9 Genomic Techniques and How to Apply Them to Marine Questions
371
Baldi P, Long AD (2001) A Bayesian framework for the analysis of microarray expression
data: regularized t-test and statistical inferences of gene changes. Bioinformatics 17(6):
509–519
Ball CA, Brazma A, Causton H et al (2004) Submission of microarray data to public repositories.
PLoS Biol 2(9):E317
Bammler T, Beyer RP, Bhattacharya S et al (2005) Standardizing global gene expression analysis
between laboratories and across platforms. Nat Methods 2(5):351–356
Barrett T, Troup DB, Wilhite SE et al (2007) NCBI GEO: mining tens of millions of expression
profiles-database and tools update. Nucleic Acids Res 35(Database issue):D760–D765
Bartels D, Kespohl S, Albaum S et al (2005) BACCardI-a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison. Bioinformatics 21(7):853–859
Bauerle RH, Margolin P (1966) The functional organization of the tryptophan gene cluster in
Salmonella typhimurium. Proc Natl Acad Sci U S A 56(1):111–118
Bekel T, Henckel K, Küster H et al (2009) The sequence analysis and management system –
SAMS-2.0: data management and sequence analysis adapted to changing requirements from
traditional sanger sequencing to ultrafast sequencing technologies. J Biotechnol 140(1–2):3–12
Bendtsen JD, Nielsen H, von Heijne G et al (2004) Improved prediction of signal peptides: SignalP
3.0. J Mol Biol 340(4):783–795
Benson DA, Karsch-Mizrachi I, Lipman DJ et al (2008) GenBank. Nucleic Acids Res 36:D25–D30
Berman H, Henrick K, Nakamura H (2003) Announcing the worldwide Protein Data Bank. Nat
Struct Biol 10(12):980
Besemer J, Borodovsky M (2005) GeneMark: web software for gene finding in prokaryotes,
eukaryotes and viruses. Nucleic Acids Res 33:W451–W454
Besemer J, Lomsadze A, Borodovsky M (2001) GeneMarkS: a self-training method for prediction
of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory
regions. Nucleic Acids Res 29(12):2607–2618
Birney E, Clamp M, Durbin R (2004) GeneWise and Genomewise. Genome Res 14(5):988–995
Black MA, Doerge RW (2002) Calculation of the minimum number of replicate spots required for
detection of significant gene expression fold change in microarray experiments. Bioinformatics
18(12):1609–1616
Brazma A, Hingamp P, Quackenbush J et al (2001) Minimum information about a microarray
experiment (MIAME)-toward standards for microarray data. Nat Genet 29(4):365–371
Brejova B, Brown DG, Li M et al (2005) ExonHunter: a comprehensive approach to gene finding.
Bioinformatics 21(Suppl 1):i57–i65
Brent MR (2007) How does eukaryotic gene prediction work? Nat Biotechnol 25(8):883–885
Brunak S, Danchin A, Hattori M et al (2002) Nucleotide sequence database policies. Science
298(5597):1333
Burge C, Karlin S (1997) Prediction of complete gene structures in human genomic DNA. J Mol
Biol 268(1):78–94
Chen YA, Lin CC, Wang CD et al (2007) An optimized procedure greatly improves EST vector
contamination removal. BMC Genomics 8:416
Chothia C, Gough J, Vogel C et al (2003) Evolution of the protein repertoire. Science
300(5626):1701–1703
Cochrane G, Bates K, Apweiler R et al (2006) Evidence standards in experimental and inferential
INSDC Third Party Annotation data. Omics 10(2):105–113
Cochrane G, Akhtar R, Aldebert P et al (2008) Priorities for nucleotide trace, sequence and annotation data capture at the ensembl trace archive and the EMBL nucleotide sequence database.
Nucleic Acids Res 36:D5–D12
Codd EF (1990) The relational model for database management: version 2. Addison-Wesley
Longman Publishing Co., Inc, New York.
