Gurinder S. Atwal

TREM2 macrophages are associated with enhanced response to PD-1 blockade in human hepatocellular carcinoma

The paper identifies TREM2-expressing macrophages as predictors of response to PD-1 blockade in HCC patients using clinical and spatial transcriptomic data.

Image guided construction of a common coordinate framework for spatial transcriptome data

This paper introduces STaCker, a deep learning algorithm that aligns spatial transcriptome slices using image registration, improving spatial concordance and enabling data integration.

PROPERMAB: an integrative framework for in silico prediction of antibody developability using machine learning

PROPERMAB predicts antibody developability properties using machine learning, enabling early assessment of biophysical characteristics to accelerate drug development.

Optimizing murine sample sizes for RNA-seq studies revealed from large-scale comparative analysis

The paper determines optimal sample sizes for bulk RNA-seq experiments in mice by analyzing large-scale comparative studies and shows that increasing sample size reduces false positives and improves discovery rates.

Designing meaningful continuous representations of T cell receptor sequences with deep generative models

This paper introduces TCR-VALID, a variational autoencoder for generating and analyzing TCR sequences, showing improved clustering and representation quality.

Identification of pan-cancer/testis genes and validation of therapeutic targeting in triple-negative breast cancer: Lin28a- and Siglece-based vaccination induces anti-tumor immunity and inhibits metastasis

The paper identifies pan-cancer/testis genes and validates their use as therapeutic targets in triple-negative breast cancer through vaccination with Lin28a and Siglece antigens, showing reduced tumor growth and metastasis.

Exome sequencing of 628,388 individuals identifies common and rare variant associations with clonal hematopoiesis phenotypes

This study uses exome sequencing of 628,388 individuals to identify genetic variants associated with clonal hematopoiesis and its health outcomes.

Noise regularization removes correlation artifacts in single-cell RNA-seq data preprocessing

This study evaluates normalization/imputation methods in scRNA-seq, finding that preprocessing introduces spurious correlations and proposes a noise regularization method to remove these artifacts.

AdRoit: an accurate and robust method to infer complex transcriptome composition

AdRoit infers cell composition from bulk or spatial transcriptome data using single-cell references, showing improved sensitivity and speed over existing methods.

Bayesian inference of power law distributions

This paper develops a Bayesian method to infer power law distributions from data, including mixture models and exponents, and provides an open-source implementation.

T-cell receptor αβ chain pairing is associated with CD4+ and CD8+ lineage specification

The paper analyzes TCR {beta} chain pairing in human T-cells to determine its role in CD4+ and CD8+ lineage specification, finding that {beta} chain pairs are more informative than individual chains for lineage prediction.

Single-cell sequencing reveals αβ chain pairing shapes the T cell repertoire

This study uses single-cell sequencing to analyze T cell receptor pairing, finding non-random β chain associations and public clone sharing, which reduce T cell repertoire diversity.

Statistical mechanics of multistable perception

This paper uses statistical mechanics to model multistable perception, showing how Bayesian inference and noise priors lead to critical dynamics and phase transitions in perception stability.