De Lima DG, Brait M, Palmieri L, Zamuner FT, Broner E, Smith KN, Westlake T, Malca O, Efroni S, Sloma I, Sidransky D · Cancer Research 83(7 Suppl), 2121 (abstract)

RepertoireCancer

2022

Distribution equality as an optimal epidemic mitigation strategy

Hacohen A, Cohen R, Efroni S, Bachelet I, Barzel B · Scientific Reports 12, 10430

Modeling and theory

A Language Model Identifies Population-Level Features of the T Cell Receptor via Self-Supervised Learning

Goldner Kabeli R, Efroni S · Fourth International Conference on Transdisciplinary AI (TransAI)

RepertoireMachine learning

PathWeigh - Quantifying the Behavior of Biochemical Pathway Cascades

Livne D, Efroni S · International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO)

Networks and pathwaysData and tools

2021

The Future of Blood Testing Is the Immunome

Arnaout RA, Luning Prak ET, Schwab N, Rubelt F, Adaptive Immune Receptor Repertoire Community · Frontiers in Immunology 12, 626793

Repertoire

A T-cell repertoire timestamp is at the core of responsiveness to CTLA-4 blockade

Philip H, Snir T, Gordin M, Shugay M, Zilberberg A, Efroni S · iScience 24

RepertoireCancer

CDR3 and V genes show distinct reconstitution patterns in T cell repertoire post-allogeneic bone marrow transplantation

Tickotsky-Moskovitz N, Louzoun Y, Dvorkin S, Rotkopf A, Kuperman AA, Efroni S · Immunogenetics

Repertoire

Breast cancer is marked by specific, Public T-cell receptor CDR3 regions shared by mice and humans

Gordin M, Philip H, Zilberberg A, Gidoni M, Margalit R, Clouser C, Adams K, Vigneault F, Cohen IR, Yaari G, Efroni S · PLOS Computational Biology

RepertoireCancer

2020

TCR and HLA analysis of patients in a phase I/IIa trial of a therapeutic CMV vaccine against recurrent glioblastoma (GBM)

Anderson DE, Zilberberg A, Philip H, Gordon M, Fluckiger AC, Efroni S, Diaz-Mitoma F · Annals of Oncology (ESMO 2020 abstract)

RepertoireCancer

Levy O, Amit G, Vaknin D, Snir T, Efroni S, Castaldi P, Liu YY, Cohen HY, Bashan A · Nature Metabolism

Single cellNetworks and pathways

T cell repertoire sequencing as a cancer's liquid biopsy: can we decode what the immune system is coding?

Snir T, Efroni S · Current Opinion in Systems Biology

RepertoireCancer

Predicting and affecting response to cancer therapy based on pathway-level biomarkers

Ben-Hamo R, Jacob Berger A, Gavert N, Miller M, Pines G, Oren R, Pikarsky E, Benes CH, Neuman T, Zwang Y, Efroni S, Getz G, Straussman R · Nature Communications 11, 3296

Networks and pathwaysCancer

Immune Computation and COVID-19 Mortality: A Rationale for IVIg

Cohen IR, Efroni S, Atlan H · Critical Reviews in Immunology

Modeling and theory

A single nucleotide variant of human PARP1 determines response to PARP inhibitors

Cashman R, Zilberberg A, Priel A, Philip H, Varvak A, Jacob A, Shoval I, Efroni S · npj Precision Oncology 4, 10

Cancer

2019

A modeling algorithm for exploring the architecture and construction of bird nests

Jessel HR, Aharoni L, Efroni S, Bachelet I · Scientific Reports

Modeling and theory

Design principles of biologically fabricated avian nests

Jessel HR, Chen S, Osovski S, Efroni S, Rittel D, Bachelet I · Scientific Reports 9, 4792

Modeling and theory

Astrocyte-specific transcriptome analysis using the ALDH1L1 bacTRAP mouse reveals novel biomarkers of astrogliosis in response to neurotoxicity

Michalovicz LT, Kelly KA, Vashishtha S, Ben-Hamo R, Efroni S, Miller JV, Locker AR, Sullivan K, Broderick G, Miller DB, O'Callaghan JP · Journal of Neurochemistry 150(4), 420-440

