Lipika R. Pal

Transient Splicing-Associated Isoform Remodeling Defines Early MAPKi Resistance Adaptation in Melanoma

The paper identifies transient isoform remodeling as a key mechanism in early MAPKi resistance in melanoma, showing it is distinct from gene expression changes and linked to splicing regulators and developmental pathways.

CRISPR-Based Gene Dependency Screens reveal Mechanism of BRAF Inhibitor Resistance in Anaplastic Thyroid Cancer

This study identifies TAZ deficiency as synthetically lethal with BRAF inhibitors in anaplastic thyroid cancer, revealing a mechanism of resistance and a potential therapeutic target.

A machine learning framework for supervised treatment response prediction from tumor transcriptomics: A large-scale pan-cancer study

This paper develops a machine learning framework, EXPRESSO, to predict treatment response from tumor transcriptomics across multiple cancer types and therapies, showing improved performance over existing methods.

Co-targeting MERTK and EGFR with a Bispecific Antibody Overcomes Drug Resistance Across Mutations in Exons 19, 20, and 21

This study develops a bispecific antibody targeting MERTK and EGFR to overcome drug resistance in lung cancer with mutations in exons 19, 20, and 21.

Pan-cancer prediction of tumor immune activation and response to immune checkpoint blockade from tumor transcriptomics and histopathology

This paper introduces TIME_ACT, a transcriptomic signature predicting immune checkpoint blockade response across cancers, validated using histopathology and multiple cohorts.

TMPRSS2-ERG confers resistance to antiandrogens: mechanism and therapeutic implications

This study shows that TMPRSS2-ERG fusion promotes resistance to antiandrogens by interacting with GR, suggesting combined GR and AR inhibition could benefit tERG-positive prostate cancer patients.

Synthetic lethality-based prediction of anti-SARS-CoV-2 targets

The paper predicts anti-SARS-CoV-2 targets by identifying synthetic lethal partners of host genes altered during infection, validated through CRISPR-Cas9 screens and siRNA experiments.

Genome-scale metabolic modeling reveals SARS-CoV-2-induced metabolic changes and antiviral targets

The paper uses genome-scale metabolic modeling to identify SARS-CoV-2-induced metabolic changes and predict antiviral targets validated through drug and genetic screens.

Matching whole genomes to rare genetic disorders: Identification of potential causative variants using phenotype-weighted knowledge in the CAGI SickKids5 clinical genomes challenge

The paper identifies potential causative variants in rare genetic disorders using a gene-centric approach and phenotype-weighted scoring, achieving partial success in matching genomes to clinical profiles.

Harnessing formal concepts of biological mechanism to analyze human disease

This paper introduces a formal framework for representing biological mechanisms and applies it to analyze human genetic disease mechanisms.