Bibliography

Below is a list of the publications referred to in our software, in the user manuals and the papers listed in the Bioinformatics Explained section.

von Ahsen et al. (2001)
N. von Ahsen; C. T. Wittwer & E. Schütz:
Oligonucleotide melting temperatures under PCR conditions: nearest-neighbor corrections for Mg(2+), deoxynucleotide triphosphate, and dimethyl sulfoxide concentrations with comparison to alternative empirical formulas.
Clin Chem, 47, 1956-1961


Allison et al. (2006)
Allison, D.B.; Cui, X.; Page, G.P. & Sabripour, M.:
Microarray data analysis: from disarray to consolidation and consensus
NATURE REVIEWS GENETICS, Nature Publishing Group, 7, 55


Altschul and Gish (1996)
S. F. Altschul & W. Gish:
Local alignment statistics.
Methods Enzymol, 266, 460-480


Altschul et al. (1990)
S. F. Altschul; W. Gish; W. Miller; E. W. Myers & D. J. Lipman:
Basic local alignment search tool.
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http://dx.doi.org/10.1006/jmbi.1990.9999


Altshuler et al. (2000)
D. Altshuler; V. J. Pollara; C. R. Cowles; W. J. Van Etten; J. Baldwin; L. Linton & E. S. Lander:
An SNP map of the human genome generated by reduced representation shotgun sequencing.
Nature, Whitehead Institute/MIT Center for Genome Research, Cambridge, Massachusetts 02142, USA., 407, 513-516
http://dx.doi.org/10.1038/35035083


Andrade et al. (1998)
M. A. Andrade; S. I. O'Donoghue & B. Rost:
Adaptation of protein surfaces to subcellular location.
J Mol Biol, 276, 517-525


Atkins (1998)
Peter Atkins:
Physical Chemistry
Freeman,

Bachmair et al. (1986)
A. Bachmair; D. Finley & A. Varshavsky:
In vivo half-life of a protein is a function of its amino-terminal residue.
Science, 234, 179-186


Baggerly et al. (2003)
Baggerly, K.A.; Deng, L.; Morris, J.S. & Aldaz, C.M.:
Differential expression in SAGE: accounting for normal between-library variation
Bioinformatics, Oxford Univ Press, 19, 1477-1483


Bairoch et al. (2005)
Amos Bairoch; Rolf Apweiler; Cathy H Wu; Winona C Barker; Brigitte Boeckmann; Serenella Ferro; Elisabeth Gasteiger; Hongzhan Huang; Rodrigo Lopez; Michele Magrane; Maria J Martin; Darren A Natale; Claire O'Donovan; Nicole Redaschi & Lai-Su L Yeh:
The Universal Protein Resource (UniProt).
Nucleic Acids Res, 33, D154-D159
http://dx.doi.org/10.1093/nar/gki070


Bateman et al. (2002)
Alex Bateman; Ewan Birney; Lorenzo Cerruti; Richard Durbin; Laurence Etwiller; Sean R Eddy; Sam Griffiths-Jones; Kevin L Howe; Mhairi Marshall & Erik L L Sonnhammer:
The Pfam protein families database.
Nucleic Acids Res, 30, 276-280


Bateman et al. (2004)
Bateman, A.; Coin, L.; Durbin, R.; Finn, R. D.; Hollich, V.; Griffiths-Jones, S.; Khanna, A.; Marshall, M.; Moxon, S.; Sonnhammer, E. L.; Studholme, D. J.; Yeats, C. & Eddy, S. R.:
The Pfam protein families database.
Nucleic Acids Res., 32, D138-D141


Bateman et al. (2004)
Alex Bateman; Lachlan Coin; Richard Durbin; Robert D Finn; Volker Hollich; Sam Griffiths-Jones; Ajay Khanna; Mhairi Marshall; Simon Moxon; Erik L L Sonnhammer; David J Studholme; Corin Yeats & Sean R Eddy:
The Pfam protein families database.
Nucleic Acids Res, 32, D138-D141
http://dx.doi.org/10.1093/nar/gkh121


Baxevanis and Ouellette (2001)
Baxevanis, A.D. & Ouellette, B.F.F.:
Bioinformatics
Wiley-Interscience,

Bendtsen et al. (2004)
Jannick Dyrløv Bendtsen; Lars Juhl Jensen; Nikolaj Blom; Gunnar Von Heijne & Søren Brunak:
Feature-based prediction of non-classical and leaderless protein secretion.
Protein Eng Des Sel, 17, 349-356
http://dx.doi.org/10.1093/protein/gzh037


