Publications

Human subcutaneous and visceral adipocyte atlases uncover classical and non-classical adipocytes and depot-specific patterns

Or Lazarescu*, Maya Ziv-Agam*, Yulia Haim*, Idan Hekselman, Juman Jubran, Ariel Shneyour, Habib Muallem, Alon Zemer, Marina Rosengarten-Levin, Daniel Kitsberg, Liron Levin, Idit F Liberty, Uri Yoel, Oleg Dukhno, Miriam Adam, Julia Braune, Claudia Müller, Nora Raulien, Martin Gericke, Antje Körner, Rinki Murphy, Matthias Blüher, Naomi Habib, Assaf Rudich#, and Esti Yeger-Lotem#

Nature Genetics 2024

Editorial: Celebrating women’s contribution to protein folding, misfolding, and degradation in honor of Susan Lindquist (1949-2016)

Anat Ben-Zvi, Serena Carra, Esti Yeger-Lotem

Frontiers in Molecular Biosciences 2024. doi:https://doi.org/10.3389/fmolb.2024.1504059

Tissue-aware interpretation of genetic variants advances the etiology of rare diseases

Argov CM, Shneyour A, Jubran J, Sabag E, Mansbach A, Sepunaru Y, Filtzer E, Gruber G, Volozhinsky M, Yogev Y, Birk O, Chalifa-Caspi V, Rokach L, Yeger-Lotem E#

Mol Syst Biol 2024. doi:https://doi.org/10.1038/s44320-024-00061-6

The landscape of cellular clearance systems across human tissues and cell types is shaped by tissue-specific proteome needs

Ekaterina Vinogradov, Lior Ravkaie, Bar Edri, Juman Jubran, Anat Ben-Zvi, Esti Yeger-Lotem

2024. doi:https://doi.org/10.1101/2024.08.26.609695

sNucConv: A bulk RNA-seq deconvolution method trained on single-nucleus RNA-seq data to estimate cell-type composition of human adipose tissues

Sorek G, Haim Y, Chalifa-Caspi V, Lazarescu O, Ziv-Agam M, Hagemann T, Nono Nankam PA, Blüher M, Liberty IF, Dukhno O, Kukeev I, Yeger-Lotem E, Rudich A, Levin L

iScience 2024. doi:https://doi.org/10.1016/j.isci.2024.110368

Machine-learning analysis reveals an important role for negative selection in shaping cancer aneuploidy landscapes

Juman Jubran, Rachel Slutsky, Nir Rozenblum, Lior Rokach, Uri Ben-David & Esti Yeger-Lotem

Genome Biology 2024. doi:https://doi.org/10.1186/s13059-024-03225-7

Affected cell types for hundreds of Mendelian diseases revealed by analysis of human and mouse single-cell data

Idan Hekselman, Assaf Vital, Maya Ziv-Agam, Lior Kerber, Ido Yairi, Esti Yeger-Lotem

eLife 2024. doi:https://doi.org/10.7554/eLife.84613

Network-based anomaly detection algorithm reveals proteins with major roles in human tissues

Dima Kagan, Juman Jubran, Esti Yeger-Lotem, Michael Fire

bioRxiv 2023. doi:https://doi.org/10.1101/2023.12.19.572354

Multicellular communities are perturbed in the aging human brain and Alzheimer’s disease

Anael Cain, Mariko Taga, Cristin McCabe, Gilad S Green, Idan Hekselman, Charles C White, Dylan I Lee, Pallavi Gaur, Orit Rozenblatt-Rosen, Feng Zhang, Esti Yeger-Lotem, David A Bennett, Hyun-Sik Yang, Aviv Regev, Vilas Menon, Naomi Habib, Philip L De Jager

Nature Neuroscience 2023. doi:DOI: 10.1038/s41593-023-01356-x

Predicting molecular mechanisms of hereditary diseases by using their tissue-selective manifestation

Eyal Simonovsky, Moran Sharon, Maya Ziv, Omry Mauer, Idan Hekselman, Juman Jubran, Ekaterina Vinogradov, Chanan M Argov, Omer Basha, Lior Kerber, Yuval Yogev, Ayellet V Segrè, Hae Kyung Im, GTEx Consortium, Ohad Birk, Lior Rokach, Esti Yeger-Lotem

