Publications

Journal papers

1. E. Rosen, X. Cheng, and Y. Shkolnisky. The G-invariant graph Laplacian Part II: Diffusion maps. Submitted for publication. PDF

2. E. Rosen, P. Hoyos, X. Cheng, J. Kileel, and Y. Shkolnisky. The G-invariant graph Laplacian Part I: Convergence rate and eigendecomposition, Applied and Computational Harmonic Analysis, 71, 101637, February 2024. PDF

3. R. Mitz and Y. Shkolnisky. ROIPCA: An online memory-restricted PCA algorithm based on rank-one updates. Information and Inference: A Journal of the IMA,  12(4):2851–2872, November 2023. PDF

4. A. Shasha Geva and Y. Shkolnisky. A common lines approach for ab-initio modeling of molecules with tetrahedral and octahedral symmetry.  SIAM Journal on Imaging Sciences, 16(4):1978-2014, October 2023. PDF

5. Y. Harpaz and Y. Shkolnisky. Three-dimensional alignment of density maps in cryo-electron microscopy. Biological Imaging, 3, E8, March 2023. PDF
   Code available at https://github.com/ShkolniskyLab/emalign

6. G. Sharon, Y. Shkolnisky, and T. Bendory. Signal enhancement for two-dimensional cryo-EM data processing.  Biological Imaging, 3, E7,March 2023 . PDF

7. A. Eldar, I. Amos, and Y. Shkolnisky. ASOCEM: Automatic Segmentation Of Contaminations in cryo-EM. Journal of Structural Biology, 214(3):107871, 2022. PDF
   MATLAB version available at https://github.com/ShkolniskyLab/kltpicker2_matlab
   Python version available at https://github.com/ShkolniskyLab/kltpicker2

8. R. Mitz and Y. Shkolnisky. A Perturbation-Based Kernel Approximation Framework. Journal of Machine Learning Research, 23(142):1−26, 2022. PDF
   Code available at https://github.com/ShkolniskyLab/perturbation_kernel_approximation

9. I. Caspy, E. Neumann, M. Fadeeva, V. Liveanu, A. Savitsky, A. Frank, Y. Levi Kalisman, Y. Shkolnisky, O. Murik, H. Treves, V. Hartmann, M. M. Nowaczyk, W. Schuhmann, M. Rögner, I. Willner, A. Kaplan, G. Schuster, N. Nelson, W. Lubitz, and R. Nechushtai. Cryo-EM photosystem I structure reveals adaptation mechanisms to extreme high light in Chlorella ohadii. Nature Plants, 7:1314–1322, September 2021. PDF

10. M. Sporny, J. Guez-Haddad, T. Khazma, A. Yaron, M. Dessau, Y. Shkolnisky, C. Mim, M. N. Isupov, R. Zalk, M. Hons, Y. Opatowsky. The structural basis for SARM1 inhibition and activation under energetic stress. eLife 2020;9:e62021. PDF

11. Y. Aizenbud, B. Landa, and Y. Shkolnisky. Rank-one Multi-Reference Factor Analysis. Statistics and Computing, 31, 8, October 2021. PDF

12. B. Gutman, M. Mrejen, G. Shabat, R. Avinery, Y. Shkolnisky, R. Beck. Angular super-resolution retrieval in small-angle X-ray scattering. Scientific Reports, 10(1):16038, September 2020. PDF

13. I. Caspy,  A. Borovikova-Sheinker, D. Klaiman, Y. Shkolnisky, and N. Nelson. The structure of a triple complex of plant photosystem I with ferredoxin and plastocyanin. Nature Plants, 6:1300–1305, September 2020. PDF

14. E. Rosen and Y. Shkolnisky. Common lines ab initio reconstruction of $D_2$-symmetric molecules in cryo-electron microscopy. SIAM Journal on Imaging Sciences, 13(4):1898-1944, August 2020. PDF

15. B. Landa and Y. Shkolnisky. Multi-Reference Factor Analysis: low-rank covariance estimation under unknown translations. Information and Inference: A Journal of the IMA, iaaa019.  PDF

16. I. Caspy, T. Malavath, D. Klaiman, M. Fadeeva, Y. Shkolnisky, N. Nelson. Structure and Energy Transfer Pathways of the Dunaliella Salina Photosystem I Supercomplex. Biochimica et Biophysica Acta (BBA) – Bioenergetics, 1861(10), October 2020.  PDF

