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Network Medicine in the Age of Biomedical Big Data

Frontiers in genetics, 2019-04, Vol.10, p.294-294

2019

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Annotation enrichment analysis: an alternative method for evaluating the functional properties of gene sets

Scientific reports, 2014-02, Vol.4 (1), p.4191-4191, Article 4191

2014

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Understanding Tissue-Specific Gene Regulation

Cell reports (Cambridge), 2017-10, Vol.21 (4), p.1077-1088

2017

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Epigenetics and pulmonary diseases in the horizon of precision medicine: a review

The European respiratory journal, 2021-06, Vol.57 (6), p.2003406

2021

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Robustness and lethality in multilayer biological molecular networks

Nature communications, 2020-11, Vol.11 (1), p.6043-6043, Article 6043

2020

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Passing messages between biological networks to refine predicted interactions

PloS one, 2013-05, Vol.8 (5), p.e64832-e64832

2013

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Using methylation data to improve transcription factor binding prediction

Epigenetics, 2024-12, Vol.19 (1), p.2309826-2309826

2024

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Single-sample network modeling on omics data

BMC biology, 2023-12, Vol.21 (1), p.296-296, Article 296

2023

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The metabolic role of vitamin D in children’s neurodevelopment: a network study

Scientific reports, 2024-07, Vol.14 (1), p.16929-15, Article 16929

2024

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Gene Regulatory Network Analysis Identifies Sex-Linked Differences in Colon Cancer Drug Metabolism

Cancer research (Chicago, Ill.), 2018-10, Vol.78 (19), p.5538-5547

2018

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CpG methylation of half-CRE sequences creates C/EBPα binding sites that activate some tissue-specific genes

Proceedings of the National Academy of Sciences - PNAS, 2010-11, Vol.107 (47), p.20311-20316

2010

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Finding New Order in Biological Functions from the Network Structure of Gene Annotations

PLoS computational biology, 2015-11, Vol.11 (11), p.e1004565

2015

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lionessR: single sample network inference in R

BMC cancer, 2019-10, Vol.19 (1), p.1003-1003, Article 1003

2019

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Estimating Sample-Specific Regulatory Networks

iScience, 2019-04, Vol.14, p.226-240

2019

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Molecular networks in Network Medicine: Development and applications

Wiley interdisciplinary reviews. Mechanisms of disease, 2020-11, Vol.12 (6), p.e1489-n/a

2020

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Developmental Control of Polycomb Subunit Composition by GATA Factors Mediates a Switch to Non-Canonical Functions

Molecular cell, 2015-01, Vol.57 (2), p.304-316

2015

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Multi-scale chromatin state annotation using a hierarchical hidden Markov model

Nature communications, 2017-04, Vol.8 (1), p.15011-15011, Article 15011

2017

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Epigenome-wide association study reveals methylation pathways associated with childhood allergic sensitization

Epigenetics, 2019-05, Vol.14 (5), p.445-466

2019

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KDM4A Lysine Demethylase Induces Site-Specific Copy Gain and Rereplication of Regions Amplified in Tumors

Cell, 2013-08, Vol.154 (3), p.541-555

2013

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Editorial: Applications and Methods in Genomic Networks

Frontiers in genetics, 2022-06, Vol.13, p.936015-936015

2022

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ETV1 directs androgen metabolism and confers aggressive prostate cancer in targeted mice and patients

Genes & development, 2013-03, Vol.27 (6), p.683-698

2013

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RNA-sequencing across three matched tissues reveals shared and tissue-specific gene expression and pathway signatures of COPD

Respiratory research, 2019-04, Vol.20 (1), p.65-65, Article 65

2019

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Functional interactors of three genome-wide association study genes are differentially expressed in severe chronic obstructive pulmonary disease lung tissue

Scientific reports, 2017-03, Vol.7 (1), p.44232-44232, Article 44232

2017

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Protein interaction networks provide insight into fetal origins of chronic obstructive pulmonary disease

Respiratory research, 2022-03, Vol.23 (1), p.69-15, Article 69

2022

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

BMC bioinformatics, 2017-10, Vol.18 (1), p.437-437, Article 437

2017

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Network Medicine in the Age of Biomedical Big Data

Annotation enrichment analysis: an alternative method for evaluating the functional properties of gene sets

Understanding Tissue-Specific Gene Regulation

Epigenetics and pulmonary diseases in the horizon of precision medicine: a review

Robustness and lethality in multilayer biological molecular networks

Passing messages between biological networks to refine predicted interactions

Using methylation data to improve transcription factor binding prediction

Single-sample network modeling on omics data

The metabolic role of vitamin D in children’s neurodevelopment: a network study

Gene Regulatory Network Analysis Identifies Sex-Linked Differences in Colon Cancer Drug Metabolism

CpG methylation of half-CRE sequences creates C/EBPα binding sites that activate some tissue-specific genes

Finding New Order in Biological Functions from the Network Structure of Gene Annotations

lionessR: single sample network inference in R

Estimating Sample-Specific Regulatory Networks

Molecular networks in Network Medicine: Development and applications

Developmental Control of Polycomb Subunit Composition by GATA Factors Mediates a Switch to Non-Canonical Functions

Multi-scale chromatin state annotation using a hierarchical hidden Markov model

Epigenome-wide association study reveals methylation pathways associated with childhood allergic sensitization

KDM4A Lysine Demethylase Induces Site-Specific Copy Gain and Rereplication of Regions Amplified in Tumors

Editorial: Applications and Methods in Genomic Networks

ETV1 directs androgen metabolism and confers aggressive prostate cancer in targeted mice and patients

RNA-sequencing across three matched tissues reveals shared and tissue-specific gene expression and pathway signatures of COPD

Functional interactors of three genome-wide association study genes are differentially expressed in severe chronic obstructive pulmonary disease lung tissue

Protein interaction networks provide insight into fetal origins of chronic obstructive pulmonary disease

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

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