92
Nunan N, Daniell TJ, Singh BK, Papert A, McNicol JW, Prosser JI (2005) Links between plant and
rhizoplane bacterial communities in grassland soils, characterized using molecular techniques.
Appl Environ Microbiol 71:6784–6792
O’Farrell PH (1975) High resolution two-dimensional electrophoresis of proteins. J Biol Chem
250:4007–4021
Ochsenreiter T, Selezi D, Quaiser A, Bonch-Osmolovskaya L, Schleper C (2003) Diversity and
abundance of Crenarchaeota in terrestrial habitats studied by 16S RNA surveys and real time
PCR. Environ Microbiol 5:787–797
Ogier JC, Son O, Gruss A, Tailliez P, Delacroix-Buchet A (2002) Identification of the bacterial microflora in dairy products by temporal temperature gradient gel electrophoresis.
Appl Environ Microbiol 68:3691–3701
Ogunseitan OA (1993) Direct extraction of proteins from environmental samples. J Microbiol
Methods 17:273–281
Ogunseitan OA (1996) Protein profile in cultivated and native freshwater microorganisms exposed
to chemical environmental pollutants. Microb Ecol 31:291–304
Ogunseitan OA (1997) Direct extraction of catalytic proteins from natural microbial communities.
J Microbiol Methods 28:55–63
Ogunseitan O (2005) Microbial diversity: form and function in prokaryotes. Blackwell Science
Ltd, Malden, p 142
Overbeek MV, Kusuma WA, Buono A (2013) Clustering metagenome fragments using growing
self organizing map. In: 2013 International conference on advanced computer science and
information systems (ICACSIS). IEEE, pp 285–289
Pandey A, Lewitter F (1999) Nucleotide sequence databases: a gold mine for biologists. Trends
Biochem Sci 24:276–280
Pandey A, Mann M (2000) Proteomics to study genes and genomes. Nature 405:837–846
Parks DH, Tyson GW, Hugenholtz P, Beiko RG (2014) STAMP: statistical analysis of taxonomic
and functional profiles. Bioinformatics 30:3123–3124
Pati A, Heath LS, Kyrpides NC, Ivanova N (2011) ClaMS: a classifier for metagenomic sequences.
Stand Genomic Sci 5:248–253
Patil KR, Roune L, McHardy AC (2012) The PhyloPythiaS web server for taxonomic assignment of metagenome sequences. PLoS One 7(6):e38581. https://doi.org/10.1371/journal.
pone.0038581
Paulson JN, Pop M, Bravo HC (2011) Metastats: an improved statistical method for analysis of
metagenomic data. Genome Biol 12:P17
Peano C, Pietrelli A, Consolandi C, Rossi E, Petiti L, Tagliabue L, Landini P (2013) An efficient rRNA removal method for RNA sequencing in GC-rich bacteria. Microb Inform Exp
3:1. https://doi.org/10.1186/2042-5783-3-1
Pedersen S, Bloch PL, Reeh S, Neidhardt FC (1978) Patterns of protein synthesis in E. coli: a
catalog of the amount of 140 individual proteins at different growth rates. Cell 14:179–190
Pell J, Hintze A, Canino-Koning R, Howe A, Tiedje JM, Brown CT (2012) Scaling metagenome sequence assembly with probabilistic de Bruijn graphs. Proc Natl Acad Sci U S A
109:13272–13277
Peng J, Elias JE, Thoreen CC, Licklider LJ, Gygi SP (2003) Evaluation of multidimensional
chromatography coupled with tandem mass spectrometry (LC/LC−MS/MS) for large-scale
protein analysis: the yeast proteome. J Proteome Res 2:43–45
Peng Y, Henry CM, Leung S, Yiu M, Francis Y, Chin L (2011) Meta-IDBA: a de Novo assembler
for metagenomic data. Bioinformatics 27:i94–i101
Peng Y, Leung HC, Yiu SM, Chin FY (2012) IDBA-UD: a de novo assembler for single-cell and
metagenomic sequencing data with highly uneven depth. Bioinformatics 28:1420–1428
Perez-Cobas AE, Gosalbes MJ, Friedrichs A, Knecht H, Artacho A, Eismann K, Otto W, Rojo
D, Bargiela R, von Bergen M, Neulinger SC, Däumer C, Heinsen FA, Latorre A, Barbas C,
Seifert J, dos Santos VM, Ott SJ, Ferrer M, Moya A (2013) Gut microbiota disturbance during antibiotic therapy: a multi-omic approach. Gut 62:1591–1601
References
Nunan N, Daniell TJ, Singh BK, Papert A, McNicol JW, Prosser JI (2005) Links between plant and
rhizoplane bacterial communities in grassland soils, characterized using molecular techniques.
