
@article{marquis_zdb_2024,
  title = {{zDB}: bacterial comparative genomics made easy},
  volume = {9},
  url = {https://journals.asm.org/doi/10.1128/msystems.00473-24},
  doi = {10.1128/msystems.00473-24},
  number = {7},
  journal = {mSystems},
  author = {Marquis, Bastian and Pillonel, Trestan and Carrara, Alessia and Bertelli, Claire},
  month = {jun},
  year = {2024},
  note = {Publisher: American Society for Microbiology},
  pages = {e00473--24},
}

@article{Pallen2010,
  author = {Pallen, Mark J and Loman, Nicholas J and Penn, Charles W},
  doi = {10.1016/j.mib.2010.08.003},
  issn = {1879-0364},
  journal = {Current opinion in microbiology},
  month = {oct},
  number = {5},
  pages = {625--31},
  pmid = {20843733},
  publisher = {Elsevier Ltd},
  title = {{High-throughput sequencing and clinical microbiology: progress, opportunities and challenges.}},
  url = {http://www.ncbi.nlm.nih.gov/pubmed/20843733},
  volume = {13},
  year = {2010}
}

@article{uniprot2018uniprot,
  title={UniProt: the universal protein knowledgebase},
  author={UniProt Consortium and others},
  journal={Nucleic acids research},
  volume={46},
  number={5},
  pages={2699},
  year={2018},
  publisher={Oxford University Press},
  url={https://www.ncbi.nlm.nih.gov/pubmed/29425356}
}

@article{blanco2018blasterjs,
	title={BlasterJS: A novel interactive JavaScript visualisation component for BLAST alignment results},
	author={Blanco-M{\'\i}guez, Aitor and Fdez-Riverola, Florentino and S{\'a}nchez, Borja and Louren{\c{c}}o, An{\'a}lia},
 	journal={PLoS One},
	volume={13},
	number={10},
	pages={e0205286},
	year={2018},
	publisher={Public Library of Science San Francisco, CA USA},
	url={https://pubmed.ncbi.nlm.nih.gov/30300406/}
}

@article{parks2015checkm,
	title={CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes},
	author={Parks, Donovan H and Imelfort, Michael and Skennerton, Connor T and Hugenholtz, Philip and Tyson, Gene W},
	journal={Genome research},
	volume={25},
	number={7},
	pages={1043--1055},
	year={2015},
	publisher={Cold Spring Harbor Lab},
	url={https://pubmed.ncbi.nlm.nih.gov/25977477/}
}

@article{altschul1990basic,
	title={Basic local alignment search tool},
	author={Altschul, Stephen F and Gish, Warren and Miller, Webb and Myers, Eugene W and Lipman, David J},
	journal={Journal of molecular biology},
	volume={215},
	number={3},
	pages={403--410},
	year={1990},
	publisher={Elsevier},
	url={https://pubmed.ncbi.nlm.nih.gov/2231712/}
}

@article{lu2020cdd,
	title={CDD/SPARCLE: the conserved domain database in 2020},
	author={Lu, Shennan and Wang, Jiyao and Chitsaz, Farideh and Derbyshire, Myra K and Geer, Renata C and Gonzales, Noreen R and Gwadz, Marc and Hurwitz, David I and Marchler, Gabriele H and Song, James S and others},
	journal={Nucleic acids research},
	volume={48},
	number={D1},
	pages={D265--D268},
	year={2020},
	publisher={Oxford University Press},
	url={https://pubmed.ncbi.nlm.nih.gov/31777944/}
}

@article{aramaki2020kofamkoala,
	title={KofamKOALA: KEGG ortholog assignment based on profile HMM and adaptive score threshold},
	author={Aramaki, Takuya and Blanc-Mathieu, Romain and Endo, Hisashi and Ohkubo, Koichi and Kanehisa, Minoru and Goto, Susumu and Ogata, Hiroyuki},
	journal={Bioinformatics},
	volume={36},
	number={7},
	pages={2251--2252},
	year={2020},
	publisher={Oxford University Press},
	url={https://pubmed.ncbi.nlm.nih.gov/31742321/}
}

