L. Pachter

Studying stochastic systems biology of the cell with single-cell genomics data

The paper develops a mathematical framework to integrate stochasticity in RNA transcription and technical variation in single-cell RNA sequencing using generating functions, applied to simulated and biological data.

The telegraph process is not a subordinator

The paper identifies limitations in a strategy for connecting steady-state distributions to process dynamics, showing it applies only to a narrow class of processes.

Biophysical modeling with variational autoencoders for bimodal, single-cell RNA sequencing data

The paper introduces biVI, a variational autoencoder for bimodal single-cell RNA sequencing data, which models biophysical processes to capture cell type structure and parameter values.

Transient and delay chemical master equations

This paper develops models with delays for transcriptional dynamics and analyzes RNA copy number distributions using single-cell RNA sequencing data.

RNA velocity unraveled

This paper analyzes RNA velocity methods, evaluates their assumptions, and proposes a framework for Markovian analysis to improve their accuracy and reliability.

Interpretable and tractable models of transcriptional noise for the rational design of single-molecule quantification experiments

Length Biases in Single-Cell RNA Sequencing of pre-mRNA

The paper identifies length biases in single-cell RNA sequencing data and proposes a length-based model to explain and correct for these biases across species.

Analytical solutions of the chemical master equation with bursty production and isomerization reactions

The paper derives analytical solutions for chemical master equations involving bursty production and isomerization reactions, validated using long-read sequencing data.

A novel approach to comparative RNA-Seq does not support a conserved set of genes underlying animal regeneration

This study uses a novel statistical method to analyze RNA-seq data from six animal regeneration datasets, finding that conserved gene clusters are enriched in structural genes rather than morphogenesis regulators.

Low-cost, scalable, and automated fluid sampling for fluidics applications

The paper introduces a low-cost, modular, and automated fluid sampling device called Colosseum for scalable fluidic applications.

Direct simulation of a stochastically driven multi-step birth-death process

The paper develops an exact stochastic simulation algorithm for a multi-step transcriptional process with an Ornstein-Uhlenbeck birth rate and validates it against known analytical results in limiting cases.

Intrinsic and extrinsic noise are distinguishable in a synthesis - export - degradation model of mRNA production

The paper distinguishes intrinsic and extrinsic noise in a mRNA synthesis-export-degradation model and shows how downstream processing aids in identifying noise sources.

Design principles for open source bioinstrumentation: the poseidon syringe pump system as an example

The paper introduces the Poseidon syringe pump system as an open-source alternative to commercial systems, highlighting design principles for open-source bioinstrumentation.