++ library and Python wrapper for ultra-large phylogenetics
Niema Moshiri
Gigabyte (2025) Vol. 2025
Open Access
Variant-specific introduction and dispersal dynamics of SARS-CoV-2 in New York City – from Alpha to Omicron
Simon Dellicour, Samuel L. Hong, Verity Hill, et al.
PLoS Pathogens (2023) Vol. 19, Iss. 4, pp. e1011348-e1011348
Open Access | Times Cited: 15
Online Phylogenetics with matOptimize Produces Equivalent Trees and is Dramatically More Efficient for Large SARS-CoV-2 Phylogenies than de novo and Maximum-Likelihood Implementations
Alexander Krämer, Bryan Thornlow, Cheng Ye, et al.
Systematic Biology (2023) Vol. 72, Iss. 5, pp. 1039-1051
Open Access | Times Cited: 15
Please Mind the Gap: Indel-Aware Parsimony for Fast and Accurate Ancestral Sequence Reconstruction and Multiple Sequence Alignment including Long Indels
Clara Iglhaut, Jūlija Pečerska, Manuel Gil, et al.
Molecular Biology and Evolution (2024) Vol. 41, Iss. 7
Open Access | Times Cited: 4
Robust expansion of phylogeny for fast-growing genome sequence data
Yongtao Ye, Marcus Ho-Hin Shum, Joseph L.-H. Tsui, et al.
PLoS Computational Biology (2024) Vol. 20, Iss. 2, pp. e1011871-e1011871
Open Access | Times Cited: 3
Please Mind the Gap: Indel-Aware Parsimony for Fast and Accurate Ancestral Sequence Reconstruction and Multiple Sequence Alignment including Long Indels
Clara Iglhaut, Jūlija Pečerska, Manuel Gil, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2024)
Open Access | Times Cited: 3
Rate variation and recurrent sequence errors in pandemic-scale phylogenetics
Nicola De Maio, Myrthe Willemsen, Zihao Guo, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2024)
Closed Access | Times Cited: 2
Applying the digital data and the bioinformatics tools in SARS-CoV-2 research
Meng How Tan, Jiaxin Xia, Haitao Luo, et al.
Computational and Structural Biotechnology Journal (2023) Vol. 21, pp. 4697-4705
Open Access | Times Cited: 6
Maximum likelihood pandemic-scale phylogenetics
Nicola De Maio, Prabhav Kalaghatgi, Yatish Turakhia, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2022)
Open Access | Times Cited: 10
Representing and extending ensembles of parsimonious evolutionary histories with a directed acyclic graph
Will Dumm, Mary Barker, William Howard-Snyder, et al.
Journal of Mathematical Biology (2023) Vol. 87, Iss. 5
Open Access | Times Cited: 5
The ongoing evolution of UShER during the SARS-CoV-2 pandemic
Angie S. Hinrichs, Cheng Ye, Yatish Turakhia, et al.
Nature Genetics (2023) Vol. 56, Iss. 1, pp. 4-7
Closed Access | Times Cited: 5
Variational Phylodynamic Inference Using Pandemic-scale Data
Caleb Ki, Jonathan Terhorst
Molecular Biology and Evolution (2022) Vol. 39, Iss. 8
Open Access | Times Cited: 8
Genomic assessment of invasion dynamics of SARS-CoV-2 Omicron BA.1
Joseph L.-H. Tsui, Ben Lambert, Sumali Bajaj, et al.
medRxiv (Cold Spring Harbor Laboratory) (2023)
Open Access | Times Cited: 4
Ranked Subtree Prune and Regraft
Lena Collienne, Chris Whidden, Alex Gavryushkin
Bulletin of Mathematical Biology (2024) Vol. 86, Iss. 3
Open Access | Times Cited: 1
Analysis-ready VCF at Biobank scale using Zarr
Eric Czech, Timothy R. Millar, Will Tyler, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2024)
Open Access | Times Cited: 1
CompactTree: A lightweight header-only C++ library for ultra-large phylogenetics
Niema Moshiri
bioRxiv (Cold Spring Harbor Laboratory) (2024)
Closed Access | Times Cited: 1
Efficient phylogenetic tree inference for massive taxonomic datasets: harnessing the power of a server to analyze 1 million taxa
César Piñeiro, Juan C. Pichel
GigaScience (2024) Vol. 13
Open Access | Times Cited: 1
Online Phylogenetics using Parsimony Produces Slightly Better Trees and is Dramatically More Efficient for Large SARS-CoV-2 Phylogenies than de novo and Maximum-Likelihood Approaches
Bryan Thornlow, Alexander Krämer, Cheng Ye, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2021)
Open Access | Times Cited: 11
ARA: a flexible pipeline for automated exploration of NCBI SRA datasets
Anand Maurya, M. Szymański, Wojciech M. Karłowski
GigaScience (2022) Vol. 12
Open Access | Times Cited: 3
F1ALA: ultrafast and memory-efficient ancestral lineage annotation applied to the huge SARS-CoV-2 phylogeny
Yongtao Ye, Marcus Ho-Hin Shum, Isaac Wu, et al.
Virus Evolution (2024) Vol. 10, Iss. 1
Open Access
Phylogenetic tree instability after taxon addition: empirical frequency, predictability, and consequences for online inference
Lena Collienne, Mary Barker, Marc A. Suchard, et al.
Systematic Biology (2024)
Open Access
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