Publications
Google Scholar |
NCBI Bibliography
Submitted
In Press
2023
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I. Fraga de Andrade,
K. D. Johnson,
C. Mehta,
C. Dewey,
U. Basu, and
E. Bresnick.
(2023)
RNA-Regulatory Exosome Complex Suppresses an Apoptotic Program to Confer Erythroid Progenitor Cell Survival in Vivo.
Blood Advances.
7(4):586-601.
doi:10.1182/bloodadvances.2022008481
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H. Toh,
A. Bagheri,
C. Dewey,
R. Stewart,
L. Yan,
D. Clegg,
J. A. Thomson, and
P. Jiang.
(2023).
A Nile Rat Transcriptomic Landscape across
22 Organs by Ultra-Deep Sequencing and Comparative RNA-Seq Pipeline (CRSP).
Computational Biology and Chemistry.
102 (February): 107795.
doi:10.1016/j.compbiolchem.2022.107795
2022
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T. Woodring,
C. Dewey,
L. Dos Santos Dias,
X. He,
H. E. Dobson,
M. Wüthrich, and
B. Klein
(2022)
Distinctive Populations of CD4+T Cells Associated
with Vaccine Efficacy.
iScience.
25(9): 104934.
doi:10.1016/j.isci.2022.104934
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B. Korte,
M. Giese,
G. Ramakrishnan,
S. Ma,
D. Bennin,
J. Rindy,
C. Dewey, and
A. Huttenlocher.
(2022)
Cell Type-Specific Transcriptome Profiling Reveals
a Role for Thioredoxin During Tumor Initiation.
Front Immunol.
13.
doi:10.3389/fimmu.2022.818893
2021
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C. Mehta,
I. Fraga de Andrade,
D. Matson,
C. Dewey, and
E. Bresnick.
(2021)
RNA-regulatory exosome complex confers cellular survival to promote erythropoiesis.
Nucleic Acids Research.
49(16):9007-9025.
doi:10.1093/nar/gkab367
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M. Bernstein and
C. Dewey.
(2021)
Annotating cell types in human single-cell RNA-seq data with CellO.
STAR Protocols.
2(3):100705.
doi:10.1016/j.xpro.2021.100705
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M. Bernstein,
Z. Ma,
M. Gleicher, and
C. Dewey.
(2021)
CellO: Comprehensive and hierarchical cell type classification of human cells with the Cell Ontology.
iScience.
24: 101913.
doi:10.1016/j.isci.2020.101913
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S. Su,
G. Chhabra,
M. Ndiaye,
C. Singh,
T. Ye,
W. Huang,
C. Dewey,
V. Setaluri, and
N. Ahmad
(2021)
PLK1 and NOTCH Positively Correlate in Melanoma and Their Combined Inhibition Results in Synergistic Modulations of Key Melanoma Pathways.
Molecular Cancer Therapeutics.
20: 161-172.
doi:10.1158/1535-7163.MCT-20-0654
2020
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P. Liu,
A. Soukup,
E. Bresnick,
C. Dewey, and
S. Keles.
(2020)
PRAM: a novel pooling approach for discovering intergenic transcripts from large-scale RNA sequencing experiments.
Genome Research.
30: 1655-1666.
doi:10.1101/gr.252445.119
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R. Houseright,
E. Rosowski,
P. Lam,
S. Tauzin,
O. Mulvaney,
C. Dewey, and
A. Huttenlocher.
(2020)
Cell type specific gene expression profiling reveals a role for complement component C3 in neutrophil responses to tissue damage.
Scientific Reports.
10: 15716.
doi:10.1038/s41598-020-72750-9.
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M. Nolte,
P. Jing,
C. Dewey, and
B. Payseur.
(2020)
Giant Island Mice Exhibit Widespread Gene Expression Changes in Key Metabolic Organs.
Genome Biology and Evolution.
12: 1277-1301.
doi:10.1093/gbe/evaa118.
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ENCODE Project Consortium.
(2020)
Expanded encyclopaedias of DNA elements in the human and mouse genomes.
Nature.
583: 699-710.
doi:10.1038/s41586-020-2493-4.
2019
2017
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K. Hewitt,
K. Katsumura,
D. Matson,
P. Devadas,
N. Tanimura,
A. Hebert,
J. Coon,
J.-S. Kim,
C. Dewey,
S. Keles,
R. Paulson, and
E. Bresnick.
(2017)
GATA Factor-Regulated Samd14 Enhancer Confers Red Blood Cell Regeneration and Survival in Severe Anemia.
