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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:

PPR-Meta: a tool for identifying phages and plasmids from metagenomic fragments using deep learning
Zhencheng Fang, Jie Tan, Shu‐Fang Vivienne Wu, et al.
GigaScience (2019) Vol. 8, Iss. 6
Open Access | Times Cited: 161

Showing 1-25 of 161 citing articles:

VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences
Kristopher Kieft, Zhichao Zhou, Karthik Anantharaman
Microbiome (2020) Vol. 8, Iss. 1
Open Access | Times Cited: 786
Identifying viruses from metagenomic data using deep learning
Jie Ren, Kai Song, Chao Deng, et al.
Quantitative Biology (2020) Vol. 8, Iss. 1, pp. 64-77
Open Access | Times Cited: 477
Identification of mobile genetic elements with geNomad
Antônio Pedro Camargo, Simon Roux, Frederik Schulz, et al.
Nature Biotechnology (2023) Vol. 42, Iss. 8, pp. 1303-1312
Open Access | Times Cited: 198
PHASTEST: faster than PHASTER, better than PHAST
David S. Wishart, Scott Han, Sukanta Saha, et al.
Nucleic Acids Research (2023) Vol. 51, Iss. W1, pp. W443-W450
Open Access | Times Cited: 171
Genomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance
Patrick Munk, Christian Brinch, Frederik Duus Møller, et al.
Nature Communications (2022) Vol. 13, Iss. 1
Open Access | Times Cited: 167
Host and infectivity prediction of Wuhan 2019 novel coronavirus using deep learning algorithm
Qian Guo, Mo Li, Chunhui Wang, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2020)
Open Access | Times Cited: 157
You can move, but you can't hide: identification of mobile genetic elements with geNomad
Antônio Pedro Camargo, Simon Roux, Frederik Schulz, et al.
bioRxiv (Cold Spring Harbor Laboratory) (2023)
Open Access | Times Cited: 46
Diverse plasmid systems and their ecology across human gut metagenomes revealed by PlasX and MobMess
Michael Yu, Emily C. Fogarty, A. Murat Eren
Nature Microbiology (2024) Vol. 9, Iss. 3, pp. 830-847
Open Access | Times Cited: 21
A unified compendium of prokaryotic and viral genomes from over 300 anaerobic digestion microbiomes
Victor Borin Centurion, Alessandro Rossi, Esteban Orellana, et al.
Environmental Microbiome (2024) Vol. 19, Iss. 1
Open Access | Times Cited: 19
Seeker: alignment-free identification of bacteriophage genomes by deep learning
Noam Auslander, Ayal B. Gussow, Sean Benler, et al.
Nucleic Acids Research (2020) Vol. 48, Iss. 21, pp. e121-e121
Open Access | Times Cited: 107
Incorporating Machine Learning into Established Bioinformatics Frameworks
Noam Auslander, Ayal B. Gussow, Eugene V. Koonin
International Journal of Molecular Sciences (2021) Vol. 22, Iss. 6, pp. 2903-2903
Open Access | Times Cited: 86
DeePhage: distinguishing virulent and temperate phage-derived sequences in metavirome data with a deep learning approach
Shu‐Fang Vivienne Wu, Zhencheng Fang, Jie Tan, et al.
GigaScience (2021) Vol. 10, Iss. 9
Open Access | Times Cited: 62
Gauge your phage: benchmarking of bacteriophage identification tools in metagenomic sequencing data
Siu Fung Stanley Ho, Nicole E. Wheeler, Andrew Millard, et al.
Microbiome (2023) Vol. 11, Iss. 1
Open Access | Times Cited: 33
PLASMe: a tool to identify PLASMid contigs from short-read assemblies using transformer
Xubo Tang, Jiayu Shang, Yongxin Ji, et al.
Nucleic Acids Research (2023) Vol. 51, Iss. 15, pp. e83-e83
Open Access | Times Cited: 31
Phage-inclusive profiling of human gut microbiomes with Phanta
Yishay Pinto, Meenakshi Chakraborty, Navami Jain, et al.
Nature Biotechnology (2023) Vol. 42, Iss. 4, pp. 651-662
Closed Access | Times Cited: 28
Benchmarking bioinformatic virus identification tools using real-world metagenomic data across biomes
Ling-Yi Wu, Yasas Wijesekara, Gonçalo J. Piedade, et al.
Genome biology (2024) Vol. 25, Iss. 1
Open Access | Times Cited: 13
Metagenomic absolute quantification of antibiotic resistance genes and virulence factor genes-carrying bacterial genomes in anaerobic digesters
Chunxiao Wang, Xiaole Yin, Xiaoqing Xu, et al.
Water Research (2024) Vol. 253, pp. 121258-121258
Closed Access | Times Cited: 12
Beneath the surface: Unsolved questions in soil virus ecology
Christina Hazard, Karthik Anantharaman, Luke S. Hillary, et al.
Soil Biology and Biochemistry (2025), pp. 109780-109780
Open Access | Times Cited: 1
Challenges of Studying the Human Virome – Relevant Emerging Technologies
Mohammadali Khan Mirzaei, Jinling Xue, Rita Costa, et al.
Trends in Microbiology (2020) Vol. 29, Iss. 2, pp. 171-181
Open Access | Times Cited: 66
Accurate identification of bacteriophages from metagenomic data using Transformer
Jiayu Shang, Xubo Tang, Ruocheng Guo, et al.
Briefings in Bioinformatics (2022) Vol. 23, Iss. 4
Open Access | Times Cited: 33
A deep learning approach reveals unexplored landscape of viral expression in cancer
Abdurrahman Elbasir, Ying Ye, Daniel E. Schäffer, et al.
Nature Communications (2023) Vol. 14, Iss. 1
Open Access | Times Cited: 20
VIRify: An integrated detection, annotation and taxonomic classification pipeline using virus-specific protein profile hidden Markov models
Guillermo Rangel-Piñeros, Alexandre Almeida, Martín Beracochea, et al.
PLoS Computational Biology (2023) Vol. 19, Iss. 8, pp. e1011422-e1011422
Open Access | Times Cited: 19
Viruses under the Antarctic Ice Shelf are active and potentially involved in global nutrient cycles
Javier López-Simón, Marina Vila‐Nistal, Aleksandra Rosenova, et al.
Nature Communications (2023) Vol. 14, Iss. 1
Open Access | Times Cited: 19
Evaluation of computational phage detection tools for metagenomic datasets
Kenneth Schackart, Jessica B. Graham, Alise J. Ponsero, et al.
Frontiers in Microbiology (2023) Vol. 14
Open Access | Times Cited: 18
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