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Items: 8

1.

scMerge leverages factor analysis, stable expression, and pseudoreplication to merge multiple single-cell RNA-seq datasets.

Lin Y, Ghazanfar S, Wang KYX, Gagnon-Bartsch JA, Lo KK, Su X, Han ZG, Ormerod JT, Speed TP, Yang P, Yang JYH.

Proc Natl Acad Sci U S A. 2019 May 14;116(20):9775-9784. doi: 10.1073/pnas.1820006116. Epub 2019 Apr 26.

2.

DCARS: differential correlation across ranked samples.

Ghazanfar S, Strbenac D, Ormerod JT, Yang JYH, Patrick E.

Bioinformatics. 2019 Mar 1;35(5):823-829. doi: 10.1093/bioinformatics/bty698.

PMID:
30102408
3.

AdaSampling for Positive-Unlabeled and Label Noise Learning With Bioinformatics Applications.

Yang P, Ormerod JT, Liu W, Ma C, Zomaya AY, Yang JYH.

IEEE Trans Cybern. 2019 May;49(5):1932-1943. doi: 10.1109/TCYB.2018.2816984. Epub 2018 Apr 2.

PMID:
29993676
4.

Integrated single cell data analysis reveals cell specific networks and novel coactivation markers.

Ghazanfar S, Bisogni AJ, Ormerod JT, Lin DM, Yang JY.

BMC Syst Biol. 2016 Dec 5;10(Suppl 5):127. doi: 10.1186/s12918-016-0370-4.

5.

A multi-step classifier addressing cohort heterogeneity improves performance of prognostic biomarkers in three cancer types.

Patrick E, Schramm SJ, Ormerod JT, Scolyer RA, Mann GJ, Mueller S, Yang JY.

Oncotarget. 2017 Jan 10;8(2):2807-2815. doi: 10.18632/oncotarget.13203.

6.

Differential distribution improves gene selection stability and has competitive classification performance for patient survival.

Strbenac D, Mann GJ, Yang JY, Ormerod JT.

Nucleic Acids Res. 2016 Jul 27;44(13):e119. doi: 10.1093/nar/gkw444. Epub 2016 May 17.

7.

A Variational Bayes Approach to the Analysis of Occupancy Models.

Clark AE, Altwegg R, Ormerod JT.

PLoS One. 2016 Feb 29;11(2):e0148966. doi: 10.1371/journal.pone.0148966. eCollection 2016.

8.

ClassifyR: an R package for performance assessment of classification with applications to transcriptomics.

Strbenac D, Mann GJ, Ormerod JT, Yang JY.

Bioinformatics. 2015 Jun 1;31(11):1851-3. doi: 10.1093/bioinformatics/btv066. Epub 2015 Feb 1.

PMID:
25644269

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