Publications – Mahamid Group

Gemin O, Armijo V, Hons M, Bissardon C, Linares R, Bowler MW, Wolff G, Kovalev K, Babenko A, Salo VT, Schneider S, Rossi C, Lecomte L, Deckers T, Lauzier K, Janocha R, Felisaz F, Sinoir J, Galej W, Mahamid J, Müller CW, Eustermann S, Mattei S, Cipriani F, Papp G

bioRxiv, 2024

doi:10.1101/2024.01.18.576170.

ColabSeg: an interactive tool for editing, processing, and visualizing membrane segmentations from cryo-ET data.

Siggel M, Jensen RK, Maurer VJ, Mahamid J, Kosinski J

Journal of structural biology, 2024

doi:10.1016/j.jsb.2024.108067.

Transport-limited growth of coccolith crystals.

Avrahami EM, Eyal Z, Varsano N, Zagoriy I, Mahamid J, Gal A

Advanced materials (Deerfield Beach, Fla.), 2023

doi:10.1002/adma.202309547.

Genetically encoded multimeric tags for subcellular protein localization in cryo-EM.

Fung HKH, Hayashi Y, Salo VT, Babenko A, Zagoriy I, Brunner A, Ellenberg J, Müller CW, Cuylen-Haering S, Mahamid J

Nature methods, 2023

doi:10.1038/s41592-023-02053-0.

Molecular mechanism of glutaminase activation through filamentation and the role of filaments in mitophagy protection.

Adamoski D, Dias MM, Quesñay JEN, Yang Z, Zagoriy I, Steyer AM, Rodrigues CT, da Silva Bastos AC, da Silva BN, Costa RKE, de Abreu FMO, Islam Z, Cassago A, van Heel MG, Consonni SR, Mattei S, Mahamid J, Portugal RV, Ambrosio ALB, Dias SMG

Nature structural & molecular biology, 2023

doi:10.1038/s41594-023-01118-0.

High-throughput cryo-ET structural pattern mining by unsupervised deep iterative subtomogram clustering.

Zeng X, Kahng A, Xue L, Mahamid J, Chang YW, Xu M

Proceedings of the National Academy of Sciences of the United States of America, 2023

doi:10.1073/pnas.2213149120.

Molecular mechanisms of stress-induced reactivation in mumps virus condensates.

Zhang X, Sridharan S, Zagoriy I, Eugster Oegema C, Ching C, Pflaesterer T, Fung HKH, Becher I, Poser I, Müller CW, Hyman AA, Savitski MM, Mahamid J

Cell, 2023

doi:10.1016/j.cell.2023.03.015.

Light and electron microscopy continuum-resolution imaging of 3D cell cultures.

D'Imprima E, Garcia Montero M, Gawrzak S, Ronchi P, Zagoriy I, Schwab Y, Jechlinger M, Mahamid J

Developmental cell, 2023

doi:10.1016/j.devcel.2023.03.001.

The distance between the plasma membrane and the actomyosin cortex acts as a nanogate to control cell surface mechanics.

Lembo S, Strauss L, Cheng D, Vermeil J, Siggel M, Toro-Nahuelpan M, Chan CJ, Kosinski J, Piel M, Roure OD, Heuvingh J, Mahamid J, Diz-Muñoz A

bioRxiv, 2023

doi:10.1101/2023.01.31.526409.

Convolutional networks for supervised mining of molecular patterns within cellular context.

de Teresa-Trueba I, Goetz SK, Mattausch A, Stojanovska F, Zimmerli CE, Toro-Nahuelpan M, Cheng DWC, Tollervey F, Pape C, Beck M, Diz-Muñoz A, Kreshuk A, Mahamid J, Zaugg JB

Nature methods, 2023

doi:10.1038/s41592-022-01746-2.

Cryo-electron tomography of reconstituted biomolecular condensates.

Tollervey F, Zhang X, Bose M, Sachweh J, Woodruff JB, Franzmann TM, Mahamid J

Methods in molecular biology (Clifton, N.J.), 2022

doi:10.1007/978-1-0716-2663-4_15.

Genetically encoded multimeric tags for intracellular protein localisation in cryo-EM.

Fung KHH, Hayashi Y, Salo TV, Babenko A, Zagoriy I, Brunner A, Ellenberg J, Müller CW, Cuylen-Haering S, Mahamid J

bioRxiv, 2022

doi:10.1101/2022.12.10.519870.

Visualizing translation dynamics at atomic detail inside a bacterial cell.

Xue L, Lenz S, Zimmermann-Kogadeeva M, Tegunov D, Cramer P, Bork P, Rappsilber J, Mahamid J

Nature, 2022

doi:10.1038/s41586-022-05255-2.

