Cryo-electron microscopy: mathematical foundations and algorithms

Project Information

CRYOMATH

Grant agreement ID: 723991

DOI 10.3030/723991

Project closed

EC signature date 13 December 2016

Start date 1 March 2017

End date 28 February 2023

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost € 1 751 250,00

EU contribution € 1 751 250,00

Coordinated by

TEL AVIV UNIVERSITY
Israel

Publications

Peer reviewed articles (18)

Three-Dimensional Alignment of Density Maps in Cryo-Electron Microscopy

Author(s): Yael Harpaz and Yoel Shkolnisky
Published in: Biological Imaging, 2023, ISSN 2633-903X
Publisher: Cambridge University Press
DOI: 10.1017/s2633903x23000089

Structure and energy transfer pathways of the Dunaliella Salina photosystem I supercomplex

Author(s): Ido Caspy, Tirupathi Malavath, Daniel Klaiman, Maria Fadeeva, Yoel Shkolnisky, Nathan Nelson
Published in: Biochimica et Biophysica Acta (BBA) - Bioenergetics, Issue 1861/10, 2020, Page(s) 148253, ISSN 0005-2728
Publisher: Elsevier BV
DOI: 10.1016/j.bbabio.2020.148253

Cryo-EM photosystem I structure reveals adaptation mechanisms to extreme high light in Chlorella ohadii

Author(s): Ido Caspy, Ehud Neumann, Maria Fadeeva, Varda Liveanu, Anton Savitsky, Anna Frank, Yael Levi Kalisman, Yoel Shkolnisky, Omer Murik, Haim Treves, Volker Hartmann, Marc M. Nowaczyk, Wolfgang Schuhmann, Matthias Rögner, Itamar Willner, Aaron Kaplan, Gadi Schuster, Nathan Nelson, Wolfgang Lubitz, Rachel Nechushtai
Published in: Nature Plants, Issue 7/9, 2021, Page(s) 1314-1322, ISSN 2055-0278
Publisher: Nature
DOI: 10.1038/s41477-021-00983-1

Signal enhancement for two-dimensional cryo-EM data processing

Author(s): Guy Sharon, Yoel Shkolnisky, and Tamir Bendory
Published in: Biological Imaging, 2023, ISSN 2633-903X
Publisher: Cambridge University Press
DOI: 10.1017/s2633903x23000065

Multi-reference factor analysis: low-rank covariance estimation under unknown translations

Author(s): Boris Landa, Yoel Shkolnisky
Published in: Information and Inference: A Journal of the IMA, 2020, ISSN 2049-8772
Publisher: Oxford University Press
DOI: 10.1093/imaiai/iaaa019

The structure of a triple complex of plant photosystem I with ferredoxin and plastocyanin

Author(s): Ido Caspy, Anna Borovikova-Sheinker, Daniel Klaiman, Yoel Shkolnisky, Nathan Nelson
Published in: Nature Plants, Issue 6/10, 2020, Page(s) 1300-1305, ISSN 2055-0278
Publisher: Springer Nature
DOI: 10.1038/s41477-020-00779-9

Rank-one multi-reference factor analysis

Author(s): Yariv Aizenbud, Boris Landa, Yoel Shkolnisky
Published in: Statistics and Computing, Issue 31/1, 2021, ISSN 0960-3174
Publisher: Kluwer Academic Publishers
DOI: 10.1007/s11222-020-09990-2

ASOCEM: Automatic Segmentation Of Contaminations in cryo-EM

Author(s): Eldar, Amitay; Amos, Ido; Shkolnisky, Yoel
Published in: Journal of Structural Biology, 2022, ISSN 1047-8477
Publisher: Academic Press
DOI: 10.1016/j.jsb.2022.107871

The Steerable Graph Laplacian and its Application to Filtering Image Datasets

Author(s): Boris Landa, Yoel Shkolnisky
Published in: SIAM Journal on Imaging Sciences, Issue 11/4, 2018, Page(s) 2254-2304, ISSN 1936-4954
Publisher: Society for Industrial and Applied Mathematics
DOI: 10.1137/18M1169394

Common lines modeling for reference free Ab-initio reconstruction in cryo-EM

Author(s): Ido Greenberg, Yoel Shkolnisky
Published in: Journal of Structural Biology, Issue 200/2, 2017, Page(s) 106-117, ISSN 1047-8477
Publisher: Academic Press
DOI: 10.1016/j.jsb.2017.09.007

A max-cut approach to heterogeneity in cryo-electron microscopy

Author(s): Yariv Aizenbud, Yoel Shkolnisky
Published in: Journal of Mathematical Analysis and Applications, Issue 479/1, 2019, Page(s) 1004-1029, ISSN 0022-247X
Publisher: Academic Press
DOI: 10.1016/j.jmaa.2019.06.064

Sampling and approximation of bandlimited volumetric data

Author(s): Rami Katz, Yoel Shkolnisky
Published in: Applied and Computational Harmonic Analysis, Issue 47/1, 2019, Page(s) 235-247, ISSN 1063-5203
Publisher: Academic Press
DOI: 10.1016/j.acha.2018.11.003

Symmetric Rank-One Updates from Partial Spectrum with an Application to Out-of-Sample Extension

Author(s): Roy Mitz, Nir Sharon, Yoel Shkolnisky
Published in: SIAM Journal on Matrix Analysis and Applications, Issue 40/3, 2019, Page(s) 973-997, ISSN 0895-4798
Publisher: Society for Industrial and Applied Mathematics
DOI: 10.1137/18m1172120

A common lines approach for ab-initio modeling of cyclically-symmetric molecules

Author(s): Gabi Pragier, Yoel Shkolnisky
Published in: Inverse Problems, 2019, ISSN 0266-5611
Publisher: Institute of Physics Publishing
DOI: 10.1088/1361-6420/ab2fb2

KLT picker: Particle picking using data-driven optimal templates

Author(s): Amitay Eldar, Boris Landa, Yoel Shkolnisky
Published in: Journal of Structural Biology, 2020, Page(s) 107473, ISSN 1047-8477
Publisher: Academic Press
DOI: 10.1016/j.jsb.2020.107473

A Perturbation-Based Kernel Approximation Framework

Author(s): Mitz, Roy; Shkolnisky, Yoel
Published in: Journal of Machine Learning Research, Issue 3, 2022, ISSN 1533-7928
Publisher: JMLR, Inc. and Microtome Publishing
DOI: 10.48550/arxiv.2009.02955

Common Lines Ab Initio Reconstruction of $D_{2}$-Symmetric Molecules in Cryo-Electron Microscopy

Author(s): Eitan Rosen, Yoel Shkolnisky
Published in: SIAM Journal on Imaging Sciences, Issue 13/4, 2020, Page(s) 1898-1944, ISSN 1936-4954
Publisher: Society for Industrial and Applied Mathematics
DOI: 10.1137/20m131535x

Method of moments for 3D single particle ab initio modeling with non-uniform distribution of viewing angles

Author(s): Nir Sharon, Joe Kileel, Yuehaw Khoo, Boris Landa, Amit Singer
Published in: Inverse Problems, Issue 36/4, 2020, Page(s) 044003, ISSN 0266-5611
Publisher: Institute of Physics Publishing
DOI: 10.1088/1361-6420/ab6139