Molecular Systems Biology (2023) e11407 2023. doi:https://doi.org/10.15252/msb.202211407

ProAct: quantifying the differential activity of biological processes in tissues, cells, and user-defined contexts

Moran Sharon, Gil Gruber, Chanan M Argov, Miri Volozhinsky, Esti Yeger-Lotem

Nucleic Acids Research 2023. doi:https://doi.org/10.1093/nar/gkad421

The Organ-Disease Annotations (ODiseA) Database of Hereditary Diseases and Inflicted Tissues

Idan Hekselman, Lior Kerber, Maya Ziv, Gil Gruber, Esti Yeger-Lotem

J Mol Biol 2022. doi:10.1016/j.jmb.2022.167619.

The TissueNet v.3 Database: Protein-protein Interactions in Adult and Embryonic Human Tissue contexts

Maya Ziv, Gil Gruber, Moran Sharon, Ekaterina Vinogradov, Esti Yeger-Lotem

J Mol Biol 2022. doi:10.1016/j.jmb.2022.167532

The differential activity of biological processes in tissues and cell subsets can illuminate disease-related processes and cell type identities

Moran Sharon, Ekaterina Vinogradov, Chanan M Argov, Or Lazarescu, Yazeed Zoabi, Idan Hekselman, Esti Yeger-Lotem

Bioinformatics 2022. doi:https://doi.org/10.1093/bioinformatics/btab883

Unraveling the hidden role of a uORF-encoded peptide as a kinase inhibitor of PKCs

Divya Ram Jayaram, Sigal Frost, Chanan Argov, Vijayasteltar Belsamma Liju, Nikhil Ponnoor Anto, Amitha Muraleedharan, Assaf Ben-Ari, Rose Sinay, Ilan Smoly, Ofra Novoplansky, Noah Isakov, Debra Toiber, Chen Keasar, Moshe Elkabets, Esti Yeger-Lotem, Etta Livneh

PNAS 2021. doi:https://doi.org/10.1073/pnas.2018899118

The landscape of molecular chaperones across human tissues reveals a layered architecture of core and variable chaperones

Netta Shemesh*, Juman Jubran*, Shiran Dror, Eyal Simonovsky, Omer Basha, Chanan Argov, Idan Hekselman, Mehtap Abu-Qarn, Ekaterina Vinogradov, Omry Mauer, Tatiana Tiago, Serena Carra, Anat Ben-Zvi & Esti Yeger-Lotem

Nature Communications 2021. doi:https://doi.org/10.1038/s41467-021-22369-9

A tissue-aware machine learning framework enhances the mechanistic understanding and genetic diagnosis of Mendelian and rare diseases

Eyal Simonovsky, Moran Sharon, Maya Ziv, Omry Mauer, Idan Hekselman, Juman Jubran, Ekaterina Vinogradov, Chanan M. Argov, Omer Basha, Lior Kerber, Yuval Yogev, Ayellet V. Segrè, Hae Kyung Im, GTEx Consortium, Ohad Birk, Lior Rokach, Esti Yeger-Lotem

bioRxiv 2021. doi:https://doi.org/10.1101/2021.02.16.430825

Dosage-sensitive molecular mechanisms are associated with the tissue-specificity of traits and diseases

Juman Jubran, Idan Hekselman, Lena Novack, Esti Yeger-Lotem

Computational and Structural Biotechnology Journal 2020 18:4024-4032. doi:https://doi.org/10.1016/j.csbj.2020.10.030

