Select Publications - Morgridge Institute for Research

Machine Learning to Predict Developmental Neurotoxicity with High-Throughput Data from 2D Bio-Engineered Tissues.
Kuusisto F, Santos Costa V, Hou Z, Thomson J, Page D, Stewart R.
IEEE Intl Conf Mach Learn Appl Proc. 2019.
- Suplementary Information
A Simple Text Mining Approach for Ranking Pairwise Associations in Biomedical Applications.
Kuusisto F, Steill J, Kuang Z, Thomson J, Page D, Stewart R.
AMIA Jt Summits Transl Sci Proc. 2017 Jul 26;2017:166-174. eCollection 2017.
PMID: 28815126
Machine Learning Assisted Discovery of Novel Predictive Lab Tests Using Electronic Health Record Data.
Kleiman R, Kuusisto F, Ross I, Peissig PL, Stewart R, Page CD, Weiss J.
AMIA Jt Summits Transl Sci Proc. 2019 May 6;2019:572-581. eCollection 2019.
PMID: 31259012
A Machine-Learning-Based Drug Repurposing Approach Using Baseline Regularization.
Kuang Z, Bao Y, Thomson J, Caldwell M, Peissig P, Stewart R, Willett R, Page D.
Methods Mol Biol. 2019;1903:255-267. doi: 10.1007/978-1-4939-8955-3_15.
PMID: 30547447
Computational Drug Repositioning Using Continuous Self-Controlled Case Series.
Kuang Z, Thomson J, Caldwell M, Peissig P, Stewart R, Page D.
KDD. 2016 Aug;2016:491-500. doi: 10.1145/2939672.2939715.
PMID: 28316874
An In Vitro Human Segmentation Clock Model Derived from Embryonic Stem Cells.
Chu LF, Mamott D, Ni Z, Bacher R, Liu C, Swanson S, Kendziorski C, Stewart R, Thomson JA.
Cell Rep. 2019 Aug 27;28(9):2247-2255.e5. doi: 10.1016/j.celrep.2019.07.090.
PMID: 31461642
Trendy: segmented regression analysis of expression dynamics in high-throughput ordered profiling experiments.
Bacher R, Leng N, Chu LF, Ni Z, Thomson JA, Kendziorski C, Stewart R.
BMC Bioinformatics. 2018 Oct 16;19(1):380. doi: 10.1186/s12859-018-2405-x.
PMID: 30326833
A Novel Approach to Single Cell RNA-Sequence Analysis Facilitates In Silico Gene Reporting of Human Pluripotent Stem Cell-Derived Retinal Cell Types.
Phillips MJ, Jiang P, Howden S, Barney P, Min J, York NW, Chu LF, Capowski EE, Cash A, Jain S, Barlow K, Tabassum T, Stewart R, Pattnaik BR, Thomson JA, Gamm DM.
Stem Cells. 2018 Mar;36(3):313-324. doi: 10.1002/stem.2755. Epub 2017 Dec 25. Erratum in: Stem Cells. 2018 Jul;36(7):1133.
PMID: 29230913
RNA-Seq of Human Neural Progenitor Cells Exposed to Lead (Pb) Reveals Transcriptome Dynamics, Splicing Alterations and Disease Risk Associations.
Jiang P, Hou Z, Bolin JM, Thomson JA, Stewart R.
Toxicol Sci. 2017 Sep 1;159(1):251-265. doi: 10.1093/toxsci/kfx129.
PMID: 28903495
Analysis of embryonic development in the unsequenced axolotl: Waves of transcriptomic upheaval and stability.
Jiang P, Nelson JD, Leng N, Collins M, Swanson S, Dewey CN, Thomson JA, Stewart R.
Dev Biol. 2017 Jun 15;426(2):143-154. doi: 10.1016/j.ydbio.2016.05.024. Epub 2016 Jul 28.
PMID: 27475628
Quality control of single-cell RNA-seq by SinQC.
Jiang P, Thomson JA, Stewart R.
Bioinformatics. 2016 Aug 15;32(16):2514-6. doi: 10.1093/bioinformatics/btw176. Epub 2016 Apr 10.
PMID: 2715361
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. 2016 May 1;32(9):1408-10. doi: 10.1093/bioinformatics/btw004. Epub 2016 Jan 6.
PMID: 26743507
EBSeq-HMM: a Bayesian approach for identifying gene-expression changes in ordered RNA-seq experiments.
Leng N, Li Y, McIntosh BE, Nguyen BK, Duffin B, Tian S, Thomson JA, Dewey CN, Stewart R, Kendziorski C.
Bioinformatics. 2015 Aug 15;31(16):2614-22. doi: 10.1093/bioinformatics/btv193. Epub 2015 Apr 5.
PMID: 25847007
MPBind: a Meta-motif-based statistical framework and pipeline to Predict Binding potential of SELEX-derived aptamers.
Jiang P, Meyer S, Hou Z, Propson NE, Soh HT, Thomson JA, Stewart R.
Bioinformatics. 2014 Sep 15;30(18):2665-7. doi: 10.1093/bioinformatics/btu348. Epub 2014 May 28.
PMID: 24872422
Comparative RNA-seq analysis in the unsequenced axolotl: the oncogene burst highlights early gene expression in the blastema.
Stewart R, Rascón CA, Tian S, Nie J, Barry C, Chu LF, Ardalani H, Wagner RJ, Probasco MD, Bolin JM, Leng N, Sengupta S, Volkmer M, Habermann B, Tanaka EM, Thomson JA, Dewey CN.
PLoS Comput Biol. 2013;9(3):e1002936. doi: 10.1371/journal.pcbi.1002936. Epub 2013 Mar 7.
PMID: 23505351
EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments.
Leng N, Dawson JA, Thomson JA, Ruotti V, Rissman AI, Smits BM, Haag JD, Gould MN, Stewart RM, Kendziorski C.
Bioinformatics. 2013 Apr 15;29(8):1035-43. doi: 10.1093/bioinformatics/btt087. Epub 2013 Feb 21. Erratum in: Bioinformatics. 2013 Aug 15;29(16):2073.
PMID: 23428641
Human DNA methylomes at base resolution show widespread epigenomic differences.
Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, Nery JR, Lee L, Ye Z, Ngo QM, Edsall L, Antosiewicz-Bourget J, Stewart R, Ruotti V, Millar AH, Thomson JA, Ren B, Ecker JR.
Nature. 2009 Nov 19;462(7271):315-22. doi: 10.1038/nature08514. Epub 2009 Oct 14.
PMID: 19829295
Induced pluripotent stem cell lines derived from human somatic cells.
Yu J, Vodyanik MA, Smuga-Otto K, Antosiewicz-Bourget J, Frane JL, Tian S, Nie J, Jonsdottir GA, Ruotti V, Stewart R, Slukvin II, Thomson JA.
Science. 2007 Dec 21;318(5858):1917-20. Epub 2007 Nov 20.
PMID: 18029452

