Publications
Submitted
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L. LeGault and
C. Dewey.
Inference of alternative splicing from RNA-Seq data with probabilistic splice graphs.
Submitted.
In Press
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B. Haas,
A. Papanicolaou,
M. Yassour,
M. Grabherr,
P. Blood,
J. Bowden,
M. Couger,
D. Eccles,
B. Li,
M. Lieber,
M. MacManes,
M. Ott,
J. Orvis,
N. Pochet,
F. Strozzi,
N. Weeks,
R. Westerman,
T. William,
C. Dewey,
R. Henschel,
R. LeDuc,
N. Friedman and
A. Regev.
De novo transcript sequence reconstruction from RNA-Seq: reference generation and analysis with Trinity.
Nature Protocols. In press.
2013
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R. Stewart,
C. Rascón,
S. Tian,
J. Nie,
C. Barry,
L. Chu,
R. Wagner,
M. Probasco,
J. Bolin,
N. Leng,
S. Sengupta,
M. Volkmer,
B. Habermann,
E. Tanaka,
J. Thomson, and
C. Dewey.
(2013)
Comparative RNA-seq analysis in the unsequenced axolotl: The oncogene burst highlights early gene expression in the blastema.
PLoS
Computational Biology.
9(3): e1002936.
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S. Li,
W. Guo,
C. Dewey,
M. Greaser.
(2013)
Rbm20 regulates titin alternative splicing as a splicing repressor.
Nucleic Acids Research.
41(4): 2659-2672. (Featured Article)
2012
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C. Langley,
K. Stevens,
C. Cardeno,
Y. Lee,
D. Schrider,
J. Pool,
S. Langley,
C. Suarez,
R. Detig-Corbett,
B. Kolaczkowski,
S. Fang,
P. Nista,
A. Holloway,
A. Kern,
C. Dewey,
Y. Song,
M. Hahn, and
D. Begun
(2012)
Genomic variation in natural populations of Drosophila
melanogaster.
Genetics.
192(2):533-98.
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C. Dewey
(2012)
Whole-genome alignment.
In M. Anisimova, editor,
Evolutionary Genomics,
volume 855 of
Methods in Molecular Biology.
Humana Press.
237-57.
2011
2010
2009
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M. White,
C. Ané,
C. Dewey,
B. Larget,
B. Payseur.
(2009)
Fine scale phylogenetic discordance across the house
mouse genome.
PLoS
Genetics
5(11): e1000729.
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R. Bradley,
A. Roberts,
M. Smoot,
S. Juvekar,
J. Do,
C. Dewey,
I. Holmes, and
L. Pachter.
(2009)
Fast Statistical Alignment.
PLoS
Computational Biology
5(5): e1000392.
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R. Arora,
C. Dewey, and
W. Sethares.
(2009)
Reconstructing latent periods in genome sequences with insertions and deletions.
IEEE
International Workshop on Genomic Signal Processing and Statistics
(GENSiPS)
2007
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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.
-
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.
2006
-
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.
2005
2004
2002
Other manuscripts