Networks and pathways

Digitizable therapeutics for decentralized mitigation of global pandemics

Hacohen A, Cohen R, Efroni S, Barzel B, Bachelet I · Scientific Reports 9, 14345

Modeling and theory

The immune system computes the state of the body: Crowd wisdom, machine learning, and immune cell reference repertoires help manage inflammation

Cohen IR, Efroni S · Frontiers in Immunology 10, 10

RepertoireModeling and theoryMachine learning

Resistance to paclitaxel is associated with a variant of the gene BCL2 in multiple tumor types

Ben-Hamo R, Zilberberg A, Cohen H, Bahar-Shany K, Wachtel C, Korach J, Aviel-Ronen S, Barshack I, Barash D, Levanon K, Efroni S · npj Precision Oncology 3, 12

Cancer

Comparing Transcriptome Profiles of Neurons Interfacing Adjacent Cells and Nanopatterned Substrates Reveals Fundamental Neuronal Interactions

Baranes K, Hibsh D, Cohen S, Yamin T, Efroni S, Sharoni A, Shefi O · Nano Letters 19(3), 1451-1459

Networks and pathways

2018

Tamoxifen-resistant breast cancer cells are resistant to DNA-damaging chemotherapy because of upregulated BARD1 and BRCA1

Zhu Y, Liu Y, Zhang C, Chu J, Wu Y, Li Y, Liu J, Li Q, Li S, Shi Q, Jin L, Zhao J, Yin D, Efroni S, Su F, Yao H, Song E, Liu Q · Nature Communications 9, 1595

Cancer

Network representation of T-Cell repertoire: A novel tool to analyze immune response to cancer formation

Priel A, Gordin M, Philip H, Zilberberg A, Efroni S · Frontiers in Immunology 9, 2913

RepertoireNetworks and pathwaysCancer

Cell studio: A platform for interactive, 3D graphical simulation of immunological processes

Liberman A, Kario D, Mussel M, Brill J, Buetow K, Efroni S, Nevo U · APL Bioengineering 2(2), 026107

Modeling and theory

Immunological analysis of phase II glioblastoma dendritic cell vaccine (Audencel) trial: immune system characteristics influence outcome and Audencel up-regulates Th1-related immunovariables

Erhart F, Buchroithner J, Reitermaier R, Fischhuber K, Klingenbrunner S, Sloma I, Hibsh D, Kozol R, Efroni S, Ricken G, Wohrer A, Haberler C, Hainfellner J, Krumpl G, Felzmann T, Dohnal AM, Marosi C, Visus C · Acta Neuropathologica Communications 6, 135

Cancer

2016

Dendritic cells in the context of human tumors: Biology and experimental tools

Volovitz I, Melzer S, Amar S, Bocsi J, Bloch M, Efroni S, Ram Z, Tarnok A · International Reviews of Immunology 35(2), 116-135

Cancer

The linker histone H1.0 generates epigenetic and functional intratumor heterogeneity

Torres CM, Biran A, Burney MJ, Patel H, Henser-Brownhill T, Cohen AS, Li Y, Ben-Hamo R, Nye E, Spencer-Dene B, Chakravarty P, Efroni S, Matthews N, Misteli T, Meshorer E, Scaffidi P · Science 353(6307)

Cancer

Experimental Support for the Ecoimmunity Theory: Distinct Phenotypes of Nonlymphocytic Cells in SCID and Wild-Type Mice

Ochayon DE, Baranovski BM, Malkin P, Schuster R, Kalay N, Ben-Hamo R, Sloma I, Levinson J, Brazg J, Efroni S, Lewis EC, Nevo U · Cell Transplantation 25(8), 1575-1588

Modeling and theory

Quantification of read species behavior within whole genome sequencing of cancer genomes for the stratification and visualization of genomic variation

Hibsh D, Buetow KH, Yaari G, Efroni S · Nucleic Acids Research 44(9), e81

CancerData and tools

Autotaxin-Lysophosphatidic Acid Axis Acts Downstream of Apoprotein B Lipoproteins in Endothelial Cells

Gibbs-Bar L, Tempelhof H, Ben-Hamo R, Ely Y, Brandis A, Hofi R, Almog G, Braun T, Feldmesser E, Efroni S, Yaniv K · Arteriosclerosis, Thrombosis, and Vascular Biology 36(10), 2058-2067

Networks and pathways

Reciprocal Regulation between SIRT6 and miR-122 Controls Liver Metabolism and Predicts Hepatocarcinoma Prognosis

