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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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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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Cancer driver mutations: predictions and reality

Trends in molecular medicine, 2023-07, Vol.29 (7), p.554-566

2023

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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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Identifying causal genes and dysregulated pathways in complex diseases

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

2011

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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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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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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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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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Stochastic Modeling of Gene Expression Evolution Uncovers Tissue- and Sex-Specific Properties of Expression Evolution in the Drosophila Genus

Journal of computational biology, 2023-01, Vol.30 (1), p.21-40

2023

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Co-SELECT reveals sequence non-specific contribution of DNA shape to transcription factor binding in vitro

Nucleic acids research, 2019-07, Vol.47 (13), p.6632-6641

2019

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ISMB/ECCB 2021 proceedings

Bioinformatics, 2021-07, Vol.37 (Supplement_1), p.i7-i8

2021

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The Bioinformatics of Aptamers: HT-SELEX Analysis with AptaSUITE

Methods in molecular biology (Clifton, N.J.), 2023, Vol.2570, p.73

2023

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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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WeSME: uncovering mutual exclusivity of cancer drivers and beyond

Bioinformatics (Oxford, England), 2017-03, Vol.33 (6), p.814-821

2017

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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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The language of a virus

Science (American Association for the Advancement of Science), 2021-01, Vol.371 (6526), p.233-234

2021

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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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GMNN2CD: identification of circRNA–disease associations based on variational inference and graph Markov neural networks

Bioinformatics, 2022-04, Vol.38 (8), p.2246-2253

2022

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Transcription-dependent dynamic supercoiling is a short-range genomic force

Nature structural & molecular biology, 2013-03, Vol.20 (3), p.396-403

2013

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Bioinformatics pipeline using JUDI: Just Do It

Bioinformatics, 2020-04, Vol.36 (8), p.2572-2574

2020

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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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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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Transfer learning via multi-scale convolutional neural layers for human–virus protein–protein interaction prediction

Bioinformatics, 2021-12, Vol.37 (24), p.4771-4778

2021

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Chapter 5: Network biology approach to complex diseases

Detecting presence of mutational signatures in cancer with confidence

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

Cancer driver mutations: predictions and reality

Global Regulation of Promoter Melting in Naive Lymphocytes

Identifying causal genes and dysregulated pathways in complex diseases

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

DNA break mapping reveals topoisomerase II activity genome-wide

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

From hype to reality: data science enabling personalized medicine

Stochastic Modeling of Gene Expression Evolution Uncovers Tissue- and Sex-Specific Properties of Expression Evolution in the Drosophila Genus

Co-SELECT reveals sequence non-specific contribution of DNA shape to transcription factor binding in vitro

ISMB/ECCB 2021 proceedings

The Bioinformatics of Aptamers: HT-SELEX Analysis with AptaSUITE

RNA Polymerase II Regulates Topoisomerase 1 Activity to Favor Efficient Transcription

WeSME: uncovering mutual exclusivity of cancer drivers and beyond

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

The language of a virus

Understanding Genotype-Phenotype Effects in Cancer via Network Approaches

GMNN2CD: identification of circRNA–disease associations based on variational inference and graph Markov neural networks

Transcription-dependent dynamic supercoiling is a short-range genomic force

Bioinformatics pipeline using JUDI: Just Do It

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

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

Transfer learning via multi-scale convolutional neural layers for human–virus protein–protein interaction prediction

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