Imaging cell biology.

Andrews B, Chang JB, Collinson L, Li D, Lundberg E, Mahamid J, Manley S, Mhlanga M, Nakano A, Schöneberg J, Van Valen D, Wu T', Zaritsky A

Nature cell biology, 2022

doi:10.1038/s41556-022-00960-6.

Mechanism of RNA polymerase I selection by transcription factor UAF.

Baudin F, Murciano B, Fung HKH, Fromm SA, Mattei S, Mahamid J, Müller CW

Science advances, 2022

doi:10.1126/sciadv.abn5725.

Liquid-to-solid phase transition of oskar ribonucleoprotein granules is essential for their function in Drosophila embryonic development.

Bose M, Lampe M, Mahamid J, Ephrussi A

Cell, 2022

doi:10.1016/j.cell.2022.02.022.

A modular platform for automated cryo-FIB workflows.

Klumpe S, Fung HKH, Goetz SK, Zagoriy I, Hampoelz B, Zhang X, Erdmann PS, Baumbach J, Müller CW, Beck M, Plitzko JM, Mahamid J

eLife, 2021

doi:10.7554/eLife.70506.

Determinants shaping the nanoscale architecture of the mouse rod outer segment.

Pöge M, Mahamid J, Imanishi SS, Plitzko JM, Palczewski K, Baumeister W

eLife, 2021

doi:10.7554/eLife.72817.

Intracellular nanoscale architecture as a master regulator of calcium carbonate crystallization in marine microalgae.

Kadan Y, Tollervey F, Varsano N, Mahamid J, Gal A

Proceedings of the National Academy of Sciences of the United States of America, 2021

doi:10.1073/pnas.2025670118.

Nuclear pores dilate and constrict in cellulo.

Zimmerli CE, Allegretti M, Rantos V, Goetz SK, Obarska-Kosinska A, Zagoriy I, Halavatyi A, Hummer G, Mahamid J, Kosinski J, Beck M

Science (New York, N.Y.), 2021

doi:10.1126/science.abd9776.

High-precision targeting workflow for volume electron microscopy.

Ronchi P, Mizzon G, Machado P, D'Imprima E, Best BT, Cassella L, Schnorrenberg S, Montero MG, Jechlinger M, Ephrussi A, Leptin M, Mahamid J, Schwab Y

The Journal of cell biology, 2021

doi:10.1083/jcb.202104069.

Locating macromolecular assemblies in cells by 2D template matching with cisTEM.

Lucas BA, Himes BA, Xue L, Grant T, Mahamid J, Grigorieff N

eLife, 2021

doi:10.7554/eLife.68946.

Interphase epichromatin: last refuge for the 30-nm chromatin fiber?

Xu P, Mahamid J, Dombrowski M, Baumeister W, Olins AL, Olins DE

Chromosoma, 2021

doi:10.1007/s00412-021-00759-8.

Multi-particle cryo-EM refinement with M visualizes ribosome-antibiotic complex at 3.5 Å in cells.

Tegunov D, Xue L, Dienemann C, Cramer P, Mahamid J

Nature methods, 2021

doi:10.1038/s41592-020-01054-7.

Liquid-to-solid phase transition of oskar RNP granules is essential for their function in the Drosophila germline.

Bose M, Mahamid J, Ephrussi A

bioRxiv, 2021

doi:10.1101/2021.03.31.437848.

Fluorescence-based 3D targeting of FIB-SEM acquisition of small volumes in large samples.

Ronchi P, Machado P, D’Imprima E, Mizzon G, Best BT, Cassella L, Schnorrenberg S, Montero MG, Jechlinger M, Ephrussi A, Leptin M, Mahamid J, Schwab Y

bioRxiv, 2021

doi:10.1101/2021.01.18.427072.

Protein condensates as aging Maxwell fluids.

Jawerth L, Fischer-Friedrich E, Saha S, Wang J, Franzmann T, Zhang X, Sachweh J, Ruer M, Ijavi M, Saha S, Mahamid J, Hyman AA, Jülicher F

Science (New York, N.Y.), 2020

doi:10.1126/science.aaw4951.

Stress fibres are embedded in a contractile cortical network.

Vignaud T, Copos C, Leterrier C, Toro-Nahuelpan M, Tseng Q, Mahamid J, Blanchoin L, Mogilner A, Théry M, Kurzawa L

Nature materials, 2020

doi:10.1038/s41563-020-00825-z.

Visualizing molecular architectures of cellular condensates: hints of complex coacervation scenarios.

