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Items: 33

1.

Pregnancy-Induced Alterations in NK Cell Phenotype and Function.

Le Gars M, Seiler C, Kay AW, Bayless NL, Starosvetsky E, Moore L, Shen-Orr SS, Aziz N, Khatri P, Dekker CL, Swan GE, Davis MM, Holmes S, Blish CA.

Front Immunol. 2019 Oct 23;10:2469. doi: 10.3389/fimmu.2019.02469. eCollection 2019.

2.

UVB-Induced Tumor Heterogeneity Diminishes Immune Response in Melanoma.

Wolf Y, Bartok O, Patkar S, Eli GB, Cohen S, Litchfield K, Levy R, Jiménez-Sánchez A, Trabish S, Lee JS, Karathia H, Barnea E, Day CP, Cinnamon E, Stein I, Solomon A, Bitton L, Pérez-Guijarro E, Dubovik T, Shen-Orr SS, Miller ML, Merlino G, Levin Y, Pikarsky E, Eisenbach L, Admon A, Swanton C, Ruppin E, Samuels Y.

Cell. 2019 Sep 19;179(1):219-235.e21. doi: 10.1016/j.cell.2019.08.032. Epub 2019 Sep 12.

3.

Infliximab-Tumor Necrosis Factor Complexes Elicit Formation of Anti-Drug Antibodies.

Bar-Yoseph H, Pressman S, Blatt A, Gerassy Vainberg S, Maimon N, Starosvetsky E, Ungar B, Ben-Horin S, Shen-Orr SS, Chowers Y; Israeli IBD Research Nucleus.

Gastroenterology. 2019 Nov;157(5):1338-1351.e8. doi: 10.1053/j.gastro.2019.08.009. Epub 2019 Aug 8.

PMID:
31401142
4.

Batch correction evaluation framework using a-priori gene-gene associations: applied to the GTEx dataset.

Somekh J, Shen-Orr SS, Kohane IS.

BMC Bioinformatics. 2019 May 28;20(1):268. doi: 10.1186/s12859-019-2855-9.

5.

A clinically meaningful metric of immune age derived from high-dimensional longitudinal monitoring.

Alpert A, Pickman Y, Leipold M, Rosenberg-Hasson Y, Ji X, Gaujoux R, Rabani H, Starosvetsky E, Kveler K, Schaffert S, Furman D, Caspi O, Rosenschein U, Khatri P, Dekker CL, Maecker HT, Davis MM, Shen-Orr SS.

Nat Med. 2019 Mar;25(3):487-495. doi: 10.1038/s41591-019-0381-y. Epub 2019 Mar 6.

6.

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.

Nat Methods. 2018 Dec;15(12):1067-1073. doi: 10.1038/s41592-018-0214-9. Epub 2018 Nov 26.

PMID:
30478323
7.

UV-Protection Timer Controls Linkage between Stress and Pigmentation Skin Protection Systems.

Malcov-Brog H, Alpert A, Golan T, Parikh S, Nordlinger A, Netti F, Sheinboim D, Dror I, Thomas L, Cosson C, Gonen P, Stanevsky Y, Brenner R, Perluk T, Frand J, Elgavish S, Nevo Y, Rahat D, Tabach Y, Khaled M, Shen-Orr SS, Levy C.

Mol Cell. 2018 Nov 1;72(3):444-456.e7. doi: 10.1016/j.molcel.2018.09.022. Epub 2018 Oct 25.

8.

Regulation of S100A8 Stability by RNF5 in Intestinal Epithelial Cells Determines Intestinal Inflammation and Severity of Colitis.

Fujita Y, Khateb A, Li Y, Tinoco R, Zhang T, Bar-Yoseph H, Tam MA, Chowers Y, Sabo E, Gerassy-Vainberg S, Starosvetsky E, James B, Brown K, Shen-Orr SS, Bradley LM, Tessier PA, Ronai ZA.

Cell Rep. 2018 Sep 18;24(12):3296-3311.e6. doi: 10.1016/j.celrep.2018.08.057.

9.

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.

Nat Biotechnol. 2018 Aug;36(7):651-659. doi: 10.1038/nbt.4152. Epub 2018 Jun 18.

10.

Cell-centred meta-analysis reveals baseline predictors of anti-TNFα non-response in biopsy and blood of patients with IBD.

