John Platig

发表

Histopathological Image QTL Discovery of Immune Infiltration Variants

John Quackenbush, H. Aerts, Joseph D Barry, 2018, iScience.

Gene Targeting in Disease Networks

Deborah A. Weighill, Marouen Ben Guebila, John Quackenbush, 2021, Frontiers in Genetics.

Understanding Tissue-Specific Gene Regulation

Abhijeet R. Sonawane, D. DeMeo, John Quackenbush, 2017, bioRxiv.

Sex Differences in Gene Expression and Regulatory Networks across 29 Human Tissues.

Abhijeet R. Sonawane, D. DeMeo, John Quackenbush, 2020, Cell reports.

Exploring regulation in tissues with eQTL networks

Abhijeet R. Sonawane, John Quackenbush, M. Fagny, 2017, Proceedings of the National Academy of Sciences.

Transcriptional landscape of cell lines and their tissues of origin

Abhijeet R. Sonawane, D. DeMeo, J. Quackenbush, 2016, bioRxiv.

Histopathological image QTL discovery of thyroid autoimmune disease variants

John Quackenbush, H. Aerts, Joseph D Barry, 2017, bioRxiv.

Making Predictions and Handling Errors in Reconstructed Biological Networks

John Platig, 2013 .

Exploiting synthetic lethality for the therapy of ABC diffuse large B cell lymphoma.

Paul Shinn, Rajarshi Guha, Marc Ferrer, 2012, Cancer cell.

Gibbs Free Energy of Protein-Protein Interactions reflects tumor stage

Alex Bloemendal, E. Rietman, J. Tuszynski, 2015, bioRxiv.

Thermodynamic measures of cancer: Gibbs free energy and entropy of protein–protein interactions

E. Rietman, J. Tuszynski, John Platig, 2016, Journal of biological physics.

Identification of an Emphysema-Associated Genetic Variant near TGFB 2 with 1 Regulatory Effects in Lung Fibroblasts 2 3

Raúl San José Estépar, G. Washko, E. Silverman, 2022 .

Understanding Tissue-Specific Gene Regulation

Abhijeet R. Sonawane, D. DeMeo, John Quackenbush, 2017, bioRxiv.

Connectivity of variants in eQTL networks dictates reproducibility and functionality

Xihong Lin, J. Quackenbush, M. Fagny, 2019, bioRxiv.

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

Deborah A. Weighill, Marouen Ben Guebila, D. DeMeo, 2022, bioRxiv.

Supplemental Information Understanding Tissue-Speci fi c Gene Regulation

Lisa, Camila, Abhijeet R. Sonawane, 2017 .

Connectivity in eQTL networks dictates reproducibility and genomic properties

J. Quackenbush, Xihong Lin, M. Fagny, 2022, Cell reports methods.

Nongenic cancer-risk SNPs affect oncogenes, tumour-suppressor genes, and immune function

Xihong Lin, John Quackenbush, M. Fagny, 2019, British Journal of Cancer.

Nongenic cancer-risk SNPs affect oncogenes, tumor suppressor genes, and immune function

Xihong Lin, J. Quackenbush, M. Fagny, 2018, bioRxiv.

Multi-omic regulatory networks capture downstream effects of kinase inhibition in Mycobacterium tuberculosis

Hanno Steen, John Quackenbush, John Platig, 2019, bioRxiv.

Regulatory network changes between cell lines and their tissues of origin

John Quackenbush, Cho-Yi Chen, Joseph N. Paulson, 2017, BMC Genomics.

Gene Regulatory Network Inference as Relaxed Graph Matching

John Quackenbush, Kimberly Glass, Deborah A. Weighill, 2020, bioRxiv.

Protein kinases PknA and PknB independently and coordinately regulate essential Mycobacterium tuberculosis physiologies and antimicrobial susceptibility

H. Steen, John Platig, R. Husson, 2020, PLoS pathogens.

GRAND: a database of gene regulatory network models across human conditions

Deborah A. Weighill, Abhijeet R. Sonawane, Marouen Ben Guebila, 2021, bioRxiv.

A network-based approach to eQTL interpretation and SNP functional characterization

Cho-Yi Chen, Joseph N. Paulson, Kimberly Glass, 2016, bioRxiv.

Nongenic cancer-risk SNPs affect oncogenes, tumour-suppressor genes, and immune function

Xihong Lin, John Quackenbush, M. Fagny, 2019, British Journal of Cancer.

Predicting genotype-specific gene regulatory networks

Deborah A. Weighill, Marouen Ben Guebila, John Quackenbush, 2021, bioRxiv.

Bipartite Community Structure of eQTLs

John Quackenbush, Peter J. Castaldi, John Platig, 2015, PLoS Comput. Biol..

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

Abhijeet R. Sonawane, J. Quackenbush, M. Padi, 2023, Genome Biology.

An online notebook resource for reproducible inference, analysis and publication of gene regulatory networks

Deborah A. Weighill, J. Quackenbush, M. Fagny, 2022, Nature Methods.

Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data

John Quackenbush, Cho-Yi Chen, Joseph N. Paulson, 2016, BMC Bioinformatics.

Multisystem Analysis of Mycobacterium tuberculosis Reveals Kinase-Dependent Remodeling of the Pathogen-Environment Interface

John Quackenbush, H. Steen, J. Paulson, 2018, mBio.

Ensemble genomic analysis in human lung tissue identifies novel genes for chronic obstructive pulmonary disease

G. Washko, E. Silverman, John Quackenbush, 2018, Human Genomics.

Alternative poly-adenylation modulates α1-antitrypsin expression in chronic obstructive pulmonary disease

E. Silverman, Lela Lackey, A. Laederach, 2021, PLoS genetics.

Robustness of Network Measures to Link Errors

Michelle Girvan, Edward Ott, John Platig, 2013, Physical review. E, Statistical, nonlinear, and soft matter physics.

Sexual dimorphism in gene expression and regulatory networks across human tissues

Cho-Yi Chen, Joseph N. Paulson, Kimberly Glass, 2016, bioRxiv.

Cigarette smoking-associated isoform switching and 3′ UTR lengthening via alternative polyadenylation

R. Bowler, A. Laederach, C. Hersh, 2021, medRxiv.

Echo phenomena in large systems of coupled oscillators.

E. Ott, M. Girvan, T. Antonsen, 2008, Chaos.

External periodic driving of large systems of globally coupled phase oscillators.

M Girvan, E Ott, E. Ott, 2007, Chaos.

Multi-omic regulatory networks capture downstream effects of kinase inhibition in Mycobacterium tuberculosis

J. Quackenbush, H. Steen, John Platig, 2021, npj Systems Biology and Applications.

Thermodynamic measures of cancer: Gibbs free energy and entropy of protein–protein interactions

E. Rietman, J. Tuszynski, John Platig, 2016, Journal of Biological Physics.

Topological Pathway Enrichment Analysis of Gene Expression in High Grade Serous Ovarian Cancer Reveals Tumor-Stoma Cross-Talk

G. Thallinger, John Platig, A. Culhane, 2017 .

Identification of an emphysema-associated genetic variant near TGFB2 with regulatory effects in lung fibroblasts

Raúl San José Estépar, G. Washko, E. Silverman, 2019, eLife.

Additional file 5: Table S1. of Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data

Abhijeet R. Sonawane, J. Quackenbush, M. Fagny, 2017 .

Complex Traits Heritability is Highly Clustered in the eQTL Bipartite Network

J. Quackenbush, M. Fagny, John Platig, 2024, bioRxiv.