376
V. Mittard-Runte et al.
Overbeek R, Larsen N, Walunas T et al (2003) The ERGO genome analysis and discovery system.
Nucleic Acids Res 31:164–171
Overbeek R, Begley T, Butler RM et al (2005) The subsystems approach to genome annotation
and its use in the project to annotate 1,000 genomes. Nucleic Acids Res 33(17):5691–5702
Page GP, Edwards JW, Gadbury GL et al (2006) The PowerAtlas: a power and sample size atlas
for microarray experimental design and research. BMC Bioinformatics 7:84
Pan W, Lin J, Le CT (2002) How many replicates of arrays are required to detect gene expression
changes in microarray experiments? A mixture model approach. Genome Biol. research0022.
Parkinson H, Kapushesky M, Shojatalab M et al (2007) ArrayExpress-a public database of
microarray experiments and gene expression profiles. Nucleic Acids Res 35:D747–D750
Parra G, Agarwal P, Abril JF et al (2003) Comparative gene prediction in human and mouse.
Genome Res 13(1):108–117
Pavlidis P, Weston J, Cai J et al (2002) Learning gene functional classifications from multiple data
types. J Comput Biol 9(2):401–411
Pearson WR, Lipman DJ (1988) Improved tools for biological sequence comparison. Proc Natl
Acad Sci U S A 85(8):2444–2448
Pertea G, Huang X, Liang F et al (2003) TIGR Gene Indices clustering tools (TGICL): a software
system for fast clustering of large EST datasets. Bioinformatics 19(5):651–652
Pieler R, Sanchez-Cabo F, Hackl H et al (2004) ArrayNorm: comprehensive normalization and
analysis of microarray data. Bioinformatics 20(12):1971–1973
Prober JM, Trainor GL, Dam RJ et al (1987) A system for rapid DNA sequencing with fluorescent
chain-terminating dideoxynucleotides. Science 238(4825):336–341
Pruitt KD, Tatusova T, Maglott DR (2007) NCBI reference sequences (RefSeq): a curated nonredundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res 35:
D61–D65
Quackenbush J (2001) Computational analysis of microarray data. Nat Rev Genet 2(6):
418–427
Quackenbush J (2002) Microarray data normalization and transformation. Nat Genet
32(Suppl):496-501
Quackenbush J (2003) Genomics. Microarrays-guilt by association. Science 302(5643):240–241
Quevillon E, Silventoinen V, Pillai S et al (2005) InterProScan: protein domains identifier. Nucleic
Acids Res 33:W116–W1120
Rayner TF, Rocca-Serra P, Spellman PT et al (2006) A simple spreadsheet-based, MIAMEsupportive format for microarray data: MAGE-TAB. BMC Bioinformatics 7:489
Reeck GR, de Haen C, Teller DC et al (1987) Homology in proteins and nucleic acids: a
terminology muddle and a way out of it. Cell 50(5):667
Reese MG, Kulp D, Tammana H et al (2000) Genie-gene finding in Drosophila melanogaster.
Genome Res 10(4):529–538
Repsilber D, Ziegler A (2005) Two-color microarray experiments. Technology and sources of
variance. Methods Inf Med 44(3):400–404
Ronaghi M, Uhlén M, Nyrén P (1998) A sequencing method based on real-time pyrophosphate.
Science 281(5375):363–365
Rutherford K, Parkhill J, Crook J et al (2000) Artemis: sequence visualization and annotation.
Bioinformatics 16(10):944–945
Saal LH, Troein C, Vallon-Christersson J et al (2002) BioArray Software Environment (BASE): a
platform for comprehensive management and analysis of microarray data. Genome Biol 3(8):
SOFTWARE0003.
Saeed AI, Sharov V, White J et al (2003) TM4: a free, open-source system for microarray data
management and analysis. Biotechniques 34(2):374–378
Saha S, Sparks AB, Rago C et al (2002) Using the transcriptome to annotate the genome. Nat
Biotechnol 20(5):508–512
Salamov AA, Solovyev VV (2000) Ab initio gene finding in Drosophila genomic DNA. Genome
Res 10(4):516–522
V. Mittard-Runte et al.
Overbeek R, Larsen N, Walunas T et al (2003) The ERGO genome analysis and discovery system.