17. A. Eldar, B. Landa, and Y. Shkolnisky.  KLT picker: Particle picking using data-driven optimal templates. Journal of Structural Biology, 210(2):107473, February 2020. PDF
    MATLAB version available at https://github.com/ShkolniskyLab/kltpicker_matlab
    Python version available at https://github.com/ShkolniskyLab/kltpicker

18. R. Mitz, N. Sharon, and Yoel Shkolnisky. Symmetric rank one updating from partial spectrum with an application to out-of-sample extension. SIAM Journal on Matrix Analysis and Applications,  40(3):973–997, August 2019. PDF

19. Y. Aizenbud and Y. Shkolnisky. A max-cut approach to heterogeneity in cryo-electron microscopy. Journal of Mathematical Analysis and Applications, 479(1):1004-1029,  November 2019. PDF

20. G. Pragier and Y. Shkolnisky. A common lines approach for ab-initio modeling of cyclically-symmetric molecules. Inverse Problems, 35(12):124005, November 2019. PDF

21. M. Salhov, O. Lindenbaum, Y. Aizenbud, A. Silberschatz, Y. Shkolnisky, A. Averbuch. Multi-view kernel consensus for data analysis. Applied and Computational Harmonic Analysis, 49(1): 208-228, July 2020.  PDF

22. R. katz and Y. Shkolnisky. Sampling and approximation of bandlimited volumetric data. Applied and Computational Harmonic Analysis, 47(1):235-247, July 2019. PDF
    Code available at https://github.com/ShkolniskyLab/PSWF3D

23. Y. Ogen, S. Faigenbaum-Golovin, A. Granot, Y. Shkolnisky, N. Goldshleger and E. Ben Dor. Removing the Moisture Effect on Soil Reflectance Properties: A Case Study of Clay-Content Prediction. Pedosphere, 29(4): 421-431, August 2019.

24. B. Landa and Y. Shkolnisky. The steerable graph Laplacian and its application to filtering image data-sets. SIAM Journal on Imaging Sciences, 11(4):2254-2304, 2018. PDF

25. N. Sharon and Y. Shkolnisky. Evaluating non-analytic functions of matrices. Journal of Mathematical Analysis and Applications, 462(1): 613-636, June 2018. PDF

26. I. Greenberg and Y. Shkolnisky. Common Lines Modeling for Reference Free Ab-Initio Reconstruction in Cryo-EM. Journal of Structural Biology, 200(2): 106-117, 2017. PDF

27. B. Landa and Y. Shkolnisky. Steerable principal components for space frequency localized images. SIAM Journal on Imaging Sciences, 10(2): 508-534, 2017. PDF

28. G. Pragier, I. Greenberg, X. Cheng, and Y. Shkolnisky. A graph partitioning approach to simultaneous angular reconstitution. IEEE Transactions Computational Imaging, 2(3): 323-333, September 2016. PDF

29. A. Averbuch, G. Shabat, and Y. Shkolnisky. Direct inversion of the 3D pseudo-polar Fourier transform. SIAM Journal on Scientific Computing 38(2): A1100-A1120, 2016. PDF

30. B. Landa and Y. Shkolnisky. Approximation scheme for essentially bandlimited and space-concentrated functions on a disk. Applied and Computational Harmonic Analysis, 43(3): 381-403, November 2017. PDF

31. V. May,. Y. Keller, N. Sharon, Y. Shkolnisky. An algorithm for improving Non-Local Means operators via low-rank approximation. IEEE Transactions on Image Processing, 25(3):1340 - 1353, 2016. PDF

32. Z. Zhao, Y. Shkolnisky, A. Singer. Fast Steerable Principal Component Analysis. IEEE Transactions on Computational Imaging, 2(1):1-12, 2016. PDF

33. N. Sharon and Y. Shkolnisky. A class of Laplacian multiwavelets bases for high-dimensional data. Applied and Computational Harmonic Analysis, 38(3): 420–451, 2015. PDF

34. S. Adar, Y. Shkolnisky, and E. Ben Dor. A new approach for thresholding spectral change detection using multispectral and hyperspectral image data, a case study over Sokolov, Czech Republic. International Journal of Remote Sensing, 35(4): 1563-1584, 2014. PDF

