Part B | 10
304 Part B Tools and Methods in Marine Biotechnology
manage, and utilize so-called big data in all sectors of
the economy, not just biotechnology. It is difficult to
extract biological meaning from such data sets. Each
of the many new analytical techniques described in this
chapter will involve rapid data acquisition accelerating
the problem still further, and it may, therefore, be in the
fields of mathematics and computing where the most interesting breakthroughs will occur in the coming years.
References
10.1
G.R. Carvalho, S. Creer, J.M. Allen, F.O. Costa,
C.S. Tsigenopoulos, M. Le Goff-Vitry, A. Magoulas,
L. Medlin, K. Metfies: Genomics in the discovery
and monitoring of marine biodiversity, Adv. Mar.
Genomics 1, 1–32 (2010)
10.2
A. Szalay, J. Gray: Computing: Science in an exponential world, Nature 440, 413–414 (2006)
10.3
M.L. Metzker: Sequencing technologies the next
generation, Nat. Rev. Genet. 11, 31–46 (2010)
10.4
F. Meyer: Genome Sequencing vs. Moore’s Law: Cyber challenges for the next decade, CTWatch Q. 2,
20–22 (2006)
10.5
Nature America, Inc.: Metagenomics versus Moore’s
law, Nat. Methods 6, 623 (2009), Editorial
10.6
J. Wilkening, A. Wilke, N. Desai, F. Meyer: Using clouds for metagenomics: A case study, IEEE
Int. Conf. Cluster Comput. Workshops, New Orleans
2009) pp. 1–6
10.7
L.R. Pomeroy: The ocean’s food-web, a changing
paradigm, BioScience 24, 499–504 (1974)
10.8
J.E. Hobbie, R.J. Daley, S. Jasper: Use of nuclepore filtres for counting bacteria by fluorescent
microscopy, Appl. Environ. Microbiol. 33, 1225–1228
(1974)
10.9
R. Zimmerman, L.A. Meyer-Reil: A new method
for fluorescence staining of bacterial populations
on membrane filters, Kiel. Meeresforsch. 30, 24–27
(1974)
10.10 C.B. Field, M.J. Behrenfeld, J.T. Randerson,
P. Falkowski: Primary production of the biosphere:
Integrating terrestrial and oceanic components,
Science 281, 237–240 (2009)
10.11 W.B. Whitman, D.C. Coleman, W.J. Wiebe: Prokaryotes: The unseen majority, Proc. Natl. Acad. Sci. USA
95, 6578–6583 (1998)
10.12 P.A. del Giorgio, C.M. Duarte: Respiration in the
open ocean, Nature 420, 379–384 (2002)
10.13 E.F. DeLong: Microbial community genomics in
the oceans, Nat. Rev. Microbiol. 3, 459–469
(2005)
10.14 C. Médigue, I. Moszer: Annotation, comparison and
databases for hundreds of bacterial genomes, Res.
Microbiol. 158, 724–736 (2007)
10.15 K. Scheibye-Alsing, S. Hoffmann, A. Frankel,
P. Jensen, P.F. Stadler, Y. Mang, N. Tommerup,
M.J. Gilchrist, A.B. Nygård, S. Cirera, C.B. Jørgensen,
M. Fredholm, J. Gorodkin: Sequence assembly,
Comput. Biol. Chem. 33, 121–136 (2009)
10.16 R.D. Finn, J. Tate, J. Mistry, P.C. Coggill, S.J. Sammut, H.-R. Hotz, G. Ceric, K. Forslund, S.R. Eddy,
E.L.L. Sonnhammer, A. Bateman: The Pfam protein
families database, Nucleic Acids Res. 36, D281–D288
(2008)
10.17 A.S. Juncker, L.J. Jensen, A. Pierleoni, A. Bernsel,
M.L. Tress, P. Bork, G. von Heijne, A. Valencia,
C.A. Ouzounis, R. Casadio, S. Brunak: Sequencebased feature prediction and annotation of proteins, Genome Biol. 10, 206 (2009)
