John Quackenbush

Career Trajectory

Research Cluster Map

Direct collaborators. Node size = influence, colour = community, dashed = past collaboration.

• LOESS and DE-SWAN can induce artifactual "waves" of molecular aging

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-06-28

• GTEx eQTL Networks

  Zenodo (CERN European Organization for Nuclear Research) · 2026-06-23

• GTEx eQTL Networks

  Zenodo (CERN European Organization for Nuclear Research) · 2026-06-23

• Leveraging Artificial Intelligence in Allergy, Asthma, and Immunology With Environmental Exposures

  Allergy · 2026-06-03

• Deploying a JupyterHub Server for Academic Research Using Netbooks as an Example

  Current Protocols · 2026-06-01

• Switch-like methylation of functional pathways distinguishes COPD and idiopathic pulmonary fibrosisPreprint

  medRxiv · 2025-12-19

• Sex differences in gene regulation and its impact on cancer incidencePreprint

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-11-22

• Regulatory network analysis identifies changes in ahr, TFAP4, and AP-1 transcription factors as top drivers of symptomatic disease progression in Waldenstrom's macroglobulinemia.

  Blood · 2025-11-03

• Multi-omics protein signaling networks identify sex-specific therapeutic candidates in lung adenocarcinoma

  Biology of Sex Differences · 2025-09-29 · 2 citations

• SEAHORSE: A Serendipity Engine Assaying Heterogeneous Omics-Related Sampling ExperimentsPreprint

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-08-21 · 1 citations

• The Importance of Regulatory Network Structure for Complex Trait Heritability and Evolution

  Molecular Biology and Evolution · 2025-07-30 · 4 citations

• Aging-associated alterations in gene regulatory networks associate with risk, prognosis and response to therapy in lung adenocarcinoma

  npj Aging · 2025-07-09 · 4 citations

• The Impact of X Chromosome Inactivation Patterns and Social Determinants of Health on COPD Outcomes in Women

  American Journal of Respiratory and Critical Care Medicine · 2025-05-01

• Abstract 7478: Lung cancer gene regulatory networks reflect smoking history and age-related metabolic pathway alterations

  Cancer Research · 2025-04-21

• BLOBFISH: Bipartite Limited Subnetworks from Multiple Observations using Breadth-First Search with Constrained HopsPreprint

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-03-13 · 1 citations

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

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-02-07 · 2 citations

• Reproducible processing of TCGA regulatory networks

  GigaScience · 2025-01-01 · 1 citations

• Reproducible processing of TCGA regulatory networksPreprint

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-11-07 · 2 citations

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

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-09-22 · 5 citations

• Higher-order correction of persistent batch effects in correlation networks

  Bioinformatics · 2024-09-01 · 7 citations