35. S. Adar, Y. Shkolnisky, and E. Ben Dor. Change detection of soils under small-scale laboratory conditions using imaging spectroscopy sensors. Geoderma, 216: 19-29, 2014. PDF

36. S. Adar, Y. Shkolnisky, G. Notesco and E. Ben Dor. Using Visible spectral information to predict long-wave infrared spectral emissivity: a case study over the Sokolov area of the Czech Republic with an airborne hyperspectral Scanner Sensor. Remote Sensing, 5(11): 5757-5782, 2013. PDF

37. V. Abrishami, A. Zaldívar-Peraza, J. M. de la Rosa-Trevín, J. Vargas, J. Otón, R. Marabini, Y. Shkolnisky, J. M. Carazo, and C. O. S. Sorzano. A pattern matching approach to the automatic selection of particles from low-contrast electron micrographs. Bioinformatics, 29 (19): 2460-2468, 2013. PDF

38. Y. Shkolnisky and A. Singer. Viewing Directions Estimation in Cryo-EM using Synchronization. SIAM Journal on Imaging Sciences, 5(3): 1088-1110, 2012.PDF

39. A. Averbuch, I. Sedelnikov, and Y. Shkolnisky. CT reconstruction from parallel and fan-beam projections by 2D discrete Radon transform. IEEE Transactions on Image Processing, 21(2): 733–741, 2012.PDF

40. N. Halko, P. G. Martinsson, Y. Shkolnisky, and M. Tygert. An algorithm for the principal component analysis of large data sets. SIAM Journal on Scientific Computing, 33(5):2580-2594, 2011.PDF
    Code available at https://github.com/ShkolniskyLab/out-of-core-svd

41. A. Singer, Z. Zhao, Y. Shkolnisky, and R. Hadani. Viewing angle classification of cryo-electron microscopy images using eigenvectors. SIAM Journal on Imaging Sciences, 4(2): 723–759, 2011.PDF

42. A. Singer and Y. Shkolnisky. Three-dimensional structure determination from common lines in cryo-EM by eigenvectors and semidefinite programming. SIAM Journal on Imaging Sciences, 4(2): 543-572, 2011.PDF

43. A. Averbuch, G. Lifschitz and Y. Shkolnisky. Accelerating X-ray data collection using pyramid beam ray casting geometries. IEEE Transactions on Image Processing, 20(2): 523-533, 2011. PDF

44. C.O.S. Sorzano, J.R. Bilbao-Castro, Y. Shkolnisky, M. Alcorlo, R. Melero, G. Caffarena-Fernandez, M. Li, G. Xu, R. Marabini, J.M. Carazo. A clustering approach to multireference alignment of single-particle projections in electron microscopy. Journal of Structural Biology, 171(2): 197-206, 2010. PDF

45. A. Singer, R. R. Coifman, F. J. Sigworth, D. W Chester, and Y. Shkolnisky. Detecting consistent common lines in cryo-EM by voting. Journal of Structural Biology, 169(3): 312-322, 2010. PDF

46. R. R. Coifman, Y. Shkolnisky, F. J. Sigworth, and A. Singer. Reference-free structure determination through eigenvectors of center of mass operators. Applied and Computational Harmonic Analysis, 28(3): 296-312, 2010. PDF

47. A. Singer, Y. Shkolnisky, and B. Nadler. Diffusion interpretation of nonlocal neighborhood filters for signal denoising. SIAM Journal on Imaging Sciences, 2(1): 118-139, 2009. PDF

48. R. R. Coifman, Y. Shkolnisky, F. J. Sigworth, and A. Singer. Graph Laplacian tomography from unknown random projections. IEEE Transactions on Image Processing, 17(10): 1891-1899, 2008. PDF

49. A. Averbuch, R.R. Coifman, D. L. Donoho, M. Israeli, Y. Shkolnisky and I. Sedelnikov. A framework for discrete integral transformations II - the 2D discrete Radon transform. SIAM Journal on Scientific Computing, 30(2):785-803, 2008. PDF

50. A. Averbuch, R. R. Coifman, D. L. Donoho, M. Israeli, and Y. Shkolnisky. A framework for discrete integral transformations I - the pseudo-polar Fourier transform. SIAM Journal on Scientific Computing, 30(2): 764-784, 2008. PDF
    Code available at https://github.com/ShkolniskyLab/PPFT2D

