Quality control of single-cell RNA-seq by SinQC

di Jiang, Peng, Thomson, James A., Stewart, Ron
Pubblicato in Bioinformatics (2016)

TimeMeter assesses temporal gene expression similarity and identifies differentially progressing genes

di Jiang, Peng, Chamberlain, Connie S, Vanderby, Ray, Thomson, James A, Stewart, Ron
Pubblicato in Nucleic Acids Res (2020)

Computational Drug Repositioning Using Continuous Self-Controlled Case Series

di Kuang, Zhaobin, Thomson, James, Caldwell, Michael, Peissig, Peggy, Stewart, Ron, Page, David
Pubblicato in KDD (2016)

Baseline Regularization for Computational Drug Repositioning with Longitudinal Observational Data

di Kuang, Zhaobin, Thomson, James, Caldwell, Michael, Peissig, Peggy, Stewart, Ron, Page, David
Pubblicato in IJCAI (U S) (2016)

A Simple Text Mining Approach for Ranking Pairwise Associations in Biomedical Applications

di Kuusisto, Finn, Steill, John, Kuang, Zhaobin, Thomson, James, Page, David, Stewart, Ron
Pubblicato in AMIA Jt Summits Transl Sci Proc (2017)

RNA-Seq of Human Neural Progenitor Cells Exposed to Lead (Pb) Reveals Transcriptome Dynamics, Splicing Alterations and Disease Risk Associations

di Jiang, Peng, Hou, Zhonggang, Bolin, Jennifer M., Thomson, James A., Stewart, Ron
Pubblicato in Toxicol Sci (2017)

AP-1(cFos/JunB)/miR-200a regulate the pro-regenerative glial cell response during axolotl spinal cord regeneration

di Sabin, Keith Z., Jiang, Peng, Gearhart, Micah D., Stewart, Ron, Echeverri, Karen
Pubblicato in Commun Biol (2019)

RNA-Seq gene expression estimation with read mapping uncertainty

di Li, Bo, Ruotti, Victor, Stewart, Ron M., Thomson, James A., Dewey, Colin N.
Pubblicazione 2010

Machine learning to predict developmental neurotoxicity with high-throughput data from 2D bio-engineered tissues

di Kuusisto, Finn, Costa, Vitor Santos, Hou, Zhonggang, Thomson, James, Page, David, Stewart, Ron
Pubblicato in Proc Int Conf Mach Learn Appl (2020)

Integrated Module and Gene-Specific Regulatory Inference Implicates Upstream Signaling Networks

di Roy, Sushmita, Lagree, Stephen, Hou, Zhonggang, Thomson, James A., Stewart, Ron, Gasch, Audrey P.
Pubblicazione 2013

A Statistical Framework for the Analysis of ChIP-Seq Data

di Kuan, Pei Fen, Chung, Dongjun, Pan, Guangjin, Thomson, James A., Stewart, Ron, Keleş, Sündüz
Pubblicato in J Am Stat Assoc (2012)

OEFinder: a user interface to identify and visualize ordering effects in single-cell RNA-seq data

di Leng, Ning, Choi, Jeea, Chu, Li-Fang, Thomson, James A., Kendziorski, Christina, Stewart, Ron
Pubblicato in Bioinformatics (2016)

CHARTS: a web application for characterizing and comparing tumor subpopulations in publicly available single-cell RNA-seq data sets

di Bernstein, Matthew N., Ni, Zijian, Collins, Michael, Burkard, Mark E., Kendziorski, Christina, Stewart, Ron
Pubblicato in BMC Bioinformatics (2021)

TF-Cluster: A pipeline for identifying functionally coordinated transcription factors via network decomposition of the shared coexpression connectivity matrix (SCCM)

di Nie, Jeff, Stewart, Ron, Zhang, Hang, Thomson, James A, Ruan, Fang, Cui, Xiaoqi, Wei, Hairong
Pubblicazione 2011

Embryonic Stem Cells/Induced Pluripotent Stem Cells: Protein Kinase C Mediated Extraembryonic Endoderm Differentiation of Human Embryonic Stem Cells

di Feng, Xuezhu, Zhang, Jiuchun, Smuga-Otto, Kimberly, Tian, Shulan, Yu, Junying, Stewart, Ron, Thomson, James A.
Pubblicazione 2012

Aggregate Culture of Human Embryonic Stem Cell-Derived Hepatocytes in Suspension Are an Improved In Vitro Model for Drug Metabolism and Toxicity Testing

di Sengupta, Srikumar, Johnson, Brian Patrick, Swanson, Scott Allen, Stewart, Ron, Bradfield, Christopher Alan, Thomson, James Alexander
Pubblicazione 2014

Evaluation of de novo transcriptome assemblies from RNA-Seq data

di Li, Bo, Fillmore, Nathanael, Bai, Yongsheng, Collins, Mike, Thomson, James A, Stewart, Ron, Dewey, Colin N
Pubblicato in Genome Biol (2014)

Characterization and target identification of a DNA aptamer that labels pluripotent stem cells

di Hou, Zhonggang, Meyer, Susanne, Propson, Nicholas E, Nie, Jeff, Jiang, Peng, Stewart, Ron, Thomson, James A
Pubblicato in Cell Res (2015)

Trendy: segmented regression analysis of expression dynamics in high-throughput ordered profiling experiments

di Bacher, Rhonda, Leng, Ning, Chu, Li-Fang, Ni, Zijian, Thomson, James A., Kendziorski, Christina, Stewart, Ron
Pubblicato in BMC Bioinformatics (2018)

A Machine-Learning Based Drug Repurposing Approach Using Baseline Regularization

di Kuang, Zhaobin, Bao, Yujia, Thomson, James, Caldwell, Michael, Peissig, Peggy, Stewart, Ron, Willett, Rebecca, Page, David
Pubblicato in Methods Mol Biol (2019)