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Items: 36

1.

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.

2.

The CTLA-4 rs231775 GG genotype is associated with favorable 90-day survival in Caucasian patients with sepsis.

Mewes C, Büttner B, Hinz J, Alpert A, Popov AF, Ghadimi M, Beissbarth T, Tzvetkov M, Shen-Orr S, Bergmann I, Mansur A.

Sci Rep. 2018 Oct 11;8(1):15140. doi: 10.1038/s41598-018-33246-9.

3.

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.

4.

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.

PMID:
29912209
5.

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. 2018 Apr 4. pii: gutjnl-2017-315494. doi: 10.1136/gutjnl-2017-315494. [Epub ahead of print]

6.

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
7.

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.

8.

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. [Epub ahead of print]

9.

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
10.

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.

11.

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.

12.

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
13.

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
14.

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.

15.

Systems Analysis of Immunity to Influenza Vaccination across Multiple Years and in Diverse Populations Reveals Shared Molecular Signatures.

Nakaya HI, Hagan T, Duraisingham SS, Lee EK, Kwissa M, Rouphael N, Frasca D, Gersten M, Mehta AK, Gaujoux R, Li GM, Gupta S, Ahmed R, Mulligan MJ, Shen-Orr S, Blomberg BB, Subramaniam S, Pulendran B.

Immunity. 2015 Dec 15;43(6):1186-98. doi: 10.1016/j.immuni.2015.11.012.

16.

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.

17.

Glycolysis-mediated changes in acetyl-CoA and histone acetylation control the early differentiation of embryonic stem cells.

Moussaieff A, Rouleau M, Kitsberg D, Cohen M, Levy G, Barasch D, Nemirovski A, Shen-Orr S, Laevsky I, Amit M, Bomze D, Elena-Herrmann B, Scherf T, Nissim-Rafinia M, Kempa S, Itskovitz-Eldor J, Meshorer E, Aberdam D, Nahmias Y.

Cell Metab. 2015 Mar 3;21(3):392-402. doi: 10.1016/j.cmet.2015.02.002.

18.

Variation in the human immune system is largely driven by non-heritable influences.

Brodin P, Jojic V, Gao T, Bhattacharya S, Angel CJ, Furman D, Shen-Orr S, Dekker CL, Swan GE, Butte AJ, Maecker HT, Davis MM.

Cell. 2015 Jan 15;160(1-2):37-47. doi: 10.1016/j.cell.2014.12.020.

19.

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.

20.

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.

21.

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.

22.

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.

23.

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.

24.

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.

25.

Apoptosis and other immune biomarkers predict influenza vaccine responsiveness.

Furman D, Jojic V, Kidd B, Shen-Orr S, Price J, Jarrell J, Tse T, Huang H, Lund P, Maecker HT, Utz PJ, Dekker CL, Koller D, Davis MM.

Mol Syst Biol. 2013 Apr 16;9:659. doi: 10.1038/msb.2013.15. Erratum in: Mol Syst Biol. 2014;10:750. Mol Syst Biol. 2013;9:680.

26.

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.

27.

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.

28.

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.

29.

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.

30.

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.

31.

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.

32.

Superfamilies of evolved and designed networks.

Milo R, Itzkovitz S, Kashtan N, Levitt R, Shen-Orr S, Ayzenshtat I, Sheffer M, Alon U.

Science. 2004 Mar 5;303(5663):1538-42.

33.

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.

Bioinformatics. 2002 Nov;18(11):1542-3.

PMID:
12424129
34.

Network motifs: simple building blocks of complex networks.

Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D, Alon U.

Science. 2002 Oct 25;298(5594):824-7.

35.

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
36.

A relational schema for both array-based and SAGE gene expression experiments.

Stoeckert C, Pizarro A, Manduchi E, Gibson M, Brunk B, Crabtree J, Schug J, Shen-Orr S, Overton GC.

Bioinformatics. 2001 Apr;17(4):300-8.

PMID:
11301298

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