Goetz SK, Mahamid J

Developmental cell, 2020

doi:10.1016/j.devcel.2020.09.003.

In-cell architecture of the nuclear pore and snapshots of its turnover.

Allegretti M, Zimmerli CE, Rantos V, Wilfling F, Ronchi P, Fung HKH, Lee CW, Hagen W, Turoňová B, Karius K, Börmel M, Zhang X, Müller CW, Schwab Y, Mahamid J, Pfander B, Kosinski J, Beck M

Nature, 2020

doi:10.1038/s41586-020-2670-5.

In-cell architecture of an actively transcribing-translating expressome.

O'Reilly FJ, Xue L, Graziadei A, Sinn L, Lenz S, Tegunov D, Blötz C, Singh N, Hagen WJH, Cramer P, Stülke J, Mahamid J, Rappsilber J

Science (New York, N.Y.), 2020

doi:10.1126/science.abb3758.

Addressing the challenge of in situ structural studies of RNP granules in light of emerging opportunities.

Zhang X, Mahamid J

Current opinion in structural biology, 2020

doi:10.1016/j.sbi.2020.06.012.

TEM bright field imaging of thick specimens: nodes in Thon ring patterns.

Tichelaar W, Hagen WJH, Gorelik TE, Xue L, Mahamid J

Ultramicroscopy, 2020

doi:10.1016/j.ultramic.2020.113023.

RNA-induced conformational switching and clustering of G3BP drive stress granule assembly by condensation.

Guillén-Boixet J, Kopach A, Holehouse AS, Wittmann S, Jahnel M, Schlüßler R, Kim K, Trussina IREA, Wang J, Mateju D, Poser I, Maharana S, Ruer-Gruß M, Richter D, Zhang X, Guck J, Chang YT, Mahamid J, Honigmann A, Pappu RV, Hyman AA, Franzmann TM, Alberti S

Cell, 2020

doi:10.1016/j.cell.2020.03.049.

Tailoring cryo-electron microscopy grids by photo-micropatterning for in-cell structural studies.

Toro-Nahuelpan M, Zagoriy I, Senger F, Blanchoin L, Théry M, Mahamid J

Nature methods, 2020

doi:10.1038/s41592-019-0630-5.

A cryo-FIB lift-out technique enables molecular-resolution cryo-ET within native caenorhabditis elegans tissue.

Schaffer M, Pfeffer S, Mahamid J, Kleindiek S, Laugks T, Albert S, Engel BD, Rummel A, Smith AJ, Baumeister W, Plitzko JM

Nature methods, 2019

doi:10.1038/s41592-019-0497-5.

Liquid-crystalline phase transitions in lipid droplets are related to cellular states and specific organelle association.

Mahamid J, Tegunov D, Maiser A, Arnold J, Leonhardt H, Plitzko JM, Baumeister W

Proceedings of the National Academy of Sciences of the United States of America, 2019

doi:10.1073/pnas.1903642116.

Cryo-EM structure of the native rhodopsin dimer in nanodiscs.

Zhao DY, Poege M, Morizumi T, Gulati S, Van Eps N, Zhang J, Miszta P, Filipek S, Mahamid J, Plitzko JM, Baumeister W, Ernst OP, Palczewski K

The Journal of biological chemistry, 2019

doi:10.1074/jbc.RA119.010089.

A hydrated crystalline calcium carbonate phase: Calcium carbonate hemihydrate.

Zou Z, Habraken WJEM, Matveeva G, Jensen ACS, Bertinetti L, Hood MA, Sun CY, Gilbert PUPA, Polishchuk I, Pokroy B, Mahamid J, Politi Y, Weiner S, Werner P, Bette S, Kolb U, Dinnebier R, Fratzl P, Zolotoyabko E

Science (New York, N.Y.), 2019

doi:10.1126/science.aav0210.

Unravelling molecular complexity in structural cell biology.

Pfeffer S, Mahamid J

Current opinion in structural biology, 2018

doi:10.1016/j.sbi.2018.08.009.

Phase separation of a yeast prion protein promotes cellular fitness

Franzmann T, Jahnel M, Pozniakovsky A, Mahamid J, Holehouse AS, Nüske E, Richter D, Baumeister W, Grill SW, Pappu RV, Hyman AA, Alberti S

2018

doi:10.1126/science.aao5654.

The centrosome is a selective phase that nucleates microtubules by concentrating tubulin

Woodruff JB, Ferreira Gomes B, Widlund PO, Mahamid J, Honigmann A and Hyman AA.

2017

doi:10.1016/j.cell.2017.05.028.