Appl Environ Microbiol 71:6784–6792
O’Farrell PH (1975) High resolution two-dimensional electrophoresis of proteins. J Biol Chem
250:4007–4021
Ochsenreiter T, Selezi D, Quaiser A, Bonch-Osmolovskaya L, Schleper C (2003) Diversity and
abundance of Crenarchaeota in terrestrial habitats studied by 16S RNA surveys and real time
PCR. Environ Microbiol 5:787–797
Ogier JC, Son O, Gruss A, Tailliez P, Delacroix-Buchet A (2002) Identification of the bacterial microflora in dairy products by temporal temperature gradient gel electrophoresis.
Appl Environ Microbiol 68:3691–3701
Ogunseitan OA (1993) Direct extraction of proteins from environmental samples. J Microbiol
Methods 17:273–281
Ogunseitan OA (1996) Protein profile in cultivated and native freshwater microorganisms exposed
to chemical environmental pollutants. Microb Ecol 31:291–304
Ogunseitan OA (1997) Direct extraction of catalytic proteins from natural microbial communities.
J Microbiol Methods 28:55–63
Ogunseitan O (2005) Microbial diversity: form and function in prokaryotes. Blackwell Science
Ltd, Malden, p 142
Overbeek MV, Kusuma WA, Buono A (2013) Clustering metagenome fragments using growing
self organizing map. In: 2013 International conference on advanced computer science and
information systems (ICACSIS). IEEE, pp 285–289
Pandey A, Lewitter F (1999) Nucleotide sequence databases: a gold mine for biologists. Trends
Biochem Sci 24:276–280
Pandey A, Mann M (2000) Proteomics to study genes and genomes. Nature 405:837–846
Parks DH, Tyson GW, Hugenholtz P, Beiko RG (2014) STAMP: statistical analysis of taxonomic
and functional profiles. Bioinformatics 30:3123–3124
Pati A, Heath LS, Kyrpides NC, Ivanova N (2011) ClaMS: a classifier for metagenomic sequences.
Stand Genomic Sci 5:248–253
Patil KR, Roune L, McHardy AC (2012) The PhyloPythiaS web server for taxonomic assignment of metagenome sequences. PLoS One 7(6):e38581. https://doi.org/10.1371/journal.
pone.0038581
Paulson JN, Pop M, Bravo HC (2011) Metastats: an improved statistical method for analysis of
metagenomic data. Genome Biol 12:P17
Peano C, Pietrelli A, Consolandi C, Rossi E, Petiti L, Tagliabue L, Landini P (2013) An efficient rRNA removal method for RNA sequencing in GC-rich bacteria. Microb Inform Exp
3:1. https://doi.org/10.1186/2042-5783-3-1
Pedersen S, Bloch PL, Reeh S, Neidhardt FC (1978) Patterns of protein synthesis in E. coli: a
catalog of the amount of 140 individual proteins at different growth rates. Cell 14:179–190
Pell J, Hintze A, Canino-Koning R, Howe A, Tiedje JM, Brown CT (2012) Scaling metagenome sequence assembly with probabilistic de Bruijn graphs. Proc Natl Acad Sci U S A
109:13272–13277
Peng J, Elias JE, Thoreen CC, Licklider LJ, Gygi SP (2003) Evaluation of multidimensional
chromatography coupled with tandem mass spectrometry (LC/LC−MS/MS) for large-scale
protein analysis: the yeast proteome. J Proteome Res 2:43–45
Peng Y, Henry CM, Leung S, Yiu M, Francis Y, Chin L (2011) Meta-IDBA: a de Novo assembler
for metagenomic data. Bioinformatics 27:i94–i101
Peng Y, Leung HC, Yiu SM, Chin FY (2012) IDBA-UD: a de novo assembler for single-cell and
metagenomic sequencing data with highly uneven depth. Bioinformatics 28:1420–1428
Perez-Cobas AE, Gosalbes MJ, Friedrichs A, Knecht H, Artacho A, Eismann K, Otto W, Rojo
D, Bargiela R, von Bergen M, Neulinger SC, Däumer C, Heinsen FA, Latorre A, Barbas C,
Seifert J, dos Santos VM, Ott SJ, Ferrer M, Moya A (2013) Gut microbiota disturbance during antibiotic therapy: a multi-omic approach. Gut 62:1591–1601
References