10.18 R. Rentzsch, C.A. Orengo: Protein function prediction – The power of multiplicity, Trends Biotechnol.
27, 210–219 (2009)
10.19 E.S. Lander, L.M. Linton, B. Birren, C. Nusbaum, M.C. Zody, J. Baldwin, K. Devon, K. Dewar,
M. Doyle, W. FitzHugh, R. Funke, D. Gage, K. Harris, A. Heaford, J. Howland, L. Kann, J. Lehoczky,
R. LeVine, P. McEwan, K. McKernan, J. Meldrim,
J.P. Mesirov, C. Miranda, W. Morris, J. Naylor,
C. Raymond, M. Rosetti, R. Santos, A. Sheridan, C. Sougnez, N.S. Thomann, N. Stojanovic,
A. Subramanian, D. Wyman, J. Rogers, J. Sulston, R. Ainscough, S. Beck, D. Bentley, J. Burton, C. Clee, N. Carter, A. Coulson, R. Deadman,
P. Deloukas, A. Dunham, I. Dunham, R. Durbin,
L. French, D. Grafham, S. Gregory, T. Hubbard, S. Humphray, A. Hunt, M. Jones, C. Lloyd,
A. McMurray, L. Matthews, S. Mercer, S. Milne,
J.C. Mullikin, A. Mungall, R. Plumb, M. Ross,
R. Shownkeen, S. Sims, R.H. Waterston, R.K. Wilson, L.W. Hillier, J.D. McPherson, M.A. Marra,
E.R. Mardis, L.A. Fulton, A.T. Chinwalla, K.H. Pepin,
W.R. Gish, S.L. Chissoe, M.C. Wendl, K.D. Delehaunty, T.L. Miner, A. Delehaunty, J.B. Kramer,
L.L. Cook, R.S. Fulton, D.L. Johnson, P.J. Minx,
S.W. Clifton, T. Hawkins, E. Branscomb, P. Predki,
P. Richardson, S. Wenning, T. Slezak, N. Doggett,
J. Cheng, A. Olsen, S. Lucas, C. Elkin, E. Uberbacher,
M. Frazier, R.A. Gibbs, D.M. Muzny, S.E. Scherer,
J.B. Bouck, E.J. Sodergren, K.C. Worley, C.M. Rives,
J.H. Gorrell, M.L. Metzker, S.L. Naylor, R.S. Kucherlapati, D.L. Nelson, G.M. Weinstock, Y. Sakaki,
A. Fujiyama, M. Hattori, T. Yada, A. Toyoda, T. Itoh,
C. Kawagoe, H. Watanabe, Y. Totoki, T. Taylor,
J. Weissenbach, R. Heilig, W. Saurin, F. Artiguenave, P. Brottier, T. Bruls, E. Pelletier, C. Robert,
P. Wincker, A. Rosenthal, M. Platzer, G. Nyakatura,
S. Taudien, A. Rump, D.R. Smith, L. DoucetteStamm, M. Rubenfield, K. Weinstock, H. Mei Lee,
J. Duboi, H. Yang, J. Yu, J. Wang, G. Huang,
J. Gu, L. Hood, L. Rowen, A. Madan, S. Qin,
R.W. Davis, N.A. Federspiel, A.P. Abola, M.J. Proc-
304 Part B Tools and Methods in Marine Biotechnology
manage, and utilize so-called big data in all sectors of
the economy, not just biotechnology. It is difficult to
extract biological meaning from such data sets. Each
of the many new analytical techniques described in this
chapter will involve rapid data acquisition accelerating
the problem still further, and it may, therefore, be in the
fields of mathematics and computing where the most interesting breakthroughs will occur in the coming years.
References
10.1
G.R. Carvalho, S. Creer, J.M. Allen, F.O. Costa,
C.S. Tsigenopoulos, M. Le Goff-Vitry, A. Magoulas,
L. Medlin, K. Metfies: Genomics in the discovery
and monitoring of marine biodiversity, Adv. Mar.
Genomics 1, 1–32 (2010)
10.2
A. Szalay, J. Gray: Computing: Science in an exponential world, Nature 440, 413–414 (2006)
10.3
M.L. Metzker: Sequencing technologies the next
generation, Nat. Rev. Genet. 11, 31–46 (2010)
10.4
F. Meyer: Genome Sequencing vs. Moore’s Law: Cyber challenges for the next decade, CTWatch Q. 2,
20–22 (2006)
10.5
Nature America, Inc.: Metagenomics versus Moore’s
law, Nat. Methods 6, 623 (2009), Editorial
10.6
J. Wilkening, A. Wilke, N. Desai, F. Meyer: Using clouds for metagenomics: A case study, IEEE
Int. Conf. Cluster Comput. Workshops, New Orleans
2009) pp. 1–6
10.7
L.R. Pomeroy: The ocean’s food-web, a changing
paradigm, BioScience 24, 499–504 (1974)
10.8
J.E. Hobbie, R.J. Daley, S. Jasper: Use of nuclepore filtres for counting bacteria by fluorescent
microscopy, Appl. Environ. Microbiol. 33, 1225–1228
(1974)
10.9
R. Zimmerman, L.A. Meyer-Reil: A new method
for fluorescence staining of bacterial populations
on membrane filters, Kiel. Meeresforsch. 30, 24–27
(1974)
10.10 C.B. Field, M.J. Behrenfeld, J.T. Randerson,
P. Falkowski: Primary production of the biosphere:
Integrating terrestrial and oceanic components,
Science 281, 237–240 (2009)
10.11 W.B. Whitman, D.C. Coleman, W.J. Wiebe: Prokaryotes: The unseen majority, Proc. Natl. Acad. Sci. USA
95, 6578–6583 (1998)
10.12 P.A. del Giorgio, C.M. Duarte: Respiration in the
open ocean, Nature 420, 379–384 (2002)
10.13 E.F. DeLong: Microbial community genomics in
the oceans, Nat. Rev. Microbiol. 3, 459–469
(2005)
10.14 C. Médigue, I. Moszer: Annotation, comparison and
databases for hundreds of bacterial genomes, Res.
