Large-scale multiple perturbation experiments have the potential to reveal a more detailed understanding of the molecular pathways that respond to genetic and environmental changes. A key question in these studies is which gene expression changes are...
Drug combination therapy has gradually become a promising treatment strategy for complex or co-existing diseases. As drug-drug interactions (DDIs) may cause unexpected adverse drug reactions, DDI prediction is an important task in pharmacology and cl...
Nanopore sequencers can enrich or deplete the targeted DNA molecules in a library by reversing the voltage across individual nanopores. However, it requires substantial computational resources to achieve rapid operations in parallel at read-time sequ...
DANCE is the first standard, generic, and extensible benchmark platform for accessing and evaluating computational methods across the spectrum of benchmark datasets for numerous single-cell analysis tasks. Currently, DANCE supports 3 modules and 8 po...
Proceedings of the National Academy of Sciences of the United States of America
38451939
Proteins are a diverse class of biomolecules responsible for wide-ranging cellular functions, from catalyzing reactions to recognizing pathogens. The ability to evolve proteins rapidly and inexpensively toward improved properties is a common objectiv...
Whole-genome sequencing (WGS) is currently making its transition from research tool into routine (clinical) diagnostic practice. The workflow for WGS includes the highly labor-intensive library preparations (LP), one of the most critical steps in the...
The effective design of combinatorial libraries to balance fitness and diversity facilitates the engineering of useful enzyme functions, particularly those that are poorly characterized or unknown in biology. We introduce MODIFY, a machine learning (...
DNA-encoded library (DEL) technology is a powerful platform for the efficient identification of novel chemical matter in the early drug discovery process enabled by parallel screening of vast libraries of encoded small molecules through affinity sele...
The bacterial retron reverse transcriptase system has served as an intracellular factory for single-stranded DNA in many biotechnological applications. In these technologies, a natural retron non-coding RNA (ncRNA) is modified to encode a template fo...