Published or In-Press
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.
PMID: 31708922
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 4. pii: S0092-8674(19)30951-1. doi: 10.1016/j.cell.2019.08.032
PMID: 31522890
Infliximab-Tumor Necrosis Factor Complexes Elicit Formation of Anti-drug Antibodies.
Bar-Yoseph H, Pressman S, Blatt A, Vainberg SG, Maimon N, Starosvetsky E, Ungar B, Ben-Horin S, Shen-Orr SS, Chowers Y
Gastroenterology. 2019 Aug 8. pii: S0016-5085(19)41201-8. doi: 10.1053/j.gastro.2019.08.009
PMID: 31401142
Simulation of single-protein nanopore sensing shows feasibility for whole-proteome identification.
Ohayon S, Girsault A, Nasser M, Shen-Orr S, Meller A
PLoS Comput Biol. 2019 May 30;15(5):e1007067. doi: 10.1371/journal.pcbi.1007067
PMID: 31145734
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
PMID: 31138121
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 6. doi: 10.1038/s41591-019-0381-y
PMID: 30842675
CTLA-4 Genetic Variants Predict Survival in Patients with Sepsis.
Mewes C, Büttner B, Hinz J, Alpert A, Popov AF, Ghadimi M, Beissbarth T, Tzvetkov M, Jensen O, Runzheimer J, Quintel M, Shen-Orr S, Bergmann I, Mansur A.
J Clin Med. 2019 Jan 10;8(1). pii: E70. doi: 10.3390/jcm8010070.
PMID: 30634576
Ulcerative colitis mucosal transcriptomes reveal mitochondriopathy and personalized mechanisms underlying disease severity and treatment response.
Haberman Y, Karns R, Dexheimer PJ, Schirmer M, Somekh J, Jurickova I, Braun T, Novak E, Bauman L, Collins MH, Mo A, Rosen MJ, Bonkowski E, Gotman N, Marquis A, Nistel M, Rufo PA, Baker SS, Sauer CG, Markowitz J, Pfefferkorn MD, Rosh JR, Boyle BM, Mack DR, Baldassano RN, Shah S, Leleiko NS, Heyman MB, Grifiths AM, Patel AS, Noe JD, Aronow BJ, Kugathasan S, Walters TD, Gibson G, Thomas SD, Mollen K, Shen-Orr S, Huttenhower C, Xavier RJ, Hyams JS, Denson LA.
Nat Commun. 2019 Jan 3;10(1):38. doi: 10.1038/s41467-018-07841-3
PMID: 30604764
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 Nov 26. doi: 10.1038/s41592-018-0214-9
PMID: 30478323
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
PMID: 30401431
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
PMID: 30310101
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
PMID: 30232010
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 Jun 18. doi: 10.1038/nbt.4152.
PMID: 29912209
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.
PMID: 29529018
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 M*, Vallania F, Bar-Yoseph H, Pressman S, Weisshof R, Rabinowitz KM, Goren I, Waterman M, Yanai H, Dotan I, Sabo E, Chowers Y*, Khatri P*, Shen-Orr SS*
Gut. 2018 Apr 4. pii: gutjnl-2017-315494. doi: 10.1136/gutjnl-2017-315494.
PMID: 29618496
Inflammatory macrophage-associated 3-gene signature predicts subclinical allograft injury and graft survival.
Azad TD, Donato M, Heylen L, Shen-Orr SS, Sweeney TE, Naesens M, Khatri P.
JCI Insight. 2018 Jan 25;3(2). pii: 95659. doi: 10.1172/jci.insight.95659
PMID:29367465
Multi-cohort analysis reveals baseline transcriptional predictors of influenza vaccination responses.
The HIPC-CHI Signatures Project Team and the HIPC-I Consortium. (*Co-senior and co-corresponding).
Science Immunology, 2017 Aug 25;2(14)
PMID: 28842433
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.
Nature Immunolgy. 2017 Mar 6. doi: 10.1038/ni.3693.
PMID: 28263321
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.
PMID: 27746093
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.
PMID: 27667365
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.
PMID: 27558986
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*. (*Co-senior author)
Nat Med. 2016 Aug;22(8):940-4. doi: 10.1038/nm.4133.
PMID: 27376577
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):419-31. doi: 10.1016/j.celrep.2016.05.084.
PMID: 27346348
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.
PMID: 26682988
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.
PMID: 25834109
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.
PMID: 25738455
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.
PMID: 25594173
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.
PMID: 25355795
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.
PMID: 24489091
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.
PMID: 24146609
Sensitivity Analysis for Inference with Partially Identifiable Covariance Matrices. Computational Statistics.
G’Sell M, Shen-Orr S, Tibshirani R
Computational Statistics. 2013 Sep 13; DOI 10.1007/s00180-013-0451-4
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.
PMID: 23591775
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.
PMID: 22323610
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.
PMID: 20515465
Extracting 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.
PMID: 20208531
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.
PMID: 19209721
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.
PMID: 18277379
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.
PMID: 15001784
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
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.
PMID: 12399590
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.
PMID: 11967538
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
Submitted or In-Revision
High resolution longitudinal immune profiling reveals immunosenescence dynamics and attractor state
Pickman Y*, Alpert A*, Starosvetsky E, Gaujoux R, Rabani H, Leipold M, Schaffert S, Furman D, Kveler K, Khatari P, Dekker CL, Maeker HT, Davis MM*, Shen-Orr SS*.
In Revision.
High Resolution Characterization of Monocytic Development in Acute Myeloid Leukemia Using Trajectories Alignment
Alpert A, Starosvetsky E, Hayun M, Ofran Y, Shen-Orr SS.
Submitted.
Found In Translation: A statistical model for improving mouse to human inference.
Normand R, Du W, Briller M, Gaujoux R, Ziv-Kenet A, Starosvetsky E, Shalev-Malul G, Tibshirani RJ, Shen-Orr SS.
In Revision.
MITF dynamics upon UVB exposure serves as the UV protection timer.
Malcov H, Alpert A, Golan T, Parikh S, Thomas L, Cosson C, Gonen P, Stanevsky Y, Brenner R, Khaled M*, Shen-Orr SS*, Levy C*. (*Co-senior author)
In Revision.
Immune cellular homeostasis in early life is determined by genetic variants of cellular production and turnover.
Dubovik T, Starosvetsky E, LeRoy B, Normand R, Admon Y, Alpert A, Ofran Y, G’Sell M, Shen-Orr SS.
Submitted. BioRxiv: https://www.biorxiv.org/content/early/2018/01/29/256073
Review Papers
ImmPort, toward repurposing of open access immunological assay data for translational and clinical research.
Bhattacharya S, Dunn P, Thomas C, Smith B, Schaefer H, Chen J, Hu Z, Zalocusky K, Shankar R, Shen-Orr S, Thomson E, Wiser J, Butte A.
Sci Data. 2018 Feb 27;5:180015. doi: 10.1038/sdata.2018.15.
PMID: 29485622
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. Review.
PMID: 24148234
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. Review.
PMID: 23953808
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.
PMID: 23908847
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.
PMID: 22647780
Books and Book Chapters
Systems Immunology: from Cells and Molecules, to a Dynamic Multi-Scale System.
Davis M, Shen-Orr S
A Handbook for Systems Biology, Elsevier Academic Press, 481-498, 2013