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Our Major Publications

for all the publications including collaborative projects please see PubMed:

2025

2025 Publications

A comprehensive overview of yeast libraries and their role in advancing cell biology

The FEBS Journal

Din Baruch, Maya Schuldiner, Ofir Klein

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Creation and validation of a proteome-wide yeast library for protein detection and analysis

Journal of Cell Science

Din Baruch, Ioannis Tsirkas, Ehud Sass, Benjamin Dubreuil,

Yeynit Asraf, Amir Aharoni, Maya Schuldiner, Ofir Klein

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A cryo-electron microscopy structure of yeast Pex5 in complex with a cargo uncovers a novel binding interface

Journal of Cell Science

Lior Peer, Orly Dym, Nadav Elad, Asa Tirosh, Jossef Jacobovitch, Ehud Sivan, Mor Angel, Shira Albeck, Maya Schuldiner, Yoav Peleg, Einat Zalckvar 

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A data-driven model for mitochondrial inner membrane remodeling as a driving force of organelle shaping

Journal of Cell Science

Noga Preminger, Ben Zucker, Sarah Hassdenteufel, Till Stephan, Stefan Jakobs, Michael M Kozlov, Maya Schuldiner

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Profiling the LAM Family of Contact Site Tethers Provides Insights into Their Regulation and Function

Contact

Emma J. Fenech, Meital Kupervaser, Angela Boshnakovska,

Shani Ravid, Inês Gomes Castro, Yeynit Asraf, Sylvie Callegari, Christof Lenz,  Henning Urlaub, Peter Rehling, Maya Schuldiner

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A proteome-wide yeast degron collection for the dynamic study of protein function

JCB

Rosario Valenti , Yotam David , Dunya Edilbi, Benjamin Dubreuil, Angela Boshnakovska, Yeynit Asraf , Tomer-Meir Salame , Ehud Sass, Peter Rehling,  Maya Schuldiner 

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2024 Publications

Analysis of mitochondrial biogenesis and protein localization by genetic screens and automated imaging

Methods in Enzymology

Yury S Bykov, Maya Schuldiner

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A systematic bi-genomic split-GFP assay illuminates the mitochondrial matrix proteome and protein targeting routes

eLife

Yury S Bykov, Solène Zuttion, Bruno Senger, Ofir Klein, Yeynit Asraf, Hadar Meyer, Hubert D Becker, Róża Kucharczyk, Maya Schuldiner

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Beyond fission and fusion—Diving into the mysteries of mitochondrial shape

PLoS Biology

Noga Preminger, Maya Schuldiner

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2023 Publications

A systematic proximity ligation approach to studying protein-substrate specificity identifies the substrate spectrum of the Ssh1 translocon

The EMBO Journal 

Nir Cohen, Naama Aviram,  Maya Schuldiner 

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A toolbox for systematic discovery of stable and transient protein interactors in baker's yeast

Molecular Systems Biology

Emma J Fenech, Nir Cohen, Meital Kupervaser, Zohar Gazi, Maya Schuldiner 

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2022 Publications

Systematic analysis of membrane contact sites in Saccharomyces cerevisiae uncovers modulators of cellular lipid distribution

eLife

Inês Gomes Castro, Shawn P Shortill, Samantha Katarzyna Dziurdzik, Angela Cadou, Suriakarthiga Ganesan, Rosario Valenti, Yotam David, Michael Davey, Carsten Mattes, Ffion B Thomas, Reut Ester Avraham, Hadar Meyer, Amir Fadel, Emma J Fenech, Robert Ernst, Vanina Zaremberg, Tim P Levine, Christopher Stefan, Elizabeth Conibear, Maya Schuldiner

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Determining the targeting specificity of the selective peroxisomal targeting factor Pex9

Biological Chemistry

Eden Yifrach, Markus Rudowitz, Luis Daniel, Cruz-Zaragoza, Asa Tirosh, Zohar Gazi, Yoav Peleg, Markus Kunze, Miriam Eisenstein, Wolfgang Schliebs, Maya Schuldiner, Ralf Erdmann, Einat Zalckvar

