User profiles for A.J. Gentles

Andrew Gentles

Stanford University
Verified email at stanford.edu
Cited by 32132

Multimodal data fusion for cancer biomarker discovery with deep learning

…, T Hernandez-Boussard, AJ Gentles… - Nature machine …, 2023 - nature.com
Technological advances have made it possible to study a patient from multiple angles with
high-dimensional, high-throughput multiscale biomedical data. In oncology, massive amounts …

Robust enumeration of cell subsets from tissue expression profiles

AM Newman, CL Liu, MR Green, AJ Gentles, W Feng… - Nature …, 2015 - nature.com
We introduce CIBERSORT, a method for characterizing cell composition of complex tissues
from their gene expression profiles. When applied to enumeration of hematopoietic subsets …

[PDF][PDF] Machine learning identifies stemness features associated with oncogenic dedifferentiation

TM Malta, A Sokolov, AJ Gentles, T Burzykowski… - Cell, 2018 - cell.com
Cancer progression involves the gradual loss of a differentiated phenotype and acquisition
of progenitor and stem-cell-like features. Here, we provide novel stemness indices for …

[PDF][PDF] The immune landscape of cancer

…, AC Culhane, EO Paull, IKA Sivakumar, AJ Gentles… - Immunity, 2018 - cell.com
We performed an extensive immunogenomic analysis of more than 10,000 tumors comprising
33 diverse cancer types by utilizing data compiled by TCGA. Across cancer types, we …

The prognostic landscape of genes and infiltrating immune cells across human cancers

AJ Gentles, AM Newman, CL Liu, SV Bratman… - Nature medicine, 2015 - nature.com
Molecular profiles of tumors and tumor-associated cells hold great promise as biomarkers of
clinical outcomes. However, existing data sets are fragmented and difficult to analyze …

Determining cell type abundance and expression from bulk tissues with digital cytometry

AM Newman, CB Steen, CL Liu, AJ Gentles… - Nature …, 2019 - nature.com
Single-cell RNA-sequencing has emerged as a powerful technique for characterizing cellular
heterogeneity, but it is currently impractical on large sample cohorts and cannot be applied …

The CD47-signal regulatory protein alpha (SIRPa) interaction is a therapeutic target for human solid tumors

…, JP Volkmer, AJ Gentles… - Proceedings of the …, 2012 - National Acad Sciences
CD47, a “don't eat me” signal for phagocytic cells, is expressed on the surface of all human
solid tumor cells. Analysis of patient tumor and matched adjacent normal (nontumor) tissue …

[HTML][HTML] Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor

O Kohany, AJ Gentles, L Hankus, J Jurka - BMC bioinformatics, 2006 - Springer
Background Repbase is a reference database of eukaryotic repetitive DNA, which includes
prototypic sequences of repeats and basic information described in annotations. Updating …

Transient rest restores functionality in exhausted CAR-T cells through epigenetic remodeling

…, Y Qi, K Sandor, LC Chen, S Prabhu, AJ Gentles… - Science, 2021 - science.org
INTRODUCTION More than 50% of patients treated with chimeric antigen receptor (CAR)–T
cells for B cell malignancies develop progressive disease after CAR therapy, and these …

Calreticulin is the dominant pro-phagocytic signal on multiple human cancers and is counterbalanced by CD47

…, AA Alizadeh, AJ Gentles… - Science translational …, 2010 - science.org
Under normal physiological conditions, cellular homeostasis is partly regulated by a balance
of pro- and anti-phagocytic signals. CD47, which prevents cancer cell phagocytosis by the …