A cellular hierarchy framework for understanding heterogeneity and predicting drug response in acute myeloid leukemia

AGX Zeng, S Bansal, L Jin, A Mitchell, WC Chen… - Nature medicine, 2022 - nature.com
The treatment landscape of acute myeloid leukemia (AML) is evolving, with promising
therapies entering clinical translation, yet patient responses remain heterogeneous, and …

Respiratory viral infections and host responses; insights from genomics

NM Troy, A Bosco - Respiratory research, 2016 - Springer
Respiratory viral infections are a leading cause of disease and mortality. The severity of
these illnesses can vary markedly from mild or asymptomatic upper airway infections to …

[HTML][HTML] Development of a primary human Small Intestine-on-a-Chip using biopsy-derived organoids

M Kasendra, A Tovaglieri, A Sontheimer-Phelps… - Scientific reports, 2018 - nature.com
Here we describe a method for fabricating a primary human Small Intestine-on-a-Chip
(Intestine Chip) containing epithelial cells isolated from healthy regions of intestinal …

Impact of molecular subtypes in muscle-invasive bladder cancer on predicting response and survival after neoadjuvant chemotherapy

R Seiler, HAD Ashab, N Erho, BWG van Rhijn… - European urology, 2017 - Elsevier
Background An early report on the molecular subtyping of muscle-invasive bladder cancer
(MIBC) by gene expression suggested that response to neoadjuvant chemotherapy (NAC) …

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 …

Preprocessing, normalization and integration of the Illumina HumanMethylationEPIC array with minfi

JP Fortin, TJ Triche Jr, KD Hansen - Bioinformatics, 2017 - academic.oup.com
The minfi package is widely used for analyzing Illumina DNA methylation array data. Here
we describe modifications to the minfi package required to support the …

Validation of a 22-gene genomic classifier in patients with recurrent prostate cancer: an ancillary study of the NRG/RTOG 9601 randomized clinical trial

FY Feng, HC Huang, DE Spratt, SG Zhao… - JAMA …, 2021 - jamanetwork.com
Importance Decipher (Decipher Biosciences Inc) is a genomic classifier (GC) developed to
estimate the risk of distant metastasis (DM) after radical prostatectomy (RP) in patients with …

MYC drives aggressive prostate cancer by disrupting transcriptional pause release at androgen receptor targets

X Qiu, N Boufaied, T Hallal, A Feit, A de Polo… - Nature …, 2022 - nature.com
Abstract c-MYC (MYC) is a major driver of prostate cancer tumorigenesis and progression.
Although MYC is overexpressed in both early and metastatic disease and associated with …

Associations of luminal and basal subtyping of prostate cancer with prognosis and response to androgen deprivation therapy

SG Zhao, SL Chang, N Erho, M Yu, J Lehrer… - JAMA …, 2017 - jamanetwork.com
Importance There is a clear need for a molecular subtyping approach in prostate cancer to
identify clinically distinct subgroups that benefit from specific therapies. Objectives To …

Tissue-based genomics augments post-prostatectomy risk stratification in a natural history cohort of intermediate-and high-risk men

AE Ross, MH Johnson, K Yousefi, E Davicioni… - European urology, 2016 - Elsevier
Background Radical prostatectomy (RP) is a primary treatment option for men with
intermediate-and high-risk prostate cancer. Although many are effectively cured with local …