Viruses as living processes

Bapteste, 2009, Prokaryotic evolution and the tree of life are two different things, Biology Direct, 4, 1

Barr, 2013, Bacteriophage adhering to mucus provide a non–host-derived immunity, Proceedings of the National Academy of Sciences, 110, 10771, 10.1073/pnas.1305923110

Bouchard, 2013

Bravo, 2012, Communication between gastrointestinal bacteria and the nervous system, Current Opinion in Pharmacology, 12, 667, 10.1016/j.coph.2012.09.010

Brüssow, 2002, Phage genomics: small is beautiful, Cell, 108, 13, 10.1016/S0092-8674(01)00637-7

Chu, 2013, Innate immune recognition of the microbiota promotes host-microbial symbiosis, Nature Immunology, 14, 668, 10.1038/ni.2635

Delwart, 2013, A roadmap to the human virome, PLoS Pathogens, 9, e1003146, 10.1371/journal.ppat.1003146

Dupré, 2005, Are there genes?, 193

Dupré, 2012

Dupré, 2009, Varieties of living things: life at the intersection of lineage and metabolism, Philosophy & Theory in Biology, 1, 10.3998/ptb.6959004.0001.003

Griffiths, 2001, Endogenous retroviruses in the human genome sequence, Genome Biology, 2, 1017, 10.1186/gb-2001-2-6-reviews1017

2016

Guttinger, S. Towards a process ontology for macromolecular biology. In J. Dupré & D. Nicholson (Eds.), Everything flows: Towards a processual philosophy of biology. Oxford University Press (in press).

Guttinger, 2009, Orchestrating nuclear envelope disassembly and reassembly during mitosis, Nature Reviews Molecular Cell Biology, 10, 178, 10.1038/nrm2641

Haig, 2012, Retroviruses and the placenta, Current Biology, 22, R609, 10.1016/j.cub.2012.06.002

Hehemann, 2010, Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota, Nature, 464, 908, 10.1038/nature08937

Henning, 2013, Of termites and men: on the ontology of collective individuals, 233

La Scola, 2008, The virophage as a unique parasite of the giant mimivirus, Nature, 455, 100, 10.1038/nature07218

Lander, 2001, Initial sequencing and analysis of the human genome, Nature, 409, 860, 10.1038/35057062

Lecuit, 2013, The human virome: new tools and concepts, Trends in Microbiology, 21, 510, 10.1016/j.tim.2013.07.001

Lieberman, 2008, Chromatin organization and virus gene expression, Journal of Cellular Physiology, 216, 295, 10.1002/jcp.21421

Méthot, 2014, What is a pathogen? Towards a process view of host-parasite interactions, Virulence, 5, 775, 10.4161/21505594.2014.960726

Mindell, 1992, Phylogenetic consequences of symbioses: eukarya and eubacteria are not monophyletic taxa, BioSystems, 27, 53, 10.1016/0303-2647(92)90046-2

Minot, 2011, The human gut virome: inter-individual variation and dynamic response to diet, Genome Research, 21, 1616, 10.1101/gr.122705.111

Noble, 2006

Nogawa, 1996, Cloning and characterization of mycovirus double-stranded RNA from the plant pathogenic fungus, Fusarium solani f. sp. Robiniae, Bioscience, Biotechnology, and Biochemistry, 60, 784, 10.1271/bbb.60.784

Philippot, 2013, Going back to the roots: the microbial ecology of the rhizosphere, Nature Reviews Microbiology, 11, 789, 10.1038/nrmicro3109

Pradeu, 2006, The self model and the conception of biological identity in immunology, Biology and Philosophy, 21, 235, 10.1007/s10539-005-8621-6

Rescher, 1996

Reyes, 2010, Viruses in the faecal microbiota of monozygotic twins and their mothers, Nature, 466, 334, 10.1038/nature09199

Rohwer, 2002, Diversity and distribution of coral-associated bacteria, Marine Ecology Progress Series, 243, 1, 10.3354/meps243001

Rosenberg, 2007, The role of microorganisms in coral health, disease and evolution, Nature Reviews Microbiology, 5, 355, 10.1038/nrmicro1635

Round, 2009, The gut microbiota shapes intestinal immune response during health and disease, Nature Reviews Immunology, 9, 313, 10.1038/nri2515

Sherratt, 1974, Bacterial plasmids, Cell, 3, 189, 10.1016/0092-8674(74)90130-5

Smillie, 2010, Mobility of plasmids, Microbiol and Molecular Biology Reviews, 74, 434, 10.1128/MMBR.00020-10

Spasova, 2014, Blowing on embers: commensal microbiota and our immune system, Frontiers in Immunology, 5, 318, 10.3389/fimmu.2014.00318

Suttle, 2007, Marine viruses — major players in the global ecosystem, Nature Reviews Microbiology, 5, 801, 10.1038/nrmicro1750

Turnbaugh, 2007, The human microbiome project, Nature, 449, 804, 10.1038/nature06244

Whitman, 1998, Prokaryotes: The unseen majority, Proceedings of the National Academy of Sciences, 95, 6578, 10.1073/pnas.95.12.6578

Wylie, 2012, Emerging view of the human virome, Translational Research: the Journal of Laboratory and Clinical Medicine, 160, 283, 10.1016/j.trsl.2012.03.006