372
V. Mittard-Runte et al.
Cover T, Hart P (1967) Nearest neighbor pattern classification. IEEE Trans Inf Theory 13(1):21–27
Dandekar T, Snel B, Huynen MA et al (1998) Conservation of gene order: a fingerprint of proteins
that physically interact. Trends Biochem Sci 23(9):324–328
Datson NA, van der Perk-de Jong J, van den Berg MP et al (1999) MicroSAGE: a modified procedure for serial analysis of gene expression in limited amounts of tissue. Nucleic Acids Res
27(5):1300–1307
Delcher AL, Bratke KA, Powers EC et al (2007) Identifying bacterial genes and endosymbiont
DNA with Glimmer. Bioinformatics 23(6):673–679
Delcher AL, Harmon D, Kasif S et al (1999) Improved microbial gene identification with
GLIMMER. Nucleic Acids Res 27(23):4636–4641
Demeter J, Beauheim C, Gollub J et al (2007) The Stanford microarray database: implementation
of new analysis tools and open source release of software. Nucleic Acids Res 35:D766–D770
Djebali S, Delaplace F, Crollius HR (2006) Exogean: a framework for annotating protein-coding
genes in eukaryotic genomic DNA. Genome Biol 7(Suppl 1):S7–S10
Dondrup M, Goesmann A, Bartels D et al (2003) EMMA: a platform for consistent storage and
efficient analysis of microarray data. J Biotechnol 106(2-3):135–146
Dondrup M, Albaum S, Griebel T et al (2009) EMMA 2 – A MAGE-compliant system for the
collaborative analysis and integration of microarray data. BMC Bioinformatics 10(1):50
Dressman D, Yan H, Traverso G et al (2003) Transforming single DNA molecules
into fluorescent magnetic particles for detection and enumeration of genetic
variations. Proc Natl Acad Sci U S A 100(15):8817–8822
Durbin R, Eddy S, Krogh A et al (1998) Biological sequence analysis. Cambridge University Press,
Cambridge.
Edwards RA, Rodriguez-Brito B, Wegley L et al (2006) Using pyrosequencing to shed light on
deep mine microbial ecology. BMC Genomics 7:57
Eisen MB, Spellman PT, Brown PO et al (1998) Cluster analysis and display of genome-wide
expression patterns. Proc Natl Acad Sci U S A 95(25):14863–14868
Elsik CG, Mackey AJ, Reese JT et al (2007) Creating a honey bee consensus gene set. Genome
Biol 8(1):R13
Emanuelsson O, Nielsen H, von Heijne G (1999) ChloroP, a neural network-based method for
predicting chloroplast transit peptides and their cleavage sites. Protein Sci 8(5):978–984
Emanuelsson O, Brunak S, von Heijne G et al (2007) Locating proteins in the cell using TargetP,
SignalP and related tools. Nat Protoc 2(4):953–971
Ewing B, Hillier L, Wendl MC et al (1998) Base-calling of automated sequencer traces using
phred. I. Accuracy assessment. Genome Res 8(3):175–185
Fedurco M, Romieu A, Williams S et al (2006) BTA, a novel reagent for DNA attachment on
glass and efficient generation of solid-phase amplified DNA colonies. Nucleic Acids Res 34(3):
e22
Fleischmann RD, Adams MD, White O et al (1995) Whole-genome random sequencing and
assembly of Haemophilus influenzae Rd. Science 269(5223):496–512
Flicek P, Aken BL, Beal K et al (2008) Ensembl 2008. Nucleic Acids Res 36:D707–D714
Florea L, Hartzell G, Zhang Z et al (1998) A computer program for aligning a cDNA sequence
with a genomic DNA sequence. Genome Res 8(9):967–974
Gaasterland T, Sczyrba A, Thomas E et al (2000) MAGPIE/EGRET annotation of the 2.9-Mb
Drosophila melanogaster Adh region. Genome Res 10:502–510
Gartemann KH, Abt B, Bekel T et al (2008) The genome sequence of the tomato-pathogenic actinomycete Clavibacter michiganensis subsp. michiganensis NCPPB382 reveals a large island
involved in pathogenicity. J Bacteriol 190(6):2138–2149
Gentleman R, Huber W, Carev VJ (eds) (2005) Bioinformatics and computational biology solutions
using R and bioconductor. Springer, New York.
