I co-organize the One World Cryo-EM online seminar series about mathematics and algorithms in cryo-electron microscopy. Please contact me if you are interested in speaking or getting involved in our activities around the seminar.

I am looking for extraordinary postdocs and extraordinary graduate students (at Yale, any graduate program). More information about postdoc positions is available here.

Office hours available here and on Canvas (internal Yale system).

Structural biology and cryo-EM: inverse problems and unsupervised learning, applications of representation theory, numerical analysis, and data organization to imaging of molecules

Computational biology: fast search algorithms, statistics of DNA, sequencing, organization of biological data

CRYO-EM (a little out of date – more updates coming soon)

Cryo-electron microscopy (cryo-EM) is a method for imaging molecules without crystallization. The Nobel Prize in Chemistry 2017 was awarded to Jacques Dubochet, Joachim Frank and Richard Henderson “for the development of cryo-electron microscopy, which both simplifies and improves the imaging of biomolecules.” I work on various problems of alignment, classification and signal processing that are motivated by application in cryo-EM with many other applications. I am particularly interested in heterogeneity, i.e. imaging of mixtures of different types of molecules.

I work on “hyper-molecules” which represent heterogeneous molecules as higher-dimension objects. The movie below is an example of a reconstruction of a continuously heterogeneous object, using the approach described in this paper and this paper.

This is one of several approaches that I am developing for the heterogeneity problem in cryo-EM, and for other aspects of cryo-EM. For more information on my work in cryo-EM, see project page.

We are interested in revisiting elements of Bayesian Inference and Variational Inference. Some (but not all) of this work is motivated by applications such as cryo-EM (although it might not be obvious at first – for example questions about inference on manifolds). Example of some recent work in these areas: Non-Canonical Hamiltonian Monte Carlo .

NUMERICAL ANALYSIS AND SIGNAL PROCESSING

Prolate Functions

The Truncated Fourier Transform and its eigenfunctions, Prolate Spheroidal Wave Functions (PSWF) and Generalized Prolate Spheroidal Functions (GPSF) (also known as Slepian Functions) are frequently encountered in mathematics, physics, signal processing, optics and other areas. Surprisingly, very few resources and code for the numerical computation of GPSFs and their eigenvalues are publicly available. Our sample implementation and associated paper are available at http://github.com/lederman/prol. The code also contains an experimental “open-source proof,” which is code for analytical proofs of some of the results that appear in this paper.

The Laplace Transform and Grunbaum Functions

The Laplace transform is frequently encountered in mathematics, physics, engineering and other areas. However, the spectral properties of the Laplace transform tend to complicate its numerical treatment; therefore, the closely related “Truncated” Laplace Transforms are often used in applications.

Lower bounds on the truncated Fourier transform and truncated Laplace transform: see paper.

GEOMETRY OF DATA

Alternating Diffusion, a method for recovering the common variable in multi-sensor experiments, is discussed in this paper, this technical report and this project webpage. A different approach to the common variable recovery problem, which also constructs representations that are invariable to unknown transformations, is discussed in this paper.

Additional Application: Assembly. The algorithm is also used to construct approximate overlap graphs. These graph are used for fast assembly. Unlike other algorithms, this algorithm allows errors in the reads, so no error-correction is necessary prior to the construction of the graph. See: paper.

Publications

Stanton, Kelly P; Jin, Jiaqi; Lederman, Roy R; Weissman, Sherman M; Kluger, Yuval

@article{stanton_ritornello_2017,
title = {Ritornello: high fidelity control-free chromatin immunoprecipitation peak calling},
author = {Kelly P Stanton and Jiaqi Jin and Roy R Lederman and Sherman M Weissman and Yuval Kluger},
url = {https://academic.oup.com/nar/article/45/21/e173/4157402},
doi = {10.1093/nar/gkx799},
issn = {0305-1048},
year = {2017},
date = {2017-01-01},
urldate = {2020-08-13},
journal = {Nucleic Acids Research},
volume = {45},
number = {21},
pages = {e173--e173},
abstract = {Abstract. With the advent of next generation high-throughput DNA sequencing technologies, omics experiments have become the mainstay for studying diverse biolo},
note = {Publisher: Oxford Academic},
keywords = {DNA sequencing, Sequencing, Software},
pubstate = {published},
tppubtype = {article}
}

Abstract. With the advent of next generation high-throughput DNA sequencing technologies, omics experiments have become the mainstay for studying diverse biolo

@techreport{lederman_permutations-based_2013,
title = {A permutations-based algorithm for fast alignment of long paired-end reads},
author = {Roy R Lederman},
year = {2013},
date = {2013-04-01},
number = {YALEU/DCS/TR-1474},
pages = {11},
institution = {Yale CS},
keywords = {Algorithms, DNA sequencing, Fast algorithms, Randomized algorithms, Sequencing},
pubstate = {published},
tppubtype = {techreport}
}