@article{buchfink2021sensitive,
	title={Sensitive protein alignments at tree-of-life scale using DIAMOND},
	author={Buchfink, Benjamin and Reuter, Klaus and Drost, Hajk-Georg},
	journal={Nature methods},
	volume={18},
	number={4},
	pages={366--368},
	year={2021},
	publisher={Nature Publishing Group},
	url={https://pubmed.ncbi.nlm.nih.gov/33828273/}
}


@article{kanehisa2015kegg,
  title={KEGG as a reference resource for gene and protein annotation},
  author={Kanehisa, Minoru and Sato, Yoko and Kawashima, Masayuki and Furumichi, Miho and Tanabe, Mao},
  journal={Nucleic acids research},
  volume={44},
  number={D1},
  pages={D457--D462},
  year={2015},
  publisher={Oxford University Press},
  url={https://www.ncbi.nlm.nih.gov/pubmed/26476454}
}

@article{bardou2014jvenn,
  title={jvenn: an interactive Venn diagram viewer},
  author={Bardou, Philippe and Mariette, Jérôme and Escudié, Fédéric and Djemiel, Christophe and Klopp, Christophe},
  journal={BMC bioinformatics},
  volume={15},
  number={1},
  pages={293},
  year={2014},
  publisher={BioMed Central},
  url={https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4261873/}
}

@article{huerta2016ete,
  title={ETE 3: reconstruction, analysis, and visualization of phylogenomic data},
  author={Huerta-Cepas, Jaime and Serra, François and Bork, Peer},
  journal={Molecular biology and evolution},
  volume={33},
  number={6},
  pages={1635--1638},
  year={2016},
  publisher={Society for Molecular Biology and Evolution},
  url={https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4868116/}
}


@article{finn2015pfam,
  title={The Pfam protein families database: towards a more sustainable future},
  author={Finn, Robert D and Coggill, Penelope and Eberhardt, Ruth Y and Eddy, Sean R and Mistry, Jaina and Mitchell, Alex L and Potter, Simon C and Punta, Marco and Qureshi, Matloob and Sangrador-Vegas, Amaia and others},
  journal={Nucleic acids research},
  volume={44},
  number={D1},
  pages={D279--D285},
  year={2015},
  publisher={Oxford University Press},
  url={https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702930/}
}

@article{galperin2014expanded,
  title={Expanded microbial genome coverage and improved protein family annotation in the COG database},
  author={Galperin, Michael Y and Makarova, Kira S and Wolf, Yuri I and Koonin, Eugene V},
  journal={Nucleic acids research},
  volume={43},
  number={D1},
  pages={D261--D269},
  year={2014},
  publisher={Oxford University Press},
  url={https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383993/}
}

@article{emms2015orthofinder,
  title={OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy},
  author={Emms, David M and Kelly, Steven},
  journal={Genome biology},
  volume={16},
  number={1},
  pages={157},
  year={2015},
  publisher={BioMed Central},
  url={https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4531804/}
}


@article{krzywinski2009circos,
  title={Circos: An information aesthetic for comparative genomics},
  author={Krzywinski, Martin and Schein, Jacqueline and Birol, Inanç and Connors, Joseph and Gascoyne, Randy and Horsman, Doug and Jones, Steven J and Marra, Marco A},
  journal={Genome Research},
  volume={19},
  number={9},
  pages={1639},
  year={2009},
  publisher={Cold Spring Harbor Laboratory Press},
  url={https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2752132/}
}

