81
References
Alberts B, Johnson A, Lewis J et al (2008) Molecular biology of the
cell. Garland Science, New York
Almeida MI, Reis RM, Calin GA (2011) MicroRNA history: discovery,
recent applications, and next frontiers. Mutat Res – Fundam Mol
Mech Mutagen 717:1–8
Amann R, Rosselló-Móra R (2016) After all, only millions? MBio
7(4):e00999–16
Andrews KR, Good JM, Miller MR et al (2016) Harnessing the power
of RADseq for ecological and evolutionary genomics. Nat Rev
Genet 17:81–92
Avery OT, Macleod CM, McCarty M (1943) Studies on the chemical
nature of the substance inducing transformation of pneumococcal
types: induction of transformation by a Desoxyribonucleic acid fraction isolated from Pneumococcus type III. J Exp Med 79:137–158
Baumgarten S, Simakov O, Esherick LY et al (2015) The genome of
Aiptasia, a sea anemone model for coral symbiosis. Proc Natl Acad
Sci USA 112:11893–11898
Beale DJ, Karpe AV, Ahmed W (2016) Beyond metabolomics: a review
of multi-omics-based approaches. In: Beale DJ, Kouremenos
KA, Palombo A (eds) Microbial metabolomics. Springer, Cham,
pp 289–312
Biagi E, Candela M, Fairweather-Tait S et al (2012) Ageing of the
human metaorganism: the microbial counterpart. Age 34:247–267
Bock C, Farlik M, Sheffield NC (2016) Multi-omics of single cells:
strategies and applications. Trends Biotechnol 34:605–608
Bosch TCG, Miller DJ (2016) The Holobiont imperative. Springer,
Vienna
Brüwer JD, Voolstra CR (2018) First insight into the viral community
of the cnidarian model metaorganism Aiptasia using RNA-Seq data.
PeerJ 6:e4449
Brüwer JD, Agrawal S, Liew YJ et al (2017) Association of coral algal
symbionts with a diverse viral community responsive to heat shock.
BMC Microbiol 17:174
Buck-Wiese H, Voolstra CR, Brüwer JD (2016) The metaorganism
frontier – incorporating microbes into the organism’s response
to environmental change. In: Bode M, Jessen C, Golz V (eds)
YOUMARES 7 conference proceedings, pp 94–102
Cherf GM, Lieberman KR, Rashid H et al (2012) Automated forward
and reverse ratcheting of DNA in a nanopore at 5-A precision. Nat
Biotechnol 30:344–348
Dahm R (2005) Friedrich Miescher and the discovery of DNA. Dev
Biol 278:274–288
Dalsgaard J, John MS, Kattner G et al (2003) Fatty acid trophic markers
in the pelagic marine environment. Adv Mar Biol 46:225–340
Delorme-Axford E, Donker RB, Mouillet J-F et al (2013) Human placental trophoblasts confer viral resistance to recipient cells. Proc
Natl Acad Sci U S A 110:12048–12053
Dewar ML, Arnould JPY, Dann P et al (2013) Interspecific variations
in the gastrointestinal microbiota in penguins. MicrobiologyOpen
2:195–204
Dewar ML, Arnould JPY, Krause L et al (2014) Influence of fasting during moult on the faecal microbiota of penguins. PLoS One 9:e99996
Dick GJ (2017) Embracing the mantra of modellers and synthesizing
omics, experiments and models. Environ Microbiol Rep 9:18–20
Epstein SS (2013) The phenomenon of microbial uncultivability. Curr
Opin Microbiol 16:636–642
Fauquet CM, Mayo MA (2001) The 7th ICTV report. Arch Virol
146:189–194
Feng Y, Zhang Y, Ying C et al (2015) Nanopore-based fourth-generation
DNA sequencing technology. Genomics Proteomics Bioinf 13:4–16
Freilich S, Zarecki R, Eilam O et al (2011) Competitive and cooperative metabolic interactions in bacterial communities. Nat Commun
2:589
Gaby JC, Buckley DH (2012) A comprehensive evaluation of PCR
primers to amplify the nifH gene of nitrogenase. PLoS One 7:e42149
Geiss GK, Bumgarner RE, Birditt B et al (2008) Direct multiplexed
measurement of gene expression with color-coded probe pairs. Nat
Biotechnol 26:317–325
Gillooly JF, Allen AP, West GB et al (2005) The rate of DNA evolution:
effects of body size and temperature on the molecular clock. Proc
Natl Acad Sci U S A 102:140–145
Gottlieb A (2017) Untersuchungen zur Expression ausgewählter Stammzellgene an embryonalen Geweben und Tumoren.