Bendtsen et al. (2005)
Jannick D Bendtsen; Lars Kiemer; Anders Fausbøll & Søren Brunak:
Non-classical protein secretion in bacteria.
BMC Microbiol, 5, 58
http://dx.doi.org/10.1186/1471-2180-5-58


Bendtsen et al. (2004)
Jannick Dyrløv Bendtsen; Henrik Nielsen; Gunnar von Heijne & Søren Brunak:
Improved prediction of signal peptides: SignalP 3.0.
J Mol Biol, 340, 783-795
http://dx.doi.org/10.1016/j.jmb.2004.05.028


Benjamini and Hochberg (1995)
Benjamini, Y. & Hochberg, Y.:
Controlling the false discovery rate: a practical and powerful approach to multiple testing
JOURNAL-ROYAL STATISTICAL SOCIETY SERIES B, ROYAL STAT MED, 57, 289-289


Bennett-Baker et al. (1996)
P. E. Bennett-Baker; S. Kiousis; S. C. Chandrasekharappa; S. E. King; K. J. Abel; F. S. Collins; B. L. Weber & J. S. Chamberlain:
Isolation of tetranucleotide repeat polymorphisms flanking the BRCA1 gene.
Genomics, 32, 163-167
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Benson et al. (2005)
Dennis A Benson; Ilene Karsch-Mizrachi; David J Lipman; James Ostell & David L Wheeler:
GenBank.
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Bernhart et al. (2006)
Stephan H Bernhart; Hakim Tafer; Ulrike Mückstein; Christoph Flamm; Peter F Stadler & Ivo L Hofacker:
Partition function and base pairing probabilities of RNA heterodimers.
Algorithms Mol Biol, 1, 3
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Blobel (2000)
Blobel, G.:
Protein targeting (Nobel lecture)
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Bolstad et al. (2003)
Bolstad, BM; Irizarry, RA; Astrand, M. & Speed, TP:
A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
Bioinformatics, Oxford Univ Press, 19, 185-193


Bommarito et al. (2000)
S. Bommarito; N. Peyret & J. SantaLucia:
Thermodynamic parameters for DNA sequences with dangling ends.
Nucleic Acids Res, 28, 1929-1934


Brockman et al. (2008)
William Brockman; Pablo Alvarez; Sarah Young; Manuel Garber; Georgia Giannoukos; William L Lee; Carsten Russ; Eric S Lander; Chad Nusbaum & David B Jaffe:
Quality scores and SNP detection in sequencing-by-synthesis systems.
Genome Res, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA., 18, 763-770
http://dx.doi.org/10.1101/gr.070227.107


Brookes (1999)
A. J. Brookes:
The essence of SNPs.
Gene, 234, 177-186


Cedano et al. (1997)
J. Cedano; P. Aloy; J. A. Pérez-Pons & E. Querol:
Relation between amino acid composition and cellular location of proteins.
J Mol Biol, 266, 594-600


Chen et al. (2004)
Gang Chen; Brent M Znosko; Xiaoqi Jiao & Douglas H Turner:
Factors affecting thermodynamic stabilities of RNA 3 x 3 internal loops.
Biochemistry, 43, 12865-12876
http://dx.doi.org/10.1021/bi049168d


Chou and Fasman (1974)
P. Y. Chou & G. D. Fasman:
Prediction of protein conformation.
Biochemistry, 13, 222-245


Chou and Fasman (1974)
P. Y. Chou & G. D. Fasman:
Conformational parameters for amino acids in helical, beta-sheet, and random coil regions calculated from proteins.
Biochemistry, 13, 211-222


CLC bio (2007)
CLC bio:
CLC Bioinformatics Cell white paper
http://www.clcbio.com


Clote et al. (2005)
Peter Clote; Fabrizio Ferré; Evangelos Kranakis & Danny Krizanc:
Structural RNA has lower folding energy than random RNA of the same dinucleotide frequency.
RNA, 11, 578-591
http://dx.doi.org/10.1261/rna.7220505


