Colin N. Dewey, Ph.D.

2006 University of California, Berkeley, Berkeley, CA 
"Colin Dewey"


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Lior Pachter grad student 2006 UC Berkeley
 (Whole -genome alignments and polytopes for comparative genomics.)


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Bo Li grad student 2008-2013 UW Madison (Computational Biology Tree)
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Liu P, Soukup AA, Bresnick EH, et al. (2020) PRAM: a novel pooling approach for discovering intergenic transcripts from large-scale RNA sequencing experiments. Genome Research
Nolte MJ, Jing P, Dewey CN, et al. (2020) Giant Island Mice Exhibit Widespread Gene Expression Changes in Key Metabolic Organs. Genome Biology and Evolution
Dewey CN. (2019) Whole-Genome Alignment. Methods in Molecular Biology (Clifton, N.J.). 1910: 121-147
Sanchez-Vazquez P, Dewey CN, Kitten N, et al. (2019) Genome-wide effects on transcription from ppGpp binding to its two sites on RNA polymerase. Proceedings of the National Academy of Sciences of the United States of America
Hewitt KJ, Katsumura KR, Matson DR, et al. (2017) GATA Factor-Regulated Samd14 Enhancer Confers Red Blood Cell Regeneration and Survival in Severe Anemia. Developmental Cell. 42: 213-225.e4
Bernstein MN, Doan A, Dewey CN. (2017) MetaSRA: normalized human sample-specific metadata for the Sequence Read Archive. Bioinformatics (Oxford, England)
Jiang P, Nelson JD, Leng N, et al. (2016) Analysis of embryonic development in the unsequenced axolotl: Waves of transcriptomic upheaval and stability. Developmental Biology
Liu P, Sanalkumar R, Bresnick EH, et al. (2016) Integrative analysis with ChIP-seq advances the limits of transcript quantification from RNA-seq. Genome Research
Tanimura N, Miller E, Igarashi K, et al. (2015) Mechanism governing heme synthesis reveals a GATA factor/heme circuit that controls differentiation. Embo Reports
Zeng X, Li B, Welch R, et al. (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: e1004491
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