[HTML][HTML] An engineered CRISPR-Cas9 mouse line for simultaneous readout of lineage histories and gene expression profiles in single cells

S Bowling, D Sritharan, FG Osorio, M Nguyen… - Cell, 2020 - cell.com
Tracing the lineage history of cells is key to answering diverse and fundamental questions in
biology. Coupling of cell ancestry information with other molecular readouts represents an …

Determining sequencing depth in a single-cell RNA-seq experiment

MJ Zhang, V Ntranos, D Tse - Nature communications, 2020 - nature.com
An underlying question for virtually all single-cell RNA sequencing experiments is how to
allocate the limited sequencing budget: deep sequencing of a few cells or shallow …

Diversity in biology: definitions, quantification and models

S Xu, L Böttcher, T Chou - Physical Biology, 2020 - iopscience.iop.org
Diversity indices are useful single-number metrics for characterizing a complex distribution
of a set of attributes across a population of interest. The utility of these different metrics or …

Classification and computation of extreme events in turbulent combustion

M Hassanaly, V Raman - Progress in Energy and Combustion Science, 2021 - Elsevier
In the design of practical combustion systems, ensuring safety and reliability is an important
requirement. For instance, reliably avoiding lean blowout, flame flashback or inlet unstart is …

Estimating the unseen: improved estimators for entropy and other properties

G Valiant, P Valiant - Journal of the ACM (JACM), 2017 - dl.acm.org
We show that a class of statistical properties of distributions, which includes such practically
relevant properties as entropy, the number of distinct elements, and distance metrics …

Chebyshev polynomials, moment matching, and optimal estimation of the unseen

Y Wu, P Yang - The Annals of Statistics, 2019 - JSTOR
We consider the problem of estimating the support size of a discrete distribution whose
minimum nonzero mass is at least 1 k. Under the independent sampling model, we show …

Minimax Estimation of the Distance

J Jiao, Y Han, T Weissman - IEEE Transactions on Information …, 2018 - ieeexplore.ieee.org
We consider the problem of estimating the L 1 distance between two discrete probability
measures P and Q from empirical data in a nonasymptotic and large alphabet setting. When …

Maximum likelihood estimation of functionals of discrete distributions

J Jiao, K Venkat, Y Han… - IEEE Transactions on …, 2017 - ieeexplore.ieee.org
We consider the problem of estimating functionals of discrete distributions, and focus on a
tight (up to universal multiplicative constants for each specific functional) nonasymptotic …

Optimal design of stochastic DNA synthesis protocols based on generative sequence models

EN Weinstein, AN Amin… - International …, 2022 - proceedings.mlr.press
Generative probabilistic models of biological sequences have widespread existing and
potential applications in analyzing, predicting and designing proteins, RNA and genomes …

Genome-wide detection of DNA double-strand breaks by in-suspension BLISS

BAM Bouwman, F Agostini, S Garnerone, G Petrosino… - Nature protocols, 2020 - nature.com
Abstract sBLISS (in-suspension breaks labeling in situ and sequencing) is a versatile and
widely applicable method for identification of endogenous and induced DNA double-strand …