RNA-Seq signatures normalized by mRNA abundance allow absolute deconvolution of human immune cell types

G Monaco, B Lee, W Xu, S Mustafah, YY Hwang… - Cell reports, 2019 - cell.com
The molecular characterization of immune subsets is important for designing effective
strategies to understand and treat diseases. We characterized 29 immune cell types within …

A multi-cohort study of the immune factors associated with M. tuberculosis infection outcomes

R Roy Chowdhury, F Vallania, Q Yang… - Nature, 2018 - nature.com
Most infections with Mycobacterium tuberculosis (Mtb) manifest as a clinically asymptomatic,
contained state, known as latent tuberculosis infection, that affects approximately one …

Cellular senescence impairs the reversibility of pulmonary arterial hypertension

DE Van Der Feen, GPL Bossers… - Science Translational …, 2020 - science.org
Pulmonary arterial hypertension (PAH) in congenital cardiac shunts can be reversed by
hemodynamic unloading (HU) through shunt closure. However, this reversibility potential is …

Multi-domain adversarial learning

A Schoenauer-Sebag, L Heinrich… - arXiv preprint arXiv …, 2019 - arxiv.org
Multi-domain learning (MDL) aims at obtaining a model with minimal average risk across
multiple domains. Our empirical motivation is automated microscopy data, where cultured …

KLRD1-expressing natural killer cells predict influenza susceptibility

E Bongen, F Vallania, PJ Utz, P Khatri - Genome medicine, 2018 - Springer
Background Influenza infects tens of millions of people every year in the USA. Other than
notable risk groups, such as children and the elderly, it is difficult to predict what …

[HTML][HTML] Integrated, multicohort analysis reveals unified signature of systemic lupus erythematosus

WA Haynes, DJ Haddon, VK Diep, A Khatri, E Bongen… - JCI insight, 2020 - ncbi.nlm.nih.gov
Systemic lupus erythematosus (SLE) is a complex autoimmune disease that follows an
unpredictable disease course and affects multiple organs and tissues. We performed an …

Complementing single-cell RNA-seq using bulk transcriptional profiles

WA Haynes, F Vallania, P Khatri - 2017 IEEE International …, 2017 - ieeexplore.ieee.org
While high-throughput single cell technologies enable in depth examination of specific cell
subsets, these experiments lack the context of these subsets in other cell types and …

[图书][B] Understanding Human Disease Through Integrated Molecular and Clinical Analyses

WA Haynes - 2018 - search.proquest.com
Traditional biomedical experiments are designed to study a single cohort for a single
disease using a single technology. I show that studying disease with a narrow lens has lead …

Blood-based signatures for diagnosis and sub-typing of inflammatory bowel disease subsets

SJ Rubin, A Habtezion - US Patent App. 17/296,941, 2021 - Google Patents
This disclosure provides a method for analyzing peripheral blood leukocytes. In some
embodiments, method may com prise:(a) labeling peripheral blood leukocytes isolated from …

A Unified Molecular Signature of Systemic Lupus Erythematosus Revealed by Integrated, Multi-Cohort Transcriptomic Analysis

WA Haynes, DJ Haddon, VK Diep, A Khatri, E Bongen… - bioRxiv, 2019 - biorxiv.org
Systemic lupus erythematosus (SLE) is a complex autoimmune disease that follows an
unpredictable disease course and affects multiple organs and tissues. We performed an …