Nucleic Acids Res 31:164–171
Overbeek R, Begley T, Butler RM et al (2005) The subsystems approach to genome annotation
and its use in the project to annotate 1,000 genomes. Nucleic Acids Res 33(17):5691–5702
Page GP, Edwards JW, Gadbury GL et al (2006) The PowerAtlas: a power and sample size atlas
for microarray experimental design and research. BMC Bioinformatics 7:84
Pan W, Lin J, Le CT (2002) How many replicates of arrays are required to detect gene expression
changes in microarray experiments? A mixture model approach. Genome Biol. research0022.
Parkinson H, Kapushesky M, Shojatalab M et al (2007) ArrayExpress-a public database of
microarray experiments and gene expression profiles. Nucleic Acids Res 35:D747–D750
Parra G, Agarwal P, Abril JF et al (2003) Comparative gene prediction in human and mouse.
Genome Res 13(1):108–117
Pavlidis P, Weston J, Cai J et al (2002) Learning gene functional classifications from multiple data
types. J Comput Biol 9(2):401–411
Pearson WR, Lipman DJ (1988) Improved tools for biological sequence comparison. Proc Natl
Acad Sci U S A 85(8):2444–2448
Pertea G, Huang X, Liang F et al (2003) TIGR Gene Indices clustering tools (TGICL): a software
system for fast clustering of large EST datasets. Bioinformatics 19(5):651–652
Pieler R, Sanchez-Cabo F, Hackl H et al (2004) ArrayNorm: comprehensive normalization and
analysis of microarray data. Bioinformatics 20(12):1971–1973
Prober JM, Trainor GL, Dam RJ et al (1987) A system for rapid DNA sequencing with fluorescent
chain-terminating dideoxynucleotides. Science 238(4825):336–341
Pruitt KD, Tatusova T, Maglott DR (2007) NCBI reference sequences (RefSeq): a curated nonredundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res 35:
D61–D65
Quackenbush J (2001) Computational analysis of microarray data. Nat Rev Genet 2(6):
418–427
Quackenbush J (2002) Microarray data normalization and transformation. Nat Genet
32(Suppl):496-501
Quackenbush J (2003) Genomics. Microarrays-guilt by association. Science 302(5643):240–241
Quevillon E, Silventoinen V, Pillai S et al (2005) InterProScan: protein domains identifier. Nucleic
Acids Res 33:W116–W1120
Rayner TF, Rocca-Serra P, Spellman PT et al (2006) A simple spreadsheet-based, MIAMEsupportive format for microarray data: MAGE-TAB. BMC Bioinformatics 7:489
Reeck GR, de Haen C, Teller DC et al (1987) Homology in proteins and nucleic acids: a
terminology muddle and a way out of it. Cell 50(5):667
Reese MG, Kulp D, Tammana H et al (2000) Genie-gene finding in Drosophila melanogaster.
Genome Res 10(4):529–538
Repsilber D, Ziegler A (2005) Two-color microarray experiments. Technology and sources of
variance. Methods Inf Med 44(3):400–404
Ronaghi M, Uhlén M, Nyrén P (1998) A sequencing method based on real-time pyrophosphate.
Science 281(5375):363–365
Rutherford K, Parkhill J, Crook J et al (2000) Artemis: sequence visualization and annotation.
Bioinformatics 16(10):944–945
Saal LH, Troein C, Vallon-Christersson J et al (2002) BioArray Software Environment (BASE): a
platform for comprehensive management and analysis of microarray data. Genome Biol 3(8):
SOFTWARE0003.
Saeed AI, Sharov V, White J et al (2003) TM4: a free, open-source system for microarray data
management and analysis. Biotechniques 34(2):374–378
Saha S, Sparks AB, Rago C et al (2002) Using the transcriptome to annotate the genome. Nat
Biotechnol 20(5):508–512
Salamov AA, Solovyev VV (2000) Ab initio gene finding in Drosophila genomic DNA. Genome
Res 10(4):516–522