51. Y. Shkolnisky. Prolate spheroidal wave functions on a disc - Integration and approximation of two-dimensional bandlimited functions. Applied and Computational Harmonic Analysis, 22(2):235-256, March 2007. PDF

52. Y. Shkolnisky, M. Tygert, and V. Rokhlin. Approximation of bandlimited functions. Applied and Computational Harmonic Analysis, 21(3):413-420, November 2006. PDF

53. Y. Keller, Y. Shkolnisky, and A. Averbuch. Volume registration using the 3-D pseudo-polar Fourier transform. IEEE Transactions on Signal Processing, 54(11):4323-4331, 2006. PDF

54. Y. Keller and Y. Shkolnisky. A signal processing approach to symmetry detection. IEEE Transactions on Image Processing, 15(8):2198-2207, 2006. PDF

55. Y. Keller, Y. Shkolnisky, and A. Averbuch. The angular difference function and its application to image registration. IEEE Transactions on Pattern Analysis and Machine Intelligence, 27(6):969-976, 2005. PDF

56. A. Averbuch and Y. Shkolnisky. 3D discrete X-ray transform. Applied and Computational Harmonic Analysis, 17(3):259-276, 2004. PDF

57. A. Averbuch and Y. Shkolnisky. 3D Fourier based discrete Radon transform. Applied and Computational Harmonic Analysis, 15(1):33-69, 2003. PDF
    Code available at https://github.com/ShkolniskyLab/PPFT3D

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Technical Reports

1. R. R. Coifman, Y. Shkolnisky, F. J. Sigworth, and A. Singer. Cryo-EM Structure Determination through Eigenvectors of Sparse Matrices. Technical Report 1389, Yale University, Department of Computer Science, November 2007. PDF

2. J. Bremer, Y. Shkolnisky, and A. Szlam. Image denoising using diffusion on curvelet-scaled Gabor filter responses, 2007. PDF

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Conference Proceedings

1. C. Vonesch, L. Wang, Y. Shkolnisky and A. Singer. Fast wavelet-based single-particle reconstruction in cryo-EM, IEEE International Symposium on Biomedical Imaging (ISBI 2011), Chicago, Illinois, USA, March 2011, pp. 1950-1953. PDF

2. Y. Keller, Y. Shkolnisky, and A. Averbuch. Accurate Multi-Dimensional Alignment, Proceedings of the IEEE International Conference on Image Processing (ICIP2005), volume 3, pages 1052-1055, September 2005.

3. Y. Keller, Y. Shkolnisky, and A. Averbuch. A non-Cartesian FFT approach to image alignment, Proceedings of the IEEE International Conference on Image Processing (ICIP2005), volume 3, pages 50-53, September 2005.

4. Y. Keller, A. Averbuch, and Y. Shkolnisky. Algebraically Accurate Volume Registration using Euler's Theorem and the 3-D Pseudo-polar FFT, IEEE Computer Society Conference on Computer Vision and Pattern Recognition (CVPR 2005), volume 2, pages 795-800, June 2005.

5. Y. Keller and Y. Shkolnisky. An algebraic approach to symmetry detection, Proceedings of the 17th International Conference on Pattern Recognition (ICPR2004), volume 3, pages 186-189, August 2004.

6. A. Averbuch and Y. Shkolnisky. Multidimensional discrete Radon transform. Wavelets and their Applications (M. Krishna, R. Radha, and S. Thangavelu editors), Allied Publishers Private Limited, 2003, pp. 63-88.

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Book Chapters

1. Y. Shkolnisky and A. Singer. Center of Mass Operators for CryoEM - Theory and Implementation. Modeling Nanoscale Imaging in Electron Microscopy, T. Vogt, W. Dahmen, and P. Binev (Eds.) Nanostructure Science and Technology Series, Springer, 2012, pp. 147–177. PDF

2. A. Averbuch, R. R. Coifman, M. Israeli, I. Sedelnikov, Y. Shkolnisky. Irregular sampling for multidimensional polar processing of integral transforms. Advances in Signal Transforms: Theory and Applications, J. Astola and L. Yaroslavsky (Editors), Hindawi Publishing Corporation, pp. 143-200 (Chapter 4), 2007.

3. A. Averbuch and Y. Shkolnisky. Multidimensional discrete Radon transform. Wavelets and their Applications (M. Krishna, R. Radha, and S. Thangavelu editors), Allied Publishers Private Limited, 2003, pp. 63–88.

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