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Citations
SHANG Jiayu edited this page Oct 23, 2024
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The PhaBOX 2.0v has not been formally published in a journal. But if you want to cite our tools, feel free to use the citations listed below:
- PhaBOX (The long-term support package)
Jiayu Shang, Cheng Peng, Herui Liao, Xubo Tang, Yanni Sun, PhaBOX: a web server for identifying and characterizing phage contigs in metagenomic data, Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad101, https://doi.org/10.1093/bioadv/vbad101
- Each independent pipeline
# PhaMer (virus identification)
Jiayu Shang, Xubo Tang, Ruocheng Guo, Yanni Sun, Accurate identification of bacteriophages from metagenomic data using Transformer, Briefings in Bioinformatics, 2022;, bbac258, https://doi.org/10.1093/bib/bbac258
# PhaGCN (taxonomy classification)
Jiayu Shang, Jingzhe Jiang, Yanni Sun, Bacteriophage classification for assembled contigs using graph convolutional network, Bioinformatics, Volume 37, Issue Supplement_1, July 2021, Pages i25–i33, https://doi.org/10.1093/bioinformatics/btab293
# Cherry (host prediction)
Jiayu Shang, Yanni Sun, CHERRY: a Computational metHod for accuratE pRediction of virus–pRokarYotic interactions using a graph encoder–decoder model, Briefings in Bioinformatics, 2022;, bbac182, https://doi.org/10.1093/bib/bbac182
# PhaTYP (Lifestyle prediction)
Jiayu Shang, Xubo Tang, Yanni Sun, PhaTYP: predicting the lifestyle for bacteriophages using BERT, Briefings in Bioinformatics, 2022;, bbac487, https://doi.org/10.1093/bib/bbac487
- PhaBOX (The long-term support package)
@article{shang2023phabox,
title={PhaBOX: a web server for identifying and characterizing phage contigs in metagenomic data},
author={Shang, Jiayu and Peng, Cheng and Liao, Herui and Tang, Xubo and Sun, Yanni},
journal={Bioinformatics advances},
volume={3},
number={1},
pages={vbad101},
year={2023},
publisher={Oxford University Press}
}
- Each independent pipeline
# PhaMer (virus identification)
@article{shang2022accurate,
title={Accurate identification of bacteriophages from metagenomic data using Transformer},
author={Shang, Jiayu and Tang, Xubo and Guo, Ruocheng and Sun, Yanni},
journal={Briefings in Bioinformatics},
volume={23},
number={4},
pages={bbac258},
year={2022},
publisher={Oxford University Press}
}
# PhaGCN (taxonomy classification)
@article{shang2021bacteriophage,
title={Bacteriophage classification for assembled contigs using graph convolutional network},
author={Shang, Jiayu and Jiang, Jingzhe and Sun, Yanni},
journal={Bioinformatics},
volume={37},
number={Supplement\_1},
pages={i25--i33},
year={2021},
publisher={Oxford University Press}
}
# Cherry (host prediction)
@article{shang2022cherry,
title={CHERRY: a Computational metHod for accuratE pRediction of virus--pRokarYotic interactions using a graph encoder--decoder model},
author={Shang, Jiayu and Sun, Yanni},
journal={Briefings in Bioinformatics},
volume={23},
number={5},
pages={bbac182},
year={2022},
publisher={Oxford University Press}
}
# PhaTYP (Lifestyle prediction)
@article{shang2023phatyp,
title={PhaTYP: predicting the lifestyle for bacteriophages using BERT},
author={Shang, Jiayu and Tang, Xubo and Sun, Yanni},
journal={Briefings in Bioinformatics},
volume={24},
number={1},
pages={bbac487},
year={2023},
publisher={Oxford University Press}
}
In the design of the PhaBOX package, we were inspired by the idea of some methods and we loaded some modules for generating the results. We acknowledge these tools and also list the names below:
- The methods we directly loaded
# Diamond
Buchfink, B., Xie, C., & Huson, D. H. (2015). Fast and sensitive protein alignment using DIAMOND. Nature methods, 12(1), 59-60.