Gaujoux R, Starosvetsky E, Maimon N, Vallania F, Bar-Yoseph H, Pressman S, Weisshof R, Goren I, Rabinowitz K, Waterman M, Yanai H, Dotan I, Sabo E, Chowers Y, Khatri P, Shen-Orr SS; Israeli IBD research Network (IIRN).

Gut. 2019 Apr;68(4):604-614. doi: 10.1136/gutjnl-2017-315494. Epub 2018 Apr 4.

11.

Alignment of single-cell trajectories to compare cellular expression dynamics.

Alpert A, Moore LS, Dubovik T, Shen-Orr SS.

Nat Methods. 2018 Apr;15(4):267-270. doi: 10.1038/nmeth.4628. Epub 2018 Mar 12.

PMID:
29529018
12.

ImmPort, toward repurposing of open access immunological assay data for translational and clinical research.

Bhattacharya S, Dunn P, Thomas CG, Smith B, Schaefer H, Chen J, Hu Z, Zalocusky KA, Shankar RD, Shen-Orr SS, Thomson E, Wiser J, Butte AJ.

Sci Data. 2018 Feb 27;5:180015. doi: 10.1038/sdata.2018.15.

13.

Inflammatory macrophage-associated 3-gene signature predicts subclinical allograft injury and graft survival.

Azad TD, Donato M, Heylen L, Liu AB, Shen-Orr SS, Sweeney TE, Maltzman JS, Naesens M, Khatri P.

JCI Insight. 2018 Jan 25;3(2). pii: 95659. doi: 10.1172/jci.insight.95659. eCollection 2018 Jan 25.

14.

Social network architecture of human immune cells unveiled by quantitative proteomics.

Rieckmann JC, Geiger R, Hornburg D, Wolf T, Kveler K, Jarrossay D, Sallusto F, Shen-Orr SS, Lanzavecchia A, Mann M, Meissner F.

Nat Immunol. 2017 May;18(5):583-593. doi: 10.1038/ni.3693. Epub 2017 Mar 6.

PMID:
28263321
15.

Defective Signaling in the JAK-STAT Pathway Tracks with Chronic Inflammation and Cardiovascular Risk in Aging Humans.

Shen-Orr SS, Furman D, Kidd BA, Hadad F, Lovelace P, Huang YW, Rosenberg-Hasson Y, Mackey S, Grisar FA, Pickman Y, Maecker HT, Chien YH, Dekker CL, Wu JC, Butte AJ, Davis MM.

Cell Syst. 2016 Oct 26;3(4):374-384.e4. doi: 10.1016/j.cels.2016.09.009. Epub 2016 Oct 13.

16.

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.

Cell Syst. 2016 Oct 26;3(4):346-360.e4. doi: 10.1016/j.cels.2016.08.011. Epub 2016 Sep 22.

17.

Tofacitinib for polyarteritis nodosa: a tailored therapy.

Rimar D, Alpert A, Starosvetsky E, Rosner I, Slobodin G, Rozenbaum M, Kaly L, Boulman N, Awisat A, Ginsberg S, Zilber K, Shen-Orr SS.

Ann Rheum Dis. 2016 Dec;75(12):2214-2216. doi: 10.1136/annrheumdis-2016-209330. Epub 2016 Aug 24. No abstract available.

PMID:
27558986
18.

Activation of the reward system boosts innate and adaptive immunity.

Ben-Shaanan TL, Azulay-Debby H, Dubovik T, Starosvetsky E, Korin B, Schiller M, Green NL, Admon Y, Hakim F, Shen-Orr SS, Rolls A.

Nat Med. 2016 Aug;22(8):940-4. doi: 10.1038/nm.4133. Epub 2016 Jul 4.

PMID:
27376577
19.

A c-Myc/miR17-92/Pten Axis Controls PI3K-Mediated Positive and Negative Selection in B Cell Development and Reconstitutes CD19 Deficiency.

Benhamou D, Labi V, Novak R, Dai I, Shafir-Alon S, Weiss A, Gaujoux R, Arnold R, Shen-Orr SS, Rajewsky K, Melamed D.

Cell Rep. 2016 Jul 12;16(2):419-431. doi: 10.1016/j.celrep.2016.05.084. Epub 2016 Jun 23.

20.

Cytomegalovirus infection enhances the immune response to influenza.