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Systematic multi-level analysis of an organelle proteome reveals new peroxisomal functions

Molecular Systems Biology

Eden Yifrach, Duncan Holbrook-Smith, Jérôme Bürgi, Alaa Othman, Miriam Eisenstein, Carlo WT van Roermund, Wouter Visser, Asa Tirosh, Markus Rudowitz, Chen Bibi, Shahar Galor, Uri Weill, Amir Fadel, Yoav Peleg, Ralf Erdmann, Hans R Waterham, Ronald J A Wanders, Matthias Wilmanns, Nicola Zamboni, Maya Schuldiner, Einat Zalckvar

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Pls1 Is a Peroxisomal Matrix Protein with a Role in Regulating Lysine Biosynthesis

Cells

Yotam David, Inês Gomes Castro, Eden Yifrach, Chen Bibi, Enas Katawi, Dekel Yahav Har-Shai, Sagie Brodsky, Naama Barkai, Tommer Ravid, Miriam Eisenstein, Shmuel Pietrokovski, Maya Schuldiner, Einat Zalckvar

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A Similarity-Based Method for Predicting Enzymatic Functions in Yeast Uncovers a New AMP Hydrolase

JMB

Nir Cohen, Amit Kahana, Maya Schuldiner

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Peroxisome function relies on organelle-associated mRNA translation

Science Advances

Noa Dahan, Yury S Bykov, Elizabeth A Boydston, Amir Fadel, Zohar Gazi, Hodaya Hochberg-Laufer, James Martenson, Vlad Denic, Yaron Shav-Tal, Jonathan S Weissman, Naama Aviram, Einat Zalckvar, Maya Schuldiner

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Beyond rare disorders: A new era for peroxisomal pathophysiology

Molecular Cell

Einat Zalckvar, Maya Schuldiner

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Show your true color: Mammalian cell surface staining for tracking cellular identity in multiplexing and beyond

Current Opinion in Chemical Biology

Sarah Hassdenteufel, Maya Schuldiner

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2021 Publications

The Fast and the Furious: Golgi Contact Sites

SAGE journals 

Yotam David , Inês G. Castro, and Maya Schuldiner

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Cnm1 mediates nucleus-mitochondria contact site formation in response to phospholipid levels

JCB journal of cell biology 

Michal Eisenberg-Bord, Naama Zung, Javier Collado, Layla Drwesh, Emma J. Fenech, Amir Fadel, Nili Dezorella, Yury S. Bykov, Doron Rapaport, Ruben Fernandez-Busnadiego, and Maya Schuldiner

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Widespread use of unconventional targeting signals in mitochondrial ribosome proteins

​The EMBO journal 

Yury S. Bykov, Tamara Flohr, Felix Boos, Naama Zung, Johannes M. Herrmann, Maya Schuldiner

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2020 Publications

New horizons in mitochondrial contact site research

Biological Chemistry 

Naama Zung​, Maya Schuldiner

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A piggybacking mechanism enables peroxisomal localization of the glyoxylate cycle enzyme Mdh2 in yeast

Journal of Cell Science 

Shiran Gabay-Maskit, Luis Daniel Cruz-Zaragoza, Nadav Shai, Miriam Eisenstein, Chen Bibi, Nir Cohen, Tobias Hansen, Eden Yifrach, Nofar Harpaz, Ruth Belostotsky, Wolfgang Schliebs,
Maya Schuldiner, Ralf Erdmann and Einat Zalckvar

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Uncovering targeting priority to yeast peroxisomes using an in-cell competition assay.

PNAS 

Rosenthal M, Metzl-Raz E, Bürgi J, Yifrach E, Drwesh L, Fadel A, Peleg Y, Rapaport D, Wilmanns M, Barkai N, Schuldiner M,
Zalckvar E.

