Dawn Lisa DeMeo

Sex differences in gene regulation and its impact on cancer incidence

The paper identifies sex-biased regulation of cancer genes in normal tissues, linking these differences to sex-specific cancer incidence patterns.

Aging-associated Alterations in the Gene Regulatory Network Landscape Associate with Risk, Prognosis and Response to Therapy in Lung Adenocarcinoma

This study identifies aging-related changes in gene regulatory networks linked to LUAD risk, prognosis, and therapy response using multi-omics data from GTEx and TCGA.

DNA-methylation markers associated with lung function at birth and childhood reveal early life programming of inflammatory pathways

The paper identifies DNA-methylation markers at birth and childhood associated with lung function and reveals sex- and genetics-related pathways linked to asthma and lung development.

Identifying Sex Differences in Lung Adenocarcinoma Using Multi-Omics Integrative Protein Signaling Networks

The paper identifies sex differences in lung adenocarcinoma by integrating multi-omics data to discover sex-biased signaling pathways and potential sex-specific therapies.

Genomic and phenotypic correlates of mosaic loss of chromosome Y in blood

The paper identifies genetic and phenotypic correlates of mosaic loss of chromosome Y in blood using whole genome sequencing data from the TOPMed program.

Selective loss of Y chromosomes in lung adenocarcinoma modulates the tumor immune environment through cancer/testis antigens

This study investigates how loss of the Y chromosome in lung adenocarcinoma affects the tumor immune environment and response to immunotherapy.

Proteomic Networks and Related Genetic Variants Associated with Smoking and Chronic Obstructive Pulmonary Disease

The paper identifies proteomic networks and genetic variants associated with smoking and COPD phenotypes using multi-ethnic proteomic data and network-based GWAS.

Bayesian Optimized sample-specific Networks Obtained ByOmics data (BONOBO)

BONOBO infers sample-specific co-expression networks to capture individual heterogeneity in gene regulation, outperforming existing methods in yeast, breast cancer, and thyroid tissue analyses.

Determinants of mosaic chromosomal alteration fitness

The paper estimates mCA fitness in the NHLBI TOPMed cohort and identifies genetic variants associated with clonal expansion rates.

Using methylation data to improve transcription factor binding prediction

The paper improves transcription factor binding prediction by integrating CpG methylation data with PWM-based scores, showing better performance than standard PWM scores for most TFs.

Clonal hematopoiesis is driven by aberrant activation of TCL1A

The paper develops PACER to infer clonal expansion rates from single timepoint data and identifies TCL1A activation as a mediator of clonal hematopoiesis fitness.

Somatic mutations in chronic lung disease are associated with reduced lung function

The paper finds that somatic mutations in diseased lung tissue correlate with reduced lung function and cell type proportions in COPD and IPF.

A robust and adaptive framework for interaction testing in quantitative traits between multiple genetic loci and exposure variables

RITSS identifies gene-environment interactions in quantitative traits using sample splitting and robust statistics, finding significant interactions in lung function and height data.

A Statistical Physics Approach for Disease Module Detection

This paper introduces a statistical physics approach using the random-field Ising model to detect disease modules, showing improved efficiency and robustness compared to existing methods.

The Network Zoo: a multilingual package for the inference and analysis of biological networks

The paper introduces netZoo, an open-source software suite for analyzing biological networks, demonstrating its use on cancer cell line data to identify drug resistance and cancer development factors.

Bidirectional Mendelian randomization supports bidirectional causality between telomere length and clonal hematopoiesis of intermediate potential

The paper uses bidirectional Mendelian randomization to show LTL lengthening increases CHIP risk, while CHIP accelerates LTL shortening, with modest mediation between CHIP and CAD via LTL.

gpuZoo: Cost-effective estimation of gene regulatory networks using the Graphics Processing Unit

gpuZoo accelerates gene regulatory network inference by using GPU acceleration, achieving faster and cheaper runtime compared to CPU-based methods.

Constructing Gene Regulatory Networks using Epigenetic Data

This paper introduces SPIDER, a method that integrates DNase-Seq data into a message passing framework to construct gene regulatory networks, showing improved accuracy over existing methods.

Whole-Genome Association Analyses of Sleep-disordered Breathing Phenotypes in the NHLBI TOPMed Program

The paper reports whole-genome association analyses of sleep-disordered breathing traits in the NHLBI TOPMed program, identifying rare and common variant associations.

Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program

Over 400 million variants, 97% below 1% frequency, emerge from deep whole-genome sequencing of 53,831 diverse TOPMed participants; TOPMed haplotypes enable imputation down to ~0.01% frequency.

Novel genetic determinants of telomere length from a trans-ethnic analysis of 109,122 whole genome sequences in TOPMed

This study identifies 59 sentinel variants and two novel genes associated with telomere length using whole genome sequences from 109,122 trans-ethnic individuals.

Two mutations in the SARS-CoV-2 spike protein and RNA polymerase complex are associated with COVID-19 mortality risk

The paper identifies two SARS-CoV-2 genome loci associated with increased COVID-19 mortality risk using logistic regression on whole-genome sequencing data.

Epigenomic prediction of cardiovascular disease risk and interactions with traditional risk metrics

The paper develops a DNA methylation-based risk score for cardiovascular disease and shows it predicts risk independently of traditional factors.

A gene-diet interaction-based score predicts response to dietary fat in the Women's Health Initiative

The paper develops a gene-diet interaction score to predict dietary fat response for cardiometabolic risk factors using the Women's Health Initiative cohort.

DNA methylation modules associate with incident cardiovascular disease and cumulative risk factor exposure

The paper identifies DNA methylation modules and regions associated with incident cardiovascular disease and cumulative risk factor exposure using data from the Women's Health Initiative and Framingham Heart Study Offspring Cohort.

New Statistical Methods for Constructing Robust Differential Correlation Networks

This paper introduces six new statistical tests for differential correlation networks that are computationally efficient and outperform existing methods in simulations and real data analysis.

Expanded genetic landscape of chronic obstructive pulmonary disease reveals heterogeneous cell type and phenotype associations

This study expands the genetic landscape of COPD by identifying 82 risk loci, revealing associations with lung function, cell types, and comorbidities.

New genetic signals for lung function highlight pathways and pleiotropy, and chronic obstructive pulmonary disease associations across multiple ancestries

The paper identifies 279 new genetic signals for lung function across multiple ancestries, showing associations with COPD and pleiotropic effects.

Gene regulatory network analysis identifies sex-linked differences in colon cancer drug metabolism processes

The paper identifies sex-linked differences in colon cancer drug metabolism via gene regulatory network analysis, showing improved survival in females with higher pathway targeting.

Detecting Differential Variable microRNAs via Model-Based Clustering

The paper introduces a model-based clustering method to detect differentially variable microRNAs, outperforming the probe-wise F test and identifying 7 novel microRNAs in hepatocellular carcinoma.