Pachter Lab Biophysics Home

Diagram


Our Motivation

As biological data becomes increasingly complex and multimodal, we need tools which can interpret the relationships between these high-dimensional, noisy measurements and illuminate the intertwined components of DNA and RNA regulation. In the Pachter Lab, we harness stochastic, biophysical models to represent these high-throughput, genomics data. With our tools, we aim to explicitly model the noise in the data, to capture and reveal important biological variation as well as technical effects of the sequencing pipeline. By treating the underlying biophysical processes which generate our molecular measurements, we can uncover how the processes of the central dogma define cellular diversity, differentiation, and perturbation.


Table of tools

Below is a table of the Pachter Lab’s current tools for biophysical modeling of high-throughput genomics data. The main features and input data types are listed across the columns. All methods require data with UMIs (molecular count data).

Tool

Task

Resolution

Modalities

Steady State?

Technical Noise?

Language

Monod: Monod: a package for CME inference from seq data

Parameter Inference

gene

U/S RNA

yes

yes (3’ seq)

Python

biVI: biVI: Biophysical modeling with variational autoencoders

Parameter Inference

cell/gene

U/S RNA

yes

coming soon

Python

meK-Means: meK-means: Biophysically interpretable inference of cell types from multimodal sequencing data

Clustering

gene

U/S RNA

yes

yes (3’ seq)

Python

Chronocell: Chronocell: trajectory inference from single-cell genomic data

Trajectory Inference

gene

U/S RNA

no

no

Python

Spatial: coming soon

Parameter Inference

gene

S RNA

yes

yes

Python

For more details on the available methods see Our Packages

Not sure which tool is best for your data? See Choose Your Tool.

Foundational Literature

Explore the foundational literature for biophysical modeling of transcription in Foundations, and the lab’s publications at Our Contributions.

Note

This project is under active development.