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Double the Fun, Double the Trouble: Paralogs and Homologs Functioning in the Endoplasmic Reticulum

Annual Review of Biochemistry 

Emma J Fenech, Shifra Ben-Dor, Maya Schuldiner

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Cytosolic Events in the Biogenesis of Mitochondrial Proteins.

Cell Press

Yury S. Bykov, Doron Rapaport, Johannes M. Herrmann and Maya Schuldiner

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2019 Publications

Protein Topology Prediction Algorithms Systematically Investigated in the Yeast Saccharomyces cerevisiae.

Bioessays

Uri Weill, Nir Cohen, Amir Fadel, Shifra Ben‐Dor, and Maya Schuldiner

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High-throughput ultrastructure screening using electron microscopy and fluorescent barcoding.

J Cell Biol

Yury S. Bykov, Nir Cohen, Natalia Gabrielli, Hetty Manenschijn, SonjaWelsch, Petr Chlanda, Wanda Kukulski, Kiran R. Patil, Maya Schuldiner, and John A.G. Briggs

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Yeast ceramide synthases, Lag1 and Lac1, have distinct substrate specificity

Journal of Cell Science  

Márton Megyeri, Rupali Prasad, Giora Volpert , Andrzej Sliwa-Gonzalez , A. Galih Haribowo, Auxiliadora Aguilera-Romero, Howard Riezman, Yves Barral , Anthony H. Futerman and Maya Schuldiner

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The Endoplasmic Reticulum-Mitochondria Encounter Structure Complex Coordinates Coenzyme Q Biosynthesis.

Contact 

Michal Eisenberg-Bord, Hui S. Tsui, Diana Antunes, Lucía Fernández-del-Río, Michelle C. Bradley, Cory D. Dunn Theresa P. T. Nguyen, Doron Rapaport, Catherine F. Clarke, and Maya Schuldiner

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Promethin Is a Conserved Seipin Partner Protein

Cells 

Inês G. Castro ,Michal Eisenberg-Bord ,Elisa Persiani ,Justin J. Rochford ,Maya Schuldiner and Maria Bohnert

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Coming together to define membrane contact sites.

Nature communications

Luca Scorrano , Maria Antonietta De Matteis , Scott Emr , Francesca Giordano , György Hajnóczky  , Benoît Kornmann , Laura L. Lackner , Tim P. Levine  , Luca Pellegrini , Karin Reinisch , Rosario Rizzuto , Thomas Simmen , Harald Stenmark , Christian Ungermann  & Maya Schuldiner

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2018 Publications

Assessment of GFP tag position on protein localization and growth fitness in yeast

J Mol Biol

Uri Weill, Gat Krieger, Zohar Avihou, Ron Milo, Maya Schuldiner, Dan Davidi.

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Defining the Mammalian Peroxisomal Proteome

Subcell Biochem

Eden Yifrach, Sven Fischer, Silke Oeljeklaus, Maya Schuldiner,
Einat Zalckvar and Bettina Warscheid

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An ER surface retrieval pathway safeguards the import of mitochondrial membrane proteins in yeast

Science

Hansen KG, Aviram N, Laborenz J, Bibi C, Meyer M, Spang A, Schuldiner M, Herrmann JM.

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Genome-wide SWAp-Tag yeast libraries for proteome exploration

Nat Methods

Weill U, Yofe I, Sass E, Stynen B, Davidi D, Natarajan J, Ben-Menachem R, Avihou Z, Goldman O, Harpaz N, Chuartzman S, Kniazev K, Knoblach B, Laborenz J, Boos F, Kowarzyk J, Ben-Dor S, Zalckvar E, Herrmann JM, Rachubinski RA, Pines O, Rapaport D, Michnick SW, Levy ED, Schuldiner M.

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Stepping outside the comfort zone of membrane contact site research

Nat Rev Mol Cell Biol

Bohnert M, Schuldiner M.

