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Items: 9

1.

Defining Reprogramming Checkpoints from Single-Cell Analyses of Induced Pluripotency.

Tran KA, Pietrzak SJ, Zaidan NZ, Siahpirani AF, McCalla SG, Zhou AS, Iyer G, Roy S, Sridharan R.

Cell Rep. 2019 May 7;27(6):1726-1741.e5. doi: 10.1016/j.celrep.2019.04.056.

2.

Integrative Approaches for Inference of Genome-Scale Gene Regulatory Networks.

Siahpirani AF, Chasman D, Roy S.

Methods Mol Biol. 2019;1883:161-194. doi: 10.1007/978-1-4939-8882-2_7.

PMID:
30547400
3.

A prior-based integrative framework for functional transcriptional regulatory network inference.

Siahpirani AF, Roy S.

Nucleic Acids Res. 2017 Feb 28;45(4):2221. doi: 10.1093/nar/gkw1160. No abstract available.

4.

A proteomic atlas of the legume Medicago truncatula and its nitrogen-fixing endosymbiont Sinorhizobium meliloti.

Marx H, Minogue CE, Jayaraman D, Richards AL, Kwiecien NW, Siahpirani AF, Rajasekar S, Maeda J, Garcia K, Del Valle-Echevarria AR, Volkening JD, Westphall MS, Roy S, Sussman MR, Ané JM, Coon JJ.

Nat Biotechnol. 2016 Nov;34(11):1198-1205. doi: 10.1038/nbt.3681. Epub 2016 Oct 17.

PMID:
27748755
5.

A prior-based integrative framework for functional transcriptional regulatory network inference.

Siahpirani AF, Roy S.

Nucleic Acids Res. 2017 Feb 28;45(4):e21. doi: 10.1093/nar/gkw963. Erratum in: Nucleic Acids Res. 2017 Feb 28;45(4):2221.

6.

A predictive modeling approach for cell line-specific long-range regulatory interactions.

Roy S, Siahpirani AF, Chasman D, Knaack S, Ay F, Stewart R, Wilson M, Sridharan R.

Nucleic Acids Res. 2016 Feb 29;44(4):1977-8. doi: 10.1093/nar/gkv1181. Epub 2015 Nov 5. No abstract available.

7.

A predictive modeling approach for cell line-specific long-range regulatory interactions.

Roy S, Siahpirani AF, Chasman D, Knaack S, Ay F, Stewart R, Wilson M, Sridharan R.

Nucleic Acids Res. 2015 Oct 15;43(18):8694-712. doi: 10.1093/nar/gkv865. Epub 2015 Sep 3. Erratum in: Nucleic Acids Res. 2016 Feb 29;44(4):1977-8.

8.

Deep Sequencing of the Medicago truncatula Root Transcriptome Reveals a Massive and Early Interaction between Nodulation Factor and Ethylene Signals.

Larrainzar E, Riely BK, Kim SC, Carrasquilla-Garcia N, Yu HJ, Hwang HJ, Oh M, Kim GB, Surendrarao AK, Chasman D, Siahpirani AF, Penmetsa RV, Lee GS, Kim N, Roy S, Mun JH, Cook DR.

Plant Physiol. 2015 Sep;169(1):233-65. doi: 10.1104/pp.15.00350. Epub 2015 Jul 14.

9.

A pan-cancer modular regulatory network analysis to identify common and cancer-specific network components.

Knaack SA, Siahpirani AF, Roy S.

Cancer Inform. 2014 Oct 28;13(Suppl 5):69-84. doi: 10.4137/CIN.S14058. eCollection 2014.

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