Machine Learning to Predict Developmental Neurotoxicity with High-Throughput Data from 2D Bio-Engineered Tissues.

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

Machine Learning Assisted Discovery of Novel Predictive Lab Tests Using Electronic Health Record Data.

A Machine-Learning-Based Drug Repurposing Approach Using Baseline Regularization.

Computational Drug Repositioning Using Continuous Self-Controlled Case Series.

An In Vitro Human Segmentation Clock Model Derived from Embryonic Stem Cells.

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

A Novel Approach to Single Cell RNA-Sequence Analysis Facilitates In Silico Gene Reporting of Human Pluripotent Stem Cell-Derived Retinal Cell Types.

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

Analysis of embryonic development in the unsequenced axolotl: Waves of transcriptomic upheaval and stability.

Quality control of single-cell RNA-seq by SinQC.

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

EBSeq-HMM: a Bayesian approach for identifying gene-expression changes in ordered RNA-seq experiments.

MPBind: a Meta-motif-based statistical framework and pipeline to Predict Binding potential of SELEX-derived aptamers.

Comparative RNA-seq analysis in the unsequenced axolotl: the oncogene burst highlights early gene expression in the blastema.

EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments.

Human DNA methylomes at base resolution show widespread epigenomic differences.

Induced pluripotent stem cell lines derived from human somatic cells.

Stewart Computational Biology Group