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Systematic mapping of contact sites reveals tethers and a function for the peroxisome-mitochondria contact

Nature communications 

Shai N, Yifrach E, van Roermund CWT, Cohen N, Bibi C, IJlst L, Cavellini L, Meurisse J, Schuster R, Zada L, Mari MC, Reggiori FM, Hughes AL, Escobar-Henriques M, Cohen MM, Waterham HR, Wanders RJA, Schuldiner M and Zalckvar E.

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Database for High Throughput Screening Hits (dHITS): a simple tool to retrieve gene specific phenotypes from systematic screens done in yeast

Yeast

Chuartzman SG, Schuldiner M.

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Creating a systematic database of secretory pathway proteins uncovers new cargo for COPI

Traffic

Weill U, Arakel EC, Goldmann O, Golan M, Chuartzman S, Munro S, Schwappach B, Schuldiner M.

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Validation of a yeast malate dehydrogenase 2 (Mdh2) antibody tested for use in western blots

F1000Res

Gabay-Maskit S, Schuldiner M, Zalckvar E

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Mind the Organelle Gap – Peroxisome Contact Sites in Disease

Trends in Biochemical Sciences

Castro G. I., Schuldiner M., Zalckvar E.

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2017
Publications

Targeting and translocation of proteins to the endoplasmic reticulum at a glance

J Cell Sci.

Aviram N, Schuldiner M.

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​Identification of seipin-linked factors that act as determinants of a lipid droplet subpopulation

J Cell Biol.

Eisenberg-Bord M, Mari M, Weill U, Rosenfeld-Gur E, Moldavski O, Castro IG, Soni KG, Harpaz N, Levine TP, Futerman AH, Reggiori F, Bankaitis VA, Schuldiner M, Bohnert M

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Iron affects Ire1 clustering propensity and the amplitude of endoplasmic reticulum stress signaling

J Cell Sci.

Cohen N, Breker M, Bakunts A, Pesek K, Chas A, Argemí J, Orsi A, Gal L, Chuartzman S, Wigelman Y, Jonas F, Walter P, Ernst R, Aragón T, van Anken E, Schuldiner M.

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Two novel effectors of trafficking and maturation of the yeast plasma membrane H+ -ATPase

Traffic.

Geva Y, Crissman J, Arakel EC, Gómez-Navarro N, Chuartzman SG, Stahmer KR, Schwappach B, Miller EA, Schuldiner M

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A different kind of love - lipid droplet contact sites

Biochim Biophys Acta.

Schuldiner M, Bohnert M.

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Mitochatting - if only we could be a fly on the cell wall

Biochim Biophys Acta.

Eisenberg-Bord M, Schuldiner M.

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Peroxisome Mini-Libraries: Systematic Approaches to Study Peroxisomes Made Easy

Methods Mol Biol.

Dahan N, Schuldiner M and Zalckvar E

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Pex35 is a regulator of peroxisome abundance

J Cell Sci.

Yofe I, Soliman K, Chuartzman SG, Morgan B, Weill U, Yifrach E, Dick TP, Cooper SJ, Ejsing CS, Schuldiner M, Zalckvar E, Thoms S.

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2016
Publications

The SND proteins constitute an alternative targeting route to the endoplasmic reticulum

Nature.

Aviram N, Ast T, Costa EA, Arakel EC, Chuartzman SG, Jan CH, Haßdenteufel S, Dudek J, Jung M, Schorr S, Zimmermann R, Schwappach B, Weissman JS, Schuldiner M.

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A Tether Is a Tether Is a Tether: Tethering at Membrane Contact Sites

Dev Cell.

Eisenberg-Bord M, Shai N, Schuldiner M, Bohnert M

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Characterization of proteome dynamics in oleate reveals a novel peroxisome targeting receptor

J Cell Sci.

Yifrach E, Chuartzman SG, Dahan N, Maskit S, Zada L, Weill U, Yofe I, Olender T, Schuldiner M, Zalckvar E.

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Making sense of the yeast sphingolipid pathway

J Mol Biol.

Megyeri M, Riezman H, Schuldiner M, Futerman AH.

