Saket Choudhary

Opposing copy number variation dynamics accompany adaptation to glucose and galactose in diploid yeast.

This study shows that copy number variations (CNVs) dominate genome evolution in yeast adapting to glucose or galactose, with opposing CNV dynamics in each environment.

A conserved logic for the development of cortical layering in tetrapods

The paper shows that cortical layering in tetrapods follows conserved developmental principles, with mammals displaying an inverted layer order.

Dictionary learning for integrative, multimodal, and scalable single-cell analysis

Dictionary learning enables assumption-free cross-modality single-cell mapping via multi-omic bridge datasets and scales single-modality integration to millions of cells in under an hour via atomic sketching.

CPA-Perturb-seq: Multiplexed single-cell characterization of alternative polyadenylation regulators

The paper introduces CPA-Perturb-seq, a multiplexed perturbation screen dataset, and uses it to identify polyA site regulators and their functional properties.

Comparison and evaluation of statistical error models for scRNA-seq

This study evaluates statistical error models for scRNA-seq, finding that negative binomial models are more appropriate than Poisson for most datasets due to overdispersion.

pysradb: A Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive

pysradb is a Python package that enables querying and downloading metadata and data from NCBI Sequence Read Archive, with examples of its use cases.

Bioconda: A sustainable and comprehensive software distribution for the life sciences

Bioconda provides a sustainable, comprehensive distribution of bioinformatics software using Conda for reproducible analysis across platforms.

BioJS-HGV Viewer: Genetic Variation Visualizer

BioJS-HGV Viewer provides an interactive tool to visualize genetic variants from multiple sources, enabling detailed exploration of variant sites and annotations.

GalDrive: Pipeline for comparative identification of driver mutations using the Galaxy framework

GalDrive provides a Galaxy-based pipeline to run multiple driver mutation prediction tools on the same dataset, enabling consensus driver identification.