Conesa A, Gotz S, Garcia-Gomez JM et al (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21(18):
3674–3676
Consortium U (2008) The universal protein resource (UniProt). Nucleic Acids Res 36:D190–D195
371
Baldi P, Long AD (2001) A Bayesian framework for the analysis of microarray expression
data: regularized t-test and statistical inferences of gene changes. Bioinformatics 17(6):
509–519
Ball CA, Brazma A, Causton H et al (2004) Submission of microarray data to public repositories.
PLoS Biol 2(9):E317
Bammler T, Beyer RP, Bhattacharya S et al (2005) Standardizing global gene expression analysis
between laboratories and across platforms. Nat Methods 2(5):351–356
Barrett T, Troup DB, Wilhite SE et al (2007) NCBI GEO: mining tens of millions of expression
profiles-database and tools update. Nucleic Acids Res 35(Database issue):D760–D765
Bartels D, Kespohl S, Albaum S et al (2005) BACCardI-a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison. Bioinformatics 21(7):853–859
Bauerle RH, Margolin P (1966) The functional organization of the tryptophan gene cluster in
Salmonella typhimurium. Proc Natl Acad Sci U S A 56(1):111–118
Bekel T, Henckel K, Küster H et al (2009) The sequence analysis and management system –
SAMS-2.0: data management and sequence analysis adapted to changing requirements from
traditional sanger sequencing to ultrafast sequencing technologies. J Biotechnol 140(1–2):3–12
Bendtsen JD, Nielsen H, von Heijne G et al (2004) Improved prediction of signal peptides: SignalP
3.0. J Mol Biol 340(4):783–795
Benson DA, Karsch-Mizrachi I, Lipman DJ et al (2008) GenBank. Nucleic Acids Res 36:D25–D30
Berman H, Henrick K, Nakamura H (2003) Announcing the worldwide Protein Data Bank. Nat
Struct Biol 10(12):980
Besemer J, Borodovsky M (2005) GeneMark: web software for gene finding in prokaryotes,
eukaryotes and viruses. Nucleic Acids Res 33:W451–W454
Besemer J, Lomsadze A, Borodovsky M (2001) GeneMarkS: a self-training method for prediction
of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory
regions. Nucleic Acids Res 29(12):2607–2618
Birney E, Clamp M, Durbin R (2004) GeneWise and Genomewise. Genome Res 14(5):988–995
Black MA, Doerge RW (2002) Calculation of the minimum number of replicate spots required for
detection of significant gene expression fold change in microarray experiments. Bioinformatics
18(12):1609–1616
Brazma A, Hingamp P, Quackenbush J et al (2001) Minimum information about a microarray
experiment (MIAME)-toward standards for microarray data. Nat Genet 29(4):365–371
Brejova B, Brown DG, Li M et al (2005) ExonHunter: a comprehensive approach to gene finding.
Bioinformatics 21(Suppl 1):i57–i65
Brent MR (2007) How does eukaryotic gene prediction work? Nat Biotechnol 25(8):883–885
Brunak S, Danchin A, Hattori M et al (2002) Nucleotide sequence database policies. Science
298(5597):1333
Burge C, Karlin S (1997) Prediction of complete gene structures in human genomic DNA. J Mol
Biol 268(1):78–94
Chen YA, Lin CC, Wang CD et al (2007) An optimized procedure greatly improves EST vector
contamination removal. BMC Genomics 8:416
Chothia C, Gough J, Vogel C et al (2003) Evolution of the protein repertoire. Science
300(5626):1701–1703
Cochrane G, Bates K, Apweiler R et al (2006) Evidence standards in experimental and inferential
INSDC Third Party Annotation data. Omics 10(2):105–113
Cochrane G, Akhtar R, Aldebert P et al (2008) Priorities for nucleotide trace, sequence and annotation data capture at the ensembl trace archive and the EMBL nucleotide sequence database.
Nucleic Acids Res 36:D5–D12
Codd EF (1990) The relational model for database management: version 2. Addison-Wesley
Longman Publishing Co., Inc, New York.
Conesa A, Gotz S, Garcia-Gomez JM et al (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21(18):
3674–3676
Consortium U (2008) The universal protein resource (UniProt). Nucleic Acids Res 36:D190–D195