Elhanati S, Ben-Hamo R, Kanfi Y, Varvak A, Glazz R, Lerrer B, Efroni S, Cohen HY · Cell Reports 14(2), 234-242

CancerNetworks and pathways

System-wide Analysis of the T Cell Response

Covacu R, Philip H, Jaronen M, Almeida J, Kenison JE, Darko S, Chao CC, Yaari G, Louzoun Y, Carmel L, Douek DC, Efroni S, Quintana FJ · Cell Reports 14(11), 2733-2744

Repertoire

hsa-miR-9 controls the mobility behavior of glioblastoma cells via regulation of MAPK14 signaling elements

Ben-Hamo R, Zilberberg A, Cohen H, Efroni S · Oncotarget 7(17), 23170-23181

CancerNetworks and pathways

2015

Fmrp Interacts with Adar and Regulates RNA Editing, Synaptic Density and Locomotor Activity in Zebrafish

Shamay-Ramot A, Khermesh K, Porath HT, Barak M, Pinto Y, Wachtel C, Zilberberg A, Lerer-Goldshtein T, Efroni S, Levanon EY, Appelbaum L · PLoS Genetics 11(12), e1005702

Networks and pathways

Distinct inhibitory effects on mTOR signaling by ethanol and INK128 in diffuse large B-cell lymphoma

Mazan-Mamczarz K, Peroutka RJ, Steinhardt JJ, Gidoni M, Zhang Y, Lehrmann E, Landon AL, Dai B, Houng S, Muniandy PA, Efroni S, Becker KG, Gartenhaus RB · Cell Communication and Signaling 13, 15

Cancer

De novo transcriptome assembly databases for the central nervous system of the medicinal leech

Hibsh D, Schori H, Efroni S, Shefi O · Scientific Data 2, 150015

Data and tools

A novel mitosis-associated lncRNA, MA-linc1, is required for cell cycle progression and sensitizes cancer cells to Paclitaxel

Bida O, Gidoni M, Ideses D, Efroni S, Ginsberg D · Oncotarget 6(29), 27880-27890

Cancer

MicroRNA regulation of molecular pathways as a generic mechanism and as a core disease phenotype

Ben-Hamo R, Efroni S · Oncotarget 6(3), 1594-1604

Networks and pathways

Synaptojanin 2 is a druggable mediator of metastasis and the gene is overexpressed and amplified in breast cancer

Ben-Chetrit N, Chetrit D, Russell R, Korner C, Mancini M, Abdul-Hai A, Itkin T, Carvalho S, Cohen-Dvashi H, Koestler WJ, Shukla K, Lindzen M, Kedmi M, Lauriola M, Shulman Z, Barr H, Seger D, Ferraro DA, Pareja F, Gil-Henn H, Lapidot T, Alon R, Milanezi F, Symons M, Ben-Hamo R, Efroni S, Schmitt F, Wiemann S, Caldas C, Ehrlich M, Yarden Y · Science Signaling 8(360), ra7

Cancer

2014

Heat acclimation memory: do the kinetics of the deacclimated transcriptome predispose to rapid reacclimation and cytoprotection?

Tetievsky A, Assayag M, Ben-Hamo R, Efroni S, Cohen G, Abbas A, Horowitz M · Journal of Applied Physiology 117(11), 1262-1277

Networks and pathways

Spatial regulation dominates gene function in the ganglia chain

Hibsh D, Schori H, Efroni S, Shefi O · Bioinformatics 30(3), 310-316

Networks and pathways

Shift in GATA3 functions, and GATA3 mutations, control progression and clinical presentation in breast cancer

Cohen H, Ben-Hamo R, Gidoni M, Yitzhaki I, Kozol R, Zilberberg A, Efroni S · Breast Cancer Research 16(6), 464

CancerNetworks and pathways

SENP5 mediates breast cancer invasion via a TGFβRI SUMOylation cascade

Cashman R, Cohen H, Ben-Hamo R, Zilberberg A, Efroni S · Oncotarget 5(4), 1071-1082

Cancer

PhenoNet: identification of key networks associated with disease phenotype

Ben-Hamo R, Gidoni M, Efroni S · Bioinformatics 30(17), 2399-2405

Networks and pathwaysData and tools

2013

IL-27 acts on DCs to suppress the T cell response and autoimmunity by inducing expression of the immunoregulatory molecule CD39