Dissertation, Universität Bremen
Graeve M, Kattner G, Hagen W (1994) Diet-induced changes in the
fatty acid composition of Arctic herbivorous copepods: experimental evidence of trophic markers. J Exp Mar Biol Ecol 182:97–110
Handelsman J (2004) Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev 68:669–685
Hernandez-Agreda A, Leggat W, Bongaerts P, Ainsworth D (2016) The
microbial signature provides insight into the mechanistic basis of
coral success across reef habitats. MBio 7:e00560–e00516
IPCC (2007) Climate change 2007: The physical science basis.
Summary for policymakers. Contribution of working group I to the
fourth assessment report of the intergovernmental panel on climate
change. Cambridge University Press, Cambridge
IPCC (2014) Climate change 2014: Synthesis report. Contribution of
working groups I, II and III to the fifth assessment report of the
intergovernmental panel on climate change. IPCC, Geneva
Jones OAH, Sdepanian S, Lofts S et al (2014) Metabolomic analysis
of soil communities can be used for pollution assessment. Environ
Toxicol Chem 33:61–64
Kanehisa M, Sato Y, Kawashima M et al (2016) KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res
44:D457–D462
Kanehisa M, Furumichi M, Tanabe M et al (2017) KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res
45:D353–D361
Kim BM, Kim J, Choi IY et al (2016) Omics of the marine medaka
(Oryzias melastigma) and its relevance to marine environmental
research. Mar Environ Res 113:141–152
Kimes NE, Callaghan AV, Aktas DF et al (2013) Metagenomic analysis and metabolite profiling of deep-sea sediments from the Gulf of
Mexico following the Deepwater Horizon oil spill. Front Microbiol
4:50
Klug WS, Spencer CA, Palladino MA (2012) Concepts of genetics,
10th edn. Pearson Education, San Francisco
Leary DH, Li RW, Hamdan LJ et al (2014) Integrated metagenomic and
metaproteomic analyses of marine biofilm communities. Biofouling
30:1211–1223
Levin RA, Voolstra CR, Weynberg KD et al (2017) Evidence for a role
of viruses in the thermal sensitivity of coral photosymbionts. ISME
J 11:808–812
Liew YJ, Li Y, Baumgarten S et al (2017) Condition-specific RNA editing in the coral symbiont Symbiodinium microadriaticum. PLoS
Genet 13:1–22
Liu Y, Beyer A, Aebersold R (2016) On the dependency of cellular protein levels on mRNA abundance. Cell 165:535–550
Llewellyn CA, Sommer U, Dupont CL et al (2015) Using community
metabolomics as a new approach to discriminate marine microbial
particulate organic matter in the western English Channel. Prog
Oceanogr 137:421–433
Lu H, Giordano F, Ning Z (2016) Oxford Nanopore MinION sequencing and genome assembly. Genomics Proteomics Bioinf 14:265–279
Luo S-S, Ishibashi O, Ishikawa G et al (2009) Human villous trophoblasts express and secrete placenta-specific microRNAs into maternal circulation via exosomes. Biol Reprod 81:717–729
Reading the Book of Life – Omics as a Universal Tool Across Disciplines
References
Alberts B, Johnson A, Lewis J et al (2008) Molecular biology of the
cell. Garland Science, New York
Almeida MI, Reis RM, Calin GA (2011) MicroRNA history: discovery,
recent applications, and next frontiers. Mutat Res – Fundam Mol
Mech Mutagen 717:1–8
Amann R, Rosselló-Móra R (2016) After all, only millions? MBio
7(4):e00999–16
Andrews KR, Good JM, Miller MR et al (2016) Harnessing the power
of RADseq for ecological and evolutionary genomics. Nat Rev