A reference map of the human protein interactome

Katja Luck, Dae-Kyum Kim, Luke Lambourne, Kerstin Spirohn, Bridget E. Begg, Wenting Bian, Ruth Brignall, Tiziana Cafarelli, Francisco J. Campos-Laborie, Benoit Charloteaux, Dongsic Choi, Atina G. Cote, Meaghan Daley, Steven Deimling, Alice Desbuleux, Amélie Dricot, Marinella Gebbia, Madeleine F. Hardy, Nishka Kishore, Jennifer J. Knapp, István A. Kovács, Irma Lemmens, Miles W. Mee, Joseph C. Mellor, Carl Pollis, Carles Pons, Aaron D. Richardson, Sadie Schlabach, Bridget Teeking, Anupama Yadav, Mariana Babor, Dawit Balcha, Omer Basha, Suet-Feung Chin, Soon Gang Choi, Claudia Colabella, Georges Coppin, Cassandra D’Amata, David De Ridder, Steffi De Rouck, Miquel Duran-Frigola, Hanane Ennajdaoui, Florian Goebels, Anjali Gopal, Ghazal Haddad, Mohamed Helmy, Yves Jacob, Yoseph Kassa, Roujia Li, Natascha van Lieshout, Andrew MacWilliams, Dylan Markey, Joseph N. Paulson, Sudharshan Rangarajan, John Rasla, Ashyad Rayhan, Thomas Rolland, Adriana San Miguel, Yun Shen, Dayag Sheykhkarimli, Gloria M. Sheynkman, Eyal Simonovsky, Murat Taşan, Alexander Tejeda, Jean-Claude Twizere, Yang Wang, Robert Weatheritt, Jochen Weile, Yu Xia, Xinping Yang, Esti Yeger-Lotem, Quan Zhong, Patrick Aloy, Gary D. Bader, Javier De Las Rivas, Suzanne Gaudet, Tong Hao, Janusz Rak, Jan Tavernier, Vincent Tropepe, David E. Hill, Marc Vidal, Frederick P. Roth, Michael A. Calderwood

Nature 2020 580(7803):402-408. doi:10.1038/s41586-020-2188-x.

Differential network analysis of human tissue interactomes highlights tissue-selective processes and genetic disorder genes

Omer Basha*, Chanan M Argov*, Raviv Artzy, Yazeed Zoabi, Idan Hekselman, Liad Alfandari, Vered Chlifa-Caspi and Esti Yeger-Lotem

Bioinformatics. 2020 pii: btaa034. doi:10.1093/bioinformatics/btaa034.

Mechanisms of tissue and cell-type specificity in heritable traits and diseases

Idan Hekselman & Esti Yeger-Lotem

Nature Reviews Genetics 2020 21(3):137-150. doi:https://doi.org/10.1038/s41576-019-0200-9; Featured on the March 2020 journal cover.

Aging promotes reorganization of the CD4 T cell landscape toward extreme regulatory and effector phenotypes.

Yehezqel Elyahu*, Idan Hekselman*, Inbal Eizenberg-Magar, Omer Berner, Itai Strominger, Maya Schiller, Kritika Mittal, Anna Nemirovsky, Ekaterina Eremenko, Assaf Vital, Eyal Simonovsky, Vered Chalifa-Caspi, Nir Friedman, Esti Yeger-Lotem, and Alon Monsonego

Science Advances 2019 5:8. doi:10.1126/sciadv.aaw8330

ResponseNet v.3: Revealing signaling and regulatory pathways connecting your proteins and genes across human tissues

Omer Basha, Omry Mauer, Eyal Simonovsky, Rotem Shpringer and Esti Yeger-Lotem

Nucleic Acids Research, In Press 2019. doi:https://doi.org/10.1093/nar/gkz421

Elucidating genotype-to-phenotype relationships via analyses of human tissue interactomes

Idan Hekselman, Moran Sharon, Omer Basha and Esti Yeger-Lotem

Analyzing Network Data in Biology and Medicine, Ed. Nataša Pržulj Cambridge, UK: Cambridge University Press 2019:459-489. doi:https://doi.org/10.1017/9781108377706

Large-scale analysis of human gene expression variability associates highly variable drug targets with lower drug effectiveness and safety

Eyal Simonovsky, Ronen Schuster and Esti Yeger-Lotem

Bioinformatics 2019 5(17):3028-3037. doi:https://doi.org/10.1093/bioinformatics/btz023

Integrating Rio1 activities discloses its nutrient-activated network in Saccharomyces cerevisiae

Maria G Iacovella, Michael Bremang, Omer Basha, Luciano Giacò, Walter Carotenuto, Cristina Golfieri, Barnabas Szakal, Marianna Dal Maschio, Valentina Infantino, Galina V Beznoussenko, Chinnu R Joseph, Clara Visintin, Alexander A Mironov, Rosella Visintin, Dana Branzei, Sébastien Ferreira-Cerca, Esti Yeger-Lotem, Peter De Wulf