Challenges of Integrating Stochastic Dynamics and Cryo-Electron Tomograms in Whole-Cell Simulations.

Earnest TM, Watanabe R, Stone JE, Mahamid J, Baumeister W, Villa E, Luthey-Schulten Z

The journal of physical chemistry. B, 2017

doi:10.1021/acs.jpcb.7b00672.

Optimized cryo-focused ion beam sample preparation aimed at in situ structural studies of membrane proteins

Schaffer M, Mahamid J, Engel BD, Laugks T, Baumeister W, Plitzko JM

Journal of structural biology, 2017

doi:10.1016/j.jsb.2016.07.010.

Polar Positioning of Phase-Separated Liquid Compartments in Cells Regulated by an mRNA Competition Mechanism

Saha S, Weber CA, Nousch M, Adame-Arana O, Hoege C, Hein MY, Osborne-Nishimura E, Mahamid J, Jahnel M, Jawerth L, Pozniakovski A, Eckmann CR, Jülicher F, Hyman AA

Cell, 2016

doi:10.1016/j.cell.2016.08.006.

Visualizing the molecular sociology at the HeLa cell nuclear periphery

Mahamid J, Pfeffer S, Schaffer M, Villa E, Danev R, Cuellar LK, Förster F, Hyman AA, Plitzko JM, Baumeister W

Science (New York, N.Y.), 2016

doi:10.1126/science.aad8857.

Site-Specific Cryo-focused Ion Beam Sample Preparation Guided by 3D Correlative Microscopy

Arnold J, Mahamid J, Lucic V, de Marco A, Fernandez JJ, Laugks T, Mayer T, Hyman AA, Baumeister W, Plitzko JM

Biophysical journal, 2016

doi:10.1016/j.bpj.2015.10.053.

A focused ion beam milling and lift-out approach for site-specific preparation of frozen-hydrated lamellas from multicellular organisms

Mahamid J, Schampers R, Persoon H, Hyman AA, Baumeister W, Plitzko JM

Journal of structural biology, 2015

doi:10.1016/j.jsb.2015.07.012.

Cryo-focused Ion Beam Sample Preparation for Imaging Vitreous Cells by Cryo-electron Tomography.

Schaffer M, Engel BD, Laugks T, Mahamid J, Plitzko JM, Baumeister W

Bio-protocol, 2015

doi:10.21769/BioProtoc.1575.

A Liquid-to-Solid Phase Transition of the ALS Protein FUS Accelerated by Disease Mutation

Patel A, Lee HO, Jawerth L, Maharana S, Jahnel M, Hein MY, Stoynov S, Mahamid J, Saha S, Franzmann TM, Pozniakovski A, Poser I, Maghelli N, Royer LA, Weigert M, Myers EW, Grill S, Drechsel D, Hyman AA, Alberti S

Cell, 2015

doi:10.1016/j.cell.2015.07.047.

Centrosomes. Regulated assembly of a supramolecular centrosome scaffold in vitro.

Woodruff JB, Wueseke O, Viscardi V, Mahamid J, Ochoa SD, Bunkenborg J, Widlund PO, Pozniakovsky A, Zanin E, Bahmanyar S, Zinke A, Hong SH, Decker M, Baumeister W, Andersen JS, Oegema K, Hyman AA

Science (New York, N.Y.), 2015

doi:10.1126/science.aaa3923.

Initial stages of calcium uptake and mineral deposition in sea urchin embryos

Vidavsky N, Addadi S, Mahamid J, Shimoni E, Ben-Ezra D, Shpigel M, Weiner S, Addadi L

Proceedings of the National Academy of Sciences of the United States of America, 2014

doi:10.1073/pnas.1312833110.

Cryo-Electron Tomography: The realization of a vision.

Mahamid J, Baumeister W

Microscopy and Analysis (Americas), 2012

doi:.

Bone mineralization proceeds through intracellular calcium phosphate loaded vesicles: a cryo-electron microscopy study.

Mahamid J, Sharir A, Gur D, Zelzer E, Addadi L, Weiner S

Journal of structural biology, 2011

doi:10.1016/j.jsb.2011.03.014.

Self-Sharpening Mechanism of the Sea Urchin Tooth

Killian CE, Metzler RA, Gong YT, Churchill TH, Olson IC, Trubetskoy V, Christensen MB, Fournelle JH, De Carlo F, Cohen S, Mahamid J, Scholl A, Young A, Doran A, Wilt FH, Coppersmith SN, Gilbert PUPA

ADVANCED FUNCTIONAL MATERIALS, 2011

doi:10.1002/adfm.201001546.