@article{haft2017refseq,
  title={RefSeq: an update on prokaryotic genome annotation and curation},
  author={Haft, Daniel H and DiCuccio, Michael and Badretdin, Azat and Brover, Vyacheslav and Chetvernin, Vyacheslav and O’Neill, Kathleen and Li, Wenjun and Chitsaz, Farideh and Derbyshire, Myra K and Gonzales, Noreen R and others},
  journal={Nucleic acids research},
  volume={46},
  number={D1},
  pages={D851--D860},
  year={2017},
  publisher={Oxford University Press},
  url={https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753331/}
}

@article{katoh2013mafft,
  title={MAFFT multiple sequence alignment software version 7: improvements in performance and usability},
  author={Katoh, Kazutaka and Standley, Daron M},
  journal={Molecular biology and evolution},
  volume={30},
  number={4},
  pages={772--780},
  year={2013},
  publisher={Society for Molecular Biology and Evolution},
  url={https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3603318/}
}

@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},
  url={https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2835736/}
}

@article{federhen2011ncbi,
  title={The NCBI taxonomy database},
  author={Federhen, Scott},
  journal={Nucleic acids research},
  volume={40},
  number={D1},
  pages={D136--D143},
  year={2011},
  publisher={Oxford University Press},
  url={https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245000/}
}


@article{kanehisa2019kegg,
  title={KEGG Mapper for inferring cellular functions from protein sequences},
  author={Kanehisa, Minoru and Sato, Yoko},
  journal={Protein Science},
  volume={-},
  number={-},
  pages={-},
  year={2019},
  publisher={Wiley Online Library},
  url={https://www.ncbi.nlm.nih.gov/pubmed/31423653}
}

@article{di2017nextflow,
  title={Nextflow enables reproducible computational workflows},
  author={Di Tommaso, Paolo and Chatzou, Maria and Floden, Evan W and Barja, Pablo Prieto and Palumbo, Emilio and Notredame, Cedric},
  journal={Nature biotechnology},
  volume={35},
  number={4},
  pages={316},
  year={2017},
  publisher={Nature Publishing Group},
  url={https://www.ncbi.nlm.nih.gov/pubmed/28398311}
}

@Article{Feldgarden2021,
  author={Feldgarden, Michael and Brover, Vyacheslav and Gonzalez-Escalona, Narjol and Frye, Jonathan G. and Haendiges, Julie and Haft, Daniel H. and Hoffmann, Maria and Pettengill, James B. and Prasad, Arjun B. and Tillman, Glenn E. and Tyson, Gregory H. and Klimke, William},
  title={AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence},
  journal={Scientific Reports},
  year={2021},
  month={Jun},
  day={16},
  volume={11},
  number={1},
  pages={12728},
  doi={10.1038/s41598-021-91456-0},
  url={https://doi.org/10.1038/s41598-021-91456-0}
}

@Article{Roder2024,
  author={Roder, Thomas and Pimentel, Gr{\'e}gory and Fuchsmann, Pascal and Stern, Mireille Tena and von Ah, Ueli and Verg{\`e}res, Guy and Peischl, Stephan and Brynildsrud, Ola and Bruggmann, R{\'e}my and B{\"a}r, Cornelia},
  title={Scoary2: rapid association of phenotypic multi-omics data with microbial pan-genomes},
  journal={Genome Biology},
  year={2024},
  month={Apr},
  day={11},
  volume={25},
  number={1},
  pages={93},
  issn={1474-760X},
  doi={10.1186/s13059-024-03233-7},
  url={https://doi.org/10.1186/s13059-024-03233-7}
}

@article{doi:10.1128/msystems.00039-17,
  author = {Morgan N. Price and Adam P. Arkin},
  title = {PaperBLAST: Text Mining Papers for Information about Homologs},
  journal = {mSystems},
  volume = {2},
  number = {4},
  pages = {10.1128/msystems.00039-17},
  year = {2017},
  doi = {10.1128/msystems.00039-17},
  URL = {https://journals.asm.org/doi/abs/10.1128/msystems.00039-17}
}

