Publications

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


JudithSomekhBatch 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

 


Ayelet Alpert-JerbiYishai PickmanA 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


 

Rachelly Normand

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, ShenOrr 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, ShenOrr 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, ShenOrr 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


 

Ksenya

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

 


 

Ayelet Alpert-Jerbi

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

 

 


Elina Starosvetsky

Renaud Gaujoux

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