Publications
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A. Stark,
M. F. Lin,
P. Kheradpour,
J. S. Pedersen,
L. Parts,
J. W. Carlson,
M. A. Crosby,
M. D. Rasmussen,
S. Roy,
A. N. Deoras,
J. G. Ruby,
J. Brennecke,
Harvard FlyBase curators,
Berkeley Drosophila Genome Project,
E. Hodges,
A. S. Hinrichs,
A. Caspi,
B. Paten,
S.-W. Park,
M. V. Han,
M. L. Maeder,
B. J. Polansky,
B. E. Robson,
S. Aerts,
J. van Helden,
B. Hassan,
D. G. Gilbert,
D. A. Eastman,
M. Rice,
M. Weir,
M. W. Hahn,
Y. Park,
C. N. Dewey,
L. Pachter,
W. J. Kent,
D. Haussler,
E. C. Lai,
D. P. Bartel,
G. J. Hannon,
T. C. Kaufman,
M. B. Eisen,
A. G. Clark,
D. Smith,
S. E. Celniker,
W. M. Gelbart,
M. Kellis.
(2007)
Discovery of functional elements in 12 drosophila genomes using evolutionary signatures.
Nature
450(7167):219-232.
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D. Begun,
A. Holloway,
K. Stevens,
L. Hillier,
Y. Poh,
M. Hahn,
P. Nista,
C. Jones,
A. Kern,
C. Dewey,
L. Pachter,
E. Myers,
C. Langley
(2007)
Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans.
PLoS Biology
5(11):e310.
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E. Margulies,
G. Cooper,
G. Asimenos,
D. Thomas,
C. Dewey,
et al.
(2007)
Analyses of deep mammalian sequence alignments and
constraint predictions for 1% of the human genome.
Genome Research
17(6):760-774.
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The ENCODE Project Consortium
(2007)
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.
Nature
447:799-816.
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C. Dewey
(2007)
Aligning multiple whole genomes with Mercator and MAVID.
In N. Bergman, editor,
Comparative Genomics,
volume 395 of
Methods in Molecular Biology.
Humana Press.
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N. Beerenwinkel,
C. Dewey, and
K. Woods.
Parametric inference of recombination in HIV genomes.
Submitted.
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C. Dewey,
I. Rogozin, and
E. Koonin
(2006)
Compensatory relationships between splice sites and
exonic splicing signals depending on the length of vertebrate
introns.
BMC Genomics
7:311.
-
C. Dewey
(2006)
Whole-genome alignments and polytopes for comparative genomics.
Ph.D. thesis,
University of California, Berkeley.
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C. Dewey,
P. Huggins,
K. Woods,
B. Sturmfels and
L. Pachter
(2006)
Parametric alignment of Drosophila genomes.
PLoS Computational Biology
2(6): e73.
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C. Dewey and
L. Pachter
(2006)
Evolution at the nucleotide level: the problem of multiple whole-genome alignment.
Human Molecular Genetics
15:R51-R56.
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S. Lall,
D. Grün,
A. Krek,
K. Chen,
Y. Wang,
C. Dewey,
P. Sood,
T. Colombo,
N. Bray,
P. MacMenamin,
H. Kao,
K. Gunsalus,
L. Pachter,
F. Piano, and
N. Rajewsky
(2006)
A genome-wide map of conserved microRNA targets in C. elegans.
Current Biology
16:460-471.
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C. Dewey and
K. Woods
(2005)
Parametric sequence alignment.
In L. Pachter and B. Sturmfels Eds.
Algebraic Statistics for Computational Biology.
Cambridge University Press.
193-205.
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International Chicken Genome Sequencing Consortium
(2004)
Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution.
Nature
432:695-716.
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The ENCODE Project Consortium
(2004)
The ENCODE (ENCyclopedia Of DNA Elements) project.
Science
306:636-640.
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C. Dewey,
J.Q. Wu,
S. Cawley,
M. Alexandersson,
R. Gibbs and
L. Pachter
(2004)
Accurate identification of novel human genes through simultaneous gene prediction in human, mouse, and rat.
Genome Research
14:661-664.
(Supplementary Web site)
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Rat Genome Sequencing Project Consortium
(2004)
Genome sequence of the Brown Norway rat yields insights into mammalian evolution.
Nature
428:493-521.
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Mouse Genome Sequencing Consortium
(2002)
Initial sequencing and comparative analysis of the mouse genome.
Nature
420:520-562.
