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Results for: Publications | Transcriptome-based Phenotyping Project


MetaSRA: normalized human sample-specific metadata for the Sequence Read Archive. Bernstein M, Doan A, Dewey C. Bioinformatics, 2017.

SCnorm: robust normalization of single-cell RNA-seq data. Bacher R, Chu LF, Leng N, Gasch A, Thomson J, Stewart R, Newton M, Kendziorski C. Nature Methods, 2017.

A statistical approach for identifying differential distributions in single-cell RNA-seq experiments. Korthauer K, Chu LF, Newton M, Li Y, Thomson J, Stewart R, Kendziorski K. Genome Biology 17:222, 2016.

Single-cell RNA-seq reveals novel regulators of human embryonic stem cell differentiation to definitive endoderm. Chu LF, Leng N, Zhang J, Hou Z, Mamott D, Vereide D, Choi J, Kendziorski C, Stewart R, Thomson J. Genome Biology 17:173.

Analysis of embryonic development in the unsequenced axolotl: waves of transcriptional upheaval and stability. Jiang P, Nelson J, Leng N, Collins M, Swanson S, Dewey C, Thomson J, Stewart R. Developmental Biology, 2016.

Integrative analysis with ChIP-seq advances the limits of transcript quantification from RNA-seq. Liu P, Sanalkumar R, Bresnick E, Keles S, Dewey C. Genome Research 26:1124–1133, 2016.

Design and computational analysis of single-cell RNA-sequencing experiments. Bacher R, Kendziorski C. Genome Biology 17:173, 2016.

IPI59: An actionable biomarker to improve treatment response in serous ovarian carcinoma patients. Choi J, Ye S, Eng K, Korthauer K, Bradley W, Rader J, Kendziorski C. Statistics in Biosciences, 2016.

OEFinder: a user interface to identify and visualize ordering effects in single-cell RNA-seq data. Leng N, Choi J, Chu LF, Thomson JA, Kendziorski C, Stewart R. Bioinformatics 32(9):1408-10, 2016.

Hematopoietic signaling mechanism revealed from a stem/progenitor cell cistrome. Hewitt KJ, Kim DH, Devadas P, Prathibha R, Zuo C, Sanalkumar R, Johnson D, Kang Y-A, Kim J-S, Dewey CN, Keles S, Bresnick EH. Molecular Cell 9(1):62–74, 2015.

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