Cryo-electron microscopy: mathematical foundations and algorithms

Publicaciones

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

Autores: Yael Harpaz and Yoel Shkolnisky
Publicado en: Biological Imaging, 2023, ISSN 2633-903X
Editor: Cambridge University Press
DOI: 10.1017/s2633903x23000089

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

Autores: Ido Caspy, Tirupathi Malavath, Daniel Klaiman, Maria Fadeeva, Yoel Shkolnisky, Nathan Nelson
Publicado en: Biochimica et Biophysica Acta (BBA) - Bioenergetics, Edición 1861/10, 2020, Página(s) 148253, ISSN 0005-2728
Editor: Elsevier BV
DOI: 10.1016/j.bbabio.2020.148253

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

Autores: 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
Publicado en: Nature Plants, Edición 7/9, 2021, Página(s) 1314-1322, ISSN 2055-0278
Editor: Nature
DOI: 10.1038/s41477-021-00983-1

Signal enhancement for two-dimensional cryo-EM data processing

Autores: Guy Sharon, Yoel Shkolnisky, and Tamir Bendory
Publicado en: Biological Imaging, 2023, ISSN 2633-903X
Editor: Cambridge University Press
DOI: 10.1017/s2633903x23000065

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

Autores: Boris Landa, Yoel Shkolnisky
Publicado en: Information and Inference: A Journal of the IMA, 2020, ISSN 2049-8772
Editor: Oxford University Press
DOI: 10.1093/imaiai/iaaa019

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

Autores: Ido Caspy, Anna Borovikova-Sheinker, Daniel Klaiman, Yoel Shkolnisky, Nathan Nelson
Publicado en: Nature Plants, Edición 6/10, 2020, Página(s) 1300-1305, ISSN 2055-0278
Editor: Springer Nature
DOI: 10.1038/s41477-020-00779-9

Rank-one multi-reference factor analysis

Autores: Yariv Aizenbud, Boris Landa, Yoel Shkolnisky
Publicado en: Statistics and Computing, Edición 31/1, 2021, ISSN 0960-3174
Editor: Kluwer Academic Publishers
DOI: 10.1007/s11222-020-09990-2

ASOCEM: Automatic Segmentation Of Contaminations in cryo-EM

Autores: Eldar, Amitay; Amos, Ido; Shkolnisky, Yoel
Publicado en: Journal of Structural Biology, 2022, ISSN 1047-8477
Editor: Academic Press
DOI: 10.1016/j.jsb.2022.107871

The Steerable Graph Laplacian and its Application to Filtering Image Datasets

Autores: Boris Landa, Yoel Shkolnisky
Publicado en: SIAM Journal on Imaging Sciences, Edición 11/4, 2018, Página(s) 2254-2304, ISSN 1936-4954
Editor: Society for Industrial and Applied Mathematics
DOI: 10.1137/18M1169394

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

Autores: Ido Greenberg, Yoel Shkolnisky
Publicado en: Journal of Structural Biology, Edición 200/2, 2017, Página(s) 106-117, ISSN 1047-8477
Editor: Academic Press
DOI: 10.1016/j.jsb.2017.09.007

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

Autores: Yariv Aizenbud, Yoel Shkolnisky
Publicado en: Journal of Mathematical Analysis and Applications, Edición 479/1, 2019, Página(s) 1004-1029, ISSN 0022-247X
Editor: Academic Press
DOI: 10.1016/j.jmaa.2019.06.064

Sampling and approximation of bandlimited volumetric data

Autores: Rami Katz, Yoel Shkolnisky
Publicado en: Applied and Computational Harmonic Analysis, Edición 47/1, 2019, Página(s) 235-247, ISSN 1063-5203
Editor: 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

Autores: Roy Mitz, Nir Sharon, Yoel Shkolnisky
Publicado en: SIAM Journal on Matrix Analysis and Applications, Edición 40/3, 2019, Página(s) 973-997, ISSN 0895-4798
Editor: Society for Industrial and Applied Mathematics
DOI: 10.1137/18m1172120

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

Autores: Gabi Pragier, Yoel Shkolnisky
Publicado en: Inverse Problems, 2019, ISSN 0266-5611
Editor: Institute of Physics Publishing
DOI: 10.1088/1361-6420/ab2fb2

KLT picker: Particle picking using data-driven optimal templates

Autores: Amitay Eldar, Boris Landa, Yoel Shkolnisky
Publicado en: Journal of Structural Biology, 2020, Página(s) 107473, ISSN 1047-8477
Editor: Academic Press
DOI: 10.1016/j.jsb.2020.107473

A Perturbation-Based Kernel Approximation Framework

Autores: Mitz, Roy; Shkolnisky, Yoel
Publicado en: Journal of Machine Learning Research, Edición 3, 2022, ISSN 1533-7928
Editor: 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

Autores: Eitan Rosen, Yoel Shkolnisky
Publicado en: SIAM Journal on Imaging Sciences, Edición 13/4, 2020, Página(s) 1898-1944, ISSN 1936-4954
Editor: 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

Autores: Nir Sharon, Joe Kileel, Yuehaw Khoo, Boris Landa, Amit Singer
Publicado en: Inverse Problems, Edición 36/4, 2020, Página(s) 044003, ISSN 0266-5611
Editor: Institute of Physics Publishing
DOI: 10.1088/1361-6420/ab6139

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