Gentleman RC, Carey VJ, Bates DM et al (2004) Bioconductor: open software development for
computational biology and bioinformatics. Genome Biol 5(10):R80
V. Mittard-Runte et al.
Cover T, Hart P (1967) Nearest neighbor pattern classification. IEEE Trans Inf Theory 13(1):21–27
Dandekar T, Snel B, Huynen MA et al (1998) Conservation of gene order: a fingerprint of proteins
that physically interact. Trends Biochem Sci 23(9):324–328
Datson NA, van der Perk-de Jong J, van den Berg MP et al (1999) MicroSAGE: a modified procedure for serial analysis of gene expression in limited amounts of tissue. Nucleic Acids Res
27(5):1300–1307
Delcher AL, Bratke KA, Powers EC et al (2007) Identifying bacterial genes and endosymbiont
DNA with Glimmer. Bioinformatics 23(6):673–679
Delcher AL, Harmon D, Kasif S et al (1999) Improved microbial gene identification with
GLIMMER. Nucleic Acids Res 27(23):4636–4641
Demeter J, Beauheim C, Gollub J et al (2007) The Stanford microarray database: implementation
of new analysis tools and open source release of software. Nucleic Acids Res 35:D766–D770
Djebali S, Delaplace F, Crollius HR (2006) Exogean: a framework for annotating protein-coding
genes in eukaryotic genomic DNA. Genome Biol 7(Suppl 1):S7–S10
Dondrup M, Goesmann A, Bartels D et al (2003) EMMA: a platform for consistent storage and
efficient analysis of microarray data. J Biotechnol 106(2-3):135–146
Dondrup M, Albaum S, Griebel T et al (2009) EMMA 2 – A MAGE-compliant system for the
collaborative analysis and integration of microarray data. BMC Bioinformatics 10(1):50
Dressman D, Yan H, Traverso G et al (2003) Transforming single DNA molecules
into fluorescent magnetic particles for detection and enumeration of genetic
variations. Proc Natl Acad Sci U S A 100(15):8817–8822
Durbin R, Eddy S, Krogh A et al (1998) Biological sequence analysis. Cambridge University Press,
Cambridge.
Edwards RA, Rodriguez-Brito B, Wegley L et al (2006) Using pyrosequencing to shed light on
deep mine microbial ecology. BMC Genomics 7:57
Eisen MB, Spellman PT, Brown PO et al (1998) Cluster analysis and display of genome-wide
expression patterns. Proc Natl Acad Sci U S A 95(25):14863–14868
Elsik CG, Mackey AJ, Reese JT et al (2007) Creating a honey bee consensus gene set. Genome
Biol 8(1):R13
Emanuelsson O, Nielsen H, von Heijne G (1999) ChloroP, a neural network-based method for
predicting chloroplast transit peptides and their cleavage sites. Protein Sci 8(5):978–984
Emanuelsson O, Brunak S, von Heijne G et al (2007) Locating proteins in the cell using TargetP,
SignalP and related tools. Nat Protoc 2(4):953–971
Ewing B, Hillier L, Wendl MC et al (1998) Base-calling of automated sequencer traces using
phred. I. Accuracy assessment. Genome Res 8(3):175–185
Fedurco M, Romieu A, Williams S et al (2006) BTA, a novel reagent for DNA attachment on
glass and efficient generation of solid-phase amplified DNA colonies. Nucleic Acids Res 34(3):
e22
Fleischmann RD, Adams MD, White O et al (1995) Whole-genome random sequencing and
assembly of Haemophilus influenzae Rd. Science 269(5223):496–512
Flicek P, Aken BL, Beal K et al (2008) Ensembl 2008. Nucleic Acids Res 36:D707–D714
Florea L, Hartzell G, Zhang Z et al (1998) A computer program for aligning a cDNA sequence
with a genomic DNA sequence. Genome Res 8(9):967–974
Gaasterland T, Sczyrba A, Thomas E et al (2000) MAGPIE/EGRET annotation of the 2.9-Mb
Drosophila melanogaster Adh region. Genome Res 10:502–510
Gartemann KH, Abt B, Bekel T et al (2008) The genome sequence of the tomato-pathogenic actinomycete Clavibacter michiganensis subsp. michiganensis NCPPB382 reveals a large island
involved in pathogenicity. J Bacteriol 190(6):2138–2149
Gentleman R, Huber W, Carev VJ (eds) (2005) Bioinformatics and computational biology solutions
using R and bioconductor. Springer, New York.
Gentleman RC, Carey VJ, Bates DM et al (2004) Bioconductor: open software development for
computational biology and bioinformatics. Genome Biol 5(10):R80