Genet 17:81–92
Avery OT, Macleod CM, McCarty M (1943) Studies on the chemical
nature of the substance inducing transformation of pneumococcal
types: induction of transformation by a Desoxyribonucleic acid fraction isolated from Pneumococcus type III. J Exp Med 79:137–158
Baumgarten S, Simakov O, Esherick LY et al (2015) The genome of
Aiptasia, a sea anemone model for coral symbiosis. Proc Natl Acad
Sci USA 112:11893–11898
Beale DJ, Karpe AV, Ahmed W (2016) Beyond metabolomics: a review
of multi-omics-based approaches. In: Beale DJ, Kouremenos
KA, Palombo A (eds) Microbial metabolomics. Springer, Cham,
pp 289–312
Biagi E, Candela M, Fairweather-Tait S et al (2012) Ageing of the
human metaorganism: the microbial counterpart. Age 34:247–267
Bock C, Farlik M, Sheffield NC (2016) Multi-omics of single cells:
strategies and applications. Trends Biotechnol 34:605–608
Bosch TCG, Miller DJ (2016) The Holobiont imperative. Springer,
Vienna
Brüwer JD, Voolstra CR (2018) First insight into the viral community
of the cnidarian model metaorganism Aiptasia using RNA-Seq data.
PeerJ 6:e4449
Brüwer JD, Agrawal S, Liew YJ et al (2017) Association of coral algal
symbionts with a diverse viral community responsive to heat shock.
BMC Microbiol 17:174
Buck-Wiese H, Voolstra CR, Brüwer JD (2016) The metaorganism
frontier – incorporating microbes into the organism’s response
to environmental change. In: Bode M, Jessen C, Golz V (eds)
YOUMARES 7 conference proceedings, pp 94–102
Cherf GM, Lieberman KR, Rashid H et al (2012) Automated forward
and reverse ratcheting of DNA in a nanopore at 5-A precision. Nat
Biotechnol 30:344–348
Dahm R (2005) Friedrich Miescher and the discovery of DNA. Dev
Biol 278:274–288
Dalsgaard J, John MS, Kattner G et al (2003) Fatty acid trophic markers
in the pelagic marine environment. Adv Mar Biol 46:225–340
Delorme-Axford E, Donker RB, Mouillet J-F et al (2013) Human placental trophoblasts confer viral resistance to recipient cells. Proc
Natl Acad Sci U S A 110:12048–12053
Dewar ML, Arnould JPY, Dann P et al (2013) Interspecific variations
in the gastrointestinal microbiota in penguins. MicrobiologyOpen
2:195–204
Dewar ML, Arnould JPY, Krause L et al (2014) Influence of fasting during moult on the faecal microbiota of penguins. PLoS One 9:e99996
Dick GJ (2017) Embracing the mantra of modellers and synthesizing
omics, experiments and models. Environ Microbiol Rep 9:18–20
Epstein SS (2013) The phenomenon of microbial uncultivability. Curr
Opin Microbiol 16:636–642
Fauquet CM, Mayo MA (2001) The 7th ICTV report. Arch Virol
146:189–194
Feng Y, Zhang Y, Ying C et al (2015) Nanopore-based fourth-generation
DNA sequencing technology. Genomics Proteomics Bioinf 13:4–16
Freilich S, Zarecki R, Eilam O et al (2011) Competitive and cooperative metabolic interactions in bacterial communities. Nat Commun
2:589
Gaby JC, Buckley DH (2012) A comprehensive evaluation of PCR
primers to amplify the nifH gene of nitrogenase. PLoS One 7:e42149
Geiss GK, Bumgarner RE, Birditt B et al (2008) Direct multiplexed
measurement of gene expression with color-coded probe pairs. Nat
Biotechnol 26:317–325
Gillooly JF, Allen AP, West GB et al (2005) The rate of DNA evolution:
effects of body size and temperature on the molecular clock. Proc
Natl Acad Sci U S A 102:140–145
Gottlieb A (2017) Untersuchungen zur Expression ausgewählter Stammzellgene an embryonalen Geweben und Tumoren.