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Ground Control to Major TOM: Mitochondria-Nucleus Communication

FEBS J.

Eisenberg-Bord M, Schuldiner M.

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One library to make them all: streamlining the creation of yeast libraries via a SWAp-Tag strategy

Nat Methods.

Yofe I, Weill U, Meurer M, Chuartzman S, Zalckvar E, Goldman O, Ben-Dor S, Schütze C, Wiedemann N, Knop M, Khmelinskii A, Schuldiner M.

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The Protease Ste24 Clears Clogged Translocons

Cell. 

Ast T, Michaelis S, Schuldiner M.

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2015
Publications

No peroxisome is an island - Peroxisome contact sites

Biochim Biophys Acta.

Shai N, Schuldiner M, Zalckvar E.

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Lam6 Regulates the Extent of Contacts between Organelles

Cell Rep.

Elbaz-Alon Y, Eisenberg-Bord M, Shinder V, Stiller SB, Shimoni E, Wiedemann N, Geiger T, Schuldiner M.

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Lipid Droplets Are Essential for Efficient Clearance of Cytosolic Inclusion Bodies.

Dev Cell.

Moldavski O, Amen T, Levin-Zaidman S, Eisenstein M, Rogachev I, Brandis A, Kaganovich D, Schuldiner M.

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Peroxisystem: harnessing systems cell biology to study peroxisomes.

Biol Cell.

Schuldiner M, Zalckvar E

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2014
Publications

The yeast ER-intramembrane protease Ypf1 refines nutrient sensing by regulating transporter abundance.

Mol Cell.

Avci D, Fuchs S, Schrul B, Fukumori A, Breker M, Frumkin I, Chen CY, Biniossek ML, Kremmer E, Schilling O, Steiner H, Schuldiner M, Lemberg MK.

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The yeast oligopeptide transporter Opt2 is localized to peroxisomes and affects glutathione redox homeostasis.

FEMS Yeast Res.

Elbaz-Alon Y, Morgan B, Clancy A, Amoako TN, Zalckvar E, Dick TP, Schwappach B, Schuldiner M.

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A dynamic interface between vacuoles and mitochondria in yeast.

Dev Cell.

Elbaz-Alon Y, Rosenfeld-Gur E, Shinder V, Futerman AH, Geiger T, Schuldiner M.

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Accurate, model-based tuning of synthetic gene expression using introns in S. cerevisiae.

PLoS Genet.

Yofe I, Zafrir Z, Blau R, Schuldiner M, Tuller T, Shapiro E, Ben-Yehezkel T.

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The emergence of proteome-wide technologies: systematic analysis of proteins comes of age

Nat Rev Mol Cell Biol.

Breker M, Schuldiner M.

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A cytosolic degradation pathway, prERAD, monitors pre-inserted secretory pathway proteins.

J Cell Sci.

Ast T, Aviram N, Chuartzman SG, Schuldiner M.

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Peroxisomes are juxtaposed to strategic sites on mitochondria.

Mol Biosyst.

Cohen Y, Klug YA, Dimitrov L, Erez Z, Chuartzman SG, Elinger D, Yofe I, Soliman K, Gärtner J, Thoms S, Schekman R, Elbaz-Alon Y, Zalckvar E, Schuldiner M.

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Embracing the void--how much do we really know about targeting and translocation to the endoplasmic reticulum?

Curr Opin Cell Biol.

Aviram N, Schuldiner M.

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The back and forth of cargo exit from the endoplasmic reticulum.

Curr Biol.

Geva Y, Schuldiner M.

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Primers-4-Yeast: a comprehensive web tool for planning primers for Saccharomyces cerevisiae.

Yeast.

Yofe I, Schuldiner M.

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2013
Publications

The yeast p5 type ATPase, spf1, regulates manganese transport into the endoplasmic reticulum

PLoS One.

Cohen Y, Megyeri M, Chen OC, Condomitti G, Riezman I, Loizides-Mangold U, Abdul-Sada A, Rimon N, Riezman H, Platt FM, Futerman AH, Schuldiner M.