Nucleic Acids Research 2018. doi:https://doi.org/10.1093/nar/gky618

Role of duplicate genes in determining the tissue-selectivity of hereditary diseases

Ruth Barshir, Idan Hekselman, Netta Shemesh, Moran Sharon, Lena Novack, Esti Yeger-Lotem

PLoS Genetics 2018. doi:https://doi.org/10.1371/journal.pgen.1007327

RSRC1 mutation affects intellect and behaviour through aberrant splicing and transcription, downregulating IGFBP3

Yonatan Perez, Shay Menascu, Idan Cohen, Rotem Kadir, Omer Basha, Zamir Shorer, Hila Romi, Gal Meiri, Tatiana Rabinski, Rivka Ofir, Esti Yeger-Lotem, Ohad S Birk

Brain 2018 141:4:961-970. doi:https://doi.org/10.1093/brain/awy045

The DifferentialNet database of differential protein–protein interactions in human tissues

Omer Basha, Rotem Shpringer, Chanan M Argov and Esti Yeger-Lotem

Nucleic Acids Research 2018 46:D1:D522-D526. doi:https://doi.org/10.1093/nar/gkx981

Genetic effects on gene expression across human tissues

GTEx Consortium

Nature 2017 550:204-213. doi:https://doi.org/10.1038/nature24277

MotifNet: a web-server for network motif analysis

Ilan Y Smoly, Eugene Lerman, Michal Ziv-Ukelson, Esti Yeger-Lotem

Bioinformatics 2017 33:12:1907-1909. doi:https://doi.org/10.1093/bioinformatics/btx056

An Asymmetrically Balanced Organization of Kinases versus Phosphatases across Eukaryotes Determines Their Distinct Impacts

Ilan Smoly, Netta Shemesh, Michal Ziv-Ukelson, Anat Ben-Zvi and Esti Yeger-Lotem

PLoS Comp. Biol. 2017. doi:https://doi.org/10.1371/journal.pcbi.1005221

The TissueNet v.2 database: A quantitative view of proteins and their interactions across human tissues

Basha O, Barshir R, Sharon M, Lerman E, Kirson B, Hekselman I and Yeger-Lotem E

Nucleic Acids Research 2017 45:D1:D427-D431

A Differentiation Transcription Factor Establishes Muscle-Specific Proteostasis in Caenorhabditis elegans

Yael Bar-Lavan, Netta Shemesh, Shiran Dror, Rivka Ofir, Esti Yeger-Lotem, Anat Ben-Zvi

PLoS Genetics 2016. doi:https://doi.org/10.1371/journal.pgen.1006531

Algorithms for Regular Tree Grammar Network Search and Their Application to Mining Human-Viral Infection Patterns

Ilan Smoly, Amir Carmel, Yonat Shemer-Avni, Esti Yeger-Lotem and Michal Ziv-Ukelson

J Comput Biol. 2016 23:3:165-179. doi:https://doi.org/10.1089/cmb.2015.0168

Human protein interaction networks across tissues and diseases

Esti Yeger-Lotem and Roded Sharan

Frontiers in Genetics 2015 6. doi:https://doi.org/10.3389/fgene.2015.00257

MyProteinNet: Build up-to-date protein interaction networks for organisms, tissues and user-defined contexts

Omer Basha, Dvir Flom, Ruth Barshir, Ilan Smoly, Shoval Tirman & Esti Yeger-Lotem

Nucleic Acids Research 2015 43:W1:W258-W263. doi:10.1093/nar/gkv515

A combination of gene expression ranking and co-expression network analysis increases discovery rate in large-scale mutant screens for novel Arabidopsis thaliana abiotic stress genes.

Vanessa Ransbotyn, Esti Yeger-Lotem, Omer Basha, Tania Acuna, Christoph Verduyn, Michal Gordon, Vered Chalifa-Caspi, Matthew A. Hannah and Simon Barak

Plant Biotechnol J. 2015 13:4:501-513. doi:10.1111/pbi.12274

Comparative Analysis of Human Tissue Interactomes Reveals Factors Leading to Tissue-Specific Manifestation of Hereditary Diseases.

Barshir R, Shwartz O, Smoly IY & Yeger-Lotem E.