Developmental Cell.
42(3):213-225.e4
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I. Sedykh,
B. Yoon,
L. Roberson,
O. Moskvin,
C. Dewey, and
Y. Grinblat.
(2017)
Zebrafish zic2 controls formation of periocular neural crest and choroid fissure morphogenesis.
Developmental Biology.
429(1):92-104.
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M. Bernstein,
A. Doan, and
C. Dewey.
(2017)
MetaSRA: normalized human sample-specific metadata for the Sequence Read Archive.
Bioinformatics.
33(18):2914-2923.
2016
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P. Liu,
R. Sanalkumar,
E. Bresnick,
S. Keles, and
C. Dewey
(2016)
Integrative analysis with RNA polymerase II ChIP-seq advances the limits of transcript quantification from RNA-seq.
Genome Research.
26(8):1124-33.
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P. Jiang,
J. Nelson,
N. Leng,
M. Collins,
S. Swanson,
C. Dewey,
J. Thomson, and
R. Stewart
(2016)
Analysis of embryonic development in the unsequenced axolotl: Waves of transcriptomic upheaval and stability.
Developmental Biology.
2016 Jul 27. pii: S0012-1606(15)30261-X.
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N. Tanimura,
E. Miller,
K. Igarashi,
D. Yang,
J. Burstyn,
C. Dewey,
E. Bresnick
(2016)
Mechanism Governing Heme Synthesis Reveals a GATA Factor-Heme Circuit that Controls Differentiation.
EMBO Reports.
17(2):249-65.
2015
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X. Zeng,
B. Li,
R. Welch,
C. Rojo,
Y. Zheng,
C. Dewey, and
S. Keles
(2015)
Perm-seq: Mapping protein-DNA interactions in segmental duplication and highly repetitive regions of genomes with prior-enhanced read mapping.
PLoS Computational Biology.
11(10):e1004491.
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K. Johnson,
G. Kong,
X. Gao,
Y-I. Chang,
K. Hewitt,
R. Sanalkumar,
R. Prathibha,
E. Ranheim,
C. Dewey,
J. Zhang,
E. Bresnick.
(2015)
Cis-regulatory mechanisms governing stem and progenitor cell transitions.
Science Advances.
1(8):e1500503-e1500503.
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K. Hewitt,
D. Kim,
P. Devadas,
R. Prathibha,
C. Zuo,
R. Sanalkumar,
K. Johnson,
Y. Kang,
J. Kim,
C. Dewey,
S. Keles,
E. Bresnick.
(2015)
Hematopoietic Signaling Mechanism Revealed from a Stem/Progenitor Cell Cistrome.
Molecular Cell.
59(1):62-74.
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N. Leng,
Y. Li,
B. McIntosh,
B. Nguyen,
B. Duffin,
S. Tian,
J. Thomson,
C. Dewey,
R. Stewart,
C. Kendziorski.
(2015)
EBSeq-HMM: a Bayesian approach for identifying gene-expression changes in ordered RNA-seq experiments.
Bioinformatics.
31(16):2614-2622.
2014
2013
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X. Gao,
K. Johnson,
Y. Chang,
M. Boyer,
C. Dewey,
J. Zhang, and
E. Bresnick.
(2013)
Gata2 cis-element is required for hematopoietic stem cell generation in the mammalian embryo.
Journal of Experimental
Medicine.
210(13):2833-42.
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Y. Zhang,
A. Cooke,
S. Park,
C. Dewey,
M. Wickens, and
M. Sheets.
(2013)
Bicaudal-C spatially controls translation of vertebrate maternal mRNAs. RNA.
19(11):1575-82.
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L. LeGault and
C. Dewey.
(2013)
Inference of alternative splicing from RNA-Seq data with probabilistic splice graphs.
Bioinformatics.
29(18):2300-2310.
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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.
(2013)
De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis.
Nature Protocols. 8(8):1494-1512.
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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.
-
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.
-
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
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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.
-
C. Dewey,
P. Huggins,
K. Woods,
B. Sturmfels and
L. Pachter
(2006)
Parametric alignment of Drosophila genomes.
PLoS Computational Biology
2(6): e73.
-
C. Dewey and
L. Pachter
(2006)
Evolution at the nucleotide level: the problem of multiple whole-genome alignment.
Human Molecular Genetics
15:R51-R56.
-
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
