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Chapter 5: Network biology approach to complex diseases

PLoS computational biology, 2012-12, Vol.8 (12), p.e1002820-e1002820

2012

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Global Regulation of Promoter Melting in Naive Lymphocytes

Cell, 2013-05, Vol.153 (5), p.988-999

2013

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Genome-wide detection of DNase I hypersensitive sites in single cells and FFPE tissue samples

Nature (London), 2015-12, Vol.528 (7580), p.142-146

2015

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From hype to reality: data science enabling personalized medicine

BMC medicine, 2018-08, Vol.16 (1), p.150-150, Article 150

2018

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Identifying causal genes and dysregulated pathways in complex diseases

PLoS computational biology, 2011-03, Vol.7 (3), p.e1001095

2011

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RNA Polymerase II Regulates Topoisomerase 1 Activity to Favor Efficient Transcription

Cell, 2016-04, Vol.165 (2), p.357-371

2016

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Large scale analysis of the mutational landscape in HT-SELEX improves aptamer discovery

Nucleic acids research, 2015-07, Vol.43 (12), p.5699-5707

2015

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Why do hubs in the yeast protein interaction network tend to be essential: reexamining the connection between the network topology and essentiality

PLoS computational biology, 2008-08, Vol.4 (8), p.e1000140-e1000140

2008

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Exploring tumor-normal cross-talk with TranNet: Role of the environment in tumor progression

PLoS computational biology, 2023-09, Vol.19 (9), p.e1011472-e1011472

2023

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AptaSUITE: A Full-Featured Bioinformatics Framework for the Comprehensive Analysis of Aptamers from HT-SELEX Experiments

Molecular therapy. Nucleic acids, 2018-06, Vol.11 (C), p.515-517

2018

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Sex- and Tissue-Specific Functions of Drosophila Doublesex Transcription Factor Target Genes

Developmental cell, 2014-12, Vol.31 (6), p.761-773

2014

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BeWith: A Between-Within method to discover relationships between cancer modules via integrated analysis of mutual exclusivity, co-occurrence and functional interactions

PLoS computational biology, 2017-10, Vol.13 (10), p.e1005695

2017

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Understanding Genotype-Phenotype Effects in Cancer via Network Approaches

PLoS computational biology, 2016-03, Vol.12 (3), p.e1004747

2016

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DNA break mapping reveals topoisomerase II activity genome-wide

International journal of molecular sciences, 2014-07, Vol.15 (7), p.13111-13122

2014

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AptaCluster – A Method to Cluster HT-SELEX Aptamer Pools and Lessons from Its Application

Research in Computational Molecular Biology, p.115-128

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Reprogramming of regulatory network using expression uncovers sex-specific gene regulation in Drosophila

Nature communications, 2018-10, Vol.9 (1), p.4061-10, Article 4061

2018

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Crystal Structures of the Outer Membrane Domain of Intimin and Invasin from Enterohemorrhagic E. coli and Enteropathogenic Y. pseudotuberculosis

Structure (London), 2012-07, Vol.20 (7), p.1233-1243

2012

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Identification of sequence-structure RNA binding motifs for SELEX-derived aptamers

Bioinformatics (Oxford, England), 2012-06, Vol.28 (12), p.i215-i223

2012

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Detecting presence of mutational signatures in cancer with confidence

Bioinformatics, 2018-01, Vol.34 (2), p.330-337

2018

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Rosalind Franklin Society Proudly Announces the 2023 Award Recipient for Journal of Computational Biology

Journal of computational biology, 2024-09, Vol.31 (9), p.783-783

Przytycka, Teresa M

2024

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Highly Constrained Bicyclic Scaffolds for the Discovery of Protease-Stable Peptides via mRNA Display

ACS chemical biology, 2017-03, Vol.12 (3), p.795-804

2017

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Influence network model uncovers relations between biological processes and mutational signatures

Genome medicine, 2023-03, Vol.15 (1), p.15-15, Article 15

2023

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Transcription Factor Networks in Drosophila melanogaster

Cell reports (Cambridge), 2014-09, Vol.8 (6), p.2031-2043

2014

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Discovering functional linkages and uncharacterized cellular pathways using phylogenetic profile comparisons: a comprehensive assessment

BMC bioinformatics, 2007-05, Vol.8 (1), p.173-173, Article 173

2007

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Direct, Competitive Comparison of Linear, Monocyclic, and Bicyclic Libraries Using mRNA Display

ACS combinatorial science, 2020-06, Vol.22 (6), p.306-310

2020

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Chapter 5: Network biology approach to complex diseases

Global Regulation of Promoter Melting in Naive Lymphocytes

Genome-wide detection of DNase I hypersensitive sites in single cells and FFPE tissue samples

From hype to reality: data science enabling personalized medicine

Identifying causal genes and dysregulated pathways in complex diseases

RNA Polymerase II Regulates Topoisomerase 1 Activity to Favor Efficient Transcription

Large scale analysis of the mutational landscape in HT-SELEX improves aptamer discovery

Why do hubs in the yeast protein interaction network tend to be essential: reexamining the connection between the network topology and essentiality

Exploring tumor-normal cross-talk with TranNet: Role of the environment in tumor progression

AptaSUITE: A Full-Featured Bioinformatics Framework for the Comprehensive Analysis of Aptamers from HT-SELEX Experiments

Sex- and Tissue-Specific Functions of Drosophila Doublesex Transcription Factor Target Genes

BeWith: A Between-Within method to discover relationships between cancer modules via integrated analysis of mutual exclusivity, co-occurrence and functional interactions

Understanding Genotype-Phenotype Effects in Cancer via Network Approaches

DNA break mapping reveals topoisomerase II activity genome-wide

AptaCluster – A Method to Cluster HT-SELEX Aptamer Pools and Lessons from Its Application

Reprogramming of regulatory network using expression uncovers sex-specific gene regulation in Drosophila

Crystal Structures of the Outer Membrane Domain of Intimin and Invasin from Enterohemorrhagic E. coli and Enteropathogenic Y. pseudotuberculosis

Identification of sequence-structure RNA binding motifs for SELEX-derived aptamers

Detecting presence of mutational signatures in cancer with confidence

Rosalind Franklin Society Proudly Announces the 2023 Award Recipient for Journal of Computational Biology

Highly Constrained Bicyclic Scaffolds for the Discovery of Protease-Stable Peptides via mRNA Display

Influence network model uncovers relations between biological processes and mutational signatures

Transcription Factor Networks in Drosophila melanogaster

Discovering functional linkages and uncharacterized cellular pathways using phylogenetic profile comparisons: a comprehensive assessment

Direct, Competitive Comparison of Linear, Monocyclic, and Bicyclic Libraries Using mRNA Display

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