Dissertation, Universität Bremen
Graeve M, Kattner G, Hagen W (1994) Diet-induced changes in the
fatty acid composition of Arctic herbivorous copepods: experimental evidence of trophic markers. J Exp Mar Biol Ecol 182:97–110
Handelsman J (2004) Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev 68:669–685
Hernandez-Agreda A, Leggat W, Bongaerts P, Ainsworth D (2016) The
microbial signature provides insight into the mechanistic basis of
coral success across reef habitats. MBio 7:e00560–e00516
IPCC (2007) Climate change 2007: The physical science basis.
Summary for policymakers. Contribution of working group I to the
fourth assessment report of the intergovernmental panel on climate
change. Cambridge University Press, Cambridge
IPCC (2014) Climate change 2014: Synthesis report. Contribution of
working groups I, II and III to the fifth assessment report of the
intergovernmental panel on climate change. IPCC, Geneva
Jones OAH, Sdepanian S, Lofts S et al (2014) Metabolomic analysis
of soil communities can be used for pollution assessment. Environ
Toxicol Chem 33:61–64
Kanehisa M, Sato Y, Kawashima M et al (2016) KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res
44:D457–D462
Kanehisa M, Furumichi M, Tanabe M et al (2017) KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res
45:D353–D361
Kim BM, Kim J, Choi IY et al (2016) Omics of the marine medaka
(Oryzias melastigma) and its relevance to marine environmental
research. Mar Environ Res 113:141–152
Kimes NE, Callaghan AV, Aktas DF et al (2013) Metagenomic analysis and metabolite profiling of deep-sea sediments from the Gulf of
Mexico following the Deepwater Horizon oil spill. Front Microbiol
4:50
Klug WS, Spencer CA, Palladino MA (2012) Concepts of genetics,
10th edn. Pearson Education, San Francisco
Leary DH, Li RW, Hamdan LJ et al (2014) Integrated metagenomic and
metaproteomic analyses of marine biofilm communities. Biofouling
30:1211–1223
Levin RA, Voolstra CR, Weynberg KD et al (2017) Evidence for a role
of viruses in the thermal sensitivity of coral photosymbionts. ISME
J 11:808–812
Liew YJ, Li Y, Baumgarten S et al (2017) Condition-specific RNA editing in the coral symbiont Symbiodinium microadriaticum. PLoS
Genet 13:1–22
Liu Y, Beyer A, Aebersold R (2016) On the dependency of cellular protein levels on mRNA abundance. Cell 165:535–550
Llewellyn CA, Sommer U, Dupont CL et al (2015) Using community
metabolomics as a new approach to discriminate marine microbial
particulate organic matter in the western English Channel. Prog
Oceanogr 137:421–433
Lu H, Giordano F, Ning Z (2016) Oxford Nanopore MinION sequencing and genome assembly. Genomics Proteomics Bioinf 14:265–279
Luo S-S, Ishibashi O, Ishikawa G et al (2009) Human villous trophoblasts express and secrete placenta-specific microRNAs into maternal circulation via exosomes. Biol Reprod 81:717–729
Reading the Book of Life – Omics as a Universal Tool Across Disciplines