Prashant Mali

Variable sparsity non-negative matrix and tensor factorization algorithms and their applications in cancer genomics

This paper introduces variable-sparsity matrix and tensor factorization algorithms for cancer genomics to improve biological interpretability and modeling of cancer subtypes and pathways.

A PERTURBATION CELL ATLAS OF HUMAN INDUCED PLURIPOTENT STEM CELLS

The paper generates a CRISPRi perturbation cell atlas in human induced pluripotent stem cells, identifies novel regulators of pluripotency and metabolism, and proposes a machine learning framework for predicting perturbation recipes.

Receptor-guided AAV Tropism Engineering via MATCH

This paper introduces MATCH, a method to engineer AAV tropism by conjugating targeting proteins, achieving efficient transduction of T cells and enhanced brain delivery in vivo.

Human dorsal root ganglia neuronal cell line to study nociceptive signaling: a new pipeline for pain therapy.

The paper develops a human-derived in vitro model of nociceptive signaling using HD10.6 cells to study pain mechanisms and drug responses.

Multiplexed Pan Soluble Ligandome Assaying via OASIS

The paper introduces OASIS, a method to screen soluble ligands by enforcing autocrine signaling, and applies it to identify self-renewal factors in hiPSCs.

Regulatable In Vivo Gene Expression via Adaptamers

This paper introduces an RNA-based system called adaptamer that allows precise, reversible control of gene expression using small molecules, demonstrating its function in cell lines and mice.

Targeting serine dehydratase supports amino acid homeostasis and skin repair

This study identifies serine dehydratase (Sds) as a regulator of serine and sphingolipid metabolism, showing that its deletion improves skin repair in diabetic mice.

A Novel Engineered U7 Small Nuclear RNA Scaffold Greatly Increases in vitro and in vivo ADAR-Mediated Programmable RNA Base Editing

This paper develops a novel U7 snRNA scaffold that significantly enhances ADAR-mediated RNA base editing in vitro and in vivo, achieving up to 76% editing efficiency in mouse models.

Cell Maps for Artificial Intelligence: AI-Ready Maps of Human Cell Architecture from Disease-Relevant Cell Lines

The paper introduces the CM4AI project, which aims to create AI-ready datasets of human cell architecture using multimodal data from cell lines.

Interface-guided phenotyping of coding variants in the transcription factor RUNX1 with SEUSS

The paper uses SEUSS to analyze the effects of 115 RUNX1 mutations on RNA profiles in myelogenous leukemia cells, categorizing them into three functional groups.

Comprehensive interrogation of the ADAR2 deaminase domain for engineering enhanced RNA base-editing activity, functionality and specificity

This study engineers ADAR2 deaminase variants to enhance RNA editing activity, specificity, and functionality through deep mutational scans, domain-wide mutagenesis, and split deaminase design.

Charting oncogenicity of genes and variants across lineages via multiplexed screens in teratomas

The paper develops a method to screen oncogenic genes across multiple lineages using teratomas and identifies drivers of proliferation in specific cell types.

Long-lasting Analgesia via Targeted in vivo Epigenetic Repression of Nav1.7

This study develops a method to achieve long-lasting, non-addictive pain relief by epigenetically repressing NaV1.7 in vivo using CRISPR-dCas9 and zinc finger proteins.

A homing CRISPR mouse resource for barcoding and lineage tracing

The paper introduces a mouse line with heritable homing guide RNAs for in vivo barcoding and lineage tracing in mammals.

Exploring protein orthogonality in immune space: a case study with AAV and Cas9 orthologs

The paper explores immune orthogonality among protein orthologs by analyzing CRISPR-Cas9 and AAV serotypes, finding high immune orthogonality in Cas9 but not in AAVs.

In vivo RNA targeting of point mutations via suppressor tRNAs and adenosine deaminases

The paper demonstrates the use of suppressor tRNAs and ADAR2 for in vivo RNA targeting to correct point mutations in mouse models of genetic diseases.

Rapidly evolving homing CRISPR barcodes

This paper introduces a homing CRISPR system that generates evolving DNA barcodes in living cells, enabling lineage tracking and molecular recording.

Genome Editing With Targeted Deaminases

This paper introduces targeted deaminases for site-specific C-to-T genomic edits without DNA cleavage, achieving 13% efficiency in E. coli and 2.5% in human cells with reduced toxicity.

CasFinder: Flexible algorithm for identifying specific Cas9 targets in genomes

CasFinder identifies specific Cas9 target sites in genomes with low off-targeting potential, generating exome-wide catalogs for human and mouse for three Cas9 variants.