Decoupling of strain- and intrastrain-level interactions of microbiomes in a sponge holobiont
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DOI: 10.1038/s41467-024-52464-6
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- Chirag Jain & Luis M. Rodriguez-R & Adam M. Phillippy & Konstantinos T. Konstantinidis & Srinivas Aluru, 2018. "High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries," Nature Communications, Nature, vol. 9(1), pages 1-8, December.
- Ravi K Patel & Mukesh Jain, 2012. "NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data," PLOS ONE, Public Library of Science, vol. 7(2), pages 1-7, February.
- Joachim Johansen & Damian R. Plichta & Jakob Nybo Nissen & Marie Louise Jespersen & Shiraz A. Shah & Ling Deng & Jakob Stokholm & Hans Bisgaard & Dennis Sandris Nielsen & Søren J. Sørensen & Simon Ras, 2022. "Genome binning of viral entities from bulk metagenomics data," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
- Darrin T. Schultz & Steven H. D. Haddock & Jessen V. Bredeson & Richard E. Green & Oleg Simakov & Daniel S. Rokhsar, 2023. "Ancient gene linkages support ctenophores as sister to other animals," Nature, Nature, vol. 618(7963), pages 110-117, June.
- Chris S. Smillie & Mark B. Smith & Jonathan Friedman & Otto X. Cordero & Lawrence A. David & Eric J. Alm, 2011. "Ecology drives a global network of gene exchange connecting the human microbiome," Nature, Nature, vol. 480(7376), pages 241-244, December.
- Hannah G. Hampton & Bridget N. J. Watson & Peter C. Fineran, 2020. "The arms race between bacteria and their phage foes," Nature, Nature, vol. 577(7790), pages 327-336, January.
- Torsten Thomas & Lucas Moitinho-Silva & Miguel Lurgi & Johannes R. Björk & Cole Easson & Carmen Astudillo-García & Julie B. Olson & Patrick M. Erwin & Susanna López-Legentil & Heidi Luter & Andia Chav, 2016. "Diversity, structure and convergent evolution of the global sponge microbiome," Nature Communications, Nature, vol. 7(1), pages 1-12, September.
- Yiqiang Chen & Yulin Wang & David Paez-Espino & Martin F. Polz & Tong Zhang, 2021. "Prokaryotic viruses impact functional microorganisms in nutrient removal and carbon cycle in wastewater treatment plants," Nature Communications, Nature, vol. 12(1), pages 1-11, December.
- Yuxuan Du & Jed A. Fuhrman & Fengzhu Sun, 2023. "ViralCC retrieves complete viral genomes and virus-host pairs from metagenomic Hi-C data," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
- Kimberley D. Seed & David W. Lazinski & Stephen B. Calderwood & Andrew Camilli, 2013. "A bacteriophage encodes its own CRISPR/Cas adaptive response to evade host innate immunity," Nature, Nature, vol. 494(7438), pages 489-491, February.
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