PLoS Comput Biol 2014 10:6:e1003632. doi:https://doi.org/10.1371/journal.pcbi.1003632

Cancer evolution is associated with pervasive positive selection on globally expressed genes.

Ostrow SL, Barshir R, DeGregori J, Yeger-Lotem E & Hershberg R.

PLoS Genet. 2014 10:3:e1004239. doi:https://doi.org/10.1371/journal.pgen.1004239

A context-sensitive framework for the analysis of human signalling pathways in molecular interaction networks

Lan A, Ziv-Ukelson M, Yeger-Lotem E

Bioinformatics 2013 29:13:i210-i216. doi:https://doi.org/10.1093/bioinformatics/btt240

ResponseNet2.0: revealing signaling and regulatory pathways connecting your proteins and genes–now with human data.

Omer Basha, Shoval Tirman, Amir Eluk and Esti Yeger-Lotem

Nucleic Acids Research 2013 41:W1:W198-W203

The TissueNet database of human tissue protein-protein interactions

Barshir R, Basha O, Eluk A, Smoly IY, Lan A, Yeger-Lotem E.

Nucleic Acids Research 2013 41:D1:D841-D844

ResponseNet: revealing signaling and regulatory networks linking genetic and transcriptomic screening data

Lan A, Smoly IY, Rapaport G, Lindquist S, Fraenkel E, Yeger-Lotem E.

Nucleic Acids Research 2011 39:W1:W424-9. doi:https://doi.org/10.1093/nar/gkr359

Compounds from an unbiased chemical screen reverse both ER-to-Golgi trafficking defects and mitochondrial dysfunction in Parkinson’s disease models.

Su LJ, Auluck PK, Outeiro TF, Yeger-Lotem E, Kritzer JA, Tardiff DF, Strathearn KE, Liu F, Cao S, Hamamichi S, Hill KJ, Caldwell KA, Bell GW, Fraenkel E, Cooper AA, Caldwell GA, McCaffery JM, Rochet JC, Lindquist S.

Disease Models & Mechanisms 2010 3:194-208. doi:https://doi.org/10.1242/dmm.004267

Bridging high-throughput genetic and transcriptional data reveals cellular responses to alpha-synuclein toxicity.

Yeger-Lotem E, Riva L, Su LJ, Gitler AD, Cashikar AG, King OD, Auluck PK, Geddie ML, Valastyan JS, Karger DR, Lindquist S, Fraenkel E.

Nature Genetics 2009 41:316-323

Alignment of metabolic pathways

Pinter RY, Rokhlenko O, Yeger-Lotem E, Ziv-Ukelson M.

Bioinformatics 2005 21:16:3401-3408. doi:https://doi.org/10.1093/bioinformatics/bti554

Chromosomal organization is shaped by the transcription regulatory network

Hershberg R, Yeger-Lotem E, Margalit H.

Trends in Genetics 2005 21:3:P138-142. doi:https://doi.org/10.1016/j.tig.2005.01.003

Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction

Yeger-Lotem E, Sattath S, Kashtan N, Itzkovitz S, Milo R, Pinter RY, Alon U, Margalit H

PNAS 2004 101:16:5934-5939. doi:https://doi.org/10.1073/pnas.0306752101

Detection of regulatory circuits by integrating the cellular networks of protein-protein interactions and transcription regulation

Yeger-Lotem E, Margalit H.

Nucleic Acids Research (Nucleic Acids Res. 2003 Oct 15;31(20):6053-61.). 2003 31:20:6053-6061. doi:https://doi.org/10.1093/nar/gkg787

The AS/400 cluster engine: A case study

Gera Goft, Esti Yeger-Lotem

Proceedings of the 1999 ICPP Workshops on Collaboration and Mobile Computing (CMC'99). Group Communications (IWGC). Internet '99 (IWI'99). Industrial Applications on Network Computing (INDAP). 1999. doi:https://doi.org/10.1109/icppw.1999.800039

Dynamic voting for consistent primary components

Danny Dolev, Idit Keidar, Esti Yeger-Lotem

PODC '97 Proceedings of the sixteenth annual ACM symposium on Principles of distributed computing 1997:63-71. doi:https://doi.org/10.1145/259380.259424