Cryo-electron microscopy: mathematical foundations and algorithms

Informazioni relative al progetto

CRYOMATH

ID dell’accordo di sovvenzione: 723991

DOI 10.3030/723991

Progetto chiuso

Data della firma CE 13 Dicembre 2016

Data di avvio 1 Marzo 2017

Data di completamento 28 Febbraio 2023

Finanziato da

• EXCELLENT SCIENCE - European Research Council (ERC)

Costo totale € 1 751 250,00

Contributo UE € 1 751 250,00

Coordinato da

TEL AVIV UNIVERSITY
Israel

Pubblicazioni

Peer reviewed articles (18)

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

Autori: Yael Harpaz and Yoel Shkolnisky
Pubblicato in: Biological Imaging, 2023, ISSN 2633-903X
Editore: Cambridge University Press
DOI: 10.1017/s2633903x23000089

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

Autori: Ido Caspy, Tirupathi Malavath, Daniel Klaiman, Maria Fadeeva, Yoel Shkolnisky, Nathan Nelson
Pubblicato in: Biochimica et Biophysica Acta (BBA) - Bioenergetics, Numero 1861/10, 2020, Pagina/e 148253, ISSN 0005-2728
Editore: Elsevier BV
DOI: 10.1016/j.bbabio.2020.148253

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

Autori: 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
Pubblicato in: Nature Plants, Numero 7/9, 2021, Pagina/e 1314-1322, ISSN 2055-0278
Editore: Nature
DOI: 10.1038/s41477-021-00983-1

Signal enhancement for two-dimensional cryo-EM data processing

Autori: Guy Sharon, Yoel Shkolnisky, and Tamir Bendory
Pubblicato in: Biological Imaging, 2023, ISSN 2633-903X
Editore: Cambridge University Press
DOI: 10.1017/s2633903x23000065

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

Autori: Boris Landa, Yoel Shkolnisky
Pubblicato in: Information and Inference: A Journal of the IMA, 2020, ISSN 2049-8772
Editore: Oxford University Press
DOI: 10.1093/imaiai/iaaa019

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

Autori: Ido Caspy, Anna Borovikova-Sheinker, Daniel Klaiman, Yoel Shkolnisky, Nathan Nelson
Pubblicato in: Nature Plants, Numero 6/10, 2020, Pagina/e 1300-1305, ISSN 2055-0278
Editore: Springer Nature
DOI: 10.1038/s41477-020-00779-9

Rank-one multi-reference factor analysis

Autori: Yariv Aizenbud, Boris Landa, Yoel Shkolnisky
Pubblicato in: Statistics and Computing, Numero 31/1, 2021, ISSN 0960-3174
Editore: Kluwer Academic Publishers
DOI: 10.1007/s11222-020-09990-2

ASOCEM: Automatic Segmentation Of Contaminations in cryo-EM

Autori: Eldar, Amitay; Amos, Ido; Shkolnisky, Yoel
Pubblicato in: Journal of Structural Biology, 2022, ISSN 1047-8477
Editore: Academic Press
DOI: 10.1016/j.jsb.2022.107871

The Steerable Graph Laplacian and its Application to Filtering Image Datasets

Autori: Boris Landa, Yoel Shkolnisky
Pubblicato in: SIAM Journal on Imaging Sciences, Numero 11/4, 2018, Pagina/e 2254-2304, ISSN 1936-4954
Editore: Society for Industrial and Applied Mathematics
DOI: 10.1137/18M1169394

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

Autori: Ido Greenberg, Yoel Shkolnisky
Pubblicato in: Journal of Structural Biology, Numero 200/2, 2017, Pagina/e 106-117, ISSN 1047-8477
Editore: Academic Press
DOI: 10.1016/j.jsb.2017.09.007

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

Autori: Yariv Aizenbud, Yoel Shkolnisky
Pubblicato in: Journal of Mathematical Analysis and Applications, Numero 479/1, 2019, Pagina/e 1004-1029, ISSN 0022-247X
Editore: Academic Press
DOI: 10.1016/j.jmaa.2019.06.064

Sampling and approximation of bandlimited volumetric data

Autori: Rami Katz, Yoel Shkolnisky
Pubblicato in: Applied and Computational Harmonic Analysis, Numero 47/1, 2019, Pagina/e 235-247, ISSN 1063-5203
Editore: 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

Autori: Roy Mitz, Nir Sharon, Yoel Shkolnisky
Pubblicato in: SIAM Journal on Matrix Analysis and Applications, Numero 40/3, 2019, Pagina/e 973-997, ISSN 0895-4798
Editore: Society for Industrial and Applied Mathematics
DOI: 10.1137/18m1172120

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

Autori: Gabi Pragier, Yoel Shkolnisky
Pubblicato in: Inverse Problems, 2019, ISSN 0266-5611
Editore: Institute of Physics Publishing
DOI: 10.1088/1361-6420/ab2fb2

KLT picker: Particle picking using data-driven optimal templates

Autori: Amitay Eldar, Boris Landa, Yoel Shkolnisky
Pubblicato in: Journal of Structural Biology, 2020, Pagina/e 107473, ISSN 1047-8477
Editore: Academic Press
DOI: 10.1016/j.jsb.2020.107473

A Perturbation-Based Kernel Approximation Framework

Autori: Mitz, Roy; Shkolnisky, Yoel
Pubblicato in: Journal of Machine Learning Research, Numero 3, 2022, ISSN 1533-7928
Editore: 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

Autori: Eitan Rosen, Yoel Shkolnisky
Pubblicato in: SIAM Journal on Imaging Sciences, Numero 13/4, 2020, Pagina/e 1898-1944, ISSN 1936-4954
Editore: 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

Autori: Nir Sharon, Joe Kileel, Yuehaw Khoo, Boris Landa, Amit Singer
Pubblicato in: Inverse Problems, Numero 36/4, 2020, Pagina/e 044003, ISSN 0266-5611
Editore: Institute of Physics Publishing
DOI: 10.1088/1361-6420/ab6139