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Network motifs in the transcriptional regulation network of Escherichia coli.
Shen-Orr SS, Milo R, Mangan S, Alon U. Shen-Orr SS, et al. Nat Genet. 2002 May;31(1):64-8. doi: 10.1038/ng881. Epub 2002 Apr 22. Nat Genet. 2002. PMID: 11967538
A Single-Cell Transcriptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure.
Baron M, Veres A, Wolock SL, Faust AL, Gaujoux R, Vetere A, Ryu JH, Wagner BK, Shen-Orr SS, Klein AM, Melton DA, Yanai I. Baron M, et al. Cell Syst. 2016 Oct 26;3(4):346-360.e4. doi: 10.1016/j.cels.2016.08.011. Epub 2016 Sep 22. Cell Syst. 2016. PMID: 27667365 Free PMC article.
Cell type-specific gene expression differences in complex tissues.
Shen-Orr SS, Tibshirani R, Khatri P, Bodian DL, Staedtler F, Perry NM, Hastie T, Sarwal MM, Davis MM, Butte AJ. Shen-Orr SS, et al. Nat Methods. 2010 Apr;7(4):287-9. doi: 10.1038/nmeth.1439. Epub 2010 Mar 7. Nat Methods. 2010. PMID: 20208531 Free PMC article.
Alignment of single-cell trajectories to compare cellular expression dynamics.
Alpert A, Moore LS, Dubovik T, Shen-Orr SS. Alpert A, et al. Nat Methods. 2018 Apr;15(4):267-270. doi: 10.1038/nmeth.4628. Epub 2018 Mar 12. Nat Methods. 2018. PMID: 29529018
Immune-centric network of cytokines and cells in disease context identified by computational mining of PubMed.
Kveler K, Starosvetsky E, Ziv-Kenet A, Kalugny Y, Gorelik Y, Shalev-Malul G, Aizenbud-Reshef N, Dubovik T, Briller M, Campbell J, Rieckmann JC, Asbeh N, Rimar D, Meissner F, Wiser J, Shen-Orr SS. Kveler K, et al. Among authors: shen orr ss. Nat Biotechnol. 2018 Aug;36(7):651-659. doi: 10.1038/nbt.4152. Epub 2018 Jun 18. Nat Biotechnol. 2018. PMID: 29912209 Free PMC article.
Found In Translation: a machine learning model for mouse-to-human inference.
Normand R, Du W, Briller M, Gaujoux R, Starosvetsky E, Ziv-Kenet A, Shalev-Malul G, Tibshirani RJ, Shen-Orr SS. Normand R, et al. Among authors: shen orr ss. Nat Methods. 2018 Dec;15(12):1067-1073. doi: 10.1038/s41592-018-0214-9. Epub 2018 Nov 26. Nat Methods. 2018. PMID: 30478323
Pairing of competitive and topologically distinct regulatory modules enhances patterned gene expression.
Yanai I, Baugh LR, Smith JJ, Roehrig C, Shen-Orr SS, Claggett JM, Hill AA, Slonim DK, Hunter CP. Yanai I, et al. Mol Syst Biol. 2008;4:163. doi: 10.1038/msb.2008.6. Epub 2008 Feb 12. Mol Syst Biol. 2008. PMID: 18277379 Free PMC article.
Network motifs: simple building blocks of complex networks.
Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D, Alon U. Milo R, et al. Science. 2002 Oct 25;298(5594):824-7. doi: 10.1126/science.298.5594.824. Science. 2002. PMID: 12399590
GeneCards 2002: towards a complete, object-oriented, human gene compendium.
Safran M, Solomon I, Shmueli O, Lapidot M, Shen-Orr S, Adato A, Ben-Dor U, Esterman N, Rosen N, Peter I, Olender T, Chalifa-Caspi V, Lancet D. Safran M, et al. Bioinformatics. 2002 Nov;18(11):1542-3. doi: 10.1093/bioinformatics/18.11.1542. Bioinformatics. 2002. PMID: 12424129
Superfamilies of evolved and designed networks.
Milo R, Itzkovitz S, Kashtan N, Levitt R, Shen-Orr S, Ayzenshtat I, Sheffer M, Alon U. Milo R, et al. Science. 2004 Mar 5;303(5663):1538-42. doi: 10.1126/science.1089167. Science. 2004. PMID: 15001784
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