@article{buchfink2015fast,
title={Fast and sensitive protein alignment using DIAMOND},
author={Buchfink, Benjamin and Xie, Chao and Huson, Daniel H},
journal={Nature methods},
volume={12},
number={1},
pages={59--60},
year={2015},
publisher={Nature Publishing Group US New York}
}
# prodigal-gv
Camargo, A. P., Roux, S., Schulz, F., Babinski, M., Xu, Y., Hu, B., ... & Kyrpides, N. C. (2023). Identification of mobile genetic elements with geNomad. Nature Biotechnology, 1-10.
@article{camargo2023identification,
title={Identification of mobile genetic elements with geNomad},
author={Camargo, Antonio Pedro and Roux, Simon and Schulz, Frederik and Babinski, Michal and Xu, Yan and Hu, Bin and Chain, Patrick SG and Nayfach, Stephen and Kyrpides, Nikos C},
journal={Nature Biotechnology},
pages={1--10},
year={2023},
publisher={Nature Publishing Group US New York}
}
# mafft
Katoh, K., Kuma, K. I., Toh, H., & Miyata, T. (2005). MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic acids research, 33(2), 511-518.
@article{katoh2008recent,
title={Recent developments in the MAFFT multiple sequence alignment program},
author={Katoh, Kazutaka and Toh, Hiroyuki},
journal={Briefings in bioinformatics},
volume={9},
number={4},
pages={286--298},
year={2008},
publisher={Oxford University Press}
}
# FastTree
Price, M. N., Dehal, P. S., & Arkin, A. P. (2010). FastTree 2–approximately maximum-likelihood trees for large alignments. PloS one, 5(3), e9490.
@article{price2010fasttree,
title={FastTree 2--approximately maximum-likelihood trees for large alignments},
author={Price, Morgan N and Dehal, Paramvir S and Arkin, Adam P},
journal={PloS one},
volume={5},
number={3},
pages={e9490},
year={2010},
publisher={Public Library of Science San Francisco, USA}
}
- The methods we were inspired from
# vOTU
Nayfach, S., Páez-Espino, D., Call, L., Low, S. J., Sberro, H., Ivanova, N. N., ... & Kyrpides, N. C. (2021). Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome. Nature microbiology, 6(7), 960-970.
@article{nayfach2021metagenomic,
title={Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome},
author={Nayfach, Stephen and P{\'a}ez-Espino, David and Call, Lee and Low, Soo Jen and Sberro, Hila and Ivanova, Natalia N and Proal, Amy D and Fischbach, Michael A and Bhatt, Ami S and Hugenholtz, Philip and others},
journal={Nature microbiology},
volume={6},
number={7},
pages={960--970},
year={2021},
publisher={Nature Publishing Group UK London}
}
# CheckV
Nayfach, S., Camargo, A. P., Schulz, F., Eloe-Fadrosh, E., Roux, S., & Kyrpides, N. C. (2021). CheckV assesses the quality and completeness of metagenome-assembled viral genomes. Nature biotechnology, 39(5), 578-585.
@article{nayfach2021checkv,
title={CheckV assesses the quality and completeness of metagenome-assembled viral genomes},
author={Nayfach, Stephen and Camargo, Antonio Pedro and Schulz, Frederik and Eloe-Fadrosh, Emiley and Roux, Simon and Kyrpides, Nikos C},
journal={Nature biotechnology},
volume={39},
number={5},
pages={578--585},
year={2021},
publisher={Nature Publishing Group US New York}
}
# CAT
Von Meijenfeldt, F. B., Arkhipova, K., Cambuy, D. D., Coutinho, F. H., & Dutilh, B. E. (2019). Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT. Genome biology, 20, 1-14.
@article{von2019robust,
title={Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT},
author={Von Meijenfeldt, FA Bastiaan and Arkhipova, Ksenia and Cambuy, Diego D and Coutinho, Felipe H and Dutilh, Bas E},
journal={Genome biology},
volume={20},
pages={1--14},
year={2019},
publisher={Springer}
}