Mascanfroni ID, Yeste A, Vieira SM, Burns EJ, Patel B, Sloma I, Wu Y, Mayo L, Ben-Hamo R, Efroni S, Kuchroo VK, Robson SC, Quintana FJ · Nature Immunology 14(10), 1054-1063

Systems analysis utilising pathway interactions identifies sonic hedgehog pathway as a primary biomarker and oncogenic target in hepatocellular carcinoma

Efroni S, Meerzaman D, Schaefer CF, Greenblum S, Soo-Lyu M, Hu Y, Cultraro C, Meshorer E, Buetow KH · IET Systems Biology 7(6), 243-251

Networks and pathwaysCancer

Altered immune pathway activity under exercise challenge in Gulf War Illness: an exploratory analysis

Broderick G, Ben-Hamo R, Vashishtha S, Efroni S, Nathanson L, Barnes Z, Fletcher MA, Klimas N · Brain, Behavior, and Immunity 28, 159-169

Networks and pathways

MicroRNA-gene association as a prognostic biomarker in cancer exposes disease mechanisms

Ben-Hamo R, Efroni S · PLoS Computational Biology 9(11), e1003351

Networks and pathwaysCancer

2012

RBM38 is a direct transcriptional target of E2F1 that limits E2F1-induced proliferation

Feldstein O, Ben-Hamo R, Bashari D, Efroni S, Ginsberg D · Molecular Cancer Research 10(9), 1169-1177

Cancer

Rep-Seq: uncovering the immunological repertoire through next-generation sequencing

Benichou J, Ben-Hamo R, Louzoun Y, Efroni S · Immunology 135(3), 183-191

Repertoire

Biomarker robustness reveals the PDGF network as driving disease outcome in ovarian cancer patients in multiple studies

Ben-Hamo R, Efroni S · BMC Systems Biology 6, 3

Networks and pathwaysCancer

2011

Reactive animation: from piecemeal experimentation to reactive biological systems

Vainas O, Harel D, Cohen IR, Efroni S · Autoimmunity 44(4), 271-281

Modeling and theory

Immune-induced evolutionary selection focused on a single reading frame in overlapping hepatitis B virus proteins

Maman Y, Blancher A, Benichou J, Yablonka A, Efroni S, Louzoun Y · Journal of Virology 85(9), 4558-4566

The PathOlogist: an automated tool for pathway-centric analysis

Greenblum SI, Efroni S, Schaefer CF, Buetow KH · BMC Bioinformatics 12, 133

Networks and pathwaysData and tools

Detecting cancer gene networks characterized by recurrent genomic alterations in a population

Efroni S, Ben-Hamo R, Edmonson M, Greenblum S, Schaefer CF, Buetow KH · PLoS One 6(1), e14437

Networks and pathwaysCancer

Gene expression and network-based analysis reveals a novel role for hsa-miR-9 and drug control over the p38 network in glioblastoma multiforme progression

Ben-Hamo R, Efroni S · Genome Medicine 3(11), 77

Networks and pathwaysCancer

The whole-organism heavy chain B cell repertoire from Zebrafish self-organizes into distinct network features

Ben-Hamo R, Efroni S · BMC Systems Biology 5, 27

RepertoireNetworks and pathways

2010

Genetic variations at loci involved in the immune response are risk factors for hepatocellular carcinoma

Clifford RJ, Zhang J, Meerzaman DM, Lyu MS, Hu Y, Cultraro CM, Finney RP, Kelley JM, Efroni S, Greenblum SI, Nguyen CV, Rowe WL, Sharma S, Wu G, Yan C, Zhang H, Chung YH, Kim JA, Park NH, Song IH, Buetow KH · Hepatology

Cancer

2009

Stem cells do play with dice: a statistical physics view of transcription

Efroni S, Melcer S, Nissim-Rafinia M, Meshorer E · Cell Cycle

Modeling and theory

2008

Superposition of transcriptional behaviors determines gene state

Efroni S, Carmel L, Schaefer CG, Buetow KH · PLoS One

Modeling and theoryNetworks and pathways

Global transcription in pluripotent embryonic stem cells

Efroni S, Duttagupta R, Cheng J, Dehghani H, Hoeppner DJ, Dash C, Bazett-Jones DP, Le Grice S, McKay RD, Buetow KH, Gingeras TR, Misteli T, Meshorer E · Cell Stem Cell