Furman D, Jojic V, Sharma S, Shen-Orr SS, Angel CJ, Onengut-Gumuscu S, Kidd BA, Maecker HT, Concannon P, Dekker CL, Thomas PG, Davis MM.

Sci Transl Med. 2015 Apr 1;7(281):281ra43. doi: 10.1126/scitranslmed.aaa2293.

21.

Systems immunology reveals markers of susceptibility to West Nile virus infection.

Qian F, Goel G, Meng H, Wang X, You F, Devine L, Raddassi K, Garcia MN, Murray KO, Bolen CR, Gaujoux R, Shen-Orr SS, Hafler D, Fikrig E, Xavier R, Kleinstein SH, Montgomery RR.

Clin Vaccine Immunol. 2015 Jan;22(1):6-16. doi: 10.1128/CVI.00508-14. Epub 2014 Oct 29.

22.

Antigen-dependent integration of opposing proximal TCR-signaling cascades determines the functional fate of T lymphocytes.

Wolchinsky R, Hod-Marco M, Oved K, Shen-Orr SS, Bendall SC, Nolan GP, Reiter Y.

J Immunol. 2014 Mar 1;192(5):2109-19. doi: 10.4049/jimmunol.1301142. Epub 2014 Jan 31.

23.

Computational deconvolution: extracting cell type-specific information from heterogeneous samples.

Shen-Orr SS, Gaujoux R.

Curr Opin Immunol. 2013 Oct;25(5):571-8. doi: 10.1016/j.coi.2013.09.015. Epub 2013 Oct 19. Review.

24.

Reconstructing the genomic content of microbiome taxa through shotgun metagenomic deconvolution.

Carr R, Shen-Orr SS, Borenstein E.

PLoS Comput Biol. 2013;9(10):e1003292. doi: 10.1371/journal.pcbi.1003292. Epub 2013 Oct 17.

25.

Variability in the immune system: of vaccine responses and immune states.

Shen-Orr SS, Furman D.

Curr Opin Immunol. 2013 Aug;25(4):542-7. doi: 10.1016/j.coi.2013.07.009. Epub 2013 Aug 13. Review.

26.

Challenges and promise for the development of human immune monitoring.

Shen-Orr SS.

Rambam Maimonides Med J. 2012 Oct 31;3(4):e0023. doi: 10.5041/RMMJ.10090. Print 2012 Oct.

27.

New tools for classification and monitoring of autoimmune diseases.

Maecker HT, Lindstrom TM, Robinson WH, Utz PJ, Hale M, Boyd SD, Shen-Orr SS, Fathman CG.

Nat Rev Rheumatol. 2012 May 31;8(6):317-28. doi: 10.1038/nrrheum.2012.66. Review. Erratum in: Nat Rev Rheumatol. 2012 Oct;8(10):562.

28.

Significance analysis of xMap cytokine bead arrays.

Won JH, Goldberger O, Shen-Orr SS, Davis MM, Olshen RA.

Proc Natl Acad Sci U S A. 2012 Feb 21;109(8):2848-53. doi: 10.1073/pnas.1112599109. Epub 2012 Feb 9.

29.

Composition and regulation of maternal and zygotic transcriptomes reflects species-specific reproductive mode.

Shen-Orr SS, Pilpel Y, Hunter CP.

Genome Biol. 2010;11(6):R58. doi: 10.1186/gb-2010-11-6-r58. Epub 2010 Jun 1.

30.

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.

Nat Methods. 2010 Apr;7(4):287-9. doi: 10.1038/nmeth.1439. Epub 2010 Mar 7.

31.

Towards a cytokine-cell interaction knowledgebase of the adaptive immune system.

Shen-Orr SS, Goldberger O, Garten Y, Rosenberg-Hasson Y, Lovelace PA, Hirschberg DL, Altman RB, Davis MM, Butte AJ.

Pac Symp Biocomput. 2009:439-50.

32.

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.

Mol Syst Biol. 2008;4:163. doi: 10.1038/msb.2008.6. Epub 2008 Feb 12.

33.

Network motifs in the transcriptional regulation network of Escherichia coli.

Shen-Orr SS, Milo R, Mangan S, Alon U.

Nat Genet. 2002 May;31(1):64-8. Epub 2002 Apr 22.

PMID:
11967538

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