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LoQAtE--Localization and Quantitation ATlas of the yeast proteomE. A new tool for multiparametric dissection of single-protein behavior in response to biological perturbations in yeast.

Nucleic Acids Res.

Breker M, Gymrek M, Moldavski O, Schuldiner M.

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The role of Djp1 in import of the mitochondrial protein Mim1 demonstrates specificity between a cochaperone and its substrate protein

Mol Cell Biol.

Papić D, Elbaz-Alon Y, Koerdt SN, Leopold K, Worm D, Jung M, Schuldiner M, Rapaport D.

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All roads lead to Rome (but some may be harder to travel): SRP-independent translocation into the endoplasmic reticulum.

Crit Rev Biochem Mol Biol.

Ast T, Schuldiner M.

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A novel single-cell screening platform reveals proteome plasticity during yeast stress responses.

J Cell Biol.

Breker M, Gymrek M, Schuldiner M.

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From rags to riches - the history of the endoplasmic reticulum.

Biochim Biophys Acta. 

Schuldiner M, Schwappach B.

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A network of cytosolic factors targets SRP-independent proteins to the endoplasmic reticulum.

Cell.

Ast T, Cohen G, Schuldiner M.

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The contribution of systematic approaches to characterizing the proteins and functions of the endoplasmic reticulum.

Cold Spring Harb Perspect Biol.

Schuldiner M, Weissman JS.

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2012
Publications

Interactions of subunit CCT3 in the yeast chaperonin CCT/TRiC with Q/N-rich proteins revealed by high-throughput microscopy analysis.

Proc Natl Acad Sci U S A.

Nadler-Holly M, Breker M, Gruber R, Azia A, Gymrek M, Eisenstein M, Willison KR, Schuldiner M, Horovitz A.

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Ergosterol content specifies targeting of tail-anchored proteins to mitochondrial outer membranes.

Mol Biol Cell.

Krumpe K, Frumkin I, Herzig Y, Rimon N, Özbalci C, Brügger B, Rapaport D, Schuldiner M.

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A systematic approach to pair secretory cargo receptors with their cargo suggests a mechanism for cargo selection by Erv14.

PLoS Biol.

Herzig Y, Sharpe HJ, Elbaz Y, Munro S, Schuldiner M.

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2011
Publications

Getting the whole picture: combining throughput with content in microscopy

J Cell Sci.

Rimon N, Schuldiner M.

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Staying in touch: the molecular era of organelle contact sites.

Trends Biochem Sci.

Elbaz Y, Schuldiner M.

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Advanced methods for high-throughput microscopy screening of genetically modified yeast libraries

Methods Mol Biol.

Cohen Y, Schuldiner M.

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2005-2010
Publications

Explorations in topology-delving underneath the surface of genetic interaction maps.

Mol Biosyst.

Breker M, Schuldiner M.

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Comprehensive characterization of genes required for protein folding in the endoplasmic reticulum.

Science. 

Jonikas MC, Collins SR, Denic V, Oh E, Quan EM, Schmid V, Weibezahn J, Schwappach B, Walter P, Weissman JS, Schuldiner M.

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The GET complex mediates insertion of tail-anchored proteins into the ER membrane.

Cell.

Schuldiner M, Metz J, Schmid V, Denic V, Rakwalska M, Schmitt HD, Schwappach B, Weissman JS.

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Identification of yeast proteins necessary for cell-surface function of a potassium channel.

Proc Natl Acad Sci U S A.

Haass FA, Jonikas M, Walter P, Weissman JS, Jan YN, Jan LY, Schuldiner M.

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Exploration of the function and organization of the yeast early secretory pathway through an epistatic miniarray profile.

Cell.

Schuldiner M, Collins SR, Thompson NJ, Denic V, Bhamidipati A, Punna T, Ihmels J, Andrews B, Boone C, Greenblatt JF, Weissman JS, Krogan NJ.

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