Cole et al. (1998)
S. T. Cole; R. Brosch; J. Parkhill; T. Garnier; C. Churcher; D. Harris; S. V. Gordon; K. Eiglmeier; S. Gas; C. E. Barry; F. Tekaia; K. Badcock; D. Basham; D. Brown; T. Chillingworth; R. Connor; R. Davies; K. Devlin; T. Feltwell; S. Gentles; N. Hamlin; S. Holroyd; T. Hornsby; K. Jagels; A. Krogh; J. McLean; S. Moule; L. Murphy; K. Oliver; J. Osborne; M. A. Quail; M. A. Rajandream; J. Rogers; S. Rutter; K. Seeger; J. Skelton; R. Squares; S. Squares; J. E. Sulston; K. Taylor; S. Whitehead & B. G. Barrell:
Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence.
Nature, 393, 537-544
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F. S. Collins:
BRCA1--lots of mutations, lots of dilemmas.
N Engl J Med, 334, 186-188


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F. S. Collins:
Ahead of schedule and under budget: the Genome Project passes its fifth birthday.
Proc Natl Acad Sci U S A, 92, 10821-10823


Collins et al. (1998)
F. S. Collins; L. D. Brooks & A. Chakravarti:
A DNA polymorphism discovery resource for research on human genetic variation.
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Consortium (2007)
The UniiProt Consortium:
The Universal Protein Resource (UniProt).
Nucleic Acids Res, 35, D193-D197


Cornette et al. (1987)
J. L. Cornette; K. B. Cease; H. Margalit; J. L. Spouge; J. A. Berzofsky & C. DeLisi:
Hydrophobicity scales and computational techniques for detecting amphipathic structures in proteins.
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Corning and Steffy (1979)
W. C. Corning & R. A. Steffy:
Taximetric strategies applied to psychiatric classification.
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Costa (2007)
Fabrício F Costa:
Non-coding RNAs: lost in translation?
Gene, 386, 1-10
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Crooks et al. (2004)
Gavin E Crooks; Gary Hon; John-Marc Chandonia & Steven E Brenner:
WebLogo: a sequence logo generator.
Genome Res, 14, 1188-1190
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Dalgaard and Pedersen (2001)
L. T. Dalgaard & O. Pedersen:
Uncoupling proteins: functional characteristics and role in the pathogenesis of obesity and Type II diabetes.
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M. O. Dayhoff & R. M. Schwartz:
Atlas of Protein Sequence and Structure
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M. O. Dayhoff; R. M. Schwartz & B. C. Orcutt:
A model of evolutionary change in protein
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Dempster, A.P.; Laird, N.M.; Rubin, D.B. & others:
Maximum likelihood from incomplete data via the EM algorithm
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Ye Ding & Charles E Lawrence:
A statistical sampling algorithm for RNA secondary structure prediction.
Nucleic Acids Res, 31, 7280-7301


Dudoit et al. (2003)
Dudoit, S.; Shaffer, J.P. & Boldrick, J.C.:
Multiple Hypothesis Testing in Microarray Experiments
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Durbin et al. (1998)
Richard Durbin; Sean R. Eddy; Anders Krogh & Graeme Mitchison:
Biological sequence analysis
Cambridge University Press, Cambridge,

Eddy (2004)
Sean R. Eddy:
Where did the BLOSUM62 alignment score matrix come from?
Nat Biotechnol, 22, 1035-1036
http://dx.doi.org/10.1038/nbt0804-1035


Eddy (2003)
Sean R. Eddy:
The HMMER User's Guide (biological sequence analysis using profile hidden Markov models)
Howard Hughes Medical Institute and Dept. of Genetics , Washington University School of Medicine, http://hmmer.wustl.edu/


Eddy (1998)
Sean R. Eddy:
Profile hidden Markov models
Bioinformatics, Oxford Univ Press, 14, 755-763


Edgar (2004)
Robert C Edgar:
MUSCLE: a multiple sequence alignment method with reduced time and space complexity.
BMC Bioinformatics, 5, 113
http://dx.doi.org/10.1186/1471-2105-5-113


Edgar (2004)
Robert C Edgar:
MUSCLE: multiple sequence alignment with high accuracy and high throughput.
Nucleic Acids Res, 32, 1792-1797
http://dx.doi.org/10.1093/nar/gkh340