Microbiol. 158, 724–736 (2007)
10.15 K. Scheibye-Alsing, S. Hoffmann, A. Frankel,
P. Jensen, P.F. Stadler, Y. Mang, N. Tommerup,
M.J. Gilchrist, A.B. Nygård, S. Cirera, C.B. Jørgensen,
M. Fredholm, J. Gorodkin: Sequence assembly,
Comput. Biol. Chem. 33, 121–136 (2009)
10.16 R.D. Finn, J. Tate, J. Mistry, P.C. Coggill, S.J. Sammut, H.-R. Hotz, G. Ceric, K. Forslund, S.R. Eddy,
E.L.L. Sonnhammer, A. Bateman: The Pfam protein
families database, Nucleic Acids Res. 36, D281–D288
(2008)
10.17 A.S. Juncker, L.J. Jensen, A. Pierleoni, A. Bernsel,
M.L. Tress, P. Bork, G. von Heijne, A. Valencia,
C.A. Ouzounis, R. Casadio, S. Brunak: Sequencebased feature prediction and annotation of proteins, Genome Biol. 10, 206 (2009)
10.18 R. Rentzsch, C.A. Orengo: Protein function prediction – The power of multiplicity, Trends Biotechnol.
27, 210–219 (2009)
10.19 E.S. Lander, L.M. Linton, B. Birren, C. Nusbaum, M.C. Zody, J. Baldwin, K. Devon, K. Dewar,
M. Doyle, W. FitzHugh, R. Funke, D. Gage, K. Harris, A. Heaford, J. Howland, L. Kann, J. Lehoczky,
R. LeVine, P. McEwan, K. McKernan, J. Meldrim,
J.P. Mesirov, C. Miranda, W. Morris, J. Naylor,
C. Raymond, M. Rosetti, R. Santos, A. Sheridan, C. Sougnez, N.S. Thomann, N. Stojanovic,
A. Subramanian, D. Wyman, J. Rogers, J. Sulston, R. Ainscough, S. Beck, D. Bentley, J. Burton, C. Clee, N. Carter, A. Coulson, R. Deadman,
P. Deloukas, A. Dunham, I. Dunham, R. Durbin,
L. French, D. Grafham, S. Gregory, T. Hubbard, S. Humphray, A. Hunt, M. Jones, C. Lloyd,
A. McMurray, L. Matthews, S. Mercer, S. Milne,
J.C. Mullikin, A. Mungall, R. Plumb, M. Ross,
R. Shownkeen, S. Sims, R.H. Waterston, R.K. Wilson, L.W. Hillier, J.D. McPherson, M.A. Marra,
E.R. Mardis, L.A. Fulton, A.T. Chinwalla, K.H. Pepin,
W.R. Gish, S.L. Chissoe, M.C. Wendl, K.D. Delehaunty, T.L. Miner, A. Delehaunty, J.B. Kramer,
L.L. Cook, R.S. Fulton, D.L. Johnson, P.J. Minx,
S.W. Clifton, T. Hawkins, E. Branscomb, P. Predki,
P. Richardson, S. Wenning, T. Slezak, N. Doggett,
J. Cheng, A. Olsen, S. Lucas, C. Elkin, E. Uberbacher,
M. Frazier, R.A. Gibbs, D.M. Muzny, S.E. Scherer,
J.B. Bouck, E.J. Sodergren, K.C. Worley, C.M. Rives,
J.H. Gorrell, M.L. Metzker, S.L. Naylor, R.S. Kucherlapati, D.L. Nelson, G.M. Weinstock, Y. Sakaki,
A. Fujiyama, M. Hattori, T. Yada, A. Toyoda, T. Itoh,
C. Kawagoe, H. Watanabe, Y. Totoki, T. Taylor,
J. Weissenbach, R. Heilig, W. Saurin, F. Artiguenave, P. Brottier, T. Bruls, E. Pelletier, C. Robert,
P. Wincker, A. Rosenthal, M. Platzer, G. Nyakatura,
S. Taudien, A. Rump, D.R. Smith, L. DoucetteStamm, M. Rubenfield, K. Weinstock, H. Mei Lee,
J. Duboi, H. Yang, J. Yu, J. Wang, G. Huang,
J. Gu, L. Hood, L. Rowen, A. Madan, S. Qin,
R.W. Davis, N.A. Federspiel, A.P. Abola, M.J. Proc-