Edgar and Batzoglou (2006)
Robert C Edgar & Serafim Batzoglou:
Multiple sequence alignment.
Curr Opin Struct Biol, 16, 368-373
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Eisen et al. (1998)
Eisen, M.B.; Spellman, P.T.; Brown, P.O. & Botstein, D.:
Cluster analysis and display of genome-wide expression patterns
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D. Eisenberg; E. Schwarz; M. Komaromy & R. Wall:
Analysis of membrane and surface protein sequences with the hydrophobic moment plot.
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Eisenberg et al. (1984)
D. Eisenberg; R. M. Weiss & T. C. Terwilliger:
The hydrophobic moment detects periodicity in protein hydrophobicity.
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Induction of hepatitis A virus-neutralizing antibody by a virus-specific synthetic peptide.
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D. M. Engelman; T. A. Steitz & A. Goldman:
Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins.
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Falcon and Gentleman (2007)
Falcon, S. & Gentleman, R.:
Using GOstats to test gene lists for GO term association
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L. Feigenbaum; K. Fujita; F. S. Collins & G. Jay:
Repression of the NF1 gene by Tax may expain the development of neurofibromas in human T-lymphotropic virus type 1 transgenic mice.
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J. Felsenstein:
Evolutionary trees from DNA sequences: a maximum likelihood approach.
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Feng and Doolittle (1987)
Feng, D. F. & Doolittle, R. F.:
Progressive sequence alignment as a prerequisite to correct phylogenetic trees
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Feng and Doolittle (1987)
D. F. Feng & R. F. Doolittle:
Progressive sequence alignment as a prerequisite to correct phylogenetic trees.
J Mol Evol, 25, 351-360


Finn et al. (2006)
Robert D Finn; Jaina Mistry; Benjamin Schuster-Böckler; Sam Griffiths-Jones; Volker Hollich; Timo Lassmann; Simon Moxon; Mhairi Marshall; Ajay Khanna; Richard Durbin; Sean R Eddy; Erik L L Sonnhammer & Alex Bateman:
Pfam: clans, web tools and services.
Nucleic Acids Res, 34, D247-D251
http://dx.doi.org/10.1093/nar/gkj149


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A molecular clock dates the common ancestor of European-type porcine reproductive and respiratory syndrome virus at more than 10 years before the emergence of disease.
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Galperin and Koonin (1998)
M. Y. Galperin & E. V. Koonin:
Sources of systematic error in functional annotation of genomes: domain rearrangement, non-orthologous gene displacement and operon disruption.
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Gardner et al. (2005)
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A benchmark of multiple sequence alignment programs upon structural RNAs
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The geneticist's approach to complex disease.
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Calculation of protein extinction coefficients from amino acid sequence data.
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O. Gotoh:
An Improved Algorithm for Matching Biological Sequences
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Guindon and Gascuel (2003)
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A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood
Systematic Biology, JSTOR, 52, 696-704


Gura (1998)
T. Gura:
Uncoupling proteins provide new clue to obesity's causes.
Science, 280, 1369-1370


Guyer and Collins (1995)
M. S. Guyer & F. S. Collins:
How is the Human Genome Project doing, and what have we learned so far?
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Hajra et al. (1996)
A. Hajra; P. P. Liu & F. S. Collins:
Transforming properties of the leukemic inv(16) fusion gene CBFB-MYH11.
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A vector-based method for drawing RNA secondary structure
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Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
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von Heijne, G.:
A new method for predicting signal sequence cleavage sites
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J. Hein:
An algorithm for statistical alignment of sequences related by a binary tree
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Amino acid substitution matrices from protein blocks.
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Recent divergence of the HLA-DRB1*04 allelic lineage from the DRB1*0701 lineage after the separation of the human and chimpanzee species.
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Hopp and Woods (1983)
T. P. Hopp & K. R. Woods:
A computer program for predicting protein antigenic determinants.
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Horikawa (1977)
Y. Horikawa:
[Louis-Bar syndrome]
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Genetic variation in the gene encoding calpain-10 is associated with type 2 diabetes mellitus.
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Rubella antibody in multiple sclerosis.
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Ensembl 2007.
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A. Ikai:
Thermostability and aliphatic index of globular proteins.
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[Encephalitis (author's transl)]
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Surface and inside volumes in globular proteins.
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An integrated software system for analyzing ChIP-chip and ChIP-seq data
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A march of genetic maps.
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Evolution of protein molecules
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Prediction of chain flexibility in proteins
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MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform.
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Thermodynamics of single mismatches in RNA duplexes.
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M. Kimura:
A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences.
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Evaluating eukaryotic secreted protein prediction.
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A likelihood ratio test for evolutionary rate shifts and functional divergence among proteins.
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